Dr. Mohammad Imran Siddiqi
 

Principal Scientist
Computational Biology & Bioinformatics Group
LSN-104, Biological Sciences, North Block
Molecular and Structural Biology Division
CSIR-Central Drug Research Institute,
Lucknow- 226031, U.P., India

 
Educational Qualifications M.Sc. (Biophysics) A.I.I.M.S., New Delhi
Ph.D. (Biophysics) A.I.I.M.S., New Delhi
Phone +91-522-2772450, 2772550 Extn. 4487 (office), 4488 (lab)
E- Mail [email protected]  [email protected]
Date of Birth 30.03.1971
 
POST-DOCTORAL RESEARCH
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University of Wuerzburg, Germany
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 Biotechnology Research Institute, Montreal , NRC Canada
 
OUR RESEARCH
Computational Biology and Bioinformatics group’s research effort are focused on studying the macromolecules and their interactions with small molecules through the concepts and methods of the computational sciences. Computer-based methods in bio-molecular sciences are an increasing complement to experiment. Particular uses are for studying molecular details that are not easily accessible to experiment and making experimentally-testable predictions, especially for drug design. We use structural bioinformatics and computational chemistry tools with specific focus on bio-molecular modeling and simulation, 3D-QSAR studies, virtual screening and development of computational predictive models towards the identification and design of small molecules as inhibitors/vaccines or chemical probes against various therapeutically important drug targets.

Focus Areas:
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 Informatics: Bio-informatics and Cheminformatics
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 Computational Structural biology: Biomolecular engineering & Modeling, Computer-Aided Molecular Design and Simulation.
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 Rational Drug design: Virtual screening, de novo design, pharmacophore perception, SAR and ADME, Molecular docking, Conformational Analysis, Binding free energy simulations and Protein Ligand interactions.
 
PRESENT GROUP MEMBERS
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 Priyanka Shah (SRF)
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  Vikash Kumar (SRF)
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 Sharat Chandra (JRF)
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 Nidhi (JRF)
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 Tanuj Sharma (JRF)
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 Shagun Krishna (Project Fellow)
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 Paroma Bhattacharya (Project Fellow)
 
REPRESENTATIVE PUBLICATIONS
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 Molecular characterization of rmsD-like rRNA methyl transferase from Wolbachia endosymbiont  of Brugia Malayi and anti-filarial activity of specific inhibitor of the enzyme. Rana, A.K., Chandra, S., Siddiqi, M.I. and Bhattacharya-Misra, S., Antimicrob. Agents Chemother. Published ahead of print 3 June, 2013, DOI: 10.1128/AAC.02269-12.
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 Structural modelling studies and immunoprophylactic  potential of Brugia malayi DEAD Box RNA helicase. Singh M, Shrivastava N, Saqib, U., Siddiqi, M.I., Misra-Bhattacharya S. Parasitology. 2013 Jul;140(8):1016-25. doi: 10.1017/S0031182013000322.
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 Novel Phytochemical-antibiotic conjugates as multi-target inhibitors of P. Aeruginosa Gyr/ParE and DHFR (2013). Jayaraman, P., Sakharkar, M.K., Lim, C.S., Siddiqi, M.I., Dhillon, S.K. and Sakharkar, M.K. Drug Des. Devel. Ther. (2013); 7, 449-475, Doi: http://dx.doi.org/10.2147/dddt.s43964
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 Hybrid drug design targeting Pseudomonas aeruginosa DHPA and DHFR. Jayaraman P, Sakharkar MK, Daniel, L.C.S., Siddiqi, M.I., Dhillon, S.K. and  Sakharkar M.K., Frontier in Biosciences  Vol. E5, June, 1, 2013, Issue 3, 864-882
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 Recycling factors for ribosome disassembly in the apicoplast and mitochondrion of Plasmodium falciparum. Gupta  A, Mir SS, Jackson KE, Lim EE, Shah P, Sinha A, Siddiqi M.I., Ralph SA and Habib SMol Microbiol. 2013 Apr 24. doi: 10.1111/mmi.12230.
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 Synthesis and Insight into the Structure−Activity Relationships of Chalcones as Antimalarial Agents, Tadigoppula N, Korthikunta V, Gupta S, Kancharla P, Khaliq T, Soni A, Srivastava RK, Srivastava K, Puri SK, Raju KS, Wahajuddin, Sijwali PS, Kumar V, Imran Siddiqi, Mohammad. J Med Chem. 2013 Jan 10;56(1):31-45. doi: 10.1021/jm300588j. Epub 2012 Dec 27.
