Puneet Kumar

I hold a degree in Biomedical Engineering and have developed into a Computational Biologist through years of interdisciplinary research and hands-on scientific experience. My work lies at the intersection of computational chemistry, structural biology, and drug discovery, where I integrate physics-based simulations with data-driven approaches to understand biomolecular mechanisms and accelerate therapeutic design.

My expertise includes molecular dynamics simulations using platforms such as GROMACS and Desmond, advanced free energy methodologies including QM/MM calculations, free energy perturbation (FEP), and metadynamics, as well as both structure- and ligand-based drug design strategies. I also apply machine learning techniques for QSAR modeling, virtual screening, and predictive analysis to identify and optimize novel therapeutic candidates.

EDUCATION

Integrated Master of Technology (M.Tech.) in Biomedical Engineering from Indian Institute of Information Technology Allahabad, India
Doctor of Philosophy ( in Computational Biology from Indian Institute of Technology Roorkee, India

RESEARCH, TEACHING, or OTHER INTERESTS

Drug Discovery, Biomedical Engineering, Cancer Research, Biophysics

Scopus Publications

An in-silico study reveals that a C-terminal fragment of the adhesion protein Fibulin7 (Fbln7-C) regulates the activation of integrin α5β1 through dynamics of VWA and the hybrid domain in the β1 subunit
Puneet Kumar, Shubham Kumar Rai, Pranita P. Sarangi
Journal of Biomolecular Structure and Dynamics, 2026
Fibulin-7 and its bioactive fragments: emerging immunomodulatory roles in disease
Saloni Gupta, Puneet Kumar, Pranita P. Sarangi
Inflammation Research, 2025
The neuroprotective role of chlorogenic acid and Fisetin in differentiated neuronal cell line-SHSY5Y against amyloid-β-induced neurotoxicity
Apoorv Sharma, Puneet Kumar, Asimul Islam, Monika Bhardwaj, Vijay Kumar, et al.
Toxicology in Vitro, 2025
Unraveling the molecular basis for effective regulation of integrin α5β1 for enhanced therapeutic interventions
Puneet Kumar, Prerna Sharma, Divya Singh, Nidhi Mishra, Pranita P. Sarangi
Biochemical and Biophysical Research Communications, 2024
Integrins a5b1 and avb3 Differentially Participate in the Recruitment and Reprogramming of Tumor-associated Macrophages in the In Vitro and In Vivo Models of Breast Tumor
Nibedita Dalpati, Shubham Kumar Rai, Shiba Prasad Dash, Puneet Kumar, Divya Singh, et al.
Journal of Immunology, 2024
Tumor-associated macrophages (TAMs) drive the protumorigenic responses and facilitate tumor progression via matrix remodeling, angiogenesis, and immunosuppression by interacting with extracellular matrix proteins via integrins. However, the expression dynamics of integrin and its correlation with TAM functional programming in the tumors remain unexplored. In this study, we examined surface integrins’ role in TAM recruitment and phenotypic programming in a 4T1-induced murine breast tumor model. Our findings show that integrin α5β1 is upregulated in CD11b+Ly6Chi monocytes in the bone marrow and blood by day 10 after tumor induction. Subsequent analysis revealed elevated integrin α5β1 expression on tumor-infiltrating monocytes (Ly6ChiMHC class II [MHCII]low) and M1 TAMs (F4/80+Ly6ClowMHCIIhi), whereas integrin αvβ3 was predominantly expressed on M2 TAMs (F4/80+Ly6ClowMHCIIlow), correlating with higher CD206 and MERTK expression. Gene profiling of cells sorted from murine tumors showed that CD11b+Ly6G−F4/80+α5+ TAMs had elevated inflammatory genes (IL-6, TNF-α, and STAT1/2), whereas CD11b+Ly6G−F4/80+αv+ TAMs exhibited a protumorigenic phenotype (IL-10, Arg1, TGF-β, and STAT3/6). In vitro studies demonstrated that blocking integrin α5 and αv during macrophage differentiation from human peripheral blood monocytes reduced cell spreading and expression of CD206 and CD163 in the presence of specific matrix proteins, fibronectin, and vitronectin. Furthermore, RNA sequencing data analysis (GEO dataset: GSE195857) from bone marrow–derived monocytes and TAMs in 4T1 mammary tumors revealed differential integrin α5 and αv expression and their association with FAK and SRC kinase. In line with this, FAK inhibition during TAM polarization reduced SRC, STAT1, and STAT6 phosphorylation. In conclusion, these findings underscore the crucial role of integrins in TAM recruitment, polarization, and reprogramming in tumors.
