Preview

Science and Innovations

Advanced search
Open Access Open Access  Restricted Access Subscription Access

Computer-aided identification of candidate molecules for tuberculosis drugs

https://doi.org/10.29235/1818-9857-2026-03-78-83

Abstract

Structure-based virtual screening of the library of bioactive compounds was used to identify novel small-molecule compounds that can inhibit the catalytic activity of Mycobacterium tuberculosis (Mtb) enoyl acyl carrier protein reductase (InhA), one of the key enzymes involved in the biosynthesis of mycolic acids of the Mtb cell wall. To do this, we employed an integrated computational approach to drug repurposing which included high-throughput docking of the InhA enzyme with small-molecule compounds from the library of bioactive molecules containing the FDA-approved drugs and investigational drug candidates, molecular dynamics simulations of the ligand/InhA-NAD+ complexes, binding free energy calculations, post-modeling analysis followed by selection of the most promising drug candidates and experimental determination of their minimum inhibitory concentration MIC90. As a result, a lead compound which showed the MIC90 value of 62.5 µM against the vaccine strain Mycobacterium bovis and Mtb was found, giving hope that this compound forms a promising scaffold for the development of novel antitubercular molecules of clinical significance with activity against an important target of Mtb.

About the Authors

A. Gonchar
Объединенный институт проблем информатики НАН Беларуси
Belarus

Anna Gonchar



K. Furs
Объединенный институт проблем информатики НАН Беларуси
Belarus

Konstantin Furs



A. Tuzikov
Объединенный институт проблем информатики НАН Беларуси
Belarus

Alexander Tuzikov



A. Andrianov
Институт биоорганической химии НАН Беларуси
Belarus

Alexander Andrianov



References

1. WHO. Global tuberculosis report 2024 / World Health Organization, 2024 // https://www.who.int/teams/global-programme-on-tuberculosis-and-lunghealth/tb-reports/global-tuberculosis-report-2024.

2. Shetye G.S. New tuberculosis drug targets, their inhibitors, and potential therapeutic impact / G.S. Shetye, S.G. Franzvlau, S. Cho // Transl. Res. 2020. Vol. 220. P. 68–97. Doi.org/10.1016/j.trsl.2020.03.007.

3. North E.J. New approaches to target the mycolic acid biosynthesis pathway for the development of tuberculosis therapeutics / E.J. North, M. Jackson, R.E. Lee // Curr. Pharm. Des. 2014. Vol. 20(27). P. 4357–4378.

4. Pawełczyk J. The molecular genetics of mycolic acid biosynthesis / J. Pawełczyk, L. Kremer // Microbiol. Spect. 2014. Vol. 2(4). MGM2-0003-2013.

5. Conditional depletion of KasA, a key enzyme of mycolic acid biosynthesis, leads to mycobacterial cell lysis / A. Bhatt [et al.] // J. Bacteriol. 2005. Vol. 187. P. 7596–7606.

6. Duan X. Crucial components of mycobacterium type II fatty acid biosynthesis (Fas-II) and their inhibitors / X. Duan, X. Xiang, J. Xie // FEMS Microbiol. Lett. 2014. Vol. 360 (2). P. 87–99. Https://doi.org/10.1111/1574-6968.12597.

7. Prasad S. Mycobacterium enoyl acyl carrier protein reductase (InhA): A key target for antitubercular drug discovery / S. Prasad, R.P. Bhole, P.B. Khedekar, R.V. Chikhale / Bioorg Chem. 2021. Vol. 115: 105242. Https://doi.org/10.1016/j.bioorg.2021.105242.

8. Kruh N. Probing mechanisms of resistance to the tuberculosis drug isoniazid: conformational changes caused by inhibition of InhA, the enoyl reductase from Mycobacterium tuberculosis / N. Kruh, R. Rawat, B.P. Ruzsicska, P.J. Tonge // Prot. Sci. 2007. Vol. 16. P. 1617–1627.

9. Rawat R. The isoniazid-NAD adduct is a slow, tightbinding inhibitor of InhA, the Mycobacterium tuberculosis enoyl reductase: Adduct affinity and drug resistance / R. Rawat, A. Whitty, P.J. Tonge // Proc. Natl. Acad. Sci. USA. 2003. Vol. 100. P. 13881– 13886. Https://doi.org/10.1073/pnas.2235848100.

