U.S. patent application number 15/934596 was filed with the patent office on 2018-08-23 for multi-specific monoclonal antibodies.
This patent application is currently assigned to BioAtla, LLC. The applicant listed for this patent is BioAtla, LLC. Invention is credited to Hwai Wen Chang, Gerhard Frey, Jay M. Short.
Application Number | 20180237543 15/934596 |
Document ID | / |
Family ID | 49551307 |
Filed Date | 2018-08-23 |
United States Patent
Application |
20180237543 |
Kind Code |
A1 |
Frey; Gerhard ; et
al. |
August 23, 2018 |
MULTI-SPECIFIC MONOCLONAL ANTIBODIES
Abstract
The present invention is relevant to the generation of
multi-specific antibodies, antibodies that are distinguished by
their ability to bind to multiple antigens with specificity and
with affinity. In particular, the present invention is related to
bi-specific antibodies.
Inventors: |
Frey; Gerhard; (San Diego,
CA) ; Chang; Hwai Wen; (San Marcos, CA) ;
Short; Jay M.; (Del Mar, CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
BioAtla, LLC |
San Diego |
CA |
US |
|
|
Assignee: |
BioAtla, LLC
San Diego
CA
|
Family ID: |
49551307 |
Appl. No.: |
15/934596 |
Filed: |
March 23, 2018 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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14399617 |
Nov 7, 2014 |
9969813 |
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PCT/US2013/040575 |
May 10, 2013 |
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15934596 |
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61645302 |
May 10, 2012 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C07K 16/468 20130101;
A61P 35/00 20180101; A01K 2267/03 20130101; C07K 2317/622 20130101;
C07K 2317/31 20130101; G01N 33/6854 20130101; C07K 2317/92
20130101; C07K 2317/14 20130101; C07K 16/005 20130101; C12N 15/1034
20130101; C07K 2317/21 20130101; C07K 2317/94 20130101 |
International
Class: |
C07K 16/46 20060101
C07K016/46; C07K 16/00 20060101 C07K016/00; C12N 15/10 20060101
C12N015/10; G01N 33/68 20060101 G01N033/68 |
Claims
1-3. (canceled)
4. The method of claim 15, wherein step (d) further comprises
screening for one or more optimized characteristics selected from
the group consisting of equilibrium dissociation constant
(K.sub.D); stability; melting temperature (T.sub.m); pI;
solubility; expression level; reduced immunogenicity; and improved
effector function.
5-9. (canceled)
10. The method of claim 15, wherein the multi-specific antibody of
step (b) specifically binds 3 epitopes.
11. The method of claim 15, wherein the multi-specific antibody of
step (b) specifically binds 4 epitopes.
12-14. (canceled)
15. A method of identifying and modifying a multi-specific
antibody, the method comprising: a. generating a library of
antibodies; b. screening the library to identify a multi-specific
antibody that binds to two or more epitopes; c. evolving the
multi-specific antibody to produce a set of modified antibodies; d.
screening the modified antibodies for optimized binding to one or
more of the two or more epitopes; and e. modifying the
multi-specific antibody such that the multi-specific antibody
comprises an organic moiety, wherein step (c) employs one or more
of comprehensive positional evolution (CPE); comprehensive
positional insertion evolution (CPI); comprehensive positional
deletion evolution (CPD); comprehensive positional evolution (CPE)
followed by combinatorial protein synthesis (CPS); and
comprehensive positional deletion evolution (CPD) followed by
combinatorial protein synthesis (CPS).
16. The method of claim 15, further comprising manufacturing the
modified, multi-specific antibody protein.
17. The method of claim 15, wherein: In step (c) the multi-specific
antibody is evolved in a manufacturing host; and further comprising
a step of f. producing the modified, multi-specific antibody
protein in the manufacturing host.
18. The method of claim 17 wherein the manufacturing host is
selected from a member of the group consisting of 3T3 mouse
fibroblast cells; BHK21 Syrian hamster fibroblast cells; MDCK, dog
epithelial cells; Hela human epithelial cells; PtK1 rat kangaroo
epithelial cells; SP2/0 mouse plasma cells; and NS0 mouse plasma
cells; HEK 293 human embryonic kidney cells; COS monkey kidney
cells; CHO, Chinese hamster ovary cells; R1 mouse embryonic cells;
E14.1 mouse embryonic cells; H1 human embryonic cells; H9 human
embryonic cells; PER C.6, human embryonic cells; S. cerevisiae
yeast cells; and pichia yeast cells.
19. The method of claim 15 wherein the screening steps comprise
fluorescence-activated cell sorting (FACS).
20. The method of claim 15 wherein the library of antibodies is
generated from an approved ethical protein therapeutic drug.
21. (canceled)
22. The method of claim 15 wherein the screening steps employ a
technique selected from the group consisting of quantitative ELISA;
affinity ELISA; ELISPOT; flow cytometry, immunocytology,
Biacore.RTM. surface plasmon resonance analysis, Sapidyne
KinExA.TM. kinetic exclusion assay; SDS-PAGE; Western blot, and
HPLC.
23. The method of claim 15 wherein the multi-specific antibody of
step (b) specifically binds 5 or more epitopes.
24. The method of claim 17, wherein the manufacturing host is
selected from CHO, HEK293 and COS-7.
25. The method of claim 17, wherein the manufacturing host uses
cell surface display.
26. The method of claim 15, wherein the organic moiety is selected
from a linear hydrophilic polymeric group, a branched hydrophilic
polymeric group, a fatty acid group, and a fatty acid ester
group.
27. The method of claim 15, wherein the organic moiety is a linear
hydrophilic polymeric group or a branched hydrophilic polymeric
group selected from a polyalkane glycol group, a carbohydrate
polymeric group, an amino acid polymeric group and a polyvinyl
pyrrolidone group.
28. The method of claim 27, wherein the organic moiety is the
carbohydrate polymeric group and is selected from a dextran group,
a cellulose group, an oligosaccharide group, and a polysaccharide
group.
29. The method of claim 27, wherein the organic moiety is the amino
acid polymeric group and is selected from a polylysine group, a
polyarginine group, and a polyaspartate group.
30. The method of claim 26, wherein the organic moiety is the fatty
acid group or the fatty acid ester group and the organic moiety
contains from about eight to about forty carbon atoms.
31. The method of claim 26, wherein the organic moiety is the fatty
acid group and is selected from an n-dodecanoate group, an
n-tetradecanoate group, an n-octadecanoate group, an n-eicosanoate
group, an n-docosanoate group, an n-triacontanoate group, an
n-tetracontanoate group, a cis-.delta. 9-octadecanoate group,
cis-.delta. 5,8,11,14-eicosatetraenoate groups, an octanedioic acid
group, a tetradecanedioic acid group, an octadecanedioic acid
group, and a docosanedioic acid group.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application is a divisional of U.S. patent application
Ser. No. 14/399,617 filed on Nov. 7, 2014, which, in turn, is a 371
continuation of International application PCT/US2013/040575 filed
on May 10, 2013, which, in turn, claims benefit of U.S. provisional
application No. 61/645,302 filed on May 10, 2012, the disclosures
of which are hereby incorporated by reference in their
entirety.
FIELD OF THE INVENTION
[0002] The present invention is relevant to the generation of
multi-specific antibodies, antibodies that are distinguished by
their ability to bind to multiple antigens with specificity and
with affinity. In particular, the present invention is related to
bi-specific antibodies. The invention is also relevant to other
multi-specific proteins that bind more than one target.
BACKGROUND AND DESCRIPTION OF THE INVENTION
[0003] While it is well known that low affinity (approximately
>1 uM) antibodies frequently bind multiple antigens, the natural
and man-made processes of affinity maturation and optimization
(directed evolution or molecular evolution) are typically designed
to increase both the affinity and specificity to only a single
epitope of a molecule at high affinity. In general, for most
applications, specificity is an important attribute; for example,
in therapeutics specificity can prevent off-target effects that are
likely to decrease the safety of a molecule. Nevertheless, there is
substantial utility in the ability to bind a limited number (for
example 2, 3, 4, 5, 6, 7, 8, 9, or 10, but preferably 2 or 3) of
selected target antigens, particularly for example for treating
diseases where there are multiple activation pathways, such as
diseases related to cancer. Immunotherapy for cancer with regular
monoclonal antibodies does not activate T-cells, because they do
not express Fc-receptors. Bi-specific antibodies (one arm binds the
tumor marker, one arm binds the T-cell specific surface antigen,
e.g. CD3) can overcome this problem and link tumor cells and
T-cells. In addition, tri-functional antibodies (IgGs with 2
different binding specificities and an intact Fc domain) can also
bind to Fc receptor expressing cells like macrophages and dendritic
cells. The tumor cell is then connected to one or two cells of the
immune system, which subsequently destroy it.
[0004] Several groups have sought to design bi-specific antibodies,
for example by making heterologous antibodies through uncoupling of
the antibody heavy chains of two independent antibodies through
disulfide bond reduction and then reassociating the antibodies
under an oxidizing environment so that the Fab's of the bivalent
IgG molecule are different and bind to separate antigens. This
approach has the disadvantage of having no avidity to the identical
target molecule and yields a costly product generation and
purification process. Other schemes have also been developed that
include sequence expansion within the Fab, effectively duplicating
the antigen binding pocket on the antibody so that each binding
pocket can have different antigen specificity on a single antibody
molecule. While this simplifies manufacturing and purification, the
structure is foreign to the human body and runs a risk of
stimulating a negative immune reaction in a patient. Still others
have employed novel covalent linkages to achieve multi-epitope
binding, creating "antibody-like" molecules.
[0005] Traditional bi-specific or multi-specific antibodies can be
difficult to manufacture. For example, these antibodies can be
constructed by expressing two separate heavy and two separate light
chains in the same cell (Quadroma technology, Milstein et al.,
1983), however, this approach is problematic because in addition to
the desired light chain1/heavy chain1-heavy chain2/light chain2
hetero-dimer, all 10 possible heavy chain and light chain
combinations will be formed (Suresh et al., 1986). The binding
affinity and specificity of unwanted light chain/heavy chain
pairings is unknown. Efforts to reduce the complexity of the
possible light chain/heavy chain assemblies of the resulting
populations includes methods such as the "knob in hole" design
(Ridgeway et al., 1996, incorporated herein by reference) where the
Fc part of the heavy chains can be modified to eliminate the
formation of some of the homo-dimers. However, the populations are
still very complex with traditional technologies, even with these
modifications. The desired bispecific (or multispecific) product is
only a small fraction of the mixture, making the purification of
the bispecific (multispecific) antibody difficult and sometimes not
feasible on a commercial scale in many cases.
[0006] Multi-specific antibodies of the present invention are
distinguished by their ability to bind to multiple antigens with
specificity and with affinity (for example, <10 nM). In one
aspect, the multi-specific antibodies of the present invention
comprise two different heavy chain variable domains (binding two or
more different antigens), a single light chain variable domain that
fits both heavy chain variable domains or has been optimized to fit
both heavy chains, and an Fc that forms heterodimers or has been
optimized to form heterodimers. Construction of multi-specific
antibodies of the present invention can be accomplished in several
ways. For example, in one approach, the variable domains of two
parent monoclonal antibodies are evolved using one of several
methods, including methods described herein, so that the same
single light chain can functionally complement both heavy chains
from the parent antibodies. One can also evolve the heavy chain of
a single parent antibody so that it can bind to a second target,
creating a new heavy chain, followed by pairing the new heavy chain
with the light chain from the parent antibody. In yet another
approach, a light chain of a single parent antibody can be evolved
so that it can bind a second target, creating a new light chain,
followed by pairing the new light chain with the heavy chain from
the parent antibody. The Fc portion that forms heterodimers of the
multi-specific antibodies of the present invention can be created
using a "knob-in-hole" type approach, or any other approach that
motivates the Fc to form or results in the Fc forming
heterodimers.
[0007] Examples of construction of multi-specific antibodies of the
present invention are further described herein.
[0008] In one embodiment, following isolation of multi-specific
antibodies of the present invention, the affinity of a
multi-specific antibody to one or more antigens or targets can be
further improved through an evolution process, for example a
comprehensive evolution process. In one aspect of the comprehensive
evolution process, up-mutants are identified during screening as
those mutants improving binding to at least one or both antigens
without causing a decrease in binding to the alternative antigen.
These up-mutants (changes can be in both the heavy and/or light
chains) can then be further mixed and matched, combinatorially, for
example.
[0009] In certain other instances, a lower affinity to one of the
target antigens and a higher affinity to another target antigen is
desirable. For example, Y. Joy Yu, et al published in Science
Translational Medicine, 25 May 2011, Vol 3, Issue 84 84ra44,
"Boosting Brain Uptake of a Therapeutic Antibody by Reducing Its
Affinity for a Transcytosis Target" that a bispecific antibody with
one arm comprising a low-affinity anti-transferrin receptor
antibody and the other arm comprising a high-affinity BACE1
antibody was able to cross the blood brain barrier and reach
therapeutic concentrations in the mouse brain. This bispecific
antibody was substantially more effective compared to a parent
monospecific antibody.
[0010] Thus, in another aspect of the comprehensive evolution
process, up-mutants are identified during screening as those
mutants improving binding to one antigen. Although the mutants that
cause a decrease in binding affinity to a second antigen are not
prioritized, they could be useful in situations where in
combinatorial fashion they lose their inhibitory effect when
combined with other mutations during the combination of mutations
process. Screening can be performed to identify lead candidates
based upon their overall affinity as well as their respective on
and off rates for antigen:antibody binding to each of the chosen
antigens.
[0011] Multi-specific antibodies of the present invention may also
be optimized for increased or decreased activity or stability in
other conditions, such as pH, oxidation, temperature, pressure, or
different ion concentrations.
BRIEF DESCRIPTION OF THE DRAWINGS
[0012] FIG. 1 illustrates one embodiment of H.sub.2L antibodies of
the present invention. The H.sub.2L antibodies have optimized
variable domains which allow the same light chain to assemble with
each of 2 heavy chains from 2 different parent antibodies (Antibody
1 and Antibody 2) without changing the binding specificity for the
particular antigen. The light chain assembles with heavy chain 1
from Antibody 1 to form "Fab-arm 1-H.sub.2L" which binds to antigen
1. The same light chain also assembles with heavy chain 2 from
Antibody 2 to form "Fab-arm 2-H.sub.2L" which binds to antigen 2.
The Fc part of the heavy chains is modified in a way that allows
only the formation of the HC1-HC2 dimer in vivo (e.g. facilitated
by a "knob in hole" design in this example, and labeled as Fc
Heterodimer). Expression of 2 heavy chains which form only
hetero-dimers and a single light chains leads to the formation of
only a single product, the "H.sub.2L mAb" antibody of the present
invention. Each molecule produced has one Fab arm binding to
antigen 1 and the other Fab arm binding to antigen 2. H.sub.2L mAbs
can be manufactured and purified just like regular IgGs.
