Computational Structural Biology Group

Total Publications: 41

  1. Purva Khodke, Dhananjay Hasurkar, Aakanksha Upadhyay, Aditi Shedge, Rhea Sippy and Bajarang Vasant Kumbhar*, B Cell Antigens: A Key to Optimizing CAR-T Cell Therapy. Accepted International Review of Immunology (IF:4.3), Q1

  2. Weronika Hanusiak, Purva Khodke, Jocelyn Mayen, Kennedy Van, Ira Sigar, Balbina J. Plotkin, Amber Kaminski, James Elste, Bajarang Kumbhar*, Vaibhav Tiwari. 3-O Sulfated Heparan Sulfate (G2) Peptide Ligand Impairs the Infectivity of Chlamydia muridarum. Biomolecules 2025, 15, 999. https://doi.org/10.3390/biom15070999 (IF: 4.8) Q1

  3. Vibhuti Saxena, Pruthanka Patil, Purva Khodke, and Bajarang Vasant Kumbhar*, Exploring purine analogues as inhibitors against Katanin, a microtubule severing enzyme using molecular modeling approach. Scientific Report, 14, 32095 (2024). https://doi.org/10.1038/s41598-024-83723-7, (IF:3.8) Q1

  4. Prem Prakash, Purva Khodke, Muthukumar Balasubramaniam, Benem-Orom Davids, Thomas Hollis, Jamaine Davis, Jui Pandhare, Bajarang Kumbhar and Chandravanu Dash. Three Prime Repair Exonuclease 1 preferentially degrades the integration-incompetent HIV-1 DNA through favorable kinetics, thermodynamic, structural, and conformational properties. Journal of Biological Chemistry (IF: 4.8).

  5. Vrinda Salvi, Purva Khodke, Pruthanka Patil, and Bajarang Vasant Kumbhar*, Identification of a Potential Anti-Viral Drug Targeting allosteric site of Papain-like Protease against Rubella using a molecular modeling approach. Under revision Journal of Biomolecular Structure and Dynamics (IF:4.4)  

  6. Purva Khodke and Bajarang Vasant Kumbhar*, Engineered CAR-T Cells: An Immunotherapeutic Approach for Cancer Treatment and Beyond. Advances in Protein Chemistry and Structural Biology: Immunology for Engineers. Vol. 140 (IF: 5.4) (Q1)

  7. Pradnya Patil; Pruthanka Patil, Padma Dandge; Prakash Bansode; Bajarang Vasant Kumbhar; Wilson Chandane; Sanket Rathod; Prafulla Choudhari; Suraj Khot; Navanath Valekar; Dattaprasad Pore, Benzylpyrazolyl naphthoquinones as potential VEGFR-2 inhibitors: synthesis, anti-cancer evaluation, molecular docking and DFT studies. Journal of Molecular Structure, 1301, 137202, ISSN No: 1872-8014, (IF 3.8) https://doi.org/10.1016/j.molstruc.2023.137202 (Q2)

  8. Richa Dwivedi, Prem Prakash, Bajarang Vasant Kumbhar, Muthukumar Balasubramaniam, and Chandravanu Dash, HIV-1 Capsid and Viral DNA Integration. mBio Journal, ISSN No: 2150-7511, (IF: 6.4) https://doi.org/10.1128/mbio.00212-22 (Q1)

  9. Anand Keshri, Rimanpreet Kaur, Suraj S Rawat, Naina Arora, Rajan K Pandey, Bajarang Vasant Kumbhar, Amit Mishra, Shweta Tripathi, Designing and development of multi-epitope chimeric vaccine against Helicobacter pylori by exploring its entire immunogenic epitopes: an immunoinformatic approach. BMC Bioinformatics, 2023 Sep 22;24(1):358. ISSN No: 1471-2105, (IF: 3.0), doi:10.1186/s12859-023-054542 (Q1)

  10. Sukhada Kanse, Mehak Khandelwal, Rajan Kumar Pandey, Manoj Khokar, Neetin Desai and Bajarang Vasant Kumbhar*. Designing a multi-epitope-based vaccine against VP1 major coat protein of JC Polyomavirus using Immunoinformatics and molecular modeling approach. Vaccines, 2023, 11(7), 1182; ISSN No: 2076-393X (IF: 7.8)  https://doi.org/10.3390/vaccines11071182 (Q1)

