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Drug resistance of pathogens, including viruses, is one of the reasons for decreased efficacy of therapy. Considering the impact of HIV type 1 (HIV-1) on the development of progressive immune dysfunction and the rapid development of drug resistance, the analysis of HIV-1 resistance is of high significance. Currently, a substantial amount of data has been accumulated on HIV-1 drug resistance that can be used to build both qualitative and quantitative models of HIV-1 drug resistance. Quantitative models of drug resistance can enrich the information about the efficacy of a particular drug in the scheme of antiretroviral therapy. In our study, we investigated the possibility of developing models for quantitative prediction of HIV-1 resistance to eight protease inhibitors based on the analysis of amino acid sequences of HIV-1 protease for 900 virus variants. We developed random forest regression (RFR), support vector regression (SVR), and self-consistent regression (SCR) models using binary vectors containing values from 0 or 1, depending on the presence of a specific peptide fragment in each amino acid sequence as independent variables, while fold ratio, reflecting the level of resistance, was the predicted variable. The SVR and SCR models showed the highest predictive performances. The models built demonstrate reasonable performances for eight out of nine (R2 varied from 0.828 to 0.909) protease inhibitors, while R2 for predicting tipranavir fold ratio was lower (R2 was 0.642). We believe that the developed approach can be applied to evaluate drug resistance of molecular targets of other viruses where appropriate experimental data are available.
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Farmacorresistência Viral , Infecções por HIV , Inibidores da Protease de HIV , Protease de HIV , HIV-1 , HIV-1/efeitos dos fármacos , HIV-1/genética , Farmacorresistência Viral/genética , Humanos , Infecções por HIV/virologia , Infecções por HIV/tratamento farmacológico , Protease de HIV/genética , Protease de HIV/metabolismo , Inibidores da Protease de HIV/farmacologia , Inibidores da Protease de HIV/uso terapêutico , Sequência de Aminoácidos , Fármacos Anti-HIV/farmacologia , Fármacos Anti-HIV/uso terapêuticoRESUMO
Classical scoring functions may exhibit low accuracy in determining ligand binding affinity for proteins. The availability of both protein-ligand structures and affinity data make it possible to develop machine-learning models focused on specific protein systems with superior predictive performance. Here, we report a new methodology named SAnDReS that combines AutoDock Vina 1.2 with 54 regression methods available in Scikit-Learn to calculate binding affinity based on protein-ligand structures. This approach allows exploration of the scoring function space. SAnDReS generates machine-learning models based on crystal, docked, and AlphaFold-generated structures. As a proof of concept, we examine the performance of SAnDReS-generated models in three case studies. For all three cases, our models outperformed classical scoring functions. Also, SAnDReS-generated models showed predictive performance close to or better than other machine-learning models such as KDEEP, CSM-lig, and ΔVinaRF20. SAnDReS 2.0 is available to download at https://github.com/azevedolab/sandres.
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Aprendizado de Máquina , Proteínas , Proteínas/química , Proteínas/metabolismo , Ligantes , Software , Simulação de Acoplamento MolecularRESUMO
Reactive oxygen species (ROS) produced by NADPH oxidases (NOX, a key source of ROS in vascular cells) are involved in the regulation of vascular tone, but this has been explored mainly for adult organisms. Importantly, the mechanisms of vascular tone regulation differ significantly in early postnatal ontogenesis and adulthood, while the vasomotor role of ROS in immature systemic arteries is poorly understood. We tested the hypothesis that the functional contribution of NADPH oxidase-derived ROS to the regulation of peripheral arterial tone is higher in the early postnatal period than in adulthood. We studied saphenous arteries from 10- to 15-day-old ("young") and 3- to 4-month-old ("adult") male rats using lucigenin-enhanced chemiluminescence, quantitative PCR, Western blotting, and isometric myography. We demonstrated that both basal and NADPH-stimulated superoxide anion radical (O2â¢-) production was significantly higher in the arteries from young in comparison to adult rats. Importantly, pan-inhibitor of NADPH oxidase VAS2870 (10 µM) reduced NADPH-induced O2â¢- production in arteries of young rats. Saphenous arteries of both young and adult rats demonstrated high levels of Nox2 and Nox4 mRNAs, while Nox1 and Nox3 mRNAs were not detected. The protein contents of NOX2 and NOX4 were significantly higher in arterial tissue of young compared to adult animals. Moreover, VAS2870 (10 µM) had no effect on methoxamine-induced contractile responses of adult arteries but decreased them significantly in young arteries; such effect of VAS2870 persisted after removal of the endothelium. Finally, NOX2 inhibitor GSK2795039 (10 µM), but not NOX1/4 inhibitor GKT137831 (10 µM) weakened methoxamine-induced contractile responses of arteries from young rats. Thus, ROS produced by NOX2 have a pronounced contractile influence in saphenous artery smooth muscle cells of young, but not adult rats, which is associated with the increased vascular content of NOX2 protein at this age.
