Resurrecting the phoenix: When an assay fails.

  title={Resurrecting the phoenix: When an assay fails.},
  author={Bharath Srinivasan and Vasudev Kantae and James Robinson},
  journal={Medicinal research reviews},
Understanding protein-small-molecule interactions is a critical component of rational drug-design. Structure-activity relationship (SAR)-guided medicinal chemistry is informed by the biological outcome, as assessed by biochemical activity or cellular effect, of chemical modifications on small molecules. The effectiveness of SAR is reliant on the sturdiness and durability of assay design and the quality of information garnered from assays. Lack of quality data at this step can lead to… 
2 Citations

A Novel High-Throughput FLIPR Tetra–Based Method for Capturing Highly Confluent Kinetic Data for Structure–Kinetic Relationship Guided Early Drug Discovery

The use of the fluorescent imaging plate reader (FLIPR), a charge-coupled device (CCD) camera technology, is described, as a potential high-throughput tool for generating biochemical kinetic data with smaller time intervals and demonstrated the collection of highly confluent time-course data for various kinase protein targets with reasonable throughput to enable SKR-guided medicinal chemistry.

Explicit Treatment of Non‐Michaelis‐Menten and Atypical Kinetics in Early Drug Discovery **

This review strives to present an overview of enzyme kinetic mechanisms that are atypical and, oftentimes, do not conform to the classical MM kinetics to enable effective screening and characterisation of small‐molecule inhibitors with desirable physiological outcomes.



Enzyme–Inhibitor Interactions and a Simple, Rapid Method for Determining Inhibition Modality

The pattern of changes in IC50 that accompany increasing substrate concentration are shown to be diagnostic of specific inhibition modalities and replots of IC50 as a function of the ratio [S]/KM are recommended as a simple and rapid means of assessing inhibition modality.

PAINS in the Assay: Chemical Mechanisms of Assay Interference and Promiscuous Enzymatic Inhibition Observed during a Sulfhydryl-Scavenging HTS

The chemical basis for assay interference and promiscuous enzymatic inhibition for several prominent chemotypes identified by this HTS, including some pan-assay interference compounds (PAINS) are characterized and identified.

Evaluation of enzyme inhibitors in drug discovery. A guide for medicinal chemists and pharmacologists.

  • R. Copeland
  • Biology, Chemistry
    Methods of biochemical analysis
  • 2005
This work has shown that knowing Inhibitor Modality is important for Structure-Based Lead Organization and Associating Cellular Effects with Target Enzyme Inhibition should Require a Certain Affinity for the target Enzyme.

An Aggregation Advisor for Ligand Discovery.

This study investigates an approach that uses lipophilicity, affinity, and similarity to known aggregators to advise on the likelihood that a candidate compound is an aggregator, and finds that 85% of the ligands acting in the 0.1 to 10 μM range in the medicinal chemistry literature are at least 85% similar to a known aggregator with these physical properties and may aggregate at relevant concentrations.

Crystal structure of the human PRMT5:MEP50 complex

The crystal structure of human PRMT5 in complex with MEP50, bound to an S-adenosylmethionine analog and a peptide substrate derived from histone H4 is determined and the structure of the surprising hetero-octameric complex reveals the close interaction between the seven-bladed β-propeller MEP50 and the N-terminal domain ofPRMT5, and delineates the structural elements of substrate recognition.

Specificity of natural and artificial substrates for human Cdc25A.

Data indicate that a significant degree of the specificity of Cdc25 toward its Cdk substrate resides within the catalytic domain itself and yet is in a region(s) that is outside the phosphate binding site of the enzyme.

Insights into the slow‐onset tight‐binding inhibition of Escherichia coli dihydrofolate reductase: detailed mechanistic characterization of pyrrolo [3,2‐f] quinazoline‐1,3‐diamine and its derivatives as novel tight‐binding inhibitors

This work demonstrates that the mode of binding of the inhibitor to the enzyme–NADPH binary complex conforms to the slow‐onset, tight‐binding model and provides novel insights into the role of substitutions on inhibitors of E. coli DHFR.