Reaching beyond HIV/HCV: Nelfinavir as a potential starting point for broad-spectrum protease inhibitors against dengue and chikungunya virus

RSC Advances

Volumn 5, Issue 104, 2015, Pages 85938-85949

  Bhakat, Soumendranath ^a   Delang, Leen ^b   Kaptein, Suzanne ^b   Neyts, Johan ^b   Leyssen, Pieter ^b   Jayaprakash, Venkatesan ^c  

^a LUND UNIVERSITY   (Sweden)

^b REGA INSTITUTE FOR MEDICAL RESEARCH   (Belgium)

^c BIRLA INSTITUTE OF TECHNOLOGY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ASSAYS; BINDING ENERGY; DISEASES; FREE ENERGY; HYDROGEN BONDS;

ANTIVIRAL ACTIVITIES; BINDING FREE ENERGY; BROAD SPECTRUM; COMPUTATIONAL ANALYSIS; PEPTIDOMIMETICS; POTENTIAL INHIBITORS; PROTEASE INHIBITOR; SELECTIVITY INDEX;

VIRUSES;

EID: 84944754654     PISSN: None     EISSN: 20462069     Source Type: Journal    
DOI: 10.1039/c5ra14469h     Document Type: Article

References (58)

1. http://www.nature.com/drugdisc/news/articles/nrd1766.html
2. C. P. Adams V. V. Brantner Estimating the cost of new drug development: is it really 802 million dollars? Health Aff. 2006 25 420 428
3. J. A. DiMasi R. W. Hansen H. G. Grabowski The price of innovation: new estimates of drug development costs J. Health Econ. 2003 22 151 185
4. Drug discovery for neglected diseases, Nat. Rev. Drug Discovery, 2008, 7, 955
5. E. Chatelain J.-R. Ioset Drug discovery and development for neglected diseases: the DNDi model Drug Des., Dev. Ther. 2011 5 175 181
6. I. H. Gilbert Drug discovery for neglected diseases: molecular target-based and phenotypic approaches J. Med. Chem. 2013 56 7719 7726
7. M. D. AbdulHameed S. Chaudhury N. Singh H. Sun A. Wallqvist G. J. Tawa Exploring polypharmacology using a ROCS-based target fishing approach J. Chem. Inf. Model. 2012 52 492 505
8. X. Hu J. R. Compton M. D. Abdulhameed C. L. Marchand K. L. Robertson D. H. Leary A. Jadhav J. R. Hershfield A. Wallqvist A. M. Friedlander P. M. Legler 3-Substituted indole inhibitors against Francisella tularensis FabI identified by structure-based virtual screening J. Med. Chem. 2013 56 5275 5287
9. J. Li S. Zheng B. Chen A. J. Butte S. J. Swamidass Z. Lu A survey of current trends in computational drug repositioning Briefings Bioinf. 2015 31 1 11
10. M. J. Keiser V. Setola J. J. Irwin C. Laggner A. I. Abbas S. J. Hufeisen N. H. Jensen M. B. Kuijer R. C. Matos T. B. Tran R. Whaley R. A. Glennon J. Hert K. L. H. Thomas D. D. Edwards B. K. Shoichet B. L. Roth Predicting new molecular targets for known drugs Nature 2009 462 175 181
11. T. T. Ashburn K. B. Thor Drug repositioning: identifying and developing new uses for existing drugs Nat. Rev. Drug Discovery 2004 3 673 683
12. S. Ekins A. J. Williams M. D. Krasowski J. S. Freundlich In silico repositioning of approved drugs for rare and neglected diseases Drug Discovery Today 2011 16 298 310
13. Z. Liu H. Fang K. Reagan X. Xu D. L. Mendrick W. Slikker Jr W. Tong In silico drug repositioning-what we need to know Drug Discovery Today 2013 18 110 115
14. D.-L. Ma D. S.-H. Chan C.-H. Leung Drug repositioning by structure-based virtual screening Chem. Soc. Rev. 2013 42 2130 2141
15. S. Bhakat W. Karubiu V. Jayaprakash M. E. S. Soliman A perspective on targeting non-structural proteins to combat neglected tropical diseases: dengue, West Nile and chikungunya viruses Eur. J. Med. Chem. 2014 87 677 702
16. M. G. Guzman, S. B. Halstead, H. Artsob, P. Buchy, J. Farrar, D. J. Gubler, E. Hunsperger, A. Kroeger, H. S. Margolis, E. Martinez, M. B. Nathan, J. L. Pelegrino, C. Simmons, S. Yoksan, and R. W. Peeling. Dengue: a continuing global threat, Nat. Rev. Microbiol., 2010, S7 S16
17. S. Bhatt P. W. Gething O. J. Brady J. P. Messina A. W. Farlow C. L. Moyes J. M. Drake J. S. Brownstein A. G. Hoen O. Sankoh M. F. Myers D. B. George T. Jaenisch G. R. W. Wint C. P. Simmons T. W. Scott J. J. Farrar S. I. Hay The global distribution and burden of dengue Nature 2013 496 504 507
