U.S. patent application number 10/188801 was filed with the patent office on 2003-02-13 for method of generating chemical compounds having desired properties.
Invention is credited to Agrafiotis, Dimitris K., Bone, Roger F., Salemme, Francis R., Soll, Richard M..
Application Number | 20030033088 10/188801 |
Document ID | / |
Family ID | 23187448 |
Filed Date | 2003-02-13 |
United States Patent
Application |
20030033088 |
Kind Code |
A1 |
Agrafiotis, Dimitris K. ; et
al. |
February 13, 2003 |
Method of generating chemical compounds having desired
properties
Abstract
A computer based, iterative process for generating chemical
entities with defined physical, chemical and/or bioactive
properties. During each iteration of the process, (1) a directed
diversity chemical library is robotically generated in accordance
with robotic synthesis instructions; (2) the compounds in the
directed diversity chemical library are analyzed to identify
compounds with the desired properties; (3) structure-property data
are used to select compounds to be synthesized in the next
iteration; and (4) new robotic synthesis instructions are
automatically generated to control the synthesis of the directed
diversity chemical library for the next iteration.
Inventors: |
Agrafiotis, Dimitris K.;
(Exton, PA) ; Bone, Roger F.; (Bridgewater,
NJ) ; Salemme, Francis R.; (Kennett Square, PA)
; Soll, Richard M.; (Lawrenceville, NJ) |
Correspondence
Address: |
STERNE, KESSLER, GOLDSTEIN & FOX PLLC
1100 NEW YORK AVENUE, N.W., SUITE 600
WASHINGTON
DC
20005-3934
US
|
Family ID: |
23187448 |
Appl. No.: |
10/188801 |
Filed: |
July 5, 2002 |
Related U.S. Patent Documents
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Application
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Patent Number |
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10188801 |
Jul 5, 2002 |
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09213156 |
Dec 17, 1998 |
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6434490 |
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09213156 |
Dec 17, 1998 |
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08904737 |
Aug 1, 1997 |
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5901069 |
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08904737 |
Aug 1, 1997 |
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08698246 |
Aug 15, 1996 |
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5684711 |
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08698246 |
Aug 15, 1996 |
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08535822 |
Sep 28, 1995 |
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5574656 |
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08535822 |
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08306915 |
Sep 16, 1994 |
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5463564 |
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Current U.S.
Class: |
506/5 ; 435/7.1;
436/518; 702/19; 702/22 |
Current CPC
Class: |
G16B 35/00 20190201;
C40B 50/08 20130101; B01J 2219/007 20130101; G16C 20/10 20190201;
B01J 2219/00599 20130101; B01J 2219/0059 20130101; G16C 20/70
20190201; B01J 2219/0072 20130101; B01J 2219/00698 20130101; C40B
40/10 20130101; B01J 2219/00725 20130101; C07K 1/047 20130101; G16B
15/30 20190201; G16C 20/60 20190201; B01J 2219/00596 20130101; G16C
20/30 20190201; B01J 2219/00695 20130101; G16C 20/62 20190201; A61P
7/02 20180101; B01J 2219/00689 20130101; B01J 2219/00592 20130101;
Y10T 436/11 20150115; B01J 19/0046 20130101; B01J 2219/00691
20130101 |
Class at
Publication: |
702/19 ; 435/7.1;
436/518; 702/22 |
International
Class: |
G01N 033/53; G06F
019/00; G01N 033/48; G01N 033/50; G01N 031/00; G01N 033/543 |
Claims
What is claimed is:
1. A computer based method of automatically generating compounds
having a prescribed set of properties, comprising the steps of: (1)
robotically synthesizing, in accordance with robotic synthesis
instructions, a directed diversity chemical library comprising a
plurality of chemical compounds; (2) robotically analyzing said
chemical compounds to obtain structure-activity data pertaining
thereto; (3) comparing, under computer control, said
structure-activity data of said chemical compounds against said
prescribed set of properties to identify any of said chemical
compounds substantially conforming to said prescribed set of
properties; (4) classifying, under computer control, said
identified chemical compounds as lead compounds; (5) analyzing,
under computer control, said structure-activity data of said
compounds and historical structure-activity data pertaining to
compounds synthesized and analyzed in the past to derive
structure-activity models having enhanced predictive and
discriminating capabilities; (6) identifying, under computer
control and in accordance with said structure-activity models,
reagents from a reagent database that, when combined, will produce
a set of compounds predicted to exhibit activity/properties more
closely matching said prescribed set of properties; (7) generating,
under computer control, robotic synthesis instructions that, when
executed, enable robotic synthesis of said set of compounds; and
(8) repeating steps (1)-(7), wherein step (1) is repeated using
said generated robotic synthesis instructions.
2. The method of claim 1, wherein step (6) comprises the step of:
identifying, under computer control and in accordance with said
structure-activity models, reagents from a reagent database that,
when combined, will produce a second set of compounds predicted to
have a superior ability to validate said structure-activity models,
wherein said first and second sets of compounds are not mutually
exclusive; wherein step (7) comprises the step of generating, under
computer control, robotic synthesis instructions that, when
executed, enable robotic synthesis of said second set of
compounds.
3. The method of claim 1, wherein step (6) comprises the step of:
identifying, under computer control and in accordance with said
structure-activity models, reagents from a reagent database that,
when combined, will produce a second set of compounds predicted to
have a superior ability to discriminate between said
structure-activity; models, wherein said first and second sets of
compounds are not mutually exclusive; wherein step (7) comprises
the step of generating, under computer control, robotic synthesis
instructions that, when executed, enable robotic synthesis of said
second set of compounds.
4. The method of claim 1, wherein step (6) comprises the step of:
identifying, under computer control and in accordance with said
structure-activity models, reagents from a reagent database that,
when combined, will produce a second set of compounds predicted to
have a superior ability to validate said structure-activity models,
and a third set of compounds predicted to have a superior ability
to discriminate between said structure-activity models, wherein
said first, second, and third sets of compounds are not mutually
exclusive; wherein step (7) comprises the step of generating, under
computer control, robotic synthesis instructions that, when
executed, enable robotic synthesis of said second and third set of
compounds.
5. The method of claim 1, wherein step (6) comprises the step of:
identifying, under computer control and in accordance with said
structure-activity models, reagents from a reagent database that,
when combined, will produce a second set of compounds predicted to
have superior three-dimensional receptor fit, wherein said first
and second sets of compounds are not mutually exclusive; wherein
step (7) comprises the step of generating, under computer control,
robotic synthesis instructions that, when executed, enable robotic
synthesis of said second set of compounds.
Description
BACKGROUND OF THE INVENTION
[0001] 1. Field of the Invention
[0002] The present invention relates generally to the generation of
chemical entities with defined physical, chemical or bioactive
properties, and particularly to the automatic generation of drug
leads via computer-based, iterative robotic synthesis and analysis
of directed diversity chemical libraries.
[0003] 2. Related Art
[0004] Conventionally, new chemical entities with useful properties
are generated by identifying a chemical compound (called a "lead
compound") with some desirable property or activity, creating
variants of the lead compound, and evaluating the property and
activity of those variant compounds. Examples of chemical entities
with useful properties include paints, finishes, plasticizers,
surfactants, scents, flavorings, and bioactive compounds, but can
also include chemical compounds with any other useful property that
depends upon chemical structure, composition, or physical state.
Chemical entities with desirable biological activities include
drugs, herbicides, pesticides, veterinary products, etc. There are
a number of flaws with this conventional approach to lead
generation, particularly as it pertains to the discovery of
bioactive compounds.
[0005] One deficiency pertains to the first step of the
conventional approach, i.e., the identification of lead compounds.
Traditionally, the search for lead compounds has been limited to an
analysis of compound banks, for example, available commercial,
custom, or natural products chemical libraries. Consequently, a
fundamental limitation of the conventional approach is the
dependence upon the availability, size, and structural diversity of
these chemical libraries. Although chemical libraries cumulatively
total an estimated 9 million identified compounds, they reflect
only a small sampling of all possible organic compounds with
molecular weights less than 1200. Moreover, only a small subset of
these libraries is usually accessible for biological testing. Thus,
the conventional approach is limited by the relatively small pool
of previously identified chemical compounds which may be screened
to identify new lead compounds.
[0006] Also, compounds in a chemical library are traditionally
screened (for the purpose of identifying new lead compounds) using
a combination of empirical science and chemical intuition. However,
as stated by Rudy M. Baum in his article "Combinatorial Approaches
Provide Fresh Leads for Medicinal Chemistry," C&EN, Feb. 7,
1994, pages 20-26, "chemical intuition, at least to date, has not
proven to be a particularly good source of lead compounds for the
drug discovery process."
[0007] Another deficiency pertains to the second step of the
conventional approach, i.e., the creation of variants of lead
compounds. Traditionally, lead compound variants are generated by
chemists using conventional chemical synthesis procedures. Such
chemical synthesis procedures are manually performed by chemists.
Thus, the generation of lead compound variants is very labor
intensive and time consuming. For example, it typically takes many
chemist years to produce even a small subset of the compound
variants for a single lead compound. Baum, in the article
referenced above, states that "medicinal chemists, using
traditional synthetic techniques, could never synthesize all of the
possible analogs of a given, promising lead compound" (emphasis
added). Thus, the use of conventional, manual procedures for
generating lead compound variants operates to impose a limit on the
number of compounds that can be evaluated as new drug leads.
