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A model of subphtalocyanine molecules ordering on Ag(111) is proposed. We have demonstrated that the driving force of the ordering into honeycomb and hexagonal close packed patterns is a balance of intermolecular and subphtalocyanine–Ag interactions which can be generally expressed by a potential with infinite exclusion in a sufficiently large number of nearest coordination spheres of Ag(111) lattice and oscillatingly decaying behavior outside the sphere of exclusion. To cope with computational problems due to large size of the molecules compared to the substrate lattice period, we introduce the rescaling of Ag(111) lattice, and took into account an infinite exclusion of first, second, and third neighbors, attraction—of fourth and fifth, and repulsion—of sixth and seventh. The phase diagram is obtained by the lattice gas model using Monte Carlo simulations. Very strong first order phase transitions, causing the two-phase coexistence, were found between disordered and honeycomb as well as between disordered and hexagonal closed packed phases.© 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Monte Carlo simulation of phase transitions to antiferromagnetic stripe phases are performed for square and triangular lattices. We employed Ising model with competing ferromagnetic nearest neighbour and antiferromagnetic dipolar interactions and calculated phase diagram for different values of exchange and dipolar interaction ratio. The order of transitions to stripe phases with different interaction ratio (stripe width) was determined. We have shown by using histogram method that for transition to the stripe phase AF1 with the smallest stripe width h = a (a is lattice constant) the order is different for square and triangular lattices. For a square lattice the first order phase transition is found only for transitions to AF2 (h = 2a) phase, the transitions to AF1 and AF3 (h = 3a) phases being continuous. For triangular lattice we determined first order phase transitions to AF1 and AF2 phases and second order phase transitions to AF3 and AF4 phases. [ABSTRACT FROM AUTHOR]

The time law of small vibrations of the center of pressure (COP) of humans in standing position (human posture) may provide useful information about health condition of an individual. Very popular method to analyze the posture stability is to draw planar or two single-dimension histograms of COP. In this paper both types of histograms are used as a discriminative tool to distinguish two classes of subjects - healthy ones and those who suffer from multiple sclerosis disability. The pattern recognition method based on solving linear programming problem is presented in this paper. The method was applied for classification of histograms. Numerical experiments demonstrate that planar histograms may be used as a discriminative tool to classify subjects into two classes - healthy and suffering from multiple sclerosis disability. A set of two single-dimension histograms failed to indicate that ability. [ABSTRACT FROM AUTHOR]

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. However, minor variations in chemical structure can significantly alter their binding properties. Over 1000 sulfonamides have been designed, synthesized and evaluated to understand the correlations between the structure and thermodynamics of their binding to the human CA isozyme family. Compound binding was determined by several binding assays: fluorescence-based thermal shift assay, stopped-flow enzyme activity inhibition assay, isothermal titration calorimetry and competition assay for enzyme expressed on cancer cell surfaces. All assays have advantages and limitations but are necessary for deeper characterization of these protein-ligand interactions. Here, the concept and importance of intrinsic binding thermodynamics is emphasized and the role of structure-thermodynamics correlations for the novel inhibitors of CA IX is discussed - an isozyme that is overexpressed in solid hypoxic tumors, and thus these inhibitors may serve as anticancer drugs. The abundant structural and thermodynamic data are assembled into the Protein-Ligand Binding Database to understand general protein-ligand recognition principles that could be used in drug discovery., (open access.)

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., Areas Covered: In this review, the authors reassess both the industry mainstays and the newest trends among the methods for protein - small-molecule affinity determination. They discuss both computational affinity predictions and experimental techniques, describing their basic principles, main limitations, and advantages. Together, this serves as initial guide to the currently most popular and cutting-edge ligand-binding assays employed in rational drug design., Expert Opinion: The affinity determination methods continue to develop toward miniaturization, high-throughput, and in-cell application. Moreover, the availability of data analysis tools has been constantly increasing. Nevertheless, cross-verification of data using at least two different techniques and careful result interpretation remain of utmost importance.

