AlphaFold is an artificial intelligence approach for predicting the three-dimensional (3D) structures of proteins with atomic accuracy. One challenge that limits the use of AlphaFold models for drug discovery is the correct prediction of folding in the absence of ligands and cofactors, which compromises their direct use. We have previously described the optimization and use of the histone deacetylase 11 (HDAC11) AlphaFold model for the docking of selective inhibitors such as FT895 and SIS17. Based on the predicted binding mode of FT895 in the optimized HDAC11 AlphaFold model, a new scaffold for HDAC11 inhibitors was designed, and the resulting compounds were tested in vitro against various HDAC isoforms. Compound 5a proved to be the most active compound with an IC50 of 365 nM and was able to selectively inhibit HDAC11. Furthermore, docking of 5a showed a binding mode comparable to FT895 but could not adopt any reasonable poses in other HDAC isoforms. We further supported the docking results with molecular dynamics simulations that confirmed the predicted binding mode. 5a also showed promising activity with an EC50 of 3.6 μM on neuroblastoma cells.
- MeSH
- Histone Deacetylases * metabolism MeSH
- Histone Deacetylase Inhibitors * pharmacology chemistry chemical synthesis MeSH
- Humans MeSH
- Molecular Structure MeSH
- Cell Line, Tumor MeSH
- Neuroblastoma * drug therapy pathology MeSH
- Antineoplastic Agents * pharmacology chemistry chemical synthesis MeSH
- Drug Design * MeSH
- Molecular Dynamics Simulation MeSH
- Molecular Docking Simulation MeSH
- Artificial Intelligence MeSH
- Dose-Response Relationship, Drug MeSH
- Structure-Activity Relationship MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
BACKGROUND: Bronchoscopic lung volume reduction (BLVR) with one-way endobronchial valves (EBV) has better outcomes when the target lobe has poor collateral ventilation, resulting in complete lobe atelectasis. High-inspired oxygen fraction (FIO2) promotes atelectasis through faster gas absorption after airway occlusion, but its application during BLVR with EBV has been poorly understood. We aimed to investigate the real-time effects of FIO2 on regional lung volumes and regional ventilation/perfusion by electrical impedance tomography (EIT) during BLVR with EBV. METHODS: Six piglets were submitted to left lower lobe occlusion by a balloon-catheter and EBV valves with FIO2 0.5 and 1.0. Regional end-expiratory lung impedances (EELI) and regional ventilation/perfusion were monitored. Local pocket pressure measurements were obtained (balloon occlusion method). One animal underwent simultaneous acquisitions of computed tomography (CT) and EIT. Regions-of-interest (ROIs) were right and left hemithoraces. RESULTS: Following balloon occlusion, a steep decrease in left ROI-EELI with FIO2 1.0 occurred, 3-fold greater than with 0.5 (p < 0.001). Higher FIO2 also enhanced the final volume reduction (ROI-EELI) achieved by each valve (p < 0.01). CT analysis confirmed the denser atelectasis and greater volume reduction achieved by higher FIO2 (1.0) during balloon occlusion or during valve placement. CT and pocket pressure data agreed well with EIT findings, indicating greater strain redistribution with higher FIO2. CONCLUSIONS: EIT demonstrated in real-time a faster and more complete volume reduction in the occluded lung regions under high FIO2 (1.0), as compared to 0.5. Immediate changes in the ventilation and perfusion of ipsilateral non-target lung regions were also detected, providing better estimates of the full impact of each valve in place. TRIAL REGISTRATION: Not applicable.