In silico identification and characterization of small-molecule inhibitors specific to RhoG/Rac1 signaling pathway
Pankaj Dipankar, Puneet Kumar, Pranita P. Sarangi
Journal of Biomolecular Structure and Dynamics, 2023
A C-terminal fragment of adhesion protein fibulin-7 inhibits growth of murine breast tumor by regulating macrophage reprogramming
Papiya Chakraborty, Shiba Prasad Dash, Nibedita Dalpati, Puneet Kumar, Deepali Jain, et al.
FEBS Journal, 2021
Recent reports have shown that a C‐terminal fragment of adhesion protein Fibulin7 (Fbln7‐C) could demonstrate both antiangiogenic and anti‐inflammatory activities. The current study investigated the potential of Fbln7‐C as a modulator of tumor‐associated macrophages (TAMs) and its potential as an anticancer therapeutic. Our in vitro data show that Fbln7‐C could inhibit the tumor cell line (MDA‐MB‐231) supernatant‐induced reprogramming of human monocytes into immunosuppressive TAMs as indicated by higher expression of pERK1/2 and pSTAT1 molecules, and reduced expression of CD206 protein and arg1, ido, and vegf transcripts in monocytes cultured in the presence of Fbln7‐C compared to controls. Interestingly, Fbln7‐C‐treated macrophages retained their altered phenotype even after the removal of Fbln7‐C, and their secretome demonstrated anticancer activities. Finally, in a 4T1‐induced murine breast tumor model, intravenous administration of Fbln7‐C, following the appearance of measurable tumors, significantly reduced the growth and weight of the tumors. Detailed phenotypic analysis of the infiltrated monocyte/macrophage populations (F480+Ly6G−CD11b+) at day 23 postinduction showed a higher percentage of inflammatory monocytes (F480+Ly6ChiCD11b+) and a delayed differentiation into anti‐inflammatory TAMs as evident by their reduced levels of CD206 expression. In conclusion, the above data suggest that Fbln7‐C could regulate the tumor environment‐induced macrophage reprogramming and has the potential for cancer therapeutics.
Functional and therapeutic relevance of Rho GTPases in innate immune cell migration and function during inflammation: An in silico perspective
Pankaj Dipankar, Puneet Kumar, Shiba Prasad Dash, Pranita P. Sarangi
Mediators of Inflammation, 2021
Systematic regulation of leukocyte migration to the site of infection is a vital step during immunological responses. Improper migration and localization of immune cells could be associated with disease pathology as seen in systemic inflammation. Rho GTPases act as molecular switches during inflammatory cell migration by cycling between Rho‐GDP (inactive) to Rho‐GTP (active) forms and play an essential role in the precise regulation of actin cytoskeletal dynamics as well as other immunological functions of leukocytes. Available reports suggest that the dysregulation of Rho GTPase signaling is associated with various inflammatory diseases ranging from mild to life‐threatening conditions. Therefore, it is crucial to understand the step‐by‐step activation and inactivation of GTPases and the functioning of different Guanine Nucleotide Exchange Factors (GEFs) and GTPase‐Activating Proteins (GAPs) that regulate the conversion of GDP to GTP and GTP to GDP exchange reactions, respectively. Here, we describe the molecular organization and activation of various domains of crucial elements associated with the activation of Rho GTPases using solved PDB structures. We will also present the latest evidence available on the relevance of Rho GTPases in the migration and function of innate immune cells during inflammation. This knowledge will help scientists design promising drug candidates against the Rho‐GTPase‐centric regulatory molecules regulating inflammatory cell migration.
A C-terminal fragment of adhesion protein Fibulin7 regulates neutrophil migration and functions and improves survival in LPS induced systemic inflammation
Papiya Chakraborty, Nibedita Dalpati, Chandra Bhan, Shiba Prasad Dash, Puneet Kumar, et al.
Cytokine, 2020
Investigation of Extracellular Matrix Protein Expression Dynamics Using Murine Models of Systemic Inflammation
Chandra Bhan, Shiba Prasad Dash, Pankaj Dipankar, Puneet Kumar, Papiya Chakraborty, et al.
Inflammation, 2019
Advanced acuity in microbial biofilm genesis, development, associated clinical infections and control
P. Kumar, S. Mishra, S. Singh
Journal Des Anti Infectieux, 2017
Structural analysis of protein lysyl oxidase: Modelling and simulation study
Journal of Biotech Research, 2017

