Biochemical characterization of CA IX, one of the most active carbonic anhydrase isozymes

Synthesis and Construction of I-124 Labeled Small Molecular Probe for Noninvasive PET Imaging of CAIX Expression

PURPOSE

Carbonic anhydrase IX (CAIX) which is high expression in the most of hypoxic tumor than normal tissue, promoting the growth, invasion, and metastasis of the tumor. Therefore, the study aimed to evaluate the retention and diagnostic ability of [124I]I-XYIMSR- 01 in CAIX-overexpression tumor by using positron emission tomography (PET) imaging.

PROCEDURES

[124/125I]I-XYIMSR- 01 was labeled by 124/125I, and its CAIX-targeting properties in different cell lines were assayed by cell uptaken study. Its diagnose and retention ability in vivo were verified in different CAIX-expression models using PET imaging and biodistribution study. Pathological tissues were obtained for immunohistochemical (IHC) and Hematoxylin-Eosin (HE) staining to explore the relationship between CAIX and hypoxic, and further analyze PET/CT results.

RESULTS

[124I]I-XYIMSR- 01 was obtained with high specific activity, good radiochemical purity, and good stability. The uptake of of [124I]I-XYIMSR- 01 in HT- 29 cells, which have high CAIX expression, was significant higher than that in HCT116 cells with low CAIX expression (12.78 ± 0.47 vs 1.06 ± 0.10, p = 0.000, at 1 h). This indicated that the probe has good targeting capability and specificity for CAIX. In Micro-PET imaging, clear molecular images lasting for 48 h were achieved in HT29 model. Quantitative biodistribution results showed that the tumor and digestive tract background tissues had a good signal-to-noise ratio within 24 h after injection, indicating [124I]I-XYIMSR- 01 could enable delayed imaging in digestive tract tumors (tumor-to-small intestine: 8.79 ± 0.98). Tumors uptakes were also confirmed by IHC pathology.

CONCLUSION

The study have shown that [124I]I-XYIMSR- 01 is an ideal molecular probe for tumor hypoxia, enabling long-term dynamic monitoring and imaging of hypoxic tumors.

Electric field-induced conformational dynamics of CA9: a potential biomarker for glioblastoma multiforme

GBM, a malignant brain tumor prevalent in adults, can be treated using Electric field (EF) therapy. However, the underlying mechanism of EF-based GBM therapy is not well understood. In this study, we used bioinformatics and MD analysis to explore CA9 in EF therapy for GBM. CA9 was identified as a differentially expressed gene (DEG) sensitive to EF stimulation in GBM using GEO and TCGA for integrated analysis. Elevated CA9 expression was associated with reduced overall survival in GBM patients, indicating that CA9 was an adverse prognostic factor. Single-cell data demonstrated that CA9 expression was significantly higher in GBM cells than in normal cells, suggesting that CA9 could be an EF-sensitive biomarker for GBM. GSVA analysis suggested that CA9 was related to hypoxia and glucose metabolism in glioblastoma. MD simulations were employed to examine the impact of EF (0 V/nm ≤ E ≤ 0.5 V/nm) on the conformation of the CA9 protein, including RMSF, RMSD, Rg, secondary structure, and dipole moment. The CA9 protein structure was altered with different EF intensities, affecting the motion of protein atoms in an EF intensity-dependent manner. The number of hydrogen bonds was significantly reduced as the EF intensity increased, indicating that EF disrupted the hydrogen bonds. Additionally, the EF intensity affected the dipole moment and characteristic time. Besides, the CA9 gene family analysis suggested that this gene family was highly conserved. Overall, CA9 showed potential as a GBM biomarker sensitive to EF, presenting a prospective target for therapeutic interventions in EF-mediated GBM treatment.

Highly Active Carbonic Anhydrase of the Thylakoid Lumen of Chlamydomonas reinhardtii

The green unicellular algae Chlamydomonas reinhardtii contains 12-13 carbonic anhydrases (CAs). For a long time, the two closely related α-CAs of the periplasmic membrane CAH1 and CAH2 were considered to be the CAs with the highest CO2 hydration activity. The recombinant protein α-CA CAH3 (rCAH3) from the thylakoid lumen obtained in the present study showed more than three times higher activity compared to CAH1 and more than 11 times higher compared to previous studies with rCAH3. Long-term sustainability of the enzyme was observed at alkaline pH (>8), with maintenance of half of its activity at 4 °C for up to 50 days. Thermostability of rCAH3 indicated the retention of the activity at 20 °C for one hour at pH 9-10 with its ~50% decrease at pH 6-7. However, the residual activity of rCAH3 after incubation at an extremely high temperature (75 °C) for 15 min led to the formation of the double-hump graph with maxima at pH 6 and 9. The enzyme demonstrated high sensitivity to ethoxyzolamide and acetazolamide at nM concentrations, to Zn2+ and Cu2+ cations at 1 mM concentrations, and L-cysteine was able to completely inhibit CA activity of rCAH3 through reduction of sulfhydryl groups. Esterase activity of rCAH3 was well detected with values comparable to those of bovine CAII, but with a maximum at pH 8 instead of pH 9, which is usual for bovine CAII. The results indicated that CAH3 may be the most active CA of C. reinhardtii and that its role in the photosynthetic apparatus function could have been underestimated in previous works.

Discovery of Carbonic Anhydrase 9 as a Novel CLEC2 Ligand in a Cellular Interactome Screen

Membrane proteins, especially extracellular domains, are key therapeutic targets due to their role in cell communication and associations. Yet, their functions and interactions often remain unclear. This study presents a general method to discover interactions of membrane proteins with immune cells and subsequently to deorphanize their respective receptors. We developed a comprehensive recombinant protein library of extracellular domains of human transmembrane proteins and proteins found in the ER-Golgi-lysosomal systems. Using this library, we conducted a flow-cytometric screen that identified several cell surface binding events, including an interaction between carbonic anhydrase 9 (CAH9/CA9/CAIX) and CD14high cells. Further analysis revealed this interaction was indirect and mediated via platelets bound to the monocytes. CA9, best known for its diverse roles in cancer, is a promising therapeutic target. We utilized our library to develop an AlphaLISA high-throughput screening assay, identifying CLEC2 as one robust CA9 binding partner. A five-amino-acid sequence (EDLPT) in CA9, identical to a CLEC2 binding domain in Podoplanin (PDPN), was found to be essential for this interaction. Like PDPN, CA9-induced CLEC2 signaling is mediated via Syk. A Hodgkin's lymphoma cell line (HDLM-2) endogenously expressing CA9 can activate Syk-dependent CLEC2 signaling, providing enticing evidence for a novel function of CA9 in hematological cancers. In conclusion, we identified numerous interactions with monocytes and platelets and validated one, CA9, as an endogenous CLEC2 ligand. We provide a new list of other putative CA9 interaction partners and uncovered CA9-induced CLEC2 activation, providing new insights for CA9-based therapeutic strategies.

Exploring Chemical Spaces in the Billion Range: Is Docking a Computational Alternative to DNA-Encoded Libraries?

The concept of DNA-encoded libraries (DELs) enables the experimental screening of billions of compounds simultaneously, offering an unprecedented boost in the coverage of chemical space. In parallel, however, dramatically increased access to supercomputers and a number of ultrahigh throughput virtual screening (uHTVS) tools have made screening of billion-membered virtual libraries available. Here, we investigate whether current, brute-force, or AI-enabled uHTVS approaches might constitute a computational alternative to DEL screening. While it is tempting to look at uHTVS as a computational analogue of DEL screening, we found specific advantages and limitations of both methodologies that suggest them being complementary rather than competitive.