- MeSH
- Pulmonary Atelectasis diagnostic imaging physiopathology MeSH
- Bronchoscopy * methods MeSH
- Time Factors MeSH
- Electric Impedance * MeSH
- Lung Volume Measurements methods MeSH
- Lung diagnostic imaging physiopathology surgery physiology MeSH
- Pneumonectomy methods MeSH
- Swine MeSH
- Tomography methods MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
Yohimbine, a natural indole alkaloid and a nonselective adrenoceptor antagonist, possesses potential benefits in treating inflammatory disorders and sepsis. Nevertheless, its broader clinical use faces challenges due to its low receptor selectivity. A structure-activity relationship study of novel yohimbine analogues identified amino esters of yohimbic acid as potent and selective ADRA2A antagonists. Specifically, amino ester 4n, in comparison to yohimbine, showed a 6-fold higher ADRA1A/ADRA2A selectivity index (SI > 556 for 4n) and a 25-fold higher ADRA2B/ADRA2A selectivity index. Compound 4n also demonstrated high plasma and microsomal stability, moderate-to-low membrane permeability determining its limited ability to cross the blood-brain barrier, and negligible toxicity on nontumor normal human dermal fibroblasts. Compound 4n represents an important complementary pharmacological tool to study the involvement of adrenoceptor subtypes in pathophysiologic conditions such as inflammation and sepsis and a novel candidate for further preclinical development to treat ADRA2A-mediated pathologies.
- MeSH
- Adrenergic alpha-2 Receptor Antagonists * pharmacology chemistry chemical synthesis MeSH
- Receptors, Adrenergic, alpha-2 * metabolism MeSH
- Humans MeSH
- Drug Design * MeSH
- Structure-Activity Relationship MeSH
- Yohimbine * pharmacology chemistry MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
Guanine quadruplex (GQ) is a noncanonical nucleic acid structure formed by guanine-rich DNA and RNA sequences. Folding of GQs is a complex process, where several aspects remain elusive, despite being important for understanding structure formation and biological functions of GQs. Pulling experiments are a common tool for acquiring insights into the folding landscape of GQs. Herein, we applied a computational pulling strategy─steered molecular dynamics (SMD) simulations─in combination with standard molecular dynamics (MD) simulations to explore the unfolding landscapes of tetrameric parallel GQs. We identified anisotropic properties of elastic conformational changes, unfolding transitions, and GQ mechanical stabilities. Using a special set of structural parameters, we found that the vertical component of pulling force (perpendicular to the average G-quartet plane) plays a significant role in disrupting GQ structures and weakening their mechanical stabilities. We demonstrated that the magnitude of the vertical force component depends on the pulling anchor positions and the number of G-quartets. Typical unfolding transitions for tetrameric parallel GQs involve base unzipping, opening of the G-stem, strand slippage, and rotation to cross-like structures. The unzipping was detected as the first and dominant unfolding event, and it usually started at the 3'-end. Furthermore, results from both SMD and standard MD simulations indicate that partial spiral conformations serve as a transient ensemble during the (un)folding of GQs.
Background There is a scarcity of validated rapid dietary screening tools for patient use in the clinical setting to improve health and reduce cardiovascular risk. The Healthy Eating Index (HEI) 2015 measures compliance with the 2015 to 2020 Dietary Guidelines for Americans but requires completion of an extensive diet assessment to compute, which is time consuming and impractical. The authors hypothesize that a 19-item dietary survey assessing consumption of common food groups known to affect health will be correlated with the HEI-2015 assessed by a validated food frequency questionnaire and can be further reduced without affecting validity. Methods and Results A 19-item Eating Assessment Tool (EAT) of common food groups was created through literature review and expert consensus. A cross-sectional survey was then conducted in adult participants from a preventive cardiology clinic or cardiac rehabilitation and in healthy volunteers (n=661, mean age, 36 years; 76% women). Participants completed an online 156-item food frequency questionnaire, which was used to calculate the HEI score using standard methods. The association between each EAT question and HEI group was analyzed by Kruskal-Wallis test. Linear regression models were subsequently used to identify univariable and multivariable predictors for HEI score for further reduction in the number of items. The final 9-item model of Mini-EAT was validated by 5-fold cross validation. The 19-item EAT had a strong correlation with the HEI score (r=0.73) and was subsequently reduced to the 9 items independently predictive of the HEI score: fruits, vegetables, whole grains, refined grains, fish or seafood, legumes/nuts/seeds, low-fat dairy, high-fat dairy, and sweets consumption, without affecting the predictive ability of the tool (r=0.71). Conclusions Mini-EAT is a 9-item validated brief dietary screener that correlates well with a comprehensive food frequency questionnaire. Future studies to test the Mini-EAT's validity in diverse populations and for development of clinical decision support systems to capture changes over time are needed.
