DIGEP-Pred 2.0: A web application for predicting drug-induced cell signaling and gene expression changes.

The analysis of drug-induced gene expression profiles (DIGEP) is widely used to estimate the potential therapeutic and adverse drug effects as well as the molecular mechanisms of drug action. However, the corresponding experimental data is absent for many existing drugs and drug-like compounds. To solve this problem, we created the DIGEP-Pred 2.0 web application, which allows predicting DIGEP and potential drug targets by structural formula of drug-like compounds. It is based on the combined use of structure-activity relationships (SARs) and network analysis. SAR models were created using PASS (Prediction of Activity Spectra for Substances) technology for data from the Comparative Toxicogenomics Database (CTD), the Connectivity Map (CMap) for the prediction of DIGEP, and PubChem and ChEMBL for the prediction of molecular mechanisms of action (MoA). Using only the structural formula of a compound, the user can obtain information on potential gene expression changes in several cell lines and drug targets, which are potential master regulators responsible for the observed DIGEP. The mean accuracy of prediction calculated by leave-one-out cross validation was 86.5 % for 13377 genes and 94.8 % for 2932 proteins (CTD data), and it was 97.9 % for 2170 MoAs. SAR models (mean accuracy-87.5 %) were also created for CMap data given on MCF7, PC3, and HL60 cell lines with different threshold values for the logarithm of fold changes: 0.5, 0.7, 1, 1.5, and 2. Additionally, the data on pathways (KEGG, Reactome), biological processes of Gene Ontology, and diseases (DisGeNet) enriched by the predicted genes, together with the estimation of target-master regulators based on OmniPath data, is also provided. DIGEP-Pred 2.0 web application is freely available at https://www.way2drug.com/digep-pred.

MetaTox 2.0: Estimating the Biological Activity Spectra of Drug-like Compounds Taking into Account Probable Biotransformations.

After the biotransformation of xenobiotics in the human body, the biological activity of the metabolites may differ from the activity of parent compounds. Therefore, to assess the overall biological activity of a drug-like compound, it is important to take into account its metabolites and their biological activity. We developed MetaTox 2.0-an updated version of the MetaTox web application that was able to predict the metabolites of xenobiotics. Innovations include estimating the biological activity profile of a compound and taking into account its metabolites. The estimation is based on the PASS (prediction of activity spectra for substances) algorithm and on the latest version of the training set covering over 1900 biological activities predicted with an average accuracy exceeding 0.97. Also, MetaTox 2.0 allows the search for similar substances among more than 2000 drugs with known metabolic networks, which were extracted from the ChEMBL, MetXBIODB, and DrugBank databases. MetaTox 2.0 is freely available on the web at https://www.way2drug.com/metatox.

HGMMX: Host Gut Microbiota Metabolism Xenobiotics Database.

The metagenome of bacteria colonizing the human intestine is a set of genes that is almost 150 times greater than the set of host genes. Some of these genes encode enzymes whose functioning significantly expands the number of potential pathways for xenobiotic metabolism. The resulting metabolites can exhibit activity different from that of the parent compound. This can decrease the efficacy of pharmacotherapy as well as induce undesirable and potentially life-threatening side effects. Thus, analysis of the biotransformation of small drug-like compounds mediated by the gut microbiota is an important step in the development of new pharmaceutical agents and repurposing of the approved drugs. In vitro research, the interaction of drug-like compounds with the gut microbiota is a multistep and time-consuming process. Systematic testing of large sets of chemical structures is associated with a number of challenges, including the lack of standardized techniques and significant financial costs to identify the structure of the final metabolites. Estimation of the compounds' ability to be biotransformed by the gut microbiota and prediction of the structures of their metabolites are possible in silico. However, the development of computational approaches is limited by the lack of information about chemical structures metabolized by microbiota enzymes. The aim of this study is to create a database containing information on the metabolism of drug-like compounds by the gut microbiota. We created the data set containing information about 368 structures metabolized and 310 structures not metabolized by the human gut microbiota. The HGMMX database is freely available at https://www.way2drug.com/hgmmx. The information presented will be useful in the development of computational approaches for analyzing the impact of the human microbiota on metabolism of drug-like molecules.

