-
1
-
-
0030039619
-
The art and practice of structure-based drug design: A molecular modeling perspective
-
Bohacek RS, McMartin C, Guida WC: The art and practice of structure-based drug design: a molecular modeling perspective. Med Res Rev 1996, 16:3-50. Review describing numerous examples of structure-based drug design 'successes'. The targets include carbonic anhydrase, cyclophilin, HIV-1 protease, neutral endopeptidase (NEP), angiotensin-converting enzyme (ACE), purine nucleoside phosphorylase (PNP), and thymidylate synthase.
-
(1996)
Med Res Rev
, vol.16
, pp. 3-50
-
-
Bohacek, R.S.1
McMartin, C.2
Guida, W.C.3
-
2
-
-
0031047662
-
Ortho-substituted benzofused macrocyclic lactams as zinc metalloprotease inhibitors
-
Ksander GM, de Jesus R, Yuan A, Ghai RD, McMartin C, Bohacek R: Ortho-substituted benzofused macrocyclic lactams as zinc metalloprotease inhibitors. J Med Chem 1997, 40:495-505. Benzofused macrocyclic lactams were designed as neutral endopeptidase (NEP) inhibitors using the crystal structure of thermolysin (TLN). A highly potent macrocycle was discovered. Good agreement was found between binding affinities predicted by modeling and those subsequently determined experimentally.
-
(1997)
J Med Chem
, vol.40
, pp. 495-505
-
-
Ksander, G.M.1
De Jesus, R.2
Yuan, A.3
Ghai, R.D.4
McMartin, C.5
Bohacek, R.6
-
3
-
-
0030009748
-
Nonpeptidic inhibitors of human neutrophil elastase. 7. Design, synthesis, and in vitro activity of a series of pyridopyrimidine trifluoromethyl ketones
-
Edwards PD, Andisik DW, Strimpler AM, Gomes B, Tuthill PA: Nonpeptidic inhibitors of human neutrophil elastase. 7. Design, synthesis, and in vitro activity of a series of pyridopyrimidine trifluoromethyl ketones. J Med Chem 1996, 39:1112-1124. Structure-based design of elastase inhibitors leading to highly active and orally available compounds.
-
(1996)
J Med Chem
, vol.39
, pp. 1112-1124
-
-
Edwards, P.D.1
Andisik, D.W.2
Strimpler, A.M.3
Gomes, B.4
Tuthill, P.A.5
-
4
-
-
0029063951
-
A priori prediction of activity for HIV-1 protease inhibitors employing energy minimization in the active site
-
Holloway MK, Wai JM, Halgren TA: A priori prediction of activity for HIV-1 protease inhibitors employing energy minimization in the active site. J Med Chem 1995, 38:305-317.
-
(1995)
J Med Chem
, vol.38
, pp. 305-317
-
-
Holloway, M.K.1
Wai, J.M.2
Halgren, T.A.3
-
5
-
-
0028036120
-
Multiple highly diverse structures complementary to enzyme binding sites: Results of extensive application of a de novo design method incorporating combinatorial growth
-
Bohacek RS, McMartin C: Multiple highly diverse structures complementary to enzyme binding sites: Results of extensive application of a de novo design method incorporating combinatorial growth. J Am Chem Soc 1994, 116:5560-5571.
-
(1994)
J Am Chem Soc
, vol.116
, pp. 5560-5571
-
-
Bohacek, R.S.1
McMartin, C.2
-
6
-
-
0026813925
-
The computer program LUDI: A new method for the de novo design of enzyme inhibitors
-
Boehm H-J: The computer program LUDI: a new method for the de novo design of enzyme inhibitors. J Comput Aided Mol Des 1992, 6:61-78.
-
(1992)
J Comput Aided Mol Des
, vol.6
, pp. 61-78
-
-
Boehm, H.-J.1
-
7
-
-
0038902210
-
Transformation of peptides into non-peptides. Synthesis of computer-generated enzyme inhibitors
-
Rich DH, Bohacek RS, Dales NA, Glunz P, Ripka AS: Transformation of peptides into non-peptides. Synthesis of computer-generated enzyme inhibitors. Chimia 1997, 51:45-47. One of the first reports of the use of a de novo program (GrowMol) in the discovery of a novel, low molecular weight pepsin inhibitor. GrowMol was used to discover novel molecular scaffolds for designing protease inhibitors. This paper describes the iterative process of selection and synthesis of computer-generated structures, determination of activity and reassessment of potency.