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 Heat shock protein 60 of filarial parasite Brugia malayi: cDNA cloning, expression, purification and in silico modeling and analysis of its ATP binding site. Misra, R. C., Verma, A. K., Verma, S. K., Kumar ,V., Siddiqui, W. A., Siddiqi, M.I. and Murthy, P. K. Experimental  Parasitol., 2012, Oct;132(2):257-66. doi: 10.1016/j.exppara.2012.07.012. 
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 Discovery of a new class of Dithiocarbamates and Rhodanine Scaffold as potent antifungal agent: Synthesis, Biology and molecular Docking, Chauhan, K., Sharma, M., Singh, P.,  Kumar, V., Shukla, P.K., Siddiqi, M.I., Chauhan, P.M.S., Med Chem Communications, 2012, 3, 1104-1110 DOI:10.1039/C2MD20109G
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 β-Amyrin acetate and β-Amyrin palmitate as Antidyslipidemic agents from Wrightia tomentosa leaves. Maurya, R., Srivastava, A., Shah, P., Siddiqi, M.I, Rajendran, S.M., Puri, A., Yadav, P.P., Phytomedicine. 2012 Jun 15;19(8-9):682-5. Epub 2012 Apr 26
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 3D-QSAR studies of triazolopyrimidine derivatives plasmodium falciparum dihydroorotate dehydrogenase inhibitors using a combination of molecular dynamics, docking and genetic algorithm based methods. Shah, P., Kumar, S., Tiwari, S. and Siddiqi, M.I.,  J. Chem. Biol. 2012, Volume 5 (3), 91-103 DOI:10.1007/s12154-012-0072-3
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 Synthesis and antifungal activity of 1,5-disubstituted-1,2,3-triazole containing fluconazole analogues. Vandana S. Pore, Manisha A. Jagtap, Sandip G. Agalave, Atindra K. Pandey, Mohammad I. Siddiqi, Vikash Kumar and Praveen K. Shukla., Med Chem Communications, 2012. 3, 484-488. DOI: 10.1039/C2MD00205A
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 Potentiating Metronidazole Scaffold against Resistant Trichomonas: Design, Synthesis, Biology and 3D–QSAR Analysis. Kumar,L., Jain,A., Lal,N., Sarswat, A,  Jangir,S. Kumar,L., Shah,P.,  Jain,S.K., Maikhuri,J.P., Siddiqi,M.I., Gupta,G., and Sharma, V.L. ACS Med Chem. Letts, 2012, 3, 83-87. (online publication Dec 16, 2011, , DOI: 10.1021/ml200161t)
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 Synthesis of hybrid 4-anilinoquinoline-triazine as potent antimalarial agents, their in silico modeling and bioevaluation as Plasmodium falciparum transketolase and β-hematin inhibitors, Sharma,M., Chauhan, k., Chauhan,S.S., Kumar,A., Singh,S.V.,  Saxena,J.K.,  Agarwal,P., Srivastava,K., Raja Kumar, S., Puri,S.K., Shah,P., Siddiqi,  M.I. and Prem M. S. Chauhan;  Med Chem Commun, 2012, 3, 71-79 DOI: 10.1039/C1MD00188D
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 Identification of Novel Inhibitors of Dipeptidylcarboxypeptidase of Leishmania donovani via Ligand Based Virtual Screening and Biological Evaluation. Gangwar S, Baig MS, Shah P, Biswas S, Batra S, Siddiqi M.I., Goyal N. Chem Biol Drug Des. 2012 Feb;79(2):149-156. doi: 10.1111/j.1747-0285.2011.01262.x. 