[0013] FIG. 2 illustrates an example of screening an arrayed human
immunoglobulin light chain library. Antigen Target A immobilized in
microtiter plates was incubated with recombinant IgGs consisting of
heavy chain HC1 and a fully human light chain (a different light
chain in each well). Bound antibody was detected after washing with
anti-human IgG-HRP conjugate. Each bar represents a unique clone.
The horizontal black line indicated the background activity; the
horizontal dotted line indicates 2.times. background. Clones with a
signal above 2.times. background were counted as primary hits. The
x-axis represents the well position; the y-axis represents OD450
values.
[0014] FIG. 3 illustrates ELISA data for the binding of the
bispecific H.sub.2L mAb to the two target antigens. Wells of a
microtiter plate were either coated with Target A (grey bars) or
Target B (black bars). Heavy chain 1 (HC1) in combination with the
wild type light chain wtLC1 or the novel light chain LC-15D10)
binds to target A, but not to target B while HC2 in combination
with wild type light chain wtLC2 or the novel light chain LC-15D10
binds to target B. The bi-specific H2L mAb consisting of HC1, HC 2
and the novel light chain LC-15D10 binds to both, targe A and targe
B. The x-axis represents clone names. The y-axis represents
OD4.sub.50 values.
DEFINITIONS OF TERMS
[0015] In order to facilitate understanding of the examples
provided herein, certain frequently occurring methods and/or terms
will be described.
[0016] The term "amino acid" as used herein refers to any organic
compound that contains an amino group (--NH.sub.2) and a carboxyl
group (--COOH); preferably either as free groups or alternatively
after condensation as part of peptide bonds. The "twenty naturally
encoded polypeptide-forming alpha-amino acids" are understood in
the art and refer to: alanine (ala or A), arginine (arg or R),
asparagine (asn or N), aspartic acid (asp or D), cysteine (cys or
C), gluatamic acid (glu or E), glutamine (gln or Q), glycine (gly
or G), histidine (his or H), isoleucine (ile or I), leucine (leu or
L), lysine (lys or K), methionine (met or M), phenylalanine (phe or
F), proline (pro or P), serine (ser or S), threonine (thr or T),
tryptophan (trp or W), tyrosine (tyr or Y), and valine (val or
V).
[0017] The term "amplification" means that the number of copies of
a polynucleotide is increased.
[0018] The term "antibody", as used herein, refers to intact
immunoglobulin molecules (including IgM, IgD, IgG, IgE, and IgA
isotypes) as well as fragments of immunoglobulin molecules, such as
Fab, Fab', (Fab')2, and Fv fragments, that are capable of binding
to an epitope of an antigen. These antibody fragments, which retain
some ability to selectively bind to an antigen (e.g., a polypeptide
antigen) of the antibody from which they are derived, can be made
using well known methods in the art (see, e.g., Harlow and Lane,
supra), and are described further, as follows.
[0019] (1) An Fab fragment consists of a monovalent antigen-binding
fragment of an antibody molecule, and can be produced by digestion
of a whole antibody molecule with the enzyme papain, to yield a
fragment consisting of an intact light chain and a portion of a
heavy chain.
[0020] (2) An Fab' fragment of an antibody molecule can be obtained
by treating a whole antibody molecule with pepsin, followed by
reduction, to yield a molecule consisting of an intact light chain
and a portion of a heavy chain. Two Fab' fragments are obtained per
antibody molecule treated in this manner.
[0021] (3) An (Fab')2 fragment of an antibody can be obtained by
treating a whole antibody molecule with the enzyme pepsin, without
subsequent reduction. A (Fab')2 fragment is a dimer of two Fab'
fragments, held together by two disulfide bonds.
[0022] (4) An Fv fragment is defined as a genetically engineered
fragment containing the variable region of a light chain and the
variable region of a heavy chain expressed as two chains.
[0023] A molecule that has a "chimeric" property is a molecule that
is: 1) in part homologous and in part heterologous to a first
reference molecule; while 2) at the same time being in part
homologous and in part heterologous to a second reference molecule;
without 3) precluding the possibility of being at the same time in
part homologous and in part heterologous to still one or more
additional reference molecules. In a non-limiting embodiment, a
chimeric molecule may be prepared by assembling a reassortment of
partial molecular sequences. In a non-limiting aspect, a chimeric
polynucleotide molecule may be prepared by synthesizing the
chimeric polynucleotide using plurality of molecular templates,
such that the resultant chimeric polynucleotide has properties of a
plurality of templates.
[0024] A "comparison window," as used herein, refers to a
conceptual segment of contiguous nucleotide positions, for example
20 or more contiguous nucleotide positions, wherein a
polynucleotide sequence may be compared to a reference sequence of
at least the same number of contiguous nucleotides and wherein the
portion of the polynucleotide sequence in the comparison window may
comprise additions or deletions (i.e., gaps) of 20 percent or less
as compared to the reference sequence (which does not comprise
additions or deletions) for optimal alignment of the two sequences.
Optimal alignment of sequences for aligning a comparison window may
be conducted by the local homology algorithm of Smith and Waterman
(1981) Adv. Appl. Math. 2: 482 by the homology alignment algorithm
of Needlemen and Wuncsch J. Mol. Biol. 48: 443 (1970), by the
search of similarity method of Pearson and Lipman Proc. Natl. Acad.
Sci. (U.S.A.) 85: 2444 (1988), by computerized implementations of
these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin
Genetics Software Package Release 7.0, Genetics Computer Group, 575
Science Dr., Madison, Wis.), or by inspection, and the best
alignment (i.e., resulting in the highest percentage of homology
over the comparison window) generated by the various methods is
selected.
[0025] As used herein, the term "complementarity-determining
region" and "CDR" refer to the art-recognized term as exemplified
by the Kabat and Chothia. CDR definitions are also generally known
as supervariable regions or hypervariable loops (Chothia and Leks,
1987; Clothia et al., 1989; Kabat et al., 1987; and Tramontano et
al., 1990). Variable region domains typically comprise the
amino-terminal approximately 105-115 amino acids of a
naturally-occurring immunoglobulin chain (e.g., amino acids 1-110),
although variable domains somewhat shorter or longer are also
suitable for forming single-chain antibodies. The CDRs are parts of
immunoglobulins that determine the specificity of said molecules
and make contact with a specific ligand. The CDRs are the most
variable part of the molecule and contribute to the diversity of
these molecules. There are three CDR regions CDR1, CDR2 and CDR3 in
each V domain. CDR-H depicts a CDR region of a variable heavy chain
and CDR-L relates to a CDR region of a variable light chain. H
means the variable heavy chain and L means the variable light
chain. The CDR regions of an Ig-derived region may be determined as
described in Kabat (1991). Sequences of Proteins of Immunological
Interest, 5th edit., NIH Publication no. 91-3242 U.S. Department of
Health and Human Services, Chothia (1987). J. Mol. Biol. 196,
901-917 and Chothia (1989) Nature, 342, 877-883.
[0026] "Conservative amino acid substitutions" refer to the
interchangeability of residues having similar side chains. For
example, a group of amino acids having aliphatic side chains is
glycine, alanine, valine, leucine, and isoleucine; a group of amino
acids having aliphatic-hydroxyl side chains is serine and
threonine; a group of amino acids having amide-containing side
chains is asparagine and glutamine; a group of amino acids having
aromatic side chains is phenylalanine, tyrosine, and tryptophan; a
group of amino acids having basic side chains is lysine, arginine,
and histidine; and a group of amino acids having sulfur-containing
side chains is cysteine and methionine. Preferred conservative
amino acids substitution groups are: valine-leucine-isoleucine,
phenylalanine-tyrosine, lysine-arginine, alanine-valine, and
asparagine-glutamine.
[0027] The term "deimmunization" as used herein relates to
production of a variant of the template binding molecule, which is
modified compared to an original wild type molecule by rendering
said variant non-immunogenic or less immunogenic in humans.
Deimmunized molecules according to the invention relate to
antibodies or parts thereof (like frameworks and/or CDRs) of
non-human origin. Corresponding examples are antibodies or
fragments thereof as described in U.S. Pat. No. 4,361,549. The term
"deimmunized" also relates to molecules, which show reduced
propensity to generate T cell epitopes. In accordance with this
invention, the term "reduced propensity to generate T cell
epitopes" relates to the removal of T-cell epitopes leading to
specific T-cell activation.
[0028] Furthermore, reduced propensity to generate T cell epitopes
means substitution of amino acids contributing to the formation of
T cell epitopes, i.e. substitution of amino acids, which are
essential for formation of a T cell epitope. In other words,
reduced propensity to generate T cell epitopes relates to reduced
immunogenicity or reduced capacity to induce antigen independent T
cell proliferation. In addition, reduced propensity to generate T
cell epitopes relates to deimmunization, which means loss or
reduction of potential T cell epitopes of amino acid sequences
inducing antigen independent T cell proliferation.
[0029] The term "T cell epitope" as used herein relates to short
peptide sequences which can be released during the degradation of
peptides, polypeptide or proteins within cells and subsequently be
presented by molecules of the major histocompatibility complex
(MHC) in order to trigger the activation of T cells; see inter alia
WO 02/066514. For peptides presented by MHC class II such
activation of T cells can then induce an antibody response by
direct stimulation of B cells to produce said antibodies.
[0030] "Digestion" of DNA refers to catalytic cleavage of the DNA
with a restriction enzyme that acts only at certain sequences in
the DNA. The various restriction enzymes used herein are
commercially available and their reaction conditions, cofactors and
other requirements were used as would be known to the ordinarily
skilled artisan. For analytical purposes, typically 1 .mu.g of
plasmid or DNA fragment is used with about 2 units of enzyme in
about 20 .mu.l of buffer solution. For the purpose of isolating DNA
fragments for plasmid construction, typically 5 to 50 .mu.g of DNA
are digested with 20 to 250 units of enzyme in a larger volume.
Appropriate buffers and substrate amounts for particular
restriction enzymes are specified by the manufacturer. Incubation
times of about 1 hour at 37.degree. C. are ordinarily used, but may
vary in accordance with the supplier's instructions. After
digestion the reaction is electrophoresed directly on a gel to
isolate the desired fragment.
[0031] As used in this invention, the term "epitope" refers to an
antigenic determinant on an antigen to which the paratope of an
antibody binds. Antigenic determinants usually consist of
chemically active surface groupings of molecules, such as amino
acids or sugar side chains, and can have specific three-dimensional
structural characteristics, as well as specific charge
characteristics. As used herein "epitope" refers to that portion of
an antigen or other macromolecule capable of forming a binding
interaction that interacts with the variable region binding body of
an antibody. Typically, such binding interaction is manifested as
an intermolecular contact with one or more amino acid residues of a
CDR.
[0032] As used herein, the term "evolution" refers to a process of
directed evolution or molecular evolution, which is a process of
experimentally modifying a biological molecule towards a desirable
property, and can be achieved by mutagenizing one or more parental
molecular templates and identifying any desirable molecules among
the progeny molecules; many methods of evolution (directed
evolution) are known and published in the art, including site
directed mutagenesis, error prone PCR, site saturation methods, and
other random and non-random methods. Any of these methods may be
used in the methods of the present invention.
[0033] The terms "fragment", "derivative" and "analog" when
referring to a reference polypeptide comprise a polypeptide which
retains at least one biological function or activity that is at
least essentially same as that of the reference polypeptide.
Furthermore, the terms "fragment", "derivative" or "analog" are
exemplified by a "pro-form" molecule, such as a low activity
proprotein that can be modified by cleavage to produce a mature
enzyme with significantly higher activity.
[0034] A method is provided herein for producing from a template
polypeptide a set of progeny polypeptides in which a "full range of
single amino acid substitutions" is represented at each amino acid
position. As used herein, "full range of single amino acid
substitutions" is in reference to the naturally encoded 20
naturally encoded polypeptide-forming alpha-amino acids, as
described herein.
[0035] The term "gene" means the segment of DNA involved in
producing a polypeptide chain; it includes regions preceding and
following the coding region (leader and trailer) as well as
intervening sequences (introns) between individual coding segments
(exons).
[0036] The term "heterologous" means that one single-stranded
nucleic acid sequence is unable to hybridize to another
single-stranded nucleic acid sequence or its complement. Thus,
areas of heterology means that areas of polynucleotides or
polynucleotides have areas or regions within their sequence which
are unable to hybridize to another nucleic acid or polynucleotide.
Such regions or areas are for example areas of mutations.
[0037] The term "homologous" or "homeologous" means that one
single-stranded nucleic acid nucleic acid sequence may hybridize to
a complementary single-stranded nucleic acid sequence. The degree
of hybridization may depend on a number of factors including the
amount of identity between the sequences and the hybridization
conditions such as temperature and salt concentrations as discussed
later. Preferably the region of identity is greater than about 5
bp, more preferably the region of identity is greater than 10
bp.
[0038] An immunoglobulin light or heavy chain variable region
consists of a "framework" region interrupted by three hypervariable
regions, also called CDR's. The extent of the framework region and
CDR's have been precisely defined (see, "Sequences of Proteins of
Immunological Interest," Kabat et al., 1987). The sequences of the
framework regions of different light or heavy chains are relatively
conserved within a species. As used herein, a "human framework
region" is a framework region that is substantially identical
(about 85 or more, usually 90-95 or more) to the framework region
of a naturally occurring human immunoglobulin. The framework region
of an antibody, that is the combined framework regions of the
constituent light and heavy chains, serves to position and align
the CDR's. The CDR's are primarily responsible for binding to an
epitope of an antigen. In accordance with this invention, a
framework region relates to a region in the V domain (VH or VL
domain) of immunoglobulins that provides a protein scaffold for the
hypervariable complementarity determining regions (CDRs) that make
contact with the antigen. In each V domain, there are four
framework regions designated FR1, FR2, FR3 and FR4. Framework 1
encompasses the region from the N-terminus of the V domain until
the beginning of CDR1, framework 2 relates to the region between
CDR1 and CDR2, framework 3 encompasses the region between CDR2 and
CDR3 and framework 4 means the region from the end of CDR3 until
the C-terminus of the V domain; see, inter alia, Janeway,
Immunobiology, Garland Publishing, 2001, 5th ed. Thus, the
framework regions encompass all the regions outside the CDR regions
in VH or VL domains.
[0039] The person skilled in the art is readily in a position to
deduce from a given sequence the framework regions and, the CDRs;
see Kabat (1991) Sequences of Proteins of Immunological Interest,
5th edit., NIH Publication no. 91-3242 U.S. Department of Health
and Human Services, Chothia (1987). J. Mol. Biol. 196, 901-917 and
Chothia (1989) Nature, 342, 877-883.
