Electrostatic Similarities between Protein and Small Molecule Ligands Facilitate the Design of Protein-Protein Interaction Inhibitors

PLoS ONE

Volumn 8, Issue 10, 2013, Pages

  Voet, Arnout ^a   Berenger, Francois ^a   Zhang, Kam Y J ^a  

^a RIKEN   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

INTEGRASE; INTEGRIN; PROTEIN INHIBITOR; PROTEIN MDM2; PROTEIN PROTEIN INTERACTION INHIBITOR; UNCLASSIFIED DRUG; X LINKED INHIBITOR OF APOPTOSIS;

ALGORITHM; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; CRYSTAL STRUCTURE; DRUG DESIGN; DRUG STRUCTURE; ELECTROSTATIC SIMILARITY; LIGAND BINDING; MOLECULAR DOCKING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; RETROSPECTIVE STUDY; STATIC ELECTRICITY;

LIGANDS; PROTEIN BINDING; PROTEINS; SOFTWARE; STATIC ELECTRICITY;

EID: 84885410322     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0075762     Document Type: Article

References (50)

1. Stumpf MPH, Thorne T, de Silva E, Stewart R, An HJ, et al. (2008) Estimating the size of the human interactome. Proc Natl Acad Sci U S A 105: 6959-64.
2. Venkatesan K, Rual JF, Vazquez A, Stelzl U, Lemmens I, et al. (2009) An empirical framework for binary interactome mapping. Nat Meth 6: 83 - 90.
3. Wells JA, McClendon CL, (2007) Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature 450: 1001-1009.
4. Verdine GL, Walensky LD, (2007) The Challenge of Drugging Undruggable Targets in Cancer: Lessons Learned from Targeting BCL-2 Family Members. Clin Cancer Res 13: 7264-7270.
5. Villoutreix BO, Labbe CM, Lagorce D, Laconde G, Sperandio O, (2012) A Leap into the Chemical Space of Protein-Protein Interaction Inhibitors. Curr Pharm Des 18: 4648-67.
6. Morelli X, Bourgeas R, Roche P (2011) Chemical and structural lessons from recent successes in protein-protein interaction inhibition (2P2I). Curr Opin Chem Biol 15: 475 - 81.
7. Dias R, de Azevedo WFJ, (2008) Molecular Docking Algorithms. Curr Drug Targets 9: 1040-7.
8. Horvath D (2011) Pharmacophore-Based Virtual Screening, volume 672 of Methods Mol Biol. Humana Press, 261-98 pp.
9. Fry DC, (2008) Drug-like inhibitors of protein-protein interactions: A structural examination of effective protein mimicry. Curr Protein Pept Sci 9: 240-7.
10. Fry DC, (2012) Small-Molecule Inhibitors of Protein-Protein Interactions: How to Mimic a Protein Partner. Curr Pharm Des 18: 4679-84.
11. Voet A, Zhang KYJ, (2012) Pharmacophore Modelling as a Virtual Screening Tool for the Discovery of Small Molecule Protein-protein Interaction Inhibitors. Curr Pharm Des 18: 4586-98.
12. Voet A, Banwell E, Sahu K, Heddle J, Zhang KYJ, (2013) Protein interface pharmacophore mapping tools for small molecule protein: Protein interaction inhibitor discovery. Curr Top Med Chem 13: 989-1001.
13. Nray-Szab G, (1993) Analysis of molecular recognition: steric electrostatic and hydrophobic complementarity. J Mol Recognit 6: 205-10.
14. Nicholls A, Honig B, (1991) A rapid finite difference algorithm, utilizing successive over-relaxation to solve the PoissonBoltzmann equation. Journal of Computational Chemistry 12: 435-445.
15. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA, (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci U S A 98: 10037-41.
16. Rohs R, West SM, Sosinsky A, Liu P, Mann RS, et al. (2009) The role of DNA shape in protein-DNA recognition. Nature 461: 1248-1253.
17. McCoy AJ, Chandana Epa V, Colman PM, (1997) Electrostatic complementarity at protein/protein interfaces. J Mol Biol 268: 570-84.
18. Blomberg N, Gabdoulline RR, Nilges M, Wade RC, (1999) Classification of protein sequences by homology modeling and quantitative analysis of electrostatic similarity. Proteins: Structure, Function, and Bioinformatics 37: 379-387.
19. Dlugosz M, Trylska J, (2008) Electrostatic similarity of proteins: Application of three dimensional spherical harmonic decomposition. The Journal of Chemical Physics 129: 015103.
20. Kieslich CA, Morikis D, Yang J, Gunopulos D, (2011) Automated computational framework for the analysis of electrostatic similarities of proteins. Biotechnology Progress 27: 316-325.
21. Gorham R, Kieslich C, Morikis D, (2011) Electrostatic Clustering and Free Energy Calculations Provide a Foundation for Protein Design and Optimization. Annals of Biomedical Engineering 39: 1252-1263.
22. Janin J, Chothia C, (1990) The structure of protein-protein recognition sites. Biol Chem 265: 16027-30.
23. Jones S, Thornton JM, (1995) Protein-protein interactions - a review of protein dimer structures. Progr Biophy molec Biol 63: 31-65.
24. Chau PL, Dean PM, (1994) Electrostatic complementarity between proteins and ligands. 1. Charge disposition, dielectric and interface effects. J Comput-Aided Mol Des 8: 51325.
