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Disease Drug Development Combinatorial Libraries
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Combinatorial Libraries

Torrey Pines Institute's drug discovery program is centered on our proprietary "high density" combinatorial libraries, otherwise known as mixture-based combinatorial libraries1,2. The utility of mixture-based combinatorial libraries has been demonstrated in more than 100 separate studies in which active compounds have been identified. These studies have been carried out by more than 50 separate research groups. Novel enzyme inhibitors3,4, agonists and antagonists to specific receptors5, antimicrobial, antifungal and antiviral compounds6, and B and T cell epitopes7 have been identified from such libraries, and have been extensively reviewed8,9.

Peptidic Combinatorial Libraries
Library Comments
Tetrapeptide

12 million compounds
Both acetylated and non-acetylated forms of the N-terminal are available. The carboxy-terminal of these libraries are amides.
Hexapeptide

47 million compounds
Both acetylated and non-acetylated forms of the N-terminal are available. The carboxy-terminal of these libraries are available both as amides and free acids.
Decapeptide

300 million compounds
Both acetylated and non-acetylated forms of the N-terminal are available. The carboxy-terminal of these libraries are amides.
Dodecapeptide

6 trillion compounds

Both acetylated and non-acetylated forms of the N-terminal are available. The carboxy-terminal of these libraries are amides.

Technology

Most combinatorial libraries at TPIMS are prepared in positional scanning format1 both to lower the cost and speed the deconvolution of the libraries. Information on synthesis, deconvolution, and screening techniques involved in combinatorial libraries can be found on this web site. For a more comprehensive discussion, please see our review "Mixture-based synthetic combinatorial libraries"2. For a more general discussion, see our review in Nature Medicine3, or for recent chemistry, see our review in the Journal of Organic Chemistry4.

Positional scanning synthetic combinatorial libraries (PS-SCLs) are composed of one sublibrary for each variable position. In the case of single position defined PS-SCLs, each compound present in a given mixture has a common individual building block at a given position, while the remaining positions are composed of mixtures of all of the building blocks used to prepare the library. A common single building block defines each relevant mixture. The sublibraries for each position represent the same collection of individual compounds, and they differ only by the location of the defined position. The screening data permit the identification of key functionalities at each diversity position. It is important to note, however, that the activity found for a mixture is due to the presence of specific active compound(s) within the mixture, and not the individual functionalities as separate independent entities. The combination of all positional functional groups identified as key elements leads to active individual compound(s).

As an illustration of the PS-SCL concept, the simple trifunctional combinatorial library composed of 27 compounds will be used. When these compounds are arranged as a PS-SCL, 9 separate mixtures (3 building blocks x 3 positions) are synthesized. It is important to note that each of the three sublibraries of mixtures, namely OXX, XOX, and XXO, contains the same compounds, and they differ only in the location of their defined functionalities.

combi-chemi_tech.gifcombi-chemi_tech.gif

This illustration assumes that only one compound (Et/F/SH) is active, with all of the other compounds being inactive. Since each sublibrary contains the same diversity of compounds, “Et/F/SH†is present in only one mixture in each of the three sublibraries. The only mixtures exhibiting activity will therefore be mixture 2 (Et/X/X) from sublibrary 1, mixture 4 (X/F/X) from sublibrary 2, and mixture 9 (X/X/SH) from sublibrary 3, since only these mixtures contain the active individual compound “Et/F/SHâ€. Following screening, one need synthesize only this one compound corresponding to the combination of these three building blocks in their respective positions to yield “Et/F/SHâ€. Testing of “Et/F/SH†in the assay of interest not only confirms that the selections made actually lead to the active compound, but also allows the determination of its biological activity. As stated above, the activity observed for each of the three mixtures (Et/X/X, X/F/X, and X/X/SH) is due to the presence of a single active compound “Et/F/SH†within each of these mixtures, and is not independently due to the individual building blocks Et, F, and SH that occupy the relevant defined positions.

