U.S. patent application number 13/300534 was filed with the patent office on 2012-12-20 for method for generating and selecting antibodies against target protein.
This patent application is currently assigned to ADIMAB LLC. Invention is credited to Shaobing Benjamin Hua, Li Zhu.
Application Number | 20120322672 13/300534 |
Document ID | / |
Family ID | 37855428 |
Filed Date | 2012-12-20 |
United States Patent
Application |
20120322672 |
Kind Code |
A1 |
Hua; Shaobing Benjamin ; et
al. |
December 20, 2012 |
METHOD FOR GENERATING AND SELECTING ANTIBODIES AGAINST TARGET
PROTEIN
Abstract
Compositions are provided that comprise antibody against
membrane proteins such as chemokine receptors. In particular,
monoclonal human antibodies against human CXCR4 are provided that
are capable of inhibiting HIV infection and chemotaxis in human
breast cancer cells. The antibodies can be used as prophylactics or
therapeutics to prevent and treat HIV infection and cancer, for
screening drugs, and for diagnosing diseases or conditions
associated with interactions with chemokine receptors.
Inventors: |
Hua; Shaobing Benjamin;
(Cupertino, CA) ; Zhu; Li; (Palo Alto,
CA) |
Assignee: |
ADIMAB LLC
Lebanon
NH
|
Family ID: |
37855428 |
Appl. No.: |
13/300534 |
Filed: |
November 18, 2011 |
Related U.S. Patent Documents
|
|
|
|
|
|
Application
Number |
Filing Date |
Patent Number |
|
|
12713357 |
Feb 26, 2010 |
|
|
|
13300534 |
|
|
|
|
11593957 |
Nov 6, 2006 |
7700302 |
|
|
12713357 |
|
|
|
|
10360828 |
Feb 7, 2003 |
7138496 |
|
|
11593957 |
|
|
|
|
10133978 |
Apr 25, 2002 |
|
|
|
10360828 |
|
|
|
|
10071866 |
Feb 8, 2002 |
|
|
|
10133978 |
|
|
|
|
10072301 |
Feb 8, 2002 |
7005503 |
|
|
10071866 |
|
|
|
|
09703399 |
Oct 31, 2000 |
6610472 |
|
|
10072301 |
|
|
|
|
10072301 |
Feb 8, 2002 |
7005503 |
|
|
10133978 |
|
|
|
|
10071866 |
Feb 8, 2002 |
|
|
|
10072301 |
|
|
|
|
09703399 |
Oct 31, 2000 |
6610472 |
|
|
10071866 |
|
|
|
|
09703399 |
Oct 31, 2000 |
6610472 |
|
|
10071866 |
|
|
|
|
09703399 |
Oct 31, 2000 |
6610472 |
|
|
10072301 |
|
|
|
|
Current U.S.
Class: |
506/9 ;
506/14 |
Current CPC
Class: |
A61K 39/39541 20130101;
C07K 16/2866 20130101; C07K 2319/00 20130101; C07K 2317/21
20130101; C07K 16/00 20130101; C07K 2317/622 20130101; C07K 2317/76
20130101; A61K 39/39541 20130101; A61K 2039/505 20130101; A61K
2300/00 20130101 |
Class at
Publication: |
506/9 ;
506/14 |
International
Class: |
C40B 30/04 20060101
C40B030/04; C40B 40/02 20060101 C40B040/02 |
Claims
1-31. (canceled)
32. A method for selecting an antibody that binds to a target
membrane protein by yeast display, comprising the step of:
contacting yeast cells that display a library of antibodies with a
target membrane protein or a peptide fragment of the target
membrane protein; selecting the yeast cell that binds to the target
membrane or the peptide fragment of the target membrane protein;
and identifying the antibody displayed by the selected yeast
cell.
33. The method of claim 32, wherein the antibodies are single-chain
antibodies each of which is fused via its C-terminus to a binding
subunit of a yeast adhesion receptor.
34. The method of claim 33, wherein the yeast adhesion receptor is
a-agglutinin or .alpha.-agglutinin.
35. The method of claim 34, wherein the yeast adhesion receptor is
an Aga2p mating adhesion receptor of Saccharomyces cerevisiae.
36. The method of claim 33, wherein the single-chain antibodies
each comprises an antibody heavy chain variable region, an antibody
light chain variable region, and a linker peptide that links the
antibody heavy chain variable region and the antibody light chain
variable region.
37. The method of claim 32, wherein the diversity of the library of
antibodies is at least 1.times.10.sup.6.
38. The method of claim 32, wherein the diversity of the library of
antibodies is at least 1.times.10.sup.7.
39. The method of claim 32, wherein the diversity of the library of
antibodies is at least 1.times.10.sup.7-1.times.10.sup.10.
40. The method of claim 32, wherein the diversity of the library of
antibodies is at least 1.times.10.sup.8-1.times.10.sup.10.
41. The method of claim 32, wherein the sequence of the antibody
heavy or light chain variable region is fully human.
42. The method of claim 32, wherein the V.sub.H and V.sub.L are
encoded by variable regions of immunoglobulin genes of a human,
non-human primate, or rodent.
43. The method of claim 32, wherein the V.sub.H and V.sub.L are
encoded respectively by a heavy-chain variable region and a
light-chain variable region of a human immunoglobulin gene.
44. The method of claim 32, wherein the V.sub.H is encoded by a
heavy-chain variable region of a first human immunoglobulin gene,
and the V.sub.L is encoded by a light chain variable region of a
second human immunoglobulin gene different from the first human
immunoglobulin gene.
45. The method of claim 32, wherein the antibody heavy or light
chain variable region is encoded by a human IgG gene.
46. The method of claim 32, wherein the target membrane protein is
selected from the group consisting of receptors for growth factors,
insulin receptor, MHC proteins, CD3 receptor, T cell receptors,
cytokine receptors, tyrosine-kinase-associated receptors and
G-protein coupled receptors.
47. The method of claim 46, wherein receptors for growth factors
are selected from the group consisting of receptors for vascular
endothelial growth factor, epidermal growth factor, transforming
growth factor, fibroblast growth factor, platelet derived growth
factor, and insulin-like growth factor.
48. The method of claim 46, wherein the MHC protein is class I or
class II MHC protein.
49. The method of claim 46, wherein the cytokine receptor is
selected from interleukin-1 receptor, interleukin-2 receptor,
interleukin-8 receptor, and interleukin-12 receptor,
50. The method of claim 46, wherein the tyrosine-kinase-associated
receptors is selected from the group consisting of Src, Yes, Fgr,
Flt, Lck, Lyn, Hck, and Blk.
51. The method of claim 32, wherein the peptide fragment of the
target membrane protein has a length of 5-100 aa.
52. The method of claim 32, wherein the peptide fragment of the
target membrane protein has a length of 10-80 aa.
53. The method of claim 32, wherein the peptide fragment of the
target membrane protein has a length of 20-60 aa.
54. The method of claim 32, wherein the peptide fragment of the
membrane protein is an extracellular domain of the target membrane
protein.
55. The method of claim 32, wherein the yeast cell that binds to
the target membrane or the peptide fragment of the target membrane
protein is selected by flow cytometric cell sorting.
56. A library of yeast cells displaying a library of antibodies on
the surface of the yeast cells, comprising: yeast cells transformed
with a library of yeast expression vectors encoding a library of
antibodies each comprising an antibody heavy chain variable region
(V.sub.H) and an antibody light chain variable region (V.sub.L),
wherein at least one yeast expression vector comprises one or more
homologous recombination sites and has undergone homologous
recombination such that a polynucleotide sequence from a first
polynucleotide sequence encoding the V.sub.H or a second
polynucleotide sequence encoding the V.sub.L is incorporated into
the yeast expression vector, and also a sequence encoding a binding
subunit of a yeast adhesion receptor.
57. The library of claim 56, wherein the yeast cells are
Saccharomyces cerevisiae cells.
58. The library of claim 56, wherein the yeast adhesion receptor is
a-agglutinin or .alpha.-agglutinin.
59. The library of claim 56, wherein a region of the V.sub.H or
V.sub.L is mutagenized.
60. The library of claim 59, wherein the region of the VH or VL is
mutagenized through mutagenesis selected from the group consisting
of error-prone PCR mutagenesis, site-directed mutagenesis, cassette
mutagenesis, DNA shuffling and combinations thereof.
61. The library of claim 56, wherein the diversity of the library
of antibodies is at least 1.times.10.sup.6.
62. The library of claim 56, wherein the diversity of the library
of antibodies is at least 1.times.10.sup.7.
63. The library of claim 56, wherein the diversity of the library
of antibodies is at least 1.times.107-1.times.10.sup.10.
64. The library of claim 56, wherein the diversity of the library
of antibodies is at least 1.times.10.sup.8-1.times.10.sup.10.
65. The library of claim 56, wherein the sequence of the antibody
heavy or light chain variable region is fully human.
66. The library of claim 56, wherein the V.sub.H and V.sub.L are
encoded by variable regions of immunoglobulin genes of a human,
non-human primate, or rodent.
67. The library of claim 56, wherein the V.sub.H and V.sub.L are
encoded respectively by a heavy-chain variable region and a
light-chain variable region of a human immunoglobulin gene.
68. The library of claim 56, wherein the V.sub.H is encoded by a
heavy-chain variable region of a first human immunoglobulin gene,
and the V.sub.L is encoded by a light chain variable region of a
second human immunoglobulin gene different from the first human
immunoglobulin gene.
69. The library of claim 56, wherein the antibody heavy or light
chain variable region is encoded by a human IgG gene.
Description
CROSS-REFERENCE
[0001] This application is a continuation of Application entitled
"HUMAN MONOCLONAL ANTIBODIES AGAINST MEMBRANE PROTEINS" application
of Ser. No. 10/360,828, filed Feb. 7, 2003, which is a
continuation-in-part of Application entitled "METHODS FOR
GENERATING MONOCLONAL ANTIBODY AGAINST FUSION PROTEIN CONTAINING
PEPTIDE GRAGMENT DERIVED FROM MEMBRANE PROTEIN", application Ser.
No. 10/133,978, filed Apr. 25, 2002, which is a
continuation-in-part of Application entitled "HUMAN MONOCLONAL
ANTIBODY AGAINST CORECEPTORS FOR HUMAN IMMUNODEFICIENCY VIRUS",
application Ser. No. 10/072,301, filed on Feb. 8, 2002, and
Application entitled "HIGH THROUGHPUT GENERATION HUMAN MONOCLONAL
ANTIBODY AGAINST PEPTIDE FRAGMENTS DERIVED FROM MEMBRANE PROTEINS",
application Ser. No. 10/071,866, filed Feb. 8, 2002. These
applications are incorporated herein by reference in their
entirety.
FIELD OF THE INVENTION
[0002] This invention relates to methods for generating monoclonal
antibody against cell membrane proteins, and, more particularly, to
methods for generating human monoclonal antibodies against cell
surface coreceptors for human immunodeficiency virus (HIV) and
using these antibodies for diagnostic or therapeutic purposes.
DESCRIPTION OF RELATED ART
[0003] HIV infection has been implicated as the primary cause of
the slowly degenerate disease of the immune system termed acquired
immune deficiency syndrome (AIDS). Barre-Sinoussi et al. (1983)
Science 220:868-870; and Gallo et al. (1984) Science 224:500-503.
Infection of the CD4+ subclass of T-lymphocytes with the HIV-1
virus leads to depletion of this essential lymphocyte subclass
which inevitably leads to opportunistic infections, neurological
disease, neoplastic growth and eventually death. HIV-1 infection
and HIV-1 associated diseases represent a major health problem and
considerable attention is currently being directed towards the
successful design of effective therapeutics.
[0004] HIV-1 is a member of the lentivirus family of retroviruses.
Teich et al. (1984) In RNA Tumor Viruses ed. R. Weiss, N. Teich, H.
Varmus, J. Coffin CSH Press, pp. 949-56. The life cycle of HIV-1 is
characterized by a period of proviral latency followed by active
replication of the virus. The primary cellular target for the
infectious HIV-1 virus is the CD4 subset of human T-lymphocytes.
Targeting of the virus to the CD4 subset of cells is due to the
fact that the CD4 cell surface protein acts as the cellular
receptor for the HIV-1 virus. Dalgleish et al. (1984) Nature
312:763-67; Klatzmann (1984) Nature 312:767-68; and Maddon et al.
(1986) Cell 47:333-48.
[0005] After binding to the cell surface, the HIV-1 virion becomes
internalized, and once inside the cell, the viral life cycle begins
by conversion of the RNA genome into linear DNA molecules. This
process is dependent on the action of the virally encoded reverse
transcriptase. Following replication of the viral genome, the
linear DNA molecule integrates into the host genome through the
action of the viral integrase protein, thus establishing the
proviral form of HIV-1.
[0006] It was later discovered that other than CD4, HIV-1 utilizes
several cell membrane proteins as its coreceptor to falitate viral
entry into the host cell. Alkhatib et al. (1996) Science 272:
1955-1958; and Deng et al. (1996) Nature 388:296-300. Examples of
chemokine receptors include CXCR4, CCR5, CCR1, CCR2b, CCR3, CCR4,
CCR8, CXCR1, CXCR2, CXCR3, and CX.sub.3CR1. Examples of chemokine
receptor-like orphan proteins include STRL33/BONZO and
GPR15/BOB.
[0007] CXCR4 (also known as "fusin") is a receptor for chemokines
such as SDF-1.alpha. and SDF-1.beta.. CCR5 is a receptor for
several CC chemokines such as MIP-1.alpha. (also named GOS19, LD78,
pAT464 gene product, TY5 (murine) and SIS.alpha. (murine)),
MIP-1.beta. (also named Act-2, G-26, pAT744 gene product, H-400
(murine) and hSIS.gamma. (murine)) and RANTES (regulated on
activation, normal T cell expressed and secreted, or CCL5). Cocchi
et al. (1995) Science 270:1811-1815; and Mellado et al. (2001)
Annu. Rev. Immunol. 19:397-421. The roles of these CC chemokine
molecules in regulating T cell fate include possible indirect
effects on antigen-presenting cells and direct effects on
differentiating T cells. Luther & Cyster (2001) Nat. Immunol.
2:102-107.
[0008] Specific chemokine receptors such as CXCR4 and CCR5
receptors play important roles in mediating HIV entry and tropism
for different target cells. See reviews by Berger (1997) AIDS 11,
Suppl. a: S3-S16; and Dimitrov (1997) Cell 91: 721-730; and Burger
et al. (1999) Annu. Rev. Immunol. 17:657-700. Macrophages-tropic
(M-tropic) strains of HIV virus can replicate in primary CD4.sup.+
T cells and macrophages and use the .alpha.-chemokine receptor CCR5
and less often, CCR3 receptor. T cell line-tropic (T-tropic) HIV
strains can also replicate in primary CD4.sup.+ T cells but can in
addition infect established CD4.sup.+ T cell lines in vitro via the
.alpha.-chemokine receptor CXCR4. Many of the T-tropic strains can
use CCR5 in addition to CXCR4. Chemokine receptor-like HIV
coreceptor STRL33 is expressed in activated peripheral blood
lymphocytes and T-cell lines and can function as an entry cofactor
for Env proteins from M-tropic, T-tropic and dual tropic strains of
HIV-1 and SIV. Other HIV coreceptors have also been identified by
numerous in vitro assays, including chemokine receptors CCR2b,
CCR3, CCR8 and CX3CR1 as well as several chemokine receptor-like
orphan receptor proteins such as GPR15/BOB and STRL33/BONZO. Each
or a set of these HIV coreceptors can mediate entry of different
strains of HIV virus into the host cell.
[0009] The CC chemokine receptor CCR5 is a principal HIV-1
coreceptor that plays a dominant role in disease transmission and
in the early course of infection. Berger et al. (1999) Annu. Rev.
Immunol. 17:657-700. Molecular epidemiology studies clearly
demonstrated that CCR5 plays critical roles in HIV-1 transmission
and pathogenesis. Individuals lacking two copies of functional CCR5
alleles (.DELTA.32 allele) are strongly protected against HIV-1
infection. Dean et al. (1996) Science 273:1856-1862. Individuals
with one .DELTA.32 and one normal CCR5 gene on average express
lower levels of CCR5 on their T cells. Wu et al. (1997) J. Exp Med.
185:1681-1691. Heterozygosity for the .DELTA.32 allele does not
protect against HIV-1 infection but does confer an improved
prognosis in the form of significantly increased AIDS-free and
overall survival periods. Husman et al. (1997) Ann. Intern. Med.
127:882-890. Moreover, CCR5 heterozygotes are overrepresented among
long-term nonprogressors, i.e., those individuals who do not
progress to AIDS after 10 or more years of infection. Dean et al.
(1996) Science 273:1856-1862. Because it is an essential coreceptor
for clinically relevant strains of HIV-1 and yet is apparently
dispensable for human health, CCR5 provides an attractive target
for new antiretroviral therapies. Liu et al. (1996) Cell
86:367-377; and Michael & Moore (1999) Nat. Med. 5:740-742.
[0010] Several approaches have been employed to target HIV
coreceptors, involving proteins, peptides and small molecules. It
has been found that some CCR5-targeting chemokines and chemokine
analogs are capable of inhibiting HIV-1 replication in vitro.
Berger et al. (1999) Annu. Rev. Immunol. 17:657-700. Of the CC
chemokines that bind CCR5, RANTES possesses significantly greater
breadth of antiviral activity than MIP-1.alpha. and MIP-1.beta.,
although all CC chemokines show interisolate variation in potency.
Trkola et al. (1998) J. Viol. 72:396-404. The antiviral activity of
the CC chemokines better correlates with their ability to
downregulate rather than to bind CCR5 on CD4 T cells, and sustained
down-regulation of CCR5 has been suggested to be a principal
mechanism of action for the chemokine analog aminooxypentane
(AOP)-RANTES. Mack et al. (1998) J. Exp. Med. 187:1215-1224. A
small non-peptide molecule designated TAK-779 was found to be an
antagonist against CCR5 presumably through binding to a hydrophobic
pocket defined by the transmembrane helices 1, 2, 3 and 7. Baba et
al. (1999) Proc. Natl. Acad. Sci. USA 96:5698-5703; Shiraishi et
al. (2000) J. Med. Chem. 43:2049-2063; and Dragic et al. (2000)
Proc. Natl. Acad. Sci. USA 97:5639-5644.
[0011] Phage display has been utilized to select for single chain
antibody against CCR5 from a human antibody library by using
CCR5-expressing CD4.sup.+ lymphocytes as the target in the presence
and absence of MIP-1.alpha.. Osbourn et al. (1998) Nature Biotech.
16:778-781. The selected phage particles were analyzed by phage
ELISA for their ability to recognize CD4.sup.+ lymphocytes,
CCR5-transfected CHO cell line, non-transfected CHO cell line, and
a BSA-conjugated peptide corresponding to the N-terminal 20 amino
acid peptide of CCR5. Osbourn et al. found that none of the
antibodies selected in the presence of MIP-1.alpha. blocked
MIP-1.alpha. binding to CD4.sup.+ lymphocytes. Among the antibodies
selected in the absence of MIP-1.alpha., around 20% inhibited
MIP-1.alpha. binding to CD4.sup.+ lymphocytes, as well as
MIP-1.alpha. mediated calcium signaling.
[0012] Mouse monoclonal antibodies have also been generated to
target CCR5 by using the whole protein of CCR5 as the antigen. For
example, Wu et al. immunized mice with the murine pre-B cell
lymphoma cell line L1.2 expressing high levels of transfected CCR5,
which generated a IgG1 monoclonal antibody, designated as mAb 2D7.
Wu et al. (1997) J. Exp. Med. 186:1373-1381. The binding site of
this monoclonal on CCR5 was mapped to the second extracellular loop
of CCR5. MAb 2D7 was shown to be able block the binding and
chemotaxis of the three natural chemokine ligands of CCR5, RANTES,
macrophage inflammatory protein MIP-1.alpha. and MIP-1.beta., to
CCR5 transfectants. MAb 2D7 failed to stimulate an increase in
intracellular calcium concentration in the CCR5 transfectants, but
blocked calcium response elicited by RANTES, MIP-1.alpha. and
MIP-1.beta. chemotactic responses of activated T cells, but not of
monocyte. In contrast, a group of mAbs that were also generated in
the same process and failed to clock chemokine binding were all
mapped to the N-terminal region of CCR5.
[0013] Using a similar strategy to Wu et al. (1997), Olson et al.
isolated 6 anti-CCR5 murine monoclonal antibodies (MAbs) by
intraperitoneally immunizing female BALB/c mice with murine L1.2
cells expressing CCR5. Olson et al. (1999) J. Virol. 73:4145-4155.
Epitope mapping of these MAbs reveals that the epitopes of these
antibodies reside in the N-terminus and/or second extracellular
loop regions of CCR5. This structural information was correlated
with the antibodies' abilities to inhibit (1) HIV-1 entry; (2)
HIV-1 envelope glycoprotein-mediated membrane fusion; (3) gp120
binding to CCR5; and (4) CC-chemokine activity. Surprisingly, each
of the antibodies displayed distinctly different activities in
different stages of HIV-1 entry. In particular, one of these MAbs,
PRO140, was shown to exert inhibitory effects on HIV-1 infection on
primary peripheral blood mononuclear cells (PBMC). Trkola et al.
(2001) J. Virol, 75:579-588.
SUMMARY OF THE INVENTION
[0014] The present invention provides innovative methods for
generating antibodies against a wide variety of proteins targets,
especially against membrane proteins. In particular, methods are
provided for eliciting monoclonal antibody against a target
membrane protein by using a fusion protein as an immunogen that
contains a peptide fragment derived from the membrane protein. More
particularly, efficient high through methods are provided for
screening fully human antibody library against membrane proteins
such as HIV coreceptors in yeast.
[0015] In one aspect of the invention, a method is provided for
eliciting antibodies against a membrane protein in a non-human
animal. The method comprises: immunizing a non-human animal with an
antigen that is a fusion protein between a peptide fragment of a
target membrane protein and a heterologous chaperon protein that
stabilizes the peptide fragment.
[0016] The step of immunizing the animal may include injecting the
antigen directly into the animal. For example, the antigen may be
injected into a mouse to elicit polyclonal antibodies, or
monoclonal antibodies by using a hybridoma technology. The animal
may be a natural animal, a transgenic animal that has been
genetically modified to produce human antibodies, such as
XENOMOUSE.RTM. and HuMab Mouse, or a transchromosome (TC)
mouse.
[0017] Optionally, the step of immunizing the animal may include
transfecting the animal with an expression vector encoding the
antigen. For example, DNA sequence encoding the antigen can be
inserted into a mammalian expression vector or a viral vector
(e.g., retroviral, adenoviral, and adeno-associated viral vectors)
and the resulting expression vector can be injected into the animal
where the expression of the antigen by the vector elicits immune
responses to the antigen. Antibodies can then be isolated from the
serum of the animal and used to target the membrane protein for
therapeutic or diagnostic purposes.
[0018] In another aspect of the invention, a method is provided for
selecting antibody against a membrane protein in vitro. The method
comprises: contacting a library of antibodies with an antigen that
is a fusion protein between a peptide fragment of a target membrane
protein and a heterologous chaperon protein that stabilizes the
peptide fragment; and selecting the antibodies that bind to the
antigen.
[0019] According to the above-described methods, the chaperon
protein may be any protein or a domain of a protein that is capable
of stabilizing the fused peptide, for example, structurally
stabilizing the conformation of the peptide under the condition of
the immunization or screening process and/or preventing degradation
of the peptide. Preferably, the chaperon protein may be a DNA
binding domain (BD) or an activation domain (AD) of a transcription
factor. More preferably, the chaperon protein may include Gal4 DNA
binding domain, LexA binding domain, lambda c1 DNA binding domain,
cdc25 or Sos (guanine nucleotide exchange factor), T18 bacterial
protein, T25 bacterial protein, the alpha and omega fragments of
beta-lactamase, glutathion-S-transferase (GST) and thioredoxin.
[0020] The library of antibodies may be a library of antibodies
mixed in solution, immobilized to a substrate in the form of an
array, or displayed by mRNA, ribosome, phage, and cells such as
yeast cells.
[0021] The antibodies in the library may be in the form of a single
chain antibody, Fab antibody and fully assembled antibody.
[0022] In yet another aspect of the invention, a method is provided
for screening a library of single chain antibodies (scFv) against a
target peptide in yeast. In one embodiment, the method
comprising:
[0023] expressing a library of scFv fusion proteins in yeast cells,
each scFv fusion protein comprising either an activation domain or
a DNA binding domain of a transcription activator and a scFv, the
scFv comprising a V.sub.H of antibody whose sequence varies within
the library, a V.sub.L of antibody whose sequence varies within the
library independently of the V.sub.H, and a linker peptide which
links the V.sub.H and V.sub.L;
[0024] expressing a target fusion protein in the yeast cells
expressing the scFv fusion proteins, the target fusion protein
comprising either the DNA binding domain or the activation domain
of the transcription activator which is not comprised in the scFv
fusion proteins, and a target peptide; and
[0025] selecting those yeast cells in which a reporter gene is
expressed, the expression of the reporter gene being activated by a
reconstituted transcriptional activator formed by binding of the
scFv fusion protein to the target fusion protein.
[0026] According to the embodiment, the diversity of the library
scFv fusion proteins is preferably higher than 1.times.10.sup.4,
more preferably higher than 1.times.10.sup.6, and most preferably
higher than 1.times.10.sup.7. Optionally, the diversity of the
library scFv fusion proteins is between
1.times.10.sup.4-1.times.10.sup.11,
1.times.10.sup.6-1.times.10.sup.10,
1.times.10.sup.7-1.times.10.sup.10,
1.times.10.sup.7-1.times.10.sup.9, or
1.times.10.sup.8-1.times.10.sup.10.
[0027] In yet another aspect of the invention, a method is provided
for screening a library of antibodies against a target peptide in
yeast. In one embodiment, the method comprising:
[0028] expressing a library of antibody fusion proteins in yeast
cells, each antibody fusion protein comprising either an activation
domain or a DNA binding domain of a transcription activator which
is fused with either V.sub.H or V.sub.L of the antibody, wherein
the sequences of V.sub.Hand V.sub.L of the antibody vary
independently within the library, and the V.sub.H, V.sub.L and
their fusions thereof are expressed as separate proteins and
assemble in yeast to form the antibody fusion proteins;
[0029] expressing a target fusion protein in the yeast cells
expressing the antibody fusion proteins, the target fusion protein
comprising either the DNA binding domain or the activation domain
of the transcription activator which is not comprised in the
antibody fusion proteins, and a target peptide; and
[0030] selecting those yeast cells in which a reporter gene is
expressed, the expression of the reporter gene being activated by a
reconstituted transcriptional activator formed by binding of the
antibody fusion protein to the target fusion protein.
[0031] According to the embodiment, the diversity of the library
antibody fusion proteins is preferably higher than
1.times.10.sup.4, more preferably higher than 1.times.10.sup.6, and
most preferably higher than 1.times.10.sup.7. Optionally, the
diversity of the library antibody fusion proteins is between
1.times.10.sup.4-1.times.10.sup.11,
1.times.10.sup.6-1.times.10.sup.10,
1.times.10.sup.7-1.times.10.sup.10,
1.times.10.sup.7-1.times.10.sup.9, or
1.times.10.sup.8-1.times.10.sup.10.
[0032] According to any of the above methods, the length of the
target peptide is preferably 5-100 aa, more preferably 10-80 aa,
and most preferably 20-60 aa.
[0033] According to any of the above methods, the target peptide or
peptide fragment may be a fragment of a protein that includes an
antigenic determinant or epitope, preferably a fragment of a
membrane protein, more preferably an extracellular domain of a
membrane protein, and most preferably an extracellular loop of a
transmembrane protein.
[0034] Examples of the membrane protein include, but are not
limited to, receptors for growth factors (e.g., vascular
endothelial growth factor (VEGF), transforming growth factor (TGF),
fibroblast growth factor (FF), platelet derived growth factor
(PDGF), insulin-like growth factor), insulin receptor, MHC proteins
(e.g. class I MHC and class II MHC protein), CD3 receptor, T cell
receptors, cytokine receptors (e.g., interleukin (IL)-1, IL-2,
IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12,
IL-13, IL-14, IL-15 receptors), tyrosine-kinase-associated
receptors such as Src, Yes, Fgr, Lck, Flt, Lyn, Hck, and Blk, and
G-protein coupled receptors such as receptors for the hormone
relaxin (LGR7 and LGR8) and chemokine receptor (e.g., CCR1, CCR2,
CCR3, CCR4, CCR5, CCR6, CCR7, CCR8, CCR9, CCR10, CCR11, CXCR1,
CXCR2, CXCR3, CXCR4, CXCR5, CXCR6, CX3CR1, and XCR1), PSGR,
beta1-adrenergic receptor, beta2-adrenergic receptor, parathyroid
hormone (PTH) receptor, EDG1, G10d, opioid receptors, neutensin
recetpors, neuropeptide Y (NPY) receptors, melatonin receptor,
adrenocorticotrophin (ACTH) receptor, leukotriene receptors,
5-hydroxytryptamine (5-HT, or serotonin) receptors (including
5-TH1a, 5-TH1b, 5-TH1d, 5-TH1e, 5-TH1f, 5-TH2a, 5-TH2b, 5-TH2c,
5-TH3, 5-TH4, 5-TH5 receptors), FSH receptor, LH/hCG receptor, TSH
receptor, formyl-methionyl peptide (fMLP) receptors (FPR1 receptor,
FPR2 receptor, FPR3 receptor), GABA receptors, endothelin (ET)
receptors, sarafotoxin receptors, dopamin receptors (D1 receptor,
D2 receptor, D3 receptor, D4 receptor, D5 receptor), cannabinoid
receptor, CGRP1 receptor, CGRP2 receptor, amylin receptor,
calcitonin receptor, C5a receptor, bradykinin receptors (B1, B2 and
B3 receptors), bombesin Receptors (BB1, BB2 and BB3 receptors),
angiotensin receptors (AT1a, AT1b and AT2 receptors), adrenaline
and noradrenaline receptors (or adrenoceptors), acetylcholine
Receptors, platelet activating factor (PAF) receptor, prostanoid
receptors (DP, EP1, EP2, EP3, FP, IP and TP receptors),
somatostanin receptors (SS1, SS2, SS3, SS4 receptors), tachykinin
Recetpors (NK1, NK2 and NK3 receptors), thrombin receptor,
vasoactive Intestinal polypeptide (VIP) receptor family (GRF,
PACAP, secretin, VIP and helodermin-preferring receptors),
stresscopin receptor, urocortin receptor, corticotropin releasing
hormone receptors, LGR4, LGR5, LGR6, LGR7 and LGR8; and GPCR orphan
receptors designated as GPR1-58 at GenBank.
