1
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Kumar R, Sharma A, Alexiou A, Ashraf GM. Artificial Intelligence in De novo Drug Design: Are We Still There? Curr Top Med Chem 2022; 22:2483-2492. [PMID: 36263480 DOI: 10.2174/1568026623666221017143244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 09/06/2022] [Accepted: 09/15/2022] [Indexed: 01/20/2023]
Abstract
BACKGROUND The artificial intelligence (AI)-assisted design of drug candidates with novel structures and desired properties has received significant attention in the recent past, so related areas of forward prediction that aim to discover chemical matters worth synthesizing and further experimental investigation. OBJECTIVES The purpose behind developing AI-driven models is to explore the broader chemical space and suggest new drug candidate scaffolds with promising therapeutic value. Moreover, it is anticipated that such AI-based models may not only significantly reduce the cost and time but also decrease the attrition rate of drug candidates that fail to reach the desirable endpoints at the final stages of drug development. In an attempt to develop AI-based models for de novo drug design, numerous methods have been proposed by various study groups by applying machine learning and deep learning algorithms to chemical datasets. However, there are many challenges in obtaining accurate predictions, and real breakthroughs in de novo drug design are still scarce. METHODS In this review, we explore the recent trends in developing AI-based models for de novo drug design to assess the current status, challenges, and opportunities in the field. CONCLUSION The consistently improved AI algorithms and the abundance of curated training chemical data indicate that AI-based de novo drug design should perform better than the current models. Improvements in the performance are warranted to obtain better outcomes in the form of potential drug candidates, which can perform well in in vivo conditions, especially in the case of more complex diseases.
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Affiliation(s)
- Rajnish Kumar
- Amity Institute of Biotechnology, Amity University Uttar Pradesh Lucknow Campus, Uttar Pradesh, India
| | - Anju Sharma
- Department of Applied Science, Indian Institute of Information Technology, Allahabad, Uttar Pradesh, India
| | - Athanasios Alexiou
- Novel Global Community Educational Foundation, Hebersham, 2770 NSW, Australia.,AFNP Med Austria, 1010 Wien, Austria
| | - Ghulam Md Ashraf
- Pre-Clinical Research Unit (PCRU), King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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2
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Inoue T, Tanaka K, Kotera M, Funatsu K. Improvement of the Structure Generator DAECS with Respect to Structural Diversity. Mol Inform 2020; 40:e2000225. [PMID: 33237627 DOI: 10.1002/minf.202000225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/29/2020] [Indexed: 11/11/2022]
Abstract
The development of novel organic compounds with desired properties is time consuming and costly. Thus, the quantitative structure-property relationship (QSPR) model is used widely for efficiently discovering compounds with the desired properties. Novel structures can be generated from a variety of input structures in silico by structure generators. We previously developed the structure generator DAECS to yield highly active drug-like structures. However, the structural diversity of the structures generated by DAECS was still small for practical applications such as drug discovery. In this paper, we present structure modification rules and the algorithm to output more diverse structures through the DAECS workflow. Two new types of structural modification rules, bond contraction and ring mergence, were added. The new algorithm, which restricts the search area and subsequently clusters structures on a two-dimensional map generated by generative topographic mapping, was implemented for the repetitive selection of seed structures. A case study was conducted to evaluate our method using ligand structures for the histamine H1 receptor. The results showed improved structural diversity than the previous method.