In more complex libraries, more than one mixture is often found to exhibit significant activity at each position. In the process of selecting building blocks for the synthesis of individual compounds, one first selects based on relative activity, then on differences in the chemical character of the building block. While positional scanning deconvolution is usually highly preferred over iterative deconvolution due to the speed in which individual compounds can be identified, iterative deconvolution may also be performed from any of the sublibraries making up a positional scanning library. An iterative deconvolution can therefore be initiated at any of the diversity positions of a positional scanning library, and typically would be initiated with the most active mixture. While the preceding description illustrates the single defined PS-SCL, the same concept has been applied to libraries having more than one defined position. For example, a dual-defined hexapeptide PS-SCL composed of three sublibraries, each composed of 400 mixtures (OOXXXX, XXOOXX, XXXXOO), was successfully generated and screened by this laboratory for the identification of novel peptides having high affinity for the Nociceptin/Orphanin FQ receptor5, ORL181, as well as for exploring antibody specificity6.

  1. Pinilla, C., Appel, J.R., Blanc, P., Houghten, R.A. Rapid identification of high affinity peptide ligands using positional scanning synthetic peptide combinatorial libraries. Biotechniques 13: 901-905, 1992.

  2. Houghten, R.A., Pinilla, C., Appel, J.R., Blondelle, S.E., Dooley, C.T., Eichler, J., Nefzi, A., Ostresh, J.M. Mixture-based synthetic combinatorial libraries. J. Med. Chem. 42:3743-3778, 1999.

  3. Pinilla, C., Appel, J.R., Borras, E., Houghten, R.A. Advances in the use of synthetic combinatorial chemistry: Mixture-based libraries. Nat. Med. 9:118-122, 2003.

  4. Nefzi, A., Ostresh, J.M., Yu, Y., Houghten, R.A. Combinatorial chemistry: libraries from libraries, the art of the diversity-oriented transformation of resin-bound peptides and chiral polyamides to low molecular weight acyclic and heterocyclic compounds. J. Org. Chem. 69:3603-3609, 2004.

  5. Dooley, C.T., Houghten, R.A. Orphanin FQ/Nociceptin receptor binding studies. Peptides 21:949-960, 2000.

  6. Appel, J.R., Buencamino, J., Houghten, R.A., Pinilla, C. Exploring antibody polyspecificity using synthetic combinatorial libraries. Mol. Div. 2:29-34, 1996.

Available Combinatorial Libraries

Non-peptidic Combinatorial Libraries
Name Structure
1,4-Disubstituted Hydantoins

32,000 compounds

  1. J. Med. Chem. 42:3743, 1999.
  2. Drug Discovery Today 5:276, 2000.
3.gif3.gif
Benzothiazepenes

4,560 compounds

  1. Tet. Lett. 40:4939, 1999.
1.gif1.gif
Bicyclic Guanidines

102,459 compounds

  1. J. Org. Chem. 63: 8622, 1998.
  2. Bioorg. Med. Chem. Lett. 8:2273, 1998.
  3. Pure Appl. Chem. 70: 2141, 1998.
  4. J.Med.Chem. 42:3743, 1999.
17.gif17.gif
Bis-cyclic Guanidines

45,864 compounds

  1. Tetrahedron 3:612, 2001.
18.gif18.gif
Bis-cyclic Thioureas

45,864 compounds

  1. J. Comb. Chem. 3:68, 2001.
21.gif21.gif
Bis-Diketopiperazines

45,864 compounds

  1. J. Comb. Chem. 3:68, 2001.
19.gif19.gif
Bis-Piperazines

45,864 compounds

  1. J. Comb. Chem. 3:68, 2001.
20.gif20.gif
C-5-Acylamino Bicyclic Guanidines

72,283 compounds

16.gif16.gif
Dialkylated Hydantoins

32,400 compounds

  1. Bioorg. Med. Chem. Lett. 8:2273, 1998.
  2. J. Med. Chem. 42:3743, 1999.
2.gif2.gif
Imidazolpyridoindoles

25,300 compounds

  1. Pure. Appl. Chem. 70:2141, 1998.
4.gif4.gif
N-6-Acylamino Bicyclic Guanidines

1,100,512 compounds

15.gif15.gif
N,N-Dialkyl Ureas

32,400 compounds

  1. Bioorg. Med. Chem. Lett. 8:2273, 1998.
  2. Pure Appl. Chem. 70:2141, 1998.
  3. J. Med. Chem. 42:3743, 1999.
2-2.gif2-2.gif
N-Acyl Triamines

