Publications

PUBLICATIONS:

• Anagha Kalle, Jian Wu, Caesar Tawfeeq, Alexandr P Kornev, Gianluigi Veglia, Rodrigo Maillard, Susan S Taylor*, Nisha Amarnath Jonniya* (2025). Local and distal changes in dynamics are caused by an L205R Cushing’s syndrome mutant in PRKACA. Proceedings of the National Academy of Sciences, 122(24), e2502898122, DOI: 10.1073/pnas.250289812. [*Corresponding Author]

• 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.