Molecular Modeling of Glycosylated Catalytic Domain of Human Carbonic Anhydrase IX

Glycans exhibit significant structural diversity due to the flexibility of glycosidic bonds linking their constituent monosaccharides and the formation of numerous hydrogen bonds. The present work searches a simulated ensemble of glycan chain conformations attached to the catalytic domain of N-glycosylated human carbonic anhydrase IX (HCA IX-c) to identify conformations pointed away or back-folded toward the protein surface guided by different amino acid residues. A series of classical molecular dynamics (MD) simulation studies for a total of 30 μs followed by accelerated MD simulations for a total of 2 μs have been performed using two different force fields to capture varying degrees of fluctuations of both glycan chain and HCA IX. From the underlying free energy profile and kinetics derived using hidden Markov state model, several stable glycan orientations are identified that extend away from the protein surface and convert among each other with rate constants of the order 107-1010 S-1. Most importantly, we have identified a rare glycan conformation which reaches close to a catalytically important amino acid residue, Glu-106. We further enlist the protein residues that couple such less frequent event of the glycan chain back-folding toward the surface of the protein.

Exploring the Redox and pH Dimension of Carbonic Anhydrases in Cancer: A Focus on Carbonic Anhydrase 3

Significance: Both redox and pH are important regulatory processes that underpin cell physiological functions, in addition to influencing cancer cell development and tumor progression. The thioredoxin (Trx) and glutathione redox systems and the carbonic anhydrase (CA) proteins are considered key regulators of cellular redox and pH, respectively, with components of the Trx system and CAs regarded as cancer therapeutic targets. However, the redox and pH axis in cancer cells is an underexplored topic of research. Recent Advances: Structural studies of a CA family member, CA3, localized two of its five cysteine residues to the protein surface. Redox-regulated modifications to CA3 have been identified, including glutathionylation. CA3 has been shown to bind to other proteins, including B cell lymphoma-2-associated athanogene 3, and squalene epoxidase, which can modulate autophagy and proinflammatory signaling, respectively, in cancer cells. Critical Issues: CA3 has also been associated with epithelial-mesenchymal transition processes, which promote cancer cell metastasis, whereas CA3 overexpression activates the phosphatidylinositol-3 kinase/protein kinase B/mammalian target of rapamycin (PI3K/AKT/mTOR) pathway, which upregulates cell growth and inhibits autophagy. It is not yet known if CA3 modulates cancer progression through its reported antioxidant functions. Future Directions: CA3 is one of the least studied CA isozymes. Further studies are required to assess the cellular antioxidant role of CA3 and its impact on cancer progression. Identification of other binding partners is also required, including whether CA3 binds to Trx in human cells. The development of specific CA3 inhibitors will facilitate these functional studies and allow CA3 to be investigated as a cancer therapeutic target. Antioxid. Redox Signal. 41, 957-975.

QSAR modeling of pyrazoline derivative as carbonic anhydrase inhibitors

The efficacy of 34 pyrazoline derivatives as carbonic anhydrase inhibitors was studied in silico. The quantum descriptors were calculated by the DFT/B3LYP method using the 6-31G(d) basis; the dataset was randomly divided into training and testing. By altering the compounds in the sets, four models were created, and they were then used to determine the predicted pIC50 values for the six chemicals in the test set. According to the OECD guidelines for QSAR model validation and the Golbraikh and Tropsha's criteria for model approval, each created model was independently validated both internally and externally, along with YRandomization. Model 3 is chosen because it has higher R2, R2test, and Q2cv values (R2 = 0.79, R2test = 0.95, Q2cv = 0.64). Only one descriptor has a proportional influence on pIC50 activity, but the other four descriptors have an inverse influence on pIC50 because of the negative contribution coefficient. Given the descriptors of the model, we could propose new molecules with remarkable inhibitory activity.

Harnessing Nitric Oxide-Donating Benzofuroxans for Targeted Inhibition of Carbonic Anhydrase IX in Cancer

We describe here the design and antitumor evaluation of benzofuroxan-based nitric oxide (NO)-donor hybrid derivatives targeting human carbonic anhydrases (hCAs) IX and XII. The most effective compounds, 27 and 28, demonstrated potent dual action, exhibiting low nanomolar inhibition constants against hCA IX and significant NO release. Notably, compound 27 showed significant antiproliferative effects against various cancer cell lines, particularly renal carcinoma A-498 cells. In these cells, it significantly reduced the expression of CA IX and iron-regulatory proteins, inducing apoptosis via mitochondrial caspase activity and ferroptosis pathways, as evidenced by increases in ROS, nitrite, and down-regulated expression of ferritin-encoding genes. In three-dimensional tumor models, compound 27 effectively reduced spheroid size and viability. In vivo toxicity studies in mice indicated that the compounds were well-tolerated, with no significant alterations in kidney function. These findings underscore the potential of benzofuroxan-based CA inhibitors for further preclinical evaluations as therapeutic agents targeting renal cell carcinoma.

Carbonic anhydrase IX: An atypical target for innovative therapies in cancer

Carbonic anhydrases (CAs), are metallo-enzymes implicated in several pathophysiological processes where tissue pH regulation is required. CA IX is a tumor-associated CA isoform induced by hypoxia and involved in the adaptation of tumor cells to acidosis. Indeed, several tumor-driving pathways can induce CA IX expression, and this in turn has been associated to cancer cells invasion and metastatic features as well as to induction of stem-like features, drug resistance and recurrence. After its functional and structural characterization CA IX targeting approaches have been developed to inhibit its activity in neoplastic tissues, and to date this field has seen an incredible acceleration in terms of therapeutic options and biological readouts. Small molecules inhibitors, hybrid/dual targeting drugs, targeting antibodies and adoptive (CAR-T based) cell therapy have been developed at preclinical level, whereas a sulfonamide CA IX inhibitor and an antibody entered Phase Ib/II clinical trials for the treatment and imaging of different solid tumors. Here recent advances on CA IX biology and pharmacology in cancer, and its therapeutic targeting will be discussed.

Ectopic expression of BmeryCA in Bombyx mori increases silk yield and mechanical properties by altering the pH of posterior silk gland

The silk glands are the specialized tissue where silk protein synthesis, secretion, and conformational transitions take place, with pH playing a critical role in both silk protein synthesis and fiber formation. In the present study, we have identified erythrocyte carbonic anhydrase (BmeryCA) belonging to the α-CA class in the silk gland, which is a Zn2+ dependent metalloenzyme capable of efficiently and reversibly catalyzing the hydrated reaction of CO2 to HCO3-, thus participating in the regulation of acid-base balance. Multiple sequence alignments revealed that the active site of BmeryCA was highly conserved. Tissue expression profiling showed that BmeryCA had relatively high expression levels in hemolymph and epidermis but is barely expressed in the posterior silk gland (PSG). By specifically overexpressing BmeryCA in the PSG, we generated transgenic silkworms. Ion-selective microelectrode (ISM) measurements demonstrated that specifically overexpression of BmeryCA in the PSG led to a shift in pH from weakly alkaline to slightly neutral conditions. Moreover, the resultant PSG-specific BmeryCA overexpression mutant strain displayed a significant increase in both silk yield and silk fiber mechanical properties. Our research provided new insights into enhancing silk yield and improving the mechanical properties of silk fibers.

Label-free detection and profiling of individual solution-phase molecules

Most chemistry and biology occurs in solution, in which conformational dynamics and complexation underlie behaviour and function. Single-molecule techniques1 are uniquely suited to resolving molecular diversity and new label-free approaches are reshaping the power of single-molecule measurements. A label-free single-molecule method2-16 capable of revealing details of molecular conformation in solution17,18 would allow a new microscopic perspective of unprecedented detail. Here we use the enhanced light-molecule interactions in high-finesse fibre-based Fabry-Pérot microcavities19-21 to detect individual biomolecules as small as 1.2 kDa, a ten-amino-acid peptide, with signal-to-noise ratios (SNRs) >100, even as the molecules are unlabelled and freely diffusing in solution. Our method delivers 2D intensity and temporal profiles, enabling the distinction of subpopulations in mixed samples. Notably, we observe a linear relationship between passage time and molecular radius, unlocking the potential to gather crucial information about diffusion and solution-phase conformation. Furthermore, mixtures of biomolecule isomers of the same molecular weight and composition but different conformation can also be resolved. Detection is based on the creation of a new molecular velocity filter window and a dynamic thermal priming mechanism that make use of the interplay between optical and thermal dynamics22,23 and Pound-Drever-Hall (PDH) cavity locking24 to reveal molecular motion even while suppressing environmental noise. New in vitro ways of revealing molecular conformation, diversity and dynamics can find broad potential for applications in the life and chemical sciences.

