Generation of virtual combinatorial libraries of compounds

FIELD OF THE INVENTION

The present invention is directed to methods for the generation of virtual combinatorial libraries of small molecules and other ligands. The members or molecules of the combinatorial libraries are generated in silico, and are designed to bind to identified target molecules in silico. The present invention also includes methods for docking the library members to desired target molecules whereby the library members are bound to such targets in silico.

BACKGROUND OF THE INVENTION

Combinatorial chemistry is a recent addition to the toolbox of chemists and represents a field of chemistry dealing with the synthesis of a large number of chemical entities. This is generally achieved by condensing a small number of reagents together in all combinations defined by a given reaction sequence. Advances in this area of chemistry include the use of chemical software tools and advanced computer hardware which has made it possible to consider possibilities for synthesis in orders of magnitude greater than the actual synthesis of the library compounds. The concept of “virtual library” is used to indicate a collection of candidate structures that would theoretically result from a combinatorial synthesis involving reactions of interest and reagents to effect those reactions. It is from this virtual library that compounds are selected to be actually synthesized.

Project Library (MDL Information Systems, Inc., San Leandro, Calif.) is said to be a desktop software system which supports combinatorial research efforts. (

Practical Guide to Combinatorial Chemistry,

A. W. Czaniik and S. H. DeWitt, eds., 1997, ACS, Washington, D.C.) The software is said to include an information-management module for the representation and search of building blocks, individual molecules, complete combinatorial libraries, and mixtures of molecules, and other modules for computational support for tracking mixture and discrete-compound libraries.

Molecular Diversity Manager (Tripos, Inc., St. Louis, Mo.) is said to be a suite of software modules for the creation, selection, and management of compound libraries. (

Practical Guide to Combinatorial Chemistry,

A. W. Czarnik and S. H. DeWitt, eds., 1997, ACS, Washington, D.C.) The LEGION and SELECTOR modules are said to be useful in creating libraries and characterizing molecules in terms of both 2-dimensional and 3-dimensional structural fingerprints, substituent parameters, topological indices, and physicochemical parameters.

Afferent Systems (San Francisco, Calif.) is said to offer combinatorial library software that creates virtual molecules for a database. It is said to do this by virtually reacting precursor molecules and selecting those that could be actually synthesized (Wilson,

C

&

EN,

Apr. 27, 1998, p.32).

While only Project Library and Molecular Diversity Manager are available commercially, these products do not provide facilities to efficiently track reagents and synthesis conditions employed for the introduction of fragments into the desired compounds being generated. Further, these products are unable to track mixtures of compounds that are generated by the introduction of multiple fragments by the use of multiple reagents. Therefore, it is desirable to have available methods for handling mixtures of compounds, as well as methods for the tracking of chemical reactions or transformations utilized in the synthesis of individual compounds and mixtures thereof.

SUMMARY OF THE INVENTION

In accordance with the present invention, there are provided methods for the generation of virtual combinatorial libraries of small molecules. These library molecules or members are generated in silico. Library members of larger molecular weight, such as those that are polymeric in nature, may also be generated using the methods of the present invention.

The present invention further provides methods for tracking and maintaining in databases, the fragments, reagents and unique combinations of these used for the in silico generation of the library members. Methods for interfacing the information necessary for the generation of libraries in silicon as instructions designed to direct the actual synthesis of the library members on an instrument such as a parallel array synthesizer, are also provided in the present invention.

The present invention also provides methods for the in silico docking of the library members to identified target molecules. According to these methods, individual library members are allowed to bind to the desired target molecule in order to identify those library members that demonstrate high affinity binding to the targets.

While there are a number of ways to identify molecular interaction sites, identify compounds likely to interact with molecular interaction sites of RNA and other biological molecules, synthesize such compounds and analyze their binding, preferred methodologies are described in U.S. patent applications filed on even date herewith and assigned to the assignee of this invention. These application bear U.S. Ser. Nos. 09/076,440, 09/076,447, 09/076,206, 09/076,214 and 09/076,404, each of which was filed May 12, 1998. All of the foregoing applications are incorporated by reference herein in their entirety.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1

shows a compound CI, dissected into its constituent fragments;

FIG. 2

shows the various identifying characteristics of the fragments comprising compound CI;

FIG. 3

shows the various identifying characteristics of the reagents used to introduce the corresponding fragments comprising compound CI;

FIG. 4

is a list of transformations that link the fragments and reagents associated with the generation of compound CI;

FIG. 5

is a schematic for the introduction of a common fragment using two different reagents;

FIG. 6

a

is a schematic for the use of a single reagent for the introduction of two different fragments into a compound;

FIG. 6

b

is a schematic showing the use of a common reagent for the introduction of a common fragment compound which can further be converted into two different fragments within the compound generated;

FIG. 7

shows the symbolic addition of fragments yielding a symbolic compound, compound CI′;

FIG. 8

is a symbolic reagent table;