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Artérias , NADPH Oxidases , Ratos , Masculino , Animais , NADPH Oxidases/genética , NADPH Oxidases/metabolismo , Espécies Reativas de Oxigênio/metabolismo , NADP , Metoxamina , Artérias/fisiologia , NADPH Oxidase 1/genética , NADPH Oxidase 4/genética , NADPH Oxidase 4/metabolismo , Superóxidos/metabolismoRESUMO
PURPOSE: The WHO reported an increasing trend in the number of new cases of breast cancer, making it the most prevalent cancer in the world. This fact necessitates the availability of highly qualified ultrasonographers, which can be achieved by the widespread implementation of training phantoms. The goal of the present work is to develop and test an inexpensive, accessible, and reproducible technology for creating an anatomical breast phantom for practicing ultrasound diagnostic skills in grayscale and elastography imaging, as well as ultrasound-guided biopsy sampling. METHODS: We used FDM 3D printer and PLA plastic for printing an anatomical breast mold. We made a phantom using a mixture of polyvinyl chloride plastisol, graphite powder, and metallic glitter to simulate soft tissues and lesions. Various degrees of elasticity were imparted using plastisols of stiffness ranging from 3 to 17 on the Shore scale. The lesions were shaped by hand. The materials and methods used are easily accessible and reproducible. RESULTS: Using the proposed technology, we have developed and tested a basic, differential, and elastographic versions of the breast phantom. The three versions of the phantom are anatomical and intended for use in medical education: the basic version is for practicing primary hand-eye coordination skills; the differential one is for practicing the differential diagnosis skills; the elastographic version helps developing the skills needed for assessing the stiffness of tissues. CONCLUSION: The proposed technology allows the creation of breast phantoms for practicing hand-eye coordination and develop the critical skills for navigation and assessment of the shape, margins, and size of the lesion, as well as performing an ultrasound-guided biopsy. It is cost-effective, reproducible, and easily implementable, and could be instrumental in generating ultrasonographers with crucial skills for accurate diagnosis of breast cancer, especially in low-resource settings.
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Neoplasias da Mama , Técnicas de Imagem por Elasticidade , Humanos , Feminino , Cloreto de Polivinila , Mama/diagnóstico por imagem , Neoplasias da Mama/diagnóstico por imagem , Técnicas de Imagem por Elasticidade/métodos , Imagens de Fantasmas , ElasticidadeRESUMO
Self-assembly of 4,4'-linked dipyrromethanes from 2-(vinyloxy)ethyl isothiocyanate, tertiary propargylamines, and alkylating agents has been discovered. The plausible reaction mechanism, the major stages of which have been confirmed experimentally, includes (1) the lithiation of propargylamine (with n-BuLi); (2) the formation of lithium N-[2-(vinyloxy)ethyl]but-2-ynimidothioate (product of the addition of monolithiated propargylamine to isothiocyanate); (3) isomerization of the latter in the corresponding allenylimidothioate (under the action of the t-BuOK/t-BuOH system); (4) low-temperature (<15 °C) intramolecular cyclization of the latter into potassium N-(5-amino-2-thienyl)-N-[2-(vinyloxy)ethyl]amide; (5) the base-induced cleavage of the C-O bond of the N-[2-(vinyloxy)ethyl] group and removal of vinyloxide-anion leading to acetaldehyde; (6) interaction of acetaldehyde with two molecules of N-(5-amino-2-thienyl)-N-[2-(vinyloxy)ethyl]amide-anion resulting in dithienomethane N-anionic intermediate; (7) recyclization of the latter into dipyrromethane S-anionic intermediate. Final S-alkylation affords synthetically challenging 4,4'-dipyrromethanes in a yield of 22-51%. The whole process is carried out in a single synthetic operation in a very short time (â¼10-15 min, excluding alkylation time).
