Structure elaboration of isoniazid: synthesis, in silico molecular docking and antimycobacterial activity of isoniazid–pyrimidine conjugates


Designing small molecule-based new drug candidates through structure modulation of the existing drugs has drawn considerable attention in view of inevitable emergence of resistance. A new series of isoniazid–pyrimidine conjugates were synthesized in good yields and evaluated for antitubercular activity against the H37Rv strain of Mycobacterium tuberculosis using the microplate Alamar Blue assay. Structure–anti-TB relationship profile revealed that conjugates 8a and 8c bearing a phenyl group at C-6 of pyrimidine scaffold were most active (MIC99 10 µM) and least cytotoxic members of the series. In silico docking of 8a in the active site of bovine lactoperoxidase as well as a cytochrome C peroxidase mutant N184R Y36A revealed favorable interactions similar to the heme enzyme catalase peroxidase (KatG) that activates isoniazid. This investigation suggests a rationale for further work on this promising series of antitubercular agents.

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Microplate Alamar Blue assay


World Health Organization


Sustainable development goals










Polyphosphate ester


Heme (ferric) enzyme catalase peroxidase




2-trans-enoyl-acyl carrier protein reductase


Adsorption, distribution, metabolism, excretion


  1. 1.

    Tanwar J, Das S, Fatima Z, Hameed S (2014) Multidrug resistance: an emerging crisis. Interdiscip Perspect Infect Dis 2014:541340

    Google Scholar 

  2. 2.

    Monge-Maillo B, Lopez-Velez R, Norman FF, Ferrere-Gonzalez F, Martınez-Perez A, Perez-Molina JA (2015) Screening of imported infectious diseases among asymptomatic sub-Saharan African and Latin American immigrants: a public health challenge. Am J Trop Med Hyg 92:848–856

    Google Scholar 

  3. 3.

    Sakamoto K (2012) The pathology of Mycobacterium tuberculosis infection. Vet Pathol 49:423–439

    CAS  Google Scholar 

  4. 4.

    Russel DG (2001) Mycobacterium tuberculosis: here today, and here tomorrow. Nat Rev Mol Cell Biol 2:569–577

    Google Scholar 

  5. 5.

    Global Tuberculosis report 2018, WHO

  6. 6.

    Uplekar M, Weil D, Lonnroth K, Jaramillo E, Lienhardt C, Dias HM, Falzon D, Floyd K, Gargioni G, Getahun H, Gilpin C, Glaziou P, Grzemska M, Mirzayev F, Nakatani H, Raviglione M (2015) WHO’s new end TB strategy. Lancet 385:1799–1801

    Google Scholar 

  7. 7.

    Lonnarth K, Raviglione M (2016) The WHO’s new end TB strategy in the post-2015 era of the sustainable development goals. Trans R Soc Trop Med Hyg 110:148–150

    Google Scholar 

  8. 8.

    Pushpakom S, Iorio F, Eyers PA, Escott KJ, Hopper S, Wells A, Doig A, Guilliams T, Latimer J, McNamee C, Norris A, Sanseau P, Cavalla D, Pirmohamed M (2019) Drug repurposing: progress, challenges and recommendations. Nat Rev Drug Discov 18:41–58

    CAS  Google Scholar 

  9. 9.

    Knowles DJ (1997) New strategies for antibacterial drug design. Trends Microbiol 5:379

    CAS  Google Scholar 

  10. 10.

    Broach JR, Thorner J (1996) High-throughput screening for drug discovery. Nature 384:14–16

    CAS  Google Scholar 

  11. 11.

    Gualano G, Capone S, Mattelli A, Palmien F (2016) New antituberculosis drugs: from clinical trial to programmatic use. Infect Dis Rep 8:6569

    Google Scholar 

  12. 12.

    Zumla A, Chakaya J, Centis R, D’Ambrosio L, Mwaba P, Bates M, Kapata N, Nyirenda T, Chanda D, Mfinanga S, Hoelscher M, Maeurer M, Migliori GB (2015) Tuberculosis treatment and management–an update on treatment regimens, trials, new drugs, and adjunct therapies. Lancet Respir Med 3:220–234

    Google Scholar 

  13. 13.

    Meunier B (2008) Hybrid molecules with a dual mode of action: dream or reality? Acc Chem Res 41:69–77

    CAS  Google Scholar 

  14. 14.

    Muregi FW, Ishih A (2010) Next-generation antimalarial drugs: hybrid molecules as a new strategy in drug design. Drug Dev Res 71:20–32

    CAS  Google Scholar 

  15. 15.

    Bass Jr JB, Farer LS, Hopewell PC, O’Brien R, Jacobs RF, Ruben F, Snider Jr DE, Thornton GS (1994) Treatment of tuberculosis and tuberculosis infection in adults and children. American Thoracic Society and The Centers for Disease Control and Prevention. Am J Respir Crit Care Med 149:1359–1374

    CAS  Google Scholar 

  16. 16.

