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Dr. Nisha Amarnath Jonniya

ABOUT
NAME: Dr. Nisha Amarnath Jonniya

M.TECH: MANIT Bhopal, Madhya Pradesh

E- MAIL: nishaj@nitandhra.ac.in

POSITION: Assistant Professor

PhD: Indian Institute of Technology Indore, M.P

PHONE: +91 0000000000


AREAS OF INTEREST: Computational Modelling of Biomolecules; Drug Discovery; Exploring Protein Structure, Dynamics, and Function Relationship; Computational Approach to Understand Disease Mutation Mechanism; Biomolecular Recognition of Protein-Protein and Protein-Ligands

PERSONAL WEB PAGE: https://sites.google.com/nitandhra.ac.in/computationalbiologygroup
PROFILE

Professional and Research Experience

  •       Assistant Professor, Department of Biotechnology, NIT Andhra Pradesh, India (Since Nov 2024)
  •       Postdoctoral Research Employee, University of California San Diego, USA (December 2022-November 2024)
  •       Research Associate I/II, Indian Institute of Technology Indore, Madhya Pradesh, India (May 2021- November 2022)
  •       Adhoc Faculty, Department of Biotechnology, NIT Raipur, Chhattisgarh, India (July 2010-June 2015) 

Publications (Citations: 932; h-index:14; i10-index:19)