  11. Asiya Rozindar, Virupakshaiah DBM, Bharati Meti, Bajarang Vasant Kumbhar, Ajay Kumar oli, Identification of potential human chymase inhibitors using molecular docking and molecular dynamics simulation, Journal of Applied and Natural Science, 15(1), 1-8, Mar 19, 2023. https://doi.org/10.31018/jans.v15i1.3324 (Q4)

  12. Bipin Raj Shekhar, Karishma Rupani, Shubhangi Raghunath Parkar, Ajita Sunil Nayak, Bajarang Vasant Kumbhar, Satyajeet P Khare, Shyla Menon, Harshavardhan Gawde, Dhanjit Kumar Das, “Identifying novel causal genes involved in glycosylation processes with familial schizophrenia: Prediction of ADAMTS9 gene variant for structural stability", Gene, 872, 1 July 2023, 147443 https://doi.org/10.1016/j.gene.2023.147443, (IF: 3.913)  ISSN No: 0300-9564. (Q2)

  13. Swapnil Doijad, Nicolas Gisch, Renate Frantz, Bajarang Vasant Kumbhar, Jane Falgenhauer, Can Imirzalioglu, Linda Falgenhauer, Alexander Mischnik, Jan Rupp, Michael Behnke, Michael Buhl, Simone Eisenbeis, Petra Gastmeier, Hanna Gölz, Nadja Käding, Winfried V. Kern, Axel Kola, Evelyn Kramme, Silke Peter, Anna M. Rohde, Harald Seifert, Evelina Tacconelli, Maria Vehreschild, Sarah Walker, Janine Zweigner, Dominik Schwudke and Trinad Chakraborty, and R-Net Study Group, Resolving colistin resistance and heteroresistance in Enterobacter species. Nature Communication, 14, 140 2023 (IF:17.69), ISSN No: 2041-1723.   https://doi.org/10.1038/s41467-022-35717-0 (Q1)

  14. Satyendra Singh, Priya Chauhan, Vinita Sharma, Abhishek Rao, Bajarang Vasant Kumbhar, Vijay Kumar Prajapati. Identification of multi-targeting natural antiviral peptides to impede SARS-CoV-2 infection. Structural Chemistry, Accepted (IF: 1.795) ISSN No: 1572-9001. https://doi.org/10.1007/s11224-022-02113-9   (Q3)

  15. Ratan W. Jadhav, Sopan M. Wagalgave, Bajarang V. kumbhar, Rushikesh M. Khadake, Ambadas B. Rode, Sidhanath V. Bhosaleb, and Sheshanath V. Bhosale Aminoglycoside Antibiotic Kanamycin Functionalized Tetraphenylethylene Molecular Probe for Highly Selective Detection of Bovine Serum Albumin Protein. Nature: Scientific Reports, 12, 11526, 2022. (IF: 4.996) ISSN No: 2045-2322. https://doi.org/10.1038/s41598-022-15890-4, (Q1)

  16. Khushnandan Rai, Bajarang Vasant Kumbhar, Dulal Panda, Ambarish Kunwar. Computational study of interaction of anti-cancer drug eribulin with human tubulin isotypes. Physical Chemistry Chemical Physics, 2022, 24, 16694-16700 (IF: 3.676) ISSN No:1463-9076. https://doi.10.1039/D1CP04454K (Q1)

  17. Harshad Lade, Sung Hee Chung, Yeonhee Lee, Jung-Min Kim, Bajarang Vasant Kumbhar, Hwang Soo Joo, Yun-Gon Kim, Yung-Hun Yange and Jae-Seok Kim. Thymol reduces agr-mediated virulence factor phenol-soluble modulin production in Staphylococcus aureus. Biomed Research International, Volume 2022 |Article ID 8221622, (IF: 3.246) ISSN No: 2314-6141. https://doi.10.1155/2022/8221622 (Q2)

  18. Anandsinha Patil, Vijay Patil, Dipak Jaiswal, Sandip Palakhe, Sandip Patil, Bajarang Vasant Kumbhar*. Investigating the novel acetonitrile derivatives as potential SARS-CoV-2 main protease inhibitor using molecular modeling approach. 2022 Journal of Biomolecular Structure and Dynamics, Apr 6; 1-13. (IF: 5.235) ISSN No:1538-0254. https://doi.org/10.1080/07391102.2022.2059568  (Q1)

