Contact


Dr. Prajwal P. Nandekar
Postdoc Research associate
Molecular and cellular modeling
Heidelberg Institute for Theoretical Studies (HITS)
Phone: +49(0)6221-533-202
Fax: +49(0)6221-533-298
Mobile: +49-151-71660851
Email: prajwal.nandekar@h-its.org
prajwal.pharm07@gmail.com

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About me


  • 3 years of postdoctoral research experience in computational biology and computer‑aided drug design.
  • Ph.D. in Pharmaceutical sciences from National Institute of Pharmaceutical Education and Research (NIPER), India and DAAD fellow for sandwich Ph.D. program.
  • Experienced in project management and mentoring students.
  • 25 research publications in peer reviewed journals with h-index of 8 and 229 citations. (ORCID ID: 0000-0003-0210-9301)

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Research interests


  • Molecular modeling and MD simulations of biomolecular complexes to study their structure-function relationships.
  • Protein-protein and protein-membrane interaction studies
  • For example: i) Cytochrome P450s (CYP450) in membrane, ii) Cytochrome P450 reductase (CPR) in membrane, iii) CYP450-CPR protein-protein complex in membrane to study drug metabolism mechanism and inter-protein electron transfer processes. iv) Actin protein filament modeling and simulations to study cell motility.
  • Molecular modeling and computer-aided drug design

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Methodologies and Software


  • Structure and ligand based drug design
  • Metabolism prediction studies
  • Software development
  • Molecular dynamics simulations: Martini coarse-grain, all-atom, Random Acceleration Molecular Dynamics (RAMD) simulations
  • Quantum chemistry
  • In vitro assay

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Professional experience and Academic details


Jan 2017 – till date

Jan 2015 – Jan 2017

Working as a Postdoctoral Research associate in Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg University, Heidelberg, Germany.

Worked as a Postdoctoral Research associate in Molecular and Cellular Modeling Group, Heidelberg Institute of Theoretical Studies (HITS), Heidelberg, Germany.

Sept 2013 – Sept 2014

As a Deutscher Akademischer Austausch Dienst (DAAD) fellow during Ph.D. tenure at MCM, HITS, Heidelberg, Germany.

July 2010 – Dec 2014

Ph.D. in Pharmacoinformatics, with cGPA of 8.50 on a 10 point scale.

Thesis title: Cytochrome P450 1A1: Molecular Modeling Guided Design and In Vitro Studies of Anticancer Compounds and Cyp1A1-Biomembrane Interactions.

Supervisor: Dr. Abhay Sangamwar, Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar and

Co-supervisor: Prof. Rebecca Wade, HITS gGmbH, Heidelberg, Germany.

July 2008 – June 2010

M. S. (Pharm.) Pharmacoinformatics, with cGPA of 9.02 on a 10 point scale.

Thesis title: Cytochrome P450 2C19 mediated metabolism of drugs: Molecular docking and MetaSite analysis

Supervisor: Prof. Prasad V. Bharatam, Department of Medicinal Chemistry, NIPER, S.A.S. Nagar.

Industry – Academia collaborative project for one year during M. S. (Pharm.).

Project: The identification of optimum protocol to solve the CYP450 mediated drug metabolism profile of NCE.

Supervisors: Dr. Prashant Desai, Eli Lilly, Department of Drug Metabolism and Disposition, Indianapolis, United States of America.

2004 – 2008

Bachelor of Pharmacy, with 65.95 % marks. First Division.

University Department of Pharmaceutical Sciences, Nagpur University, Nagpur, India

2003

Higher Secondary School Certificate Exam, with 81.03% marks.

Nabira Mahavidyalaya, Katol, Dist. Nagpur, India

2001

Secondary School Certificate Exam, with 80.60% marks.

Nagar Parishad High School, Katol, Dist. Nagpur


Teaching experience


  • Assistance in conducting practical classes for M.S. (Pharm.) students, taught Chemoinformatics in drug discovery at National Institute of Pharmaceutical Education and Research (NIPER), SAS Nagar, India
  • Conducted “Training and practical session on MetaSite and TOPKAT software” in Drug Metabolism and Pharmacokinetics (DMPK) symposium 2010, 2011, 2012 and 2013 at NIPER, S.A.S. Nagar, India
  • Teaching assistance in Basic Bioinformatics course for Undergraduates at University of Heidelberg, in 2016, 2017, taught practical aspects of protein modeling, structure‑based and ligand‑based drug design.

