PhD in Computational Biology from Indian Institute of Technology Indore
M.Tech in Bioinformatics from Maulana Azad National Institute of Technology Bhopal
B.Tech in Biotechnology from National Institute of Technology Raipur
RESEARCH INTERESTS
Computational Biology, Biophysics, Drug Design, Bioinformatics
27
Scopus Publications
1095
Scholar Citations
15
Scholar h-index
22
Scholar i10-index
Scopus Publications
Local and distal changes in dynamics are caused by an L205R Cushing’s syndrome mutant in PRKACA Anagha Kalle, Jian Wu, Caesar Tawfeeq, Alexandr P. Kornev, Gianluigi Veglia, et al. Proceedings of the National Academy of Sciences of the United States of America, 2025 Cushing’s syndrome (CS) is an abnormal condition characterized by elevated cortisol levels, often resulting from genetic alterations in the PRKACA gene, which encodes the catalytic subunit of cAMP-dependent protein kinase A (PKA-C). The most common CS mutation, L205R, lies at the P + 1 loop. Understanding how this mutation alters the internal allosteric network within PKA-C and changes nucleotide and substrate cooperativity is a major goal. Using molecular dynamics (MD) simulations and protein residue networks based on local spatial pattern (LSP) method, we compare crystal structures of wild-type PKA-C and L205R. Our findings indicate that L205R not only locally disrupts the P + 1 hydrophobic pocket, leading to the displacement of the P + 1-residue and altered substrate specificity, but also has long-range effects in the linker connecting the A helix to β strand 1. The MD simulations and LSP analyses also reveal critical changes at the phosphoryl transfer site. Some of these changes are captured in the L205R crystal structure while others are not. With this strategy, we also show how the dynamics of local and distal allosteric networks are differentially influenced by backbone and side-chain dynamics.
Molecular dynamics simulations reveal phosphorylation-induced conformational dynamics of the fibroblast growth factor receptor 1 kinase Subhasmita Mahapatra, Nisha Amarnath Jonniya, Suman Koirala, Parimal Kar Journal of Biomolecular Structure and Dynamics, 2024 The Fibroblast Growth Factor Receptor1 (FGFR1) kinase wields exquisite control on cell fate, proliferation, differentiation, and homeostasis. An imbalance of FGFR1 signaling leads to several pathogeneses of diseases ranging from multiple cancers to allergic and neurodegenerative disorders. In this study, we investigated the phosphorylation-induced conformational dynamics of FGFR1 in apo and ATP-bound states via all-atom molecular dynamics simulations. All simulations were performed for 2 × 2 µs. We have also investigated the energetics of the binding of ATP to FGFR1 using the molecular mechanics Poisson-Boltzmann scheme. Our study reveals that the FGFR1 kinase can reach a fully active configuration through phosphorylation and ATP binding. A 3-10 helix formation in the activation loop signifies its rearrangement leading to stability upon ATP binding. The interaction of phosphorylated tyrosine (pTyr654) with positively charged residues forms strong salt-bridge interactions, driving the compactness of the structure. The dynamic cross-correlation map reveals phosphorylation enhances correlated motions and reduces anti-correlated motions between different domains. We believe that the mechanistic understanding of large-conformational changes upon the activation of the FGFR1 kinase will aid the development of novel targeted therapeutics.Communicated by Ramaswamy H. Sarma.
