Class Of Carbonic Anhydrase Inhibitors Research Articles

Exploring the binding mode of phenyl and vinyl boronic acids to human carbonic anhydrases

Boronic acids are an interesting but still poorly studied class of carbonic anhydrase inhibitors. Previous investigations proved that derivatives incorporating aromatic, arylalkyl, and arylalkenyl moieties are low micromolar to millimolar inhibitors for several α- and β-CAs involved in pathologic states.Here we report a high-resolution X-ray study on two classes of boronic acids (phenyl and vinyl) in complex with hCA II. Our results unambiguously clarify the binding mode of these molecules to the human carbonic anhydrase active site, which occurs through their tetrahedral anionic form, regardless of the nature of the organic scaffold. Data here presented contribute to the understanding of the inhibition mechanism of boronic acids that can be fruitfully used for the rational design of novel and effective isozyme-specific carbonic anhydrase inhibitors.

Design, synthesis, and structure-activity studies of new rhodanine derivatives as carbonic anhydrase II, IX inhibitors.

Rhodanine and its derivatives are an important class of heterocycles with diverse biological properties, including anticancer, antibacterial, and anti-mycobacterial activities. In the present work, four series of new Rhodanine derivatives were synthesized and evaluated for their inhibitory activity against carbonic anhydrase I, II, IX, and XII isoforms. Interestingly, the tested compounds exhibited good inhibitory activity against the cytosolic isoform human carbonic anhydrase (hCA) II and tumor-associated hCA IX. While the Rhodanine-benzylidene derivatives (3a-l) and Rhodanine-hydrazine derivatives (6a-e) are found to be selective against hCA II, the Rhodanine-N-carboxylate derivatives (8a-d) are found to be highly selective toward hCA IX. The Rhodanine-linked isoxazole and 1,2,4-oxadiazole derivatives (8ba, 8da, and 8db) exhibited inhibitory activity against hCA II and hCA IX. Among the tested compounds, 3b, 3j, 6d, and 8db were found to inhibit hCA II with Ki values of 9.8, 46.4, 7.7, and 4.7 µM, respectively. Furthermore, their mechanism of action is supported by molecular docking studies. Notably, the synthesized Rhodanine derivatives belong to a nonsulfonamide class of carbonic anhydrase inhibitors.

A Combined in Silico and Structural Study Opens New Perspectives on Aliphatic Sulfonamides, a Still Poorly Investigated Class of CA Inhibitors

Aliphatic sulfonamides are an interesting class of carbonic anhydrase inhibitors (CAIs) proven to be effective for several carbonic anhydrase (CA) isoforms involved in pathologic states. Here we report the crystallographic structures of hCA II in complex with two aliphatic sulfonamides incorporating coumarin rings, which showed a good inhibition and selectivity for this isoform. Although these two molecules have a very similar chemical structure, differing only in the substitution of the two aliphatic hydrogen atoms with two fluorine atoms, they adopt a significantly different binding mode within the enzyme active site. Theoretical binding free energy calculations, performed to rationalize these data, showed that a delicate balance of electrostatic and steric effects modulate the protein-ligand interactions. Data presented here can be fruitfully used for the rational design of novel and effective isozyme-specific inhibitor molecules.

Benzoselenoates: A novel class of carbonic anhydrase inhibitors

A series of benzoselenoates has been prepared and their inhibitory properties against the most relevant human Carbonic Anhydrases (CAs) isoforms, among which hCA I, II, IV, VII, IX, and XII were investigated. These inhibitors were designed considering the carboxylates and mono-/dithiocarbamates as lead and led to the observation that the COSe- is a new zinc-binding group (ZBG) for metalloenzymes possessing zinc ions at their active site. The substitution pattern on aromatic ring of the benzoselenoates is the crucial structural element influencing selectivity towards various isoforms. We elucidated the binding mode of benzoselenoates to hCA I and hCA II by using X-ray crystallography. The negatively charged selenium atom from the new ZBG was observed coordinated to the zinc ion from the CA active site at a distance of 2.30–2.40 Å from it. Overall, these data might be useful for the development of new inhibitors with higher selectivity and efficacy for various hCAs.

