Carbonic anhydrase IX inhibition as a path to treat neuroblastoma.

Background And Purpose: Tumour hypoxia frequently presents a major challenge in the treatment of neuroblastoma (NBL). The neuroblastoma cells produce carbonic anhydrase IX (CA IX), an enzyme crucial for the survival of cancer cells in low-oxygen environments.

Experimental Approach: We designed and synthesised a novel high-affinity inhibitor of CA IX.

From X-ray crystallographic structure to intrinsic thermodynamics of protein-ligand binding using carbonic anhydrase isozymes as a model system.

Carbonic anhydrase (CA) was among the first proteins whose X-ray crystal structure was solved to atomic resolution. CA proteins have essentially the same fold and similar active centers that differ in only several amino acids. Primary sulfonamides are well defined, strong and specific binders of CA.

Recent advances in computational and experimental protein-ligand affinity determination techniques.

Introduction: Modern drug discovery revolves around designing ligands that target the chosen biomolecule, typically proteins. For this, the evaluation of affinities of putative ligands is crucial. This has given rise to a multitude of dedicated computational and experimental methods that are constantly being developed and improved.

Intrinsic Solubility of Ionizable Compounds from p Shift.

Aqueous solubility of pharmaceutical substances plays an important role in small molecule drug discovery and development, with ionizable groups often employed to enhance solubility. Drug candidate compounds often contain ionizable groups to increase their solubility. Recognizing that the electrostatically charged form of the compound is much more soluble than the uncharged form, this work proposes a model to explore the relationship between the p shift of the ionizable group and dissolution equilibria.

PLBD: protein-ligand binding database of thermodynamic and kinetic intrinsic parameters.

We introduce a protein-ligand binding database (PLBD) that presents thermodynamic and kinetic data of reversible protein interactions with small molecule compounds. The manually curated binding data are linked to protein-ligand crystal structures, enabling structure-thermodynamics correlations to be determined. The database contains over 5500 binding datasets of 556 sulfonamide compound interactions with the 12 catalytically active human carbonic anhydrase isozymes defined by fluorescent thermal shift assay, isothermal titration calorimetry, inhibition of enzymatic activity and surface plasmon resonance.

Aberrant pancreas adenocarcinoma in the stomach: A case report and literature review.

Rationale: Aberrant pancreatic tissue in the gastrointestinal tract is a relatively common finding. However, malignant transformation is extremely rare. Herein, we report a case of ectopic pancreatic ductal adenocarcinoma in the stomach wall.

Picomolar fluorescent probes for compound affinity determination to carbonic anhydrase IX expressed in live cancer cells.

Numerous human cancers, especially hypoxic solid tumors, express carbonic anhydrase IX (CAIX), a transmembrane protein with its catalytic domain located in the extracellular space. CAIX acidifies the tumor microenvironment, promotes metastases and invasiveness, and is therefore considered a promising anticancer target. We have designed a series of high affinity and high selectivity fluorescein-labeled compounds targeting CAIX to visualize and quantify CAIX expression in cancer cells.

Factors, associated with elevated concentration of soluble carbonic anhydrase IX in plasma of women with cervical dysplasia.

Unlabelled: Precancerous lesions of human cervix uteri have a tendency for regression or progression. In cervical intraepithelial neoplasia grade 2 (CINII) case there is an uncertainty if a lesion will progress or regress. The carbonic anhydrase IX (CAIX) enzyme is overexpressed in cervical cancer which is more sensitive to radiotherapy.

Denaturant- or ligand-induced changes in protein volume by pressure shift assay.

A complete thermodynamic description of protein-ligand binding includes parameters related to pressure and temperature. The changes in the protein volume and compressibility upon binding a ligand are pressure-related parameters that are often neglected due to the lack of routine methods for their determination. Fluorescent pressure shift assay (FPSA) is based on pressure-induced protein unfolding and its stabilization by a ligand and offers a universal approach to determine protein-ligand binding volumes.

Suspected and Confirmed Acute Appendicitis During the COVID-19 Pandemic: First and Second Quarantines-a Prospective Study.

Purpose: COVID-19 posed an unprecedented modern global healthcare crisis affecting both elective and urgent surgeries. The aim of this study is to evaluate the difference in the presentation of acute appendicitis (AA) before and during the COVID-19 era, the first and second quarantines.

Methods: We performed a prospective study from December 2018 to May 2021.

Interactions between S100A9 and Alpha-Synuclein: Insight from NMR Spectroscopy.

S100A9 is a pro-inflammatory protein that co-aggregates with other proteins in amyloid fibril plaques. S100A9 can influence the aggregation kinetics and amyloid fibril structure of alpha-synuclein (α-syn), which is involved in Parkinson's disease. Currently, there are limited data regarding their cross-interaction and how it influences the aggregation process.

Thermott: A comprehensive online tool for protein-ligand binding constant determination.

The thermal shift assay is one of the most universal techniques to determine protein-ligand affinities ranging from millimolar to picomolar levels in a single ligand dosing experiment. However, the complexity of thermodynamic data analysis leads to an underuse of this technique. We have developed a user-friendly, open-source, free online analysis software to study any protein-ligand interaction thermal shift data and yield a comprehensive thermodynamic characterization of the binding reaction.

Short-term clinical and functional results of rectal wall suture defect after transanal endoscopic microsurgery-a prospective cohort study.

