Insights into the binding mode of sulphamates and sulphamides to hCA II: crystallographic studies and binding free energy calculations

Abstract

Sulphamate and sulphamide derivatives have been largely investigated as carbonic anhydrase inhibitors (CAIs) by means of different experimental techniques. However, the structural determinants responsible for their different binding mode to the enzyme active site were not clearly defined so far. In this paper, we report the X-ray crystal structure of hCA II in complex with a sulphamate inhibitor incorporating a nitroimidazole moiety. The comparison with the structure of hCA II in complex with its sulphamide analogue revealed that the two inhibitors adopt a completely different binding mode within the hCA II active site. Starting from these results, we performed a theoretical study on sulphamate and sulphamide derivatives, demonstrating that electrostatic interactions with residues within the enzyme active site play a key role in determining their binding conformation. These findings open new perspectives in the design of effective CAIs using the sulphamate and sulphamide zinc binding groups as lead compounds. ARTICLE HISTORY

Native mass spectrometry of human carbonic anhydrase I and its inhibitor complexes

“…In this case, the kinetic energy applied to the system results too high to keep intact the inhibitors bound to the protein. Since the main signal in all the spectra at 300 V belongs to the holo-CA (see SI), this is suggestive for a different binding energy between Zn-protein and inhibitor-Zn adduct, resulting this latter one less stable with higher acceleration energy [ 74 – 76 ]. This is perfectly consistent with the great stabilization that the Zn ion receives from the coordination to the three histidine residues, while the inhibitor establishes only one bond with the metal ion [ 76 ].…”

Benzamide-4-Sulfonamides Are Effective Human Carbonic Anhydrase I, II, VII, and IX Inhibitors

“…The inhibition constants were obtained by non-linear least-squares methods using PRISM 3 and the Cheng-Prusoff equation, as reported earlier [ 62 , 63 , 64 , 65 , 66 , 67 , 68 , 69 , 70 , 71 , 72 , 73 , 74 , 75 ]. All CAs were recombinant proteins produced as reported earlier by our groups [ 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 , 65 , 66 , 67 , 68 , 69 , 70 , 71 , 72 , 73 , 74 , 75 , 76 ].…”

Inhibition of carbonic anhydrase IX targets primary tumors, metastases, and cancer stem cells: Three for the price of one

“…All these studies allowed the detailed understanding of the factors governing activity and selectivity for inhibiting CA IX over other CA isoforms, and are summarized below: the zinc‐binding group of the sulfonamide, sulfamate, and sulfamide is not highly influential for obtaining potent and CA IX‐selective inhibitors. In fact, many classes of such derivatives show similar CA IX inhibitory/selectivity profiles, such as various sulfonamides, sulfamates, and sulfamides The scaffold of the potent and isoform‐selective CA IX inhibitors of this type incorporates aromatic,…”

“…the zinc‐binding group of the sulfonamide, sulfamate, and sulfamide is not highly influential for obtaining potent and CA IX‐selective inhibitors. In fact, many classes of such derivatives show similar CA IX inhibitory/selectivity profiles, such as various sulfonamides, sulfamates, and sulfamides …”

“…In fact, many classes of such derivatives show similar CA IX inhibitory/selectivity profiles, such as various sulfonamides, [124][125][126][127][130][131][132][133][134][135]140,[142][143][144][145]152,156,173,174,[179][180][181][182][183][189][190][191][192][193][194][195] sulfamates, [149][150][151]156,188,196,199 and sulfamides. 149,152,156,197,202 (ii) The scaffold of the potent and isoform-selective CA IX inhibitors of this type incorporates aromatic, 12 196,199 sugar, [133][134]…”