FIG. 9

is a symbolic fragment table;

FIG. 10

is a symbolic transformation table;

FIG. 11

shows the generation of individual compounds, compounds C

1

and C

4

, and a mixture, mixture M

1

;

FIG. 12

shows the generation of further mixture, mixture M

2

;

FIG. 13

shows the generation of an additional mixture, mixture M

3

;

FIGS. 14

a

and

14

b

show the generation of an additional mixture, mixture M

4

;

FIG. 15

shows tables for tracking compound C

1

by the fragments added and or transformations performed;

FIG. 16

shows tables for tracking mixture M

1

by the transformations performed;

FIG. 17

shows tables for tracking mixture M

2

by the transformations performed; and

FIG. 18

shows tables for tracking mixture M

3

by the transformations performed.

The present invention is directed to computational methods employed for the in silico design and synthesis of combinatorial libraries of small molecules. The library members are generated in silico. The present invention also encompasses methods for tracking and storing the information generated during the in silico creation of library members into relational databases for later access and use. For the purposes of this specification, in silico refers to the creation in a computer memory, i.e., on a silicon or other like chip. Stated otherwise in silico means “virtual.”

According to the methods of the present invention, each compound or library member is dissected into its component or constituent parts referred to as fragments. Thus each compound that is generated is considered to be comprised of constituent fragments such that the sum of the molecular formulas of each of the fragments when added together totals the molecular formula of the compound generated. This dissection can be done in a variety of ways using chemical intuition. Thus a variety of components of fragments may be identified, each of which lend themselves to readily available reagents or reactions to generate diverse compounds. Further, each fragment is associated with at least one reagent, which represents the necessary chemical to be used to introduce that desired fragment into the compound being generated in silico. Dissection of compounds is based on the ease of synthesis of the reagents, commercial availability of the reagents, or a combination of both. Each of the fragments and reagents are stored in a relational database and are described in terms of identifying characteristics in the database. A fragment may be available from a variety of starting materials or reaction schemes. So when a library is being generated, which entails building a database, the fragments used in building that library can be stored in the database using the corresponding set of reagents and reaction conditions. When another library is to be generated, the fragment information stored in the database is now available for use in the generation of the new library of compounds. Similarly, when a third library is being generated, an even greater quantity of fragment, reagent, and reaction information is available in the database. Thus the methods of the present invention represent a dynamic method of building a database associated with building libraries of compounds. Initial library generation requires database input for fragments, reagents and transformations necessary for desired library. As the database grows, however, an increasing number of fragments and reagents are available in the database, which simplifies the generation of subsequent libraries of compounds and makes for more routine combinatorial synthetic efforts which can be accomplished with increasing ease and efficacy.

Fragments that are recorded in the database may be defined using identifying characteristics. Identifying characteristics defining fragments include a structural representation (as a 2-dimensional or 3-dimensional file), name, molecular weight, molecular formula, and attachment points or nodes (which denote sites of attachment or linkage of the fragment to other fragments of the compound being generated in silico). For the purpose of describing this invention, 2-dimensional representations are used, which are further simplified by the use of symbolic representations without reference to any particular chemical entities. The symbolic representations as used herein merely shows how fragments can be tracked to further the methods of the present invention. Other identifying characteristics may also be added to the database. Any characteristic that is desired to be tracked may be included in the database, including biological data, chemical reactivity rates, or other physical or chemical properties. Further, a fragment may also be created by modifying a reagent, and such modifications can be added to the database in terms of changes made to the reagent structure. Some of the identifying characteristics associated with any fragment may be common to those of the corresponding reagent. The related fragment thus created can then be stored in the relational database.

Identifying characteristics defining reagents include a structural representation, name, molecular weight, molecular formula, and source, such as a commercial source or a unique compound defined by the user. In case of a commercial source for the reagent, a catalog number or a link to a web page can be provided. Some commonalities may exist between the identifying characteristics associated with a reagent and those associated with the related fragment.

Further, in accordance with the present invention, a compound is the sum of various transformations. Transformation is the nomenclature attributed according to the present invention to a chemical synthesis. A transformation is a 1:1 link between a fragment and a reagent. Thus each transformation describes a unique conversion of a reagent into the corresponding fragment as introduced into a compound. When the compound being generated in silico is broken down into its component fragments, and the corresponding reagents have been identified, each fragment is linked to the corresponding reagent in a 1:1 relationship in order to describe a transformation. Thus, according to the present invention, a transformation may be viewed as the source of a fragment, thereby linking that fragment to a particular synthetic method or reaction. This description of a transformation according to the methods of the present invention also includes any auxiliary reagents or conditions used to effect the reaction denoted by the transformation, such as temperature and pressure requirements, catalysts, activators, solvents, or other additives.