TCR-Pred: A new web-application for prediction of epitope and MHC specificity for CDR3 TCR sequences using molecular fragment descriptors.

The search for the relationships between CDR3 TCR sequences and epitopes or MHC types is a challenging task in modern immunology. We propose a new approach to develop the classification models of structure-activity relationships (SAR) using molecular fragment descriptors MNA (Multilevel Neighbourhoods of Atoms) to represent CDR3 TCR sequences and the naïve Bayes classifier algorithm. We have created the freely available TCR-Pred web application (http://way2drug.com/TCR-pred/) to predict the interactions between α chain CDR3 TCR sequences and 116 epitopes or 25 MHC types, as well as the interactions between ß chain CDR3 TCR sequences and 202 epitopes or 28 MHC types. The TCR-Pred web application is based on the data (more 250 000 unique CDR3 TCR sequences) from VDJdb, McPAS-TCR, and IEDB databases and the proposed approach. The average AUC values of the prediction accuracy calculated using a 20-fold cross-validation procedure varies from 0.857 to 0.884. The created web application may be useful in studies related with T-cell profiling based on CDR3 TCR sequences.

SAV-Pred: A Freely Available Web Application for the Prediction of Pathogenic Amino Acid Substitutions for Monogenic Hereditary Diseases Studied in Newborn Screening.

Next Generation Sequencing (NGS) technologies are rapidly entering clinical practice. A promising area for their use lies in the field of newborn screening. The mass screening of newborns using NGS technology leads to the discovery of a large number of new missense variants that need to be assessed for association with the development of hereditary diseases. Currently, the primary analysis and identification of pathogenic variations is carried out using bioinformatic tools. Although extensive efforts have been made in the computational approach to variant interpretation, there is currently no generally accepted pathogenicity predictor. In this study, we used the sequence-structure-property relationships (SSPR) approach, based on the representation of protein fragments by molecular structural formula. The approach predicts the pathogenic effect of single amino acid substitutions in proteins related with twenty-five monogenic heritable diseases from the Uniform Screening Panel for Major Conditions recommended by the Advisory Committee on Hereditary Disorders in Newborns and Children. In order to create SSPR models of classification, we modified a piece of cheminformatics software, MultiPASS, that was originally developed for the prediction of activity spectra for drug-like substances. The created SSPR models were compared with traditional bioinformatic tools (SIFT 4G, Polyphen-2 HDIV, MutationAssessor, PROVEAN and FATHMM). The average AUC of our approach was 0.804 ± 0.040. Better quality scores were achieved for 15 from 25 proteins with a significantly higher accuracy for some proteins (IVD, HADHB, HBB). The best SSPR models of classification are freely available in the online resource SAV-Pred (Single Amino acid Variants Predictor).

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.

RHIVDB: A Freely Accessible Database of HIV Amino Acid Sequences and Clinical Data of Infected Patients.

Human immunodeficiency virus (HIV) infection remains one of the most severe problems for humanity, particularly due to the development of HIV resistance. To evaluate an association between viral sequence data and drug combinations and to estimate an effect of a particular drug combination on the treatment results, collection of the most representative drug combinations used to cure HIV and the biological data on amino acid sequences of HIV proteins is essential. We have created a new, freely available web database containing 1,651 amino acid sequences of HIV structural proteins [reverse transcriptase (RT), protease (PR), integrase (IN), and envelope protein (ENV)], treatment history information, and CD4+ cell count and viral load data available by the user's query. Additionally, the biological data on new HIV sequences and treatment data can be stored in the database by any user followed by an expert's verification. The database is available on the web at http://www.way2drug.com/rhivdb.

MetaPASS: A Web Application for Analyzing the Biological Activity Spectrum of Organic Compounds Taking into Account their Biotransformation.