The FGF/FGFR signalling mediated anti-cancer drug resistance and therapeutic intervention Subhasmita Mahapatra, Nisha Amarnath Jonniya, Suman Koirala, Kapil Dattatray Ursal, Parimal Kar Journal of Biomolecular Structure and Dynamics, 2023 Fibroblast Growth Factor (FGF) ligands and their receptors are crucial factors driving chemoresistance in several malignancies, challenging the efficacy of currently available anti-cancer drugs. The Fibroblast growth factor/receptor (FGF/FGFR) signalling malfunctions in tumor cells, resulting in a range of molecular pathways that may impact its drug effectiveness. Deregulation of cell signalling is critical since it can enhance tumor growth and metastasis. Overexpression and mutation of FGF/FGFR induce regulatory changes in the signalling pathways. Chromosomal translocation facilitating FGFR fusion production aggravates drug resistance. Apoptosis is inhibited by FGFR-activated signalling pathways, reducing multiple anti-cancer medications' destructive impacts. Angiogenesis and epithelial-mesenchymal transition (EMT) are facilitated by FGFRs-dependent signalling, which correlates with drug resistance and enhances metastasis. Further, lysosome-mediated drug sequestration is another prominent method of resistance. Inhibition of FGF/FGFR by following a plethora of therapeutic approaches such as covalent and multitarget inhibitors, ligand traps, monoclonal antibodies, recombinant FGFs, combination therapy, and targeting lysosomes and micro RNAs would be helpful. As a result, FGF/FGFR suppression treatment options are evolving nowadays. To increase positive impacts, the processes underpinning the FGF/FGFR axis' role in developing drug resistance need to be clarified, emphasizing the need for more studies to develop novel therapeutic options to address this significant problem. Communicated by Ramaswamy H. Sarma.
Functional Loop Dynamics and Characterization of the Inactive State of the NS2B-NS3 Dengue Protease due to Allosteric Inhibitor Binding Nisha Amarnath Jonniya, Parimal Kar Journal of Chemical Information and Modeling, 2022 Dengue virus, a flavivirus that causes dengue shock syndrome and dengue hemorrhagic fever, is currently prevalent worldwide. A two-component protease (NS2B-NS3) is essential for maturation, representing an important target for designing anti-flavivirus drugs. Previously, consideration has been centered on developing active-site inhibitors of NS2B-NS3pro. However, the flat and charged nature of its active site renders difficulties in developing inhibitors, suggesting an alternative strategy for identifying allosteric inhibitors. The allosterically sensitive site of the dengue protease is located near Ala125, between the 120s loop and 150s loop. Using atomistic molecular dynamics simulations, we have explored the protease's conformational dynamics upon binding of an allosteric inhibitor. Furthermore, characterization of the inherent flexible loops (71-75s loop, 120s loop, and 150s loop) is carried out for allosteric-inhibitor-bound wild-type and mutant A125C variants and a comparison is performed with its unbound state to extract the structural changes describing the inactive state of the protease. Our study reveals that compared to the unliganded system, the inhibitor-bound system shows large structural changes in the 120s loop and 150s loop in contrast to the rigid 71-75s loop. The unliganded system shows a closed-state pocket in contrast to the open state for the wild-type complex that locks the protease into the open and inactive-state conformations. However, the mutant complex fluctuates between open and closed states. Also, we tried to see how mutation and binding of an allosteric inhibitor perturb the connectivity in a protein structure network (PSN) at contact levels. Altogether, our study reveals the mechanism of conformational rearrangements of loops at the molecular level, locking the protein in an inactive conformation, which may be useful for developing allosteric inhibitors.
Effect of Sulfation on the Conformational Dynamics of Dermatan Sulfate Glycosaminoglycan: A Gaussian Accelerated Molecular Dynamics Study Rajarshi Roy, Nisha Amarnath Jonniya, Parimal Kar Journal of Physical Chemistry B, 2022 Glycosaminoglycans (GAGs) are anionic biopolymers present on cell surfaces as a part of proteoglycans. The biological activities of GAGs depend on the sulfation pattern. In our study, we have considered three octadecasaccharide dermatan sulfate (DS) chains with increasing order of sulfation (dp6s, dp7s, and dp12s) to illuminate the role of sulfation on the GAG units and its chain conformation through 10 μs-long Gaussian accelerated molecular dynamics simulations. DS is composed of repeating disaccharide units of iduronic acid (IdoA) and N-acetylgalactosamine (N-GalNAc). Here, N-GalNAc is linked to IdoA via β(1-4), while IdoA is linked to N-GalNAc through α(1-3). With the increase in sulfation, the DS structure becomes more rigid and linear, as is evident from the distribution of root-mean-square deviations (RMSDs) and end-to-end distances. The tetrasaccharide linker region of the main chain shows a rigid conformation in terms of the glycosidic linkage. We have observed that upon sulfation (i.e., dp12s), the ring flip between two chair forms vanished for IdoA. The dynamic cross-correlation analysis reveals that the anticorrelation motions in dp12s are reduced significantly compared to dp6s or dp7s. An increase in sulfation generates relatively more stable hydrogen-bond networks, including water bridging with the neighboring monosaccharides. Despite the favorable linear structures of the GAG chains, our study also predicts few significant bendings related to the different puckering states, which may play a notable role in the function of the DS. The relation between the global conformation with the micro-level parameters such as puckering and water-mediated hydrogen bonds shapes the overall conformational space of GAGs. Overall, atomistic details of the DS chain provided in this study will help understand their functional and mechanical roles, besides developing new biomaterials.
