Dr. Amit Nargotra

Discovery Informatics Division
CSIR - Indian Institute of Integrative Medicine,Canal Road, Jammu – 180001
Email: anargotra[at]iiim[dot]ac[dot]in, amitnargotra[at]yahoo[dot]com

Positions Held  
Position Held Date Organization
Senior Scientist 2013 - Present CSIR-IIIM
Scientist 2009 - 2013 CSIR-IIIM
Scientist B 2006 - 2009 CSIR-IIIM
Information Officer 2001 - 2006 CSIR-IIIM
Engineer D&D 2000 - 2001 Tata Elxsi Limited, Banglore
Trainee Engineer D&D 1999 - 2000 Tata Elxsi Limited, Banglore
Honours & Awards  
  • Received Merit Scholarship throughout the course in BITS Pilani during Engineering.

  • Gold Medal awarded for securing second position in JK Board in Higher Secondary School.

  • Received Momento from Mrs Governer for being topper in CBSE Secondary School Examination
Membership and Proffessional activities  
  • Life Member of The Indian Science Congress

  • Life Member of The Essential Oil Association of India

  • External Examiner for HMV, Jallandhar (affiliated to GNDU Amritsar)

  • Peer Reviewer for European Journal of Medicinal Chemistry

  • Paper Setter & External Examiner for Bioinformatics at GNDU Amritsar.

  • External Examiner for Bioinformatics Course at NDRI Karnal

Major research areas:

Cheminformatics approach to design new inhibitors of Cancer, Tuberculosis and Malarial targets.  

The screening of large numbers of natural and synthetic compounds for drug discovery using in vivo experiments is not the only practically effective approach, particularly since this strategy makes the whole process eco-unfriendly, time consuming and centered on the sacrifice of a huge number of test animals. The role of molecular modeling and cheminformatics in the development, research and drug design can be significant in terms of developing alternative methodologies where in the animal sacrifices is either totally not involved or minimized quite drastically. Besides, several successful examples wherein the aid of molecular modeling has been instrumental in designing new drugs, the role of this approach is very well supported by the fact that quite a number of scientific journals are purely dedicated to this field.

We are involved in all the major target based drug discovery programs at IIIM with in silico support for designing molecules effective for cancer, tuberculosis and malaria. We develop robust ligand-based and structure-based models, as per the availability of the data, and then strategically combine these models to screen the Institutional compound repository. The potent compounds are thus, fetched from the repository for its biological evaluation and further optimization.

Application of protein fold imprints of natural products in drug discovery

ChemBioChem 2007, 8, 788 – 798

One of the ways where in silico research can contribute effectively in drug discovery is by exploring the concept of fold-based selection of natural products. Natural Products represent a very attractive starting point for drug discovery. An apposite selection of ‘Hit’ and ‘Lead’ plays a significant role in the identification of a new chemical entity. The biological relevance, design and diversity of a compound library are far more important than the library size. Hence a warily chosen starting point lays the foundation for drug discovery and would certainly prove very effective at later stages of the drug discovery and development process

Network pharmacology application for understanding mechanism of action and identifying new starting points for drug discovery

Current paradigm of developing highly selective ligands has been challenged mainly due to high late-stage clinical attrition rates. When a drug is taken it interacts polypharmacologically (drug interact with multiple targets), and these unintended interactions between drug and the therapeutic targets leads to the cause of these side effects and toxicity problems.
Instead of looking for a single disease-causing gene and drugs which acts solely on the appropriate individual target, the whole disease network is considered with the aim of finding multiple nodes which can be modulated via Multi-target drugs or Drug combinations. Thereby designing a magic shrapnel instead of designing a magic bullet. At Discovery Informatics Division, IIIM Jammu, we are trying to explore the Institutional compound repository and existing target based inhibitors for an effective rational combination by the application of network pharmacology approach through in silico means.      

Exploring and establishing plant based systems as models for CNS diseases in humans

The Arabidopsis genome contains 25,498 genes encoding proteins from 11,000 families, similar to the functional diversity of Drosophila and Caenorhabditis elegans -the other sequenced multicellular eukaryotes. Arabidopsis has many families of new proteins but also lacks several common protein families, these common sets of proteins have undergone differential expansion and contraction in these multicellular eukaryotes. Research has suggests that 70% of gene similarities are there with eukaryotes.  This research information motivates us to find the functional similarities of the orthologous present in Arabidopsis thaliana in contexts to neurodegenerative disorders. This idea can be a novel research to use Arabidopsis as a plant model to understand the human neuro disorder and to find its solution for the therapeutics.


