Docking and 3D-QSAR investigations of pyrrolidine derivatives as potent neuraminidase inhibitors

Chemical Biology and Drug Design

Volumn 79, Issue 5, 2012, Pages 863-868

  Sun, Jiaying ^a   Mei, Hu ^b  

^a SICHUAN UNIVERSITY OF ARTS AND SCIENCE   (China)

^b CHONGQING UNIVERSITY   (China)

Author keywords

3D QSAR; Docking; Pyrrolidine derivatives

Indexed keywords

AMINO ACID; PYRROLIDINE DERIVATIVE; SIALIDASE INHIBITOR; ZANAMIVIR;

ALMOND MODEL; ANIMAL EXPERIMENT; ANIMAL MODEL; ARTICLE; COMFA MODEL; COMSIA MODEL; CONTROLLED STUDY; CRYSTAL STRUCTURE; DRUG DESIGN; DRUG SCREENING; ELECTROSTATIC PRECIPITATION; HYDROGEN BOND; HYDROPHOBICITY; INFLUENZA VIRUS A; MOLECULAR DOCKING; MOLECULAR INTERACTION; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTOMOL; QUANTITATIVE STRUCTURE ACTIVITY RELATION; RAT; THREE DIMENSIONAL IMAGING; TOPOMER COMFA MODEL;

ANIMALS; ANTIVIRAL AGENTS; BINDING SITES; DRUG DESIGN; HUMANS; HYDROGEN BONDING; MODELS, MOLECULAR; NEURAMINIDASE; ORTHOMYXOVIRIDAE; ORTHOMYXOVIRIDAE INFECTIONS; PYRROLIDINES; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84862800270     PISSN: 17470277     EISSN: 17470285     Source Type: Journal    
DOI: 10.1111/j.1747-0285.2012.01330.x     Document Type: Article

References (37)