Overall, the traditional approach to new lead generation is an
inefficient, labor-intensive, time consuming process of limited
scope.
[0008] Recently, attention has focused on the use of combinatorial
chemical libraries to assist in the generation of new chemical
compound leads. A combinatorial chemical library is a collection of
diverse chemical compounds generated by either chemical synthesis
or biological synthesis by combining a number of chemical "building
blocks" such as reagents. For example, a linear combinatorial
chemical library such as a polypeptide library is formed by
combining a set of chemical building blocks called amino acids in
every possible way for a given compound length (i.e., the number of
amino acids in a polypeptide compound). Millions of chemical
compounds theoretically can be synthesized through such
combinatorial mixing of chemical building blocks. For example, one
commentator has observed that the systematic, combinatorial mixing
of 100 interchangeable chemical building blocks results in the
theoretical synthesis of 100 million tetrameric compounds or 10
billion pentameric compounds (Gallop et al., "Applications of
Combinatorial Technologies to Drug Discovery, Background and
Peptide Combinatorial Libraries," Journal of Medicinal Chemistry,
Volume 37, Number 9, pages 1233-1250, Apr. 29, 1994).
[0009] To date, most work with combinatorial chemical libraries has
been limited only to peptides and oligonucleotides for the purpose
of identifying bioactive agents; little research has been performed
using non-peptide, non-nucleotide based combinatorial chemical
libraries. It has been shown that the compounds in peptide and
oligonucleotide based combinatorial chemical libraries can be
assayed to identify ones having bioactive properties. However,
there is no consensus on how such compounds (identified as having
desirable bioactive properties and desirable profile for medicinal
use) can be used.
[0010] Some commentators speculate that such compounds could be
used as orally efficacious drugs. This is unlikely, however, for a
number of reasons. First, such compounds would likely lack
metabolic stability. Second, such compounds would be very expensive
to manufacture, since the chemical building blocks from which they
are made most likely constitute high priced reagents. Third, such
compounds would tend to have a large molecular weight, such that
they would have bioavailability problems (i.e., they could only be
taken by injection).
[0011] Others believe that the compounds from a combinatorial
chemical library that are identified as having desirable biological
properties could be used as lead compounds. Variants of these lead
compounds could be generated and evaluated in accordance with the
conventional procedure for generating new bioactive compound leads,
described above. However, the use of combinatorial chemical
libraries in this manner does not solve all of the problems
associated with the conventional lead generation procedure.
Specifically, the problem associated with manually synthesizing
variants of the lead compounds is not resolved.
[0012] In fact, the use of combinatorial chemical libraries to
generate lead compounds exacerbates this problem. Greater and
greater diversity has often been achieved in combinatorial chemical
libraries by using larger and larger compounds (that is, compounds
having a greater number of variable subunits, such as pentameric
compounds instead of tetrameric compounds in the case of
polypeptides). However, it is more difficult, time consuming, and
costly to synthesize variants of larger compounds. Furthermore, the
real issues of structural and functional group diversity are still
not directly addressed; bioactive agents such as drugs and
agricultural products possess diversity that could never be
achieved with available peptide and oligonucleotide libraries since
the available peptide and oligonucleotide components only possess
limited functional group diversity and limited topology imposed
through the inherent nature of the available components. Thus, the
difficulties associated with synthesizing variants of lead
compounds are exacerbated by using typical peptide and
oligonucleotide combinatorial chemical libraries to produce such
lead compounds. The issues described above are not limited to
bioactive agents but rather to any lead generating paradigm for
which a chemical agent of defined and specific activity is
desired.
[0013] Thus, the need remains for a system and method for
efficiently and effectively generating new leads designed for
specific utilities.
SUMMARY OF THE INVENTION
[0014] The present invention is directed to a computer based system
and method for automatically generating chemical entities with
desired physical, chemical and/or biological properties. The
present invention is also directed to the chemical entities
produced by this system and method. For purposes of illustration,
the present invention is described herein with respect to the
production of drug leads. However, the present invention is not
limited to this embodiment.
[0015] Specifically, the present invention is directed to an
iterative process for generating new chemical compounds with a
prescribed set of physical, chemical and/or biological properties,
and to a system for implementing this process. During each
iteration of the process, (1) a directed diversity chemical library
is robotically generated in accordance with robotic synthesis
instructions; (2) the compounds in the directed diversity chemical
library are analyzed under computer control, and
structure-activity/structure-property models (collectively referred
to as structure-activity models hereafter) are constructed and/or
refined; and (3) new robotic synthesis instructions are generated
to control the synthesis of the directed diversity chemical library
for the next iteration.
[0016] More particularly, during each iteration of the process, the
system of the present invention robotically synthesizes, in
accordance with robotic synthesis instructions, a directed
diversity chemical library comprising a plurality of chemical
compounds. The chemical compounds are robotically analyzed to
obtain structure-activity/structure-property data (collectively
referred to as structure-activity data hereafter) pertaining
thereto. The structure-activity data is stored in a
structure-activity/structure-property database (referred to as
structure-activity database hereafter). The structure-activity
database also stores therein structure-activity data pertaining to
previously synthesized compounds.
[0017] The system of the present invention evaluates, under
computer control, the structure-activity data of the chemical
compounds obtained from all previous iterations (or a subset of all
previous iterations as specified by user input, for example) and
constructs structure-activity models that substantially conform to
the observed data.
[0018] The system of the present invention then identifies, under
computer control, reagents, from a reagent database, which, when
combined, will produce compounds which are predicted to (1) exhibit
improved activity/properties, (2) test the validity of the current
structure-activity models, and/or (3) discriminate between the
various structure-activity models. Under the system of the present
invention, a plurality of structure-activity models may be tested
and evaluated in parallel.
[0019] Then, the system of the present invention generates, under
computer control, new robotic synthesis instructions which, when
executed, enable robotic synthesis of chemical compounds from
selected combinations of the identified reagents. Such new robotic
synthesis instructions are used to generate a new directed
diversity chemical library during the next iteration.
[0020] Further features and advantages of the present invention, as
well as the structure and operation of various embodiments of the
present invention, are described in detail below with reference to
the accompanying drawings. In the drawings, like reference numbers
indicate identical or functionally similar elements. Also, the
leftmost digit(s) of the reference numbers identify the drawings in
which the associated elements are first introduced.
BRIEF DESCRIPTION OF THE FIGURES
[0021] The present invention will be described with reference to
the accompanying drawings, wherein:
[0022] FIG. 1 is a block diagram of a lead generation system
according to a preferred embodiment of the present invention;
[0023] FIG. 2 is a flow diagram depicting the preferred flow of
data and materials among elements of the lead generation system of
the present invention;
[0024] FIGS. 3-6 are flowcharts depicting the operation of the lead
generation system according to a preferred embodiment of the
present invention;
[0025] FIG. 7 is a preferred block diagram of a structure-activity
database which forms a part of the lead generation system of the
present invention;
[0026] FIG. 8 illustrates a preferred database record format common
to records in the structure-activity database;
[0027] FIG. 9 is a preferred block diagram of analysis robots which
are part of the lead generation system of the present
invention;
[0028] FIG. 10 illustrates an embodiment of the present invention
in which candidate compounds are ranked according to their
predicted three-dimensional receptor fit;
[0029] FIG. 11 is used to describe the preferred, high level
operation of the present invention; and
[0030] FIG. 12 is a schematic of an example thrombin directed
diversity chemical library.
DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
[0031] 1. General Overview
[0032] The present invention is directed to the computer-aided
generation of chemical entities with a prescribed set of physical,
chemical and/or bioactive properties via computer-based, iterative
robotic synthesis and analysis of directed diversity chemical
libraries. The present invention is also directed to the new
chemical entities generated by operation of the present
invention.
[0033] According to the present invention, a directed diversity
chemical library is not the same as a combinatorial chemical
library. As discussed above, a combinatorial chemical library
comprises a plurality of chemical compounds which are formed by
combining, in every possible way for a given compound length (i.e.,
the number of building blocks in a compound), a set of chemical
building blocks. For example, suppose that three chemical building
blocks (designated as A, B, and C) are used to generate a
combinatorial chemical library. Also suppose that the length of the
compounds in the combinatorial chemical library is equal to two. In
this case, the following compounds would be generated: AA, AB, AC,
BA, BB, BC, CA, CB, and CC.
[0034] In contrast, a directed diversity chemical library comprises
a plurality of chemical compounds which are formed by selectively
combining a particular set of chemical building blocks. Thus,
whereas discovery using combinatorial chemical libraries tends to
be scattershot and random (essentially constituting a "needle in a
haystack" research paradigm), the use by the present invention of
directed diversity chemical libraries results in an optimization
approach which is focused and directed.
[0035] As shown in FIG. 11, the present invention includes a
Chemical Synthesis Robot 112 which operates in accordance with
robotic synthesis instructions 204 to synthesize a Directed
Diversity Chemical Library 208. The Chemical Synthesis Robot 112
synthesizes the Directed Diversity Chemical Library 208 by
selectively mixing a set of chemical building blocks from a Reagent
Repository 114 in accordance with the robotic synthesis
instructions 204.