  • Jian Wu#, Nisha A. Jonniya#, Sophia P. Hirakis, Cristina Olivieri, Gianluigi Veglia, Alexandr P. Kornev, Susan S. Taylor* (2024). Role of the αC-β4 loop in protein kinase structure and dynamics. eLife, Structural Biology and Molecular Biophysics, doi: 10.7554/eLife.91980.[# Equal contributors]
  • Jonniya, N. A., Poddar, S., Mahapatra, S., Kar, P.*(2023). Computer-aided Affinity Enhancement of a Cross-reactive Antibody against Dengue Virus Envelope Domain III. Cell Biochemistry and Biophysics, 81(4), 737-755, doi: 10.1007/s12013-023-01175-8.
  • Mahapatra, S., Jonniya, N.A., Koirala, P.* (2023).  Molecular dynamics simulations reveal phosphorylation-induced conformational dynamics of the fibroblast growth factor receptor 1 kinase. Journal of Biomolecular Structure and Dynamics, 42(6), 2929-2941,doi: 10.1080/07391102.2023.2209189.
  • Mahapatra, S., Jonniya, N.A., Koirala, S. Ursal, K.D., P.* (2023).  The FGF/FGFR signalling mediated anti-cancer drug resistance and therapeutic intervention. Journal of Biomolecular Structure and Dynamics, 41(22), 13509-13533, doi: 10.1080/07391102.2023.2191721.
  • Jonniya, N. A.* and Kar, P.*(2022).  Functional Loop Dynamics and Characterization of the Inactive State of the NS2B-NS3 Dengue Protease due to Allosteric Inhibitor Binding. Journal of Chemical Information and Modeling, 62(16), 3800-3813, doi: 10.1021/acs.jcim.2c00461. (* Corresponding Authors)
  • Sk, M. F.; Jonniya, N. A.; Roy, R.; Kar, P.* (2022).  Phosphorylation-Induced Conformational Dynamics and Inhibition of Janus Kinase1 by Suppressors of Cytokine Signaling1. Journal of Physical Chemistry B, 126(17), 3224-3239, doi:10.1021/acs.jpcb.1c10733.
  • Roy,R.#; Jonniya, N. A.#; Sk, M.F.; Kar, P.* (2022).  Comparative structural dynamics of isoforms of Helicobacter pylori adhesin BabA bound to Lewis b hexasaccharide via multiple replica molecular dynamics simulations, Frontiers in Molecular Biosciences, 9, 852895, doi: 10.3389/fmolb.2022.852895. [# Equal contributors]
  • Jonniya, N.A.; Sk, M.F.; Roy, R.; Kar, P.* (2022).   Discovery of potential competitive inhibitors against With-No-Lysine 1 for treating hypertension by virtual screening, inverse pharamcophore-based lead optimization and molecular dynamics simulations. SAR and QSAR in Environmental Research, 33(2), 63-87, doi: 10.1080/1062936X.2021.2023218.
  • Jonniya, N. A; Sk, M. F.; Kar, P.* (2022).   A comparative study of structural and conformational properties of WNK kinase isoforms bound to an inhibitor: insights from molecular dynamic simulations, Journal of Biomolecular Structure and Dynamics, 40(3), 1400-1415, doi: 10.1080/07391102.2020.1827035.  
  • Indari, Omakri.; Sk, M.F.; Jakhmola, S.; Jonniya, N.A.; Jha, H.C*.; Kar, P.* (2022).   Decoding the Host-Parasite Protein Interactions Involved in Cerebral Malaria Through Glares of Molecular Dynamics Simulations. The Journal of Physical Chemistry B, 126(2), 387-402, doi: 10.1021/acs.jpcb.1c07850.
  • Sk, M. F.; Jonniya, N. A.; Roy, R.; Kar, P.* (2022). Unraveling the Molecular Mechanism of Recognition of Selected Next Generation Anti-Rheumatoid Arthritis Inhibitors by Janus Kinase 1. ACS Omega, 7(7), 6195-6209, doi: 10.1021/acsomega.1c06715.
  •  Roy, R.; Jonniya, N. A.; Kar, P.* (2022).  Effect of Sulfation on the Conformational Dynamics of Dermatan Sulfate Glycosaminoglycan: A Gaussian Accelerated Molecular Dynamics Study. Journal of Physical Chemistry B, 126 (21), 3852-3866, doi: 10.1021/acs.jpcb.2c01807.
  • Jonniya, N. A; Sk, M. F.; Kar, P.* (2021).   Characterizing an allosteric inhibitor-induced inactive state in with-no-lysine kinase 1 using Gaussian accelerated molecular dynamics simulations, Physical Chemistry Chemical Physics, 12(23), 7343-7358, doi: /10.1039/D0CP05733A.
  • Jonniya, N. A.; Sk, M. F.; Kar, P.* (2021).   Elucidating specificity of an allosteric inhibitor WNK476 among WNK isoforms using molecular dynamic simulations, Chemical Biology and Drug Design, 98(3), 405-420, doi: 10.1111/cbdd.13863.
  • Jonniya, N. A.; Sk, M. F.; Kar, P.* (2021).   Molecular Mechanism of Inhibiting WNK Binding to OSR1 by Targeting the Allosteric Pocket of the OSR1-CCT Domain with Potential Antihypertensive Inhibitors: An In Silico Study, The Journal of Physical Chemistry B, 125 (32), 9115-9129, doi: 10.1021/acs.jpcb.1c04672.
  • Roy,R.# ; Jonniya, N. A.# ; Poddar, S.; Sk, M.F.; Kar, P.* (2021).   Unraveling the Molecular Mechanism of Recognition of Human Interferon-Stimulated Gene Product 15 by Coronavirus Papain-Like Proteases: A Multiscale Simulation Study, Journal of Chemical and Information Modelling, 61(12), 6038-6052, doi: 10.1021/acs.jcim.1c00918. [# Equal contributors]
  •  Jhakmola, S.#; Jonniya, N.A. #; Sk, M. F; Jha H. C*.; Kar, P.* (2021).   Identification of Potential Inhibitors against Epstein–Barr Virus Nuclear Antigen 1 (EBNA1): An Insight from Docking and Molecular Dynamic Simulations, ACS Chemical Neuroscience, 12(16), 3060-3072, doi:  10.1021/acschemneuro.1c00350. [# Equal contributors]
  • Pyasi, S#; Jonniya, N. A.#; Sk, M. F.; Nayak, D.; Kar, P.* (2021).   Finding potential inhibitors against RNA-dependent RNA polymerase (RdRp) of Bovine Ephemeral Fever Virus (BEFV): An in-silico study, Journal of Biomolecular Structure and Dynamics, 40(20), 10403-10421, doi: 10.1080/07391102.2021.1946714. [# Equal contributors]
  • Pyasi, S.; Sharma, V.; Dipti, K.; Jonniya, N. A.; Nayak D.* (2021).   Immunoinformatics approach to design multi-epitope-subunit vaccine against bovine ephemeral fever disease. Vaccines, 9 (8), 925, doi: 10.3390/vaccines9080925.
  • Sk, M. F.#; Jonniya, N. A.#; Roy, R.; Poddar, S.; Kar, P.* (2020).  Computational investigation of structural dynamics of SARS-CoV-2 methyltransferase-stimulatory factor heterodimer nsp16/nsp10 bound to the cofactor SAM, Frontiers in Molecular Biosciences, 7, 590165, doi: 10.3389/fmolb.2020.590165. [# Equal contributors]
  • Roy, R.; Sk, M. F.; Jonniya, N. A; Poddar, S.; Kar, P.* (2020).  Finding potent inhibitors against SARS-CoV-2 main protease through virtual screening, ADMET, and molecular dynamic simulation studies, Journal of Biomolecular Structure and Dynamics, 40(14), 6556-6568, doi: 10.1080/07391102.2021.1897680.
  • Jonniya, N. A. and Kar, P.* (2019).   Investigating specificity of the anti-hypertensive inhibitor WNK463 against With-No-Lysine kinase family isoforms via multiscale simulations. Journal of Biomolecular Structure and Dynamics, 38(5), 1306-1321, doi: 10.1080/07391102.2019.1602079.
  • Jonniya, N. A; Sk, M. F.; Kar, P.* (2019).   Investigating phosphorylation-induced conformational changes in WNK1 kinase by molecular dynamics simulations, ACS Omega, 17(4), 17404-17416, doi: 10.1021/acsomega.9b02187.
  • Sk, M. F.; Jonniya, N. A; Kar, P.* (2020).  Exploring the energetics basis of binding of currently used drugs against HIV-1 subtype CRF01-AE protease via molecular dynamics simulations, Journal of Biomolecular Structure and Dynamics, 39(16), 5892-5909, doi: 10.1080/07391102.2020.1794965.
  • Sk, M. F.; Roy, R.; Jonniya, N. A.; Poddar, S.; Kar, P.* (2020).  Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations, Journal of Biomolecular Structure and Dynamics, 39(10), 3649-3661, doi: 10.1080/07391102.2020.1768149.