    Srivastava S, Pasipanodya J, Meek C, Leff R, Gumbo T (2011) Multidrug-resistant tuberculosis not due to noncompliance but to between-patient pharmacokinetic variability. J Infect Dis 204:1951–1959

    CAS  Google Scholar 

  17. 17.

    Singh M, Sasi P, Rai G, Gupta VH, Amarapurkar D, Wangikar PP (2011) Studies on toxicity of antitubercular drugs namely isoniazid, rifampicin, and pyrazinamide in an in vitro model of HepG2 cell line. Med Chem Res 20:1611–1615

    CAS  Google Scholar 

  18. 18.

    Hu Y-Q, Zhang S, Zhao F, Gao C, Feng L-S, Lv Z-S, Xu Z, Wu X (2017) Isoniazid derivatives and their anti-tubercular activity. Eur J Med Chem 133:255–267

    CAS  Google Scholar 

  19. 19.

    Tripathi M, Taylor D, Khan SI, Tekwani BL, Ponnan P, Das US, Velpandian T, Rawat DS (2019) Hybridization of fluoro-amodiaquine (FAQ) with pyrimidines: synthesis and antimalarial efficacy of FAQ-pyrimidines. ACS Med Chem Lett 10:714–719

    CAS  Google Scholar 

  20. 20.

    Singh K, Kaur T (2016) Pyrimidine-based antimalarials: design strategies and antiplasmodial effects. Med Chem Commun 7:749–768

    CAS  Google Scholar 

  21. 21.

    Kaur H, Chibale K, Smith P, de Kock C, Singh K (2015) Synthesis, antiplasmodial activity and mechanistic studies of pyrimidine-5-carbonitrile and quinoline hybrids. Eur J Med Chem 101:52–62

    CAS  Google Scholar 

  22. 22.

    Kaur H, Machado M, Chibale K, Prudêncio M, Singh K (2015) Primaquine–pyrimidine hybrids: synthesis and dual-stage antiplasmodial activity. Eur J Med Chem 101:266–273

    CAS  Google Scholar 

  23. 23.

    Singh K, Kaur H, Smith P, de Kock C, Chibale K, Balzarini J (2014) Quinoline-pyrimidine hybrids: synthesis, antiplasmodial activity, SAR, and mode of action studies. J Med Chem 57:435–448

    CAS  Google Scholar 

  24. 24.

    Romeo R, Iannazzo D, Veltri L, Gabriele B, Macchi B, Frezza C, Merlo FM, Giofre SV (2019) Pyrimidine 2,4-diones in the design of new HIV RT inhibitors. Molecules 24:1718

    CAS  Google Scholar 

  25. 25.

    Okazaki S, Mizuhara T, Shimura K, Murayama H, Ohno H, Oishi S, Matsuoka M, Fujii N (2015) Identification of anti-HIV agents with a novel benzo[4,5]isothiazolo[2,3-a]pyrimidine scaffold. Bioorg Med Chem 23:1447–1452

    CAS  Google Scholar 

  26. 26.

    Varano F, Catarzi D, Vincenzi F, Betti M, Falsini M, Ravani A, Borea PA, Colotta V, Varani K (2016) Design, synthesis, and pharmacological characterization of 2-(2-Furanyl)thiazolo[5,4-d]pyrimidine-5,7-diamine derivatives: new highly potent A2A adenosine receptor inverse agonists with antinociceptive activity. J Med Chem 59:10564–10576

    CAS  Google Scholar 

  27. 27.

    Bookser BC, Ugarkar BG, Matelich MC, Lemus RH, Allan M, Tsuchiya M, Nakane M, Nagahisa A, Wiesner JB, Erion MD (2005) Adenosine kinase inhibitors. 6. Synthesis, water solubility, and antinociceptive activity of 5-phenyl-7-(5-deoxy-β-d-ribofuranosyl)pyrrolo[2,3-d]pyrimidines substituted at C4 with glycinamides and related compounds. J Med Chem 48:7808–7820

    CAS  Google Scholar 

  28. 28.

    Wu W, Chen M, Wang R, Tu H, Yang M, Ouyang G (2019) Novel pyrimidine derivatives containing an amide moiety: design, synthesis, and antifungal activity. Chem Pap 73:719–729

    Google Scholar 

  29. 29.

    Maddila S, Gorle S, Seshadri N, Lavanya P, Jonnalagadda SB (2016) Synthesis, antibacterial and antifungal activity of novel benzothiazole pyrimidine derivatives. Arab J Chem 9:681–687

    CAS  Google Scholar 

  30. 30.

    Ma Z, Gao G, Fang K, Sun H (2019) Development of novel anticancer agents with a scaffold of tetrahydropyrido[4,3-d]pyrimidine-2,4-dione. ACS Med Chem Lett 10:191–195

    CAS  Google Scholar 

  31. 31.

    Gokhale N, Dalimba U, Kums M (2017) Facile synthesis of indole-pyrimidine hybrids and evaluation of their anticancer and antimicrobial activity. J Saudi Chem Soc 21:761–775

    CAS  Google Scholar 

  32. 32.