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The feasibility of risk assessment of a Siberian silk moth (Dendrolimus sibiricus Tschetv.) outbreak was analyzed by means of landscape and weather characteristics and tree condition parameters. Difficulties in detecting forest pest outbreaks (especially in Siberian conditions) are associated with the inability to conduct regular ground surveillance in taiga territories, which generally occupy more than 2 million km2. Our analysis of characteristics of Siberian silk moth outbreak zones under mountainous taiga conditions showed that it is possible to distinguish an altitudinal belt between 400 and 800 m above sea level where an outbreak develops and trees are damaged. It was found that to assess the resistance of forest stands to pest attacks, researchers can employ new parameters: namely, characteristics of a response of remote sensing variables to changes in land surface temperature. Using these parameters, it is possible to identify in advance (2-3 years before an outbreak) forest stands that are not resistant to the pest. Thus, field studies in difficult-to-access taiga forests are not needed to determine these parameters, and hence the task of monitoring outbreaks of forest insects is simplified substantially.
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Predicting viral drug resistance is a significant medical concern. The importance of this problem stimulates the continuous development of experimental and new computational approaches. The use of computational approaches allows researchers to increase therapy effectiveness and reduce the time and expenses involved when the prescribed antiretroviral therapy is ineffective in the treatment of infection caused by the human immunodeficiency virus type 1 (HIV-1). We propose two machine learning methods and the appropriate models for predicting HIV drug resistance related to amino acid substitutions in HIV targets: (i) k-mers utilizing the random forest and the support vector machine algorithms of the scikit-learn library, and (ii) multi-n-grams using the Bayesian approach implemented in MultiPASSR software. Both multi-n-grams and k-mers were computed based on the amino acid sequences of HIV enzymes: reverse transcriptase and protease. The performance of the models was estimated by five-fold cross-validation. The resulting classification models have a relatively high reliability (minimum accuracy for the drugs is 0.82, maximum: 0.94) and were used to create a web application, HVR (HIV drug Resistance), for the prediction of HIV drug resistance to protease inhibitors and nucleoside and non-nucleoside reverse transcriptase inhibitors based on the analysis of the amino acid sequences of the appropriate HIV proteins from clinical samples.
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Fármacos Anti-HIV , Infecções por HIV , Humanos , Fármacos Anti-HIV/farmacologia , Fármacos Anti-HIV/uso terapêutico , Teorema de Bayes , Substituição de Aminoácidos , Reprodutibilidade dos Testes , Transcriptase Reversa do HIV/genética , Inibidores da Transcriptase Reversa/farmacologia , Infecções por HIV/tratamento farmacológico , Farmacorresistência Viral/genética , Protease de HIV/genéticaRESUMO
Introduction: There are difficulties in creating direct antiviral drugs for all viruses, including new, suddenly arising infections, such as COVID-19. Therefore, pathogenesis-directed therapy is often necessary to treat severe viral infections and comorbidities associated with them. Despite significant differences in the etiopathogenesis of viral diseases, in general, they are associated with significant dysfunction of the immune system. Study of common mechanisms of immune dysfunction caused by different viral infections can help develop novel therapeutic strategies to combat infections and associated comorbidities. Methods: To identify common mechanisms of immune functions disruption during infection by nine different viruses (cytomegalovirus, Ebstein-Barr virus, human T-cell leukemia virus type 1, Hepatitis B and C viruses, human immunodeficiency virus, Dengue virus, SARS-CoV, and SARS-CoV-2), we analyzed the corresponding transcription profiles from peripheral blood mononuclear cells (PBMC) using the originally developed pipeline that include transcriptome data collection, processing, normalization, analysis and search for master regulators of several viral infections. The ten datasets containing transcription data from patients infected by nine viruses and healthy people were obtained from Gene Expression Omnibus. The analysis of the data was performed by Genome Enhancer pipeline. Results: We revealed common pathways, cellular processes, and master regulators for studied viral infections. We found that all nine viral infections cause immune activation, exhaustion, cell proliferation disruption, and increased susceptibility to apoptosis. Using network analysis, we identified PBMC receptors, representing proteins at the top of signaling pathways that may be responsible for the observed transcriptional changes and maintain the current functional state of cells. Discussion: The identified relationships between some of them and virus-induced alteration of immune functions are new and have not been found earlier, e.g., receptors for autocrine motility factor, insulin, prolactin, angiotensin II, and immunoglobulin epsilon. Modulation of the identified receptors can be investigated as one of therapeutic strategies for the treatment of severe viral infections.
