204
Views
12
CrossRef citations to date
0
Altmetric
Research Articles

High-throughput virtual screening, ADME analysis, and estimation of MM/GBSA binding-free energies of azoles as potential inhibitors of Mycobacterium tuberculosis H37Rv

, , , &
Pages 312-320 | Received 07 May 2019, Accepted 24 Aug 2019, Published online: 28 Oct 2019

References

  • de Souza MV. Current status and future prospects for new therapies for pulmonary tuberculosis. Curr Opin Pulm Med. 2006;12:167–171.
  • World Health Organization. Global Tuberculosis Report 2018. Geneva: WHO, 2018.
  • Scior T, Garces-Eisele S. Isoniazid is not a lead compound for its pyridyl ring derivatives, isonicotinoyl amides, hydrazides, and hydrazones: a critical review. Curr Med Chem. 2006;13(18):2205–2219.
  • Robert SW, Markus M, Peter M, et al. Tuberculosis—advances in development of new drugs, treatment regimens, host-directed therapies, and biomarkers. Lancet Infect Dis. 2016;16:34–46.
  • Baldwin PR, Reeves AZ, Powell KR, et al. Monocarbonyl analogs of curcumin inhibit growth of antibiotic sensitive and resistant strains of Mycobacterium tuberculosis. Eur J Med Chem. 2015;92:693–699.
  • Jankute M, Cox JG, Harrison J, et al. Assembly of the mycobacterial cell wall. Annu Rev Microbiol. 2015;69:405–423.
  • Vollmer W, Blanot D, de Pedro MA. Peptidoglycan structure and architecture. FEMS Microbiol Rev. 2008;32(2):149–167.
  • Alderwick LJ, Harrison J, Georgina SL, et al. The mycobacterial cell wall—peptidoglycan and arabinogalactan. Cold Spring Harb Perspect Med. 2015;5(8):a021113.
  • Brennan PJ. Structure, function, and biogenesis of the cell wall of Mycobacterium tuberculosis. Tuberculosis. 2003;83(1–3):91–97.
  • Chiaradia L, Lefebvre C, Parra J, et al. Dissecting the mycobacterial cell envelope and defining the composition of the native mycomembrane. Sci Rep. 2017;7(1):12807.
  • Marrakchi H, Laneelle G, Quemard A. InhA, a target of the antituberculous drug isoniazid, is involved in a mycobacterial fatty acid elongation system, FAS-II. Microbiology. 2000;146(2):289–296.
  • Cole ST, Brosch R, Parkhill J, et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature. 1998;393(6685):537–544.
  • McLean KJ, Clift D, Lewis DG, et al. The preponderance of P450s in the Mycobacterium tuberculosis genome. Trends Microbiol. 2006;14(5):220–228.
  • McLean KJ, Carroll P, Lewis DG, et al. Characterization of active site structure in CYP121. A cytochrome P450 essential for viability of Mycobacterium tuberculosis H37Rv. J Biol Chem. 2008;283(48):33406–33416.
  • Ouellet H, Johnston JB, Montellano POD. The Mycobacterium tuberculosis cytochrome P450 system. NIH Public Access Syst. 2010;493:82–95.
  • Fleischmann RD, Alland D, Eisen JA, et al. Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. J Bacteriol. 2002;184(19):5479–5490.
  • Sundaramurthi JC, Kumar S, Silambuchelvi K, et al. Molecular docking of azole drugs and their analogs on CYP121 of Mycobacterium tuberculosis. Bioinformation. 2011;7(3):130–133.
  • Winde FGr, Collins PB. Inhibition by isoniazid of synthesis of mycolic acids in Mycobacterium tuberculosis. J Gen Microbiol. 1970;63:41–48.
  • Quemard A, Lacave C, Laneelle G. Isoniazid inhibition of mycolic acid synthesis by cell extracts of sensitive and resistant strains of Mycobacterium aurum. Antimicrob Agents Chemother. 1991;35(6):1035–1039.
  • Ahmad Z, Sharma S, Khuller GK. Azole antifungals as novel chemotherapeutic agents against murine tuberculosis. FEMS Microbiol Lett. 2006;261(2):181–186.