Benzyl alcohol inhibits carbonic anhydrases by anchoring to the zinc coordinated water molecule

Up to date alcohols have been scarcely investigated as carbonic anhydrase (CA) inhibitors. To get more insights into the CA inhibition properties of this class of molecules, in this paper, by means of inhibition assays and X-ray crystallographic studies we report a detailed characterization of the CA inhibition properties and the binding mode to human CA II of benzyl alcohol. Results show that, although possessing a very simple scaffold, this molecule acts as a micromolar CA II inhibitor, which anchors to the enzyme active site by means of an H-bond interaction with the zinc bound solvent molecule. Taken together our results clearly indicate primary alcohols as a class of CA inhibitors that deserve to be more investigated.

Benzilydene and thiourea derivatives as new classes of carbonic anhydrase inhibitors: an in vitro and molecular docking study

Carbonic anhydrase-II (CA-II) catalyzes reversible hydration of carbon dioxide leading to the formation of bicarbonate and a proton. CA-II inhibitors act as biomarkers and therapeutic targets for various diseases such as epilepsy, glaucoma, leukemia, and cystic fibrosis. In the present work, a number of thiourea and benzylidene derivatives were evaluated as CA-II inhibitors. For this, detection of CA-II inhibition was tested through high throughput biochemical mechanism-based assay. Results indicated that thiourea derivatives exhibit remarkable inhibition activity with IC50 values ranging from 1.90 ± 1.30 to 25.90 ± 2.05 µM, when compared with the standard inhibitor acetazolamide IC50 = 0.13 ± 0.05. On the other hand, bezylidene derivatives showed weak inhibition potential with IC50 values in the range of 52.68 ± 0.47 to 348.57 ± 3.32 µM when compared with the thiourea derivatives; the Ez-Fit enzyme kinetics software was used for IC50 calculations from the percentage inhibition. In addition, 3T3 normal cell line was employed to determine the toxicity profile of identified inhibitors of CA-II. In silico modeling was performed to decipher the molecular nature of thiourea and benzylidene derivatives with key residues of carbonic anhydrase; results were in agreement with experiments related to inhibition of carbonic anhydrase.

N-aryl-N'-ureido-O-sulfamates as potent and selective inhibitors of hCA VB over hCA VA: Deciphering the binding mode of new potential agents in mitochondrial dysfunctions.

N-aryl-N'-ureido-O-sulfamates (AUSs) were recently reported as new class of Carbonic Anhydrase Inhibitors (CAIs), endowed of high potency and selectivity against hCA VII and XII. In this work, we extended the investigational study on this new class of CAIs profiling them against the mitochondrial CA isoforms hCA VA and VB. The results revealed a very interesting selectivity profile, with dramatic selectivity against hCA VB over the VA isoform observed for all the analyzed compounds 2-22. On derivative 15, selected as one of the most promising among the series, molecular modeling studies were conducted, highlighting the importance of small residue substitution between the two isoforms in substantially changing the tail orientation and interaction with the enzymes.

2-Mercaptobenzoxazoles: a class of carbonic anhydrase inhibitors with a novel binding mode to the enzyme active site.

2-Mercaptobenzoxazole is a widely used organic scaffold in medicinal chemistry. By means of kinetic and structural studies, we demonstrate that this molecule can effectively be used to inhibit hCAs showing a peculiar binding mode. The results reported here can pave the way for the development of selective CA inhibitors.

Catechols: a new class of carbonic anhydrase inhibitors

To date, catechols have been only poorly investigated as carbonic anhydrase (CA) inhibitors. Here we report the first structural information on the CA inhibition mechanism of these molecules, showing that they adopt a peculiar binding mode to the enzyme active site which involves the zinc-bound water molecule and the "deep water".