Most drug-like compounds can interact with several pharmacological targets and exhibit complex biological activity spectra. Analysis of these spectra helps find and optimize new pharmaceutical agents or identify new uses for approved and investigational drugs (drug repurposing). Since most pharmaceuticals usually undergo biotransformation in the human body, it is reasonable during drug discovery to take into account biological activity spectra of metabolites. A new freely available MetaPASS web application (http://www.way2drug.com/metapass) has been developed for analyzing the probable biological activity spectra of drug-like organic compounds taking into account their metabolites - integrated activity profile. To obtain an integrated biological activity profile, one can create a biotransformation network for any compound or analyze known networks for more than 950 compounds from ChEBML and DrugBank. Biological activity profile prediction is based on the PASS Refined software that predicts 1,333 biological activities with an average accuracy (IAP, calculated by leave-one-out cross-validation procedure) exceeded 0.97.

AntiHIV-Pred: web-resource for in silico prediction of anti-HIV/AIDS activity.

MOTIVATION: Identification of new molecules promising for treatment of HIV-infection and HIV-associated disorders remains an important task in order to provide safer and more effective therapies. Utilization of prior knowledge by application of computer-aided drug discovery approaches reduces time and financial expenses and increases the chances of positive results in anti-HIV R&D. To provide the scientific community with a tool that allows estimating of potential agents for treatment of HIV-infection and its comorbidities, we have created a freely-available web-resource for prediction of relevant biological activities based on the structural formulae of drug-like molecules. RESULTS: Over 50 000 experimental records for anti-retroviral agents from ChEMBL database were extracted for creating the training sets. After careful examination, about seven thousand molecules inhibiting five HIV-1 proteins were used to develop regression and classification models with the GUSAR software. The average values of R2 = 0.95 and Q2 = 0.72 in validation procedure demonstrated the reasonable accuracy and predictivity of the obtained (Q)SAR models. Prediction of 81 biological activities associated with the treatment of HIV-associated comorbidities with 92% mean accuracy was realized using the PASS program. AVAILABILITY AND IMPLEMENTATION: Freely available on the web at http://www.way2drug.com/hiv/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

AntiBac-Pred: A Web Application for Predicting Antibacterial Activity of Chemical Compounds.

Discovery of new antibacterial agents is a never-ending task of medicinal chemistry. Every new drug brings significant improvement to patients with bacterial infections, but prolonged usage of antibacterials leads to the emergence of resistant strains. Therefore, novel active structures with new modes of action are required. We describe a web application called AntiBac-Pred aimed to help users in the rational selection of the chemical compounds for experimental studies of antibacterial activity. This application is developed using antibacterial activity data available in ChEMBL and PASS software. It allows users to classify chemical structures of interest into growth inhibitors or noninhibitors of 353 different bacteria strains, including both resistant and nonresistant ones.

Prediction of Drug-Drug Interactions Related to Inhibition or Induction of Drug-Metabolizing Enzymes.

Drug-drug interaction (DDI) is the phenomenon of alteration of the pharmacological activity of a drug(s) when another drug(s) is co-administered in cases of so-called polypharmacy. There are three types of DDIs: pharmacokinetic (PK), pharmacodynamic, and pharmaceutical. PK is the most frequent type of DDI, which often appears as a result of the inhibition or induction of drug-metabolising enzymes (DME). In this review, we summarise in silico methods that may be applied for the prediction of the inhibition or induction of DMEs and describe appropriate computational methods for DDI prediction, showing the current situation and perspectives of these approaches in medicinal and pharmaceutical chemistry. We review sources of information on DDI, which can be used in pharmaceutical investigations and medicinal practice and/or for the creation of computational models. The problem of the inaccuracy and redundancy of these data are discussed. We provide information on the state-of-the-art physiologically- based pharmacokinetic modelling (PBPK) approaches and DME-based in silico methods. In the section on ligand-based methods, we describe pharmacophore models, molecular field analysis, quantitative structure-activity relationships (QSAR), and similarity analysis applied to the prediction of DDI related to the inhibition or induction of DME. In conclusion, we discuss the problems of DDI severity assessment, mention factors that influence severity, and highlight the issues, perspectives and practical using of in silico methods.

