Rationalization and prediction of drug resistant mutations in targets for clinical anti-tubercular drugs

Journal of Biomolecular Structure and Dynamics

Volumn 31, Issue 1, 2013, Pages 44-58

  Padiadpu, Jyothi ^a   Mukherjee, Sumanta ^a   Chandra, Nagasuma ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

Decrease in drug binding; Mutability index; Mutant structures; Residue conservation index; TB drug targets

Indexed keywords

AMIKACIN; AMINOSALICYLIC ACID; ETHAMBUTOL; ETHIONAMIDE; ISONIAZID; KANAMYCIN; POLYPEPTIDE; PYRAZINAMIDE; QUINOLINE DERIVED ANTIINFECTIVE AGENT; RIFAMPICIN; STREPTOMYCIN; TUBERCULOSTATIC AGENT;

AMINO ACID SEQUENCE; ANTIBIOTIC RESISTANCE; BACTERIUM MUTANT; BINDING AFFINITY; CONFERENCE PAPER; DRUG BINDING SITE; DRUG DESIGN; DRUG TARGETING; GENE MUTATION; GENETIC CONSERVATION; GENETIC DATABASE; MICROARRAY ANALYSIS; MOLECULAR DOCKING; MOLECULAR INTERACTION; MOLECULAR STABILITY; MYCOBACTERIUM TUBERCULOSIS; POINT MUTATION; PREDICTION; PRIORITY JOURNAL; PROTEIN TARGETING; SEQUENCE HOMOLOGY; WILD TYPE;

ANTITUBERCULAR AGENTS; BINDING SITES; DATABASES, CHEMICAL; DRUG DESIGN; DRUG RESISTANCE, BACTERIAL; MOLECULAR DOCKING SIMULATION; MYCOBACTERIUM TUBERCULOSIS; POINT MUTATION; PROTEIN STABILITY; TUBERCULOSIS, PULMONARY;

BACTERIA (MICROORGANISMS); MYCOBACTERIUM TUBERCULOSIS;

EID: 84871231098     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2012.691361     Document Type: Conference Paper

References (56)