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 Discovery of a new class of HMG-CoA reductase inhibitor from Polyalthia longifolia as potential antidyslipidemic agent. Sashidhara, K.V., Singh, S.P., Srivastava, A, Puri, A , Chhonker, Y.S. , Bhatta, R.S.,  Shah, P.  and  Siddiqi, M.I., Eur J Med Chem.  2011 Oct;46(10):5206-11 , Epub 2011 August12 , doi:10.1016/j.ejmech.2011.08.012
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 Singh, N., Pandey, S.K., Anand, N., Dwiwedi, R., Singh, S., Sinha, S.K., Chaturvedi, V., Jaiswal, N., Srivastava, A.K., Shah, P., Siddiqi, M. I., Tripathi, R.P., Synthesis, molecular modeling and bio-evaluation of cycloalkyl fused 2-aminopyrimidines as anti-tubercular and anti-diabetic agents, Bioorganic & Medicinal Chemistry Letters (2011), Aug 1;21(15):4404-8, doi: 10.1016/j.bmcl.2011.06.040
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 Interaction between SufB and SufC: evidence for an iron-sulfur cluster biogenesis pathway in the apicoplast of Plasmodium falciparum. Kumar, B., Chaubey,S., Shah, P.,  Tanveer,A., Charan,M., Siddiqi, M.I. and Habib, S. Int J Parasitol.  2011 Aug 1;41(9):991-9. Epub 2011 Jun 16
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 Interaction of a ruthenium(II)–chalcone complex with double stranded DNA: Spectroscopic, molecular docking and nuclease properties   Gaur,R., Khan,R.A., Tabassum,S., Shah,P., Siddiqi,M.I, and  Mishra, L.J Photochem Photobiol A Chem Volume 220, Issues 2-3, 20 May 2011, Pages 145-152 doi:10.1016/j.jphotochem.2011.04.005 
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 Bile Acid Receptor Agonist GW4064 Regulates PPAR{gamma} Coactivator-1{alpha} Expression Through Estrogen Receptor-Related Receptor {alpha}. Dwivedi SK, Singh N, Kumari R, Mishra JS, Tripathi S, Banerjee P, Shah P, Kukshal V, Tyagi AM, Gaikwad AN, Chaturvedi RK, Mishra DP, Trivedi AK, Sanyal S, Chattopadhyay N, Ramachandran R, Siddiqi M.I., Bandyopadhyay A, Arora A, Lundåsen T, Anakk SP, Moore DD, Sanyal S. Mol Endocrinol. 2011 Jun;25(6):922-32. Epub 2011 Apr 14.
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 Structural Investigations of Anthranilimide Derivatives by CoMFA and CoMSIA 3D-QSAR Studies Reveal Novel Insight into Their Structures toward glycogen phosphorylase  Inhibition, Saqib, U and  Siddiqi, M.I. SAR QSAR Environ Res. 2011 2011 Jul-Sep;22(5-6):411-49. Epub 2011 May 27 ,DOI: 10.1080/1062936X.2011.569898
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 Insights into structure and function of SHIP2-SH2: homology modeling, docking, and molecular dynamics study Uzma Saqib and Siddiqi, M.I. J. Chem. Biol. 2011 Volume 4, Number 4, 149-158, doi: 10.1007/s12154-011-0057-7)
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 Interaction of apicoplast-encoded elongation factor (EF) EF-Tu with nuclear-encoded EF-Ts mediates translation in the Plasmodium falciparum plastid. Biswas, S.,   Lim, E.E., Gupta, A., Mir, S.S., Siddiqi, M.I., Ralph, S.A., and Habib, S. Int J Parasitol. 2011 Mar;41(3-4):417-27. Epub 2010 Dec 14.
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 4-anilinoquinoline triazines: a novel class of hybrid antimalarial agents.Kumar A, Srivastava K, Kumar SR, Siddiqi M.I., Puri SK, Saxena JK, Chauhan PM. Eur J Med Chem. 2011 Feb;46(2):676-90.
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 Identification of potential P. Falciparum transketolase inhibitors: pharmacophore design, in silico screening and docking studies. Joshi, S., Singh, A.R., Saqib, U., Misra, P.C., Siddiqi, M.I. and Saxena, J.K. J. Biophys. Chem., 2010 Vol 1(2): 96-104.
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 3D-QSAR studies on triclosan derivatives as Plasmodium falciparum enoyl acyl carrier reductase inhibitors. Shah, P., Siddiqi, M.I., SAR QSAR Environ Res. 2010 Jul;21(5):527-45
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 Synthesis And Molecular Docking Studies Of 1-Phenyl-4-Glycosyl Dihydropyridines As Potent Anti-leishmanial Agents, Pandey VP, Bisht SS, Mishra M, Kumar A, Siddiqi MI, Verma A, Mittal M, Sane SA, Gupta S, Tripathi RP. Eur J Med Chem. 2010 Jun;45(6):2381-8. Epub 2010 Feb 12.