Direct and straightforward access to substituted alkyl selenols as novel carbonic anhydrase inhibitors

Functionalised aliphatic selenols, straightforwardly obtained through ring-opening reaction of strained heterocycles, represent a new chemotype acting as carbonic anhydrase inhibitors (CAIs). These compounds showed pronounced selectivity towards the cytosolic human (h) isoforms such as the hCA I, II and VII rather than the membrane tumor associate hCA IX. In addition, we reported for the first time the X-ray crystal structure of an aliphatic selenol bound to the hCA I zinc ion, and that afforded the opportunity to decipher in detail the inhibition mechanism underpinning such a new class of CAIs. In this context selenols are interesting leads worth developing for the obtainment of novel and efficient selective CAIs potentially useful for the management of a variety of diseases including glaucoma, retinitis pigmentosa, epilepsy and arthritis.

Mycobacterium tuberculosis β-Carbonic Anhydrases: Novel Targets for Developing Antituberculosis Drugs.

The genome of Mycobacterium tuberculosis (Mtb) encodes three β-carbonic anhydrases (CAs, EC 4.2.1.1) that are crucial for the life cycle of the bacterium. The Mtb β-CAs have been cloned and characterized, and the catalytic activities of the enzymes have been studied. The crystal structures of two of the enzymes have been resolved. In vitro inhibition studies have been conducted using different classes of carbonic anhydrase inhibitors (CAIs). In vivo inhibition studies of pathogenic bacteria containing β-CAs showed that β-CA inhibitors effectively inhibited the growth of pathogenic bacteria. The in vitro and in vivo studies clearly demonstrated that β-CAs of not only mycobacterial species, but also other pathogenic bacteria, can be targeted for developing novel antimycobacterial agents for treating tuberculosis and other microbial infections that are resistant to existing drugs. In this review, we present the molecular and structural data on three β-CAs of Mtb that will give us better insights into the roles of these enzymes in pathogenic bacterial species. We also present data from both in vitro inhibition studies using different classes of chemical compounds and in vivo inhibition studies focusing on M. marinum, a model organism and close relative of Mtb.

N-aryl-N’-ureido-O-sulfamates: Potent and selective inhibitors of the human Carbonic Anhydrase VII isoform with neuropathic pain relieving properties

Herein we report for the first time an efficient synthetic procedure for the preparation of N-aryl-N’-ureido-O-sulfamates (AUSs) as a new class of Carbonic Anhydrase Inhibitors (CAIs). The compounds were tested for the inhibition of several human (h) Carbonic Anhydrase (CA; EC 4.2.1.1) isoforms. Interesting inhibition activity and high selectivity against CA VII and XII versus CA I and II, with KIs in the low nanomolar range, were observed. Molecular modeling studies allowed us to decipher the structural features underpinning the selective inhibitory profile of AUSs towards isoforms CAs VII and XII. A selection of sulfamates showed promising neuropathic pain modulating effects in an in vivo animal model of oxaliplatin induced pain.

Selenols: a new class of carbonic anhydrase inhibitors.

Stable aryl selenols were obtained through a convenient procedure. Selenols represent a new chemotype acting as carbonic anhydrase inhibitors (CAIs), inhibiting four human isoforms, CAs I, II, VII and the tumor-associated CA IX. X-ray crystallographic, physical and computational studies provided insights into the binding mode of this conceptually new class of CAIs.