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COVID-19 , Vírus , Humanos , Leucócitos Mononucleares , Transcriptoma , Antivirais/farmacologia , ImunidadeRESUMO
Studies on virus-host interactions are of high significance for a number of reasons [...].
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Antivirais , Interações Hospedeiro-Patógeno , Antivirais/farmacologia , Antivirais/uso terapêutico , Replicação ViralRESUMO
The study of the mechanisms of regulation of vascular tone is an urgent task of modern science, since diseases of the cardiovascular system remain the main cause of reduction in the quality of life and mortality of the population. Myography (isometric and isobaric) of isolated blood vessels is one of the most physiologically relevant approaches to study the function of cells in the vessel wall. On the one hand, cell-cell interactions as well as mechanical stretch of the vessel wall remain preserved in myography studies, in contrast to studies on isolated cells, e.g., cell culture. On the other hand, in vitro studies in isolated vessels allow control of numerous parameters that are difficult to control in vivo. The aim of this review was to 1) discuss the specifics of experimental design and interpretation of data obtained by myography and 2) highlight the importance of the combined use of myography with various complementary techniques necessary for a deep understanding of vascular physiology.
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Exploiting 2-(alkylsulfonyl)pyridines as 1,3-N,S-ligands, herein we have constructed 1D CuI-based coordination polymers (CPs) bearing unprecedented (CuI)n chains and possessing remarkable photophysical properties. At room temperature, these CPs show efficient TADF, phosphorescence or dual emission in the deep-blue to red range with outstandingly short decay times of 0.4-2.0 µs and good quantum performance. Owing to great structural diversity, the CPs demonstrate a variety of emissive mechanisms, spanning from TADF of 1(M + X)LCT type to 3CC and 3(M + X)LCT phosphorescence. Moreover, the designed compounds emit strong X-ray radioluminescence with the quantum efficiency of up to an impressive 55% relative to all-inorganic BGO scintillators. The presented findings push the boundaries in designing TADF and triplet emitters with very short decay times.
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BACKGROUND: The idea of scoring function space established a systems-level approach to address the development of models to predict the affinity of drug molecules by those interested in drug discovery. OBJECTIVE: Our goal here is to review the concept of scoring function space and how to explore it to develop machine learning models to address protein-ligand binding affinity. METHOD: We searched the articles available in PubMed related to the scoring function space. We also utilized crystallographic structures found in the protein data bank (PDB) to represent the protein space. RESULTS: The application of systems-level approaches to address receptor-drug interactions allows us to have a holistic view of the process of drug discovery. The scoring function space adds flexibility to the process since it makes it possible to see drug discovery as a relationship involving mathematical spaces. CONCLUSION: The application of the concept of scoring function space has provided us with an integrated view of drug discovery methods. This concept is useful during drug discovery, where we see the process as a computational search of the scoring function space to find an adequate model to predict receptor-drug binding affinity.
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Viruses cause various infections that may affect human lifestyle for durations ranging from several days to for many years. Although preventative and therapeutic remedies are available for many viruses, they may still have a profound impact on human life. The human immunodeficiency virus type 1 is the most common cause of HIV infection, which represents one of the most dangerous and complex diseases since it affects the immune system and causes its disruption, leading to secondary complications and negatively influencing health-related quality of life. While highly active antiretroviral therapy may decrease the viral load and the velocity of HIV infection progression, some individual peculiarities may affect viral load control or the progression of T-cell malfunction induced by HIV. Our study is aimed at the text-based identification of molecular mechanisms that may be involved in viral infection progression, using HIV as a case study. Specifically, we identified human proteins and genes which commonly occurred, overexpressed or underexpressed, in the collections of publications relevant to (i) HIV infection progression and (ii) acute and chronic stages of HIV infection. Then, we considered biological processes that are controlled by the identified protein and genes. We verified the impact of the identified molecules in the associated clinical study.
