Commikuanoids A-C: New cycloartane triterpenoids with exploration of carbonic anhydrase-II inhibition from the resins of Commiphora kua by in vitro and in silico molecular docking.

Three new cycloartane triterpenoids, commikuanoids A-C (1-3), together with four known compounds 4-7, were isolated from the resin of Commiphora kua. Their structures were confirmed by advanced NMR techniques such as 1D (1H and 13C) and 2D (HMBC, HSQC, COSY, NOESY and NOE) and high-resolution mass spectrometry (HRMS). Five compounds (1-5) were screened for in vitro carbonic anhydrase II (CA II) inhibitory activity. All the tested compounds demonstrated significant activity against CA II with IC50 values ranging from 4.9-19.6 µM. Moreover, the binding pattern of each compound in the binding site of CA-II was predicted through in silico molecular docking approach. It was observed that compounds 2, 4, and 5 binds with the Zn ion present in the active site of CA II, while compounds 1 and 3 mediated hydrogen bonding with Thr199 of CA-II, and all the compounds showed good binding score (> - 5 kcal/mol).

Microsecond simulation analysis of carbonic anhydrase - II in complex with (+)-cathechin revealed molecular interactions responsible for its amelioration effect on fluoride toxicity.

Fluorosis is a chronic condition caused by overexposure to fluoride, marked by impaired dental, skeletal, and non-skeletal health. In presence of excess fluoride ions, in severe cases calcification of the ligaments observed. Earlier studies have suggested that the disruption of carbonic anhydrase activity via ionic homeostasis change was associated with F toxicity. In a recent study, it was demonstrated that Tamarind fruit extract was effective in increasing the urinary F excretion in male Wistar rats via studying the mRNA expression of carbonic anhydrase II (CA II) in kidney homogenates using western blotting, immunohistochemistry and quantitative Realtime PCR based studies. We have carried out this study to understand the detailed molecular level interactions responsible for this tamarind extract based (+)-cathechin compound towards lowering the F toxicity via targeting CA-II. From our study, it was revealed that due to the ability of (+)-cathechin compound to bind tightly filling complete available space at the catalytically important site forming metal coordinated ionic bonds with His94, His96 and His119 residues helps in restricting F ions to interact with Zn ion located at the core of catalytic site responsible for its functionality. On the other hand, interaction of (+)-cathechin compound with Gln92 was observed to be critically important towards inducing conformational changes in CA-II, thus allowing (+)-cathechin compound to burry even deeply inside the catalytic site.Communicated by Ramaswamy H. Sarma.

New Carbonic Anhydrase-II Inhibitors from Marine Macro Brown Alga Dictyopteris hoytii Supported by In Silico Studies.

In continuation of phytochemical investigations of the methanolic extract of Dictyopteris hoytii, we have obtained twelve compounds (1-12) through column chromatography. Herein, three compounds, namely, dimethyl 2-bromoterepthalate (3), dimethyl 2,6-dibromoterepthalate (4), and (E)-3-(4-(dimethoxymethyl)phenyl) acrylic acid (5) are isolated for the first time as a natural product, while the rest of the compounds (1, 2, 6-12) are known and isolated for the first time from this source. The structures of the isolated compounds were elucidated by advanced spectroscopic 1D and 2D NMR techniques including 1H, 13C, DEPT, HSQC, HMBC, COSY, NEOSY, and HR-MS and comparison with the reported literature. Furthermore, eight compounds (13-20) previously isolated by our group from the same source along with the currently isolated compounds (1-12) were screened against the CA-II enzyme. All compounds, except 6, 8, 14, and 17, were evaluated for in vitro bovine carbonic anhydrase-II (CA-II) inhibitory activity. Eventually, eleven compounds (1, 4, 5, 7, 9, 10, 12, 13, 15, 18, and 19) exhibited significant inhibitory activity against CA-II with IC50 values ranging from 13.4 to 71.6 µM. Additionally, the active molecules were subjected to molecular docking studies to predict the binding behavior of those compounds. It was observed that the compounds exhibit the inhibitory potential by specifically interacting with the ZN ion present in the active site of CA-II. In addition to ZN ion, two residues (His94 and Thr199) play an important role in binding with the compounds that possess a carboxylate group in their structure.

