Abstract
In view of the role of DHFR in design and development of antimicrobials, we have attempted to develop a rigorously validated structure-based pharmacophore model comprising of two hydrogen bond donors, one hydrogen bond acceptor and two hydrophobic features. The model was used as a query to screen the National Cancer Institute and Maybridge database leading to retrieval of many hits which were screened on the basis of estimated activity, fit value and Lipinski’s violation. Three most potent hits with zero lipinski’s violation were subjected to docking studies which resulted into visualization of potential interaction capabilities of compounds in line to pharmacophoric features. All the three hits were subjected to in vitro antimicrobial evaluation, and the order of activity against various microbial strains was found to be HTS00987 > NSC47793 > NSC5475. Since HTS00987 appeared to be most active, it was subjected to permeability studies using in vitro everted intestinal sac permeation method. The results revealed that HTS00987 has good permeability proving its potential as druggable antimicrobial agent.
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Allegra CJ, Kovacs JA, Drake JC (1987a) Potent in vitro and in vivo antitoxoplasma activity of the lipid-soluble antifolate trimetrexate. J Clin Invest 79:478–482
Allegra CJ, Kovacs JA, Drake JC, Swan JC (1987b) Activity of antifolates against Pneumocystis carinii dihydrofolate reductase and identification of a potent new agent. J Exp Med 165:926
Barlett MS, Smith JW (1991) Pneumocystis carinii, an opportunist in immunocompromized patients. Clin Microbiol Rev 4:137–149
Behbahani R, Moshfeghi M, Baxter JD (1995) Therapeutic approaches for AIDS-related toxoplasmosis. Ann Pharmacother 29:760–768
Doweyko AM (1994) Three-dimensional pharmacophores from binding data. J Med Chem 37:1769–1778
Gangjee A, Devraj R, McGuire JJ, Queener SF (1994) Classical and nonclassical furo [2,3 d] pyrimidines as novel antifolates: synthesis and biological activities. J Med Chem 37:1169–1176
Gangjee A, Vasudevan A, Queener SF (1996a) 2,4-Diamino-5-deaza-6-substituted pyrido[2,3-d]pyrimidine antifolates as potent and selective nonclassical inhibitors of dihydrofolate reductases. J Med Chem 39:1438–1446
Gangjee A, Zhu Y, Queener SF, Broom AD (1996b) Nonclassical 2,4-diamino-8-deazafolate analogues as inhibitors of dihydrofolate reductase from rat liver, Pneumocystis carinii and Toxoplasma gondii. J Med Chem 39:1836–1845
Gangjee A, Vidwans A, Elzein E, McGuire JJ, Queener SF, Kisliuk RL (2001) Synthesis, antifolate, and antitumor activities of classical and nonclassical 2-amino-4-oxo-5-substituted-pyrrolo [2,3-d] pyrimidines. J Med Chem 44:1993–2003
Gangjee A, Adair OO, Queener SF (2003) Synthesis and biological evaluation of 2,4-diamino-6-(arylaminomethyl) pyrido [2,3-d] pyrimidines as inhibitors of Pneumocystis carinii and Toxoplasma gondii dihydrofolate reductase and as antiopportunistic infection and antitumor agents. J Med Chem 46:5074–5082
Gangjee A, Adair OO, Pagley M, Queener SF (2008) N9 substituted 2,4-diaminoquinazolines: synthesis and biological evaluation of lipophilic inhibitors of Pneumocystis carinii and Toxoplasma gondii dihydrofolate reductase. J Med Chem 51:6195–6200
Güner OF, Henry DR (2000) Metric for analyzing hit lists and pharmacophores. In: Güner OF (ed) Pharmacophore perception, development and use in drug design. IUL biotechnology series. International University Line, La Jolla, pp 191–212
Güner OF, Waldman M, Hoffmann RD, Kim JH (2000) Strategies for database mining and pharmacophore development. In: Güner OF (ed) Pharmacophore perception, development, and use in drug design. IUL biotechnology series, 1st edn. International University Line, La Jolla, CA, pp 213–236
Hou TJ, Xu XJ (2004) Recent development and application of virtual screening in drug discovery: an overview. Curr Pharm Des 10:1011–1033
Jorgensen WL (2004) The many roles of computation in drug discovery. Science 303:1813–1816
Kovacs JA, Allegra CJ, Swan JC, Darke JC (1988) Potent antipneumocystis and antitoxoplasma activities of piritrexim, a lipid-soluble antifolate. Antimicrob Agents Chemother 32:430–433
Kovacs JA, Allegra CJ, Beaver J, Boarman D (1989) Characterization of de novo folate synthesis in Pneumocystis carinii and Toxoplasma gondii: potential for screening therapeutic agents. J Infect Dis 160:312–320
Kroemer RT (2007) Structure-based drug design: docking and scoring. Curr Protein Pept Sci 8:312–328
Mittal A, Paliwal S, Sharma M, Singh A, Sharma S (2014) Pharmacophore based virtual screening, molecular docking and biological evaluation to identify novel PDE5 inhibitors with vasodilatory activity. Bioorg Med Chem Lett 24:3137–3141
Paliwal S, Yadav D, Yadav R, Paliwal S (2010) In silico structure-based drug design approach to develop novel pharmacophore model of human peroxisome proliferatoractivated receptor γ agonists. Med Chem Res 20:656–659
Parikh KS, Vyas SP (2012) Synthesis, characterization and antimicrobial activity of a new series of s-triazines derived with pyrimidine. Am J Pharmtech Res 2:571–576
Piper JR, Johnson CA, Krauth CA, Queener SF (1996) Lipophilic antifolates as agents against opportunistic infections. 1. Agents superior to trimetrexate and piritrexim against Toxoplasma gondii and Pneumocystis carinii in vitro evaluations. J Med Chem 39:1271–1280
Schneider G, Fechner U (2005) Computer-based de novo design of drug-like molecules. Nat Rev Drug Discov 4:649–663
Wilson TH, Wiseman G (1954) The use sacs of everted small intestine for the study of transference of substances from the mucosal to the serosal surface. J Physiol 123:116–125
Xiang M, Lei K, Fan W, Lin Y (2013) In silico identification of EGFR-T790M inhibitors with novel scaffolds: start with extraction of common features. Drug Des Devel Ther 7:789–839
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We gratefully acknowledge support for this research from Indian Council of Medical Research Centre (ICMR), New Delhi, and the authors also thank Vice Chancellor, Banasthali University for extending all the necessary facilities.
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Mishra, R., Paliwal, S., Agarwal, A. et al. Discovery of a potent broad spectrum antimicrobial agent through pharmacophore modeling, virtual screening, in vitro antimicrobial evaluation and gastrointestinal permeation studies. Med Chem Res 24, 4050–4057 (2015). https://doi.org/10.1007/s00044-015-1445-2
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DOI: https://doi.org/10.1007/s00044-015-1445-2