125,000 compounds

  1. Mol. Div. 4:91, 1999.
4-2.gif4-2.gif
N-Alkyl Dipeptidomimetics

57,500 compounds

  1. Bioorg. Med. Chem. 4:709, 1996.
3-2.gif3-2.gif
N-Benzyl Aminocyclic Ureas

118,400 compounds

  1. Bioorg. Med. Chem. Lett. 8:2273, 1998.
  2. Pure Appl. Chem. 70: 2141, 1998.
  3. J. Comb. Chem. 1:195, 1999.
  4. J. Med. Chem. 42:3743, 1999.
6.gif6.gif
N-Benzyl Diketopiperazines

31,320 compounds

  1. Tetrahedron 56:3319, 2000.
11.gif11.gif
N-Benzyl Piperazines

31,320 compounds

13.gif13.gif
N-Methyl Aminocyclic Thioureas

118,400 compounds

  1. Bioorg. Med. Chem. Lett. 8:2273, 1998.
  2. Pure Appl. Chem. 70, 2141, 1998.
  3. J. Comb. Chem. 1:195, 1999.
  4. J. Med. Chem. 42:3743, 1999.
9.gif9.gif
N-Methyl Aminocylic Ureas

118,400 compounds

  1. Bioorg. Med. Chem. Lett. 8:2273, 1998.
  2. Pure Appl. Chem. 70: 2141, 1998.
  3. J. Comb. Chem. 1:195, 1999.
  4. J. Med. Chem. 42:3743, 1999.
7.gif7.gif
N-Methyl Diketopiperazines

31,320 compounds

  1. Tetrahedron 56:3319, 2000.
10.gif10.gif
N-Methyl Piperazines

31,320 compounds

12.gif12.gif
N-Methyltriamines

31,320 compounds

6-2.gif6-2.gif
N-Per-Allylated Tetrapeptidomimetics

7,311,616 compounds

12-2.gif12-2.gif
N-Per-Benzylated Pentamines

7,311,616 compounds

  1. Mol. Div. 4:91, 1999.
11-2.gif11-2.gif
N-Per-Benzylated Tetrapeptidomimetics

7,311,616 compounds

  1. Mol. Div. 4:91, 1999.
13-2.gif13-2.gif
N-Per-Ethylated Pentamines

7,311,616 compounds

10-2.gif10-2.gif
N-Per-Methylated Pentamines

7,311,616 compounds

9-2.gif9-2.gif
N-Per-Methylated Tetrapeptidomimetics

7,311,616 compounds

7-2.gif7-2.gif
Pentamines

7,311,616 compounds

  1. J. Org. Chem. 63: 8622, 1998.
  2. Tetrahedron 55:335, 1999.
  3. Mol. Div. 4:91, 1999.
8-2.gif8-2.gif
Reduced Dipeptidomimetics

42,320 compounds

  1. Proc. Natl. Acad. Sci. USA 98:3519, 2001.
5.gif5.gif
Thiohydantoins

6,525 compounds

  1. Drug Discovery Today 5:276, 2000.
5-2.gif5-2.gif
Triphenylureas

85,248 compounds

  1. Bioorg. Med. Chem. Lett. 8:2273, 1998.
  2. Cancer Cell 5:25, 2004.
1-2.gif1-2.gif
Urea Linked Bicyclic Guanidines

47,600 compounds

  1. J. Comb. Chem. 3:189, 2001.
14.gif14.gif