How to Achieve Better Results Using PASS-Based Virtual Screening: Case Study for Kinase Inhibitors.

Discovery of new pharmaceutical substances is currently boosted by the possibility of utilization of the Synthetically Accessible Virtual Inventory (SAVI) library, which includes about 283 million molecules, each annotated with a proposed synthetic one-step route from commercially available starting materials. The SAVI database is well-suited for ligand-based methods of virtual screening to select molecules for experimental testing. In this study, we compare the performance of three approaches for the analysis of structure-activity relationships that differ in their criteria for selecting of "active" and "inactive" compounds included in the training sets. PASS (Prediction of Activity Spectra for Substances), which is based on a modified Naïve Bayes algorithm, was applied since it had been shown to be robust and to provide good predictions of many biological activities based on just the structural formula of a compound even if the information in the training set is incomplete. We used different subsets of kinase inhibitors for this case study because many data are currently available on this important class of drug-like molecules. Based on the subsets of kinase inhibitors extracted from the ChEMBL 20 database we performed the PASS training, and then applied the model to ChEMBL 23 compounds not yet present in ChEMBL 20 to identify novel kinase inhibitors. As one may expect, the best prediction accuracy was obtained if only the experimentally confirmed active and inactive compounds for distinct kinases in the training procedure were used. However, for some kinases, reasonable results were obtained even if we used merged training sets, in which we designated as inactives the compounds not tested against the particular kinase. Thus, depending on the availability of data for a particular biological activity, one may choose the first or the second approach for creating ligand-based computational tools to achieve the best possible results in virtual screening.

Which cytochrome P450 metabolizes phenazepam? Step by step in silico, in vitro, and in vivo studies.

BACKGROUND: Phenazepam (bromdihydrochlorphenylbenzodiazepine) is the original Russian benzodiazepine tranquilizer belonging to 1,4-benzodiazepines. There is still limited knowledge about phenazepam's metabolic liver pathways and other pharmacokinetic features. METHODS: To determine phenazepam's metabolic pathways, the study was divided into three stages: in silico modeling, in vitro experiment (cell culture study), and in vivo confirmation. In silico modeling was performed on the specialized software PASS and GUSAR to evaluate phenazepam molecule affinity to different cytochromes. The in vitro study was performed using a hepatocytes' cell culture, cultivated in a microbioreactor to produce cytochrome P450 isoenzymes. The culture medium contained specific cytochrome P450 isoforms inhibitors and substrates (for CYP2C9, CYP3A4, CYP2C19, and CYP2B6) to determine the cytochrome that was responsible for phenazepam's metabolism. We also measured CYP3A activity using the 6-betahydroxycortisol/cortisol ratio in patients. RESULTS: According to in silico and in vitro analysis results, the most probable metabolizer of phenazepam is CYP3A4. By the in vivo study results, CYP3A activity decreased sufficiently (from 3.8 [95% CI: 2.94-4.65] to 2.79 [95% CI: 2.02-3.55], p=0.017) between the start and finish of treatment in patients who were prescribed just phenazepam. CONCLUSIONS: Experimental in silico and in vivo studies confirmed that the original Russian benzodiazepine phenazepam was the substrate of CYP3A4 isoenzyme.

CLC-Pred: A freely available web-service for in silico prediction of human cell line cytotoxicity for drug-like compounds.