1. Abbadi, S.H., Sameaa, G.A., Morlock, G., & Cooksey, R.C. (2009). Molecular identification of mutations associated with anti-Tuberculosis drug resistance among strains of Mycobacterium tuberculosis. International Journal of Infectious Diseases, 13, 673-678.
2. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., & Lipman, D.J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215, 403-410.
3. Anand, P., Sankaran, S., Mukherjee, S., Yeturu, K., Laskowski, R., Bhardwaj, A. Brahmachari, S.K., & Chandra, N. (2011). Structural annotation of Mycobacterium tuberculosis proteome. PLoS ONE, 6, e27044.
4. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H.,Bourne, P.E. (2000). The protein data bank. Nucleic Acids Research, 28, 235-242.
5. Borea, P.A., Varani, K., Gessi, S., Gilli, P., & Dalpiaz, A. (1998). Receptor binding thermodynamics as a tool for linking drug efficacy and affinity. Farmaco, 53, 249-254.
6. Brown, K.M., Costanzo, M.S., Xu, W., Roy, S., Lozovsky, E. R., & Hartl, D.L. (2010). Compensatory mutations restore fitness during the evolution of dihydrofolate reductase. Molecular Biology and Evolution, 27, 2682-2690.
7. Cade, C.E., Dlouhy, A.C., Medzihradszky, K.F., Salas-Castillo, S.P., & Ghiladi, R.A. (2010). Isoniazid-resistance conferring mutations in Mycobacterium tuberculosis KatG: Catalase, peroxidase, and INH-NADH adduct formation activities. Protein Science, 19, 458-474.
8. Campbell, E.A., Korzheva, N., Mustaev, A., Murakami, K., Nair, S., Goldfarb, A., & Darst, S.A. (2001). Structural mechanism for rifampicin inhibition of bacterial RNA polymerase. Cell, 104, 901-912.
9. Cunningham, B.C., & Wells, J.A. (1989). High-resolution epitope mapping of hGH-receptor interactions by alanine-scanning mutagenesis. Science, 244, 1081-1085.
10. Dehouck, Y., Grosfils, A., Folch, B., Gilis, D., Bogaerts, P., & Rooman, M. (2009). Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0. Bioinformatics, 25, 2537-2543.
11. Ghiladi, R.A., Knudsen, G.M., Medzihradszky, K.F., & Ortiz de Montellano, P.R. (2005). The Met-Tyr-Trp cross-link in Mycobacterium tuberculosis catalase-peroxidase (KatG): Autocatalytic formation and effect on enzyme catalysis and spectroscopic properties. Journal of Biological Chemistry, 280, 22651-22663.
12. Hess, B., Kutzner, C., van der Spoel, D., & Lindahl, E. (2008). GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 4, 435-447.
13. Hetenyi, C., Maran, U., Garcia-Sosa, A.T., & Karelson, M. (2007). Structure-based calculation of drug efficiency indices. Bioinformatics, 23, 2678-2685.
14. Huang, N., Shoichet, B.K., & Irwin, J.J. (2006). Benchmarking sets for molecular docking. Journal of Medicinal Chemistry, 49, 6789-6801.
15. Huey, R., Morris, G.M., Olson, A.J., & Goodsell, D.S. (2007). A semiempirical free energy force field with charge-based desolvation. Journal of Computational Chemistry, 28, 1145-1152.
16. Jenkins, C. (2005). Rifampicin resistance in tuberculosis outbreak, London, England. Emerging Infectious Diseases, 11, 931-934.
17. Kabsch, W. (1976). A solution for the best rotation to relate two sets of vectors. Acta Crystallographica, A32, 922-923.
18. Kalidas, Y., & Chandra, N. (2008). PocketDepth: A new depth based algorithm for identification of ligand binding sites in proteins. Journal of Structural Biology, 161, 31-42.
19. Kaneko, T., Cooper, C., & Mdluli, K. (2011). Challenges and opportunities in developing novel drugs for TB. Future Medicinal Chemistry, 3, 1373-1400.
20. Kohanski, M.A., Dwyer, D.J., & Collins, J.J. (2010). How antibiotics kill bacteria: from targets to networks. Nature Reviews Microbiology, 8, 423-435.
21. Krivov, G.G., Shapovalov, M.V., & Dunbrack, R.L.Jr. (2009). Improved prediction of protein side-chain conformations with SCWRL4. Proteins, 77, 778-795.
22. Larijani, M., Frieder, D., Basit, W., & Martin, A. (2005). The mutation spectrum of purified AID is similar to the mutability index in Ramos cells and in ung(-/-)msh2(-/-) mice. Immunogenetics, 56, 840-845.
23. Lee, A.S., Lim, I.H., Tang, L.L., & Wong, S.Y. (2005). High frequency of mutations in the rpoB gene in rifampin-resistant clinical isolates of Mycobacterium tuberculosis from Singapore. Journal of Clinical Microbiology, 43, 2026-2027.
24. Lemaitre, N., Callebaut, I., Frenois, F., Jarlier, V., & Sougakoff, W. (2001). Study of the structure-Activity relationships for the pyrazinamidase (PncA) from Mycobacterium tuberculosis. Biochemical Journal, 353, 453-458.
25. Li, Q., Cheng, T., Wang, Y., & Bryant, S.H. (2010). PubChem as a public resource for drug discovery. Drug Discovery Today, 15, 1052-1057.
26. Mathys, V., Wintjens, R., Lefevre, P., Bertout, J., Singhal, A., Kiass, M.,Bifani, P. (2009). Molecular genetics of para-Aminosalicylic acid resistance in clinical isolates and spontaneous mutants of Mycobacterium tuberculosis. Antimicrobial Agents and Chemotherapy, 53, 2100-2109.
27. Morar, M., & Wright, G.D. (2010). The genomic enzymology of antibiotic resistance. Annual Review of Genetics, 44, 25-51.
28. Morlock, G.P., Metchock, B., Sikes, D., Crawford, J.T., & Cooksey, R.C. (2003). EthA, inhA, and katG loci of ethionamide-resistant clinical Mycobacterium tuberculosis isolates. Antimicrobial Agents and Chemotherapy, 47, 3799-3805.
29. Morrison, K.L., & Weiss, G.A. (2001). Combinatorial alaninescanning. Current Opinion in Chemical Biology, 5, 302-307.