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 K a shift of the ionizable group and dissolution equilibria. The model considers three forms of a compound: dissolved-charged, dissolved-uncharged, and aggregated-uncharged. It analyzes two linked equilibria: the protonation of the ionizable group and the dissolution-aggregation of the uncharged form, with the observed p K a shift depending on the total concentration of the compound. The active concentration of the aggregates determines this shift. The model was explored through the determination of the p K a shift and intrinsic solubility of specific compounds, such as ICPD47, a high-affinity inhibitor of the Hsp90 chaperone protein and anticancer target, as well as benzoic acid and benzydamine. The model holds the potential for a more nuanced understanding of intrinsic solubility and may lead to advancements in drug discovery and development., Competing Interests: The authors declare no competing financial interest., (© 2023 The Authors. Published by American Chemical Society.)

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. In the PLBD, the intrinsic thermodynamic parameters of interactions are provided, which account for the binding-linked protonation reactions. In addition to the protein-ligand binding affinities, the database provides calorimetrically measured binding enthalpies, providing additional mechanistic understanding. The PLBD can be applied to investigations of protein-ligand recognition and could be integrated into small molecule drug design. Database URL https://plbd.org/., (© The Author(s) 2023. Published by Oxford University Press.)

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., Patient Concerns: A 38 year old male presented with nausea, bloating, abdominal distention and weight loss for 4 months., Diagnoses: Endoscopy of upper gastrointestinal tract was performed twice with 2 months interval and a stenotic pyloric part was observed with a suspected submucosal lesion. It was sampled both times, however the pathology findings of the mucosal biopsies were unremarkable with no identifiable neoplastic structures. CT scan and MRI was performed and showed a thickened pyloric wall with a submucosal lesion 15 × 15 mm in diameter. Blood levels of tumor markers carcinoembrionic antigen and carbohydrate antigen 19-9 were within a normal range., Interventions: Pyloric stenosis progressed and the patient underwent a Billroth type I distal gastric resection with D2 lymphadenectomy. Pathologic examination revealed a well differentiated ductal adenocarcinoma arising in the heterotopic pancreatic tissue (Heinrich type III). The resection margins and lymph nodes were free of tumor. The patient received adjuvant chemotherapy with 6 courses of XELOX., Outcomes: No disease recurrence is reported in 12 months follow-up., Lessons: Aberrant pancreatic ductal adenocarcinoma in the stomach is a rare finding, however this pathology should be included in the differential diagnosis of gastric submucosal lesion causing pyloric stenosis., Competing Interests: The authors have no conflicts of interest to disclose., (Copyright © 2023 the Author(s). Published by Wolters Kluwer Health, Inc.)

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. The competitive binding model enabled the determination of common CA inhibitors' dissociation constants for CAIX expressed in exponentially growing cancer cells. All tested sulfonamide compounds bound the proliferating cells with similar affinity as to recombinantly purified CAIX. The probes are applicable for the design of selective drug-like compounds for CAIX and the competition strategy could be applied to other drug targets., (© 2022. The Author(s).)

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. CAIX is associated with poor prognosis in solid hypoxic tumors. The aim of this study was to determine factors related to elevated soluble CAIX (s-CAIX) in high-grade intraepithelial lesion (HSIL) cases., Methods: Patients diagnosed with HSIL (N = 77) were included into the research group whereas without HSIL (N = 72)-the control group. Concentration of the soluble CAIX (s-CAIX) in plasma was determined by the DIANA ligand-antibody-based method. C. trachomatis was detected from cervical samples by PCR. Primary outcomes were risk factors elevating s-CAIX level in HSIL group. Non-parametric statistical analysis methods were used to calculate correlations., Results: The s-CAIX level in patients with HSIL was elevated among older participants (r s  = 0.27, p = 0.04) and with C. trachomatis infection (p = 0.028). Among heavy smokers with HSIL, the concentration of s-CAIX was higher in older women (r s  = 0.52, p = 0.005), but was not related to the age of heavy smokers' controls (τ = 0.18 p = 0.40)., Conclusion: The concentration of s-CAIX was higher among older, heavy smoking and diagnosed with C. trachomatis patients. All these factors increased the risk for HSIL progression., (© 2022. The Author(s).)

