1
|
Agea MI, Čmelo I, Dehaen W, Chen Y, Kirchmair J, Sedlák D, Bartůněk P, Šícho M, Svozil D. Chemical space exploration with Molpher: Generating and assessing a glucocorticoid receptor ligand library. Mol Inform 2024:e202300316. [PMID: 38979783 DOI: 10.1002/minf.202300316] [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: 11/10/2023] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 07/10/2024]
Abstract
Computational exploration of chemical space is crucial in modern cheminformatics research for accelerating the discovery of new biologically active compounds. In this study, we present a detailed analysis of the chemical library of potential glucocorticoid receptor (GR) ligands generated by the molecular generator, Molpher. To generate the targeted GR library and construct the classification models, structures from the ChEMBL database as well as from the internal IMG library, which was experimentally screened for biological activity in the primary luciferase reporter cell assay, were utilized. The composition of the targeted GR ligand library was compared with a reference library that randomly samples chemical space. A random forest model was used to determine the biological activity of ligands, incorporating its applicability domain using conformal prediction. It was demonstrated that the GR library is significantly enriched with GR ligands compared to the random library. Furthermore, a prospective analysis demonstrated that Molpher successfully designed compounds, which were subsequently experimentally confirmed to be active on the GR. A collection of 34 potential new GR ligands was also identified. Moreover, an important contribution of this study is the establishment of a comprehensive workflow for evaluating computationally generated ligands, particularly those with potential activity against targets that are challenging to dock.
Collapse
Affiliation(s)
- M Isabel Agea
- Department of Informatics and Chemistry & CZ-OPENSCREEN: National Infrastructure for Chemical Biology, Faculty of Chemical Technology, University of Chemistry and Technology, Prague, 16628, Czech Republic
| | - Ivan Čmelo
- Department of Informatics and Chemistry & CZ-OPENSCREEN: National Infrastructure for Chemical Biology, Faculty of Chemical Technology, University of Chemistry and Technology, Prague, 16628, Czech Republic
| | - Wim Dehaen
- Department of Informatics and Chemistry & CZ-OPENSCREEN: National Infrastructure for Chemical Biology, Faculty of Chemical Technology, University of Chemistry and Technology, Prague, 16628, Czech Republic
- Department of Organic Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology, Prague, 16628, Czech Republic
| | - Ya Chen
- Center for Bioinformatics (ZBH), Department of Informatics, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, 20146, Hamburg, Germany
- Division of Pharmaceutical Chemistry, Department of Pharmaceutical Sciences, Faculty of Life Sciences, University of Vienna, 1090, Vienna, Austria
| | - Johannes Kirchmair
- Center for Bioinformatics (ZBH), Department of Informatics, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, 20146, Hamburg, Germany
- Division of Pharmaceutical Chemistry, Department of Pharmaceutical Sciences, Faculty of Life Sciences, University of Vienna, 1090, Vienna, Austria
| | - David Sedlák
- CZ-OPENSCREEN: National Infrastructure for Chemical Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, 14220, Czech Republic
| | - Petr Bartůněk
- CZ-OPENSCREEN: National Infrastructure for Chemical Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, 14220, Czech Republic
| | - Martin Šícho
- Department of Informatics and Chemistry & CZ-OPENSCREEN: National Infrastructure for Chemical Biology, Faculty of Chemical Technology, University of Chemistry and Technology, Prague, 16628, Czech Republic
| | - Daniel Svozil
- Department of Informatics and Chemistry & CZ-OPENSCREEN: National Infrastructure for Chemical Biology, Faculty of Chemical Technology, University of Chemistry and Technology, Prague, 16628, Czech Republic
- CZ-OPENSCREEN: National Infrastructure for Chemical Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, 14220, Czech Republic
| |
Collapse
|
2
|
Kos J, Jampilek J. Editorial of Special Issue "Current Trends in Chemistry Towards Biology". Int J Mol Sci 2024; 25:7307. [PMID: 39000415 PMCID: PMC11242065 DOI: 10.3390/ijms25137307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 06/28/2024] [Indexed: 07/16/2024] Open
Abstract
One of the definitions of chemical biology is that it is a scientific discipline spanning the fields of chemistry, biology, and physics; it primarily involves the application of chemical techniques, tools, analyses, and often compounds (also known as chemical probes), which are produced through synthetic chemistry, in order to study and manipulate biological systems [...].