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Professional recognitions / Awards / Fellowships


  • Won the BioSolveIT Scientific challenge ‘Spring 2016’ at first place.
  • First prize for Hackathon session on “Setting up simulation” and “Software carpentry” in the Macromolecular simulation software workshop, at CECAM- Forschungszentrum Jülich GmbH, DE-JUELICH, 12-17 Oct. 2015.
  • Deutscher Akademischer Austausch Dienst (DAAD) fellowship awarded by the German Academic Exchange Service for Sandwich model Ph.D. to perform one year research at Heidelberg Institute of Theoretical Studies (HITS), Heidelberg, Germany from Sept. 2013 to Sept. 2014.

  • Young Scientist International Travel Grant awarded by Council of Scientific and Industrial Research (CSIR), to attend the European Conference on Computational Biology (ECCB’2012), 9-12 Sept. 2012, Basel Switzerland.

  • NIPER fellowship for Doctoral study awarded by NIPER S.A.S. Nagar (July 2010 – Dec. 2014).

  • Secured All India Rank 179 in NIPER-JEE-2008 conducted by NIPER, Mohali.

  • MHRD fellowship awarded for Master’s study (July 2008 – June 2010)

  • Secured All India Rank 527 with 98.08 percentile in Graduate Aptitude Test in Engineering (GATE) 2008 (Pharmaceutical Sciences) conducted by IISc. Bangalore.

 


Project granted


  • High Performance Supercomputing time granted at HLRS, Stuttgart, Germany during year 2016-2017.
  • Research funding proposal to Department of Biotechnology, India (year 2011-2014). “Molecular Dynamics Studies of the Homology model of CYP1A1, Structure Based Drug Design And Virtual Screening of Potential Ligands that Modulates the Biological Function of CYP1A1”

 


Technical expertise


  • Data Mining/Statistics software used: R package, MATLAB, RapidMiner, Sigmastat, GNU plot, SQL Data mining add-in in MS Excel

  • Programing/Scripting skills: C++, Perl, Python, Bash shell scripting

  • Hardware and operating systems worked on: Sun workstation, Core Cluster on Linux, SGI Tezro, Fuel, Windows, IRIX, LINUX

  • Chem-Bio software used:

    • Chemoinformatics: Tripos Sybyl 7.1, Schrödinger Suite, Accelrys Discovery Studio, CCG MOE, Cambridge ChemOffice 2010

    • Docking: FlexX, Glide, InduceFit, Autodock, GOLD, LeadIT, CDOCKER

    • Visualizer: Maestro, Silver, BiosolveIT, Pymol, VMD, Chimera

    • Homology modeling: Modeller, Prime, Biopolymer

    • ADMET prediction: GastroPlus (Simulations Plus, Inc), Dragon, TOPKAT, DEREK, MetaSite, ADMET predictor, ACD labs, QuickProp

    • Molecular dynamics: Gromacs, Amber, NAMD

    • Quantum chemistry: Gaussian

    • Scientific workflow system: Pipeline Pilot and KNIME

  • Other software used: MS Access, M.S. Excel, Endnote, etc.

 


Research projects


 

  • Postdoctoral Research project: “Understanding the differences in Rabbit and Plasmodium actin filament structure”

Supervisor: Prof. Dr. Rebecca Wade, Heidelberg Institute of Theoretical Studies (HITS), Heidelberg, Germany and Prof. Dr. Friedrich Frischknecht, Department of Infectious Diseases, Parasitology Heidelberg University

Currently, I am working as a Postdoc Research Associate in Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg, Germany. Here, my role was to design, coordinate, and work on research projects. I have also been responsible for creating new collaborations with other experimental research groups that are working in same research area.  I am working on a research project funded by Heidelberg University Frontier Program. The project aims to understand the structural and mechanistic differences between Rabbit and Plasmodium Actin filament. We use molecular modelling and molecular dynamics simulation methods to study the filament properties at atomic level. We work in close collaboration with experimental research groups from UniversitätsKlinikum Heidelberg, to validate the computational outcomes. The ultimate aim of work is to design an effective strategy against the invasion malaria parasite into the human skin.

  • Postdoctoral Research Project: Molecular modeling and simulations of Cytochrome P450-Cytochrome P450 Reductase to study protein-protein interactions”.