Design, synthesis and in silico insights of novel 1,2,3-triazole benzenesulfonamide derivatives as potential carbonic anhydrase IX and XII inhibitors with promising anticancer activity

Novel 1,2,3-triazole benzenesulfonamide derivatives were designed as inhibitors for the tumor- related hCA IX and XII isoforms. Most of the synthesized compounds showed good inhibitory activity against hCA IX and hCA XII isoforms. Compounds 4d, 5h and 6b, exhibited remarkable activity as hCA IX inhibitors, with Ki values in the range of 0.03 to 0.06 µM, more potent than AAZ. Additionally, compounds 5b and 6d, efficiently inhibited hCA XII isoform, with Ki value of 0.02 µM, respectively, similar to AAZ. Further investigation for those potent derivatives against MCF-7, Hep-3B and WI-38 cell lines was achieved. Compounds 4d and 6d exerted dual cytotoxic activity against MCF-7 and Hep-3B cell lines, with IC50 values of 3.35 & 2.12 µM against MCF-7 cell line and 1.72 & 1.56 µM against Hep-3B cell line, with high SI values ranged from 8.92 to 17.38 on both of the cell lines. Besides, they showed a high safety profile against normal human cell line, WI-38. Moreover, compound 5h had better cytotoxic effect on MCF-7 than the reference, DOX, with IC50 value of 4.02 µM. While, compounds 5b and 6b showed higher activity against Hep-3B if compared to the reference drug, 5-FU. From ADME study, compounds 4d, 5b, 6b and 6d obeyed Lipinski's rule of five, and they might be orally active derivatives, while, compound 5h exerted less oral bioavailability than the reference standard acetazolamide. Molecular docking and MDS studies predicted the binding mode and the stability of the target compounds inside hCA IX and hCA XII active sites, especially for compounds 5b and 6b.

Carbonic anhydrase, its inhibitors and vascular function

It has been known for some time that Carbonic Anhydrase (CA, EC 4.2.1.1) plays a complex role in vascular function, and in the regulation of vascular tone. Clinically employed CA inhibitors (CAIs) are used primarily to lower intraocular pressure in glaucoma, and also to affect retinal blood flow and oxygen saturation. CAIs have been shown to dilate vessels and increase blood flow in both the cerebral and ocular vasculature. Similar effects of CAIs on vascular function have been observed in the liver, brain and kidney, while vessels in abdominal muscle and the stomach are unaffected. Most of the studies on the vascular effects of CAIs have been focused on the cerebral and ocular vasculatures, and in particular the retinal vasculature, where vasodilation of its vessels, after intravenous infusion of sulfonamide-based CAIs can be easily observed and measured from the fundus of the eye. The mechanism by which CAIs exert their effects on the vasculature is still unclear, but the classic sulfonamide-based inhibitors have been found to directly dilate isolated vessel segments when applied to the extracellular fluid. Modification of the structure of CAI compounds affects their efficacy and potency as vasodilators. CAIs of the coumarin type, which generally are less effective in inhibiting the catalytically dominant isoform hCA II and unable to accept NO, have comparable vasodilatory effects as the primary sulfonamides on pre-contracted retinal arteriolar vessel segments, providing insights into which CA isoforms are involved. Alterations of the lipophilicity of CAI compounds affect their potency as vasodilators, and CAIs that are membrane impermeant do not act as vasodilators of isolated vessel segments. Experiments with CAIs, that shed light on the role of CA in the regulation of vascular tone of vessels, will be discussed in this review. The role of CA in vascular function will be discussed, with specific emphasis on findings with the effects of CA inhibitors (CAI).

CAH3 from Chlamydomonas reinhardtii: Unique Carbonic Anhydrase of the Thylakoid Lumen

CAH3 is the only carbonic anhydrase (CA) present in the thylakoid lumen of the green algae Chlamydomonas reinhardtii. The monomer of the enzyme has a molecular weight of ~29.5 kDa with high CA activity. Through its dehydration activity, CAH3 can be involved either in the carbon-concentrating mechanism supplying CO2 for RuBisCO in the pyrenoid or in supporting the maximal photosynthetic activity of photosystem II (PSII) by accelerating the removal of protons from the active center of the water-oxidizing complex. Both proposed roles are considered in this review, together with a description of the enzymatic parameters of native and recombinant CAH3, the crystal structure of the protein, and the possible use of lumenal CA as a tool for increasing biomass production in higher plants. The identified involvement of lumenal CAH3 in the function of PSII is still unique among green algae and higher plants and can be used to understand the mechanism(s) of the functional interconnection between PSII and the proposed CA(s) of the thylakoid lumen in other organisms.

Synthesis and biological evaluation of new 3-substituted coumarin derivatives as selective inhibitors of human carbonic anhydrase IX and XII

The Carbonic anhydrase isoforms IX and XII play a significant role in regulating the intracellular and extracellular pH in hypoxic tumours abetting the metastasis of solid tumours. Selective and potent inhibitors targeting carbonic anhydrase IX and XII reduce the activity of these isoforms in hypoxic tumours, representing an antitumor and antimetastatic mechanism. Coumarin-based derivatives are selective inhibitors of CA isoforms IX and XII. In this study, we report the design and synthesis of new 3-substituted coumarin derivatives with different functional moieties and their inhibitory activity against various carbonic anhydrase isoforms. We found that the tertiary sulphonamide derivative 6c showed selective inhibition against CA IX with IC₅₀ of 4.1 µM. Similarly, the carbothioamides 7c, 7b and oxime ether derivative 20a exhibited good inhibition against CA IX and CA XII. Additionally, the binding mode was predicted and validated using molecular docking and dynamic simulations.

Rheumatoid Arthritis Has Won the Battle but Not the War: How Many Joints Will We Save Tomorrow?

Rheumatoid arthritis refers to joint diseases of unclear etiology whose final stages can lead to unbearable pain and complete immobility of the affected joints. As one of the most widely known diseases of the joints, it serves as a study target for a large number of research groups and pharmaceutical companies. Modern treatment with anti-inflammatory drugs, including janus kinase (JAK) inhibitors, monoclonal antibodies, and botanicals (polyphenols, glycosides, alkaloids, etc.) has achieved some success and hope for improving the course of the disease. However, existing drugs against RA have a number of side effects which push researchers to elaborate on more selective and effective drug candidates. The avant-garde of research, which aims to develop treatment of rheumatoid arthritis using antisense oligonucleotides along with nonsteroidal drugs and corticosteroids against inflammation, increases the chances of success and expands the arsenal of drugs. The primary goal in the treatment of this disease is to find therapies that allow patients with rheumatoid arthritis to move their joints without pain. The main purpose of this review is to show the victories and challenges for the treatment of rheumatoid arthritis and the tortuous but promising path of research that aims to help patients experience the joy of freely moving joints without pain.