Collapse
Affiliation(s)
- Jiri Kos
- Department of Biochemistry, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 842 15 Bratislava, Slovakia
| | - Josef Jampilek
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 842 15 Bratislava, Slovakia
- Department of Chemical Biology, Faculty of Science, Palacky University Olomouc, Slechtitelu 27, 783 71 Olomouc, Czech Republic
| |
Collapse
|
3
|
Parvatikar PP, Patil S, Khaparkhuntikar K, Patil S, Singh PK, Sahana R, Kulkarni RV, Raghu AV. Artificial intelligence: Machine learning approach for screening large database and drug discovery. Antiviral Res 2023; 220:105740. [PMID: 37935248 DOI: 10.1016/j.antiviral.2023.105740] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 10/17/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023]
Abstract
Recent research in drug discovery dealing with many faces difficulties, including development of new drugs during disease outbreak and drug resistance due to rapidly accumulating mutations. Virtual screening is the most widely used method in computer aided drug discovery. It has a prominent ability in screening drug targets from large molecular databases. Recently, a number of web servers have developed for quickly screening publicly accessible chemical databases. In a nutshell, deep learning algorithms and artificial neural networks have modernised the field. Several drug discovery processes have used machine learning and deep learning algorithms, including peptide synthesis, structure-based virtual screening, ligand-based virtual screening, toxicity prediction, drug monitoring and release, pharmacophore modelling, quantitative structure-activity relationship, drug repositioning, polypharmacology, and physiochemical activity. Although there are presently a wide variety of data-driven AI/ML tools available, the majority of these tools have, up to this point, been developed in the context of non-communicable diseases like cancer, and a number of obstacles have prevented the translation of these tools to the discovery of treatments against infectious diseases. In this review various aspects of AI and ML in virtual screening of large databases were discussed. Here, with an emphasis on antivirals as well as other disease, offers a perspective on the advantages, drawbacks, and hazards of AI/ML techniques in the search for innovative treatments.
Collapse
Affiliation(s)
- Prachi P Parvatikar
- Department of Biotechnology, Allied Health Science, BLDE (Deemed-to-be University), Vijayapur 586103, Karnataka, India.
| | - Sudha Patil
- Department of Pharmaceutics, BLDEA's SSM College of Pharmacy and Research Centre, Vijayapur 586 103, Karnataka, India
| | - Kedar Khaparkhuntikar
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, 500037, India
| | - Shruti Patil
- Department of Biotechnology, Allied Health Science, BLDE (Deemed-to-be University), Vijayapur 586103, Karnataka, India
| | - Pankaj K Singh
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, 500037, India
| | - R Sahana
- Department of Computer Science and Engineering, RV Institute of Technology and Management, 560076, Bengaluru, India
| | - Raghavendra V Kulkarni
- Department of Biotechnology, Allied Health Science, BLDE (Deemed-to-be University), Vijayapur 586103, Karnataka, India; Department of Pharmaceutics, BLDEA's SSM College of Pharmacy and Research Centre, Vijayapur 586 103, Karnataka, India
| | - Anjanapura V Raghu
- Department of Science and Technology, BLDE (Deemed-to-be University), Vijayapur 586103, Karnataka, India.
