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Biochemistry, Biophysics, and Structural Biology Commons™
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- 12-6-4 (1)
- 2′-O-MT (1)
- 3CLpro (1)
- 3CLpro enzymatic assay (1)
- Anti-Viral assay (1)
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- Biomedical engineering (1)
- Biophysical models (1)
- COVID-19 (1)
- Drug repurposing (1)
- Electronics phototonics and device physics (1)
- ExoN (1)
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- Fluctuating charge model (1)
- Force field (1)
- Helicase (1)
- Intracellular recording (1)
- Ion-induced dipole interaction (1)
- Isindolylmaleimide (BIM) IX (1)
- MD simulations (1)
- MM-GBSA (1)
- Metal ion (1)
- Metalloproteins (1)
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- NendoU (1)
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- PLpro (1)
- RdRP (1)
- SARS-CoV-2 (1)
- Transcranial magnetic stimulation (1)
- Virtual screening (1)
Articles 1 - 3 of 3
Full-Text Articles in Biochemistry, Biophysics, and Structural Biology
Bisindolylmaleimide Ix: A Novel Anti-Sars-Cov2 Agent Targeting Viral Main Protease 3clpro Demonstrated By Virtual Screening Pipeline And In-Vitro Validation Assays, Yash Gupta, Dawid Maciorowski, Samantha E. Zak, Krysten A. Jones, Rahul S. Kathayat, Saara-Anne Azizi, Raman Mathur, Catherine M. Pearce, David J. Ilc, Hamza Husein, Andrew S. Herbert, Ajay Bharti, Brijesh Rathi, Ravi Durvasula, Daniel P. Becker, Bryan C. Dickinson, John M. Dye, Prakasha Kempaiah
Bisindolylmaleimide Ix: A Novel Anti-Sars-Cov2 Agent Targeting Viral Main Protease 3clpro Demonstrated By Virtual Screening Pipeline And In-Vitro Validation Assays, Yash Gupta, Dawid Maciorowski, Samantha E. Zak, Krysten A. Jones, Rahul S. Kathayat, Saara-Anne Azizi, Raman Mathur, Catherine M. Pearce, David J. Ilc, Hamza Husein, Andrew S. Herbert, Ajay Bharti, Brijesh Rathi, Ravi Durvasula, Daniel P. Becker, Bryan C. Dickinson, John M. Dye, Prakasha Kempaiah
Chemistry: Faculty Publications and Other Works
SARS-CoV-2, the virus that causes COVID-19 consists of several enzymes with essential functions within its proteome. Here, we focused on repurposing approved and investigational drugs/compounds. We targeted seven proteins with enzymatic activities known to be essential at different stages of the viral cycle including PLpro, 3CLpro, RdRP, Helicase, ExoN, NendoU, and 2′-O-MT. For virtual screening, energy minimization of a crystal structure of the modeled protein was carried out using the Protein Preparation Wizard (Schrodinger LLC 2020-1). Following active site selection based on data mining and COACH predictions, we performed a high-throughput virtual screen of drugs and investigational molecules (n = …
Bridging The 12-6-4 Model And The Fluctuating Charge Model, Pengfei Li
Bridging The 12-6-4 Model And The Fluctuating Charge Model, Pengfei Li
Chemistry: Faculty Publications and Other Works
Metal ions play important roles in various biological systems. Molecular dynamics (MD) using classical force field has become a popular research tool to study biological systems at the atomic level. However, meaningful MD simulations require reliable models and parameters. Previously we showed that the 12-6 Lennard-Jones nonbonded model for ions could not reproduce the experimental hydration free energy (HFE) and ion-oxygen distance (IOD) values simultaneously when ion has a charge of +2 or higher. We discussed that this deficiency arises from the overlook of the ion-induced dipole interaction in the 12-6 model, and this term is proportional to 1/r …
Somatic Inhibition By Microscopic Magnetic Stimulation, Hui Ye
Somatic Inhibition By Microscopic Magnetic Stimulation, Hui Ye
Biology: Faculty Publications and Other Works
Electric currents can produce quick, reversible control of neural activity. Externally applied electric currents have been used in inhibiting certain ganglion cells in clinical practices. Via electromagnetic induction, a miniature-sized magnetic coil could provide focal stimulation to the ganglion neurons. Here we report that high-frequency stimulation with the miniature coil could reversibly block ganglion cell activity in marine mollusk Aplysia californica, regardless the firing frequency of the neurons, or concentration of potassium ions around the ganglion neurons. Presence of the ganglion sheath has minimal impact on the inhibitory effects of the coil. The inhibitory effect was local to the …