[0035] The target peptide or peptide fragment may also be derived
from a viral surface or core protein. Examples of these viral
proteins include, but are not limited to, glycoproteins (or surface
antigens, e.g., GP120 and GP41) and capsid proteins (or structural
proteins, e.g., P24 protein); surface antigens or core proteins of
hepatitis A, B, C, D or E virus (e.g. small hepatitis B surface
antigen (SHBsAg) of hepatitis B virus and the core proteins of
hepatitis C virus, NS3, NS4 and NS5 antigens); glycoprotein
(G-protein) or the fusion protein (F-protein) of respiratory
syncytial virus (RSV); surface and core proteins of herpes simplex
virus HSV-1 and HSV-2 (e.g., glycoprotein D from HSV-2).
[0036] In one particular variation of the embodiment, the target
peptide comprises an extracellular domain of human CCR5 selected
from the group consisting of N-terminal domain, loop 2, loop 4, and
loop 6 of human CCR5. Preferably, the extracellular domain of human
CCR5 comprises a sequence selected from the group consisting of SEQ
ID Nos: 2, 3, 8, and 9.
[0037] In another particular variation of the embodiment, the
target peptide comprises an extracellular domain of human CXCR4
selected from the group consisting of N-terminal domain, loop 2,
loop 4, and loop 6 of human CXCR4. Preferably, the extracellular
domain of human CXCR4 comprises SEQ ID NO: 58.
[0038] Also according to the embodiment, the activation domain or
the DNA binding domain of the transcription activator may
optionally be fused to C-terminus of the scFv, or to the N-terminus
of the scFv.
[0039] Also according to the embodiment, the activation domain or
the DNA binding domain of the transcription activator may
optionally be fused to C-terminus of the target peptide, or to the
N-terminus of the target peptide.
[0040] According to the embodiment, the step of expressing the
library of scFv fusion proteins in yeast cells may include
transforming a library of scFv expression vectors into the yeast
cells which contain the reporter gene.
[0041] Optionally, the step of expressing the target fusion
proteins includes transforming a target expression vector into the
yeast cells simultaneously or sequentially with the library of scFv
expression vectors.
[0042] Also according to the embodiment, the steps of expressing
the library of scFv fusion proteins and expressing the target
fusion protein may optionally include causing mating between first
and second populations of haploid yeast cells of opposite mating
types.
[0043] The first population of haploid yeast cells comprises a
library of scFv expression vectors for the library of scFv fusion
proteins. The second population of haploid yeast cells comprises a
target expression vector. Either the first or second population of
haploid yeast cells comprises the reporter gene.
[0044] The haploid yeast cells of opposite mating types may
preferably be .alpha. and a type strains of yeast. The mating
between the first and second populations of haploid yeast cells of
.alpha. and a type strains may be conducted in a rich nutritional
culture medium.
[0045] It should be noted that the above-described target peptide
fragment derived from a membrane protein may be screened against an
antibody library in other organisms or in vitro. For example, the
target peptide may be expressed as a fusion protein with another
protein and screened against an antibody library co-expressed in
mammalian cells. The target peptide may also be immobilized to a
substrate as a single peptide or a fusion protein and selected
against a library of antibodies displayed by mRNA, ribosome, phage
or cells such as yeast cells. In addition, the target peptide may
be introduced to a xenomouse, a HuMab mouse, or a transchromosomal
mouse that contains a library of human antibody, and selected for
monoclonal human antibodies with specific binding affinity to
target peptide and/or the target membrane protein.
[0046] In yet another aspect of the invention, compositions that
comprise at least one of the heavy chain and light chain variable
region of an antibody are provided which recognize epitopes on the
extracellular domains of human CCR5.
[0047] In one embodiment, the composition comprises an antibody
that binds to loop 6 of human CCR5. In a variation, the antibody is
capable of inhibiting HIV-1 infection of human cells.
[0048] It is noted the antibody may be a polyclonal or a monoclonal
antibody, including but not limited to fully assembled antibody,
single chain antibody, Fab fragment, and chimeric antibody.
[0049] Optionally, CDR2 of the heavy chain variable region of the
antibody comprises amino acid sequence GSTX.sub.1YNPSL [SEQ ID NO:
32], wherein X.sub.1 is asparagine (N) or threonine (T).
[0050] Optionally, CDR2 of the light chain variable region of the
antibody comprises amino acid sequence DAX.sub.2 X.sub.3L [SEQ ID
NO: 33], wherein X.sub.2 is threonine (T) or serine (S), and
X.sub.3 is threonine (T) or aspartic acid (D).
[0051] Optionally, CDR2 of the heavy chain variable region of the
antibody comprises amino acid sequence GSTX.sub.1YNPSL [SEQ ID NO:
32]; and CDR2 of the light chain variable region of the antibody
comprises amino acid sequence DAX.sub.2 X.sub.3L [SEQ ID NO: 33],
wherein X.sub.1 is asparagine (N) or threonine (T), X.sub.2 is
threonine (T) or serine (S), and X.sub.3 is threonine (T) or
aspartic acid (D).
[0052] Optionally, CDR3 of the heavy chain variable region of the
monoclonal antibody comprises 5, 6, 7, 8, 9 or more consecutive
amino acids of a sequence elected from the group consisting of
TABLE-US-00001 RLKGAWLLSEPPYFSSDGMDV, [SEQ ID NO: 43] RTVAGTSDY,
[SEQ ID NO: 44] and HEQYYYDTSGQPYYFDF. [SEQ ID NO: 45]
[0053] Optionally, CDR3 of the light chain variable region of the
monoclonal antibody comprises 5, 6, 7, 8, 9 or more consecutive
amino acids of a sequence elected from the group consisting of
TABLE-US-00002 AAWDESLNGVV, [SEQ ID NO: 46] LQHDNFPLT, [SEQ ID NO:
47] and QQSDYLPLT. [SEQ ID NO: 48]
[0054] Optionally, CDR3 of the heavy chain variable region of the
monoclonal antibody comprises an amino acid sequence selected from
the group consisting of SEQ ID Nos: 43-45; and CDR3 of the light
chain variable region of the monoclonal antibody comprises an amino
acid sequence selected from the group consisting of SEQ ID Nos:
46-48.
[0055] It is noted that the above-described different CDR regions
may all be included in the antibody independent of each other, or
in combination with one or more of each other.
[0056] Optionally, CDR3 of the heavy chain variable region of the
antibody comprises an amino acid sequence selected from the group
consisting of SEQ ID Nos: 43-45; and CDR3 of the light chain
variable region of the antibody comprises an amino acid sequence
selected from the group consisting of SEQ ID Nos: 46-48.
[0057] Optionally, the heavy chain variable region of the antibody
comprises an amino acid sequence selected from SEQ ID Nos: 36, 38,
and 40.
[0058] Optionally, the light chain variable region of the antibody
comprises an amino acid sequence selected from SEQ ID Nos: 37, 39,
and 41.
[0059] In yet another aspect of the invention, compositions that
comprise at least one of the heavy chain and light chain variable
region of an antibody are provided which recognize epitopes on the
extracellular domains of human CXCR4.
[0060] In one embodiment, the composition comprises an antibody
that binds to loop 6 of human CXCR4. In a variation, the antibody
is capable of inhibiting HIV-1 infection of human cells. In another
variation, the antibody is capable of inhibiting chemotaxis of
cells, optionally human cancer cells, optionally human breast
cancer cells.
[0061] It is noted the antibody may be a polyclonal or a monoclonal
antibody, including but not limited to fully assembled antibody,
single chain antibody, Fab fragment, and chimeric antibody. For
example, the antibody is a single chain antibody encoded by DNA SEQ
ID NO: 59 or 62.
[0062] Optionally, the heavy chain variable region of the antibody
comprises an amino acid sequence with SEQ ID NO: 60 or 63.
[0063] Optionally, the light chain variable region of the antibody
comprises an amino acid sequence with SEQ ID NO: 61 or 64.
[0064] The antibody of the present invention may be produced by
expression in bacteria, yeast, plant, and animal cells in any form
including but not limited to single chain, Fab, full length IgA,
secretion form sIgA, or IgG.
[0065] The antibody of present invention may be used for the
prevention or treatment of HIV infection. For example, the
antibodies against human CCR5 may be administered to an individual
with high risk of HIV infection or already infected with HIV to
block the entry of HIV-1 into the cells.
[0066] The antibody of present invention may also be conjugated
with a molecule such as an antiviral drug and a radio-isotope to
specifically target cells expressing human CCR5 and/or CXCR4.
[0067] The antibody of the present invention may be used in a
therapy for the treatment of various diseases such as cancer,
autoimmune diseases, and viral infection. The antibody may also be
used in a combination therapy in conjunction with other therapeutic
agents such as anti-viral agents (e.g., nucleoside or
non-nucleoside HIV reverse transcriptase inhibitors, HIV protease
inhibitors, and HIV integrase inhibitors), and anti-neoplastic
agents.
[0068] Examples of the nucleoside HIV reverse transcriptase
inhibitor include, but are not limited to zidovudine (AZT),
didanosine (ddI), zalcitabine (ddC), lamivudine (3TC), stavudine
(d4T), abacavir (1592U89), and adefovir dipivoxil (bis(POM)-PMEA).
Examples of the non-nucleoside HIV reverse transcriptase inhibitor
include, but are not limited to nevirapine (BI-RG-587), delavirdine
(BHAP, U-90152) and efavirenz (DMP 266). Examples of the HIV
protease inhibitors include, but are not limited to indinavir
(MK-639), ritonavir (ABT-538), saqinavir (Ro-31-8959), nelfinavir
(AG-1343), and amprenavir (141W94).
[0069] Examples of anti-neoplastic agents include, but are not
limited to, alkylating agents (e.g., cyclophosphamide and
cisplatin), antibiotic agents (e.g., doxorubicin, mitomycin C, and
bleomycin), antimetabolic agents (e.g., fluorouracil (5-FU) and
methotrexate), hormonal agents (e.g., tamoxifen), plant-derived
agents (paclitaxel, vincristine and camptothecin), and biologic
agents (e.g., monoclonal antibodies such as HERCEPTIN.RTM.
(Trastruzumab) and RITUXAN.RTM. (Rituximab), and cytokines).
[0070] The antibody of the present invention may be administered to
a mammal, preferably a human, via a variety of routes, including
but not limited to, orally, parenterally, intraperitoneally,
intravenously, intraarterially, topically, transdermally,
sublingually, intramuscularly, rectally, transbuccally,
intranasally, liposomally, via inhalation, vaginally,
intraoccularly, via local delivery (for example by catheter or
stent), subcutaneously, intraadiposally, intraarticularly, or
intrathecally. The antibody may also be delivered to the host
locally (e.g., via stents or cathetors) and/or in a timed-release
manner.
[0071] Additionally, the antibody of the present invention may be
used for diagnosis of diseases associated with membrane proteins
interactions such as CXCR4 and CCR5, the co-receptors of HIV.
Moreover, the antibody may be used in assays for screening
therapeutic agents against these diseases.
BRIEF DESCRIPTION OF THE FIGURES
[0072] FIG. 1A shows the amino acid sequence of human CCR5.
[0073] FIG. 1B shows the amino acid sequences of peptide fragments
derived from human CCR5 that are used as target peptides for
eliciting antibody according to the present invention.
[0074] FIG. 1C shows and a model of the secondary structure of
human CCR5.
[0075] FIG. 2A illustrates an embodiment of the method of present
invention for screening of scFv against a target peptide derived
from a membrane protein via transformation of yeast cells.
[0076] FIG. 2B illustrates another embodiment of the method of
present invention for screening of scFv against a target peptide
derived from a membrane protein via mating of two yeast
strains.
[0077] FIG. 3 illustrates a method of constructing a human scFv
antibody library via homologous recombination in yeast.
[0078] FIG. 4 illustrates a method of affinity maturation of an
antibody lead.
[0079] FIG. 5 shows DNA and amino acid sequences of four distinct
scFv antibodies against human CCR5 fragments.
[0080] FIG. 6 shows DNA and amino acid sequences of variants of the
four scFv antibodies against human CCR5 fragments.
[0081] FIG. 7 shows a homology alignment of amino acid sequences of
three scFv antibodies against human CCR5 Loop6.
[0082] FIG. 8 shows amino acid sequences of V.sub.H and V.sub.L of
the four scFv antibodies against human CCR5 fragments.
[0083] FIGS. 9A-C show HIV-1 reverse transcriptase (RT) activity in
a culture of human monocytes infected by HIV-1 in the present or
absent of antibody on day 4, 8, and 12 post infection,
respectively.
[0084] FIGS. 10A-C show viability of a culture of human monocytes
infected by HIV-1 in the present or absent of antibody on day 4, 8,
and 12 post infection, respectively.
[0085] FIGS. 11A-C show HIV-1 reverse transcriptase (RT) activity
in a culture of human monocytes infected by HIV-1 in the present or
absent of antibody at lower concentrations than those in FIGS. 9A-C
on day 4, 8, and 12 post infection, respectively.
[0086] FIG. 12 shows a Western blot of CCR5 expressed by human
macrophage probed by scFv against human CCR5 Loop 6.
[0087] FIG. 13 is a graph showing that two scFv against human CCR5
Loop 6 are both capable of blocking the binding of MIP-1.alpha. to
CCR5 on human monocyte-derived macrophages.
[0088] FIG. 14 is a graph showing that non-labeled CCR5 ligands,
MIP-1.alpha. and RANTES, can compete with radio-labeled
MIP-1.alpha. in binding with CCR5 on human monocyte-derived
macrophages.
[0089] FIG. 15 shows DNA sequence, amino acid sequences of V.sub.H
and V.sub.L of single chain antibodies Ab124 and Ab125.
[0090] FIG. 16 is a graph showing that single chain antibodies
Ab124 and Ab125 can inhibit SDF-1 induced chemotaxis in human
breast cancer line MDA-MB-231.
DETAILED DESCRIPTION OF THE INVENTION
[0091] The present invention provides innovative methods for
efficient, high throughput screening of antibody library against a
wide variety of target proteins, especially membrane proteins. In
particular, the methods can be used to systematically and
efficiently screen human antibody against epitopes on a target
protein and select for antibodies with high affinity and efficacy
in regulating the biological functions of the target protein. More
particularly, fully human antibodies can be selected by using these
methods to target therapeutically significant membrane proteins,
such as cell surface co-receptors for HIV envelope protein (e.g.,
CXCR4 and CCR5).
[0092] Membrane proteins are generally considered to be evasive
targets for screening agents for therapeutic intervention and
rational drug design because of difficulties associated with
isolation and purification, as well as the structural uncertainty
of the isolated protein adopted in vitro. As described in the
section of "Background of the Invention", skilled artisans resorted
to using cells expressing the whole protein of the membrane protein
such as CCR5 as an immunogen to elicit monoclonal antibody against
it.
[0093] Surprisingly, the inventors discovered that peptide
fragments of a membrane protein, as opposed to the whole protein,
can be excellent targets against which high affinity antibody can
be selected in a yeast two-hybrid system. The peptide fragment is
expressed as a target fusion protein with the DNA-binding domain
(BD) (or the activation domain (AD)) of a transcription activator
in yeast cells. A library of fully human single-chain antibody is
expressed as tester fusion proteins with the AD (or the BD) of the
transcription activator in the same yeast cells. Binding of the
antibody to the peptide target triggers expression of a reporter
gene in the yeast cell, which facilitates identification and
isolation of the clones containing the monoclonal human antibody.
The ability of the selected monoclonal antibodies in blocking HIV
entry and inhibiting infection has been validated. See the
"EXAMPLE" section below.
[0094] Not wishing to be bound by the theory, the inventors believe
that a peptide fragment derived from a membrane protein, when fused
with a heterologous protein that acts like a chaperon to stabilize
the conformation adopted by the peptide in isolation from the
membrane protein, can serve as an immunogen to elicit antibody in
an animal or as a target ligand in screening assays in vitro. The
fusion protein formed by the peptide and the chaperon protein may
present the peptide in a conformation similar to that adopted by
the peptide in its native context, i.e., in the membrane protein
located on the cell. In particular, extracellular loops adopted by
stretches of peptide sequences in the membrane protein are
attractive targets because these loops can serve as accessible
epitopes for extracellular binding with antibodies to block
downstream signal transduction mediated by the membrane protein.
This feature is desirable for therapeutic and diagnostic
applications targeting cells expressing the membrane protein.
[0095] In one aspect, a method is provided for eliciting antibodies
against a membrane protein in a non-human animal. The method
comprises: immunizing a non-human animal with an antigen that is a
fusion protein between a peptide fragment of a target membrane
protein and a heterologous chaperon protein that stabilizes the
peptide fragment.
[0096] The step of immunizing the animal may include injecting the
antigen directly into the animal. For example, the antigen may be
injected into a mouse to elicit polyclonal antibodies, or
monoclonal antibodies by using a conventional hybridoma technology,
examples of which are described in detail in Section 2 below. The
animal may be a natural animal, a transgenic animal that has been
genetically modified to produce human antibodies, such as
XENOMOUSE.RTM. and HuMab Mouse, or a transchromosome (TC) mouse
(Tomizuka et al. (2000) Proc Natl Acad Sci USA. 97:722-727. This
document, and all documents cited to herein, are incorporated by
reference as if fully reproduced below).
[0097] For example, the fusion protein formed by the peptide and
the chaperon protein may be administered into a XENOMOUSE.RTM. by
following protocols described in U.S. Pat. Nos. 6,075,181 and
6,114,598 which are incorporated herein by reference. Briefly, two
to six xenomice aged 6-30 weeks are age-matched and immunized
intraperitoneally with 10-100 .mu.g of the fusion protein in
complete Freund's adjuvant for primary immunization and in
incomplete Freund's adjuvant for subsequent injections. The mice
received 6 injections 2-3 weeks apart. Serum titers are determined
after the second dose and following each dose thereafter. Bleeds
are performed 6-7 days after injections from the retrobulbar
plexus. The blood is allowed to clot at room temperature for about
2 hours and then incubated at 4.degree. C. for at least 2 hours
before separating and collecting the sera. The sera of the
immunized xenomice (or the supernatants from immortalized B cells)
are titrated for antigen specific human antibodies using a standard
ELISA assay. In this assay, the antigen used for immunization,
i.e., the fusion protein, was immobilized onto wells of microtiter
plates. The plates are washed and blocked and the sera (or
supernatants) are added as serial dilutions for 1-2 hours of
incubation. After washing, bound antibody having human
characteristics are detected by adding the appropriate antispecies
Ig (typically antihuman .kappa. or antihuman .mu.) conjugated to
horseradish peroxidase (HRP) for one hour. The bound antibodies may
be tested for murine characteristics using antimurine antibodies,
typically antimurine .gamma.. After again washing, the chromogenic
reagent o-phenylene diamine (OPD) substrate and hydrogen peroxide
are added and the plates are read 30 minutes later at 492 nm using
a microplate reader. The hybridoma secreting the target
antigen-binding antibodies is used to obtain the cDNA encoding
fully human variable regions. Such xenogeneic antibodies can then
converted to fully human antibodies by cloning the variable region
sequences into plasmids containing the coding sequences for human
antibodies. Queens et al. Proc. Natl. Acad. Sci. (1989)
86:10029.
[0098] Optionally, the step of immunizing the animal may include
transfecting the animal with an expression vector encoding the
antigen. For example, DNA sequence encoding the antigen can be
inserted into a mammalian expression vector or a viral vector
(e.g., retroviral, adnoviral, and adeno-associated viral vectors)
and the resulting expression vector can be injected into the animal
where the expression of the antigen by the vector elicits immune
responses to the antigen. Antibodies can then be isolated from the
serum of the animal and used to target the membrane protein for
therapeutic or diagnostic purposes.
[0099] In another aspect, a method is provided for selecting
antibody against a membrane protein in vitro. The method comprises:
contacting a library of antibodies with an antigen that is a fusion
protein between a peptide fragment of a target membrane protein and
a heterologous chaperon protein that stabilizes the peptide
fragment; and selecting the antibodies that bind to the
antigen.
[0100] The library of antibodies may be a library of antibodies
mixed in solution, immobilized to a substrate in the form of an
array, or displayed by mRNA, ribosome, phage, and cells such as
yeast cells.
[0101] The antibodies in the library may be in the form of a single
chain antibody, Fab antibody and fully assembled antibody.
[0102] The chaperon protein may be any protein or a domain of a
protein that is heterologous to the membrane protein and capable of
stabilizing the fused peptide, for example, structurally
stabilizing the conformation of the peptide under the condition of
the immunization or screening process and/or preventing degradation
of the peptide. Preferably, the chaperon protein may be a DNA
binding domain (BD) or an activation domain (AD) of a transcription
factor. More preferably, the chaperon protein may include Gal4 DNA
binding domain, LexA binding domain, lambda cl DNA binding domain,
cdc25 or Sos (guanine nucleotide exchange factor), T18 bacterial
protein, T25 bacterial protein, the alpha and omega fragments of
beta-lactamase, glutathion-S-transferase (GST) and thioredoxin.
[0103] In yet another aspect, the present invention provides a
method for selecting monoclonal single chain antibody (scFv)
against a peptide target. A single chain antibody generally
includes a heavy chain variable region (V.sub.H) of antibody
covalently linked to a light chain variable region (V.sub.L) of
antibody via a peptide linker. In one embodiment, the method
comprising:
[0104] expressing a library of scFv fusion proteins in yeast cells,
each scFv fusion protein comprising either an activation domain or
a DNA binding domain of a transcription activator and a scFv, the
scFv comprising a V.sub.H of antibody whose sequence varies within
the library, a V.sub.L of antibody whose sequence varies within the
library independently of the V.sub.H, and a linker peptide which
links the V.sub.H and V.sub.L;
[0105] expressing a target fusion protein in the yeast cells
expressing the scFv fusion proteins, the target fusion protein
comprising either the DNA binding domain or the activation domain
of the transcription activator which is not comprised in the scFv
fusion proteins, and a target peptide having a length of 5-100
amino acid residues (aa); and
[0106] selecting those yeast cells in which a reporter gene is
expressed, the expression of the reporter gene being activated by a
reconstituted transcriptional activator formed by binding of the
scFv fusion protein to the target fusion protein.
[0107] According to the embodiment, the diversity of the library
scFv fusion proteins is preferably higher than 1.times.10.sup.4,
more preferably higher than 1.times.10.sup.6, and most preferably
higher than 1.times.10.sup.7.
[0108] Also according to the embodiment, the length of the target
peptide is preferably 10-80 aa, more preferably 20-60 aa, and most
preferably 30-50 aa.
[0109] Also according to the embodiment, the target peptide is
preferably a fragment of a membrane protein, more preferably an
extracellular domain of a membrane protein, and most preferably an
extracellular loop of a transmembrane protein.
[0110] By using the methods of present invention, antibodies with
high affinity and specificity can be selected against the target
peptide expressed as a fusion protein in vivo and in vitro. In
particular, compared to conventional approaches of generating
monoclonal antibody by hybridoma technology and the recently
developed XENOMOUSE.RTM. technology, the inventive method for
screening in yeast may provide a more efficient and economical way
to screen for fully human antibodies against virtually any target
peptide in a much shorter period of time. More importantly, the
screening of the antibody libraries can be readily adopted for high
throughput screening in vivo.
[0111] In a particular embodiment, the method of the present
invention has been used for screening fully human antibody library
against HIV coreceptors such as CCR5 and CXCR4 in yeast.
Significantly, single chain antibodies against fragments of CCR5
have been selected and demonstrated to bind to human CCR5 with high
affinity and inhibit HIV-1 infection at sub-nanomolar
concentrations.
[0112] The overall process of screening in yeast is very efficient
and high throughput. For any targeted membrane protein, each domain
(or fragment) of the protein can be can systematically screened
against the same library of human antibody with high diversity
(>1.times.10.sup.7). Since the peptide comprising the domain is
expressed intracellularly and screened for binding with the library
of antibody intracellulary, the peptide needs not be isolated or
synthesized in vitro, thus greatly simplifying the process and
reducing labor and cost.
[0113] Further, the fast proliferation rate of yeast cells and ease
of handling makes a process of "molecular evolution" dramatically
shorter than the natural process of antibody affinity maturation in
a mammal. Therefore, antibody repertoires with extremely high
diversity can be produced and screened directly against the fusion
protein containing the target peptide in yeast cells at a much
lower cost and higher efficiency than prior processes such as the
painstaking, stepwise "humanization" of monoclonal murine
antibodies isolated by using the conventional hybridoma technology
(a "protein redesign") or the recently-developed XENOMOUSE.TM.
technology.
[0114] According to the "protein redesign" approach, murine
monoclonal antibodies of desired antigen specificity are modified
or "humanized" in vitro in an attempt to reshape the murine
antibody to resemble more closely its human counterpart while
retaining the original antigen-binding specificity. Riechmann et
al. (1988) Nature 332:323-327. This humanization demands extensive,
systematic genetic engineering of the murine antibody, which could
take months, if not years. Additionally, extensive modification of
the backbone of the murine monoclonal antibody may result in
reduced specificity and affinity.
[0115] In comparison, by using the inventive method for screening
in yeast, fully human antibodies with high affinity to a specified
target peptide can be screened and isolated directly from yeast
cells without going through site-by-site modification of the
antibody, and without sacrifice of specificity and affinity of the
selected antibodies.
[0116] By using the methods of the present invention, any peptide
fragment derived from the target protein can be expressed as a
fusion protein with a chaperon protein, such as a DNA-binding
domain (or an activation domain) of a transcription activator and
selected against the library of antibody in vivo or in vitro (e.g.,
in a yeast-2-hybrid system). Moreover, multiple peptide targets may
be arrayed in multiple-well plates and screened against the library
of antibodies in a high throughput and automated manner.
[0117] Various aspects of the present invention are described in
detail in the following sections.
[0118] 1. Peptide Fragment from a Membrane Protein as the Target
Peptide
[0119] In a preferred embodiment, the target peptide is a fragment
of a membrane protein. The target peptide is expressed in yeast as
a target fusion protein with either a DNA binding domain or an
activation domain of a transcription activator which is not
comprised in the scFv fusion proteins. The epitope on the target
peptide is presented by the target fusion protein in yeast and
recognized by some member(s) in the library of scFv fusion
proteins. Such interactions trigger expression of a reporter gene
within the same cell, allowing identification of the yeast clones
expressing the binding scFv fusion protein.
[0120] Member protein is a protein that is associated with the
plasma membrane of a cell. Plasma membrane encloses the cell by
forming a selective permeability barrier, defines its boundaries,
and maintains the essential differences between the cytosol and the
extracellular environment. The plasma membrane consists lipids,
proteins, and some carbohydrates. Lipids form a bilayer in which
the membrane proteins are embedded to varying degrees.
[0121] Different membrane proteins are associated with the
membranes in different ways. Many membrane proteins extend through
the lipid bilayer, with part of their mass on either side. These
transmembrane proteins are amphipathic, having regions that are
hydrophobic and regions that are hydrophilic. Their hydrophilic
regions are exposed to water on one or the other side of the
membrane. Other membrane proteins are located entirely in the
cytosol and are associated with the bilayer only by means of one or
more covalently attached fatty acid chains or other types of lipid
chains called prenyl groups. Yet other membrane proteins are
entirely exposed at the external cell surface, being attached to
the bilayer only the covalent linkage (e.g., via a specific
oligosaccharide) to phosphatidylinositol in the outer lipid
monolayer of the plasma membrane.
[0122] In a more preferred embodiment, the membrane protein is a
transmembrane protein. Typically, a transmembrane protein has its
cytoplasmic and extracellular domains which are separated by the
membrane-spanning segments of the polypeptide chain. The
membrane-spanning segments contact the hydrophobic environment of
the lipid bilayer and are composed largely of amino acid residues
with non-polar side chains. The great majority of transmembrane
proteins are glycosylated. The oligosaccharide chains are usually
present in the excellular domain. Further, the reducing environment
of the cytosol prevents the formation of intrachain (and
interchain) disulfide (S--S) bonds between cysteine residues on the
cytosolic side membranes. These disulfide bonds do form on the
extracellular side, e.g., between the N-terminal domain and an
extracellular loop.
[0123] Transmembrane proteins are notoriously difficult to
crystallize for X-ray structural studies. The folded
three-dimensional structures are quite uncertain for the isolated
forms of these proteins. Thus, these features present a problem in
the attempt to use the whole transmembrane protein as a target for
isolating molecules that would bind to it in vitro.
[0124] According to the present invention, a peptide fragment
derived from one of the extracellular domains of the transmembrane
protein could serve as the target peptide. Antibody selected by
using the screening methods of present invention binds to the
exacelluar cellular domain, thereby effectively blocking
interactions of the transmembrane protein with its excellular
ligand.