  19. Rajan Kumar Pandey; Rupal Ojha; Moodu Devender; Prince Sebastian; Madhulika Namdeo; Bajarang Vasant Kumbhar; Shyam Sundar; Radheshyam Maurya, Vijay Prajapati, Febrifugine dihydrochloride as a new oral chemotherapeutic agent against visceral leishmaniasis infection, Experimental Parasitology, 236–237, May–June 2022, 108250, https://doi.10.1016/j.exppara.2022.108250, (IF: 2.132) ISSN No:0014-4894. (Q2)

  20. Brijesh Krishnappa, Sneha Arya, Anurag R Lila, Vijaya Sarathi, Saba Samad Memon, Rohit Barnabas, Bajarang Vasant Kumbhar, Vishwambhar Vishnu Bhandare, Virendra Patil, Nalini S Shah, Ambarish Kunwar, Tushar Bandgar. 17β hydroxysteroid dehydrogenase 3 deficiency in 46, XY disorders of sex development: our experience and a gender role-focused systematic review, Clinical Endocrinology (Oxf), 2022 Feb 16. http://doi:10.1111/cen.14694 (IF: 3.478) ISSN No: 1365-2265. (Q1)

  21. Somnath D. Bhinge, Namdeo R. Jadhav, Dheeraj S. Randive, Mangesh B. Bhutkar, Rohankumar chavan, Bajarang Vasant Kumbhar, Isolation and identification of Hair growth potential Fraction from Active Plant Extract of Blumea eriantha DC Grown in Western Ghat of India: In Silico Study, Journal of Ayurveda and Integrative Medicine, 13 (2) 2022, 100542. https://doi.10.1016/j.jaim.2022.100542, ISSN No: 0975-9476. Impact Factor 2.4 (Q2)

  22. Jitesh Kumar, Ravi Ranjan Kumar, Dilip Kumar Das, Auroshikha Mohanty, Kumari Rajani, Namaste Kumari, Vinod Kumar, Sunil Kumar, Bajarang Vasant Kumbhar and Tushar Ranjan. Knockdown of capsid protein encoding novel ATPase domain inhibits genome packaging in potato leafroll virus. 3Biotech, 2022 Mar;12(3):66. http://doi.10.1007/s13205-021-03085-z, (IF: 2.8) ISSN No: 2190-5738. (Q3)

  23. Prasanna S Patil, Vijay R Salunkhe, Somnath D Bhinge, Sandeep B Patil, Bajarang V Kumbhar. Formulation optimization and evaluation of Glycyrrhetinic Acid Loaded PLARosome using Factorial design: In-vitro anti-ulcer activity and in silico PASS Prediction. Journal of the Indian Chemical Society. 98, 11, November 2021, 100199. (IF: 1.3), ISSN No: 0019-4522. https://doi.10.1016/j.jics.2021.100199, (Q4)

 

  1. Alka Dwivedi, Atharva Karulkar, Sarbari Ghosh, Srisathya Srinivasan, Bajarang Vasant Kumbhar, Ankesh Kumar Jaiswal, Atish Kizhakeyil, Sweety Asija, Afrin Rafiq, Sushant Kumar, Albeena Nisar, Deepali Pandit, Minal Poojary, Hasmukh Jain, Shripad D. Banavali, Steven L. Highfill, David F. Stroncek, Nirali N. Shah, Terry J. Fry, Gaurav Narula, Rahul Purwar. “Robust anti-tumor activity and low cytokine production by novel humanized CD19 CART-cells”. American Association for Cancer Research, Molecular Cancer Therapeutics. 2021 May; 20(5):846-858. (IF: 6.009), ISSN No: 1535-7163. https://doi.org/10.1158/1535-7163.MCT-20-0476

  2. Shipra Sharma, Vibha Kumari, Bajarang Vasant Kumbhar, Amrita Mukherjee, Ruchika Pandey, and Kiran Kondabagil. Immunoinformatics approach for a novel multi-epitope subunit vaccine design against various subtypes of Influenza A virus. Immunobiology, 226, 2, 152053, 2021. https://doi.org/10.1016/j.imbio.2021.152053  (IF: 3.152), ISSN No: 0171-2985.

  3. Amit Bhatti, Sangeeta Ravat, Karan Desai, Bipin Raj Shekhar, Bajarang Vasant Kumbhar, Ambarish Kunwar, Neeraj Jain, Dhanjit Kumar Das, ‘Spectrum of Clinical Variability with SEPT9 gene Mutation in Hereditary Neuralgic Amyotrophy: Understanding the Pathogenesis using Molecular Dynamics Simulation study.’ Neurology India, (IF: 1.663), ISSN No: 0028-3886.

