Bio-sketch

Dr. Sonika Bhatnagar completed her Ph.D. and Post-Doctoral work in Department of Biophysics, AIIMS. She has been involved with the BSE Department since its inception. She has worked towards developing the curricula, laboratories and other infrastructure in the Department.

She carried out an international consultancy assignment and was awarded the Innocentive solver award for shortlisting of five top therapeutic targets for obesity in 2003. Her work lies in the area of systems biology and structural study of protein -protein interactions as novel drug targets using machine learning, and genomics & proteomics for infectious and cardiovascular diseases. 

Administrative positions

• Dean, faculty of Science since October 2024 
• Chief Proctor, NSUT since 2023
• HOD, Department of BSE, NSUT from Sept. 2018-2024
• HOD, Department of BSE, NSIT since Sept. 2017-18

Areas of Interest

• Infectious disease
• Cardiovascular Disease 
• Molecular mechanisms of disease
• Drug target selection
• Drug design and Repurposing
• Pharmacogenomics
• Viral evolution
• Host-pathogen interactions 

Thesis supervision

• Akanksha Gupta, Structural Bioinformatics Studies on Proteins Involved in Pathogenesis of Cardiovascular Disease under D.U. Completed   2018.
• Shikha Joon, Identification and characterization of a novel GTP-sensing protein CodY in Bacillus anthracis under D.U.  Completed   2018.
• Pallavi Mohanty, Structure, Dynamics and Interactions of Focal Adhesion Kinase in Cardiac Hypertrophy under  D.U.  Completed 2019.
• Sneha Rai, Systems and Structural Study of Lipid-Protein Interactions in Hyperlipidemia Induced Diseases under D.U.  Completed 2020.
• Nirupma  Singh, Network Biology and Machine learning for Mining of Drug Targets in Microbial CVDs for Structure Based Drug Design, under D.U.  Completed 2023.

Financial support received 

• PI from NSUT: National Network Project on Bioinformatics Funded by DBT for Rs. 60.0 Lakhs (2024-29) 
• PI: ICMR funded project: Implementation of Machine learning for improvement of patient care in Covid-19 for Rs. 29.36 Lakhs (2022-25) 
•  PI: ICMR funded project: System level Host pathogen interaction studies in COVID- 19 for therapeutics and pharmacovigilance. Rs. 36.82 Lakhs (2022-25). 
•  Project mentor: CSIR funded JRF “Development of novel inhibitors for atherosclerosis” 2017-2022  
•  PI: Sonika Bhatnagar and Co-PI: Rakesh Bhatnagar.   Collaborative project between NSIT and JNU entitled “Development of novel antibiotics of control of infectious diseases in pathogenic bacteria through induction of programmed cell death”. 2012-15. 
• Project mentor: ICMR funded SRF, Ms. Pallavi Mohanty working in a project entitled Modeling of Protein-Protein Interactions in Cardiovascular Disease for Mining of Novel Drug Targets under Dr. Sonika Bhatnagar from 2013-2016.  
• PI, DST young scientist project – Structure-based design of peptide inhibitors of mammalian 15-lipoxygenase, a target in atherogenesis. 2002- 2005. 
• CSIR research project – Design of specific antagonists for the human endothelin A receptor. 2000-2002.

Awards received 

•  Commendable Research Award from NSUT on 2nd March 2022. 
•  Dr. Sarvepalli Radhakrishnan distinguished Professor of Biotechnology Award from IMRF in 2021 
•  Kalpana Chawla Memorial Excellence Award for Woman achiever in Higher Education at Guru Kashi University, Bathinda, India on 1st February, 2020. 
•  Awardee, Identification of the top 5 biological targets for the discovery and development of pharmaceuticals to treat Obesity for Innocentive Inc., an e business venture of Eli Lilly, 25th September, 2003.
   

Publications in International Journals

• Kulshreshtha A, Bhatnagar S. Structural effect of the H992D/H418D mutation of angiotensin-converting enzyme in the Indian population: implications for health and disease. J Biomol Struct Dyn. 2024 
• Singh V, Kumar Y, Bhatnagar S. Robustaflavone as a novel scaffold for inhibitors of native and auto-proteolysed human neutrophil elastase. SAR QSAR Environ Res. 2024 ;35(8):729-756.

• Tayal S, Bhatnagar S. Role of molecular mimicry in the SARS-CoV-2-human interactome for pathogenesis of cardiovascular diseases: An update to ImitateDB. Comput Biol Chem. 2023 ;106:107919.

• Gupta S, Gupta D, Bhatnagar S. Analysis of SARS-CoV-2 genome evolutionary patterns. Microbiol Spectr. 2024 ;12(2):e0265423.