Research supervisor: Prof. Rebecca Wade, Heidelberg Institute of Theoretical Studies (HITS), Heidelberg, Germany

I worked as a Postdoc research associate in the Molecular and Cellular Modeling Group at the Heidelberg Institute of Theoretical Studies (HITS), Heidelberg, Germany under the supervision of Prof. Dr. Rebecca Wade. Here, my role is to design, coordinate, and work on research projects. I have also been responsible for creating new collaborations with other experimental research groups that are working in same research area. I am working on the research project on molecular dynamics simulations to study CYP450-CYP450 Reductase (protein-protein) interactions using Brownian dynamics, coarse-grained, and atomic-resolutions simulation methodologies.

  • Ph.D. Research Project Title: Cytochrome P450 1A1: Molecular Modeling Guided Design and In Vitro Studies of Anticancer Compounds and Cyp1A1-Biomembrane Interactions.

Doctoral thesis project July 2010-Dec.2014

Project Supervisor: Dr. Abhay T. Sangamwar, Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar and

Co-supervisor: Prof. Rebecca Wade, Heidelberg Institute of Theoretical Studies (HITS), Heidelberg, Germany

Developments in molecular oncology and pharmacoinformatics, has converted the pattern of new drug discovery (NDD) from pharmacology mode of “drug-receptor-gene” to retro-molecular pharmacology mode of “gene-receptor-drugs”. So, the oncologists have become more aware of the fact that NDD must target the developing mechanism of tumerogenesis to improve the therapeutic efficacy of antineoplastic drugs. The trend of anticancer drug studies has been oriented to target the multi-links of mechanism of tumerogenesis, such as targeting interrelated enzymes, interrupting cell signal transduction pathway, cell apoptosis and cell metabolism. The drugs designed are expected to have high affinity towards the novel targets selectively. The concept of overexpression of individual forms of cytochrome P450 (CYP450) enzymes in tumor cells is now becoming well recognized. Indeed, a growing body of research highlights the overexpression of CYP450s, particularly cytochrome P450 1A1 (CYP1A1), in tumor cells as representing novel targets for anticancer therapy. During the Ph.D. project, various in silico methodologies such as homology modeling, molecular docking, molecular dynamics simulations, quantum chemical studies, QSAR, pharmacophore mapping and the prediction of metabolism of chemotherapeutic agents were effectively applied for CYP1A1 mediated anticancer drug designing. The designed compounds were synthesized and tested against various cancer cell lines. The experimental validation of the designed molecules was performed to increase confidence level of strategy. The coarse grain and all atom molecular dynamics simulations were performed to understand the CYP1A1-membrane interactions. The RAMD simulation was also performed to study the CYP1A1-membrane, substrate and product interactions.

Minor Projects

  • DNA binding and off-target identification studies of 5F-203 and 5-amino flavone as CYP1A1 mediated antitumor compounds were performed using in silico techniques.

  • Quantum chemical based descriptor calculation of available CYP1A1 mediated antitumor compounds and designing of novel antitumor compounds acting on CYP1A1.

  • Predicting drug metabolism by CYP1A1, CYP1A2, and CYP1B1: insights from MetaSite, molecular docking and quantum chemical calculations.

  • Comparative Proteomics Among Cytochrome P450 Family 1 for Differential Substrate Specificity.

  • Characterization of Differences in Substrate Specificity among CYP1A1, CYP1A2 and CYP1B1: An Integrated approach employing Molecular Docking, Molecular Dynamics Simulations and Access Channel Analysis.

Collaborative Projects

  • Mechanistic Insights into PEPT1-Mediated Transport of a Novel Antiepileptic, NP-647

Project Supervisor: Dr. Arvind K. Bansal, Department of Pharmaceutics, NIPER, S.A.S. Nagar)

It is aimed to uncover the properties of the transport mechanism or mechanisms responsible for the uptake of NP-647 into Caco-2 cells and, in particular, to understand whether it is a substrate for the intestinal oligopeptide transporter, PEPT1. NP-647 showed a carrier-mediated, saturable transport with Michaelis-Menten parameters. The effect of pH, sodium ion (Na+), glycylsarcosine and amoxicillin (substrates of PEPT1), and Na+/K+-ATPase inhibitor on the flux rate of NP-647 was determined. Molecular docking and molecular dynamics simulation studies were carried out to investigate molecular interactions of NP-647 with transporter using homology model of human PEPT1.

