Kalyan Giri

Assistant Professor

About-

My Research interest is to build a significant research program on the structure and function of different viral proteins and their role in viral pathogenesis like HIV-1 and Dengue virus among many others. The HIV-1 genome encodes four accessory proteins that include Vif, Nef, Vpu and Vpr. These proteins employ an array of strategies to manipulate host cellular factors and distinguish HIV-1 as a complex retrovirus. The goal of this research is to determine the mechanisms by which HIV accessory proteins recruit their cellular binding partners, pinpoint the molecular interactions that stabilize the virus-host protein complexes, and develop strategies to screen for molecules that have inhibitory potential against these viral proteins. My focus is also on the study of conformational dynamics of the dengue virus proteins and the multiple roles they play in different stages of the dengue virus life cycle using enhanced sampling methods. I am also interested in developing novel computational tools for virtual screening against the Dengue virus proteins in order to inhibit their pathogenic functions.I am also interested on designing of peptide based vaccines to target the various viral surface proteins utilizing the host immune system besides major focus on designing, development and optimization of novel molecules with therapeutic potential as well repurposing of available FDA approved drugs against a myriad of virus proteins in order to curb their infective potential.

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Biography+

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Teaching / Other Experience+

Post Graduate Supervision+

Academic Memberships+

Publications+

Chaudhuri D, Ghosh M, Majumder S. Giri K (2024) Repurposing of FDA?approved drugs against oligomerization domain of dengue virus NS1 protein: a computational approach. Molecular Diversity https://doi.org/10.1007/s11030-024-10936-3

Chaudhuri D, Majumder S, Datta J, Giri K (2024) Repurposing of therapeutic antibodies against dengue virus envelope protein receptor binding domain. Archives of Microbiology 206(7):312.

Dey D, Chakravarti R, Bhattacharjee O, Majumder S, Chaudhuri D, Ahmed KT, Roy D, Bhattacharya B, Arya M, Gautam A, Singh R, Gupta R, Ravichandiran V, Chattopadhyay D, Ghosh A, Giri K, Roy S, Ghosh D (2024) A mechanistic study on the tolerance of PAM distal end mismatch by SpCas9. Journal of Biological Chemistry 300(7):107439.

Chaudhuri D, Datta J, Majumder S, Giri K (2024) Peptide based vaccine designing against endemic causing mammarenavirus using reverse vaccinology approach. Archives of Microbiology 206(5):217.

Majumder S, Deganutti G, Pipitò L, Chaudhuri D, Datta J, Giri K (2024) Computational Insights into the Conformational Dynamics of HIV-1 Vpr in a Lipid Bilayer for Ion Channel Modeling. Journal of Chemical Information and Modeling 64(8):3360-3374.

Chaudhuri D, Majumder S, Giri K (2024) Repurposing of drugs targeting heparan sulphate binding site of dengue virus envelope protein: an in silico competitive binding study. Molecular Diversity doi: 10.1007/s11030-024-10834-8.

Chaudhuri D, Datta J, Majumder S. Giri K (2024) In Silico Designing of Antimicrobial Peptide Cocktail Drug Against SARS-CoV-1 and SARS-CoV-2 Replisome Complex. Proc. Natl. Acad. Sci., India, Sect. B Biol. Sci. 94, 145–159.

Chaudhuri D, Majumder S, Datta J, Giri K. (2023) In silico designing of an epitope-based peptide vaccine cocktail against Nipah virus: an Indian population-based epidemiological study. Archives of Microbiology 205(12):380.

Chaudhuri D, Majumder S, Datta J, Giri K (2023) Exploring the chemical space for potential inhibitors against cell surface binding protein of Mpox virus using molecular fingerprint based screening approach. Journal of Biomolecular Structure and Dynamics doi: 10.1080/07391102.2023.2238087.

Majumder S, Deganutti G, Pipitò L, Chaudhuri D, Datta J, Giri K (2023) Computer-aided de novo design and optimization of novel potential inhibitors of HIV-1 Nef protein. Computational Biology and Chemistry 104:107871.

Chaudhuri D, Datta J, Majumder S, Giri K (2023) Repurposing of drug molecules from FDA database against Hepatitis C virus E2 protein using ensemble docking approach. Molecular Diversity doi: 10.1007/s11030-023-10646-2.

