ArGan'sLab for Biocomputing and Therapeutic Discovery

Peer reviewed manuscripts (>2017)

1. Maya Petgrave*, Shubham Devesh Ramgoolam*, Aravindhan Ganesan. 2024. Deciphering the molecular association of Human CRIP1a with an agonist-bound cannabinoid receptor 1. 64(2):499-517. Link.

2. Tran, N., Dasari, S.et al. 2023. The H163A mutation unravels an oxidized conformation of the SARS-CoV-2 main protease. Nature Communications. 14, 5625. Link.

3. Joseph P. Clarke, Patricia A. Thibault, Sakina Fatima*, et al. 2023. Sequence- and Structure-specific RNA oligonucleotide biding attenuates heterogeneous nuclar ribonucleoprotein A1 dysfunction. 10. Link.

4. Sandhya Chahal, Payal Rani, et al, 2023. Design and Development of COX-II Inhibitors: Current Scenario and Future Prospective. ACS Omega. 8(2): 17446-17498. Link.

5. Marawan Ahmed, Aravindhan Ganesan, Khaled Barakat. 2022. Leveraging structural and 2D-QSAR to investigate the role of functional group substitutions, conserved surface residues and desolvation in triggering the small molecule-induced dimerization of hPD-L1. BMC Chemistry, 16, Article number: 49. Link.

6. Shirin Khanna*, Aravindhan Ganesan, Subha Kalyaanamoorthy. 2022. Exploring the potentials of phytochemicals for targeting coronavirus. The Natural Products Journal. 12(6):1-10. Link. 

7. Ying Lin Weng*, Shiv Rakesh Naik*, Nadia Dingelstad*, Miguel R. Lugo*, Subha Kalyaanamoorthy, Aravindhan Ganesan. 2021. Molecular dynamics and in silico mutagenesis on the reversible inhibitor-bound SARS-CoV-2 main protease complexes reveal the role of a lateral pocket in enhancing the ligand affinity. Scientific Reports. 11(1), 1-22.Link.

8. Mirfath Mesbahuddin, Aravindhan Ganesan, Subha Kalyaanamoorthy. 2021. Engineering carbonic anhydrases for CO2 capture: A critical review. Protein Engineering, Design, and Selection. 34:gzab021.

9. Patricia A Thibault, Aravindhan Ganesan, Subha Kalyaanamoorthy, Joseph-Patrick WE Clarke, Hannah E Salapa, Michael C Levin. 2021. hnRNP A/B Proteins: An encylopedic assessment of their roles in homeostasis and diseases. Biology. 10(8) 721.

10. Shiv Rakesh Naik*, Prashant Bharadwaj, Nadia Dingelstad*, Subha Kalyaanamoorthy, Subhash C Mandal, Aravindhan Ganesan, Debprasad Chattopadhyay, Partha Palit. 2021. Structure-based virtual screening, molecular dynamics, and binding affinity calculations of potential phytocompounds against SARS-CoV-2. Journal of Biomolecular Structure and Dynamics. DOI: 10.1080/07391102.2021.1891969.                     

11. Rui Chen#, Aravindhan Ganesan#, Elena Arutyunova, Joanne M. Lemieux, Khaled Barakat. 2020. Targeting B7-1 in Immunotherapy. Medicinal Research Reviews. 40(2), 654-682. 

12. Aravindhan Ganesan, Marawan Ahmed, Isobel Okoye, Elena Arutyunova, Dinesh Babu, Will L. Turnbull, Joydeb Kumar Kundu, Justin Shields, Katharine Cheryl Agopsowicz, Lai Xu, Guangzhi Zhang, Tae Chul Moon, Seyedeh Nargess Hosseini, Mary Hitt, John Walker, Michael Smylie, Frederick G. West, Arno G. Siraki, Joanne M. Lemieux, Shokrollah Elahi, D. Lorne Tyrrell, Michael Houghton and Khaled Barakat. 2020. Comprehensive in vitro characterization of PD-L1 inhibitors. Scientific Reports. 9 (1) 2054-2322. 

13. Tianhua Feng, Subha Kalyaanamoorthy, Aravindhan Ganesan, Khaled Barakat. 2019. Atomistic modeling and molecular dynamics analysis of human CaV1.2 channel using external electric field and ion pulling simulations. Biochemica et Biophysica Acta-General Subjects. 1863 (6), 1116-1126.

14. Aravindhan Ganesan, Tae Chul, Khaled Barakat. 2018. Revealing the atomistic details behind the binding of B7-1 to CD28 and CTLA-4: A comprehensive protein-protein modelling study. Biochemica et Biophysica Acta-General Subjects. 1862 (12): 2764-2778.

15. Shawkat Islam, Aravindhan Ganesan, Rebecca Auchettl, Oksana Plekan, Robert G. Acres, Feng Wang and Kevin Prince. 2018. Electronic structure and intramolecular interactions in three methoxyphenol isomers. The Journal of Chemical Physics. 149 (13):134312.

16. Aravindhan Ganesan, Theinmozhi Arulraj, Tahir Choulli, Khaled Barakat. 2018. A mathematical modelling tool for unravelling the antibody-mediated effects on CTLA-4 interactions. BMC Medical Informatics and Decision Making. 18:37. 1-17. 

17. Jalily H. Horia#, Aravindhan Ganesan#, Marawan Ahmed, Khaled Barakat. 2018. Effects of protein-protein interactions and ligand binding on the ion permeation in KCNQ1 potassium channel. PloS one. 13(2). e0191905.  2-26. *Rile first authors. 

18. Aravindhan Ganesan, Michelle Coote, Khaled Barakat. 2017. Molecular time-machines to unravel key biological events for drug design. WIREs: Computational Molecular Science. 7. e1306. 1-21. [Impact Factor: 8.836].

19. Mitchelle D Nothling, Aravindhan Ganesan, Karmen Condic-Jurkic,Eric Pressley,Ashley Davalos, Michael R. Gotrik, Zeyun Xiao, Ezat Koshdel, Craig J. Hawker, Megan L. OMara, Michelle Coote, Luke A. Connal. 2017. Simple design of an enzyme inspired supported catalyst based on a catalytic triad. Chem. 2. 732-745.  

20.   Aravindhan Ganesan, Khaled Barakat. 2017. Applications of computer-aided approaches in the development of Hepatitis C antiviral agents. Expert Opinion on Drug Discovery. 12. 407-425. [Impact Factor: 4.692].

21.   Marawan Ahmed, Jalily H. Horia#, Aravindhan Ganesan#, Michael Houghton, Khaled Barkat. 2017. Modeling the human Nav1.5 sodium channel: structural and mechanistic insights of ion permeation and drug blockade. Drug Design, Development and Therapy. 11. 2301-232. 

22.  Aravindhan Ganesan, Khaled Barakat. 2017. Solubility: A speed-breaker on the drug discovery highway, MOJ Bioequivalence & Bioavailability. 3. 00033. 

23.  Aravindhan Ganesan, Michelle Coote, Khaled Barakat. 2017. Molecular dynamics-driven drug discovery: Leaping forward with confidence. Drug Discovery Today. 22. 249-269. [Impact Factor: 6.848].

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Book chapter

Justine C Williams, Stanley Opare, Senthil Kumar Sugadoss, Aravindhan Ganesan, Subha Kalyaanamoorthy. 2021. Chapter X. Virtual screening techniques in Pharmaceutical Research. Edited by Marianna Torok. Contemporary Chemical Approaches for Green and Sustainable Drugs. Elsevier, United States. Accepted, in press.