[0125] Examples of the membrane protein include, but are not
limited to, receptors for growth factors (e.g., vascular
endothelial growth factor (VEGF), transforming growth factor (TGF),
fibroblast growth factor (FF), platelet derived growth factor
(PDGF), insulin-like growth factor), insulin receptor, MHC proteins
(e.g. class I MHC and class II MHC protein), CD3 receptor, T cell
receptors, cytokine receptors (e.g., interleukin (IL)-1, IL-2,
IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12,
IL-13, IL-14, IL-15 receptors), tyrosine-kinase-associated
receptors such as Src, Yes, Fgr, Lck, Flt, Lyn, Hck, and Blk, and
G-protein coupled receptors such as receptors for the hormone
relaxin (LGR7 and LGR8) and chemokine receptors (e.g., CCR1, CCR2,
CCR3, CCR4, CCR5, CCR6, CCR7, CCR8, CCR9, CCR10, CCR11, CXCR1,
CXCR2, CXCR3, CXCR4, CXCR5, CXCR6, CX3CR1, and XCR1), PSGR,s
beta1-adrenergic receptor, beta2-adrenergic receptor, parathyroid
hormone (PTH) receptor, EDG1, G10d, opioid receptors, neutensin
recetpors, neuropeptide Y (NPY) receptors, melatonin receptor,
adrenocorticotrophin (ACTH) receptor, leukotriene receptors,
5-hydroxytryptamine (5-HT, or serotonin) receptors (including
5-TH1a, 5-TH1b, 5-TH1d, 5-TH1e, 5-TH1f, 5-TH2a, 5-TH2b, 5-TH2c,
5-TH3, 5-TH4, 5-TH5 receptors), FSH receptor, LH/hCG recetpor, TSH
receptor, formyl-methionyl peptide (fMLP) receptors (FPR1 receptor,
FPR2 receptor, FPR3 receptor), GABA receptors, endothelin (ET)
receptors, sarafotoxin receptors, dopamin receptors (D1 receptor,
D2 receptor, D3 receptor, D4 receptor, D5 receptor), cannabinoid
receptor, CGRP 1 receptor, CGRP2 receptor, amylin receptor,
calcitonin receptor, C5a receptor, bradykinin receptors (B1, B2 and
B3 receptors), bombesin Receptors (BB1, BB2 and BB3 receptors),
angiotensin receptors (AT1a, AT1b and AT2 receptors), adrenaline
and noradrenaline receptors (or adrenoceptors), acetylcholine
Receptors, platelet activating factor (PAF) receptor, prostanoid
receptors (DP, EP1, EP2, EP3, FP, IP and TP receptors),
somatostanin receptors (SS1, SS2, SS3, SS4 receptors), tachykinin
Recetpors (NK1, NK2 and NK3 receptors), thrombin receptor,
[0126] vasoactive Intestinal polypeptide (VIP) receptor family
(GRF, PACAP, secretin, VIP and helodermin-preferring receptors),
stresscopin receptor, urocortin receptor, corticotropin releasing
hormone receptors, LGR4, LGR5, LGR6, LGR7 and LGR8, and GPCR orphan
receptors designated as GPR1-58 at GenBank.
[0127] G protein-coupled receptors (GPCR) are a superfamily of
transmembrane proteins that play important roles in the signal
transduction process of a cell. GPCR mediates the cellular
responses to an enormous diversity of signaling molecules,
including hormones, neurotransmitters, and local mediators. The
signal molecules vary in their structure and function, including
proteins, small peptides, as well as amino acid and fatty acid
derivatives. See reviews by Watson S., and Arkinstall S.: "The
G-Protein Linked Receptor Facts Book". 1994, Academic Press,
Harcourt Brace & Company, Publishers. London, San Diego, New
York; Proudfoot A.E.I.: "Chemokine Receptors: Multifaceted
Therapeutic Targets." 2002, Nature Review Immunology 2:106-115; and
Ji T. H., Grossman M. and Ji I.: "G Protein-coupled Receptors."
1998, J. Biol. Chem. 273:17299-17302. These documents, and all
documents cited to herein, are incorporated by reference as if
fully reproduced below.
[0128] For example, receptors for the hormone relaxin (LGR7 and
LGR8) have been found recently to be G-protein coupled receptors.
Hsu et al. (2002) Science 295:671-674. Relaxin is a hormone
important for the growth and remodeling of reproductive and other
tissues during pregnancy. Hsu et al demonstrated that two orphan
heterotrimeric guanine nucleotide binding protein (G-protein)
receptors, LGR7 and LGR8 are capable of mediating the action of
relaxin through an adenosine 3',5'-monophosphate (cAMP)-dependent
pathway distinct from that of the structurally related insulin and
insulin-like growth factor. These receptors for relaxin are
implicated to play roles in reproductive, brain, renal,
cardiovascular and other functions.
[0129] Despite the chemical and functional diversity of the
signaling molecules that bind to them, all of GPCRs share a
structural similarity in that the polypeptide chain threads back
and forth across the lipid bilayer several times, e.g., seven times
to form 7 transmembrane domains which are connected by 3
extracellular loops and 3 intracellular loops.
[0130] Both CCR5 and CXCR4 are chemokine receptors are members of
the GPCR superfamily. CCR5 is a receptor for several CC chemokines
such as MIP-1.alpha. (also named GOS19, LD78, pAT464 gene product,
TY5 (murine) and SIS.alpha. (murine)), MIP-1.beta. (also named
Act-2, G-26, pAT744 gene product, H-400 (murine) and hSIS.gamma.
(murine)) and RANTES (regulated on activation, normal T cell
expressed and secreted, or CCL5). Cocchi et al. (1995) Science
270:1811-1815; and Mellado et al. (2001) Annu. Rev. Immunol.
19:397-421. CXCR4 (also named LESTR or fusin before) is a human
chemokine receptor with the C--X--C motif, and is highly expressed
in leukocytes. Loetscher M, et al (1994) J Biol Chem. 269:232-237.
The lymphocyte chemoattractant stromal cell derived factor-1 (or
SDF-1) or CXCL12 is a ligand for CXCR4 (Bleul C C, et al. (1996)
Nature. 382:829-833). CXCR4 acts as a coreceptor of HIV-1 (Feng Y,
(1996) Science 272:872-877). Its expression is also correlated with
cancer, including prostate cancer (Taichman R S, et al (2002)
Cancer Res. 62:1832-1837) and breast caner metastasis (Muller A, et
al (2001) Nature. 410:50-56; and Moore M A. (2001) Bioessays.
23:674-676). Thus, the inventive methodology disclosed herein can
be used to generate antibodies against these chemokine receptors.
The resultant antibodies can then be used for the prevention and/or
treatment of HIV infection, cancer and other diseases associated
with abnormal chemokine activities. As will be shown in the Example
section below, human monoclonal single chain antibodies against
CCR5 and CXCR4 were generated using the inventive methods and used
to inhibit HIV infection of peripheral blood mononuclear cells and
chemotaxis in breast cancer cells, respectively.
[0131] FIG. 1A shows the amino acid sequence of human CCR5 with 7
transmembrane domains that are connected by loops 2, 4, and 6 which
are extracellular loops and by loops 1, 3, 5 which are
intracellular loops. FIG. 1B shows a model of the secondary
structure of human CCR5. Blanpain et al. (1999) J. Biol. Chem.
274:34719-34727.
[0132] In particular, peptides derived from excellular loops of the
membrane protein could serve an ideal target for screening against
the library of antibody.
[0133] Other than CCR5 and CXCR4, examples of a chemokine receptor
or a chemokine receptor-like orphan receptor also include, but are
not limited to, CCR1, CCR2b, CCR3, CCR4, CCR8, CXCR1, CXCR2, CXCR3,
CX3CR1, STRL33/BONZO and GPR15/BOB. Berger, E. a. (1997) AIDS 11,
Suppl. a: S3-S16; and Dimitrov, D. S. (1997) Cell 91: 721-730. Each
or a set of these HIV coreceptors can mediate entry of different
strains of HIV virus into the host cell.
[0134] By using the method of the present invention, high affinity
monoclonal antibodies can be generated against a peptide fragment
of a chemokine receptor efficiently and in a high throughput
manner. Administering one or more of these antibodies to a host may
offer protection against or inhibit infection of HIV strains with
broad-spectrum tropisms.
[0135] Other membrane proteins described above, the target peptide
may be derived from any protein. For example, the target peptide
may be derived from a disease-associated antigen, such as tumor
surface antigen such as B-cell idiotypes, CD20 on malignant B
cells, CD33 on leukemic blasts, and HER2/neu on breast cancer.
Antibody selected against these antigens can be used in a wide
variety of therapeutic and diagnostic applications, such as
treatment of cancer by direct administration of the antibody itself
or the antibody conjugated with a radioisotope or cytotoxic drug,
and in a combination therapy involving coadministration of the
antibody with a chemotherapeutic agent, or in conjunction with
radiation therapy.
[0136] Alternatively, the target peptide may be derived from a
growth factor receptor. Examples of the growth factor include, but
are not limited to, epidermal growth factors (EGFs), transferrin,
insulin-like growth factor, transforming growth factors (TGFs),
interleukin-1, and interleukin-2. For example, high expression of
EGF receptors have been found in a wide variety of human epithelial
primary tumors. TGF-.alpha. have been found to mediate an autocrine
stimulation pathway in cancer cells. Several murine monoclonal
antibody have been demonstrated to be able to bind EGF receptors,
block the binding of ligand to EGF receptors, and inhibit
proliferation of a variety of human cancer cell lines in culture
and in xenograft medels. Mendelsohn and Baselga (1995) "Antibodies
to growth factors and receptors", in Biologic Therapy of Cancer,
2.sup.nd Ed., J B Lippincott, Philadelphia, pp 607-623; Leget and
Czuczman (1998) "Use of rituximab, the new FDA-approved antibody'.
Curr Opin Oncol. 10:548-551; and Goldenberg (1999) "Trastuzumab, a
recombinant DNA-derived humanized monoclonal antibody, a novel
agent for the treatment of metastatic breast cancer. Clin Ther.
21:309-318). Thus, fully human antibodies selected against these
growth factors by using the method of the present invention can be
used to treat a variety of cancer.
[0137] The target peptide may also be derived from a cell surface
protein or receptor associated with coronary artery disease such as
platelet glycoprotein Iib/IIIa receptor, autoimmune diseases such
as CD4, CAMPATH-1 and lipid A region of the gram-negative bacterial
lipopolysaccharide. Humanized antibodies against CD4 has been
tested in clinical trials in the treatment of patients with mycosis
fungoides, generalized postular psoriasis, severe psorisis, and
rheumatoid arthritis. Antibodies against lipid A region of the
gram-negative bacterial lipopolysaccharide have been tested
clinically in the treatment of septic shock. Antibodies against
CAMPATH-1 has also been tested clinically in the treatment of
against refractory rheumatoid arthritis. Thus, fully human
antibodies selected against these growth factors by using the
method of the present invention can be used to treat a variety of
autoimmune diseases (Vaswani et al. (1998) "Humanized antibodies as
potential therapeutic drugs" Annals of Allergy, Asthma and
Immunology 81:105-115); inflammation (Present et al. (1999)
"Infliximab for the treatment of fistulas in patients with Crohn's
disease" N Engl J Med. 340:1398-1405); and immuno-rejection in
transplantation (Nashan et al. (1999) "Reduction of acute renal
allograft rejection by daclizumab. Daclizumab Double Therapy Study
Group", Transplantation 67:110-115.
[0138] The target peptide may also be derived from proteins
associated with human allergic diseases, such as those inflammatory
mediator protein, e.g. Interleukin-1 (IL-1), tumor necrosis factor
(TNF), leukotriene receptor and 5-lipoxygenase, and adhesion
molecules such as V-CAM/VLA-4. In addition, IgE may also serve as
the target antigen because IgE plays pivotal role in type I
immediate hypersensitive allergic reactions such as asthma. Studies
have shown that the level of total serum IgE tends to correlate
with severity of diseases, especially in asthma. Burrows et al.
(1989) "Association of asthma with serum IgE levels and skin-test
reactivity to allergens" New Engl. L. Med. 320:271-277. Thus, fully
human antibodies selected against IgE by using the method of the
present invention may be used to reduce the level of IgE or block
the binding of IgE to mast cells and basophils in the treatment of
allergic diseases without having substantial impact on normal
immune functions.
[0139] The target peptide may also be derived from a viral surface
or core protein which may serve as an antigen to trigger immune
response of the host. Examples of these viral proteins include, but
are not limited to, glycoproteins (or surface antigens, e.g., GP120
and GP41) and capsid proteins (or structural proteins, e.g., P24
protein); surface antigens or core proteins of hepatitis A, B, C, D
or E virus (e.g. small hepatitis B surface antigen (SHBsAg) of
hepatitis B virus and the core proteins of hepatitis C virus, NS3,
NS4 and NS5 antigens); glycoprotein (G-protein) or the fusion
protein (F-protein) of respiratory syncytial virus (RSV); surface
and core proteins of herpes simplex virus HSV-1 and HSV-2 (e.g.,
glycoprotein D from HSV-2). For example, humanized monoclonal
antibody has been developed for the prevention of respiratory
syncytial virus (RSV) infection. Storch (1998) "Humanized
monoclonal antibody for prevention of respiratory syncytial virus
infection" Pediatrics. 102:648-651.
[0140] The target peptide may also be derived from a mutated tumor
suppressor gene that have lost its tumor-suppressing function and
may render the cells more susceptible to cancer. Tumor suppressor
genes are genes that function to inhibit the cell growth and
division cycles, thus preventing the development of neoplasia.
Mutions in tumor suppressor genes cause the cell to ignore one or
more of the components of the network of inhibitory signals,
overcoming the cell cycle check points and resulting in a higher
rate of controlled cell growth--cancer. Examples of the tumor
suppressor genes include, but are not limited to, DPC-4, NF-1,
NF-2, RB, p5.3, WT1, BRCA1 and BRCA2.
[0141] DPC-4 is involved in pancreatic cancer and participates in a
cytoplasmic pathway that inhibits cell division. NF-1 codes for a
protein that inhibits Ras, a cytoplasmic inhibitory protein. NF-1
is involved in neurofibroma and pheochromocytomas of the nervous
system and myeloid leukemia. NF-2 encodes a nuclear protein that is
involved in meningioma, schwanoma, and ependymoma of the nervous
system. RB codes for the pRB protein, a nuclear protein that is a
major inhibitor of cell cycle. RB is involved in retinoblastoma as
well as bone, bladder, small cell lung and breast cancer. P53 codes
for p53 protein that regulates cell division and can induce
apoptosis. Mutation and/or inaction of p53 is found in a wide
ranges of cancers. WT1 is involved in Wilms tumor of the kidneys.
BRCA1 is involved in breast and ovarian cancer, and BRCA2 is
involved in breast cancer. Thus, fully human antibodies selected
against a mutated tumor suppressor gene product by using the method
of the present invention can be used to block the interactions of
the gene product with other proteins or biochemicals in the
pathways of tumor onset and development.
[0142] 2. Antibody Against Loop 6 of CCR5
[0143] The inventors also discovered that certain fragments derived
from loop 6 of CCR5 (designated hereafter "CCR5 Loop 6") present
excellent epitopes for recognition by antibodies. The epitope(s) on
CCR5 Loop 6 can be used to elicit antibody by using the method of
present invention or other methods for generating antibody known in
the art.
[0144] CCR5 Loop 6 includes amino acid residue aa 261-277:
[0145] qeffglnncsssnrldq [SEQ ID NO:2] (shown in FIG. 1A). As
demonstrated in the section of "EXAMPLE", a peptide fragment
containing most of the Loop 6 region and a portion of transmembrane
domain 7, effglnncs ssnrldqamq vtetlgmthc [SEQ ID NO:3], could
elicit monoclonal antibodies that bind to CCR5 with high affinity
and inhibit HIV-1 infection at sub-nanomolar concentrations.
[0146] According to the present invention, a peptide comprising a
substantial portion of Loop 6 may serve as an epitope for elicit
antibodies by using the method of the present invention or
conventional methods such as hybridoma techniques and bacteriophage
display panning. In particular, the loop 6 peptide may be fused
with a chaperon protein such as Gal4 DNA binding domain to form a
fusion protein.
[0147] Such a fusion protein can be used as an immunogen for
eliciting antibodies in animals or as a ligand for screening an
antibody library in vitro. The antibodies against CCR5 Loop 6
include but are not limited to polyclonal, monoclonal, Fab
fragments, single chain antibodies, chimeric antibodies (e.g.,
humanized antibodies), etc.
[0148] For the production of antibodies against CCR5 Loop 6,
various host animals may be immunized by injection with an
immunogen containing a peptide derived from CCR5 Loop 6. Such host
animals may include but are not limited to rabbits, mice, and rats,
to name but a few. Various adjuvants may be used to increase the
immunological response, depending on the host species, including
but not limited to Freund's (complete and incomplete), mineral gels
such as aluminum hydroxide, surface active substances such as
lysolecithin, pluronic polyols, polyanions, peptides, oil
emulsions, keyhole limpet hemocyanin, dinitrophenol, and
potentially useful human adjuvants such as BCG (bacille
Calmette-Guerin) and Corynebacterium parvum.
[0149] Polyclonal antibodies are heterogeneous populations of
antibody molecules derived from the sera of animals immunized with
an antigen, such as a peptide derived from CCR5 Loop 6 or its
fusion with a chaperon protein, or an antigenic functional
derivative thereof. For the production of polyclonal antibodies,
host animals such as those described above, may be immunized by
injection with a peptide comprising a portion of CCR5 Loop 6
supplemented with adjuvants as also described above. It may be
useful to conjugate the peptide to a protein that is immunogenic in
the species to be immunized, e.g., keyhole limpet hemocyanin (KLH),
serum albumin, bovine thyroglobulin, or soybean trypsin inhibitor,
by using a bifunctional or derivatizing agent, for example,
maleimidobenzoyl sulfosuccinimide ester (conjugation through
cysteine residues), N-hydroxysuccinimide (through lysine residues),
glutaraldehyde, succinic anhydrid or SOCl.sub.2.
[0150] Briefly, animals are immunized against CCR5 Loop 6 peptide
or its immunogenic conjugates by combining, e.g., 100 .mu.g or 5
.mu.g of the protein or conjugate (for rabbits or mice,
respectively) with 3 volumes of Freund's complete adjuvant and
injecting the solution intradermally at multiple sites. One month
later the animals are boosted with 1/5 or 1/10 the original amount
of peptide or conjugate in Freund's complete adjuvant by
subcutaneous injection at multiple sites. Seven to 14 days later
the animals are bled and the serum is assayed for antibody titer.
Animals are boosted until the titer plateaus. Preferably, the
animal is boosted with conjugate of the same antigen, but
conjugated to a different protein and/or through a different
cross-linking reagent. Conjugates can also be made in recombinant
cell culture as protein fusions. In addition, aggregating agents
such as alum are suitably used to enhance the immune response.
[0151] Monoclonal antibodies, which are homogeneous populations of
antibodies to a particular antigen, may be obtained by any
technique which provides for the production of antibody molecules
by continuous cell lines in culture. These include, but are not
limited to the hybridoma technique of Kohler and Milstein (1975)
Nature 256:495-497; and U.S. Pat. No. 4,376,110, the human B-cell
hybridoma technique (Kosbor et al. (1983) Immunology Today 4:72;
Cole et al. (1983) Proc. Natl. Acad. Sci. USA 80:2026-2030, and the
EBV-hybridoma technique (Cole et al. (1985) Monoclonal Antibodies
And Cancer Therapy, Alan R. Liss, Inc., pp. 77-96). Such antibodies
may be of any immunoglobulin class including IgG, IgM, IgE, IgA,
IgD and any subclass thereof. The hybridoma producing the mAb of
this invention may be cultivated in vitro or in vivo.
[0152] In the hybridoma method, a mouse or other appropriate host
animal, such as hamster or macaque monkey, is immunized as herein
above described to elicit lymphocytes that produce or are capable
of producing antibodies that will specifically bind to the antigen
used for immunization. Alternatively, lymphocytes may be immunized
in vitro. Lymphocytes are then fused with myeloma cells using a
suitable fusing agent, such as polyethylene glycol, to form a
hybridoma cell. Goding (1986) "Monoclonal Antibodies: Principles
and Practice", pp. 59-103, Academic Press.
[0153] The hybridoma cells thus prepared are seeded and grown in a
suitable culture medium that preferably contains one or more
substances that inhibit the growth or survival of the unfused,
parental myeloma cells. For example, if the parental myeloma cells
lack the enzyme hypoxanthaine guanine phosphoribosyl transferase
(HGPRT or HPRT), the culture medium for the hybridoma typically
will include hypoxanthine, aminopterin, and thymidine (HAT medium),
which substances prevent the growth of HGPRT-deficient cells.
[0154] Preferred meyloma cells are those that fuse efficiently,
support stable high-level production of antibody by the selected
antibody-producing cells, and are sensitive to a medium such as HAT
medium. Among these, preferred myeloma cell lines are murine
myeloma lines, such as those derived from MOP-21 and M.C.-11 mouse
tumors, SP-2 or X63-Ag8-653 cells available from the American
Typeure Collection (ATCC), Rockville, Md. Human myeloma and
mouse-human heteromyeloma cell lines also have been described for
the production of human monoclonal antibodies.
[0155] Culture medium in which hybridoma cell are growing is
assayed for production of monoclonal antibodies directed against
CCR5 Loop 6 antigen. Preferably, the binding specificity of
monoclonal antibodies produced by hybridoma cells is determined by
immunoprecipitation or by an in vitro binding assay, such as
radioimmunoassay (RIA) or enzyme-linked immunoabsorbent assay
(ELISA).
[0156] After hybridoma cells are identified that produce antibodies
of the desired specificity, affinity, and/or activity, the clones
may be subcloned by limiting dilution procedures and grown by
standard methods. Suitable culture media for this purpose include,
for example, DEME or RPMI-1640 medium. In addition, hybridoma cell
may be grown in vivo as ascites tumors in an animal.
[0157] The monoclonal antibodies secreted by the subclones are
suitably separated from the culture medium, ascites fluid, or
serum, by conventional immunoglobulin purification procedures such
as protein A-Sepharose, hydroxylapatite chromatography, gel
electrophoresis, dialysis, or affinity chromatography.
[0158] DNA encoding the monoclonal antibodies is readily isolated
and sequenced using conventional procedures (e.g., by using
oligonucleotide probes that are capable of binding specifically to
genes encoding the heavy and light chains of the monoclonal
antibodies). The hybridoma cells serve as a preferred source of
such DNA. Once isolated, the DNA may be placed into expression
vectors, which are then transferred into host cell such as E. coli
cells, simian COS cells, Chinese hamster ovary (CHO) cells, or
myeloma cells that do not otherwise produce immunoglobulin protein,
to obtain the synthesis of monoclonal antibodies in the recombinant
host cells.
[0159] Monoclonal antibodies against CCR5 Loop 6 may also be
generated by using bacteriophage display. Combinatorial libraries
of antibodies have been generated in bacteriophage lambda
expression systems which are screened as bacteriophage plaques or
as colonies of lysogens (Huse et al. (1989) Science 246: 1275;
Caton and Koprowski (1990) Proc. Natl. Acad. Sci. (U.S.A.) 87:
6450; Mullinax et al (1990) Proc. Natl. Acad. Sci. (U.S.A.) 87:
8095; Persson et al. (1991) Proc. Natl. Acad. Sci. (U.S.A.) 88:
2432). Various embodiments of bacteriophage antibody display
libraries and lambda phage expression libraries have been described
(Kang et al. (1991) Proc. Natl. Acad. Sci. (U.S.A.) 88: 4363;
Clackson et al. (1991) Nature 352: 624; McCafferty et al. (1990)
Nature 348: 552; Burton et al. (1991) Proc. Natl. Acad. Sci.
(U.S.A.) 88: 10134; Hoogenboom et al. (1991) Nucleic Acids Res. 19:
4133; Chang et al. (1991) J. Immunol. 147: 3610; Breitling et al.
(1991) Gene 104: 147; Marks et al. (1991) J. Mol. Biol. 222: 581;
Barbas et al. (1992) Proc. Natl. Acad. Sci. (U.S.A.) 89: 4457;
Hawkins and Winter (1992) J. Immunol. 22: 867; Marks et al. (1992)
Biotechnology 10: 779; Marks et al. (1992) J. Biol. Chem. 267:
16007; Lowman et al (1991) Biochemistry 30: 10832; Lerner et al.
(1992) Science 258: 1313). Also see review by Rader, C. and Barbas,
C. F. (1997) "Phage display of combinatorial antibody libraries"
Curr. Opin. Biotechnol. 8:503-508.
[0160] Various scFv libraries displayed on bacteriophage coat
proteins have been described. Marks et al. (1992) Biotechnology 10:
779; Winter G and Milstein C (1991) Nature 349: 293; Clackson et
al. (1991) op.cit.; Marks et al. (1991) J. Mol. Biol. 222: 581;
Chaudhary et al. (1990) Proc. Natl. Acad. Sci. (USA) 87: 1066;
Chiswell et al. (1992) TIBTECH 10: 80; and Huston et al. (1988)
Proc. Natl. Acad. Sci. (USA) 85: 5879.
[0161] Generally, a phage library is created by inserting a library
of a random oligonucleotide or a cDNA library encoding antibody
fragment such as V.sub.L and V.sub.H into gene 3 of M13 or fd
phage. Each inserted gene is expressed at the N-terminal of the
gene 3 product, a minor coat protein of the phage. As a result,
peptide libraries that contain diverse peptides can be constructed.
The phage library is then affinity screened against immobilized
target molecule of interest, such as a peptide comprising a portion
of CCR5 Loop6 or its fusion with a chaperon protein, and
specifically bound phages are recovered and amplified by infection
into Escherichia coli host cells. Typically, the target molecule of
interest, such as a peptide comprising a portion of CCR5 Loop6 or
its fusion with a chaperon protein (e.g., Gal4 DNA binding domain),
is immobilized by covalent linkage to a chromatography resin to
enrich for reactive phage by affinity chromatography) and/or
labeled for screen plaques or colony lifts. This procedure is
called biopanning. Finally, amplified phages can be sequenced for
deduction of the specific antibody sequences.
[0162] In addition, techniques developed for the production of
"chimeric antibodies" or "humanized antibodies" may be utilized to
modify mouse monoclonal antibodies to reduce immunogenicity of
non-human antibodies. Morrison et al. (1984) Proc. Natl. Acad. Sci.
81:6851-6855; Neuberger et al. (1984) Nature, 312:604-608; Takeda
et al. (1985) Nature, 314:452-454. Such antibodies are generated by
splicing the genes from a mouse antibody molecule of appropriate
antigen specificity together with genes from a human antibody
molecule of appropriate biological activity can be used. A chimeric
antibody is a molecule in which different portions are derived from
different animal species, such as those having a variable region
derived from a murine mAb and a human immunoglobulin constant
region.
[0163] Alternatively, techniques described for the production of
single chain antibodies (U.S. Pat. No. 4,946,778; Bird (1988)
Science 242:423-426; Huston et al. (1988) Proc. Natl. Acad. Sci.
USA 85:5879-5883; and Ward et al. (1989) Nature 334:544-546) can be
adapted to produce differentially expressed or pathway gene-single
chain antibodies. Single chain antibodies are formed by linking the
heavy and light chain fragments of the Fv region via an amino acid
bridge, resulting in a single chain polypeptide.
[0164] Antibody fragments which recognize specific epitopes may be
generated by known techniques. For example, such fragments include
but are not limited to: the F(ab')2 fragments which can be produced
by pepsin digestion of the antibody molecule and the Fab fragments
which can be generated by reducing the disulfide bridges of the
F(ab')2 fragments. Alternatively, Fab expression libraries may be
constructed (Huse et al. (1989) Science 246:1275-1281) to allow
rapid and easy identification of monoclonal Fab fragments with the
desired specificity.
[0165] By using the inventive method for screening a fully human
antibody library in a yeast two-hybrid system, three monoclonal
scFv antibodies were selected. FIG. 7 shows a homology alignment of
the amino acid sequences of the three scFv antibodies. As shown in
FIG. 7, other than the framework regions, there is also substantial
homology between the three scFv antibodies in heavy chain CDR2 (in
sequence GSTX.sub.1YNPSL [SEQ ID NO: 32], X.sub.1=N or T) and light
chain CDR2 (DAX.sub.2 X.sub.3L [SEQ ID NO: 33], X.sub.2=T or S, and
X.sub.3=T or D) regions. Thus, mutants of the three antibodies may
be generated while conserving the consensus sequences in the heavy
and/or light chain CDR2 regions.
[0166] In one embodiment, an antibody is provided that binds to
loop 6 of human CCR5. In a variation, the antibody is capable of
inhibiting HIV-1 infection of human cells.
[0167] Optionally, CDR2 of the heavy chain variable region of the
antibody comprises amino acid sequence GSTX.sub.1YNPSL [SEQ ID NO:
32], wherein X1 is asparagine (N) or threonine (T).
[0168] Optionally, CDR2 of the light chain variable region
comprises amino acid sequence DAX.sub.2 X.sub.3L [SEQ ID NO: 33],
wherein X.sub.2 is threonine (T) or serine (S), and X.sub.3 is
threonine (T) or aspartic acid (D).
[0169] Optionally, CDR2 of the heavy chain variable region of the
antibody comprises amino acid sequence GSTX.sub.1YNPSL [SEQ ID NO:
32]; and CDR2 of the light chain variable region comprises amino
acid sequence DAX.sub.2 X.sub.3L [SEQ ID NO: 33], wherein X.sub.1
is asparagine (N) or threonine (T), X.sub.2 is threonine (T) or
serine (S), and X.sub.3 is threonine (T) or aspartic acid (D).
[0170] Optionally, CDR3 of the heavy chain variable region of the
monoclonal antibody comprises 5, 6, 7, 8, 9 or more consecutive
amino acids of a sequence elected from the group consisting of
TABLE-US-00003 RLKGAWLLSEPPYFSSDGMDV, [SEQ ID NO: 43] RTVAGTSDY,
[SEQ ID NO: 44] and HEQYYYDTSGQPYYFDF. [SEQ ID NO: 45]
[0171] Optionally, CDR3 of the light chain variable region of the
monoclonal antibody comprises 5, 6, 7, 8, 9 or more consecutive
amino acids of a sequence elected from the group consisting of
TABLE-US-00004 AAWDESLNGVV, [SEQ ID NO: 46] LQHDNFPLT, [SEQ ID NO:
47] and QQSDYLPLT. [SEQ ID NO: 48]
[0172] Optionally, CDR3 of the heavy chain variable region of the
monoclonal antibody comprises an amino acid sequence selected from
the group consisting of SEQ ID Nos: 43-45; and CDR3 of the light
chain variable region of the monoclonal antibody comprises an amino
acid sequence selected from the group consisting of SEQ ID Nos:
46-48.
[0173] It is noted that the above-described different CDR regions
may all be included in the antibody independent of each other, or
in combination with one or more of each other.
