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Here you will find information about the research publications I’ve been involved with. Throughout my research, I’ve had the opportunity to work on many interesting projects that have enriched my understanding and paved the path towards my successful Researcher career. I’m proud to showcase my hard work with the list of publications below.

2024

  1. Uttarkar, A., Niranjan, V. A comparative insight into peptide folding with quantum CVaR-VQE algorithm, MD simulations and structural alphabet analysis. Quantum Inf Process 23, 48 (2024). https://doi.org/10.1007/s11128-024-04261-9

  2. Uttarkar, A., Rao, V., Bhat, D. et al. Disaggregation of amyloid-beta fibrils via natural metabolites using long timescale replica exchange molecular dynamics simulation studies. J Mol Model 30, 61 (2024). https://doi.org/10.1007/s00894-024-05860-0

  3. Vidya Niranjan, Anagha S. Setlur, K. Chandrashekar, Akshay Uttarkar, Sinosh Skariyachan Deciphering the scope of in silico screening of novel natural lead molecules against putative molecular targets of multidrug-resistant bacterial pathogens, Nanotechnology and In Silico Tools, Elsevier, 2024, Pages 269-284 https://doi.org/10.1016/B978-0-443-15457-7.00001-0.

2023

  1. Sujitha, D., Kumar, H.G.J., Thapliayal, G. Uttarkar A, et al. Transcription factors controlling the expression of oxidative stress associated genes in rice (Oryza sativa L.). Plant Biotechnol Rep (2023). https://doi.org/10.1007/s11816-023-00819-8

  2. Niranjan V, Rao P, Uttarkar A, Kumar J (2023) Protocol for the development of coarse-grained structures for macromolecular simulation using GROMACS. PLoS ONE 18(8): e0288264. https://doi.org/10.1371/journal.pone.0288264

  3. Niranjan, Vidya, Akshay Uttarkar, Ananya Ramakrishnan, Anagha Muralidharan, Abhay Shashidhara, Anushri Acharya, Avila Tarani, and Jitendra Kumar. 2023. "De Novo Design of Anti-COVID Drugs Using Machine Learning-Based Equivariant Diffusion Model Targeting the Spike Protein" Current Issues in Molecular Biology 45, no. 5: 4261-4284. https://doi.org/10.3390/cimb45050271

  4. Anagha S Setlur, Chandrashekar Karunakaran, V. Anusha, Aditya A Shendre, Akshay Uttarkar, Vidya Niranjan, H. G. Ashok Kumar & Raviraj Kusanur, Investigating the Molecular Interactions of Quinoline Derivatives for Antibacterial Activity Against Bacillus subtilis: Computational Biology and In Vitro Study Interpretations. Mol Biotechnol (2023). https://doi.org/10.1007/s12033-023-00933-6

  5. Skariyachan, S, Praveen, PKU, Uttarkar, A, Niranjan, V. Computational design of prospective molecular targets for Burkholderia cepacia complex by molecular docking and dynamic simulation studies. Proteins. 2023; 1- 15. doi:10.1002/prot.26462.

  6. Niranjan Vidya*, R Vibha, Philip Sarah, Uttarkar Akshay, Kusanur Raviraj and Kumar Jitendra, Design of novel Imidazopyrazine derivative against breast cancer via targeted NPY1R antagonist, Anti-Cancer Agents in Medicinal Chemistry 2023; 23() . https://dx.doi.org/10.2174/1871520623666230505100031

  7. Shraddha Rana, Sinosh S, Akshay Uttarkar and Vidya Niranjan. Carboxymuconolactone decarboxylase is a prospective molecular target for multi-drug resistant Acinetobacter baumannii-computational modeling, molecular docking and dynamic simulation studies. Computers in biology and medicine (2023). https://doi.org/10.1016/j.compbiomed.2023.106793

  8. Niranjan, V., Uttarkar, A., Kaul, A., Varghese, M. (2023). A Machine Learning-Based Approach Using Multi-omics Data to Predict Metabolic Pathways. In: Selvarajoo, K. (eds) Computational Biology and Machine Learning for Metabolic Engineering and Synthetic Biology. Methods in Molecular Biology, vol 2553. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2617-7_19

  9. Niranjan, V.; Jayaprasad, S.; Uttarkar, A.; Kusanur, R.; Kumar, J. Design of Novel Coumarin Derivatives as NUDT5 Antagonists That Act by Restricting ATP Synthesis in Breast Cancer Cells. Molecules 2023, 28, 89. https://doi.org/10.3390/molecules28010089