Each combination of a fragment and reagent in a 1:1 link comprises a different transformation. Therefore, each transformation is unique. The present invention allows the tracking of fragments in terms of the reaction or transformation in which those fragments are introduced into the compounds of the library. Thus the database describes not only the compounds generated in terms of their constituent fragments, but also in terms of the synthetic pathways to produce those compounds, i.e. the related transformations to generate the library compounds. In this manner, a user of the present invention can generate a virtual library of compounds by simply selecting the fragments desired. Alternately, a user can also generate the compounds by selecting the chemical pathways required for actual synthesis of the compounds. This is accomplished by selecting the appropriate transformation associated with the generation of the desired compounds. Here, the user uses intuition or an in silico expert system to assist in selecting those transformations that are expected to allow generation or synthesis of the desired compounds. Each of the transformations created in silico is stored in the relational database and described in terms of identifying characteristics. Identifying characteristics defining transformations include the fragment, the reagent, and any auxiliary reagent or conditions necessary to effect the conversion of the reagent into the fragment as incorporated into the compound.

For example, consider in

FIG. 1

the in silico generation of compound CI according to the methods of the present invention. As shown in

FIG. 1

, upon dissection of CI (molecular formula of C

12

H

18

N

2

O

5

S

1

), its constituent fragments can be denoted as F

1

(molecular formula of H

2

NO), F

ii

(molecular formula of C

5

H

9

NO), and F

iii

(molecular formula of C

7

H

7

O

3

S). F

i

can also be a hydroxyl amine moiety linked to a solid support, i.e. P-O-NH, wherein P is a solid support. The sum of the molecular formulas of each of the fragments totals the molecular formula of compound CI.

As shown in

FIG. 2

, each of the fragments, F

i

, F

ii

, and F

iii

, are stored in a relational database, and are described in terms of identifying characteristics including a structural representation (which may be 2-dimensional or 3-dimensional), an identifier or name, molecular formula and attachment points or nodes which signify sites on the fragment which are linked to other fragments in compound CI. Other information such as molecular weight can also be associated with the fragment in the database.

As shown in

FIG. 3

, each of the corresponding reagents (R

i

, R

ii

, and R

iii

) are also stored in the relational database, and described in terms of identifying characteristics. Identifying characteristics used to define the reagents include a structural representation, and identifier or name and molecular formula. As with the fragment, other associated information such as molecular weight and source (such as a commercial source verses user-supplied, amount on hand, special handling, etc.) can also be stored in database in association with the individual reagents.

Next, each of the transformations associated with the in silico generation of compound CI are also stored in the relational database. As shown in

FIG. 4

, transformation T

i

links reagent R

i

with fragment F

i

, T

ii

links R

ii

with F

ii

, and T

iii

links R

iii

with F

iii

in a 1:1 relationship. Also, associated with each transformation is the necessary reaction condition, so that transformation T

i

is associated with reaction condition alpha, T

ii

with reaction condition beta, and T

iii

with reaction condition gamma. In the case of transformation T

iii

, reagent R

iii

may be a hydroxyl amine attached to a solid support so that fragment F

iii

can be represented as a hydroxyl amine moiety attached to a solid support.

While each fragment may be arrived at or generated by a unique corresponding reagent, the present invention also encompasses common fragments that may be generated via two or more reagents, so that two or more transformations can lead to the same fragment. As shown in

FIG. 5

, the common fragment CH

3

-CH

2

-C(═O)- may be arrived at via transformation A, which employs reagent X (an acid chloride), CH

3

-CH

2

-C(═O)Cl. The common fragment can also be introduced into a compound being generated in silico via transformation B, which employs reagent Y (an acid anhydride), CH

3

-CH

2

-C(═O)-O-C(═O)-CH

2

-CH

3

. Therefore, in accordance with the methods of the present invention, a common fragment can be introduced into the compound via two or more different reagents, and thus via two or more distinct transformations.

Alternately, a common reagent may be employed to effect two or more conversions forming two or more different fragments. This then represents two or more different transformations associated with different conditions. For example, as shown in

FIG. 6

a,

common reagent Z, CH

3

-CH

2

-NH

2

, can be employed to introduce an alkene fragment into the compound under conditions favoring Schiffs base formation. This represents transformation X. The same common reagent Z, however, can also be employed to introduce an amide fragment into the compound by using a different set of conditions, constituting transformation Y. Thus, a common reagent can introduce two or more different fragments into final compounds being generated in silico, and can be associated with two or more transformations depending upon the conditions associated with each of those transformations.

Additionally, once a fragment has been introduced into a compound, it can be further modified and converted into yet another fragment without effecting any other chemical changes within the compound formed. As an example, shown in

FIG. 6

b,

consider common reagent Z′, CH

3

-CH

2

-C(═O)CH

2

-Cl. Common reagent Z′ corresponds to a fragment having the structure CH

3

-CH

2

-C(═O)CH

2

-. Common reagent Z′ may be used to introduce an alkene fragment into the final compound, representing transformation X′, under conditions favoring reduction and dehydration. Common reagent Z′, however, can also be used to introduce a hydroxyalkyl fragment into the final compound under conditions favoring reduction. This represents transformation Y′.

