3
|
Poroikov VV. [Computer-aided drug design: from discovery of novel pharmaceutical agents to systems pharmacology]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2020; 66:30-41. [PMID: 32116224 DOI: 10.18097/pbmc20206601030] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
New drug discovery is based on the analysis of public information about the mechanisms of the disease, molecular targets, and ligands, which interaction with the target could lead to the normalization of the pathological process. The available data on diseases, drugs, pharmacological effects, molecular targets, and drug-like substances, taking into account the combinatorics of the associative relations between them, correspond to the Big Data. To analyze such data, the application of computer-aided drug design methods is necessary. An overview of the studies in this area performed by the Laboratory for Structure-Function Based Drug Design of IBMC is presented. We have developed the approaches to identifying promising pharmacological targets, predicting several thousand types of biological activity based on the structural formula of the compound, analyzing protein-ligand interactions based on assessing local similarity of amino acid sequences, identifying likely molecular mechanisms of side effects of drugs, calculating the integral toxicity of drugs taking into account their metabolism, have been developed in the human body, predicting sustainable and sensitive options strains and evaluating the effectiveness of combinations of antiretroviral drugs in patients, taking into account the molecular genetic characteristics of the clinical isolates of HIV-1. Our computer programs are implemented as the web-services freely available on the Internet, which are used by thousands of researchers from many countries of the world to select the most promising substances for the synthesis and determine the priority areas for experimental testing of their biological activity.
Collapse
Affiliation(s)
- V V Poroikov
- Institute of Biomedical Chemistry, Moscow, Russia
| |
Collapse
|
5
|
Morenikeji OB, Thomas BN. In silico analyses of CD14 molecule reveal significant evolutionary diversity, potentially associated with speciation and variable immune response in mammals. PeerJ 2019; 7:e7325. [PMID: 31338263 PMCID: PMC6628885 DOI: 10.7717/peerj.7325] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 06/19/2019] [Indexed: 12/23/2022] Open
Abstract
The cluster differentiation gene (CD14) is a family of monocyte differentiating genes that works in conjunction with lipopolysaccharide binding protein, forming a complex with TLR4 or LY96 to mediate innate immune response to pathogens. In this paper, we used different computational methods to elucidate the evolution of CD14 gene coding region in 14 mammalian species. Our analyses identified leucine-rich repeats as the only significant domain across the CD14 protein of the 14 species, presenting with frequencies ranging from one to four. Importantly, we found signal peptides located at mutational hotspots demonstrating that this gene is conserved across these species. Out of the 10 selected variants analyzed in this study, only six were predicted to possess significant deleterious effect. Our predicted protein interactome showed a significant varying protein–protein interaction with CD14 protein across the species. This may be important for drug target and therapeutic manipulation for the treatment of many diseases. We conclude that these results contribute to our understanding of the CD14 molecular evolution, which underlays varying species response to complex disease traits.
Collapse
Affiliation(s)
| | - Bolaji N Thomas
- Department of Biomedical Sciences, Rochester Institute of Technology, Rochester, NY, USA
| |
Collapse
|
6
|
Ivanov S, Semin M, Lagunin A, Filimonov D, Poroikov V. In Silico Identification of Proteins Associated with Drug-induced Liver Injury Based on the Prediction of Drug-target Interactions. Mol Inform 2017; 36. [PMID: 28145637 DOI: 10.1002/minf.201600142] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 01/16/2017] [Indexed: 12/13/2022]
Abstract
Drug-induced liver injury (DILI) is the leading cause of acute liver failure as well as one of the major reasons for drug withdrawal from clinical trials and the market. Elucidation of molecular interactions associated with DILI may help to detect potentially hazardous pharmacological agents at the early stages of drug development. The purpose of our study is to investigate which interactions with specific human protein targets may cause DILI. Prediction of interactions with 1534 human proteins was performed for the dataset with information about 699 drugs, which were divided into three categories of DILI: severe (178 drugs), moderate (310 drugs) and without DILI (211 drugs). Based on the comparison of drug-target interactions predicted for different drugs' categories and interpretation of those results using clustering, Gene Ontology, pathway and gene expression analysis, we identified 61 protein targets associated with DILI. Most of the revealed proteins were linked with hepatocytes' death caused by disruption of vital cellular processes, as well as the emergence of inflammation in the liver. It was found that interaction of a drug with the identified targets is the essential molecular mechanism of the severe DILI for the most of the considered pharmaceuticals. Thus, pharmaceutical agents interacting with many of the identified targets may be considered as candidates for filtering out at the early stages of drug research.
