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2000
Volume 22, Issue 6
  • ISSN: 1570-1638
  • E-ISSN: 1875-6220

Abstract

Introduction

After COVID-19, tuberculosis remained the world's second most infectious fatal disease in 2022, with about 410 million people developing MDR TB, according to WHO. The fast increase of MDR and XDR-TB has posed a significant clinical problem in tuberculosis treatment. Bedaquiline, the first FDA-approved medicine for MDR-TB treatment, has caused cardiotoxicity and hepatotoxicity due to high lipophilicity or hERG potassium channel blockage throughout the last four decades. To overcome medication resistance and toxicity, there is an urgent need to create innovative drugs with improved efficacy against specific enzymes.

Methods

The work focused on the biological importance of the Quinazoline pharmacophore scaffold, and it involved the virtual screening and development of 180 novel Quinazoline derivatives in order to find potential hit candidates against molecular dual targets (Pks-13 esterase and DNA ). Based on docking scores lower than (-7.5, -7.6 kcal/mol) of the standard compound, 80 drug molecules were screened using AUTODOCK Vina and filtered by ADMET profile. The top five HIT compounds developed with good binding interactions, acceptable ADME features that obeys the Lipinski Rule of Five, and no toxicity produced as compared to standard bedaquiline were chosen.

Results and Discussion

Docking scores showed that compound RBSI64 had a substantial binding affinity against dual targets (-11.6, -8.2 kcal/mol) than Bedaquiline (-7.5, -7.6 kcal/mol). MD simulation at 100 ns was carried out to investigate the protein's dynamic behaviour with the standard and ligand complex.

Conclusion

The results indicated that RBSI64 could be a useful template for developing MDR and XDR-TB inhibitors. The current study contributes to the identification of promising antitubercular candidates against targeted enzymes.

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2025-10-19
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References