Symposium

  • Presented “Multiscale simulations of WNK kinases associated with hypertension” at the 1st In-house Symposium on Advances in Biosciences and Bioengineering, at the Indian Institute of Technology (IIT), Indore, India, on February 23, 2019. [Best oral presentation]

Conferences

  • Presented "Capturing Domain Dynamics of Protein Kinase A Associated with Cushing Syndrome Mutation Using Local Spatial Pattern Method" in the Gordan Research Conference on Phosphorylation and G-Protein Mediated Signaling Networks, Waterville Valley, New Hampshire, USA between June 9-14, 2024.
  • Presented (Online Mode) "Molecular Mechanism of Inhibiting WNK Binding to OSR1 by Targeting the Allosteric Pocket of the OSR1 CCT Domain with Potential Antihypertensive Inhibitors: An In Silico Study" in the Hybrid Workshop COMPUTER SIMULATION AND THEORY OF MACROMOLECULES, at Max Planck Institute for Multidisciplinary Science Theoretical and Computational Biophysics, Germany between April 8-9, 2022.
  • Presented (Online Mode) "Characterizing an allosteric inhibitor-induced inactive state in with-no-lysine kinase 1 using Gaussian accelerated molecular dynamics simulations" in the 44th Indian Biophysical Society meeting entitled Conceptual Advances in Biophysics and its Applications, at Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India between March 30-31, April 1, 2022.
  • Presented (Online Mode) "Allosteric inhibitor-induced inactive state in WNK1 kinase: A structural insight using Gaussian accelerated Molecular Dynamic simulations (GaMD)", at the 8th Annual Research Symposium at Centre for BioSystem Science and Engineering, at the Indian Institute of Science between January 28–29, 2022.
  • Presented “Energetics of binding of WNK463 to With-No-Lysine (WNK) kinase isoforms”, at the International Conference on Emerging Area in Biosciences and Biomedical Technologies-2 (ebbt-2), at the Indian Institute of Technology (IIT), Indore, India, between February 7-9, 2020.
  • Presented “Energetics of binding of WNK463 to With-No-Lysine (WNK) kinase isoforms”, in the workshop on Computational Biology and Bioinformatics (CBB, 2019), at the Indian Institute of Technology, Jodhpur, India, on July 31-August 1, 2019.
  • Presented “Investigating the effectiveness of currently used protease inhibitor against HIV-1 subtype D by using multiscale” at the International Conference on Mathematical Modeling and Scientific Computing (ICMMSC-2018), at the Indian Institute of Technology, Indore, between July 19-21, 2018.
  • Presented “Energetics of binding WNk463 to With-No-Lysine (WNK) kinase isoforms”, at the International Conference on Emerging Area in Biosciences and Biomedical Technologies-1 (ebbt-1), between January 5-6, 2018.
  • Presented “Molecular Recognition of Drugs by Receptor Proteins via Multiscale Simulation Methods” at the 5th Industry Academia Conclave (IAC), at the Indian Institute of Technology (IIT), Indore, India, on September 6, 2017.