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Affiliation(s)
- Takahiro Inoue
- Department of Chemical System Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Kenichi Tanaka
- Department of Chemical System Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Masaaki Kotera
- Department of Chemical System Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Kimito Funatsu
- Department of Chemical System Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
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3
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Vázquez J, López M, Gibert E, Herrero E, Luque FJ. Merging Ligand-Based and Structure-Based Methods in Drug Discovery: An Overview of Combined Virtual Screening Approaches. Molecules 2020; 25:E4723. [PMID: 33076254 PMCID: PMC7587536 DOI: 10.3390/molecules25204723] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/06/2020] [Accepted: 10/11/2020] [Indexed: 12/20/2022] Open
Abstract
Virtual screening (VS) is an outstanding cornerstone in the drug discovery pipeline. A variety of computational approaches, which are generally classified as ligand-based (LB) and structure-based (SB) techniques, exploit key structural and physicochemical properties of ligands and targets to enable the screening of virtual libraries in the search of active compounds. Though LB and SB methods have found widespread application in the discovery of novel drug-like candidates, their complementary natures have stimulated continued efforts toward the development of hybrid strategies that combine LB and SB techniques, integrating them in a holistic computational framework that exploits the available information of both ligand and target to enhance the success of drug discovery projects. In this review, we analyze the main strategies and concepts that have emerged in the last years for defining hybrid LB + SB computational schemes in VS studies. Particularly, attention is focused on the combination of molecular similarity and docking, illustrating them with selected applications taken from the literature.
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Affiliation(s)
- Javier Vázquez
- Pharmacelera, Plaça Pau Vila, 1, Sector C 2a, Edificio Palau de Mar, 08039 Barcelona, Spain;
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, Institute of Biomedicine (IBUB), and Institute of Theoretical and Computational Chemistry (IQTC-UB), University of Barcelona, Av. Prat de la Riba 171, E-08921 Santa Coloma de Gramanet, Spain
| | - Manel López
- AB Science, Parc Scientifique de Luminy, Zone Luminy Enterprise, Case 922, 163 Av. de Luminy, 13288 Marseille, France;
| | - Enric Gibert
- Pharmacelera, Plaça Pau Vila, 1, Sector C 2a, Edificio Palau de Mar, 08039 Barcelona, Spain;
| | - Enric Herrero
- Pharmacelera, Plaça Pau Vila, 1, Sector C 2a, Edificio Palau de Mar, 08039 Barcelona, Spain;
| | - F. Javier Luque
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, Institute of Biomedicine (IBUB), and Institute of Theoretical and Computational Chemistry (IQTC-UB), University of Barcelona, Av. Prat de la Riba 171, E-08921 Santa Coloma de Gramanet, Spain
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4
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Shibayama S, Marcou G, Horvath D, Baskin II, Funatsu K, Varnek A. Application of the mol2vec Technology to Large-size Data Visualization and Analysis. Mol Inform 2020; 39:e1900170. [PMID: 32090493 DOI: 10.1002/minf.201900170] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/11/2020] [Indexed: 11/09/2022]
Abstract
Generative Topographic Mapping (GTM) is a dimensionality reduction method, which is widely used for both data visualization and structure-activity modeling. Large dimensionality of the initial data space may require significant computational resources and slow down the GTM construction. Therefore, it may be meaningful to reduce the number of descriptors used for encoding molecular structures. The Principal Component Analysis (PCA), a standard preprocessing tool, suffers from the information loss upon the dimensionality reduction. As an alternative, we propose to use substructure vector embedding provided by the mol2vec technique. In addition to the data dimensionality reduction, this technology also accounts for proximity of substructures in molecular graphs. In this study, dimensionality of large descriptor spaces of ISIDA fragment descriptors or Morgan fingerprints were reduced using either the PCA or the mol2vec method. The latter significantly speeds up GTM training without compromising its predictive power in bioactivity classification tasks.