[0036] In one example of the present invention, discussed here to
generally illustrate the present invention, these chemical building
blocks comprise approximately 100 commercially available reagents
suitable for generating thrombin inhibitors. However, it should be
understood that the present invention is not limited to this
example. Preferably, the Chemical Synthesis Robot 112 combines
these reagents using well known synthetic chemistry techniques to
synthesize inhibitors of the enzyme thrombin. Each inhibitor is
generally composed of, but not restricted to, three chemical
building blocks. Thus, the Directed Diversity Chemical Library 208
preferably comprises a plurality of thrombin inhibitors generally
composed of, but not restricted to, three sites of variable
structure (i.e., trimers).
[0037] Again, however, it should be understood that the present
invention is not limited to this thrombin example. The present
invention is equally adapted and intended to generate chemical
compounds (other than thrombin inhibitors) having other desired
properties, such as paints, finishes, plasticizers, surfactants,
scents, flavorings, bioactive compounds, drugs, herbicides,
pesticides, veterinary products, etc., and/or lead compounds for
any of the above. In fact, the present invention is adapted and
intended to generate chemical compounds having any useful
properties that depend upon structure, composition, or state.
[0038] Still referring to FIG. 11, the Directed Diversity Chemical
Library 208 generated by the Chemical Synthesis Robot 112 is
provided to an analysis robot 116. The analysis robot 116 analyzes
(chemically, biochemically, physically, and/or biophysically) the
compounds in the Directed Diversity Chemical Library 208 to obtain
structure-activity/stru- cture-property data (called herein
Structure-Activity Data) 210 pertaining to the compounds. Such
structure-activity/structure-property data 210 includes well known
structure-activity/structure property relationship data
(collectively referred to as structure-activity relationships or
SAR hereafter) pertaining to the relationship(s) between a
compound's activity/properties and its chemical structure.
Preferably, the analysis robot 116 assays the compounds in the
Directed Diversity Chemical Library 208 to obtain, for example,
enzyme activity data, cellular activity data, toxicology data,
and/or bioavailability data pertaining to the compounds.
Optionally, the analysis robot 116 also analyzes the compounds to
identify which of the compounds were adequately synthesized, and
which of the compounds were not adequately synthesized. This could
be useful, since not all combinations of chemical building blocks
may interact as expected. The analysis robot 116 further analyzes
the compounds to obtain other pertinent data, such as data
pertaining to the compounds' composition, structure and electronic
structure.
[0039] This data obtained by the analysis robot 116 (i.e., physical
data, synthesis data, enzyme activity data, cellular activity data,
toxicology data, bioavailability data, etc.) collectively
represents the Structure-Activity Data 210 shown in FIG. 11. The
Structure-Activity Data 210 is stored in a Structure-Activity
Database 122, and is provided to a Synthesis Protocol Generator
104.
[0040] The Synthesis Protocol Generator 104 uses the
Structure-Activity Data 210 of the chemical compounds in the
Directed Diversity Chemical Library 208, as well as historical
structure-activity data 212 pertaining to chemical compounds that
were previously synthesized (or known), to derive and/or refine
structure-activity models that substantially conform to the
observed data.
[0041] The synthesis protocol generator then identifies, under
computer control, reagents, from a Reagent Repository 114, which,
when combined with each other, will produce compounds which are
predicted (by the structure-activity models) to (1) exhibit
improved activity/properties, (2) test the validity of the current
structure-activity models, and/or (3) discriminate between the
various structure-activity models. Under the system of the present
invention, one or more structure-activity models may be tested and
evaluated in parallel.
[0042] In addition, the Synthesis Protocol Generator 104 classifies
any compounds which possess the desired activity/properties as new
leads (lead compounds) 216.
[0043] After performing this analysis, the Synthesis Protocol
Generator 104 generates new robotic synthesis instructions 204
which pertain to the synthesis of chemical compounds from
combinations of the identified reagents. These new robotic
synthesis instructions 204 are provided to the Chemical Synthesis
Robot 112.
[0044] Then, the process described above is repeated. In
particular, the Chemical Synthesis Robot 112 operates in accordance
with the new robotic synthesis instructions 204 to synthesize a new
Directed Diversity Chemical Library 208 by selectively combining
the identified reagents. The analysis robot 116 analyzes the new
Directed Diversity Chemical Library 208 to obtain
Structure-Activity Data 210 pertaining to the compounds in the new
Directed Diversity Chemical Library 208. The Synthesis Protocol
Generator 104 analyzes the Structure-Activity Data 210 pertaining
to the compounds in the new Directed Diversity Chemical Library 208
to improve the structure-activity models, and to generate new
robotic synthesis instructions 204.
[0045] Thus, the present invention is an iterative process for
generating new chemical entities having a set of physical, chemical
and/or biological properties optimized towards a prescribed target.
During each iteration, a Directed Diversity Chemical Library 208 is
generated, the compounds in the Directed Diversity Chemical Library
208 are analyzed, structure-activity models are derived and
elaborated, and robotic synthesis instructions 204 are generated to
control the synthesis of the Directed Diversity Chemical Library
208 for the next iteration.
[0046] Preferably, elements of the present invention are controlled
by a data processing device, such as a computer operating in
accordance with software. Consequently, it is possible in the
present invention to store massive amounts of data, and to utilize
this data in a current iteration to generate robotic synthesis
instructions 204 for the next iteration. In particular, since the
elements of the present invention are controlled by a data
processing device, it is possible to store the Structure-Activity
Data 210 obtained during each iteration. It is also possible to
utilize the historical structure-activity data 212 obtained during
previous iterations, as well as other pertinent structure-activity
data obtained by other experiments, to generate robotic synthesis
instructions 204 for the next iteration. In other words, the
synthesis of the Directed Diversity Chemical Library 208 for the
next iteration is guided by the results of all previous iterations
(or any subset of the previous iterations, as determined by user
input, for example). Put another way, the present invention
"learns" from its past performance such that the present invention
is "intelligent". As a result, the leads 216 identified in
subsequent iterations are better (i.e., exhibit physical, chemical
and/or biological properties closer to the prescribed values) than
the leads 216 identified in prior iterations.
[0047] According to a preferred embodiment of the present
invention, one or more robots (i.e., the Chemical Synthesis Robot
112) are used to robotically synthesize the Directed Diversity
Chemical Library 208 during each iteration. Also, one or more
robots (i.e. the analysis robot 116) are used to robotically
analyze the compounds contained in the Directed Diversity Chemical
Library 208 during each iteration. As used herein, the term "robot"
refers to any automated device that automatically performs
functions specified by instructions, such as the robotic synthesis
instructions 204 which the Chemical Synthesis Robot 112 receives
from the Synthesis Protocol Generator 104. The integrated use of
data processing devices (i.e., the Synthesis Protocol Generator
104) and robots (i.e., the Chemical Synthesis Robot 112 and the
analysis robot 116) in the present invention enables the automatic
and intelligent synthesis and screening of very large numbers of
chemical compounds.
[0048] The structure and operation of the present invention shall
now be described in greater detail.
[0049] 2. Structure of the Present Invention
[0050] FIG. 1 is a structural block diagram of a lead
generation/optimization system 102 according to a preferred
embodiment of the present invention. The drug lead generation
system 102 comprises a central processing unit (CPU), such as a
processor 106, which operates according to control logic 108.
According to the present invention, the processor 106 and the
control logic 108 collectively represent a Synthesis Protocol
Generator 104.
[0051] The control logic 108 preferably represents a computer
program such that the processor 106 operates according to software
instructions contained in the control logic 108. Alternatively, the
processor 106 and/or the control logic 108 are implemented as a
hardware state machine.
[0052] A suitable form for the processor 106 is an Indigo, Indy,
Onyx, Challenge, or Power Challenge computer made by Silicon
Graphics, Inc., of Mountain View, Calif. Another suitable form for
the processor 106 is a Connection Machine computer made by Thinking
Machines Corporation of Boston, Mass. Any other suitable computer
system could alternatively be used.
[0053] A communication medium 110, comprising one or more data
buses and/or IO (input/output) interface devices, connect the
Synthesis Protocol Generator 104 to a number of peripheral devices,
such as an input device 121, an output device 123, a Chemical
Synthesis Robot 112, one or more analysis robots 116, and a data
storage device 118.
[0054] The input device 121 receives input (such as data, commands,
etc.) from human operators and forwards such input to the Synthesis
Protocol Generator 104 via the communication medium 110. Any well
known, suitable input device may be used in the present invention,
such as a keyboard, pointing device (mouse, roller ball, track
ball, light pen, etc.), touch screen, etc. User input may also be
stored and then retrieved, as appropriate, from data/command
files.
[0055] The output device 123 outputs information to human
operators. The Synthesis Protocol Generator 104 transfers such
information to the output device 123 via the communication medium
110. Any well known, suitable output device may be used in the
present invention, such as a monitor, a printer, a floppy disk
drive, a text-to-speech synthesizer, etc.
[0056] The Chemical Synthesis Robot 112 receives robotic synthesis
instructions from the Synthesis Protocol Generator 104 via the
communication medium 110. The Chemical Synthesis Robot 112 operates
according to the robotic synthesis instructions to selectively
combine a particular set of reagents from a Reagent Repository 114
to thereby generate structurally and functionally diverse chemical
compounds. These chemical compounds form a Directed Diversity
Chemical Library 208.