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Infecções por HIV , HIV-1 , Humanos , Qualidade de Vida , Terapia Antirretroviral de Alta Atividade , Mineração de Dados , Carga ViralRESUMO
In vitro cell-line cytotoxicity is widely used in the experimental studies of potential antineoplastic agents and evaluation of safety in drug discovery. In silico estimation of cytotoxicity against hundreds of tumor cell lines and dozens of normal cell lines considerably reduces the time and costs of drug development and the assessment of new pharmaceutical agent perspectives. In 2018, we developed the first freely available web application (CLC-Pred) for the qualitative prediction of cytotoxicity against 278 tumor and 27 normal cell lines based on structural formulas of 59,882 compounds. Here, we present a new version of this web application: CLC-Pred 2.0. It also employs the PASS (Prediction of Activity Spectra for Substance) approach based on substructural atom centric MNA descriptors and a Bayesian algorithm. CLC-Pred 2.0 provides three types of qualitative prediction: (1) cytotoxicity against 391 tumor and 47 normal human cell lines based on ChEMBL and PubChem data (128,545 structures) with a mean accuracy of prediction (AUC), calculated by the leave-one-out (LOO CV) and the 20-fold cross-validation (20F CV) procedures, of 0.925 and 0.923, respectively; (2) cytotoxicity against an NCI60 tumor cell-line panel based on the Developmental Therapeutics Program's NCI60 data (22,726 structures) with different thresholds of IG50 data (100, 10 and 1 nM) and a mean accuracy of prediction from 0.870 to 0.945 (LOO CV) and from 0.869 to 0.942 (20F CV), respectively; (3) 2170 molecular mechanisms of actions based on ChEMBL and PubChem data (656,011 structures) with a mean accuracy of prediction 0.979 (LOO CV) and 0.978 (20F CV). Therefore, CLC-Pred 2.0 is a significant extension of the capabilities of the initial web application.
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Antineoplásicos , Software , Humanos , Teorema de Bayes , Antineoplásicos/farmacologia , Antineoplásicos/química , Prednisona , Linhagem Celular TumoralRESUMO
Introduction: Functional tests and training regimens intensity-controlled by an individual are used in sport practice, clinical rehabilitation, and space medicine. The model of voluntary wheel running in rats can be used to explore molecular mechanisms of such training regimens in humans. Respiratory and locomotor muscles demonstrate diverse adaptations to treadmill exercise, but the effects of voluntary exercise training on these muscle types have not been compared yet. Therefore, this work aimed at the effects of voluntary ET on rat triceps brachii and diaphragm muscles with special attention to reactive oxygen species, which regulate muscle plasticity during exercise. Methods: Male Wistar rats were distributed into exercise trained (ET) and sedentary (Sed) groups. ET group had free access to running wheels, running activity was continuously recorded and analyzed using the original hardware/software complex. After 8 weeks, muscle protein contents were studied using Western blotting. Results: ET rats had increased heart ventricular weights but decreased visceral/epididymal fat weights and blood triglyceride level compared to Sed. The training did not change corticosterone, testosterone, and thyroid hormone levels, but decreased TBARS content in the blood. ET rats demonstrated higher contents of OXPHOS complexes in the triceps brachii muscle, but not in the diaphragm. The content of SOD2 increased, and the contents of NOX2 and SOD3 decreased in the triceps brachii muscle of ET rats, while there were no such changes in the diaphragm. Conclusion: Voluntary wheel running in rats is intensive enough to govern specific adaptations of muscle fibers in locomotor, but not respiratory muscle.