Datta J, Majumder S, Chaudhuri D, Giri K (2023) In silico investigation of binding propensity of hematoxylin derivative and damnacanthal for their potential inhibitory effect on HIV-1 Vpr from different subtypes. Journal of Biomolecular Structure and Dynamics 41(24):14977-14988.

Chaudhuri D, Majumder S, Datta J, Giri K (2023) Designing of nanobodies against Dengue virus Capsid: a computational affinity maturation approach. Journal of Biomolecular Structure and Dynamics 41(6):2289-2299.

Sarkar D, Majumder S, Giri K, Sabnam N (2022) In silico characterization, molecular docking, and dynamic simulation of a novel fungal cell-death suppressing effector, MoRlpA as potential cathepsin B-like cysteine protease inhibitor during rice blast infection. Journal of Biomolecular Structure and Dynamics 41(18):9039-9056.

Saha J, Chaudhuri D, Kundu A, Bhattacharya S, Roy S, Giri K (2023) Phylogenetic, structural, functional characterisation and effect of exogenous spermidine on rice (Oryza sativa) HAK transporters under salt stress. Functional Plant Biology 50(2):160-182.

Chaudhuri D, Datta J, Majumder S, Giri K (2022) In silico study on miRNA regulation and NSs protein interactome characterization of the SFTS virus. Journal of Molecular Graphics and Modelling 117:108291.

Chaudhuri D, Datta J, Majumder S, Giri K (2022) Prediction of infectivity of SARS-CoV-2 virus based on Spike-hACE-2 interaction. VirusDisease 33(3):244-250.

Majumder S, Giri K (2022) An insight into the binding mechanism of Viprinin and its morpholine and piperidine derivatives with HIV-1 Vpr: molecular dynamics simulation, principal component analysis and binding free energy calculation study. Journal of Biomolecular Structure and Dynamics 40(21):10918-10930.

Chaudhuri D, Majumder S, Datta J, Giri K (2021) In Silico Study of Mutational Stability of SARS-CoV-2 Proteins. The Protein Journal 40(3):328-340.

Majumder S, Chaudhuri D, Datta J, Giri K (2021) Exploring the intrinsic dynamics of SARS-CoV-2, SARS-CoV and MERS-CoV spike glycoprotein through normal mode analysis using anisotropic network model. Journal of Molecular Graphics and Modelling 102:107778.

Saha J, Giri K, Roy S (2020) Identification and characterization of differentially expressed genes in the rice root following exogenous application of spermidine during salt stress. Genomics 112(6):4125-4136.

Chaudhuri D, Datta J, Majumder S, Giri K (2020) In silico designing of peptide based vaccine for Hepatitis viruses using reverse vaccinology approach. Infection Genetics and Evolution 84:104388.

Saha J, Giri K (2017) Molecular phylogenomic study and the role of exogenous spermidine in the metabolic adjustment of endogenous polyamine in two rice cultivars under salt stress. Gene 609:88-103.

Ghosh U, Giri K, Bhattacharyya NP (2009) Interaction of aurintricarboxylic acid (ATA) with four nucleic acid binding proteins DNase I, RNase A, reverse transcriptase and Taq polymerase. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 74(5):1145-51.

Giri K, Scott RA, Maynard EL (2009) Molecular structure and biochemical properties of the HCCH-Zn2+ site in HIV-1 Vif. Biochemistry 48(33):7969-78.

Giri K, Maynard EL (2009) Conformational analysis of a peptide approximating the HCCH motif in HIV-1 Vif. Biopolymers 92(5):417-25.

Raychaudhuri S, Majumder P, Sarkar S, Giri K, Mukhopadhyay D, Bhattacharyya NP (2008) Huntingtin interacting protein HYPK is intrinsically unstructured. Proteins. 2008 71(4):1686-98.

Giri K, Bhattacharyya NP, Basak S (2007) pH-dependent self-assembly of polyalanine peptides. Biophysical Journal 92(1):293-302.

Giri K, Ghosh U, Bhattacharyya NP, Basak S (2003) Caspase 8 mediated apoptotic cell death induced by beta-sheet forming polyalanine peptides. FEBS Letters 555(2):380-4.

Address

Presidency University,
86/1 College Street, Kolkata - 700073,
West Bengal, India

CV Not Available
Email: kalyan.biochem at presiuniv.ac.in
alternate E-mail: kalyan.giri at gmail.com

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