    Liu P, Yang Y, Tang Y, Yang T, Liu Z, Zhang T, Luo Y (2019) Design and synthesis of novel pyrimidine derivatives as potent antitubercular agents. Eur J Med Chem 163:169–182

    CAS  Google Scholar 

  33. 33.

    Ke S, Shi L, Zhang Z, Yang Z (2017) Steroidal[17,16-d]pyrimidines derived from dehydroepiandrosterone: a convenient synthesis, antiproliferation activity, structure-activity relationships, and role of heterocyclic moiety. Sci Rep 7:44439

    Google Scholar 

  34. 34.

    Singh K, Singh K, Wan B, Franzblau S, Chibale K, Balzarini J (2011) Facile transformation of Biginelli pyrimidin-2(1H)-ones to pyrimidines. In vitro evaluation as inhibitors of Mycobacterium tuberculosis and modulators of cytostatic activity. Eur J Med Chem 46:2290–2294

    CAS  Google Scholar 

  35. 35.

    Vekariya MK, Vekariya RH, Patel KD, Raval NP, Shah PU, Rajani DP, Shah NK (2018) Pyrimidine‐pyrazole hybrids as morpholinopyrimidine‐based pyrazole carboxamides: synthesis, characterisation, docking, ADMET study and biological evaluation. ChemistrySelect 3:6998–7008

    CAS  Google Scholar 

  36. 36.

    Chatterji M, Shandil R, Manjunatha MR, Solapure S, Ramachandran V, Kumar N, Saralaya R, Panduga V, Reddy J, Prabhakar KR, Sharma S, Sadler C, Cooper CB, Mdluli K, Iyer PS, Narayanan S, Shirude PS (2014) 1, 4-Azaindole, a potential drug candidate for treatment of tuberculosis. Antimicrob Agents Chemother 58:5325–5331

    Google Scholar 

  37. 37.

    Biginelli P, Gazz P (1893) Synthesis of 3,4-Dihydropyrimidin-2(1H)-Ones. Chim Ital 23:360–416

    Google Scholar 

  38. 38.

    Singh K (2012) Biginelli condensation: synthesis and structure diversification of 3,4-dihydropyrimidin-2(1H)-one derivatives. In: Katritzky AR (ed) Advances in heterocyclic chemistry, vol 105. Academic Press, Cambridge, pp 223–308

    Google Scholar 

  39. 39.

    Kappe CO (2003) The generation of dihydropyrimidine libraries utilizing Biginelli multicomponent chemistry. QSAR Comb Sci 22:630–645

    CAS  Google Scholar 

  40. 40.

    Falsone FS, Kappe CO (2001) The Biginelli dihydropyrimidone synthesis using polyphosphate ester as a mild and efficient cyclocondensation/dehydration reagent. Arkivoc 2:122–134

    CAS  Google Scholar 

  41. 41.

    Shaabani A, Bazgir A, Teimouri F (2003) Ammonium chloride-catalyzed one-pot synthesis of 3, 4-dihydropyrimidin-2-(1H)-ones under solvent-free conditions. Tetrahedron Lett 44:857–859

    CAS  Google Scholar 

  42. 42.

    Strohmeier GA, Kappe CO (2002) Rapid parallel synthesis of polymer-bound enones utilizing microwave-assisted solid-phase chemistry. J Comb Chem 4:154–161

    CAS  Google Scholar 

  43. 43.

    Puchala A, Belaj F, Bergman J, Kappe CO (2001) On the reaction of 3,4-dihydropyrimidones with nitric acid. Preparation and x–ray structure analysis of a stable nitrolic acid. J Heterocycl Chem 38:1345–1352

    CAS  Google Scholar 

  44. 44.

    Metcalfe C, Macdonald IK, Murphy EJ, Brown KA, Raven EL, Moody PCE (2008) The tuberculosis prodrug isoniazid bound to activating peroxidases. J Biol Chem 283:6193–6200

    CAS  Google Scholar 

  45. 45.

    Singh AK, Kumar RP, Pandey N, Singh N, Sinha M, Bhushan A, Kaur P, Sharma S, Singh TP (2010) Mode of binding of the tuberculosis prodrug isoniazid to heme peroxidases: binding studies and crystal structure of bovine lactoperoxidase with isoniazid at 2.7 A resolution. J Biol Chem 285:1569–1576

    CAS  Google Scholar 

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We gratefully acknowledge financial assistance from CSIR, New Delhi (Project 02(0268)/16/EMR-II). We also thank Ronnett Seldon and Dale Taylor for antimycobacterial and cytotoxicity screening, respectively. KS thanks Schrodinger, India, for complimentary license.

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The manuscript was written through contributions of all authors. All authors have given approval to the final version of the manuscript.

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Correspondence to Kamaljit Singh.

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Kaur, H., Singh, L., Chibale, K. et al. Structure elaboration of isoniazid: synthesis, in silico molecular docking and antimycobacterial activity of isoniazid–pyrimidine conjugates. Mol Divers 24, 949–955 (2020).

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  • Isoniazid
  • Pyrimidine
  • Conjugates
  • Tuberculosis
  • Drug resistance
  • Molecular docking
  • ADME