Recent advances in pharmacophore modeling and its application to anti-influenza drug discovery

Expert Opinion on Drug Discovery

Volumn 8, Issue 4, 2013, Pages 411-426

  Shin, Woo Jin ^a   Seong, Baik Lin ^a,b  

^a Department of Biotechnology   (South Korea)

^b Yonsei University   (South Korea)

Author keywords

Antiviral; Drug discovery; Influenza virus; Pharmacophore modeling; Virtual screening

Indexed keywords

2 MERCAPTO 1,3,4 OXADIAZINE; 2 THIOXO THIAZOLIDIN 4 ONE; A 315675; CALCIUM CALMODULIN DEPENDENT PROTEIN KINASE II; CALCIUM CALMODULIN DEPENDENT PROTEIN KINASE IIBETA; FIBROBLAST GROWTH FACTOR RECEPTOR; GLYCOGEN SYNTHASE KINASE 3BETA; INFLUENZA VACCINE; INITIATION FACTOR 3; L 735 882; LANINAMIVIR; LANINAMIVIR OCTANOATE; MITOGEN ACTIVATED PROTEIN KINASE KINASE 3; NUCLEOPROTEIN; NUCLEOZIN; OSELTAMIVIR; PERAMIVIR; SIALIDASE; TRIMETHOXYBENZENE; UNCLASSIFIED DRUG; ZANAMIVIR;

ALGORITHM; ANTIVIRAL ACTIVITY; BINDING AFFINITY; CONFORMATIONAL TRANSITION; COST EFFECTIVENESS ANALYSIS; CRYSTAL STRUCTURE; DRUG DESIGN; DRUG STRUCTURE; DRUG TARGETING; DRUG USE; HIGH THROUGHPUT SCREENING; IC 50; INFLUENZA VIRUS A; MOLECULAR RECOGNITION; NONHUMAN; PH; PHARMACOPHORE; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN PROTEIN INTERACTION; QUANTITATIVE STRUCTURE ACTIVITY RELATION; REVIEW; VIRION; VIRUS REPLICATION;

ANTIVIRAL AGENTS; DRUG DESIGN; HUMANS; INFLUENZA, HUMAN; MODELS, THEORETICAL; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84875383056     PISSN: 17460441     EISSN: 1746045X     Source Type: Journal    
DOI: 10.1517/17460441.2013.767795     Document Type: Review

References (94)

