SAnDReS 2.0: Development of machine-learning models to explore the scoring function space.

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.

Self-Assembly of 4,4'-Linked Dipyrromethanes from Unconventional Reactants─Propargylamines, 2-(Vinyloxy)ethyl Isothiocyanate, and Alkylating Agents under Basic Conditions.

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 (∼10-15 min, excluding alkylation time).

HIV-1 drug resistance profiling using amino acid sequence space cartography.

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.

Current Perspectives in Antiviral Research.

Studies on virus-host interactions are of high significance for a number of reasons [...].

Identification of Molecular Mechanisms Involved in Viral Infection Progression Based on Text Mining: Case Study for HIV Infection.

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.

CLC-Pred 2.0: A Freely Available Web Application for In Silico Prediction of Human Cell Line Cytotoxicity and Molecular Mechanisms of Action for Druglike Compounds.

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.

The Effects of Acidosis on eNOS in the Systemic Vasculature: A Focus on Early Postnatal Ontogenesis.

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.

Extraction of Data on Parent Compounds and Their Metabolites from Texts of Scientific Abstracts.

The growing amount of experimental data on chemical objects includes properties of small molecules, results of studies of their interaction with human and animal proteins, and methods of synthesis of organic compounds (OCs). The data obtained can be used to identify the names of OCs automatically, including all possible synonyms and relevant data on the molecular properties and biological activity. Utilization of different synonymic names of chemical compounds allows researchers to increase the completeness of data on their properties available from publications. Enrichment of the data on the names of chemical compounds by information about their possible metabolites can help estimate the biological effects of parent compounds and their metabolites more thoroughly. Therefore, an attempt at automated extraction of the names of parent compounds and their metabolites from the texts is a rather important task. In our study, we aimed at developing a method that provides the extraction of the named entities (NEs) of parent compounds and their metabolites from abstracts of scientific publications. Based on the application of the conditional random fields' algorithm, we extracted the NEs of chemical compounds. We developed a set of rules allowing identification of parent compound NEs and their metabolites in the texts. We evaluated the possibility of extracting the names of potential metabolites based on cosine similarity between strings representing names of parent compounds and all other chemical NEs found in the text. Additionally, we used conditional random fields to fetch the names of parent compounds and their metabolites from the texts based on the corpus of texts labeled manually. Our computational experiments showed that usage of rules in combination with cosine similarity could increase the accuracy of recognition of the names of metabolites compared to the rule-based algorithm and application of a machine-learning algorithm (conditional random fields).

The Cyclicity of coronavirus cases: "Waves" and the "weekend effect".

INTRODUCTION: Medical statistics is one of the "milestones" of current medical systems. It is the foundation for many protocols, including medical care systems, government recommendations, epidemic planning, etc. At this time of global COVID-19, credible data on epidemic spread can help governments make better decisions. This study's aim is to evaluate the cyclicity in the number of daily diagnosed coronavirus patients, thus allowing governments to plan how to allocate their resources more effectively. METHODS: To assess this cycle, we consider the time series of the first and second differences in the number of registered patients in different countries. The spectral densities of the time series are calculated, and the frequencies and amplitudes of the maximum spectral peaks are estimated. RESULTS: It is shown that two types of cycles can be distinguished in the time series of the case numbers. Cyclical fluctuations of the first type are characterized by periods from 100 to 300 days. Cyclical fluctuations of the second type are characterized by a period of about seven days. For different countries, the phases of the seven-day fluctuations coincide. It is assumed that cyclical fluctuations of the second type are associated with the weekly cycle of population activity. CONCLUSIONS: These characteristics of cyclical fluctuations in cases can be used to predict the incidence rate.

Remodeling of Arterial Tone Regulation in Postnatal Development: Focus on Smooth Muscle Cell Potassium Channels.

Maturation of the cardiovascular system is associated with crucial structural and functional remodeling. Thickening of the arterial wall, maturation of the sympathetic innervation, and switching of the mechanisms of arterial contraction from calcium-independent to calcium-dependent occur during postnatal development. All these processes promote an almost doubling of blood pressure from the moment of birth to reaching adulthood. This review focuses on the developmental alterations of potassium channels functioning as key smooth muscle membrane potential determinants and, consequently, vascular tone regulators. We present evidence that the pattern of potassium channel contribution to vascular control changes from Kir2, Kv1, Kv7 and TASK-1 channels to BKCa channels with maturation. The differences in the contribution of potassium channels to vasomotor tone at different stages of postnatal life should be considered in treatment strategies of cardiovascular diseases associated with potassium channel malfunction.