[0040] The term "identical" or "identity" means that two nucleic
acid sequences have the same sequence or a complementary sequence.
Thus, "areas of identity" means that regions or areas of a
polynucleotide or the overall polynucleotide are identical or
complementary to areas of another polynucleotide or the
polynucleotide.
[0041] The term "isolated" means that the material is removed from
its original environment (e.g., the natural environment if it is
naturally occurring). For example, a naturally-occurring
polynucleotide or enzyme present in a living animal is not
isolated, but the same polynucleotide or enzyme, separated from
some or all of the coexisting materials in the natural system, is
isolated. Such polynucleotides could be part of a vector and/or
such polynucleotides or enzymes could be part of a composition, and
still be isolated in that such vector or composition is not part of
its natural environment.
[0042] By "isolated nucleic acid" is meant a nucleic acid, e.g., a
DNA or RNA molecule, that is not immediately contiguous with the 5'
and 3' flanking sequences with which it normally is immediately
contiguous when present in the naturally occurring genome of the
organism from which it is derived. The term thus describes, for
example, a nucleic acid that is incorporated into a vector, such as
a plasmid or viral vector; a nucleic acid that is incorporated into
the genome of a heterologous cell (or the genome of a homologous
cell, but at a site different from that at which it naturally
occurs); and a nucleic acid that exists as a separate molecule,
e.g., a DNA fragment produced by PCR amplification or restriction
enzyme digestion, or an RNA molecule produced by in vitro
transcription. The term also describes a recombinant nucleic acid
that forms part of a hybrid gene encoding additional polypeptide
sequences that can be used, for example, in the production of a
fusion protein.
[0043] As used herein "ligand" refers to a molecule, such as a
random peptide or variable segment sequence, that is recognized by
a particular receptor. As one of skill in the art will recognize, a
molecule (or macromolecular complex) can be both a receptor and a
ligand. In general, the binding partner having a smaller molecular
weight is referred to as the ligand and the binding partner having
a greater molecular weight is referred to as a receptor.
[0044] "Ligation" refers to the process of forming phosphodiester
bonds between two double stranded nucleic acid fragments (Maniatis
et al, 1982, p. 146). Unless otherwise provided, ligation may be
accomplished using known buffers and conditions with 10 units of T4
DNA ligase ("ligase") per 0.5 .mu.s of approximately equimolar
amounts of the DNA fragments to be ligated.
[0045] As used herein, "linker" or "spacer" refers to a molecule or
group of molecules that connects two molecules, such as a DNA
binding protein and a random peptide, and serves to place the two
molecules in a preferred configuration, e.g., so that the random
peptide can bind to a receptor with minimal steric hindrance from
the DNA binding protein.
[0046] As used herein, a "property to be evolved" includes
reference to molecules comprised of a polynucleotide sequence,
molecules comprised of a polypeptide sequence, and molecules
comprised in part of a polynucleotide sequence and in part of a
polypeptide sequence. Particularly relevant--but by no means
limiting--examples of properties to be evolved include binding
affinity, specificity and activities at specified conditions, such
as related to temperature; salinity; pressure; pH; and
concentration of glycerol, DMSO, detergent, and/or any other
molecular species with which contact is made in a reaction
environment. Additional particularly relevant--but by no means
limiting examples of properties to be evolved include
stabilities--e.g., the amount of a residual property that is
present after a specified exposure time to a specified
environment.
[0047] The term "multi-specific antibody" means an antibody that
has the ability to bind to two or more antigens with specificity;
multi-specific antibodies include bi-specific antibodies,
antibodies that have the ability to bind two antigens.
[0048] The term "mutations" means changes in the sequence of a
wild-type nucleic acid sequence or changes in the sequence of a
peptide. Such mutations may be point mutations such as transitions
or transversions. The mutations may be deletions, insertions or
duplications.
[0049] As used herein, the degenerate "N,N,G/T" nucleotide sequence
represents 32 possible triplets, where "N" can be A, C, G or T.
[0050] As used herein, the degenerate "N,N,N" nucleotide sequence
represents 64 possible triplets, where "N" can be A, C, G or T.
[0051] The term "naturally-occurring" as used herein as applied to
the object refers to the fact that an object can be found in
nature. For example, a polypeptide or polynucleotide sequence that
is present in an organism (including viruses) that can be isolated
from a source in nature and which has not been intentionally
modified by man in the laboratory is naturally occurring.
Generally, the term naturally occurring refers to an object as
present in a non-pathological (un-diseased) individual, such as
would be typical for the species.
[0052] As used herein, a "nucleic acid molecule" is comprised of at
least one base or one base pair, depending on whether it is
single-stranded or double-stranded, respectively. Furthermore, a
nucleic acid molecule may belong exclusively or chimerically to any
group of nucleotide-containing molecules, as exemplified by, but
not limited to, the following groups of nucleic acid molecules:
RNA, DNA, genomic nucleic acids, non-genomic nucleic acids,
naturally occurring and not naturally occurring nucleic acids, and
synthetic nucleic acids. This includes, by way of non-limiting
example, nucleic acids associated with any organelle, such as the
mitochondria, ribosomal RNA, and nucleic acid molecules comprised
chimerically of one or more components that are not naturally
occurring along with naturally occurring components.
[0053] Additionally, a "nucleic acid molecule" may contain in part
one or more non-nucleotide-based components as exemplified by, but
not limited to, amino acids and sugars. Thus, by way of example,
but not limitation, a ribozyme that is in part nucleotide-based and
in part protein-based is considered a "nucleic acid molecule".
[0054] In addition, by way of example, but not limitation, a
nucleic acid molecule that is labeled with a detectable moiety,
such as a radioactive or alternatively a non-radioactive label, is
likewise considered a "nucleic acid molecule".
[0055] The terms "nucleic acid sequence coding for" or a "DNA
coding sequence of" or a "nucleotide sequence encoding" a
particular enzyme--as well as other synonymous terms--refer to a
DNA sequence which is transcribed and translated into an enzyme
when placed under the control of appropriate regulatory sequences.
A "promotor sequence" is a DNA regulatory region capable of binding
RNA polymerase in a cell and initiating transcription of a
downstream (3' direction) coding sequence. The promoter is part of
the DNA sequence. This sequence region has a start codon at its 3'
terminus. The promoter sequence does include the minimum number of
bases where elements necessary to initiate transcription at levels
detectable above background. However, after the RNA polymerase
binds the sequence and transcription is initiated at the start
codon (3' terminus with a promoter), transcription proceeds
downstream in the 3' direction. Within the promotor sequence will
be found a transcription initiation site (conveniently defined by
mapping with nuclease Si) as well as protein binding domains
(consensus sequences) responsible for the binding of RNA
polymerase.
[0056] The terms "nucleic acid encoding an enzyme (protein)" or
"DNA encoding an enzyme (protein)" or "polynucleotide encoding an
enzyme (protein)" and other synonymous terms encompasses a
polynucleotide which includes only coding sequence for the enzyme
as well as a polynucleotide which includes additional coding and/or
non-Cq3 coding sequence.
[0057] In one preferred embodiment, a "specific nucleic acid
molecule species" is defined by its chemical structure, as
exemplified by, but not limited to, its primary sequence. In
another preferred embodiment, a specific "nucleic acid molecule
species" is defined by a function of the nucleic acid species or by
a function of a product derived from the nucleic acid species.
Thus, by way of non-limiting example, a "specific nucleic acid
molecule species" may be defined by one or more activities or
properties attributable to it, including activities or properties
attributable its expressed product.
[0058] The instant definition of "assembling a working nucleic acid
sample into a nucleic acid library" includes the process of
incorporating a nucleic acid sample into a vector-based collection,
such as by ligation into a vector and transformation of a host. A
description of relevant vectors, hosts, and other reagents as well
as specific non-limiting examples thereof are provided hereinafter.
The instant definition of "assembling a working nucleic acid sample
into a nucleic acid library" also includes the process of
incorporating a nucleic acid sample into a non-vector-based
collection, such as by ligation to adaptors. Preferably the
adaptors can anneal to PCR primers to facilitate amplification by
PCR.
[0059] Accordingly, in a non-limiting embodiment, a "nucleic acid
library" is comprised of a vector-based collection of one or more
nucleic acid molecules. In another preferred embodiment a "nucleic
acid library" is comprised of a non-vector-based collection of
nucleic acid molecules. In yet another preferred embodiment a
"nucleic acid library" is comprised of a combined collection of
nucleic acid molecules that is in part vector-based and in part
non-vector-based. Preferably, the collection of molecules
comprising a library is searchable and separable according to
individual nucleic acid molecule species.
[0060] The present invention provides a "nucleic acid construct" or
alternatively a "nucleotide construct" or alternatively a "DNA
construct". The term "construct" is used herein to describe a
molecule, such as a polynucleotide, that may optionally be
chemically bonded to one or more additional molecular moieties,
such as a vector, or parts of a vector. In a specific--but by no
means limiting--aspect, a nucleotide construct is exemplified by a
DNA expression DNA expression constructs suitable for the
transformation of a host cell.
[0061] An "oligonucleotide" (or synonymously an "oligo") refers to
either a single stranded polydeoxynucleotide or two complementary
polydeoxynucleotide strands which may be chemically synthesized.
Such synthetic oligonucleotides may or may not have a 5' phosphate.
Those that do not will not ligate to another oligonucleotide
without adding a phosphate with an ATP in the presence of a kinase.
A synthetic oligonucleotide will ligate to a fragment that has not
been dephosphorylated. To achieve polymerase-based amplification
(such as with PCR), a "32-fold degenerate oligonucleotide that is
comprised of, in series, at least a first homologous sequence, a
degenerate N,N,G/T sequence, and a second homologous sequence" is
mentioned. As used in this context, "homologous" is in reference to
homology between the oligo and the parental polynucleotide that is
subjected to the polymerase-based amplification.
[0062] As used herein, the term "operably linked" refers to a
linkage of polynucleotide elements in a functional relationship. A
nucleic acid is "operably linked" when it is placed into a
functional relationship with another nucleic acid sequence. For
instance, a promoter or enhancer is operably linked to a coding
sequence if it affects the transcription of the coding sequence.
Operably linked means that the DNA sequences being linked are
typically contiguous and, where necessary to join two protein
coding regions, contiguous and in reading frame.
[0063] A coding sequence is "operably linked to" another coding
sequence when RNA polymerase will transcribe the two coding
sequences into a single mRNA, which is then translated into a
single polypeptide having amino acids derived from both coding
sequences. The coding sequences need not be contiguous to one
another so long as the expressed sequences are ultimately processed
to produce the desired protein.
[0064] As used herein the term "physiological conditions" refers to
temperature, pH, ionic strength, viscosity, and like biochemical
parameters which are compatible with a viable organism, and/or
which typically exist intracellularly in a viable cultured yeast
cell or mammalian cell. For example, the intracellular conditions
in a yeast cell grown under typical laboratory culture conditions
are physiological conditions. Suitable in vitro reaction conditions
for in vitro transcription cocktails are generally physiological
conditions. In general, in vitro physiological conditions comprise
50-200 mM NaCl or KCl, pH 6.5-8.5, 20-45.degree. C. and 0.001-10 mM
divalent cation (e.g., Mg++, Ca++); preferably about 150 mM NaCl or
KCl, pH 7.2-7.6, 5 mM divalent cation, and often include 0.01-1.0
percent nonspecific protein (e.g., BSA). A non-ionic detergent
(Tween, NP-40, Triton X-100) can often be present, usually at about
0.001 to 2%, typically 0.05-0.2% (v/v). Particular aqueous
conditions may be selected by the practitioner according to
conventional methods. For general guidance, the following buffered
aqueous conditions may be applicable: 10-250 mM NaCl, 5-50 mM Tris
HC1, pH 5-8, with optional addition of divalent cation(s) and/or
metal chelators and/or non-ionic detergents and/or membrane
fractions and/or anti-foam agents and/or scintillants.
[0065] The term "population" as used herein means a collection of
components such as polynucleotides, portions or polynucleotides or
proteins. A "mixed population: means a collection of components
which belong to the same family of nucleic acids or proteins (i.e.,
are related) but which differ in their sequence (i.e., are not
identical) and hence in their biological activity.
[0066] A molecule having a "pro-form" refers to a molecule that
undergoes any combination of one or more covalent and noncovalent
chemical modifications (e.g., glycosylation, proteolytic cleavage,
dimerization or oligomerization, temperature-induced or pH-induced
conformational change, association with a co-factor, etc.) en route
to attain a more mature molecular form having a property difference
(e.g. an increase in activity) in comparison with the reference
pro-form molecule. When two or more chemical modification (e.g. two
proteolytic cleavages, or a proteolytic cleavage and a
deglycosylation) can be distinguished en route to the production of
a mature molecule, the reference precursor molecule may be termed a
"pre-pro-form" molecule.
[0067] As used herein, the term "pseudorandom" refers to a set of
sequences that have limited variability, such that, for example,
the degree of residue variability at another position, but any
pseudorandom position is allowed some degree of residue variation,
however circumscribed.
[0068] As used herein "random peptide library" refers to a set of
polynucleotide sequences that encodes a set of random peptides, and
to the set of random peptides encoded by those polynucleotide
sequences, as well as the fusion proteins contain those random
peptides.
[0069] As used herein, "random peptide sequence" refers to an amino
acid sequence composed of two or more amino acid monomers and
constructed by a stochastic or random process. A random peptide can
include framework or scaffolding motifs, which may comprise
invariant sequences.
[0070] As used herein, "receptor" refers to a molecule that has an
affinity for a given ligand. Receptors can be naturally occurring
or synthetic molecules. Receptors can be employed in an unaltered
state or as aggregates with other species. Receptors can be
attached, covalently or non-covalently, to a binding member, either
directly or via a specific binding substance. Examples of receptors
include, but are not limited to, antibodies, including monoclonal
antibodies and antisera reactive with specific antigenic
determinants (such as on viruses, cells, or other materials), cell
membrane receptors, complex carbohydrates and glycoproteins,
enzymes, and hormone receptors.
[0071] "Recombinant" enzymes refer to enzymes produced by
recombinant DNA techniques, i.e., produced from cells transformed
by an exogenous DNA construct encoding the desired enzyme.
"Synthetic" enzymes are those prepared by chemical synthesis.
[0072] The term "related polynucleotides" means that regions or
areas of the polynucleotides are identical and regions or areas of
the polynucleotides are heterologous.
[0073] "Reductive reassortment", as used herein, refers to the
increase in molecular diversity that is accrued through deletion
(and/or insertion) events that are mediated by repeated
sequences.
[0074] The following terms are used to describe the sequence
relationships between two or more polynucleotides: "reference
sequence," "comparison window," "sequence identity," "percentage of
sequence identity," and "substantial identity."