[0174] Optionally, the heavy chain variable region of the
monoclonal antibody comprises an amino acid sequence selected from
SEQ ID Nos: 36, 38, and 40 (shown in FIG. 8).
[0175] Optionally, the light chain variable region of the
monoclonal antibody comprises an amino acid sequence selected from
SEQ ID Nos: 37, 39, and 41 (shown in FIG. 8).
[0176] It should be appreciated that the present invention also
provides for analogs of antibodies against CCR5 Loop 6 obtained
according to the methods described above. Analogs may differ from
naturally occurring proteins by conservative amino acid sequence
differences or by modifications which do not affect sequence, or by
both.
[0177] For example, conservative amino acid changes may be made,
which although they alter the primary sequence of the peptide, do
not normally alter its function. Conservative amino acid
substitutions typically include substitutions within the following
groups:
[0178] glycine, alanine;
[0179] valine, isoleucine, leucine;
[0180] aspartic acid, glutamic acid;
[0181] asparagine, glutamine;
[0182] serine, threonine;
[0183] lysine, arginine;
[0184] phenylalanine, tyrosine.
[0185] Modifications of the antibodies include in vivo, or in vitro
chemical derivatization of proteins, e.g., acetylation, or
carboxylation. Also included are modifications of glycosylation,
e.g., those made by modifying the glycosylation patterns of a
protein during its synthesis and processing or in further
processing steps; e.g., by exposing the protein to enzymes which
affect glycosylation, e.g., mammalian glycosylating or
deglycosylating enzymes. Also embraced are sequences which have
phosphorylated amino acid residues, e.g., phosphotyrosine,
phosphoserine, or phosphothreonine.
[0186] Also included are antibodies which have been modified using
ordinary molecular biological techniques so as to improve their
resistance to proteolytic degradation or to optimize solubility
properties. Analogs of such proteins include those containing
residues other than naturally occurring L-amino acids, e.g.,
D-amino acids or non-naturally occurring synthetic amino acids. The
proteins of the invention are not limited to products of any of the
specific exemplary processes listed herein.
[0187] 3. Use of antibody Against HIV Coreceptors for Prevention
and Treatment of HIV Infection
[0188] The antibodies of the present invention selected against
target peptides derived from HIV coreceptors may be used for
prevention and treatment of HIV infection in vitro and in vivo.
[0189] To inhibit infection of cells by HIV in vitro, cells are
treated with the antibody of the invention, or a derivative
thereof, either prior to or concurrently with the addition of
virus. Inhibition of infection of the cells by the antibody of the
present invention is assessed by measuring the replication of virus
in the cells, by identifying the presence of viral nucleic acids
and/or proteins in the cells, for example, by performing PCR,
Southern, Northern or Western blotting analyses, reverse
transcriptase (RT) assays, or by immunofluorescence or other viral
protein detection procedures. The amount of antibody and virus to
be added to the cells will be apparent to one skilled in the art
from the teaching provided herein.
[0190] To prevent or inhibit infection of cells by HIV in vivo, the
antibody of the present invention, or a derivative thereof, is
administered to a human subject who is either at risk of acquiring
HIV infection, or who is already infected with HIV.
[0191] The antibody of the present invention may be formulated for
delivery via various routes of administration, including but not
limited to, orally, parenterally, intraperitoneally, intravenously,
intraarterially, topically, transdermally, sublingually,
intramuscularly, rectally, transbuccally, intranasally,
liposomally, via inhalation, vaginally, intraoccularly, via local
delivery (for example by catheter or stent), subcutaneously,
intraadiposally, intraarticularly, or intrathecally.
[0192] In an embodiment, the antibody is in an injectable
formulation. The formulation is suitable for parenteral
administration by injection, e.g., by bolus injection or continuous
infusion. Formulations for injection may be presented in unit
dosage form, e.g., in ampules or in multidose containers, with an
added preservative. The compositions may take such forms as
suspensions, solutions or emulsions in oily or aqueous vehicles,
and may contain formulatory agents such as suspending, stabilizing
and/or dispersing agents.
[0193] Prior to administration, the antibody, or a derivative
thereof, is suspended in a pharmaceutically acceptable formulation
such as a saline solution or other physiologically acceptable
solution which is suitable for the chosen route of administration
and which will be readily apparent to those skilled in the art of
antibody preparation and administration. The dose of antibody to be
used may vary dependent upon any number of factors including the
age of the individual, the route of administration and the extent
of HIV infection in the individual. The antibody is prepared for
administration by being suspended or dissolved in a
pharmaceutically acceptable carrier such as saline, salt solution
or other formulations apparent to those skilled in such
administration.
[0194] Typically, the antibody is administered in a range of 0.1
.mu.g to 1 g of protein per dose. Approximately 1-10 doses are
administered to the individual at intervals ranging from once per
day to once every few years.
[0195] The antibody may optionally be administered orally to a
human. For example, the antibody of the present invention would be
formulated in propylene glycol solution by attaching the antibody a
polymer carrier. Polymers or liposomes can stabilize the protein
and desensitize it to digestive enzymes by encapsulating the
protein within.
[0196] Also optionally, the antibody may be formulated for
pulmonary delivery via inhalation. For example, the antibody could
be delivered as aerosolized powder to a host using an inhaler. The
lung provides an excellent site for delivery of protein or peptide
drug because the drugs are absorbed quickly into the blood-stream
due to the huge surface area of the lung. In addition, the layer
separating airflow from blood vessels is very narrow, so that the
drug does not have far to travel to enter blood.
[0197] Also optionally, the antibody of the invention may be
administered to a host in a sustained release formulation using a
biodegradable biocompatible polymer, or by on-site delivery using
micelles, gels and liposomes, or rectally (e.g., by suppository or
enema). For example, the antibody is formulated with a polymer such
as pluronic F127. The gel formulation may be injected
subcutaneously or intramuscularly to allow the antibody to be bled
out over a period of time to ensure efficacy.
[0198] Also optionally, the antibody of the invention may be
administered to a host in a topical formulation. The antibody may
be formulated with suitable pharmaceutically acceptable carrier
that does not denature or inactivate the protein in the form of
lotion, cream, gel or suppository. For example, the anti-human CCR5
antibody of the present invention may be used as prophylactic or
therapeutic to prevent or treat infection of HIV (or other sexually
transmitted diseases or STD) via skin or mucosa of the body. The
topical formulation of the antibody may be applied to all areas of
skin likely to come in intimate contact during sexual activity,
especially to any area that has sores or breaks in the skin. For
example, cream or lotion containing the antibody may be applied to
the surfaces of the penis, the base of the penis and scrotum, the
upper vagina, the inner and outer lips of the vulva, the inner
thighs, pubic and perianal regions. The antibody may also be
applied to the anus and/or delivered directly to the rectum via the
penis. In addition, the antibody may be incorporated into an
intrauterine device or an intravaginal device that timely releases
the antibody into the uterus or into the vagina to provide
continuous protection against infection of viruses. For example,
the antibody may be formulated as co-polymer with ethylene-vinyl
acetate which forms a soft, rubber-like material. The procedures
for forming an antibody co-polymer with ethylene-vinyl acetate are
described in U.S. Pat. No. 4,391,797 which is incorporated herein
by reference in its entirety.
[0199] Applying the antibody to the skin and mucosa of the body is
advantageous in that the surfaces of skin and mucus epithelia that
are exposed to semen and other body fluids during sexual activity
are most at risk of exposure to HIV or other STD pathogens. It is
believed that the major roles of secreted antibodies are to block
the adhesive groups that enable a pathogen to adhere to its target
cell. The antibody of the present invention can be used to block
the adhesion of HIV to its target cells such as CD4.sup.+ cells by
binding to HIV coreceptor such as CCR5 and CXCR4. With the
occupation of the antibody on the coreceptors on the host's cells,
HIV carried by body fluid such as semen and blood of another
individual can be prevented from entry into the host's cells, thus
significantly reducing the risk of infection.
[0200] The antibody of the present invention may be used in
combination with a variety of anti-retroviral drugs for prevention
or treatment of HIV infection. Anti-retroviral drugs include many
small molecule drugs (e.g. organic compounds) and macromolecule
drugs (antisense DNAs/RNAs, ribozymes, viral surface
protein-binding proteins or nucleotides, etc.).
[0201] Anti-retroviral drugs against HIV have been developed since
the discovery of correlation between HIV and AIDS. In particular,
many anti-retroviral drugs have been developed to target critical
enzymes of retroviruses and inhibit replication of the virus inside
the host cell. For example, nucleoside or nucleotide analogs such
as AZT, dideoxycytidine (ddC), and dideoxyinosine (ddI) were
developed to inhibit reverse transcriptase (RT) of retroviruses by
acting as competitive inhibitors and chain terminators.
Non-nucleoside or nucleotide inhibitors have also been found to
inhibit reverse transcriptase activity of retroviruses by exerting
an allosteric effect by binding to a hydrophobic pocket close to
the active site of RT. The protease (PRO) inhibitors in current use
are targeted at the active site of the enzyme.
[0202] In addition to the RT and PRO inhibitors of HIV infection,
other classes of antiviral agents targeting different components of
HIV or interfering with different stages of HIV life cycle may be
also be used in conjunction with the antibody to achieve
efficacious clinical results. For example, synthetic peptides have
been modeled to mimic the coiled-coiled helical bundle formed by
heptad repeat sequences of one of the two subunits of HIV envelop
glycoprotein, the transmembrane glycoprotein (gp41). Wild C. T. et
al. "A synthetic peptide inhibitor of HIV replication: correlation
between solution structure and viral inhibition" Proc. Natl. Acad.
Sci. USA 89: 10537-10541 (1992). These heptad sequences play
important roles in the conformational changes essential for
membrane fusion of HIV with host cells. The synthetic peptides, DP
107 and DP 178, have been shown to inhibit infection in vitro by
disrupting the gp41 conformational changes associated with membrane
fusion. Wild, C. et al. "Peptides corresponding to a predictive
alpha-helical domain of HIV-1 gp41 are potent inhibitors of virus
infection" Proc. Natl. Acad. Sci. USA 91: 9770-9774 (1994). In
particular, a 36-amino acid peptide (T-20), corresponding to DP
178, functions as a potent inhibitor of the HIV-1 envelop-cell
membrane fusion and viral entry. Wild, C. et al. "A synthetic
peptide from HIV-1 gp41 is a potent inhibitor of virus-mediated
cell-cell fusion" AIDS Res. Hum. Retroviruses 9:1051-1053 (1993).
When used in monotherapy, T-20 demonstrated potent antiviral
activity in vivo when administered as an intravenous subcutaneous
infusion in trials of 28 days or less. Lalezari, J. et al "Safety,
pharmacokinetics, and antiviral activity of T-20 as a single agent
in heavily pretreated patients" 6.sup.th Conference on Retroviruses
and Opportunistic Infections, Chicago, February 1999 [Abstract
LB13]. Such inhibitors of HIV fusion and entry into the host cells
may be combined with the antibodies of the present invention, as
well as other anti-retroviral agents to inhibit HIV infection at
different stages of the retroviral life cycle.
[0203] Further, inhibitors of retroviral integrase may be used in
conjunction with in combination with the antibodies of the present
invention according to the present invention. A variety of
inhibitors of HIV integrase have been identified that inhibit HIV
integration at different stages. In general, retroviral integration
occurs in the following three biochemical stages: 1) assembly of a
stable complex with specific DNA sequences at the end of the HIV-1
long terminal repeat (LTR) regions, (2) endonucleolytic processing
of the viral DNA to remove the terminal dinucleotide from each 3'
end, and (3) strand transfer in which the viral DNA 3' ends are
covalently linked to the cellular (target) DNA. Pommier, Y. and
Neamati, N. in Advances in Viral Research, K. Maramorosch, et al.
eds. Academic Press, New York (1999), pp 427-458. Compounds have
been identified to interfere with assembly of the stable complex in
assays with purified, recombinant integrase. Hazuda, D. J. et al.
Drug Des. Discovery 15: 17 (1997). In a random screening of more
than 250,000 samples. A variety of compounds have been discovered
as inhibitors of strand transfer reaction catalyzed by integrase.
Hazuda, D. J. et al. "Inhibitors of strand transfer that prevent
integration and inhibit HIV-1 replication in cells" Science
287:646-650 (2000). The most potent and specific compounds each
contained a distinct diketo acid moiety, such as compound
L-731,988, L-708,906, L-731,927, and L-731,942. Hazuda, D. J. et
al. (2000), supra. Such inhibitors of HIV integration into the host
genome may be combined with in combination with the antibodies of
the present invention, as well as other anti-retroviral agents to
inhibit HIV infection at different stages of the retroviral life
cycle.
[0204] In the pharmaceutical compositions of the present invention,
nucleoside reverse transcriptase inhibitors, non-nucleoside reverse
transcriptase inhibitors, protease inhibitors, fusion inhibitors
and integrase inhibitors are the preferred anti-retroviral drugs in
combination with the antibody. Examples of the nucleoside HIV
reverse transcriptase inhibitor include, but are not limited to
zidovudine (AZT), didanosine (ddI), zalcitabine (ddC), lamivudine
(3TC), stavudine (d4T), abacavir (1592U89), and adefovir dipivoxil
(bis(POM)-PMEA). Examples of the non-nucleoside HIV reverse
transcriptase inhibitor include, but are not limited to nevirapine
(BI-RG-587), delavirdine (BHAP, U-90152) and efavirenz (DMP 266).
Examples of the HIV protease inhibitors include, but are not
limited to indinavir (MK-639), ritonavir (ABT-538), saqinavir
(Ro-31-8959), nelfinavir (AG-1343), and amprenavir (141W94).
[0205] The antibody of the present invention may be used in
combination with any one or more of the antiretroviral drugs,
preferably with a "cocktail" of nucleoside reverse transcriptase
inhibitors, non-nucleoside HIV reverse transcriptase inhibitors,
and protease inhibitors. For example, the antibody of the present
invention may be combined with two nucleoside reverse transcriptase
inhibitors (e.g. zidovudine (AZT) and lamivudine (3TC)), and one
protease inhibitor (e.g. indinavir (MK-639)). The antibody of the
present invention may also be combined with one nucleoside reverse
transcriptase inhibitor (e.g. stavudine (d4T)), one non-nucleoside
reverse transcriptase inhibitor (e.g. nevirapine (BI-RG-587)), and
one protease inhibitor (e.g. nelfmavir (AG-1343)). Alternatively,
the antibody of the present invention may be combined with one
nucleoside reverse transcriptase inhibitor (e.g. zidovudine (AZT)),
and two protease inhibitors (e.g. nelfmavir (AG-1343) and saqinavir
(Ro-31-8959)).
[0206] Optionally, the pharmaceutical composition of the present
invention further includes one or more general antiviral agents.
Examples of general antiviral agents include, but are not limited
to acyclovir, ganciclovir, trisodium phosphonoformate, novapren
(Novaferon Labs, Inc., Akron, Ohio), Peptide T Octapeptide Sequence
(Peninsula Labs, Belmont, Calif.), ansamycin LM 427 (Adria
Laboratories, Dublin, Ohio), dextran sulfate, virazole, ribavirin
(Virateck/ICN, Costa Mesa, Calif.), .alpha.-interferon, and
.beta.-interferon. General antiviral agents can be used to prevent
or inhibit opportunistic infections of other viruses.
[0207] 4. Use of Antibody Against HIV Coreceptors for Screening
Anti-HIV Agents
[0208] The antibody of the present invention may also be used in a
method of screening agents for anti-HIV activity. A test agent
(e.g., a compound) is first screened for the ability to bind to the
antibody of the invention. Compounds which bind to the antibody are
likely to share structural and perhaps biological activities with
the HIV coreceptor (e.g., CCR5) and thus, may serve as competitive
inhibitors for inhibition of the interaction of HIV envelope
protein with CD4 and/or CCR5 plus CD4. An antibody-binding compound
is further tested for antiviral activity by treating cells with the
compound either prior to or concurrently with the addition of virus
to the cells. Alternatively, the virus and the compound may be
mixed together prior to the addition of the mixture to the cells.
The ability of the compound to affect virus infection is assessed
by measuring virus replication in the cells using any one of the
known techniques, such as a RT assay, immunofluorescence assays and
other assays known in the art useful for detection of viral
proteins or nucleic acids in cells. Generation of newly replicated
virus may also be measured using known virus assays such as those
which are described herein.
[0209] The antibody of the present invention may also be used in
competition assays to screen for compounds that bind to the HIV
coreceptor (e.g., CCR5) and which therefore prevent binding of the
antibody to the coreceptor. Such compounds, once identified, may be
examined further to determine whether or not they prevent entry of
virus into cells. Compounds which prevent entry of virus into cells
are useful as anti-viral compounds.
[0210] Additional uses for the antibody of the present invention
include the identification of cells in the body which are potential
targets for infection by HIV. These cells express HIV coreceptor(s)
and are therefore capable of being infected by HIV. For example,
cells which are potential targets for HIV infection may be
identified by virtue of the presence of CCR5 on their surface. The
antibody of the present invention facilitates identification of
these cells as follows.
[0211] The antibody of the present invention is first combined with
an identifiable marker, such as an immunofluorescent or radioactive
marker. Cells which are obtained from a human subject are then
reacted with the tagged antibody. Binding of the antibody to cells
is an indication that such cells are potential targets for HIV
infection. The identification of cells which may be infected with
HIV is important for the design of therapies for the prevention of
HIV infection. In the case of individuals who are infected with
HIV, the identification of target cells provides an immune profile
of these individuals which provides useful information regarding
the progress of their infection.
[0212] In addition to the aforementioned uses for the monoclonal
antibody of the present invention, the antibody may be useful for
the detection of CCR5 on a variety of cell types on which CCR5 may
be expressed.
[0213] The monoclonal antibody of the present invention may be
useful for monitoring CCR5 expression levels on a variety of cell
types, which expression may be an indication of a disease state in
a human, including, but not limited to HIV infection,
atherosclerosis, and the like.
[0214] 5. Construction of scFv Library via Homologous Recombination
in Yeast
[0215] The library of scFv proteins may be produced in vivo or in
vitro by using any methods known in the art. In a preferred
embodiment, the library of scFv proteins is constructed in yeast by
exploiting the intrinsic property of yeast--homologous
recombination at an extremely high level of efficiency.
[0216] FIG. 3 shows a flow chart delineating a method for
generating and screening highly diverse libraries of single-chain
human antibodies (scFv) in yeast. As illustrated in FIG. 3, a
highly complex library of scFv is constructed in yeast cells. In
particular, cDNA libraries of the heavy and light chain variable
regions (V.sub.H and V.sub.L) are transferred into a yeast
expression vector by direct homologous recombination between the
sequences encoding V.sub.H and V.sub.L, and the yeast expression
vector containing homologous recombination sites. The resulting
expression vector is called scFv expression vector. This primary
antibody library may reach a diversity preferably between
10.sup.6-10.sup.12, more preferably between 10.sup.7-10.sup.12, and
most preferably between 10.sup.8-10.sup.12.
[0217] The diversity of V.sub.H and V.sub.L within the library of
scFv fusion proteins may be preferably between 10.sup.3-10.sup.8,
more preferably between 10.sup.4-10.sup.8, and most preferably
between 10.sup.5-10.sup.8.
[0218] Optionally, AD is an activation domain of yeast GAL 4
transcription activator; and BD is a DNA binding domain of yeast
GAL 4 transcription activator.
[0219] The linker sequence L may have a specific sequence, or vary
within the library of the yeast expression vectors.
[0220] The linker sequences L in the library of expression vectors
is preferably between 30-120 by in length, more preferably between
45-102 by in length, and most preferably between 45-63 by in
length. The linker sequence in the library of expression vectors
preferably comprises a nucleotide sequence encoding an amino acid
sequence of Gly-Gly-Gly-Gly-Ser in 3 or 4 tandem repeats.
[0221] The linker peptides expressed by the library of expression
vectors preferably provide a substantially conserved conformation
between the first and second polypeptide subunits across the fusion
proteins expressed by the library of expression vectors. For
example, a linker peptide Gly-Gly-Gly-Gly-Ser [SEQ ID NO: 42] in 4
tandem repeats (G.sub.4S).sub.4 [SEQ ID NO: 4] is believed to
provide a substantially conserved conformation of scFv antibodies
which preserves its antigen-binding site in the variable regions of
the corresponding full antibody.
[0222] DNA sequences encoding human antibody V.sub.H and V.sub.L
segments may be polynucleotide segments of at least 30 contiguous
base pairs substantially encoding genes of the immunoglobulin
superfamily. A. F. Williams and A. N. Barclay (1989) "The
Immunoglobulin Gene Superfamily", in Immunoglobulin Genes, T.
Honjo, F. W. Alt, and T. H. Rabbitts, eds., Academic Press: San
Diego, Calif., pp.361-387. The V.sub.H and V.sub.L genes are most
frequently encoded by human, non-human primate, avian, porcine,
bovine, ovine, goat, or rodent heavy chain and light chain gene
sequences.
[0223] The library of DNA sequences encoding human antibody V.sub.H
and V.sub.L segments may be derived from a variety of sources. For
example, mRNA encoding the human antibody V.sub.H and V.sub.L
libraries may be extracted from cells or organs from immunized or
non-immunized animals or humans. Preferably, organs such as human
fetal spleen and lymph nodes may be used. Peripheral blood cells
from non-immunized humans may also be used. The blood samples may
be from an individual donor, from multiple donors, or from combined
blood sources.
[0224] The human antibody V.sub.H- and V.sub.L-coding sequences may
be derived and amplified by using sets of oligonucleotide primers
to amplify the cDNA of human heavy and light chains variable
domains by polymerase chain reaction (PCR). Orlandi et al. (1989)
Proc. Natl. Acad. Sci. USA 86: 3833-3837. For example, blood sample
may be from healthy volunteers and B-lymphocyte in the blood can be
isolated. RNA can be prepared by following standard procedures.
Cathala et al. (1983) DNA 3:329. The cDNA can be made from the
isolated RNA by using reverse transcriptase.
[0225] Alternatively, the V.sub.H- and V.sub.L-coding sequences may
be derived from an artificially rearranged immunoglobulin gene or
genes. For example, immunoglobulin genes may be rearranged by
joining of germ line V segments in vitro to J segments, and, in the
case of V.sub.H domains, D segments. The joining of the V, J and D
segments may be facilitated by using PCR primers which have a
region of random or specific sequence to introduce artificial
sequence or diversity into the products.
[0226] The fusion protein formed by linking V.sub.H and V.sub.L
polypeptides is also referred as a single-chain antibody, scFv. A
typical scFv comprises a V.sub.H domain and a V.sub.L domain in
polypeptide linkage, generally linked via a spacer/linker peptide
L. The linker peptide sequence L may encode an appropriately
designed linker peptide, such as (Gly-Gly-Gly-Gly-Ser)4 [SEQ. ID
NO: 4] or equivalent linker peptide(s). The linker bridges the
C-terminus of the first V region and N-terminus of the second,
ordered as either V.sub.H-L-V.sub.L or V.sub.L-L-V.sub.H.
[0227] A scFv may comprise additional amino acid sequences at the
amino- and/or carboxy-termini. For example, a single-chain antibody
may comprise a tether segment for linking to the constant regions
of a complete or full antibody. A functional single-chain antibody
generally contains a sufficient portion of an immunoglobulin
superfamily gene product so as to retain the property of binding to
a specific target molecule, typically a receptor or antigen
(epitope).
[0228] In a preferred embodiment, the expression vector is based on
a yeast plasmid, especially one from Saccharomyces cerevisiae.
After transformation of yeast cells, the exogenous DNA encoding
scFv fusion proteins are uptaken by the cells and subsequently
expressed by the transformed cells.
[0229] More preferably, the expression vector may be a
yeast-bacteria shuttle vector which can be propagated in either
Escherichia coli or yeast Struhl, et al. (1979) Proc. Natl. Acad.
Sci. 76:1035-1039. The inclusion of E. coli plasmid DNA sequences,
such as pBR322, facilitates the quantitative preparation of vector
DNA in E. coli, and thus the efficient transformation of yeast
[0230] The types of yeast plasmid vector that may serve as the
shuttle may be a replicating vector or an integrating vector. A
replicating vector is yeast vector that is capable of mediating its
own maintenance, independent of the chromosomal DNA of yeast, by
virtue of the presence of a functional origin of DNA replication.
An integrating vector relies upon recombination with the
chromosomal DNA to facilitate replication and thus the continued
maintenance of the recombinant DNA in the host cell. A replicating
vector may be a 2.mu.-based plasmid vector in which the origin of
DNA replication is derived from the endogenous 2.mu. plasmid of
yeast. Alternatively, the replicating vector may be an autonomously
replicating (ARS) vector, in which the "apparent" origin of
replication is derived from the chromosomal DNA of yeast.
Optionally, the replicating vector may be a centromeric (CEN)
plasmid which carries in addition to one of the above origins of
DNA replication a sequence of yeast chromosomal DNA known to harbor
a centromere.
[0231] The vectors may be transformed into yeast cells in a closed
circular form or in a linear form. Transformation of yeast by
integrating vectors, although with inheritable stability, may not
be efficient when the vector is in in a close circular form (e.g.
1-10 transformants per ug of DNA). Linearized vectors, with free
ends located in DNA sequences homologous with yeast chromosomal
DNA, transforms yeast with higher efficiency (100-1000 fold) and
the transforming DNA is generally found integrated in sequences
homologous to the site of cleavage. Thus, by cleaving the vector
DNA with a suitable restriction endonuclease, it is possible to
increase the efficiency of transformation and target the site of
chromosomal integration. Integrative transformation may be
applicable to the genetic modification of brewing yeast, providing
that the efficiency of transformation is sufficiently high and the
target DNA sequence for integration is within a region that does
not disrupt genes essential to the metabolism of the host cell.
[0232] ARS plasmids, which have a high copy number (approximately
20-50 copies per cell) (Hyman et al., 1982), tend to be the most
unstable, and are lost at a frequency greater than 10% per
generation. However, the stability of ARS plasmids can be enhanced
by the attachment of a centromere; centromeric plasmids are present
at 1 or 2 copies per cell and are lost at only approximately 1% per
generation.
[0233] The expression vector of the present invention is preferably
based on the 2.mu. plasmid. The 2.mu. plasmid is known to be
nuclear in cellular location, but is inherited in a non-Mendelian
fashion. Cells that lost the 2.mu. plasmid have been shown to arise
from haploid yeast populations having an average copy number of 50
copies of the 2.mu. plasmid per cell at a rate of between 0.001%
and 0.01% of the cells per generation. Futcher & Cox (1983) J.
Bacteriol. 154:612. Analysis of different strains of S. cerevisiae
has shown that the plasmid is present in most strains of yeast
including brewing yeast. The 2.mu. plasmid is ubiquitous and
possesses a high degree of inheritable stability in nature.
[0234] The 2.mu. plasmid harbors a unique bidirectional origin of
DNA replication which is an essential component of all 2.mu.-based
vectors. The plasmid contains four genes, REP1, REP2, REP3 and FLP
which are required for the stable maintenance of high plasmid copy
number per cell Jaysram et al. (1983) Cell 34:95. The REP 1 and
REP2 genes encode trans-acting proteins which are believed to
function in concert by interacting with the REP3 locus to ensure
the stable partitioning of the plasmid at cell division. In this
respect, the REP3 gene behaves as a cis acting locus which effects
the stable segregation of the plasmid, and is phenotypically
analogous to a chromosomal centromere. An important feature of the
2.mu. plasmid is the presence of two inverted DNA sequence repeats
(each 559 base-pairs in length) which separate the circular
molecule into two unique regions. Intramolecular recombination
between the inverted repeat sequences results in the inversion of
one unique region relative to the other and the production in vivo
of a mixed population of two structural isomers of the plasmid,
designated A and B. Recombination between the two inverted repeats
is mediated by the protein product of a gene called the FLP gene,
and the FLP protein is capable of mediating high frequency
recombination within the inverted repeat region. This site specific
recombination event is believed to provide a mechanism which
ensures the amplification of plasmid copy number. Murray et al.
(1987) EMBO J. 6:4205.
[0235] The expression vector may also contain an Escherichia coli
origin of replication and E. coli antibiotic resistance genes for
propagation and antibiotic selection in bacteria. Many E. coli
origins are known, including ColE1, pMB1 and pBR322, The ColE
origin of replication is preferably used in this invention. Many E.
coli drug resistance genes are known, including the ampicillin
resistance gene, the chloramphenicol resistance gene and the
tetracycline resistance gene. In one particular embodiment, the
ampicillin resistance gene is used in the vector.
[0236] The transformants that carry the scFv library may be
selected by using various selection schemes. The selection is
typically achieved by incorporating within the vector DNA a gene
with a discernible phenotype. In the case of vectors used to
transform laboratory yeast, prototrophic genes, such as LEU2, URA3
or TRP1, are usually used to complement auxotrophic lesions in the
host. However, in order to transform brewing yeast and other
industrial yeasts, which are frequently polyploid and do not
display auxotrophic requirements, it is necessary to utilize a
selection system based upon a dominant selectable gene. In this
respect replicating transformants carrying 2.mu.-based plasmid
vectors may be selected based on expression of marker genes which
mediate resistance to: antibiotics such as G418, hygromycin B and
chloramphenicol, or otherwise toxic materials such as the herbicide
sulfometuron methyl, compactin and copper.
[0237] 6. Screening of scFv Library Against the Target Peptide in
Yeast Two-Hybrid System
[0238] The present invention provides efficient methods for
screening the scFv library against any target peptide in a yeast
two-hybrid system.
[0239] The two-hybrid system is a selection scheme designed to
screen for polypeptide sequences which bind to a predetermined
polypeptide sequence present in a fusion protein. Chien et al.
(1991) Proc. Natl. Acad. Sci. (USA) 88: 9578). This approach
identifies protein-protein interactions in vivo through
reconstitution of a transcriptional activator. Fields and Song
(1989) Nature 340: 245), the yeast Gal 4 transcription protein. The
method is based on the properties of the yeast Gal 4 protein, which
consists of separable domains responsible for DNA-binding and
transcriptional activation. Polynucleotides encoding two hybrid
proteins, one consisting of the yeast Gal 4 DNA-binding domain (BD)
fused to a polypeptide sequence of a known protein and the other
consisting of the Gal4 activation domain (AD) fused to a
polypeptide sequence of a second protein, are constructed and
introduced into a yeast host cell. Intermolecular binding between
the two fusion proteins reconstitutes the Gal4 DNA-binding domain
with the Gal4 activation domain, which leads to the transcriptional
activation of a reporter gene (e.g., lacZ, HIS3) which is operably
linked to a Gal4 binding site.