The present invention may be described more generally, in terms of symbolic representations. Symbolic representations are used to describe the methods of the present invention because such representations are not limited to any particular chemistry. Symbolic representations merely denote the manner of using the present invention with multiple chemical entities. Each symbol used in the representations describing the present invention may represent one compound or multiple compounds because the present invention is not limited to tracking a single compound, but may be used to track a vast variety of compounds that can be generated.

FIG. 7

shows the symbolic addition of fragments which yields compound CI′. The fragments have structures F

i′

, F

ii′

, and F

iii

that are added sequentially to yield compound CI′. Structures F

i′

, F

ii′

, and F

iii′

are symbolic representations of the fragments that constitute compound CI′. These fragments can be stored in the relational database with the corresponding identifying characteristics for each of them, including the structural representation, name, molecular formula, and attachment sites or nodes. A visual inspection of compounds C

1

and C

1

′ revels the commonality between the chemical compound C

1

and the symbolic representation of a compound C

1

′ as well as the chemical structure of the fragments and the symbolic structure of the fragments.

A symbolic reagent table is shown in FIG.

8

. Reagents R

1

to R

10

can be described in terms of their structure, name, molecular formula, molecular weight, and source as well as other information that might be desired to be associated with the reagents.. R

3

and R

4

are two different reagents, but may be used to introduce the same fragment into a compound. This depends upon the reaction conditions used as reagent R

3

is used in a transformation associated with one set of conditions, while reagent R

4

is used in another transformation associated with a different set of conditions. Also, reagent R

5

is comprised of a mixture of two reagents or components. These may be (R)- and (S)-stereoisomers, D- and L-isomers, or may be two completely different reagents. While R

5

here is represented as a mixture of only two reagents or components, it will be recognized by the art-skilled that the methods of the present invention may be practiced using a mixture of two or more reagents. Typical reagent mixtures used in constructing libraries might have four, five or more individual reagent constituting the mixture.

FIG. 9

shows a symbolic fragment table. Fragments F

1

to F

8

are stored in the relational database with identifying characteristics that include a structural representation, name, molecular weight, molecular formula, and attachment sites or nodes. This table depicts symbolic representations of the various fragments that are introduced into the compounds of the library by the use of reagents symbolized in FIG.

8

. Thus it can be seen that fragment F

1

can be introduced into the compound by employing reagent R

1

. In fragment F

1

, X is an identifier for an attachment site. This indicates that X is the site at which F

1

attaches to another fragment in a compound. Similarly, fragment F

2

may be introduced into a compound (attaching at its X site) by employing reagent R

2

.

Fragment F

3

, however, can be introduced into the compound by the use of either reagent R

3

or R

4

. This allows for selection in the choice of the reagent used, and also allows for the consideration of the compatibility of the chemistries involved in the introduction of other fragments into the compound. Next, fragment F

4

(which is a mixture of fragments) can be introduced via the use of reagent R

5

, which is a mixture of reagents, as shown in FIG.

8

.

Fragment F

5

has two attachment sites, indicating that other fragments can attach at sites X and Y when F

5

has been incorporated into a compound. The presence of two attachment sites indicates that two attachments may be undertaken to build a compound when dealing with F

5

. Here again, as before, F

5

can be introduced into the compound using either of reagents R

6

or R

7

, depending upon the reaction conditions used and the chemistries involved when introducing other fragments to build the compound.

Fragments F

7

and F

8

can be introduced into a compound being created in silico by employing reagents R

9

and R

10

, respectively. Both these fragments have three attachment sites, indicating that three attachments to other fragments can occur when using these fragments to build a compound in silico. While fragments F

7

and F

8

have three attachment sites, it is recognized by the art-skilled that more than three attachment sites may be present in a fragment, allowing for more attachments to the fragment upon introduction into a compound (with the use of an appropriate reagent).

With the fragment and reagent tables in place in the relational database, a transformation table is created in accordance with the methods of the present invention, by linking a fragment with a reagent to form a unique transformation.

FIG. 10

shows a symbolic transformation table where a fragment is linked to a reagent in a 1:1 relationship. The identifying characteristics describing each transformation include a 1:1 link (a one to one link) between a fragment and a reagent, and the reaction conditions which include, solvent, concentration, temperature and pressure requirements, or auxiliary reagents necessary to effect the introduction of the fragment into the compound by using an appropriate reagent. Auxiliary reagents include catalysts, activators, acids, bases or other chemicals or additives necessary to effect the fragment introduction described. For example a base can always be added with an alkyl halide to scavenge the acid generated with use of the alkyl halide.

