Skip to content
Log in
Sponsored Have an interesting project or opportunity? → Hire me ↗
Sponsored Artificial Intelligence: A Modern Approach, Global Edition Artificial Intelligence: A Modern Approach, Global Edition

Author

Ke Chen

View on Semantic Scholar

2 papers indexed here

We haven’t gathered this author’s papers yet. Follow them and we’ll fetch their work.

Not the right person? Other researchers publish under this name.

Jul 2026

Biochemical characterization and assay development for adenylosuccinate synthetase Rv0357c from Mycobacterium tuberculosis.

The global rise of drug-resistant Mycobacterium tuberculosis (Mtb) underscores an urgent need for antitubercular agents with novel targets and mechanisms of action. Among these, the de novo purine biosynthesis pathway is essential for Mtb growth and survival, making its constituent enzymes attractive targets for therapeutic intervention. Within this pathway, adenylosuccinate (ADS) synthetase (ADSS) Rv0357c catalyzes the first committed step in biosynthesis of adenosine monophosphate (AMP) by converting inosine monophosphate (IMP) to ADS through a GTP-dependent reaction with l-aspartate. Despite its importance, Mtb ADSS remains poorly characterized at the biochemical level. In this study, we report the expression, purification, and enzymatic characterization of recombinant Mtb ADSS. To overcome the challenge of the enzyme being predominantly expressed as inclusion bodies in Escherichia coli, we established both protein refolding and chaperone-assisted expression strategies to obtain soluble, catalytically active protein. Using complementary spectrophotometric, colorimetric, and fluorescence-based assays, we determined steady-state kinetic parameters and confirmed robust ADSS activity consistent with Michaelis-Menten behaviour. Furthermore, we developed scalable, nonradioactive assays compatible with high-throughput screening (HTS), enabling the quantitative monitoring of ADSS activity via GTP hydrolysis and phosphate release. As a proof of concept, the MESG assay successfully detected inhibition of Mtb ADSS by the previously reported ADSS inhibitor Aurodox, demonstrating its utility for inhibitor characterization and screening. Collectively, these results provide the first comprehensive biochemical framework for studying Mtb ADSS and establish a foundation for structure-guided inhibitor discovery targeting purine biosynthesis as a novel antitubercular strategy.

Vigyasa Singh, Ran Zhang, Ke Chen et al. · 0 citations
Open access Aug 2026

A Medicinal Chemistry-Centered Evaluation of AlphaFold 3 and Boltz-2 Across Diverse Binding Modalities

AlphaFold 3 (AF3) and Boltz-2 are state-of-the-art AI-based tools for biomolecular structure prediction, but whether their predictions provide useful guidance for lead optimization, SAR interpretation, and virtual screening remains insufficiently characterized. We benchmarked their performance using newly determined soluble epoxide hydrolase co-crystal structures and matched activity data together with a curated post-training-cutoff dataset spanning kinases, allosteric modulators, covalent systems, PROTACs, molecular glues, fragments, membrane proteins, RNA binders, and activity-cliff pairs. Both models recovered canonical orthosteric enzyme and kinase complexes, including key DFG/αC conformational states, whereas allosteric, membrane-protein, and induced-proximity complexes remained challenging. Pharmacophore RMSD was often lower than overall ligand RMSD, indicating preservation of key recognition features despite imperfect whole-ligand alignment. AF3 minPAE correlated with pose accuracy, and very low minPAE values (<0.85 Å) were strongly enriched for accurate poses. Model confidence scores were not associated with experimental activity, whereas Boltz-2 predicted affinity captured relative activity trends and distinguished the activity-cliff pair, although its performance varied across ligand series.

Ke Chen, Zuo-Huang Qi, Omar Lozano Ramos et al. · 0 citations