Intracellular Binding/Unbinding Kinetics of Approved Drugs to Carbonic Anhydrase II Observed by in-Cell NMR.

Candidate drugs rationally designed in vitro often fail due to low efficacy in vivo caused by low tissue availability or because of unwanted side effects. To overcome the limitations of in vitro rational drug design, the binding of candidate drugs to their target needs to be evaluated in the cellular context. Here, we applied in-cell NMR to investigate the binding of a set of approved drugs to the isoform II of carbonic anhydrase (CA) in living human cells. Some compounds were originally developed toward other targets and were later found to inhibit CAs. We observed strikingly different dose- and time-dependent binding, wherein some drugs exhibited a more complex behavior than others. Specifically, some compounds were shown to gradually unbind from intracellular CA II, even in the presence of free compound in the external medium, therefore preventing the quantitative formation of a stable protein-ligand complex. Such observations could be correlated to the known off-target binding activity of these compounds, suggesting that this approach could provide information on the pharmacokinetic profiles of lead candidates at the early stages of multitarget drug design.

Secondary metabolites of Helichrysum plicatum DC. subsp. plicatum flowers as strong carbonic anhydrase, cholinesterase and α-glycosidase inhibitors.

Helichrysum plicatum species are used in Turkish folk medicine as lithagogue, diuretic, and nephritic. Research on the methanol (MeOH) extract of flowers of H. plicatum DC. subsp. plicatum resulted in the isolation of eight known compounds (1-8). The chemical structures of the compounds were determined as ß-sitosterol (1), apigenin (2), nonacosanoic acid (3), astragalin (4), ß-sitosterol-3-O-ß-D-glucopyranoside (5), helichrysin A (6), helichrysin B (7), and isosalipurposide (8) by spectroscopic and chromatographic/spectrometric methods, including 1D and 2D nuclear magnetic resonance and liquid chromatography-tandem mass spectrometry. Nonacosanoic acid (3) was isolated for the first time from H. plicatum DC. subsp. plicatum. The MeOH extract and isolated compounds were evaluated for their in vitro human carbonic anhydrase I (hCAI) and II (hCAII), acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and α-glycosidase inhibitory activities. The IC50 values of H. plicatum DC. subsp. plicatum MeOH extract for hCAI, hCAII, AChE, BChE, and α-glycosidase were found to be 77.87, 52.90, 115.50, 117.46, and 81.53 mg/mL, respectively. The compounds showed IC50 values of 1.43-4.47, 1.40-4.32, 1.69-2.90, 1.09-3.89, and 1.61-3.80 µM against hCAI, hCAII, AChE, BChE, and α-glycosidase, respectively. In summary, H. plicatum DC. subsp. plicatum secondary metabolites demonstrated strong inhibitory effects especially against hCAI and hCAII, whereas the MeOH extract showed a weak inhibitory effect on all enzymes.

On-DNA hit validation methodologies for ligands identified from DNA-encoded chemical libraries.

DNA-encoded chemical libraries (DECLs) are large compound collections attached to DNA fragments, serving as amplifiable barcodes, which can be screened on target proteins of pharmaceutical interest. In DECL selections, ligands are identified by high-throughput DNA sequencing, by comparing their frequency before and after the affinity capture step. Hits identified using this procedure need to be validated by resynthesis and by performing affinity measurements. Here we report novel on-DNA hit validation strategies, which enable the facile confirmation of ligand-protein interaction as well as the determination of equilibrium and kinetic binding constants. The experimental procedures, which had been inspired by enzyme-linked immunosorbent assays (ELISA), were validated using ligands of different affinity to carbonic anhydrase II and IX.