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. Seven to 10 days after TEM, clinical data were recorded, and digital rectal examination and rigid proctoscopy were performed. After at least 6 months, bowel function was evaluated using low anterior resection syndrome (LARS) and Wexner questionnaires., Results: Forty-five men with an average age of 67 ± 10.1 (40-85) were included. TEM sutures were recorded as intact in 48/70 (68%) and as dehiscent in 22/70 (32%). It did not have any significant clinical manifestation and was not related with longer postoperative stay or incidence of postoperative complications. Eight of 22 (36.4%) patients with suture dehiscence had per rectal bleeding or febrile temperature without any need for intervention or treatment. The only risk factor for wound dehiscence was a posteriorly located defect. In late postoperative period, there was no difference between groups in LARS or Wexner questionnaire (p value 0.72 and 0.85, respectively)., Conclusions: Our study suggests that 1/3 of the patients' rectal wall defect after TEM will undergo dehiscence in early postoperative period and will not transfer to clinically significant manifestation (without a need of hospitalization or prolonging it). In late postoperative period, there is no difference in bowel function., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

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., Competing Interests: Conflicts of interest The authors declare no competing interests., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

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. Extremely high pressures are required to unfold most proteins and protein-ligand complexes. Thus, guanidinium hydrochloride (GdmHCl) is used as a protein-destabilizing agent. We determined that GdmHCl unfolds carbonic anhydrase isoforms in a different pathway, but the destabilization effect is linear in a particular concentration range. We developed a concept for the FPSA experiment, where both - the ligand and GdmHCl - concentrations are varied. This approach enabled us to determine protein-ligand binding volumes that otherwise would be impossible due to the equipment-unreachable pressures of protein unfolding.

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. Four nested models of different complexities were examined and compared for goodness-of-fit using chi-squared difference testing. Measurement invariance testing was conducted across heterogeneous neuroscience and seizure disorder samples to test generality of the factor model., Results: After removing items with limited variability (very easy or very hard; 12 of 40 items), a four-factor model was found to be best-fitting in the present patient samples. The four factors were "recreational", "functional", "material", and "symbolic", each representing semantic knowledge associated with the function of the target word referent. This model subsequently met the criteria for the strict measurement invariance, showing good overall fit when factor loadings, thresholds, and residuals were held to equality across samples., Conclusions: The results of this study provide further evidence that "arbitrary" associations between word pairs in VPA items have an underlying semantic structure, challenging the idea that unrelated hard-pairs are semantic-free. These results suggest that a semantic-structure model may be implemented as an alternative scoring in future editions of the WMS to facilitate interpretation., (© The Author(s) 2021. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