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 Leishmania actin binds and nicks kDNA as well as inhibits decatenation activity of type II topoisomerase. Kapoor, P, Kumar, A., Naik, R., Ganguli, M., Siddiqi, M.I., Sahasrabuddhe, A., Gupta, C.M., Nucleic Acids Res. 2010 Jun;38(10):3308-17. Epub 2010 Feb 10.doi:10.1093/nar/gkq051
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 Alkaline pH dependent differential unfolding characteristics of mesophilic and thermophilic homologs of dimeric serine hydroxymethyltransferase , Anant Narayan Bhatt, A.N., Bhakuni,V., Kumar,A., Khan, M.Y., and  Siddiqi, M.I., Biochim Biophys Acta.2010 Jun;1804(6):1294-300. Epub 2010 Feb 10. doi:10.1016/j.bbapap.2010.01.023
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 Receptor based 3D-QSAR to identify putative binders of Mycobacterium tuberculosis Enoyl acyl carrier protein reductase. Kumar, A. and Siddiqi, M.I. J. Mol. Model. 2010 May;16(5):877-93. Epub 2009 Sep 25DOI: 10.1007/s00894-009-0584-0
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 3D-QSAR studies on quinazoline antifolate thymidylate synthase inhibitors by CoMFA and CoMSIA models. Srivastava V, Gupta SP, Siddiqi M.I., Mishra B.N., Eur J Med Chem. 2010 Apr;45(4):1560-71. Epub 2010 Jan 13.doi:10.1016/j.ejmech.2009.12.065
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 New molecular scaffolds for the design of Mycobacterium tuberculosis Type II dehydroquinase inhibitors identified using ligand and receptor based virtual screening. Kumar, A., Siddiqi, M. I., Miertus, S., J. Mol. Model. 2010 Apr;16(4):693-712. Epub 2009 Oct 9.
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 Characterization of dipeptidylcarboxypeptidase of Leishmania donovani: A molecular model for structure based design of antileishmanials, Baig, M.S., Kumar, A., Siddiqi, M.I., and Goyal, N. J Comput Aided Mol Des. 2010 Jan;24(1):77-87. Epub 2009 Dec 29 DOI: 10.1007/s10822-009-9315-y
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 Molecular docking studies on quinazoline antifolate derivatives as human thymidylate synthase inhibitors. Srivastava V, Gupta SP, Siddiqi M.I., Mishra B.N. Bioinformation. 4(8) 357-36,  (2010)
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 3D-QSAR studies on triazolopiperazine amide inhibitors of dipeptidyl peptidase-IVas anti-diabetic agents, Saqib, U. and Siddiqi,M.I., 2009, SAR and QSAR in Environmental Research, Volume 20, Issue 5 & 6 July 2009 , pages 519 – 535.
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 Review of Knowledge for Rational Design and Identification of Anti-tubercular compounds, Siddiqi, M. I. and Kumar, A. Expert Opin. Drug Discov. (2009) 4(10): 1005-1015. Invited article. DOI 10.1517/17460440903253876.
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 An orally effective dihydropyrimidone (DHPM) analogue induces apoptosis-like cell death in clinical isolates of Leishmania donovani overexpressing pteridine reductase 1. Singh, N., Kaur, J., Kumar, P., Gupta, S., Singh, N., Ghosal, A., Dutta, A., Kumar, A., Tripathi, R., Siddiqi, M.I., Mandal, C., Dube, A.  Parasitol Res.  2009 Oct;105(5):1317-25
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 Knowledge based identification of potent anti-tubercular compounds using structure based virtual screening and structure interaction fingerprints. Kumar, A., Chaturvedi,V., Bhatnagar, S., Sinha, S.,  and  Siddiqi, M.I. (J. Chem. Info. and model.,2009, 49(1) 35-42, http://pubs.acs.org/doi/abs/10.1021/ci8003607)
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 3D-QSAR studies of xanthone derivatives as human alpha glucosidase inhibitors. Saqib, U. and Siddiqi, M.I., Int. Journal  of Integrative Biology, 2009,Vol 5(1); 13-19.
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 Molecular docking studies on DMDP derivatives as human DHFR inhibitors. Srivastava, V., Kumar, A., Mishra, B.N., and  Siddiqi, M.I. Bioinformation, 2008, 3(4), 180-188.