Abeliophyllum distichum Nakai alleviates postmenopausal osteoporosis in ovariectomized rats and prevents RANKL-induced osteoclastogenesis in vitro.

ETHNOPHARMACOLOGICAL RELEVANCE: Abeliophyllum distichum Nakai (AD), called Miseon, is one of Korea's monotypic endemic species. As a folk remedy, the AD has been used to treat inflammatory disease, stomachaches, diarrhea, and gynecologic disease in Korea. Some researchers have reported that the AD has anti-cancer, anti-inflammatory, and anti-oxidant effects. But the protective effect of AD leaf for osteoporosis has not been reported yet. AIM OF THE STUDY: This study aimed to analyze the effects and mechanism of AD-ethyl acetate fraction (EA) extract on the osteoporosis, one of the gynecologic disease. MATERIALS AND METHODS: The RAW 264.7 cells were used as a model for RANKL-induced osteoclastogenesis. We measured the TRAcP activity, expressions of NFATc1, c-fos, and MAPK to investigate the effect of AD-EA. OVX-induced osteoporosis rat model was used as menopausal osteoporosis. After both ovaries were removed through a surgical procedure, and AD-EA or 17b-estradiol was orally administered for 8 weeks. BMD of femurs was measured as well as the bone morphometric parameter, such as BV/TV, trabecular thickness, number and surface using a micro CT. RESULTS: AD-EA significantly inhibited TRAcP activity, actin ring formation, pit formation and the expressions of osteoclast-related genes in a dose-dependent manner through the inhibition of the MAPK and c-fos/NFATc1 pathway. In addition, low dose administration of AD-EA improved the deterioration of trabecular bone microarchitecture caused by OVX through the inhibition of bone resorption by TRAcP and CTK. CONCLUSIONS: These results suggest that AD-EA may contribute to the therapy of osteoporosis caused by menopause in women.

Screening of benzenesulfonamide in combination with chemically diverse fragments against carbonic anhydrase by differential scanning fluorimetry.

The differential scanning fluorimetry (DSF) screening of 5.692 fragments in combination with benzenesulfonamide (BSA) against bovine carbonic anhydrase (bCA) delivered >100 hits that either caused, on their own, a significant thermal shift (ΔTm, °C) in the protein melting temperature or significantly influenced the thermal shift observed for BSA alone. Three hits based on 1,2,3-triazole moiety represent the periphery of the recently reported potent inhibitors of hCA II, IX and XII which were efficacious in vivo. Such a re-discovery of suitable BSA periphery essentially validates the new fragment-based approach to the discovery of future CAIs. Structures of other validated fragment hits are reported.

Further validation of strecker-type α-aminonitriles as a new class of potent human carbonic anhydrase II inhibitors: hit expansion within the public domain using differential scanning fluorimetry leads to chemotype refinement.

Testing of an expanded, 800-compound set of analogues of the earlier described Strecker-type α-aminonitriles (selected from publicly available Enamine Ltd. Screening Collection) in thermal shift assay against bovine carbonic anhydrase (bCA) led to further validation of this new class of inhibitors and identification a new, refined chemotype represented by inhibitors with 10-improved potency. [Formula: see text].

Syntesis of thio- and seleno-acetamides bearing benzenesulfonamide as potent inhibitors of human carbonic anhydrase II and XII.

A novel series of thio- and seleno-acetamides bearing benzenesulfonamide were synthetized and tested as human carbonic anhydrase inhibitors. These compounds were tested for the inhibition of four human (h) isoforms, hCA I, II, IX, and XII, involved in pathologies such as glaucoma (CA II and XII) or cancer (CA IX/XII). Several derivatives showed potent inhibition activity in low nanomolar range such as 3a, 4a, 7a and 8a. Furthermore, based on the tail approach we explain the interesting and selective inhibition profile of compound such as 5a and 9a, which were more selective for hCA I, 9b which was selective for hCA II, 3f selective for hCA IX and finally, 3e and 4b selective for hCA XII, over the other three isoforms. They are interesting leads for the development of more effective and isoform-selective inhibitors.

