Publications

2023

1. Singh, V.K., Thakur, D.C., Rajak, N., Giri, R. and Garg, N., 2023. Immunomodulatory potential of bioactive glycoside syringin: a network pharmacology and molecular modeling approach. Journal of Biomolecular Structure and Dynamics, pp.1-14.

2. Kumar, A., Kumar, P., Mishra, P.M. and Giri, R., 2023. Investigating the folding dynamics of NS2B protein of Zika virus. Virology.

3. Bhardwaj, T., Gadhave, K., Kapuganti, S.K. et al. Amyloidogenic proteins in the SARS-CoV and SARS-CoV-2 proteomes. Nat Commun 14, 945 (2023). https://doi.org/10.1038/s41467-023-36234-4

2022

1. Kumar, A., Kumar, P., Mishra, P. M., & Giri, R. (2022). Investigating the folding dynamics of NS2B protein of Zika virus. bioRxiv, 2022-12.

4. Kumar, A. A., Kumar, D., Jose, J., Giri, R., & Mysorekar, I. U. (2022). Drugs to limit Zika virus infection and implication for maternal-fetal health. Frontiers in Virology, 64.

5. Kumar, A., Kumar, D., Kumar, P., Jones, B. L., Mysorekar, I. U., & Giri, R. (2022). Discovery And Characterization of Small Molecule Inhibitors of Zika Virus Replication. bioRxiv, 2022-12.

6. Bhardwaj, T., Kumar, P., & Giri, R. (2022). Investigating the conformational dynamics of Zika virus NS4B protein. Virology.

7. Kapuganti, S. K., Bhardwaj, A., Nayak, N., Bhardwaj, T., Kumar, P., & Giri, R. (2022). Vaccine Omics: role of bioinformatics in vaccinology. System Vaccinology: The History, the Translational Challenges and the Future, 33.

8. Yadav, P., Beura, S. K., Panigrahi, A. R., Bhardwaj, T., Giri, R., & Singh, S. K. (2022). Platelet-derived microvesicles activate human platelets via intracellular calcium mediated reactive oxygen species release. Blood Cells, Molecules, and Diseases, 102701.

9. Kumar, A. A., Kumar, D., Jose, J., Giri, R., & Mysorekar, I. U. Drugs to limit Zika virus infection and implication for maternal-fetal health. Frontiers in Virology, 64.

10. Kapuganti, S. K., Bhardwaj, A., Kumar, P., Bhardwaj, T., Nayak, N., Uversky, V. N., & Giri, R. (2022). Role of structural disorder in the multi-functionality of flavivirus proteins. Expert Review of Proteomics, DOI: 10.1080/14789450.2022.2085563.

11. Singh, A., Kumar, P., Sarvagalla, S., Bharadwaj, T., Nayak, N., Coumar, M.S., Giri, R. and Garg, N. (2022). Functional inhibition of c-Myc using novel inhibitors identified through “hot spot” targeting. Journal of Biological Chemistry, 298(5).

12. Gehi, B. R., Gadhave, K., Uversky, V. N., & Giri, R. (2022). Intrinsic disorder in proteins associated with oxidative stress-induced JNK signaling. Cellular and Molecular Life Sciences, 79(4), 1-32.

13. Bhardwaj, A., Kumar, P., Kapuganti, S. K., Uversky, V. N., & Giri, R. (2022). Coronavirus Epidemics and the Current COVID-19 Pandemic. COVID-19: From Bench to Bedside.

14. Kumar, P., Bhardwaj, T., & Giri, R. (2022). Mitoxantrone dihydrochloride, an FDA approved drug, binds with SARS-CoV-2 NSP1 C-terminal. RSC Advances, 12(9), 5648-5655.

15. Sharma, N., Gadhave, K., Kumar, P., & Giri, R. (2022). Transactivation domain of Adenovirus Early Region 1A (E1A): Investigating folding dynamics and aggregation. Current Research in Structural Biology.

16. Nag, N., Chetri, P. B., Uversky, V. N., Giri, R., & Tripathi, T. (2022). Experimental methods to study intrinsically disordered proteins. In Advances in Protein Molecular and Structural Biology Methods (pp. 505-533). Academic Press.