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. Two cohorts were analysed, one with patients who presented to the emergency department (ED) with suspected AA and the second with confirmed AA. Both cohorts were divided into four groups: before COVID-19, during the first quarantine, between the first and second quarantine, and during the second quarantine. Data such as demographics, the time to first contact with the healthcare provider and time to operation, laboratory tests, clinical stage of AA, length of stay, and COVID-19 status were collected. A total of 469 patients were enrolled., Results: A total of 209 patients were male (45%) and 260 were female (55%), with the median age being 33 years (24-45). In the first cohort of suspected AA, there was no difference in sex; however, more older patients presented to the ED during the first quarantine (41 years) compared with other groups (28.5, 36, and 32.5 years), p  < 0.000. Before the pandemic, there was a shorter duration of symptoms to first contact with the healthcare provider (13 h) compared with other groups, p  = 0.001. In the second cohort of confirmed AA, there was a shorter period of time to operation from first symptoms before the pandemic (22 h) compared with other groups (30, 35, 30.5 h), p  < 0.000. There were more complicated gangrenous, perforated appendicitis or periappendicular abscess in Group 2 and 3 (26, 22 and 10%, and 26, 22 and 2%, respectively) compared with Group 1 (20, 4 and 3%) and Group 4 (22, 12, and 2%), p  = 0.009. Hospital stay was longer during the first quarantine (3 days) compared with other groups (2 days), p  = 0.009. Six patients were COVID-19 positive: one from Group 3 and five from Group 4 ( p  > 0.05)., Conclusions: Our study suggests that during the first quarantine of the COVID-19 pandemic, there was delayed presentation to the ED with suspected AA and there was a greater proportion of complicated appendicitis and longer hospitalization in confirmed cases as well., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Petrauskas, Poskus, Luksaite -Lukste, Kryzauskas, Petrulionis, Strupas and Poskus.)

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. In this work, we analyzed this interaction using solution 19F and 2D 15 N- 1 H HSQC NMR spectroscopy and studied the aggregation properties of these two proteins. Here, we show that α-syn interacts with S100A9 at specific regions, which are also essential in the first step of aggregation. We also demonstrate that the 4-fluorophenylalanine label in alpha-synuclein is a sensitive probe to study interaction and aggregation using 19F NMR spectroscopy.

Background: Our aim was to compare the bowel function and oncologic outcomes following these two treatment modalities. Materials and methods: 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. We performed a case-matched analysis: we matched the patients by age, cancer stage, and comorbidities. Duration of operation, postoperative complications, length of hospital stay, and long-term functional and oncological outcomes were compared. We calculated oncological outcomes using Kaplan-Meier Cox diagrams. In addition, we used a low anterior resection syndrome (LARS) score for the bowel function assessment. Results: Mean operation time in the LE group was 58.8 ± 45 min compared with the TME group that was 121.1 ± 42 min ( p = 0.032). Complications were seen in 5.7% in LE group and 15.62% in TME group ( p = 0.043). ~85.2% of the patients had no LARS in LE group compared with 54.5% in TME group ( p = 0.018). Minor LARS was 7.4% in LE group compared with 31.8% in TME group ( p = 0.018); major LARS was 7.4 and 13.7%, respectively ( p = 0.474). Hospital stay was 2.77 days in LE group compared with 9.21 days in TME group ( p = 0.036). The overall survival was 68.78 months in LE group compared with 74.81 months in TME group ( p = 0.964). Conclusion: Our results of a small sample size showed that local excision ± chemoradiation is a rather safe method for early rectal cancer compared with gold standard treatment. In addition, better bowel function is preserved with less postoperative complications and shorter hospital stays., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Pacevicius, Petrauskas, Pilipavicius and Dulskas.)

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. S100A9 is a calcium-binding, pro-inflammation protein, which is also found in such amyloid plaques. To understand the influence of S100A9 on the aggregation of α-synuclein, we analyzed their co-aggregation kinetics and the resulting amyloid fibril structure by Fourier-transform infrared spectroscopy and atomic force microscopy. We found that the presence of S100A9 alters the aggregation kinetics of α-synuclein and stabilizes the formation of a particular amyloid fibril structure. We also show that the solution's ionic strength influences the interplay between S100A9 and α-synuclein, stabilizing a different structure of α-synuclein fibrils.

