A5005434924- Protein Structure and Dynamics
- Computational Drug Discovery Methods
- RNA and protein synthesis mechanisms
- Prostate Cancer Treatment and Research
- Enzyme Structure and Function
- Chemical Synthesis and Analysis
- Bioinformatics and Genomic Networks
- Influenza Virus Research Studies
- Respiratory viral infections research
- Monoclonal and Polyclonal Antibodies Research
- Machine Learning in Bioinformatics
- Cellular Mechanics and Interactions
- Antimicrobial Peptides and Activities
- CRISPR and Genetic Engineering
- Biochemical and Structural Characterization
- Epigenetics and DNA Methylation
- Advanced biosensing and bioanalysis techniques
- Microtubule and mitosis dynamics
- Wnt/β-catenin signaling in development and cancer
- Lipid Membrane Structure and Behavior
- RNA Research and Splicing
- RNA Interference and Gene Delivery
- Force Microscopy Techniques and Applications
- Bioactive Compounds and Antitumor Agents
- Cell Adhesion Molecules Research
University of Georgia
2018-2025
Drug Discovery Laboratory (Norway)
2018
Albert Einstein College of Medicine
2014-2017
Yeshiva University
2014-2017
The Bronx Defenders
2015
Institute of Biomedical Sciences, Academia Sinica
2005-2014
National Yang Ming Chiao Tung University
2005-2012
Per- and polyfluoroalkyl substances (PFAS) are synthetic chemicals used in various products, such as firefighting foams non-stick cookware, due to their resistance heat degradation. However, these same properties make them persistent the environment human body, raising public health concerns. This study selected eleven PFAS commonly found drinking water exposed Caenorhabditis elegans concentrations ranging from 0.1 200 µM assess neurodevelopmental toxicity using a high-throughput,...
CRISPR/Cas9 genome editing is a very promising avenue for the treatment of variety genetic diseases. However, it still challenging to encapsulate machinery delivery. Protein N-myristoylation an irreversible co/post-translational modification that results in covalent attachment myristoyl-group N-terminus target protein. It serves as anchor protein associate with cell membrane and determines its intracellular trafficking activity. Extracellular vesicles (EVs) are secreted mediate cell-cell...
Chemoresistance is a major obstacle in prostate cancer (PCa) treatment. We sought to understand the underlying mechanism of PCa chemoresistance and discover new treatments overcome docetaxel resistance.
The interactions of bio-molecules constitute the key steps cellular functions. However, in vivo binding properties differ significantly from their vitro measurements due to heterogeneity environments. Here we introduce a coarse-grained model based on rigid-body representation study how factors such as crowding and membrane confinement affect molecular binding. macroscopic parameters equilibrium constant kinetic rate are calibrated by adjusting microscopic coefficients used numerical...
Abstract The RNA-guided CRISPR-associated Cas9 proteins have been widely applied in programmable genome recombination, base editing or gene regulation both prokaryotes and eukaryotes. SpCas9 from Streptococcus pyogenes is the most extensively engineered with robust manifold functionalities. However, one inherent limitation of its stringent 5′-NGG-3′ PAM requirement that significantly restricts DNA target range. Here, to repurpose as a universal repressor, we generate screen variants...
A good scoring function is essential for molecular docking computations. In conventional functions, energy terms modeling pairwise interactions are cumulatively summed, and the best solution selected. Here, we propose to transform protein-ligand into three-dimensional geometric networks, from which recurring network substructures, or motifs, selected used provide probability-ranked interaction templates with score solutions. novel docking, MotifScore, was developed. It non-energy-based, is,...
Knowledge about the site at which a ligand binds provides an important clue for predicting function of protein and is also often prerequisite performing docking computations in virtual drug design screening. We have previously shown that certain ligand-interacting triangles atoms, called triangles, tend to occur more frequently ligand-binding sites than other parts protein.In this work, we describe new prediction method was developed based on binding site-enriched triangles. The tested 2...