•  Tayal S, Singh V, Bhatnagar S. 3D-QSAR and ADMET studies of morpholino-pyrimidine inhibitors of DprE1 from Mycobacterium tuberculosis. J Biomol Struct Dyn. 2023 Dec 19:1-20.

•  Singh V, Singh N, Pradhan A, Kumar Y, Bhatnagar S. Structure-activity relationships of dihydropyrimidone inhibitors against native and auto-processed human neutrophil elastase. Comput Biol Med. 2023 Jul;161:107004.

• Tayal S, Bhatia V, Mehrotra T, Bhatnagar S. ImitateDB: A database for domain and motif mimicry incorporating host and pathogen protein interactions. Amino Acids. 2022;54(6):923-934.

• Singh N, Rai S, Bhatnagar R, Bhatnagar S. Network analysis of host-pathogen protein interactions in microbe induced cardiovascular diseases. In Silico Biol. 2021;14(3-4):115-133.

• Singh, N. and Bhatnagar, S. Machine Learning for Prediction of Drug Targets in Microbe Associated Cardiovascular Diseases by Incorporating Host-pathogen Interaction Network Parameters. Mol. Inf. 2021;2100115. 
• Rai, S, Bhatia, V and Bhatnagar, S. Drug Repurposing for Hyperlipidemia Associated Disorders: An Integrative Network Biology and Machine Learning Approach. Computational Biology and Chemistry 2021

• Singh N, Bhatia V, Singh S, Bhatnagar S. MorCVD: A Unified Database for Host- Pathogen Protein-Protein Interactions of Cardiovascular Diseases Related to Microbes. Sci Rep. 2019 Mar 11;9(1):4039. doi: 10.1038/s41598-019-40704-5.

• 11.  Kandari D, Gopalani M, Gupta M, Joshi H, Bhatnagar S, Bhatnagar R. Identification, Functional Characterization, and Regulon Prediction of the Zinc Uptake Regulator (zur) of Bacillus anthracis - An Insight Into the Zinc Homeostasis of the Pathogen. Front Microbiol. 2019 Jan 11;9:3314.

• Rai S, Mohanty P, Bhatnagar S. Modeling, dynamics and phosphoinositide binding of the pleckstrin homology domain of two novel PLCs: η1 and η2. J Mol Graph Model. 2018 Oct; 85:130-144.

• Mohanty P, Bhatnagar S. Structure of focal adhesion kinase in healthy heart versus pathological cardiac hypertrophy: A modeling and simulation study. J Mol Graph Model. 2018 Mar; 80:15-24.

• Joon S, Gopalani M, Rahi A, Kulshreshtha P, Gogoi H, Bhatnagar S, et al. Biochemical characterization of the GTP-sensing protein, CodY of Bacillus anthracis. Pathog Dis. 2017 Jun 01;75(4).

• Rai S, Bhatnagar S. Novel Lipidomic Biomarkers in Hyperlipidemia and Cardiovascular Diseases: An Integrative Biology Analysis. OMICS. 2017 Mar;21(3):132-42.

• Dhiman A, Rahi A, Gopalani M, Bajpai S, Bhatnagar S, Bhatnagar R. Role of the recognition helix of response regulator WalR from Bacillus anthracis in DNA binding and specificity. Int J Biol Macromol. 2017 Mar;96:257-264.
• Mohanty P, Bhatnagar S. Structural basis of focal adhesion targeting domain- mediated signaling in cardiac hypertrophy. J Recept Signal Transduct Res. 2016 Apr 8:1-13.
•  Calcium-induced conformational changes of Thrombospondin-1 signature domain: implications for vascular disease. Gupta A, Agarwal R, Singh A, Bhatnagar S. J Recept Signal Transduct Res. 2016 Aug 2:1-13.

• A Network Biology Approach to Decipher Stress Response in Bacteria Using Escherichia coli As a Model. Nagar SD, Aggarwal B, Joon S, Bhatnagar R, Bhatnagar S. OMICS. 2016 May;20(5):310-24.

• Gupta A, Bhatnagar S. Vasoregression: A Shared Vascular Pathology Underlying Macrovascular And Microvascular Pathologies? OMICS. 2015 Dec;19(12):733-53.

• Integrative analysis of ocular complications in atherosclerosis unveils pathway convergence and crosstalk (2014) Gupta A, Mohanty P, Bhatnagar S. J Recept Signal Transduct Res. Jul 23:1-16.

• Structural basis of Bacillus anthracis MoxXT disruption and the modulation of MoxT ribonuclease activity by rationally designed peptides (2014) Verma S, Kumar S, Gupta VP, Gourinath S, Bhatnagar S, Bhatnagar R Epub J Biomol Struct Dyn.