25. Kieslich CA, Morikis D, (2012) The Two Sides of Complement C3d: Evolution of Electrostatics in a Link between Innate and Adaptive Immunity. PLoS Comput Biol 8: e1002840.
26. Dlugosz M, Antosiewicz JM, Zielinski P, Trylska J, (2012) Contributions of Far-Field Hydrodynamic Interactions to the Kinetics of Electrostatically Driven Molecular Association. J Phys Chem B 116: 5437-5447.
27. Muchmore SW, Souers AJ, Akritopoulou-Zanze I, (2006) The Use of Three-Dimensional Shape and Electrostatic Similarity Searching in the Identification of a Melanin-Concentrating Hormone Receptor 1 Antagonist. Chem Biol Drug Des 67: 174-176.
28. Naylor E, Arredouani A, Vasudevan SR, Lewis AM, Parkesh R, et al. (2009) Identification of a chemical probe for NAADP by virtual screening. Nat Chem Biol 5: 220-226.
29. OpenEye Scientific Software, Inc (2010) OEChem 1.7.4. Santa Fe, NM, USA: OpenEye Scientific Software, Inc.
30. Armstrong M, Morris G, Finn P, Sharma R, Moretti L, et al. (2010) ElectroShape: fast molecular similarity calculations incorporating shape, chirality and electrostatics. Journal of Computer-Aided Molecular Design 24: 789-801.
31. Cavalluzzo C, Voet A, Christ F, Singh BK, Sharma A, et al. (2012) De novo design of small molecule inhibitors targeting the LEDGF/p75-HIV integrase interaction. RSC Advances 2: 974-84.
32. Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA, (2004) PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res 32: W665-7.
33. Carbó R, Leyda L, Arnau M, (1980) How similar is a molecule to another? An electron density measure of similarity between two molecular structures. International Journal of Quantum Chemistry 17: 1185-1189.
34. Hodgkin EE, Richards WG, (1987) Molecular similarity based on electrostatic potential and electric field. International Journal of Quantum Chemistry 32: 105-110.
35. Leroy X, Doligez D, Frisch A, Garrigue J, Rémy D, et al. (2011) The OCaml system release 3.12 Documentation and user's manual. INRIA, France.
36. Danelutto M, Di Cosmo R (2012) A "Minimal Disruption" Skeleton Experiment: Seamless Map and Reduce Embedding in OCaml. Procedia Computer Science 9: 1837 - 1846.
37. Wade RC, Gabdoulline RR, De Rienzo F, (2001) Protein interaction property similarity analysis. International Journal of Quantum Chemistry 83: 122-127.
38. Davis ME, Madura JD, Luty BA, McCammon J (1991) Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian dynamics program. Computer Physics Communications 62: 187 - 197.
39. Petke J, (1993) Cumulative and discrete similarity analysis of electrostatic potentials and fields. Journal of Computational Chemistry 14: 928-933.
40. Hartman G, Egbertson M, Halczenko W, Laswell WL, Duggan ME, et al. (1992) Non-peptide fibrinogen receptor antagonists. 1. Discovery and design of exosite inhibitors. J Med Chem 35: 46402.
41. Christ F, Voet A, Marchand A, Nicolet S, Desimmie B, et al. (2010) Rational design of small-molecule inhibitors of the LEDGF/p75-integrase interaction and HIV replication. Nat Chem Biol 6: 442-8.
42. Arkin MR, Randal M, DeLano WL, Hyde J, Luong TN, et al. (2003) Binding of small molecules to an adaptive proteinprotein interface. Proc Natl Acad Sci U S A 100: 1603-8.
43. Press WH, Teukolsky SA, Vetterling WT, Flannery BP (2007) Numerical Recipes 3rd Edition: The Art of Scientific Computing. New York, NY, USA: Cambridge University Press.
44. Irwin JJ, Shoichet BK, (2005) ZINC A Free Database of Commercially Available Compounds for Virtual Screening. J Chem Inf Model 45: 177-82.
45. Huang N, Shoichet BK, Irwin JJ, (2006) Benchmarking Sets for Molecular Docking. J Med Chem 49: 6789-801.
46. Mysinger MM, Carchia M, Irwin JJ, Shoichet BK, (2012) Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking. J Med Chem 55: 6582-94.
47. Chemical Computing Group Inc (2011) Molecular Operating Environment (MOE) 10th edition. 1010 Sherbooke St. West, Suite #910, Montreal, QC, Canada, H3A 2R7: Chemical Computing Group Inc.
48. Naim M, Bhat S, Rankin KN, Dennis S, Chowdhury SF, et al. (2007) Solvated interaction energy (SIE) for scoring protein-ligand binding affinities. 1. Exploring the parameter space. J Chem Inf Model 47: 122-33.
49. Neudert G, Klebe G, (2011) fconv: Format conversion, manipulation and feature computation of molecular data. Bioinformatics 27: 1021-2.
50. Ullmann GM, Hauswald M, Jensen A, Kostić NM, Knapp EW, (1997) Comparison of the Physiologically Equivalent Proteins Cytochrome c6 and Plastocyanin on the Basis of Their Electrostatic Potentials. Tryptophan 63 in Cytochrome c6 May Be Isofunctional with Tyrosine 83 in Plastocyanin. Biochemistry 36: 16187-16196.