  10. Niranjan V, Setlur AS, Chandrashekar K, Uttarkar A, Skariyachan S. Deciphering the scope of in silico screening of novel natural lead molecules against putative molecular targets of multidrug-resistant bacterial pathogens. Nanotechnology and In Silico Tools 2024 Jan 1 (pp. 269-284). Elsevier, https://doi.org/10.1016/B978-0-443-15457-7.00001-0

2022

  1. Akshay Uttarkar, Alice Preethi Kishore, Sudhanva M. Srinivas, Shobith Rangappa, Raviraj Kusanur ,Vidya Niranjan, "Coumarin derivative as a potent drug candidate against triple negative breast cancer targeting the frizzled receptor of wingless-related integration site signaling pathway", Journal of Biomolecular Structure and Dynamics, 2022,  DOI: 10.1080/07391102.2021.2022536

  2. Akshay Uttarkar & Vidya Niranjan, "Brefeldin A variant via combinatorial screening acts as an effective antagonist inducing structural modification in EPAC2", Molecular Simulation,2022,  DOI: 10.1080/08927022.2022.2110271

  3. Niranjan, V.; Uttarkar, A.; Murali, K.; Niranjan, S.; Gopal, J.; Kumar, J. Mycobacterium Time-Series Genome Analysis Identifies AAC2′ as a Potential Drug Target with Naloxone Showing Potential Bait Drug Synergism. Molecules 2022, 27, 6150. https://doi.org/10.3390/molecules27196150

  4. Vanitha, P., Vijayaraghavareddy, P., Uttarkar, A., Dawane, A., Sujitha, D., Ashwin, V., Babitha, K., Niranjan, V., Sheshshayee, M., Anuradha, C., Makarla, U. and Vemanna, R.S. (2022), Novel small molecules targeting bZIP23 TF improve stomatal conductance and photosynthesis under mild drought stress by regulating ABA. FEBS J. 289: 6058-6077,  https://doi.org/10.1111/febs.16461

  5. Vanitha Adhinarayanreddy, Preethi Vijayraghavareddy, Ashwin Vargheese, Sujitha Dadi, Akshay Uttarkar, Vidya Niranjan, Anuradha C V, Sheshshayee M. Sreeman, Ramu Vemanna "Simple and Rapid Oxidative Stress Screening Method of Small Molecules for Functional Studies of Transcription Factor", Rice Science,2022,,Vol 29(5): 402-406, https://doi.org/10.1016/j.rsci.2022.07.002

  6. Niranjan, V., Setlur, A.S., Karunakaran, Uttarkar, A., Kumar, K. M., Skariyachan, S (2022) Scope of repurposed drugs against the potential targets of the latest variants of SARS-CoV-2. Struct Chem. DOI: https://doi.org/10.1007/s11224-022-02020-z

  7. Shaban Ahmad, Piyush Bhanu, Jitendra Kumar, Ravi Kant Pathak, Dharmendra Mallick, Akshay Uttarkar, Vidya Niranjan & Vachaspati Mishra "Molecular dynamics simulation and docking analysis of NF-κB protein binding with sulindac acid", Bioinformation 18(3): 170-179 , 2022, DOI: 10.6026/97320630018170

  8. Vidya Niranjan and Akshay Uttarkar, (2022), "Triple-Negative Breast Cancer and Recent Advancements in Treatment". J Oncol Res Treat 7(2):182. DOI: 10.4172/aot-1000182

  9. Vidya Niranjan, Akshay Uttarkar and Jitendra Kumar (2022) "Recent Advancement in Drug Delivery for Treatment of Leukemia" . J Leuk 10(4):298. DOI: 10.35248/2329-6917.22.10.298

 

2021

  1. Sinosh Skariyachan, Dharshini Gopal, Dhrithi Deshpande, Anusha Joshi, Akshay Uttarkar, Vidya Niranjan, "Carbon fullerene and nanotube are probable binders to multiple targets of SARS-CoV-2: Insights from computational modeling and molecular dynamic simulation studies", Infection, Genetics and Evolution,2021,105155,https://doi.org/10.1016/j.meegid.2021.105155.

  2. Sinosh Skariyachan, Dharshini Gopal, Aditi G. Muddebihalkar, Akshay Uttarkar, Vidya Niranjan,”Structural insights on the interaction potential of natural leads against major protein targets of SARS-CoV-2: Molecular modelling, docking and dynamic simulation studies”, Computers in Biology and Medicine, 2021, 104325, https://doi.org/10.1016/j.compbiomed.2021.104325.