MAPKs Are Highly Abundant but Do Not Contribute to α1-Adrenergic Contraction of Rat Saphenous Arteries in the Early Postnatal Period.

Previously, the abundance of p42/44 and p38 MAPK proteins had been shown to be higher in arteries of 1- to 2-week-old compared to 2- to 3-month-old rats. However, the role of MAPKs in vascular tone regulation in early ontogenesis remains largely unexplored. We tested the hypothesis that the contribution of p42/44 and p38 MAPKs to the contraction of peripheral arteries is higher in the early postnatal period compared to adulthood. Saphenous arteries of 1- to 2-week-old and 2- to 3-month-old rats were studied using wire myography and western blotting. The α1-adrenoceptor agonist methoxamine did not increase the phosphorylation level of p38 MAPK in either 1- to 2-week-old or 2- to 3-month-old rats. Accordingly, inhibition of p38 MAPK did not affect arterial contraction to methoxamine in either age group. Methoxamine increased the phosphorylation level of p42/44 MAPKs in arteries of 2- to 3-month-old and of p44 MAPK in 1- to 2-week-old rats. Inhibition of p42/44 MAPKs reduced methoxamine-induced contractions in arteries of 2- to 3-month-old, but not 1- to 2-week-old rats. Thus, despite a high abundance in arterial tissue, p38 and p42/44 MAPKs do not regulate contraction of the saphenous artery in the early postnatal period. However, p42/44 MAPK activity contributes to arterial contractions in adult rats.

Intrauterine Nitric Oxide Deficiency Weakens Differentiation of Vascular Smooth Muscle in Newborn Rats.

Nitric oxide (NO) deficiency during pregnancy is a key reason for preeclampsia development. Besides its important vasomotor role, NO is shown to regulate the cell transcriptome. However, the role of NO in transcriptional regulation of developing smooth muscle has never been studied before. We hypothesized that in early ontogeny, NO is important for the regulation of arterial smooth muscle-specific genes expression. Pregnant rats consumed NO-synthase inhibitor L-NAME (500 mg/L in drinking water) from gestational day 10 till delivery, which led to an increase in blood pressure, a key manifestation of preeclampsia. L-NAME reduced blood concentrations of NO metabolites in dams and their newborn pups, as well as relaxations of pup aortic rings to acetylcholine. Using qPCR, we demonstrated reduced abundances of the smooth muscle-specific myosin heavy chain isoform, α-actin, SM22α, and L-type Ca2+-channel mRNAs in the aorta of newborn pups from the L-NAME group compared to control pups. To conclude, the intrauterine NO deficiency weakens gene expression specific for a contractile phenotype of arterial smooth muscle in newborn offspring.

Pannexin 1 Transgenic Mice: Human Diseases and Sleep-Wake Function Revision.

In humans and other vertebrates pannexin protein family was discovered by homology to invertebrate gap junction proteins. Several biological functions were attributed to three vertebrate pannexins members. Six clinically significant independent variants of the PANX1 gene lead to human infertility and oocyte development defects, and the Arg217His variant was associated with pronounced symptoms of primary ovarian failure, severe intellectual disability, sensorineural hearing loss, and kyphosis. At the same time, only mild phenotypes were observed in Panx1 knockout mice. In addition, a passenger mutation was identified in a popular line of Panx1 knockout mice, questioning even those effects. Using CRISPR/Cas9, we created a new line of Panx1 knockout mice and a new line of mice with the clinically significant Panx1 substitution (Arg217His). In both cases, we observed no significant changes in mouse size, weight, or fertility. In addition, we attempted to reproduce a previous study on sleep/wake and locomotor activity functions in Panx1 knockout mice and found that previously reported effects were probably not caused by the Panx1 knockout itself. We consider that the pathological role of Arg217His substitution in Panx1, and some Panx1 functions in general calls for a re-evaluation.

Intrauterine L-NAME Exposure Weakens the Development of Sympathetic Innervation and Induces the Remodeling of Arterial Vessels in Two-Week-Old Rats.

