Ann Varghese, Ph.D.

ORISE Postdoctoral Research Fellow in Computational Chemistry. Experienced in using computational tools and techniques to analyze biological systems and uncover valuable insights to contribute to the development of novel pharmaceutical solutions. Committed to continuous learning, and professional growth and successful at managing multiple priorities with a positive attitude.

• Experienced in performing MD, QM and QM/MM calculations
• Parallel computing: CUDA, MPI
• Software: Turbomole, Chemshell, GAMESS, Firefly electronic package, Gaussian, ORCA
• Shell scripting: Bash (beginner)
• Simulation tools: AMBER, VMD, Chimera, PyMOL, Schrodinger (beginner)
• Utility programs: Chemcraft, Gauss View, GRACE
• Applications: HPC, Windows, Linux, Microsoft Office (Word, Excel, Powerpoint)

• Varghese, A., Liu, B.; Li, Z. et al. Exploring the 3D structures of SARS CoV-2 PLpro (Manuscript in preparation).
• Liu, B.; Huang, R.; Xia, M; Dong, F.; Guo, W.; Li, B.; Varghese, A. et al. Exploring Leachables and Extractables from Medical Devices: Sources, Detection Methods, and Future Prospects (Manuscript in preparation).
• Li, Z.; Huang, R.; Xia, M.; Chan, N.; Guo, W.; Liu, J.; Dong, F.; Liu, B.; Varghese, A. et al. Decoding the κ Opioid Receptor: Advancements in Structural Understanding and Implications for Opioid Analgesic Development (Manuscript in preparation).
• Gorantla, K.; Waheed, S.O.; Krishnan, A.; Varghese, A. et al. Novel Insights into the Catalytic Mechanism of Collagenolysis by Zn (II)-Dependent Matrix Metalloproteinase-1 (Requested revision in process, Biochem).
• Krishnan, A.; Waheed, S. O.; Varghese, A. et al. Unusual Catalytic Strategy by Non-Heme Fe(II)/2- Oxoglutarate-Dependent Aspartyl Hydroxylase AspH. RSC Chem Sci. 2024, 15, 3466-3484.V
• Varghese, A.; Waheed, S. O.; Gorantla, K. et al. Catalytic Mechanism of Collagen Hydrolysis by Zinc(II)-Dependent Matrix Metalloproteinase-1. J. Phys. Chem. B. 2023, 127(45), 9697-9709.
• Varghese, A.; Waheed, S. O.; Chaturvedi, S. S.; et al. Revealing the Catalytic Strategy of FTO. Chem Catal. 2023.
• Waheed, S. O.; Varghese, A.; DiCastri, I. et al. Mechanism of the Early Catalytic Events in the Collagenolysis by Matrix Metalloproteinase-1 ChemPhysChem 2022, 24(3), e202200649.
• Waheed, S. O.; Varghese, A.; Chaturvedi, S. S. et al. How Human TET2 Enzyme Catalyzes the Oxidation of Unnatural Cytosine Modifications in Double-Stranded DNA ACS Catal. 2022, 12, 5327-5344.
• Mathew, C. M.; Varghese, A.; Sugunan, S. K. et al. Rapid Computational approach towards designing singlet-fission chromophores by tuning diradical character of heteroatom-doped polycyclic aromatic hydrocarbons using atom-specific Fukui function. . Phys. Chem. A. 2022, 126(10), 1579-1590.
• Varghese, A.; Chaturvedi, S. S.; DiCastri, I. et al. Effects of the Nature of Metal Ion, Protein and Substrate on the Catalytic Center in Matrix Metalloproteinase-1: Insights from Multilevel MD, QM/MM and QM studies. ChemPhysChem 2021 23(4) e202100680.
• Varghese, A.; Chaturvedi, S. S.; Fields, G. B.; et al. A Synergy between the Catalytic and Structural Zn(II) Ions and the Enzyme and Substrate Dynamics Underlies the Structure–Function Relationships of Matrix Metalloproteinase Collagenolysis. . Biol. Inorg. Chem. 2021, 26(5), 583–597.

• Varghese, A.; Chaturvedi, S. S.; Fields, G. B.; et al. Computational studies on the effect of the Zn(II) ions and the substrate in Matrix Metalloproteinase-1. ACS Upper Peninsula Local Section (UPLS) Meeting Fall 2022, Northern Michigan University, Marquette, MI.
• Varghese, A.; Chaturvedi, S. S.; Fields, G. B.; et al. Computational study of the Synergy between the Catalytic and Structural Zn(II) Ions and the Protein Environment in Matrix Metalloproteinase-1. ACS National Meeting Fall 2022, Bioinorganic Chemistry Session, Chicago, IL.
• Varghese, A.; Chaturvedi, S. S.; Fields, G. B.; et al. Computational studies on the role of the Zn(II) ions in the enzyme•substrate complex of MMP-1. Chemistry Department Poster Session Fall 2021, Michigan Technological University, Houghton, MI.
• Varghese, A.; Chaturvedi, S. S.; Fields, G. B.; et al. Computational studies on the role of the Zn(II) ions in the enzyme•substrate complex of MMP-1. ACS Upper Peninsula Local Section (UPLS) Meeting Fall 2021, Northern Michigan University, Marquette, MI.
• Varghese, A.; Chaturvedi, S. S.; Fields, G. B.; et al. Computational studies on the role of the Zn(II) ions in the enzyme•substrate complex of MMP-1. ACS National Meeting Fall 2021, Bioinorganic Chemistry Session, Virtual.