Collapse
Affiliation(s)
- Sergey Ivanov
- Institute of Biomedical Chemistry 10 building 8, Pogodinskaya str., 119121, Moscow, Russia.,Pirogov Russian National Research Medical University, Medico-Biological Faculty 1, Ostrovitianova str., 117997, Moscow, Russia
| | - Maxim Semin
- Institute of Biomedical Chemistry 10 building 8, Pogodinskaya str., 119121, Moscow, Russia.,Pirogov Russian National Research Medical University, Medico-Biological Faculty 1, Ostrovitianova str., 117997, Moscow, Russia
| | - Alexey Lagunin
- Institute of Biomedical Chemistry 10 building 8, Pogodinskaya str., 119121, Moscow, Russia.,Pirogov Russian National Research Medical University, Medico-Biological Faculty 1, Ostrovitianova str., 117997, Moscow, Russia
| | - Dmitry Filimonov
- Institute of Biomedical Chemistry 10 building 8, Pogodinskaya str., 119121, Moscow, Russia
| | - Vladimir Poroikov
- Institute of Biomedical Chemistry 10 building 8, Pogodinskaya str., 119121, Moscow, Russia
| |
Collapse
|
7
|
Wang RS, Loscalzo J. Illuminating drug action by network integration of disease genes: a case study of myocardial infarction. MOLECULAR BIOSYSTEMS 2016; 12:1653-66. [PMID: 27004607 PMCID: PMC4846559 DOI: 10.1039/c6mb00052e] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Drug discovery has produced many successful therapeutic agents; however, most of these drugs were developed without a deep understanding of the system-wide mechanisms of action responsible for their indications. Gene-disease associations produced by molecular and genetic studies of complex diseases provide great opportunities for a system-level understanding of drug activity. In this study, we focused on acute myocardial infarction (MI) and conducted an integrative network analysis to illuminate drug actions. We integrated MI drugs, MI drug interactors, drug targets, and MI disease genes into the human interactome and showed that MI drug targets are significantly proximate to MI disease proteins. We then constructed a bipartite network of MI-related drug targets and MI disease proteins and derived 12 drug-target-disease (DTD) modules. We assessed the biological relevance of these modules and demonstrated the benefits of incorporating disease genes. The results indicate that DTD modules provide insights into the mechanisms of action of MI drugs and the cardiovascular (side) effects of non-MI drugs.
Collapse
Affiliation(s)
- Rui-Sheng Wang
- Department of Medicine, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA.
| | - Joseph Loscalzo
- Department of Medicine, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
8
|
Boland MR, Jacunski A, Lorberbaum T, Romano JD, Moskovitch R, Tatonetti NP. Systems biology approaches for identifying adverse drug reactions and elucidating their underlying biological mechanisms. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2015; 8:104-22. [PMID: 26559926 DOI: 10.1002/wsbm.1323] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 09/30/2015] [Accepted: 10/01/2015] [Indexed: 01/06/2023]
Abstract
Small molecules are indispensable to modern medical therapy. However, their use may lead to unintended, negative medical outcomes commonly referred to as adverse drug reactions (ADRs). These effects vary widely in mechanism, severity, and populations affected, making ADR prediction and identification important public health concerns. Current methods rely on clinical trials and postmarket surveillance programs to find novel ADRs; however, clinical trials are limited by small sample size, whereas postmarket surveillance methods may be biased and inherently leave patients at risk until sufficient clinical evidence has been gathered. Systems pharmacology, an emerging interdisciplinary field combining network and chemical biology, provides important tools to uncover and understand ADRs and may mitigate the drawbacks of traditional methods. In particular, network analysis allows researchers to integrate heterogeneous data sources and quantify the interactions between biological and chemical entities. Recent work in this area has combined chemical, biological, and large-scale observational health data to predict ADRs in both individual patients and global populations. In this review, we explore the rapid expansion of systems pharmacology in the study of ADRs. We enumerate the existing methods and strategies and illustrate progress in the field with a model framework that incorporates crucial data elements, such as diet and comorbidities, known to modulate ADR risk. Using this framework, we highlight avenues of research that may currently be underexplored, representing opportunities for future work.