| |
Collapse
|
4
|
Soklou KE, Marzag H, Vallée B, Routier S, Plé K. Synthesis of Heterospirocycles through Gold‐(I) Catalysis: Useful Building Blocks for Medicinal Chemistry. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202101080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Kossi Efouako Soklou
- Institut de Chimie Organique et Analytique University of Orléans, CNRS UMR 7311 45067 Orléans Cedex 2 France
| | - Hamid Marzag
- Institut de Chimie Organique et Analytique University of Orléans, CNRS UMR 7311 45067 Orléans Cedex 2 France
| | - Béatrice Vallée
- Centre de Biophysique Moléculaire, CNRS, UPR 4301 University of Orléans and INSERM 45071 Orléans Cedex 2 France
| | - Sylvain Routier
- Institut de Chimie Organique et Analytique University of Orléans, CNRS UMR 7311 45067 Orléans Cedex 2 France
| | - Karen Plé
- Institut de Chimie Organique et Analytique University of Orléans, CNRS UMR 7311 45067 Orléans Cedex 2 France
| |
Collapse
|
5
|
Sicho M, Liu X, Svozil D, van Westen GJP. GenUI: interactive and extensible open source software platform for de novo molecular generation and cheminformatics. J Cheminform 2021; 13:73. [PMID: 34563271 PMCID: PMC8465716 DOI: 10.1186/s13321-021-00550-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 09/05/2021] [Indexed: 03/05/2023] Open
Abstract
Many contemporary cheminformatics methods, including computer-aided de novo drug design, hold promise to significantly accelerate and reduce the cost of drug discovery. Thanks to this attractive outlook, the field has thrived and in the past few years has seen an especially significant growth, mainly due to the emergence of novel methods based on deep neural networks. This growth is also apparent in the development of novel de novo drug design methods with many new generative algorithms now available. However, widespread adoption of new generative techniques in the fields like medicinal chemistry or chemical biology is still lagging behind the most recent developments. Upon taking a closer look, this fact is not surprising since in order to successfully integrate the most recent de novo drug design methods in existing processes and pipelines, a close collaboration between diverse groups of experimental and theoretical scientists needs to be established. Therefore, to accelerate the adoption of both modern and traditional de novo molecular generators, we developed Generator User Interface (GenUI), a software platform that makes it possible to integrate molecular generators within a feature-rich graphical user interface that is easy to use by experts of diverse backgrounds. GenUI is implemented as a web service and its interfaces offer access to cheminformatics tools for data preprocessing, model building, molecule generation, and interactive chemical space visualization. Moreover, the platform is easy to extend with customizable frontend React.js components and backend Python extensions. GenUI is open source and a recently developed de novo molecular generator, DrugEx, was integrated as a proof of principle. In this work, we present the architecture and implementation details of GenUI and discuss how it can facilitate collaboration in the disparate communities interested in de novo molecular generation and computer-aided drug discovery.
Collapse
Affiliation(s)
- M. Sicho
- CZ-OPENSCREEN: National Infrastructure for Chemical Biology, Department of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague, Czech Republic
| | - X. Liu
- Computational Drug Discovery, Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Einsteinweg 55, Leiden, The Netherlands
| | - D. Svozil
- CZ-OPENSCREEN: National Infrastructure for Chemical Biology, Department of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague, Czech Republic
- CZ-OPENSCREEN: National Infrastructure for Chemical Biology, Institute of Molecular Genetics of the ASCR, v. v. i., Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - G. J. P. van Westen
- Computational Drug Discovery, Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Einsteinweg 55, Leiden, The Netherlands
| |
Collapse
|
6
|
Santana K, do Nascimento LD, Lima e Lima A, Damasceno V, Nahum C, Braga RC, Lameira J. Applications of Virtual Screening in Bioprospecting: Facts, Shifts, and Perspectives to Explore the Chemo-Structural Diversity of Natural Products. Front Chem 2021; 9:662688. [PMID: 33996755 PMCID: PMC8117418 DOI: 10.3389/fchem.2021.662688] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 02/25/2021] [Indexed: 12/22/2022] Open
Abstract
Natural products are continually explored in the development of new bioactive compounds with industrial applications, attracting the attention of scientific research efforts due to their pharmacophore-like structures, pharmacokinetic properties, and unique chemical space. The systematic search for natural sources to obtain valuable molecules to develop products with commercial value and industrial purposes remains the most challenging task in bioprospecting. Virtual screening strategies have innovated the discovery of novel bioactive molecules assessing in silico large compound libraries, favoring the analysis of their chemical space, pharmacodynamics, and their pharmacokinetic properties, thus leading to the reduction of financial efforts, infrastructure, and time involved in the process of discovering new chemical entities. Herein, we discuss the computational approaches and methods developed to explore the chemo-structural diversity of natural products, focusing on the main paradigms involved in the discovery and screening of bioactive compounds from natural sources, placing particular emphasis on artificial intelligence, cheminformatics methods, and big data analyses.
