Shashi Kumar

@ivanov-group.org

Postdoctorlal Research Associate
Georgia State University Atlanta

Shashi Kumar


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https://researchid.co/shashikumar

RESEARCH, TEACHING, or OTHER INTERESTS

Chemical Engineering, Biochemistry, Artificial Intelligence, Multidisciplinary
14

Scopus Publications

301

Scholar Citations

6

Scholar h-index

5

Scholar i10-index

Scopus Publications

  • Tailoring spacer architecture in cationic Geminis: Effects on physicochemical behaviour, transfection efficiency, and antibacterial efficacy
    Homen Dahal, Sadhana Roy, Shashi Kumar, Joykrishna Dey, Somdeb Bose Dasgupta
    Journal of Drug Delivery Science and Technology, 2026
  • Advanced Techniques for Polymer Characterization
    Nikhil Kumar, Komal Agarwal, Shashi Kumar, Biswajoy Ghosh
    Polymer Characterization Structure to Applications, 2026
  • Unravelling the self-assembly of a novel cationic pseudo-gemini surfactant and its monomeric counterpart: interactions with DNA and BSA in aqueous medium at neutral pH
    Homen Dahal, Sachin Soren, Shashi Kumar, Joykrishna Dey
    Soft Matter, 2025
    Novel pseudo-gemini surfactant developed via electrostatic interaction avoiding complex synthesis, shows stable self-assembly and strong DNA/BSA binding, enabling biomedical applications.
  • High-Throughput Ligand Dissociation Kinetics Predictions Using Site Identification by Ligand Competitive Saturation
    Wenbo Yu, Shashi Kumar, Mingtian Zhao, David J. Weber, Alexander D. MacKerell
    Journal of Chemical Theory and Computation, 2025
    The dissociation or off rate, koff, of a drug molecule has been shown to be more relevant to efficacy than affinity for selected systems, motivating the development of predictive computational methodologies. These are largely based on enhanced-sampling molecular dynamics (MD) simulations that come at a high computational cost limiting their utility for drug design where a large number of ligands need to be evaluated. To overcome this, presented is a combined physics- and machine learning (ML)-based approach that uses the physics-based site identification by ligand competitive saturation (SILCS) method to enumerate potential ligand dissociation pathways and calculate ligand dissociation free-energy profiles along those pathways. The calculated free-energy profiles along with molecular properties are used as features to train ML models, including tree and neural network approaches, to predict koff values. The protocol is developed and validated using 329 ligands for 13 proteins showing robustness of the ML workflow built upon the SILCS physics-based free-energy profiles. The resulting SILCS-Kinetics workflow offers a highly efficient method to study ligand dissociation kinetics, providing a powerful tool to facilitate drug design including the ability to generate quantitative estimates of atomic and functional groups contributions to ligand dissociation.
  • Unravelling and Quantifying the Biophysical– Biochemical Descriptors Governing Protein Thermostability by Machine Learning
    Shashi Kumar, Vinay Kumar Duggineni, Vibhuti Singhania, Swayam Prabha Misra, Parag A. Deshpande
    Advanced Theory and Simulations, 2023
    Analysis of protein thermostability is vital in protein science to aid the understanding of evolutionary aspects of organic life as well as in protein engineering for modern day industrial applications. In the present study, supervised machine learning (ML) algorithms are employed to unravel potential patterns behind protein thermostability. This computational analysis conclusively shows inverse gamma turns, VIII turns, and the propensity of cysteine (Cys) to be the most important biophysical–biochemical attributes responsible for protein thermostability. From the propensity analysis of amino acids, polar residues, specifically glutamine (Gln) and serine (Ser), and charged residues, specifically glutamic acid (Glu) and lysine (Lys), are found to favor the enhancement of protein thermostability. The study demonstrates the feasibility of assigning quantifiable descriptors of thermostability which is expected to aid protein engineering.
  • Efficient proton shuttle makes SazCA an excellent CO2 hydration enzyme
    Shashi Kumar, Parag A. Deshpande
    Journal of Biomolecular Structure and Dynamics, 2023
    The fastest member of the carbonic anhydrase family catalysing the reversible hydration of carbon dioxide to bicarbonate ions has been recently reported to be SazCA. While thermostable, this enzyme shows exceptional activity at 353 K for the reaction. This study explores the molecular basis for the exceptional activity of SazCA, in contrast to SspCA, probed using molecular dynamics simulations. Our simulations, carried out at different temperatures, indicate the presence of efficient proton shuttle between the active zinc centre and His64 residue in the two enzymes. The proton accepting His64 residue was identified to have in and out conformations with the in conformations being supportive to proton acceptance. Our simulations show a large population of in conformations in SazCA making the enzyme exhibit an exceptional activity. The RMSF and H-bonds analysis confirmed the role of His2 and His207 in supporting the attainment of in conformations in SazCA resulting in exceptional activity. Communicated by Ramaswamy H. Sarma