17. Kumar, P., Bhardwaj, A., Uversky, V. N., Tripathi, T., & Giri, R. (2022). Computational methods to study intrinsically disordered proteins. In Advances in Protein Molecular and Structural Biology Methods (pp. 489-504). Academic Press.

18. Kumar, P., Bhardwaj, T., Garg, N., & Giri, R. (2022). Microsecond simulations and CD spectroscopy reveals the intrinsically disordered nature of SARS-CoV-2 spike-C-terminal cytoplasmic tail (residues 1242–1273) in isolation. Virology, 566, 42-55.

2021

1. 1. Bhardwaj, T., Kumar, P., & Giri, R. (2021). Investigating the conformational dynamics of Zika virus NS4B protein. bioRxiv.

   2. Gadhave, K., Bhardwaj, T., Uversky, V. N., Vendruscolo, M., & Giri, R. (2021). The signal peptide of the amyloid precursor protein forms amyloid-like aggregates and enhances Aβ42 aggregation. Cell Reports Physical Science, 100599.

   3. Kumar, A., Kumar, P., Saumya, K. U., & Giri, R. (2021). Investigating the conformational dynamics of SARS-CoV-2 NSP6 protein with emphasis on non-transmembrane 91-112 & 231-290 regions. Microbial Pathogenesis, 105236.

   4. Singh, A., Singh, A. K., Giri, R., Kumar, D., Sharma, R., Valis, M., ... & Garg, N. (2021). The role of microRNA-21 in the onset and progression of cancer. Future Medicinal Chemistry, (0).

   5. Kumar, P., Bhardwaj, T., Kumar, A., Garg, N., & Giri, R. (2021). One Microsecond MD simulations of the SARS-CoV-2 main protease and Hydroxychloroquine complex reveal the intricate nature of binding. Journal of Biomolecular Structure and Dynamics. doi: https://dx.doi.org/10.1080/07391102.2021.1948447

   6. Singh A, Kumar A, Kumar P, Nayak N, Bhardwaj T, Giri R, Garg N, A novel inhibitor L755507 efficiently blocks c-Myc/MAX heterodimerization and induces apoptosis in cancer cells, Journal of Biological Chemistry (2021), doi: https://doi.org/10.1016/j.jbc.2021.100903. 

   7. Sharma, N. R., Gadhave, K., Kumar, P., Saif, M., Khan, M. M., Sarkar, D. P., ... & Giri, R. (2021). Analysis of the dark proteome of Chandipura virus reveals maximum propensity for intrinsic disorder in phosphoprotein. Scientific reports, 11(1), 1-17.

   8. Saumya, K. U., Gadhave, K., Kumar, A., & Giri, R. (2021). Zika virus capsid anchor forms cytotoxic amyloid-like fibrils. Virology, 560, 8-16.

   9. Kumar, P., Kumar, A., Garg, N., & Giri, R. (2021). An insight into SARS-CoV-2 membrane protein interaction with spike, envelope, and nucleocapsid proteins. Journal of Biomolecular Structure and Dynamics, 1-10.

   10. Bhardwaj, T., Gadhave, K., Kapuganti, S. K., Kumar, P., Brotzakis, Z. F., Saumya, K. U., ... & Giri, R. (2021). Amyloidogenic proteins in the SARS-CoV and SARS-CoV-2 proteomes. bioRxiv.

   11. Gadhave, K., Kumar, P., Kumar, A., Bhardwaj, T., Garg, N., & Giri, R. (2021). Conformational dynamics of 13 amino acids long NSP11 of SARS-CoV-2 under membrane mimetics and different solvent conditions. Microbial Pathogenesis, 105041.

   12. Singh, A., Kumar, A., Kumar, P., Bhardwaj, T., Giri, R., & Garg, N. (2021). Salvianolic acid B noncovalently interacts with disordered c-Myc: a computational and spectroscopic-based study. Future Medicinal Chemistry, (0).

   13. Gadhave, K., Kapuganti, S. K., Mishra, P. M., & Giri, R. (2021). P53 TAD2 Domain (38-61) Forms Amyloid-like Aggregates in Isolation. bioRxiv.

   14. Kumar, A., Kumar, A., Kumar, P., Garg, N., & Giri, R. (2021). SARS-CoV-2 NSP1 C-terminal (residues 131-180) is an intrinsically disordered region in isolation. . Current Research in Virological Science, 100007.

