Exploration of the residues modulating the catalytic features of human carbonic anhydrase XIII by a site-specific mutagenesis approach

Bacterial α-CAs: a biochemical and structural overview

Carbonic anhydrases belonging to the α-class are widely distributed in bacterial species. These enzymes have been isolated from bacteria with completely different characteristics including both Gram-negative and Gram-positive strains. α-CAs show a considerable similarity when comparing the biochemical, kinetic and structural features, with only small differences which reflect the diverse role these enzymes play in Nature. In this chapter, we provide a comprehensive overview on bacterial α-CA data, with a highlight to their potential biomedical and biotechnological applications.

Investigation of novel alkyl/benzyl (4-sulphamoylphenyl)carbamimidothioates as carbonic anhydrase inhibitors

A library of novel alkyl/benzyl (4-sulphamoylphenyl)carbamimidothioates was synthesised by selective S-alkylation of the easily accessible 4-thioureidobenzenesulphonamide. The compounds were assayed as inhibitors of four human (h) carbonic anhydrase isoforms hCA I, II, VII, and XIII, as well as three bacterial enzymes belonging to the β-CA class, MscCA from Mammaliicoccus (Staphylococcus) sciuri and StCA1 and StCA2, from Salmonella enterica (serovar Typhimurium). Most compounds investigated here exhibited moderate to low nanomolar inhibition constants against hCA I, II, and VII. The cytosolic hCA XIII was also inhibited by these compounds, but not as effective as hCA I, II, and VII. Several compounds were very effective against MscCA and StCA1. StCA2 was less inhibited compared to MscCA and StCA1. Some compounds showed considerable selectivity for inhibiting some CA isoforms. They may thus be considered as interesting starting points for the discovery and development of novel therapeutic agents belonging to this class of enzyme inhibitors.

Efficient proton shuttle makes SazCA an excellent CO2 hydration enzyme

The fastest member of the carbonic anhydrase family catalysing the reversible hydration of carbon dioxide to bicarbonate ions has been recently reported to be SazCA. While thermostable, this enzyme shows exceptional activity at 353 K for the reaction. This study explores the molecular basis for the exceptional activity of SazCA, in contrast to SspCA, probed using molecular dynamics simulations. Our simulations, carried out at different temperatures, indicate the presence of efficient proton shuttle between the active zinc centre and His64 residue in the two enzymes. The proton accepting His64 residue was identified to have in and out conformations with the in conformations being supportive to proton acceptance. Our simulations show a large population of in conformations in SazCA making the enzyme exhibit an exceptional activity. The RMSF and H-bonds analysis confirmed the role of His2 and His207 in supporting the attainment of in conformations in SazCA resulting in exceptional activity.Communicated by Ramaswamy H. Sarma.

Experimental Approaches to Identify Selective Picomolar Inhibitors for Carbonic Anhydrase IX

BACKGROUND

Carbonic anhydrases (CAs) regulate pH homeostasis via the reversible hydration of CO₂, thereby emerging as essential enzymes for many vital functions. Among 12 catalytically active CA isoforms in humans, CA IX has become a relevant therapeutic target because of its role in cancer progression. Only two CA IX inhibitors have entered clinical trials, mostly due to low affinity and selectivity properties.

OBJECTIVE

The current review presents the design, development, and identification of the selective nano- to picomolar CA IX inhibitors VD11-4-2, VR16-09, and VD12-09.

METHODS AND RESULTS

Compounds were selected from our database, composed of over 400 benzensulfonamides, synthesized at our laboratory, and tested for their binding to 12 human CAs. Here we discuss the CA CO₂ hydratase activity/inhibition assay and several biophysical techniques, such as fluorescent thermal shift assay and isothermal titration calorimetry, highlighting their contribution to the analysis of compound affinity and structure- activity relationships. To obtain sufficient amounts of recombinant CAs for inhibitor screening, several gene cloning and protein purification strategies are presented, including site-directed CA mutants, heterologous CAs from Xenopus oocytes, and native endogenous CAs. The cancer cell-based methods, such as clonogenicity, extracellular acidification, and mass spectrometric gas-analysis are reviewed, confirming nanomolar activities of lead inhibitors in intact cancer cells.

CONCLUSIONS

Novel CA IX inhibitors are promising derivatives for in vivo explorations. Furthermore, the simultaneous targeting of several proteins involved in proton flux upon tumor acidosis and the disruption of transport metabolons might improve cancer management.

Intrinsically disordered features of carbonic anhydrase IX proteoglycan-like domain

hCA IX is a multi-domain protein belonging to the family of hCAs which are ubiquitous zinc enzymes that catalyze the reversible hydration of CO2 to HCO3- and H+. hCA IX is a tumor-associated enzyme with a limited distribution in normal tissues, but over-expressed in many tumors, and is a promising drug target. Although many studies concerning the CA IX catalytic domain were performed, little is known about the proteoglycan-like (PG-like) domain of hCA IX which has been poorly investigated so far. Here we attempt to fill this gap by providing an overview on the functional, structural and therapeutic studies of the PG-like domain of hCA IX which represents a unique feature within the CA family. The main studies and recent advances concerning PG role in modulating hCA IX catalytic activity as well as in tumor spreading and migration are here reported. Special attention has been paid to the newly discovered disordered features of the PG domain which open new perspectives about its molecular mechanisms of action under physiological and pathological conditions, since disorder is likely involved in mediating interactions with partner proteins. The emerged disordered features of PG domain will be explored for putative diagnostic and therapeutic applications involving CA IX targeting in tumors.

Coumarin-Thiourea Hybrids Show Potent Carbonic Anhydrase IX and XIII Inhibitory Action

A series of coumarin-thiourea hybrids (4 a-o) has been synthesized, and the compounds have been evaluated against the tumour associated transmembrane isoform, human (h) carbonic anhydrase (CA) hCA IX and the less-explored cytosolic isoform, hCA XIII. All compounds exhibited potent inhibition of both isoforms, with K_I values of <100 nM against hCA IX. Compound 4 b was the best inhibitor (K_I =78.5 nM). All the compounds inhibited hCA XIII in the low-nanomolar to sub-micromolar range, with compound 4 b again showing the best inhibition (K_I =76.3 nM). With compound 4 b as a lead, more-selective inhibitors of hCA IX and hCA XIII or dual hCA IX/XIII inhibitors might be developed.

Activation studies of the β-carbonic anhydrases from Malassezia restricta with amines and amino acids

The β-carbonic anhydrase (CA, EC 4.2.1.1) from the genome of the opportunistic pathogen Malassezia restricta (MreCA), which was recently cloned and characterised, herein has been investigated for enzymatic activation by a panel of amines and amino acids. Of the 24 compounds tested in this study, the most effective MreCA activators were L-adrenaline (KA of 15 nM), 2-aminoethyl-piperazine/morpholine (KAs of 0.25-0.33 µM), histamine, L-4-amino-phenylalanine, D-Phe, L-/D-DOPA, and L-/D-Trp (KAs of 0.32 - 0.90 µM). The least effective activators were L-/D-Tyr, L-Asp, L-/D-Glu, and L-His, with activation constants ranging between 4.04 and 12.8 µM. As MreCA is involved in dandruff and seborrhoeic dermatitis, these results are of interest to identify modulators of the activity of enzymes involved in the metabolic processes of such fungi.