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Affiliation(s)
- Shojiro Shibayama
- Department of Chemical System Engineering, School of Engineering, University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, Japan.,Department, Institution Laboratoire de Chemoinformatique, UMR7140 University of Strasbourg-CNRS, 4, rue Blaise Pascal, 67000, Strasbourg, France
| | - Gilles Marcou
- Department, Institution Laboratoire de Chemoinformatique, UMR7140 University of Strasbourg-CNRS, 4, rue Blaise Pascal, 67000, Strasbourg, France
| | - Dragos Horvath
- Department, Institution Laboratoire de Chemoinformatique, UMR7140 University of Strasbourg-CNRS, 4, rue Blaise Pascal, 67000, Strasbourg, France
| | - Igor I Baskin
- Faculty of Physics, Lomonosov Moscow State University, Leninskie Gory, 119991, Moscow, Russian Federation
| | - Kimito Funatsu
- Department of Chemical System Engineering, School of Engineering, University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Alexandre Varnek
- Department, Institution Laboratoire de Chemoinformatique, UMR7140 University of Strasbourg-CNRS, 4, rue Blaise Pascal, 67000, Strasbourg, France.,Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21 Nishi 10, Kita-ku, 001-0021, Sapporo, Japan
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5
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Gantzer P, Creton B, Nieto-Draghi C. Inverse-QSPR for de novo Design: A Review. Mol Inform 2019; 39:e1900087. [PMID: 31682079 DOI: 10.1002/minf.201900087] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 11/04/2019] [Indexed: 11/09/2022]
Abstract
The use of computer tools to solve chemistry-related problems has given rise to a large and increasing number of publications these last decades. This new field of science is now well recognized and labelled Chemoinformatics. Among all chemoinformatics techniques, the use of statistical based approaches for property predictions has been the subject of numerous research reflecting both new developments and many cases of applications. The so obtained predictive models relating a property to molecular features - descriptors - are gathered under the acronym QSPR, for Quantitative Structure Property Relationships. Apart from the obvious use of such models to predict property values for new compounds, their use to virtually synthesize new molecules - de novo design - is currently a high-interest subject. Inverse-QSPR (i-QSPR) methods have hence been developed to accelerate the discovery of new materials that meet a set of specifications. In the proposed manuscript, we review existing i-QSPR methodologies published in the open literature in a way to highlight developments, applications, improvements and limitations of each.
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Affiliation(s)
- Philippe Gantzer
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852, Rueil-Malmaison, France
| | - Benoit Creton
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852, Rueil-Malmaison, France
| | - Carlos Nieto-Draghi
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852, Rueil-Malmaison, France
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6
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Yang X, Wang Y, Byrne R, Schneider G, Yang S. Concepts of Artificial Intelligence for Computer-Assisted Drug Discovery. Chem Rev 2019; 119:10520-10594. [PMID: 31294972 DOI: 10.1021/acs.chemrev.8b00728] [Citation(s) in RCA: 346] [Impact Index Per Article: 69.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Artificial intelligence (AI), and, in particular, deep learning as a subcategory of AI, provides opportunities for the discovery and development of innovative drugs. Various machine learning approaches have recently (re)emerged, some of which may be considered instances of domain-specific AI which have been successfully employed for drug discovery and design. This review provides a comprehensive portrayal of these machine learning techniques and of their applications in medicinal chemistry. After introducing the basic principles, alongside some application notes, of the various machine learning algorithms, the current state-of-the art of AI-assisted pharmaceutical discovery is discussed, including applications in structure- and ligand-based virtual screening, de novo drug design, physicochemical and pharmacokinetic property prediction, drug repurposing, and related aspects. Finally, several challenges and limitations of the current methods are summarized, with a view to potential future directions for AI-assisted drug discovery and design.