- MeSH
- Diet * MeSH
- Fruit MeSH
- Cross-Sectional Studies MeSH
- Surveys and Questionnaires MeSH
- Vegetables * MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
A miniature probe for electromembrane extraction is developed and constructed. The tubular probe with an internal volume of 1.1 μL is made of polypropylene hollow fiber with a supported liquid membrane of 85% nitrophenyloctyl ether (NPOE) with 15% bis(2-ethylhexyl)phosphonic acid (DEHP). The probe is connected on-line to the electrophoresis with short separation capillary via an air assisted flow gating interface cast from poly (dimethylsiloxane). The compact instrument is computer controlled via LabView. The probe parameters are tested for extraction of creatinine and basic amino acids from artificial solution and human urine. The sensitivity of the electrophoretic determination after 300 s extraction at 150 V compared to the sensitivity without extraction is 4.9-fold and 2.6-fold higher for creatinine and arginine, respectively. The RSDs for peak area measured from 5 repeated extractions of 50 μM solutions are 7.5%, 7.2%, 8.6% and 9.2% for Crea, Lys, Arg and His, respectively. The probe can be used for all-day measurements. The preparation of the probe is simple and requires no special tool.
- MeSH
- Electrophoresis, Capillary * methods MeSH
- Ethers * chemistry MeSH
- Creatinine MeSH
- Humans MeSH
- Membranes, Artificial MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
ORPs are lipid-transport proteins belonging to the oxysterol-binding protein family. They facilitate the transfer of lipids between different intracellular membranes, such as the ER and plasma membrane. We have solved the crystal structure of the ORP8 lipid transport domain (ORD8). The ORD8 exhibited a β-barrel fold composed of anti-parallel β-strands, with three α-helices replacing β-strands on one side. This mixed alpha-beta structure was consistent with previously solved structures of ORP2 and ORP3. A large cavity (≈1860 Å3) within the barrel was identified as the lipid-binding site. Although we were not able to obtain a lipid-bound structure, we used computer simulations based on our crystal structure to dock PS and PI4P molecules into the putative lipid-binding site of the ORD8. Comparative experiments between the short ORD8ΔLid (used for crystallography) and the full-length ORD8 (lid containing) revealed the lid's importance for stable lipid binding. Fluorescence assays revealed different transport efficiencies for PS and PI4P, with the lid slowing down transport and stabilizing cargo. Coarse-grained simulations highlighted surface-exposed regions and hydrophobic interactions facilitating lipid bilayer insertion. These findings enhance our comprehension of ORD8, its structure, and lipid transport mechanisms, as well as provide a structural basis for the design of potential inhibitors.
Monkeypox, or mpox, is a disease that has recently resurfaced and spread across the globe. Despite the availability of an FDA-approved vaccine (JYNNEOS) and an effective drug (tecovirimat), concerns remain over the possible recurrence of a viral pandemic. Like any other virus, mpox virus must overcome the immune system to replicate. Viruses have evolved various strategies to overcome both innate and adaptive immunity. Poxviruses possess an unusual nuclease, poxin, which cleaves 2'-3'-cGAMP, a cyclic dinucleotide, which is an important second messenger in the cGAS-STING signaling pathway. Here, we present the crystal structure of mpox poxin. The structure reveals a conserved, predominantly β-sheet fold and highlights the high conservation of the cGAMP binding site and of the catalytic residues His17, Tyr138, and Lys142. This research suggests that poxin inhibitors could be effective against multiple poxviruses.
