Optimization of TRPV6 Calcium Channel Inhibitors Using a 3D Ligand‐Based Virtual Screening Method

Abstract

Herein, we report the discovery of the first potent and selective inhibitor of TRPV6, a calcium channel overexpressed in breast and prostate cancer, and its use to test the effect of blocking TRPV6-mediated Ca(2+)-influx on cell growth. The inhibitor was discovered through a computational method, xLOS, a 3D-shape and pharmacophore similarity algorithm, a type of ligand-based virtual screening (LBVS) method described briefly here. Starting with a single weakly active seed molecule, two successive rounds of LBVS followed by optimization by chemical synthesis led to a selective molecule with 0.3 μM inhibition of TRPV6. The ability of xLOS to identify different scaffolds early in LBVS was essential to success. The xLOS method may be generally useful to develop tool compounds for poorly characterized targets.

Natural product inspired optimization of a selective TRPV6 calcium channel inhibitor

“…9). Similar to 1, 17 39 did not activate nor inhibit TRPV1, which is the only known TRP target of capsaicin (Fig. S2 †).…”

Identification of potent and selective small molecule inhibitors of the cation channel TRPM4

“…To identify potent TRPM4 inhibitors, we performed a focused screening campaign using LBVS with xLOS (Simonin et al ., ) to search a catalogue of 900 000 commercially available drug‐like small molecules for analogues of the known but relatively weak TRPM4 inhibitors 9‐phenanthrol, FFA and glibenclamide (Figure ). We selected 214 compounds among the top scoring virtual hits, purchased 1 mg solid samples that we conditioned as 10 mM stock solution in DMSO and screened these compounds for inhibition of TRPM4 at 10 μM using 9‐phenanthrol (25 μM) as positive control (Figure A, panel i).…”

“…Recently, virtual screening methods have emerged as an efficient approach for identifying potent and specific inhibitors for different ion channels (Langer and Krovat, ; Fernández‐Ballester et al ., ; Simonin et al ., ). In this study, we carried out an initial virtual screening using an in‐house developed pharmacophore similarity search algorithm: xLOS, which compared the spatial overlap between a catalogue of commercially available drug‐like small molecules to the three reference TRPM4 inhibitors, 9‐phenanthrol, glibenclamide and FFA.…”

“…The first round of virtual screening ( VS ) was performed in the Princeton database, which contains 900 000 purchasable compounds, using three different reference compounds, namely, 9‐phenanthrol, glibenclamide and flufenamic acid. The VS was carried out with an in‐house developed extended Ligand Overlap Score (xLOS) method, which computes the 3D‐shape and –pharmacophore similarity between any two compounds (typically reference and database compounds) (Simonin et al ., ). The single lowest energy 3D‐models of reference and database molecules were generated using the CORINA programme available from Molecular Networks Pvt.…”

“…We performed LBVS with the 3D‐shape and pharmacophore similarity algorithm xLOS (atom category eXtended Ligand Overlap Score) as a similarity measure. xLOS is a scaffold‐hopping algorithm (Schneider et al ., ) that recently proved its validity in related searches for selective Ca 2+ channel (Simonin et al ., ) and kinase inhibitors (Kilchmann et al ., ). Activity screening of a small series of compounds selected by the LBVS procedure allowed us to rapidly identify anthranilic amides 4 and 5 , two analogues of FFA with a 10‐fold stronger and more selective inhibition of TRPM4 compared with 9‐phenanthrol (Figure ).…”