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Bouhedjar K, Boukelia A, Khorief Nacereddine A, Boucheham A, Belaidi A, Djerourou A. A natural language processing approach based on embedding deep learning from heterogeneous compounds for quantitative structure-activity relationship modeling. Chem Biol Drug Des 2021; 96:961-972. [PMID: 33058460 DOI: 10.1111/cbdd.13742] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 05/27/2020] [Accepted: 05/31/2020] [Indexed: 12/15/2022]
Abstract
Over the past decade, rapid development in biological and chemical technologies such as high-throughput screening, parallel synthesis, has been significantly increased the amount of data, which requires the creation and the integration of new analytical methods, especially deep learning models. Recently, there is an increasing interest in deep learning utilization in computer-aided drug discovery due to its exceptional successful application in many fields. The present work proposed a natural language processing approach, based on embedding deep neural networks. Our method aims to transform the Simplified Molecular Input Line Entry System format into word embedding vectors to represent the semantics of compounds. These vectors are fed into supervised machine learning algorithms such as convolutional long short-term memory neural network, support vector machine, and random forest to build up quantitative structure-activity relationship models on toxicity data sets. The obtained results on toxicity data to the ciliate Tetrahymena pyriformis (IGC50 ), and acute toxicity rat data expressed as median lethal dose of treated rats (LD50 ) show that our approach can eventually be used to predict the activities of chemical compounds efficiently. All material used in this study is available online through the GitHub portal (https://github.com/BoukeliaAbdelbasset/NLPDeepQSAR.git).
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Affiliation(s)
- Khalid Bouhedjar
- Laboratoire de Synthèse et Biocatalyse Organique, Département de Chimie, Faculté des Sciences, Université Badji Mokhtar Annaba, Annaba, Algeria.,Laboratoire Bioinformatique, Centre de Recherche en Biotechnologie (CRBt), Constantine, Algeria
| | - Abdelbasset Boukelia
- Laboratoire Bioinformatique, Centre de Recherche en Biotechnologie (CRBt), Constantine, Algeria.,Computer Science Department, Faculty of NTIC University of Constantine 2 - Abdelhamid Mehri, Constantine, Algeria
| | - Abdelmalek Khorief Nacereddine
- Laboratory of Physical Chemistry and Biology of Materials, Department of Physics and Chemistry, Higher Normal School of Technological Education-Skikda, Skikda, Algeria
| | - Anouar Boucheham
- University Salah Boubnider Constantine, Constantine, Algeria.,Laboratory of Molecular and Cellular Biology, Constantine, Algeria
| | - Amine Belaidi
- Laboratoire Bioinformatique, Centre de Recherche en Biotechnologie (CRBt), Constantine, Algeria
| | - Abdelhafid Djerourou
- Laboratoire de Synthèse et Biocatalyse Organique, Département de Chimie, Faculté des Sciences, Université Badji Mokhtar Annaba, Annaba, Algeria
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2
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Warr WA. Many InChIs and quite some feat. J Comput Aided Mol Des 2015; 29:681-94. [PMID: 26081259 DOI: 10.1007/s10822-015-9854-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 06/10/2015] [Indexed: 12/14/2022]
Affiliation(s)
- Wendy A Warr
- Wendy Warr & Associates, Holmes Chapel, Crewe, Cheshire, CW4 7HZ, UK,
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3
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Quashie PK, Mesplède T, Wainberg MA. HIV Drug Resistance and the Advent of Integrase Inhibitors. Curr Infect Dis Rep 2013. [PMID: 23180144 DOI: 10.1007/s11908-012-0305-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This review focuses on the topic of HIV integrase inhibitors that are potent antiretroviral drugs that efficiently decrease viral load in patients. However, emergence of resistance mutations against this new class of drugs represents a threat to their long-term efficacy. Here, we provide new information about the most recent mutations identified and other mutations that confer resistance to several integrase inhibitors, such as new resistance mutations-for example, G118R, R263K, and S153Y-that have been identified through in vitro selection studies with second-generation integrase strand transfer inhibitors (INSTIs). These add to the three main resistance pathways involving mutations at positions Y143, N155, and Q148. Deep sequencing, structural modeling, and biochemical analyses are methods that currently help in the understanding of the mechanisms of resistance conferred by these mutations. Although the new resistance mutations appear to confer only low levels of cross-resistance to second-generation drugs, the Q148 pathway with numerous secondary mutations has the potential to significantly decrease susceptibility to all drugs of the INSTI family of compounds.