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. In this study, the affinities of twelve CA isoforms have been determined for nineteen clinically used drugs used to treat hypertension related diseases, i.e. thiazides, indapamide, and metolazone. Their affinities were determined using a fluorescent thermal shift assay. Stopped flow assay and isothermal titration calorimetry were also employed on a subset of compounds and proteins to confirm inhibition of CA enzymatic activity and verify the quantitative agreement between different assays. The findings of this study showed that pharmaceuticals could bind to human CA isoforms with variable affinities and inhibit their catalytic activity, even though the drug was intended to interact with a different (non-CA) protein target. Relatively minor structural changes of the compounds may cause significant changes in affinity and selectivity for a particular CA isoform., Competing Interests: The authors have read the journal’s policy and have the following competing interests: Authors LB and DM declare that they are authors of several patents and patent applications on carbonic anhydrase inhibitors. None of the patents or patent applications are directly related to the compounds described in this manuscript. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

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) 1 H- 15 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. This approach required a significantly lower amount of protein and NMR time to determine the protein-ligand binding volume of two carbonic anhydrase isozymes upon binding their ligands. The proposed method can be used in other protein-ligand systems and expand the knowledge about protein volume changes upon small-molecule binding.

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. To enhance drug development for CA XII we used a reverse engineering approach where mutation of the key six amino acids in the active site of human CA XII into the CA II isoform was performed to provide a protein chimera (chCA XII) which is amenable to structure-based compound optimization. Through determination of structural detail and affinity measurement of the interaction with over 60 compounds we observed that the compounds that bound CA XII more strongly than CA II, switched their preference and bound more strongly to the engineered chimera, chCA XII, based on CA II, but containing the 6 key amino acids from CA XII, behaved as CA XII in its compound recognition profile. The structures of the compounds in the chimeric active site also resembled those determined for complexes with CA XII, hence validating this protein engineering approach in the development of new inhibitors., (© 2021 The Authors. Published by Wiley-VCH GmbH.)

Equilibrium binding constants (K b ) 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., in lead compound discovery processes and in comparing computational predictions with experimental results. Uncertainties in measured K b values are commonly represented by a symmetric normal distribution, often quoted in terms of the experimental value plus-minus the standard deviation. However, in general, the distributions of measured K b (and equivalent K d ) values and the corresponding free energy change ΔG b are all asymmetric to varying degree. Here, using a simulation approach, we illustrate the effect of asymmetric K b distributions within the realm of isothermal titration calorimetry (ITC) experiments. Further we illustrate the known, but perhaps not widely appreciated, fact that when distributions of any of K b , K d and ΔG b are transformed into each other, their degree of asymmetry is changed. Consequently, we recommend that a more accurate way of expressing the uncertainties of K b , K d , and ΔG b values is to consistently report 95% confidence intervals, in line with other authors' suggestions. The ways to obtain such error ranges are discussed in detail and exemplified for a binding reaction obtained by ITC.

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. The assay has a wide dynamic range enabling simultaneous determination of affinities in the milimolar to picomolar range. The assay could be used for essentially any protein that is sufficiently soluble and stable in the studied aqueous solution. Here we provide examples and typical experimental protocols for both affinity and stability determinations.

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 (Panc10.05, Panc215, A6L) in a dose-response manner, and the inhibitor in vitro effect on cell growth was evaluated. Seven of novel Hsp90 inhibitors based on resorcinol fragment and 5 commercially available Hsp90 inhibitors (17-AAG, AT-13387, AUY-922, ganetespib, and rifabutin) as well as control compound triptolide were tested yielding IC50 values in 2- and 3-dimensional assays., Results: The novel Hsp90 inhibitors exhibited strong effects on all 3 tested pancreatic cell line cultures (Panc10.05, Panc215, A6L) reaching the IC50 of 300 to 600 nM in 2- and 3-dimensional assays., Conclusions: Novel Hsp90 inhibitors can be developed as antipancreatic cancer agents. Their chemical structures are simpler, and they are likely to exhibit lower side effects than the much more complex inhibitors used as controls., Competing Interests: E.K. and D.M. declare that they have authored a patent on heat shock protein 90 inhibitor use. Other authors declare no conflicts of interest., (Copyright © 2021 Wolters Kluwer Health, Inc. All rights reserved.)