  • Ahmad Z, Sharma S, Khuller GK. The potential of azole antifungals against latent/persistent tuberculosis. FEMS Microbiol Lett. 2006;258(2):200–203.
  • Ahmad Z, Sharma S, Khuller GK. Chemotherapeutic evaluation of alginate nanoparticle-encapsulated azole antifungal and antitubercular drugs against murine tuberculosis. Nanomedicine: Nanotechnol Biol Med. 2007;3(3):239–243.
  • Como JA, Dismukes WE. Oral azole drugs as systemic antifungal therapy. N Engl J Med. 1994;330(4):263–272.
  • McLean KJ, Cheesman MR, Rivers SL, et al. Expression, purification and spectroscopic characterization of the cytochrome P450 CYP121 from Mycobacterium tuberculosis. J Inorg Biochem. 2002;91(4):527–541.
  • Janin YL. Antituberculosis drugs: ten years of research. Bioorg Med Chem. 2007;15(7):2479–2513.
  • Sterling T, Irwin JJ. ZINC 15-ligand discovery for everyone. J Chem Inf Model. 2015;55(11):2324–2337.
  • Momen-Roknabadi A, Sadeghi M, Pezeshk H, et al. Impact of residue accessible surface area on the prediction of protein secondary structures. BMC Bioinformatics. 2008;9(1):357.
  • Seward HE, Roujeinikova A, McLean KJ, et al. Crystal structure of the Mycobacterium tuberculosis P450 CYP121-fluconazole complex reveals new azole drug –P450 binding mode. J Biol Chem. 2006;281(51):39437–39443.
  • Shivakumar D, Williams J, Wu Y, et al. Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field. J Chem Theory Comput. 2010;6(5):1509–1519.
  • Saikiran RP, Sreekanth S, Vijjulatha M. An integrated molecular modeling approach for in silico design of new tetracyclic derivatives as ALK inhibitors. J Recept Signal Transduction. 2016;36:1–17.
  • Greenwood JR, Calkins D, Sullivan AP, et al. Towards the comprehensive, rapid, and accurate prediction of the favourable tautomeric states of drug-like molecules in aqueous solution. J Comput Aided Mol Des. 2010;24(6–7):591–604.
  • Centers for Disease Control and Prevention. Available from: http://www.cdc.gov/tb/topic/treatment/ (accessed 17.10.15).
  • Friesner RA, Murphy RB, Repasky MP, et al. Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J Med Chem. 2006;49(21):6177–6196.
  • Li J, Abel R, Zhu K, et al. The VSGB 2.0 Model: a next generation energy model for high resolution protein structure modeling. Proteins. 2011;79(10):2794–2812.
  • Ioakimidis L, Thoukydidis L, Mirza A, et al. Benchmarking the reliability of QikProp. Correlation between experimental and predicted values. QSAR Comb Sci. 2008;27(4):445–456.
  • Kavanagh ME, Gray JL, Gilbert SH, et al. Substrate fragmentation for the design of M. tuberculosis CYP121 inhibitors. ChemMedChem. 2016;11(17):1924–1935.
  • Gaulton A, Hersey A, Nowotka M, et al. The ChEMBL database in 2017. Nucleic Acids Res. 2017;45(D1):D945–D954.
  • Irwin JJ, Sterling T, Mysinge MM, et al. ZINC: a free tool to discover chemistry for biology. J Chem Inf Model. 2012;52(7):1757–1768.
  • Kim S, Chen J, Cheng T, et al. PubChem 2019 update: improved access to chemical data. Nucleic Acids Res. 2019;47(D1):D1102–D1109.
  • Embi N, Rylatt DB, Cohen P. Glycogen synthase kinase-3 formrabbit skeletal muscle: separation from cylic-AMP-dependent proteinkinase and phosphorylase kinase. Eur J Biochem. 2005;107(2):519–527.
  • McLean KJ, Dunford AJ, Neeli R, et al. Munro structure, function and drug targeting in Mycobacterium tuberculosis cytochrome P450 systems. Arch Biochem Biophys. 2007;464(2):228–240.
  • Lipinski C, Lombardo F, Dominy BW, et al. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev. 2012;64:4–17.
  • Jorgensen WL. Efficient drug lead discovery and optimization. Acc Chem Res. 2009;42(6):724–733.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.