As seen in

FIG. 10

, transformation T

1

links fragment F

1

with reagent R

1

. T

1

also specifies the reaction conditions (a) associated with this 1:1 link. Similarly, T

2

links F

2

with R

2

under conditions &bgr;. Transformations T

3

and T

4

are each unique transformations despite being associated with a common fragment, F

3

. Transformation T

3

links common fragment F

3

with reagent R

3

under conditions &agr;, while transformation T

4

links the common fragment F

3

with another reagent, R

4

, under the different conditions, conditions &dgr;. For example reagent R

3

might be an alkyl chloride while R

4

might be an alkyl iodide. While these reagents are similar (they are both alkyl halides), they might be used under different reaction conditions. Use of different reagents to effect the introduction of the same fragment into the compound being generated in silico represents two unique transformations. This indicates two distinct or unique synthetic ways of introducing the same fragment into the compound. Depending upon the totality of the chemical steps involved in synthesizing the compound, one transformation may be preferred over other transformations that introduce the same fragment into the compound.

Transformation T

5

links fragment F

4

with reagent R

5

. R

5

is a mixture of reagents, such as (R)- and (S)-stereoisomers, D- and L-isomers, or two or more different reagents. As a result, use of R

5

leads to the introduction of a mixture of fragments F

4

into the compound. The art-skilled will recognize that the multiple reagents in R

5

are selected such that they are capable of being mixed together, do not react with each other, and react under similar reaction conditions. For example, R

5

may be comprised of a mixture of acid halides. These do not react with each other, but do react similarly with a nucleophile under similar conditions. It is also recognized by the art-skilled that a reagent is not limited to only one or two components or constituent reagents, but in fact may comprise of two, three, four, five or more reagents or components.

When using a mixture of reagents, each of the individual component reagents may have different chemical reactivity rates. If a correction is not made for this, this could result in their products being unequally represented in the product compounds. This is solved by adjusting the concentration of each reagent in the reaction mixture relative to the other reagents in the mixture such that the relative rates are the same. This is effected by comparing to the reactivity of each of the reagents to a chosen standard reagent. The standardized reactivity rates can then be used to adjust the concentration of each constituent reagent in the reagent mixture to compensate for the varied reaction rates. Thus a mixture of reagents with different reaction rates may be used in one reagent mixture to still generate equivalent quantities of the desired compounds in the library.

Transformations T

6

and T

7

are similar to transformations T

3

and T

4

except that conditions identifying each of these transformations are different. Transformation T

6

links fragment F

5

with reagent R

6

under conditions &egr;, while transformation T

7

links the same fragment F

5

with a different reagent R

7

under different conditions (condition &agr;). As the conditions associated with transformations T

6

and T

7

are different, this allows selection of compatible chemistries with other fragments during any particular synthesis being used. This is a very useful and very important consideration in actually synthesizing real libraries. When it is desired to introduce fragment F

5

into the compound, the actual chemistries used to build the compound can be initially be considered in selecting transformation T

6

or T

7

, and thus reagents R

6

or R

7

. This is in direct opposition to any chemical database generator that only considers the compound structure not the actual chemistries necessary to build a compound.

Transformations T

9

and T

10

link fragment F

7

with reagent R

9

and fragment F

8

with reagent R

10

, respectively. Both transformations are identified to be associated with reaction conditions &ggr;. Fragments F

7

and F

8

have three attachment sites, but it is recognized that these fragments may have more than three attachment sites, thereby increasing the complexity of the compounds generated, and increasing the number of rounds that may be employed to attach other fragments. For the three sites illustrated, if three sets of different reagent mixtures each have five reagents in the set are used, then 125 compounds will be generated for fragment F

7

and a further 125 compounds will be generated for fragment F

8

.

The methods of the present invention may be used to generate single compounds or mixtures of compounds. A mixture comprises two or more compounds and may involve the use of two or more reagents (thus introduction of two or more fragments) at the outset of library generation, introduction of a mixture of reagents (thus a mixture of fragments) at a subsequent stage of library generation, or a combination of both such techniques.

FIGS. 11 and 12

illustrate this aspect of the present invention.

As shown in

FIG. 11

, the methods of the present invention may be used to generate single compounds such as C

1

and C

4

, or may also be used to generate a mixture of compounds, M

1

, comprising compounds C

2

and C

3

. Library generation commences with selecting fragment F

7

(with three attachment sites), in the first round (i.e. round n). In the second synthesis round (i.e. round n+1), F

7

is combined with fragment F

2

, constituting synthetic pathway P

1

a

, and resulting in the formation of complex fragment CF

1

. F

7

possesses three attachment sites (i.e. X, Y and Z). Thus round n+1 will not be complete until each of X, Y and Z have been used, if desired, to attach other fragments to. Stepping around each of X, Y and Z, and attaching fragments to these sites, occurs in that sequential order. Once sites X, Y and Z of the fragment selected in the first synthesis round (i.e. round n) have been exhausted, stepping around the attachment sites present in the next added fragment constitutes the next synthesis round (i.e. the third synthesis round, or round n+2). Here again, when all desired attachment sites on this fragment have been used, that particular synthesis round is complete. This attachment iteration around the desired and available attachment sites of the fragments added continues until the desired compounds have been generated.