10. Transfer of a point mutation in Mycobacterium tuberculosis inhA resolves the target of isoniazid / C. Vilchèze [et al.] // Nat. Med. 2006. Vol. 12. P. 1027–1029. Https://doi.org/10.1038/nm1466.

11. Pan P. Targeting InhA, the FASII enoyl-ACP reductase: SAR studies on novel inhibitor scaffolds / P. Pan, P.J. Tonge // Curr. Top. Med. Chem. 2012. Vol. 12. P. 672–693. Https://doi.org/10.2174/156802612799984535.

12. DrugBank 5.0: a major update to the DrugBank database for 2018 / D.S. Wishart [et al.] // Nucl. Acids Res. 2017. Vol. 46. P. D1074–D1082. Https://doi.org/10.1093/nar/gkx1037.

13. Sterling T. ZINC 15 – Ligand discovery for everyone / T. Sterling, J.J. Irwin // J. Chem. Inf. Model. 2015. Vol. 55(11). P. 2324–2337. Https://doi.org/10.1021/acs.jcim.5b00559.

14. Trott O. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading / O. Trott, A.J. Olson // J. Comp. Chem. 2010. Vol. 31. P. 455–461. Https://doi.org/10.1002/jcc.21334.

15. Pyrrolidine carboxamides as a novel class of inhibitors of enoyl acyl carrier protein reductase from Mycobacterium tuberculosis / X. He [et al.] // J. Med. Chem. 2006. Vol. 49(21). P. 6308–6323. Https: // doi: 10.1021/jm060715y.

16. Wójcikowski M. Performance of machine-learning scoring functions in structure-based virtual screening / M. Wójcikowski, P. Ballester, P. Siedlecki // Sci. Rep. 2017. Vol. 7. P. 46710. Https://doi.org/10.1038/srep46710.

17. Durrant J.D. NNScore 2.0: A neural-network receptor–ligand scoring function / J.D. Durrant, J.A. McCammon // J. Chem. Inf. Model. 2011. Vol. 51(11). P. 2897–2903. Https://doi.org/10.1021/ci2003889.

18. Palacio-Rodríguez K. Exponential consensus ranking improves the outcome in docking and receptor ensemble docking / K. Palacio-Rodríguez, I. Lans, C.N. Cavasotto, P. Cossio // Sci. Rep. 2019. Vol. 9(1). Article No. 5142. Https://doi.org/10.1038/s41598-019-41594-3.

19. AMBER 2018 / D.A. Case [et al.] // University of California, 2018.

20. Comparison of simple potential functions for simulating liquid water / W.L. Jorgensen [et al.] // J. Chem. Phys. 1983. Vol. 79 (2). P. 926–935. Https://doi.org/10.1063/1.445869.

21. Ryckaert J.P. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes / J.P. Ryckaert, G. Ciccotti, H.J.C. Berendsen // J. Comput. Phys. 1977. Vol. 23 (3). P. 327–341. Https://doi.org/10.1016/0021-9991(77)90098-5.

22. A smooth particle mesh Ewald method / U. Essmann [et al.] // J. Chem. Phys. 1995. Vol. 103. P. 8577–8593. Https://doi.org/10.1063/1.470117.

23. Genheden S. The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinity / S. Genheden, U. Ryde // Expert Opin. Drug Discov. 2015. Vol. 10(5). P. 449–461. Https://doi.org/10.1517/17460441.2015.1032936.

24. Targeting tuberculosis and malaria through inhibition of enoyl reductase / M.R. Kuo [et al.] // J. Biol. Chem. 2003. Vol. 278(23). P. 20851–20859. Https://doi.org/10.1074/jbc.m211968200.


Review

For citations:


Gonchar A., Furs K., Tuzikov A., Andrianov A. Computer-aided identification of candidate molecules for tuberculosis drugs. Science and Innovations. 2026;(3):78-83. (In Russ.) https://doi.org/10.29235/1818-9857-2026-03-78-83

Views: 77

JATS XML

ISSN 1818-9857 (Print)
ISSN 2412-9372 (Online)