  4. Sneha Arya, Ankita Tiwari, Anurag Lila, Vijaya Sarathi, Vishwambhar Vishnu Bhandare, Bajarang Vasant Kumbhar, Khushnandan Rai, Ambarish Kunwar, Hemangini Thakkar, Kunal Thakkar, Saba Samad Memon, Swati Ramteke-Jadhav, Nalini S Shah, Tushar Bandgar. “Homozygous p.Val89Leu plays an important pathogenic role in 5α-reductase type 2 deficiency patients with homozygous p.Arg246Gln in SRD5A2”. European Journal of Endocrinology, 2020 Jun 1; EJE-19-1050.R2, https://doi.org/10.1530/EJE-19-1050  (IF: 6.664), ISSN No: 0804-4643.

  5. Bajarang Vasant Kumbhar* and Vishwambhar Vishnu Bhandare. ‘Exploring the interaction of peloruside-A with drug resistant αβII and αβIII tubulin isotypes present in human ovarian carcinoma using molecular modeling approach.’ Journal of Biomolecular Structure and Dynamics, 2020, Apr 3; 1-13 (IF: 5.235), ISSN No: 1538-0254. https://doi.org/10.1080/07391102.2020.1745689 

  6. Vishwambhar V Bhandare, Bajarang Vasant Kumbhar and Ambarish Kunwar, Differential binding affinity of tau repeat region R2 with neuronal-specific β-tubulin isotypes, Nature: Scientific Reports, July 25, 9 (1–12):10795, 2019 (IF: 4.525), ISSN No: 2045-2322. https://doi.org/10.1038/s41598-019-47249-7 

  7. Bajarang Vasant Kumbhar, Vishwambhar Vishnu bhandare, Dulal Panda, Ambarish Kunwar, Delineating the Interaction of Combretastatin A-4 with αβ tubulin Isotypes present in Drug Resistant Human Lung Carcinoma using a Molecular Modeling Approach. Journal of Biomolecular Structure and Dynamics, 2019, Mar 4:1-13 (IF: 5.235), ISSN No: 1538-0254. https://doi.org/10.1080/07391102.2019.1577174 

  8. Bajarang Vasant Kumbhar, Dulal Panda and Ambarish Kunwar. Interaction of microtubule depolymerizing agent indanocine with different human αβ tubulin isotypes. PLoS One, Mar 27, 2018, 13(3): e0194934 (IF: 3.240), ISSN No: 1932-6203. https://doi.org/10.1371/journal.pone.0194934

  9. Bajarang Vasant Kumbhar, Anubhaw Borogaon, Dulal Panda, Ambarish Kunwar. “Exploring the Origin of Differential Binding Affinities of Human Tubulin Isotypes αβII, αβIII and αβIV for DAMA-Colchicine using Homology Modeling, Molecular Docking and Molecular Dynamics Simulations” PLoS One, May 26, 2016 ;11(5): e0156048. https://doi.org/10.1371/journal.pone.0156048 (IF: 3.752), ISSN No:1932-6203. 

  10. Rajan Kumar Pandey, Bajarang Vasant Kumbhar, Shyam Sundar, Ambarish Kunwar and Vijay Kumar Prajapati. Structure based virtual screening, molecular docking, ADMET and molecular simulations to develop benzoxaborole analogues as a potential inhibitor against Leishmania donovani trypanothione reductase. Journal of Receptors and Signal Transduction, https://doi.org/10.3109/10799893.2016.117134 2017, 5:1-11. (IF: 2.2), ISSN No:1079-9893.

  11. Rajan Kumar Pandey, Bajarang Vasant Kumbhar, Shubham Srivastava, Ruchi Malik, Shyam Sundar, Ambarish Kunwar and Vijay Kumar Prajapati. Febrifugine analogues as Leishmaniadonovani trypanothione reductase inhibitors: binding energy analysis assisted by molecular docking ADMET, and molecular dynamics simulation. Journal of Biomolecular Structure and Dynamics, 2017, 4:1-18. (IF: 5.235), ISSN No: 1538-0254. https://doi.org/10.1080/07391102.2015.1135298

