Non-stoichiometric inhibition in integrated lead finding – a literature review

Abstract

Over the last few years, awareness of non-stoichiometric inhibitors within screening libraries and HTS hit lists has considerably increased, not only in the pharmaceutical industry but also in the academic drug discovery community. This has resulted in a variety of methods to detect and handle such compounds. These range from in silico approaches to flag suspicious compounds, and counterassays to measure non-stoichiometric inhibition, to biophysical methods that positively demonstrate stoichiometric binding. In addition, novel technologies to verify target engagement within cells are becoming available. While still a time- and resource-consuming nuisance, non-stoichiometric inhibitors therefore do not fundamentally jeopardize the discovery of low molecular weight lead and drug candidates. Rather, they should be viewed as a manageable issue that with appropriate expertise can be overcome through integration of the above-mentioned approaches.

The Role of the Phosphorus Atom in Drug Design

“…Phosphonate‐containing compounds have also been shown for allosteric inhibitors of FPPS according to an integrated lead finding approach . Salicylic acid and quinoline derivatives 79 – 81 are representative allosteric inhibitors, the binding site for which is located close to the homoallylic site.…”

“…[90] Molecular modeling studies through ah omology model from P. vivax indicated that this compound binds at the allylic site of the enzymec oordinating three Mg 2 + ions. [90] Phosphonate-containing compounds have also been shown for allosterici nhibitors of FPPS accordingt oa nintegratedl ead finding [93] approach. [94,95] Salicylica cid and quinoline derivatives 79-81 are representative allosterici nhibitors, the binding site for which is located closet ot he homoallylic site.…”

Computational Multitarget Drug Design

“…Again, aggregation itself is not a definite exclusion criteria and can be detected by light scattering, flow cytometry, or NMR integrated with other established assays. 91 The pharmacophore-and docking-based multitarget drug design methods will continue to evolve. As the number of available chemical compounds increases, the gap between in silico chemoinformatics and biological exploration will narrow.…”

“…Emphasis on polypharmacology as a lead discovery strategy does not mean choosing any promiscuous lead for optimization. While computational methods are less expensive than HTS, ligands selected from in silico methods should also be carefully examined, to avoid nonspecific activities . In recent years, the Pan-Assay INterference compoundS (PAINS) criteria have been widely used to avoid false positive compounds that are chemically reactive, interfere with fluorescent assays, or aggregate. − This type of analysis only accounts for possible false activity.…”

“…This method could be helpful for early-stage-compound consideration, especially for validation using nonionic detergents in the screening assay. Again, aggregation itself is not a definite exclusion criteria and can be detected by light scattering, flow cytometry, or NMR integrated with other established assays …”