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Aim: TASK-1 channels are established regulators of pulmonary artery tone but their contribution to the regulation of vascular tone in systemic arteries is poorly understood. We tested the hypothesis that TASK-1 channel functional impact differs among systemic vascular beds, that this is associated with differences in their expression and may increase with alkalization of the extracellular environment. Therefore, we evaluated the expression level of TASK-1 channels and their vasomotor role in mesenteric and renal arteries. Methods: Pulmonary, mesenteric and renal arteries from male Wistar rats were used for TASK-1 channel mRNA (qPCR) and protein content (Western blotting) measurements. The functional role of TASK-1 channels was studied by wire myography using the TASK-1 channel blocker AVE1231. In some experiments, the endothelium was removed with a rat whisker. Results: Expression levels of both mRNA and protein of the TASK-1 channel pore-forming subunit were highest in pulmonary arteries, lowest in mesenteric arteries and had an intermediate value in renal arteries. Blockade of TASK-1 channels by 1 µM AVE1231 increased U46619-induced contractile responses of pulmonary arteries but did not affect basal tone and contractile responses to methoxamine of mesenteric and renal arteries at physiological extracellular pH (pHo = 7.41). At alkaline extracellular pH = 7.75 (increase of NaHCO3 to 52 mM) AVE1231 evoked the development of basal tone and increased contractile responses to low concentrations of methoxamine in renal but not mesenteric arteries. This effect was independent of the endothelium. Conclusion: In the rat systemic circulation, TASK-1 channels are abundant in renal arteries and have an anticontractile function under conditions of extracellular alkalosis.
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The activity of many vasomotor signaling pathways strongly depends on extracellular/intracellular pH. Nitric oxide (NO) is one of the most important vasodilators produced by the endothelium. In this review, we present evidence that in most vascular beds of mature mammalian organisms metabolic or respiratory acidosis increases functional endothelial NO-synthase (eNOS) activity, despite the observation that direct effects of low pH on eNOS enzymatic activity are inhibitory. This can be explained by the fact that acidosis increases the activity of signaling pathways that positively regulate eNOS activity. The role of NO in the regulation of vascular tone is greater in early postnatal ontogenesis compared to adulthood. Importantly, in early postnatal ontogenesis acidosis also augments functional eNOS activity and its contribution to the regulation of arterial contractility. Therefore, the effect of acidosis on total peripheral resistance in neonates may be stronger than in adults and can be one of the reasons for an undesirable decrease in blood pressure during neonatal asphyxia. The latter, however, should be proven in future studies.
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Acidose , Endotélio Vascular , Acidose/metabolismo , Adulto , Animais , Pressão Sanguínea , Endotélio Vascular/metabolismo , Humanos , Recém-Nascido , Mamíferos/metabolismo , Óxido Nítrico/metabolismo , Óxido Nítrico Sintase Tipo III/metabolismo , Vasodilatadores/farmacologiaRESUMO
Ritonavir-boosted atazanavir is an option for second-line therapy in low- and middle-income countries (LMICs). We analyzed publicly available HIV-1 protease sequences from previously PI-naïve patients with virological failure (VF) following treatment with atazanavir. Overall, 1497 patient sequences were identified, including 740 reported in 27 published studies and 757 from datasets assembled for this analysis. A total of 63% of patients received boosted atazanavir. A total of 38% had non-subtype B viruses. A total of 264 (18%) sequences had a PI drug-resistance mutation (DRM) defined as having a Stanford HIV Drug Resistance Database mutation penalty score. Among sequences with a DRM, nine major DRMs had a prevalence >5%: I50L (34%), M46I (33%), V82A (22%), L90M (19%), I54V (16%), N88S (10%), M46L (8%), V32I (6%), and I84V (6%). Common accessory DRMs were L33F (21%), Q58E (16%), K20T (14%), G73S (12%), L10F (10%), F53L (10%), K43T (9%), and L24I (6%). A novel nonpolymorphic mutation, L89T occurred in 8.4% of non-subtype B, but in only 0.4% of subtype B sequences. The 264 sequences included 3 (1.1%) interpreted as causing high-level, 14 (5.3%) as causing intermediate, and 27 (10.2%) as causing low-level darunavir resistance. Atazanavir selects for nine major and eight accessory DRMs, and one novel nonpolymorphic mutation occurring primarily in non-B sequences. Atazanavir-selected mutations confer low-levels of darunavir cross resistance. Clinical studies, however, are required to determine the optimal boosted PI to use for second-line and potentially later line therapy in LMICs.