[0075] A "reference sequence" is a defined sequence used as a basis
for a sequence comparison; a reference sequence may be a subset of
a larger sequence, for example, as a segment of a full-length cDNA
or gene sequence given in a sequence listing, or may comprise a
complete cDNA or gene sequence. Generally, a reference sequence is
at least 20 nucleotides in length, frequently at least 25
nucleotides in length, and often at least 50 nucleotides in length.
Since two polynucleotides may each (1) comprise a sequence (i.e., a
portion of the complete polynucleotide sequence) that is similar
between the two polynucleotides and (2) may further comprise a
sequence that is divergent between the two polynucleotides,
sequence comparisons between two (or more) polynucleotides are
typically performed by comparing sequences of the two
polynucleotides over a "comparison window" to identify and compare
local regions of sequence similarity.
[0076] The term "sequence identity" means that two polynucleotide
sequences are identical (i.e., on a nucleotide-by-nucleotide basis)
over the window of comparison. The term "percentage of sequence
identity" is calculated by comparing two optimally aligned
sequences over the window of comparison, determining the number of
positions at which the identical nucleic acid base (e.g., A, T, C,
G, U, or I) occurs in both sequences to yield the number of matched
positions, dividing the number of matched positions by the total
number of positions in the window of comparison (i.e., the window
size), and multiplying the result by 100 to yield the percentage of
sequence identity. This "substantial identity", as used herein,
denotes a characteristic of a polynucleotide sequence, wherein the
polynucleotide comprises a sequence having at least 80 percent
sequence identity, preferably at least 85 percent identity, often
90 to 95 percent sequence identity, and most commonly at least 99
percent sequence identity as compared to a reference sequence of a
comparison window of at least 25-50 nucleotides, wherein the
percentage of sequence identity is calculated by comparing the
reference sequence to the polynucleotide sequence which may include
deletions or additions which total 20 percent or less of the
reference sequence over the window of comparison.
[0077] As known in the art "similarity" between two enzymes is
determined by comparing the amino acid sequence and its conserved
amino acid substitutes of one enzyme to the sequence of a second
enzyme. Similarity may be determined by procedures which are
well-known in the art, for example, a BLAST program (Basic Local
Alignment Search Tool at the National Center for Biological
Information).
[0078] As used herein, the term "single-chain antibody" refers to a
polypeptide comprising a VH domain and a VL domain in polypeptide
linkage, generally liked via a spacer peptide (e.g.,
[Gly-Gly-Gly-Gly-Ser].sub.x), and which 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 encoding polynucleotide. As an example a scFv is a
single-chain antibody. Single-chain antibodies are generally
proteins consisting of one or more polypeptide segments of at least
10 contiguous amino substantially encoded by genes of the
immunoglobulin superfamily (e.g., see Williams and Barclay, 1989,
pp. 361-368, which is incorporated herein by reference), most
frequently encoded by a rodent, non-human primate, avian, porcine
bovine, ovine, goat, or human heavy chain or light chain gene
sequence. 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).
[0079] The members of a pair of molecules (e.g., an
antibody-antigen pair or a nucleic acid pair) are said to
"specifically bind" to each other if they bind to each other with
greater affinity than to other, non-specific molecules. For
example, an antibody raised against an antigen to which it binds
more efficiently than to a non-specific protein can be described as
specifically binding to the antigen. (Similarly, a nucleic acid
probe can be described as specifically binding to a nucleic acid
target if it forms a specific duplex with the target by base
pairing interactions (see above).)
[0080] "Specific hybridization" is defined herein as the formation
of hybrids between a first polynucleotide and a second
polynucleotide (e.g., a polynucleotide having a distinct but
substantially identical sequence to the first polynucleotide),
wherein substantially unrelated polynucleotide sequences do not
form hybrids in the mixture.
[0081] The term "specific polynucleotide" means a polynucleotide
having certain end points and having a certain nucleic acid
sequence. Two polynucleotides wherein one polynucleotide has the
identical sequence as a portion of the second polynucleotide but
different ends comprises two different specific
polynucleotides.
[0082] "Stringent hybridization conditions" means hybridization
will occur only if there is at least 90% identity, preferably at
least 95% identity and most preferably at least 97% identity
between the sequences. See Sambrook et al, 1989, which is hereby
incorporated by reference in its entirety.
[0083] A "substantially identical" amino acid sequence is a
sequence that differs from a reference sequence only by
conservative amino acid substitutions, for example, substitutions
of one amino acid for another of the same class (e.g., substitution
of one hydrophobic amino acid, such as isoleucine, valine, leucine,
or methionine, for another, or substitution of one polar amino acid
for another, such as substitution of arginine for lysine, glutamic
acid for aspartic acid, or glutamine for asparagine).
[0084] Additionally a "substantially identical" amino acid sequence
is a sequence that differs from a reference sequence or by one or
more non-conservative substitutions, deletions, or insertions,
particularly when such a substitution occurs at a site that is not
the active site the molecule, and provided that the polypeptide
essentially retains its behavioural properties. For example, one or
more amino acids can be deleted from a polypeptide, resulting in
modification of the structure of the polypeptide, without
significantly altering its biological activity. For example, amino-
or carboxyl-terminal amino acids that are not required for
biological activity can be removed. Such modifications can result
in the development of smaller active polypeptides.
[0085] As used herein, "substantially pure" means an object species
is the predominant species present (i.e., on a molar basis it is
more abundant than any other individual macromolecular species in
the composition), and preferably substantially purified fraction is
a composition wherein the object species comprises at least about
50 percent (on a molar basis) of all macromolecular species
present. Generally, a substantially pure composition will comprise
more than about 80 to 90 percent of all macromolecular species
present in the composition. Most preferably, the object species is
purified to essential homogeneity (contaminant species cannot be
detected in the composition by conventional detection methods)
wherein the composition consists essentially of a single
macromolecular species. Solvent species, small molecules (<500
Daltons), and elemental ion species are not considered
macromolecular species.
[0086] As used herein, "syngenic" means genetically identical, or
sufficiently identical and immunologically compatible.
[0087] As used herein, "templates", "template antibodies" or
"parent antibodies" mean protein(s) from which the multi-functional
antibodies of the present invention are made. As will be
appreciated by those in the art, any number of templates find use
in the present invention. Specifically included within the
definition of "proteins" or "oligopeptides" are fragments and
domains of known proteins, including functional domains such as
enzymatic domains, binding domains, etc., and smaller fragments,
such as turns, loops, etc. That is, portions of proteins may be
used as well. In addition, "protein" as used herein includes
proteins, oligopeptides and peptides. In addition, protein
variants, i.e., non-naturally occurring protein analog structures,
may be used.
[0088] Suitable proteins include, but are not limited to,
pharmaceutical proteins, including ligands, cell surface receptors,
antigens, antibodies, cytokines, hormones, transcription factors,
signaling modules, cytoskeletal proteins and enzymes. Suitable
protein backbones include, but are not limited to, all of those
found in the protein data base compiled and serviced by the
Research Collaboratory for Structural Bioinformatics (RCSB,
formerly the Brookhaven National Lab).
[0089] As used herein, the term "variable segment" refers to a
portion of a nascent peptide which comprises a random,
pseudorandom, or defined kernel sequence. A variable segment"
refers to a portion of a nascent peptide which comprises a random
pseudorandom, or defined kernel sequence. A variable segment can
comprise both variant and invariant residue positions, and the
degree of residue variation at a variant residue position may be
limited: both options are selected at the discretion of the
practitioner. Typically, variable segments are about 5 to 20 amino
acid residues in length (e.g., 8 to 10), although variable segments
may be longer and may comprise antibody portions or receptor
proteins, such as an antibody fragment, a nucleic acid binding
protein, a receptor protein, and the like.
[0090] The term "wild-type" means that the polynucleotide does not
comprise any mutations. A "wild type" protein means that the
protein will be active at a level of activity found in nature and
will comprise the amino acid sequence found in nature.
DESCRIPTION OF THE INVENTION
[0091] Generation of Multi-Functional Antibodies of the Present
Invention
[0092] Antibodies with different properties (improved affinity,
avidity and pharmacokinetics, for example) and structures,
including fully human antibodies, chimeric antibodies with both
human and non-human elements, Fab antibodies, and other antibody
structures, have been constructed in the laboratory using molecular
biology techniques, such as cloning, phage display, transgenic mice
and mutagenesis. Multi-functional antibodies of the present
invention can be generated from antibodies that are used as
starting molecules, or templates. Parent antibodies can be fully
human antibodies, rodent, rabbit, canine, bovine, artiodactyla,
fish, chondrichthyes, chimeric antibodies, humanized antibodies,
partially human antibodies or other antibodies. Methods for
generating such antibodies are well known in the art. Considerable
information has been published and is known about monoclonal
antibodies and their utility in research, diagnosis, and in the
treatment of multiple diseases, including cancer. For example, over
a dozen monoclonal antibodies have government regulatory approval
for therapeutic use in patients.
[0093] The deciphering of the human genome has opened new
opportunities to build fully human antibodies that can be used as
therapeutics. The human immune system is able to generate
antibodies against all immunogenic molecules from a limited number
of germline antibody genes. Diversity is generated by sloppy
(flexible) recombination of V, D, and J fragments (heavy chain),
and V and J fragments for the light chain. The resulting variable
antibody domains consist of three complementarity determining
regions (CDRs) and four framework regions. The frame works provide
the scaffold to give the CDR loops the proper spatial orientation
for optimal binding to the antigen. In one aspect of the present
invention, a fully human, de novo, antibody library can be
generated and screened to identify templates for the present
invention in accordance with methods well known in the art.
[0094] Monoclonal antibodies that can be used as parent antibodies
for the molecules of the present invention can also be produced by
immunization of a rodent or other host animal with the target
antigen, and subsequent generation of a hybridoma cell line using
methods well known in the art.
[0095] In the methods of the present invention, it is also
envisioned that any antibody that binds an epitope on one or more
targets (known or unknown) can also be evolved to bind a second or
third or multiple epitopes on the one or more targets. Thus parent
antibodies can be one or more antibodies.
[0096] Antibody libraries can also be screened using a variety of
known methods, such as those described herein, to generate one or
more parent antibodies.
[0097] Protein engineering via site-directed mutagenesis and, more
recently, molecular evolution has been successfully employed to
improve therapeutic properties in antibodies. Characteristics such
as thermostability, specificity, binding affinity and other
characteristics have all been altered to better adapt antibodies
for specific purposes.
[0098] Since its inception, many different methods for molecular
evolution have been described and applied to improve
characteristics of the target protein. Very often sets of single
point mutants are generated and screened for up mutants. Beneficial
single amino acid substitutions can then be recombined and screened
to further optimize the desired characteristics in the target
molecule.
[0099] In the present invention, evolution methods are employed to
identify mutant polypeptides formed from, or based upon, a template
polypeptide(s) of the dual binding, multi-specific antibodies
previously identified (or the mono-functional antibody, as the case
may be).
[0100] For example, one method to evolve these polypeptides is
referred to herein as Comprehensive Positional Evolution (CPE)
followed optionally by Combinatorial Protein Synthesis (CPS). Other
methods include comprehensive positional insertion evolution (CPI),
comprehensive positional deletion evolution (CPD); comprehensive
positional deletion evolution (CPD) followed by combinatorial
protein synthesis (CPS); or comprehensive positional deletion
evolution (CPD) followed by combinatorial protein synthesis (CPS).
Such methods, are described in detail in the patent publication
WO2012/009026 entitled Novel Methods of Protein Evolution
(incorporated herein in its entirety by reference).
[0101] Evolution may be employed to multi-specific antibodies of
the present invention to reduce protein-protein aggregation,
improve of protein solubility, optimize pharmacokinetics via
glycosylation libraries, optimize protein secondary and tertiary
structure and for deimmunization of antigenic sites directly via
either mutation sets or indirectly through glycosylation
masking.
[0102] Evolution may also be used for deimmunization to eliminate
immunogenicity while maintaining function. Evolution deimmunization
can be performed by masking immunogenicity with glycosylation,
identifying human hypersomatic mutation spectra amino acid
substitutions that may eliminate immunogenicity while maintaining
function, reduction of dose for evading immunogenicity potential,
and minimization of non-surface amino acid residue changes.
Further, immunogenicity databases and algorithms can be used to
identify and replace potential MHC binding epitopes.
[0103] Reduced propensity to generate T-cell epitopes and/or
deimmunization may be measured by techniques known in the art.
Preferably, deimmunization of proteins may be tested in vitro by T
cell proliferation assay. In this assay PBMCs from donors
representing >80% of HLA-DR alleles in the world are screened
for proliferation in response to either wild type or deimmunized
peptides. Ideally cell proliferation is only detected upon loading
of the antigen-presenting cells with wild type peptides. Additional
assays for deimmunization include human in vitro PBMC
re-stimulation assays (e.g. interferon gamma (TH1) or IL4 (TH2)
ELISA. Alternatively, one may test deimmunization by expressing
HLA-DR tetramers representing all haplotypes. In order to test if
de-immunized peptides are presented on HLA-DR haplotypes, binding
of e.g. fluorescence-labeled peptides on PBMCs can be measured.
Measurement of HLA Class I and Class II transgenic mice for
responses to target antigen (e.g. interferon gamma or IL4).
Alternatively epitope library screening with educated T cells (MHCI
9mer; MHCII 20mer) from PBMC and/or transgenic mouse assays.
Furthermore, deimmunization can be proven by determining whether
antibodies against the deimmunized molecules have been generated
after administration in patients.
[0104] Evolution techniques can also be utilized for expression
optimization. In one aspect, the present invention discloses the
utilization of protein engineering methods to develop silent
mutation codon optimized Fc variants with improved expression in
mammalian cells. A silent mutation is is one in which the variation
of the DNA sequence does not result in a change in the amino acid
sequence of the protein. In one aspect, codon mutagenesis is
performed in the constant region for optimization of mammalian cell
expression. A codon optimized Fc variant with improved expression
properties while retaining the capacity to mediate effector
functions improves the production of therapeutic antibodies. In
this aspect, for example, a constant region of an antibody molecule
can be evolved for screening in different expression hosts, for
example, mammalian cell lines expression screening utilizing CHO,
HEK293 and COS-7.
[0105] The term template may refer to a base polypeptide or a
polynucleotide encoding such polypeptide. As would be appreciated
by one of skill in this art, any template may be used in the
methods and compositions of the present invention. Templates that
can be mutated and thereby evolved can be used to guide the
synthesis of another polypeptide or library of polypeptides as
described in the present invention. As described in more detail
herein, the evolvable template encodes the synthesis of a
polypeptide and can be used later to decode the synthetic history
of the polypeptide, to indirectly amplify the polypeptide, and/or
to evolve (i.e., diversify, select, and amplify) the polypeptide.
The evolvable template is, in certain embodiments, a nucleic acid.
