Carbonic anhydrase inhibitors: binding of indanesulfonamides to the human isoform II

Indanesulfonamides are interesting lead compounds for designing selective inhibitors of the different isoforms of the zinc enzyme Carbonic Anhydrase (CA). Herein, we report for the first time the X-ray crystal structure of two such derivatives, namely indane-5-sulfonamide and indane-2-valproylamido-5-sulfonamide, in complex with the physiologically dominant human isoform II. The structural analysis reveals that, although these two inhibitors have quite similar chemical structures, the arrangement of their indane ring within the enzyme active site is significantly diverse. Thus, our findings suggest that the introduction of bulky substituents on the indane-sulfonamide ring may alter the binding mode of this potent class of CA inhibitors, although retaining good inhibitory properties. Accordingly, the introduction of bulky tail moieties on the indane-sulfonamide scaffold may represent a powerful strategy to induce a desired physicochemical property to an aromatic sulfonamide or to obtain inhibitors with diverse inhibition profiles and selectivity for various mammalian CAs.     

Carbonic anhydrase textile structured packing for efficient CO2 absorption in methyldiethanolamine solvent

Carbonic anhydrase (CA) is an attractive biodegradable catalyst for CO₂ absorption in solvent-based CO₂ capture. However, maintaining the stability of CA as a homogeneous component of the solvents is a challenge. Solvent regeneration temperature typically exceeds the enzyme thermal tolerance, which leads to CA deactivation. To reduce the need for frequent CA replenishment and to avoid inactive CA accumulation in the solvent, this work shows the benefits of an immobilization strategy where CA is fixed in a second-generation design of textile structured packing (CATSP-2) modules. The enzyme-immobilized packing showed 1.5 times better performance in CO₂ separation compared with traditional structured packing with a corresponding increased CO₂ loading in the rich solvent. The modules exhibited good CA activity retention of ~80% during the tests without any CA replenishment. Applying CATSP-2 could potentially decrease the packing height and absorber column size for a lower cost per amount of CO₂ captured.     

Model studies for molecular recognition of carbonic anhydrase and carboxypeptidase

Model studies using Zn(2+) complexes of various derivatives of macrocyclic triamines ([12]aneN(3)) and tetraamines (cyclen) have been found to be useful in elucidating and understanding the intrinsic properties of substrate or inhibitor recognition by zinc ions at the active centers of carbonic anhydrase and carboxypeptidase.     

Comparison of different ranking methods in protein-ligand binding site prediction

In recent years, although many ligand-binding site prediction methods have been developed, there has still been a great demand to improve the prediction accuracy and compare different prediction algorithms to evaluate their performances. In this work, in order to improve the performance of the protein-ligand binding site prediction method presented in our former study, a comparison of different binding site ranking lists was studied. Four kinds of properties, i.e., pocket size, distance from the protein centroid, sequence conservation and the number of hydrophobic residues, have been chosen as the corresponding ranking criterion respectively. Our studies show that the sequence conservation information helps to rank the real pockets with the most successful accuracy compared to others. At the same time, the pocket size and the distance of binding site from the protein centroid are also found to be helpful. In addition, a multi-view ranking aggregation method, which combines the information among those four properties, was further applied in our study. The results show that a better performance can be achieved by the aggregation of the complementary properties in the prediction of ligand-binding sites.     

Carbonic anhydrase inhibitors. Part 54: metal complexes of heterocyclic sulfonamides: a new class of antiglaucoma agents

Metal complexes of heterocyclic sulfonamides possessing carbonic anhydrase (CA) inhibitory properties were recently shown to be useful as intraocular pressure (IOP) lowering agents in experimental animals, and might be developed as a novel class of antiglaucoma drugs. Here we report the synthesis of a heterocyclic sulfonamide CA inhibitor and of the metal complexes containing main group metal ions, such as Be(II), Mg(II), Al(III), Zn(II), Cd(II) and Hg(II) and the new sulfonamide as well as 5-amino-1,3,4-thiadiazole-2-sulfonamide as ligands. The new complexes were characterized by standard physico-chemical procedures, and assayed as inhibitors of three CA isozymes, CA I, II and IV. Some of them (but not the parent sulfonamides) strongly lowered IOP in rabbits when administered as a 2% solution into the eye.     