[0240] Typically, the two-hybrid method is used to identify novel
polypeptide sequences which interact with a known protein. Silver
and Hunt (1993) Mol. Biol. Rep. 17: 155; Durfee et al. (1993) Genes
Devel. 7; 555; Yang et al. (1992) Science 257: 680; Luban et al.
(1993) Cell 73: 1067; Hardy et al. (1992) Genes Devel. 6; 801;
Bartel et al. (1993) Biotechniques 14: 920; and Vojtek et al.
(1993) Cell 74: 205. The two-hybrid system was used to detect
interactions between three specific single-chain variable fragments
(scFv) and a specific antigen. De Jaeger et al. (2000) FEBS Lett.
467:316-320. The two-hybrid system was also used to screen against
cell surface proteins or receptors such as receptors of
hematopoietic super family in yeast. Ozenberger, B. A., and Young,
K. H. (1995) "Functional interaction of ligands and receptors of
hematopoietic superfamily in yeast" Mol Endocrinol.
9:1321-1329.
[0241] Variations of the two-hybrid method have been used to
identify mutations of a known protein that affect its binding to a
second known protein Li and Fields (1993) FASEB J. 7: 957; Lalo et
al. (1993) Proc. Natl. Acad. Sci. (USA) 90: 5524; Jackson et al.
(1993) Mol. Cell. Biol. 13; 2899; and Madura et al. (1993) J. Biol.
Chem. 268: 12046.
[0242] Two-hybrid systems have also been used to identify
interacting structural domains of two known proteins or domains
responsible for oligomerization of a single protein. Bardwell et
al. (1993) Med. Microbiol. 8: 1177; Chakraborty et al. (1992) J.
Biol. Chem. 267: 17498; Staudinger et al. (1993) J. Biol. Chem.
268: 4608; and Milne G T; Weaver D T (1993) Genes Devel. 7; 1755;
Iwabuchi et al. (1993) Oncogene 8; 1693; Bogerd et al. (1993) J.
Virol. 67: 5030).
[0243] Variations of two-hybrid systems have been used to study the
in vivo activity of a proteolytic enzyme. Dasmahapatra et al.
(1992) Proc. Natl. Acad. Sci. (USA) 89: 4159. Alternatively, an E.
coli/BCCP interactive screening system was used to identify
interacting protein sequences (i.e., protein sequences which
heterodimerize or form higher order heteromultimers). Germino et
al. (1993) Proc. Natl. Acad. Sci. (U.S.A.) 90: 933; and Guarente L
(1993) Proc. Natl. Acad. Sci. (U.S.A.) 90: 1639.
[0244] Typically, selection of binding protein using a two-hybrid
method relies upon a positive association between two Gal4 fusion
proteins, thereby reconstituting a functional Gal4 transcriptional
activator which then induces transcription of a reporter gene
operably linked to a Gal4 binding site. Transcription of the
reporter gene produces a positive readout, typically manifested
either (1) as an enzyme activity (e.g., .beta.-galactosidase) that
can be identified by a colorimetric enzyme assay or (2) as enhanced
cell growth on a defined medium (e.g., HIS3 and Ade 2). Thus, the
method is suited for identifying a positive interaction of
polypeptide sequences, such as antibody-antigen interactions.
[0245] False positives clones that indicate activation of the
reporter gene irrespective of the specific interaction between the
two hybrid proteins, may arise in the two-hybrid screening. Various
procedures have developed to reduce and eliminate the false
positive clones from the final positives. For example, 1)
prescreening the clones that contains the target vector and shows
positive in the absence of the two-hybrid partner (Bartel, P. L.,
et al. (1993) "Elimination of false positives that arise in using
the two-hybrid system" BioTechniques 14:920-924); 2) by using
multiple reporters such as His3, .beta.-galactosidase, and Ade2
(James, P. et al. (1996) "Genomic libraries and a host strain
designed for highly efficient two-hybrid selection in yeast"
Genetics 144:1425-1436); 3) by using multiple reporters each of
which is under different GAL 4--responsive promoters such as those
in yeast strain Y190 where each of the His 3 and .beta.-Gal
reporters is under the control of a different promoter Gal 1 or Gal
10, but both response to Gal 4 signaling (Durfee, T., et al (1993)
"The retinoblastoma protein associates with the protein phosphatase
type 1 catalytic subunit" Genes Devel. 7:555-569); and 4) by
post-screening assays such as testing isolates with target
consisting of GAL 4-BD alone.
[0246] In addition, the false positive clones may also be
eliminated by using unrelated targets to confirm specificity. This
is a standard control procedure in the two-hybrid system which can
be performed after the library isolate is confirmed by the
above-described 1)-4) procedures. Typically, the library clones are
confirmed by co-transforming the initially isolated library clones
back into the yeast reporter strain with one or more control
targets unrelated to the target used in the original screening.
Selection is conducted to eliminate those library clones that show
positive activation of the reporter gene and thus indicate
non-specific interactions with multiple, related proteins.
[0247] When the library of scFv fusion proteins are expressed by
the expression vector in yeast cells, such as cells from the
Saccharomyces cerevisiae strains, the scFv fusion protein undergoes
a process of protein folding to adopt one or more conformations.
The peptide sequence encoded by the linker sequence L also
facilitates the folding by providing a flexible hinge between the
V.sub.H and V.sub.L. The conformation(s) adopted by the scFv fusion
protein may have suitable binding site(s) for a specific target
peptide expressed as fusion protein with the domain BD of a
transcription activator. The AD domain of the scFv fusion protein
should be able to activate transcription of gene(s) once the AD and
BD domains are reconstituted to form an active transcription
activator in vitro or in vivo by a two-hybrid method.
[0248] In a preferred embodiment, the highly complex primary
antibody libraries is screened against the peptide target, for
example a 30 aa peptide derived from loop 6 of CCR5. This screening
for antibody-antigen interaction is conveniently carried out in
yeast by using a yeast two-hybrid method. The library of scFv
expression vectors are introduced into yeast cells. Expression of
the scFv antibody library in the yeast cells produces a library of
scFv fusion proteins, each fusion protein comprising a scFv and an
activation domain (AD) of a transcription activator. The yeast
cells are also modified to express a recombinant fusion protein
comprising a DNA-binding domain (BD) of the transcription activator
and the target peptide. The yeast cells are also modified to
express a reporter gene whose expression is under the control of a
specific DNA binding site. Upon binding of the scFv antibody from
the library to the target antigen, the AD is brought into close
proximity of BD, thereby causing transcriptional activation of a
reporter gene downstream from a specific DNA binding site to which
the BD binds. It is noted that the library of scFv expression
vectors may contain the BD domain while the modified yeast cells
express a fusion protein comprising the AD domain and the target
peptide.
[0249] These scFv expression vectors may be introduced to yeast
cells by co-transformation of diploid yeast cells or by direct
mating between two strains of haploid yeast cells. For example, the
scFv expression vectors and an expression vector containing the
target peptide can be used to co-transform diploid yeast cells in a
form of yeast plasmid or bacteria-yeast shuttle plasmid.
Alternatively, two strains haploid yeast cells (e.g. .alpha.- and
a-type strains of yeast), each containing the scFv expression
vector and the target peptide expression vector, respectively, are
mated to produce a diploid yeast cell containing both expression
vectors. Preferably, the haploid yeast strain containing the target
peptide expression vector also contains the reporter gene
positioned downstream of the specific DNA binding site.
[0250] The yeast clones containing scFv antibodies with binding
affinity to the target peptide are selected based on phenotypes of
the cells or other selectable markers. The plasmids encoding these
primary antibody leads can be isolated and further characterized.
The affinity and biological activity of the primary antibody leads
can be determined using assays particularly designed based on the
specific target protein from which the target peptide is
derived.
[0251] FIG. 2A illustrates a flow diagram of a preferred embodiment
of the above described method. As illustrated in FIG. 2A, the
sequence library containing scFv fused with an AD domain upstream
is carried by a library of expression vectors, the AD-scFv vectors.
The coding sequence of the target peptide (labeled as "Target") is
contained in another expression vector and fused with a BD domain,
forming the BD-Target vector.
[0252] The AD-scFv vector and the BD-Target vector may be
co-transformed into a yeast cell by using method known in the art.
Gietz, D. et al. (1992) "Improved method for high efficiency
transformation of intact yeast cells" Nucleic Acids Res. 20:1425.
The construct carrying the specific DNA binding site and the
reporter gene (labeled as "Reporter") may be stably integrated into
the genome of the host cell or transiently transformed into the
host cell. Upon expression of the sequences in the expression
vectors, the library of scFv fusion proteins undergo protein
folding in the host cell and adopt various conformations. Some of
the scFv fusion proteins may bind to the Target protein expressed
by the BD-Target vector in the host cell, thereby bringing the AD
and BD domains to a close proximity in the promoter region (i.e.,
the specific DNA binding site) of the reporter construct and thus
reconstituting a functional transcription activator composed of the
AD and BD domains. As a result, the AD activates the transcription
of the reporter gene downstream from the specific DNA binding site,
resulting in expression of the reporter gene, such as the lacZ
reporter gene. Clones showing the phenotype of the reporter gene
expression are selected, and the AD-scFv vectors are isolated. The
coding sequences for scFv are identified and characterized.
[0253] Alternatively, the steps of expressing the library of scFv
fusion proteins and expressing the target fusion protein includes
causing mating between first and second populations of haploid
yeast cells of opposite mating types. The first population of
haploid yeast cells comprises a library of scFv expression vectors
for the library of tester fusion proteins. The second population of
haploid yeast cells comprises a target expression vector. Either
the first or second population of haploid yeast cells comprises a
reporter construct comprising the reporter gene whose expression is
under transcriptional control of the transcription activator.
[0254] In this method, the haploid yeast cells of opposite mating
types may preferably be .alpha. and a type strains of yeast. The
mating between the first and second populations of haploid yeast
cells of .alpha. and a type strains may be conducted in a rich
nutritional culture medium.
[0255] FIG. 2B illustrates a flow diagram of a preferred embodiment
of the above described method. As illustrated in FIG. 2B, the
sequence library containing scFv fused with an AD domain upstream
is carried by a library of expression vectors, the AD-scFv vectors.
The library of the AD-scFv vectors are transformed into haploid
yeast cells such as the a type strain of yeast.
[0256] The coding sequence of the target protein (labeled as
"Target") is contained in another expression vector and fused with
a BD domain, forming the BD-Target vector. The BD-Target vector is
transformed into haploid cells of opposite mating type of the
haploid cells containing the the AD-scFv vectors, such as the
.alpha. type strain of yeast. The construct carrying the specific
DNA binding site and the reporter gene (labeled as "Reporter") may
be transformed into the haploid cells of either the type a or type
.alpha. strain of yeast
[0257] The haploid cells of the type a and type a strains of yeast
are mated under suitable conditions such as low speed of shaking in
liquid culture, physical contact in solid medium culture, and rich
medium such as YPD. Bendixen, C. et al. (1994) "A yeast
mating-selection scheme for detection of protein-protein
interactions", Nucleic Acids Res. 22: 1778-1779. Finley, Jr., R. L.
& Brent, R. (1994) "Interaction mating reveals lineary and
ternery connections between Drosophila cell cycle regulators",
Proc. Natl. Acad. Sci. USA, 91:12980-12984. As a result, the
AD-scFv, the BD-Target expression vectors and the Reporter
construct are taken into the parental diploid cells of the a and
type .alpha. strain of haploid yeast cells.
[0258] Upon expression of the sequences in the expression vectors
in the parental diploid cells, the library of scFv fusion proteins
undergo protein folding in the host cell and adopt various
conformations. Some of the AD-scFv fusion proteins may bind to the
Target protein expressed by the BD-Target vector in the parental
diploid cell, thereby bringing the AD and BD domains to a close
proximity in the promoter region (i.e., the specific DNA binding
site) of the reporter construct and thus reconstituting a
functional transcription activator composed of the AD and BD
domains. As a result, the AD activates the transcription of the
reporter gene downstream from the specific DNA binding site,
resulting in expression of the reporter gene, such as the lacZ
reporter gene. Clones showing the phenotype of the reporter gene
expression are selected, and the AD-scFv vectors are isolated. The
coding sequences for scFv are identified and characterized.
[0259] A wide variety of reporter genes may be used in the present
invention. Examples of proteins encoded by reporter genes include,
but are not limited to, easily assayed enzymes such as
.beta.-galactosidase, .alpha.-galactosidase, luciferase,
.beta.-glucuronidase, chloramphenicol acetyl transferase (CAT),
secreted embryonic alkaline phosphatase (SEAP), fluorescent
proteins such as green fluorescent protein (GFP), enhanced blue
fluorescent protein (EBFP), enhanced yellow fluorescent protein
(EYFP) and enhanced cyan fluorescent protein (ECFP); and proteins
for which immunoassays are readily available such as hormones and
cytokines. The expression of these reporter genes can also be
monitored by measuring levels of mRNA transcribed from these
genes.
[0260] When the screening of the scFv library is conducted in yeast
cells, certain reporter(s) are of nutritional reporter which allows
the yeast to grow on the specific selection medium plate. This is a
very powerful screening process, as has been shown by many
published papers. Examples of the nutritional reporter include, but
are not limited to, His3, Ade2, Leu2, Ura3, Trp1and Lys2. The His3
reporter is described in Bartel, P. L. et al. (1993) "Using the
two-hybrid system to detect protein-protein interactions", in
Cellular interactions in Development: A practical approach, ed.
Hastley, D. A., Oxford Press, pages 153-179. The Ade2 reporter is
described in Jarves, P. et al. (1996) "Genomic libraries and a host
strain designed for highly efficient two-hybrid selection in yeast"
Genetics 144:1425-1436.
[0261] For example, a library of scFv expression vectors that
contains a scFv fused with an AD domain of GAL 4 transcription
activator (the AD-scFv library) may be transformed into haploid
cells of the .alpha. mating type of yeast strain. A BD domain of
GAL 4 transcription activator is fused with the sequence encoding
the target protein to be selected against the scFV library in a
plasmid. This plasmid is transformed into haploid cells of the a
mating type of yeast strain.
[0262] Equal volume of AD-scFv library-containing yeast stain
(.alpha.-type) and the BD-target-containing yeast strain (a-type)
are inoculated into selection liquid medium and incubated
separately first. These two cultures are then mixed and allowed to
grow in rich medium such as 1xYPD and 2xYPD. Under the rich
nutritional culture condition, the two haploid yeast strains will
mate and form diploid cells. At the end of this mating process,
these yeast cells are plated into selection plates. A
multiple-marker selection scheme may be used to select yeast clones
that show positive interaction between the scFVs in the library and
the target. For example, a scheme of SD/-Leu-Trp-His-Ade may be
used. The first two selections (Leu-Trp) are for markers (Leu and
Trp) expressed from the AD-scFv library and the BD-Target vector,
respectively. Through this dual-marker selection, diploid cells
retaining both BD and AD vectors in the same yeast cells are
selected. The latter two markers, His-Ade, are used to screen for
those clones that express the reporter gene from parental strain,
presumably due to affinity binding between the scFv in the library
and the target.
[0263] After the screening by co-transformation, or by mating
screening as described above, the putative interaction between the
gene probe and the library clone isolates can be further tested and
confirmed in vitro or in vivo.
[0264] In vitro binding assays may be used to confirm the positive
interaction between the scFv expressed by the clone isolate and the
target peptide. For example, the in vitro binding assay may be a
"pull-down" method, such as using GST (glutathione
S-transferase)-fused gene probe as matrix-binding protein, and with
in vitro expressed library clone isolate that are labeled with a
radioactive or non-radioactive group. While the probe is bound to
the matrix through GST affinity substrate (glutathione-agarose),
the library clone isolate will also bind to the matrix through its
affinity with the gene probe. The in vitro binding assay may also
be a Co-immuno-precipitation (Co-IP) method using two affinity tag
antibodies. In this assay, both the target gene probe and the
library clone isolate are in vitro expressed fused with peptide
tags, such as HA (haemaglutinin A) or Myc tags. The gene probe is
first immuno-precipitated with an antibody against the affinity
peptide tag (such as HA) that the target gene probe is fused with.
Then the second antibody against a different affinity tag (such as
Myc) that is fused with the library clone isolate is used for
reprobing the precipitate.
[0265] In vivo assays may also be used to confirm the positive
interaction between the scFv expressed by the clone isolate and the
target peptide. For example, a mammalian two-hybrid system may
serve as a reliable verification system for the yeast two-hybrid
library screening. In this system, the target gene probe and
library clone are fused with Gal 4 DNA-binding domain or an
mammalian activation domain (such as VP-16) respectively. These two
fusion proteins under control of a strong and constitutive
mammalian promoter (such as CMV promoter) are introduced into
mammalian cells by transfection along with a reporter responsive to
Gal 4. The reporter can be CAT gene (chloramphenical acetate
transferase) or other commonly used reporters. After 2-3 days of
transfection, CAT assay or other standard assays will be performed
to measure the strength of the reporter which is correlated with
the strength of interaction between the gene probe and the library
clone isolate.
[0266] It should be noted that the antibody library described above
may be screened against a target peptide fragment derived from a
membrane protein in other organisms or in vitro. For example, the
target peptide may be expressed as a fusion protein with another
protein and screened against the antibody library co-expressed in
mammalian cells. The target peptide may also be immobilized to a
substrate as a single peptide or a fusion protein and selected
against a library of antibodies displayed by
bacteriophagedisplayed, mRNA, ribosome or cells such as yeast
cells. In addition, the target peptide may be introduced to a
xenomouse, HuMab mouse, or a transchromosomal mouse which contains
a library of human antibody, and selected for monoclonal human
antibodies with specific binding affinity to target peptide and/or
the target membrane protein.
[0267] For example, the library of human antibodies may be screened
against a target peptide derived from a membrane protein (e.g.,
CCR5) by using ribosome display. Ribosome display is a form of
protein display for in vitro selection against a target ligand. In
this system, mRNA encoding the tester protein (e.g. an antibody)
and the translated tester protein are associated through the
ribosome complex, also called an antibody-ribosome-mRNA (ARM)
complex. He and Taussig (1997) Nucleic Acid Research 25:5132-5134.
The principle behind this approach is that single chain antibody
can be functionally produced in an in vitro translation system
(e.g. rabbit reticulocyte lysate), and in the absence of a stop
codon, individual nascent proteins remain associated with their
corresponding mRNa as stable ternary polypeptide-ribosome-mRNA
complexes in such a cell-free system.
[0268] In the ribosome display assay, each member of the library of
human antibody sequences includes a bacterial phage T7 promoter and
protein synthesis initiation sequence attached to the 5' end of the
cDNA encoding the antibody (e.g., scFv) and no stop codon in the 3'
end. Because the cDNA pool is depleted of the stop codon, when the
mRNA is transcribed from the cDNA and is subject to in vitro
translation, the mRNA will still be attached to the ribosome and
mRNA, forming the ARM complex. The library of human scFv antibody
that is translated from the cDNA gene pool and displayed on the
surface of the ribosome can be screened against the target peptide
as a single peptide or as a fusion protein with a protein other
than the target membrane protein. The in vitro transcription and
translation of this library may be carried out in rabbit
reticulocyte lysate in the presence of methionine at 30.degree. C.
by using the commercially available systems, such as TNT T7 Quick
Coupled Transcription/Translation System (Promega, Madison,
Wis.).
[0269] The target peptide or its fusion protein may be immobilized
to a solid substrate, such as a chromatography resin by covalent
linkage to enrich for those ribosomes with high affinity humanized
antibody attached. By affinity chromatography, the ribosomes with
high affinity scFv antibody attached are isolated. The mRNA
encoding the high affinity scFv antibody is recovered from the
isolated ARM complexes and subject to reverse transcriptase
(RT)/PCR to synthesize and amplify the cDNA of the selected
antibody. This completes the first cycle of the panning process for
antibody isolation and its coding sequence characterization. Such a
panning process may be repeated until scFv antibody with desirably
affinity is isolated.
[0270] Optionally, the library of human antibodies may be screened
against a target peptide derived from a membrane protein (e.g.,
CCR5) by using mRNA display. Wilson et al. (2001) Proc Natl Acad
Sci USA. 98:3750-3755; and Keefe and Szostak (2001) Nature
410:715-718. These documents, and all documents cited to herein,
are incorporated by reference as if fully reproduced below. Each of
the antibodies can be covalently linked through the carboxy
terminus if the antibody is a single chain antibody or through the
carboxy terminus of the light or heavy chain if the antibody is a
Fv, Fab or a fully assembled antibody to the 3' end of its encoding
mRNA.
[0271] The target peptide or its fusion protein may be immobilized
to a solid substrate, such as a chromatography resin by covalent
linkage to enrich for the mRNA to which high affinity humanized
antibody is linked. The mRNA encoding the high affinity antibody is
recovered from the isolated the mRNA-antibody conjugate and subject
to reverse transcriptase (RT)/PCR to synthesize and amplify the
cDNA of the selected antibody. This completes the first cycle of
the panning process for antibody isolation and its coding sequence
characterization. Such a panning process may be repeated until
antibody with desirably affinity is isolated.
[0272] Also optionally, the library of human antibodies may be
screened against a target peptide derived from a membrane protein
(e.g., CCR5) by using yeast display. Boder et al. (2000) Proc Natl
Acad Sci USA. 97:10701-10705; and Boder and Wittrup (1997) Nat
Biotechnol. 15:553-557. These documents, and all documents cited to
herein, are incorporated by reference as if fully reproduced below.
For example, the library of antibodies may be display on the
surface of yeast cells via C-terminal fusion to the Aga2p mating
adhesion receptor of Saccharomyces cerevisiae. The displayed
antibodies can be selected for binding to the target peptide or its
fusion with a chaperon protein. Such a eukaryotic host may
alleviate expression biases present in bacterially propagated
combinatorial libraries.
[0273] The target peptide or its fusion protein may be immobilized
to a solid substrate or present in a solution. For example, the
target peptide or its fusion may be mixed with yeast cells which
display the library of antibodies on the cell surface. The cell
displaying the antibody that binds to the target may be selected by
using flow cytometric cell sorting. The cDNA encoding the selected
antibody can be recovered from the isolated cell. This completes
the first cycle of the selection process for antibody isolation and
its coding sequence characterization. Such a selection process may
be repeated until antibody with desirably affinity is isolated.
[0274] 7. Affinity Maturation of scFv Leads Positively Selected
Against Target Peptide
[0275] The binding affinity of the primary scFv antibody leads can
be improved by using an in vitro affinity maturation process
according to the present invention. The coding sequences of these
protein leads may be mutagenized in vitro or in vivo to generated a
secondary library more diverse than these leads. The mutagenized
leads can be selected against the target peptide again in vivo
following similar procedures described for the selection of the
primary library carrying scFv. Such mutagenesis and selection of
primary antibody leads effectively mimics the affinity maturation
process naturally occurring in a mammal that produces antibody with
progressive increase in the affinity to the immunizing antigen.
[0276] The sequences encoding V.sub.H and V.sub.L of the primary
antibody leads are mutagenized in vitro to produce a secondary
antibody library. The V.sub.H and V.sub.L sequences can be randomly
mutagenized by "poison" PCR (or error-prone PCR), by DNA shuffling,
or by any other way of random or site-directed mutagenesis (or
cassette mutagenesis). After mutagenesis in the regions of V.sub.H
and V.sub.L, the secondary antibody library formed by the mutants
of the primary antibody can be screened against the peptide target
by using the yeast two-hybrid system or other screening method.
Mutants with higher affinity than the primary antibody lead can be
isolated.
[0277] The coding sequences of the scFv leads may be mutagenized by
using a wide variety of methods. Examples of methods of mutagenesis
include, but are not limited to site-directed mutagenesis,
error-prone PCR mutagenesis, cassette mutagenesis, random PCR
mutagenesis, DNA shuffling, and chain shuffling.
[0278] Site-directed mutagenesis or point mutagenesis may be used
to gradually change the V.sub.H and V.sub.L sequences in specific
regions. This is generally accomplished by using
oligonucleotide-directed mutagenesis. For example, a short sequence
of a scFv antibody lead may be replaced with a synthetically
mutagenized oligonucleotide. The method may not be efficient for
mutagenizing large numbers of V.sub.H and V.sub.L sequences, but
may be used for fine toning of a particular lead to achieve higher
affinity toward a specific target protein.
[0279] Cassette mutagenesis may also be used to mutagenize the
V.sub.H and V.sub.L sequences in specific regions. In a typical
cassette mutagenesis, a sequence block, or a region, of a single
template is replaced by a completely or partially randomized
sequence. However, the maximum information content that can be
obtained may be statistically limited by the number of random
sequences of the oligonucleotides. Similar to point mutagenesis,
this method may also be used for fine toning of a particular lead
to achieve higher affinity toward a specific target protein.
[0280] Error-prone PCR, or "poison" PCR, may be used to the V.sub.H
and V.sub.L sequences by following protocols described in Caldwell
and Joyce (1992) PCR Methods and Applications 2:28-33. Leung, D. W.
et al. (1989) Technique 1:11-15. Shafikhani, S. et al. (1997)
Biotechniques 23:304-306. Stemmer, W. P. et al. (1994) Proc. Natl.
Acad. Sci. USA 91:10747-10751.
[0281] FIG. 4 illustrates an example of the method of the present
invention for affinity maturation of antibody leads selected from
the primary scFv library. As illustrated in FIG. 4, the coding
sequences of the scFv leads selected from clones containing the
primary scFv library are mutagenized by using a poison PCR method.
Since the coding sequences of the scFV library are contained in the
expression vectors isolated from the selected clones, one or more
pairs of PCR primers may be used to specifically amplify the
V.sub.H and V.sub.L region out of the vector. The PCR fragments
containing the V.sub.H and V.sub.L sequences are mutagenized by the
poison PCR under conditions that favors incorporation of mutations
into the product.
[0282] Such conditions for poison PCR may include a) high
concentrations of Mn2+ (e.g. 0.4-0.6 mM) that efficiently induces
malfunction of Taq DNA polymerase; and b) disproportionally high
concentration of one nucleotide substrate (e.g., dGTP) in the PCR
reaction that causes incorrect incorporation of this high
concentration substrate into the template and produce mutations.
Additionally, other factors such as, the number of PCR cycles, the
species of DNA polymerase used, and the length of the template, may
affect the rate of mis-incorporation of "wrong" nucleotides into
the PCR product. Commercially available kits may be utilized for
the mutagenesis of the selected scFv library, such as the
"Diversity PCR random mutagenesis kit" (catalog No. K1830-1,
Clontech, Palo Alto, Calif.).
[0283] The PCR primer pairs used in mutagenesis PCR may preferably
include regions matched with the homologous recombination sites in
the expression vectors. This design allows re-introduction of the
PCR products after mutagenesis back into the yeast host strain
again via homologous recombination. This also allows the modified
V.sub.H and V.sub.L region to be fused with the AD domain directly
in the expression vector in the yeast.
[0284] Still referring to FIG. 4, the mutagenized scFv fragments
are inserted into the expression vector containing an AD domain via
homologous recombination in haploid cells of .alpha. type yeast
strain. Similarly to the selection of scFv clones from the primary
antibody library, the AD-scFv containing haploid cells are mated
with haploid cells of opposite mating type (e.g. a type) that
contains the BD-Target vector and the reporter gene construct. The
parental diploid cells are selected based on expression of the
reporter gene and other selection criteria as described in detail
in Section 5.
[0285] Other PCR-based mutagenesis method can also be used, alone
or in conjunction with the poison PCR described above. For example,
the PCR amplified V.sub.H and V.sub.L segments may be digested with
DNase to create nicks in the double DNA strand. These nicks can be
expanded into gaps by other exonucleases such as Bal 31. The gaps
may be then be filled by random sequences by using DNA Klenow
polymerase at low concentration of regular substrates dGTP, dATP,
dTTP, and dCTP with one substrate (e.g., dGTP) at a
disproportionately high concentration. This fill-in reaction should
produce high frequency mutations in the filled gap regions. These
method of DNase I digestion may be used in conjunction with poison
PCR to create highest frequency of mutations in the desired V.sub.H
and V.sub.L segments.
[0286] The PCR amplified V.sub.H and V.sub.L segments or the scFv
segments amplified from the primary antibody leads may be
mutagenized in vitro by using DNA shuffling techniques described by
Stemmer (1994) Nature 370:389-391; and Stemmer (1994) Proc. Natl.
Acad. Sci. USA 91:10747-10751. The V.sub.H, V.sub.L or scFV
segments from the primary antibody leads are digested with DNase I
into random fragments which are then reassembled to their original
size by homologous recombination in vitro by using PCR methods. As
a result, the diversity of the library of primary antibody leads
are increased as the numbers of cycles of molecular evolution
increase in vitro.
[0287] The V.sub.H, V.sub.L or scFv segments amplified from the
primary antibody leads may also be mutagenized in vivo by
exploiting the inherent ability of mutton in pre-B cells. The Ig
gene in pre-B cells is specifically susceptible to a high-rate of
mutation in the development of pre-B cells. The Ig promoter and
enhancer facilitate such high rate mutations in a pre-B cell
environment while the pre-B cells proliferate. Accordingly, V.sub.H
and V.sub.L gene segments may be cloned into a mammalian expression
vector that contains human Ig enhancer and promoter. This construct
may be introduced into a pre-B cell line, such as 38B9, which
allows the mutation of the V.sub.H and V.sub.L gene segments
naturally in the pre-B cells. Liu, X., and Van Ness, B. (1999) Mol.
Immunol. 36:461-469. The mutagenized V.sub.H and V.sub.L segments
can be amplified from the cultured pre-B cell line and
re-introduced back into the AD-containing yeast strain via, for
example, homologous recombination.