   15. Kumar, Prateek, Nitin Sharma, Amit Kumar, and Rajanish Giri. "Molecular Dynamic Simulation of Intrinsically Disordered Proteins and Relevant Forcefields." In Innovations and Implementations of Computer Aided Drug Discovery Strategies in Rational Drug Design, pp. 317-333. Springer, Singapore, 2021.

   16. Khan, A. N., Gadhave, K., Furkan, M., Kumar, P., Siddiqi, M. K., Giri, R., & Khan, R. H. (2021). Anti-tuberculotic thionamide antibiotics show antioxidative and neuronal cytoprotective nature by inhibiting amyloid formation in human insulin and amyloid β-42. Journal of Molecular Liquids, 326, 115396.

   17. Salehi, Bahare, Javad Sharifi-Rad, Patrick Valere Tsouh Fokou, Gail B. Mahady, Hafiz Ansar Rasul Suleria, Shivani Krishna Kapuganti, Gadhave et al. "Naturally-Occurring Bioactives as Antivirals: Emphasis on Coronavirus Infection." Frontiers in Pharmacology 12 (2021): 502.

   18. Kumar, Ankur, Prateek Kumar, Murali Aarthy, Sanjeev Kumar Singh, and Rajanish Giri. "Experiments and simulation on ZIKV NS2B-NS3 protease reveal its complex folding." Virology 556 (2021): 110-123.

2020

1. 19. Singh, Ashutosh, Sandesh Kumar Patel, Prateek Kumar, Kanhu Charan Das, Deepanshu Verma, Rohit Sharma, Timir Tripathi, Rajanish Giri, Natália Martins, and Neha Garg. "Quercetin acts as a P-gp modulator via impeding signal transduction from nucleotide-binding domain to transmembrane domain." Journal of Biomolecular Structure and Dynamics (2020): 1-9.

   20. Kumar, Deepak, Ankur Kumar, Taniya Bhardwaj, and Rajanish Giri. "Zika virus NS4A N-Terminal region (1-48) acts as a cofactor for inducing NTPase activity of NS3 helicase but not NS3 protease." Archives of Biochemistry and Biophysics 695 (2020): 108631.

   21. Kumar, Prateek, Taniya Bhardwaj, Ankur Kumar, Bhuvaneshwari R. Gehi, Shivani K. Kapuganti, Neha Garg, Gopal Nath, and Rajanish Giri. "Reprofiling of approved drugs against SARS-CoV-2 main protease: an in-silico study." Journal of Biomolecular Structure and Dynamics (2020): 1-15.

   22. Kumar, Ankur, Prateek Kumar, and Rajanish Giri. "Zika virus NS4A cytosolic region (residues 1–48) is an intrinsically disordered domain and folds upon binding to lipids." Virology 550 (2020): 27-36.

   23. Saumya, Kumar Udit, Deepak Kumar, Prateek Kumar, and Rajanish Giri. "Unlike dengue virus, the conserved 14–23 residues in N-terminal region of Zika virus capsid is not involved in lipid interactions." Biochimica et Biophysica Acta (BBA)-Biomembranes 1862, no. 11 (2020): 183440.

   24. Sharma, Nitin, Oliver Prosser, Prateek Kumar, Andrew Tuplin, and Rajanish Giri. "Small molecule inhibitors possibly targeting the rearrangement of Zika virus envelope protein." Antiviral Research 182 (2020): 104876.

   25. Kumar, Amit, Prateek Kumar, Kumar Udit Saumya, Shivani K. Kapuganti, Taniya Bhardwaj, and Rajanish Giri. "Exploring the SARS-CoV-2 structural proteins for multi-epitope vaccine development: an in-silico approach." Expert review of vaccines 19, no. 9 (2020): 887-898.

   26. Bhardwaj, Taniya, Kumar Udit Saumya, Prateek Kumar, Nitin Sharma, Kundlik Gadhave, Vladimir N. Uversky, and Rajanish Giri. "Japanese encephalitis virus–exploring the dark proteome and disorder–function paradigm." The FEBS Journal 287, no. 17 (2020): 3751-3776.

   27. Kumar, Deepak, Pushpendra Mani Mishra, Kundlik Gadhave, and Rajanish Giri. "Conformational dynamics of p53 N-terminal TAD2 region under different solvent conditions." Archives of Biochemistry and Biophysics 689 (2020): 108459.

