Binding affinity of bicarboxylate ions for cobalt (II) bovine carbonic anhydrase

Machine Learning-Enhanced Quantum Chemistry-Assisted Refinement of the Active Site Structure of Metalloproteins

Understanding the fine structural details of inhibitor binding at the active site of metalloenzymes can have a profound impact on the rational drug design targeted to this broad class of biomolecules. Structural techniques such as NMR, cryo-EM, and X-ray crystallography can provide bond lengths and angles, but the uncertainties in these measurements can be as large as the range of values that have been observed for these quantities in all the published structures. This uncertainty is far too large to allow for reliable calculations at the quantum chemical (QC) levels for developing precise structure-activity relationships or for improving the energetic considerations in protein-inhibitor studies. Therefore, the need arises to rely upon computational methods to refine the active site structures well beyond the resolution obtained with routine application of structural methods. In a recent paper, we have shown that it is possible to refine the active site of cobalt(II)-substituted MMP12, a metalloprotein that is a relevant drug target, by matching to the experimental pseudocontact shifts (PCS) those calculated using multireference ab initio QC methods. The computational cost of this methodology becomes a significant bottleneck when the starting structure is not sufficiently close to the final one, which is often the case with biomolecular structures. To tackle this problem, we have developed an approach based on a neural network (NN) and a support vector regression (SVR) and applied it to the refinement of the active site structure of oxalate-inhibited human carbonic anhydrase 2 (hCAII), another prototypical metalloprotein target. The refined structure gives a remarkably good agreement between the QC-calculated and the experimental PCS. This study not only contributes to the knowledge of CAII but also demonstrates the utility of combining machine learning (ML) algorithms with QC calculations, offering a promising avenue for investigating other drug targets and complex biological systems in general.

Natural deep eutectic solvents as green and biocompatible reaction medium for carbonic anhydrase catalysis

Easy deactivation of free enzymes under non-native condition has become a stumbling block to the industrial application of biocatalysis. Natural deep eutectic solvent (NADES) has been exploited as a novel reaction medium for improving enzyme stability. The present work focused on preserving and enhancing the activity of carbonic anhydrase (CA) in a more economical and biocompatible NADES system. We synthesized six choline chloride/betaine-based NADES and analyzed the effects of compositions and concentrations of NADES on their physicochemical properties. The Bet-Gly (1: 2) NADES (55%) was proved to be more suitable as reaction medium for CA by analyzing enzyme activity in the presence of NADES. The enhancement in the stability of CA was found to be as a result of a three-dimensional hydrogen bonding network, rather than the individual or the synergistic effect of betaine and glyceride. The conformational change of CA to become more compact was confirmed both by fluorescence spectrum analysis and circular dichroism analysis. It is worth mentioning that a remarkable thermal stability was maintained when CA was incubated at temperature below 60 °C, and about 96% of activity was still restored in 55% NADES at 60 °C for 12 h.

Reconsidering anion inhibitors in the general context of drug design studies of modulators of activity of the classical enzyme carbonic anhydrase

Inorganic anions inhibit the metalloenzyme carbonic anhydrase (CA, EC 4.2.1.1) generally by coordinating to the active site metal ion. Cyanate was reported as a non-coordinating CA inhibitor but those erroneous results were subsequently corrected by another group. We review the anion CA inhibitors (CAIs) in the more general context of drug design studies and the discovery of a large number of inhibitor classes and inhibition mechanisms, including zinc binders (sulphonamides and isosteres, dithiocabamates and isosteres, thiols, selenols, benzoxaboroles, ninhydrins, etc.); inhibitors anchoring to the zinc-coordinated water molecule (phenols, polyamines, sulfocoumarins, thioxocoumarins, catechols); CAIs occluding the entrance to the active site (coumarins and derivatives, lacosamide), as well as compounds that bind outside the active site. All these new chemotypes integrated with a general procedure for obtaining isoform-selective compounds (the tail approach) has resulted, through the guidance of rigorous X-ray crystallography experiments, in the development of highly selective CAIs for all human CA isoforms with many pharmacological applications.