1. Das K, Aramini JM, Ma L-C, et al. Structures of influenza A proteins and insights into antiviral drug targets. Nat Struct Mol Biol 2010;17(5):530-8
2. Medina RA, Garcia-Sastre A. Influenza A viruses: new research developments. Nat Rev Microbiol 2011;9(8):590-603
3. Tong S, Li Y, Rivailler P, et al. A distinct lineage of influenza A virus from bats. Proc Natl Acad Sci 2012;2012;109(11):4269-74
4. Zambon M. Lessons from the 1918 influenza. Nat Biotechnol 2007;25(4):433-4
5. Neumann G, Kawaoka Y. The first influenza pandemic of the new millennium. Influenza Other Respir Viruses 2011;5(3):157-66
6. Taubenberger JK, Kash JC. Influenza virus evolution, host adaptation, and pandemic formation. Cell Host Microbe 2010;7(6):440-51
7. Johnson NP, Mueller J. Updating the accounts: global mortality of the 1918-1920 "Spanish" influenza pandemic. Bull Hist Med 2002;76(1):105-15
8. Taubenberger JK, Reid AH, Lourens RM, et al. Characterization of the 1918 influenza virus polymerase genes. Nature 2005;437(7060):889-93
9. Treanor J. Weathering the Influenza Vaccine Crisis. N Engl J Med 2004;351(20):2037-40
10. von Itzstein M, Wu W-Y, Kok GB, et al. Rational design of potent sialidase-based inhibitors of influenza virus replication. Nature 1993;363(6428):418-23
11. Kim CU, Lew W, Williams MA, et al. Influenza neuraminidase inhibitors possessing a novel hydrophobic interaction in the enzyme active site: design, synthesis, and structural analysis of carbocyclic sialic acid analogues with potent anti-influenza activity. J Am Chem Soc 1997;119(4):681-90
12. Pinto LH, Lamb RA. Understanding the mechanism of action of the anti-influenza virus drug amantadine. Trends Microbiol 1995;3(7):271
13. De Clercq E. Antiviral agents active against influenza A viruses. Nat Rev Drug Discov 2006;5(12):1015-25
14. Hay AJ, Wolstenholme AJ, Skehel JJ, Smith MH. The molecular basis of the specific anti-influenza action of amantadine. EMBO J 1985;4(11):3021-4
15. Claas EC, Osterhaus AD, van Beek R, et al. Human influenza A H5N1 virus related to a highly pathogenic avian influenza virus. Lancet 1998;351(9101):472-7
16. Maines TR, Jayaraman A, Belser JA, et al. Transmission and pathogenesis of swine-origin 2009 A(H1N1) influenza viruses in ferrets and mice. Science 2009;325(5939):484-7
17. van der Vries E, Stelma FF, Boucher CA. Emergence of a multidrug-resistant pandemic influenza A (H1N1) virus. N Engl J Med 2010;363(14):1381-2
18. Kim KH, Kim ND, Seong BL. Discovery and development of anti-HBV agents and their resistance. Molecules 2010;15(9):5878-908
19. Safety fears raised over Tamiflu after teenage suicides in Japan. Br J Infection Control 2005;6(6):8
20. Yang SY. Pharmacophore modeling and applications in drug discovery: challenges and recent advances. Drug Discov Today 2010;15(11-12):444-50
21. Van Drie JH. Monty kier and the origin of the pharmacophore concept. Internet Electron J Mol Des 2007;6:271-9
22. Kier LB. Molecular orbital calculation of preferred conformations of acetylcholine, muscarine, and muse. Mol Pharmacol 1967;3(5):487-94
23. Kier LB. Molecular orbital theory in drug research. Academic Press, New York, NY, USA;1971;1-258
24. Wermuth C-G, Ganellin CR, Lindberg P, Mitscher LA. Chapter 36. Glossary of terms used in medicinal chemistry (IUPAC Recommendations 1997). In: James AB, editor. Annual reports in medicinal chemistry. Academic Press; 1998. p. 385-95
25. Sotriffer C, Klebe G. Identification and mapping of small-molecule binding sites in proteins: computational tools for structure-based drug design. Farmaco 2002;57(3):243-51
26. Langer T. Pharmacophores in drug research. Mol Informatics 2010;29(6-7):470-5
27. Löower M, Proschak E. Structure-based pharmacophores for virtual screening. Mol Inf 2011;30(5):398-404
28. Ortuso F, Langer T, Alcaro S. GBPM: GRID-based pharmacophore model: concept and application studies to protein-protein recognition. Bioinformatics 2006;22(12):1449-55
29. Foloppe N, Chen IJ. Conformational sampling and energetics of drug-like molecules. Curr Med Chem 2009;16(26):3381-413
30. Hahn M. Three-dimensional shape-based searching of conformationally flexible compounds. J Chem Inf Comput Sci 1997;37(1):80-6
31. Bowman AL, Makriyannis A. Approximating protein flexibility through dynamic pharmacophore models: application to fatty acid amide hydrolase (FAAH). J Chem Inf Model 2011;51(12):3247-53
32. Toba S, Srinivasan J, Maynard AJ, Sutter J. Using pharmacophore models to gain insight into structural binding and virtual screening: an application study with CDK2 and human DHFR. J Chem Inf Model 2006;46(2):728-35
33. Kubinyi H. Structure-based design of enzyme inhibitors and receptor ligands. Curr Opin Drug Discov Devel 1998;1(1):4-15
34. Wolber G, Langer T. LigandScout: 3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters. J Chem Inf Model 2005;45(1):160-9