In silico methods of phenotypic screening are necessary to reduce the time and cost of the experimental in vivo screening of anticancer agents through dozens of millions of natural and synthetic chemical compounds. We used the previously developed PASS (Prediction of Activity Spectra for Substances) algorithm to create and validate the classification SAR models for predicting the cytotoxicity of chemicals against different types of human cell lines using ChEMBL experimental data. A training set from 59,882 structures of compounds was created based on the experimental data (IG50, IC50, and % inhibition values) from ChEMBL. The average accuracy of prediction (AUC) calculated by leave-one-out and a 20-fold cross-validation procedure during the training was 0.930 and 0.927 for 278 cancer cell lines, respectively, and 0.948 and 0.947 for cytotoxicity prediction for 27 normal cell lines, respectively. Using the given SAR models, we developed a freely available web-service for cell-line cytotoxicity profile prediction (CLC-Pred: Cell-Line Cytotoxicity Predictor) based on the following structural formula: http://way2drug.com/Cell-line/.

ROSC-Pred: web-service for rodent organ-specific carcinogenicity prediction.

Motivation: Identification of rodent carcinogens is an important task in risk assessment of chemicals. SAR methods were proposed to reduce the number of animal experiments. Most of these methods ignore information about organ-specificity of tumorigenesis. Our study was aimed at the creation of classification models and a freely available online service for prediction of rodent carcinogens considering the species (rats, mice), sex and tissue-specificity from structural formula of compounds. Results: The data from Carcinogenic Potency Database for 1011 organic compounds evaluated on the standard two-year rodent carcinogenicity bioassay was used for the creation of training sets. Structure-activity relationships models for prediction of rodent organ-specific carcinogenicity were created by PASS software, which was based on Bayesian-like approach and Multilevel Neighborhoods of Atoms descriptors. The average prediction accuracy for training sets calculated by leave-one-out and 10-fold cross-validation was 79 and 78.2%, respectively. Availability and implementation: Freely available on the web at http://www.way2drug.com/ROSC. Contact: alexey.lagunin@ibmc.msk.ru. Supplementary information: Supplementary data are available at Bioinformatics online.

ADVERPred-Web Service for Prediction of Adverse Effects of Drugs.

Application of structure-activity relationships (SARs) for the prediction of adverse effects of drugs (ADEs) has been reported in many published studies. Training sets for the creation of SAR models are usually based on drug label information which allows for the generation of data sets for many hundreds of drugs. Since many ADEs may not be related to drug consumption, one of the main problems in such studies is the quality of data on drug-ADE pairs obtained from labels. The information on ADEs may be included in three sections of the drug labels: "Boxed warning," "Warnings and Precautions," and "Adverse reactions." The first two sections, especially Boxed warning, usually contain the most frequent and severe ADEs that have either known or probable relationships to drug consumption. Using this information, we have created manually curated data sets for the five most frequent and severe ADEs: myocardial infarction, arrhythmia, cardiac failure, severe hepatotoxicity, and nephrotoxicity, with more than 850 drugs on average for each effect. The corresponding SARs were built with PASS (Prediction of Activity Spectra for Substances) software and had balanced accuracy values of 0.74, 0.7, 0.77, 0.67, and 0.75, respectively. They were implemented in a freely available ADVERPred web service ( http://www.way2drug.com/adverpred/ ), which enables a user to predict five ADEs based on the structural formula of compound. This web service can be applied for estimation of the corresponding ADEs for hits and lead compounds at the early stages of drug discovery.

MetaTox: Web Application for Predicting Structure and Toxicity of Xenobiotics' Metabolites.

A new freely available web-application MetaTox ( http://www.way2drug.com/mg ) for prediction of xenobiotic's metabolism and calculation toxicity of metabolites based on the structural formula of chemicals has been developed. MetaTox predicts metabolites, which are formed by nine classes of reactions (aliphatic and aromatic hydroxylation, N- and O-glucuronidation, N-, S- and C-oxidation, and N- and O-dealkylation). The calculation of probability for generated metabolites is based on analyses of "structure-biotransformation reactions" and "structure-modified atoms" relationships using a Bayesian approach. Prediction of LD50 values is performed by GUSAR software for the parent compound and each of the generated metabolites using quantitative structure-activity relationahip (QSAR) models created for acute rat toxicity with the intravenous type of administration.