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. The first assay uses Sypro Orange™ and monitors the thermal stability of POT1 and its binding under a variety of conditions. This assay is useful for the quality control of POT1 preparations, for biophysical characterization of its DNA binding and, potentially, as an efficient screening tool for binding of small molecule drug candidates. The second assay uses a FRET-labeled human telomeric G-quadruplex structure that reveals the effects of POT1 binding on thermal stability from the DNA frame of reference. These complementary assays provide efficient biophysical approaches for the quantitative characterization of multiple aspects of POT1 structure and function. The results from these assays provide thermodynamics details of POT1 folding, the sequence selectivity of its DNA binding and the thermodynamic profile for its binding to its preferred DNA binding sequence. Most significantly, results from these assays elucidate two mechanisms for the inhibition of POT1 -DNA interactions. The first is by competitive inhibition at the POT1 DNA binding site. The second is indirect and is by stabilization of G-quadruplex formation within the normal POT1 single-stranded DNA sequence to prevent POT1 binding., Competing Interests: The authors have declared that no competing interests exist.

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. Patients with a temporary ileostomy who underwent rectal cancer surgery and did not have anastomotic leakage or other. Early closure (EC; 30 days after creation) and standard closure (SC; 90 days after creation) of ileostomy were compared. Thirty-six months (17-97) after stoma closure, we contacted patients by phone and filled in two questionnaires-The European Organization for Research and Treatment of Cancer Quality of Life Questionnaire Core 30 (EORTC QLQ-C30) and low anterior resection syndrome (LARS) score. This index trial was not powered to assess the difference in bowel function between the two groups. All the patients in the SC group had anastomosis <6 cm from the anal verge compared to 42 of 43 (97.7%) in the EC group. There were no statistically significant differences between EC (26 patients) and SC (25 patients) groups in the EORTC QLQ-C30 and LARS questionnaires. Global quality of life was 37.2 (0-91.7; ±24.9) in the EC group vs. 34.3 (0-100; ±16.2) in the SC ( p = 0.630). Low anterior resection syndrome was present in 46% of patients in the EC and 56% in the SC group ( p = 0.858). Major LARS was found more often in younger patients. However, no statistical significance was found ( p = 0.364). The same was found with quality of life ( p = 0.219). Age, gender, ileostomy closure timing, neoadjuvant treatment, complications had no effect of worse bowel function or quality of life. There was no difference in quality of life or bowel function in the late postoperative period after the early vs. late closure of ileostomy based on two questionnaires and small sample size. None of our assessed risk factors had a negative effect on bowel function o quality of life.

Interactions between charges play a role in protein stability and contribute to the energetics of binding between various charged ligands. Ionic surfactants are charged molecules, whose interactions with proteins are still rather poorly understood despite their wide applications. Here, we show by isothermal titration calorimetry that cationic alkylammonium surfactants bind to negatively charged polyaspartate and polyglutamate homopolymers stoichiometrically, i.e., one surfactant molecule per charged amino acid. Similarly, negatively charged alkyl sulfates (e.g., sodium dodecyl sulfate) and alkane sulfonates bind stoichiometrically to positively charged polylysine, polyornithine, and polyarginine homopolymers. In these reactions, the interacting counterparts form ion pairs and the resulting electrostatically neutral complex coprecipitates from solution. The enthalpies and heat capacities are determined for various pairs of ionic surfactants and charged amino acid homopolymers. These results show the energetic contributions of ionic headgroups and the CH 2 group to surfactant interactions with proteins., Competing Interests: The authors declare no competing financial interest., (Copyright © 2019 American Chemical Society.)