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Affiliation(s)
- Peter K Quashie
- McGill University AIDS Centre, Lady Davis for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
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4
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Wainberg MA. The Need for Development of New HIV-1 Reverse Transcriptase and Integrase Inhibitors in the Aftermath of Antiviral Drug Resistance. SCIENTIFICA 2012; 2012:238278. [PMID: 24278679 PMCID: PMC3820659 DOI: 10.6064/2012/238278] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 11/01/2012] [Indexed: 05/20/2023]
Abstract
The use of highly active antiretroviral therapy (HAART) involves combinations of drugs to achieve maximal virological response and reduce the potential for the emergence of antiviral resistance. There are two broad classes of reverse transcriptase inhibitors, the nucleoside reverse transcriptase inhibitors (NRTIs) and nonnucleoside reverse transcriptase inhibitors (NNRTIs). Since the first classes of such compounds were developed, viral resistance against them has necessitated the continuous development of novel compounds within each class. This paper considers the NRTIs and NNRTIs currently in both preclinical and clinical development or approved for second line therapy and describes the patterns of resistance associated with their use, as well as the underlying mechanisms that have been described. Due to reasons of both affordability and availability, some reverse transcriptase inhibitors with low genetic barrier are more commonly used in resource-limited settings. Their use results to the emergence of specific patterns of antiviral resistance and so may require specific actions to preserve therapeutic options for patients in such settings. More recently, the advent of integrase strand transfer inhibitors represents another major step forward toward control of HIV infection, but these compounds are also susceptible to problems of HIV drug resistance.
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Affiliation(s)
- Mark A. Wainberg
- Lady Davis Institute, McGill University AIDS Centre, Jewish General Hospital, Montreal, QC, Canada H3T 1E2
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5
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Gajewicz A, Rasulev B, Dinadayalane TC, Urbaszek P, Puzyn T, Leszczynska D, Leszczynski J. Advancing risk assessment of engineered nanomaterials: application of computational approaches. Adv Drug Deliv Rev 2012; 64:1663-93. [PMID: 22664229 DOI: 10.1016/j.addr.2012.05.014] [Citation(s) in RCA: 161] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Revised: 05/20/2012] [Accepted: 05/25/2012] [Indexed: 02/06/2023]
Abstract
Nanotechnology that develops novel materials at size of 100nm or less has become one of the most promising areas of human endeavor. Because of their intrinsic properties, nanoparticles are commonly employed in electronics, photovoltaic, catalysis, environmental and space engineering, cosmetic industry and - finally - in medicine and pharmacy. In that sense, nanotechnology creates great opportunities for the progress of modern medicine. However, recent studies have shown evident toxicity of some nanoparticles to living organisms (toxicity), and their potentially negative impact on environmental ecosystems (ecotoxicity). Lack of available data and low adequacy of experimental protocols prevent comprehensive risk assessment. The purpose of this review is to present the current state of knowledge related to the risks of the engineered nanoparticles and to assess the potential of efficient expansion and development of new approaches, which are offered by application of theoretical and computational methods, applicable for evaluation of nanomaterials.
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Affiliation(s)
- Agnieszka Gajewicz
- Laboratory of Environmental Chemometrics, Institute for Environmental and Human Health Protection, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
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6
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Quashie PK, Sloan RD, Wainberg MA. Novel therapeutic strategies targeting HIV integrase. BMC Med 2012; 10:34. [PMID: 22498430 PMCID: PMC3348091 DOI: 10.1186/1741-7015-10-34] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 04/12/2012] [Indexed: 01/17/2023] Open
Abstract
Integration of the viral genome into host cell chromatin is a pivotal and unique step in the replication cycle of retroviruses, including HIV. Inhibiting HIV replication by specifically blocking the viral integrase enzyme that mediates this step is an obvious and attractive therapeutic strategy. After concerted efforts, the first viable integrase inhibitors were developed in the early 2000s, ultimately leading to the clinical licensure of the first integrase strand transfer inhibitor, raltegravir. Similarly structured compounds and derivative second generation integrase strand transfer inhibitors, such as elvitegravir and dolutegravir, are now in various stages of clinical development. Furthermore, other mechanisms aimed at the inhibition of viral integration are being explored in numerous preclinical studies, which include inhibition of 3' processing and chromatin targeting. The development of new clinically useful compounds will be aided by the characterization of the retroviral intasome crystal structure. This review considers the history of the clinical development of HIV integrase inhibitors, the development of antiviral drug resistance and the need for new antiviral compounds.
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Affiliation(s)
- Peter K Quashie
- McGill University AIDS Centre, Lady Davis Institute, Montreal, Canada
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Mouchlis VD, Melagraki G, Mavromoustakos T, Kollias G, Afantitis A. Molecular Modeling on Pyrimidine-Urea Inhibitors of TNF-α Production: An Integrated Approach Using a Combination of Molecular Docking, Classification Techniques, and 3D-QSAR CoMSIA. J Chem Inf Model 2012; 52:711-23. [DOI: 10.1021/ci200579f] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
| | - Georgia Melagraki
- Department
of Chemoinformatics, NovaMechanics, Ltd., Nicosia, Cyprus
| | - Thomas Mavromoustakos
- Laboratory
of Organic Chemistry,
Department of Chemistry, University of Athens, Athens 15771, Greece
| | - George Kollias
- Institute
of Immunology, Biomedical Sciences Research Center “Alexander Fleming”, Athens, Greece
| | - Antreas Afantitis
- Department
of Chemoinformatics, NovaMechanics, Ltd., Nicosia, Cyprus
- Institute
of Immunology, Biomedical Sciences Research Center “Alexander Fleming”, Athens, Greece
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