Affinity Enhancement of Protein Ligands by Reversible Covalent Modification of Neighboring Lysine Residues.

The discovery of protein ligands, capable of forming a reversible covalent bond with amino acid residues on a protein target of interest, may represent a general strategy for the discovery of potent small-molecule inhibitors. We analyzed the ability of different aromatic aldehydes to form imines by reaction with lysine using 1 H NMR techniques. 2-Hydroxybenzaldehyde derivatives were found to efficiently form imines in the millimolar concentration range. These benzaldehyde derivatives could increase the binding affinity of protein ligands towards the cognate protein target. Affinity maturation was achieved not only by displaying ligand and aldehyde moieties on two complementary locked nucleic acid strands but also by incorporating the binding fragments in a single small-molecule ligand. The affinity gain was only observed when lysine residues were accessible in the immediate surroundings of the ligand-binding site and could be abrogated by quenching with a molar excess of hydroxylamine.

Discovery of ß-Adrenergic Receptors Blocker-Carbonic Anhydrase Inhibitor Hybrids for Multitargeted Antiglaucoma Therapy.

The combination of a ß-adrenergic receptors (AR) blocker and a carbonic anhydrase (CA, EC 4.2.1.1) inhibitor in eye drops formulations is one of the most clinically used treatment for glaucoma. A novel approach consisting of single-molecule, multitargeted compounds for the treatment of glaucoma is proposed here by designing compounds which concomitantly interact with the ß-adrenergic and CA targets. Most derivatives of the two series of benzenesulfonamides incorporating 2-hydroxypropylamine moieties reported here exhibited striking efficacy against the target hCA II and XII, whereas a subset of compounds also showed significant modulation of ß1- and ß2-ARs. X-ray crystallography studies provided rationale for the observed hCA inhibition. The best dual-agents decreased IOP more effectively than clinically used dorzolamide, timolol, and the combination of them in an animal model of glaucoma. The reported evidence supports the proof-of-concept of ß-ARs blocker-CAI hybrids for antiglaucoma therapy with an innovative mechanism of action.

Development of drug discovery screening system by molecular interaction kinetics-mass spectrometry.

RATIONALE: Drug discovery studies invariably require qualitative and quantitative analyses of target compounds at every stage of drug discovery. We have developed a system combining molecular interaction analysis and mass spectrometry (LC-MS) using the principle of nanopore optical interferometry (nPOI) called molecular interaction kinetics-mass spectrometry (MIK-MS). Since nPOI has high binding capacity, the bond-dissociated compound can be directly detected using LC-MS. In this study, we use carbonic anhydrase II (CAII) as a ligand and apply six small compounds as analytes and report the affinity analysis using MIK-MS. METHODS: CAII was immobilized onto a COOH sensor chip using standard amine coupling. A reference surface was prepared by activating and subsequently blocking the surface under identical conditions. An amount of 50 µL of mix solution was injected over the reference channel and sample channel for CAII immobilization. The solutions eluting from the sensor chip were collected from the waste-line of the SKi Pro system every 30 s. Reconstructed elution samples were then injected into the LC-MS/MS system. RESULTS: A mixture containing furosemide, acetazolamide, 4-sulfamoylbenzoic acid, 5-(dimethylamino)-1-naphthalene sulfonamide (DNSA), sulfanilamide and sulpiride (15 µM each) was injected into the CAII-immobilized sensor chip, and the fractions eluted from the SKi Pro system were collected and subjected to selected reaction monitoring LC-MS characterization. Specific results were obtained for acetazolamide, DNSA, furosemide and sulpiride. The results suggest that the association-dissociation curve of a mixed sample can be obtained by one-time MIK-MS analysis. CONCLUSIONS: Six small-molecule binders of CAII were analyzed quantitatively using nPOI and MIK-MS, and the results were compared to published surface plasmon resonance (SPR) results. The nPOI and SPR results show good agreement, confirming the reliability of the analysis. Time-dependent binding results may be obtained by our MS sensorgram approach. Drugs that meet medical needs in a short period are required; this nPOI-LC-MS system is considered an important tool for rapid drug discovery.