Spleen is typically injured in blunt abdominal trauma. Spleen injuries make 42% of all blunt abdominal injuries. The aim of this study was to perform a retrospective assessment of the cases of acute and subacute isolated traumatic spleen ruptures.A retrospective study performed on 50 patients, whose cause of death was isolated spleen rupture and bleeding into the abdominal cavity.An acute spleen rupture was diagnosed in 47 cases, whereas the rest 3 cases demonstrated a subacute rupture. In cases of acute spleen rupture, the mean weight of spleen was 309.6 g, whereas in 3 cases of subacute rupture the mean weight of the organ achieved 710 g. The mean weight of spleen in the control group with no spleen rupture was 144.7 g.Recording of the cases of isolated acute and subacute traumatic spleen ruptures and morphological assessment of them are important in forensic pathology science and in clinical practice as well.

The aim of rational drug design is to develop small molecules using a quantitative approach to optimize affinity. This should enhance the development of chemical compounds that would specifically, selectively, reversibly, and with high affinity interact with a target protein. It is not yet possible to develop such compounds using computational (i.e., in silico) approach and instead the lead molecules are discovered in high-throughput screening searches of large compound libraries. The main reason why in silico methods are not capable to deliver is our poor understanding of the compound structure-thermodynamics and structure-kinetics correlations. There is a need for databases of intrinsic binding parameters (e.g., the change upon binding in standard Gibbs energy (ΔGint), enthalpy (ΔHint), entropy (ΔSint), volume (ΔVintr), heat capacity (ΔCp,int), association rate (ka,int), and dissociation rate (kd,int)) between a series of closely related proteins and a chemically diverse, but pharmacophoric group-guided library of compounds together with the co-crystal structures that could help explain the structure-energetics correlations and rationally design novel compounds. Assembly of these data will facilitate attempts to provide correlations and train data for modeling of compound binding. Here, we report large datasets of the intrinsic thermodynamic and kinetic data including over 400 primary sulfonamide compound binding to a family of 12 catalytically active human carbonic anhydrases (CA). Thermodynamic parameters have been determined by the fluorescent thermal shift assay, isothermal titration calorimetry, and by the stopped-flow assay of the inhibition of enzymatic activity. Kinetic measurements were performed using surface plasmon resonance. Intrinsic thermodynamic and kinetic parameters of binding were determined by dissecting the binding-linked protonation reactions of the protein and sulfonamide. The compound structure-thermodynamics and kinetics correlations reported here helped to discover compounds that exhibited picomolar affinities, hour-long residence times, and million-fold selectivities over non-target CA isoforms. Drug-lead compounds are suggested for anticancer target CA IX and CA XII, antiglaucoma CA IV, antiobesity CA VA and CA VB, and other isoforms. Together with 85 X-ray crystallographic structures of 60 compounds bound to six CA isoforms, the database should be of help to continue developing the principles of rational target-based drug design.

Human heat shock protein 90 (Hsp90) is a key player in the homeostasis of the proteome and plays a role in numerous diseases, such as cancer. For the design of Hsp90 ATPase activity inhibitors, it is important to understand the relationship between an inhibitor structure and its inhibition potential. The volume of inhibitor binding is one of the most important such parameters that are rarely being studied. Here, the volumes of binding of several ligands to recombinant Hsp90 were obtained by three independent experimental techniques: fluorescent pressure shift assay, vibrating tube densitometry, and high-pressure NMR. Within the error range, all techniques provided similar volumetric parameters for the investigated protein-ligand systems. Protein-ligand binding volumes were negative, suggesting that the protein-ligand complex, together with its hydration shell, occupies less volume than the separate constituents with their hydration shells. Binding volumes of tightly binding, subnanomolar ligands were significantly more negative than those of weakly binding, millimolar ligands. The volumes of binding could be useful for designing inhibitors with desired recognition properties and further development as drugs.

