Conformational Aspects in the Design of Inhibitors for Serine Hydroxymethyltransferase (SHMT): Biphenyl, Aryl Sulfonamide, and Aryl Sulfone Motifs

Abstract

Malaria remains a major threat to mankind due to the perpetual emergence of resistance against marketed drugs. Twenty-one pyrazolopyran-based inhibitors bearing terminal biphenyl, aryl sulfonamide, or aryl sulfone motifs were synthesized and tested towards serine hydroxymethyltransferase (SHMT), a key enzyme of the folate cycle. The best ligands inhibited Plasmodium falciparum (Pf) and Arabidopsis thaliana (At) SHMT in target, as well as PfNF54 strains in cell-based assays in the low nanomolar range (18-56 nm). Seven co-crystal structures with P. vivax (Pv) SHMT were solved at 2.2-2.6 Å resolution. We observed an unprecedented influence of the torsion angle of ortho-substituted biphenyl moieties on cell-based efficacy. The peculiar lipophilic character of the sulfonyl moiety was highlighted in the complexes with aryl sulfonamide analogues, which bind in their preferred staggered orientation. The results are discussed within the context of conformational preferences in the ligands.

Potent Inhibitors of Plasmodial Serine Hydroxymethyltransferase (SHMT) Featuring a Spirocyclic Scaffold

“…The overall conformation of the spirocyclic system in each co‐crystal structure is in good agreement with the small‐molecule X‐ray crystal structure of (±)‐ 42 (Supporting Information, Section S5.3.2, Figure S22). The binding mode of these ligands resembles that of previous pyrazolopyran‐based molecules; however, subtle differences are distinguishable. The pyrazolopyran core forms three strong hydrogen‐bonding interactions through the vinylogous cyanamide with the side chain of Thr357 and the backbone C=O of Leu124 and Gly128 (Figure A and Supporting Information, Section S5.1, Figure S15 A).…”

“…Molecular modeling with MOLOC, by using previously obtained co‐crystal structures with pyrazolopyran‐based inhibitors, was used to guide the structural modifications of the ligands. As shown in the schematic representation of the binding mode of carboxylate (+)‐ 18 at the active site of Pv SHMT (PDB ID: https://www.rcsb.org/structure/5GVN, 2.3 Å resolution) (Figure ), two sub‐pockets are distinguishable: the pyrazolopyran core binds into the pterin binding pocket, which normally hosts the pterin core of H 4 F (PDB ID: https://www.rcsb.org/structure/4OYT, 2.4 Å), whereas the bicyclic scaffold occupies the para ‐aminobenzoate ( p ABA) channel.…”

“…The ligands reported herein feature a spirocyclic motif on the 4‐position of the pyran ring to address a small lipophilic pocket within the pterin binding site (see below). The choice of fragments occupying the p ABA channel was guided by the results of our previous structure–activity relationship (SAR) studies …”

“…Amino acid analogues, such as d ‐serine, d ‐threonine, and thiosemicarbazide, were also investigated, but no significant inhibition was observed either . We recently demonstrated that pyrazolopyran‐based inhibitors, such as carboxylate (±)‐ 18 (Figure ), could inhibit Pf SHMT in the lower nanomolar IC 50 range and were highly effective (half‐maximal effective concentration (EC 50 )) in cell‐based assays against the Pf NF54 strain . Several co‐crystal structures with Pv SHMT showed that these highly preorganized ligands nicely occupy the H 4 F binding pocket of the enzyme.…”

“…[27] We recently demonstrated that pyrazolopyran-based inhibitors, such as carboxylate (AE)-18 ( Figure 1), could inhibit PfSHMT in the lower nanomolarI C 50 range and were highly effective (half-maximaleffective concentration (EC 50 )) in cell-based assays against the PfNF54 strain. [32][33][34] Several co-crystal structures with PvSHMT showed that theseh ighly preorganized ligands nicely occupy the H 4 F bindingp ocket of the enzyme. Finally,w ev alidated SHMT as a druggable target for antimalarials by achieving significant in vivo efficacy in a P. falciparum severe combined immunodeficiency (SCID) mousemodel.…”