35. Jones G, Willett P, Glen RC. A genetic algorithm for flexible molecular overlay and pharmacophore elucidation. J Comput Aided Mol Des 1995;9(6):532-49
36. Wolber G, Dornhofer AA, Langer T. Efficient overlay of small organic molecules using 3D pharmacophores. J Comput Aided Mol Des 2006;20(12):773-88
37. Tresadern G, Bemporad D. Modeling approaches for ligand-based 3D similarity. Future Med Chem 2010;2(10):1547-61
38. Kubinyi H. QSAR and 3D QSAR in drug design Part 1: methodology. Drug Discov Today 1997;2(11):457-67
39. Kubinyi H. Combinatorial and computational approaches in structure-based drug design. Curr Opin Drug Discov Devel 1998;1(1):16-27
40. Hoffren AM, Murray CM, Hoffmann RD. Structure-based focusing using pharmacophores derived from the active site of 17beta-hydroxysteroid dehydrogenase. Curr Pharm Des 2001;7(7):547-66
41. Richmond NJ, Abrams CA, Wolohan PR, et al. GALAHAD: 1. pharmacophore identification by hypermolecular alignment of ligands in 3D. J Comput Aided Mol Des 2006;20(9):567-87
42. Dixon SL, Smondyrev AM, Knoll EH, et al. PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results. J Comput Aided Mol Des 2006;20(10-11):647-71
43. Dixon SL, Smondyrev AM, Rao SN. PHASE: a novel approach to pharmacophore modeling and 3D database searching. Chem Biol Drug Des 2006;67(5):370-2
44. Schneidman-Duhovny D, Dror O, Inbar Y, et al. PharmaGist: a webserver for ligand-based pharmacophore detection. Nucleic Acids Res 2008;36(Web Server issue):W223-8
45. Rester U. From virtuality to reality-virtual screening in lead discovery and lead optimization: a medicinal chemistry perspective. Curr Opin Drug Discov Devel 2008;11(4):559-68
46. Sun H. Pharmacophore-based virtual screening. Curr Med Chem 2008;15(10):1018-24
47. Gao Q, Yang L, Zhu Y. Pharmacophore based drug design approach as a practical process in drug discovery. Curr Comput Drug Des 2010;6(1):37-49
48. Liwo A, Czaplewski C, Oldziej S, Scheraga HA. Computational techniques for efficient conformational sampling of proteins. Curr Opin Struct Biol 2008;18(2):134-9
49. Kim do Y, Kim KH, Kim ND, et al. Design and biological evaluation of novel tubulin inhibitors as antimitotic agents using a pharmacophore binding model with tubulin. J Med Chem 2006;49(19):5664-70
50. Huang Q, Li LL, Yang SY. PhDD: a new pharmacophore-based de novo design method of drug-like molecules combined with assessment of synthetic accessibility. J Mol Graph Model 2010;28(8):775-87
51. Schneider G, Fechner U. Computer-based de novo design of drug-like molecules. Nat Rev Drug Discov 2005;4(8):649-63
52. Köonig R, Stertz S, Zhou Y, et al. Human host factors required for influenza virus replication. Nature 2010;463(7282):813-17
53. Karlas A, Machuy N, Shin Y, et al. Genome-wide RNAi screen identifies human host factors crucial for influenza virus replication. Nature 2010;463(7282):818-22
54. Nelson N, Perzov N, Cohen A, et al. The cellular biology of proton-motive force generation by V-ATPases. J Exp Biol 2000;203(Pt 1):89-95
55. Ornitz DM, Itoh N. Fibroblast growth factors. Genome Biol 2001;2(3):3005.1-3005.12
56. Bertrand JA, Thieffine S, Vulpetti A, et al. Structural characterization of the GSK-3beta active site using selective and non-selective ATP-mimetic inhibitors. J Mol Biol 2003;333(2):393-407
57. Yamauchi T. Neuronal Ca2+/Calmodulin-dependent protein kinase II: discovery, progress in a quarter of a century, and perspective: implication for learning and memory. Biol Pharm Bull 2005;28(8):1342-54
58. Ferraris O, Lina B. Mutations of neuraminidase implicated in neuraminidase inhibitors resistance. J Clin Virol 2008;41(1):13-19
59. Babu YS, Chand P, Bantia S, et al. BCX-1812 (RWJ-270201): discovery of a novel, highly potent, orally active, and selective influenza neuraminidase inhibitor through structure-based drug design. J Med Chem 2000;43(19):3482-6
60. Kati WM, Montgomery D, Carrick R, et al. In vitro characterization of A-315675, a highly potent inhibitor of A and B strain influenza virus neuraminidases and influenza virus replication. Antimicrob Agents Chemother 2002;46(4):1014-21
61. Kati WM, Montgomery D, Maring C, et al. Novel alpha-and beta-amino acid inhibitors of influenza virus neuraminidase. Antimicrob Agents Chemother 2001;45(9):2563-70
62. Yamashita M, Tomozawa T, Kakuta M, et al. CS-8958, a prodrug of the new neuraminidase inhibitor R-125489, shows long-acting anti-influenza virus activity. Antimicrob Agents Chemother 2009;53(1):186-92
63. Knapp S, Zhao D. Synthesis of the sialidase inhibitor Siastatin B. Org Lett 2000;2(25):4037-40
64. Collins PJ, Haire LF, Lin YP, et al. Crystal structures of oseltamivir-resistant influenza virus neuraminidase mutants. Nature 2008;453(7199):1258-61
65. Russell RJ, Haire LF, Stevens DJ, et al. The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design. Nature 2006;443(7107):45-9