Nitric oxide (NO) has been shown to stimulate differentiation and increase the survival of ganglionic sympathetic neurons. The proportion of neuronal NOS-immunoreactive sympathetic preganglionic neurons is particularly high in newborn rats and decreases with maturation. However, the role of NO in the development of vascular sympathetic innervation has never been studied before. We tested the hypothesis that intrauterine NO deficiency weakened the development of vascular sympathetic innervation and thereby changed the contractility of peripheral arteries and blood pressure level in two-week-old offspring. Pregnant rats consumed NOS inhibitor L-NAME (250 mg/L in drinking water) from gestational day 10 until delivery. Pups in the L-NAME group had a reduced body weight and blood level of NO metabolites at 1-2 postnatal days. Saphenous arteries from two-week-old L-NAME offspring demonstrated a lower density of sympathetic innervation, a smaller inner diameter, reduced maximal active force and decreased α-actin/ß-actin mRNA expression ratio compared to the controls. Importantly, pups in the L-NAME group exhibited decreased blood pressure levels before, but not after, ganglionic blockade with chlorisondamine. In conclusion, intrauterine L-NAME exposure is followed by the impaired development of the sympathetic nervous system in early postnatal life, which is accompanied by the structural and functional remodeling of arterial blood vessels.

A Computational Approach for the Prediction of Treatment History and the Effectiveness or Failure of Antiretroviral Therapy.

Human Immunodeficiency Virus Type 1 (HIV-1) infection is associated with high mortality if no therapy is provided. Currently, the treatment of an HIV-1 positive patient requires that several drugs should be taken simultaneously. The resistance of the virus to an antiretroviral drug may lead to treatment failure. Our approach focuses on predicting the exposure of a particular viral variant to an antiretroviral drug or drug combination. It also aims at the prediction of drug treatment success or failure. We utilized nucleotide sequences of HIV-1 encoding protease and reverse transcriptase to perform such types of prediction. The PASS (Prediction of Activity Spectra for Substances) algorithm based on the naive Bayesian classifier was used to make a prediction. We calculated the probability of whether a sequence belonged (P1) or did not belong (P0) to the class associated with exposure of the viral sequence to the set of drugs that can be associated with resistance to the set of drugs. The accuracy calculated as the average Area Under the ROC (Receiver Operating Characteristic) Curve (AUC/ROC) for classifying exposure of the sequence to the HIV-1 protease inhibitors was 0.81 (±0.07), and for HIV-1 reverse transcriptase, it was 0.83 (±0.07). To predict cases of treatment effectiveness or failure, we used P1 and P0 values, obtained in PASS, along with the binary vector constructed based on short nucleotide descriptors and the applied random forest classifier. Average AUC/ROC prediction accuracy for the prediction of treatment effectiveness or failure for the combinations of HIV-1 protease inhibitors was 0.82 (±0.06) and of HIV-1 reverse transcriptase was 0.76 (±0.09).

Data and Text Mining Help Identify Key Proteins Involved in the Molecular Mechanisms Shared by SARS-CoV-2 and HIV-1.

Viruses can be spread from one person to another; therefore, they may cause disorders in many people, sometimes leading to epidemics and even pandemics. New, previously unstudied viruses and some specific mutant or recombinant variants of known viruses constantly appear. An example is a variant of coronaviruses (CoV) causing severe acute respiratory syndrome (SARS), named SARS-CoV-2. Some antiviral drugs, such as remdesivir as well as antiretroviral drugs including darunavir, lopinavir, and ritonavir are suggested to be effective in treating disorders caused by SARS-CoV-2. There are data on the utilization of antiretroviral drugs against SARS-CoV-2. Since there are many studies aimed at the identification of the molecular mechanisms of human immunodeficiency virus type 1 (HIV-1) infection and the development of novel therapeutic approaches against HIV-1, we used HIV-1 for our case study to identify possible molecular pathways shared by SARS-CoV-2 and HIV-1. We applied a text and data mining workflow and identified a list of 46 targets, which can be essential for the development of infections caused by SARS-CoV-2 and HIV-1. We show that SARS-CoV-2 and HIV-1 share some molecular pathways involved in inflammation, immune response, cell cycle regulation.

Pro-contractile role of chloride in arterial smooth muscle: Postnatal decline potentially governed by sympathetic nerves.