• Linkage, Mobility, and Selfishness in the MazF Family of Bacterial Toxins: A Snapshot of Bacterial Evolution (2013) Chopra N, Pathak A, Bhatnagar R, Bhatnagar S. Genome biol and evol 5, 2268-2284.

• Modeling of Plasmodium falciparum Telomerase Reverse Transcriptase Ternary Complex: Repurposing of Nucleoside Analog Inhibitors (2014) Mohanty P, Gupta A, and Bhatnagar S. Drug Repurposing, Rescue, and Repositioning.
• 25.  Functional characterization of WalRK: A two-component signal transduction system from Bacillus anthracis (2014) Dhiman A, Bhatnagar S, Kulshreshtha P, Bhatnagar R. FEBS Open Bio. 4: 65-76.

•  Positive selection and evolution of dengue type-3 virus in the Indian subcontinent. Bedi SK, Prasad A, Mathur K, Bhatnagar S. (2013) J Vector Borne Dis. 50,188-96.

• Modeling of the structure and interactions of the B. anthracis antitoxin, MoxX: deletion mutant studies highlight its modular structure and repressor function (2011) Chopra N, Agarwal S, Verma S, Bhatnagar S, Bhatnagar R. J Comput Aided Mol Des. 25, 275-91.

•  Mining human genome for novel purinergic P2Y receptors: a sequence analysis and molecular modeling approach (2011) Bhatnagar S, Mishra S, Pathak R. J Recept Signal Transduct Res. 31, 75-84.

• The PemK Toxin of Bacillus anthracis is a ribonuclease: An insight into its active site, structure and function. (2010) Agarwal S, Mishra NK, Bhatnagar S, Bhatnagar R J. Biol. Chem. 285, 7254-70.

• Singh A, Thakur PK, Meena M, Dhiraj K, Bhatnagar S, Dubey AK, et al. Interaction between Basic 7S Globulin and Leginsulin in Soybean [Glycine max]: A Structural Insight Letters in Drug Design & Discovery. 2014;11(2): 231-239.

•  Dhiman A, Bhatnagar S, Kulshreshtha P, Bhatnagar R. Functional characterization of WalRK: A two-component signal transduction system from Bacillus anthracis. FEBS Open Bio. 2014;4:65-76.

• Chopra N, Saumitra, Pathak A, Bhatnagar R, Bhatnagar S. Linkage, mobility, and selfishness in the MazF family of bacterial toxins: a snapshot of bacterial evolution. Genome Biol Evol. 2013;5(12):2268-84.

• Bedi SK, Prasad A, Mathur K, Bhatnagar S. Positive selection and evolution of dengue type-3 virus in the Indian subcontinent. J Vector Borne Dis. 2013 Sep;50(3):188-96.

• Chopra N, Agarwal S, Verma S, Bhatnagar S, Bhatnagar R. Modeling of the structure and interactions of the B. anthracis antitoxin, MoxX: deletion mutant studies highlight its modular structure and repressor function. J Comput Aided Mol Des. 2011 Mar;25(3):275-91.

• Bhatnagar S, Mishra S, Pathak R. Mining human genome for novel purinergic P2Y receptors: a sequence analysis and molecular modeling approach. J Recept Signal Transduct Res. 2011 Feb;31(1):75-84.

• Agarwal S, Mishra NK, Bhatnagar S, Bhatnagar R. PemK toxin of Bacillus anthracis is a ribonuclease: an insight into its active site, structure, and function. J Biol Chem. 2010 Mar 5;285(10):7254-70.

• Pathak R, Bhatnagar S, Dubey AK. Mechanisms underlying the opposing effects of P2Y receptors on the cell cycle. J Recept Signal Transduct Res. 2008;28(6):505-29.

• Bhatnagar S, Srivastava D, Jayadev MS, Dubey AK. Molecular variants and derivatives of insulin for improved glycemic control in diabetes. Prog Biophys Mol Biol. 2006 Jul;91(3):199-228.

• Structure based design of a potent, mutation resilient, small peptide inhibitor of HIV-1 reverse transcriptase. J Biomol Struct Dyn. 2003 Oct;21(2):171-8.

• Rao GS, Bhatnagar S, and Ahuja V. Structure-based design of a novel peptide inhibitor of HIV-1 integrase: a computer modeling approach. J Biomol Struct Dyn. 2002;20(1): p. 31-8.

• Bhatnagar S, Rao GS. Molecular modeling of the complex of endothelin-1 (ET- 1) with the endothelin type A (ET(A)) receptor and the rational design of a peptide antagonist. J Biomol Struct Dyn. 2000 Jun;17(6):957-64.

• Bhatnagar S, Rao GS, Singh TP. The role of dehydro-alanine in the design of peptides. Biosystems. 1995;34(1-3): p. 143-8.