  • Design, synthesis and in silico studies of novel and specific substrates for thyrotropin releasing hormone receptor-2 (TRHR-2) as anti-epileptic agents

Project Supervisor: Dr. Rahul Jain, Department of Medicinal Chemistry, NIPER, S.A.S. Nagar

The various drugs are available as thyrotropin releasing hormone (TRH) analogues as to treat epilepsy a CNS disorder. The TRHR-2 as a novel target for TRH analogues were identified and validated by researchers. The novel substrates as TRH analogues were designed and synthesized and tested for their anti-epileptic activity. We have performed in silico studies such as homology modeling of TRHR-1 and TRHR-2 to study the 3D structural features of receptor target. The molecular docking and molecular dynamics simulation studies were also performed to study the substrate-receptor binding and substrate specificity towards TRHR-2. The results were also validated using in vitro substrate binding assay.

  • Cytochrome P450 2C19 mediated metabolism of drugs: Molecular docking and MetaSite analysis

M.S. (Pharm.) thesis project from March 2009 to June 2010

Project Supervisor: Prof. Prasad V. Bharatam, Department of Pharmacoinformatics, NIPER, S.A.S. Nagar.

This work is on predicting the site of metabolism of drugs using computational tools which helps in improving DMPK profile of NCE. During the work, performance of one free and three commercial docking software were compared and consensus ranking by all four software was evaluated on more than 60 drugs on CYP2C19 isoform. Preference of drugs for isoform of cytochrome P450 2C19 will be predicted using docking.

  • The identification of optimum protocol to solve the CYP450 mediated drug metabolism profile of NCE

Worked in Industry – Academia collaborative project for one year during M. S. (Pharm.)

Project Supervisors: Prof. Prasad V. Bharatam, Department of Pharmacoinformatics, NIPER, S.A.S. Nagar. and Dr. Prashant V. Desai, Eli Lilly, Department of Drug Metabolism and Disposition, Indianapolis, United States.

This work involves the identification of optimum protocol to solve the DMPK profile of NCE. This leads to generation of huge amount of data which is to be summarized and reported. We categorize events, identify the key influencers on the success rates in different protocols and by recursive partitioning, decision trees are designed which defines optimum pathway. We have used MetaSite, data mining add-in in MS Excel, RapidMiner in addition to computational Chemistry, chemoinformatics software and C++ Programming.

Key achievements: A group member of five team members to look for overall progress and training of personnel which resulted in increased efficiency of team to successfully submit two quarterly reports even before deadline.

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Research publications

More info: http://scholar.google.co.in/citations?user=-PDYwgwAAAAJ&hl=en (Note: *: Author with equal contribution as first author.)