[0057] The Chemical Synthesis Robot 112 is preferably capable of
mix-and-split, solid phase chemistry for coupling chemical building
blocks. The Chemical Synthesis Robot 112 preferably performs
selective microscale solid state synthesis of a specific
combinatorial library of directed diversity library compounds. The
Chemical Synthesis Robot 112 preferably cleaves and separates the
compounds of the Directed Diversity Chemical Library 208 (FIG. 2)
from support resin and distributes the compounds into preferably 96
wells with from 1 to 20 directed diversity library compounds per
well, corresponding to an output of 96 to 1920 compounds per
synthetic cycle iteration. This function may alternatively be
performed by a well known liquid transfer robot (not shown).
Chemical synthesis robots suitable for use with the present
invention are well known and are commercially available from a
number of manufacturers, such as the following:
1TABLE 1 Manufacturer City State Model Advanced ChemTech Louisville
KY 357 MPS 390 MPS Rainin Woburn MA Symphony Perkin-Elmer
Corporation Applied Foster City CA 433A Biosystems Division
Millipore Bedford MA 9050 Plus
[0058] All of the instruments listed in Table 1 perform solid
support-based peptide synthesis only. The Applied Biosystems and
the Millipore instruments are single peptide synthesizers. The
Rainin Symphony is a multiple peptide synthesizer capable of
producing up to 20 peptides simultaneously. The Advanced ChemTech
instruments are also multiple peptide synthesizers, but the 357 MPS
has a feature utilizing an automated mix-and-split technology. The
peptide synthesis technology is preferred in producing the directed
diversity libraries associated with the present invention. See, for
example, Gallop, M. A. et al., J. Med. Chem. 37, 1233-1250 (1994),
which is herein incorporated by reference in its entirety.
[0059] Peptide synthesis is by no means the only approach
envisioned and intended for use with the present invention. Other
chemistries for generating chemical diversity libraries can also be
used. For example, the following are suitable: peptoids (PCT
Publication No WO 91/19735, Dec. 26, 1991), encoded peptides (PCT
Publication WO 93/20242, Oct. 14, 1993), random bio-oligomers (PCT
Publication WO 92/00091, Jan. 9, 1992), benzodiazepines (U.S. Pat.
No. 5,288,514), diversomeres such as hydantoins, benzodiazepines
and dipeptides (Hobbs DeWitt, S. et al., Proc. Nat. Acad. Sci. USA
90:6909-6913 (1993)), vinylogous polypeptides (Hagihara et al., J.
Amer. Chem. Soc. 114 : 6568 (1992)), nonpeptidal peptidormimetics
with a Beta-D-Glucose scaffolding (Hirschmann, R. et al., J. Amer.
Chem. Soc. 114 : 9217-9218 (1992)), analogous organic syntheses of
small compound libraries (Chen, C. et al., J. Amer. Chem. Soc. 116:
2661(1994)), oligocarbamates (Cho, C. Y. et al., Science 261:1303
(1993)), and/or peptidyl phosphonates (Campbell, D. A. et al., J.
Org. Chem. 59:658(1994)). See, generally, Gordon, E. M. et al., J.
Med. Chem. 37: 1385 (1994). The contents of all of the
aforementioned publications are incorporated herein by
reference.
[0060] A number of well known robotic systems have also been
developed for solution phase chemistries. These systems include
automated workstations like the automated synthesis apparatus
developed by Takeda Chemical Industries, LTD. (Osaka, Japan) and
many robotic systems utilizing robotic arms (Zymate II, Zymark
Corporation, Hopkinton, Mass.; Orca, Hewlett-Packard, Palo Alto,
Calif.) which mimic the manual synthetic operations performed by a
chemist.
[0061] Any of the above devices are suitable for use with the
present invention. The nature and implementation of modifications
to these devices (if any) so that they can operate as discussed
herein will be apparent to persons skilled in the relevant art.
[0062] The analysis robots 116 receive the chemical compounds
synthesized by the Chemical Synthesis Robot 112. This is indicated
by arrow 113. The analysis robots 116 analyze these compounds to
obtain structure-activity data pertaining to the compounds.
[0063] FIG. 9 is a more detailed structural block diagram of the
analysis robots 116. The analysis robots 116 include one or more
assay modules 902, such as an enzyme activity assay module 904, a
cellular activity assay module 906, a toxicology assay module 908,
and/or a bioavailability assay module 910. The enzyme activity
assay module 904 assays the compounds synthesized by the Chemical
Synthesis Robot 112 using well known procedures to obtain enzyme
activity data relating to the compounds. The cellular activity
assay module 906 assays the compounds using well known procedures
to obtain cellular activity data relating to the compounds. The
toxicology assay module 908 assays the compounds using well known
procedures to obtain toxicology data relating to the compounds. The
bioavailability assay module 910 assays the compounds using well
known procedures to obtain bioavailability data relating to the
compounds.
[0064] The enzyme activity assay module 904, cellular activity
assay module 906, toxicology assay module 908, and bioavailability
assay module 910 are implemented in a well known manner to
facilitate the preparation of solutions, initiation of the
biological or chemical assay, termination of the assay (optional
depending on the type of assay) and measurement of the results,
commonly using a counting device, spectrophotometer, fluorometer or
radioactivity detection device. Each of these steps can be done
manually or by robots in a well known manner. Raw data is collected
and stored on magnetic media under computer control or input
manually into a computer. Useful measurement parameters such as
dissociation constants or 50% inhibition concentrations can then be
manually or automatically calculated from the observed data, stored
on magnetic media and output to a relational database.
[0065] The analysis robots 116 optionally include a structure and
composition analysis module 914 to obtain two dimensional structure
and composition data relating to the compounds. Preferably, the
structure and composition analysis module 914 is implemented using
a liquid chromatograph device and/or a mass spectrometer. In one
embodiment, a sampling robot (not shown) transfers aliquots from
the 96 wells to a coupled liquid chromatography-mass spectrometry
system to perform sample analysis.
[0066] The structure and composition analysis module 914 may be
utilized to determine product composition and to monitor reaction
progress by comparison of the experimental results to the
theoretical results predicted by the Synthesis Protocol Generator
104. The analysis module may use, but is not limited to, infra-red
spectroscopy, decoding of a molecular tag, mass spectrometry (MS),
gas chromatography (GC), liquid chromatography (LC), or
combinations of these techniques (i.e., GC-MS, LC-MS, or MS-MS).
Preferably, the structure and composition analysis module 914 is
implemented using a mass spectrometric technique such as Fast Atom
Bombardment Mass Spectrometry (FABSMS) or triple quadrapole ion
spray mass spectrometry, optionally coupled to a liquid
chromatograph, or matrix-assisted laser desorption ionization
time-of-flight mass spectrometry (MALDI-TOF MS). MALDI-TOF MS is
well known and is described in a number of references, such as:
Brummell et al., Science 264:399 (1994); Zambias et al.,
Tetrahedron Lett. 35:4283 (1994), both incorporated herein by
reference in their entireties.
[0067] Liquid chromatograph devices, gas chromatograph devices, and
mass spectrometers suitable for use with the present invention are
well known and are commercially available from a number of
manufacturers, such as the following:
2TABLE 2 GAS CHROMATOGRAPHY Manufacturer City State Model
Hewlett-Packard Company Palo Alto CA 5890 Varian Associates Palo
Alto CA Shimadzu Scientific Inst. Columbia MD GC-17A Fisons
Instruments Beverly MA GC 8000
[0068]
3TABLE 3 LIQUID CHROMATOGRAPHY Manufacturer City State Model
Hewlett-Packard Company Palo Alto CA 1050, 1090 Varian Associates
Inc. Palo Alto CA Rainin Instrument Co. Woburn MA Shimadzu
Scientific Inst. Columbia MD LC-10A Waters Chromatography Milford
MA Millennium Perkin-Elmer Corporation Norwalk CT Hitachi
Instruments Inc. San Jose CA
[0069]
4TABLE 4 MASS SPECTROSCOPY Manufacturer City State Model
Hewlett-Packard Company Palo Alto CA Varian Associates Inc. Palo
Alto CA Kratos Analytical Inc. Ramsey NJ MS80RFAQ Finnigan MAT San
Jose CA Vision 2000, TSQ-700 Fisons Instruments Beverly MA API
LC/MS, AutoSpec Perkin-Elmer Sciex Norwalk CT API-III
[0070] Modifications to these devices may be necessary to fully
automate both the loading of samples on the systems as well as the
comparison of the experimental and predicted results. The extent of
the modification may vary from instrument to instrument. The nature
and implementation of such modifications will be apparent to
persons skilled in the art.
[0071] The analysis robots 116 may optionally further include a
chemical synthesis indicia generator 912 which analyzes the
structure and composition data obtained by the structure and
composition analysis module 914 to determine which compounds were
adequately synthesized by the Chemical Synthesis Robot 112, and
which compounds were not adequately synthesized by the Chemical
Synthesis Robot 112. Preferably, the chemical synthesis indicia
generator 912 is implemented using a processor, such as processor
106, operating in accordance with appropriate control logic, such
as control logic 108. Preferably, the control logic 108 represents
a computer program such that the processor 106 operates in
accordance with instructions in the control logic 108 to determine
which compounds were adequately synthesized by the Chemical
Synthesis Robot 112, and which compounds were not adequately
synthesized by the Chemical Synthesis Robot 112. Persons skilled in
the relevant art will be able to produce such control logic 108
based on the discussion of the chemical synthesis indicia generator
912 contained herein.