As shown in

FIG. 11

, CF

1

is next subjected to synthetic pathway P

1

b

wherein fragment F

1

is introduced into CF

1

, thereby forming complex fragment CF

2

. CF

2

is then subjected to synthetic pathway P

1

c

wherein fragment F

5

is added to CF

2

, leading to the formation of complex fragment CF

3

. This completes synthesis round n+1 (i.e. the second round of fragment introduction, or synthesis, to build the compound). As fragment F

5

has two attachment sites, CF

3

has an available attachment site (i.e. site Y). Introduction of fragments to this site (Y site) constitutes synthesis round n+2 (i.e. the third round) because all the desired attachment sites on the previously added fragment have been exhausted. Next, CF

3

is subjected to synthetic pathway P

2

wherein fragment F

4

is introduced into CF

3

at attachment site Y. As F

4

is a mixture of two components, a mixture (M

1

) of two compounds, C

2

and C

3

, is generated.

A single compound, however, may also be generated using the present scheme of fragment introduction. Thus, compound C

1

can be generated by subjecting CF

3

to synthetic pathway P

1

d

wherein CF

3

is combined with fragment F

3

, which attaches to site Y in CF

3

. The introduction of fragment F

3

into CF

3

constitutes the third synthesis round (i.e. round n+2), leading to the generation of C

1

.

Alternately, CF

3

can be subjected to synthetic pathway P

3

a

wherein fragment F

6

is introduced into CF

3

to form CF

4

. This represents the third synthesis round (i.e. round n+2). CF

4

has one more available attachment site (i.e. site Y) to which fragment F

2

may be attached via synthetic pathway P

3

b.

This leads to the generation of compound C

4

which is a compound of increased complexity because of the number of attachment sites on the chosen fragments and synthetic pathways employed. The addition of fragment F

6

to CF

4

constitutes the third synthesis round (i.e. round n+2). Addition of fragment F

2

to CF

4

represents the fourth synthesis round, or round n+

3

, because P

3

b

involves addition of a fragment (fragment F

2

) onto a site (i.e. site Y in CF

4

) which has been generated by adding fragment F

6

to CF

3

, thus exhausting the available attachment sites on the previously added fragment in CF

4

(i.e. fragment F

5

). That is, the addition of fragment F

6

completed round n+2 (or the third synthesis round) because F

6

attached to the last available attachment site on CF

3

(i.e. site Y in CF

3

).

For the reactions effected at path P

1

c

in

FIG. 11

, a single fragment (F

5

) can be added to CF

2

via use of either reagents R

6

or R

7

(as thus via the transformations associated with R

6

and R

7

). While these additions are represented as two unique transformations for the purpose of tracking in the database on the invention, these additions in effect perform the same chemical conversion. Thus, the simultaneous tracking of compounds generated according to the methods of the invention is useful not only in working with virtual libraries of compounds, but also provide the user with a choice of synthetic pathways along which the compounds can be actually synthesized. This tracking aspect of the present invention is, therefore, a novel and unique way to account for the fragments being introduced, the related transformations (or reactions) associated with the fragments, and the alternate transformations that lead to the introduction of a common fragment into the desired compounds. The present invention allows not only the tracking of individual compounds that are generated by the use of multiple reagents, but also allows for the simultaneous tracking of multiple compounds that are generated via multiple transformations. While the methods described herein represent the tracking aspects of the invention in terms of symbolic representations or tables, it is recognized by the art-skilled that a variety of computer algorithmic codes and techniques may be employed for the individual or simultaneous tracking aspects described above.

The present invention further provides methods for the one-pot generation of mixtures of compounds by commencing the library generation using different starting fragments in a one-pot fashion. One-pot generation or synthesis of compounds refers to the formation of multiple compounds in a single reaction vessel (i.e. one pot). This is possible if compatible chemistries are selected. Examples of such single vessels include but are not limited to multiple well plates, e.g. a 96-well plate, reactions flasks, e.g. a 25 mL flask, or even an industrial reactor. The reactions, or transformations, are performed in one vessel regardless of the size of the reaction vessel. The concept of one-pot synthesis is irrelevant to the generation of virtual libraries of compounds as these virtual libraries are merely generated in silico. The concept of one-pot synthesis becomes relevant, however, when the actual synthesis of libraries of compounds is to be undertaken. Thus the compounds can be tracked separately for compound building in order to generate distinct chemical structures, however, they can be group together for synthesis allowing them to be made in the same “pot.” An example of a one-pot synthesis was shown in

FIG. 11

with the addition of the complex reagent R

5

to form mixture M

1

. A further one-pot synthesis is shown in

FIG. 12

, where a further mixture of compounds is generated. Mixture M

2

comprising compounds C

1

and C

5

can be generated by starting with fragments F

7

and F

8

in the first synthesis round (i.e. round n). Each of these fragments have three attachment sites onto which other fragments can be introduced. As a result, subjecting the two fragments to synthetic pathway P