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".

Sliding Window Adduct Removal Method (SWARM) for Enhanced Electrospray Ionization Mass Spectrometry Binding Data

Electrospray ionization mass spectrometry (ESI-MS) screening of compound libraries against target proteins enables the rapid identification of ligands and measurement of the stoichiometry and affinity of the interactions. However, non-specific association of buffer or salts (added or present as impurities) to the protein ions during gas-phase ion formation can complicate the analysis of ESI-MS data acquired for mixtures of compounds with similar molecular weights. Spectral overlap of ions corresponding to free protein and protein-ligand complexes and their corresponding adducts can hinder the identification of ligands and introduce errors in the measured affinities. Here, we present a straightforward approach, called the sliding window adduct removal method (SWARM), to quantitatively correct ESI mass spectra of low-to-moderate resolution for signal overlap associated with adducts. The method relies on the statistical nature of adduct formation in ESI and the assumption that the distributions of adducts associated with a given protein (free protein and ligand-bound forms) are identical at a given charge state. Analysis of ESI mass spectra measured for protein-oligosaccharide interactions using solutions that produced either low- or high-abundance adducts provides support for this assumption. Implementation of SWARM involves the stepwise subtraction of the adduct signal associated with the detected protein-ligand complexes from the mass spectrum. This is accomplished using the adduct distribution measured for an appropriate reference species (usually free protein). To demonstrate the utility of the method, we applied SWARM to ESI-MS screening data acquired for libraries of oligosaccharides and bifunctional ligands consisting of a sulfonamide moiety linked to human glycan structures. Graphical Abstract.

Long-range paramagnetic NMR data can provide a closer look on metal coordination in metalloproteins

Paramagnetic NMR data can be profitably incorporated in structural refinement protocols of metalloproteins or metal-substituted proteins, mostly as distance or angle restraints. However, they could in principle provide much more information, because the magnetic susceptibility of a paramagnetic metal ion is largely determined by its coordination sphere. This information can in turn be used to evaluate changes occurring in the coordination sphere of the metal when ligands (e.g.: inhibitors) are bound to the protein. This gives an experimental handle on the molecular structure in the vicinity of the metal which falls in the so-called blind sphere. The magnetic susceptibility anisotropy tensors of cobalt(II) and nickel(II) ions bound to human carbonic anhydrase II in free and inhibited forms have been determined. The change of the magnetic susceptibility anisotropy is directly linked to the binding mode of different ligands in the active site of the enzyme. Indication about the metal coordination sphere in the presence of an inhibitor in pharmaceutically relevant proteins could be important in the design of selective drugs with a structure-based approach.

Out of the active site binding pocket for carbonic anhydrase inhibitors

2-Benzylsulfinylbenzoic acid binds to human carbonic anhydrase II in a mode completely different from any other class of carbonic anhydrase inhibitors investigated so far.

Inhibition of the β-class carbonic anhydrases from Mycobacterium tuberculosis with carboxylic acids

The growth of Mycobacterium tuberculosis is strongly inhibited by weak acids although the mechanism by which these compounds act is not completely understood. A series of substituted benzoic acids, nipecotic acid, ortho- and para-coumaric acid, caffeic acid and ferulic acid were investigated as inhibitors of three β-class carbonic anhydrases (CAs, EC 4.2.1.1) from this pathogen, mtCA 1 (Rv1284), mtCA 2 (Rv3588c) and mtCA 3 (Rv3273). All three enzymes were inhibited with efficacies between the submicromolar to the micromolar one, depending on the scaffold present in the carboxylic acid. mtCA 3 was the isoform mostly inhibited by these compounds (K(I)s in the range of 0.11-0.97 µM); followed by mtCA 2 (K(I)s in the range of 0.59-8.10 µM), whereas against mtCA 1, these carboxylic acids showed inhibition constants in the range of 2.25-7.13 µM. This class of relatively underexplored β-CA inhibitors warrant further in vivo studies, as they may have the potential for developing antimycobacterial agents with a diverse mechanism of action compared to the clinically used drugs for which many strains exhibit multi-drug or extensive multi-drug resistance.