18. M. G. Guzman and E. Harris, Dengue, Lancet, 2015, 385, 453 465
19. D. J. Gubler Dengue and Dengue Hemorrhagic Fever Clin. Microbiol. Rev. 1998 11 480 496
20. S. Murrell S.-C. Wu M. Butler Review of dengue virus and the development of a vaccine Biotechnol. Adv. 2011 29 239 247
21. S.-W. Wan C.-F. Lin S. Wang Y.-H. Chen T.-M. Yeh H.-S. Liu R. Anderson Y.-S. Lin Current progress in dengue vaccines J. Biomed. Sci. 2013 20 37
22. A. A. Rashad S. Mahalingam P. A. Keller Chikungunya virus: emerging targets and new opportunities for medicinal chemistry J. Med. Chem. 2014 57 1147 1166
23. O. Schwartz M. L. Albert Biology and pathogenesis of chikungunya virus Nat. Rev. Microbiol. 2010 8 491 500
24. J. E. Staples R. F. Breiman A. M. Powers Chikungunya Fever: An Epidemiological Review of a Re-Emerging Infectious Disease Clin. Infect. Dis. 2009 49 942 948
25. M. P. Manns T. von Hahn Novel therapies for hepatitis C [mdash] one pill fits all? Nat. Rev. Drug Discovery 2013 12 595 610
26. J. Pokorná L. Machala P. Řezáčová J. Konvalinka Current and Novel Inhibitors of HIV Protease Viruses 2009 1 1209 1239
27. E. D. Clercq The design of drugs for HIV and HCV Nat. Rev. Drug Discovery 2007 6 1001 1018
28. C. G. Noble C. C. Seh A. T. Chao P. Y. Shi Ligand-bound structures of the dengue virus protease reveal the active conformation J. Virol. 2012 86 438 446
29. http://www.rcsb.org/pdb/explore/explore.do?structureId=3TRK
30. P. Erbel N. Schiering A. D'Arcy M. Renatus M. Kroemer S. P. Lim Z. Yin T. H. Keller S. G. Vasudevan U. Hommel Structural basis for the activation of flaviviral NS3 proteases from dengue and West Nile virus Nat. Struct. Mol. Biol. 2006 13 372 373
31. http://www.chemspider.com/
32. Y. Maharaj S. Bhakat M. E. S. Soliman Computer-aided Identification of Novel DprE1 Inhibitors as Potential Anti-TB Lead Compounds: A Hybrid Virtual-screening and Molecular Dynamics Approach Lett. Drug Des. Discovery 2015 12 302 313
33. O. Trott A. J. Olson AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading J. Comput. Chem. 2010 31 455 461
34. C. D. Lau M. J. Levesque S. Chien S. Date J. H. Haga ViewDock TDW: high-throughput visualization of virtual screening results Bioinformatics 2010 26 1915 1917
35. E. F. Pettersen T. D. Goddard C. C. Huang G. S. Couch D. M. Greenblatt E. C. Meng T. E. Ferrin UCSF Chimera-a visualization system for exploratory research and analysis J. Comput. Chem. 2004 25 1605 1612
36. P. D. Lyne M. L. Lamb J. C. Saeh Accurate Prediction of the Relative Potencies of Members of a Series of Kinase Inhibitors Using Molecular Docking and MM-GBSA Scoring J. Med. Chem. 2006 49 4805 4808
37. G. Rastelli A. D. Rio G. Degliesposti M. Sgobba Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA J. Comput. Chem. 2010 31 797 810
38. H. Sun Y. Li M. Shen S. Tian L. Xu P. Pan Y. Guan T. Hou Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoring Phys. Chem. Chem. Phys. 2014 16 22035 22045
39. M. D. Abdulhameed A. Hamza C. G. Zhan Microscopic modes and free energies of 3-phosphoinositide-dependent kinase-1 (PDK1) binding with celecoxib and other inhibitors J. Phys. Chem. B 2006 110 26365 26374
40. N. Li R. I. Ainsworth B. Ding T. Hou W. Wang Using Hierarchical Virtual Screening To Combat Drug Resistance of the HIV-1 Protease J. Chem. Inf. Model. 2015 55 1400 1412
41. P. A. Greenidge C. Kramer J. C. Mozziconacci W. Sherman Improving Docking Results via Reranking of Ensembles of Ligand Poses in Multiple X-ray Protein Conformations with MM-GBSA J. Chem. Inf. Model. 2014 54 2697 2717
42. S. Sirin R. Kumar C. Martinez M. J. Karmilowicz P. Ghosh Y. A. Abramov V. Martin W. Sherman A Computational Approach to Enzyme Design: Predicting ω-Aminotransferase Catalytic Activity Using Docking and MM-GBSA Scoring J. Chem. Inf. Model. 2014 54 2334 2346
