In Silico Exploration for New Antimalarials: Arylsulfonyloxy Acetimidamides as Prospective Agents

Journal of Chemical Information and Modeling

Volumn 55, Issue 8, 2015, Pages 1708-1719

  Verma, Saroj ^a   Debnath, Utsab ^a   Agarwal, Pooja ^a   Srivastava, Kumkum ^a   Prabhakar, Yenamandra S ^a  

^a CENTRAL DRUG RESEARCH INSTITUTE   (India)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL ENGINEERING; CHEMISTRY;

ANTIMALARIAL AGENT; BIOLOGICAL TARGETS; DATABASE ENTRY; DRUG RESISTANCE; IN-SILICO SCREENING; MOLECULAR DYNAMICS SIMULATIONS; P. FALCIPARUM; VIRTUAL SCREENING;

MOLECULAR DYNAMICS;

AMIDE; ANTIMALARIAL AGENT; CHOLINE KINASE; CYTIDINE TRIPHOSPHATE SYNTHASE; ENZYME INHIBITOR; GLUTATHIONE TRANSFERASE; LIGASE; SULFUR DERIVATIVE;

ANTAGONISTS AND INHIBITORS; CHEMISTRY; COMPUTER SIMULATION; DRUG DATABASE; DRUG DEVELOPMENT; DRUG EFFECTS; DRUG RESISTANCE; ENZYMOLOGY; HUMAN; IC50; MALARIA, FALCIPARUM; METABOLISM; MOLECULAR DOCKING; MOLECULAR DYNAMICS; PARASITOLOGY; PLASMODIUM FALCIPARUM;

AMIDES; ANTIMALARIALS; CARBON-NITROGEN LIGASES; CHOLINE KINASE; COMPUTER SIMULATION; DATABASES, PHARMACEUTICAL; DRUG DISCOVERY; DRUG RESISTANCE; ENZYME INHIBITORS; GLUTATHIONE TRANSFERASE; HUMANS; INHIBITORY CONCENTRATION 50; MALARIA, FALCIPARUM; MOLECULAR DOCKING SIMULATION; MOLECULAR DYNAMICS SIMULATION; PLASMODIUM FALCIPARUM; SULFUR COMPOUNDS;

EID: 84940214308     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/acs.jcim.5b00392     Document Type: Article

References (48)