  • Computational analysis of the effect of Gly100Ala mutation on the thermostability of SazCA
    Shashi Kumar, Soumya Biswas, Parag A. Deshpande
    Journal of Biomolecular Structure and Dynamics, 2023
    Maintaining the protein stability upon mutation is a challenging task in protein engineering. In the present computational study, we induced a single point Gly100Ala mutation in SazCA and examined the factors governing the stability and flexibility of the mutated form, and compared it to that of the wildtype using molecular dynamics simulations. We observed higher structural stability and lesser residual mobility in the mutated SazCA. Improved H-bonding due to Gly100Ala was observed. Ala100 was responsible for the increased helical contents in the mutated SazCA while Gly100 compromised the secondary structure contents in the wildtype. A strong network of salt bridges and high local ordering of the solvent molecules at the protein surface contributed to the enhanced stability of the mutated protein. Our simulations conclusively highlight Gly100Ala mutation as a step towards designing a more robust and thermostable SazCA. Communicated by Ramaswamy H. Sarma
  • Enzyme-substrate interactions in orotate-mimetic OPRT inhibitor complexes: a QM/MM analysis
    Shashi Kumar, N. N. Subrahmanyeswara Rao, K. S. S. V. Prasad Reddy, Manjusha C. Padole, Parag A. Deshpande
    Physical Chemistry Chemical Physics, 2022
    QM/MM analysis of orotate-mimetic inhibitors of orotate phosphoribosyltransferase revealed 4-Hydroxy-6-methylpyridin-2(1H)-one be the best inhibitor among the tested ones for the inhibition of OPRT action.
  • Biomimetic CO2hydration activity of boronic acids
    Manju Verma, V. Sai Phani Kumar, Shashi Kumar, Parag A. Deshpande
    Physical Chemistry Chemical Physics, 2021
    Inspired by the recent experimental reports on boron containing compounds to be active and biomimetic for carbon capture, we report the mechanistic details of CO2 hydration activities of boronic acids using density functional theory calculations.
  • Structural and thermodynamic analysis of factors governing the stability and thermal folding/unfolding of SazCA
    Shashi Kumar, Parag A. Deshpande
    Plos One, 2021
    Molecular basis of protein stability at different temperatures is a fundamental problem in protein science that is substantially far from being accurately and quantitatively solved as it requires an explicit knowledge of the temperature dependence of folding free energy of amino acid residues. In the present study, we attempted to gain insights into the thermodynamic stability of SazCA and its implications on protein folding/unfolding. We report molecular dynamics simulations of water solvated SazCA in a temperature range of 293-393 K to study the relationship between the thermostability and flexibility. Our structural analysis shows that the protein maintains the highest structural stability at 353 K and the protein conformations are highly flexible at temperatures above 353 K. Larger exposure of hydrophobic surface residues to the solvent medium for conformations beyond 353 K were identified from H-bond analysis. Higher number of secondary structure contents exhibited by SazCA at 353 K corroborated the conformations at 353 K to exhibit the highest thermal stability. The analysis of thermodynamics of protein stability revealed that the conformations that denature at higher melting temperatures tend to have greater maximum thermal stability. Our analysis shows that 353 K conformations have the highest melting temperature, which was found to be close to the experimental optimum temperature. The enhanced protein stability at 353 K due the least value of heat capacity at unfolding suggested an increase in folding. Comparative Gibbs free energy analysis and funnel shaped energy landscape confirmed a transition in folding/unfolding pathway of SazCA at 353 K.
  • Molecular dynamics simulations identify the regions of compromised thermostability in SazCA
    Shashi Kumar, Deepak Seth, Parag Arvind Deshpande
    Proteins Structure Function and Bioinformatics, 2021
  • Slip-enhanced flow through thin packed column with superhydrophobic wall
    Tamoghna Saha, Shashi Kumar, Soubhik Kumar Bhaumik
    Sensors and Actuators B Chemical, 2017
  • Minimizing axial dispersion in narrow packed column using superhydrophobic wall
    Tamoghna Saha, Shashi Kumar, Soubhik Kumar Bhaumik
    Korean Journal of Chemical Engineering, 2016
  • Hydrothermal conversion of lignin to substituted phenols and aromatic ethers
    Rawel Singh, Aditya Prakash, Shashi Kumar Dhiman, Bhavya Balagurumurthy, Ajay K. Arora, S.K. Puri, Thallada Bhaskar
    Bioresource Technology, 2014