Role of Carbonic Anhydrase in Cerebral Ischemia and Carbonic Anhydrase Inhibitors as Putative Protective Agents

Ischemic stroke is a leading cause of death and disability worldwide. The only pharmacological treatment available to date for cerebral ischemia is tissue plasminogen activator (t-PA) and the search for successful therapeutic strategies still remains a major challenge. The loss of cerebral blood flow leads to reduced oxygen and glucose supply and a subsequent switch to the glycolytic pathway, which leads to tissue acidification. Carbonic anhydrase (CA, EC 4.2.1.1) is the enzyme responsible for converting carbon dioxide into a protons and bicarbonate, thus contributing to pH regulation and metabolism, with many CA isoforms present in the brain. Recently, numerous studies have shed light on several classes of carbonic anhydrase inhibitor (CAI) as possible new pharmacological agents for the management of brain ischemia. In the present review we summarized pharmacological, preclinical and clinical findings regarding the role of CAIs in strokes and we discuss their potential protective mechanisms.     

Spin labels as a tool to identify and characterize protein-ligand interactions by NMR spectroscopy

NMR spectroscopy based discovery and optimization of lead compounds for a given molecular target requires the development of methods with maximum sensitivity and robustness. It is shown here that organic nitroxide radicals ("spin labels") can be used to boost the sensitivity of NMR spectroscopic screening in drug discovery research. The concept of utilizing spin labels in NMR spectroscopy is summarized, examples for successful first-site and second-site NMR spectroscopic screens are given, and guidelines for linker design are presented.     

Carbonic anhydrase inhibitors. Part 91. Metal complexes of heterocyclic sulfonamides as potential pharmacological agents in the treatment of gastric Acid secretion imbalances

Zinc, magnesium, aluminum and copper complexes of several potent, clinically used carbonic anhydrase (CA) sulfonamide inhibitors, such as acetazolamide, methazolamide, ethoxzolamide and benzolamide were tested for their possible applications as antacids, in experimental animals. Gastric acid secretion parameters 3 days after treatment with these CA inhibitors (2 x 500 mg, twice a day), in dogs with chronic gastric fistulas, led to the observation that the gastric acid parameters BAO (the basal acid output), and MAO (the maximal acid output after stimulation with histamine) were drastically reduced, as compared to the same parameters in animals that did not receive these enzyme inhibitors. These are promising results for the possible use of metal complexes of heterocyclic sulfonamides as treatment alternatives (alone or in combination with other drugs) for gastric acid secretion imbalances.     

Definition of a model fat for crystallization-in-emulsion studies

Numerous food products are dispersed in droplet emulsions in which fat is partially crystallized. A model fat allowing the study of crystallization in emulsion, obtained by the mixing of two fats (one solid and one liquid at room temperature) with simple triacylglycerol (TG) composition, is defined and characterized. Cocoa butter (CB), a vegetable fat mainly composed of monounsaturated long-chain fatty acids (POP, POST, StOSt, where P=palmitic, O=oleic, St=stearic), and miglyol, a synthetic oil made from capric and caprylic fatty acids, were chosen, respectively. The thermal behaviors of CB, miglyol, and their mixtures are studied using high-sensitivity differential scanning calorimetry (DSC). The CB/miglyol ratio was optimized (i) in order to make stable emulsions as a function of time, (ii) so that the mixture displays several solid phases on cooling that result from CB polymorphism, and (iii) in order to keep, even at low temperature, a liquid moiety facilitating the phase transitions. The CB 75%/miglyol 25% composition is defined as the model mixture. This mixture is characterized on cooling at 0.5°C/min by coupled X-ray diffraction as a function of temperature and DSC experiments. First and α 2L (49.3 Å) variety is formed. Then, co-crystallization of both CB and miglyol TG shows the simultaneous formation of longitudinal stackings of 44.5 and 34.5 Å with a lateral organization of β′ form. An unusual TG packing corresponding to compound formation is proposed to explain the observation of a 34.5 Å long-spacing. The crystallization behavior of the model fat mixture dispersed in emulsion droplets is also monitored in order to validate its use.     