   28. Gadhave, Kundlik, Deepak Kumar, Vladimir N. Uversky, and Rajanish Giri. "A multitude of signaling pathways associated with Alzheimer's disease and their roles in AD pathogenesis and therapy." Medicinal Research Reviews (2020).

   29. Sharma, Nitin, Prateek Kumar, and Rajanish Giri. "Polysaccharides like pentagalloylglucose, parishin A and stevioside inhibits the viral entry by binding the Zika virus envelope protein." Journal of Biomolecular Structure and Dynamics (2020): 1-13.

   30. Kumar, Deepak, Nitin Sharma, Murali Aarthy, Sanjeev Kumar Singh, and Rajanish Giri. "Mechanistic insights into Zika virus NS3 helicase inhibition by Epigallocatechin-3-gallate." ACS omega 5, no. 19 (2020): 11217-11226.

   31. Gadhave, Kundlik, Prateek Kumar, Shivani K. Kapuganti, Vladimir N. Uversky, and Rajanish Giri. "Unstructured biology of proteins from ubiquitin-proteasome system: roles in cancer and neurodegenerative diseases." Biomolecules 10, no. 5 (2020): 796.

   32. Bramson, Jonathan, Christopher W. Helsen, Galina Denisova, Rajanish Giri, and Kenneth Anthony Mwawasi. "Trifunctional T cell-antigen coupler and methods and uses thereof." U.S. Patent 10,435,453, issued October 8, 2019.

   33. Gadhave, Kundlik, Ankur Kumar, Prateek Kumar, Shivani K. Kapuganti, Neha Garg, Michele Vendruscolo, and Rajanish Giri. "Environmental Dependence of the Structure of the C-terminal Domain of the SARS-CoV-2 Envelope Protein." bioRxiv (2020).

   34. Khrustalev, Vladislav Victorovich, Rajanish Giri, Tatyana Aleksandrovna Khrustaleva, Shivani Krishna Kapuganti, Aleksander Nicolaevich Stojarov, and Victor Vitoldovich Poboinev. "Translation-associated mutational U-pressure in the first ORF of SARS-CoV-2 and other coronaviruses." Frontiers in Microbiology 11 (2020): 2336.

   35. Giri, Rajanish, Taniya Bhardwaj, Meenakshi Shegane, Bhuvaneshwari R. Gehi, Prateek Kumar, Kundlik Gadhave, Christopher J. Oldfield, and Vladimir N. Uversky. "Understanding COVID-19 via comparative analysis of dark proteomes of SARS-CoV-2, human SARS and bat SARS-like coronaviruses." Cellular and Molecular Life Sciences 78, no. 4 (2021): 1655-1688.

   36. A Kumar, P Kumar, S Kumari, VN Uversky, Giri R*. Folding and structural polymorphism of p53 C-terminal domain: One peptide with many conformations. Archives of Biochemistry and Biophysics. 2020 May 15. 

   37. K Gadhave, Giri R*. Amyloid formation by intrinsically disordered trans-activation domain of cMyb. Biochemical and Biophysical Research Communications. 2020 Jan 30. 

   38. R Yadav, C Selvaraj, M Aarthy, P Kumar, A Kumar, SK Singh, Giri R*. Investigating into the molecular interactions of flavonoids targeting NS2B-NS3 protease from ZIKA virus through in-silico approaches. Journal of Biomolecular Structure and Dynamics. 2020 Jan 13.

   39. Mayank, D Kumar, N Kaur*, Giri R* N Singh*. Biscoumarin scaffold as an efficient anti-Zika virus lead with NS3-Helicase inhibitory potential: in-vitro and in-silico Investigation. New Journal of Chemistry. 2020 Jan 3. 

   40. Gadhave K, Gehi BR, Kumar P, Xue B, Uversky VN, Giri R*. The dark side of Alzheimer's disease: unstructured biology of proteins from the amyloid cascade signaling pathway. Cell Mol Life Sci. 2020 Jan 2. 

   41. Khrustalev VV*, Khrustaleva TA, Stojarov AN, Sharma N, Bhaskar B, Giri R Giri R.• The history of mutational pressure changes during the evolution of adeno-associated viruses: A message to gene therapy and DNA-vaccine vectors designers. Infect Genet Evol. 2020 Jan;77:104100.