- MeSH
- Humans MeSH
- Mpox, Monkeypox * MeSH
- Poxviridae * MeSH
- Drug Design MeSH
- Signal Transduction MeSH
- Monkeypox virus MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
Imunoterapie jako samostatná léčebná modalita nebo v kombinaci s chemoterapií se stala novým zlatým standardem léčby nemocných s recidivujícími či metastazujícími nádory hlavy a krku s vyčerpanými možnostmi lokoregionální terapie. V naší kazuistice prezentujeme pacienta s recidivou nádoru hlasivky po kurativní radioterapii a následně první linii paliativní léčby cisplatinou s 5-fluorouracilem s rychlou progresí onemocnění, druhou linií imunoterapie nivolumabem, po které následovala opět progrese, a teprve po třetí linii s docetaxelem došlo k dlouhodobé kompletní remisi onemocnění. Tuto skutečnost si vysvětlujeme buď opožděnou aktivací imunitního systému, nebo imunomodulačním účinkem docetaxelu, jelikož dlouhodobá kompletní remise po třetí linii paliativní léčby docetaxelem se nedá úplně očekávat.
Immunotherapy as monotherapy or in combination with chemotherapy represents the new gold standard for the treatment of the relapsed or metastatic head and neck cancer where local therapy is not possible. In our case report we present the patient with laryngeal cancer relapse after radical radiotherapy and first line palliative chemotherapy cisplatin and 5-fluorouracil with rapid disease progression followed by second line palliative treatment with immunotherapy nivolumab, again with progression and finally followed by third line palliative treatment with docetaxel with long term complete remission. This excellent result can be explained by delayed activation of the immune system or immunomudulatory effect of the docetaxel, since long term remission cannot be expected solely after third line docetaxel palliative treatment.
- MeSH
- Chemotherapy, Adjuvant MeSH
- Survival Analysis MeSH
- Cetuximab therapeutic use MeSH
- Cisplatin therapeutic use MeSH
- Docetaxel therapeutic use MeSH
- Fluorouracil therapeutic use MeSH
- Vocal Cords pathology MeSH
- Immunotherapy MeSH
- Clinical Trials, Phase III as Topic MeSH
- Humans MeSH
- Neoplasm Recurrence, Local MeSH
- Neoplasm Metastasis MeSH
- Laryngeal Neoplasms * drug therapy MeSH
- Nivolumab therapeutic use MeSH
- Positron Emission Tomography Computed Tomography MeSH
- Disease Progression MeSH
- Antineoplastic Agents, Immunological therapeutic use MeSH
- T-Lymphocytes, Regulatory drug effects MeSH
- Aged MeSH
- Carcinoma, Squamous Cell MeSH
- Check Tag
- Humans MeSH
- Male MeSH
- Aged MeSH
- Publication type
- Case Reports MeSH
BACKGROUND: Recently, deep neural networks have been successfully applied in many biological fields. In 2020, a deep learning model AlphaFold won the protein folding competition with predicted structures within the error tolerance of experimental methods. However, this solution to the most prominent bioinformatic challenge of the past 50 years has been possible only thanks to a carefully curated benchmark of experimentally predicted protein structures. In Genomics, we have similar challenges (annotation of genomes and identification of functional elements) but currently, we lack benchmarks similar to protein folding competition. RESULTS: Here we present a collection of curated and easily accessible sequence classification datasets in the field of genomics. The proposed collection is based on a combination of novel datasets constructed from the mining of publicly available databases and existing datasets obtained from published articles. The collection currently contains nine datasets that focus on regulatory elements (promoters, enhancers, open chromatin region) from three model organisms: human, mouse, and roundworm. A simple convolution neural network is also included in a repository and can be used as a baseline model. Benchmarks and the baseline model are distributed as the Python package 'genomic-benchmarks', and the code is available at https://github.com/ML-Bioinfo-CEITEC/genomic_benchmarks . CONCLUSIONS: Deep learning techniques revolutionized many biological fields but mainly thanks to the carefully curated benchmarks. For the field of Genomics, we propose a collection of benchmark datasets for the classification of genomic sequences with an interface for the most commonly used deep learning libraries, implementation of the simple neural network and a training framework that can be used as a starting point for future research. The main aim of this effort is to create a repository for shared datasets that will make machine learning for genomics more comparable and reproducible while reducing the overhead of researchers who want to enter the field, leading to healthy competition and new discoveries.