6-Aminocoumarin oxime-ether/sulfonamides as selective hCA IX and XII inhibitors: Synthesis, evaluation, and molecular dynamics studies

Carbonic anhydrase isoforms IX and XII are overexpressed in hypoxic tumor cells regulating various physiological processes such as cell proliferation, invasion, and metastasis, resulting in the onset and spread of cancer. Selective inhibition of these enzymes is a promising strategy for anticancer therapy. Coumarin derivatives were identified as selective and potent inhibitors of these isoforms. This study reports 6-aminocoumarin sulfonamide and oxime ether derivatives linked through a chloroacetyl moiety tethered to piperazine and piperidone, respectively, showing selective inhibition against human carbonic anhydrase (hCA) IX and XII with Ki ranging from 0.51 to 1.18 µM and 0.89-4.43 µM. While the sulfonamide derivative 8a exhibited submicromolar inhibition against hCA IX and XII with Ki 0.89 and 0.51 µM, the oxime ether derivatives showed lower activity than the sulfonamides, with the compound 5n inhibiting hCA IX and hCA XII with a Ki of 1.055 and 0.70 µM, respectively. The above results demonstrate the potential of these derivatives as selective, potent inhibitors of carbonic anhydrase IX and XII and provide a foundation for further optimization and development as effective anticancer agents. Further, the binding mode of the synthesized derivatives in the active site were examined using molecular docking and dynamic simulation studies.

Molecular Resonance Imaging of the CAIX Expression in Mouse Mammary Adenocarcinoma Cells

The carbonic anhydrase isoform IX (hCAIX) is one of the main players in extracellular tumor pH regulation, and it is known to be overexpressed in breast cancer and other common tumors. hCA IX supports the growth and survival of tumor cells, and its expression is correlated with metastasis and resistance to therapies, making it an interesting biomarker for diagnosis and therapy. The aim of this work deals with the development of an MRI imaging probe able to target the extracellular non-catalytic proteoglycan-like (PG) domain of CAIX. For this purpose, a specific nanoprobe, LIP_PepC, was designed by conjugating a peptidic interactor of the PG domain on the surface of a liposome loaded with Gd-bearing contrast agents. A Mouse Mammary Adenocarcinoma Cell Line (TS/A) was chosen as an in vitro breast cancer model to test the developed probe. MRI results showed a high selectivity and sensitivity of the imaging probe toward hCAI-expressing TS/A cells. This approach appears highly promising for the in vivo translation of a diagnostic procedure based on the targeting of hCA IX enzyme expression.

Carbonic anhydrase IX subcellular localization in normoxic and hypoxic SH-SY5Y neuroblastoma cells is assisted by its C-terminal protein interaction domain

The human carbonic anhydrase IX (CA IX) is a hypoxia-induced transmembrane protein belonging to the α-CA enzyme family. It has a crucial role in pH regulation in hypoxic cells and acts by buffering intracellular acidosis induced by hypoxia. Indeed, it is frequently expressed in cancer cells, where it contributes to tumor progression. CA IX is also able to localize in the nucleus, where it contributes to 47S rRNA precursor genes transcription; however, the mechanisms assisting its nuclear translocation still remain unclear. The aim of our study was to deepen the understanding of the mechanisms involved in CA IX subcellular distribution. To this purpose, we implemented a site-directed mutagenesis approach targeting the C-terminal domain of CA IX and evaluated the subcellular distribution of the wild-type and mutant proteins in the SH-SY5Y cell line. The mutant proteins showed impaired binding ability and altered subcellular distribution in both normoxic and hypoxic conditions. Our data suggest that CA IX nuclear translocation depends on its transit through the secretory and the endocytic pathways.

Deep Learning Approach for the Discovery of Tumor-Targeting Small Organic Ligands from DNA-Encoded Chemical Libraries

DNA-Encoded Chemical Libraries (DELs) have emerged as efficient and cost-effective ligand discovery tools, which enable the generation of protein-ligand interaction data of unprecedented size. In this article, we present an approach that combines DEL screening and instance-level deep learning modeling to identify tumor-targeting ligands against carbonic anhydrase IX (CAIX), a clinically validated marker of hypoxia and clear cell renal cell carcinoma. We present a new ligand identification and hit-to-lead strategy driven by machine learning models trained on DELs, which expand the scope of DEL-derived chemical motifs. CAIX-screening datasets obtained from three different DELs were used to train machine learning models for generating novel hits, dissimilar to elements present in the original DELs. Out of the 152 novel potential hits that were identified with our approach and screened in an in vitro enzymatic inhibition assay, 70% displayed submicromolar activities (IC₅₀ < 1 μM). To generate lead compounds that are functionalized with anticancer payloads, analogues of top hits were prioritized for synthesis based on the predicted CAIX affinity and synthetic feasibility. Three lead candidates showed accumulation on the surface of CAIX-expressing tumor cells in cellular binding assays. The best compound displayed an in vitro K_D of 5.7 nM and selectively targeted tumors in mice bearing human renal cell carcinoma lesions. Our results demonstrate the synergy between DEL and machine learning for the identification of novel hits and for the successful translation of lead candidates for in vivo targeting applications.

Genes transcriptional activity features in different histological subtypes of tongue squamous cell carcinoma

Introduction. Over the past decade, tongue cancer has maintained a leading position in the overall structure of the incidence of head and neck malignant tumors. Squamous cell carcinoma of the tongue is an aggressive form and has a clinically unpredictable prognosis. Currently, there are several histological subtypes of this disease. And the search for new prognostic factors that could reflect the actual state of tumor progression and give an objective prognosis of disease development is an important research area in molecular oncology. Such factors may be certain transcriptomic characteristics of tumors, which determine the features of pathogenesis in each specific case.

Aim. To research genes transcriptional activity features in various histological subtypes of tongue squamous cell carcinoma using bioinformatic and molecular approaches.

Materials and methods. The stage of screening bioinformatics analysis was performed using an interactive web server for analyzing data on messenger RNA expression of 9736 tumors and 8587 normal samples from the The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) projects using a standard processing pipeline (GEPIA). The main (validation) stage of the study was performed on 300 patients with locally advanced malignant tumors of the tongue. The quantitative real-time polymerase chain reaction method was used to determine the values of the relative expression of genes identified at the stage of bioinformatic analysis.

Results. Bioinformatic analysis identified 1488 genes that increase expression and 589 genes that decrease expression in tongue squamous cell carcinoma. Of these 2077 genes, 23 genetic loci were selected that most strongly alter expression in tumor tissue relative to normal tissue of the tongue. Of these, when validated by polymerase chain reaction, only 14 changed their transcriptional profile in tumor tissue relative to normal: MMP1, MMP11, CA9, PTHLH, MMP9, LAMC2, MMP3, ANXA1, MT-ND6, CRNN, MAL, TGM3, IL1RN and CLU. The analysis of polymerase chain reaction data revealed significant heterogeneity in a number of biological samples studied. Cluster analysis made it possible to divide the total sample of 300 patients into 3 groups differing in gene expression: cluster 1 (n = 90), cluster 2 (n = 101) and cluster 3 (n = 109), corresponding to the basaloid, acantholytic and usual histological subtypes. Thus, the study made it possible to identify a number of molecular markers of tongue squamous cell carcinoma (MMP1, MMP11, CA9, PTHLH, MMP9, LAMC2, MMP3, ANXA1, MT-ND6, CRNN, MAL, TGM3, IL1RN and CLU), as well as to reveal the transcriptional features of various histological subtypes of this disease.

Label-free observation of individual solution phase molecules

The vast majority of chemistry and biology occurs in solution, and new label-free analytical techniques that can help resolve solution-phase complexity at the single-molecule level can provide new microscopic perspectives of unprecedented detail. Here, we use the increased light-molecule interactions in high-finesse fiber Fabry-Pérot microcavities to detect individual biomolecules as small as 1.2 kDa with signal-to-noise ratios >100, even as the molecules are freely diffusing in solution. Our method delivers 2D intensity and temporal profiles, enabling the distinction of sub-populations in mixed samples. Strikingly, we observe a linear relationship between passage time and molecular radius, unlocking the potential to gather crucial information about diffusion and solution-phase conformation. Furthermore, mixtures of biomolecule isomers of the same molecular weight can also be resolved. Detection is based on a novel molecular velocity filtering and dynamic thermal priming mechanism leveraging both photo-thermal bistability and Pound-Drever-Hall cavity locking. This technology holds broad potential for applications in life and chemical sciences and represents a major advancement in label-free in vitro single-molecule techniques.