1

a

wherein F

7

and F

8

are combined with fragment F

5

at site X, results in the one-pot formation of complex fragments CF

1

and CF

5

. CF

1

and CF

5

are next subjected to synthetic pathway P

1

b

wherein fragment F

1

is introduced into CF

1

and CF

5

at site Y, thereby forming complex fragments CF

2

and CF

6

. CF

2

and CF

6

are next subjected to synthetic pathway P

1

c

wherein fragment F

5

is introduced into these complex fragments at site Z, forming CF

3

and CF

7

. This completes the second synthetic round (i.e. round n+1). As fragment F

5

contains two attachment sites, after introduction into CF

3

and CF

7

, there is still available an attachment site (i.e. site Y) for further introduction of another fragment Thus CF

3

and CF

7

are converted to a mixture (M

2

) of compounds C

1

and C

5

via synthetic pathway P

1

d

wherein CF

3

and CF

7

are combined with fragment F

3

which attaches to the Y site on fragment F

5

in CF

3

and CF

7

. The introduction of fragment F

3

at site Y in CF

3

and CF

7

represents the third synthetic round (i.e. round n+2).

Yet another symbolic example of the one-pot generation of mixtures of compounds, in accordance with the present invention, is shown in FIG.

13

. In silico generation of compounds commences with the selection of fragment F

7

, which has three sites of attachment (X, Y, and Z). This represents the first synthesis round (i.e. round n). Next, F

7

is subjected to synthetic pathway P

1

a

wherein F

7

is combined with fragment F

2

. F

2

attaches to site X on fragment F

7

, forming complex fragment CF

1

. At this stage, CF

1

is subjected to two synthetic pathways, P

1

b

and P

1

b

′. P

1

b

employs fragment F

1

which is introduced onto site Y on CF

1

, thereby forming complex fragment CF

2

, while P

1

b′

employs fragment F

3

which is introduced onto site Y on CF

1

, thereby forming complex fragment CF

8

. Thus a mixture of complex fragments (CF

2

and CF

8

) are formed. Both fragments, F

1

and F

3

can be introduced together (such as from a single reagent bottle when actual synthesis is being undertaken) for the one-pot generation of compounds if the chemistries associated with introduction of these fragments into the compounds are compatible. If not, these fragments can be introduced separately. Next, CF

2

and CF

8

are subjected to synthetic pathway P

1

c

wherein both complex fragments are combined with fragment F

5

which attaches to site Z on CF

2

and CF

8

, thereby forming complex fragments CF

3

and CF

9

. The formation of CF

3

and CF

9

completes the second synthesis round (i.e. round n+1). As fragment F

5

has two sites of attachment, site Y is still available for attachment to another fragment. Therefore, CF

3

is subjected to synthetic pathway P

3

wherein CF

3

is combined with fragment F

4

. Introduction of F

4

represents the third synthesis round (i.e. round n+2). F

4

is a mixture of fragments (and introduced by adding a mixture of reagents), as shown in FIG.

9

. As a result, synthetic pathway P

2

leads to the generation of compounds C

2

and C

3

. Simultaneously, CF

9

combines with fragment F

4

, via synthetic pathway P

2

′, leading to the generation of compounds C

7

and C

8

. Thus mixture M

3

is formed comprising compounds C

2

, C

3

, C

7

and C

8

.

The present invention also provides methods for the generation of increasingly complex mixtures of compounds. An example is shown in

FIGS. 14

a

and

14

b

where mixture M

4

is generated and comprises sixteen compounds. The compounds in mixture M

4

can be generated by starting with fragments F

7

and F

8

in the first synthesis round (i.e. round n). These fragments can then be combined with fragment F

2

, which is introduced at site X in each of F

7

and F

8

, forming complex fragment CF

1

and CF

5

. Following this, a mixture of fragments F

1

and F

3

are introduced into CF

1

and CF

5

at site Y of these complex fragments, leading to the formation of four complex fragments, CF

2

, CF

6

, CF

8

and CF

11

. These complex fragments are next combined with a mixture of fragments F

5

and F

6

. Both F

5

and F

6

have two attachment sites such that site X on F

5

and F

6

attaches to site Z on CF

2

, CF

6

, CF

8

and CF

11

forming a mixture of eight complex fragments, CF

3

, CF

7

, CF

9

, CF

12

, CF

13

, CF

14

, CF

15

and CF

16

. This completes the second synthesis round (i.e. round n+1). As fragments F

5

and F

6

have two attachment sites, X and Y, the abovementioned eight complex fragments have one more available attachment site (i.e. site Y) onto which another fragment may be introduced. Attachment of a fragment to site Y on these eight complex fragments represents the third synthesis round (i.e. round n+2). Next, fragment F

4

is introduced into CF

3

, CF

7

, CF

9

, CF

12

, CF

13

, CF

14

, CF

15

and CF

16

. As fragment F

4

is a mixture of two constituent fragments, sixteen compounds are generated: C

2

, C

3

, C

7

, C

8

, C

9

, C

10

, C

11

, C

12

, C

13

, C

14

, C

15

, C

16

, C

17

, C

18

, C

19

and C

20

. Thus it can be seen that by using multiple fragments in a one-pot fashion and combining with mixtures of fragments, mixtures of compounds of increasing complexity can be generated. The example in

FIGS. 14

a

and

14

b

shows sixteen unique compounds being generated as mixture M

4

when the library is generated by starting with two fragments. It is recognized by the art-skilled that if the library generation is commenced with more than two fragments or multiple fragments are added to the same precursor fragment, even more complex mixtures of compounds can be generated.