  1. World TB. World TB Day 20242024Available from: https://www.who.int/europe/news-room/events/item/2024/03/24/default-calendar/world-tb-day-2024#:~:text=World%20Tuberculosis%20(TB)%20Day%2C,We%20can%20end%20TB%E2%80%9D
  2. WHO Global tuberculosis report.2023Available from: [https://iris.who.int/bitstream/handle/10665/373828/9789240083851-eng.pdf]
    [Google Scholar]
  3. WangX. ZhaoW. WangB. Identification of inhibitors targeting polyketide synthase 13 of Mycobacterium tuberculosis as antituberculosis drug leads.Bioorg. Chem.202111410511010.1016/j.bioorg.2021.105110
    [Google Scholar]
  4. DartoisV.A. RubinE.J. Anti-tuberculosis treatment strategies and drug development: Challenges and priorities.Nat. Rev. Microbiol.2022201168570110.1038/s41579‑022‑00731‑y35478222
    [Google Scholar]
  5. SeungK.J. KeshavjeeS. RichM.L. Multidrug-resistant tuberculosis and extensively drug-resistant tuberculosis.Cold Spring Harb. Perspect. Med.201559a01786310.1101/cshperspect.a01786325918181
    [Google Scholar]
  6. MaseS.R. ChorbaT. Treatment of drug-resistant tuberculosis.Clin. Chest Med.201940477579510.1016/j.ccm.2019.08.00231731984
    [Google Scholar]
  7. DooleyK.E. RosenkranzS.L. ConradieF. QT effects of bedaquiline, delamanid, or both in patients with rifampicin-resistant tuberculosis: A phase 2, open-label, randomised, controlled trial.Lancet Infect. Dis.202121797598310.1016/S1473‑3099(20)30770‑233587897
    [Google Scholar]
  8. UppumavuluriN.T. KrovvidiS.R. MailavaramR.P. MohantyS.K. DebP.K. VenugopalaK.N. Pks 13 inhibitors: A promising target for future antitubercular agents.Med. Chem. Res.20233281574158810.1007/s00044‑023‑03107‑w
    [Google Scholar]
  9. WilsonC. RayP. ZuccottoF. Optimization of TAM16, a Benzofuran that inhibits the thioesterase activity of Pks13: Evaluation toward a preclinical candidate for a novel antituberculosis clinical target.J. Med. Chem.202165140934910486
    [Google Scholar]
  10. VillainP. CatchpoleR. ForterreP. ObertoJ. da CunhaV. BastaT. Expanded dataset reveals the emergence and evolution of DNA gyrase in archaea.Mol. Biol. Evol.2022398msac15510.1093/molbev/msac15535811376
    [Google Scholar]
  11. PortevinD. de Sousa-D’AuriaC. HoussinC. A polyketide synthase catalyzes the last condensation step of mycolic acid biosynthesis in mycobacteria and related organisms.Proc. Natl. Acad. Sci. USA2004101131431910.1073/pnas.030543910114695899
    [Google Scholar]
  12. GavaldaS. BardouF. LavalF. The polyketide synthase Pks13 catalyzes a novel mechanism of lipid transfer in mycobacteria.Chem. Biol.201421121660166910.1016/j.chembiol.2014.10.01125467124
    [Google Scholar]
  13. WilsonR. KumarP. ParasharV. Antituberculosis thiophenes define a requirement for Pks13 in mycolic acid biosynthesis.Nat. Chem. Biol.20139849950610.1038/nchembio.127723770708
    [Google Scholar]
  14. LehmannJ. ChengT.Y. AggarwalA. Antibacterial β-lactone kills Mycobacterium tuberculosis by disrupting mycolic acid biosynthesis.Angew. Chem. Int. Ed.201857134835310.1002/anie.20170936529067779
    [Google Scholar]
  15. AggarwalA. ParaiM.K. ShettyN. Development of a novel lead that targets M. tuberculosis polyketide synthase 13.Cell20171702249259.e2510.1016/j.cell.2017.06.02528669536
    [Google Scholar]
  16. ZhangW. LunS. WangS.H. Identification of novel coumestan derivatives as polyketide synthase 13 inhibitors against Mycobacterium tuberculosis.J. Med. Chem.201861379180310.1021/acs.jmedchem.7b0131929328655
    [Google Scholar]
  17. ShirudeP.S. MadhavapeddiP. TuckerJ.A. Aminopyrazinamides: Novel and specific GyrB inhibitors that kill replicating and nonreplicating Mycobacterium tuberculosis.ACS Chem. Biol.20138351952310.1021/cb300510w23268609
    [Google Scholar]
  18. SachanR.S.K. MistryV. DholariaM. Overcoming Mycobacterium tuberculosis drug resistance: Novel medications and repositioning strategies.ACS Omega2023836322443225710.1021/acsomega.3c0256337720746
    [Google Scholar]
  19. CollinF. KarkareS. MaxwellA. Exploiting bacterial DNA gyrase as a drug target: Current state and perspectives.Appl. Microbiol. Biotechnol.201192347949710.1007/s00253‑011‑3557‑z21904817
    [Google Scholar]
  20. CharifsonP.S. GrillotA.L. GrossmanT.H. Novel dual-targeting benzimidazole urea inhibitors of DNA gyrase and topoisomerase IV possessing potent antibacterial activity: Intelligent design and evolution through the judicious use of structure-guided design and structure-activity relationships.J. Med. Chem.200851175243526310.1021/jm800318d18690678
