Prajwal Nandekar, Ph.D.
Pharmaceutical Sciences (Pharmacoinformatics)
Currently working as Manager - Bioinformatics (Drug Discovery) with Elanco IAC.
4 years worked as Senior Scientist II (Application Science) with Schrödinger Inc.
4 years of postdoctoral research experience in computational biophysics and computer‑aided drug design at Heidelberg University, Germany with Prof. Dr. Rebecca Wade.
Ph.D. in Pharmaceutical Sciences from National Institute of Pharmaceutical Education and Research (NIPER), India.
DAAD fellow for sandwich Ph.D. program.
Experienced in project management and mentoring students.
33 research publications in peer-reviewed international journals with an h-index of 19, 801 citations and a total impact factor of 109. Google Scholar
Research focus
My research focuses on computer-aided drug design, virtual screening, and multi‑scale molecular dynamics (MD) simulations to understand the structure-function relationships of proteins at the atomic‑level and to use these insights for drug design. The fundamental questions I am trying to answer are: What are the sequence and structural determinants of stability of protein assemblies and their functional dynamics? What are the fundamentals of ligand binding and protein-protein interactions? How can we translate this knowledge into the design of new and better drug candidates?
I develop and apply approaches to model and simulate large biomolecular complexes involved in important cellular processes namely cell motility (actin filaments), xenobiotic metabolism (cytochrome P450 and redox proteins) and inter-protein electron transfer processes using multi-scale molecular dynamics (MD) simulation methodologies, - at the heart of which is the aim of reaching a sufficiently long time scale while maintaining a realistic description. Therefore, based on expertise I gained so far, I have been successfully using a multi-scale MD simulations approach in which I combine efficient sampling techniques at a Martini coarse-grained level, 4 atoms to 1 bead coarse-grain force field for biomolecules (http://cgmartini.nl/), with more expensive but more detailed atomistic models in high‑performance computational tools such as Gromacs, Amber, NAMD MD simulation packages.
During my Ph.D. and postdoctoral tenure, I have brought several major and auxiliary projects to successful completion. Several of these studies have been published in peer-reviewed international journals and a few manuscripts are under review/preparation. Collectively, I have 26 research publications with an author’s h-index of 9 and 246 citations (https://scholar.google.com).
Research Interests
Molecular modeling and MD simulations of biomolecular complexes to understand their structure-function relationships.
Molecular dynamics simulations: Martini coarse-grain, all-atom, Random Acceleration Molecular Dynamics (RAMD) simulations
Protein-protein and protein-membrane interaction studies For example,
Cytochrome P450s (CYP450) in a membrane,
Cytochrome P450 reductase (CPR) in a membrane,
CYP450-CPR protein-protein complex in a membrane to study drug metabolism mechanism and inter-protein electron transfer processes.
Actin protein filament modeling and simulations to study cell motility.
Molecular modeling and computer-aided drug design, structure-based and ligand-based drug design
In silico drug Metabolism prediction studies
Software development
Quantum chemistry
In vitro assays
Contact Information:
Office:
Dr. Prajwal P. Nandekar
Manager - Bioinformatics (Drug Discovery)
Elanco IAC, Bengaluru, India