AutoGrow 3.0: An improved algorithm for chemically tractable, semi-automated protein inhibitor design1

Journal of Molecular Graphics and Modelling

Volumn 44, Issue , 2013, Pages 104-112

  Durrant, Jacob D ^a   Lindert, Steffen ^b   Andrew McCammon, J ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Autogrow; Click chemistry; Computational chemistry; Drug design

Indexed keywords

AUTOMATION; BINDING ENERGY; CATALYSIS; COMPUTATIONAL CHEMISTRY; COMPUTER OPERATING SYSTEMS; CYTOLOGY; MOLECULES; OPEN SOURCE SOFTWARE; OPEN SYSTEMS; SYNTHESIS (CHEMICAL);

AUTOGROW; AUTOMATED OPTIMIZATION; BINDING AFFINITIES; CLICK CHEMISTRY; DRUG DESIGN; IMPROVED * ALGORITHM; INHIBITOR DESIGN; OPEN-SOURCE SOFTWARES; PROPERTY; PROTEIN INHIBITORS;

LIGANDS;

DIHYDROFOLATE REDUCTASE; LIGASE; LIGASE 1; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA; PROTEIN INHIBITOR; UNCLASSIFIED DRUG;

ARTICLE; AUTOGROW 3.0; BINDING AFFINITY; CLICK CHEMISTRY; COMPUTER PROGRAM; CONTROLLED STUDY; DRUG DESIGN; EVOLUTIONARY ALGORITHM; PRIORITY JOURNAL; RNA EDITING; TRYPANOSOMA BRUCEI;

TRYPANOSOMA BRUCEI;

AUTOGROW; CLICK CHEMISTRY; COMPUTATIONAL CHEMISTRY; DRUG DESIGN;

ALGORITHMS; DRUG DESIGN; FOLIC ACID ANTAGONISTS; LIGANDS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; PROTEIN BINDING; PROTEINS; SOFTWARE; TETRAHYDROFOLATE DEHYDROGENASE;

EID: 84885121005     PISSN: 10933263     EISSN: 18734243     Source Type: Journal    
DOI: 10.1016/j.jmgm.2013.05.006     Document Type: Article

References (47)

