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Articles 1 - 6 of 6
Full-Text Articles in Entire DC Network
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 = …
Oxygen-Induced Surface Reconstructions On Curved Ag(111), Marie Turano, Ludo B. F. Juurlink, Maxwell Z. Gillum, Elizabeth A. Jamka, George Hildebrandt, Faith J. Lewis, Daniel Killelea
Oxygen-Induced Surface Reconstructions On Curved Ag(111), Marie Turano, Ludo B. F. Juurlink, Maxwell Z. Gillum, Elizabeth A. Jamka, George Hildebrandt, Faith J. Lewis, Daniel Killelea
Chemistry: Faculty Publications and Other Works
The adsorption of oxygen and the resultant O-induced surface reconstructions are key components in heterogeneously catalyzed reactions on silver metal surfaces. O uptake and reconstructions on planar Ag(111) are well-characterized, and in this paper, we show that curved Ag(111) features similar O adsorption and reconstructions. Through a systematic scanning tunneling microscope study of a curved Ag(111) single crystal exposed to gas-phase atomic oxygen at a temperature of 525 K, we observed Oad and, upon higher coverages, saw p(4 4) and p(4 5 p3) reconstructions form on both the A-type and B-type steps. Exposures at low temperatures (< 500 K) resulted in the formation of subsurface oxygen and the appearance of a stripe pattern and amorphous phase on the surface. Upon heating, stable surface reconstructions were formed. Although the geometric arrangement of atoms along the steps were different, A-type and B-type steps formed the same reconstructions. In addition, the B-type steps also saw the formation of several different features atop the oxygen reconstructions.
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 …
Cyclobutanone Inhibitor Of Cobalt-Functionalized Metallo-Γ-Lactonase Aiia With Cyclobutanone Ring Opening In The Active Site, Cory T. Reidl, Romila Mascarenhas, Thahani S. Habeeb Mohammad, Marlon R. Lutz Jr, Pei W. Thomas, Walter Fast, Dali Liu, Daniel P. Becker Ph.D.
Cyclobutanone Inhibitor Of Cobalt-Functionalized Metallo-Γ-Lactonase Aiia With Cyclobutanone Ring Opening In The Active Site, Cory T. Reidl, Romila Mascarenhas, Thahani S. Habeeb Mohammad, Marlon R. Lutz Jr, Pei W. Thomas, Walter Fast, Dali Liu, Daniel P. Becker Ph.D.
Chemistry: Faculty Publications and Other Works
An α-amido cyclobutanone possessing a C10 hydrocarbon tail was designed as a potential transition-state mimetic for the quorum-quenching metallo-γ-lactonase autoinducer inactivator A (AiiA) with the support of in-house modeling techniques and found to be a competitive inhibitor of dicobalt(II) AiiA with an inhibition constant of Ki = 0.007 ± 0.002 mM. The catalytic mechanism of AiiA was further explored using our product-based transition-state modeling (PBTSM) computational approach, providing substrate-intermediate models arising during enzyme turnover and further insight into substrate–enzyme interactions governing native substrate catalysis. These interactions were targeted in the docking of cyclobutanone hydrates into the active site of …
Gcn5-Related N-Acetyltransferases (Gnats) With A Catalytic Serine Residue Can Play Ping-Pong Too, Jackson T. Baumgartner, Thahani S. Habeeb Mohammad, Mateusz P. Czub, Karolina A. Majorek, Xhulio Arolli, Cillian Variot, Madison Anonick, Wladek Minor, Miguel A. Ballicora, Daniel P. Becker Ph.D., Misty L. Kuhn
Gcn5-Related N-Acetyltransferases (Gnats) With A Catalytic Serine Residue Can Play Ping-Pong Too, Jackson T. Baumgartner, Thahani S. Habeeb Mohammad, Mateusz P. Czub, Karolina A. Majorek, Xhulio Arolli, Cillian Variot, Madison Anonick, Wladek Minor, Miguel A. Ballicora, Daniel P. Becker Ph.D., Misty L. Kuhn
Chemistry: Faculty Publications and Other Works
Enzymes in the Gcn5-related N-acetyltransferase (GNAT) superfamily are widespread and critically involved in multiple cellular processes ranging from antibiotic resistance to histone modification. While acetyl transfer is the most widely catalyzed reaction, recent studies have revealed that these enzymes are also capable of performing succinylation, condensation, decarboxylation, and methylcarbamoylation reactions. The canonical chemical mechanism attributed to GNATs is a general acid/base mechanism; however, mounting evidence has cast doubt on the applicability of this mechanism to all GNATs. This study shows that the Pseudomonas aeruginosa PA3944 enzyme uses a nucleophilic serine residue and a hybrid ping-pong mechanism for catalysis instead …
Atomic-Resolution 1.3 Å Crystal Structure, Inhibition By Sulfate, And Molecular Dynamics Of The Bacterial Enzyme Dape, Matthew Kochert, Boguslaw P. Nocek, Thahani S. Habeeb Mohammad, Elliot Gild, Kaitlyn Lovato, Tahirah K. Heath, Richard C. Holz, Kenneth W. Olsen, Daniel P. Becker Ph.D.
Atomic-Resolution 1.3 Å Crystal Structure, Inhibition By Sulfate, And Molecular Dynamics Of The Bacterial Enzyme Dape, Matthew Kochert, Boguslaw P. Nocek, Thahani S. Habeeb Mohammad, Elliot Gild, Kaitlyn Lovato, Tahirah K. Heath, Richard C. Holz, Kenneth W. Olsen, Daniel P. Becker Ph.D.
Chemistry: Faculty Publications and Other Works
We report the atomic-resolution (1.3 Å) X-ray crystal structure of an open conformation of the dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE, EC 3.5.1.18) from Neisseria meningitidis. This structure [Protein Data Bank (PDB) entry 5UEJ] contains two bound sulfate ions in the active site that mimic the binding of the terminal carboxylates of the N-succinyl-l,l-diaminopimelic acid (l,l-SDAP) substrate. We demonstrated inhibition of DapE by sulfate (IC50 = 13.8 ± 2.8 mM). Comparison with other DapE structures in the PDB demonstrates the flexibility of the interdomain connections of this protein. This high-resolution structure was then utilized as the …