Sr. no. Authors Title of research article / paper(s) Name of journal (with city/ country) Month & year of publication, volume, no. & page nos. Impact Factor Type of authorship
# Ross G. Douglas, Prajwal Nandekar, Julia-Elisabeth Aktories, Hirdesh Kumar, Rebekka Weber, Mirko Singer, Simone Lepper,  Kashif S. Sadiq, Rebecca C. Wade, and, Friedrich Frischknecht Inter-subunit interactions drive divergent dynamics in mammalian and Plasmodium actin filaments PLOS Biology Under review Co-author
1 Prajwal P Nandekar*, Kailas Khomane, Vikas Chaudhary, Vijay P Rathod, Roshan M Borkar, Murali Mohan Bhandi, R Srinivas, Abhay T Sangamwar, Sankar K Guchhait, Arvind K Bansal  Identification of leads for antiproliferative activity on MDA-MB-435 human breast cancer cells through pharmacophore and CYP1A1-mediated metabolism European journal of medicinal chemistry, Elsevier Masson, France 10 June 2016, Volume 115, Pages 82–93 4.519 First author
2 Xiaofeng Yu, Prajwal Nandekar, Ghulam Mustafa, Vlad Cojocaru, Galina I. Lepesheva, Rebecca C. Wade Ligand tunnels in T. brucei and human CYP51: Insights for parasite-specific drug design Biochimica et Biophysica Acta (BBA) – General Subject, Elsevier Masson, France Jan. 2016, Volume 1860 (1), Part A, Pages 67-78 4.702  Co-author
3 Siddharth S Kesharwani, Prajwal P Nandekar*, Preeti Pragyan, Vijay Rathod, Abhay T Sangamwar Characterization of differences in substrate specificity among CYP1A1, CYP1A2 and CYP1B1: an integrated approach employing molecular docking and molecular dynamics simulations Journal of Molecular Recognition, Wiley Online Library, United Kingdom 1 Sept. 2016, Volume 29 (8), Pages 370-390 2.175  First author
4 Vishnu K Sharma, Prajwal P Nandekar*, Abhay Sangamwar, Horacio Pérez-Sánchez, Subhash Mohan Agarwal Structure guided design and binding analysis of EGFR inhibiting analogues of erlotinib and AEE788 using ensemble docking, molecular dynamics and MM-GBSA RSC Advances, Royal Society of Chemistry,  United Kingdom 05 Jul 2016, Volume 6 (70), Pages 370-390 3.108  First author
5 Chhuttan L Meena, Avinash Thakur, Prajwal P Nandekar, Shyam S Sharma, Abhay T Sangamwar, Rahul Jain Synthesis and biology of ring-modified l-Histidine containing thyrotropin-releasing hormone (TRH) analogues European journal of medicinal chemistry, Elsevier Masson, France 23 March 2016, Volume 111, Pages 72-83 4.519  Co-author
6 Roshan M Borkar, Murali Mohan Bhandi, Ajay P Dubey, V Ganga Reddy, Prashanth Komirishetty, Prajwal P Nandekar, Abhay T Sangamwar, Ahmed Kamal, Sanjay K Banerjee, R Srinivas An evaluation of the CYP2D6 and CYP3A4 inhibition potential of metoprolol metabolites and their contribution to drug–drug and drug–herb interaction by LC‐ESI/MS/MS Biomedical Chromatography, Wiley Online Library, United Kingdom 1 Oct. 2016, Volume 30 (10), Pages 1556-1572 1.613  Co-author
7 Ghulam Mustafa, Prajwal P Nandekar*, Xiaofeng Yu, Rebecca C Wade On the application of the MARTINI coarse-grained model to immersion of a protein in a phospholipid bilayer The Journal of chemical physics, American Institute of Physics, United States 28 Dec. 2015, Volume 143 (24), Pages 12B621_1 2.965  First author
8 Roshan M Borkar, Murali Mohan Bhandi, Ajay P Dubey, Prajwal P Nandekar, Abhay T Sangamwar, Sanjay K Banerjee, R Srinivas Plasma protein binding, pharmacokinetics, tissue distribution and CYP450 biotransformation studies of fidarestat by ultra high performance liquid chromatography–high resolution mass spectrometry Journal of Pharmaceutical and Biomedical Analysis, Elsevier, Netherlands 5 Jan. 2015, Volume 102, Pages 386-399 3.255  Co-author
9 Chhuttan L Meena, Shubdha Ingole, Satyendra Rajpoot, Avinash Thakur, Prajwal P Nandekar, Abhay T Sangamwar, Shyam S Sharma, Rahul Jain Discovery of a low affinity thyrotropin-releasing hormone (TRH)-like peptide that exhibits potent inhibition of scopolamine-induced memory impairment in mice RSC Advances, Royal Society of Chemistry,  United Kingdom 23 June 2015, Volume 5 (70), Pages 56872-56884 3.108  Co-author
10 Chhuttan L Meena, Avinash Thakur, Prajwal P Nandekar, Abhay T Sangamwar, Shyam S Sharma, Rahul Jain Synthesis of CNS active thyrotropin-releasing hormone (TRH)-like peptides: Biological evaluation and effect on cognitive impairment induced by cerebral ischemia in mice Bioorganic and Medicinal Chemistry, Pergamon,
Elsevier, U.S.A
1 Sept. 2015, Volume 23 (17), Pages 5641-5653 2.930  Co-author