-
(1997)
Chimia
, vol.51
, pp. 45-47
-
-
Rich, D.H.1
Bohacek, R.S.2
Dales, N.A.3
Glunz, P.4
Ripka, A.S.5
-
8
-
-
85030047129
-
Combinatorial docking
-
Lausanne, Switzerland, in press
-
Boehm H-J: Combinatorial docking. In Proceedings of the 11th European Symposium on Quantitative Structure-Activity Relationships, Lausanne, Switzerland, 1997 in press. The de novo program LUDI was used to generate molecules in the active site of thrombin. Upon synthesis, one of these novel, low molecular weight compounds was found to inhibit thrombin. This is one of the first reports of the use of a de novo program in the discovery of enzyme inhibitors.
-
(1997)
Proceedings of the 11th European Symposium on Quantitative Structure-Activity Relationships
-
-
Boehm, H.-J.1
-
9
-
-
0029062889
-
De novo design of enzyme inhibitors by Monte Carlo ligand generation
-
Gehlhaar DK, Moerder KE, Zichi D, Sherman CJ, Ogden RC, Freer ST: De novo design of enzyme inhibitors by Monte Carlo ligand generation. J Med Chem 1995, 38:466-472.
-
(1995)
J Med Chem
, vol.38
, pp. 466-472
-
-
Gehlhaar, D.K.1
Moerder, K.E.2
Zichi, D.3
Sherman, C.J.4
Ogden, R.C.5
Freer, S.T.6
-
10
-
-
0348242299
-
CONCEPTS: New dynamic algorithm for de novo drug suggestions
-
Pearlman DA, Murcko MA: CONCEPTS: New dynamic algorithm for de novo drug suggestions. J Med Chem 1993, 10:1184-1193.
-
(1993)
J Med Chem
, vol.10
, pp. 1184-1193
-
-
Pearlman, D.A.1
Murcko, M.A.2
-
11
-
-
0029586802
-
An automated method for dynamic ligand design
-
Miranker A, Karplus M: An automated method for dynamic ligand design. Proteins 1995, 23:472-490.
-
(1995)
Proteins
, vol.23
, pp. 472-490
-
-
Miranker, A.1
Karplus, M.2
-
12
-
-
0027517544
-
Confirmation of usefulness of a structure construction program based on three-dimensional receptor structure for rational lead generation
-
Nishibata U, Itai A: Confirmation of usefulness of a structure construction program based on three-dimensional receptor structure for rational lead generation. J Med Chem 1993, 36:2921-2928.
-
(1993)
J Med Chem
, vol.36
, pp. 2921-2928
-
-
Nishibata, U.1
Itai, A.2
-
13
-
-
0039979333
-
Combinatorial design and combinatorial synthesis of enzyme inhibitors
-
Amsterdam: Elsevier
-
Rich DJ, Bohacek RS, Dales NA, Glunz P, Ripka AS: Combinatorial design and combinatorial synthesis of enzyme inhibitors. In Actualities de Chimie Therapeutic-22e serie. Amsterdam: Elsevier; 1996:101-111.
-
(1996)
Actualities de Chimie Therapeutic-22e Serie
, pp. 101-111
-
-
Rich, D.J.1
Bohacek, R.S.2
Dales, N.A.3
Glunz, P.4
Ripka, A.S.5
-
14
-
-
0026345685
-
Computer design of bioactive molecules: A method for receptor-based de novo ligand design
-
Moon JB, Howe WJ: Computer design of bioactive molecules: a method for receptor-based de novo ligand design. Proteins - Struct Funct Genet 1991, 11:314-328.
-
(1991)
Proteins - Struct Funct Genet
, vol.11
, pp. 314-328
-
-
Moon, J.B.1
Howe, W.J.2
-
15
-
-
0025988461
-
Automatic creation of drug candidate structures based on receptor structure. Starting point for artificial lead generation
-
Nishibata Y, Itai A: Automatic creation of drug candidate structures based on receptor structure. Starting point for artificial lead generation. Tetrahedron 1991, 47:8985-8990.
-
(1991)
Tetrahedron
, vol.47
, pp. 8985-8990
-
-
Nishibata, Y.1
Itai, A.2
-
16
-
-
0025916872
-
Functionality maps of binding sites: A multiple copy simultaneous search method
-
Miranker A, Karplus M: Functionality maps of binding sites: a multiple copy simultaneous search method. Proteins 1991, 11:29-34.
