Assistant Professor of Chemistry and Biochemistry

Research Area
Research in Saha lab will involve development and application of novel computational chemistry and biophysics approaches to gain fundamental understanding of remarkable biological processes and their relation to complex diseases. This knowledge will further be used to design small molecules either to inhibit or to enhance particular biological function facilitating drug discovery for cancer and neurodegenerative diseases (e.g., Alzheimer’s, Parkinson’s, Dementia). To achieve this goal, state-of-the-art computer aided drug discovery techniques will be implemented in collaboration with medicinal chemistry, biochemistry and experimental biophysical research groups (both in academia and in pharmaceutical industry). Researchers in Saha lab will develop skills and expertise in advanced molecular modeling techniques (e.g., Machine Learning, Coarse grained Molecular Dynamics, Quantum Mechanics/Molecular Mechanics, Cheminformatics) as well as simulated exposure to computational drug discovery research as in Big Pharma.

Projects

• Understanding protein misfolding through machine learning and large-scale molecular dynamics simulation.
• Design of covalent inhibitors for ubiquitin proteasome system through computational enzymology.
• Understanding mechanochemical process in motor proteins through electrostatic-enhanced coarse-grained molecular dynamics.

Selected Publications (*Corresponding author)

• Deepa Jonnalagadda,† Yasuyuki Kihara,† Aran Groves,† Manisha Ray, Arjun Saha, Hyeon-Cheol Lee, Tomomi Furihata, Takehiko Yokomizo, Edward V. Quadros, Richard Rivera, Jerold Chun “Fingolimod Manipulates Vitamin B₁₂-TCN2-CD320 System to Safeguard against Neuroinflammatory Demyelination” (Under review) (†Co-First author).
• Jiao Zhou, Arjun Saha*, Ziwei Huang*, Arieh Warshel* “Fast and Accurate Prediction of Absolute Binding Free Energies of Covalent Inhibitors for SARS-COV-2 and Proteasome” Journal of the American Chemical Society, 2022, 144, 7568.
• Arjun Saha, Arieh Warshel* “Simulating the Directional Translocation of the Substrate by 26S Proteasome AAA+ Motor in 26S Proteasome” Proceedings of the National Academy of Sciences of the United States of America, 2021, 118, e2104245118.
• Vikrant Tripathy, Arjun Saha,* Krishnan Raghavachari,* “Electrostatically Embedded Molecules-in-Molecules Approach and its Application to Molecular Clusters” Journal of Computational Chemistry, 2021, 42, 719.
• Arjun Saha, Gabriel Oanca, Dibyendu Mondal and Arieh Warshel* “Exploring the Proteolysis Mechanism of the Proteasome” Journal of Physical Chemistry B 2020, 124, 5626.
• Gabriel Oanca, Mojgan Asadi, Arjun Saha, Balajee Ramachandran, Arieh Warshel* “Exploring the Catalytic Reaction of Cysteine Protease” Journal of Physical Chemistry B2020, 124, 11349.
• Arjun Saha, Teena Varghese, Annie Liu, Tara Mirzadegan and Michael Hack* “An Analysis of Different Components of High-Throughput Screening Library” Journal of Chemical Information and Modeling, 2018, 58, 2057.
• Arjun Saha, Amy Shih, Tara Mirzadegan and Mark Seierstad* “Predicting the Binding of Fatty Acid Amide Hydrolase Inhibitors by Free Energy Perturbation” Journal of Chemical Theory and Computation, 2018, 14, 5815.
• Manisha Ray, Arjun Saha, Krishnan Raghavachari, “Hydrogen Evolution from Water using Mo-Oxide Clusters in the Gas Phase: DFT Modeling of a Complete Catalytic Cycle using a Mo₂O₄‾/Mo₂O₅‾ Cluster Couple” Chem. Chem. Phys., 2016, 18, 25687.
• Krishnan Raghavachari* and Arjun Saha, “Accurate Composite Quantum Chemical Models for Large Molecules” Chemical Reviews, 2015, 115, 5643.