Phosphorylation-Induced Conformational Dynamics and Inhibition of Janus Kinase 1 by Suppressors of Cytokine Signaling 1 Md Fulbabu Sk, Nisha Amarnath Jonniya, Rajarshi Roy, Parimal Kar Journal of Physical Chemistry B, 2022 The dysfunction of the JAK/STAT (Janus kinase/signal transducers and activators of transcription) pathway results in several pathophysiological conditions, including autoimmune disorders. The negative feedback regulators of the JAK/STAT signaling pathway, suppressors of cytokine signaling (SOCS), act as a natural inhibitor of JAK and inhibit aberrant activity. SOCS1 is the most potent member of the SOCS family, whose kinase inhibitory region targets the substrate-binding groove of JAK with high affinity and blocks the phosphorylation of JAK kinases. Overall, we performed an aggregate of 13 μs molecular dynamics simulations on the activation loop's three different phosphorylation (double and single) states. Results from our simulations show that the single Tyr1034 phosphorylation could stabilize the JAK1/SOCS1 complex as well as the flexible activation segment. The phosphate-binding loop (P-loop) shows conformational variability at dual and single phosphorylated states. Principal component analysis and protein structure network (PSN) analysis reveal that the different phosphorylation states and SOCS1 binding induce intermediate inactive conformations of JAK1, which could be a better target for future JAK1 selective drug design. PSN analysis suggests that the com-pY1034 system is stabilized due to higher values of network hubs than the other two complex systems. Moreover, the binding free energy calculations suggest that pTyr1034 states show a higher affinity toward SOCS1 than the dual and pTyr1035 states. We believe that the mechanistic understanding of JAK1/SOCS1 complexation will aid future studies related to peptide inhibitors based on SOCS1.
Comparative Structural Dynamics of Isoforms of Helicobacter pylori Adhesin BabA Bound to Lewis b Hexasaccharide via Multiple Replica Molecular Dynamics Simulations Rajarshi Roy, Nisha Amarnath Jonniya, Md Fulbabu Sk, Parimal Kar Frontiers in Molecular Biosciences, 2022 BabA of Helicobacter pylori is the ABO blood group antigen-binding adhesin. Despite considerable diversity in the BabA sequence, it shows an extraordinary adaptation in attachment to mucosal layers. In the current study, multiple replica molecular dynamics simulations were conducted in a neutral aqueous solution to elucidate the conformational landscape of isoforms of BabA bound to Lewis b (Leb) hexasaccharide. In addition, we also investigated the underlying molecular mechanism of the BabA-glycan complexation using the MM/GBSA scheme. The conformational dynamics of Leb in the free and protein-bound states were also studied. The carbohydrate-binding site across the four isoforms was examined, and the conformational variability of several vital loops was observed. The cysteine–cysteine loops and the two diversity loops (DL1 and DL2) were identified to play an essential role in recognizing the glycan molecule. The flexible crown region of BabA was stabilized after association with Leb. The outward movement of the DL2 loop vanished upon ligand binding for the Spanish specialist strain (S381). Our study revealed that the S831 strain shows a stronger affinity to Leb than other strains due to an increased favorable intermolecular electrostatic contribution. Furthermore, we showed that the α1-2-linked fucose contributed most to the binding by forming several hydrogen bonds with key amino acids. Finally, we studied the effect of the acidic environment on the BabA-glycan complexation via constant pH MD simulations, which showed a reduction in the binding free energy in the acidic environment. Overall, our study provides a detailed understanding of the molecular mechanism of Leb recognition by four isoforms of H. pylori that may help the development of therapeutics targeted at inhibiting H. pylori adherence to the gastric mucosa.