    [Google Scholar]
  21. TanitameA. OyamadaY. OfujiK. Synthesis and antibacterial activity of a novel series of DNA gyrase inhibitors: 5-[(E)-2-arylvinyl]pyrazoles.Bioorg. Med. Chem. Lett.200515194299430310.1016/j.bmcl.2005.06.10316087337
    [Google Scholar]
  22. EastS P WhiteCB BarkerO DNA gyrase (GyrB)/topoisomerase IV (ParE) inhibitors: Synthesis and antibacterial activityBioorg Med Chem Lett 200919389410.1016/j.bmcl.2008.11.102
    [Google Scholar]
  23. BansodeD. JainN. GoelT. ThakarS. JadhavM. An explicative review on the progress of quinazoline scaffold as bioactive agents in the past decade.Med. Chem.202319321124510.2174/157340641866622060609320235670342
    [Google Scholar]
  24. PanneerselvamT. SivakumarA. ArumugamS. JoshiS.D. Design, docking analysis, identification, and synthesis of novel 3-(substituted phenyl) amino)methyl)-2-methylquinazolin-4(3H)-one compounds to fight tuberculosis.Drug Discov. Ther.201610418819410.5582/ddt.2016.0104827594295
    [Google Scholar]
  25. GroverG. KiniS.G. Synthesis and evaluation of new quinazolone derivatives of nalidixic acid as potential antibacterial and antifungal agents.Eur. J. Med. Chem.200641225626210.1016/j.ejmech.2005.09.00216260068
    [Google Scholar]
  26. TiwariA.K. SinghV.K. BajpaiA. ShuklaG. SinghS. MishraA.K. Synthesis and biological properties of 4-(3H)-quinazolone derivatives.Eur. J. Med. Chem.20074291234123810.1016/j.ejmech.2007.01.00217321640
    [Google Scholar]
  27. ChandrikaP.M. YakaiahT. RaoA.R.R. Synthesis of novel 4,6-disubstituted quinazoline derivatives, their anti-inflammatory and anti-cancer activity (cytotoxic) against U937 leukemia cell lines.Eur. J. Med. Chem.200843484685210.1016/j.ejmech.2007.06.01017689837
    [Google Scholar]
  28. GiriR.S. ThakerH.M. GiordanoT. Design, synthesis and characterization of novel 2-(2,4-disubstituted-thiazole-5-yl)-3-aryl-3H-quinazoline-4-one derivatives as inhibitors of NF-κB and AP-1 mediated transcription activation and as potential anti-inflammatory agents.Eur. J. Med. Chem.20094452184218910.1016/j.ejmech.2008.10.03119064304
    [Google Scholar]
  29. JatavV. MishraP. KashawS. StablesJ.P. CNS depressant and anticonvulsant activities of some novel 3-[5-substituted 1,3,4-thiadiazole-2-yl]-2-styryl quinazoline-4(3H)-ones.Eur. J. Med. Chem.20084391945195410.1016/j.ejmech.2007.12.00318222569
    [Google Scholar]
  30. KumarA SharmaS Archana Some new 2,3,6-trisubstituted quinazolinones as potent anti-inflammatory, analgesic and COX-II inhibitors.Bioorg. Med. Chem.200311235293529910.1016/S0968‑0896(03)00501‑714604693
    [Google Scholar]
  31. ConnollyD.J. CusackD. O’SullivanT.P. GuiryP.J. Synthesis of quinazolinones and quinazolines.Tetrahedron20056143101531020210.1016/j.tet.2005.07.010
    [Google Scholar]
  32. MosaadS.M. MohammedK.I. AhmedM.A. Abdel-HamiS.G. Synthesis of certain new 6-iodoquinazolines as potential antitubercular agents.J. Appl. Sci. (Faisalabad)20044230230710.3923/jas.2004.302.307
    [Google Scholar]
  33. EfremovR. ChugunovA. PyrkovT. PriestleJ. ArsenievA. JacobyE. Molecular lipophilicity in protein modeling and drug design.Curr. Med. Chem.200714439341510.2174/09298670777994105017305542
    [Google Scholar]
  34. HarbutM.B. YangB. LiuR. Small molecules targeting Mycobacterium tuberculosis type II NADH dehydrogenase exhibit antimycobacterial activity.Angew. Chem. Int. Ed.201857133478348210.1002/anie.20180026029388301
    [Google Scholar]
  35. PanditU. DodiyaA. Synthesis and antitubercular activity of novel pyrazole–quinazolinone hybrid analogs.Med. Chem. Res.20132273364337110.1007/s00044‑012‑0351‑0
    [Google Scholar]
  36. PrestinaciF. PezzottiP. PantostiA. Antimicrobial resistance: A global multifaceted phenomenon.Pathog. Glob. Health2015109730931810.1179/2047773215Y.000000003026343252
    [Google Scholar]
  37. MaiaE.H.B. AssisL.C. de OliveiraT.A. da SilvaA.M. TarantoA.G. Structure-based virtual screening: From classical to artificial intelligence.Front Chem.2020834310.3389/fchem.2020.0034332411671
    [Google Scholar]
  38. 7VJT: Crystal Structure of Mtb Pks13-TE in complex with inhibitor coumestan derivative 8.2022Available from:https://www.rcsb.org/structure/7VJT
  39. 3IG0: crystal structure of the second part of the Mycobacterium tuberculosis DNA gyrase reaction core: The TOPRIM domain at 2.1 A resolution2010Available from: https://www.rcsb.org/structure/3ig0