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Affiliation(s)
- Xin Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital , Sichuan University , Chengdu , Sichuan 610041 , China
| | - Yifei Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital , Sichuan University , Chengdu , Sichuan 610041 , China
| | - Ryan Byrne
- ETH Zurich , Department of Chemistry and Applied Biosciences , Vladimir-Prelog-Weg 4 , CH-8093 Zurich , Switzerland
| | - Gisbert Schneider
- ETH Zurich , Department of Chemistry and Applied Biosciences , Vladimir-Prelog-Weg 4 , CH-8093 Zurich , Switzerland
| | - Shengyong Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital , Sichuan University , Chengdu , Sichuan 610041 , China
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7
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Miyao T, Funatsu K, Bajorath J. Three-Dimensional Activity Landscape Models of Different Design and Their Application to Compound Mapping and Potency Prediction. J Chem Inf Model 2018; 59:993-1004. [DOI: 10.1021/acs.jcim.8b00661] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Tomoyuki Miyao
- Data Science Center and Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Kimito Funatsu
- Data Science Center and Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Endenicher Allee 19c, D-53115 Bonn, Germany
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8
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Kaneko H. Data Visualization, Regression, Applicability Domains and Inverse Analysis Based on Generative Topographic Mapping. Mol Inform 2018; 38:e1800088. [PMID: 30259699 DOI: 10.1002/minf.201800088] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 08/30/2018] [Indexed: 01/11/2023]
Abstract
This paper introduces two generative topographic mapping (GTM) methods that can be used for data visualization, regression analysis, inverse analysis, and the determination of applicability domains (ADs). In GTM-multiple linear regression (GTM-MLR), the prior probability distribution of the descriptors or explanatory variables (X) is calculated with GTM, and the posterior probability distribution of the property/activity or objective variable (y) given X is calculated with MLR; inverse analysis is then performed using the product rule and Bayes' theorem. In GTM-regression (GTMR), X and y are combined and GTM is performed to obtain the joint probability distribution of X and y; this leads to the posterior probability distributions of y given X and of X given y, which are used for regression and inverse analysis, respectively. Simulations using linear and nonlinear datasets and quantitative structure-activity relationship (QSAR) and quantitative structure-property relationship (QSPR) datasets confirm that GTM-MLR and GTMR enable data visualization, regression analysis, and inverse analysis considering appropriate ADs. Python and MATLAB codes for the proposed algorithms are available at https://github.com/hkaneko1985/gtm-generativetopographicmapping.
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Affiliation(s)
- Hiromasa Kaneko
- Department of Applied Chemistry, Meiji University 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan
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9
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Segler MHS, Kogej T, Tyrchan C, Waller MP. Generating Focused Molecule Libraries for Drug Discovery with Recurrent Neural Networks. ACS CENTRAL SCIENCE 2018; 4:120-131. [PMID: 29392184 PMCID: PMC5785775 DOI: 10.1021/acscentsci.7b00512] [Citation(s) in RCA: 665] [Impact Index Per Article: 110.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Indexed: 05/20/2023]
Abstract
In de novo drug design, computational strategies are used to generate novel molecules with good affinity to the desired biological target. In this work, we show that recurrent neural networks can be trained as generative models for molecular structures, similar to statistical language models in natural language processing. We demonstrate that the properties of the generated molecules correlate very well with the properties of the molecules used to train the model. In order to enrich libraries with molecules active toward a given biological target, we propose to fine-tune the model with small sets of molecules, which are known to be active against that target. Against Staphylococcus aureus, the model reproduced 14% of 6051 hold-out test molecules that medicinal chemists designed, whereas against Plasmodium falciparum (Malaria), it reproduced 28% of 1240 test molecules. When coupled with a scoring function, our model can perform the complete de novo drug design cycle to generate large sets of novel molecules for drug discovery.