[0072] The analysis robots 116 may also include a three dimensional
(3D) receptor mapping module 918 to obtain three dimensional
structure data relating to a receptor binding site. The 3D receptor
mapping module 918 preferably determines the three dimensional
structure of a receptor binding site empirically through x-ray
crystallography and/or nuclear magnetic resonance spectroscopy,
and/or as a result of the application of extensive 3D QSAR
(quantitative structure-activity relationship) and receptor field
analysis procedures, well known to persons skilled in the art and
described in: "Strategies for Indirect Computer-Aided Drug Design",
Gilda H. Loew et al., Pharmaceutical Research, Volume 10, No. 4,
pages 475-486 (1993); "Three Dimensional Structure Activity
Relationships", G. R. Marshall et al., Trends In Pharmaceutical
Science, 9: 285-289 (1988). Both of these documents are herein
incorporated by reference in their entireties.
[0073] The analysis robots 116 may additionally include a physical
and/or electronic property analysis module(s) 916 which analyzes
the compounds synthesized by the Chemical Synthesis Robot 112 to
obtain physical and/or electronic property data relating to the
compounds. Such properties may include water/octanol partition
coefficients, molar refractivity, dipole moment, fluorescence etc.
Such properties may either be measured experimentally or computed
using methods well known to persons skilled in the art.
[0074] Referring again to FIG. 1, the data storage device 118 is a
read/write high storage capacity device such as a tape drive unit
or a hard disk unit. Data storage devices suitable for use with the
present invention are well known and are commercially available
from a number of manufacturers, such as the 2 gigabyte Differential
System Disk, part number FTO-SD8-2NC, and the 10 gigabyte DLT tape
drive, part number P-W-DLT, both made by Silicon Graphics, Inc., of
Mountain View, Calif. A reagent database 120 and a
Structure-Activity Database 122 are stored in the data storage
device 118.
[0075] The reagent database 120 contains information pertaining to
the reagents in the Reagent Repository 114. In particular, the
reagent database 120 contains information pertaining to the
chemical substructures, chemical properties, physical properties,
biological properties, and electronic properties of the reagents in
the Reagent Repository 114.
[0076] The Structure-Activity Database 122 stores
Structure-Activity Data 210, 212 (FIG. 2) pertaining to the
compounds which were synthesized by the Chemical Synthesis Robot
112. Such Structure-Activity Data 210, 212 is obtained as a result
of the analysis of the compounds performed by the analysis robots
116, as described above. The Structure-Activity Data 210, 212
obtained by the analysis robots 116 is transferred to and stored in
the Structure-Activity Database 122 via the communication medium
110.
[0077] FIG. 7 is a more detailed block diagram of the
Structure-Activity Database 122. The Structure-Activity Database
122 includes a structure and composition database 702, a physical
and electronic properties database(s) 704, a chemical synthesis
database 706, a chemical properties database 708, a 3D receptor map
database 710, and a biological properties database 712. The
structure and composition database 702 stores structure and
composition data 714 pertaining to compounds synthesized by the
Chemical Synthesis Robot 112 and analyzed by the analysis robots
116. Similarly, the physical and electronic properties database
704, chemical synthesis database 706, chemical properties database
708, 3D receptor map database 710, and biological properties
database 712 store physical and electronic properties data 716,
chemical synthesis indicia 718, chemical properties data 720, 3D
receptor map data 722, and biological properties data 724,
respectively, pertaining to compounds synthesized by the Chemical
Synthesis Robot 112 and analyzed by the analysis robots 116. The
structure and composition data 714, electronic properties data 716,
chemical synthesis indicia 718, chemical properties data 720,
receptor map data 722, and biological properties data 724
collectively represent the Structure-Activity Data 210, 212.
[0078] Preferably, the structure and composition database 702,
physical and electronic properties database 704, chemical synthesis
database 706, chemical properties database 708, 3D receptor map
database 710, and biological properties database 712 each include
one record for each chemical compound synthesized by the Chemical
Synthesis Robot 112 and analyzed by the analysis robots 116. (Other
database structures could alternatively be used.) FIG. 8 depicts a
preferred database record format 802 for these records.
[0079] Each database record includes: (1) a first field 804
containing information identifying the compound; (2) a second field
806 containing information identifying the reagents from the
Reagent Repository 114 that were combined to produce the compound;
(3) a third field 808 containing information indicating the
predicted mass and structure of the compound and information
identifying the label assigned to the compound (the information
contained in the third field 808 is described below); (4) a fourth
field 810 indicating the rating factor (described below) assigned
to the compound; and (5) a fifth field 812 containing
structure-activity data. The information stored in the fifth field
812 is database specific (also, the fifth field 812 may include one
or more sub-fields). For example, the fifth field 812 in records of
the structure and composition database 702 stores structure and
composition data 714, whereas the fifth field 812 in records of the
electronic properties database 704 stores electronic properties
data 716.
[0080] 3. Operation of the Present Invention
[0081] The operation of the lead generation/optimization system 102
shall now be described in detail with reference to a flowchart 302
shown in FIG. 3, and a flow diagram 202 shown in FIG. 2. Flowchart
302 represents the preferred operation of the present invention.
The flow diagram 202 depicts the preferred flow of data and
materials between the elements of the lead generation system
102.
[0082] As stated above, the lead generation/optimization system 102
implements an iterative process where, during each iteration, (1) a
Directed Diversity Chemical Library 208 is generated; (2) the
compounds in the Directed Diversity Chemical Library 208 are
analyzed and new lead compounds 216 are classified,
structure-activity/structure-property models with enhanced
predictive and discriminating capabilities are constructed, and
compounds which are predicted to exhibit improved
activity/properties are identified for synthesis during the next
iteration; and (3) robotic synthesis instructions 204 are generated
to control the synthesis of the Directed Diversity Chemical Library
208 for the next iteration. The steps of flowchart 302 (that is,
steps 304-316) are performed during each iteration of this
iterative process as indicated by control line 317 in flowchart
302. Generally, (1) the Directed Diversity Chemical Library 208 is
generated during step 304; (2) the compounds in the Directed
Diversity Chemical Library 208 are analyzed and new lead compounds
216 are classified, structure-activity/structure-p- roperty models
with enhanced predictive and discriminating capabilities are
constructed, and compounds which are predicted to exhibit improved
activity/properties are identified for synthesis during the next
iteration during steps 306-314; and (3) robotic synthesis
instructions 204 are generated to control the synthesis of the
Directed Diversity Chemical Library 208 for the next iteration
during step 316 . The operation of the lead generation/optimization
system 102 according to the steps of flowchart 302 shall now be
discussed in detail.
[0083] As represented by step 304, the Chemical Synthesis Robot 112
robotically synthesizes a plurality of chemical compounds in
accordance with robotic synthesis instructions 204 (flow arrow 252
in FIG. 2). Preferably, the Chemical Synthesis Robot 112
synthesizes the chemical compounds by selective mixing of reagents
206 from a Reagent Repository 114 (flow arrows 274 and 276 in FIG.
2) in accordance with the robotic synthesis instructions 204. The
chemical compounds synthesized by the Chemical Synthesis Robot 112
collectively represent a Directed Diversity Chemical Library 208
(flow arrow 254 in FIG. 2).
[0084] The robotic synthesis instructions 204 are generated by a
Synthesis Protocol Generator 104 in a manner which is described
below (flow arrow 250 in FIG. 2). The robotic synthesis
instructions 204 identify which reagents 206 from the Reagent
Repository 114 are to be mixed by the Chemical Synthesis Robot 112.
The robotic synthesis instructions 204 also identify the manner in
which such reagents 206 are to be mixed by the Chemical Synthesis
Robot 112 (i.e., which of the reagents 206 are to be mixed
together, and under what chemical and/or physical conditions, such
as temperature, length of time, stirring, etc.).
[0085] As represented by step 306, analysis robots 116 receive the
Directed Diversity Chemical Library 208 generated by the Chemical
Synthesis Robot 112 (flow arrow 256 in FIG. 2). The analysis robots
116 robotically analyze the chemical compounds in the Directed
Diversity Chemical Library 208 to obtain Structure-Activity Data
210 pertaining to such compounds (flow arrow 258 in FIG. 2).
[0086] As represented by step 308, the analysis robots 116 store
the Structure-Activity Data 210 in a Structure-Activity Database
122 contained in a data storage device 118 (flow arrow 260 in FIG.
2). This structure-activity database 112 also stores
structure-activity data pertaining to chemical compounds which were
synthesized and analyzed in previous iterations by the Chemical
Synthesis Robot 112 and the analysis robots 116, respectively, as
well as other pertinent structure-activity data obtained from
independent experiments.
[0087] The operation of the lead generation/optimization system 102
while performing steps 306 and 308 shall now be discussed in
greater detail.
[0088] During step 306, assay modules 902 (FIG. 9) robotically
assay the chemical compounds in the Directed Diversity Chemical
Library 208 to obtain physical properties data 716, chemical
properties data 720 and biological properties data 724 (FIG. 7)
pertaining to the chemical compounds. For example, the enzyme
activity assay module 904 robotically assays the chemical compounds
using well known assay techniques to obtain enzyme activity data
relating to the compounds. Such enzyme activity data includes
inhibition constants K.sub.1, maximal velocity V.sub.max, etc. The
cellular activity assay module 906 robotically assays the compounds
using well known assay techniques to obtain cellular activity data
relating to the compounds. The toxicology assay module 908
robotically assays the compounds using well known assay techniques
to obtain toxicology data relating to the compounds. The
bioavailability assay module 910 robotically assays the compounds
using well know assay techniques to obtain bioavailability data
relating to the compounds. Such enzyme activity data, cellular
activity data, toxicology data, and bioavailability data represent
the physical properties data 716, chemical properties data 720 and
the biological properties data 724 shown in FIG. 7. Alternatively,
physical properties data 716 may be obtained by the physical and
electronic property analysis module 916. In step 308, the physical
properties data 716 is stored in the physical properties database
704, the chemical properties data 720 is stored in the chemical
properties database 706 and the biological properties data 724 is
stored in the biological properties database 712.