  40. PitonJ. PetrellaS. DelarueM. Structural insights into the quinolone resistance mechanism of Mycobacterium tuberculosis DNA gyrase.PLoS One201058e12245e510.1371/journal.pone.001224520805881
    [Google Scholar]
  41. CASTpComputed atlas of surface topography of proteins.2018Available from: [http://sts.bioe.uic.edu/]
    [Google Scholar]
  42. PDBsumPictorial database of 3D structures in theProtein Data BankAvailable from: [https://www.ebi.ac.uk/thornton-srv/databases/pdbsum/]
    [Google Scholar]
  43. YangC. ChenE.A. ZhangY. Protein–ligand docking in the machine-learning era.Molecules20222714456810.3390/molecules2714456835889440
    [Google Scholar]
  44. SwissADME: SwissDrugDesignAvailable from:http://www.swissadme.ch/
  45. GowthamK SurendraKumar Open access in silico tools for drug likeness analysis, toxicity, ADME properties and molecular docking studies.Inter J Pharm Res App202276127130
    [Google Scholar]
  46. MolinspirationC. Calculation of molecular properties and bioactivity score.2011Available from: http://www.molinspiration.com/cgi-bin/propertiesor https://www.molinspiration.com/
    [Google Scholar]
  47. TrottO. OlsonA.J. AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading.J. Comput. Chem.201031245546110.1002/jcc.2133419499576
    [Google Scholar]
  48. Remya Surajambika Ramachandran Palanikarasu P. 2D-QSAR modeling, docking, synthesis and in-vitro evaluation of novelflavone derivatives as anticancer agents.Curr. Bioact. Compd.20242031910.2174/1573407219666230522112102
    [Google Scholar]
  49. OSIRIS Property ExplorerAvailable from: https://www.organic-chemistry.org/prog/peo/
  50. pred-herg 5.0: Unlocking the full potential of predictive modeling for precise hERG activity predictionsAvailable from:http://predherg.labmol.com.br/
  51. BanerjeeP. EckertA.O. SchreyA.K. PreissnerR. ProTox-II: A webserver for the prediction of toxicity of chemicals.Nucleic Acids Res.201846W1W257-6310.1093/nar/gky31829718510
    [Google Scholar]
  52. ProTox 3.0: Prediction of toxicity of chemicals.Available from: https://tox.charite.de/protox3/
  53. GopinathP. KathriavanM.K. Docking studies and molecular dynamics simulation of triazole benzene sulfonamide derivatives with human carbonic anhydrase IX inhibition activity.RSC Advances20211160380793809310.1039/D1RA07377J35498092
    [Google Scholar]
  54. BalakrishnanV. GanapathyS. VeerasamyV. SubramaniyanS. Mohamed HussainS.A. DuraisamyR. Modifying effects of nerolidol on cell surface glycoconjugates and suppressed inflammation during DMBA-induced oral carcinogenesis: An in vivo and in silico.Biologia (Bratisl.)202278252954110.1007/s11756‑022‑01260‑y
    [Google Scholar]
  55. AzamF. TabanI.M. EidE.E.M. An in-silico analysis of ivermectin interaction with potential SARS-CoV-2 targets and host nuclear importin α.J. Biomol. Struct. Dyn.20224062851286410.1080/07391102.2020.184102833131430
    [Google Scholar]
  56. AhamedN.A. ArifI.A. Finding potential inhibitors for Main protease (Mpro) of SARS-CoV-2 through virtual screening and MD simulation studies.Saudi J. Biol. Sci.2023301210384510.1016/j.sjbs.2023.10384538020225
    [Google Scholar]
  57. DilipkumarS. KarthikV. GowrammaB. In-silico screening and molecular dynamics simulation of quinazolinone derivatives as PARP1 and STAT3 dual inhibitors: A novel DML approaches.J. Biomol. Struct. Dyn.20234220108241083437735921
    [Google Scholar]
  58. AhmadI. JadhavH. ShindeY. JagtapV. GiraseR. PatelH. Optimizing Bedaquiline for cardiotoxicity by structure based virtual screening, DFT analysis and molecular dynamic simulation studies to identify selective MDR-TB inhibitors.In Silico Pharmacol.2021912310.1007/s40203‑021‑00086‑x33854869
    [Google Scholar]
  59. GuendouziA. BelkhiriL. GuendouziA. TaharM.T.D. DjekounA. A combined approaches of 2D-QSAR, molecular docking, molecular dynamics and ADMET prediction of anti-cancer inhibitor activity for actinonin derivatives.J. Biomol. Struct. Dyn.202342111913336995063
    [Google Scholar]
  60. TambeP.M. BhowmickS. ChaudharyS.K. Structure-based screening of DNA gyrase B inhibitors for therapeutic applications in tuberculosis: A pharmacoinformatics study.Appl. Biochem. Biotechnol.202019241107112310.1007/s12010‑020‑03374‑y32686004
    [Google Scholar]
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  • Article Type:
    Research Article
Keyword(s): AutoDock and ADMET; DNA gyrase; lipophilicity; PKS-13; tuberculosis; virtual screening
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