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Affiliation(s)
- Marwin H. S. Segler
- Institute of Organic
Chemistry & Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Thierry Kogej
- Hit Discovery, Discovery Sciences, AstraZeneca R&D, Gothenburg, Sweden
| | - Christian Tyrchan
- Department of Medicinal
Chemistry, IMED RIA, AstraZeneca R&D, Gothenburg, Sweden
| | - Mark P. Waller
- Department of Physics & International Centre for Quantum and
Molecular Structures, Shanghai University, Shanghai, China
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10
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Allen WJ, Fochtman BC, Balius TE, Rizzo RC. Customizable de novo design strategies for DOCK: Application to HIVgp41 and other therapeutic targets. J Comput Chem 2017; 38:2641-2663. [PMID: 28940386 DOI: 10.1002/jcc.25052] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 08/03/2017] [Indexed: 12/12/2022]
Abstract
De novo design can be used to explore vast areas of chemical space in computational lead discovery. As a complement to virtual screening, from-scratch construction of molecules is not limited to compounds in pre-existing vendor catalogs. Here, we present an iterative fragment growth method, integrated into the program DOCK, in which new molecules are built using rules for allowable connections based on known molecules. The method leverages DOCK's advanced scoring and pruning approaches and users can define very specific criteria in terms of properties or features to customize growth toward a particular region of chemical space. The code was validated using three increasingly difficult classes of calculations: (1) Rebuilding known X-ray ligands taken from 663 complexes using only their component parts (focused libraries), (2) construction of new ligands in 57 drug target sites using a library derived from ∼13M drug-like compounds (generic libraries), and (3) application to a challenging protein-protein interface on the viral drug target HIVgp41. The computational testing confirms that the de novo DOCK routines are robust and working as envisioned, and the compelling results highlight the potential utility for designing new molecules against a wide variety of important protein targets. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- William J Allen
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, 11794
| | - Brian C Fochtman
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, 11794
| | - Trent E Balius
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, 94158
| | - Robert C Rizzo
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, 11794.,Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, New York, 11794.,Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, 11794
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11
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Maeda I, Hasegawa K, Kaneko H, Funatsu K. Novel Method Proposing Chemical Structures with Desirable Profile of Activities Based on Chemical and Protein Spaces. Mol Inform 2017; 36. [PMID: 28857513 DOI: 10.1002/minf.201700075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 08/09/2017] [Indexed: 11/06/2022]
Abstract
Active molecules among numerous chemical structures in a chemical database can be searched easily by statistical prediction of compound-protein interactions. However, constructing a simple prediction model against one protein does not aid drug design, because detecting chemical structures that act similarly against multiple proteins is necessary for preventing side effects of the potential drug. To tackle this problem, we propose a new method that visualizes chemical and protein spaces. For simultaneous visualization of both spaces, we employ a counterpropagation neural network (CPNN) and develop a new visualization method named multi-input CPNN (MICPNN). In a case study of the kinase protein family, the MICPNN model predicted accurately the complex relationships between compounds and proteins. The proposed method identified chemical structures with promising activity against kinases. Our proposed method is also applicable to other protein families, such as G-protein coupled receptors, ion channels and transporters.
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Affiliation(s)
- Iwao Maeda
- The University of Tokyo, School of Engineering, Department of Chemical System Engineering, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656
| | - Kiyoshi Hasegawa
- Chugai Pharmaceutical Company, Kamakura Research Laboratories, 200 Kajiwara, Kamakura, Kanagawa, 247-8530, Japan
| | - Hiromasa Kaneko
- The University of Tokyo, School of Engineering, Department of Chemical System Engineering, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656
| | - Kimito Funatsu
- The University of Tokyo, School of Engineering, Department of Chemical System Engineering, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656
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12
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Takeda S, Kaneko H, Funatsu K. Chemical-Space-Based de Novo Design Method To Generate Drug-Like Molecules. J Chem Inf Model 2016; 56:1885-1893. [PMID: 27632418 DOI: 10.1021/acs.jcim.6b00038] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
To discover drug compounds in chemical space containing an enormous number of compounds, a structure generator is required to produce virtual drug-like chemical structures. The de novo design algorithm for exploring chemical space (DAECS) visualizes the activity distribution on a two-dimensional plane corresponding to chemical space and generates structures in a target area on a plane selected by the user. In this study, we modify the DAECS to enable the user to select a target area to consider properties other than activity and improve the diversity of the generated structures by visualizing the drug-likeness distribution and the activity distribution, generating structures by substructure-based structural changes, including addition, deletion, and substitution of substructures, as well as the slight structural changes used in the DAECS. Through case studies using ligand data for the human adrenergic alpha2A receptor and the human histamine H1 receptor, the modified DAECS can generate high diversity drug-like structures, and the usefulness of the modification of the DAECS is verified.