Ellagitannin and flavonoid constituents from Agrimonia pilosa Ledeb. with their protein tyrosine phosphatase and acetylcholinesterase inhibitory activities.

A new ellagitannin, agritannin (1), a new flavone glycoside, agriflavone (2), and another flavone glycoside with spectroscopic data reported for the first time, kaempferol-3-O-[(S)-3-hydroxy-3-methylglutaryl (1→6)]-ß-d-glucoside (3), along with 16 known compounds were isolated from the aerial parts of Agrimonia pilosa Ledeb. These compounds were evaluated for PTP1B inhibitory activity. Among them, compounds 9 and 18 displayed potential inhibitory activity against PTP1B with IC50 values of 7.14±1.75 and 7.73±0.24µM, respectively. In addition, compound 1 showed significant inhibitory effect with an IC50 value of 17.03±0.09µM. Furthermore, these compounds were tested in AChE inhibitory assays. Most of them were found to have moderate inhibitory effects, with IC50 values ranging from 60.20±1.09 to 92.85±1.12µM. Except compounds 3, 8, and 18 were inactive.

3D QSAR studies, pharmacophore modeling, and virtual screening of diarylpyrazole-benzenesulfonamide derivatives as a template to obtain new inhibitors, using human carbonic anhydrase II as a model protein.

A 3D-QSAR modeling was performed on a series of diarylpyrazole-benzenesulfonamide derivatives acting as inhibitors of the metalloenzyme carbonic anhydrase (CA, EC 4.2.1.1). The compounds were collected from two datasets with the same scaffold, and utilized as a template for a new pharmacophore model to screen the ZINC database of commercially available derivatives. The datasets were divided into training, test, and validation sets. As the first step, comparative molecular field analysis (CoMFA), CoMFA region focusing and comparative molecular similarity indices analysis (CoMSIA) in parallel with docking studies were applied to a set of 41 human (h) CA II inhibitors. The validity and the prediction capacity of the resulting models were evaluated by leave-one-out (LOO) cross-validation approach. The reliability of the model for the prediction of possibly new CA inhibitors was also tested.

A spectroscopic study on the absorption of carbonic anhydrase onto the nanoporous silica nanoparticle.

Herein, KIT-6 nanoporous silica nanoparticles were used as a solid support for immobilization of bovine carbonic anhydrase, isoform II (BCA II). The zeta potential study revealed that KIT-6 and BCA II provided negative (-13.58±1.95mV) and positive (4.23±0.72mV) charge distribution, respectively. Dynamic light scattering (DLS) analysis also showed that the hydrodynamic radius of KIT-6 is less than 100nm. In addition, the structural studies of free and immobilized BCA II against urea-induced denaturation were investigated by circular dichroism (CD) and fluorescence spectroscopy. CD studies showed that the absorbed BCA II, in comparison with the free enzyme, demonstrated higher stability against rising urea concentration. Fluorescence spectroscopy showed lower values of Stern- Volmer constant (KSV) for immobilized BCA II relative to free enzyme, reflecting the relative enzyme stability of BCA II after immobilization. Melting temperature (Tm) measurement of free and immobilized BCA II showed that immobilized enzyme had a more stable structure (Tm=71.9°C) relative to the free counterpart (Tm=64.7°C). In addition, the immobilized BCA II showed pronounced stability against pH and thermal deactivation. This study may provide new and complementary details regarding the design and development of enzymes in industrial applications.

Investigation of the inhibitory properties of some phenolic standards and bee products against human carbonic anhydrase I and II.