-
(1991)
Proteins
, vol.11
, pp. 29-34
-
-
Miranker, A.1
Karplus, M.2
-
17
-
-
0027193713
-
GroupBuild: A fragment-based method for de novo drug design
-
Rotstein SH, Murcko MA: GroupBuild: a fragment-based method for de novo drug design. J Med Chem 1993, 36:1700-1710.
-
(1993)
J Med Chem
, vol.36
, pp. 1700-1710
-
-
Rotstein, S.H.1
Murcko, M.A.2
-
18
-
-
0027586682
-
SPROUT: A program for structure generation
-
Gillet V, Johnson P, Mata P, Sike S, Williams P: SPROUT: a program for structure generation. J Comput Aided Mol Des 1993, 7:127-153.
-
(1993)
J Comput Aided Mol Des
, vol.7
, pp. 127-153
-
-
Gillet, V.1
Johnson, P.2
Mata, P.3
Sike, S.4
Williams, P.5
-
19
-
-
0029320501
-
PROLIGAND: An approach to de novo molecular design. 1. Application to the design of organic molecules
-
Clark DE, Frenkel D, Levy S, Li J, Murray CW, Robson B, Waszkowycz B, Westhead DR: PROLIGAND: An approach to de novo molecular design. 1. Application to the design of organic molecules. J Comput Aided Mol Des 1995, 9:13-32.
-
(1995)
J Comput Aided Mol Des
, vol.9
, pp. 13-32
-
-
Clark, D.E.1
Frenkel, D.2
Levy, S.3
Li, J.4
Murray, C.W.5
Robson, B.6
Waszkowycz, B.7
Westhead, D.R.8
-
20
-
-
0029348176
-
The atom assignment problem in automated de novo drug design. 1. Transferability of molecular fragment properties
-
Barakat MT, Dean PM: The atom assignment problem in automated de novo drug design. 1. Transferability of molecular fragment properties. J Comput Aided Mol Des 1995, 9:341-350.
-
(1995)
J Comput Aided Mol Des
, vol.9
, pp. 341-350
-
-
Barakat, M.T.1
Dean, P.M.2
-
21
-
-
0029320812
-
BUILDER v.2: Improving the chemistry of a de novo design strategy
-
Roe DC, Kuntz ID: BUILDER v.2: Improving the chemistry of a de novo design strategy. J Comput Aided Mol Des 1995, 9:269-282.
-
(1995)
J Comput Aided Mol Des
, vol.9
, pp. 269-282
-
-
Roe, D.C.1
Kuntz, I.D.2
-
22
-
-
0026696669
-
Definition and display of steric, hydrophobic, and hydrogen-bonding properties of ligand binding sites in proteins using Lee and Richards accessible surface: Validation of a high resolution graphical tool for drug design
-
Bohacek RS, McMartin C: Definition and display of steric, hydrophobic, and hydrogen-bonding properties of ligand binding sites in proteins using Lee and Richards accessible surface: validation of a high resolution graphical tool for drug design. J Med Chem 1992, 35:1671-1684.
-
(1992)
J Med Chem
, vol.35
, pp. 1671-1684
-
-
Bohacek, R.S.1
McMartin, C.2
-
23
-
-
0028454828
-
The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
-
Boehm H-J: The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. J Comput Aided Mol Des 1994, 8:243-256.
-
(1994)
J Comput Aided Mol Des
, vol.8
, pp. 243-256
-
-
Boehm, H.-J.1
-
24
-
-
0029623184
-
Computational methods to predict binding free energy in ligand-receptor complexes
-
Ajay, Murcko MA: Computational methods to predict binding free energy in ligand-receptor complexes. J Med Chem 1995, 38:4953-4967.
-
(1995)
J Med Chem
, vol.38
, pp. 4953-4967
-
-
Ajay, M.M.A.1
-
25
-
-
0029995624
-
VALIDATE: A new method for the receptor-based prediction of binding affinities of novel ligands
-
Head RD, Smythe ML, Oprea TJ, Waller CL, Green SM, Marshall GR: VALIDATE: A new method for the receptor-based prediction of binding affinities of novel ligands. J Am Chem Soc 1996, 118:3959-3969. A method for predicting binding affinity based on calculated physicochemical properties of the ligand and receptor-ligand complexes. Enthalpy of the binding is computed with molecular mechanics, whereas entropy of binding is estimated using properties such as complementary hydrophobic surface area. Three different sets of data were used to demonstrate the ability of VALIDATE to predict binding affinity. Excellent correlation between predicted and experimentally determined binding affinities were obtained for two of the data sets.
