Captopril scaffold and key pharmacophoric features

Captopril is an angiotensin converting enzyme inhibitor widely used as an antihypertensive agent and has been repurposed as a starting scaffold for the design of NDM-1 inhibitors [16,30-43]. Captopril is an experimentally validated inhibitor of NDM-1 as it can interact with the active site via metal coordination. Crystallographic evidence confirmed that captopril binds in the NDM-1 active site, supporting its role as a lead compound for inhibitor design [26,39]. The inhibitory activity of captopril is based on a defined pharmacophore composed of a 3-mercapto-2-methylpropanoyl fragment attached to a proline moiety, as shown in Figure 2.

Figure 2.: Chemical structure of captopril, highlighting key pharmacophoric features

The thiol group is the main anchor, which coordinates the binuclear Zn (II) centre and, therefore, disrupts the catalytic activity, while the proline moiety prevents conformational flexibility and promotes a binding geometry favourable for enzyme inhibition [36-39]. Simplification studies without altering the thiol group have produced more active analogues with low-micromolar IC50 values [40]. Stereochemistry plays a significant role in the activity of captopril. D-captopril has been shown to be significantly more potent against NDM-1 than L-captopril in the same assay format, with reported IC50 values of 20.1±1.5 and 157.4±1.3 μM, respectively [39], whereas previously measured values were 7.9 μM for D-captopril and 39 μM for L-captopril, demonstrating the same pattern [40], even though absolute potency varied according to assay conditions. Such stereochemical effects were attributed to variation in the binding orientation and geometry of metal coordination in the active site of NDM-1, where the D-configuration places the thiol group in a favourable position within the NDM-1 active site [39]. For both captopril structures, the pyrrolidine ring of the proline moiety participates in hydrophobic interactions with valine (V73) from the L3 loop, whereas the carboxylate group is involved in a hydrogen bond with the backbone amine of asparagine (N220). D-captopril adopts an altered binding orientation to maximize interactions with the enzyme by increasing hydrophobic interactions with methionine (M67) and phenylalanine (F70) residues. Additionally, the carboxylate group of D-captopril forms water-mediated hydrogen-bonding interactions with lysine (K211), leucine (L218), and histidine (H189) residues. The methyl group of captopril is also involved in the interaction with the enzyme through hydrophobic interactions with methionine (M67) and tryptophan (W93) [39], as shown in Figure 3.

Figure 3.: A: Two-dimensional interaction map of captopril within the NDM-1 active site, highlighting dual zinc coordination, hydrogen bonding, electrostatic and hydrophobic interactions; B: Corresponding three-dimensional structure demonstrating thiol-mediated coordination. Figure is generated by the author using BIOVIA Discovery Studio based on publicly available Protein Data Bank data (PDB ID: 5ZJ2) [38]