CV Venkata Krishnan Ramaswamy

OBJECTIVE

To be actively involved in challenging projects in drug discovery research and carve a niche for myself to evolve as a competitive research scientist in the field of Computer Aided Drug Design.

AREAS OF INTERESTS

Computer aided drug design, Molecular modeling, Chemoinformatics and Bioinformatics

RESEARCH EXPERIENCE

Senior Research Fellowin Dr. Prasad V. Bharatam`s Research Group, Department of Medicinal Chemistry, NIPER, S.A.S. Nagar, India

This CSIR-OSDD project of mine involves working in close collaboration with informaticians, wet lab scientists, contract research organizations, and a few others of the OSDD team to develop an open source scientific workflow platform to aid drug discovery science in India and other developing and economically challenged nations. The main objective of my work here includes development of cheminformatics software tools for drug discovery and development that can be used either as a stand-alone program or can be incorporated in the Galaxy workflow. This is aimed at solving the complex problems associated with discovering novel therapies for neglected tropical diseases like Malaria, Tuberculosis, Leshmaniasis, etc.

Other responsibilities include teaching software programming (C++) for M.S. (Pharm.) Pharmacoinformatics students and train them in software tools development that can be used in-house for enhancing the process of drug discovery and development.

RESEARCH PROJECTS

An Insight into the Effect of pH and Temperature on the Structural Stability of CD47 using Molecular Dynamics Approach [M.S. (Pharm.)Thesis Work]

This study is aimed at understanding the stability of CD47 under varying conditions of pH and temperature by examining its atomic level conformational changes especially at its interacting region with SIRPα using molecular dynamics simulations. This study would be beneficial as anti-CD47 antibody treatment and CD47-marked nanoparticles are beginning to gain attention in anti-cancer therapies.

Structural basis of conformational variance inphosphorylated and non-phosphorylated states of PKCβII

PKCβII activation is achieved by primary phosphorylation at three phosphorylation sites, followed by addition of secondary messengers for full activation. Phosphorylation is essential for enzyme maturation, and the associated conformational changes are known to modulate the enzyme activation. In this study, a comprehensive analysis of conformational changes of PKCβII in both phosphorylated and non-phosphorylated states complexed with ATP and ruboxistaurin was done to probe into the structural basis of the observed changes that can be exploited in the design and development of novel and potent PKCβII inhibitors.

In SilicoDesigning of Novel and Potent PknB Inhibitors as Anti-tubercular Agents

The already reported PknB inhibitors were found to be less potent against whole cells due to the cell wall permeability factor in these cells. By structure baseddenovodesignapproach, we designed novel and potent PknB inhibitors with improved permeability. The designed compounds were analyzed by molecular docking, ADMET, quantitative estimation of drug likeness, synthetic accessibility, and binding-free energy calculations using MM-GBSA method to finally arrive at two molecules that can be prospective potential PknB inhibitors.

Structure Based De NovoDesign of IspDInhibitors as Anti-Tubercular Agents

The absence of2-C-methyl-D-erythritol-4-phosphate cytidyltransferase (IspD) in mammals and its essentiality in bacteria makes it an attractive target for the discovery of novel antibiotics. In the study, we designed novel and potent inhibitors for IspD receptor by employing structure based drug design approach. Molecular docking studies, ADMET, and synthetic accessibility filters were used to screen the designed molecules. Finally, ten compounds were selected and subsequently submitted for the synthesis and in vitro studies as IspD inhibitors.

Formulation and Evaluation of Sintered Matrix Tablets of Diltiazem Hydrochloride[B.Pharm.]

Diltiazemhydrochloride,awatersolubledrug,hasashorthalf-lifeof3to4.5hoursandalimitedwindowof absorption. To extend the release of this drug, we formulated controlled release tablets using polymers HPMC K4M and HPMC K15Mcoupled with sintering technique. The formulated tablets were also subjected to various quality control tests to characterize them.

SOFTWARE TOOLS DEVELOPED

CPMD IFGen server (SOFTWARE TOOLS)

An input file (*.inp) for CPMD (Car-ParrinelloMolecular Dynamics) calculations lists the coordinates of every element in the input molecule collectively as a group apart from the other simulation related specifications. This has to be manually prepared by the user. We developed a PHP based web application to semi-automate the input file preparation. This server can be accessed at http://www.databases.niper.ac.in/IFGen/.

C++ library in Predictor P450 software

I was the core programmer in the development team of a C++ library that generates Atom type SMARTS Fragment Molecular Descriptor from *.mol and *.mol2 files. This library is currently used in Predictor P450 software (in-house software to predict the site of metabolism).

EDUCATIONAL QUALIFICATIONS

M.S. (Pharm.), NIPER, S.A.S. Nagar, 2011-2013, 9.20/10 (Percentage/CGPA)

B.Pharm., The Tamil Nadu Dr.M.G.R. Medical University, 2006-2010, 76.19% (Percentage/CGPA)

HSC, Board of Intermediate Education, Andhra Pradesh, 2004-2006, 93.10% (Percentage/CGPA)

SSC, State Board of Andhra Pradesh, 2003-2004, 90.66% (Percentage/CGPA)

CERTIFICATIONS

Basic Java of C-DAC, GIST PACE programme
Professional Diploma in Intellectual Property Rights (PDIPR)from Satrishi Institute of Clinical Research, Noida, India
General Course on Intellectual Propertyfrom World Intellectual Property Organization (WIPO), Geneva
Professional Diploma in Drug Regulatory Affairs (PDDRA)from Satrishi Institute of Clinical Research, Noida, India
Completed 2 levels of French course from Alliance Française with 96% in DELF A1