RECENT SCHOLAR PUBLICATIONS

AI in designing novel cancer treatments
P Kumar, M Umar, A Naeem, E Khan
Artificial Intelligence for Enhanced Diagnosis in Oncology, 149-168 , 2026
2026
Fibulin-7 and its bioactive fragments: emerging immunomodulatory roles in disease
S Gupta, P Kumar, PP Sarangi
Inflammation Research 74 (1), 101 , 2025
2025
Citations: 2
The neuroprotective role of chlorogenic acid and Fisetin in differentiated neuronal cell line-SHSY5Y against amyloid-β-induced neurotoxicity
A Sharma, P Kumar, A Islam, M Bhardwaj, V Kumar, H Prakash
Toxicology in Vitro, 106110 , 2025
2025
Citations: 1
An in-silico study reveals that a C-terminal fragment of the adhesion protein Fibulin7 (Fbln7- C) regulates the activation of integrin α5β1 through dynamics of VWA and the …
P Kumar, SK Rai, PP Sarangi
Journal of Biomolecular Structure and Dynamics, 1-20 , 2024
2024
Citations: 4
Unraveling the molecular basis for effective regulation of integrin α5β1 for enhanced therapeutic interventions
P Kumar, P Sharma, D Singh, N Mishra, PP Sarangi
Biochemical and Biophysical Research Communications 734 (150627) , 2024
2024
Citations: 5
Integrins α5β1 and αvβ3 Differentially Participate in the Recruitment and Reprogramming of Tumor-associated Macrophages in the In Vitro and In Vivo Models of Breast Tumor
N Dalpati, SK Rai, SP Dash, P Kumar, D Singh, PP Sarangi
The Journal of Immunology , 2024
2024
Citations: 14
In silico identification and characterization of small-molecule inhibitors specific to RhoG/Rac1 signaling pathway
P Dipankar, P Kumar, PP Sarangi
Journal of biomolecular structure and dynamics 41 (2), 560-580 , 2023
2023
Citations: 16
Functional and Therapeutic Relevance of Rho GTPases in Innate Immune Cell Migration and Function during Inflammation: An In Silico Perspective
P Dipankar, P Kumar, SP Dash, PP Sarangi
Mediators of inflammation 2021 (1), 6655412 , 2021
2021
Citations: 31
A C-terminal fragment of adhesion protein Fibulin7 regulates neutrophil migration and functions and improves survival in LPS induced systemic inflammation
P Chakraborty, N Dalpati, C Bhan, SP Dash, P Kumar, PP Sarangi
Cytokine 131 (155113) , 2020
2020
Citations: 10
AC‐terminal fragment of adhesion protein fibulin‐7 inhibits growth of murine breast tumor by regulating macrophage reprogramming
P Chakraborty, SP Dash, N Dalpati, P Kumar, D Jain, PP Sarangi
The FEBS journal 288 (3), 803-817 , 2020
2020
Citations: 17
Investigation of extracellular matrix protein expression dynamics using murine models of systemic inflammation
C Bhan, SP Dash, P Dipankar, P Kumar, P Chakraborty, PP Sarangi
Inflammation 42 (6), 2020-2031 , 2019
2019
Citations: 13
Novel drug delivery system for herbal formulation in cancer treatment
D Mishra, G Panda, P Kumar, S Singh
World Journal of Pharmaceutical Research 6 (15), 341-353 , 2017
2017
Citations: 10
Advanced acuity in microbial biofilm genesis, development, associated clinical infections and control
P Kumar, S Mishra, S Singh
Journal des Anti-infectieux 19 (1), 20-31 , 2017
2017
Citations: 8
Structural analysis of protein lysyl oxidase: modelling and simulation study
S Mishra, P Kumar, S Singh
Journal of Biotech Research 8, 9 , 2017
2017
Citations: 5