2019

1. 42. Kumar P, Saumya KU, Giri R*.• Identification of peptidomimetic compounds as potential inhibitors against MurA enzyme of Mycobacterium tuberculosis. J Biomol Struct Dyn. . 2019 Dec 4:1-17

   43. Kumar D, Singh A, Kumar P, Uversky VN, Rao CD*,Giri R*.• Understanding the penetrance of intrinsic protein disorder in rotavirus proteome. Int J Biol Macromol.. 2019 Nov 15. 

   44. Sharma N, Fonin AV, Shpironok OG, Silonov SA, Turoverov KK, Uversky VN, Kuznetsova IM, Giri R*.• Folding perspectives of an intrinsically disordered transactivation domain and its single mutation breaking the folding propensity. Int J Biol Macromol.. 2019 Nov 13. 

   45. Kumar D, Aarthy M, Kumar P, Singh SK, Uversky VN, Giri R*.• Targeting the NTPase site of Zika virus NS3 helicase for inhibitor discovery. J Biomol Struct Dyn.. 2019 Nov 14:1-11.

   46. Kumar P, Kumar D, Giri R*.• Targeting the nsp2 Cysteine Protease of Chikungunya Virus Using FDA Approved Library and Selected Cysteine Protease Inhibitors. Pathogens. 2019 Aug 15; 8(3). 

   47. Gour S, Kumar V, Singh A, Gadhave K, Goyal P, Pandey J, Giri R. Yadav JK*.• Mammalian antimicrobial peptide protegrin-4 self assembles and forms amyloid-like aggregates: Assessment of its functional relevance. J Pept Sci. 2019 March;25 (3):e3151.

   48. Kumar V, Gour S, Verma N, Kumar S, Gadhave K, Mishra PM, Goyal P, Pandey J, Giri R. Yadav JK*.• The mechanism of phosphatidylcholine-induced interference of PAP (248-286) aggregation. J Pept Sci. 2019 Feb 19:e3152.

2018

1. 49. P Kalita, H Shukla, K Gadhave, Giri R. T Tripathi* • Role of the glutaredoxin domain and FAD in the stabilization of thioredoxin glutathione reductase. Archives of biochemistry and biophysics. 2018, Oct 15;656:38-45.

   50. Kumar, A, Liang B, Aarthy M, Singh S, Garg N, Mysorekar I, Giri R*. • Hydroxychloroquine inhibits Zika virus NS2B-NS3 protease. ACS Omega. 2018, 3, 18132-18141.

   51. Singh A,Kumar A, Uversky VN*, Giri R*. • Understanding the interactability of chikungunya virus proteins via molecular recognition feature analysis. RSC Advances.. 2018,8, 27293-27303.

   52. Singh A, Kumar A, Yadav R, Uversky VN, Giri R*. • Deciphering the dark proteome of Chikungunya virus. Scientific Reports. 2018 Apr 11;8(1):5822.

   53. Murali A, Kumar D, Giri R ,Singh S K. E7 oncoprotein of human papillomavirus: Structural dynamics and inhibitor screening study. Gene. 2018. 

2017

1. 54. Kalita J, Shukla R, Shukla H, Gadhave K, Giri R , Tripathi T. Comprehensive analysis of the catalytic and structural properties of a mu-class glutathione s-transferase from Fasciola gigantica. Sci Rep. 2017 Dec 13 doi: 10.1038/s41598-017-17678-3.

   55. Mishra PM, Uversky VN*, Giri R*. Molecular Recognition Features in Zika Virus Proteome. Journal of Molecular Biology. 2017 November 7 doi: 10.1016/j.jmb.2017.10.018.

   56. Sharma N, Murali A, Singh SK*, Giri R*. Epigallocatechin gallate, an active green tea compound inhibits the Zika virus entry into host cells via binding the envelope protein. Int J Biol Macromol.. 2017 June 28; 104(Pt A): 1046-1054

   57. Kumar D, Sharma N and Giri R*. Therapeutic Interventions of Cancers Using Intrinsically Disordered Proteins as Drug Targets: c-Myc as Model System. Cancer Inform. 2017 March 16

   58. Khrustalev VV*, Khrustaleva TA,Sharma N and Giri R*. Mutational Pressure in Zika Virus:Local ADAR-Editing Areas Associated with Pauses in Translation and Replication. Front Cell Infect Microbiol.. 2017 Feb 22;7:44.