Expression Dynamics of CA IX Epitope in Cancer Cells under Intermittent Hypoxia Correlates with Extracellular pH Drop and Cell Killing by Ureido-Sulfonamide CA IX Inhibitors

Carbonic anhydrase IX (CA IX) is a membrane-bound CA isozyme over-expressed in many hypoxic tumor cells, where it ensures pH homeostasis and has been implicated in tumor survival, metastasis and resistance to chemotherapy and radiotherapy. Given the functional importance of CA IX in tumor biochemistry, we investigated the expression dynamics of CA IX in normoxia, hypoxia and intermittent hypoxia, which are typical conditions experienced by tumor cells in aggressive carcinomas. We correlated the CA IX epitope expression dynamics with extracellular pH acidification and with viability of CA IX-expressing cancer cells upon treatment with CA IX inhibitors (CAIs) in colon HT-29, breast MDA-MB-231 and ovarian SKOV-3 tumor cell models. We observed that the CA IX epitope expressed under hypoxia by these cancer cells is retained in a significant amount upon reoxygenation, probably to preserve their proliferation ability. The extracellular pH drop correlated well with the level of CA IX expression, with the intermittent hypoxic cells showing a similar pH drop to fully hypoxic ones. All cancer cells showed higher sensitivity to CA IX inhibitors (CAIs) under hypoxia as compared to normoxia. The tumor cell sensitivity to CAIs under hypoxia and intermittent hypoxia were similar and higher than in normoxia and appeared to be correlated with the lipophilicity of the CAI.

Novel Thiopyrano[2,3-d]thiazole-pyrazole Hybrids as Potential Nonsulfonamide Human Carbonic Anhydrase IX and XII Inhibitors: Design, Synthesis, and Biochemical Studies

In recent years, molecular hybridization strategies have developed into a potent strategy for drug discovery. A series of novel thiopyrano[2,3-d]thiazoles linked to the pyrazole moiety was designed and developed as anticancer agents by a molecular hybridization. Target compounds were synthesized and characterized by spectroscopic tools as well as X-ray crystallography analysis as in the case of thiopyrano[2,3-d]thiazole derivative 5a. The MTT assay was used to demonstrate the in vitro efficacy of compounds 5a-g and 7a-j on MCF-7 and HePG-2. The results showed that some cycloadducts such as bromophenyl-4-thioxo-2-thiazolidinone 3e, 4-methylphenyl derivative of thiopyrano[2,3-d]thiazole 5d, and 6-substituted-thiopyrano[2,3-d]thiazoles 7e-j displayed good to excellent IC₅₀ in the range of 10.08 ± 1.5 to 25.95 ± 2.8 μg/mL against the MCF-7 cell line and from 7.83 ±2.1 to 13.37 ± 1.2 μg/mL against the HePG-2 cell line. To explore the enzymatic tests for isozymes hCAIX and hCAXII, the most promising eight compounds 3e, 5d, and 7e-j with IC₅₀ ranging from 7.83 ± 2.1 to 25.95 ± 2.8 μM were chosen. Compound 7e exhibited an IC₅₀ (0.067 ± 0.003 μM) similar to that of the standard drug AZA against CAIX (0.059 ± 0.003 μM)). For CAXII, the compound 7i had an IC₅₀ equal to 0.123 ± 0.007 μM compared to that of AZA (0.083 ± 0.005 μM). In addition, using flow cytometry, cell cycle analysis and apoptosis studies in HePG-2 were performed for the two potent anticancer and selective carbonic anhydrase agents (7e and 7i). An enzymatic assay of these two compounds against caspase-9 was also examined. Interestingly, the molecular docking studies revealed that compounds 7e and 7i successfully embedded themselves in the active pockets of the CAIX and CAXII enzymes through different interactions. Overall, the novel thiopyrano[2,3-d]thiazole-pyrazole hybrids (7e and 7i) were suggested to be potent and selective inhibitors of CAIX and CAXII.

The immunolocalization of HIF-2α, GLUT1 and CAIX in porcine oviduct during the estrous cycle

Oxygen (O₂ ) rates in the oviduct are essential to human and animal reproduction. These rates are regulated by the activity of hypoxia markers such as the hypoxia-inducible factors (HIFs), the glucose transporters (GLUT), and the carbonic anhydrase (CA). In the porcine model, scarce studies have been reported regarding these markers and their effects in reproduction are unknown. The objective was to characterize the immunolocalization of HIF-2α, GLUT1, and CAIX in porcine oviducts throughout the estrous cycle. Oviducts (ampulla and isthmus) of adult sows (n = 45) were collected for histological and immunohistochemical analysis with HIF-2α, GLUT1, and CAIX markers. The percentage of immunopositive area was quantified, and the differences among phases of the estrous cycle were analyzed (folicular, early luteal, and late luteal). The three markers showed epithelial presence mainly. Significantly lower expression of HIF-2α was found in the luteal phases, especially in the isthmus. GLUT1 expression did not change throughout the estrous cycle, but differences were found between the ampulla and isthmus. CAIX expression showed the highest, with a significant downward trend throughout estrous cycle. The ubiquitous expression of hypoxia markers shows the porcine oviduct physiology in relation to O₂ . The differential expression of HIF-2α, GLUT1, and CAIX in different subcompartments of the oviduct throughout the estrous cycle contributes to improve the knowledge of the cell physiology of the oviduct, which can be useful in fertilization studies.

Carbonic anhydrase IX: A tumor acidification switch in heterogeneity and chemokine regulation

The primary physiological process of respiration produces carbon dioxide (CO₂) that reacts with water molecules which subsequently liberates bicarbonate (HCO-₃) and protons. Carbonic anhydrases (CAs) are the primary catalyst involved in this conversion. More than 16 isoforms of human CAs show organ or subcellular specific activity. Dysregulation of each CA is associated with multiple pathologies. Out of these members, the overexpression of membrane-bound carbonic anhydrase IX (CAIX) is associated explicitly with hypoxic tumors or various solid cancers. CAIX helps tumors deal with higher CO₂ by sequestering it with bicarbonate ions and helping cancer cells to grow in a comparatively hypoxic or acidic environment, thus acting as a pH adaptation switch. CAIX-mediated adaptations in cancer cells include angiogenesis, metabolic alterations, tumor heterogeneity, drug resistance, and regulation of cancer-specific chemokines. This review comprehensively collects and describe the cancer-specific expression mechanism and role of CAIX in cancer growth, progression, heterogeneity, and its structural insight to develop future combinatorial targeted cancer therapies.

The production and biochemical characterization of α-carbonic anhydrase from Lactobacillus rhamnosus GG

Abstract

We report the production and biochemical characterization of an α-carbonic anhydrase (LrhCA) from gram-positive probiotic bacteria Lactobacillus rhamnosus GG. CAs form a family of metalloenzymes that catalyze hydration of CO₂/interconversion between CO₂ and water to bicarbonate ions and protons. They are divided into eight independent gene families (α, β, γ, δ, ζ, η, θ, and ι). Interestingly, many pathogens have been identified with only β- and/or γ-CAs, which can be targeted with CA-specific inhibitors (CAIs) acting as anti-pathogen drugs. Since it is important to study the potential off-target effects of CAIs for both the human body and its commensal bacteria, we took L. rhamnosus GG as our study subject. To date, only a single α-CA has been identified in L. rhamnosus GG, which was successfully produced and biochemically characterized. LrhCA showed moderate catalytic activity with the following kinetic parameters: k_cat of 9.86 × 10⁵ s⁻¹ and k_cat/K_M of 1.41 × 10⁷ s⁻¹ M⁻¹. Moderate inhibition was established with 11 of the 39 studied sulfonamides. The best inhibitors were 5-((4-aminophenyl)sulfonamido)-1,3,4-thiadiazole-2-sulfonamide, 4-(2-hydroxymethyl-4-nitrophenyl-sulfonamidoethyl)-benzenesulfonamide, and benzolamide with K_i values of 319 nM, 378 nM, and 387 nM, respectively. The other compounds showed weaker inhibitory effects. The K_i of acetazolamide, a classical CAI, was 733 nM. In vitro experiments with acetazolamide showed that it had no significant effect on cell growth in L. rhamnosus GG culture. Several sulfonamides, including acetazolamide, are in use as clinical drugs, making their inhibition data highly relevant to avoid any adverse off-target effects towards the human body and its probiotic organisms.