The present invention also provides methods for keeping track of fragment addition in the various synthesis rounds. This system of accounting is accomplished by tabulation of the synthesis rounds which are correlated with addition of fragments. While for the purposes of illustration of the invention, a tabulation method of tracking fragment addition is described herein, it will be recognized by the art-skilled that other algorithms, algorithmic codes, computer readable mediums and various software coding techniques know to those skilled in the computer arts may be used for such tracking. The tables tracking fragment addition can be used to produce structural representations of compounds and create virtual libraries where actual synthesis of the compounds is not desired. Tables tracking transformations, however, can be used to synthesize compounds by selecting the appropriate transformations, and in the case of multiple transformations, selecting the preferable transformations to introduce the required fragment into the compounds being synthesized.

FIG. 15

is descriptive of compound C

1

in terms of the fragments added in each synthesis round. The first synthesis round (i.e. round n) commences with the selection of fragment F

7

. This is followed by the sequential addition of fragments F

2

, F

1

and F

5

in the second synthesis round (i.e. round n+1). Finally, compound C

1

is generated by the addition of fragment F

3

in the third synthesis round (i.e. round n+2). The compounds thus generated can be stored as a 2-dimensional virtual library, or may be converted to a 3-dimensional virtual library that can be used for in silico docking to desired target molecules.

For the generation of virtual libraries of compounds and for docking the library members onto target molecules, it suffices to add compounds to the relational database in terms of its fragments to track the addition of fragments in the various synthetic rounds. However, when the actual synthesis of desired compounds of a library is to be undertaken, it becomes necessary to specify the actual synthetic steps, reagents, solvents, concentrations, auxiliary compounds needed and other various synthetic factors in order to effect such an actual synthesis of real chemical compounds. Such synthetic steps, reagents, solvents, concentrations and auxiliary compounds are, in fact, incorporated in to the above described transformations. Thus by employing the concept of transformations, the present invention provides methods to track the compounds generated not only in terms of the fragments added but as well as the synthetic parameters necessary for each synthesis round.

FIG. 15

also shows the generation of compound C

1

in terms of the various transformations employed in the synthesis rounds. Four synthesis pathways lead to the synthesis of compound C

1

because of the availability of multiple transformations that can introduce the same fragment into the compound being synthesized. Thus, as seen in

FIG. 15

, selection of fragment F

7

constitutes transformation T

9

in the first synthesis round (i.e. round n). This is followed by the addition of fragment F

2

which is achieved by employing transformation T

2

. Next, fragment F

1

is added via transformation T

1

. Fragment F

5

, however, may be added by employing either reagent R

6

via transformation T

6

along synthesis paths

1

and

3

, or reagent R

7

via transformation T

7

along synthesis paths

2

and

4

. Similarly, the final fragment F

3

can be added by using either reagent R

3

via transformation T

3

along synthesis paths

1

and

2

, or reagent R

4

via transformation T

4

along synthesis paths

3

and

4

. Thus

FIG. 15

shows that compound C

1

can be actually synthesized via one of four different synthetic schemes which can be tracked or tabulated and accounted for using the methods of the present invention. Each of the four tables is completely descriptive of each of the four synthetic pathways for the preparation of C

1

. Thus, a user of the present invention has available all the alternate pathways of performing the same reaction (i.e. introducing the same fragment), and can select the preferable or most appropriate synthetic route to preparing the desired compounds.

FIG. 16

shows a similar transformation tracking table for compounds C

2

and C

3

in mixture M

1

. Synthesis of compounds C

2

and C

3

commences with selection of fragment F

7

which represents transformation T

9

(step

1

in

FIG. 16

) in the first synthesis round (i.e. round n). Next, F

7

is combined with fragment F

2

via transformation T

2

in the second synthesis round (i.e. round n+1) (step

2

). In the same round, fragment F

1

, via transformation T

1

, and fragment F

5

, via transformation

7

are added sequentially (steps

3

and

4

). Finally, fragment F

4

is added in the third synthesis round (i.e. round n+2). As F

4

is a mixture of two constituent fragments (because of two constituent reagents), the table is duplicated at this stage (step

5

) to account for the different synthetic ways in which transformation T

5

may be accomplished (i.e. T

5

′ and T

5

2

). Step

5