In certain embodiment of the present invention, the template is
based on a nucleic acid. In other embodiments, the template is a
polypeptide.
[0106] The nucleic acid templates used in the present invention are
made of DNA, RNA, a hybrid of DNA and RNA, or a derivative of DNA
and RNA, and may be single- or double-stranded. The sequence of the
template is used to encode the synthesis of a polypeptide,
preferably a compound that is not, or does not resemble, a nucleic
acid or nucleic acid analog (e.g., an unnatural polymer or a small
molecule). In the case of certain unnatural polymers, the nucleic
acid template is used to align the monomer units in the sequence
they will appear in the polymer and to bring them in close
proximity with adjacent monomer units along the template so that
they will react and become joined by a covalent bond. In certain
other embodiments, the template can be utilized to generate
non-natural polymers by PCR amplification of a synthetic DNA
template library consisting of a random region of nucleotides.
[0107] It will be appreciated that the template can vary greatly in
the number of bases. For example, in certain embodiments, the
template may be 10 to 10,000 bases long, preferably between 10 and
1,500 bases long, more preferably between 10 and 1,000 bases long.
The length of the template will of course depend on the length of
the codons, complexity of the library, length of the unnatural
polymer to be synthesized, complexity of the small molecule to be
synthesized, use of space sequences, etc. The nucleic acid sequence
may be prepared using any method known in the art to prepare
nucleic acid sequences. These methods include both in vivo and in
vitro methods including PCR, plasmid preparation, endonuclease
digestion, solid phase synthesis, in vitro transcription, strand
separation, etc. The nucleic acid template can also be synthesized
using an automated DNA synthesizer.
[0108] Because of the high efficiency with which all 19 amino acid
substitutions can be generated at a single residue, it is possible
to perform saturation mutagenesis on numerous residues of interest,
either independently or in combination with other mutations within
the protein. As used herein, "complete saturation" mutagenesis is
defined as replacing a given amino acid within a protein, with the
other 19 naturally-occurring amino acids. For example, gene site
saturation mutagenesis, which systematically explores minimally all
possible single amino acid substitutions along a protein sequence,
is disclosed in Kretz et al., Methods in Enzymology, 2004,
388:3-11, Short U.S. Pat. No. 6,171,820, and Short U.S. Pat. No.
6,562,594, each of which is incorporated herein by reference.
[0109] Codon primers (containing a degenerate N,N,G/T sequence) can
be used to introduce point mutations into a polynucleotide, so as
to generate a set of progeny polypeptides in which a full range of
single amino acid substitutions is represented at each amino acid
position (see U.S. Pat. No. 6,171,820; see also, U.S. Pat. No.
5,677,149, each incorporated herein by reference). The oligos used
are comprised contiguously of a first homologous sequence, a
degenerate N,N,G/T sequence, and preferably but not necessarily a
second homologous sequence. The downstream progeny translational
products from the use of such oligos include all possible amino
acid changes at each amino acid site along the polypeptide, because
the degeneracy of the N,N,G/T sequence includes codons for all 20
amino acids.
[0110] Codon usage is one of the important factors in mammalian
gene expression. The frequencies with which different codons are
used vary significantly between different hosts, and between
proteins expressed at high or low levels within the same organism.
The most likely reason for this variation is that preferred codons
correlate with the abundance of cognate tRNAs available within the
cell. It is possible that codon usage and tRNA acceptor
concentrations have coevolved, and that the selection pressure for
this co-evolution is more pronounced for highly expressed genes
than genes expressed at low levels.
[0111] One such degenerate oligo (comprised of one degenerate
N,N,G/T cassette) can be used for subjecting each original codon in
a parental polynucleotide template to a full range of codon
substitutions. Further, at least two degenerate N,N,G/T cassettes
can be used--either in the same oligo or not, for subjecting at
least two original codons in a parental polynucleotide template to
a full range of codon substitutions. Thus, more than one N,N,G/T
sequence can be contained in one oligo to introduce amino acid
mutations at more than one site. This plurality of N,N,G/T
sequences can be directly contiguous, or separated by one or more
additional nucleotide sequence(s). Oligos serviceable for
introducing additions and deletions can also be used either alone
or in combination with the codons containing an N,N,G/T sequence,
to introduce any combination or permutation of amino acid
additions, deletions, and/or substitutions.
[0112] The template polypeptide may be any protein, however
proteins which have a convenient assay for activity such as
catalytic activity or ligand binding are preferred. As used herein,
a ligand is any molecule which binds specifically to a different
molecule, such as small molecule binding to a protein.
Representative examples of target interactions include catalysis,
enzyme-substrate interactions, protein-nucleic acid interactions,
receptor-ligand interactions, protein-metal interactions and
antibody-antigen interactions. Representative target proteins
include enzymes, antibodies, cytokines, receptors, DNA binding
proteins, chelating agents, and hormones.
[0113] Templates can be discovered by generating and screening
antibody libraries. Various methods for generation and screening of
antibody libraries are known in the art, as indicated. For example,
fully human antibody display libraries can be utilized. The
"library" in this case is a population of antibodies displayed on
the surface of host cell(s). Preferably, the antibody library is
representative of the human repertoire of antibodies in that they
have broad capability of binding to a wide range of antigens. Also,
the library preferably has thousands of bivalent antibodies
displayed. Because the antibodies are displayed on the surface of
cells, the effective affinity (due to avidity) of each antibody in
the library is increased. Unlike other popular library types, such
as phage display libraries, where avidity of the antibodies for
screening and identification purposes is less desirable, the super
avidity provided by cell surface display in the present invention,
is desirable. Cell surface display libraries enable the
identification of low, medium and high binding affinity antibodies,
as well as the identification of non-immunogenic and weak epitopes
in the screening or selection step. Any chemical synthetic or
recombinant mutagenic method may be used to generate the population
of mutant polypeptides. The practice of the present invention may
employ, unless otherwise indicated, conventional techniques of cell
biology, cell culture, molecular biology, transgenic biology,
microbiology, recombinant DNA, and immunology, which are within the
skill of the art. Such techniques are explained fully in the
literature. See, for example, Molecular Cloning A Laboratory
Manual, 2nd Ed., ed. by Sambrook, Fritsch and Maniatis (Cold Spring
Harbor Laboratory Press: 1989); DNA Cloning, Volumes I and II (D.
N. Glover ed., 1985); Oligonucleotide Synthesis (M. J. Gait ed.,
1984); Mullis et al. U.S. Pat. No. 4,683,195; Nucleic Acid
Hybridization (B. D. Hames & S. J. Higgins eds. 1984);
Transcription And Translation (B. D. Hames & S. J. Higgins eds.
1984); Culture Of Animal Cells (R. I. Freshney, Alan R. Liss, Inc.,
1987); Immobilized Cells And Enzymes (IRL Press, 1986); B. Perbal,
A Practical Guide To Molecular Cloning (1984); the treatise,
Methods In Enzymology (Academic Press, Inc., N.Y.); Gene Transfer
Vectors For Mammalian Cells (J. H. Miller and M. P. Cabs eds.,
1987, Cold Spring Harbor Laboratory); Methods In Enzymnology, Vols.
154 and 155 (Wu et al. eds.), Immunochemical Methods In Cell And
Molecular Biology (Mayer and Walker, eds., Academic Press, London,
1987); Handbook Of Experimental Immunology, Volumes I-IV (D. M.
Weir and C. C. Blackwell, eds., 1986); Manipulating the Mouse
Embryo, (Cold Spring Harbor Laboratory Press, Cold Spring Harbor,
N.Y., 1986).
[0114] In the preferred embodiment, the template polypeptide is an
antibody. The antibody is subjected to the methods described herein
to, for example, map and understand which positions within the CDR
effect binding affinity. The techniques for preparing and using
various antibody-based constructs and fragments thereof are well
known in the art. An important aspect of the present invention is
the identification of residues that play, or are likely to play, a
role in the interaction of interest (e.g., antigen-antibody
interaction, metal chelation, receptor binding, substrate binding,
etc). Any antibody or antibody fragment may be used according to
the present invention. The specificity of an antibody is determined
by the complementarity determining regions (CDRs) within the light
chain variable regions (VL) and heavy chain variable regions (VH).
The Fab fragment of an antibody, which is about one-third the size
of a complete antibody contains the heavy and light chain variable
regions, the complete light chain constant region and a portion of
the heavy chain constant region. Fab molecules are stable and
associate well due to the contribution of the constant region
sequences. However, the yield of functional Fab expressed in
bacterial systems is lower than that of the smaller Fv fragment
which contains only the variable regions of the heavy and light
chains. The Fv fragment is the smallest portion of an antibody that
still retains a functional antigen binding site. The Fv fragment
has the same binding properties as the Fab, however without the
stability conferred by the constant regions, the two chains of the
Fv can dissociate relatively easily in dilute conditions.
[0115] To overcome this problem, VH and VL regions may be fused via
a polypeptide linker (Huston et al., 1991) to stabilize the antigen
binding site. This single polypeptide Fv fragment is known as a
single chain antibody (scFv). The VH and VL can be arranged with
either domain first. The linker joins the carboxy terminus of the
first chain to the amino terminus of the second chain.
[0116] One of skill in the art will recognize that heavy or light
chain Fv or Fab fragments may also be used with this system. A
heavy or light chain can be mutagenized followed by the addition of
the complementary chain to the solution. The two chains are then
allowed to combine and form a functional antibody fragment.
Addition of random non-specific light or heavy chain sequences
allows for the production of a combinatorial system to generate a
library of diverse members.
[0117] Generally, a single-chain expression polynucleotide is
generated. This expression polynucleotide contains: (1) a
single-chain antibody cassette consisting of a V.sub.H domain,
spacer peptide, and V.sub.L domain operably linked to encode a
single-chain antibody, (2) a promoter suitable for in vitro
transcription (e.g., T7 promoter, SP6 promoter, and the like)
operably linked to ensure in vitro transcription of the
single-chain antibody cassette forming a mRNA encoding a
single-chain antibody, and (3) a transcription termination sequence
suitable for functioning in an in vitro transcription reaction.
Optionally, the expression polynucleotide may also comprise an
origin of replication and/or a selectable marker. An example of a
suitable expression polynucleotide is pLM166.
[0118] The V.sub.H and V.sub.L sequences can be conveniently
obtained from a library of V.sub.H and V.sub.L sequences produced
by PCR amplification using V gene family-specific primers or V
gene-specific primers (Nicholls et al. (1993) J. Immunol. Meth.
165: 81; WO93/12227) or are designed according to standard
art-known methods based on available sequence information.
Typically, mouse or human V.sub.H and V.sub.L sequences are
isolated. The V.sub.H and V.sub.L sequences are then ligated,
usually with an intervening spacer sequence (e.g., encoding an
in-frame flexible peptide spacer), forming a cassette encoding a
single-chain antibody. Typically, a library comprising a plurality
of V.sub.H and V.sub.L sequences is used (sometimes also with a
plurality of spacer peptide species represented), wherein the
library is constructed with one or more of the V.sub.H and V.sub.L
sequences mutated to increase sequence diversity particularly at
CDR residues, sometimes at framework residues. V region sequences
can be conveniently cloned as cDNAs or PCR amplification products
for immunoglobulin-expressing cells. For example, cells from human
hybridoma, or lymphoma, or other cell line that synthesizes either
cell surface or secreted immunoglobulin may be used for the
isolation of polyA+RNA. The RNA is then used for the synthesis of
oligo dT primed cDNA using the enzyme reverse transcriptase (for
general methods see, Goodspeed et al. (1989) Gene 76: 1; Dunn et
al. (1989) J. Biol. Chem. 264: 13057). Once the V-region CDNA or
PCR product is isolated, it is cloned into a vector to form a
single-chain antibody cassette.
[0119] To accomplish construction of antibodies and antibody
fragments, the encoding genes are isolated and identified. The
genes can be modified to permit cloning into an expression vector
or an in vitro transcription/translation. Although methods can be
used such as probing the DNA for VH and VL from hybridoma cDNA
(Maniatis et al., 1982) or constructing a synthetic gene for VH and
VL (Barbas et al., 1992), a convenient mode is to use template
directed methods to amplify the antibody sequences. A diverse
population of antibody genes can be amplified from a template
sample by designing primers to the conserved sequences at the 3'
and 5' ends of the variable region known as the framework or to the
constant regions of the antibody (Iverson et al., 1989). Within the
primers, restriction sites can be placed to facilitate cloning into
an expression vector. By directing the primers to these conserved
regions, the diversity of the antibody population is maintained to
allow for the construction of diverse libraries. The specific
species and class of antibody can be defined by the selection of
the primer sequences as illustrated by the large number of
sequences for all types of antibodies given in Kabat et al., 1987,
hereby incorporated by reference.
[0120] Messenger RNA isolated from the spleen or peripheral blood
of an animal can also be used as the template for the amplification
of an antibody library. In certain circumstances, where it is
desirable to display a homogeneous population of antibody fragments
on the cell surface, mRNA may be isolated from a population of
monoclonal antibodies. Messenger RNA from either source can be
prepared by standard methods and used directly or for the
preparation of a cDNA template. Generation of mRNA for cloning
antibody purposes is readily accomplished by following the
well-known procedures for preparation and characterization of
antibodies (see, e.g., Antibodies: A Laboratory Manual, 1988;
incorporated herein by reference).
[0121] Generation of monoclonal antibodies (MAbs) follows generally
the same procedures as those for preparing polyclonal antibodies.
Briefly, a polyclonal antibody is prepared by immunizing an animal
with an immunogenic composition in accordance and collecting
antisera from that immunized animal. A wide range of animal species
can be used for the production of antisera. Typically the animal
used for production of anti-antisera is a rabbit, a mouse, a rat, a
hamster, a guinea pig or a goat. Because of the relatively large
blood volume of rabbits, rabbits are usually preferred for
production of polyclonal antibodies.
[0122] Immunogenic compositions often vary in immunogenicity. It is
often necessary therefore to boost the host immune system, as may
be achieved by coupling a peptide or polypeptide immunogen to a
carrier. Exemplary and preferred carriers are keyhole limpet
hemocyanin (KLH) and bovine serum albumin (BSA). Other albumins
such as ovalbumin, mouse serum albumin or rabbit serum albumin can
also be used as carriers. Recognized means for conjugating a
polypeptide to a carrier protein are well known and include
glutaraldehyde, m-maleimidobenzoyl-N-hydroxysuccinimide ester,
carbodiimides and bis-diazotized benzidine.
[0123] The immunogenicity of a particular immunogen composition may
be enhanced by the use of non-specific stimulators of the immune
response, known as adjuvants. Exemplary and preferred adjuvants
include complete Freund's adjuvant (a non-specific stimulator of
the immune response containing killed Mycobacterium tuberculosis),
incomplete Freund's adjuvants and aluminum hydroxide adjuvant.