Key points

• The α-carbonic anhydrase from Lactobacillus rhamnosus GG (LrhCA) is 24.3 kDa.

• LrhCA has significant catalytic activity with a kcat of 9.9 × 105 s-1.

• Acetazolamide resulted in a marginal inhibitory effect on cell growth.

New 1H-indole-2,3-dione 3-thiosemicarbazones with 3-sulfamoylphenyl moiety as selective carbonic anhydrase inhibitors

1-Methyl/ethyl/benzyl-5-(un)substituted 1H-indole-2,3-diones (2, 3, and 4) were synthesized by reaction of 5-(un)substituted 1H-indole-2,3-diones (1) with methyl iodide, ethyl chloride, and benzyl bromide. (3-Sulfamoylphenyl)isothiocyanate (6) was obtained by the treatment of 3-aminobenzenesulfonamide (5) with thiophosgene. Compound 6 was reacted with hydrazine to yield 4-(3-sulfamoylphenyl)thiosemicarbazide (7). Novel 1-(un)substituted/methyl/ethyl/benzyl-5-(un)substituted 1H-indole-2,3-dione 3-[4-(3-sulfamoylphenyl)thiosemicarbazone] derivatives (8-11) were prepared by condensation of 7 and 1-4. The structures of the synthesized compounds were confirmed by elemental analysis and spectral data. Inhibition of the widely distributed cytosolic off-targets human carbonic anhydrases (hCAs) I and II, and two tumor-associated membrane-bound isoforms (hCAs IX and XII), by 8-11 was investigated. The hCA II inhibitory effects of all tested compounds were in the subnanomolar to low nanomolar levels (K_i  = 0.32-83.3 nM), and generally high selectivity for hCA II isoenzyme over hCA I, IX, and XII isoenzymes was observed. The strongest inhibitors of hCA II, 1-benzyl-5-(trifluoromethoxy)-substituted 11c (K_i  = 0.32 nM) and 1-ethyl-5-chloro-substituted 10e (K_i  = 0.35 nM), were docked within the enzyme active site. Molecular modeling studies with the most effective hCA IX and XII inhibitors were also carried out.

Carbonic Anhydrases in Metazoan Model Organisms: Molecules, Mechanisms, and Physiology

During the past three decades, mice, zebrafish, fruit flies, and Caenorhabditis elegans have been the primary model organisms used for the study of various biological phenomena. These models have also been adopted and developed to investigate the physiological roles of carbonic anhydrases (CAs) and carbonic anhydrase-related proteins (CARPs). These proteins belong to eight CA families and are identified by Greek letters: α, β, γ, δ, ζ, η, θ, and ι. Studies using model organisms have focused on two CA families, α-CAs and β-CAs, which are expressed in both prokaryotic and eukaryotic organisms with species-specific distribution patterns and unique functions. This review covers the biological roles of CAs and CARPs in light of investigations performed in model organisms. Functional studies demonstrate that CAs are not only linked to the regulation of pH homeostasis, the classical role of CAs but also contribute to a plethora of previously undescribed functions.

Discovery of new carbonic anhydrase IX inhibitors as anticancer agents by toning the hydrophobic and hydrophilic rims of the active site to encounter the dual-tail approach

The hydrophobic and the hydrophilic rims in the active site of human carbonic anhydrase IX (hCA IX) which as well contains a zinc ion as part of the catalytic core, were simultaneously matched to design and synthesize potent and selective inhibitors using a dual-tail approach. Seventeen new compounds, 5a-q, were designed to have the benzenesulfonamide moiety as a zinc binding group. In addition, N-substituted hydrazone and N-phenyl fragments were chosen as the hydrophilic and hydrophobic parts, respectively to achieve favorable interactions with the corresponding halves of the active site. All synthesized compounds successfully suppressed the CA IX, with IC₅₀ values in nanomolar range from 13.3 to 259 nM. Compounds, 5h, 5c, 5m, 5e, and 5k were the top-five compounds efficiently inhibited the tumor-related CA IX isoform in the low nanomolar range (K_I = 13.3, 22.6, 25.8, 26.9 and 27.2 nM, respectively). The target compounds 5a-q developed remarkable selectivity toward the tumor-associated isoforms (hCA IX and XII) over the off-target isoforms (hCA I and II). Furthermore, they were assessed for their anti-proliferative activity, according to US-NCI protocol, against a panel of fifty-nine cancer cell lines. Compounds 5d, 5k and 5o were passed the criteria for activity and scheduled automatically for evaluation at five concentrations with 10-fold dilutions. Compound 5k exhibited significant in vitro anticancer activity with GI₅₀-MID; 8.68 μM compared to compounds 5d and 5o with GI₅₀-MID; 25.76 μM and 34.97 μM respectively. The most selective compounds 5h and 5k were further screened for their in vitro cytotoxic activity against SK-MEL-5, HCC-2998 and RXF 393 cancer cell lines under hypoxic conditions. Furthermore, 5k was screened for cell cycle disturbance, apoptosis induction and intracellular reactive oxygen species (ROS) production in SK-MEL-5 cancer cells. Finally, molecular docking studies were performed to gain insights for the plausible binding interactions and affinities for selected compounds within hCA IX active site.

Photodegradation of carbonic anhydrase IX via a binding-enhanced ruthenium-based photosensitizer

A binding-enhanced ruthenium-based photosensitizer is reported for photodegradation of carbonic anhydrase IX.

Carbonic Anhydrases as Potential Targets Against Neurovascular Unit Dysfunction in Alzheimer’s Disease and Stroke

The Neurovascular Unit (NVU) is an important multicellular structure of the central nervous system (CNS), which participates in the regulation of cerebral blood flow (CBF), delivery of oxygen and nutrients, immunological surveillance, clearance, barrier functions, and CNS homeostasis. Stroke and Alzheimer Disease (AD) are two pathologies with extensive NVU dysfunction. The cell types of the NVU change in both structure and function following an ischemic insult and during the development of AD pathology. Stroke and AD share common risk factors such as cardiovascular disease, and also share similarities at a molecular level. In both diseases, disruption of metabolic support, mitochondrial dysfunction, increase in oxidative stress, release of inflammatory signaling molecules, and blood brain barrier disruption result in NVU dysfunction, leading to cell death and neurodegeneration. Improved therapeutic strategies for both AD and stroke are needed. Carbonic anhydrases (CAs) are well-known targets for other diseases and are being recently investigated for their function in the development of cerebrovascular pathology. CAs catalyze the hydration of CO₂ to produce bicarbonate and a proton. This reaction is important for pH homeostasis, overturn of cerebrospinal fluid, regulation of CBF, and other physiological functions. Humans express 15 CA isoforms with different distribution patterns. Recent studies provide evidence that CA inhibition is protective to NVU cells in vitro and in vivo, in models of stroke and AD pathology. CA inhibitors are FDA-approved for treatment of glaucoma, high-altitude sickness, and other indications. Most FDA-approved CA inhibitors are pan-CA inhibitors; however, specific CA isoforms are likely to modulate the NVU function. This review will summarize the literature regarding the use of pan-CA and specific CA inhibitors along with genetic manipulation of specific CA isoforms in stroke and AD models, to bring light into the functions of CAs in the NVU. Although pan-CA inhibitors are protective and safe, we hypothesize that targeting specific CA isoforms will increase the efficacy of CA inhibition and reduce side effects. More studies to further determine specific CA isoforms functions and changes in disease states are essential to the development of novel therapies for cerebrovascular pathology, occurring in both stroke and AD.