Carbonic Anhydrase IX Inhibitors as Candidates for Combination Therapy of Solid Tumors

Combination therapy is becoming imperative for the treatment of many cancers, as it provides a higher chance of avoiding drug resistance and tumor recurrence. Among the resistance-conferring factors, the tumor microenvironment plays a major role, and therefore, represents a viable target for adjuvant therapeutic agents. Thus, hypoxia and extracellular acidosis are known to select for the most aggressive and resilient phenotypes and build poorly responsive regions of the tumor mass. Carbonic anhydrase (CA, EC 4.2.1.1) IX isoform is a surficial zinc metalloenzyme that is proven to play a central role in regulating intra and extracellular pH, as well as modulating invasion and metastasis processes. With its strong association and distribution in various tumor tissues and well-known druggability, this protein holds great promise as a target to pharmacologically interfere with the tumor microenvironment by using drug combination regimens. In the present review, we summarized recent publications revealing the potential of CA IX inhibitors to intensify cancer chemotherapy and overcome drug resistance in preclinical settings.     

A standardized and biocompatible preparation of aggregate-free amyloid beta peptide for biophysical and biological studies of Alzheimer's disease

We provide a validated and rapid protocol for the solubilization of amyloid β-peptide (Aβ). This procedure involves sequential solubilization using structure-breaking organic solvents hexafluoroisopropanol and DMSO followed by column purification. The low solubility and tendency of Aβ to aggregate considerably impede the in vitro handling and biophysical or biological investigation of Aβ, despite the interest in this peptide because of its implication in Alzheimer's disease. The main advantage of the proposed protocol over others is that it results in standardized aggregate-free Aβ peptide samples that are biocompatible for cell culture studies and yield reproducible aggregation kinetics and cytotoxicities. This three-step protocol also enables the co-solubilization of the longer Aβ42 variant with Aβ40 in ratios relevant to Alzheimer's disease.     

Thienothiopyransulfonamides as complexing agents for the preparation of dual carbonic anhydrase inhibitors

Co(II); Zn(II) and Cu(II) complexes of two new sulfonamide carbonic anhydrase (CA) inhibitors, derivatives of thienothiopyran-2-sulfonamide, were prepared and characterized by analytic, spectroscopic, magnetic and conductimetric measurements. The new complexes are more potent CA inhibitors than the parent sulfonamides, with IC(50) values around 0.1 nM, against isozyme CA II.     

Peptides and proteins as a continuing exciting source of inspiration for peptidomimetics

Despite their enormous diversity in biological function and structure, peptides and proteins are endowed with properties that have induced and stimulated the development of peptidomimetics. Clearly, peptides can be considered as the "stem" of a phylogenetic molecular development tree from which branches of oligomeric peptidomimetics such as peptoids, peptidosulfonamides, urea peptidomimetics, as well as β-peptides have sprouted. It is still a challenge to efficiently synthesize these oligomeric species, and study their structural and biological properties. Combining peptides and peptidomimetics led to the emergence of peptide-peptidomimetic hybrids in which one or more (proteinogenic) amino acid residues have been replaced with these mimetic residues. In scan-like approaches, the influence of these replacements on biological activity can then be studied, to evaluate to what extent a peptide can be transformed into a peptidomimetic structure while maintaining, or even improving, its biological properties. A central issue, especially with the smaller peptides, is the lack of secondary structure. Important approaches to control secondary structure include the introduction of α,α-disubstituted amino acids, or (di)peptidomimetic structures such as the Freidinger lactam. Apart from intra-amino acid constraints, inter-amino acid constraints for formation of a diversity of cyclic peptides have shaped a thick branch. Apart from the classical disulfide bridges, the repertoire has been extended to include sulfide and triazole bridges as well as the single-, double- and even triple-bond replacements, accessible by the extremely versatile ring-closing alkene/alkyne metathesis approaches. The latter approach is now the method of choice for the secondary structure that presents the greatest challenge for structural stabilization: the α-helix.     