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Affiliation(s)
- Shunichi Takeda
- Department of Chemical Systems Engineering, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hiromasa Kaneko
- Department of Chemical Systems Engineering, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kimito Funatsu
- Department of Chemical Systems Engineering, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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13
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Kaneko H, Funatsu K. Applicability Domains and Consistent Structure Generation. Mol Inform 2016; 36. [DOI: 10.1002/minf.201600032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 04/25/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Hiromasa Kaneko
- Department of Chemical System Engineering The University of Tokyo 7-3-1 Hongo Bunkyo-ku, Tokyo 113-8656 Japan
| | - Kimito Funatsu
- Department of Chemical System Engineering The University of Tokyo 7-3-1 Hongo Bunkyo-ku, Tokyo 113-8656 Japan
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14
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Jindalertudomdee J, Hayashida M, Zhao Y, Akutsu T. Enumeration method for tree-like chemical compounds with benzene rings and naphthalene rings by breadth-first search order. BMC Bioinformatics 2016; 17:113. [PMID: 26932529 PMCID: PMC4774041 DOI: 10.1186/s12859-016-0962-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 02/19/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Drug discovery and design are important research fields in bioinformatics. Enumeration of chemical compounds is essential not only for the purpose, but also for analysis of chemical space and structure elucidation. In our previous study, we developed enumeration methods BfsSimEnum and BfsMulEnum for tree-like chemical compounds using a tree-structure to represent a chemical compound, which is limited to acyclic chemical compounds only. RESULTS In this paper, we extend the methods, and develop BfsBenNaphEnum that can enumerate tree-like chemical compounds containing benzene rings and naphthalene rings, which include benzene isomers and naphthalene isomers such as ortho, meta, and para, by treating a benzene ring as an atom with valence six, instead of a ring of six carbon atoms, and treating a naphthalene ring as two benzene rings having a special bond. We compare our method with MOLGEN 5.0, which is a well-known general purpose structure generator, to enumerate chemical structures from a set of chemical formulas in terms of the number of enumerated structures and the computational time. The result suggests that our proposed method can reduce the computational time efficiently. CONCLUSIONS We propose the enumeration method BfsBenNaphEnum for tree-like chemical compounds containing benzene rings and naphthalene rings as cyclic structures. BfsBenNaphEnum was from 50 times to 5,000,000 times faster than MOLGEN 5.0 for instances with 8 to 14 carbon atoms in our experiments.
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Affiliation(s)
- Jira Jindalertudomdee
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Gokasho, Japan
| | - Morihiro Hayashida
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Gokasho, Japan.
| | - Yang Zhao
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Gokasho, Japan
| | - Tatsuya Akutsu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Gokasho, Japan.
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15
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Li Y, Zhao Z, Liu Z, Su M, Wang R. AutoT&T v.2: An Efficient and Versatile Tool for Lead Structure Generation and Optimization. J Chem Inf Model 2016; 56:435-53. [DOI: 10.1021/acs.jcim.5b00691] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Yan Li
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Collaborative
Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People’s Republic of China
| | - Zhixiong Zhao
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Collaborative
Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People’s Republic of China
| | - Zhihai Liu
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Collaborative
Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People’s Republic of China
| | - Minyi Su
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Collaborative
Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People’s Republic of China
| | - Renxiao Wang
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Collaborative
Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People’s Republic of China
- State
Key Laboratory of Quality Research in Chinese Medicine, Macau Institute
for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, People’s Republic of China
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16
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Foscato M, Houghton BJ, Occhipinti G, Deeth RJ, Jensen VR. Ring Closure To Form Metal Chelates in 3D Fragment-Based de Novo Design. J Chem Inf Model 2015; 55:1844-56. [DOI: 10.1021/acs.jcim.5b00424] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Marco Foscato
- Department
of Chemistry, University of Bergen, Allégaten 41, N-5007 Bergen, Norway
| | - Benjamin J. Houghton
- Inorganic
Computational Chemistry Group, Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, Great Britain
| | - Giovanni Occhipinti
- Department
of Chemistry, University of Bergen, Allégaten 41, N-5007 Bergen, Norway
| | - Robert J. Deeth
- Inorganic
Computational Chemistry Group, Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, Great Britain
| | - Vidar R. Jensen
- Department
of Chemistry, University of Bergen, Allégaten 41, N-5007 Bergen, Norway
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