[0288] The secondary antibody library produced by mutagenesis in
vitro (e.g. PCR) or in vivo, i.e., by passing through a mammalian
pre-B cell line may be cloned into an expression vector and
screened against the same target protein as in the first round of
screening using the primary antibody library. For example, the
expression vectors containing the secondary antibody library may be
transformed into haploid cells of .alpha. type yeast strain. These
a cells are mated with haploid cells a type yeast strain containing
the BD-target expression vector and the reporter gene construct.
The positive interaction of scFvs from the secondary antibody
library is screened by following similar procedures as described
for the selection of the primary antibody leads in yeast
[0289] Alternatively, since the secondary antibody library may be
relatively low in complexity (e.g.,10.sup.4-10.sup.5 independent
clones) as compared to the primary libraries
(e.g.,10.sup.7-10.sup.14), the screening of the secondary antibody
library may be performed without mating between two yeast strains.
Instead, the linearized expression vectors containing the AD domain
and the mutagenized V.sub.H and V.sub.L segments may be directly
co-transformed into yeast cells containing the BD-target expression
vector and the reporter gene construct. Via homologous
recombination in yeast, the secondary antibody library are
expressed by the recombined AD-scFv vector and screened against the
target protein expressed by the BD-target vector by following
similar procedures as described for the selection of the primary
antibody leads in yeast.
[0290] 8. Functional Expression and Purification of Selected
Antibody
[0291] The library of scFv fusion proteins that are generated and
selected in the screening against the target protein(s) may be
expressed in hosts after the V.sub.H and V.sub.L sequences are
operably linked to an expression control DNA sequence, including
naturally-associated or heterologous promoters, in an expression
vector. By operably linking the V.sub.H and V.sub.L sequences to an
expression control sequence, the V.sub.H and V.sub.L coding
sequences are positioned to ensure the transcription and
translation of these inserted sequences. The expression vector may
be replicable in the host organism as episomes or as an integral
part of the host chromosomal DNA. The expression vector may also
contain selection markers such as antibiotic resistance genes (e.g.
neomycin and tetracycline resistance genes) to permit detection of
those cells transformed with the expression vector.
[0292] Preferably, the expression vector may be a eukaryotic vector
capable of transforming or transfecting eukaryotic host cells. Once
the expression vector has been incorporated into the appropriate
host cells, the host cells are maintained under conditions suitable
for high level expression of the single-chains polypeptide encoded
by a scFv. The polypeptides expressed are collected and purified
depending on the expression system used.
[0293] The scFv, Fab, or fully assembled antibodies selected by
using the methods of the present invention may be expressed in
various scales in any host system such as bacteria (e.g. E. coli),
yeast (e.g. S. cerevisiae), and mammalian cells (COS). The bacteria
expression vector may preferably contain the bacterial phage T7
promoter and express a single chain variable fragment (scFv). The
yeast expression vector may contain a constitutive promoter (e.g.
ADGI promoter) or an inducible promoter such as (e.g. GCN4 and Gal
1 promoters). All three types of antibody, scFv, Fab, and full
antibody, may be expressed in a yeast expression system.
[0294] The expression vector may be a mammalian express vector that
can be used to express the single-chains polypeptide encoded by
V.sub.H and V.sub.L in mammalian cell culture transiently or
stably. Examples of mammalian cell lines that may be suitable of
secreting immunoglobulins include, but are not limited to, various
COS cell lines, HeLa cells, myeloma cell lines, CHO cell lines,
transformed B-cells and hybridomas.
[0295] Typically, a mammalian expression vector includes certain
expression control sequences, such as an origin of replication, a
promoter, an enhancer, as well as necessary processing signals,
such as ribosome binding sites, RNA splice sites, polyadenylation
sites, and transcriptional terminator sequences. Examples of
promoters include, but are not limited to, insulin promoter, human
cytomegalovirus (CMV) promoter and its early promoter, simian virus
SV40 promoter, Rous sarcoma virus LTR promoter/enhancer, the
chicken cytoplasmic .beta.-actin promoter, promoters derived from
immunoglobulin genes, bovine papilloma virus and adenovirus.
[0296] One or more enhancer sequence may be included in the
expression vector to increase the transcription efficiency.
Enhancers are cis-acting sequences of between 10 to 300 by that
increase transcription by a promoter. Enhancers can effectively
increase transcription when positioned either 5' or 3' to the
transcription unit. They may also be effective if located within an
intron or within the coding sequence itself. Examples of enhancers
include, but are not limited to, SV40 enhancers, cytomegalovirus
enhancers, polyoma enhancers, the mouse immunoglobulin heavy chain
enhancer, and adenovirus enhancers.
[0297] The mammalian expression vector may also typically include a
selectable marker gene. Examples of suitable markers include, but
are not limited to, the dihydrofolate reductase gene (DHFR), the
thymidine kinase gene (TK), or prokaryotic genes conferring
antibiotic resistance. The DHFR and TK genes prefer the use of
mutant cell lines that lack the ability to grow without the
addition of thymidine to the growth medium. Transformed cells can
then be identified by their ability to grow on non-supplemented
media. Examples of prokaryotic drug resistance genes useful as
markers include genes conferring resistance to. G418, mycophenolic
acid and hygromycin.
[0298] The expression vectors containing the scFv sequences can
then be transferred into the host cell by methods known in the art,
depending on the type of host cells. Examples of transfection
techniques include, but are not limited to, calcium phosphate
transfection, calcium chloride transfection, lipofection,
electroporation, and microinjection.
[0299] The V.sub.H and V.sub.L sequences may also be inserted into
a viral vector such as adenoviral vector that can replicate in its
host cell and produce the polypeptide encoded by V.sub.H and
V.sub.L in large amounts.
[0300] In particular, the scFv, Fab, or fully assembled antibody
may be expressed in mammalian cells by using a method described by
Persic et al. (1997) Gene, 187:9-18. The mammalian expression
vector that is described by Persic and contains EF-.alpha. promoter
and SV40 replication origin is preferably utilized. The SV40 origin
allows a high level of transient expression in cells containing
large T antigen such as COS cell line. The expression vector may
also include secretion signal and different antibiotic markers
(e.g. neo and hygro) for integration selection.
[0301] Once expressed, polypeptides encoded by V.sub.H and V.sub.L
may be isolated and purified by using standard procedures of the
art, including ammonium sulfate precipitation, fraction column
chromatography, and gel electrophoresis. Once purified, partially
or to homogeneity as desired, the polypeptides may then be used
therapeutically or in developing, performing assay procedures,
immunofluorescent stainings, and in other biomedical and industrial
applications. In particular, the antibodies generated by the method
of the present invention may be used for diagnosis and therapy for
the treatment of various diseases such as cancer, autoimmune
diseases, or viral infections.
[0302] In a preferred embodiment, the scFv human antibody with
V.sub.H and V.sub.L segments that are generated and screened by
using the methods of the present invention may be expressed
directly in yeast. According to this embodiment, the V.sub.H and
V.sub.L regions from the selected expression vectors may be PCR
amplified with primers that simultaneously add appropriate
homologous recombination sequences to the PCR products. These PCR
segments of V.sub.H and V.sub.L may then be introduced into a yeast
strain together with a linearized expression vector containing
desirable promoters, expression tags and other transcriptional or
translational signals.
[0303] For example, the PCR segments of V.sub.H and V.sub.L regions
may be homologously recombined with a yeast expression vector that
already contains a desirable promoter in the upstream and stop
codons and transcription termination signal in the downstream. The
promoter may be a constitutive expression promoter such as ADH1, or
an inducible expression promoter, such as Gal 1, or GCN4 (A.
Mimran, I. Marbach, and D. Engelberg, (2000) Biotechniques
28:552-560). The latter inducible promoter may be preferred because
the induction can be easily achieved by adding 3-AT into the
medium.
[0304] The yeast expression vector to be used for expression of the
scFv antibody may be of any standard strain with nutritional
selection markers, such as His 3, Ade 2, Leu 2, Ura 3, Trp 1 and
Lys 2. The marker used for the expression of the selected scFv may
preferably be different from the AD vector used in the selection of
scFv in the two-hybrid system. This may help to avoid potential
carryover problem associated with multiple yeast expression
vectors.
[0305] For expressing the scFv antibody in a secreted form in
yeast, the expression vector may include a secretion signal in the
5' end of the V.sub.H and V.sub.L segments, such as an alpha factor
signal and a 5-pho secretion signal. Certain commercially available
vectors that contain a desirable secretion signal may also be used
(e.g., pYEX-S1, catalog #6200-1, Clontech, Palo Alto, Calif.).
[0306] The scFv antibody fragments generated may be analyzed and
characterized for their affinity and specificity by using methods
known in the art, such as ELISA, western, and immune staining.
Those scFv antibody fragments with reasonably good affinity (with
dissociation constant preferably lower than 10.sup.-6M) and
specificity can be used as building blocks in Fab expression
vectors, or can be further assembled with the constant region for
full length antibody expression. These fully assembled human
antibodies may also be expressed in yeast in a secreted form.
[0307] The V.sub.H sequence encoding the selected scFv protein may
be linked with the constant regions of a full antibody, C.sub.H1,
C.sub.H2 and C.sub.H3. Similarly, the V.sub.L sequence may be
linked with the constant region C.sub.L. The assembly of two units
of V.sub.H-C.sub.H 1-C.sub.H2-C.sub.H3 and V.sub.L-C.sub.L leads to
formation of a fully functional antibody. The present invention
provides a method for producing fully functional antibody in yeast.
Fully functional antibody retaining the rest of the constant
regions may have a higher affinity (or avidity) than a scFv or a
Fab. The full antibody should also have a higher stability, thus
allowing more efficient purification of antibody protein in large
scale.
[0308] The method is provided by exploiting the ability of yeast
cells to uptake and maintain multiple copies of plasmids of the
same replication origin. According to the method, different vectors
may be used to express the heavy chain and light chain separately,
and yet allows for the assembly of a fully functional antibody in
yeast. This approach has been successfully used in a two-hybrid
system design where the BD and AD vectors are identical in backbone
structure except the selection markers are distinct. This approach
has been used in a two-hybrid system design for expressing both BD
and AD fusion proteins in the yeast. The BD and AD vectors are
identical in their backbone structures except the selection markers
are distinct. Both vectors can be maintained in yeast in high copy
numbers. Chien, C. T., et al. (1991) "The two-hybrid system: a
method to identify and clone genes for proteins that interact with
a protein of interest" Proc. Natl. Acad. Sci. USA 88:9578-9582.
[0309] In the present invention, the heavy chain gene and light
chain genes are placed in two different vectors. Under a suitable
condition, the V.sub.H-C.sub.H1-C.sub.H2-C.sub.H3 and
V.sub.L-C.sub.L sequences are expressed and assembled in yeast,
resulting in a fully functional antibody protein with two heavy
chains and two light chains. This fully functional antibody may be
secreted into the medium and purified directly from the
supernatant.
[0310] The scFv with a constant region, Fab, or fully assembled
antibody can be purified using methods known in the art.
Conventional techniques include, but are not limited to,
precipitation with ammonium sulfate and/or caprylic acid, ion
exchange chromatography (e.g. DEAE), and gel filtration
chromatography. Delves (1997) "Antibody Production: Essential
Techniques", New York, John Wiley & Sons, pages 90-113.
Affinity-based approaches using affinity matrix based on Protein A,
Protein G or Protein L may be more efficiency and results in
antibody with high purity. Protein A and protein G are bacterial
cell wall proteins that bind specifically and tightly to a domain
of the Fc portion of certain immunoglobulins with differential
binding affinity to different subclasses of IgG. For example,
Protein G has higher affinities for mouse IgG1 and human IgG3 than
does Protein A. The affinity of Protein A of IgG 1 can be enhanced
by a number of different methods, including the use of binding
buffers with increased pH or salt concentration. Protein L binds
antibodies predominantly through kappa light chain interactions
without interfering with the antigen-binding site. Chateau et al.
(1993) "On the interaction between Protein L and immunoglobulins of
various mammalian species" Scandinavian J. Immunol., 37:399-405.
Protein L has been shown to bind strongly to human kappa light
chain subclasses I, III and IV and to mouse kappa chain subclasses
I. Protein L can be used to purify relevant kappa chain-bearing
antibodies of all classes (IgG, IgM, IgA, IgD, and IgE) from a wide
variety of species, including human, mouse, rat, and rabbit.
Protein L can also be used for the affinity purification of scFv
and Fab antibody fragments containing suitable kappa light chains.
Protein L-based reagents is commercially available from Actigen,
Inc., Cambridgem, England. Actigen can provide a line of
recombinant Protein products, including agarose conjugates for
affinity purification and immobilized forms of recombinant Protein
L and A fusion protein which contains four protein A
antibody-binding domains and four protein L kappa-binding
domains.
[0311] Other affinity matrix may also be used, including those that
exploit peptidomimetic ligands, anti-immunoglobulins, mannan
binding protein, and the relevant antigen. Peptidomimetic ligands
resemble peptides but they do not correspond to natural peptides.
Many of Peptidomimetic ligands contain unnatural or chemically
modified amino acids. For example, peptidomimetic ligands designed
for the affinity purification of antibodies of the IGA and IgE
classes are commercially available from Tecnogen, Piana di Monte
Verna, Italy. Mannan binding protein (MBP) is a mannose- and
N-acetylglucosamine-specific lectin found in mammalian sera. This
lectin binds IgM. The MBP-agarose support for the purification IgM
is commercially available from Pierce.
[0312] Immunomagnetic methods that combine an affinity reagent
(e.g. protein A or an anti-immunoglobulin) with the ease of
separation conferred by paramagnetic beads may be used for
purifying the antibody produced. Magnetic beads coated with Protein
or relevant secondary antibody may be commercially available from
Dynal, Inc., NY; Bangs Laboratories, Fishers, Ind.; and Cortex
Biochem Inc., San Leandro, Calif.
[0313] Direct expression and purification of the selected antibody
in yeast is advantageous in various aspects. As a eukaryotic
organism, yeast is more of an ideal system for expressing human
proteins than bacteria or other lower organisms. It is more likely
that yeast will make the scFv, Fab, or fully assembled antibody in
a correct conformation (folded correctly), and will add
post-translation modifications such as correct disulfide bond(s)
and glycosylations.
[0314] Yeast has been explored for expressing many human proteins
in the past. Many human proteins have been successfully produced
from the yeast, such as human serum albumin (Kang, H. A. et al.
(2000) Appl. Microbiol. Biotechnol. 53:578-582) and human
telomerase protein and RNA complex (Bachand, F., et al. (2000) RNA
6:778-784).
[0315] Yeast has fully characterized secretion pathways. The
genetics and biochemistry of many if not all genes that regulate
the pathways have been identified. Knowledge of these pathways
should aid in the design of expression vectors and procedures for
isolation and purification of antibody expressed in the yeast.
[0316] Moreover, yeast has very few secreted proteases. This should
keep the secreted recombinant protein quite stable. In addition,
since yeast does not secrete many other and/or toxic proteins, the
supernatant should be relatively uncontaminated. Therefore,
purification of recombinant protein from yeast supernatant should
be simple, efficient and economical.
[0317] Additionally, simple and reliable methods have been
developed for isolating proteins from yeast cells. Cid, V. J. et
al. (1998) "A mutation in the Rho&GAP-encoding gene BEM2 of
Saccharomyces cerevisiae affects morphogenesis and cell wall
functionality" Microbiol. 144:25-36. Although yeast has a
relatively thick cell wall that is not present in either bacterial
or mammalian cells, the yeast cells can still keep the yeast strain
growing with the yeast cell wall striped from the cells. By growing
the yeast strain in yeast cells without the cell wall, secretion
and purification of recombinant human antibody may be made more
feasible and efficient.
[0318] By using yeast as host system for expression, a streamlined
process can be established to produce recombinant antibodies in
fully assembled and purified form. This may save tremendous time
and efforts as compared to using any other systems such as
humanization of antibody in vitro and production of fully human
antibody in transgenic animals.
[0319] In summary, the compositions, kits and methods provided by
the present invention should be very useful for selecting proteins
such as human antibodies with high affinity and specificity against
a wide variety of targets including, but not limited to, soluble
proteins (e.g. growth factors, cytokines and chemokines),
membrane-bound proteins (e.g. cell surface receptors), and viral
antigens. The whole process of library construction, functional
screening and expression of highly diverse repertoire of human
antibodies can be streamlined, and efficiently and economically
performed in yeast in a high throughput and automated manner. The
selected proteins can have a wide variety of applications. For
example, they can be used in therapeutics and diagnosis of diseases
including, but not limited to, autoimmune diseases, cancer,
transplant rejection, infectious diseases and inflammation.
EXAMPLE
[0320] 1. Construction of Human Single Chain Antibody Library
[0321] A human scFv library was constructed in a yeast two-hybrid
vector pACT2 that contains sequence encoding Gal4 activation domain
(AD) (Li et al. (1994) "Specific association between the human DNA
repair proteins XPA and ERCC1" Proc Natl Acad Sci USA.
91:5012-5016). cDNA encoding the variable regions of heavy
(V.sub.H) and light chain (V.sub.L) were amplified by RT-PCR from
poly A.sup.+ RNA of human spleen, bone marrow, fetal liver and
peripheral blood leukocytes (PBL). The V.sub.H and V.sub.L cDNA
fragments were linked by a linker encoding [(Gly).sub.4Ser].sub.4
(Nicholls et al. (1993) "An improved method for generating
single-chain antibodies from hybridomas" J Immunol Methods
165:81-91), and are flanked by sequences of approximately 60 by at
each end that are homologous to the pACT2 multiple cloning sites
(MCS) (Hua, et al, (1998) "Construction of a modular yeast
two-hybrid cDNA library from human EST clones for the human genome
protein linkage map" Gene. 215:143-152). Such assembled PCR
products were cloned into pACT2 by homologous recombination (Hua et
al, 1997) in yeast cells (MAT.alpha. strains Y187 or MaV203)
(Harper et al, (1993) "The p21 Cdk-interacting protein Cip1 is a
potent inhibitor of G1 cyclin-dependent kinases" Cell 75:805-16;
Vidal et al. (1996) "Reverse two-hybrid and one-hybrid systems to
detect dissociation of protein-protein and DNA-protein
interactions" Proc Natl Acad Sci USA. 93:10315-10320). Such derived
human scFvs are fused in-frame with the Gal4 activation domain. A
total of 5.times.10.sup.7 independent yeast colonies were harvested
and stored at -80.degree. C.
[0322] More specifically, poly A.sup.+RNA from human bone marrow,
human fetal liver, human spleen and human peripheral blood
leukocytes were purchased from Clontech Laboratories (Palo Alto,
Calif.). First strand cDNA were made from the poly A.sup.+ RNA
using random primer and PowerScript reverse transcriptase kit
(Clontech Laboratories, Palo Alto, Calif.). A set of
oligonucleotides designed by Sblattero and Bradbury (Sblattero and
Bradbury (1998) "A definitive set of oligonucleotide primers for
amplifying human V regions" Immunotechnology. 3:271-278) that
recognize all functional V genes were used to amplify all variable
regions of heavy chain and light chain of human antibodies in PCR
(Marks et al. (1991) "By-passing immunization: Human antibodies
from V-gene libraries displayed on phage" J Mol Biol.
222:581-597).
[0323] The cDNA of heavy chain variable region (V.sub.H) and light
chain variable region (V.sub.L) were linked by a short linker
sequence encoding [(Gly).sub.4Ser].sub.4 (5'-GGC GGT GGT GGA TCA
GGC GGC GGA GGA TCT GGC GGA GGT GGC AGC GGT GGT GGA GGC AGT-3' [SEQ
ID NO: 5]) (Nicholls et al. (1993) "An improved method for
generating single-chain antibodies from hybridomas" J Immunol
Methods 165:81-91). The V.sub.H-linker-V.sub.L cassettes were
flanked by 60 base pairs (bp) at its 5' end and 57 by at its 3' end
of sequence homologous to the sequence adjacent to multiple cloning
site of the yeast two-hybrid vector pACT2 (Hua et al, (1997),
supra, Hua et al (1998), supra).
[0324] The 5' (1.3.a) and 3' homologous sequence (1.3.b) are as
follows:
TABLE-US-00005 1.3.a: [SEQ ID NO: 6] 5'-ACC CCA CCA AAC CCA AAA AAA
GAG ATC TGT ATG GCT TAC CCA TAC GAT GTT CCA GAT TAC 1.3.b: [SEQ ID
NO: 7] 5'-GAG ATG GTG CAC GAT GCA CAG TTG AAG TGA ACT TGC GGG GTT
TTT CAG TAT CTA CGA
[0325] The above-assembled PCR products containing scFv were
co-transformed with linearized pACT2 DNA (Hua et al. (1997), supra)
into yeast strains Y187 (MAT.alpha., ura3-52, his3-200, ade2-101,
lys2-801, trp1-901, leu2-3,112, gal4.DELTA., gal80.DELTA.,
URA3::GAL1.sub.UAS-GAL1.sub.TATA-lacZ) (Harper et al, 1993) or
MaV203 (MAT.alpha., ura3-52, his3.DELTA.200, ade2-101, trp1-901,
leu2-3,112, cyh2.sup.R, can1.sup.R, gal4.DELTA., gal80.DELTA.,
GAL1::lacZ, HIS3 .sub.UASGALl::HIS3@LYS2, SPAL10::URA3) (Vidal et
al. (1996) "Reverse two-hybrid and one-hybrid systems to detect
dissociation of protein-protein and DNA-protein interactions" Proc
Natl Acad Sci USA. 93:10315-10320). The transformants were plated
on yeast synthetic medium lacking leucine (SD/-L) and incubated at
30.degree. C. for 2 days. A total of approximately 5.times.10.sup.7
independent colonies of the yeast two-hybrid scFv library were
harvested and stored at -80.degree. C.
[0326] 2. Construction of a Yeast Expression Vector Encoding
Peptide Fragments Derived from Human CCR5
[0327] Peptide fragments derived from human CCR5 were used as
target peptides against which the scFv library constructed above
was screened. Three extracellular domains of human CCR5 cDNA, an
N-terminal fragment, the 4.sup.th loop (or loop 4) and the 6.sup.th
loop (or loop 6), were separately PCR-amplified from human
leukocyte cDNA (Clontech Laboratories, Inc., Palo Alto, Calif.)
using the following oligonucleotide primers.
[0328] For amplification of the N-terminus of human CCR5 (aa 1-36),
the primer pair are:
TABLE-US-00006 13.13.L [SEQ ID NO: 49] 5'-GGA GAA TTC
GATTATCAAGTGTCAAGTCCA 13.13.M [SEQ ID NO: 50] 5'-CGC GGA TCC TTA
GAGCGGAGGCAGGAGGCGG
[0329] Primer 13.13.L corresponds to the N-terminus of CCR5, with
an Eco R1 site added. Primer 13.13.M complements the sequence at
the end of N-terminal extracellular domain (aa 36) of CCR5, with
Bam HI and Stop codon added.
[0330] For amplification of the 4.sup.th loop of human CCR5 (aa
167-198), the primer pair are:
TABLE-US-00007 13.13.N [SEQ ID NO: 51] 5'-GGA GAA TTC
ACCAGATCTCAAAAAGAAGG 13.13.O [SEQ ID NO: 52] 5'-CGC GGA TCC TTA
TATCTTTAATGTCTGGAAATT
[0331] Primer 13.13.N corresponds the sequence at the N-terminus of
4.sup.th loop of CCR5 (aa 167), with Eco RI site added. Primer
13.13.O complements the sequence at the C-terminus of 4.sup.th loop
of CCR5 (aa 198), with Bam HI and Stop codon added.
[0332] For amplification of the 6.sup.th loop of CCR5 (aa 262-290),
the primer pair are:
TABLE-US-00008 13.13.P [SEQ ID NO: 53] 5'-CAG GAA TTC TTTGGCCTGAAT
13.13.Q [SEQ ID NO: 54] 5'-CGC GGA TCC TCA GCAGTGCGTCATCCCAAGA
[0333] Primer 13.13.P corresponds the sequence at the N-terminus of
6.sup.th loop of hCCR5 (aa 262) at the Eco RI site. Primer 13.13.Q
complements the sequence at the C-terminus of 6.sup.th loop of CCR5
(aa 290), with Bam HI and Stop codon added.
[0334] The PCR product of each of the domains was cloned into an
Eco RI/Bam HI-digested cloning vector pGBKT7 (Clontech
Laboratories, Palo Alto, Calif.) with the Gal4 DNA binding domain
(DNA-BD) at its carboxy terminus. The resulting plasmids were
designated as follows:
[0335] pG90: pGBKT7-CCR5 N-terminus;
[0336] pG91: pGBKT7-CCR5 loop 4;
[0337] pG92: pGBKT7-CCR5 loop 6.
[0338] Each of the above plasmids encoding CCR5 peptide fragments
was transformed into yeast strain AH109 (MATa, ura3-52, his3-200,
ade2-101, trp1-901, leu2-3,112, gal4.DELTA., gal80.DELTA.,
LYS2::GAL1.sub.UAS-GAL1.sub.TATA-HIS3,
GAL2.sub.UAS-GAL2.sub.TATA-ADE2,
URA3::MEL1.sub.UAS-MEL1.sub.TATA-lacZ) (Clontech Laboratories, Palo
Alto, Calif.). The transformants were selected on synthetic medium
lacking tryptophan (SD/-W).
[0339] 3. Screening of a Human scFv Library Against Extracellular
Domains of Human CCR5
[0340] To screen the scFv library against the extracellular domains
of human CCR5, the AH109 transformants containing one of the three
extracellular domains were mated with MAT.alpha. type yeast cells
(Y 187 or MaV203 strain) containing the scFv library following the
protocols from Clontech Laboratories. The scFv library-containing
vector pACT2 contains a LEU2 gene, whereas the pGBKT7 plasmids
contain a TRP1 gene. Cells harboring both plasmids can grow in the
yeast synthetic medium lacking leucine and tryptophan (SD/-LW).
Interactions between a scFv and the target CCR5 domain activated
expression of reporter genes ADE2 and HIS3 built in genome of the
strains, thus allowing the cells to grow on medium lacking adenine,
histidine, leucine and tryptophan (SD/-AHLW). Colonies that were
able to grow on SD/-ALHW medium were picked. These colonies were
assayed for the expression of additional reporter gene lacZ in the
.beta.-galactosidase colony-lifting assay as described in the
instruction manual from Clontech Laboratories. Plasmid DNA of pACT2
containing the scFv fragment was retrieved from the yeast
cells.
[0341] To analyze the specificity of those scFv clones isolated
from the above-mentioned library screening, pGBKT7 plasmids
encoding CCR5 domains, empty vector pGBKT7 and pGBKT7-Lam
(Clontech) (which contains sequence of human lamin C), were
co-transformed, respectively, with individual scFv plasmids into
yeast cells, followed by growth selection on SD/-LW or SD/-AHLW
media. Yeast colonies grown on the selection media were subjected
to .beta.-galactosidase activity assays. The sequences of those
scFv clones specific to human CCR5 domains were determined with an
ABI automatic sequencer.
[0342] From the above library screening and specificity analysis,
one specific scFv clone (clone 15.186.35) was obtained against the
N-terminal fragment of human CCR5, and 3 specific scFv clones
against Loop 6 of human CCR5: clones 15.150.11, 15.150.12, and
15.150.24. The DNA and amino acid sequences encoding these four
clones are listed in FIG. 5. In addition, some variants of the four
clones with slight modifications in the sequences in the framework
regions are listed in FIG. 6.
[0343] 4. Inhibition of HIV-1 Infection by the Selected Human
Monoclonal Antibody
[0344] ScFv clones 15.150.11 and 15.150.12 were cloned into E. coli
expression vector pET27b(+) (Novagen) to facilitate expression of
scFv antibodies of Ab32 and Ab33, respectively. ScFv proteins were
expressed and purified from the periplasmic space of the bacteria.
The ability of the selected anti-CCR5 scFv antibodies, Ab32 and
Ab33, to inhibit HIV-1 infection was determined by using an assay
described in Cotter et al. (2001) J. Virol. 75:4308-4320. The
control scFv antibody used was anti-human p53 scFv antibody.
[0345] Human monocytes were recovered from peripheral blood
mononuclear cells of HIV-1-, HIV-2-, and hepatitis B
virus-seronegative donors after leukapheresis and then purified by
countercurrent centrifugal elutriation. Monocytes were cultured as
adherent monolayers and differentiated for 7 days into macrophages
(monocyte-derived macrophages or MDM). MDM were first incubated
with different concentrations of scFv antibodies, then infected
with HIV-1. HIV-1 reverse transcriptase (RT) activity was
determined at Day 4, Day 8 and Day 12, as incorporation of
[.sup.3H]TTP (Cotter et al, 2001, J. Virol. 75:4308-4320).
Radiolabeled nucleotides were precipitated with cold 10%
trichloroacetic acid on paper filters in an automatic cell
harvester and washed with 95% ethanol. Radioactivity was estimated
by liquid scintillation spectroscopy. The cell viability was
determined by MTT assay. Briefly, MTT
(3-{4,5-Dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide, from
Sigma) was dissolved in cell culture medium without phenol red.
Live cells will convert MTT into purple dye inside cells. The dye
was solubilized with acidic isopropanol and absorbance (OD) of the
converted dye was measured at 570 nm. Mossman T., 1983, J. Immunol.
Methods 65:55.
[0346] FIGS. 9A-C show HIV-1 RT activity in monocytes infected by
HIV-1 in the presence or absence of two selected scFv antibodies
against human CCR5 Loop (Ab32 and AB33) of the present invention on
day 4, 8, and 12 post infection, respectively. As shown in FIGS.
9A-C, both Ab32 and AB33 effectively inhibit HIV-1 RT activity at
concentrations 20, 2.0 and 0.2 .mu.g/mL. In contrast, a
non-specific antibody which is elicited against the tumor
suppressor p53 protein), Ab 16, is completely ineffective in
inhibition of HIV-1 RT activity. The positive control, a murine
monoclonal antibody 2D7 (available from Pharmingen, San Diego,
Calif.) could inhibit HIV-1 RT activity at a concentration of 10
.mu.g/mL. In the absence of antibodies or with addition of mere
buffer the HIV RT activity is completely uninhibited. Throughout
the incubation period, the HIV-infected monocytes had normal
viability in the presence or absence of these antibodies, as shown
in FIGS. 10A-C.