  3. Vidya Niranjan, Akshay Uttarkar, Sujitha Dadi, Akashata Dawane, Ashwin Vargheese, Jalendra Kumar H. G., Udayakumar Makarla, and Vemanna S. Ramu  “Stress-Induced Detoxification Enzymes in Rice Have Broad Substrate Affinity”, ACS Omega, 2021, https://doi.org/10.1021/acsomega.0c05961

  4. Ishu Khangwal, Sinosh Skariyachan, Akshay Uttarkar, Aditi G. Muddebihalkar, Vidya Niranjan and Pratyoosh Shukla "Understanding the Xylooligosaccharides Utilization Mechanism of Lactobacillus brevis and Bifidobacterium adolescentis: Proteins Involved and Their Conformational Stabilities for Effectual Binding." Molecular Biotechnology. 2021.  https://doi.org/10.1007/s12033-021-00392-x

  5. Niranjan Vidya, Rao Amulya , Janaki B, Uttarkar Akshay , Setlur S Anagha , K Chandrashekar and M Udayakumar, Molecular Docking and Interaction Studies of Identified Abscisic Acid Receptors in Oryza sativa: An In-Silico Perspective on Comprehending Stress Tolerance Mechanisms, Current Genomics 2022; 23() . https://dx.doi.org/10.2174/1389202923666211222161006

  6. Akshay Uttarkar, Vidya Niranjan, Shivam Pandit and Srividya Subash, "Study of SARS-nCOV2 Indian isolates gaining insights into mutation frequencies, protein stability and prospective effect on its pathogenicity", Coronaviruses, 2021, Volume 2(1), https://doi.org/10.2174/2666796702666210118155636

  7. Dayanand Patagar, Akshay Uttarkar, Swarna M. Patra, Jagadish H. Patil, Raviraj Kusanur, Vidya Niranjan, and H. G. Ashok Kumar “Spiro Benzodiazepine Substituted Fluorocoumarins as Potent Anti-Anxiety Agents” Russian Journal of Bioorganic Chemistry, 2021, Vol. 47, No. 2, pp. 390–398. https://doi.org/10.1134/S1068162021020199.

 

2020

  1. Sinosh Skariyachan, Dharshini Gopal, Shweta Chakrabarti, Priya Kempanna, Akshay Uttarkar, Aditi G. Muddebihalkar, Vidya Niranjan, “Structural and molecular basis of the interaction mechanism of selected drugs towards multiple targets of SARS-CoV-2 by molecular docking and dynamic simulation studies- Deciphering the scope of repurposed drugs”, Computers in Biology and Medicine, 2020, 104054, https://doi.org/10.1016/j.compbiomed.2020.104054.

  2. Skariyachan S, Ravishankar R, Gopal D, Muddebihalkar AG, Uttarkar A, Praveen PKU, et al. Response regulator GacA and transcriptional activator RhlR proteins involved in biofilm formation of Pseudomonas aeruginosa are prospective targets for natural lead molecules: Computational modelling, molecular docking and dynamic simulation studies. Infection, Genetics and Evolution. 2020;85:104448.https://doi.org/10.1016/j.meegid.2020.104448

  3. Skariyachan, S., Muddebihalkar, A. G., Badrinath, V., Umashankar, B., Eram, D., Uttarkar, A., & Niranjan, V. (2020). Natural epiestriol-16 act as potential lead molecule against prospective molecular targets of multidrug resistant Acinetobacter baumannii-Insight from in silico modelling and in vitro investigations. Infection, Genetics and Evolution, 82, 104314, 2020. doi: https://doi.org/10.1016/j.meegid.2020.104314

  4. Sinosh Skariyachan, Darshani Gopal, Sanjana Pratab Kadam, Aditi G Muddebihalkar, Akshay Uttarkar and Vidya Niranjan, “Carbon fullerene act as a potential lead molecule against prospective molecular targets to biofilm producing multidrug resistant Acinetobacter baumanni and Psuedomonas aeruginosa: Computational modelling and MD simulation”  Journal of biomolecular structure and dynamics, 2020, accepted. https://doi.org/10.1080/07391102.2020.1726821

  5. Dharshani Gopal, Aditi G Muddebhihalkar, Sinosh Skarriyachan, Akshay Uttarkar C, Prinith Kaveramma, Ulluvangada Praveen, Roshini Ravishankar, Tejaswini V and Vidya Niranjan, “ Mitogen activated protein kinase-1 and cell division control protein-42 are putative targets for the binding of novel natural lead molecules: a therapeutic intervention against Candida albicans, Journal of biomolecular structure and dynamics, 2019, accepted. DOI: 10.1080/07391102.2019.1682053.

 

2017

  1. Utpal S Tatu, Shuba Varshini Alampalli, Akshay C Uttarkar, Suchithra Ventakesh, Sivarajan T Chettinar, Rishi Kumar Nageshan, Vidya Niranjan. “Genome Resequencing Reveals Single Nucleotide Polymorphism and Repeat Regions in Giardia lamblia Indian Isolate” Next Generation Sequencing and Applications, Vol 4(3), 2017

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