RECENT SCHOLAR PUBLICATIONS

  • High-Throughput Ligand Dissociation Kinetics Predictions Using Site Identification by Ligand Competitive Saturation
    W Yu, S Kumar, M Zhao, DJ Weber, AD MacKerell Jr
    Journal of Chemical Theory and Computation 21 (9), 4964-4978 , 2025
    2025
    Citations: 8
  • Unravelling the self-assembly of a novel cationic pseudo-gemini surfactant and its monomeric counterpart: interactions with DNA and BSA in aqueous medium at neutral pH
    H Dahal, S Soren, S Kumar, J Dey
    Soft Matter 21 (27), 5515-5528 , 2025
    2025
  • Computational study of ligand dissociation pathways and free-energy barriers using the site-identification by ligand competitive saturation (SILCS) method
    W Yu, S Kumar, M Zhao, AD MacKerell
    Biophysical Journal 123 (3), 471a , 2024
    2024
  • Computational analysis of the effect of Gly100Ala mutation on the thermostability of SazCA
    S Kumar, S Biswas, PA Deshpande
    Journal of Biomolecular Structure and Dynamics 41 (21), 12363-12371 , 2023
    2023
    Citations: 1
  • Efficient proton shuttle makes SazCA an excellent CO 2 hydration enzyme
    S Kumar, PA Deshpande
    Journal of Biomolecular Structure and Dynamics 41 (13), 6001-6010 , 2023
    2023
    Citations: 1
  • Development of SILCS kinetics methodology for the determination of ligand dissociation pathways and free energy barriers
    S Kumar, M Zhao, AD MacKerell Jr
    2023
  • Development of SILCS Kinetics Methodology for the Determination of Ligand Dissociation Pathways and Free Energy Barriers
    K Shashi, A D. MacKerell Jr
    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY , 2023
    2023
  • Unravelling and quantifying the biophysical–biochemical descriptors governing protein thermostability by machine learning
    S Kumar, VK Duggineni, V Singhania, SP Misra, PA Deshpande
    Advanced Theory and Simulations 6 (3), 2200703 , 2023
    2023
    Citations: 5
  • Enzyme–substrate interactions in orotate-mimetic OPRT inhibitor complexes: a QM/MM analysis
    S Kumar, NNS Rao, KP Reddy, MC Padole, PA Deshpande
    Physical Chemistry Chemical Physics 25 (4), 3472-3484 , 2023
    2023
    Citations: 4
  • Structural and thermodynamic analysis of factors governing the stability and thermal folding/unfolding of SazCA
    S Kumar, PA Deshpande
    PLoS One 16 (4), e0249866 , 2021
    2021
    Citations: 31
  • Molecular dynamics simulations identify the regions of compromised thermostability in SazCA
    S Kumar, D Seth, PA Deshpande
    Proteins: Structure, Function, and Bioinformatics 89 (4), 375-388 , 2021
    2021
    Citations: 24
  • Biomimetic CO 2 hydration activity of boronic acids
    M Verma, VSP Kumar, S Kumar, PA Deshpande
    Physical Chemistry Chemical Physics 23 (15), 9561-9570 , 2021
    2021
  • Comparison of Biomolecular Force-fields and High Temperature Molecular Dynamics Simulations for Thermostable SazCA
    S Kumara, PA Deshpande
    2019
  • Comparison of force fields for structure and dynamics of carbonic anhydrase isozymes
    S Kumar, D Seth, P Deshpande
    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 258 , 2019
    2019
  • Computational Insights into Carbonic Anhydrase Action
    S Kumar, PA Deshpande
    2018
  • Slip-enhanced flow through thin packed column with superhydrophobic wall
    T Saha, S Kumar, SK Bhaumik
    Sensors and Actuators B: Chemical 240, 468-476 , 2017
    2017
    Citations: 18
  • Minimizing axial dispersion in narrow packed column using superhydrophobic wall
    T Saha, S Kumar, SK Bhaumik
    Korean Journal of Chemical Engineering 33 (12), 3337-3342 , 2016
    2016
    Citations: 6
  • Treatment of pulp and paper mill effluents using novel biodegradable polymeric flocculants based on anionic polysaccharides: a new way to treat the waste water
    S Kumar, T Saha, S Sharma
    Int Res J Eng Technol 2 (4), 1-14 , 2015
    2015
    Citations: 29
  • Methane clathrate: dirty fuel or energy savior: a new form of ice to store energy
    S Kumar
    International Research Journal of Engineering Technology 2, 1429-1438 , 2015
    2015
    Citations: 5
  • LOTUS-LEAF EFFECT AND ITS APPLICATION IN DRAG REDUCTION
    S Kumar, T Saha, A Das, SK Bhaumik
    2015