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 Virtual screening against Mycobacterium tuberculosis Dihydrofolatreductase: Suggested workflow for compound prioritization using structure interaction fingerprints. Kumar, A., and  Siddiqi, M.I. J. Mol. Graph. and Model., November, 2008; 27(4) : 476-488.doi:10.1016/j.jmgm.2008.08.005
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 CoMFA based de novo design of pyrilidone carboxamides as inhibitors of enoyl acyl carrier protein reductase from Mycobacterium tuberculosis. Kumar, A. and Siddiqi, M.I.,   J. Mol. Model, October, 2008 ; 14 (10) : 923-35. http://dx.doi.org/10.1007/s00894-008-0326-8.
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 Leishmania donovani Pteridine Reductase 1: Biochemical Properties and Structure-Modeling studies. Kumar, P., kumar, A., Verma,S.S.,  Dwivedi,N., Singh, N., Siddiqi, M.I., Tripathi, R.P., Dubey, A., and Singh, N. Experimental  Parasitol., September 2008, Volume 120, (1): 73-79,  doi:10.1016/j.exppara.2008.05.005 
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 An unconventional form of actin in protozoan haemoflagellate, Leishmania.  Kapoor,P.,  Sahasrabuddhe,A.A., Kumar,A., Mitra,K., Siddiqi, M.I. , and   Gupta, C.M.  J. Biol. Chem., 2008, August 15; 283 (33): 22760-73. doi:10.1074/jbc.M800213200
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 Molecular and biochemical characterization of plasmodium falciparum transketolase. Joshi, S., Singh, A.K., Kumar, A., Mishra, P.C., Siddiqi, M.I. and Saxena, J.K.  Mol Biochem Parasitol. 2008 Jul;160 (1):32-41
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 Synthesis, Molecular Docking and PTP1B Inhibitory Activity of Functionalized 4,5-Dihydronaphthofurans and Dibenzofurans, Dixit, M., Saeed, U., Kumar, A., Siddiqi, M.I., Tamrakar, A.K.,  Srivastava, A.K. and Goel, A.  Medicinal Chemistry, 2008, Jan, 4(1): 18-24.
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 Probing ligand binding interactions of human alpha glucosidase by homology modeling and molecular docking. Saqib, U. and Siddiqi, M.I.  Int. Journal  of Integrative Biology, 2008, Vol 2, (2) : 116-121.
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 Nuclear gyrB encodes a functional subunit of the Plasmodium falciparum gyrase that is involved in apicoplast DNA replication.  Raghu Ram, EVS, Kumar, A., Biswas, S., Kumar, A., Chaubey, S., Siddiqi, M.I. and Habib, S., Mol Biochem. Parasit. 2007, July, 154: 30-39.
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 Ligand based Virtual Screening and Biological Evaluation of  Inhibitors of Chorismate Mutase (Rv1885c) from Mycobacterium tuberculosis H37Rv. Agrawal, H.,  Kumar,  A., Bal, N.C., Siddiqi M.I., and Ashish Arora,  Bioorg. Med. Chem. Letts, 2007; Jun 1;17(11):3053-3058. Epub 2007 Mar 21.
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 Amino acid based enantiomerically pure 3-substituted benzodiazepine-ones : a new class of  anti-ischemic agents. Mishra, J.K., Garg, P., Doohare, P., Kumar, A., Siddiqi, M.I. Ray, M. and Panda, G. Bioorg Med Chem Lett. 2007 Mar 1;17(5):1326-1331. Epub 2006 Dec 3.
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 Solvated interaction energy (SIE) for scoring protein-ligand binding affinities. 1. Exploring the parameter space. Naim, M., Bhat, Sathesh,  Rankin; K. N., Dennis, S., Chowdhury, S. F., Siddiqi, M. I., Drabik, P., Sulea T., Bayly, C.,  Jakalian ,A. and Purisima, E.O.  J. Chem. Info. and model., 2007, Jan 22, 47(1) : 122-133.
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 Molecular Docking   Studies on 4-Thiazolidinones as HIV-1 RT Inhibitors. Ravindra K. Rawal, Ashutosh kumar, Siddiqi, M. I. and  S.B. Katti. J Mol  Model, 2007, Jan;13(1):155-61. Epub 2006 Sep 13.
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 CoMFA and CoMSIA based 3D-QSAR  Analysis of Diaryloxy methano phenanthrene Analogues asAnti-tuberculosis Agents. Shagufta, Ashutosh Kumar, Gautam Panda and Siddiqi, M.I., J Mol Model. 2007, Jan;13(1):99-109. Epub 2006 Jun 21.