(In)organic anions as carbonic anhydrase inhibitors

Carbonic anhydrases (CAs, EC 4.2.1.1) are widespread enzymes in all life kingdoms with five distinct genetic families known to date, the α-, β-, γ-, δ- and ζ-CAs. With the exception of the δ-class, which is less investigated to date, enzymes from the remaining classes found in vertebrates, corals, fungi, bacteria and archaea have been studied for their inhibition with simple inorganic anions as well as more complex inorganic and organic ones. In this paper we review the available data for the inhibition of these enzymes with all anions except sulfonamides and their bioisosteres (sulfamates, sulfamides) which have been reviewed earlier. Anion inhibitors are important both for understanding the inhibition/catalytic mechanisms of these enzymes and for designing novel types of inhibitors which may have clinical applications for the management of a variety of disorders in which CAs are involved. Environmental aspects of CO(2) fixation by CAs present in plants, corals, algae or diatoms and how this may be affected by inhibitors are also discussed.

Thermodynamic parameters of the interaction between Co(II) bovine carbonic anhydrase and anionic inhibitors

The pH dependence of the apparent affinity constants of perchlorate for cobalt(II)bovine carbonic anhydrase II has been measured by electronic absorption spectroscopy. The obtained data have been analyzed in terms of the ionization of two acidic groups of CoBCAII, and the affinity of perchlorate for the two water-containing species of the enzyme have been estimated. Furthermore, the affinity constants of nitrate, perchlorate, and azide for CoBCAII in the temperature range 5 degrees C-30 degrees C have been determined by spectrophotometric titrations at pH 7. The affinity constants for these ligands decrease with increasing temperatures. The temperature dependence of binding was used to estimate the enthalpy and entropy parameters for the formation of the corresponding 1:1 adducts. The obtained results indicate that binding of these anions to the cobalt enzyme is an enthalpy driven process which is opposed by a moderate entropy change.

Interaction of amide inhibitors with the active site of carbonic anhydrase: metal-induced deprotonation of the bound amide group is indicated by slow binding kinetics, by visible spectra of complexes with cobalt enzyme, and by pH effects on binding affinity

Most carbonic anhydrase (CA) inhibitors bind at the active site metal and either are anions or are capable of deprotonation to yield anions. Much less is known about the interaction of CA with inhibitors that have hitherto been considered to bind as neutral species. We report a study of the reversible amide inhibition of Co(II)-substituted CA by iodoacetamide and ethyl carbamate (urethane), as well as the ambivalent oxamate, the monoamide of oxalate. Visible cobalt spectral changes indicate coordination of all these inhibitors to the metal. The pH dependence of the affinity of carbonic anhydrase isozyme I (CA I) for ethyl carbamate and iodoacetamide is formally consistent with their binding either as anionic species to the acid form of the enzyme or as neutral species to the basic form of the enzyme. The former view is in better accord with the spectral data. Most strikingly, reversible binding of iodoacetamide and ethyl carbamate leads to uniquely slow kinetics of ligand association and dissociation that could be followed by simple mixing. The slow association kinetics suggest the involvement of energetically unfavorable deprotonation of the amide group preceding final coordination. The complex pH profile for inhibition of CA I by the ambivalent oxamate is consistent with coordination through the carboxylate group at low pH and through the deprotonated amide group at high pH. The visible spectrum of the complex of Co(II)CA I with oxamate shows a parallel dependence on pH, reflecting this dual coordination mode. Similarly, oxamate dissociation kinetics were biphasic and could be correlated with the pH-dependent spectral changes.(ABSTRACT TRUNCATED AT 250 WORDS)