MOST CITED SCHOLAR PUBLICATIONS

  • Hydrothermal conversion of lignin to substituted phenols and aromatic ethers
    R Singh, A Prakash, SK Dhiman, B Balagurumurthy, AK Arora, SK Puri, ...
    Bioresource technology 165, 319-322 , 2014
    2014
    Citations: 169
  • Structural and thermodynamic analysis of factors governing the stability and thermal folding/unfolding of SazCA
    S Kumar, PA Deshpande
    PLoS One 16 (4), e0249866 , 2021
    2021
    Citations: 31
  • Treatment of pulp and paper mill effluents using novel biodegradable polymeric flocculants based on anionic polysaccharides: a new way to treat the waste water
    S Kumar, T Saha, S Sharma
    Int Res J Eng Technol 2 (4), 1-14 , 2015
    2015
    Citations: 29
  • Molecular dynamics simulations identify the regions of compromised thermostability in SazCA
    S Kumar, D Seth, PA Deshpande
    Proteins: Structure, Function, and Bioinformatics 89 (4), 375-388 , 2021
    2021
    Citations: 24
  • Slip-enhanced flow through thin packed column with superhydrophobic wall
    T Saha, S Kumar, SK Bhaumik
    Sensors and Actuators B: Chemical 240, 468-476 , 2017
    2017
    Citations: 18
  • High-Throughput Ligand Dissociation Kinetics Predictions Using Site Identification by Ligand Competitive Saturation
    W Yu, S Kumar, M Zhao, DJ Weber, AD MacKerell Jr
    Journal of Chemical Theory and Computation 21 (9), 4964-4978 , 2025
    2025
    Citations: 8
  • Minimizing axial dispersion in narrow packed column using superhydrophobic wall
    T Saha, S Kumar, SK Bhaumik
    Korean Journal of Chemical Engineering 33 (12), 3337-3342 , 2016
    2016
    Citations: 6
  • Unravelling and quantifying the biophysical–biochemical descriptors governing protein thermostability by machine learning
    S Kumar, VK Duggineni, V Singhania, SP Misra, PA Deshpande
    Advanced Theory and Simulations 6 (3), 2200703 , 2023
    2023
    Citations: 5
  • Methane clathrate: dirty fuel or energy savior: a new form of ice to store energy
    S Kumar
    International Research Journal of Engineering Technology 2, 1429-1438 , 2015
    2015
    Citations: 5
  • Enzyme–substrate interactions in orotate-mimetic OPRT inhibitor complexes: a QM/MM analysis
    S Kumar, NNS Rao, KP Reddy, MC Padole, PA Deshpande
    Physical Chemistry Chemical Physics 25 (4), 3472-3484 , 2023
    2023
    Citations: 4
  • Computational analysis of the effect of Gly100Ala mutation on the thermostability of SazCA
    S Kumar, S Biswas, PA Deshpande
    Journal of Biomolecular Structure and Dynamics 41 (21), 12363-12371 , 2023
    2023
    Citations: 1
  • Efficient proton shuttle makes SazCA an excellent CO 2 hydration enzyme
    S Kumar, PA Deshpande
    Journal of Biomolecular Structure and Dynamics 41 (13), 6001-6010 , 2023
    2023
    Citations: 1
  • Unravelling the self-assembly of a novel cationic pseudo-gemini surfactant and its monomeric counterpart: interactions with DNA and BSA in aqueous medium at neutral pH
    H Dahal, S Soren, S Kumar, J Dey
    Soft Matter 21 (27), 5515-5528 , 2025
    2025
  • Computational study of ligand dissociation pathways and free-energy barriers using the site-identification by ligand competitive saturation (SILCS) method
    W Yu, S Kumar, M Zhao, AD MacKerell
    Biophysical Journal 123 (3), 471a , 2024
    2024
  • Development of SILCS kinetics methodology for the determination of ligand dissociation pathways and free energy barriers
    S Kumar, M Zhao, AD MacKerell Jr
    2023
  • Development of SILCS Kinetics Methodology for the Determination of Ligand Dissociation Pathways and Free Energy Barriers
    K Shashi, A D. MacKerell Jr
    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY , 2023
    2023
  • Biomimetic CO 2 hydration activity of boronic acids
    M Verma, VSP Kumar, S Kumar, PA Deshpande
    Physical Chemistry Chemical Physics 23 (15), 9561-9570 , 2021
    2021
  • Comparison of Biomolecular Force-fields and High Temperature Molecular Dynamics Simulations for Thermostable SazCA
    S Kumara, PA Deshpande
    2019
  • Comparison of force fields for structure and dynamics of carbonic anhydrase isozymes
    S Kumar, D Seth, P Deshpande
    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 258 , 2019
    2019
  • Computational Insights into Carbonic Anhydrase Action
    S Kumar, PA Deshpande
    2018