Collapse
Affiliation(s)
- Kauê Santana
- Instituto de Biodiversidade, Universidade Federal do Oeste do Pará, Santarém, Brazil
| | | | - Anderson Lima e Lima
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil
| | - Vinícius Damasceno
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil
| | - Claudio Nahum
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil
| | | | - Jerônimo Lameira
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| |
Collapse
|
7
|
Investigation of the Click-Chemical Space for Drug Design Using ZINClick. Methods Mol Biol 2021. [PMID: 33759118 DOI: 10.1007/978-1-0716-1209-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
This chapter provides a brief overview of the applications of ZINClick virtual library. In the last years, we have investigated the click-chemical space covered by molecules containing the triazole ring and generated a database of 1,2,3-triazoles called ZINClick, starting from literature reported alkynes and azides synthesizable in no more than three synthetic steps from commercially available products. This combinatorial database contains millions of 1,4-disubstituted 1,2,3-triazoles that are easily synthesizable. The library is regularly updated and can be freely downloaded from http://www.ZINClick.org . This virtual library is a good starting point to explore a new portion of chemical space.
Collapse
|
8
|
Yang T, Li Z, Chen Y, Feng D, Wang G, Fu Z, Ding X, Tan X, Zhao J, Luo X, Chen K, Jiang H, Zheng M. DrugSpaceX: a large screenable and synthetically tractable database extending drug space. Nucleic Acids Res 2021; 49:D1170-D1178. [PMID: 33104791 PMCID: PMC7778939 DOI: 10.1093/nar/gkaa920] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/11/2020] [Accepted: 10/05/2020] [Indexed: 02/07/2023] Open
Abstract
One of the most prominent topics in drug discovery is efficient exploration of the vast drug-like chemical space to find synthesizable and novel chemical structures with desired biological properties. To address this challenge, we created the DrugSpaceX (https://drugspacex.simm.ac.cn/) database based on expert-defined transformations of approved drug molecules. The current version of DrugSpaceX contains >100 million transformed chemical products for virtual screening, with outstanding characteristics in terms of structural novelty, diversity and large three-dimensional chemical space coverage. To illustrate its practical application in drug discovery, we used a case study of discoidin domain receptor 1 (DDR1), a kinase target implicated in fibrosis and other diseases, to show DrugSpaceX performing a quick search of initial hit compounds. Additionally, for ligand identification and optimization purposes, DrugSpaceX also provides several subsets for download, including a 10% diversity subset, an extended drug-like subset, a drug-like subset, a lead-like subset, and a fragment-like subset. In addition to chemical properties and transformation instructions, DrugSpaceX can locate the position of transformation, which will enable medicinal chemists to easily integrate strategy planning and protection design.