11 Varun Kumar, Mahesh Rachamalla, Prajwal Nandekar, Gopal L Khatik, Abhay T Sangamwar, Kulbhushan Tikoo, Vipin A Nair Design and synthesis of optically pure 3-aryl-6-methyl-2-thioxotetrahydropyrimidin-4 (1 H)-ones as anti-prostate cancer agents RSC Advances, Royal Society of Chemistry,  United Kingdom 06 Aug. 2014, Volume 4 (71), Pages 37868-37877 3.108  Co-author
12 Pravin Bagul, Kailas S Khomane, Siddhakrth S Kesharwani, Preeti Pragyan, Prajwal P Nandekar*, Chhuttan Lal Meena, Arvind K Bansal, Rahul Jain, Kulbhushan Tikoo, Abhay T Sangamwar Intestinal transport of TRH analogs through PepT1: the role of in silico and in vitro modeling Journal of Molecular Recognition, Wiley Online Library, United Kingdom 1 Oct. 2014, Volume 27 (10), Pages 609-617 2.175  First author
13 Sumit Jain, Vijay Rathod, Rameshwar Prajapati, Prajwal P Nandekar, Abhay T Sangamwar Pregnane X Receptor and P-glycoprotein: a connexion for Alzheimer’s disease management Molecular Diversity, Springer International Publishing, Switzerland 1 Nov. 2014, Volume 18 (4), Pages 895-909 1.752  Co-author
14 Khaled M Tumbi, Prajwal P Nandekar, Naeem Shaikh, Siddharth S Kesharwani, Abhay T Sangamwar Molecular dynamics simulation studies for DNA sequence recognition by reactive metabolites of anticancer compounds Journal of Molecular Recognition, Wiley Online Library, United Kingdom 1 March 2014, Volume 27 (3), Pages 138-150 2.175  Co-author
15 Inderjit S Yadav, Prajwal P Nandekar, Shambhavi Shrivastava, Abhay Sangamwar, Ashok Chaudhury, Subhash Mohan Agarwal Ensemble docking and molecular dynamics identify knoevenagel curcumin derivatives with potent anti-EGFR activity Gene, Elsevier, Netherlands 10 April 2014, Volume 540 (1), Pages 82-90 2.415  Co-author
16 Pradipbhai D Kalariya, B Raju, Roshan M Borkar, Deepak Namdev, S Gananadhamu, Prajwal P Nandekar, Abhay T Sangamwar, R Srinivas Characterization of forced degradation products of ketorolac tromethamine using LC/ESI/Q/TOF/MS/MS and in silico toxicity prediction Journal of Mass Spectrometry, Wiley Online Library, United Kingdom 1 May 2014, Volume 49 (5), Pages 380-391 2.422  Co-author
17 Preeti Pragyan, Siddharth S Kesharwani, Prajwal P Nandekar*, Vijay Rathod, Abhay T Sangamwar Predicting drug metabolism by CYP1A1, CYP1A2, and CYP1B1: insights from MetaSite, molecular docking and quantum chemical calculations Molecular Diversity, Springer International Publishing, Switzerland 1 Nov. 2014, Volume 18 (4), Pages 865-878 1.752  First author
18 Siddharth S Kesharwani, Prajwal P Nandekar*, Preeti Pragyan, Abhay T Sangamwar Comparative proteomics among cytochrome P450 family 1 for differential substrate specificity Protein journal, Springer U.S.A. 1 Dec 2014, Volume 33 (6), Pages 536-548 1.139  First author
19 Prajwal P Nandekar*, Khaled M Tumbi, Nitu Bansal, Vijay P Rathod, Leena B Labhsetwar, Neelagiri Soumya, Sushma Singh, Abhay T Sangamwar Chem-bioinformatics and in vitro approaches for candidate optimization: a case study of NSC745689 as a promising antitumor agent Medicinal Chemistry Research, Springer U.S.A. 4 Dec. 2013, Volume 22 (8), Pages 3728-3742 1.277 First author
20 Vijay Rathod, Sumit Jain, Prajwal Nandekar, Abhay T Sangamwar Human pregnane X receptor: a novel target for anticancer drug development Drug Discovery Today, Elsevier Masson, France 31 Jan. 2013, Volume 19 (1), Pages 63-70 6.369  Co-author
21 Sameer R Modi, Ajay KR Dantuluri, Vibha Puri, Yogesh B Pawar, Prajwal Nandekar, Abhay T Sangamwar, Sathyanarayana R Perumalla, Changquan Calvin Sun, Arvind K Bansal Impact of crystal habit on biopharmaceutical performance of celecoxib Crystal Growth and Design, American Chemical Society, U.S.A. 30 May 2013, Volume 13 (7), Pages 2824-2832 4.055  Co-author
22 Prajwal P Nandekar*, Abhay T Sangamwar Cytochrome P450 1A1-mediated anticancer drug discovery: in silico findings Expert opinion on Drug Discovery, Taylor & Francis, United Kingdom 1 Sept. 2012, Volume 7 (9), Pages 771-789 3.876  First author
23 Kailas S Khomane, Prajwal P Nandekar, Banrida Wahlang, Pravin Bagul, Naeem Shaikh, Yogesh B Pawar, Chhuttan Lal Meena, Abhay T Sangamwar, Rahul Jain, K Tikoo, Arvind K Bansal Mechanistic insights into PEPT1-mediated transport of a novel antiepileptic, NP-647 Molecular Pharmaceutics, American Chemical Society, U.S.A. 26 July 2012, Volume 9 (9), Pages 2458-2468 4.440  Co-author
24 Santosh S Chobe, Bhaskar S Dawane, Khaled M Tumbi, Prajwal P Nandekar, Abhay T Sangamwar An ecofriendly synthesis and DNA binding interaction study of some pyrazolo [1, 5-a] pyrimidines derivatives Bioorganic & Medicinal Chemistry Letters, Pergamon,
Elsevier, U.S.A
15 Dec. 2012, Volume 22 (24), Pages 7566-7572 2.454  Co-author