-
(1996)
J Am Chem Soc
, vol.118
, pp. 3959-3969
-
-
Head, R.D.1
Smythe, M.L.2
Oprea, T.J.3
Waller, C.L.4
Green, S.M.5
Marshall, G.R.6
-
26
-
-
0000934205
-
SMoG: A de novo design method based on simple, fast, and accurate free energy estimates. 1. Methodology and supporting evidence
-
DeWitte RS, Shakhnovich E: SMoG: a de novo design method based on simple, fast, and accurate free energy estimates. 1. Methodology and supporting evidence. J Am Chem Soc 1996, 118:11733-11744. A de novo computer program which uses a scoring function that is related to the free energy of binding through a knowledge-based potential.
-
(1996)
J Am Chem Soc
, vol.118
, pp. 11733-11744
-
-
DeWitte, R.S.1
Shakhnovich, E.2
-
27
-
-
33845377127
-
Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
-
Miyazawa S, Jernigan RL: Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules 1985, 18:534-552.
-
(1985)
Macromolecules
, vol.18
, pp. 534-552
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
28
-
-
0029119320
-
A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease inhibitor design
-
Wallqvist A, Jernigan RL, Covell DG: A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease inhibitor design. Protein Sci 1995, 4:1881-1903.
-
(1995)
Protein Sci
, vol.4
, pp. 1881-1903
-
-
Wallqvist, A.1
Jernigan, R.L.2
Covell, D.G.3
-
29
-
-
0029965861
-
CONCERTS: Dynamic connection of fragments as an approach to de novo ligand design
-
Pearlman DA, Murcko MA: CONCERTS: dynamic connection of fragments as an approach to de novo ligand design. J Med Chem 1996, 39:1651-1663. A de novo program which uses molecular fragments to build molecules in 3D binding sites. The fragments are continually reoriented in the active site using molecular dynamics and connected to form molecules when the geometry between proximal fragments is appropriate. When applied to the HIV-1 protease binding site, CONCERTS suggested ligands similar to known inhibitors.
-
(1996)
J Med Chem
, vol.39
, pp. 1651-1663
-
-
Pearlman, D.A.1
Murcko, M.A.2
-
30
-
-
0025225682
-
X-ray cristallographic structure of a complex between a synthetic protease of human immunodeficiency virus 1 and a substrate-based hydroxyethylamine inhibitor
-
Swain AL, Miller MM, Green J, Rich DH, Schneider J, Kent SBH, Wlodawer A: X-ray cristallographic structure of a complex between a synthetic protease of human immunodeficiency virus 1 and a substrate-based hydroxyethylamine inhibitor. Proc Natl Acad Sci USA 1990, 87:8805-8809.
-
(1990)
Proc Natl Acad Sci USA
, vol.87
, pp. 8805-8809
-
-
Swain, A.L.1
Miller, M.M.2
Green, J.3
Rich, D.H.4
Schneider, J.5
Kent, S.B.H.6
Wlodawer, A.7
-
31
-
-
0030076313
-
Functionality map analysis of the active site cleft of human thrombin
-
Grootenhuis PD, Karplus M: Functionality map analysis of the active site cleft of human thrombin. J Comput Aided Mol Des 1996, 10:1-10.
-
(1996)
J Comput Aided Mol Des
, vol.10
, pp. 1-10
-
-
Grootenhuis, P.D.1
Karplus, M.2
-
32
-
-
0030256270
-
Computational combinatorial ligand design: Application to human α-thrombin
-
Caflisch A: Computational combinatorial ligand design: application to human α-thrombin. J Comput Aided Mol Des 1996, 10:372-396.
-
(1996)
J Comput Aided Mol Des
, vol.10
, pp. 372-396
-
-
Caflisch, A.1
-
33
-
-
0028899391
-
Exploring the universe of molecules for new drugs
-
Bohacek R, McMartin C: Exploring the universe of molecules for new drugs. Nat Med 1995, 1:177-178.
-
(1995)
Nat Med
, vol.1
, pp. 177-178
-
-
Bohacek, R.1
McMartin, C.2
-
34
-
-
0030204057
-
Towards the automatic design of synthetically accessible protein ligands: Peptides, amides and peptidomimetics
-
Boehm H-J: Towards the automatic design of synthetically accessible protein ligands: Peptides, amides and peptidomimetics. J Comput Aided Mol Des 1996, 10:265-272. The original version of LUDI has been extended so that it is now able to take into account the synthetic accessibility of the constructed molecules. The program was applied to the enzymes elastase, renin and thermolysin.