Collapse
Affiliation(s)
- Tianbiao Yang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- Department of Pharmacy, University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
| | - Zhaojun Li
- School of Information Management, Dezhou University, No. 566 University Rd. West, Dezhou 253023, Shandong, China
| | - Yingjia Chen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- Department of Pharmacy, University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Dan Feng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai, China
| | - Guangchao Wang
- School of Information Management, Dezhou University, No. 566 University Rd. West, Dezhou 253023, Shandong, China
| | - Zunyun Fu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- Nanjing University of Chinese Medicine, 138 Xianlin Road, Jiangsu, Nanjing 210023, China
| | - Xiaoyu Ding
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- Department of Pharmacy, University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Xiaoqin Tan
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- Department of Pharmacy, University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Jihui Zhao
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- Department of Pharmacy, University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Xiaomin Luo
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- Department of Pharmacy, University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Kaixian Chen
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- Department of Pharmacy, University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Hualiang Jiang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- Department of Pharmacy, University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
- School of Life Science and Technology, ShanghaiTech University, 393 Huaxiazhong Road, Shanghai 200031, China
| | - Mingyue Zheng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- Department of Pharmacy, University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| |
Collapse
|
9
|
Cheminformatics Explorations of Natural Products. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2019; 110:1-35. [PMID: 31621009 DOI: 10.1007/978-3-030-14632-0_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The chemistry of natural products is fascinating and has continuously attracted the attention of the scientific community for many reasons including, but not limited to, biosynthesis pathways, chemical diversity, the source of bioactive compounds and their marked impact on drug discovery. There is a broad range of experimental and computational techniques (molecular modeling and cheminformatics) that have evolved over the years and have assisted the investigation of natural products. Herein, we discuss cheminformatics strategies to explore the chemistry and applications of natural products. Since the potential synergisms between cheminformatics and natural products are vast, we will focus on three major aspects: (1) exploration of the chemical space of natural products to identify bioactive compounds, with emphasis on drug discovery; (2) assessment of the toxicity profile of natural products; and (3) diversity analysis of natural product collections and the design of chemical collections inspired by natural sources.
Collapse
|
10
|
Pawar G, Madden JC, Ebbrell D, Firman JW, Cronin MTD. In Silico Toxicology Data Resources to Support Read-Across and (Q)SAR. Front Pharmacol 2019; 10:561. [PMID: 31244651 PMCID: PMC6580867 DOI: 10.3389/fphar.2019.00561] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 05/03/2019] [Indexed: 12/14/2022] Open
Abstract
A plethora of databases exist online that can assist in in silico chemical or drug safety assessment. However, a systematic review and grouping of databases, based on purpose and information content, consolidated in a single source, has been lacking. To resolve this issue, this review provides a comprehensive listing of the key in silico data resources relevant to: chemical identity and properties, drug action, toxicology (including nano-material toxicity), exposure, omics, pathways, Absorption, Distribution, Metabolism and Elimination (ADME) properties, clinical trials, pharmacovigilance, patents-related databases, biological (genes, enzymes, proteins, other macromolecules etc.) databases, protein-protein interactions (PPIs), environmental exposure related, and finally databases relating to animal alternatives in support of 3Rs policies. More than nine hundred databases were identified and reviewed against criteria relating to accessibility, data coverage, interoperability or application programming interface (API), appropriate identifiers, types of in vitro, in vivo,-clinical or other data recorded and suitability for modelling, read-across, or similarity searching. This review also specifically addresses the need for solutions for mapping and integration of databases into a common platform for better translatability of preclinical data to clinical data.
Collapse
Affiliation(s)
| | | | | | | | - Mark T. D. Cronin
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| |
Collapse
|
11
|
Interrogating dense ligand chemical space with a forward-synthetic library. Proc Natl Acad Sci U S A 2019; 116:11496-11501. [PMID: 31113876 DOI: 10.1073/pnas.1818718116] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Forward-synthetic databases are an efficient way to enumerate chemical space. We explored here whether these databases are good sources of novel protein ligands and how many molecules are obtainable and in which time frame. Based on docking calculations, series of molecules were selected to gain insights into the ligand structure-activity relationship. To evaluate the novelty of compounds in a challenging way, we chose the β2-adrenergic receptor, for which a large number of ligands is already known. Finding dissimilar ligands is thus the exception rather than the rule. Here we report on the results, the successful synthesis of 127/240 molecules in just 2 weeks, the discovery of previously unreported dissimilar ligands of the β2-adrenergic receptor, and the optimization of one series to a K D of 519 nM in only one round. Moreover, the finding that only 3 of 240 molecules had ever been synthesized before indicates that large parts of chemical space are unexplored.