Collapse
Affiliation(s)
- Mary Regina Boland
- Department of Biomedical Informatics, Columbia University, New York, NY, USA.,Department of Systems Biology, Columbia University, New York, NY, USA.,Department of Medicine, Columbia University, New York, NY, USA.,Observational Health Data Science and Informatics (OHDSI), New York, NY, USA
| | - Alexandra Jacunski
- Department of Biomedical Informatics, Columbia University, New York, NY, USA.,Department of Systems Biology, Columbia University, New York, NY, USA.,Department of Medicine, Columbia University, New York, NY, USA.,Integrated Program in Cellular, Molecular and Biomedical Studies, Columbia University, New York, NY, USA
| | - Tal Lorberbaum
- Department of Biomedical Informatics, Columbia University, New York, NY, USA.,Department of Systems Biology, Columbia University, New York, NY, USA.,Department of Medicine, Columbia University, New York, NY, USA.,Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
| | - Joseph D Romano
- Department of Biomedical Informatics, Columbia University, New York, NY, USA.,Department of Systems Biology, Columbia University, New York, NY, USA.,Department of Medicine, Columbia University, New York, NY, USA
| | - Robert Moskovitch
- Department of Biomedical Informatics, Columbia University, New York, NY, USA.,Department of Systems Biology, Columbia University, New York, NY, USA.,Department of Medicine, Columbia University, New York, NY, USA
| | - Nicholas P Tatonetti
- Department of Biomedical Informatics, Columbia University, New York, NY, USA.,Department of Systems Biology, Columbia University, New York, NY, USA.,Department of Medicine, Columbia University, New York, NY, USA.,Observational Health Data Science and Informatics (OHDSI), New York, NY, USA
| |
Collapse
|
9
|
Pogodin PV, Lagunin AA, Filimonov DA, Poroikov VV. PASS Targets: Ligand-based multi-target computational system based on a public data and naïve Bayes approach. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2015; 26:783-793. [PMID: 26305108 DOI: 10.1080/1062936x.2015.1078407] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Estimation of interactions between drug-like compounds and drug targets is very important for drug discovery and toxicity assessment. Using data extracted from the 19th version of the ChEMBL database ( https://www.ebi.ac.uk/chembl ) as a training set and a Bayesian-like method realized in PASS software ( http://www.way2drug.com/PASSOnline ), we developed a computational tool for the prediction of interactions between protein targets and drug-like compounds. After training, PASS Targets became able to predict interactions of drug-like compounds with 2507 protein targets from different organisms based on analysis of structure-activity relationships for 589,107 different chemical compounds. The prediction accuracy, estimated as AUC ROC calculated by the leave-one-out cross-validation and 20-fold cross-validation procedures, was about 96%. Average AUC ROC value was about 90% for the external test set from approximately 700 known drugs interacting with 206 protein targets.
Collapse
Affiliation(s)
- P V Pogodin
- a Department for Bioinformatics; Institute of Biomedical Chemistry , Pirogov Russian National Research Medical University , Moscow , Russia
- b Medico-Biological Faculty , Pirogov Russian National Research Medical University , Moscow , Russia
| | - A A Lagunin
- a Department for Bioinformatics; Institute of Biomedical Chemistry , Pirogov Russian National Research Medical University , Moscow , Russia
- b Medico-Biological Faculty , Pirogov Russian National Research Medical University , Moscow , Russia
| | - D A Filimonov
- a Department for Bioinformatics; Institute of Biomedical Chemistry , Pirogov Russian National Research Medical University , Moscow , Russia
| | - V V Poroikov
- a Department for Bioinformatics; Institute of Biomedical Chemistry , Pirogov Russian National Research Medical University , Moscow , Russia
- b Medico-Biological Faculty , Pirogov Russian National Research Medical University , Moscow , Russia
| |
Collapse
|
10
|
In silico assessment of adverse drug reactions and associated mechanisms. Drug Discov Today 2015; 21:58-71. [PMID: 26272036 DOI: 10.1016/j.drudis.2015.07.018] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 07/15/2015] [Accepted: 07/31/2015] [Indexed: 12/31/2022]
Abstract
During recent years, various in silico approaches have been developed to estimate chemical and biological drug features, for example chemical fragments, protein targets, pathways, among others, that correlate with adverse drug reactions (ADRs) and explain the associated mechanisms. These features have also been used for the creation of predictive models that enable estimation of ADRs during the early stages of drug development. In this review, we discuss various in silico approaches to predict these features for a certain drug, estimate correlations with ADRs, establish causal relationships between selected features and ADR mechanisms and create corresponding predictive models.
Collapse
|