Electrostatic interactions between the positively and negatively charged amino acids in proteins play an important role in macromolecular stability, binding, and recognition. Numerous amino acids in proteins are ionizable and may exist in negatively (e.g., Glu, Asp, Cys, Tyr) or positively (e.g., Arg, Lys, His, Orn) charged form dependent on pH and their pKas. In this work, isothermal titration calorimetry was used to determine the average standard values of thermodynamic parameters (the Gibbs free energy, enthalpy, entropy, and the heat capacity) of interaction between the positively charged amino acid homopolymers (polyarginine, polylysine, and polyornithine) and the negatively charged homopolymers (polyaspartic and polyglutamic acids). These values are of potential use in the computational models of interacting proteins and other biological macromolecules. The study showed that oppositely charged poly(amino acid)s bound each other with the stoichiometry of one positive to one negative charge. Arginine bound to the negatively charged amino acids with exothermic enthalpy and higher affinity than lysine. This result also suggests that positive charges in proteins should not be considered entirely equivalent if carried by lysine or arginine. The difference in binding energy of arginine and lysine association with the negatively charged amino acids was attributed to the enthalpy of the second ionic hydrogen bond formation between the guanidine and carboxylic groups. Despite the favorable enthalpic contribution, all such ion pair formation reactions were largely entropy-driven. Consistent with previously observed ionic interactions, the positive heat capacity was always observed during the amino acid ion pair formation.

Human carbonic anhydrase IX (CA IX) is highly expressed in tumor tissues, and its selective inhibition provides a potential target for the treatment of numerous cancers. Development of potent, highly selective inhibitors against this target remains an unmet need in anticancer therapeutics. A series of fluorinated benzenesulfonamides with substituents on the benzene ring was designed and synthesized. Several of these exhibited a highly potent and selective inhibition profile against CA IX. Three fluorine atoms significantly increased the affinity by withdrawing electrons and lowering the pKa of the benzenesulfonamide group. The bulky ortho substituents, such as cyclooctyl or even cyclododecyl groups, fit into the hydrophobic pocket in the active site of CA IX but not CA II, as shown by the compound's co-crystal structure with chimeric CA IX. The strongest inhibitor of recombinant human CA IX's catalytic domain in human cells achieved an affinity of 50 pM. However, the high affinity diminished the selectivity. The most selective compound for CA IX exhibited 10 nM affinity. The compound that showed the best balance between affinity and selectivity bound with 1 nM affinity. The inhibitors described in this work provide the basis for novel anticancer therapeutics targeting CA IX.

Volume changes that accompany protein unfolding and ligand binding are important but largely neglected thermodynamic parameters that may facilitate rational drug design. Here, we determined the volume of lead compound ICPD47 binding to an anticancer target, heat shock protein 90 N-terminal domain, using a pressure shift assay (PressureFluor). The ligand exhibited a stabilizing effect on the protein by increasing its melting pressure and temperature. The Gibbs free energy of unfolding depends on the absence or presence of ligand and has an elliptical shape. Ellipse size increases upon addition of the strongly binding ligand, which stabilizes the protein. The three-dimensional (3D) ellipsoidal surface of the Gibbs free energy of unfolding was calculated with increasing ligand concentrations. The negative volume of ligand binding was relatively large and significantly exceeded the volume of protein unfolding. The pressure shift assay technique could be used to determine the volume changes associated with both protein unfolding as well as ligand binding to protein.

The interaction between positively and negatively charged linear surfactants is an interesting system for the understanding of the fundamental interplay of hydrophobic and ionic forces in lipid membranes and proteins. We used isothermal titration calorimetry to dissect the Gibbs free energies, enthalpies, entropies, and heat capacities of interaction into hydrophobic and ionic contributions for alkylamine interaction with alkyl sulfates and alkane sulfonates. Dependence on aliphatic chain length, surfactant concentration, temperature, and ionic strength provided a detailed thermodynamic description of this interaction. Reactions of surfactants with tails longer than approximately 10 carbon atoms were primarily driven by enthalpy changes arising from solid-phase interactions between aliphatic tails. Entropic contributions were small relative to enthalpic ones. Contributions of methylene groups were additive. The binding reaction can yield a solid or liquid complex, depending on temperature. Thermodynamic dissection yielded the parameters of the phase transition., (© 2012 American Chemical Society)