[0347] More significantly, when the concentrations of both Ab32 and
AB33 were lowered to 0.02 .mu.g/mL, these two scFv antibodies were
still effectively inhibit inhibit HIV-1 RT activity. FIGS. 11A-C
show HIV-1 RT activity in monocytes infected by HIV-1 in the
presence or absence of Ab32 and AB33 at various concentrations on
day 4, 8, and 12 post infection, respectively. At a concentration
as lower as 0.02 .mu.g/mL (.about.0.8 nM), both Ab32 and AB33 could
inhibit HIV-1 RT activity by 75% on day 12 post infection of the
monocytes.
[0348] 5. Binding of the Selected Human Monoclonal Antibody to
CCR5
[0349] The ability of the human monoclonal scFv antibodies Ab32 and
Ab33 to bind with their target protein was confirmed by Western
blot. Briefly, lysate of human macrophage (expressing CCR5) was
separated on SDS-PAGE, and transferred to nitrocellulose membrane.
The membrane was then probed either with the scFv selected in the
above-described process (Ab32 and Ab33) or positive control
antibody (murine monoclonal antibody 2D7 from Pharmingen, San
Diego), or a negative control (Ab16, an anti-p53 scFv antibody).
The positive control (MAb 2D7) blot was then probed with goat
anti-mouse IgG conjugated with HRP (horse radish peroxidase). The
scFv-probed blots were incubated with mouse anti-HSV tag antibody
followed by goat anti-mouse IgG conjugated HRP. The CCR5 band was
then detected with ECL (Enhanced Chemilluminence, from
Amersham-Pharmacia).
[0350] FIG. 12 shows the Western blot of CCR5 expressed by human
macrophage probed by Ab32 and Ab33. As shown in FIG. 12, both Ab32
and Ab33 were capable of binding to CCR5, just like the positive
control MAb 2D7. In contrast, a non-specific scFv antibody elicited
against human p53 protein, AB 16, is incapable of binding to
CCR5.
[0351] These results indicate that the monoclonal scFv antibodies
selected against a peptide fragment derived from CCR5 Loop 6 can
specifically recognize and bind to human CCR5 in vitro.
[0352] 6. Inhibition of Chemokine Binding to CCR5 by the Selected
Human Monoclonal Antibody
[0353] The ability of the human monoclonal scFv antibodies Ab32 and
Ab33 to bind with their target protein was further validated by
conducting competition binding assay using described in Wu et al.
(1997) J. Exp. Med. 186:1373-1381. Briefly, human MDMs
(monocyte-derived macrophages) were plated in 48-well plates. The
attached cells were incubated with antibodies (Ab32, Ab33, or the
mouse monoclonal antibody 2D7) at 37.degree. C. for 30 minutes.
Radio-labeled human CCR5 ligand, .sup.125I MIP1-.alpha. (Amersham),
was added to each well to a final concentration of 100 pM (2
.mu.Ci/pmole) and the cultures were incubated at 37.degree. C. for
two hours. After removal of the medium, the cultures were washed 3
times with cold PBS buffer. Cells were lysed with 0.3 ml of 1%
Triton X-100 in PBS for 30 min at room temperature. Radioactivity
in the lysates were measured by a gamma counter (Packard). The
results were shown in FIG. 13.
[0354] As shown in FIG. 13, the human monoclonal scFv antibodies
Ab32 and Ab33 effectively blocked the binding of .sup.125I MIP
1-.alpha. to its cognate receptor CCR5 on human MDMs.
Significantly, both Ab32 and Ab33 exhibited slightly stronger
binding affinity to human CCR5 than the mouse monoclonal antibody
2D7. In contrast, a non-specific human scFv against human p53,
Ab16, could not inhibit the binding of .sup.125I MIP1-.alpha. to
CCR5.
[0355] To ensure that the results obtained in above-described assay
were obtained in a normally-behaving binding assay, non-labeled
MIP1-.alpha. was used to compete with .sup.125I MIP1-.alpha. for
binding to CCR5. As shown in FIG. 14, MIP1-.alpha. could compete
with .sup.125I MIP1-.alpha. for binding to CCR5 at a concentration
of 25 nm. Similarly, another cognate ligand of human CCR5, RANTES,
could also compete with .sup.125I MIP1-.alpha. for binding to CCR5
at a concentration of 25 nm. These results indicate that the
radio-labeled human CCR5 ligand, .sup.125I MIP1-.alpha. did bind to
its cognate receptor CCR5 on human MDMs and the binding could be
inhibited by the human monoclonal scFv antibodies Ab32 and Ab33
selected using the method of the present invention.
[0356] 7. Construction of a Yeast Expression Vector Encoding
Peptide Fragments Derived from Human CXCR4
[0357] In one embodiment of the present invention, the last
extracellular loop of human CXCR4, loop 6, was used as the target
peptide fragment for eliciting monoclonal antibodies against CXCR4
in yeast. The cDNA encoding CXCR4 loop 6 was amplified from human
leukocyte Quick-clone cDNA (purchased from BD-Clontech, Cat.
#7182-1) using primers 13.12.G and 13.12.H.
TABLE-US-00009 13.12.G [SEQ ID NO: 55] 5'-GGA GAA TTC
ATCGACTCCTTCATCCTCCTG 13.12.H [SEQ ID NO: 56] 5'-CGC GGA TCC TTA
AGCTAGGGCCTCGGTGATGGA
[0358] The PCR product was cloned into Eco RI/Bam HI sites of
pGBK-T7, resulting a plasmid (designated as pG88) encoding CXCR4
loop 6 with the Gal4 DNA binding domain fused at its carboxy
terminus. The DNA sequence of the coding region of human CXCR4
loop6 is as follows:
TABLE-US-00010 [SEQ ID NO: 57]
5'ATCGACTCCTTCATCCTCCTGGAAATCATCAAGCAAGGGTGTGAGTTTGAGAACACTGTGCACAAGT
GGATTTCCATCACCGAGGCCCTAGCT-3'
[0359] The amino acid sequence encoded by the above DNA sequence is
as follows:
TABLE-US-00011 [SEQ ID NO: 58] IDSFILLEIIKQGCEFENTVHKWISITEALA
[0360] 8. Screening of a Human scFv Antibody Library Against Human
CXCR4 Loop 6 in Yeast Two-Hybrid System
[0361] Plasmid DNA of pG88 was transformed into yeast cells of
strain AH109. Transformed cells were mated with a fully human scFv
library as described in Section 1 of "EXAMPLE" above. The mated
cells were selected on medium SD/-Leu-Trp-His-Ade. Cells grown on
the selection medium were assayed for .beta.-gal activities.
Non-specific scFv clones were ruled out by assaying with control
bait plasmids (pGBK-T7 and pGBK-Lam). DNA sequences of the scFv
inserts from the human CXCR4 loop 6-specific clones were
determined. Two clones with complete scFv inserts were obtained.
These two scFv clones were designated Ab124 and Ab125. Their
nucleotide and amino acid sequences are listed in FIG. 15.
[0362] 9. Inhibition of SDF-1 Induced Chemotaxis by the Selected
Human Monoclonal Antibodies Against CXCR4 in Human Breast Cancer
Cells
[0363] ScFv clones encoding Ab124 and Ab125 were cloned into E.
coli expression vector pET27b(+) (Novagen) to facilitate expression
of these 2 scFv antibodies. ScFv proteins were expressed and
purified from the periplasmic space of the bacteria. The ability of
these selected anti-CXCR4 scFv antibodies to inhibit SDF-1 induced
chemotaxis was determined by using an assay described in Harvath L,
et al. (1980) J Immunol Methods. 37:39-45. SDF-1 (Stromal cell
Derived Factor-1) is a ligand of CXCR4 which can cause chemotaxis
of certain cell types, including the breast cancer cell line
MDA-MB-231. In the present invention, the selected antibodies were
tested for their ability to inhibit SDF-1 induced chemotaxis in
MDA-MB-231 cells.
[0364] Cells of breast cancer cell line MDA-MB-231 were incubated
with i) medium only, ii) mouse anti-CXCR4 monoclonal antibody
(R&D System), iii) isotype control mouse monoclonal antibody,
iv) control scFv Ab16, v) scFv Ab124, or vi) scFv Ab125, followed
by the chemotaxis assay. Numbers of MDA-MB-231 cells that migrated
toward the chamber containing SDF-1 were counted under a
microscope.
[0365] The results are shown in FIG. 16. These results demonstrate
that Ab124 and Ab125 can block SDF-1 induced chemotaxis in the
breast cancer cell line MDA-MB-231, suggesting that the Ab124 and
Ab 125 can bind to CXCR4 and block the function of a CXCR4 ligand,
SDF-1.
Sequence CWU 1
1
641352PRTHomo sapiens 1Met Asp Tyr Gln Val Ser Ser Pro Ile Tyr Asp
Ile Asn Tyr Tyr Thr 1 5 10 15 Ser Glu Pro Cys Gln Lys Ile Asn Val
Lys Gln Ile Ala Ala Arg Leu 20 25 30 Leu Pro Pro Leu Tyr Ser Leu
Val Phe Ile Phe Gly Phe Val Gly Asn 35 40 45 Met Leu Val Ile Leu
Ile Leu Ile Asn Cys Lys Arg Leu Lys Ser Met 50 55 60 Thr Asp Ile
Tyr Leu Leu Asn Leu Ala Ile Ser Asp Leu Phe Phe Leu 65 70 75 80 Leu
Thr Val Pro Phe Trp Ala His Tyr Ala Ala Ala Gln Trp Asp Phe 85 90
95 Gly Asn Thr Met Cys Gln Leu Leu Thr Gly Leu Tyr Phe Ile Gly Phe
100 105 110 Phe Ser Gly Ile Phe Phe Ile Ile Leu Leu Thr Ile Asp Arg
Tyr Leu 115 120 125 Ala Val Val His Ala Val Phe Ala Leu Lys Ala Arg
Thr Val Thr Phe 130 135 140 Gly Val Val Thr Ser Val Ile Thr Trp Val
Val Ala Val Phe Ala Ser 145 150 155 160 Leu Pro Gly Ile Ile Phe Thr
Arg Ser Gln Lys Glu Gly Leu His Tyr 165 170 175 Thr Cys Ser Ser His
Phe Pro Tyr Ser Gln Tyr Gln Phe Trp Lys Asn 180 185 190 Phe Gln Thr
Leu Lys Ile Val Ile Leu Gly Leu Val Leu Pro Leu Leu 195 200 205 Val
Met Val Ile Cys Tyr Ser Gly Ile Leu Lys Thr Leu Leu Arg Cys 210 215
220 Arg Asn Glu Lys Lys Arg His Arg Ala Val Arg Leu Ile Phe Thr Ile
225 230 235 240 Met Ile Val Tyr Phe Leu Phe Trp Ala Pro Tyr Asn Ile
Val Leu Leu 245 250 255 Leu Asn Thr Phe Gln Glu Phe Phe Gly Leu Asn
Asn Cys Ser Ser Ser 260 265 270 Asn Arg Leu Asp Gln Ala Met Gln Val
Thr Glu Thr Leu Gly Met Thr 275 280 285 His Cys Cys Ile Asn Pro Ile
Ile Tyr Ala Phe Val Gly Glu Lys Phe 290 295 300 Arg Asn Tyr Leu Leu
Val Phe Phe Gln Lys His Ile Ala Lys Arg Phe 305 310 315 320 Cys Lys
Cys Cys Ser Ile Phe Gln Gln Glu Ala Pro Glu Arg Ala Ser 325 330 335
Ser Val Tyr Thr Arg Ser Thr Gly Glu Gln Glu Ile Ser Val Gly Leu 340
345 350 217PRTHomo sapiens 2Gln Glu Phe Phe Gly Leu Asn Asn Cys Ser
Ser Ser Asn Arg Leu Asp 1 5 10 15 Gln 332PRTHomo sapiens 3Thr Arg
Ser Gln Lys Glu Gly Leu His Tyr Thr Cys Ser Ser His Phe 1 5 10 15
Pro Tyr Ser Gln Tyr Gln Phe Trp Lys Asn Phe Gln Thr Leu Lys Ile 20
25 30 420PRTArtificial SequenceG4S Linker 4Gly Gly Gly Gly Ser Gly
Gly Gly Gly Ser Gly Gly Gly Gly Ser Gly 1 5 10 15 Gly Gly Gly Ser
20 560DNAArtificial SequenceDNA of G4S Linker 5ggcggtggtg
gatcaggcgg cggaggatct ggcggaggtg gcagcggtgg tggaggcagt
60660DNAArtificial Sequence5' Homologous Sequence 6accccaccaa
acccaaaaaa agagatctgt atggcttacc catacgatgt tccagattac
60757DNAArtificial Sequence3' Homologous Sequence 7gagatggtgc
acgatgcaca gttgaagtga acttgcgggg tttttcagta tctacga 57836PRTHomo
sapiens 8Met Asp Tyr Gln Val Ser Ser Pro Ile Tyr Asp Ile Asn Tyr
Tyr Thr 1 5 10 15 Ser Glu Pro Cys Gln Lys Ile Asn Val Lys Gln Ile
Ala Ala Arg Leu 20 25 30 Leu Pro Pro Leu 35 932PRTHomo sapiens 9Thr
Arg Ser Gln Lys Glu Gly Leu His Tyr Thr Cys Ser Ser His Phe 1 5 10
15 Pro Tyr Ser Gln Tyr Gln Phe Trp Lys Asn Phe Gln Thr Leu Lys Ile
20 25 30 1030DNAArtificial SequencePrimer 10ggagaattcg attatcaagt
gtcaagtcca 301131DNAArtificial SequencePrimer 11cgcggatcct
tagagcggag gcaggaggcg g 311229DNAArtificial SequencePrimer
12ggagaattca ccagatctca aaaagaagg 291333DNAArtificial
SequencePrimer 13cgcggatcct tatatcttta atgtctggaa att
331421DNAArtificial SequencePrimer 14caggaattct ttggcctgaa t
211531DNAArtificial SequencePrimer 15cgcggatcct cagcagtgcg
tcatcccaag a 3116759DNAArtificial SequenceClone 15.186.35
16caggttacct tgaaggagtc tggtcctacg ttggtgaaac ccacacagac cctcacgctg
60acctgcacct tgtctgggtt ctcactcagc actagtggag tgagtgtggg ctggatccgt
120cagcccccag gaaaggccct tgagtggctt gcaagcataa attggaatga
tgataagtgc 180tacagcccat ctctgaaaag caggctcacc atcaccaagg
acacccccaa aaaccaggtg 240gtccttgcaa tgagcaacat ggaccctgcg
gacacagcca catattcctg tgcactcgat 300atgccccccc atgatagtgg
cccgcaatct tttgatgctt ctgatgtctg gggcccaggg 360acaatggtca
ccgtctcttc aggcggtggt ggatcaggcg gcggaggatc tggcggaggt
420ggcagcggtg gtggaggcag ttcctatgag ctgatgcagc taccctcagt
gtccgtgtcc 480ccaggacaga cagccagcat cacctgctct ggagataatt
tgggggataa atatgcctgc 540tggtatcaac agaagccagg ccggtcccct
gtgctggtca tttatggaga taacaagcgg 600ccctcaggga tccctgagcg
attctctggc tccaactctg ggaacacagc cactctgacc 660atcagcggga
cccaggctat ggatgaggct gactattact gtcaggcgtg ggacaccagc
720actgctgtct tcggaactgg gaccaagctc accgtccta 75917253PRTArtificial
SequenceClone 15.186.35 17Gln Val Thr Leu Lys Glu Ser Gly Pro Thr
Leu Val Lys Pro Thr Gln 1 5 10 15 Thr Leu Thr Leu Thr Cys Thr Leu
Ser Gly Phe Ser Leu Ser Thr Ser 20 25 30 Gly Val Ser Val Gly Trp
Ile Arg Gln Pro Pro Gly Lys Ala Leu Glu 35 40 45 Trp Leu Ala Ser
Ile Asn Trp Asn Asp Asp Lys Cys Tyr Ser Pro Ser 50 55 60 Leu Lys
Ser Arg Leu Thr Ile Thr Lys Asp Thr Pro Lys Asn Gln Val 65 70 75 80
Val Leu Ala Met Ser Asn Met Asp Pro Ala Asp Thr Ala Thr Tyr Ser 85
90 95 Cys Ala Leu Asp Met Pro Pro His Asp Ser Gly Pro Gln Ser Phe
Asp 100 105 110 Ala Ser Asp Val Trp Gly Pro Gly Thr Met Val Thr Val
Ser Ser Gly 115 120 125 Gly Gly Gly Ser Gly Gly Gly Gly Ser Gly Gly
Gly Gly Ser Gly Gly 130 135 140 Gly Gly Ser Ser Tyr Glu Leu Met Gln
Leu Pro Ser Val Ser Val Ser 145 150 155 160 Pro Gly Gln Thr Ala Ser
Ile Thr Cys Ser Gly Asp Asn Leu Gly Asp 165 170 175 Lys Tyr Ala Cys
Trp Tyr Gln Gln Lys Pro Gly Arg Ser Pro Val Leu 180 185 190 Val Ile
Tyr Gly Asp Asn Lys Arg Pro Ser Gly Ile Pro Glu Arg Phe 195 200 205
Ser Gly Ser Asn Ser Gly Asn Thr Ala Thr Leu Thr Ile Ser Gly Thr 210
215 220 Gln Ala Met Asp Glu Ala Asp Tyr Tyr Cys Gln Ala Trp Asp Thr
Ser 225 230 235 240 Thr Ala Val Phe Gly Thr Gly Thr Lys Leu Thr Val
Leu 245 250 18762DNAArtificial SequenceClone 15.150.11 18caggtgcagc
tgcaggagtc gggcccagga ctggtgaagc cttcggagac cctgtccctc 60acttgcactg
tctctggtgg ctccatcggt catgactact ggagctggat acggcagccc
120ccaggggagg gactggagtg gattggtttc atcttcttcg atgggagcac
caactacaac 180ccctccctca acggtcgagt caccatctca ctcgacacgt
cgaagaatca gctctccctg 240aggctgacct ctgtgaccgc tgcggacacg
gccgtgtatt tctgtgcgag actaaagggg 300gcgtggttat tgtctgaacc
cccttacttc agctccgacg gcatggacgt ctggggccaa 360gggaccacgg
tcaccgtccc ctcaggcggt ggtggatcag gcggcggagg atctggcgga
420ggtggcagcg gtggtggagg cagtaatttt atgctgactc agcccccctc
agcgtctggg 480acccccgggc agagggtcag catctcttgt tctgggagca
gctccgacat cggaagtaat 540actgtaaact ggtaccagca actcccagga
acggccccca aactcctcat ctatagtaat 600aatcagcggc cctcaggggt
ccctgaccga ttctctggct tcaagtctgg cacctcagcc 660tccctggtca
tcagtggcct ccagtctgag gatgaggctg attattattg tgcagcatgg
720gatgagagcc tgaatggtgt ggtgttcggc ggaggaccaa gg
76219254PRTArtificial SequenceClone 15.150.11 19Gln Val Gln Leu Gln
Glu Ser Gly Pro Gly Leu Val Lys Pro Ser Glu 1 5 10 15 Thr Leu Ser
Leu Thr Cys Thr Val Ser Gly Gly Ser Ile Gly His Asp 20 25 30 Tyr
Trp Ser Trp Ile Arg Gln Pro Pro Gly Glu Gly Leu Glu Trp Ile 35 40
45 Gly Phe Ile Phe Phe Asp Gly Ser Thr Asn Tyr Asn Pro Ser Leu Asn
50 55 60 Gly Arg Val Thr Ile Ser Leu Asp Thr Ser Lys Asn Gln Leu
Ser Leu 65 70 75 80 Arg Leu Thr Ser Val Thr Ala Ala Asp Thr Ala Val
Tyr Phe Cys Ala 85 90 95 Arg Leu Lys Gly Ala Trp Leu Leu Ser Glu
Pro Pro Tyr Phe Ser Ser 100 105 110 Asp Gly Met Asp Val Trp Gly Gln
Gly Thr Thr Val Thr Val Pro Ser 115 120 125 Gly Gly Gly Gly Ser Gly
Gly Gly Gly Ser Gly Gly Gly Gly Ser Gly 130 135 140 Gly Gly Gly Ser
Asn Phe Met Leu Thr Gln Pro Pro Ser Ala Ser Gly 145 150 155 160 Thr
Pro Gly Gln Arg Val Ser Ile Ser Cys Ser Gly Ser Ser Ser Asp 165 170
175 Ile Gly Ser Asn Thr Val Asn Trp Tyr Gln Gln Leu Pro Gly Thr Ala
180 185 190 Pro Lys Leu Leu Ile Tyr Ser Asn Asn Gln Arg Pro Ser Gly
Val Pro 195 200 205 Asp Arg Phe Ser Gly Phe Lys Ser Gly Thr Ser Ala
Ser Leu Val Ile 210 215 220 Ser Gly Leu Gln Ser Glu Asp Glu Ala Asp
Tyr Tyr Cys Ala Ala Trp 225 230 235 240 Asp Glu Ser Leu Asn Gly Val
Val Phe Gly Gly Gly Pro Arg 245 250 20750DNAArtificial
SequenceClone 15.150.12 20caggtgcagc tacagcagtg gggcgcagga
ctgttgaagt cttggggaac cctgtccctc 60acctgcgctg tctctggtgc gtcgtttagt
ggttattatt ggagctggat ccgccagccc 120ccagggaagg ggctggagtg
gattggggag atcaatcatc gtggaagcac tacctacaac 180ccgtccctcg
acggtcgagt caccatatca ttagacacat ctaccaacca gatctccctt
240aaactgacct ctatgaccgc cgcggacacg gccgtgtatt actgtgcgag
gacagtggct 300ggtactagtg actactgggg ccagggaacc ctggtcaccg
tttcctcagg gagtgcatcc 360gccccaacgg gcggtggtgg atcaggcggc
ggaggatctg gcggaggtgg cagcggtggt 420ggaggcagta aaacgacact
cacgcagtct ccagcattca tgtcagcgac tccaggagac 480aaagtcagca
tctcctgcaa agccagccga gacgttgatg atgatgtgaa ctggtaccaa
540cagagaccag gagaagctcc tattttcatt attgaagatg ctactactct
cgttcctgga 600atctcacctc gattcagtgg cagcgggtat ggaaccgatt
ttaccctcac aattaataac 660atcgattctg aggatgctgc atattatttc
tgtctacaac atgataattt cccgctcacc 720ttcggcggag ggaccaaggt
ggagatcaaa 75021250PRTArtificial SequenceClone 15.150.12 21Gln Val
Gln Leu Gln Gln Trp Gly Ala Gly Leu Leu Lys Ser Trp Gly 1 5 10 15
Thr Leu Ser Leu Thr Cys Ala Val Ser Gly Ala Ser Phe Ser Gly Tyr 20
25 30 Tyr Trp Ser Trp Ile Arg Gln Pro Pro Gly Lys Gly Leu Glu Trp
Ile 35 40 45 Gly Glu Ile Asn His Arg Gly Ser Thr Thr Tyr Asn Pro
Ser Leu Asp 50 55 60 Gly Arg Val Thr Ile Ser Leu Asp Thr Ser Thr
Asn Gln Ile Ser Leu 65 70 75 80 Lys Leu Thr Ser Met Thr Ala Ala Asp
Thr Ala Val Tyr Tyr Cys Ala 85 90 95 Arg Thr Val Ala Gly Thr Ser
Asp Tyr Trp Gly Gln Gly Thr Leu Val 100 105 110 Thr Val Ser Ser Gly
Ser Ala Ser Ala Pro Thr Gly Gly Gly Gly Ser 115 120 125 Gly Gly Gly
Gly Ser Gly Gly Gly Gly Ser Gly Gly Gly Gly Ser Lys 130 135 140 Thr
Thr Leu Thr Gln Ser Pro Ala Phe Met Ser Ala Thr Pro Gly Asp 145 150
155 160 Lys Val Ser Ile Ser Cys Lys Ala Ser Arg Asp Val Asp Asp Asp
Val 165 170 175 Asn Trp Tyr Gln Gln Arg Pro Gly Glu Ala Pro Ile Phe
Ile Ile Glu 180 185 190 Asp Ala Thr Thr Leu Val Pro Gly Ile Ser Pro
Arg Phe Ser Gly Ser 195 200 205 Gly Tyr Gly Thr Asp Phe Thr Leu Thr
Ile Asn Asn Ile Asp Ser Glu 210 215 220 Asp Ala Ala Tyr Tyr Phe Cys
Leu Gln His Asp Asn Phe Pro Leu Thr 225 230 235 240 Phe Gly Gly Gly
Thr Lys Val Glu Ile Lys 245 250 22759DNAArtificial SequenceClone
15.150.24 22caggtcacct tgaaggagtc tggtcctacg ctggtgaaac ccacacagac
cctcacgctg 60acctgcacct tctctgggtt ctcactcaga actactggag agggtgtggg
ctgggtccgt 120cagcccccag gaaaggccct ggaatggctt gcactcattt
attgggatga tgataagcgc 180tacagcccat ctctgaagag caggctcacc
atcaccaagg acacctccaa aaagcaggtg 240gtccttacaa tgaccaacgt
ggacccagcg gacacagcca cctattactg tacacacgag 300caatactatt
atgatactag tggtcagcca tactactttg acttctgggg ccagggcacc
360ctggtcaccg tctcctcagg cggtggtgga tcaggcggcg gaggatctgg
cggaggtggc 420agcggtggtg gaggcagtaa catccaggtg acccagtctc
catcctccct gtctgcatct 480gtaggagaca gagtcaccat gacttgccgg
gcgagtcagg acattaggaa gaatttaaat 540tggtatcagc aaaaaccagg
gaaagcccct aaggtcctga tctacgatgc atccgatttg 600gaaacaggga
tcccatcaag gttcagtgga agtggatctg ggacagattt tatcctcacc
660atcagcagcc tgcagcctga agatattgca acatactact gtcaacagtc
tgattattta 720ccgctcactt tcggcggagg gaccaaagtg gatatcaaa
75923253PRTArtificial SequenceClone 15.150.24 23Gln Val Thr Leu Lys
Glu Ser Gly Pro Thr Leu Val Lys Pro Thr Gln 1 5 10 15 Thr Leu Thr
Leu Thr Cys Thr Phe Ser Gly Phe Ser Leu Arg Thr Thr 20 25 30 Gly
Glu Gly Val Gly Trp Val Arg Gln Pro Pro Gly Lys Ala Leu Glu 35 40
45 Trp Leu Ala Leu Ile Tyr Trp Asp Asp Asp Lys Arg Tyr Ser Pro Ser
50 55 60 Leu Lys Ser Arg Leu Thr Ile Thr Lys Asp Thr Ser Lys Lys
Gln Val 65 70 75 80 Val Leu Thr Met Thr Asn Val Asp Pro Ala Asp Thr
Ala Thr Tyr Tyr 85 90 95 Cys Thr His Glu Gln Tyr Tyr Tyr Asp Thr
Ser Gly Gln Pro Tyr Tyr 100 105 110 Phe Asp Phe Trp Gly Gln Gly Thr
Leu Val Thr Val Ser Ser Gly Gly 115 120 125 Gly Gly Ser Gly Gly Gly
Gly Ser Gly Gly Gly Gly Ser Gly Gly Gly 130 135 140 Gly Ser Asn Ile
Gln Val Thr Gln Ser Pro Ser Ser Leu Ser Ala Ser 145 150 155 160 Val
Gly Asp Arg Val Thr Met Thr Cys Arg Ala Ser Gln Asp Ile Arg 165 170
175 Lys Asn Leu Asn Trp Tyr Gln Gln Lys Pro Gly Lys Ala Pro Lys Val