Book Chapter

Sr. no. Title Author’s name Publisher Year of publication
1. Dynathor: Dynamics of the Complex of Cytochrome P450 and Cytochrome P450 Reductase in a Phospholipid Bilayer X Yu, DB Kokh, P Nandekar, G Mustafa, S Richter, RC Wade Springer International Publishing Switzerland 2015

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Conferences/ Workshops/ presentations


Sl. No. Talk/ Poster Title/Subject of paper presented Subject of Conference / Seminar / Symposium / Workshop Organizing Institution/ and Name of City/ Country Duration From __ to__
1 Talk Dynathor: Dynamics of the Complex of Cytochrome P450 and Cytochrome P450 Reductase in a Phospholipid Bilayer 18th Results and Review Workshop of the HLRS High Performance Computing Center Stuttgart, Allmandring 30, 70569 Stuttgart, Germany 2 days 5-6 Oct. 2015
2 Talk Simulation of Human Drug-metabolizing Cytochrome P450s – Membrane, Substrate and Product Interactions Indo-US Conference on Molecular Modeling and Informatics in Drug Design (M2ID2) National Institute of Pharmaceutical Education and research (NIPER) SAS Nagar, Punjab, India 4 days 3-6 Nov. 2014
3 Talk Pharmacophore based in silico virtual screening: An effective strategy for CYP1A1 mediated anticancer drug discovery 5th International Symposium on Drug Metabolism and Pharmacokinetics-2013 Symposium (DMPK-2013) NIPER, S.A.S. Nagar, India 4 days 7-10 March 2013
4 Talk NSC745689, a new pyrimidobenzothiazole shows promising antitumor properties and an in silico insights for candidate optimization 4th International Symposium on Drug Metabolism and Pharmacokinetics-2012 Symposium (DMPK-2012) NIPER, S.A.S. Nagar, India 3 days 16-19 Feb. 2012
5 Poster Understanding the Differences in Rabbit and Plasmodium Actin Filament Structure Using Molecular Dynamics Simulations eCheminfo Euro 2017 Department of Pharmaceutical Sciences, Via L. Mangiagalli, 25 / 20133 Milano, Italy 5 days 17-21 July 2017
6 Poster Dynamics of the Complex of Cytochrome P450 and Cytochrome P450 Reductase in a Phospholipid Bilayer Hünfeld 2017 Workshop on Computer Simulation and Theory of Macromolecules Max Planck Institute for Biophysical Chemistry, Gottingen, Germany 2 days 24-25, March 2017
7 Poster Dynamics of the Complex of Cytochrome P450 and Cytochrome P450 Reductase in a Phospholipid Bilayer Drug Innovation in Academia 2016 Helmholtz Drug Research. – at DKFZ, Heidelberg, Germany 2 days  8-9th Dec. 2016
8 Poster Identification of New Anticancer Compounds Through Computer-Aided Drug Designing Approaches IT For Life Science @ Bayer Bayer AG, Leverkusen, Germany. 2 days 12-13 May 2015
9 Poster Simulation of human drug-metabolizing cytochrome P450s – membrane, substrate, and product interactions 20th International Symposium on Microsomes and Drug Oxidations (MDO) Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany 5 days 18th – 22nd May 2014
10 Poster Molecular dynamics simulation to study the importance of loop flexibility in CYP1A1 3rd Indo-German Conference on Modelling Chemical And Biological (Re)activity NIPER & IISER Mohali, India. 4 days 26th February – 1st March, 2013
11 Poster Homology Modeling and molecular dynamics simulation to study the importance of loop flexibility in CYP1A1 ECCB’12 – The European Conference on Computational Biology at Congress Center Basel, Switzerland Swiss Institute of Bioinformatics, Basel, Switzerland 4 days 9-12. September 2012
12 Poster Homology modeling and molecular dynamics simulation to study the importance of loop flexibility in CYP1A1 4th International Symposium on Drug Metabolism and Pharmacokinetics (DMPK) symposium 2012 National Institute of Pharmaceutical Education and research (NIPER) SAS Nagar, Punjab, India 3 days 16-19 Feb. 2012
13 Poster Homology modeling and docking studies on cytochrome P450 2C19: Prediction of site of metabolism on drugs Current Trends in Drug Discovery Research (CTDDR-2010) CDRI, Lucknow, India 5 days 17–21st February 2010
14 Poster Metabolism studies of cytochrome P450 2C19 substrates using computational approaches: Use of homology modeling, molecular docking and MetaSite 2nd International Symposium on Drug Metabolism and Pharmacokinetics (DMPK): Applications toward Drug Discovery and Development National Institute of Pharmaceutical Education and research (NIPER) SAS Nagar, Punjab, India 2 days 27-28 Feb 2010