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MOTIVATION: Human immunodeficiency virus (HIV) drug resistance is a global healthcare issue. The emergence of drug resistance influenced the efficacy of treatment regimens, thus stressing the importance of treatment adaptation. Computational methods predicting the drug resistance profile from genomic data of HIV isolates are advantageous for monitoring drug resistance in patients. However, existing computational methods for drug resistance prediction are either not suitable for emerging HIV strains with complex mutational patterns or lack interpretability, which is of paramount importance in clinical practice. The approach reported here overcomes these limitations and combines high accuracy of predictions and interpretability of the models. RESULTS: In this work, a new methodology based on generative topographic mapping (GTM) for biological sequence space representation and quantitative genotype-phenotype relationships prediction purposes was introduced. The GTM-based resistance landscapes allowed us to predict the resistance of HIV strains based on sequencing and drug resistance data for three viral proteins [integrase (IN), protease (PR) and reverse transcriptase (RT)] from Stanford HIV drug resistance database. The average balanced accuracy for PR inhibitors was 0.89 ± 0.01, for IN inhibitors 0.85 ± 0.01, for non-nucleoside RT inhibitors 0.73 ± 0.01 and for nucleoside RT inhibitors 0.84 ± 0.01. We have demonstrated in several case studies that GTM-based resistance landscapes are useful for visualization and analysis of sequence space as well as for treatment optimization purposes. Here, GTMs were applied for the in-depth analysis of the relationships between mutation pattern and drug resistance using mutation landscapes. This allowed us to predict retrospectively the importance of the presence of particular mutations (e.g. V32I, L10F and L33F in HIV PR) for the resistance development. This study highlights some perspectives of GTM applications in clinical informatics and particularly in the field of sequence space exploration. AVAILABILITY AND IMPLEMENTATION: https://github.com/karinapikalyova/ISIDASeq. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Infecções por HIV , HIV-1 , Humanos , HIV-1/genética , HIV-1/metabolismo , Sequência de Aminoácidos , Infecções por HIV/tratamento farmacológico , Estudos Retrospectivos , Transcriptase Reversa do HIV/química , Transcriptase Reversa do HIV/genética , Transcriptase Reversa do HIV/metabolismo , Mutação , Protease de HIV/genética , Protease de HIV/metabolismo , Resistência a Medicamentos , Farmacorresistência Viral/genética , GenótipoRESUMO
BACKGROUND: Antenatal/early postnatal hypothyroidism weakens NO-mediated anticontractile influence of endothelium in coronary arteries of adult rats, but it remains unclear whether this occurs in other vascular regions. We hypothesized that developmental thyroid deficiency is followed by region-specific changes in the endothelial NO-pathway activity in systemic vasculature. To explore this, we estimated the effects of antenatal/early postnatal hypothyroidism on NO-pathway activity and its potential local control mechanisms in rat mesenteric and skeletal muscle (sural) arteries. METHODS: Dams were treated with 6-propyl-2-thiouracil (PTU) in drinking water (0.0007%) during pregnancy and 2 weeks postpartum; control (CON) females received PTU-free water. Adult offspring (10-12-weeks) arteries were studied by wire myography, qPCR, and Western blotting. RESULTS: Endothelium removal or inhibition of NO-synthase with L-NNA augmented contractile responses to α1-adrenoceptor agonist methoxamine. In PTU compared to CON group, these effects were stronger in sural arteries, but did not differ in mesenteric arteries. The responses of both arteries to NO-donor DEA/NO were similar in CON and PTU rats. mRNA contents of deiodinase 2 and thyroid hormone receptor α were similar in mesenteric arteries of two groups but were elevated in sural arteries of PTU group compared to CON. The abundance of eNOS protein was higher in sural arteries of PTU compared to CON rats. CONCLUSION: Antenatal/early postnatal hypothyroidism is followed by an increase in NO-mediated anticontractile influence in sural, but not in mesenteric arteries of adult animals. The diversity of hypothyroidism effects may be due to different alterations of local T3 synthesis/reception in different vascular beds.