1. H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, et al., The protein data bank, Nucleic Acids Research 28 (2000) 235-242. (Pubitemid 30047768)
2. T.T. Talele, S.A. Khedkar, A.C. Rigby, Successful applications of computer aided drug discovery: moving drugs from concept to the clinic, Current Topics in Medicinal Chemistry 10 (2010) 127-141.
3. G. Schneider, U. Fechner, Computer-based de novo design of drug-like molecules, Nature Reviews Drug Discovery 4 (2005) 649.
4. J.A. McCammon, Computer-aided drug discovery: two antiviral drugs for HIV/AIDS, in: T. Schlick (Ed.), Innovations in Biomolecular Modeling and Simulations, vol. 2, Royal Society of Chemistry, 2012, pp. 316-319.
5. J.D. Durrant, R.E. Amaro, J.A. McCammon, AutoGrow: a novel algorithm for protein inhibitor design, Chemical Biology and Drug Design 73 (2009) 168-178.
6. V. Gillet, A.P. Johnson, P. Mata, S. Sike, P. Williams, SPROUT: a program for structure generation, Journal of Computer-Aided Molecular Design 7 (1993) 127.
7. J.B. Moon, W.J. Howe, Computer design of bioactive molecules: a method for receptor-based de novo ligand design, Proteins: Structure, Function, and Genetics 11 (1991)314.
8. H.-J. Bohm, The computerprogram LUDI: anew method forthede novo design of enzyme inhibitors, Journal of Computer-Aided Molecular Design 6 (1992) 61.
9. V.A. Gillet, A.P. Johnson, P. Mata, S. Sike, Automated structure design in 3D, Tetrahedron 3 (1990) 681.
10. S.H. Rotstein, M.A. Murcko, GroupBuild: a fragment-based method forde novo drug design, Journal of Medicinal Chemistry 36(1993) 1700.
11. R.S. Bohacek, C. McMartin, Multiple highly diverse structures complementary to enzyme binding-sites-results of extensive application of a de-novo design method incorporating combinatorial growth, Journal of the American Chemical Society 116(1994) 5560.
12. D.E. Clark, D. Frenkel, S.A. Levy, J. Li, C.W. Murray, B. Robson, et al., PROLIGAND: an approach to de novo molecular design. 1. Application to the design of organic molecules, Journal of Computer-Aided Molecular Design 9 (1995) 13.
13. D.R. Westhead, D.E. Clark, D. Frenkel, J. Li, C.W. Murray, B. Robson, et al., PROLIGAND: an approach to de novo molecular design. 1. Application to the design of organic molecules, Journal of Computer-Aided Molecular Design 9 (1995) 139.
14. R.S. DeWitte, E.I. Shakhnovich, SMoG: de novo design method based on simple, fast, and accurate free energy estimates. 1. Methodology and supporting evidence, Journal of the American Chemical Society 118 (1996) 11733.
15. CA. Lipinski, F. Lombardo, B.W. Dominy, P.J. Feeney, Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings, Advanced Drug Delivery Reviews 46 (2001) 3-26. (Pubitemid 33653411)
16. A.K. Ghose, V.N. Viswanadhan, J.J. Wendoloski, A knowledge-based approach in designing combinatorial or medicinal chemistry libraries for drug discovery. 1. A qualitative and quantitative characterization of known drug databases, Journal of Combinatorial Chemistry 1 (1999) 55-68.
17. M.F. Sanner, Python: a programming language for software integration and development, Journal of Molecular Graphics and Modelling 17 (1999) 57-61. (Pubitemid 30029318)
18. N.M. O'Boyle, M. Banck, CA. James, C Morley, T. Vandermeersch, G.R. Hutchison, Open Babel: an open chemical toolbox, Journal of Cheminformatics 3 (2011)33.
19. O. Trott, A.J. Olson, AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading, Journal of Computational Chemistry 31 (2009) 455-461.
20. E. Jones, T. Oliphant, P. Peterson, SciPy: Open Source Scientific Tools for Python, 2001.
21. J.D. Durrant, J.A. McCammon, AutoClickChem: click chemistry in silico, PLoS Computational Biology 8 (2012) e1002397.
22. S. Lindert, J.D. Durrant, J.A. McCammon, LigMerge: a fast algorithm to generate models of novel potential ligands from sets of known binders, Chemical Biology and Drug Design 80 (2012) 358-365.
23. J.D. Durrant, J.A. McCammon, NNScore: a neural-network-based scoring function forthe characterization of protein-ligand complexes, Journal of Chemical Information and Modeling 50 (2010) 1865-1871.
24. J.D. Durrant, J.A. McCammon, NNScore 2.0: a neural-network receptor-ligand scoring function, Journal of Chemical Information and Modeling 51 (2011) 2897-2903.
25. J.J. Irwin, B.K. Shoichet, ZINC-a free database of commercially available compounds for virtual screening, Journal of Chemical Information and Modeling 45 (2005) 177-182. (Pubitemid 40736970)