[0124] The amount of immunogen composition used in the production
of polyclonal antibodies varies upon the nature of the immunogen as
well as the animal used for immunization. A variety of routes can
be used to administer the immunogen (subcutaneous, intramuscular,
intradermal, intravenous and intraperitoneal). The production of
polyclonal antibodies may be monitored by sampling blood of the
immunized animal at various points following immunization. A
second, booster injection, may also be given. The process of
boosting and titering is repeated until a suitable titer is
achieved. When a desired level of immunogenicity is obtained, the
immunized animal can be bled and the serum isolated, stored and the
spleen harvested for the isolation of mRNA from the polyclonal
response or the animal can be used to generate MAbs for the
isolation of mRNA from a homogeneous antibody population.
[0125] MAbs may be readily prepared through use of well-known
techniques, such as those exemplified in U.S. Pat. No. 4,196,265,
incorporated herein by reference. Typically, this technique
involves immunizing a suitable animal with a selected immunogen
composition, e.g. a small molecule hapten conjugated to a carrier,
a purified or partially purified protein, polypeptide or peptide.
The immunizing composition is administered in a manner effective to
stimulate antibody producing cells. Rodents such as mice and rats
are frequently used animals; however, the use of rabbit, sheep frog
cells is also possible. The use of rats may provide certain
advantages (Goding, pp. 60-61, 1986), but mice are preferred,
particularly the BALB/c mouse as this is most routinely used and
generally gives a higher percentage of stable fusions.
[0126] Following immunization, somatic cells with the potential for
producing antibodies, specifically B lymphocytes (B cells), are
selected for use in the MAb generating protocol. These cells may be
obtained from biopsied spleens, tonsils or lymph nodes, or from
blood samples. Spleen cells and blood cells are preferable, the
former because they are a rich source of antibody-producing cells
that are in the dividing plasmablast stage, and the latter because
blood is easily accessible. Often, a panel of animals will have
been immunized and the spleen of animal with the highest antibody
titer will be removed and the spleen lymphocytes obtained by
homogenizing the spleen with a syringe. Typically, a spleen from an
immunized mouse contains approximately 5.times.107 to 2.times.108
lymphocytes.
[0127] The antibody-producing B lymphocytes from the immunized
animal are then fused with cells of an immortal myeloma cell,
generally one of the same species as the animal that was immunized.
Myeloma cell lines suited for use in hybridoma-producing fusion
procedures preferably are non-antibody-producing, have high fusion
efficiency, and enzyme deficiencies that render then incapable of
growing in certain selective media which support the growth of only
the desired fused cells (hybridomas).
[0128] Any one of a number of myeloma cells may be used, as are
known to those of skill in the art (Goding, pp. 65-66, 1986;
Campbell, 1984). For example, where the immunized animal is a
mouse, one may use P3-X63/Ag8, X63-Ag8.653, NS1/1.Ag 4 1,
Sp210-Ag14, FO, NSO/U, MPC-11, MPC11-X45-GTG 1.7 and 5194/5XX0 Bul;
for rats, one may use R210.RCY3, Y3-Ag 1.2.3, IR983F and 4B210; and
U-266, GM1500-GRG2, LICR-LON-HMy2 and UC729-6 are all useful in
connection with human cell fusions.
[0129] One preferred murine myeloma cell is the NS-1 myeloma cell
line (also termed P3-NS-1-Ag4-1), which is readily available from
the NIGMS Human Genetic Mutant Cell Repository by requesting cell
line repository number GM3573. Another mouse myeloma cell line that
may be used is the 8-azaguanine-resistant mouse murine myeloma
SP2/0 non-producer cell line.
[0130] Methods for generating hybrids of antibody-producing spleen
or lymph node cells and myeloma cells usually comprise mixing
somatic cells with myeloma cells in a 2:1 proportion, though the
proportion may vary from about 20:1 to about 1:1, respectively, in
the presence of an agent or agents (chemical or electrical) that
promote the fusion of cell membranes. Fusion methods using Sendai
virus have been described by Kohler & Milstein (1975; 1976),
and those using polyethylene glycol (PEG), such as 37% (v/v) PEG,
by Gefter et al., 1977). The use of electrically induced fusion
methods is also appropriate (Goding pp. 71-74, 1986).
[0131] Fusion procedures usually produce viable hybrids at low
frequencies, about 1.times.10.sup.-6 to 1.times.10.sup.-8. However,
this does not pose a problem, as the viable, fused hybrids are
differentiated from the parental, unfused cells (particularly the
unfused myeloma cells that would normally continue to divide
indefinitely) by culturing in a selective medium. The selective
medium is generally one that contains an agent that blocks the de
novo synthesis of nucleotides in the tissue culture media.
Exemplary and preferred agents are aminopterin, methotrexate, and
azaserine. Aminopterin and methotrexate block de novo synthesis of
both purines and pyrimidines, whereas azaserine blocks only purine
synthesis. Where aminopterin or methotrexate is used, the media is
supplemented with hypoxanthine and thymidine as a source of
nucleotides (HAT medium). Where azaserine is used, the media is
supplemented with hypoxanthine.
[0132] The preferred selection medium is HAT. Only cells capable of
operating nucleotide salvage pathways are able to survive in HAT
medium. The myeloma cells are defective in key enzymes of the
salvage pathway, e.g., hypoxanthine phosphoribosyl transferase
(HPRT), and they cannot survive. The B cells can operate this
pathway, but they have a limited life span in culture and generally
die within about two weeks. Therefore, the only cells that can
survive in the selective media are those hybrids formed from
myeloma and B cells.
[0133] This culturing provides a population of hybridomas from
which specific hybridomas are selected. Typically, selection of
hybridomas is performed by culturing the cells by single-clone
dilution in microtiter plates, followed by testing the individual
clonal supernatants (after about two to three weeks) for the
desired reactivity. Simple and rapid assays include
radioimmunoassays, enzyme immunoassays, cytotoxicity assays, plaque
assays, dot immunobinding assays, and the like.
[0134] The selected hybridomas are serially diluted and cloned into
individual antibody-producing cell lines from which clones can then
be propagated indefinitely to provide MAbs. The cell lines may be
exploited for MAb production in two basic ways. A sample of the
hybridoma can be injected (often into the peritoneal cavity) into a
histocompatible animal of the type that was used to provide the
somatic and myeloma cells for the original fusion. The injected
animal develops tumors secreting the specific monoclonal antibody
produced by the fused cell hybrid. The body fluids of the animal,
such as serum or ascites fluid, can then be tapped to provide MAbs
in high concentration. The individual cell lines could also be
cultured in vitro, where the MAbs are naturally secreted into the
culture medium from which they can be readily obtained in high
concentrations. MAbs produced by either means may be further
purified, if desired, using filtration, centrifugation and various
chromatographic methods such as HPLC or affinity
chromatography.
[0135] Following the isolation and characterization of the desired
monoclonal antibody, the mRNA can be isolated using techniques well
known in the art and used as a template for amplification of the
target sequence.
[0136] A number of template dependent processes are available to
amplify the target sequences before and after mutagenesis. For
example, one of the best known amplification methods is the
polymerase chain reaction (referred to as PCR) which is described
in detail in U.S. Pat. Nos. 4,683,195, 4,683,202 and 4,800,159, and
in Innis et al. (1990), each of which is incorporated herein by
reference in its entirety. Briefly, in PCR, two primer sequences
are prepared which are complementary to regions on opposite
complementary strands of the target sequence. An excess of
deoxynucleoside triphosphates are added to a reaction mixture along
with a DNA polymerase, e.g., Taq polymerase. If the target sequence
is present in a sample, the primers will bind to the target and the
polymerase will cause the primers to be extended along the target
sequence by adding on nucleotides. By raising and lowering the
temperature of the reaction mixture, the extended primers will
dissociate from the target to form reaction products, excess
primers will bind to the target and to the reaction products and
the process is repeated. Preferably a reverse transcriptase PCR
amplification procedure may be performed in order to quantify the
amount of target amplified. Polymerase chain reaction methodologies
are well known in the art. Using enzymatic amplification techniques
such as PCR, desired control elements may be designed into the
primer and thus, will be incorporated into the DNA product.
[0137] Many other amplification methods are known in the art.
[0138] One advantage to the solid phase method of gene synthesis is
the opportunity for mutagenesis using combinatorial synthesis
techniques. Combinatorial synthesis techniques are defined as those
techniques producing large collections or libraries of compounds
simultaneously, by sequentially linking different building blocks.
Libraries can be constructed using compounds free in solution, but
preferably the compound is linked to a solid support such as a
bead, solid particle or even displayed on the surface of a
microorganism.
[0139] Several methods exist for combinatorial synthesis (Holmes et
al., 1995; Burbaum et al., 1995; Martin et al., 1995; Freier et
al., 1995; Pei et al., 1991; Bruce et al., 1995; Ohlmeyer et al.,
1993), including split synthesis or parallel synthesis.
Alternatively, the technique known as parallel synthesis may be
conducted either in solid phase or solution. Using combinatorial
methods, a large number of mutant gene templates may be
synthesized.
[0140] Mutants genes also may be generated by semisynthetic methods
known in the art (Barbas et al., 1992). Using the conserved regions
of an antibody fragment as a framework, variable regions can be
inserted in random combinations one or more at a time to alter the
specificity of the antibody fragment and generate novel binding
sites, especially in the generation of antibodies to antigens not
conducive to immunization such as toxic or labile compounds. Along
the same lines, a known antibody sequence may be varied by
introducing mutations randomly or non-randomly.
[0141] Prokaryotic in vitro techniques for protein production were
the first to be used (Zubay et al., 1970). Subsequently eukaryotic
systems were developed using wheat germ (Roberts, 1973) and rabbit
reticulocytes (Pelham, 1976). Several new developments have
increased the efficiency of these techniques. Examples include, the
development of nuclease deficient strains of E. coli to improve the
results using linear DNA templates (Yang, 1980) and treatment of
reticulocyte lysates with micrococcal nuclease to lower any
background expression from the system.
[0142] The most recent systems developed for in vitro
transcription/translation are based on transcription by phage RNA
polymerases including SP6 and SP7 (Krieg, 1987, Studier, 1990). DNA
placed under the control of T7 promoter elements can be used as a
template for in vitro transcription by T7 RNA polymerase or for
complete in vitro transcription/translation with the polymerase
added to either a prokaryotic or eukaryotic protein synthesis
system. While the methods of the present invention can be used with
any in vitro transcription/translation system, the T7 system is
preferred for transcription and the use of a prokaryotic
translation system is preferred as no capping of the RNA is
required.
[0143] Using in vitro methods for translation, amino acid
derivatives may be incorporated into the protein by addition of the
derivatized amino acid to the protein synthesis system mixture.
Varying the concentration of the derivatives, with respect to the
normal amino acid, permits one to create a mixed population and
measure relative effects. G. Characterization
[0144] Mutant polypeptides generated by the present invention may
be characterized using a variety of techniques. In general, protein
products may be analyzed for the correct apparent molecular weight
using SDS-PAGE. This provides an initial indication that the
polypeptide was, in fact, synthesized. When compared to the natural
molecule, it also indicates whether normal folding or processing is
taking place with the mutant. In this regard, it may prove useful
to label the polypeptide. Alternatively, the polypeptide may be
identified by staining of the gel.
[0145] Beyond mere synthesis, proteins may be characterized
according to various properties and an extensive range of
functions. Properties include isoelectric point, thermal stability,
sedimentation rate and folding. One manner of examining folding is
the ability to be recognized by a cognate binding partner. The
prime example of this function is the antibody-antigen interaction.
A wide variety of different immunoassay formats are available for
this purpose and are well known in the art. Principally, changes in
either affinity or specificity can be determined when the protein
is contacted with a specific ligand or panels of related
ligands.
[0146] Immunoassays can be generally divided into two types:
heterogeneous assays requiring multiple separation steps, and
homogeneous assays which are performed directly. Heterogeneous
immunoassays in general involve a ligand or antibody immobilized on
a solid matrix. A sample containing a ligand is contacted with the
immobilized antibody and the amount of complex formed on the matrix
support is determined from a label attached directly or indirectly
to the immobilized complex. As used in the context of the present
invention, ligand is defined as a species that interacts with a
non-identical molecule to form a tightly bound, stable complex. For
practical purposes, the binding affinity is usually greater than
about 106 M.sup.-1 and is preferably in the range of
10.sup.9-10.sup.15 M.sup.-1. The ligand may be any of several types
of organic molecules, including alicyclic hydrocarbons, polynuclear
aromatics, halogenated compounds, benzenoids, polynuclear
hydrocarbons, nitrogen heterocyclics, sulfur heterocyclics, oxygen
heterocyclics, and alkane, alkene alkyne hydrocarbons, etc.
Biological molecules are of particular interest, including amino
acids, peptides, proteins, lipids, saccharides, nucleic acids and
combinations thereof. Of course it will be understood that these
are by way of example only and that contemplated immunoassay
methods are applicable to detecting an extraordinarily wide range
of compounds, so long as one can obtain an antibody that binds with
the ligand of interest.
[0147] Heterogeneous immunoassays may be performed as sandwich
assays in which a molecule of interest is reacted with an
immobilized antibody that specifically binds that molecule with
high affinity. In a second step, a conjugate formed from the same
or different antibody to the antigen and a marker molecule is
reacted with the antigen-antibody complex on the immobilization
matrix. After removal of excess free marker conjugate, the bound
marker conjugate, which is proportional to the amount of ligand in
the sample, is measured.
[0148] Detection of immunocomplex formation is well known in the
art and may be achieved through the application of numerous
approaches. These approaches are typically based upon the detection
of a label or marker, such as any of the radioactive, fluorescent,
chemiluminescent, electrochemiluminescent, biological or enzymatic
tags or labels known in the art. U.S. patents concerning the use of
such labels include U.S. Pat. Nos. 3,817,837; 3,850,752; 3,939,350;
3,996,345; 4,277,437; 4,275,149 and 4,366,241, each incorporated
herein by reference. Of course, one may find additional advantages
through the use of a secondary binding ligand such as a second
antibody or a biotin/avidin ligand binding arrangement, as is known
in the art.
[0149] Preferred methods for detection includes radioimmunoassay
(RIA) or enzyme-linked immunosorbent assay (ELISA) with ELISA being
most preferred due to generally increased sensitivity. ELISAs are
extensively used in biotechnology applications, particularly as
immunoassays for a wide range of antigenic substances. The
sensitivity of ELISA is based on the enzymatic amplification of the
signal
[0150] Other preferred proteins contemplated for use in accordance
with the present invention are those which have a convenient assay
for activity. Representative examples of target interactions
include catalysis, enzyme-substrate interactions, protein-nucleic
acid interactions, receptor-ligand interactions and protein-metal
interactions. In these assays the mutant proteins can be compared
with the wild-type protein for changes in the ability to perform
any of the foregoing functions.