Workshops

  • Participated in the "61st Hands-On Workshop on Computational Biophysics presented by the NIH Center for Macromolecular Modeling and Visualization of the University of Illinois at Urbana-Champaign", at AUBURN University, USA, June 22-28, 2024.
  •  Participated in the "Computational Approaches in Drug Design and Therapeutics", at AMITY University, Chhattisgarh, Feb 20-2021.
  •  Attended and qualified in the Assessment Test for the “Introduction to Computational Drug Design” workshop organized by the Schrodinger and Pharmacy Council of India, from 21st Sep-23rd Oct 2020.
  • Participated in the 10-Days Short Term Course on “Data Science and Analytics” sponsored by the Technical Education Quality Improvement Programme, MHRD, at the Indian Institute of Technology (IIT), Indore, India, March 02-12, 2020.
  • Participated in the workshop on Computational Biology and Bioinformatics (CBB, 2019), at the Indian Institute of Technology, Jodhpur, India, on July 31-August 1, 2019.
  • Participated in the 5-Days Active Learning Course on “GPU Computing in Computational Biology” sponsored by Global Initiative of Academic Network, MHRD, at the Indian Institute of Technology (IIT), Indore, India, July 15-19, 2019
  • Attended a workshop on “Business Analytics using R”, at the Indian Institute of Management (IIM), Indore, India, on January 20th, 2019.
  • Attended a workshop on "Practical Protein Crystallography using PX Beamline at Indus-2 Synchroton", Raja Ramanna Centre for Advanced Technology (RRCAT), Indore, on March 27- 28, 2018.

Mentored

  • Bachelor’s Project Guided at University of California San Diego, USA:   [01 B.Tech student from PES, Bangalore]
  • Bachelor’s Project  Guided at NIT Raipur, India:   [03 B.Tech students from NIT Raipur]
  • Bachelor’s Project Co-Guided at IIT Indore, India:  [02  B.Tech student from Guwahati University, Guwahati]; [ 01 B.Tech student from IISER Trivandrum, Kerala];  [01 B.Tech student from NIT Rourkela, Odisha]; [01 B.Tech student from the Institute of Bioinformatics and Biotechnology SPPU, Pune, Maharashtra]
  •  Master's Project Co-Guided at IIT Indore:  [01 M.Sc student from Devi Ahilya Vishwavidyalaya, Indore, Madhya Pradesh]
  • Trained one student of Class-XI, Yashwant Public School, Indore, Madhya Pradesh, India for a project in the subject of Biology for one week under “Vigyan Jyoti Programme” funded by the Department of Science and Technology under a project titled: ‘Knowledge, Personality and Skill development activities for aspiring school-girls’, at the Indian Institute of Technology, Indore, India, May 21st-10th June 2018.

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