Unraveling the Molecular Mechanism of Recognition of Selected Next-Generation Antirheumatoid Arthritis Inhibitors by Janus Kinase 1 Md Fulbabu Sk, Nisha Amarnath Jonniya, Rajarshi Roy, Parimal Kar ACS Omega, 2022 Rheumatoid arthritis (RA) is a chronic immune-related condition, primarily of joints, and is highly disabling and painful. The inhibition of Janus kinase (JAK)-related cytokine signaling pathways using small molecules is prevalent nowadays. The JAK family belongs to nonreceptor cytoplasmic protein tyrosine kinases (PTKs), including JAK1, JAK2, JAK3, and TYK2 (tyrosine kinase 2). JAK1 has received significant attention after being identified as a promising target for developing anti-RA therapeutics. Currently, no crystal structure is available for JAK1 in complex with the next-generation anti-RA drugs. In the current study, we investigated the mechanism of binding of baricitinib, filgotinib, itacitinib, and upadacitinib to JAK1 using a combined method of molecular docking, molecular dynamics simulation, and binding free energy calculation via the molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) scheme. We found that the calculated binding affinity decreases in the order upadacitinib > itacitinib > filgotinib > baricitinib. Due to the increased favorable intermolecular electrostatic contribution, upadacitinib is more selective to JAK1 compared to the other three inhibitors. The cross-correlation and principal component analyses showed that different inhibitor bindings significantly affect the binding site dynamics of JAK1. Furthermore, our studies indicated that the hydrophobic residues and hydrogen bonds from the hinge region (Glu957 and Leu959) of JAK1 played an essential role in stabilizing the inhibitors. Protein structural network analysis reveals that the total number of links and hubs in JAK1/baricitinib (354, 48) is more significant than those in apo (328, 40) and the other three complexes. The JAK1/baricitinib complex shows the highest probability of the highest-ranked community, indicating a compact network of the JAK1/baricitinib complex, consistent with its higher stability than the rest of the four systems. Overall, our study may be crucial for the rational design of JAK1-selective inhibitors with better affinity.
Decoding the Host–Parasite Protein Interactions Involved in Cerebral Malaria Through Glares of Molecular Dynamics Simulations Omkar Indari, Md Fulbabu Sk, Shweta Jakhmola, Nisha Amarnath Jonniya, Hem Chandra Jha, et al. Journal of Physical Chemistry B, 2022 Malaria causes millions of deaths every year. The malaria parasite spends a substantial part of its life cycle inside human erythrocytes. Inside erythrocytes, it synthesizes and displays various proteins onto the erythrocyte surface, such as Plasmodium falciparum erythrocytic membrane protein-1 (PfEMP1). This protein contains cysteine-rich interdomain region (CIDR) domains which have many subtypes based on sequence diversity and can cross-talk with host molecules. The CIDRα1.4 subtype can attach host endothelial protein C receptor (EPCR). This interaction facilitates infected erythrocyte adherence to brain endothelium and subsequent development of cerebral malaria. Through molecular dynamics simulations in conjunction with the molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) method, we explored the mechanism of interaction in the CIDRα1-EPCR complex. We examined the structural behavior of two CIDRα1 molecules (encoded by HB3-isolate var03-gene and IT4-isolate var07-gene) with EPCR unbound and bound (complex) forms. HB3var03CIDRα1 in apo and complexed with EPCR was comparatively more stable than IT4var07CIDRα1. Both of the complexes adopted two distinct conformational energy states. The hydrophobic residues played a crucial role in the binding of both complexes. For HB3var03CIDRα1-EPCR, the dominant energetic components were total polar interactions, while in IT4var07CIDRα1-EPCR, the primary interaction was van der Waals and nonpolar solvation energy. The study also revealed details such as correlated conformational motions and secondary structure evolution. Further, it elucidated various hotspot residues involved in protein-protein recognition. Overall, our study provides additional information on the structural behavior of CIDR molecules in unbound and receptor-bound states, which will help to design potent inhibitors.