[0151] As used herein, the term "contacting" is defined as bringing
the reaction components into close enough proximity to each other
to allow the desired interaction to occur. Contacting may be
accomplished by mixing the components in solution, for example, or
by heterogeneous interaction such as by flow contact through a
column or immobilizing matrix that binds to one of the
components.
[0152] For mutant proteins having a catalytic activity, the
appropriate reaction may be monitored for a change in catalytic
rate or an alteration in specificity.
[0153] DNA expression constructs will typically include an
expression control DNA sequence operably linked to the coding
sequences, including naturally-associated or heterologous promoter
regions. Preferably, the expression control sequences will be
eukaryotic promoter systems in vectors capable of transforming or
transfecting eukaryotic host cells. Once the vector has been
incorporated into the appropriate host, the host is maintained
under conditions suitable for high level expression of the
nucleotide sequences, and the collection and purification of the
mutant "engineered" antibodies.
[0154] DNA sequences will be expressed in hosts after the sequences
have been operably linked to an expression control sequence (i.e.,
positioned to ensure the transcription and translation of the
structural gene). These expression vectors are typically replicable
in the host organisms either as episomes or as an integral part of
the host chromosomal DNA. Commonly, expression vectors will contain
selection markers, e.g., tetracycline or neomycin, to permit
detection of those cells transformed with the desired DNA sequences
(see, e.g., U.S. Pat. No. 4,704,362, which is incorporated herein
by reference).
[0155] In addition to eukaryotic microorganisms such as yeast,
mammalian tissue cell culture may also be used to produce the
polypeptides of the present invention (see, Winnacker, "From Genes
to Clones," VCH Publishers, N.Y., N.Y. (1987), which is
incorporated herein by reference). Eukaryotic cells are preferred,
because a number of suitable host cell lines capable of secreting
intact immunoglobulins have been developed in the art, and include
the CHO cell lines, various COS cell lines, HeLa cells, myeloma
cell lines, etc, but preferably transformed B-cells or hybridomas.
Expression vectors for these cells can include expression control
sequences, such as an origin of replication, a promoter, an
enhancer (Queen et al. (1986) Immunol. Rev. 89: 49), and necessary
processing information sites, such as ribosome binding sites, RNA
splice sites, polyadenylation sites, and transcriptional terminator
sequences. Preferred expression control sequences are promoters
derived from immunoglobulin genes, cytomegalovirus, SV40,
Adenovirus, Bovine Papilloma Virus, and the like.
[0156] Eukaryotic DNA transcription can be increased by inserting
an enhancer sequence into the vector. Enhancers are cis-acting
sequences of between 10 to 30 obp that increase transcription by a
promoter. Enhancers can effectively increase transcription when
either 5' or 3' to the transcription unit. They are also effective
if located within an intron or within the coding sequence itself.
Typically, viral enhancers are used, including SV40 enhancers,
cytomegalovirus enhancers, polyoma enhancers, and adenovirus
enhancers. Enhancer sequences from mammalian systems are also
commonly used, such as the mouse immunoglobulin heavy chain
enhancer.
[0157] Mammalian expression vector systems will also typically
include a selectable marker gene. Examples of suitable markers
include, the dihydrofolate reductase gene (DHFR), the thymidine
kinase gene (TK), or prokaryotic genes conferring drug resistance.
The first two marker 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.
[0158] The vectors containing the DNA segments of interest can be
transferred into the host cell by well-known methods, depending on
the type of cellular host. For example, calcium chloride
transfection is commonly utilized for prokaryotic cells, whereas
calcium phosphate treatment. lipofection, or electroporation may be
used for other cellular hosts. Other methods used to transform
mammalian cells include the use of Polybrene, protoplast fusion,
liposomes, electroporation, and microinjection (see, generally,
Sambrook et al., supra).
[0159] Once expressed, the antibodies, individual mutated
immunoglobulin chains, mutated antibody fragments, and other
immunoglobulin polypeptides of the invention can be purified
according to standard procedures of the art, including ammonium
sulfate precipitation, fraction column chromatography, gel
electrophoresis and the like (see, generally, Scopes, R., Protein
Purification, Springer-Verlag, N.Y. (1982)). Once purified,
partially or to homogeneity as desired, the polypeptides may then
be used therapeutically or in developing and performing assay
procedures, immunofluorescent stainings, and the like (see,
generally, Immunological Methods, Vols. I and II, Eds. Lefkovits
and Pernis, Academic Press, N.Y. N.Y. (1979 and 1981)).
[0160] Once the template peptide has been mapped, a variety of
techniques can be used to diversity the template or members of the
peptide library to construct ligands with improved properties.
Oligonucleotides can be synthesized based on these peptide
sequences, employing all bases at each step at concentrations
designed to produce slight variations of the primary
oligonucleotide sequences. This mixture of (slightly) degenerate
oligonucleotides is then cloned into the random peptide library
expression vector as described herein. This method produces
systematic, controlled variations of the starting peptide sequences
but requires, however, that individual positive vectors be
sequenced before mutagenesis. This method is useful for expanding
the diversity of small numbers of recovered vectors.
[0161] Yet another approach for diversifying a selected random
peptide vector involves the mutagenesis of a pool, or subset, of
recovered vectors. Recombinant host cells transformed with vectors
recovered from panning are pooled and isolated. The vector DNA is
mutagenized by treating the cells with, e.g., nitrous acid, formic
acid, hydrazine, or by use of a mutator strain as described below.
These treatments produce a variety of mutations in the vector DNA.
The segment containing the sequence encoding the variable peptide
can optionally be isolated by cutting with restriction nuclease(s)
specific for sites flanking the variable region and then recloned
into undamaged vector DNA. Alternatively, the mutagenized vectors
can be used without recloning of the mutagenized random peptide
coding sequence.
[0162] In the second general approach for diversifying a set of
peptide ligands, that of adding additional amino acids to a peptide
or peptides found to be active, a variety of methods are available.
In one, the sequences of peptides selected in early panning are
determined individually and near oligonucleotides, incorporating
all or part of the determined sequence and an adjoining degenerate
sequence, are synthesized. These are then cloned to produce a
secondary library.
[0163] Unless modified during or after synthesis by the translation
machinery, recombinant peptide libraries consist of sequences of
the 20 normal L-amino acids. While the available structural
diversity for such a library is large, additional diversity can be
introduced by a variety of means, such as chemical modifications of
the amino acids. For example, as one source of added diversity a
peptide library of the invention can be subjected to carboxy
terminal amidation. Carboxy terminal amidation is necessary to the
activity of many naturally occurring bioactive peptides. This
modification occurs in vivo through cleavage of the N--C bond of a
carboxy terminal Gly residue in a two-step reaction catalyzed by
the enzymes peptidylglycine alpha-amidation monooxygenase (PAM) and
hydroxyglycine aminotransferase (HGAT). See Eipper et al., J. Biol.
Chem. 266, 7827-7833 (1991); Mizuno et al., Biochem. Biophys. Res.
Comm. 137(3), 984-991 (1986); Murthy et al., J. Biol. Chem. 261(4),
1815-1822 (1986); Katopodis et al., Biochemistry 29, 6115-6120
(1990); and Young and Tamburini, J. Am. Chem. Soc. 111, 1933-1934
(1989), each of which are incorporated herein by reference.
[0164] Amidation can be performed by treatment with enzymes, such
as PAM and HGAT, in vivo or in vitro, and under conditions
conducive to maintaining the structural integrity of the fusion
protein/vector complex. In a random peptide library of the present
invention, amidation will occur on a library subset, i.e., those
peptides having a carboxy terminal Gly. A library of peptides
designed for amidation can be constructed by introducing a Gly
codon at the end of the variable region domain of the library.
After amidation, an enriched library serves as a particularly
efficient source of ligands for receptors that preferentially bind
amidated peptides.
[0165] Other modifications found in naturally occurring peptides
and proteins can be introduced into the libraries to provide
additional diversity and to contribute to a desired biological
activity. For example, the variable region library can be provided
with codons that code for amino acid residues involved in
phosphorylation, glycosylation, sulfation, isoprenylation (or the
addition of other lipids), etc. Modifications not catalyzed by
naturally occurring enzymes can be introduced by chemical means
(under relatively mild conditions) or through the action of, e.g.,
catalytic antibodies and the like. In most cases, an efficient
strategy for library construction involves specifying the enzyme
(or chemical) substrate recognition site within or adjacent to the
variable nucleotide region of the library so that most members of
the library are modified. The substrate recognition site added can
be simply a single residue (e.g., serine for phosphorylation) or a
complex consensus sequence, as desired.
[0166] One disadvantage of generating, producing or manufacturing
bispecific antibodies using traditional technologies is that in
general, expression of 2 antibodies in a single cell leads to the
formation of 10 possible LC/HC antibody combinations (with 2 heavy
and 2 light chains per antibody), only one of which is the desired
bispecific product; thus, the desired bispecific product is only a
small fraction of the mixture and purification of the bispecific
antibody if very difficult on a commercial scale. For example, if
the first antibody (antibody 1) has a left LC (1-LC1) and a left HC
(1-HC1) and a right LC (r-LC1) and a right HC (r-HC1), and the
second antibody (antibody 2) has a left LC (1-LC2) and a left HC
(1-HC2) and a right LC (r-LC2) and a right HC (r-HC2), expression
of antibody 1 and antibody 2 in a single cell leads to the
formation of the following possible LC/HC combinations: (1)
1-LC1/1-HC1 with r-LC1/r-HC1; (2) 1-LC1/1-HC1 with r-LC2/r-HC1; (3)
1-LC1/1-HC1 with r-LC1/r-HC2; (4) 1-LC2/1-HC1 with r-LC2/r-HC1; (5)
1-LC2/1-HC2 with r-LC2/r-HC2; (6) 1-LC2/1-HC2 with r-HC2/r-LC1; (7)
1-LC2/1-HC1 with r-HC2/r-LC2; (8) 1-LC1/1-HC2 with r-HC2/r-LC1; (9)
1-LC2/1-HC1 with r-LC2/r-HC2; (10) 1-LC1/1-HC1 with r-LC2/r-HC2.
Only one of the combinations binds to both antigens (1-LC1/1-HC1
with r-LC2/r-HC2). Further, the binding affinity and specificity of
unwanted LC/HC pairings is unknown. Modifications to the heavy
chain CH3 domain (such as knob-in-hole designs) can eliminate the
formation of heavy chain homo-dimers, and reduce the number of
possible LC/HC antibody combinations produced down to 4 different
products (coexpression of 2 different light chains with the one
heavy chain pair). For example, in the knob-in-hole design, the 4
different products would be: (1) 1-LC1/1-HC1 with r-LC2/r-HC2; (2)
1-LC1/1-HC1 with r-LC1/r-HC2; (3) 1-LC2/1-HC1 with r-LC1/r-HC2; (4)
1-LC2/1-HC1 with r-LC2/r-HC2.
[0167] The H2L multispecific antibodies of the present invention
overcome these production/manufacturing difficulties. The H2L
antibodies of the present invention have optimized variable domains
which allow the same light chain to assemble with each of the 2
heavy chains without changing the binding specificity for the
particular antigen. The light chain assembles with heavy chain 1 to
form a Fab-arm which binds to antigen 1. The light chain can also
assemble with heavy chain 2 to form a Fab arm which binds to
antigen 2. The Fc part of the heavy chains is modified in a way
that allows only the formation of the HC1-HC2 dimer in vivo (e.g.
facilitated by, for example, a "knob in hole" design). Expression
of 2 heavy chains which form only hetero-dimers and a single light
chains leads to the formation of only a single product, the H2L
multispecific antibody of the present invention. Each molecule
produced has one Fab arm binding to antigen 1 and the other Fab arm
binding to antigen 2. H2L mAbs. The single light chain has been
optimized in accordance with the methods of the present invention
to be able to assemble with both heavy chains and form functional
Fab-arms binding to either antigen 1 or antigen 2. H2L antibodies
of the present invention can be manufactured and purified just like
regular IgGs, processes well known in the art.
[0168] Construction of H2L mAbs
[0169] Starting parent antibodies can be known binders (LC1/HC1
pairs comprising antibody 1, and LC2/HC2 pairs comprising antibody
2, for example) to different antigens (antibody 1 binds antigen 1
and antibody 2 binds antigen 2, for example), and can be non-human,
humanized, or fully human antibodies.
[0170] In a first step, the 2 different light chains of both
antibodies (LC1 and LC2) are replaced by a single light chain
(new-LC). This process can begin with a library of light chains.
Libraries of potential new light chains (new-LC) of the present
invention can be generated in several ways. For example, all
functional human germline kappa light chain (Vk) variable regions
are published and can be obtained from publicly available
databases. Variable genes can be selected for library construction.
Light chain variable genes can be amplified from human genomic DNA
using gene specific primers. In the event genes are amplified in
pieces, partial genes can be combined by overlap PCR, as published.
Rearranged kappa and lambda light chains can also be amplified from
human cDNA (derived, for example, from PBMCs from a pool of
non-immunized donors) using forward primers specific for the 5' end
of the light chain secretion signals and reverse primer specific
for the 3' end of the kappa or lambda constant domain. LC libraries
can also be generated by taking LC from each known parent antibody
(LC1 and LC2) and evolving one (or both) in accordance with
evolution methods described herein, or other methods, to generate a
population or library of LCs (LC1 library and LC2 library).
[0171] In one method of the present invention, the HC of antibody 1
(HC1) is co-expressed with the human LC1 library, for example a LC1
library generated as described herein, and this HC1-LC1 library is
then screened for binders, or hits, to antigen 1, followed by
isolation of the light chains of the binders, or hits. The HC2 of
antibody 2 (HC2) is co-expressed with the human LC2 library, for
example a LC1 library generated as described herein, and this
HC2-LC2 library is screened for binders, or hits, to antigen 2,
followed by isolation of the light chains of the binders, or hits.
Screening can be done be FACS (if the LC/HC combinations are
expressed on the cell surface, for example) or by ELISA (using
secreted or cell surface bound libraries).
[0172] Isolated light chains of identified hits in the HC1-LC1
library are co-expressed with the heavy chain from antibody 2 (HC2)
and this HC2-LC1 library is screened for binders, or hits, to
antigen 2. Isolated light chains of identified hits in the HC2-LC2
library are also isolated, co-expressed with the heavy chain from
antibody 1 (HC1), and screened for binders, or hits, to antigen 1.
This process identifies a population of clones containing light
chains that can functionally complement both HC1 and HC2. These
clones, containing light chains that can functionally complement
both HC1 and HC2, are further characterized (e.g. by competition
ELISA with wild type antigen 1 or antigen 2) to verify the
conservation of the binding specificity of each clone to either
antigen 1 and/or antigen 2, and the same epitope on antigen 1
and/or antigen 2 as the respective parental molecules (antibody 1
and/or antibody 2). Light chains of these clones can be also
re-tested with both HC1 and HC2 to confirm that they retain
capability of functionally complementing both HC1 and HC2.
