Protein dynamics and activation/deactivation mechanism: Use molecular dynamics (MD) simulations with advance sampling techniques and protein network analysis to gain detailed insight into the conformational dynamics associated with ligand recognition and activation/deactivation mechanism in proteins. Research will also focus on identifying the local motif(s) that play central role in switching the activation – deactivation dynamics, with an aim of rational drug designing.
Allostery and structure-based drug discovery: Understanding the protein flexibility is central to the structure-based drug discovery. Our research uses co- solvent MD simulations to incorporate dynamic nature of proteins into the drug discovery pipeline to identify allosteric/cryptic sites, that are potentially druggable.
Green chemistry and enzyme catalysis
Contributions to Teaching:
At Department of Biotechnology, Kannur University (from November 2020 to present):
MSMBY01E01: Fundamentals of Biostatistics (M Sc course)
Research Projects undertaken
Developing applications of cosolvent simulations for mapping druggable hotspots on protein surfaces and pharmacophore modelling (University of Michigan, USA)
In silico investigation of ligand recognition and ion permeation properties of IP 3 receptors (University of Cambridge, UK)
Exploring allosteric druggable pockets in nuclear receptors for rational drug designing (Indian Institute of Science, India)
12-10-2020 – Present: Assistant Professor, Department of Biotechnology and Microbiology, Kannur University, Kerala, India
Feb 2019 – Jan 2020: Postdoctoral Fellow, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA
Mar 2017 – Dec 2018: Postdoctoral Fellow, Molecular Biophysics Unit, Indian Institute of Science, India
Jan 2018 – Feb 2018: Visiting Researcher (Newton alumnus support grant), Department of Pharmacology, University of Cambridge, UK
Feb 2015 – Feb 2017: Royal Society Newton International Postdoctoral Fellow, Department of Pharmacology, University of Cambridge, Cambridge, UK
Aug 2012 - Jan 2015: Dr. D. S. Kothari Postdoctoral Fellow, Molecular Biophysics Unit, Indian Institute of Science, India
J. C. Greenhalgh, A. Chandran, G. Ladds, M. T. Harper, T. Rahman. Proposed model of the Dictyostelium cAMP receptors bound to cAMP. J Mol Graph Model 100, 107662, 2020
B. Vyhlidalova, K. Krasulova, P. Pecinkova, K. Poulikova, R. Vrzal, Q. Yang, A. P. Li, Z. Andrysik, A. Chandran, S. Mani, Z. Dvorak. Antimigraine drug avitriptan is a ligand and agonist of human aryl hydrocarbon receptor that induces cyp1a1 in hepatic and intestinal cells. Int J Mol Sci 21, 2799, 2020.
Z. Dvořák, F. Kopp, C. M. Costello, J. S. Kemp., H. Li, A. Vrzalová, M. Štěpánková, I. Bartoňková, E. Jiskrová, K. Poulíková, B. Vyhlídalová, C. Karunaratne, K. Abbott, C. Chaudhury, A. De, S. R. Pondugula, H. Ranhotra, K. S. Mun, N. Anjaparavanda, I. Murray, G. H. Perdew, J. Brtko, L. Toporova, A. Schon, E. Nieves, K. Sun, A. Beck, S. Kortagere, P. Mallick, R. Ghosh, V. Dou, A. Yang, V. DesMarais, M. C. Neary, Q. Liu, A. Akki, J. M. Albanese, Y. Qiu, I. J. Kurland, D. J. Lukin, T. Ullmann, O. C. Aroniadis, B. A. Coffin, M. Longo, Z. W. Mei, J. Hart, A. Chandran, S. Vishveshwara, M. M. Cavalluzzi, G. Lentini, J. Y. Cui, H. Gu , J. C. March, A. P. Li, S. Mani. Targeting the pregnane X receptor using microbial metabolite mimicry. EMBO Mol Med 12, e11621, 2020.
K. L. Abbott, C. S. Chaudhury, A. Chandran, S. Vishveshwara, Z. Dvorak, E. Jiskrova, K. Poulikova, B. Vyhlidalova, S. Mani, S. R. Pondugula. Belinostat, at its clinically relevant concentrations, inhibits rifampicin induced CYP3A4 and MDR1 gene expression. Mol Pharmacol 95,324-334, 2019.
A. Chandran*, X. Chee, D. L. Prole, T. Rahman. Exploration of inositol 1,4,5- trisphosphate (IP 3 ) regulated dynamics of N-terminal domain of IP 3 receptor reveals early phase molecular events during receptor activation. Sci Rep 9,2454, 2019.
A. Chandran, S. Vishveshwara. Exploration of the conformational landscape in pregnane X receptor reveals a new binding pocket. Protein Sci 25, 1989-2005, 2016.
A. Chandran, D.Ghoshdastidar, S. Senapati. Groove binding mechanism of ionic liquids: A key factor in long-term stability of DNA in hydrated ionic liquids? J. Am. Chem. Soc. 134, 20330−20339, 2012.
A. Chandran, K. Prakash, S. Senapati. Self-assembled inverted micelles stabilize ionic liquid domains in supercritical CO 2 . J. Am. Chem. Soc. 132, 12511-12516, 2010.
A. Chandran, K. Prakash, S. Senapati. Structure and dynamics of acetate anion based ionic liquids from molecular dynamics study. Chem. Phys. 374, 46-54, 2010.
S.N. Gummadi, S. Kumar, Aneesh CNA. Effect of salts on growth and pectinases production by halotolerant yeast, Debaryomyces nepalensis NCYC 3413. CurrenT Microbiol. 54, 472-476, 2007.