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Courses and Practices undertaken


Major courses

  • Ph. D credit courses: Structural bioinformatics and macromolecular Crystallography, Strategies in Lead Optimization, Biotransformation and Stereoselective Biocatalysis of Pharmaceutically important Compounds, Advanced Course in Intellectual Property Rights and technology Management, Regulatory Toxicology and Drug Safety Evaluation, Advanced Topics in Drug Action and Drug Design.

  • M.S.(Pharm.): Pharmacoinformatics- the Tool and Methodology, Bioinformatics, Molecular biology, Genomics, Proteomics and Systems Biology, , Informatics and Information Technology, Drug Design, Structure and Function of Biomolecules, Basis of Drug Action, Dosage Form Design Parameters, Drug Metabolism, Toxicity and Metabolic Disorders, Pharmacological Screening and Assays, IPRs, Pharmacy Practices, and Clinical Pharmacy.

  • B. Pharmacy : Pharmacology, Biochemistry, Medicinal Chemistry, Mathematics and Statistics, Organic Chemistry, Microbiology and Biotechnology, Pharmaceutical Analysis, Pharmaceutics, Pharmacognosy, Natural Products, Inorganic and Physical Chemistry, Anatomy and Physiology, Physical Pharmacy, Clinical Pharmacy.

Practicals performed

  • Pharmaceutics: Dosage form preparation, Dosage form evaluation parameter determination, Instrument handling, Instrument designing, etc.
  • Pharmaceutical Analysis: Assay of pharmaceutical ingredients, using UV, IR, Fluorimetry, Flame photometry, pH meter, Polarimeter, etc.
  • Medicinal chemistry: Synthesis of drugs, Evaluation of drug, etc
  • Pharmacognosy: Microscopic studies of different sections of part of medicinal plants, etc.
  • Microbiology: Culture development, culture preservation, staining methods, identification of cultures, etc.
  • Pharmacology: Animal handling, Studies of CRC for different drugs on isolated parts of frog and rat, etc.
  • Biochemistry: Various blood tests such as TLC, DLC, RBC count, Hemoglobin count, urine test, etc.
  • Biophysics: Studies of biological physics on isolated parts of animals, etc.

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Extra curricular


  • Worked in organizing committee of “Drug Metabolism and Pharmacokinetics, Symposium (DMPK)” at NIPER, S. A. S. Nagar, Feb, 2010, 2011, 2012, 2013.

  • General course on IPR from WIPO, Geneva, through distance learning program, 2009.

  • Object oriented C++ programming from NIIT center, Mohali.

  • Attended Five days seminars on IPR, Patent design, Patent filing and content specification, Trademark applications at National Institute of Intellectual property Management, Nagpur on dated 15-19 Dec. 2008.

  • Industrial Training: Unijules Life Science, Nagpur, Maharashatra, Duration: 1 month during 3rd year of bachelor degree.

  • Worked as treasurer and cultural secretary in college annual gathering in Dec. 2007.

  • Participated in various sports events (Cricket, Vollyball, Chess)