Collapse
|
12
|
Saldívar-González FI, Pilón-Jiménez BA, Medina-Franco JL. Chemical space of naturally occurring compounds. PHYSICAL SCIENCES REVIEWS 2019. [DOI: 10.1515/psr-2018-0103] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
AbstractThe chemical space of naturally occurring compounds is vast and diverse. Other than biologics, naturally occurring small molecules include a large variety of compounds covering natural products from different sources such as plant, marine, and fungi, to name a few, and several food chemicals. The systematic exploration of the chemical space of naturally occurring compounds have significant implications in many areas of research including but not limited to drug discovery, nutrition, bio- and chemical diversity analysis. The exploration of the coverage and diversity of the chemical space of compound databases can be carried out in different ways. The approach will largely depend on the criteria to define the chemical space that is commonly selected based on the goals of the study. This chapter discusses major compound databases of natural products and cheminformatics strategies that have been used to characterize the chemical space of natural products. Recent exemplary studies of the chemical space of natural products from different sources and their relationships with other compounds are also discussed. We also present novel chemical descriptors and data mining approaches that are emerging to characterize the chemical space of naturally occurring compounds.
Collapse
|
13
|
Pathak V, Pathak AK, Reynolds RC. Synthesis of Aza-acyclic Nucleoside Libraries of Purine, Pyrimidine, and 1,2,4-Triazole. ACS COMBINATORIAL SCIENCE 2019; 21:183-191. [PMID: 30653914 DOI: 10.1021/acscombsci.8b00136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Under the aegis of the Pilot Scale Library Program of the NIH Roadmap Initiative, a new library of propan-1-amine containing aza acyclic nucleosides was designed and prepared, and we now report a diverse set of 157 purine, pyrimidine, and 1,2,4-triazole- N-acetamide analogues. These new nucleoside analogues were prepared in a parallel high throughput solution-phase format. A set of diverse amines was reacted with several nucleobase N-propaldehydes utilizing reductive amination with sodium triacetoxyborohydride coupling to produce a small and diverse aza acyclic nucleoside library. All reactions were performed using 24-well reaction blocks and an automatic reagent-dispensing platform under an inert atmosphere. Final targets were purified on an automated system using solid sample loading prepacked cartridges and prepacked silica gel columns. All compounds were characterized by NMR and HRMS and were analyzed for purity by HPLC prior to submission to the Molecular Libraries Small Molecule Repository (MLSMR). Initial screening through the Molecular Libraries Probe Production Centers Network (MLPCN) demonstrated diverse and interesting biological activities.
Collapse
Affiliation(s)
- Vibha Pathak
- Chemistry Department, Drug Discovery Division, Southern Research, 2000 Ninth Avenue South, Birmingham, Alabama 35205, United States
| | - Ashish K. Pathak
- Chemistry Department, Drug Discovery Division, Southern Research, 2000 Ninth Avenue South, Birmingham, Alabama 35205, United States
| | - Robert C. Reynolds
- Department of Medicine, Division of Hematology and Oncology, University of Alabama at Birmingham, NP 2540 J, 1720 Second Avenue South, Birmingham, Alabama 35294-3300, United States
| |
Collapse
|
14
|
Kunkel C, Schober C, Oberhofer H, Reuter K. Knowledge discovery through chemical space networks: the case of organic electronics. J Mol Model 2019; 25:87. [DOI: 10.1007/s00894-019-3950-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 01/29/2019] [Indexed: 12/14/2022]
|
15
|
Reynisson J. Generation of Quality Hit Matter for Successful Drug Discovery Projects. Molecules 2019; 24:molecules24030381. [PMID: 30678174 PMCID: PMC6384824 DOI: 10.3390/molecules24030381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 01/18/2019] [Indexed: 11/26/2022] Open