MOST CITED SCHOLAR PUBLICATIONS

Functional and Therapeutic Relevance of Rho GTPases in Innate Immune Cell Migration and Function during Inflammation: An In Silico Perspective
P Dipankar, P Kumar, SP Dash, PP Sarangi
Mediators of inflammation 2021 (1), 6655412 , 2021
2021
Citations: 31
AC‐terminal fragment of adhesion protein fibulin‐7 inhibits growth of murine breast tumor by regulating macrophage reprogramming
P Chakraborty, SP Dash, N Dalpati, P Kumar, D Jain, PP Sarangi
The FEBS journal 288 (3), 803-817 , 2020
2020
Citations: 17
In silico identification and characterization of small-molecule inhibitors specific to RhoG/Rac1 signaling pathway
P Dipankar, P Kumar, PP Sarangi
Journal of biomolecular structure and dynamics 41 (2), 560-580 , 2023
2023
Citations: 16
Integrins α5β1 and αvβ3 Differentially Participate in the Recruitment and Reprogramming of Tumor-associated Macrophages in the In Vitro and In Vivo Models of Breast Tumor
N Dalpati, SK Rai, SP Dash, P Kumar, D Singh, PP Sarangi
The Journal of Immunology , 2024
2024
Citations: 14
Investigation of extracellular matrix protein expression dynamics using murine models of systemic inflammation
C Bhan, SP Dash, P Dipankar, P Kumar, P Chakraborty, PP Sarangi
Inflammation 42 (6), 2020-2031 , 2019
2019
Citations: 13
A C-terminal fragment of adhesion protein Fibulin7 regulates neutrophil migration and functions and improves survival in LPS induced systemic inflammation
P Chakraborty, N Dalpati, C Bhan, SP Dash, P Kumar, PP Sarangi
Cytokine 131 (155113) , 2020
2020
Citations: 10
Novel drug delivery system for herbal formulation in cancer treatment
D Mishra, G Panda, P Kumar, S Singh
World Journal of Pharmaceutical Research 6 (15), 341-353 , 2017
2017
Citations: 10
Advanced acuity in microbial biofilm genesis, development, associated clinical infections and control
P Kumar, S Mishra, S Singh
Journal des Anti-infectieux 19 (1), 20-31 , 2017
2017
Citations: 8
Unraveling the molecular basis for effective regulation of integrin α5β1 for enhanced therapeutic interventions
P Kumar, P Sharma, D Singh, N Mishra, PP Sarangi
Biochemical and Biophysical Research Communications 734 (150627) , 2024
2024
Citations: 5
Structural analysis of protein lysyl oxidase: modelling and simulation study
S Mishra, P Kumar, S Singh
Journal of Biotech Research 8, 9 , 2017
2017
Citations: 5
An in-silico study reveals that a C-terminal fragment of the adhesion protein Fibulin7 (Fbln7- C) regulates the activation of integrin α5β1 through dynamics of VWA and the …
P Kumar, SK Rai, PP Sarangi
Journal of Biomolecular Structure and Dynamics, 1-20 , 2024
2024
Citations: 4
Fibulin-7 and its bioactive fragments: emerging immunomodulatory roles in disease
S Gupta, P Kumar, PP Sarangi
Inflammation Research 74 (1), 101 , 2025
2025
Citations: 2
The neuroprotective role of chlorogenic acid and Fisetin in differentiated neuronal cell line-SHSY5Y against amyloid-β-induced neurotoxicity
A Sharma, P Kumar, A Islam, M Bhardwaj, V Kumar, H Prakash
Toxicology in Vitro, 106110 , 2025
2025
Citations: 1
AI in designing novel cancer treatments
P Kumar, M Umar, A Naeem, E Khan
Artificial Intelligence for Enhanced Diagnosis in Oncology, 149-168 , 2026
2026