[0089] Also during step 306, the electronic property analysis
module 916 automatically analyzes the chemical compounds contained
in the Directed Diversity Chemical Library 208 to obtain electronic
properties data 716 pertaining to the chemical compounds. Such
electronic properties data 716 is stored in the electronic
properties database 704 during step 308.
[0090] Additionally during step 306, the 3D receptor mapping module
918 obtains receptor map data 722 representing the three
dimensional structure pertaining to a receptor binding site being
tested. The 3D receptor mapping module 918 preferably determines
the three dimensional structure of the receptor binding site
empirically through x-ray crystallography, nuclear magnetic
resonance spectroscopy, and/or as result of the application of
extensive 3D QSAR and receptor field analysis procedures. Such
receptor map data 722 is stored in the 3D receptor map database 710
during step 308.
[0091] Also during step 306, an optional structure and composition
analysis module 914 analyzes the chemical compounds contained in
the Directed Diversity Chemical Library 208 to obtain structure and
composition data 714 pertaining to the chemical compounds. Such
structure and composition data 714 is stored in the structure and
composition database 702 during step 308.
[0092] The operation of the structure and composition analysis
module 914 (and also the chemical synthesis indicia generator 912)
during steps 306 and 308 shall now be further described with
reference to a flowchart depicted in FIG. 4.
[0093] As represented by step 404, the structure and composition
analysis module 914 analyzes the chemical compounds in the Directed
Diversity Chemical Library 208 to obtain structure and composition
data 714 pertaining to the compounds. Preferably, the structure and
composition analysis module 914 analyzes the chemical compounds
using well known mass spectra analysis techniques.
[0094] As represented by step 405, the structure and composition
data 714 is stored in a structure and composition database 702
which forms part of the Structure-Activity Database 122 (FIG.
7).
[0095] As represented by step 406, the chemical synthesis indicia
generator 912 receives the structure and composition data 714. The
chemical synthesis indicia generator 912 also retrieves from the
Structure-Activity Database 122 the predicted mass and structural
data relating to the compounds in the Directed Diversity Chemical
Library 208. Such data (i.e., the predicted mass and structural
data) is preferably retrieved from the third field 808 (FIG. 8) of
the records of the Structure-Activity Database 122 pertaining to
the compounds in the Directed Diversity Chemical Library 208. The
manner in which the predicted mass and structural data is generated
and stored in the Structure-Activity Database 122 is considered in
an ensuing discussion pertaining to steps 504 and 508 of FIG.
5.
[0096] As represented by step 408, the chemical synthesis indicia
generator 912 compares the structure and composition data 714
(obtained by the structure and composition analysis module 914)
with the predicted mass and structural data (retrieved from the
Structure-Activity Database 122) to generate chemical synthesis
indicia 718. The chemical synthesis indicia 718 indicates which of
the chemical compounds from the Directed Diversity Chemical Library
208 were adequately synthesized, and which were not adequately
synthesized.
[0097] Preferably, during step 408 the chemical synthesis indicia
generator 912 compares, for each compound, the measured mass of the
compound (which is part of the structure and composition data 714)
to the predicted mass of the compound. If the measured mass and the
predicted mass differ by less than a predetermined amount, then the
chemical synthesis indicia generator 912 determines that the
chemical compound was adequately synthesized. If the measured mass
and the predicted mass differ by more than the predetermined
amount, then the chemical synthesis indicia generator 912
determines that the chemical compound was not adequately
synthesized. This predetermined amount depends on the sensitivity
of the instrument used for the structure and composition
analysis.
[0098] As represented by step 410, the chemical synthesis indicia
generator 912 generates chemical synthesis indicia 718 pertaining
to the compounds in the Directed Diversity Chemical Library 208,
and stores such chemical synthesis indicia 718 in the chemical
synthesis database 706. Such chemical synthesis indicia 718 for
each compound is a first value (such as "1") if the compound was
adequately synthesized (as determined in step 408), and is a second
value (such as "0") if the compound was not adequately
synthesized.
[0099] The performance of steps 306 and 308 is complete after the
completion of step 410. After step 410 is completed, control passes
to step 310 (FIG. 3).
[0100] As represented by step 310, the Structure-Activity Data 210
pertaining to the compounds in the Directed Diversity Chemical
Library 208 is provided to the Synthesis Protocol Generator 104
(flow arrow 262 in FIG. 2). The Synthesis Protocol Generator 104
also receives data pertaining to the desired activity/properties
214 (flow arrow 272 in FIG. 2). This is also called "desired
structure/property profile 214" or the "prescribed set". Such data
pertaining to desired activity/properties 214 was previously
entered by human operators using the input device 121, or read from
a file. The Synthesis Protocol Generator 104 compares the
Structure-Activity Data 210 of the compounds in the Directed
Diversity Chemical Library 208 against the desired
activity/properties 214 to determine whether any of the compounds
substantially conforms to the desired activity/properties 214.
[0101] Preferably, the Synthesis Protocol Generator 104 in step 312
assigns a rating factor to each compound in the Directed Diversity
Chemical Library 208, based on how closely the compound's
activity/properties match the desired activity/property profile
214. The rating factor may be represented by either numerical or
linguistic values. Numerical rating factors represent a sliding
scale between a low value (corresponding to an activity/property
profile far from the prescribed set 214) and a high value
(corresponding to an activity/property profile identical, or very
similar, to the prescribed set 214). Linguistic rating factors take
values such as "poor," "average," "good," "very good," etc.
Preferably, the Synthesis Protocol Generator 104 stores the rating
factors of the compounds in the fourth field 810 (FIG. 8) of their
respective records in the Structure-Activity Database 122.
[0102] Also in step 312, any compound from the Directed Diversity
Chemical Library 208 that substantially conforms to the desired
activity/properties profile 214 is classified as a new lead
compound. The rating factor may also be used to select new leads if
an insufficient number of compounds substantially exhibiting the
desired activity/properties 214 is found.
[0103] As represented by step 314, the Synthesis Protocol Generator
104 retrieves from the Structure-Activity Database 122 historical
structure-activity data 212 pertaining to the chemical compounds
synthesized in previous iterations (flow arrows 264 and 266). Also
during step 314, the Synthesis Protocol Generator 104 accesses the
reagent information database 120 and retrieves data 218 pertaining
to reagents contained in the Reagent Repository 114 (flow arrows
268 and 270 in FIG. 2). The synthesis protocol generator uses the
reagent data 218 and the Structure-Activity Data 210, 212 to
identify, under computer control, reagents from the Reagent
Repository 114 which, when combined, will produce compounds which
are predicted to (1) exhibit improved activity/properties, (2) test
the validity of the current structure-activity models, and/or (3)
discriminate between the various structure-activity models. Under
the system of the present invention, one or more structure-activity
models may be tested and evaluated in parallel.
[0104] Preferably, during the first iteration of flowchart 302, the
Synthesis Protocol Generator 104 uses structural, electronic and
physicochemical diversity criteria and, optionally, receptor fit
criteria to generate an initial Directed Diversity Chemical Library
208. The initial choice is aimed at maximizing the information
content of the resulting chemical library within the domain of
interest, as measured by the presence of chemical functionalities,
hydrogen bonding characteristics, electronic properties,
topological and topographical parameters, etc.
[0105] The operation of the Synthesis Protocol Generator 104 while
performing step 314 shall now be further described with reference
to a flowchart shown in FIG. 6.
[0106] As represented by step 602, the Synthesis Protocol Generator
104 analyzes the Structure-Activity Data 210 pertaining to the
compounds in the directed diversity library 208 and the historical
structure-activity data 212 obtained from previous iterations, and
constructs structure-activity models with enhanced predictive and
discriminating ability.
[0107] In a preferred embodiment of the present invention, step 602
involves the construction of functional structure-activity models,
and in particular models wherein the activity is represented as a
linear combination of basis functions of one or more molecular
features. Such molecular features may include topological indices,
physicochemical properties, electrostatic field parameters, volume
and surface parameters, etc., and their number may range from a few
tens to tens of thousands. The coefficients are preferably
determined using linear regression techniques. If many features are
used, linear regression may be combined with principal component
analysis, which is a well known technique for selecting the most
important set of features from a large table.
[0108] In a preferred embodiment of the present invention, the
basis functions used in the linear regression procedure are
selected using a well known genetic function approximation (GFA)
algorithm as described in Rogers and Hopfinger, J. Chem. Inf.
Comput. Sci. 34:854 (1994), which is herein incorporated by
reference in its entirety. In the GFA algorithm, a
structure-activity model is represented as a linear string which
encodes the features and basis functions employed by the model. A
population of linearly encoded structure-activity models is then
initialized by a random process, and allowed to evolve through the
repeated application of genetic operators, such as crossover,
mutation and selection. Selection is based on the relative fitness
of the models, as measured by a least squares error procedure, for
example. Friedman's lack-of-fit algorithm, described in J.