  • Creation and management of the Institutional compound library of natural, semi-synthetic and synthetic compounds from within the Institute as well as procured from commercial libraries.
  • Identification of hits from Institutional compound repository for selected targets based on ligand and structural based approach
  • Development of cheminformatics tools and Interactive Interfaces for wide usage of the databases and tools developed.



  • Mehra, R.; Rajput, V.S.; Gupta, M.; Chib, R.; Kumar, A.; Wazir, P.; Khan, I.A.; Nargotra, A. Benzothiazole Derivative as a Novel Mycobacterium tuberculosis Shikimate Kinase Inhibitor: Identification and Elucidation of Its Allosteric Mode of Inhibition. ACS Journal of Chemical Information and Modeling (2016) 56(5): 930-40 DOI: 10.1021/acs.jcim.6b00056.

  • Rajput, V.S. ; Mehra, R.; K, Sanjay.; Nargotra, A; Singh, P.P.; Khan, I.A. Screening of antitubercular compound library identifies novel shikimate kinase inhibitors of Mycobacterium tuberculosis. Applied Microbiology and Biotechnology (2016) 100(12): 5415-5426.

  • Alam, M. I.; Alam, M. A. ; Alam, O.; Nargotra, A.; Taneja, S.C.; Koul, S. Molecular modeling and snake venom phospholipase A2 inhibition by phenolic compounds: structure-activity relationship. European Journal of Medicinal Chemistry (2016) 114: 209-219 doi:10.1016/j.ejmech.2016.03.008.

  • Mehra, R.; Rani, C.; Mahajan, P.; Vishwakarma, R. A.; Khan, I.A.; Nargotra, A. Computationally Guided Identification of Novel Mycobacterium tuberculosis GlmU Inhibitory Leads, Their Optimization, and in Vitro Validation. ACS Combinatorial Science (2016) 18(2): 100–116. DOI: 10.1021/acscombsci.5b00019.

  • Sharma, R.; Rani, C .; Mehra, R.; Nargotra, A.; Chib, R.; Rajput, V.S.; Kumar, S.; Singh, S.; Sharma, P.R.; Khan, I.A. Identification and characterization of novel small molecule inhibitors of the acetyltransferase activity of Escherichia coli N-acetylglucosamine-1-phosphate-uridyltransferase/glucosamine-1-phosphate-acetyltransferase (GlmU). Applied Microbiology and Biotechnology (2016) 100(7): 3071-3085. doi:10.1007/s00253-015-7123-y.

  • Rani, C.; Mehra, R.; Sharma, R.; Chib, R.; Wazir, P.; Nargotra, A.; Khan, I.A. High-throughput screen identifies small molecule inhibitors targeting acetyltransferase activity of Mycobacterium tuberculosis GlmU. Tuberculosis (2015), 95(6),664–677. doi:10.1016/j.tube.2015.06.003.

  • Mehra, R .; Chib, R.; Munagala, G .; Yempalla, K.R.; Khan, I.A.; Singh, P.P.; Khan, F.G.; Nargotra. A Discovery of new Mtb proteasome inhibitors using a knowledge-based computational screening approach. Molecular Diversity (2015), 19(4), 1003-1019. DOI: 10.1007/s11030-015-9624-0.

  • Venkateswarlu, V.; Pathania, A.S.; Kumar, K.A.A.; Mahajan, P.; Nargotra, A.; Vishwakarma, R.A.; Malik, F.A.; Sawant, S.D.  4-(N-Phenyl-N'-substituted benzenesulfonyl)-6-(4-hydroxyphenyl)quinolines as inhibitors of mammalian target of rapamycin. Bioorganic & Medicinal Chemistry (2015) 23(15), 4237–4247.

  • Sawant, S.D.; Reddy, G.L.; Dar, M. I.; Srinivas, M.; Gupta, G.; Sahu, P.K.; Mahajan, P.; Nargotra, A.; Singh, S.; Sharma, S.C.; Tikoo, M.; Singh, G.; Vishwakarma, R.A.; Syed, S. H. Discovery of novel pyrazolopyrimidinone analogs as potent inhibitors of phosphodiesterase type-5. Bioorganic & Medicinal Chemistry (2015), 23(9), 2121–2128. doi:10.1016/j.bmc.2015.03.005.

  • Mehra, R.; Sharma, R.; Khan, I. A.; Nargotra. A. Identification and optimization of Escherichia coli GlmU inhibitors: An in silico approach with validation thereof. European Journal of Medicinal Chemistry (2015), 92(6), 78–90. doi:10.1016/j.ejmech.2014.12.030.