Carbohydrazones as new class of carbonic anhydrase inhibitors: Synthesis, kinetics, and ligand docking studies

Discovery and development of carbonic anhydrase inhibitors is crucial for their clinical use as antiepileptic, diurectic and antiglaucoma agents. Keeping this in mind, we have synthesized carbohydrazones 1–27 and evaluated them for their in vitro carbonic anhydrase inhibitory potential. Out of twenty-seven compounds, compounds 1 (IC50=1.33±0.01µM), 2 (IC50=1.85±0.24µM), 3 (IC50=1.37±0.06µM), and 9 (IC50=1.46±0.12µM) have showed carbonic anhydrase inhibition better than the standard drug zonisamide (IC50=1.86±0.03µM). Moreover, compounds 4 (IC50=2.32±0.04µM), 5 (IC50=3.96±0.35µM), 7 (IC50=2.33±0.02µM), and 8 (IC50=2.67±0.01µM) showed good inhibitory activity. Cheminformatic analysis has shown that compounds 1 and 2 possess lead-like properties. In addition, kinetic and molecular docking studies were also performed to investigate the binding interaction between carbohydrazones and carbonic anhydrase enzyme. This study has identified a novel and potent class of carbonic anhydrase inhibitors with the potential to be investigated further.

Active Components of Essential Oils as Anti-Obesity Potential Drugs Investigated by in Silico Techniques.

In this study, for the first time, we have considered essential oils (EOs) as possible resources of carbonic anhydrase inhibitors (CAIs), in particular against the mitochondrial isoform VA that, actually, represents an innovative target for the obesity treatment. In silico structure-based virtual screening was performed in order to speed up the identification of promising antiobesity agents. The potential hit compounds were submitted to in vitro assays and experimental results, corroborated by molecular modeling studies, showed EOs components as a new class of CAIs with a competitive mechanism of action due to the zinc ion coordination within the active sites of these metallo-enzymes.

Out of the active site binding pocket for carbonic anhydrase inhibitors.

A structural study of the adduct which 2-benzylsulfinylbenzoic acid forms with human carbonic anhydrase II is reported, showing a binding mode completely different from any other class of carbonic anhydrase inhibitors investigated so far; this carboxylate binds in a pocket situated out of the enzyme active site.

Abstract 4980: Inhibiting carbonic anhydrase IX targets hypoxic small cell lung cancer cells

Abstract Small-cell lung cancer (SCLC) is an extremely aggressive disease, exhibiting acquired resistance to therapy and poor patient prognosis. Therapy resistance can in part be attributed to tumor hypoxia. Hypoxic SCLC cells up-regulate carbonic anhydrase IX (CA IX) in order to survive. CA IX is involved in pH maintenance of cells and presents a novel therapeutic target for SCLC. This study aimed to investigate the potential of inhibiting CA IX in SCLC as a novel therapeutic target. Hypoxic conditions (0.1% O2) increased CA IX expression over 24 hours in both COR-L24 and DMS 79 SCLC cells in culture. S4 belongs to a sulfamate class of carbonic anhydrase inhibitors and has shown anti-metastatic properties in breast cancer xenografts. Treatment with 30μM and 100μM S4 significantly decreased CA IX protein levels in hypoxic COR-L24 and DMS 79 SCLC cells, respectively (p<0.05 for both treatments). Exposure to S4 for 24 hours resulted in predominantly hypoxic cell death in both cell lines (p<0.05). Combining S4 with etoposide (0.3µM) and cisplatin (0.5µM) chemotherapeutic agents resulted in additional cell death, which was also seen under normoxic conditions (20% O2). Sub-cutaneous xenograft tumors were grown in nude mice using either COR-L24 or DMS 79 SCLC cells. Resultant tumors (1000mm3) expressed CA IX largely adjacent to regions of necrosis. Treating mice with 50mg/kg S4 on two consecutive days each week resulted in greater necrosis than saline controls, coupled with up-regulation of CA IX. Analyzing tumors for characteristic neuroendocrine (pro-opiomelanocortin) and epithelial (cytokeratin) markers revealed heterogeneous expression; however, this did not correlate with CA IX expression and is not altered in response to treatment. In summary, CA IX is upregulated in hypoxic SCLC cells and tumors. Inhibition of CA IX resulted in hypoxic cell death and had an additive effect to the response observed with chemotherapy treatment alone. This suggests that directly targeting hypoxic SCLC cells via CA IX inhibition holds promise in improving treatment outcome for this aggressive disease. Citation Format: Jennifer L. Bryant, Suzanne L. Meredith, Roben G. Gieling, Brian A. Telfer, Muhammad Babur, Claudiu T. Supuran, Kaye J. Williams, Anne White. Inhibiting carbonic anhydrase IX targets hypoxic small cell lung cancer cells. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4980. doi:10.1158/1538-7445.AM2014-4980