Friedman, Technical Report No. 102, Laboratory for Computational
Statistics, Department of Statistics, Stanford University,
Stanford, Calif., November 1988, herein incorporated by reference
in its entirety, or other suitable metrics well known to persons
skilled in the art, may also be used. GFA can build models using
linear polynomials as well as higher-order polynomials, splines and
Gaussians. Upon completion, the procedure yields a population of
models, ranked according to their fitness score.
[0109] The present invention employs a plurality of analytic
filters (represented by steps 604 and 606) to intelligently select
reagents (from the Reagent Repository 114) to use during the next
iteration, and to more intelligently select compounds to synthesize
during the next iteration. The use of such analytic filters
increases the probability that the compounds ultimately selected
for synthesis during the next iteration will exhibit improved
activity/properties. Since the method only synthesizes and analyzes
compounds which have a high probability of having the desired
activity/properties 214, the present invention is much more
efficient, effective, and expedient than conventional lead
generation processes.
[0110] As represented by step 604, the Synthesis Protocol Generator
104 applies a first sequence of analytic filters to identify
candidate reagents from the Reagent Repository 114 which are
appropriate for the generation of the directed diversity chemical
library for the next iteration. Such filters may identify and
select reagents based on a number of factors, including (but not
limited to) the cost of the reagents, the presence or absence of
certain functional groups and/or hydrogen bonding characteristics,
conformational flexibility, predicted receptor fit, etc.
[0111] As represented by step 606, the Synthesis Protocol Generator
104 generates a list of compounds based on the reagents selected in
step 604. Each of these compounds incorporates one or more of the
reagents identified in step 604 . In one embodiment of the
invention, the Synthesis Protocol Generator 104 generates the list
of compounds by combining these reagents in every possible way for
a given compound length, such as three (in which case the compounds
in the list would be trimers).
[0112] Not all of these compounds in the list will be synthesized
during the next iteration. The Synthesis Protocol Generator 104 in
step 606 applies a second sequence of analytic filters to identify
candidate compounds from the list of compounds which are
appropriate for the generation of the Directed Diversity Chemical
Library 208 for the next iteration. These analytic filters base
their analysis on a number of factors, including (but not limited
to) total volume and surface area, conformational flexibility,
receptor complementarity, etc. These analytic filters may also base
their analysis on whether a compound was previously successfully or
unsuccessfully synthesized (as indicated by the chemical synthesis
indicia 718, described above). According to an embodiment of the
present invention, the candidate compounds identified by operation
of the first and second sequences of filters are synthesized during
the next iteration to generate a new Directed Diversity Chemical
Library 208.
[0113] According to an alternate embodiment of the present
invention, the primary use of the first and second sequence of
filters, particularly the filters employed in step 606, is to
eliminate unsuitable compounds from further consideration, rather
than to select a set of compounds to synthesize for the next
iteration. In this alternate embodiment, the selection of a set of
compounds to synthesize for the next iteration is performed in step
608. The set of compounds determined in step 608 is an optimal or
near-optimal one.
[0114] As represented by step 608, the Synthesis Protocol Generator
104 ranks the candidate compounds identified in step 606,
individually or in combination, according to their predicted
ability to (1) exhibit improved activity/properties, (2) test the
validity of the current structure-activity models, and/or (3)
discriminate between the various structure-activity models. The
candidate compounds may also be ranked according to their predicted
three-dimensional receptor fit. The phrase "individually or in
combination" means that the Synthesis Protocol Generator 104
analyzes and ranks the candidate compounds each standing alone, or,
alternatively, analyzes and ranks sets of the candidate
compounds.
[0115] In a preferred embodiment of the present invention, the
highest-ranking models identified in step 602 are used in step 608
to select a set of compounds which, as a set, best satisfy the
following requirements: (1) exhibit improved activity as predicted
by the highest ranking structure-activity models, (2) test the
validity of the highest ranking structure-activity models, and/or
(3) discriminate between the highest ranking structure-activity
models. Requirements (2) and (3) allow for the selection of
compounds which need not necessarily exhibit improved activity but,
rather, prove or disprove some of the highest ranking
structure-activity models, or discriminate most effectively between
them. In other words, requirements (2) and (3) enable the
elaboration or improvement of the models from one iteration to the
next. The final set of compounds may contain compounds which
satisfy one, two or all three of the conditions listed above. Which
requirement is emphasized in any iteration depends on the amount
and quality of structure-activity data, the predictive power of the
current structure-activity models, and how closely the
activity/properties of the compounds in the last directed diversity
chemical library match the desired activity/properties. Typically,
as more and more directed diversity chemical libraries are
generated, emphasis will shift from requirements (2) and (3) to
requirement (1).
[0116] The task in step 608 of selecting the optimal set of
compounds for the next directed diversity chemical library involves
a search over the entire set of subsets of the candidate compounds
(identified during step 606), wherein each subset has k members,
where k may vary from one subset to the next and is preferably
within the following range: 1000.ltoreq.k.ltoreq.5000. Given a list
of n compounds produced during step 606, the present invention in
step 608 identifies which subset of k compounds best satisfies
requirements (1), (2) and (3) outlined above. The number of
distinct k-subsets of an n-set S is given by EQ. 1: 1 N = k = k 1 k
2 n ! k ! ( n - k ) ! EQ.1
[0117] where k.sub.1 and k.sub.2 represent the minimum and maximum
number of members in a subset, respectively. As indicated above,
k.sub.1is preferably equal to 1000 and k.sub.2 is preferably equal
to 5000. This task is combinatorially explosive, i.e., in all but
the simplest cases, N is far too large to allow for the
construction and evaluation of each individual subset given current
data processing technology. As a result, a variety of stochastic
modeling techniques can be employed, which are capable of providing
good approximate solutions to combinatorial problems in realistic
time frames. However, the present invention envisions and includes
the construction and evaluation of each individual subset once
computer technology advances to an appropriate point.
[0118] In a preferred embodiment of the present invention, in step
608 each subset of candidate compounds is represented as a binary
string which uniquely encodes the number and indices of the
candidate compounds comprising the subset. A population of binary
encoded subsets is then initialized by a random process, and
allowed to evolve through the repeated application of genetic
operators, such as crossover, mutation and selection. Selection is
based on the relative fitness of the subsets, as measured by their
ability to satisfy requirements (1), (2) and (3) discussed above.
Upon completion, the present invention yields a population of
subsets, ranked according to their ability to satisfy requirements
(1), (2) and (3). The highest ranking set is then processed in
accordance with step 610.
[0119] In a preferred embodiment of the present invention,
candidate compounds may also be ranked according to their predicted
three-dimensional receptor fit. This is conceptually illustrated in
FIG. 10, wherein candidate trimer compounds are generated in step
606 from available building blocks (reagents) A, B, and C
(identified in step 604), to produce a list of candidate compounds.
These candidate compounds are then evaluated and ranked in step 608
based on their three-dimensional receptor complementarity as well
as other criteria (as described herein). FIG. 10 depicts, for
illustrative purposes, an example candidate compound 1004
interacting with a three-dimensional receptor map 1002. The highest
ranking set 1006 is then processed in accordance with step 610.
[0120] As represented by step 610, based on the rankings determined
in step 608, the Synthesis Protocol Generator 104 generates a list
of compounds to be synthesized during the next iteration, and a
list of reagents which, when combined, will produce these
compounds, and the manner in which these reagents are to be
combined. The Synthesis Protocol Generator 104 also generates a
description of how the compounds are to be distributed amongst the
individual wells of the Directed Diversity Chemical Library 208.
Upon the creation of this data, step 314 is complete, and control
passes to step 316 (FIG. 3).
[0121] Referring again to FIG. 3, in step 316 the Synthesis
Protocol Generator 104 generates robotic synthesis instructions 204
(flow arrow 250 in FIG. 2) which, when executed by the Chemical
Synthesis Robot 112, enable the Chemical Synthesis Robot 112 to
robotically synthesize (during step 304 of the next iteration of
flowchart 302) the chemical compounds from selected combinations of
particular reagents 206 from the Reagent Repository 114, as
specified in step 314. Such chemical compounds collectively
represent a new Directed Diversity Chemical Library 208. The
operation of the Synthesis Protocol Generator 104 while performing
step 316 shall now be described with reference to a flowchart shown
in FIG. 5.
[0122] As represented by step 504, the Synthesis Protocol Generator
104 predicts the molecular mass and structure of the compounds
identified in step 314 using well known procedures.
[0123] As represented by step 508, the Synthesis Protocol Generator
104 assigns a unique label to each of the compounds. Preferably,
compounds are stored in 96 well plates, and each unique label is
associated with a code that references the wells and plates in
which the compound is stored. The purpose of these labels is to
track the synthesis, analysis and storage of each individual
compound and its associated data. The Synthesis Protocol Generator
104 creates a record in the Structure-Activity Database 122 for
each compound. In practice, for each compound, the Synthesis
Protocol Generator 104 creates a record in each database of the
Structure-Activity Database 122 (see FIG. 7). These records
preferably have the format shown in FIG. 8. The Synthesis Protocol
Generator 104 stores the labels and the predicted mass and
structure information (determined in step 504) associated with the
compounds in the third field 808 of these new records.