30. Ng, P.C., & Henikoff, S. (2006). Predicting the effects of amino acid substitutions on protein function. Annual Review of Genomics and Human Genetics, 7, 61-80.
31. Payne, D.J., Gwynn, M.N., Holmes, D.J., & Pompliano, D.L. (2007). Drugs for bad bugs: Confronting the challenges of antibacterial discovery. Nature Reviews Drug Discovery, 6, 29-40.
32. Perron, G.G., Lee, A.E., Wang, Y., Huang, W.E., & Barraclough, T.G. (2012). Bacterial recombination promotes the evolution of multi-drug-resistance in functionally diverse populations. Proceedings: Biological Sciences, 279, 1477-1484.
33. Pieper, U., Eswar, N., Webb, B.M., Eramian, D., Kelly, L., Barkan, D.T., Sali, A. (2009). MODBASE, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Research, 37, D347-354.
34. Pym, A.S., Saint-Joanis, B., & Cole, S.T. (2002). Effect of katG mutations on the virulence of Mycobacterium tuberculosis and the implication for transmission in humans. Infection and Immunity, 70, 4955-4960.
35. Raman, K., & Chandra, N. (2008). Mycobacterium tuberculosis interactome analysis unravels potential pathways to drug resistance. BMC Microbiology, 8, 234.
36. Ramaswamy, S.V., Reich, R., Dou, S.J., Jasperse, L., Pan, X., Wanger, A. Graviss, E.A. (2003). Single nucleotide polymorphisms in genes associated with isoniazid resistance in Mycobacterium tuberculosis. Antimicrobial Agents and Chemotherapy, 47, 1241-1250.
37. Rawat, R., Whitty, A., & Tonge, P.J. (2003). The isoniazid-NAD adduct is a slow, tight-binding inhibitor of InhA, the Mycobacterium tuberculosis enoyl reductase: Adduct affinity and drug resistance. Proceedings of the National Academy of Sciences of the USA, 100, 13881-13886.
38. Sandgren, A., Strong, M., Muthukrishnan, P., Weiner, B.K., Church, G.M., & Murray, M.B. (2009). Tuberculosis drug resistance mutation database. PLoS Medicine, 6, e2.
39. Scorpio, A., Lindholm-Levy, P., Heifets, L., Gilman, R., Siddiqi, S., Cynamon, M., & Zhang, Y. (1997). Characterization of pncA mutations in pyrazinamide-resistant Mycobacterium tuberculosis. Antimicrobial Agents and Chemotherapy, 41, 540-543.
40. Sekiguchi, J., Miyoshi-Akiyama, T., Augustynowicz-Kopec, E., Zwolska, Z., Kirikae, F., Toyota, E.,Kirikae, T. (2007). Detection of multidrug resistance in Mycobacterium tuberculosis. Journal of Clinical Microbiology, 45, 179-192.
41. Shenoi, S., & Friedland, G. (2009). Extensively drug-resistant tuberculosis: A new face to an old pathogen. Annual Review of Medicine, 60, 307-320.
42. Sousa, S.F., Fernandes, P.A., & Ramos, M.J. (2006). Proteinligand docking: Current status and future challenges. Proteins, 65, 15-26.
43. Spies, F.S., da Silva, P.E., Ribeiro, M.O., Rossetti, M.L., & Zaha, A. (2008). Identification of mutations related to streptomycin resistance in clinical isolates of Mycobacterium tuberculosis and possible involvement of efflux mechanism. Antimicrobial Agents and Chemotherapy, 52, 2947-2949.
44. Srivastava, S., Garg, A., Ayyagari, A., Nyati, K.K., Dhole, T. N., & Dwivedi, S.K. (2006). Nucleotide polymorphism associated with ethambutol resistance in clinical isolates of Mycobacterium tuberculosis. Current Microbiology, 53, 401-405.
45. Strait, B.J., & Dewey, T.G. (1996). The Shannon information entropy of protein sequences. Biophysical Journal, 71, 148-155.
46. Tetko, I.V., Gasteiger, J., Todeschini, R., Mauri, A., Livingstone, D., Ertl, P.,Prokopenko, V.V. (2005). Virtual computational chemistry laboratory-design and description. Journal of Computer-Aided Molecular Design, 19, 453-463.
47. The UniProt Consortium (2010). The universal protein resource (UniProt) in 2010. Nucleic Acids Research, 38, D142-D148.
48. Thompson, J.D., Higgins, D.G., & Gibson, T.J. (1994). CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positionspecific gap penalties and weight matrix choice. Nucleic Acids Research, 22, 4673-4680.
49. Tomioka, H., Tatano, Y., Sano, C., & Shimizu, T. (2011). Development of new antituberculous drugs based on bacterial virulence factors interfering with host cytokine networks. Journal of Infection and Chemotherapy, 17, 302-317.
50. Toprak, E., Veres, A., Michel, J.B., Chait, R., Hartl, D.L., & Kishony, R. (2011). Evolutionary paths to antibiotic resistance under dynamically sustained drug selection. Nature Genetics, 44, 101-105.
51. Trott, O., & Olson, A.J. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31, 455-461.
52. Van Petegem, F., Duderstadt, K.E., Clark, K.A., Wang, M., & Minor, D.L. Jr. (2008). Alanine-scanning mutagenesis defines a conserved energetic hotspot in the CaValpha1 AID-CaVbeta interaction site that is critical for channel modulation. Structure, 16, 280-294.
53. Vilcheze, C., Wang, F., Arai, M., Hazbon, M.H., Colangeli, R., Kremer, L.,Jacobs, W.R.Jr. (2006). Transfer of a point mutation in Mycobacterium tuberculosis inhA resolves the target of isoniazid. Nature Medicine, 12, 1027-1029.
54. WHO (2010). Multidrug and extensively drug-resistant TB (M/XDR-TB): 2010 global report on surveillance and response.
55. Wright, G.D. (2007). The antibiotic resistome: The nexus of chemical and genetic diversity. Nature Reviews Microbiology, 5, 175-186.
56. Zhang, Y. (2005). The magic bullets and tuberculosis drug targets. Annual Review of Pharmacology and Toxicology, 45, 529-564.