[0173] The new light chain(s) identified can further be evolved
(e.g. by evolution methods described herein), to improve affinity
in order to match or surpass the binding affinities of the parental
molecules, or to modify other characteristics such as
thermostability, specificity, binding affinity and/or other
characteristics.
[0174] The HC1 variable domain is cloned in frame with a modified
IgG constant domain which has been modified, for example with
knob-in-hole technology as described herein, such that it can no
longer assemble with itself to form HC1 homo-dimers. In parallel,
the HC2 variable domain is cloned in frame with a modified IgG
constant domain which has been modified, for example with
knob-in-hole technology as described herein, such that it can no
longer assemble with itself to form HC2 homo-dimers. Modifications
in HC1 and HC2 eliminate the formation of homo-dimers, but are
designed to allow for the formation of HC1-HC2 heterodimers.
Knob-in-hole technology is described in detail in Ridgway J B,
Presta L G, Carter P (1996) `Knobs-into-holes` engineering of
antibody CH3 domains for heavy chain heterodimerization. Protein
Eng 9:617-621. In the knob-in-hole technology, large amino acid
side chains are introduced into the CH3 domain of a heavy chain
that fit into an appropriately designed cavity in the CH3 domain of
the other heavy chain.
[0175] In the present invention, expression of an optimized light
chain (which functionally complements both heavy chains) together
with HC1 and HC2 in the same cell leads to the direct assembly of a
bi-specific antibody.
[0176] If the staring parent antibody single antibody, the parental
antibody HC variable domain is evolved (by any evolution method,
such as those described herein) to bind to a second (or more)
target. One of the new, evolved HCs can be then combined with one
of the original HCs from the parent antibody, and an original LC
from the parent antibody to form an H2L antibody of the present
invention.
[0177] The full length IgGs can also be converted into smaller
fragments (e.g. skipping CH2 or making F(ab')2) for certain
applications where high tissue penetration and/or shorter half life
is important.
[0178] In another aspect, the invention relates to multi-functional
antibodies and antigen-binding fragments, as described herein,
which are modified by the covalent attachment of an organic moiety.
Such modification can produce an antibody or antigen-binding
fragment with improved pharmacokinetic properties (e.g., increased
in vivo serum half-life). The organic moiety can be a linear or
branched hydrophilic polymeric group, fatty acid group, or fatty
acid ester group. In particular embodiments, the hydrophilic
polymeric group can have a molecular weight of about 800 to about
120,000 Daltons and can be a polyalkane glycol (e.g., polyethylene
glycol (PEG), polypropylene glycol (PPG)), carbohydrate polymer,
amino acid polymer or polyvinyl pyrolidone, and the fatty acid or
fatty acid ester group can comprise from about eight to about forty
carbon atoms.
[0179] The modified multi-functional antibodies and antigen-binding
fragments of the invention can comprise one or more organic
moieties that are covalently bonded, directly or indirectly, to the
antibody. Each organic moiety that is bonded to an antibody or
antigen-binding fragment of the invention can independently be a
hydrophilic polymeric group, a fatty acid group or a fatty acid
ester group. As used herein, the term "fatty acid" encompasses
mono-carboxylic acids and di-carboxylic acids. A "hydrophilic
polymeric group," as the term is used herein, refers to an organic
polymer that is more soluble in water than in octane. For example,
polylysine is more soluble in water than in octane. Thus, an
antibody modified by the covalent attachment of polylysine is
encompassed by the invention. Hydrophilic polymers suitable for
modifying antibodies of the invention can be linear or branched and
include, for example, polyalkane glycols (e.g., PEG,
monomethoxy-polyethylene glycol (mPEG), PPG and the like),
carbohydrates (e.g., dextran, cellulose, oligosaccharides,
polysaccharides and the like), polymers of hydrophilic amino acids
(e.g., polylysine, polyarginine, polyaspartate and the like),
polyalkane oxides (e.g., polyethylene oxide, polypropylene oxide
and the like) and polyvinyl pyrolidone. Preferably, the hydrophilic
polymer that modifies the antibody of the invention has a molecular
weight of about 800 to about 150,000 Daltons as a separate
molecular entity. For example PEG.sub.5000 and PEG.sub.20,000,
wherein the subscript is the average molecular weight of the
polymer in Daltons, can be used. The hydrophilic polymeric group
can be substituted with one to about six alkyl, fatty acid or fatty
acid ester groups. Hydrophilic polymers that are substituted with a
fatty acid or fatty acid ester group can be prepared by employing
suitable methods. For example, a polymer comprising an amine group
can be coupled to a carboxylate of the fatty acid or fatty acid
ester, and an activated carboxylate (e.g., activated with
N,N-carbonyl diimidazole) on a fatty acid or fatty acid ester can
be coupled to a hydroxyl group on a polymer.
[0180] Fatty acids and fatty acid esters suitable for modifying
multi-functional antibodies of the invention can be saturated or
can contain one or more units of unsaturation. Fatty acids that are
suitable for modifying antibodies of the invention include, for
example, n-dodecanoate (C.sub.12, laurate), n-tetradecanoate
(C.sub.14, myristate), n-octadecanoate (C.sub.18, stearate),
n-eicosanoate (C.sub.20, arachidate), n-docosanoate (C.sub.22,
behenate), n-triacontanoate (C.sub.30), n-tetracontanoate
(C.sub.40), cis-.delta. 9-octadecanoate (C.sub.18, oleate), all
cis-.delta. 5,8,11,14-eicosatetraenoate (C.sub.20, arachidonate),
octanedioic acid, tetradecanedioic acid, octadecanedioic acid,
docosanedioic acid, and the like. Suitable fatty acid esters
include mono-esters of dicarboxylic acids that comprise a linear or
branched lower alkyl group. The lower alkyl group can comprise from
one to about twelve, preferably one to about six, carbon atoms.
[0181] The modified multi-functional antibodies and antigen-binding
fragments can be prepared using suitable methods, such as by
reaction with one or more modifying agents. A "modifying agent" as
the term is used herein, refers to a suitable organic group (e.g.,
hydrophilic polymer, a fatty acid, a fatty acid ester) that
comprises an activating group. An "activating group" is a chemical
moiety or functional group that can, under appropriate conditions,
react with a second chemical group thereby forming a covalent bond
between the modifying agent and the second chemical group. For
example, amine-reactive activating groups include electrophilic
groups such as tosylate, mesylate, halo (chloro, bromo, fluoro,
iodo), N-hydroxysuccinimidyl esters (NHS), and the like. Activating
groups that can react with thiols include, for example, maleimide,
iodoacetyl, acrylolyl, pyridyl disulfides, 5-thiol-2-nitrobenzoic
acid thiol (TNB-thiol), and the like. An aldehyde functional group
can be coupled to amine- or hydrazide-containing molecules, and an
azide group can react with a trivalent phosphorous group to form
phosphoramidate or phosphorimide linkages. Suitable methods to
introduce activating groups into molecules are known in the art
(see for example, Hernanson, G. T., Bioconjugate Techniques,
Academic Press: San Diego, Calif. (1996)). An activating group can
be bonded directly to the organic group (e.g., hydrophilic polymer,
fatty acid, fatty acid ester), or through a linker moiety, for
example a divalent C.sub.1-C.sub.12 group wherein one or more
carbon atoms can be replaced by a heteroatom such as oxygen,
nitrogen or sulfur. Suitable linker moieties include, for example,
tetraethylene glycol, --(CH.sub.2).sub.3--,
--NH--(CH.sub.2).sub.6--NH--, --(CH.sub.2).sub.2--NH-- and
--CH.sub.2--O--CH.sub.2--CH.sub.2--O--CH.sub.2--CH.sub.2--O--CH--NH--.
Modifying agents that comprise a linker moiety can be produced, for
example, by reacting a mono-Boc-alkyldiamine (e.g.,
mono-Boc-ethylenediamine, mono-Boc-diaminohexane) with a fatty acid
in the presence of 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide
(EDC) to form an amide bond between the free amine and the fatty
acid carboxylate. The Boc protecting group can be removed from the
product by treatment with trifluoroacetic acid (TFA) to expose a
primary amine that can be coupled to another carboxylate as
described, or can be reacted with maleic anhydride and the
resulting product cyclized to produce an activated maleimido
derivative of the fatty acid. (See, for example, Thompson, et al.,
WO 92/16221 the entire teachings of which are incorporated herein
by reference.)
[0182] The modified multi-functional antibodies of the invention
can be produced by reacting a multi-functional antibody or
antigen-binding fragment with a modifying agent. For example, the
organic moieties can be bonded to the antibody in a non-site
specific manner by employing an amine-reactive modifying agent, for
example, an NHS ester of PEG. Modified multi-functional antibodies
or antigen-binding fragments can also be prepared by reducing
disulfide bonds (e.g., intra-chain disulfide bonds) of an antibody
or antigen-binding fragment. The reduced antibody or
antigen-binding fragment can then be reacted with a thiol-reactive
modifying agent to produce the modified multi-functional antibody
of the invention. Modified multi-functional antibodies and
antigen-binding fragments comprising an organic moiety that is
bonded to specific sites of a multi-functional antibody of the
present invention can be prepared using suitable methods, such as
reverse proteolysis (Fisch et al., Bioconjugate Chem., 3:147-153
(1992); Werlen et al., Bioconjugate Chem., 5:411-417 (1994);
Kumaran et al., Protein Sci. 6(10):2233-2241 (1997); Itoh et al.,
Bioorg. Chem., 24(1): 59-68 (1996); Capellas et al., Biotechnol.
Bioeng., 56(4):456-463 (1997)), and the methods described in
Hermanson, G. T., Bioconjugate Techniques, Academic Press: San
Diego, Calif. (1996).
[0183] The multi-functional antibodies of the present invention can
be used for diagnosis and therapy. By way of illustration and not
limitation, multi-functional antibodies can be used to treat
cancer, autoimmune diseases, or viral infections. For treatment of
cancer, the multi-functional antibodies will typically bind to an
antigen expressed preferentially on cancer cells, such as erbB-2,
CEA, CD33, and many other antigens well known to those skilled in
the art. For treatment of autoimmune disease, the antibodies will
typically bind to an antigen expressed on T-cells, such as CD4, the
IL-2 receptor, the various T-cell antigen receptors and many other
antigens well known to those skilled in the art (e.g., see
Fundamental Immunology, 2nd ed., W. E. Paul, ed., Raven Press: New
York, N.Y., which is incorporated herein by reference). For
treatment of viral infections, the antibodies will typically bind
to an antigen expressed on cells infected by a particular virus
such as the various glycoproteins (e.g., gB, gD, gE) of herpes
simplex virus and cytomegalovirus, and many other antigens well
known to those skilled in the art (e.g., see Virology, 2nd ed., B.
N. Fields et al., eds., (1990), Raven Press: New York, N.Y.).
[0184] The multi-functional antibodies of the present invention can
be used to treat diseases of the central nervous system. Bispecific
antibodies have been described that cross the blood brain barrier
and bind brain proteins, potentially for therapy (Yu Y J, et al,
"Boosting brain uptake of a therapeutic antibody by reducing its
affinity for a transcytosis target", Sci Transl Med 2011 May 25;
3(84):84ra44; incorporated herein by reference). The methods of the
present invention are particularly useful for making such
antibodies.
[0185] The methods of the present invention can be used to create
conditionally active proteins as described in pending patent
application PCT/US10/26611, entitled "Mirac Proteins", and
incorporated herein by reference. Conditionally active proteins are
biologic proteins, in particular therapeutic proteins, and which
are reversibly or irreversibly inactivated at wild type, normal
physiological conditions. For example, conditionally active
proteins are virtually inactive at body temperature, but are active
at lower temperatures. Conditionally active proteins are
potentially useful for treating a variety of diseases, as
described. In the methods of the present invention, multi-specific
antibodies are identified that are conditionally active proteins.
These multi-specific antibodies that are conditionally active can
further be modified with organic moieties, creating conjugated,
conditionally active, multi-specific antibodies.
[0186] Pharmaceutical compositions comprising antibodies of the
present invention are useful for parenteral administration, i.e.,
subcutaneously, intramuscularly or intravenously. The compositions
for parenteral administration will commonly comprise a solution of
the antibody or a cocktail thereof dissolved in an acceptable
carrier, preferably an aqueous carrier. A variety of aqueous
carriers can be used, e.g., water, buffered water, 0.4% saline,
0.3% glycine and the like. These solutions are sterile and
generally free of particulate matter. These compositions may be
sterilized by conventional, well known sterilization techniques.
The compositions may contain pharmaceutically acceptable auxiliary
substances as required to approximate physiological conditions such
as pH adjusting and buffering agents, toxicity adjusting agents and
the like, for example sodium acetate, sodium chloride, potassium
chloride, calcium chloride, sodium lactate, etc. The concentration
of the mutant antibodies in these formulations can vary widely,
i.e., from less than about 0.01%, usually at least about 0.1% to as
much as 5% by weight and will be selected primarily based on fluid
volumes, viscosities, etc., in accordance with the particular mode
of administration selected.
[0187] Thus, a typical pharmaceutical composition for intramuscular
injection could be made up to contain 1 ml sterile buffered water,
and about 1 mg of mutant antibody. A typical composition for
intravenous infusion can be made up to contain 250 ml of sterile
Ringer's solution, and 10 mg of mutant antibody. Actual methods for
preparing parenterally administrable compositions will be known or
apparent to those skilled in the art and are described in more
detail in, for example, Remington's Pharmaceutical Science, 20th
Ed., Mack Publishing Company, Easton, Pa. (2000), which is
incorporated herein by reference.
[0188] The benefits of this invention extend to "industrial
applications" (or industrial processes), which term is used to
include applications in commercial industry proper (or simply
industry) as well as non-commercial industrial applications (e.g.
biomedical research at a non-profit institution). Relevant
applications include those in areas of diagnosis, medicine,
agriculture, manufacturing, and academia.
[0189] All documents, including but not limited to publications,
patents and patent applications, cited herein are herein
incorporated by reference, including U.S. Pat. No. 6,171,820 and
U.S. Pat. No. 5,677,149.
[0190] Without further elaboration, it is believed that one skilled
in the art can, using the preceding description, utilize the
present invention to its fullest extent. The following examples are
to be considered illustrative and thus are not limiting of the
remainder of the disclosure in any way whatsoever.
Sequence CWU 1
1
115PRTArtificialSynthetic sequence used as a linker between a VH
domain and a VL domain in a single-chain antibody. This linker may
be repeated two or more times. 1Gly Gly Gly Gly Ser 1 5
* * * * *