Reaction of N,N-diethyldithiocarbamate and other bidentate ligands with Zn, Co and Cu bovine carbonic anhydrases. Inhibition of the enzyme activity and evidence for stable ternary enzyme-metal-ligand complexes

The reactions with N,N-diethyldithiocarbamate (DDC) of zinc, cobalt and copper carbonic anhydrase from bovine erythrocytes were investigated. The native zinc enzyme was inhibited by DDC, but no removal of zinc could be detected even at a very high [ligand]/[protein] ratio. At identical pH values a larger inhibitory effect was found for the cobalt enzyme. The metal was removed by DDC from the protein at pH less than 7.0. No cobalt removal occurred at pH 10, where a stable ternary complex with the enzyme-bound Co(II) was detected. Its optical and EPR spectra are indicative of five-coordinate Co(II). The reaction of the Cu(II) enzyme with stoichiometric chelating agent was marked by the appearance of an electronic transition at 390 nm (epsilon = 4300 M-1 X cm-1). Metal removal from the copper enzyme readily occurred as the ligand was in excess over the metal, with parallel appearance of a band at 440 nm, which was attributed to the free Cu(II)-DDC complex. Also, in the case of the copper enzyme an alkaline pH was found to stabilize the ternary adduct with the diagnostic 390 nm band. EPR spectra showed that the ternary adduct is a mixture of two species, both characterized by the presence in the EPR spectrum of a superhyperfine structure from two protein nitrogens and by a low g parallel value, indicative of coordination to sulfur ligands. It is suggested that the two species contain the metal as penta- and hexacoordinated, respectively. Measurements of the longitudinal relaxation time, T1, of the water protons suggested that water coordination is retained in the latter case. Hexacoordination with retention of water is also proposed for the Cu(II) derivatives with the bidentate oxalate and bicarbonate anions, unlike the corresponding Co(II) derivatives, which are pentacoordinated. Different coordination of Co(II) and Cu(II) adducts may be relevant to the difference of activity of the two substituted enzymes.

Metal coordination geometry of ternary complex between cobalt-bovine carbonic anhydrase and multidentate ligands

Interaction of cobalt(II) bovine carbonic anhydrase with 3- and 4-pyridinecarboxylates, 2-pyridinecarboxylate, and 2,6-pyridinedicarboxylate has been investigated by the spectrophotometric method. The apparent formation constant of the ternary complex (ligand : cobalt ion : apoenzyme = 1 : 1 : 1) was determined from spectral data. The spectroscopic data of the ternary complex indicate that the 3- or 4-pyridinecarboxylate adduct has a five-coordination geometry through three donor atoms of the protein part of the enzyme, the carboxyl group of 3- or 4-pyridinecarboxylate, and a water molecule. 3- or 4-Pyridinecarboxylate behaves as a monodentate ligand. The spectrum of the ternary complex of 2-pyridinecarboxylate was very different from that of 3- or 4-pyridinecarboxylate. The spectra data indicate that 2-pyridinecarboxylate adduct has a five-coordination geometry and that it behaves as a bidentate ligand. The ternary complex of 2,6-pyridinedicarboxylate was so unstable that the spectrum of the ternary complex was determined by the indirect method. The spectrum of 2,6-pyridinedicarboxylate adduct shows lower molar absorption than that of 2-pyridinecarboxylate adduct. This result indicates that 2,6-pyridine dicarboxylate behaves possibly as a tridentate ligand.

Investigation of the system cobalt(II) bovine carbonic anhydrase B-trichloroacetaldehyde

The interactions between hydrated trichloroacetaldehyde and cobalt(II)bovine carbonic anhydrase B have been investigated as a function of pH by means of electronic spectroscopy of FT nmr spectroscopy. The hydrated aldehyde is bound to the metal ion and its apparent affinity constant is pH dependent with a bell-shaped profile. The kinetic parameters of the dissociation process have also been determined.