Rufomycins constitute a class of cyclic heptapeptides isolated from actinomycetes. They are secondary metabolites that show promising treatment against Mycobacterium tuberculosis infections by inhibiting novel drug target. Several nonproteinogenic amino acids integrated into rufomycins, including conserved 3-nitro-tyrosine. RufO, cytochrome P450 (CYP)-like enzyme, was proposed to catalyze the formation 3-nitro-tyrosine in presence O2 and NO. To define its biological function, interaction...
Abstract Protein–protein interactions dominate all major biological processes in living cells. We have developed a new Monte Carlo-based simulation algorithm to study the kinetic process of protein association. tested our method on previously used large benchmark set 49 complexes. The predicted rate was overestimated test compared experimental results for group hypothesized that this resulted from molecular flexibility at interface regions interacting proteins. After applying machine...
Abstract Membrane proteins are among the most functionally important in cells. Unlike soluble proteins, they only possess two translational degrees of freedom on cell surfaces, and experience significant constraints their rotations. As a result, it is currently challenging to characterize situ binding membrane proteins. Using receptors CD2 CD58 as testing system, we developed multiscale simulation framework study differences protein kinetics between 3D 2D environments. The association...
The COVID-19 pandemic has caused unprecedented health and economic crisis throughout the world. However, there is no effective medication or therapeutic strategy for treatment of this disease currently. Here, to elucidate inhibitory effects, we first tested binding affinities 11 HIV-1 protease inhibitors their pharmacoenhancers docked onto SARS-CoV-2 main (Mpro), 12 nucleotide-analog RNA dependent polymerase (RdRp). To further obtain drug candidates, screened 728 approved drugs via virtual...
LISE is a web server for novel method predicting small molecule binding sites on proteins. It differs from number of servers currently available such predictions in two aspects. First, rather than relying knowledge similar protein structures, identification surface cavities or estimation energy, computes score by counting geometric motifs extracted sub-structures interaction networks connecting and ligand atoms. These network take into account spatial physicochemical properties...
Wnt signaling and cadherin-mediated adhesion have been implicated in both processes of embryonic development the progression carcinomas. Recent experimental studies revealed that cell close crosstalk with each other. A comprehensive model investigates dynamic balance β-catenins will improve our understanding to We constructed a network evaluate interplay between signaling. The is decomposed into three interdependent modules: adhesion, degradation circle transcriptional regulation. In module,...
Speeding up the drug discovery process is of great significance. To achieve that, high-efficiency methods should be exploited. The conventional wet-bench hardly meet high-speed demand due to time-consuming experiments. Conversely, in silico approaches are much more efficient for and design. However, usually serve as a supportive role research processes. fully exert strength computational methods, we propose protocol which integrates various approaches, from de novo protein structure...
Although scientists around the world have put lots of effort into development new treatments for COVID-19 since outbreak, no drugs except Veklury (remdesivir) been approved by FDA. There is an urgent need to discover some alternative antiviral treatment COVID-19. Because polyphenols shown possess activities, here we conducted a large-scale virtual screening more than 400 polyphenols. Several lead compounds such as Petunidin 3-O-(6″-p-coumaroyl-glucoside) were identified promising binding...
Resveratrol, the most widely studied natural phytochemical, has been shown to interact with different target proteins. Previous studies show that resveratrol binds and inhibits DNA polymerases some other enzymes; however, binding functioning mechanisms remain unknown. The elucidated knowledge of inhibitory will assist us in new drug discovery. We utilized molecular docking dynamics (MD) simulation reveal how structurally similar compounds bind various nucleotide-dependent enzymes,...
An increasing number of studies have demonstrated the antiviral nature polyphenols, and many polyphenols been proposed to inhibit SARS-CoV or SARS-CoV-2. Our previous study revealed inhibitory mechanisms against DNA polymerase α HIV reverse transcriptase show that can block elongation by competing with incoming NTPs. Here we applied computational approaches examine if some also RNA (RdRp) in SARS-CoV-2, identified better candidates than remdesivir, FDA-approved drug RdRp, terms estimated...