NEW FINDINGS: What is the topic of this review? This symposium report discusses the previously unrecognized pro-contractile role of chloride ions in rat arteries at early stages of postnatal development. What advances does it highlight? It highlights the postnatal decline in the contribution of chloride ions to regulation of arterial contractile responses and potential trophic role of sympathetic nerves in these developmental alterations. ABSTRACT: Chloride ions are important for smooth muscle contraction in adult vasculature. Arterial smooth muscle undergoes structural and functional remodelling during early postnatal development, including changes in K+ currents, Ca2+ handling and sensitivity. However, developmental change in the contribution of Cl- to regulation of arterial contraction has not yet been explored. Here, we provide the first evidence that the role of Cl- in α1 -adrenergic arterial contraction prominently decreases during early postnatal ontogenesis. The trophic influence of sympathetic nerves is a potential mechanism for postnatal decline of the contribution of Cl- to the vascular contraction.

Data Mining Approach for Extraction of Useful Information About Biologically Active Compounds from Publications.

A lot of high quality data on the biological activity of chemical compounds are required throughout the whole drug discovery process: from development of computational models of the structure-activity relationship to experimental testing of lead compounds and their validation in clinics. Currently, a large amount of such data is available from databases, scientific publications, and patents. Biological data are characterized by incompleteness, uncertainty, and low reproducibility. Despite the existence of free and commercially available databases of biological activities of compounds, they usually lack unambiguous information about peculiarities of biological assays. On the other hand, scientific papers are the primary source of new data disclosed to the scientific community for the first time. In this study, we have developed and validated a data-mining approach for extraction of text fragments containing description of bioassays. We have used this approach to evaluate compounds and their biological activity reported in scientific publications. We have found that categorization of papers into relevant and irrelevant may be performed based on the machine-learning analysis of the abstracts. Text fragments extracted from the full texts of publications allow their further partitioning into several classes according to the peculiarities of bioassays. We demonstrate the applicability of our approach to the comparison of the endpoint values of biological activity and cytotoxicity of reference compounds.

Changes in Endothelial Nitric Oxide Production in Systemic Vessels during Early Ontogenesis-A Key Mechanism for the Perinatal Adaptation of the Circulatory System.

Nitric oxide (NO) produced in the wall of blood vessels is necessary for the regulation of vascular tone to ensure an adequate blood supply of organs and tissues. In this review, we present evidence that the functioning of endothelial NO-synthase (eNOS) changes considerably during postnatal maturation. Alterations in NO-ergic vasoregulation in early ontogeny vary between vascular beds and correlate with the functional reorganization of a particular organ. Importantly, the anticontractile effect of NO can be an important mechanism responsible for the protectively low blood pressure in the immature circulatory system. The activity of eNOS is regulated by a number of hormones, including thyroid hormones which are key regulators of the perinatal developmental processes. Maternal thyroid hormone deficiency suppresses the anticontractile effect of NO at perinatal age. Such alterations disturb perinatal cardiovascular homeostasis and lead to delayed occurring cardiovascular pathologies in adulthood. The newly discovered role of thyroid hormones may have broad implications in cardiovascular medicine, considering the extremely high prevalence of maternal hypothyroidism in human society.

Antenatal/early postnatal hypothyroidism increases the contribution of Rho-kinase to contractile responses of mesenteric and skeletal muscle arteries in adult rats.

BACKGROUND: Maternal thyroid deficiency can increase Rho-kinase procontractile influence in arteries of 2-week-old progeny. Here we hypothesized that augmented role of Rho-kinase persists in arteries from adult progeny of hypothyroid rats. 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. At the age of 10-12-weeks, serum T3/T4 levels did not differ between PTU and CON male offspring. Cutaneous (saphenous), mesenteric, and skeletal muscle (sural) arteries were studied by wire myography, qPCR, and Western blotting. RESULTS: Saphenous arteries of PTU and CON groups showed similar responses to α1-adrenoceptor agonist methoxamine and were equally suppressed by Rho-kinase inhibitor Y27632. Responses of mesenteric arteries also did not differ between PTU and CON, but the effects of Y27632 were more prominent in the PTU group. Sural arteries of PTU rats compared to CON demonstrated augmented responses to methoxamine, increased RhoA mRNA contents and higher levels of MYPT1 phosphorylation at Thr855. Intergroup differences in contractile responses and phospho-MYPT1-Thr855 were eliminated by Y27632. CONCLUSION: Rho-kinase contribution to contractile responses of mesenteric and especially sural arteries is augmented in adult PTU rats. Therefore, maternal thyroid deficiency may have long-term detrimental consequences for vasculature in adult offspring.