Local and distal changes in dynamics are caused by an L205R Cushing’s syndrome mutant in PRKACA A Kalle, J Wu, C Tawfeeq, AP Kornev, G Veglia, R Maillard, SS Taylor, ... Proceedings of the National Academy of Sciences 122 (24), e2502898122 , 2025 2025 Citations: 1
Role of the αC-β4 loop in protein kinase structure and dynamics J Wu, NA Jonniya, SP Hirakis, C Olivieri, G Veglia, AP Kornev, SS Taylor Elife 12, RP91980 , 2024 2024 Citations: 7
Molecular dynamics simulations reveal phosphorylation-induced conformational dynamics of the fibroblast growth factor receptor 1 kinase S Mahapatra, NA Jonniya, S Koirala, P Kar Journal of Biomolecular Structure and Dynamics 42 (6), 2929-2941 , 2024 2024 Citations: 12
The FGF/FGFR signalling mediated anti-cancer drug resistance and therapeutic intervention S Mahapatra, NA Jonniya, S Koirala, KD Ursal, P Kar Journal of Biomolecular Structure and Dynamics 41 (22), 13509-13533 , 2023 2023 Citations: 23
Computer-aided affinity enhancement of a cross-reactive antibody against dengue virus envelope domain III NA Jonniya, S Poddar, S Mahapatra, P Kar Cell Biochemistry and Biophysics 81 (4), 737-755 , 2023 2023 Citations: 3
Protein kinase structure and dynamics: role of the αc-β4 loop J Wu, NA Jonniya, SP Hirakis, C Olivieri, G Veglia, AP Kornev, SS Taylor biorxiv , 2023 2023 Citations: 7
Finding potential inhibitors against RNA-dependent RNA polymerase (RdRp) of bovine ephemeral fever virus (BEFV): an in - silico study S Pyasi, NA Jonniya, MF Sk, D Nayak, P Kar Journal of Biomolecular Structure and Dynamics 40 (20), 10403-10421 , 2022 2022 Citations: 6
Finding potent inhibitors against SARS-CoV-2 main protease through virtual screening, ADMET, and molecular dynamics simulation studies R Roy, MF Sk, NA Jonniya, S Poddar, P Kar Journal of Biomolecular Structure and Dynamics 40 (14), 6556-6568 , 2022 2022 Citations: 25
Functional loop dynamics and characterization of the inactive state of the NS2B-NS3 dengue protease due to allosteric inhibitor binding NA Jonniya, P Kar Journal of Chemical Information and Modeling 62 (16), 3800-3813 , 2022 2022 Citations: 7
Effect of Sulfation on the Conformational Dynamics of Dermatan Sulfate Glycosaminoglycan: A Gaussian Accelerated Molecular Dynamics Study R Roy, NA Jonniya, P Kar The Journal of Physical Chemistry B 126 (21), 3852-3866 , 2022 2022 Citations: 15
Comparative Structural Dynamics of Isoforms of Helicobacter pylori Adhesin BabA Bound to Lewis b Hexasaccharide via Multiple Replica Molecular Dynamics … R Roy, NA Jonniya, MF Sk, P Kar Frontiers in Molecular Biosciences 9, 852895 , 2022 2022 Citations: 7
Phosphorylation-induced conformational dynamics and inhibition of Janus Kinase 1 by suppressors of cytokine signaling 1 MF Sk, NA Jonniya, R Roy, P Kar The Journal of Physical Chemistry B 126 (17), 3224-3239 , 2022 2022 Citations: 10
Unraveling the molecular mechanism of recognition of selected next-generation antirheumatoid arthritis inhibitors by Janus kinase 1 MF Sk, NA Jonniya, R Roy, P Kar ACS omega 7 (7), 6195-6209 , 2022 2022 Citations: 25
A comparative study of structural and conformational properties of WNK kinase isoforms bound to an inhibitor: insights from molecular dynamic simulations NA Jonniya, MF Sk, P Kar Journal of Biomolecular Structure and Dynamics 40 (3), 1400-1415 , 2022 2022 Citations: 17