Correlation between imaging and tissue biomarkers of hypoxia in squamous cell cancer of the head and neck

The aim of this study was to correlate endogenous tissue biomarkers of hypoxia with quantitative imaging parameters derived from ¹⁸F-fluoro-misonidazole (F-MISO) and ¹⁸F-fluoro-deoxy-glucose (FDG) positron emission tomography/computed tomography (PET/CT) and clinical outcomes in locoregionally advanced head and neck squamous cell carcinoma (HNSCC). Tumor-tissue blocks of HNSCC patients with pretreatment F-MISO-PET/CT and FDG-PET/CT were de-archived for expression of hypoxia-inducible factor-1 alpha (HIF-1α) subunit, carbonic anhydrase-IX (CA-IX), and glucose transporter subunit-1 (GLUT-1) using immunohistochemistry (IHC). The intensity of staining was graded and correlated with quantitative imaging parameters and with disease-related outcomes. Tissue blocks were analyzed for 14 of 20 patients. On IHC, median H-scores for HIF-1α, CA-IX, and GLUT-1 were 130, 0, and 95, respectively. No significant correlation of tissue biomarkers of hypoxia with quantitative imaging parameters was found. However, borderline significant correlation was seen for H-scores of CA-IX with hypoxic tumor volume (HTV) (r = 0.873, P = 0.054) and fractional hypoxic volume (r = 0.824, P = 0.086) derived from F-MISO-PET/CT. At a median follow-up of 43 months, 5-year Kaplan-Meier estimates of locoregional control, disease-free survival, and overall survival were 53%, 43%, and 40%, respectively. Increased expression of HIF-1α or GLUT-1 (dichotomized by median H-scores) was not individually associated with disease-related outcomes. However, a combination of high HTV (>4.89cc) with above median H-scores of either HIF-1α (>130) and/or GLUT-1 (>95) was associated with worse clinical outcomes. None of the three patients with such "adverse hypoxic profile" were long-term survivors. There is no significant correlation of endogenous tissue biomarkers of hypoxia (HIF-1α, CA-IX, and GLUT-1) with quantitative imaging parameters (on F-MISO-PET/CT and FDG-PET/CT) or long-term outcomes in HNSCC. However, a combination of both can identify a subgroup of patients with adverse outcomes.

Biochemical and structural characterization of beta-carbonic anhydrase from the parasite Trichomonas vaginalis

Abstract

Trichomonas vaginalis is a unicellular parasite and responsible for one of the most common sexually transmittable infections worldwide, trichomoniasis. Carbonic anhydrases (CAs) are enzymes found in all lifeforms and are known to play a vital role in many biochemical processes in organisms including the maintenance of acid–base homeostasis. To date, eight evolutionarily divergent but functionally convergent forms of CAs (α, β, γ, δ, ζ, η, θ, and ι) have been discovered. The human genome contains only α-CAs, whereas many clinically significant pathogens express only β-CAs and/or γ-CAs. The characterization of pathogenic β- and γ-CAs provides important knowledge for targeting these biomolecules to develop novel anti-invectives against trichomoniasis. Here, we report the recombinant production and characterization of the second β-CA of T. vaginalis (TvaCA2). Light scattering analysis revealed that TvaCA2 is a dimeric protein, which was further supported with in silico modeling, suggesting similar structures between TvaCA2 and the first β-CA of T. vaginalis (TvaCA1). TvaCA2 exhibited moderate catalytic activity with the following kinetic parameters: k_cat of 3.8 × 10⁵ s⁻¹ and k_cat/K_M of 4.4 × 10⁷ M⁻¹ s⁻¹. Enzyme activity inhibition was studied with a set of clinically used sulfonamides and sulfonamide derivates. Twenty-seven out of the 39 compounds resulted in inhibition with a nanomolar range. These initial results encourage for future work entailing the design of more potent inhibitors against TvaCA2, which may provide new assets to fight trichomoniasis.

Key messages

• Protozoan parasite Trichomonas vaginalis has two β-carbonic anhydrases (TvaCA1/2).

• TvaCA1/TvaCA2 represents promising targets for antitrichomonal drug development.

• TvaCA2 is a dimer of 20.3 kDa and possesses moderate catalytic activity.

• The most efficient inhibitor was clinical drug acetazolamide with K_I of 222.9 nM.

• The 39 tested sulfonamides form the basis for the design of more potent inhibitors.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00109-021-02148-1.

Carbonic Anhydrase IX and Survivin in Colorectal Adenocarcinoma Cells: Slovakian Population Study

Simple Summary

This retrospective study (Slovakian population study) brings information about immunohistochemical detection of CAIX and survivin in 74 samples of human colorectal adenocarcinoma and comparison their expression with expression in healthy colon tissue. Our results show that all of samples with healthy colon tissue were CAIX and survivin-negative and there is no statistically significant dependence of these proteins and the chosen clinicopathological parameters. These findings demonstrate that detection of these proteins could be useful for tumor diagnostic and prognostic and CAIX and survivin could represent independent negative prognostic markers of colorectal cancer.

Abstract

The aim of this study was to detect carbonic anhydrase IX (CAIX) and survivin in the colorectal adenocarcinoma cells of the Slovakian population. We used an indirect three-step immunohistochemical method with DAB staining for the localization of the proteins and investigation their expression. We compared their expression with expression in healthy colorectal tissue. In 74 tissues of colorectal adenocarcinomas, 42% showed CAIX positivity and 20% showed survivin positivity. Brown membrane immunostaining was visible in CAIX-positive tumors. Survivin-positive tumors had strong brown cytoplasmic immunostaining. Co-expression of both proteins was present in five specimens (7%). The samples of normal colorectal tissue (without carcinoma) were CAIX-negative and survivin-negative. We also applied the Chi-squared test for evaluation statistically significant association between the expression of proteins and selected clinical and histopathological parameters. We did not find any statistically significant correlations between CAIX or survivin expression and sex of patients, the grade of the tumor, nodal status and presence of metastasis (p > 0.05). The fact that all samples of normal colorectal tissue were CAIX- and survivin-negative could lead to the possibility of using these two proteins as potential tumor diagnostic markers. On the basic of the available publications and data, we suggest that CAIX and survivin could be negative independent prognostic markers of colorectal cancer, which could affect response to therapy.

Post-translational modifications in tumor-associated carbonic anhydrases

Human carbonic anhydrases IX (hCA IX) and XII (hCA XII) are two proteins associated with tumor formation and development. These enzymes have been largely investigated both from a biochemical and a functional point of view. However, limited data are currently available on the characterization of their post-translational modifications (PTMs) and the functional implication of these structural changes in the tumor environment. In this review, we summarize existing literature data on PTMs of hCA IX and hCA XII, such as disulphide bond formation, phosphorylation, O-/N-linked glycosylation, acetylation and ubiquitination, highlighting, when possible, their specific role in cancer pathological processes.

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.

The structural basis for the selectivity of sulfonamido dicarbaboranes toward cancer-associated carbonic anhydrase IX

Human carbonic anhydrase IX (CA IX), a protein specifically expressed on the surface of solid tumour cells, represents a validated target both for anticancer therapy and diagnostics. We recently identified sulfonamide dicarbaboranes as promising inhibitors of CA IX with favourable activities both in vitro and in vivo. To explain their selectivity and potency, we performed detailed X-ray structural analysis of their interactions within the active sites of CA IX and CA II. Series of compounds bearing various aliphatic linkers between the dicarbaborane cluster and sulfonamide group were examined. Preferential binding towards the hydrophobic part of the active site cavity was observed. Selectivity towards CA IX lies in the shape complementarity of the dicarbaborane cluster with a specific CA IX hydrophobic patch containing V131 residue. The bulky side chain of F131 residue in CA II alters the shape of the catalytic cavity, disrupting favourable interactions of the spherical dicarbaborane cluster.