  • Nargotra, A.; Mehra, R.; Shakir, A.; Koul, S. Structural Characterization of Bacillus subtilis Membrane Protein Bmr: An In Silico Approach. Current Computer-Aided Drug Design (2014), 10(3), 226-236.

  • Reddya, G. L.; Gurub, S.K.; Srinivasa, M.; Pathania, A.S.; Mahajan, P.; Nargotra, A.; Bhushan, S.; Vishwakarma, R.A.; Sawant, S.D. Synthesis of novel 1,2,3-triazole based benzoxazolinones: Their TNF-a based molecular docking with in-vivo anti-inflammatory, antinociceptive activities and ulcerogenic risk evaluation. European Journal of Medicinal Chemistry (2014): 80, 201-208. http://dx.doi.org/10.1016/j.ejmech.2014.04.051.

  • Rayees, S.; Satti, N. K.; Mehra, R.; Nargotra, A.; Rasool, S.; Sharma, A.; Sahu, P.K.; Rajnikant, Gupta, V.K.; Nepali, K.; Singh, G. Anti-asthmatic activity of azepino [2, 1-b] quinazolones, synthetic analogues of vasicine, an alkaloid from Adhatoda vasica. Medicinal Chemistry Research (2014), 23(9). DOI:10.1007/s00044-014-0996-y.

  • Mungala.; Gurunandham.; Yempalla, K.R.; Aithagani, S.K.; Kalia, N.P.; Ali, F.; Ali, I .; Rajput, V.S.; Rani, C.; Chib, R.; Mehra, R.; Nargotra, A.; Khan, I.A.; Vishwakarma, R.A.; Singh, P.P. Synthesis and Biological Evaluation of Substituted N-Alkylphenyl-3, 5-Dinitrobenzamide Analogs as Anti-TB Agents. MedChemComm (2014) 5: 521-527. DOI: 10.1039/C3MD00366C.

  • Bhat, W.W.; Dhar, N.; Razdan, S.; Rana, S.; Mehra, R.; Nargotra, A.; Dhar, R.S.; Ashraf, N.; Vishwakarma, R.; Lattoo, S.K. Molecular Characterization of UGT94F2 and UGT86C4, Two Glycosyltransferases from Picrorhiza kurrooa: Comparative Structural Insight and Evaluation of Substrate Recognition. PLOS One (Published Sept 16, 2013). DOI: 10.1371/journal.pone.0073804.

  • Haider, S.; Alam, M.S.; Hamid, H.; Shafi, S.; Nargotra, A.; Mahajan, P.; Nazreen, S.; Kalle, A.M.; Kharbanda, C.; Ali, Y.; Alam, A.; Panda, A.K. Synthesis of novel 1,2,3-triazole based benzoxazolinones: Their TNF-a based molecular docking with in-vivo anti-inflammatory, antinociceptive activities and ulcerogenic risk evaluation. European Journal of Medicinal Chemistry (2013): 70, 579-588.

  • Mehra, R.; Nargotra, A.; Shah, B. A.; Taneja, S. C.; Vishwakarma, R.; Koul, S. Pro-apoptotic properties of parthenin analogs: a quantitative structure–activity relationship study. Medicinal Chemistry Research (2013) 22: 2303-2311. doi:10.1007/s00044-012-0225-5.

  • Kalia, N.P.; Mahajan, P.; Mehra, R.; Nargotra, A.; Sharma, J. P .; Koul, S.; Khan, I.A. Capsaicin, a novel inhibitor of the NorA efflux pump, reduces the intracellular invasion of Staphylococcus aureus. Journal of Antimicrobial Chemotherapy (2012) 67; 2401-2408.

  • Kalia, N.P.; Mahajan, P .; Mehra, R.; Nargotra, A .; Sharma, J.P .; Koul, S.; Khan, I.A. Capsaicin, a novel inhibitor of the NorA efflux pump, reduces the intracellular invasion of Staphylococcus aureus. Journal of Antimicrobial Chemotherapy (2012) 67; 2401-2408.

  • Sharma, D. K. ; Rah, B. A. ; Lambu, M. R.; Hussain, A.; Yousuf, S.K. ; Tripathi, A.K. ; Singh, B.; Jamwal, G.; Ahmed, Z.; Chanauria, N .; Nargotra, A.; Goswami, A .; Mukherjee, D. Design and synthesis of novel N,N'-glycoside derivatives of 3,3'-diindolylmethanes as potential antiproliferative agents . Med Chem Comm. (2012) 3: 1082-1091. Doi: 10.1039/C2MD20098H.