Discovery of potential competitive inhibitors against With-No-Lysine kinase 1 for treating hypertension by virtual screening, inverse pharmacophore-based lead optimization, and … NA Jonniya, MF Sk, R Roy, P Kar SAR and QSAR in Environmental Research 33 (2), 63-87 , 2022 2022 Citations: 6
Decoding the host–parasite protein interactions involved in cerebral malaria through glares of molecular dynamics simulations O Indari, MF Sk, S Jakhmola, NA Jonniya, HC Jha, P Kar The Journal of Physical Chemistry B 126 (2), 387-402 , 2022 2022 Citations: 14
Unraveling the molecular mechanism of recognition of human interferon-stimulated gene product 15 by coronavirus papain-like proteases: A multiscale simulation study R Roy, NA Jonniya, S Poddar, MF Sk, P Kar Journal of Chemical Information and Modeling 61 (12), 6038-6052 , 2021 2021 Citations: 11
Exploring the energetic basis of binding of currently used drugs against HIV-1 subtype CRF01_AE protease via molecular dynamics simulations MF Sk, NA Jonniya, P Kar Journal of Biomolecular Structure and Dynamics 39 (16), 5892-5909 , 2021 2021 Citations: 16
Elucidating specificity of an allosteric inhibitor WNK476 among With‐No‐Lysine kinase isoforms using molecular dynamic simulations N Amarnath Jonniya, MF Sk, P Kar Chemical Biology & Drug Design 98 (3), 405-420 , 2021 2021 Citations: 11
Immunoinformatics approach to design multi-epitope-subunit vaccine against bovine ephemeral fever disease S Pyasi, V Sharma, K Dipti, NA Jonniya, D Nayak Vaccines 9 (8), 925 , 2021 2021 Citations: 41
MOST CITED SCHOLAR PUBLICATIONS
Current and novel therapeutic molecules and targets in Alzheimer's disease A Kumar, CM Nisha, C Silakari, I Sharma, K Anusha, N Gupta, P Nair, ... Journal of the Formosan Medical Association 115 (1), 3-10 , 2016 2016 Citations: 204
Molecular Docking and In Silico ADMET Study Reveals Acylguanidine 7a as a Potential Inhibitor of β ‐Secretase CM Nisha, A Kumar, P Nair, N Gupta, C Silakari, T Tripathi, A Kumar Advances in bioinformatics 2016 (1), 9258578 , 2016 2016 Citations: 181
Docking and ADMET prediction of few GSK-3 inhibitors divulges 6-bromoindirubin-3-oxime as a potential inhibitor CM Nisha, A Kumar, A Vimal, BM Bai, D Pal, A Kumar Journal of Molecular Graphics and modelling 65, 100-107 , 2016 2016 Citations: 129
Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations MF Sk, R Roy, NA Jonniya, S Poddar, P Kar Journal of Biomolecular Structure and Dynamics 39 (10), 3649-3661 , 2021 2021 Citations: 92
Investigating phosphorylation-induced conformational changes in WNK1 kinase by molecular dynamics simulations NA Jonniya, MF Sk, P Kar ACS omega 4 (17), 17404-17416 , 2019 2019 Citations: 57
Identification of potential inhibitors against Epstein–Barr virus nuclear antigen 1 (EBNA1): An insight from docking and molecular dynamic simulations S Jakhmola, NA Jonniya, MF Sk, A Rani, P Kar, HC Jha ACS Chemical Neuroscience 12 (16), 3060-3072 , 2021 2021 Citations: 51
Computational investigation of structural dynamics of SARS-CoV-2 methyltransferase-stimulatory factor heterodimer nsp16/nsp10 bound to the cofactor SAM MF Sk, NA Jonniya, R Roy, S Poddar, P Kar Frontiers in Molecular Biosciences 7, 590165 , 2020 2020 Citations: 48