1. World malaria report 2014; World Health Organization: Geneva, 2014; pp 1-227; http://www.who.int/malaria/publications/world-malaria-report-2014/wmr-2014-no-profiles.pdf.
2. Flannery, E. L.; Chatterjee, A. K.; Winzeler, E. A. Antimalarial Drug Discovery-Approaches and Progress Towards New Medicines Nat. Rev. Microbiol. 2013, 11, 849-862 10.1038/nrmicro3138
3. Njogu, P. M.; Chibale, K. Recent Developments in Rationally Designed Multitarget Antiprotozoan Agents Curr. Med. Chem. 2013, 20, 1715-1742 10.2174/0929867311320130010
4. Li, K.; Schurig-Briccio, L. A.; Feng, X.; Upadhyay, A.; Pujari, V.; Lechartier, B.; Fontes, F. L.; Yang, H.; Rao, G.; Zhu, W.; Gulati, A.; No, J. H.; Cintra, G.; Bogue, S.; Liu, Y. L.; Molohon, K.; Orlean, P.; Mitchell, D. A.; Freitas-Junior, L.; Ren, F.; Sun, H.; Jiang, T.; Li, Y.; Guo, R. T.; Cole, S. T.; Gennis, R. B.; Crick, D. C.; Oldfield, E. Multitarget Drug Discovery for Tuberculosis and other Infectious Diseases J. Med. Chem. 2014, 57, 3126-3139 10.1021/jm500131s
5. White, N. J. Antimalarial Drug Resistance J. Clin. Invest. 2004, 113, 1084-1092 10.1172/JCI21682
6. Bloland, P. B. Drug Resistance in Malaria; World Health Organization: Geneva, 2001; pp 1-27; http://www.who.int/csr/resources/publications/drugresist/malaria.pdf.
7. Gardner, M. J.; Hall, N.; Fung, E.; White, O.; Berriman, M.; Hyman, R. W.; Carlton, J. M.; Pain, A.; Nelson, K. E.; Bowman, S.; Paulsen, I. T.; James, K.; Eisen, J. A.; Rutherford, K.; Salzberg, S. L.; Craig, A.; Kyes, S.; Chan, M. S.; Nene, V.; Shallom, S. J.; Suh, B.; Peterson, J.; Angiuoli, S.; Pertea, M.; Allen, J.; Selengut, J.; Haft, D.; Mather, M. W.; Vaidya, A. B.; Martin, D. M.; Fairlamb, A. H.; Fraunholz, M. J.; Roos, D. S.; Ralph, S. A.; McFadden, G. I.; Cummings, L. M.; Subramanian, G. M.; Mungall, C.; Venter, J. C.; Carucci, D. J.; Hoffman, S. L.; Newbold, C.; Davis, R. W.; Fraser, C. M.; Barrell, B. Genome Sequence of the Human Malaria Parasite Plasmodium Falciparum Nature 2002, 419, 498-511 10.1038/nature01097
8. Hendriks, E. F.; O'Sullivan, W. J.; Stewart, T. S. Molecular Cloning and Characterization of the Plasmodium Falciparum Cytidine Triphosphate Synthetase Gene Biochim. Biophys. Acta, Gene Struct. Expression 1998, 1399, 213-218 10.1016/S0167-4781(98)00108-0
9. Ancelin, M. L.; Vial, H. J. Quaternary Ammonium Compounds Efficiently Inhibit Plasmodium Falciparum Growth in Vitro by Impairment of Choline Transport Antimicrob. Agents Chemother. 1986, 29, 814-820 10.1128/AAC.29.5.814
10. Hiller, N.; Fritz-Wolf, K.; Deponte, M.; Wende, W.; Zimmermann, H.; Becker, K. Plasmodium Falciparum Glutathione S-transferase - Structural and Mechanistic Studies on Ligand Binding and Enzyme Inhibition Protein Sci. 2006, 15, 281-289 10.1110/ps.051891106
11. Schomburg, I.; Chang, A.; Placzek, S.; Sohngen, C.; Rother, M.; Lang, M.; Munaretto, C.; Ulas, S.; Stelzer, M.; Grote, A.; Scheer, M.; Schomburg, D. BRENDA in 2013: Integrated Reactions, Kinetic Data, Enzyme Function Data, Improved Disease Classification: New Options and Contents in BRENDA Nucleic Acids Res. 2013, 41, D764-D772 10.1093/nar/gks1049
12. Irwin, J. J.; Shoichet, B. K. ZINC - a Free Database of Commercially Available Compounds for Virtual Screening J. Chem. Inf. Model. 2005, 45, 177-182 10.1021/ci049714+
13. SYBYL, version 7.3; Tripos Associates, St. Louis, MO, 2006.
14. Morris, G. M.; Huey, R.; Lindstrom, W.; Sanner, M. F.; Belew, R. K.; Goodsell, D. S.; Olson, A. J. AutoDock4 and AutoDockTools4: Automated Docking with Selective Receptor Flexibility J. Comput. Chem. 2009, 30, 2785-2791 10.1002/jcc.21256
15. Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kale, L.; Schulten, K. Scalable Molecular Dynamics with NAMD J. Comput. Chem. 2005, 26, 1781-1802 10.1002/jcc.20289
16. Wilkins, M. R.; Gasteiger, E.; Bairoch, A.; Sanchez, J. C.; Williams, K. L.; Appel, R. D.; Hochstrasser, D. F. Protein Identification and Analysis Tools in the ExPASy Server Methods Mol. Biol. 1999, 112, 531-552 10.1385/1-59259-584-7:531
17. Muller, S. A.; Kohajda, T.; Findeiss, S.; Stadler, P. F.; Washietl, S.; Kellis, M.; von Bergen, M.; Kalkhof, S. Optimization of Parameters for Coverage of low Molecular Weight Proteins Anal. Bioanal. Chem. 2010, 398, 2867-2881 10.1007/s00216-010-4093-x
18. Altschul, S. F.; Gish, W.; Miller, W.; Myers, E. W.; Lipman, D. J. Basic Local Alignment Search Tool J. Mol. Biol. 1990, 215, 403-410 10.1016/S0022-2836(05)80360-2
19. Kelley, L. A.; Sternberg, M. J. Protein Structure Prediction on the Web: a Case Study Using the Phyre Server Nat. Protoc. 2009, 4, 363-371 10.1038/nprot.2009.2
20. Cole, C.; Barber, J. D.; Barton, G. J. The Jpred 3 Secondary Structure Prediction Server Nucleic Acids Res. 2008, 36, W197-W201 10.1093/nar/gkn238
21. Webb, B.; Sali, A. Comparative Protein Structure Modeling Using MODELLER Curr. Protoc. Bioinformatics 2014, 47, 5.6.1-5.6.32 10.1002/0471250953.bi0506s47
22. Linding, R.; Jensen, L. J.; Diella, F.; Bork, P.; Gibson, T. J.; Russell, R. B. Protein Disorder Prediction: Implications for Structural Proteomics Structure 2003, 11, 1453-1459 10.1016/j.str.2003.10.002
23. Marchler-Bauer, A.; Derbyshire, M. K.; Gonzales, N. R.; Lu, S.; Chitsaz, F.; Geer, L. Y.; Geer, R. C.; He, J.; Gwadz, M.; Hurwitz, D. I.; Lanczycki, C. J.; Lu, F.; Marchler, G. H.; Song, J. S.; Thanki, N.; Wang, Z.; Yamashita, R. A.; Zhang, D.; Zheng, C.; Bryant, S. H. CDD: NCBI's Conserved Domain Database Nucleic Acids Res. 2015, 43, D222-D226 10.1093/nar/gku1221
24. Hall, T. A. BioEdit: a User-Friendly Biological Sequence Alignment Editor and Analysis Program for Windows 95/98/NT Nucl. Acids. Symp. Ser. 1999, 41, 95-98
25. Laskowski, R. A.; MacArthur, M. W.; Moss, D. S.; Thornton, J. M. PROCHECK: a Program to Check the Stereochemical Quality of Protein Structures J. Appl. Crystallogr. 1993, 26, 283-291 10.1107/S0021889892009944
26. Wiederstein, M.; Sippl, M. J. ProSA-Web: Interactive Web Service for the Recognition of Errors in Three-Dimensional Structures of Proteins Nucleic Acids Res. 2007, 35, W407-10 10.1093/nar/gkm290
27. Schuler, L. D.; Daura, X.; van Gunsteren, W. F. An Improved GROMOS96 Force Field for Aliphatic Hydrocarbons in the Condensed Phase J. Comput. Chem. 2001, 22, 1205-1218 10.1002/jcc.1078
28. Guex, N.; Peitsch, M. C.; Schwede, T. Automated Comparative Protein Structure Modeling with SWISS-MODEL and Swiss-PdbViewer: a Historical Perspective Electrophoresis 2009, 30, S162-S173 10.1002/elps.200900140
29. Humphrey, W.; Dalke, A.; Schulten, K. VMD: Visual Molecular Dynamics J. Mol. Graphics 1996, 14, 33-38 10.1016/0263-7855(96)00018-5
30. Pedretti, A.; Villa, L.; Vistoli, G. VEGA - an Open Platform to Develop Chemo-Bio-informatics Applications, Using Plug-in Architecture and Script Programming J. Comput.-Aided Mol. Des. 2004, 18, 167-173 10.1023/B:JCAM.0000035186.90683.f2
31. Video match. http://gromada.com/main/download.php (accessed June 16, 2015).
32. Lin, C. C.; Hsieh, T. H.; Liao, P. Y.; Liao, Z. Y.; Chang, C. W.; Shih, Y. C.; Yeh, W. H.; Chien, T. C. Practical Synthesis of N-substituted Cyanamides via Tiemann Rearrangement of Amidoximes Org. Lett. 2014, 16, 892-895 10.1021/ol403645y
