Docking-Based Virtual Screening of Covalently Binding Ligands: An Orthogonal Lead Discovery Approach

Abstract

In pharmaceutical industry, lead discovery strategies and screening collections have been predominantly tailored to discover compounds that modulate target proteins through noncovalent interactions. Conversely, covalent linkage formation is an important mechanism for a quantity of successful drugs in the market, which are discovered in most cases by hindsight instead of systematical design. In this article, the implementation of a docking-based virtual screening workflow for the retrieval of covalent binders is presented considering human cathepsin K as a test case. By use of the docking conditions that led to the best enrichment of known actives, 44 candidate compounds with unknown activity on cathepsin K were finally selected for experimental evaluation. The most potent inhibitor, 4-(N-phenylanilino)-6-pyrrolidin-1-yl-1,3,5-triazine-2-carbonitrile (CP243522), showed a K(i) of 21 nM and was confirmed to have a covalent reversible mechanism of inhibition. The presented approach will have great potential in cases where covalent inhibition is the desired drug discovery strategy.

Development of N-(Functionalized benzoyl)-homocycloleucyl-glycinonitriles as Potent Cathepsin K Inhibitors

“…It is worth mentioning that compound 6 has at least 3-fold greater selectivity ratio over Cat L compared to Balicatib ( As nitriles are known to be reversible inhibitors of cathepsins, we next checked the reversibility of Cat K inhibition by compounds 5, 6 and 9 as described earlier for Cat K by rapid 100-fold dilution of the preformed enzyme-inhibitor complexes into the buffer solution containing the substrate. 41 The irreversible cysteine Cat inhibitor E-64 42 was used as a test control. As shown in Figure S2, upward curvatures were observed for all three compounds, characteristic for reversible inhibitors, but not for E-64, in agreement with previous findings.…”

“…Initially, reversibility of binding of compounds 5, 6, and 9 to Cat K was first evaluated as described elsewhere. 41 Briefly, the compounds (5 µM) and Cat K (1 µM) were incubated for 30 minutes, which is sufficient for completion of the reaction, before rapidly diluted 100-fold in the reaction buffer containing the substrate. Progress of the reaction was then monitored continuously as described above.…”

Acoplamiento Molecular: Avances Recientes y Retos

“…In contrast, instances where covalent ligands are useful have gained notoriety such as Romidepsin, a histone deacetylase inhibitor and prodrug (VanderMolen, McCulloch, Pearce & Oberlies, 2011). Actually, covalent modifiers may be more selective and effective, and more specific for infectious diseases (Schröder et al, 2013). The overall interest towards rational design and development of covalent inhibitors is growing.…”

Protein Ligand Docking in Drug Discovery

“…The main stream of rational drug design relies on non-covalent interactions as the mechanism of the functionality of the drugs [178,179], which in itself justifies the emphasis precisely on non-covalent interactions. However, some specific drugs, called covalent drugs, employ as part of their binding mechanism the formation of a covalent interaction with the target.…”