Affiliation(s)
- Jóhannes Reynisson
- School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| |
Collapse
|
16
|
Saldívar-González FI, Valli M, Andricopulo AD, da Silva Bolzani V, Medina-Franco JL. Chemical Space and Diversity of the NuBBE Database: A Chemoinformatic Characterization. J Chem Inf Model 2018; 59:74-85. [DOI: 10.1021/acs.jcim.8b00619] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Fernanda I. Saldívar-González
- School of Chemistry, Department of Pharmacy, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Mexico City 04510, Mexico
| | - Marilia Valli
- Nuclei of Bioassays, Biosynthesis and Ecophysiology of Natural Products (NuBBE), Department of Organic Chemistry, Institute of Chemistry, Sao Paulo State University - UNESP, 14800-060 Araraquara, Sao Paulo, Brazil
| | - Adriano D. Andricopulo
- Laboratório de Química Medicinal e Computacional (LQMC), Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, Institute of Physics of Sao Carlos, University of Sao Paulo - USP, 13563-120 Sao Carlos, Sao Paulo, Brazil
| | - Vanderlan da Silva Bolzani
- Nuclei of Bioassays, Biosynthesis and Ecophysiology of Natural Products (NuBBE), Department of Organic Chemistry, Institute of Chemistry, Sao Paulo State University - UNESP, 14800-060 Araraquara, Sao Paulo, Brazil
| | - José L. Medina-Franco
- School of Chemistry, Department of Pharmacy, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Mexico City 04510, Mexico
| |
Collapse
|
17
|
Levré D, Arcisto C, Mercalli V, Massarotti A. ZINClick v.18: Expanding Chemical Space of 1,2,3-Triazoles. J Chem Inf Model 2018; 59:1697-1702. [PMID: 30419167 DOI: 10.1021/acs.jcim.8b00615] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
In the last years, we have investigated the click-chemical space covered by molecules containing the triazole ring and generated a database of 1,2,3-triazoles called ZINClick, starting from literature-reported alkynes and azides synthesizable in no more than three synthetic steps from commercially available products. This combinatorial database contains millions of 1,4-disubstituted 1,2,3-triazoles that are easily synthesizable. The library is regularly updated and can be freely downloaded from http://www.ZINClick.org . In this communication, the new implementation of ZINClick will be discussed as well as our new strategy for clustering the chemical space covered by 1,4-disubstituted 1,2,3-triazoles around their availability: from direct purchase to different degrees of synthetic feasibility of the compounds.
Collapse
Affiliation(s)
- Doriana Levré
- Dipartimento di Scienze del Farmaco , Università degli Studi del Piemonte Orientale "A. Avogadro" , Largo Donegani 2 , 28100 Novara , Italy
| | - Chiara Arcisto
- Dipartimento di Scienze del Farmaco , Università degli Studi del Piemonte Orientale "A. Avogadro" , Largo Donegani 2 , 28100 Novara , Italy
| | - Valentina Mercalli
- Dipartimento di Scienze del Farmaco , Università degli Studi del Piemonte Orientale "A. Avogadro" , Largo Donegani 2 , 28100 Novara , Italy
| | - Alberto Massarotti
- Dipartimento di Scienze del Farmaco , Università degli Studi del Piemonte Orientale "A. Avogadro" , Largo Donegani 2 , 28100 Novara , Italy
| |
Collapse
|
18
|
Alonso F, Quezada MJ, Gola GF, Richmond V, Cabrera GM, Barquero AA, Ramírez JA. A Minimalist Approach to the Design of Complexity-Enriched Bioactive Small Molecules: Discovery of Phenanthrenoid Mimics as Antiproliferative Agents. ChemMedChem 2018; 13:1732-1740. [DOI: 10.1002/cmdc.201800295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Fernando Alonso
- Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales; Universidad de Buenos Aires, Ciudad Universitaria; Ciudad Autónoma de Buenos Aires C1428EGA Argentina
- CONICET - Universidad de Buenos Aires; Unidad de Microanálisis y Métodos Físicos Aplicados a Química Orgánica (UMYMFOR), Ciudad Universitaria; Ciudad Autónoma de Buenos Aires C1428EGA Argentina