Prediction of reacting atoms for the major biotransformation reactions of organic xenobiotics.

BACKGROUND: The knowledge of drug metabolite structures is essential at the early stage of drug discovery to understand the potential liabilities and risks connected with biotransformation. The determination of the site of a molecule at which a particular metabolic reaction occurs could be used as a starting point for metabolite identification. The prediction of the site of metabolism does not always correspond to the particular atom that is modified by the enzyme but rather is often associated with a group of atoms. To overcome this problem, we propose to operate with the term "reacting atom", corresponding to a single atom in the substrate that is modified during the biotransformation reaction. The prediction of the reacting atom(s) in a molecule for the major classes of biotransformation reactions is necessary to generate drug metabolites. RESULTS: Substrates of the major human cytochromes P450 and UDP-glucuronosyltransferases from the Biovia Metabolite database were divided into nine groups according to their reaction classes, which are aliphatic and aromatic hydroxylation, N- and O-glucuronidation, N-, S- and C-oxidation, and N- and O-dealkylation. Each training set consists of positive and negative examples of structures with one labelled atom. In the positive examples, the labelled atom is the reacting atom of a particular reaction that changed adjacency. Negative examples represent non-reacting atoms of a particular reaction. We used Labelled Multilevel Neighbourhoods of Atoms descriptors for the designation of reacting atoms. A Bayesian-like algorithm was applied to estimate the structure-activity relationships. The average invariant accuracy of prediction obtained in leave-one-out and 20-fold cross-validation procedures for five human isoforms of cytochrome P450 and all isoforms of UDP-glucuronosyltransferase varies from 0.86 to 0.99 (0.96 on average). CONCLUSIONS: We report that reacting atoms may be predicted with reasonable accuracy for the major classes of metabolic reactions-aliphatic and aromatic hydroxylation, N- and O-glucuronidation, N-, S- and C-oxidation, and N- and O-dealkylation. The proposed method is implemented as a freely available web service at http://www.way2drug.com/RA and may be used for the prediction of the most probable biotransformation reaction(s) and the appropriate reacting atoms in drug-like compounds.Graphical abstract.

SOMP: web server for in silico prediction of sites of metabolism for drug-like compounds.

UNLABELLED: A new freely available web server site of metabolism predictor to predict the sites of metabolism (SOM) based on the structural formula of chemicals has been developed. It is based on the analyses of 'structure-SOM' relationships using a Bayesian approach and labelled multilevel neighbourhoods of atoms descriptors to represent the structures of over 1000 metabolized xenobiotics. The server allows predicting SOMs that are catalysed by 1A2, 2C9, 2C19, 2D6 and 3A4 isoforms of cytochrome P450 and enzymes of the UDP-glucuronosyltransferase family. The average invariant accuracy of prediction that was calculated for the training sets (using leave-one-out cross-validation) and evaluation sets is 0.9 and 0.95, respectively. AVAILABILITY AND IMPLEMENTATION: Freely available on the web at http://www.way2drug.com/SOMP.

Metabolism site prediction based on xenobiotic structural formulas and PASS prediction algorithm.

A new ligand-based method for the prediction of sites of metabolism (SOMs) for xenobiotics has been developed on the basis of the LMNA (labeled multilevel neighborhoods of atom) descriptors and the PASS (prediction of activity spectra for substances) algorithm and applied to predict the SOMs of the 1A2, 2C9, 2C19, 2D6, and 3A4 isoforms of cytochrome P450. An average IAP (invariant accuracy of prediction) of SOMs calculated by the leave-one-out cross-validation procedure was 0.89 for the developed method. The external validation was made with evaluation sets containing data on biotransformations for 57 cardiovascular drugs. An average IAP of regioselectivity for evaluation sets was 0.83. It was shown that the proposed method exceeds accuracy of SOM prediction by RS-Predictor for CYP 1A2, 2D6, 2C9, 2C19, and 3A4 and is comparable to or better than SMARTCyp for CYP 2C9 and 2D6.