66. Li Q, Qi J, Zhang W, et al. The 2009 pandemic H1N1 neuraminidase N1 lacks the 150-cavity in its active site. Nat Struct Mol Biol 2010;17(10):1266-8
67. Obayashi E, Yoshida H, Kawai F, et al. The structural basis for an essential subunit interaction in influenza virus RNA polymerase. Nature 2008;454(7208):1127-31
68. He X, Zhou J, Bartlam M, et al. Crystal structure of the polymerase PAC-PB1N complex from an avian influenza H5N1 virus. Nature 2008;454(7208):1123- 6
69. Muratore G, Goracci L, Mercorelli B, et al. Small molecule inhibitors of influenza A and B viruses that act by disrupting subunit interactions of the viral polymerase. Proc Natl Acad Sci USA 2012;109(16):6247-52
70. Tomassini J, Selnick H, Davies ME, et al. Inhibition of cap (m7GpppXm)-dependent endonuclease of influenza virus by 4-substituted 2, 4-dioxobutanoic acid compounds. Antimicrob Agents Chemother 1994;38(12):2827-37
71. Hastings JC, Selnick H, Wolanski B, Tomassini JE. Anti-influenza virus activities of 4-substituted 2, 4-dioxobutanoic acid inhibitors. Antimicrob Agents Chemother 1996;40(5):1304-7
72. Tomassini JE, Davies ME, Hastings JC, et al. A novel antiviral agent which inhibits the endonuclease of influenza viruses. Antimicrob Agents Chemother 1996;40(5):1189-93
73. Parkes KE, Ermert P, Fassler J, et al. Use of a pharmacophore model to discover a new class of influenza endonuclease inhibitors. J Med Chem 2003;46(7):1153-64
74. Kim J, Lee C, Chong Y. Identification of potential influenza virus endonuclease inhibitors through virtual screening based on the 3D-QSAR model. SAR QSAR Environ Res 2009;20(1-2):103-18
75. Portela A, Digard P. The influenza virus nucleoprotein: a multifunctional RNA-binding protein pivotal to virus replication. J Gen Virol 2002;83(Pt 4):723-34
76. Bishop DH, Obijeski JF, Simpson RW. Transcription of the influenza ribonucleic acid genome by a virion polymerase. I. Optimal conditions for in vitro activity of the ribonucleic acid-dependent ribonucleic acid polymerase. J Virol 1971;8(1):66-73
77. Kao RY, Yang D, Lau LS, et al. Identification of influenza A nucleoprotein as an antiviral target. Nat Biotechnol 2010;28(6):600-5
78. Ye Q, Krug RM, Tao YJ. The mechanism by which influenza A virus nucleoprotein forms oligomers and binds RNA. Nature 2006;444(7122):1078-82
79. Shen YF, Chen YH, Chu SY, et al. E339..R416 salt bridge of nucleoprotein as a feasible target for influenza virus inhibitors. Proc Natl Acad Sci USA 2011;108(40):16515-20
80. Pinto LH, Holsinger LJ, Lamb RA. Influenza virus M2 protein has ion channel activity. Cell 1992;69(3):517-28
81. Tu Q, Pinto LH, Luo G, et al. Characterization of inhibition of M2 ion channel activity by BL-1743, an inhibitor of influenza A virus. J Virol 1996;70(7):4246-52
82. Tran L, Choi SB, Al-Najjar BO, et al. Discovery of potential M2 channel inhibitors based on the amantadine scaffold via virtual screening and pharmacophore modeling. Molecules 2011;16(12):10227-55
83. Russell RJ, Kerry PS, Stevens DJ, et al. Structure of influenza hemagglutinin in complex with an inhibitor of membrane fusion. Proc Natl Acad Sci USA 2008;105(46):17736-41
84. Smee DF, Bailey KW, Wong MH, et al. Treatment of influenza A (H1N1) virus infections in mice and ferrets with cyanovirin-N. Antiviral Res 2008;80(3):266-71
85. Nandi T. Proposed lead molecules against Hemagglutinin of avian influenza virus (H5N1). Bioinformation 2008;2(6):240-4
86. Stevens TH, Forgac M. Structure, function and regulation of the vacuolar (H+)-ATPase. Annu Rev Cell Dev Biol 1997;13:779-808
87. Jang YH, Byun YH, Lee YJ, et al. Cold-adapted pandemic 2009 H1N1 influenza live vaccine elicits cross-reactive immune responses against seasonal and H5 influenza A viruses. J Virol 2012;86(10):5953-8
88. Kim K-H, Kim ND, Seong B-L. Pharmacophore-based virtual screening: a review of recent applications. Expert Opin Drug Discov 2010;5(3):205-22
89. Catana C. Simple idea to generate fragment and pharmacophore descriptors and their implications in chemical informatics. J Chem Inf Model 2009;49(3):543-8
90. Dror O, Schneidman-Duhovny D, Inbar Y, et al. Novel approach for efficient pharmacophore-based virtual screening: method and applications. J Chem Inf Model 2009;49(10):2333-43
91. Wang R, Wang S. How does consensus scoring work for virtual library screening? An idealized computer experiment. J Chem Inf Comput Sci 2001;41(5):1422-6
92. Hayden F. Developing new antiviral agents for influenza treatment: what does the future hold? Clin Infect Dis 2009;48(Suppl 1):S3-13
93. Stouffer AL, Acharya R, Salom D, et al. Structural basis for the function and inhibition of an influenza virus proton channel. Nature 2008;451(7178):596-9
94. Cheng LS, Amaro RE, Xu D, et al. Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase. J Med Chem 2008;51(13):3878-94