  • Johri, S.; Bhat, A .; Sayed, S .; Nargotra, A.; Qazi, G. N. Novel thermostable lipase from Bacillus circulans IIIB153: Comparison with the mesostable homologue at sequence and structure level. World J Microb. Biotechnol. (2012) 28: 193-203.

  • Nargotra, A.; Sharma, S.; Alam, M.I.; Ahmed, Z.; Bhagat, A.; Taneja, S.C.; Qazi, G.N .; Koul, S. In silico identification of viper phospholipase A2 inhibitors: validation by in vitro, in vivo studies. Journal of Molecular Modeling (2011)  : 17: 3063-3073 DOI 10.1007/s00894-011-0994-7.

  • Sharma, S.; Kumar, M.; Sharma, S.; Nargotra, A.; Koul, S.; Khan, I.A. Piperine as an inhibitor of Rv1258c, a putative multidrug efflux pump of Mycobacterium tuberculosis. Journal of Antimicrobial Chemotherapy (2010) 65: 1694-1701.

  • Shah, B. A.; Chib, R.; Gupta, P.; Sethi, V. K.; Koul, S.; Andotra, S. S.; Nargotra, A.; Sharma, S.; Pandey, A.; Bani, S.; Purnima, B.; Taneja, S.C. Saponins as novel TNF-a inhibitors: Isolation of saponins and a nor-pseudoguaianolide from Parthenium hysterophorus. Organic & Biomolecular Chemistry (2009) 7, 3230–3235.

  • Nargotra, A.; Sharma, S .; Koul, J. L.; Sangwan, P.L.; Khan, I. A.; Kumar, A.; Taneja, S.C.; Koul, S. Quantitative Structure Activity Relationship (QSAR) of piperine analogs for bacterial NorA efflux pump inhibitors. European Journal of Medicinal Chemistry (2009) 44(10), 4128-4135.

  • Nargotra, A.; Koul, S .; Sharma, S.; Khan, I. A.; Kumar, A.; Thota, N.; Koul, J. L.; Taneja, S.C.; Qazi, G. N. Quantitative Structure Activity Relationship (QSAR) of aryl alkenyl amides/imines for bacterial efflux pump inhibitors. European Journal of Medicinal Chemistry (2009) 44(1), 229-38.

  • Maqbool1, Q.A.; Johri1, S.; Rasool, S.; Hassan, S.R.; Verma, V.; Nargotra, A.; Koul, S.; Qazi, GN. Molecular cloning of enantioselective carboxylesterase gene and biochemical characterisation of encoded protein from Bacillus subtilis. Journal of Biotechnology (2006) 125(1):1-10.


  • Novel 1,3,5 -triazine based PI3K inhibitors as anticancer agents and a process for the preparation thereof (Indian Patent Filed: 3369DEL2014).

  • 6-nitro-2,3-dihydroimidazo[2,1-B] oxazoles and a process for the preparation thereofanti-mycobacterial agents (WO Patent Application No. PCT/IN2014/000202, TW Patent Application No. 103120596).
  • (EN) Boronic acid bearing liphagane compounds as inhibitors of PI3K-α and/or β (FR) Composés liphagane porteurs d'acide boronique servant d'inhibiteurs de PI3K-α et/ou β. (WO Patent No. WO/2013/14041 A1).

  • Novel pyrazolopyrimidinones as PDE-5 inhibitors (Patent Application No. PCT/IN2014/000662).

  • Design, synthesis and Biological evaluation of isoform selective analogs of Tetrazolyl Quinazolinone scaffold as anticancer agents: PI3K-α/δ inhibitors ; Patent Application Filed, 2012.
  • Analogs of liphagane scaffold as anticancer agents and inhibitors of PI3K α/β and process for the preparation thereof. Patent Application Filed 0794DEL2012; Prov. Dated:19/03/2012.

  • Novel diamides as potentiators of the bioefficacy of drugs. NF042/2011 (Feb 2011). 864DEL2011.

  • Novel snake venom Phospholipase A2 inhibitors NF 0236/2006 dated 12.10.2006 and 0532DEL2008 dated 05.03.2008.

Group Members


Priya Mahajan

Rakhi Talwar

Manas Ranjan Barik

Harshita Tiwari

Monika Gupta



Schrodinger : Molecular modelling studies
Desmond : Molecular Dynamic studies
Discovery studio : Quantitative structure-activity relationship 
Auto-dock : Molecular docking studies
Instant Jchem : Create, manage and analyse chemical structures and their data.