33. Singh, S.; Srivastava, R. K.; Srivastava, M.; Puri, S. K.; Srivastava, K. In-Vitro Culture of Plasmodium Falciparum: Utility of Modified (RPNI) Medium for Drug-Sensitivity Studies using SYBR Green I Assay Exp. Parasitol. 2011, 127, 318-3121 10.1016/j.exppara.2010.08.007
34. Sharma, M.; Chauhan, K.; Chauhan, S. S.; Kumar, A.; Singh, S. V.; Saxena, J. K.; Agarwal, A.; Srivastava, K.; Kumar, S. R.; Puri, S. K.; Shah, P.; Siddiqi, M. I.; Chauhan, P. M. S. Synthesis of Hybrid 4-Anilinoquinoline Triazine as Potent Antimalarial Agents, their in Silico Modeling and Bioevaluation as Plasmodium Falciparum Transketolase and β-Hematin Inhibitors. Med MedChemComm 2012, 3, 71-79 10.1039/C1MD00188D
35. Lauritsen, I.; Willemoes, M.; Jensen, K. F.; Johansson, E.; Harris, P. Structure of the Dimeric form of CTP Synthase from Sulfolobus Solfataricus Acta Crystallogr., Sect. F: Struct. Biol. Cryst. Commun. 2011, 67, 201-208 10.1107/S1744309110052334
36. Goto, M.; Omi, R.; Nakagawa, N.; Miyahara, I.; Hirotsu, K. Crystal Structures of CTP Synthetase Reveal ATP, UTP, and Glutamine Binding Sites Structure 2004, 12, 1413-23 10.1016/j.str.2004.05.013
37. Binkowski, T. A.; Naghibzadeh, S.; Liang, J. CASTp: Computed Atlas of Surface Topography of Proteins Nucleic Acids Res. 2003, 31, 3352-3355 10.1093/nar/gkg512
38. MOE; The Molecular Operating Environment from Chemical Computing Group Inc., Montreal, Quebec, Canada; http://www.chemcomp.com.
39. Wernimont, A. K.; Pizarro, J. C.; Artz, J. D.; Amaya, M. F.; Xiao, T.; Lew, J.; Wasney, G.; Senesterra, G.; Kozieradzki, I.; Cossar, D.; Vedadi, M.; Schapira, M.; Bochkarev, A.; Arrowsmith, C. H.; Bountra, C.; Weigelt, J.; Edwards, A. M.; Hui, R.; Hills, T. Crystal Structure of Choline Kinase from Plasmodium Falciparum, PF14-0020. PDB; DOI: 10.2210/pdb3fi8/pdb.
40. Hiller, N.; Fritz-Wolf, K.; Deponte, M.; Wende, W.; Zimmermann, H.; Becker, K. Plasmodium Falciparum Glutathione S-Transferase - Structural and Mechanistic Studies on Ligand Binding and Enzyme Inhibition Protein Sci. 2006, 15, 281-289 10.1110/ps.051891106
41. Hofer, A.; Steverding, D.; Chabes, A.; Brun, R.; Thelander, L. Trypanosoma Brucei CTP synthetase: a Target for the Treatment of African Sleeping Sickness Proc. Natl. Acad. Sci. U. S. A. 2001, 98, 6412-6416 10.1073/pnas.111139498
42. Torres-Rivera, A.; Landa, A. Glutathione Transferases from Parasites: a Biochemical View Acta Trop. 2008, 105, 99-112 10.1016/j.actatropica.2007.08.005
43. Choubey, V.; Maity, P.; Guha, M.; Kumar, S.; Srivastava, K.; Puri, S. K.; Bandyopadhyay, U. Inhibition of Plasmodium Falciparum Choline Kinase by Hexadecyltrimethylammonium Bromide: a Possible Antimalarial Mechanism Antimicrob. Agents Chemother. 2007, 51, 696-706 10.1128/AAC.00919-06
44. Alberge, B.; Gannoun-Zaki, L.; Bascunana, C.; Tran van Ba, C.; Vial, H.; Cerdan, R. Comparison of the Cellular and Biochemical Properties of Plasmodium falciparum Choline and Ethanolamine Kinases Biochem. J. 2010, 425, 149-158 10.1042/BJ20091119
45. Hansch, C.; Leo, A. In Substituent Constants for Correlation Analysis in Chemistry and Biology; Wiley: New York, 1979; Chapter 6, pp 48-63.
46. Shan, Y.; Kim, E. T.; Eastwood, M. P.; Dror, R. O.; Seeliger, M. A.; Shaw, D. E. How does a Drug Molecule find its Target Binding Site? J. Am. Chem. Soc. 2011, 133, 9181-9183 10.1021/ja202726y
47. Stjernschantz, E.; Oostenbrink, C. Improved Ligand-Protein Binding Affinity Predictions using Multiple Binding Modes Biophys. J. 2010, 98, 2682-2691 10.1016/j.bpj.2010.02.034
48. Genheden, S.; Ryde, U. Improving the Efficiency of Protein-Ligand Binding Free-Energy Calculations by System Truncation J. Chem. Theory Comput. 2012, 8, 1449-1458 10.1021/ct200853g