1. Verma R.P., Hansch C. (2006) A QSAR study on influenza neuraminidase inhibitors. Bioorg Med Chem;14:982-996.
2. Helenius A. (1992) Unpacking the incoming influenza virus. Cell;69:577-578.
3. Kim C.U., Lew W., Williams M.A., Liu H., Zhang L., Swaminathan S., Bischofberger N., Chen M.S., Mendel D.B., Tai C.Y., Laver W.G., Stevens R.C. (1997) 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;119:681-690.
4. Chand P., Babu Y.S., Bantia S., Rowland S., Dehghani A., Kotian P.L., Hutchison T.L., Ali S., Brouillette W., El-Kattan Y., Lin T.H. (2004) Synthesis and inhibitory activity of benzoic acid and pyridine derivatives on influenza neuraminidase. J Med Chem;47:1919-1929.
5. Maring C.J., Stoll V.S., Zhao C., Sun M., Krueger A.C., Stewart K.D., Madigan D.L. et al. (2005) Structure-based characterization and optimization of novel hydrophobic binding interactions in a series of pyrrolidine influenza neuraminidase inhibitors. J Med Chem;48:3980-3990.
6. Hollister A.S., Sheridan W.P. (2011) The emergency use authorization of peramivir IV: a view from the manufacturer. Clin Pharmacol Ther;89:172-174.
7. Gonzalez R., Massoomi F., Neff W. (2009) Emergency-use authorization of peramivir. Am J Health Syst Pharm;66:2162-2163.
8. Birnkrant D., Cox E. (2009) The emergency use authorization of peramivir for treatment of 2009 H1N1 influenza. N Engl J Med;361:2204-2207.
9. O'Donoghue S.I., Goodsell D.S., Frangakis A.S., Jossinet F., Laskowski R.A., Nilges M., Saibil H.R., Schafferhans A., Wade R.C., Westhof E., Olson A.J. (2010) Visualization of macromolecular structures. Nat Methods;7(Suppl):42-55.
10. Verma J., Khedkar V.M., Coutinho E.C. (2010) 3D-QSAR in drug design - a review. Curr Top Med Chem;10:95-115.
11. Jain A.N. (2003) Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine. J Med Chem;46:499-511.
12. Lee S.-H., Van H.T.M., Yang S.H., Lee K.-T., Kwon Y., Cho W.-J. (2009) Molecular design, synthesis and docking study of benz[b]oxepines and 12-oxobenzo[c]phenanthridinones as topoisomerase 1 inhibitors. Bioorg Med Chem Lett;19:2444-2447.
13. Ruppert J., Welch W., Jain A.N. (1997) Automatic identification and representation of protein binding sites for molecular docking. Protein Sci;6:524-533.
14. Clark R.D., Strizhev A., Leonard J.M., Blake J.F., Matthew J.B. (2002) Consensus scoring for ligand/protein interactions. J Mol Graph Model;20:281.
15. Jones G., Willet P., Glen R.C., Leach A.R., Taylor R. (1997) Development and validation of a genetic algorithm for flexible docking. J Mol Biol;267:727.
16. Muegge I., Martin Y.C. (1999) A general and fast scoring function for protein-ligand interactions: a simplified potential approach. J Med Chem;42:791-804.
17. Kuntz I.D., Blaney J.M., Oatley S.J., Langridge R., Ferrin T.E. (1982) A geometric approach to macromolecule-ligand interactions. J Mol Biol;161:269-288.
18. Eldridge M.D., Murray C.W., Auton T.R., Paolini G.V., Mee R.P. (1997) The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J Comput Aid Mol Des;11:425-445.
19. Varghese J.N., Epa V.C., Colman P.M. (1995) Three-dimensional structure of the complex of 4-guanidino-Neu5Ac2en and influenza virus neuraminidase. Protein Sci;4:1081-1087.
20. Smith B.J., McKimm-Breshkin J.L., McDonald M., Fernley R.T., Varghese J.N., Colman P.M. (2002) Structural studies of the resistance of influenza virus neuramindase to inhibitors. J Med Chem;45:2207-2212.
21. Varghese J.N., Smith P.W., Sollis S.L., Blick T.J., Sahasrabudhe A., McKimm-Breschkin J.L., Colman P.M. (1998) Drug design against a shifting target: a structural basis for resistance to inhibitors in a variant of influenza virus neuraminidase. Structure;6:735-746.
22. Muthas D., Sabnis Y.A., Lundborg M., Karlén A. (2008) Is it possible to increase hit rates in structure-based virtual screening by pharmacophore filtering? An investigation of the advantages and pitfalls of post-filtering J Mol Graph Model;26:1237-1251.
23. Clark R.D. (2008) A ligand's-eye view of protein binding. J Comput Aid Mol Des;22:507-521.
24. Pastor M., Cruciani G., McLay I., Pickett S., Clementi S. (2000) A novel class of alignment-independent three-dimensional molecular descriptors. J Med Chem;43:3233-3243.
25. Cramer R.D. III, Patterson D.E., Bunce J.D. (1988) Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. J Am Chem Soc;110:5959-5967.
26. Klebe G., Abraham U. (1999) Comparative molecular similarity index analysis (CoMSIA) to study hydrogen bonding properties and to score combinatorial libraries. J Comput Aid Mol Des;13:1-10.
27. Böhm M., Stürzebecher J., Klebe G. (1999) 3D QSAR analyses using CoMFA and CoMSIA to elucidate selectivity differences of inhibitors binding to trypsin, thrombin and factor Xa. J Med Chem;42:458-477.
28. Bush B.L., Nachbar R.B. (1993) Sample-distance partial least-squares-PLS optimized for many variables, with application to CoMFA. J Comput Aid Mol Des;7:587-619.
29. Cramer R.D., Cruz P., Stahl G., Curtiss W.C., Campbell B., Masek B.B., Soltanshahi F. (2008) Virtual screening for R-groups, including predicted pIC50 contributions, within large structural databases, using Topomer CoMFA. J Chem Inf Model;48:2180-2195.
30. Cramer R.D. (2003) Topomer CoMFA: a design methodology for rapid lead optimization. J Med Chem;46:374-388.
31. Cramer R.D., Wendt B. (2007) Pushing the boundaries of 3D-QSAR. J Comput Aided Mol Des;21:23-32.
32. Renner S., Derksen S., Radestock S., Mörchen F. (2008) Maximum common binding modes (MCBM): consensus docking scoring using multiple ligand information and interaction fingerprints. J Chem Inf Model;48:319-332.
33. 2. J Mol Graph Model;20:269-276.
34. Wang G.T., Chen Y.W., Wang S., Gentles R., Sowin T., Kati W., Muchmore S., Giranda V., Stewart K.t., Sham H., Kempf D., Graeme Laver W. (2001) Design, synthesis, and structural analysis of influenza neuraminidase inhibitors containing pyrrolidine cores. J Med Chem;44:1192-1201.
35. Zhang J., Wang Q., Fang H., Xu W.F., Liu A.L., Du G.H. (2007) Design, synthesis, inhibitory activity, and SAR studies of pyrrolidine derivatives as neuraminidase inhibitors. Bioorg Med Chem;15:2749-2758.
36. Krueger A.C., Xu Y., Kati W.M., Kempf D.J., Maring C.J., McDaniel K.F., Molla A., Montgomery D., Kohlbrenner W.E. (2008) Synthesis of potent pyrrolidine influenza neuraminidase inhibitors. Bioorg Med Chem Lett;18:1692-1695.
37. Wallace A.C., Laskowski R.A., Thornton J.M. (1995) LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng;8:127-134.