  1. Asmita D. Kamble, Bajarang V. Kumbhar, Susmit B. Sambhare, Rohit S. Bavi, and Kailas D. Sonawane, “Conformational preferences of modified nucleoside 5-taurinomethyluridine, τm5U occur at 'wobble' 34th position in the anticodon loop of tRNA in tRNA”. Cell Biochemistry and Biophysics, 2015, 71; 1589-1603, (IF: 2.989), ISSN No: 1085-9195. https://doi.org/10.1007/s12013-014-0382-x 

  2. Susmit Balkrishna Sambhare, Bajarang V Kumbhar, Asmita D Kamble, Rohit S Bavi, Navanath M Kumbhar and Kailas Dasharath Sonawane “Structural significance of modified nucleosides k2C and t6Ade present in the anticodon loop of tRNAIle”. RSC Advances, 2014, 4; 14176-14188 (IF: 4.036), ISSN No: 2046-2069.

  3. Bajarang V. Kumbhar, Asmita D. Kamble, Kailas D. Sonawane. “Conformational Preferences of Modified Nucleoside N(4)-Acetylcytidine, ac4C Occur at ‘‘Wobble’’ 34th Position in the Anticodon Loop of tRNA”. Cell Biochemistry and Biophysics, 2013, 66; 797-816, (IF: 2.989), https://doi.org/10.1007/s12013-013-9525-8 ISSN No: 1085-9195. **Citation in the Cell, Nature, ACS, RNA etc**

  4. Navanath M. Kumbhar, Bajarang V. Kumbhar and Kailas D. Sonawane, Structural significance of hypermodified nucleic acid base hydroxywybutine (OHyW) which occur at 37th position in the anticodon loop of yeast tRNAPhe. Journal of Molecular Graphics and Modeling, 2012, 38; 174-185. (IF: 2.942), ISSN No: 1093-3263.  https://doi.org/10.1016/j.jmgm.2012.07.005   

  5. Bajarang V Kumbhar, Navanath M. Kumbhar and Kailas D. Sonawane, “Conformational preferences and MD simulation studies of the hypermodified nucleic acid base, mS2hn6Ade present at 3'-adjacent (37th) position in the anticodon loop of hyperthermophilic tRNAs. Internet Electronic Journal of Molecular Design, 2012, 11; 33-48. ISSN No: 1538-6414.

  6. Rohit S. Bavi, Asmita D. Kamble, Navanath M. Kumbhar, Bajarang V. Kumbhar and Kailas D. Sonawane, “Conformational preferences of modified nucleoside N2-methylguanosine (m2G) and its derivative N2, N2-methylguanosine (m22G) occur at 26th position (hinge region) in tRNA”. Cell Biochemistry and Biophysics, 2011, 61; 507-521, (IF: 2.989), https://doi.org/10.1007/s12013-011-9233-1 ISSN No: 1085-9195.

  7. Bajarang V Kumbhar and Kailas D Sonawane, Molecular modeling study of hypermodified nucleic acid base 3-hydroxynorvalylcarbamoyl adenine, hn6Ade present at 3’-adjacent position in anticodon loop of hyperthermophilic tRNAs” IRSAPS Bulletin 2012, 3; 8-15.

  8. Kailas D. Sonawane, Bajarang V. Kumbhar, Navanath M. Kumbhar, Susmit B. Sambhare and Asmita D. Kamble. “Quantum chemical study to investigate the effects of 5′-3′ diphosphate backbone on the conformation of hypermodified nucleotide lysidine (K2C) occurs at wobble (34th) position in the anticodon loop of tRNAIle”. International Journal of Bioinformatics Research, 2011, 3; 148-160. ISSN No: 0975–3087. http://dx.doi.org/10.9735/0975-3087.3.1.148-160  

  9. Navanath M. Kumbhar, Bajarang V. Kumbhar, and Kailas D. Sonawane. Molecular modeling studies of hypermodified nucleosides present in Anticodon loop of tRNA. Journal of Natural Science, Biology, and Medicines, 2011, 2; 3:42. ISSN No: 2229-7707.

  10. Susmit B. Sambhare, Navanath M. Kumbhar, Asmita D. Kamble, Bajarang V.   Kumbhar and Kailas D. Sonawane “Molecular modeling study to investigate   conformational preferences and base stacking interactions of hypermodified nucleoside lysidine (k2C) incorporated in the trinucleotide segment of anticodon loop of tRNAIle”. Bionanofrontier, 2011, 4; 191-196. ISSN No: 2320-9593.