Immunoinformatics approach to design multi-epitope-subunit vaccine against bovine ephemeral fever disease S Pyasi, V Sharma, K Dipti, NA Jonniya, D Nayak Vaccines 9 (8), 925 , 2021 2021 Citations: 41
Investigating specificity of the anti-hypertensive inhibitor WNK463 against With-No-Lysine kinase family isoforms via multiscale simulations NA Jonniya, P Kar Journal of Biomolecular Structure and Dynamics , 2020 2020 Citations: 33
Finding potent inhibitors against SARS-CoV-2 main protease through virtual screening, ADMET, and molecular dynamics simulation studies R Roy, MF Sk, NA Jonniya, S Poddar, P Kar Journal of Biomolecular Structure and Dynamics 40 (14), 6556-6568 , 2022 2022 Citations: 25
Unraveling the molecular mechanism of recognition of selected next-generation antirheumatoid arthritis inhibitors by Janus kinase 1 MF Sk, NA Jonniya, R Roy, P Kar ACS omega 7 (7), 6195-6209 , 2022 2022 Citations: 25
The FGF/FGFR signalling mediated anti-cancer drug resistance and therapeutic intervention S Mahapatra, NA Jonniya, S Koirala, KD Ursal, P Kar Journal of Biomolecular Structure and Dynamics 41 (22), 13509-13533 , 2023 2023 Citations: 23
Characterizing an allosteric inhibitor-induced inactive state in with-no-lysine kinase 1 using Gaussian accelerated molecular dynamics simulations NA Jonniya, MF Sk, P Kar Physical Chemistry Chemical Physics 23 (12), 7343-7358 , 2021 2021 Citations: 23
A comparative study of structural and conformational properties of WNK kinase isoforms bound to an inhibitor: insights from molecular dynamic simulations NA Jonniya, MF Sk, P Kar Journal of Biomolecular Structure and Dynamics 40 (3), 1400-1415 , 2022 2022 Citations: 17
Exploring the energetic basis of binding of currently used drugs against HIV-1 subtype CRF01_AE protease via molecular dynamics simulations MF Sk, NA Jonniya, P Kar Journal of Biomolecular Structure and Dynamics 39 (16), 5892-5909 , 2021 2021 Citations: 16
Effect of Sulfation on the Conformational Dynamics of Dermatan Sulfate Glycosaminoglycan: A Gaussian Accelerated Molecular Dynamics Study R Roy, NA Jonniya, P Kar The Journal of Physical Chemistry B 126 (21), 3852-3866 , 2022 2022 Citations: 15
Decoding the host–parasite protein interactions involved in cerebral malaria through glares of molecular dynamics simulations O Indari, MF Sk, S Jakhmola, NA Jonniya, HC Jha, P Kar The Journal of Physical Chemistry B 126 (2), 387-402 , 2022 2022 Citations: 14
Molecular dynamics simulations reveal phosphorylation-induced conformational dynamics of the fibroblast growth factor receptor 1 kinase S Mahapatra, NA Jonniya, S Koirala, P Kar Journal of Biomolecular Structure and Dynamics 42 (6), 2929-2941 , 2024 2024 Citations: 12
Unraveling the molecular mechanism of recognition of human interferon-stimulated gene product 15 by coronavirus papain-like proteases: A multiscale simulation study R Roy, NA Jonniya, S Poddar, MF Sk, P Kar Journal of Chemical Information and Modeling 61 (12), 6038-6052 , 2021 2021 Citations: 11
Elucidating specificity of an allosteric inhibitor WNK476 among With‐No‐Lysine kinase isoforms using molecular dynamic simulations N Amarnath Jonniya, MF Sk, P Kar Chemical Biology & Drug Design 98 (3), 405-420 , 2021 2021 Citations: 11