-
(1996)
J Comput Aided Mol Des
, vol.10
, pp. 265-272
-
-
Boehm, H.-J.1
-
35
-
-
0029242926
-
DBMAKER: A set of programs to generate three-dimensional databases based upon user-specified criteria
-
Ho CMW, Marshall GR: DBMAKER: a set of programs to generate three-dimensional databases based upon user-specified criteria. J Comput Aided Mol Des 1995, 9:69-86.
-
(1995)
J Comput Aided Mol Des
, vol.9
, pp. 69-86
-
-
Ho, C.M.W.1
Marshall, G.R.2
-
36
-
-
0023965741
-
SMILES, a chemical language and information system. 1. introduction to methodology and encoding rules
-
Weiniger D: SMILES, a chemical language and information system. 1. introduction to methodology and encoding rules. J Chem Inform Comput Sci 1988, 28:31-38.
-
(1988)
J Chem Inform Comput Sci
, vol.28
, pp. 31-38
-
-
Weiniger, D.1
-
37
-
-
0009485610
-
-
Univ of Texas at Austin and Tripos Assoc: St Louis, MO
-
Rusinko IA, Skell JM, Balducci R, McGarity CM, Pearlman RS: Concord: a program for the rapid generation of high quality approximate 3-dimensional molecular structures. Univ of Texas at Austin and Tripos Assoc: St Louis, MO, 1988.
-
(1988)
Concord: a Program for the Rapid Generation of High Quality Approximate 3-dimensional Molecular Structures
-
-
Rusinko, I.A.1
Skell, J.M.2
Balducci, R.3
McGarity, C.M.4
Pearlman, R.S.5
-
38
-
-
0029687909
-
MOLMAKER: De novo generation of 3D databases for use in drug design
-
Clark DE, Firth MA, Murray CW: MOLMAKER: De novo generation of 3D databases for use in drug design. J Chem Inform Comput Sci 1996, 36:137-145. A computer program, MOLMAKER, is described which can generate de novo 3D databases. Structures are first generated in 2D using graph theory algorithms, converted to 3D using CONCORD, and entered into a database. This database can then be searched with 3D pharmacophore queries.
-
(1996)
J Chem Inform Comput Sci
, vol.36
, pp. 137-145
-
-
Clark, D.E.1
Firth, M.A.2
Murray, C.W.3
-
39
-
-
0028195186
-
Conformational searching in ISIS/3D databases
-
Moock TE, Henry DR, Ozkabak AG, Alamgir M: Conformational searching in ISIS/3D databases. J Chem Inform Comput Sci 1994, 34:184-189.
-
(1994)
J Chem Inform Comput Sci
, vol.34
, pp. 184-189
-
-
Moock, T.E.1
Henry, D.R.2
Ozkabak, A.G.3
Alamgir, M.4
-
40
-
-
0029988211
-
BOOMSLANG: A program for combinatorial structure generation
-
Cosgrove DA, Kenny PW: BOOMSLANG: A program for combinatorial structure generation. J Mol Graphics 1996, 14:1-5. This work describes an intriguing new method for generating user-specified chemical structures. Structures are first assembled combinatorially from user-defined 2D fragments. The resulting structures are converted to 3D. Low energy conformers of each structure are then generated and overlaid onto a pharmacophore. Finally, the structures are ranked according to strain energy and degree of overlap with the pharmacophore.
-
(1996)
J Mol Graphics
, vol.14
, pp. 1-5
-
-
Cosgrove, D.A.1
Kenny, P.W.2
-
41
-
-
0030220147
-
Current computational tools for de novo ligand design
-
Boehm H-J: Current computational tools for de novo ligand design. Curr Opin Biotechnol 1996, 7:433-436.
-
(1996)
Curr Opin Biotechnol
, vol.7
, pp. 433-436
-
-
Boehm, H.-J.1
-
42
-
-
0030474049
-
What can we learn from molecular recognition in protein-ligand complexes for the design of new drugs?
-
Boehm H-J, Klebe G: What can we learn from molecular recognition in protein-ligand complexes for the design of new drugs? Angew Chem Int Ed 1996, 35:2588-2614. A good introduction to the current understanding of noncovalent interactions observed in protein-ligand complexes. This review draws heavily on structural information. Computational methods for predicting ligand binding affinities, ligand binding conformations and for generating new ligands de novo in binding sites are also presented.
-
(1996)
Angew Chem Int Ed
, vol.35
, pp. 2588-2614
-
-
Boehm, H.-J.1
Klebe, G.2
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