[0124] In step 510, the Synthesis Protocol Generator 104 generates
robotic synthesis instructions 204 to synthesize the chemical
compounds identified in step 314. The manner in which the Synthesis
Protocol Generator 104 generates such robotic synthesis
instructions 204 is implementation dependent and is contingent on
the particular characteristics of the chemical synthesis robot
which is used in the lead generation system 102. The manner in
which the Synthesis Protocol Generator 104 generates the robotic
synthesis instructions 204 will be apparent to persons skilled in
the relevant art.
[0125] The performance of step 316 is complete after the completion
of step 510. Then, control passes to step 304 (FIG. 3) to begin the
next iteration of flowchart 302.
[0126] In summary, the present invention is a system and method for
automatically generating chemical compounds having desired
properties. It should be noted that the terms and phrases
"automatically" and "computer controlled" (and the like) as used
herein mean that the present invention is capable of operating
without human intervention. This is achieved by using automated
devices, such as computers and robots. However, it should be
understood that the present invention allows and envisions human
intervention (i.e., operator aid, operator input, and/or operator
control), particularly when selecting compounds for synthesis
during the next iteration, and when generating robotic synthesis
instructions. Thus, the phrase "computer control" does not rule out
the possibility that optional human intervention may be involved in
the process. For example, the robotic synthesis instructions may be
generated manually in accordance with well known procedures using
information provided by the Synthesis Protocol Generator 104. Such
human intervention is allowed but optional; the present invention
can operate without any human intervention.
[0127] In an alternative embodiment of the present invention, a
plurality of systems 102 operate in parallel to generate and
analyze lead compounds. This is called distributed directed
diversity. The systems 102 are preferably centrally controlled by a
master computer system (not shown). Details of this master computer
system will be apparent to persons skilled in the relevant art.
EXAMPLE
Generation of Lead Thrombin Inhibitor
[0128] One example of the present invention is directed towards the
generation and analysis of libraries of thrombin inhibitors. This
example shall now be discussed.
[0129] Thrombin is a serine protease involved in both the blood
coagulation cascade and platelet activation. When the circulatory
system is injured, a cascade of reactions is initiated which leads
to the production of thrombin. Thrombin catalyzes the conversion of
fibrinogen to fibrin, which forms polymers, and the activation of
factor XIII, which catalyzes fibrin crosslinking leading to the
formation of fibrin clots. Thrombin also activates the thrombin
receptor, which together with other signals induces platelet
aggregation, adhesion and activation, and the formation of
haemostatic plugs. Aberrant activation or regulation of the
coagulation cascade is a major cause of morbidity and mortality in
numerous diseases of the cardiovascular system and their associated
surgical treatment. Current medical opinion holds that a triad of
treatment regimes, including thrombolytic, antiplatelet and
anticoagulant therapy, should be used in a variety of cardiac
diseases, including recurrent acute myocardial infarction,
peripheral arterial disease, atrial fibrillation and the prevention
of thromboembolic complications during valvular replacement,
orthopedic surgery and percutaneous angioplasty. There is also an
unmet therapeutic need for orally active anticoagulants in deep
vein thrombosis. Since thrombin catalyzes the terminal step in the
clotting cascade, and also plays a major role in platelet
activation, thrombin inhibitors should prove therapeutically
effective as anticoagulants, and should additionally possess
antiplatelet activity.
[0130] In the example being considered herein, the desired
bioactivity property is potent inhibition of the thrombin enzyme
which is involved in blood clotting. Competitive inhibition of
thrombin would prevent both the coagulation and platelet activation
processes mediated by thrombin. However, many other proteases in
blood and other tissues have specificity profiles similar to
thrombin. In particular, plasmin and tissue plasminogen activator,
which promote the hydrolysis of fibrin clots and thus have
functions crucial to the elimination of circulatory system
occlusions, are proteases with primary specificities similar to
thrombin. It is also desirable that therapeutically useful thrombin
inhibitors do not inhibit these proteases or other enzymes involved
in fibrinolysis. Therefore, the properties which are to be
optimized include potent thrombin inhibition, but weak or no
inhibition of enzymes such as plasmin, tissue plasminogen activator
and urokinase.
[0131] Each thrombin inhibitor generated by the present invention
preferably comprises three sites of variable structure. The use of
thrombin inhibitors having three sites is based on the goal, in
medicinal drug research, of obtaining a great deal of diversity
(both functional and structural) while minimizing molecular space
and weight. Trimers are preferably used since, generally, trimers
are smaller and lighter than compounds comprising greater numbers
of units, such as tetrameric compounds and pentameric compounds.
Obtaining drugs with minimum size and molecular weight is an
advantage because it generally minimizes cost and maximizes oral
bioavailability.
[0132] The present example (shown in FIG. 12) is directed towards
the generation and analysis of libraries of thrombin inhibitors of
type 1202 related to D-Phe-Pro-Arg 1204, wherein the initial
directed diversity library is composed of Y-proline-Z, where Y may
be one of ten D-Phe substitutes and Z one of 100-500 commercially
available primary amines from a Reagent Repository 114. The choice
of amines Z and D-Phe substitutes Y is determined under computer
control using the Synthesis Protocol Generator 104. The D-Phe
substitutes may be derived from any carboxylic acid or sulfonic
acid for compounds of type 1206 or, separately, may be a primary or
secondary amine linked to the peptide backbone as a urea for
compounds of type 1208. Preferably, the directed diversity library
208 for compounds of type 1206 is assembled by the Chemical
Synthesis Robot 112 using well known solid phase methods and is
released as mixtures of 10 compounds per well in a 96 well format
in accordance with the robotic synthesis instructions 204 received
from the Synthesis Protocol Generator 104. The initial directed
diversity library 208 is assembled using one amine Z and ten D-Phe
variants Y per well. More than one 96 well plate may be used, and
the resulting directed diversity library 208 may contain 1000-5000
members. The library 208 is then submitted to the analysis robot
116, which analyses the library 208 and generates data pertaining
thereto that can be used to evaluate the degree of inhibition of
thrombin and other enzymes of interest (such data is called
Structure-Activity Data 210).
[0133] Based on criteria set forth in the desired activity/property
profile 214 (FIG. 2) and the SAR data 210 obtained from the initial
directed diversity library, the second iteration directed diversity
library is generated using the ten best amines Z. The second
iteration directed diversity library 208 is synthesized using solid
phase methods and is released as one compound per well in a 96 well
format in accordance with the robotic synthesis instructions 204
received from the Synthesis Protocol Generator 104. The directed
diversity library 208 is generated from the ten selected amines Z
(one amine per well) using D-Phe and D-Phe substitutes Y producing
one D-Phe or D-Phe variant per well. This directed diversity
library 208 thus contains 100 members. The library 208 is then
submitted to the analysis robot 116, to evaluate the degree of
inhibition of thrombin and other enzymes of interest (as
represented by SAR data 210). This establishes the most active
members of the directed diversity library 208 as defined by the
criteria set forth in the desired property profile 214.
[0134] A third iteration directed diversity library is then
assembled based on SAR data 210 obtained from the second iteration
library as defined by the criteria set forth in the desired
property profile 214 using the ten best amines Z and additional
100-500 D-Phe substitutes Y chosen under computer control. The
D-Phe substitute Y may be derived from carboxylic acids or sulfonic
acids. The directed diversity library 208 is assembled using well
known solid phase methods and released as mixtures of ten compounds
per well in a 96 well format according to the robotic synthesis
instructions 204 received from the Synthesis Protocol Generator
104. Thus, the third iteration directed diversity library 208 is
assembled from ten amines and 100-500 D-Phe substitutes in a manner
analogous to the first iteration directed diversity library to
produce a 1000-5000 member library. The third iteration library 208
is then submitted to the analysis robot 116, to evaluate the degree
of inhibition of thrombin and other enzymes of interest (as
represented by SAR data 210).
[0135] Based on criteria set forth in the desired property profile
214 and SAR data 210 obtained from the third iteration directed
diversity library, the fourth iteration directed diversity library
is then generated from the 10 most active mixtures in the third
iteration directed diversity library. The fourth iteration directed
diversity library 208 is synthesized using solid phase methods
analogous to the first iteration directed diversity library and is
released as one compound per well in a 96 well format according to
the robotic synthesis instructions 204 received from the Synthesis
Protocol Generator 104. The fourth iteration directed diversity
library 208 is generated from the ten selected D-Phe variants using
the ten amines Z from the third iteration directed diversity
library. The fourth iteration library 208 is then submitted to the
analysis robot 116, to evaluate the degree of inhibition of
thrombin and other enzymes of interest (as represented by SAR data
210). This fourth iteration directed diversity library 208 thus
contains 100 members and establishes the most active members of the
library 208 as defined by the criteria set forth in the desired
property profile 214.
[0136] This process may be repeated any number of times (as
specified by user input, for example) under computer control.
[0137] Additionally, this iterative process is repeated for
compounds 1208. The new iterations of directed diversity libraries
208 are related to D-Phe substitutes wherein primary or secondary
amines are linked to the peptide backbone as a urea moiety. Four
generations of directed diversity libraries are performed as above
with these new D-Phe substitutes to produce a new chemically
distinct series of chemical leads.
[0138] While various embodiments of the present invention have been
described above, it should be understood that they have been
presented by way of example only, and not limitation. Thus, the
breadth and scope of the present invention should not be limited by
any of the above-described exemplary embodiments, but should be
defined only in accordance with the following claims and their
equivalents.
* * * * *