Polyphenols are important secondary products of plants with the potential to inhibit carbonic anhydrases. The aim of this study was to investigate the inhibition effects of various phenolic standards, honey, propolis, and pollen species on human carbonic anhydrase I and II. The inhibition values (IC50) of the phenolics (gallic acid, protocatechuic acid, quercetin, catechin, tannic acid, and chrysin) ranged from 0.009 to 0.32 µg/mL, tannic acid emerging as the best inhibitor. The inhibition values of three different types of honey, heather, rhododendron, and chestnut ranged between 2.32 and 25.10 µg/mL, the chestnut honeys exhibiting the best inhibition. The ethanolic extracts of pollen and propolis exhibited good inhibitory properties, with IC50 values between 0.486 and 3.320 µg/mL. In order to evaluate the phenolic composition of bee products, phenolic profiles and total phenolic contents (TFC) were also measured. The inhibition ranking among the natural products studied was phenolic standards > propolis > pollen > honeys, and inhibition was related to TFC.

Microwave-assisted extraction, HPLC analysis, and inhibitory effects on carbonic anhydrase I, II, VA, and VII isoforms of 14 blueberry Italian cultivars.

The multi-component fingerprint and the biological evaluation of plant-derived material are indispensable for the pharmaceutical field, in food quality control procedures, and in all plant-based products. We investigated the quantitative content of biologically active compounds (anthocyanins and chlorogenic acid) of microwave-assisted blueberry extracts from 14 different Italian cultivars, using validated high-performance liquid chromatography-photodiode array detector (HPLC-PDA) method and routinely instrument configuration. The carbonic anhydrase (CA, EC 4.2.1.1) inhibition profiles against several pharmacologically relevant CA isoforms of blueberry extracts and some bioactive compounds were also investigated. The various cultivars showed a highly variable content in anthocyanins and chlorogenic acid, and their CA inhibitory effects were also highly variable. Overall these data prove that antioxidant natural products found in blueberries may be useful for designing pharmacological agents in which various CAs are involved, e.g., antiobesity, antitumor, or anticonvulsants agents.

Native State Mass Spectrometry, Surface Plasmon Resonance, and X-ray Crystallography Correlate Strongly as a Fragment Screening Combination.

Fragment-based drug discovery (FBDD) is contingent on the development of analytical methods to identify weak protein-fragment noncovalent interactions. Herein we have combined an underutilized fragment screening method, native state mass spectrometry, together with two proven and popular fragment screening methods, surface plasmon resonance and X-ray crystallography, in a fragment screening campaign against human carbonic anhydrase II (CA II). In an initial fragment screen against a 720-member fragment library (the "CSIRO Fragment Library") seven CA II binding fragments, including a selection of nonclassical CA II binding chemotypes, were identified. A further 70 compounds that comprised the initial hit chemotypes were subsequently sourced from the full CSIRO compound collection and screened. The fragment results were extremely well correlated across the three methods. Our findings demonstrate that there is a tremendous opportunity to apply native state mass spectrometry as a complementary fragment screening method to accelerate drug discovery.

Inhibition studies of bacterial, fungal and protozoan ß-class carbonic anhydrases with Schiff bases incorporating sulfonamide moieties.

A series of new Schiff bases derived from sulfanilamide, 3-fluorosulfanilamide or 4-(2-aminoethyl)-benzenesulfonamide containing either a hydrophobic or a hydrophilic tail, have been investigated as inhibitors of three ß-carbonic anhydrases (CA, EC 4.2.1.1) from three different microorganisms. Their antifungal, antibacterial and antiprotozoan activities have been determined against the pathogenic fungus Cryptococcus neoformans, the bacterial pathogen Brucella suis and the protozoan parasite Leishmania donovani chagasi, responsible for Leishmaniasis. The results of these inhibition studies show that all three enzymes were efficiently inhibited by the Schiff base sulfonamides with KI values in the nanomolar or submicromolar range, depending on the nature of the tail, coming from the aryl/heteroaryl moiety present in the starting aldehyde employed in the synthesis. Furthermore, the compounds hereby investigated revealed high ß-CAs selectivity over the ubiquitous, physiologically relevant and off-target human isoforms (CA I and II) and to be more potent as antifungal and antibacterial than as antiprotozoan potential drugs.