Tricyclic Sulfonamides Incorporating Benzothiopyrano[4,3-c]pyrazole and Pyridothiopyrano[4,3-c]pyrazole Effectively Inhibit α- and β-Carbonic Anhydrase: X-ray Crystallography and Solution Investigations on 15 Isoforms

Carbonic anhydrases (CAs, EC 4.2.1.1) are ubiquitous isozymes involved in crucial physiological and pathological events, representing the targets of inhibitors with several therapeutic applications. In this connection, we report a new class of carbonic anhydrase inhibitors, based on the thiopyrano-fused pyrazole scaffold to which a pendant 4-sulfamoylphenyl moiety was attached. The new sulfonamides 3a-e were designed as constrained analogues of celecoxib and valdecoxib. The most interesting feature of sulfonamides 3 was their predominantly strong inhibition of human (h) CA I and II, as well as those of the mycobacterial β-class enzymes (Rv1284, Rv3273, and Rv3588c), whereas their inhibitory action against hCA III, IV, VA, VB, VI, VII, IX, XII, XIII, and XIV was found to be at least 2 orders of magnitude lower. X-ray crystallography and structural superposition studies made it possible to explain the very distinct inhibition profile of the tricyclic sulfonamides, different from those of celecoxib and valdecoxib.

Dithiocarbamates: a new class of carbonic anhydrase inhibitors. Crystallographic and kinetic investigations

The zinc enzyme carbonic anhydrase (CA, EC 4.2.1.1) is inhibited by several classes of zinc-binders (sulfonamides, sulfamates, and sulfamides) as well as by compounds which do not interact with the metal ion (phenols, polyamines and coumarins). Here we report a new class of potent CA inhibitors which bind the zinc ion: the dithiocarbamates (DTCs). They coordinate to the zinc ion from the enzyme active site in monodentate manner and establish many favorable interactions with amino acid residues nearby. Several low nanomolar CA I, II and IX inhibitors were detected.

3-Phenyl-1H-Indole-5-Sulfonamides: Structure-Based Drug Design of a Promising Class of Carbonic Anhydrase Inhibitors

A series of 2-(hydrazinocarbonyl)-3-substituted-phenyl-1H-indole-5-sulfonamides possessing various 2-, 3- or 4- substituted phenyl groups with methyl-, halogeno- and methoxy- functionalities, as well as the perfluorophenyl moiety have been synthesized and evaluated as inhibitors of both α- and β-class carbonic anhydrases (CAs, EC 4.2.1.1). All human isoforms with medicinal chemistry applications were included in such studies, among which CA I, II, VA, VB, VII, IX and XII. Several low nanomolar, sometimes isoform-selective compounds were thus detected. Two β-CAs from the pathogenic bacterium Mycobacterium tuberculosis encoded by the genes Rv1284 Rv3588c were also highly inhibited (sometimes in the sub-nanomolar range) by some pyridinium derivatives incoprorating this scaffold, obtained from the corresponding 2-(hydrazinocarbonyl)-3-substituted-phenyl-1H-indole-5-sulfonamides by reaction with pyrylium salts. The fungal β-CAs from Candida albicans (Nce103) and Cryptococcus neoformans (Can2) were also investigated for their inhibition with this family of sulfonamides and some highly effective inhibitors detected. As the X-ray crystal structure of one such sulfonamide with the human isoform CA II is also know, the 3-substituted-phenyl-1H-indole-5-sulfonamides represent a totally new class of inhibitors obtained by structure-based drug design, which show efficiency in inhibiting both α- and β-CAs from several species.