180 185 190 Leu Ile Tyr Asp Ala Ser Asp Leu Glu Thr Gly Ile Pro Ser
Arg Phe 195 200 205 Ser Gly Ser Gly Ser Gly Thr Asp Phe Ile Leu Thr
Ile Ser Ser Leu 210 215 220 Gln Pro Glu Asp Ile Ala Thr Tyr Tyr Cys
Gln Gln Ser Asp Tyr Leu 225 230 235 240 Pro Leu Thr Phe Gly Gly Gly
Thr Lys Val Asp Ile Lys 245 250 24759DNAArtificial SequenceClone
15.186.35 Variant 24caggtcacct tgaaggagtc tggtcctacg ttggtgaaac
ccacacagac cctcacgctg 60acctgcacct tgtctgggtt ctcactcagc actagtggag
tgagtgtggg ctggatccgt 120cagcccccag gaaaggccct tgagtggctt
gcaagcataa attggaatga tgataagtgc 180tacagcccat ctctgaaaag
caggctcacc atcaccaagg acacccccaa aaaccaggtg 240gtccttgcaa
tgagcaacat ggaccctgcg gacacagcca catattcctg tgcactcgat
300atgccccccc atgatagtgg cccgcaatct tttgatgctt ctgatgtctg
gggcccaggg 360acaatggtca ccgtctcttc aggcggtggt ggatcaggcg
gcggaggatc tggcggaggt 420ggcagcggtg gtggaggcag ttcctatgag
ctgatgcagc taccctcagt gtccgtgtcc 480ccaggacaga cagccagcat
cacctgctct ggagataatt tgggggataa atatgcctgc 540tggtatcaac
agaagccagg ccggtcccct gtgctggtca tttatggaga taacaagcgg
600ccctcaggga tccctgagcg attctctggc tccaactctg ggaacacagc
cactctgacc 660atcagcggga cccaggctat ggatgaggct gactattact
gtcaggcgtg ggacaccagc 720actgctgtct tcggaactgg gaccaagctc
accgtccta
75925253PRTArtificial SequenceClone 15.186.35 Variant 25Gln Val Thr
Leu Lys Glu Ser Gly Pro Thr Leu Val Lys Pro Thr Gln 1 5 10 15 Thr
Leu Thr Leu Thr Cys Thr Leu Ser Gly Phe Ser Leu Ser Thr Ser 20 25
30 Gly Val Ser Val Gly Trp Ile Arg Gln Pro Pro Gly Lys Ala Leu Glu
35 40 45 Trp Leu Ala Ser Ile Asn Trp Asn Asp Asp Lys Cys Tyr Ser
Pro Ser 50 55 60 Leu Lys Ser Arg Leu Thr Ile Thr Lys Asp Thr Pro
Lys Asn Gln Val 65 70 75 80 Val Leu Ala Met Ser Asn Met Asp Pro Ala
Asp Thr Ala Thr Tyr Ser 85 90 95 Cys Ala Leu Asp Met Pro Pro His
Asp Ser Gly Pro Gln Ser Phe Asp 100 105 110 Ala Ser Asp Val Trp Gly
Pro Gly Thr Met Val Thr Val Ser Ser Gly 115 120 125 Gly Gly Gly Ser
Gly Gly Gly Gly Ser Gly Gly Gly Gly Ser Gly Gly 130 135 140 Gly Gly
Ser Ser Tyr Glu Leu Met Gln Leu Pro Ser Val Ser Val Ser 145 150 155
160 Pro Gly Gln Thr Ala Ser Ile Thr Cys Ser Gly Asp Asn Leu Gly Asp
165 170 175 Lys Tyr Ala Cys Trp Tyr Gln Gln Lys Pro Gly Arg Ser Pro
Val Leu 180 185 190 Val Ile Tyr Gly Asp Asn Lys Arg Pro Ser Gly Ile
Pro Glu Arg Phe 195 200 205 Ser Gly Ser Asn Ser Gly Asn Thr Ala Thr
Leu Thr Ile Ser Gly Thr 210 215 220 Gln Ala Met Asp Glu Ala Asp Tyr
Tyr Cys Gln Ala Trp Asp Thr Ser 225 230 235 240 Thr Ala Val Phe Gly
Thr Gly Thr Lys Leu Thr Val Leu 245 250 26774DNAArtificial
SequenceClone 15.150.11 Variant 26caggtgcagc tgcaggagtc gggcccagga
ctggtgaagc cttcggagac cctgtccctc 60acttgcactg tctctggtgg ctccatcggt
catgactact ggagctggat acggcagccc 120ccaggggagg gactggagtg
gattggtttc atcttcttcg atgggagcac caactacaac 180ccctccctca
acggtcgagt caccatctca ctcgacacgt cgaagaatca gctctccctg
240aggctgacct ctgtgaccgc tgcggacacg gccgtgtatt tctgtgcgag
actaaagggg 300gcgtggttat tgtctgaacc cccttacttc agctccgacg
gcatggacgt ctggggccaa 360gggaccacgg tcaccgtctc ctcaggcggt
ggtggatcag gcggcggagg atctggcgga 420ggtggcagcg gtggtggagg
cagtaatttt atgctgactc agcccccctc agcgtctggg 480acccccgggc
agagggtcag catctcttgt tctgggagca gctccgacat cggaagtaat
540actgtaaact ggtaccagca actcccagga acggccccca aactcctcat
ctatagtaat 600aatcagcggc cctcaggggt ccctgaccga ttctctggct
tcaagtctgg cacctcagcc 660tccctggtca tcagtggcct ccagtctgag
gatgaggctg attattattg tgcagcatgg 720gatgagagcc tgaatggtgt
ggtgttcggc ggaggaacca aggtgaccgt ccta 77427258PRTArtificial
SequenceClone 15.150.11 Variant 27Gln Val Gln Leu Gln Glu Ser Gly
Pro Gly Leu Val Lys Pro Ser Glu 1 5 10 15 Thr Leu Ser Leu Thr Cys
Thr Val Ser Gly Gly Ser Ile Gly His Asp 20 25 30 Tyr Trp Ser Trp
Ile Arg Gln Pro Pro Gly Glu Gly Leu Glu Trp Ile 35 40 45 Gly Phe
Ile Phe Phe Asp Gly Ser Thr Asn Tyr Asn Pro Ser Leu Asn 50 55 60
Gly Arg Val Thr Ile Ser Leu Asp Thr Ser Lys Asn Gln Leu Ser Leu 65
70 75 80 Arg Leu Thr Ser Val Thr Ala Ala Asp Thr Ala Val Tyr Phe
Cys Ala 85 90 95 Arg Leu Lys Gly Ala Trp Leu Leu Ser Glu Pro Pro
Tyr Phe Ser Ser 100 105 110 Asp Gly Met Asp Val Trp Gly Gln Gly Thr
Thr Val Thr Val Ser Ser 115 120 125 Gly Gly Gly Gly Ser Gly Gly Gly
Gly Ser Gly Gly Gly Gly Ser Gly 130 135 140 Gly Gly Gly Ser Asn Phe
Met Leu Thr Gln Pro Pro Ser Ala Ser Gly 145 150 155 160 Thr Pro Gly
Gln Arg Val Ser Ile Ser Cys Ser Gly Ser Ser Ser Asp 165 170 175 Ile
Gly Ser Asn Thr Val Asn Trp Tyr Gln Gln Leu Pro Gly Thr Ala 180 185
190 Pro Lys Leu Leu Ile Tyr Ser Asn Asn Gln Arg Pro Ser Gly Val Pro
195 200 205 Asp Arg Phe Ser Gly Phe Lys Ser Gly Thr Ser Ala Ser Leu
Val Ile 210 215 220 Ser Gly Leu Gln Ser Glu Asp Glu Ala Asp Tyr Tyr
Cys Ala Ala Trp 225 230 235 240 Asp Glu Ser Leu Asn Gly Val Val Phe
Gly Gly Gly Thr Lys Val Thr 245 250 255 Val Leu 28750DNAArtificial
SequenceClone 15.150.12 Variant 28caggtgcagc tacagcagtg gggcgcagga
ctgttgaagt cttggggaac cctgtccctc 60acctgcgctg tctctggtgc gtcgtttagt
ggttattatt ggagctggat ccgccagccc 120ccagggaagg ggctggagtg
gattggggag atcaatcatc gtggaagcac tacctacaac 180ccgtccctcg
acggtcgagt caccatatca ttagacacat ctaccaacca gatctccctt
240aaactgacct ctatgaccgc cgcggacacg gccgtgtatt actgtgcgag
gacagtggct 300ggtactagtg actactgggg ccagggaacc ctggtcaccg
tttcctcagg gagtgcatcc 360gccccaacgg gcggtggtgg atcaggcggc
ggaggatctg gcggaggtgg cagcggtggt 420ggaggcagtg aaacgacact
cacgcagtct ccagcattca tgtcagcgac tccaggagac 480aaagtcagca
tctcctgcaa agccagccga gacgttgatg atgatgtgaa ctggtaccaa
540cagagaccag gagaagctcc tattttcatt attgaagatg ctactactct
cgttcctgga 600atctcacctc gattcagtgg cagcgggtat ggaaccgatt
ttaccctcac aattaataac 660atcgattctg aggatgctgc atattatttc
tgtctacaac atgataattt cccgctcacc 720ttcggcggag ggaccaaggt
ggagatcaaa 75029250PRTArtificial SequenceClone 15.150.12 Variant
29Gln Val Gln Leu Gln Gln Trp Gly Ala Gly Leu Leu Lys Ser Trp Gly 1
5 10 15 Thr Leu Ser Leu Thr Cys Ala Val Ser Gly Ala Ser Phe Ser Gly
Tyr 20 25 30 Tyr Trp Ser Trp Ile Arg Gln Pro Pro Gly Lys Gly Leu
Glu Trp Ile 35 40 45 Gly Glu Ile Asn His Arg Gly Ser Thr Thr Tyr
Asn Pro Ser Leu Asp 50 55 60 Gly Arg Val Thr Ile Ser Leu Asp Thr
Ser Thr Asn Gln Ile Ser Leu 65 70 75 80 Lys Leu Thr Ser Met Thr Ala
Ala Asp Thr Ala Val Tyr Tyr Cys Ala 85 90 95 Arg Thr Val Ala Gly
Thr Ser Asp Tyr Trp Gly Gln Gly Thr Leu Val 100 105 110 Thr Val Ser
Ser Gly Ser Ala Ser Ala Pro Thr Gly Gly Gly Gly Ser 115 120 125 Gly
Gly Gly Gly Ser Gly Gly Gly Gly Ser Gly Gly Gly Gly Ser Glu 130 135
140 Thr Thr Leu Thr Gln Ser Pro Ala Phe Met Ser Ala Thr Pro Gly Asp
145 150 155 160 Lys Val Ser Ile Ser Cys Lys Ala Ser Arg Asp Val Asp
Asp Asp Val 165 170 175 Asn Trp Tyr Gln Gln Arg Pro Gly Glu Ala Pro
Ile Phe Ile Ile Glu 180 185 190 Asp Ala Thr Thr Leu Val Pro Gly Ile
Ser Pro Arg Phe Ser Gly Ser 195 200 205 Gly Tyr Gly Thr Asp Phe Thr
Leu Thr Ile Asn Asn Ile Asp Ser Glu 210 215 220 Asp Ala Ala Tyr Tyr
Phe Cys Leu Gln His Asp Asn Phe Pro Leu Thr 225 230 235 240 Phe Gly
Gly Gly Thr Lys Val Glu Ile Lys 245 250 30759DNAArtificial
SequenceClone 15.150.24 Variant 30caggtcacct tgaaggagtc tggtcctacg
ctggtgaaac ccacacagac cctcacgctg 60acctgcacct tctctgggtt ctcactcaga
actactggag agggtgtggg ctgggtccgt 120cagcccccag gaaaggccct
ggaatggctt gcactcattt attgggatga tgataagcgc 180tacagcccat
ctctgaagag caggctcacc atcaccaagg acacctccaa aaagcaggtg
240gtccttacaa tgaccaacgt ggacccagcg gacacagcca cctattactg
tacacacgag 300caatactatt atgatactag tggtcagcca tactactttg
acttctgggg ccagggcacc 360ctggtcaccg tctcctcagg cggtggtgga
tcaggcggcg gaggatctgg cggaggtggc 420agcggtggtg gaggcagtaa
catccaggtg acccagtctc catcctccct gtctgcatct 480gtaggagaca
gagtcaccat gacttgccgg gcgagtcagg acattaggaa gaatttaaat
540tggtatcagc aaaaaccagg gaaagcccct aaggtcctga tctacgatgc
atccgatttg 600gaaacaggga tcccatcaag gttcagtgga agtggatctg
ggacagattt tatcctcacc 660atcagcagcc tgcagcctga agatattgca
acatactact gtcaacagtc tgattattta 720ccgctcactt tcggcggagg
gaccaaagtg gatatcaaa 75931253PRTArtificial SequenceClone 15.150.24
Variant 31Gln Val Thr Leu Lys Glu Ser Gly Pro Thr Leu Val Lys Pro
Thr Gln 1 5 10 15 Thr Leu Thr Leu Thr Cys Thr Phe Ser Gly Phe Ser
Leu Arg Thr Thr 20 25 30 Gly Glu Gly Val Gly Trp Val Arg Gln Pro
Pro Gly Lys Ala Leu Glu 35 40 45 Trp Leu Ala Leu Ile Tyr Trp Asp
Asp Asp Lys Arg Tyr Ser Pro Ser 50 55 60 Leu Lys Ser Arg Leu Thr
Ile Thr Lys Asp Thr Ser Lys Lys Gln Val 65 70 75 80 Val Leu Thr Met
Thr Asn Val Asp Pro Ala Asp Thr Ala Thr Tyr Tyr 85 90 95 Cys Thr
His Glu Gln Tyr Tyr Tyr Asp Thr Ser Gly Gln Pro Tyr Tyr 100 105 110
Phe Asp Phe Trp Gly Gln Gly Thr Leu Val Thr Val Ser Ser Gly Gly 115
120 125 Gly Gly Ser Gly Gly Gly Gly Ser Gly Gly Gly Gly Ser Gly Gly
Gly 130 135 140 Gly Ser Asn Ile Gln Val Thr Gln Ser Pro Ser Ser Leu
Ser Ala Ser 145 150 155 160 Val Gly Asp Arg Val Thr Met Thr Cys Arg
Ala Ser Gln Asp Ile Arg 165 170 175 Lys Asn Leu Asn Trp Tyr Gln Gln
Lys Pro Gly Lys Ala Pro Lys Val 180 185 190 Leu Ile Tyr Asp Ala Ser
Asp Leu Glu Thr Gly Ile Pro Ser Arg Phe 195 200 205 Ser Gly Ser Gly
Ser Gly Thr Asp Phe Ile Leu Thr Ile Ser Ser Leu 210 215 220 Gln Pro
Glu Asp Ile Ala Thr Tyr Tyr Cys Gln Gln Ser Asp Tyr Leu 225 230 235
240 Pro Leu Thr Phe Gly Gly Gly Thr Lys Val Asp Ile Lys 245 250
329PRTArtificial SequenceVH CDR2 32Gly Ser Thr Xaa Tyr Asn Pro Ser
Leu 1 5 335PRTArtificial SequenceVL CDR2 33Asp Ala Xaa Xaa Leu 1 5
34127PRTHomo sapiens 34Gln Val Thr Leu Lys Glu Ser Gly Pro Thr Leu
Val Lys Pro Thr Gln 1 5 10 15 Thr Leu Thr Leu Thr Cys Thr Leu Ser
Gly Phe Ser Leu Ser Thr Ser 20 25 30 Gly Val Ser Val Gly Trp Ile
Arg Gln Pro Pro Gly Lys Ala Leu Glu 35 40 45 Trp Leu Ala Ser Ile
Asn Trp Asn Asp Asp Lys Cys Tyr Ser Pro Ser 50 55 60 Leu Lys Ser
Arg Leu Thr Ile Thr Lys Asp Thr Pro Lys Asn Gln Val 65 70 75 80 Val
Leu Ala Met Ser Asn Met Asp Pro Ala Asp Thr Ala Thr Tyr Ser 85 90
95 Cys Ala Leu Asp Met Pro Pro His Asp Ser Gly Pro Gln Ser Phe Asp
100 105 110 Ala Ser Asp Val Trp Gly Pro Gly Thr Met Val Thr Val Ser
Ser 115 120 125 35106PRTHomo sapiens 35Ser Tyr Glu Leu Met Gln Leu
Pro Ser Val Ser Val Ser Pro Gly Gln 1 5 10 15 Thr Ala Ser Ile Thr
Cys Ser Gly Asp Asn Leu Gly Asp Lys Tyr Ala 20 25 30 Cys Trp Tyr
Gln Gln Lys Pro Gly Arg Ser Pro Val Leu Val Ile Tyr 35 40 45 Gly
Asp Asn Lys Arg Pro Ser Gly Ile Pro Glu Arg Phe Ser Gly Ser 50 55
60 Asn Ser Gly Asn Thr Ala Thr Leu Thr Ile Ser Gly Thr Gln Ala Met
65 70 75 80 Asp Glu Ala Asp Tyr Tyr Cys Gln Ala Trp Asp Thr Ser Thr
Ala Val 85 90 95 Phe Gly Thr Gly Thr Lys Leu Thr Val Leu 100 105
36126PRTHomo sapiens 36Gln Val Gln Leu Gln Glu Ser Gly Pro Gly Leu
Val Lys Pro Ser Glu 1 5 10 15 Thr Leu Ser Leu Thr Cys Thr Val Ser
Gly Gly Ser Ile Gly His Asp 20 25 30 Tyr Trp Ser Trp Ile Arg Gln
Pro Pro Gly Glu Gly Leu Glu Trp Ile 35 40 45 Gly Phe Ile Phe Phe
Asp Gly Ser Thr Asn Tyr Asn Pro Ser Leu Asn 50 55 60 Gly Arg Val
Thr Ile Ser Leu Asp Thr Ser Lys Asn Gln Leu Ser Leu 65 70 75 80 Arg
Leu Thr Ser Val Thr Ala Ala Asp Thr Ala Val Tyr Phe Cys Ala 85 90
95 Arg Leu Lys Gly Ala Trp Leu Leu Ser Glu Pro Pro Tyr Phe Ser Ser
100 105 110 Asp Gly Met Asp Val Trp Gly Gln Gly Thr Thr Val Thr Val
115 120 125 37104PRTHomo sapiens 37Asn Phe Met Leu Thr Gln Pro Pro
Ser Ala Ser Gly Thr Pro Gly Gln 1 5 10 15 Arg Val Ser Ile Ser Cys
Ser Gly Ser Ser Ser Asp Ile Gly Ser Asn 20 25 30 Thr Val Asn Trp
Tyr Gln Gln Leu Pro Gly Thr Ala Pro Lys Leu Leu 35 40 45 Ile Tyr
Ser Asn Asn Gln Arg Pro Ser Gly Val Pro Asp Arg Phe Ser 50 55 60
Gly Phe Lys Ser Gly Thr Ser Ala Ser Leu Val Ile Ser Gly Leu Gln 65
70 75 80 Ser Glu Asp Glu Ala Asp Tyr Tyr Cys Ala Ala Trp Asp Glu
Ser Leu 85 90 95 Asn Gly Val Val Phe Gly Gly Gly 100 38116PRTHomo
sapiens 38Gln Val Gln Leu Gln Gln Trp Gly Ala Gly Leu Leu Lys Ser
Trp Gly 1 5 10 15 Thr Leu Ser Leu Thr Cys Ala Val Ser Gly Ala Ser
Phe Ser Gly Tyr 20 25 30 Tyr Trp Ser Trp Ile Arg Gln Pro Pro Gly
Lys Gly Leu Glu Trp Ile 35 40 45 Gly Glu Ile Asn His Arg Gly Ser
Thr Thr Tyr Asn Pro Ser Leu Asp 50 55 60 Gly Arg Val Thr Ile Ser
Leu Asp Thr Ser Thr Asn Gln Ile Ser Leu 65 70 75 80 Lys Leu Thr Ser
Met Thr Ala Ala Asp Thr Ala Val Tyr Tyr Cys Ala 85 90 95 Arg Thr
Val Ala Gly Thr Ser Asp Tyr Trp Gly Gln Gly Thr Leu Val 100 105 110
Thr Val Ser Ser 115 39106PRTHomo sapiens 39Thr Thr Leu Thr Gln Ser
Pro Ala Phe Met Ser Ala Thr Pro Gly Asp 1 5 10 15 Lys Val Ser Ile
Ser Cys Lys Ala Ser Arg Asp Val Asp Asp Asp Val 20 25 30 Asn Trp
Tyr Gln Gln Arg Pro Gly Glu Ala Pro Ile Phe Ile Ile Glu 35 40 45
Asp Ala Thr Thr Leu Val Pro Gly Ile Ser Pro Arg Phe Ser Gly Ser 50
55 60 Gly Tyr Gly Thr Asp Phe Thr Leu Thr Ile Asn Asn Ile Asp Ser
Glu 65 70 75 80 Asp Ala Ala Tyr Tyr Phe Cys Leu Gln His Asp Asn Phe
Pro Leu Thr 85 90 95 Phe Gly Gly Gly Thr Lys Val Glu Ile Lys 100
105 40126PRTHomo sapiens 40Gln Val Thr Leu Lys Glu Ser Gly Pro Thr
Leu Val Lys Pro Thr Gln 1 5 10 15 Thr Leu Thr Leu Thr Cys Thr Phe
Ser Gly Phe Ser Leu Arg Thr Thr 20 25 30 Gly Glu Gly Val Gly Trp
Val Arg Gln Pro Pro Gly Lys Ala Leu Glu 35 40 45 Trp Leu Ala Leu
Ile Tyr Trp Asp Asp Asp Lys Arg Tyr Ser Pro Ser 50 55 60 Leu Lys
Ser Arg Leu Thr Ile Thr Lys Asp Thr Ser Lys Lys Gln Val 65 70 75 80
Val Leu Thr Met Thr Asn Val Asp Pro Ala Asp Thr Ala Thr Tyr Tyr 85
90 95 Cys Thr His Glu Gln Tyr Tyr Tyr Asp Thr Ser Gly Gln Pro Tyr
Tyr 100 105 110 Phe Asp Phe Trp Gly Gln Gly Thr Leu Val Thr Val Ser
Ser 115 120 125 41107PRTHomo sapiens 41Asn Ile Gln Val Thr Gln Ser
Pro Ser Ser Leu Ser Ala Ser Val Gly 1 5 10 15 Asp Arg Val Thr Met
Thr Cys Arg Ala Ser Gln Asp Ile Arg Lys Asn
20 25 30 Leu Asn Trp Tyr Gln Gln Lys Pro Gly Lys Ala Pro Lys Val
Leu Ile 35 40 45 Tyr Asp Ala Ser Asp Leu Glu Thr Gly Ile Pro Ser
Arg Phe Ser Gly 50 55 60 Ser Gly Ser Gly Thr Asp Phe Ile Leu Thr
Ile Ser Ser Leu Gln Pro 65 70 75 80 Glu Asp Ile Ala Thr Tyr Tyr Cys
Gln Gln Ser Asp Tyr Leu Pro Leu 85 90 95 Thr Phe Gly Gly Gly Thr
Lys Val Asp Ile Lys 100 105 425PRTArtificial SequenceLinker
Sequence 42Gly Gly Gly Gly Ser 1 5 4321PRTHomo sapiens 43Arg Leu
Lys Gly Ala Trp Leu Leu Ser Glu Pro Pro Tyr Phe Ser Ser 1 5 10 15
Asp Gly Met Asp Val 20 449PRTHomo sapiens 44Arg Thr Val Ala Gly Thr
Ser Asp Tyr 1 5 4517PRTHomo sapiens 45His Glu Gln Tyr Tyr Tyr Asp
Thr Ser Gly Gln Pro Tyr Tyr Phe Asp 1 5 10 15 Phe 4611PRTHomo
sapiens 46Ala Ala Trp Asp Glu Ser Leu Asn Gly Val Val 1 5 10
479PRTHomo sapiens 47Leu Gln His Asp Asn Phe Pro Leu Thr 1 5
489PRTHomo sapiens 48Gln Gln Ser Asp Tyr Leu Pro Leu Thr 1 5
4930DNAArtificial SequencePrimer 49ggagaattcg attatcaagt gtcaagtcca
305031DNAArtificial SequencePrimer 50cgcggatcct tagagcggag
gcaggaggcg g 315129DNAArtificial SequencePrimer 51ggagaattca
ccagatctca aaaagaagg 295233DNAArtificial SequencePrimer
52cgcggatcct tatatcttta atgtctggaa att 335321DNAArtificial
SequencePrimer 53caggaattct ttggcctgaa t 215431DNAArtificial
SequencePrimer 54cgcggatcct cagcagtgcg tcatcccaag a
315530DNAArtificial SequencePrimer 13.12.G 55ggagaattca tcgactcctt
catcctcctg 305633DNAArtificial SequencePrimer 13.12.H 56cgcggatcct
taagctaggg cctcggtgat gga 335793DNAHomo sapiens 57atcgactcct
tcatcctcct ggaaatcatc aagcaagggt gtgagtttga gaacactgtg 60cacaagtgga
tttccatcac cgaggcccta gct 935831PRTHomo sapiens 58Ile Asp Ser Phe
Ile Leu Leu Glu Ile Ile Lys Gln Gly Cys Glu Phe 1 5 10 15 Glu Asn
Thr Val His Lys Trp Ile Ser Ile Thr Glu Ala Leu Ala 20 25 30
59765DNAArtificial SequenceDNA of scFv Ab124 59caggtgcagc
tgcaggagtc cggcccagga ctggtgaagc cttcggagac cctgtccctc 60acctgcactg
tctctggtgg ctccatcagc agtagtagtt actactgggg ctggatccgc
120cagcccccag ggaaggggct ggagtggatt gggagtatct attatagtgg
gagcacctac 180tacaacccgt ccctcaagag tcgagtcacc atatccgtag
acacgtccaa gaaccagttc 240tccctgaagc tgagctctgt gaccgccgca
gacacggctg tgtattactg tgcgagacat 300attcttacga aagcagctgg
ctactggtac ttcgatctct ggggccgtgg caccctggtc 360accgtctcct
ctggcggtgg tggatcaggc ggcggaggat ctggcggagg tggcagcggt
420ggtggaggca gtcagtctgt tctgattcag cctcgctcag tgtccgggtc
tcctggacag 480tcagtcacca tctcctgcac tggaaccagc agtgatgttg
gtggttataa ctatgtctcc 540tggtaccaac agcacccagg caaagccccc
aaactcatga tttatgatgt cagtaagcgg 600ccctcagggg tccctgatcg
cttctctggc tccaagtctg gcaacacggc ctccctgacc 660atctctgggc
tccaggctga ggatgaggct gattattact gctgctcata tgcaggcagc
720tacagggatt atgtcttcgg aactgggacc aagctgaccg tccta
76560124PRTArtificial SequenceVH of scFv Ab124 60Gln Val Gln Leu
Gln Glu Ser Gly Pro Gly Leu Val Lys Pro Ser Glu 1 5 10 15 Thr Leu
Ser Leu Thr Cys Thr Val Ser Gly Gly Ser Ile Ser Ser Ser 20 25 30
Ser Tyr Tyr Trp Gly Trp Ile Arg Gln Pro Pro Gly Lys Gly Leu Glu 35
40 45 Trp Ile Gly Ser Ile Tyr Tyr Ser Gly Ser Thr Tyr Tyr Asn Pro
Ser 50 55 60 Leu Lys Ser Arg Val Thr Ile Ser Val Asp Thr Ser Lys
Asn Gln Phe 65 70 75 80 Ser Leu Lys Leu Ser Ser Val Thr Ala Ala Asp
Thr Ala Val Tyr Tyr 85 90 95 Cys Ala Arg His Ile Leu Thr Lys Ala
Ala Gly Tyr Trp Tyr Phe Asp 100 105 110 Leu Trp Gly Arg Gly Thr Leu
Val Thr Val Ser Ser 115 120 61111PRTArtificial SequenceVL of scFv
Ab124 61Gln Ser Val Leu Ile Gln Pro Arg Ser Val Ser Gly Ser Pro Gly
Gln 1 5 10 15 Ser Val Thr Ile Ser Cys Thr Gly Thr Ser Ser Asp Val
Gly Gly Tyr 20 25 30 Asn Tyr Val Ser Trp Tyr Gln Gln His Pro Gly
Lys Ala Pro Lys Leu 35 40 45 Met Ile Tyr Asp Val Ser Lys Arg Pro
Ser Gly Val Pro Asp Arg Phe 50 55 60 Ser Gly Ser Lys Ser Gly Asn
Thr Ala Ser Leu Thr Ile Ser Gly Leu 65 70 75 80 Gln Ala Glu Asp Glu
Ala Asp Tyr Tyr Cys Cys Ser Tyr Ala Gly Ser 85 90 95 Tyr Arg Asp
Tyr Val Phe Gly Thr Gly Thr Lys Leu Thr Val Leu 100 105 110
62828DNAArtificial SequenceDNA of scFv Ab125 62caggtgcagc
tacagcagtg gggcgcagga ctgttgaagc cttcggagac cctgtccctc 60acctgcgctg
tctatggtgg gtccttcagt ggttactact ggagctggat ccgccagccc
120ccagggaagg ggctggagtg gattggggaa atcaatcata gtggaagcac
caactacaac 180ccgtccctca agagtcgagt caccatatca gtagacacgt
ccaaaaacca attctccctg 240aagctgagct ctgtgaccgc cgcggacacg
gctgtgtatt actgtgcgag aggccgacgt 300agtatagcag ctcgtccgtt
ttcttttgat atctggggcc aagggacaat ggtcaccgtc 360tcttcaggcg
gtggtggatc aggcggcaca atggtcaccg tctcttctgg cggtggtgga
420tcaggcggcg gaggatctgg cggtggtgga tcaggcggcg gaggatctgg
cggaggtggc 480agcggtggtg gaggcagtca gcctgtgctg actcaatcac
cctcagcgtc tgggaccccc 540ggccagaggg tcaccatctc ttgttctgga
agcagctcca acatcggaat taatcctgta 600aactggtacc agcagctccc
aggagcggct cccaaactcc tcatctacac tactaatcag 660cggccctcag
gggtccctga ccgattctct gcctccaagt ctggcacctc ggcctccccg
720gccatcagtg gactccagtc tgcggatgag gctgattatt actgtgcagc
gtgggatgac 780aggctgaatg gtgtggtttt cggcggtggg accaagctca ccgtcctc
82863122PRTArtificial SequenceVH of scFv Ab125 63Gln Val Gln Leu
Gln Gln Trp Gly Ala Gly Leu Leu Lys Pro Ser Glu 1 5 10 15 Thr Leu
Ser Leu Thr Cys Ala Val Tyr Gly Gly Ser Phe Ser Gly Tyr 20 25 30
Tyr Trp Ser Trp Ile Arg Gln Pro Pro Gly Lys Gly Leu Glu Trp Ile 35
40 45 Gly Glu Ile Asn His Ser Gly Ser Thr Asn Tyr Asn Pro Ser Leu
Lys 50 55 60 Ser Arg Val Thr Ile Ser Val Asp Thr Ser Lys Asn Gln
Phe Ser Leu 65 70 75 80 Lys Leu Ser Ser Val Thr Ala Ala Asp Thr Ala
Val Tyr Tyr Cys Ala 85 90 95 Arg Gly Arg Arg Ser Ile Ala Ala Arg
Pro Phe Ser Phe Asp Ile Trp 100 105 110 Gly Gln Gly Thr Met Val Thr
Val Ser Ser 115 120 64110PRTArtificial SequenceVL of scFv Ab125
64Gln Pro Val Leu Thr Gln Ser Pro Ser Ala Ser Gly Thr Pro Gly Gln 1
5 10 15 Arg Val Thr Ile Ser Cys Ser Gly Ser Ser Ser Asn Ile Gly Ile
Asn 20 25 30 Pro Val Asn Trp Tyr Gln Gln Leu Pro Gly Ala Ala Pro
Lys Leu Leu 35 40 45 Ile Tyr Thr Thr Asn Gln Arg Pro Ser Gly Val
Pro Asp Arg Phe Ser 50 55 60 Ala Ser Lys Ser Gly Thr Ser Ala Ser
Pro Ala Ile Ser Gly Leu Gln 65 70 75 80 Ser Ala Asp Glu Ala Asp Tyr
Tyr Cys Ala Ala Trp Asp Asp Arg Leu 85 90 95 Asn Gly Val Val Phe
Gly Gly Gly Thr Lys Leu Thr Val Leu 100 105 110
* * * * *