Purpose: Our goal was to assess the outcomes of rectal wall suture during the early and late periods after transanal endoscopic microsurgery (TEM) and long-term bowel function.

Methods: Patients who underwent TEM for rectal neoplasms from May 2017 to March 2021 were prospectively included. A total of 70 patients were enrolled.

Latent Semantic Structure of the WMS-III Verbal Paired-Associates.

Objective: To investigate the factor structure of the verbal paired-associates (VPA) subtest in the WMS-III using a theoretically driven model of semantic processing previously found to be well-fitting for the WMS-IV version of the test.

Method: Archival data were used from 267 heterogeneous neurosciences patients and 223 seizure disorder patients who completed the WMS-III as part of a standard neuropsychological evaluation. Confirmatory factor analysis was used to test theoretically driven models for VPA based on principles of semantic processing.

Local Excision ± Chemoradiotherapy vs. Total Mesorectal Excision for Early Rectal Cancer: Case-Matched Analysis of Long-Term Results.

Our aim was to compare the bowel function and oncologic outcomes following these two treatment modalities. This was a single-center study with 67 patients included between 2009 and 2018. A total of 32 patients underwent total mesorectal excision (TME) group and 35 transanal local excisions (LE) ± chemoradiation.

S100A9 Alters the Pathway of Alpha-Synuclein Amyloid Aggregation.

The formation of amyloid fibril plaques in the brain creates inflammation and neuron death. This process is observed in neurodegenerative disorders, such as Alzheimer's and Parkinson's diseases. Alpha-synuclein is the main protein found in neuronal inclusions of patients who have suffered from Parkinson's disease.

Thiazide and other Cl-benzenesulfonamide-bearing clinical drug affinities for human carbonic anhydrases.

Twelve carbonic anhydrase (CA) isoforms catalyze carbon dioxide hydration to bicarbonate and acid protons and are responsible for many biological functions in human body. Despite their vital functions, they are also responsible for, or implicated in, numerous ailments and diseases such as glaucoma, high altitude sickness, and cancer. Because CA isoforms are highly homologous, clinical drugs designed to inhibit enzymatic activity of a particular isoform, can also bind to others with similar affinity causing toxic side effects.

Protein-Ligand Binding Volume Determined from a Single 2D NMR Spectrum with Increasing Pressure.

Proteins undergo changes in their partial volumes in numerous biological processes such as enzymatic catalysis, unfolding-refolding, and ligand binding. The change in the protein volume upon ligand binding-a parameter termed the protein-ligand binding volume-can be extensively studied by high-pressure NMR spectroscopy. In this study, we developed a method to determine the protein-ligand binding volume from a single two-dimensional (2D) H-N heteronuclear single quantum coherence (HSQC) spectrum at different pressures, if the exchange between ligand-free and ligand-bound states of a protein is slow in the NMR time-scale.

Switching the Inhibitor-Enzyme Recognition Profile via Chimeric Carbonic Anhydrase XII.

A key part of the optimization of small molecules in pharmaceutical inhibitor development is to vary the molecular design to enhance complementarity of chemical features of the compound with the positioning of amino acids in the active site of a target enzyme. Typically this involves iterations of synthesis, to modify the compound, and biophysical assay, to assess the outcomes. Selective targeting of the anti-cancer carbonic anhydrase isoform XII (CA XII), this process is challenging because the overall fold is very similar across the twelve CA isoforms.

Heat Shock Protein 90 Inhibitor Effects on Pancreatic Cancer Cell Cultures.

Objectives: Pancreatic ductal adenocarcinoma is one of the deadliest cancers for which few curative therapies are available to date. Heat shock protein 90 (Hsp90) inhibitors have shown activity against numerous cancers in vitro; therefore, we tested whether they could be used to target pancreatic ductal adenocarcinoma.

Methods: Inhibitors of Hsp90 ATPase activity were applied on low-passage pancreatic cell line cultures (Panc10.

Standard operating procedure for fluorescent thermal shift assay (FTSA) for determination of protein-ligand binding and protein stability.

A standard operating procedure for a fluorescence-based thermal shift assay (FTSA) is provided describing its typical applications, advantages and limitations. FTSA is a simple, robust, universal and quick assay to determine protein-ligand binding affinities and protein stabilities in the presence of various excipients and solution conditions. Therefore, the assay is very useful for the straightforward characterization of new recombinantly produced proteins.

Uncertainty in protein-ligand binding constants: asymmetric confidence intervals versus standard errors.

Equilibrium binding constants (K) between chemical compounds and target proteins or between interacting proteins provide a quantitative understanding of biological interaction mechanisms. Reported uncertainties of measured experimental parameters are critical for decision-making in many scientific areas, e.g.

POT1 stability and binding measured by fluorescence thermal shift assays.

The protein POT1 (Protection of Telomeres 1) is an integral part of the shelterin complex that protects the ends of human chromosomes from degradation or end fusions. It is the only component of shelterin that binds single-stranded DNA. We describe here the application of two separate fluorescent thermal shift assays (FTSA) that provide quantitative biophysical characterization of POT1 stability and its interactions.

Quality of Life and Bowel Function Following Early Closure of a Temporary Ileostomy in Patients with Rectal Cancer: A Report from a Single-Center Randomized Controlled Trial.

The aim of this study was to assess quality of life and bowel function in patients undergoing early vs. standard ileostomy closure. We retrospectively assessed patients from our previous randomized controlled trial.