Exploration of the binding mode of indanesulfonamides as selective inhibitors of human carbonic anhydrase type VII by targeting Lys 91

Convulsions are common neurological disorders in clinical medicine and are triggered by several mechanisms. The enhancement of neuronal excitability can be related, among other factors, to GABAergic depolarization. Carbonic anhydrase (CA) VII contributes to this electrophysiological behavior by providing bicarbonate anion, which can mediate current through channels coupled to GABA(A) receptors. Among the cytosolic CAs, the mechanism of action and inhibition of CA VII is less understood. We present herein the pharmacological evaluation of both enantiomers of an indanesulfonamide compound substituted by a pentafluorophenyl moiety against CA VII and five other human CA isoforms to evaluate their selectivity. The investigated compounds are powerful inhibitors of hCA VII, with K(i) values in the range of 1.7-3.3 nM, but their selectivity needs to be improved. A molecular modeling study was conducted to rationalize the structure-activity relationships and provide useful insight into the future design of selective hCA VII inhibitors.     

Roles of Carbonic Anhydrases and Carbonic Anhydrase Related Proteins in Zebrafish

During recent decades, zebrafish (Danio rerio) have become one of the most important model organisms in which to study different physiological and biological phenomena. The research field of carbonic anhydrases (CAs) and carbonic anhydrase related proteins (CARPs) is not an exception to this. The best-known function of CAs is the regulation of acid–base balance. However, studies performed with zebrafish, among others, have revealed important roles for these proteins in many other physiological processes, some of which had not yet been predicted in the light of previous studies and suggestions. Examples include roles in zebrafish pigmentation as well as motor coordination. Disruption of the function of these proteins may generate lethal outcomes. In this review, we summarize the current knowledge of CA-related studies performed in zebrafish from 1993–2021 that was obtained from PubMed search.     

Multicolored nanometre-resolution mapping of single protein-ligand binding complexes using far-field photostable optical nanoscopy (PHOTON)

Mapping of individual ligand molecules and their binding sites in single protein-ligand complexes at nanometer resolution in real-time would enable probing their structures and functions in vitro and in vivo. In this study, we have developed far-field photostable optical nanoscopy (PHOTON) for mapping single ligand molecules (biotin) and their binding sites in individual protein-ligand complexes (streptavidin-biotin) with 1.2 nm spatial resolution and 100 ms temporal resolution. PHOTON includes one standard far-field optical microscope with a halogen-lamp illuminator; single-molecule-nanoparticle-optical-biosensors (SMNOBS) with exceptionally high quantum-yield (QY) of Rayleigh scattering and photostability (non-photobleaching, non-photoblinking) as imaging probes; and Multispectral Imaging System (MSIS) for spectral isolation of individual SMNOBS with 1 nm wavelength resolution. Intrinsic size- and shape- dependent localized-surface-plasmon-resonance (LSPR) spectra of single SMNOBS provide multiple-spectral (color) nanoprobes for sub-diffraction imaging, offering feasibility of probing of binding structures and functions of single protein-ligand complexes at nm (potentially achieving ?ngstrom) resolution in real-time.     

Enantioselective proteins: selection, binding studies and molecular modeling of antibodies with affinity towards hydrophobic BINOL derivatives

In this paper, the initial steps towards the design of novel artificial metalloenzymes that exploit proteins as a second coordination sphere for traditional metal-ligand catalysis are described. Phage display was employed to select and study antibody fragments capable of recognizing hydrophobic BINOL derivatives designed to mimic BINAP, a widely used ligand in asymmetric metal-catalyzed reactions. The binding affinities of the selected antibodies towards a series of haptens were evaluated by using ELISA assays. A homology model of one of the most selective antibodies was constructed, and a computer-assisted ligand-docking study was carried out to elucidate the binding of the hapten. It was shown that, due to the hydrophobic nature of the haptens, a higher level of theoretical treatment was required to identify the correct binding modes. A small selection of the antibodies was found to discriminate between enantiomers and small structural modifications of the BINOL derivatives. The selectivities arise from hydrophobic interactions, and we propose that the identified set of antibodies provides a foundation for a novel route to artificial metalloenzymes.