43. I. Slynko M. Scharfe T. Rumpf J. Eib E. Metzger R. Schüle M. Jung W. Sippl Virtual Screening of PRK1 Inhibitors: Ensemble Docking, Rescoring Using Binding Free Energy Calculation and QSAR Model Development J. Chem. Inf. Model. 2014 54 138 150
44. D. A. Case, V. Babin, J. T. Berryman, R. M. Betz, Q. Cai, D. S. Cerutti, T. E. Cheatham, III, T. A. Darden, R. E. Duke, H. Gohlke, A. W. Goetz, S. Gusarov, N. Homeyer, P. Janowski, J. Kaus, I. Kolossváry, A. Kovalenko, T. S. Lee, S. LeGrand, T. Luchko, R. Luo, B. Madej, K. M. Merz, F. Paesani, D. R. Roe, A. Roitberg, C. Sagui, R. Salomon-Ferrer, G. Seabra, C. L. Simmerling, W. Smith, J. Swails, R. C. Walker, J. Wang, R. M. Wolf, X. Wu and P. A. Kollman, AMBER 14, University of California, San Francisco, 2014
45. S. Bhakat A. J. M. Martin M. E. S. Soliman An integrated molecular dynamics, principal component analysis and residue interaction network approach reveals the impact of M184V mutation on HIV reverse transcriptase resistance to lamivudine Mol. BioSyst. 2014 10 2215 2228
46. D. R. Roe T. E. Cheatham PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data J. Chem. Theory Comput. 2013 9 3084 3095
47. W. Humphrey A. Dalke K. Schulten VMD: Visual molecular dynamics J. Mol. Graphics 1996 14 33 38
48. L. Delang N. Segura Guerrero A. Tas G. Querat B. Pastorino M. Froeyen K. Dallmeier D. Jochmans P. Herdewijn F. Bello E. J. Snijder X. de Lamballerie B. Martina J. Neyts M. J. van Hemert P. Leyssen Mutations in the chikungunya virus non-structural proteins cause resistance to favipiravir (T-705), a broad-spectrum antiviral J. Antimicrob. Chemother. 2014 69 2770 2784
49. S. J. F. Kaptein T. de Burghgraeve M. Froeyen B. Pastorino M. M. F. Alen J. A. Mondotte P. Herdewijn M. Jacobs X. de Lamballerie D. Schols A. V. Gamarnik F. Sztaricskai J. Neyts A Derivate of the Antibiotic Doxorubicin Is a Selective Inhibitor of Dengue and Yellow Fever Virus Replication In Vitro Antimicrob. Agents Chemother. 2010 54 5269 5280
50. J. Deng N. Li H. Liu Z. Zuo O. W. Liew W. Xu G. Chen X. Tong W. Tang J. Zhu J. Zuo H. Jiang C.-G. Yang J. Li W. Zhu Discovery of Novel Small Molecule Inhibitors of Dengue Viral NS2B-NS3 Protease Using Virtual Screening and Scaffold Hopping J. Med. Chem. 2012 55 6278 6293
51. R. Takhampunya S. Ubol H. S. Houng C. E. Cameron R. Padmanabhan Inhibition of dengue virus replication by mycophenolic acid and ribavirin J. Gen. Virol. 2006 87 1947 1952
52. D. R. Koes C. J. Camacho ZINCPharmer: pharmacophore search of the ZINC database Nucleic Acids Res. 2012 40 W409 W414
53. S. Toma T. Yamashiro S. Arakaki J. Shiroma T. Maeshiro K. Hibiya N. Sakamoto F. Kinjo M. Tateyama J. Fujita Inhibition of intracellular hepatitis C virus replication by nelfinavir and synergistic effect with interferon-alpha Journal of Viral Hepatitis 2009 16 506 512
54. M. Kraus J. Bader H. Overkleeft C. Driessen Nelfinavir augments proteasome inhibition by bortezomib in myeloma cells and overcomes bortezomib and carfilzomib resistance Blood Cancer Journal 2013 3 e103
55. C. Nitsche V. N. Schreier M. A. Behnam A. Kumar R. Bartenschlager C. D. Klein Thiazolidinone-peptide hybrids as dengue virus protease inhibitors with antiviral activity in cell culture J. Med. Chem. 2013 56 8389 8403
56. G. C. Zhou Z. Weng X. Shao F. Liu X. Nie J. Liu D. Wang C. Wang K. Guo Discovery and SAR studies of methionine-proline anilides as dengue virus NS2B-NS3 protease inhibitors Bioorg. Med. Chem. Lett. 2013 23 6549 6554
57. M. Yildiz S. Ghosh J. A. Bell W. Sherman J. A. Hardy Allosteric inhibition of the NS2B-NS3 protease from dengue virus ACS Chem. Biol. 2013 8 2744 2752
58. V. K. Ganesh N. Muller K. Judge C. H. Luan R. Padmanabhan K. H. Murthy Identification and characterization of nonsubstrate based inhibitors of the essential dengue and West Nile virus proteases Bioorg. Med. Chem. 2005 13 257 264