AIMC Topic: Molecular Docking Simulation

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How Feasible Is Docking of PROTACs to POI-E3L Complexes? Testing Physics-Based and ML-Based Docking Tools.

Journal of chemical information and modeling
Targeted protein degradation (TPD) is an innovative drug discovery approach that leverages small molecules to induce proximity between a protein of interest (POI) and an E3 ubiquitin ligase (E3L) for selective degradation. Among TPD modalities, prote...

Selective cytotoxicity of anhydroicaritin in ER-positive breast cancer via ESR1-mediated MAPK and apoptotic signaling.

Chemico-biological interactions
Anhydroicaritin (AHI), a chemically characterized prenylated flavonoid, exhibits strong and selective cytotoxicity against estrogen receptor-positive (ER+) breast cancer cells. In this study, we aimed to elucidate its molecular and cellular toxicolog...

Design of Carbon Nanotube Inhibitors for Main Proteinase of SARS-CoV-2: A Combined Deep Learning and Molecular Dynamics Simulation Study.

The journal of physical chemistry. B
The rapid development of machine learning (ML) and deep learning (DL) methods provides new opportunities for innovative drug discovery. While these techniques are widely used in docking organic molecules (drugs) with protein, an evaluation of the per...

Synergistic approach utilizing bioinformatics, machine learning, and traditional screening for the identification of novel CSK inhibitors targeting hepatocellular carcinoma.

Journal of computer-aided molecular design
The overexpression or activation of C-terminal Src kinase (CSK) has been recognized as a pivotal factor in the progression of hepatocellular carcinoma (HCC), positioning CSK as a promising therapeutic target. Despite this potential, no CSK-specific i...

Drug repurposing identifies novel Wee1 kinase inhibitors for triple negative breast cancer therapeutics.

European journal of medicinal chemistry
Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer with limited treatment options. Wee1 kinase, a critical regulator of the G2/M checkpoint and DNA replication, is a promising therapeutic target. However, dose dependent as...

Multi-omics and machine learning identify GBP2 as a key therapeutic target of Qingre Kasen granules in lupus nephritis via NF-kappaB modulation.

Renal failure
Lupus nephritis (LN), a severe renal complication of systemic lupus erythematosus (SLE), results from immune abnormalities. Qingre Kasen granules (QS), which have chicory as the main ingredient, play a significant role in treating various inflammator...

Integrating multi-omics and machine learning to decipher the role of GSTP1 in endocrine-disrupting chemical-induced prostate cancer pathogenesis.

European journal of pharmacology
Prostate cancer (PCa) pathogenesis involves complex interactions between genetic susceptibility and exposure to endocrine-disrupting chemicals (EDCs). This study aimed to systematically identify key genes linking EDC exposure to PCa using an integrat...

Insights into ionic liquid-enhanced membrane protein stability through machine learning and molecular simulations.

Physical chemistry chemical physics : PCCP
Protein stability plays a critical role in structural elucidation, enzyme activity, and the storage of protein drugs, where ionic liquids (ILs) have emerged as promising protein stabilizers due to their exceptional biocompatibility and superior solub...

Modeling protein-small molecule conformational ensembles with PLACER.

Proceedings of the National Academy of Sciences of the United States of America
Modeling the conformational heterogeneity of protein-small molecule interactions is important for understanding natural systems and evaluating designed systems but remains an outstanding challenge. We reasoned that while residue-level descriptions of...

Design, synthesis, deep learning-guided prediction, and biological evaluation of novel pyridine-thiophene-based imine-benzalacetophenone hybrids as promising antimicrobial agent.

Journal of computer-aided molecular design
Antimicrobial resistance (AMR) remains a global health crisis, necessitating the development of novel therapeutics against multidrug-resistant pathogens. In this study, ten (10) hybrid imine-benzalacetophenone derivatives (7a-7j), incorporating pyrid...