| | - María Josefina Quezada
- CONICET - Universidad de Buenos Aires; Instituto de Quimica Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Ciudad Universitaria; Ciudad Autónoma de Buenos Aires C1428EGA Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales; Universidad de Buenos Aires, Ciudad Universitaria; Ciudad Autónoma de Buenos Aires C1428EGA Argentina
| | - Gabriel F. Gola
- Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales; Universidad de Buenos Aires, Ciudad Universitaria; Ciudad Autónoma de Buenos Aires C1428EGA Argentina
- CONICET - Universidad de Buenos Aires; Unidad de Microanálisis y Métodos Físicos Aplicados a Química Orgánica (UMYMFOR), Ciudad Universitaria; Ciudad Autónoma de Buenos Aires C1428EGA Argentina
| | - Victoria Richmond
- Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales; Universidad de Buenos Aires, Ciudad Universitaria; Ciudad Autónoma de Buenos Aires C1428EGA Argentina
- CONICET - Universidad de Buenos Aires; Unidad de Microanálisis y Métodos Físicos Aplicados a Química Orgánica (UMYMFOR), Ciudad Universitaria; Ciudad Autónoma de Buenos Aires C1428EGA Argentina
| | - Gabriela M. Cabrera
- Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales; Universidad de Buenos Aires, Ciudad Universitaria; Ciudad Autónoma de Buenos Aires C1428EGA Argentina
- CONICET - Universidad de Buenos Aires; Unidad de Microanálisis y Métodos Físicos Aplicados a Química Orgánica (UMYMFOR), Ciudad Universitaria; Ciudad Autónoma de Buenos Aires C1428EGA Argentina
| | - Andrea A. Barquero
- CONICET - Universidad de Buenos Aires; Instituto de Quimica Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Ciudad Universitaria; Ciudad Autónoma de Buenos Aires C1428EGA Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales; Universidad de Buenos Aires, Ciudad Universitaria; Ciudad Autónoma de Buenos Aires C1428EGA Argentina
| | - Javier A. Ramírez
- Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales; Universidad de Buenos Aires, Ciudad Universitaria; Ciudad Autónoma de Buenos Aires C1428EGA Argentina
- CONICET - Universidad de Buenos Aires; Unidad de Microanálisis y Métodos Físicos Aplicados a Química Orgánica (UMYMFOR), Ciudad Universitaria; Ciudad Autónoma de Buenos Aires C1428EGA Argentina
| |
Collapse
|
19
|
Aydın A, Tugcu G. Toxicological assessment of epinephrine and norepinephrine by analog approach. Food Chem Toxicol 2018; 118:726-732. [PMID: 29913233 DOI: 10.1016/j.fct.2018.06.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 06/13/2018] [Accepted: 06/15/2018] [Indexed: 11/27/2022]
Abstract
Epinephrine and norepinephrine have been used in the management of anaphylactic reactions and cardiac resuscitation, along with treatment of asthma and glaucoma extensively, but their toxicological profiles are not yet completed. Based on this circumstance, various toxicological endpoints of epinephrine and norepinephrine were explored. Since there is a paucity of some endpoints' data, readacross was applied to fill the data gaps using analog approach. Along with structural similarity, biological and mechanistic plausibility were also considered in analog selection. The similarity justification and supporting experimental data were provided for uncertainty evaluation. Short term repeated dose toxicity values as NOAEL and LOAEL belonging to epinephrine were used to estimate the repeated dose toxicity of norepinephrine. The in vivo and in vitro mutagenicity tests were considered representative of genotoxicity. Both chemicals are showed to be non-genotoxic. They are experimentally reported to cause developmental and reproductive toxicity. For the carcinogenicity endpoint, a conclusion could not be reached because similar compounds were seen to show conflicting results.
Collapse
Affiliation(s)
- Ahmet Aydın
- Yeditepe University, Faculty of Pharmacy, Department of Toxicology, 34755, Ataşehir, İstanbul, Turkey.
| | - Gulcin Tugcu
- Yeditepe University, Faculty of Pharmacy, Department of Toxicology, 34755, Ataşehir, İstanbul, Turkey
| |
Collapse
|