Sulphonamide inhibition profile of Staphylococcus aureus β-carbonic anhydrase

This paper presents the production and kinetic and inhibitory characterisation of β-carbonic anhydrase from the opportunistic bacterium Staphylococcus aureus (SauBCA). From the eight different carbonic anhydrase (CA) families known to date, humans have only the α-form, whereas many clinically relevant pathogens have β- and/or γ-form(s). Based on this discovery, β- and γ-CAs have been introduced as promising new anti-infective targets. The results of this study revealed that recombinant SauBCA possesses significant CO₂ hydration activity with a k_cat of 1.46 × 10⁵ s^-1 and a k_cat/K_M of 2.56 × 10⁷ s^{- 1}M^-1. Its enzymatic function was inhibited by various sulphonamides in the nanomolar - micromolar range, and the K_i of acetazolamide was 628 nM. The best inhibitor was the clinically used sulfamide agent famotidine (K_i of 71 nM). The least efficient inhibitors were zonisamide and dorzolamide. Our work encourages further investigations of SauBCA in an attempt to discover novel drugs against staphylococcal infections.

Developments of small molecules as inhibitors for carbonic anhydrase isoforms

Carbonic anhydrases are ubiquitous, and their role in the hydration of carbon dioxide is essential for the survival of many tissues and organs. However, their association with many pathological diseases, especially in glaucoma, Alzheimer's, obesity, epilepsy, and tumorigenesis, has prompted the design and synthesis of novel carbonic anhydrase inhibitors (CAIs). Herein we describe (1) approaches used in the design of CAIs and (2) synthesis of small molecules as CAIs within the last five years. Despite the active research in this area, there are still more avenues to explore, especially selective inhibition of CA I, CA IX, and XII. These isoforms would continue to open up a diversity of carbonic anhydrase inhibitors containing 1,2,3-triazoles, imidazolone, pyrrolidone, thiadiazole, isatin, and glycoconjugates as part of their molecular frameworks.

Natural Plant Extracts and Compounds for Rheumatoid Arthritis Therapy

Natural plant extracts and compounds (NPECs), which originate from herbs or plants, have been used in the clinical treatment of rheumatoid arthritis (RA) for many years. Over the years, many scientists have carried out a series of studies on the treatment of RA by NPEC. They found a high quantity of active NPECs with broad application prospects. In view of various complex functions of these NPECs, exploring their potential as medicines for RA treatment will be beneficial for RA patients. Thus, to help advance the development of high-quality NPECs for RA, we herein aimed to review the research progress of NPECs in the treatment of RA in recent years. Our findings showed that, from the pharmacological perspective, natural plant extracts or mixed herbal compounds effectively regulate the immune system to alleviate RA by inhibiting pro-inflammatory cytokines. Further, individualized medication can be applied according to each patient's physical condition. However, the pathogenesis of RA and its immune mechanism has not been fully understood and requires further studies.

Oxygen-independent disulfide bond formation in VEGF-A and CA9

Low levels of oxygen (hypoxia) occurs in many (patho)physiological situations. Adaptation to hypoxia is in part mediated by proteins expressed in the extracellular space that mature in the endoplasmic reticulum (ER) prior to traversing the secretory pathway. The majority of such ER cargo proteins require disulfide bonds for structural stability. Disulfide bonds are formed co- and posttranslationally in a redox relay that requires a terminal electron acceptor such as oxygen. We have previously demonstrated that some ER cargo proteins such as low-density lipoprotein receptor (LDLR) and influenza hemagglutinin (Flu-HA) are unable to complete disulfide bond formation in the absence of oxygen, limiting their ability to pass ER quality control and their ultimate expression. Here, using radioactive pulse-chase immunoprecipitation analysis, we demonstrate that hypoxia-induced ER cargo proteins such as carbonic anhydrase 9 (CA9) and vascular endothelial growth factor A (VEGF-A) complete disulfide bond formation and mature with similar kinetics under hypoxia and normoxia. A global in silico analysis of ER cargo revealed that hypoxia-induced proteins on average contain fewer free cysteines and shorter-range disulfide bonds in comparison to other ER cargo proteins. These data demonstrate the existence of alternative electron acceptors to oxygen for disulfide bond formation in cellulo. However, the ability of different proteins to utilize an oxygen-independent pathway for disulfide bond formation varies widely, contributing to differential gene expression in hypoxia. The superior ability of hypoxia-induced proteins such as VEGF-A and CA9 to mature in hypoxia may be conferred by a simpler disulfide architecture.

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.

Biochemical and structural characterisation of a protozoan beta-carbonic anhydrase from Trichomonas vaginalis

We report the biochemical and structural characterisation of a beta-carbonic anhydrase (β-CA) from Trichomonas vaginalis, a unicellular parasite responsible for one of the world’s leading sexually transmitted infections, trichomoniasis. CAs are ubiquitous metalloenzymes belonging to eight evolutionarily divergent groups (α, β, γ, δ, ζ, η, θ, and ι); humans express only α-CAs, whereas many clinically significant pathogens express only β- and/or γ-CAs. For this reason, the latter two groups of CAs are promising biomedical targets for novel antiinfective agents. The β-CA from T. vaginalis (TvaCA1) was recombinantly produced and biochemically characterised. The crystal structure was determined, revealing the canonical dimeric fold of β-CAs and the main features of the enzyme active site. The comparison with the active site of human CA enzymes revealed significant differences that can be exploited for the design of inhibitors selective for the protozoan enzyme with respect to the human ones.

Engineering stable carbonic anhydrases for CO2 capture: a critical review

Targeted inhibition of misregulated protein-protein interactions (PPIs) has been a promising area of investigation in drug discovery and development for human diseases. However, many constraints remain, including shallow binding surfaces and dynamic conformation changes upon interaction. A particularly challenging aspect is the undesirable off-target effects caused by inherent structural similarity among the protein families. To tackle this problem, phage display has been used to engineer PPIs for high-specificity binders with improved binding affinity and greatly reduced undesirable interactions with closely related proteins. Although general steps of phage display are standardized, library design is highly variable depending on experimental contexts. Here in this review, we examined recent advances in the structure-based combinatorial library design and the advantages and limitations of different approaches. The strategies described here can be explored for other protein-protein interactions and aid in designing new libraries or improving on previous libraries.

Inhibition of Carbonic Anhydrase Using SLC-149: Support for a Noncatalytic Function of CAIX in Breast Cancer

Carbonic anhydrase IX (CAIX) is considered a target for therapeutic intervention in solid tumors. In this study, the efficacy of the inhibitor, 4-(3-(2,4-difluorophenyl)-oxoimidazolidin-1-yl)benzenesulfonamide (SLC-149), is evaluated on CAIX and a CAIX-mimic. We show that SLC-149 is a better inhibitor than acetazolamide against CAIX. Binding of SLC-149 thermally stabilizes CAIX-mimic at lower concentrations compared to that of CAII. Structural examinations of SLC-149 bound to CAIX-mimic and CAII explain binding preferences. In cell culture, SLC-149 is a more effective inhibitor of CAIX activity in a triple-negative breast cancer cell line than previously studied sulfonamide inhibitors. SLC-149 is also a better inhibitor of activity in cells expressing CAIX versus CAXII. However, SLC-149 has little effect on cytotoxicity, and high concentrations are required to inhibit cell growth, migration, and invasion. These data support the hypothesis that CAIX activity, shown to be important in regulating extracellular pH, does not underlie its ability to control cell growth.