TECHNICALSKILLS

Bio/Cheminformatics- Molecular dynamics(AMBER, GROMACS), Molecular Docking(Maestro, Discovery Studio, AutoDock), Homology Modeling(Modeller, Prime), LigBuilder, VMD, PyMOL

ADME/T- GastroPlus, TOPKAT, DEREK, MetaSite

Programming/Scripting Languages- C/C++, Java, Bash Shell scripting, Python, PHP, Perl

Statistical Computing- R language

Operating Systems- Linux and Windows

Writing Skills- Scientific writing

Miscellaneous Software- MS Office, Endnote X, WYSIWYG WebBuilder

Scientific Workflow Systems- Galaxy

PUBLICATIONS

Varikoti, R. A., Gangwal, R. P., Dhoke, G. V., Ramaswamy, V. K., & Sangamwar, A. T., “Structure Based De NovoDesign of IspD Inhibitors As Anti-Tubercular Agents”.Nature Precedings, 1-9,doi:10.1038/npre.2012.7088.1, 2012.
Panicker, P. S., Krishnan, R. V., & Repaka, S., “Formulation and Evaluation of Sintered Matrix Tablets of Diltiazem Hydrochloride”.Research J. Pharm. and Tech. 4(6), 907-912, 2011.
Sobhia,M. E.,Krishnan, R. V., Thapaswini,P., Ankit Geete, & Khaled M. Tumbi, “A Comprehensive Review on Antibody Targeted Therapy: Application Towards Cancer and Viral Diseases”.CRIPS, 13(3), 2012.
Grewal, B. K., R.VenkataKrishnan, & Sobhia, M. E. “Structural basis of conformational variance in phosphorylated and non-phosphorylated states of PKCβII”. Proteins: Structure, Function, and Bioinformatics, doi:10.1002/prot.24500, 2013
Krishnan, R. V.,& Sobhia, M. E., “Effect of Extra-Cellular pH and Temperature on Structural Conformation of CD47: A Molecular Dynamics Study”. [Under Preparation]

POSTER PRESENTATIONS

R.Venkata Krishnan, Rahul P. Gangwal, Gaurao V. Dhoke, Abhay T. Sangamwar, “Computer Aided Drug Design (CADD) Approach to Design Novel and Potent PknB Inhibitors as Anti-Tubercular Agents”, Open Source for Computer Aided Translational Medicine (OSCAT),CSIR-IMTECH,Chandigarh, India, 2012
R.Venkata Krishnan, V.Balu, P.S.S.Ram Kumar, “Regulatory Aspects of Herbal Products”, Advances and Regulatory Aspects for Pharmaceutical and Herbal Products, ChitkaraCollege of Pharmacy, Punjab, India, 2009
R. Srikanth, R. Venkata Krishnan, R.Uma Maheswari,“Role of Biowaiver in Regulatory Affairs”,Advances and Regulatory Aspects for Pharmaceutical and Herbal Products,Chitkara College of Pharmacy, Punjab, India, 2009

IN-HOUSE SEMINARS

SILCS: Site Identification by Ligand Competitive Saturation
Folding@Home: Distributed Computing
In Silico Prediction of Metabolism: A Perspective on MetaSite

CONFERENCES/WORKSHOP/INDUSTRIAL TRAINING

5thInternational Symposium on Drug Metabolism and Pharmacokinetics (DMPK),NIPER, S.A.S. Nagar (Punjab), India, 2013
3rdIndo-German conference on Modeling Chemical and Biological Reactivity(MCBR-3), NIPER &IISER, Mohali (Punjab), India,2013
National conference on New Trends in Bioinformatics, Indian Institute of Technology, New Delhi, India, 2012
4thInternational Symposium on Drug Metabolism and Pharmacokinetics (DMPK), NIPER, S.A.S. Nagar (Punjab), India,2012
Seminar on Modeling and Simulation using GastroPlusTM, NIPER, S.A.S. Nagar (Punjab), India, 2012
International conference Phytocongress-2010,SASTRAUniversity, Thanjavur (Tamil Nadu),India, 2010
National seminar Herbal Focus-2009,SrimadAndavanArts & ScienceCollege, Tiruchirapalli (Tamil Nadu), India, 2009
48thNational Pharmacy Week Celebrations, Ultra College of Pharmacy, Madurai(Tamil Nadu), India, 2009
60thIndian Pharmaceutical Congress (IPC), New Delhi, India, 2008
Industrial training for 10 days in Analysis of Raw Materials and Finished Products through chemical and instrumental methods at ATOZ Pharmaceuticals Pvt. Ltd., Chennai (Tamil Nadu), India, 2010
Industrial training for 1 week in Production and Quality Control of Pharmaceutical Productsat Pharmafabrikon, Madurai(Tamil Nadu),India, 2008

DISTINCTIVE HIGHLIGHTS

Stood college first in B.Pharm. University Examinations
Secured state first in SSCEnglish Examination
Scored 96 inTOEFL iBT and 7.5 in IELTS (Academic)in 2013
Securedan All India Rank of 454 inNIPER-JEE,2011
Secured an All India Rank of 2597 among 40048 applicants in Graduate Pharmacy Aptitude Test (GPAT), 2011
Scored a total of 1160 inGRE-General, 2010

COMMUNITY SERVICES

Volunteer of HelpAge India in creating awareness and raising funds to help the elderly people live a healthy and dignified life
Participated in Blood Donation programs conducted by the Tamil Nadu AIDS control organization

PERSONAL INFORMATION

Date of Birth:30 December 1988

Nationality: Indian

Languages known: English, French, Hindi, Tamiland Telugu