2016

1. 59. Giri R*, Kumar D, Sharma N, Uversky VN*. Intrinsically Disordered Side of the Zika Virus Proteome. Front Cell Infect Microbiol.. 2016 Nov 4;6:144.

Previous publications (From Ph.D. and Post Doc of Dr. Giri)

1. 60. Camilloni C, Bonetti D, Morrone A, Giri R, Dobson CM, Brunori M, Gianni S, Vendruscolo M. Towards a structural biology of the hydrophobic effect in protein folding. Sci Rep. 2016 Jul 27;6:28285.

   61. Toto A, Camilloni C, Giri R, Brunori M, Vendruscolo M, Gianni S. Molecular Recognition by Templated Folding of an Intrinsically Disordered Protein. Sci Rep. 2016 Feb 25;6:21994.

   62. Dey G, Gaur P, Giri R*, Ghosh S*. Optical signaling in biofluids: a nondenaturing photostable molecular probe for serum albumins. Chem Commun. 2016 Jan 21;52(9):1887-90. 

   63. VanSchouwen B, Selvaratnam R, Giri R, Lorenz R, Herberg FW, Kim C, Melacini G. " Mechanism of cAMP Partial Agonism in Protein Kinase G (PKG).J Biol Chem, 2015 Nov 27;290(48):28631-41.

   64. Gianni S, Camilloni C, Giri R , Toto A, Bonetti D, Morrone A, Sormanni P, Brunori M, Vendruscolo M. “Understanding the frustration arising from the competition between function, misfolding and aggregation in a globular protein”. Proc Natl Acad Sci U S A. 2014 Sep 30;111(39):14141-6.

   65. Toto A, Giri R, Brunori M, and Gianni S. " The mechanism of binding of the KIX domain to the Mixed Lineage Leukemia protein and its allosteric role in the recognition of c-Myb ". Protein Sci. 2014;23(7):962-9.

   66. Boulton S, Akimoto M, Vanschouwen B, Moleschi K, Selvaratnam R, Giri R, Melacini G. " Tapping the translation potential of cAMP signalling: molecular basis for selectivity in cAMP agonism and antagonism as revealed by NMR ". Biochemical Society transactions, 2014, 42(2):302-7.

   67. Bonetti D, Toto A, Giri R, Morrone A, Sanfelice D, Pastore A, Temussi P, Gianni S and Brunori M. "The kinetics of folding of frataxin". Physical Chemistry Chemical Physics 2014 Apr 14, 16:6391-7.

   68. Giri R, Travaglini-Allocatelli C, Gianni S, Giardina G and Brunori M. ""Morphogenesis of proteins: classic views and challenges ahead". Journal of Proteins and Proteomics, 2013.

   69. Giri R, Morrone A, Toto A, Brunori M, Gianni S, “Structure of the transition state for the binding of c-Myb and KIX highlights an unexpected order for a disordered system”. Proc Natl Acad Sci U S A. 2013,110(37):14942-7.

   70. Gianni S , Morrone A , Giri R , Brunori M, "A folding-after-binding mechanism describes the recognition between the transactivation domain of c-Myb and the KIX domain of the CREB-binding protein.", Biochemical and biophysical research communications, 2012, 428(2).

   71. Morrone A , Giri R , Brunori M , Gianni S, "Reassessing the folding of the KIX domain: evidence for a two-state mechanism.", Protein science , 2012, 21(11).

   72. Giri R , Morrone A , Travaglini-Allocatelli C , Jemth P , Brunori M , Gianni S, "Folding pathways of proteins with increasing degree of sequence identities but different structure and function.", Proc Natl Acad Sci U S A. 2012;109(44):17772-6.

   73. Brunori M , Gianni S , Giri R , Morrone A , Travaglini-Allocatelli C, "Morphogenesis of a protein: folding pathways and the energy landscape.", Biochemical Society Transactions, 2012, 40(2).

   74. Morrone A , Giri R , Toofanny RD , Travaglini-Allocatelli C , Brunori M , Daggett V , Gianni S, "GB1 is not a two-state folder: identification and characterization of an on-pathway intermediate.", Biophysical Journal, 2011, 101(8).