26. W.L. Jorgensen, D.S. Maxwell, J. TiradoRives, Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids, Journal of the American Chemical Society 118 (1996) 11225-11236. (Pubitemid 26399746)
27. G.A. Kaminski, R.A. Friesner, J. TiradoRives, W.L. Jorgensen, Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides, Journal of Physical Chemistry B105(2001)6474-6487. (Pubitemid 35339015)
28. J. Deng, A. Schnaufer, R. Salavati, K.D. Stuart, W.G. Hol, High resolution crystal structure of a key editosome enzyme from Trypanosoma brucei: RNA editing ligase 1, Journal of Molecular Biology 343 (2004) 601-613. (Pubitemid 39311608)
29. R.T. Gampe, V.G. Montana, M.H. Lambert, A.B. Miller, R.K. Bledsoe, M.V. Milburn, et al., Asymmetry in the PPAR gamma/RXR alpha crystal structure reveals the molecular basis of heterodimerization among nuclear receptors, Molecular Cell 5 (2000)545-555.
30. J.T. Bolin, D.J. Filman, D.A. Matthews, R.C. Hamlin, J. Kraut, Crystal-structures of Escherichia coli and Lactobacillus casei dihydrofolate-reductase refined at 1.7 a resolution.1. General features and binding of methotrexate, Journal of Biological Chemistry 257 (1982) 3650-3662.
31. T.J. Dolinsky, P. Czodrowski, H. Li, J.E. Nielsen, J.H. Jensen, G. Klebe, et al., PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations, Nucleic Acids Research 35 (2007) W5-W522.
32. T.J. Dolinsky, J.E. Nielsen, J.A. McCammon, N.A. Baker, PDB2PQR: an automated pipeline forthe setup of Poisson-Boltzmann electrostatics calculations, Nucleic Acids Research 32 (2004) W7-W665.
33. N. Huang, B.K. Shoichet, J.J. Irwin, Benchmarking sets for molecular docking, Journal of Medicinal Chemistry 49(2006) 6789-6801. (Pubitemid 44749746)
34. J.A. Hiss, M. Hartenfeller, G. Schneider, Concepts and applications of "natural computing" techniques in de novo drug and peptide design, Current Pharmaceutical Design 16 (2010) 1656-1665.
35. S.Q. Wang, X.C. Cheng, W.L. Dong, R.L. Wang, K.C Chou, Three new powerful oseltamivir derivatives for inhibiting the neuraminidase of influenza virus, Biochemical and Biophysical Research Communications 401 (2010) 188-191.
36. J.D. Durrant, J.A. McCammon, Potential drug-like inhibitors ofgroup 1 influenza neuraminidase identified through computer-aided drug design, Computational Biology and Chemistry 34(2010) 97-105.
37. J.D. Durrant, JA McCammon, Towards the development of novel Trypanosoma brucei RNA editing ligase 1 inhibitors, BMC Pharmacology 11 (2011)9.
38. S. Lindert, W. Zhu, Y.L. Liu, R. Pang, E. Oldfield, JA McCammon, Farnesyl diphosphate synthase inhibitors from in silico screening, Chemical Biology and Drug Design 81 (6) (2013) 742-748.
39. A. Schnaufer, A.K. Panigrahi, B. Panicucci, R.P. Igo Jr., R. Salavati, K. Stuart, An RNA ligase essential for RNA editing and survival of the bloodstream form of Trypanosoma brucei, Science 291 (2001) 2159-2162. (Pubitemid 32224448)
40. R.E. Amaro, A. Schnaufer, H. Interthal, W. Hol, K.D. Stuart, J.A. McCammon, Discovery of drug-like inhibitors of an essential RNA-editing ligase in Trypanosoma brucei, Proceedings of the National Academy of Sciences 105 (2008) 17278-17283.
41. R.E. Amaro, R.V. Swift, J.A. McCammon, Functional and structural insights revealed by molecular dynamics simulations of an essential RNA editing ligase in Trypanosoma brucei, PLOS Neglected Tropical Diseases 1 (2007) e68.
42. J.D. Durrant, R.E. Amaro, L. Xie, M.D. Urbaniak, M.A. Ferguson, A. Haapalainen, et al., A multidimensional strategy to detect polypharmacological targets in the absence of structural and sequence homology, PLoS Computational Biology 6 (2010)e1000648.
43. J.D. Durrant, L. Hall, R.V. Swift, M. Landon, A. Schnaufer, R.E. Amaro, Novel naphthalene-based inhibitors of Trypanosoma brucei RNA editing ligase 1, PLOS Neglected Tropical Diseases 4 (2010) e803.
44. R.L. Then, Antimicrobial dihydrofolate reductase inhibitors-achievements and future options: review, Journal of Chemotherapy 16 (2004)3-12. (Pubitemid 38519726)
45. A.A. Adjei, A review of the pharmacology and clinical activity of new chemotherapy agents for the treatment of colorectal cancer, British Journal of Clinical Pharmacology 48 (1999) 265-277. (Pubitemid 29417708)
46. T. Liu, Y. Lin, X. Wen, R.N. Jorissen, M.K. Gilson, BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities, Nucleic Acids Research 35 (2007) D198-D201. (Pubitemid 46056198)
47. M.O. Sinnokrot, E.F. Valeev, CD. Sherrill, Estimates of the ab initio limit for pi-pi interactions: the benzene dimer, Journal of the American Chemical Society 124 (2002)10887-10893.