Chemical Multiverse: An Expanded View of Chemical Space

Molecular Informatics, Journal Year: 2022, Volume and Issue: 41(11)

Published: Aug. 2, 2022

Technological advances and practical applications of the chemical space concept in drug discovery, natural product research, other research areas have attracted scientific community's attention. The large- ultra-large spaces are associated with significant increase number compounds that can potentially be made exist increasing experimental calculated descriptors, emerging encode molecular structure and/or property aspects molecules. Due to importance continued evolution compound libraries, herein, we discuss definitions proposed literature for emphasize convenience, discussed use complementary descriptors obtain a comprehensive view data sets. In this regard, introduce term multiverse refer analysis sets through several spaces, each defined by different set representations. is contrasted related idea: consensus space.

Language: Английский

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Molecular similarity: Theory, applications, and perspectives

Artificial Intelligence Chemistry, Journal Year: 2024, Volume and Issue: 2(2), P. 100077 - 100077

Published: Aug. 31, 2024

Molecular similarity pervades much of our understanding and rationalization chemistry. This has become particularly evident in the current data-intensive era chemical research, with measures serving as backbone many Machine Learning (ML) supervised unsupervised procedures. Here, we present a discussion on role molecular drug design, space exploration, "art" generation, representations, more. We also discuss more recent topics similarity, like ability to efficiently compare large libraries.

Language: Английский

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The pursuit of accurate predictive models of the bioactivity of small molecules

Chemical Science, Journal Year: 2024, Volume and Issue: 15(6), P. 1938 - 1952

Published: Jan. 1, 2024

Property prediction is a key interest in chemistry. For several decades there has been continued and incremental development of mathematical models to predict properties. As more data generated accumulated, seems be areas opportunity develop with increased accuracy. The same true if one considers the large developments machine deep learning models. However, along development, issues challenges remain and, data, new emerge such as quality quantity reliability model reproducibility. Herein, we discuss status accuracy predictive present authors' perspective direction field, emphasizing on good practices. We focus bioactive properties small molecules relevant for drug discovery, agrochemical, food chemistry, natural product research, related fields.

Language: Английский

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Toward structure–multiple activity relationships (SMARts) using computational approaches: A polypharmacological perspective

Drug Discovery Today, Journal Year: 2024, Volume and Issue: 29(7), P. 104046 - 104046

Published: May 27, 2024

Language: Английский

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Chemical space as a unifying theme for chemistry

Journal of Cheminformatics, Journal Year: 2025, Volume and Issue: 17(1)

Published: Jan. 16, 2025

Chemistry has diversified from a basic understanding of the elements to studying millions highly diverse molecules and materials, which together are conceptualized as chemical space. A map this space where distances represent similarities between compounds can mutual relationships different subfields chemistry help discipline be viewed understood globally.

Language: Английский

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Chemoinformatics and artificial intelligence colloquium: progress and challenges in developing bioactive compounds

Journal of Cheminformatics, Journal Year: 2022, Volume and Issue: 14(1)

Published: Dec. 2, 2022

We report the main conclusions of first Chemoinformatics and Artificial Intelligence Colloquium, Mexico City, June 15-17, 2022. Fifteen lectures were presented during a virtual public event with speakers from industry, academia, non-for-profit organizations. Twelve hundred ninety students academics more than 60 countries. During meeting, applications, challenges, opportunities in drug discovery, de novo design, ADME-Tox (absorption, distribution, metabolism, excretion toxicity) property predictions, organic chemistry, peptides, antibiotic resistance discussed. The program along recordings all sessions are freely available at https://www.difacquim.com/english/events/2022-colloquium/ .

Language: Английский

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Navigating the Chemical Space and Chemical Multiverse of a Unified Latin American Natural Product Database: LANaPDB

Pharmaceuticals, Journal Year: 2023, Volume and Issue: 16(10), P. 1388 - 1388

Published: Sept. 30, 2023

The number of databases natural products (NPs) has increased substantially. Latin America is extraordinarily rich in biodiversity, enabling the identification novel NPs, which encouraged both development and implementation those that are being created or under development. In a collective effort from several American countries, herein we introduce first version Natural Products Database (LANaPDB), public compound collection gathers chemical information NPs contained diverse this geographical region. current LANaPDB unifies six countries contains 12,959 structures. structural classification showed most abundant compounds terpenoids (63.2%), phenylpropanoids (18%) alkaloids (11.8%). From analysis distribution properties pharmaceutical interest, it was observed many satisfy some drug-like rules thumb for physicochemical properties. concept multiverse employed to generate multiple spaces two different fingerprints dimensionality reduction techniques. Comparing with FDA-approved drugs major open-access repository COCONUT, concluded space covered by completely overlaps COCONUT and, regions, drugs. will be updated, adding more each database, plus addition other countries.

Language: Английский

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Art driven by visual representations of chemical space

Journal of Cheminformatics, Journal Year: 2023, Volume and Issue: 15(1)

Published: Oct. 21, 2023

Science and art have been connected for centuries. With the development of new computational methods, scientific disciplines emerged, such as chemistry, related fields, cheminformatics. Chemoinformatics is grounded on chemical space concept: a multi-descriptor in which structures are described. In several practical applications, visual representations compound datasets low-dimensional plots helpful identifying patterns. However, authors propose that can also be used artistic expressions. This manuscript introduces an approach to merging with chemoinformatics through space. As case studies, we portray food chemicals other compounds generate visually appealing graphs twofold benefits: sharing knowledge developing pieces driven by chemoinformatics. The visualization will help increase application chemistry contribute general education dissemination All code data sets reproduce representation presented freely available at https://github.com/DIFACQUIM/Art-Driven-by-Visual-Representations-of-Chemical-Space- . Scientific contribution: Chemical concept create digital tool train introduce students

Language: Английский

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Chemical Multiverse and Diversity of Food Chemicals

Journal of Chemical Information and Modeling, Journal Year: 2024, Volume and Issue: 64(4), P. 1229 - 1244

Published: Feb. 15, 2024

Food chemicals have a fundamental role in our lives, with an extended impact on nutrition, disease prevention, and marked economic implications the food industry. The number of chemical compounds public databases has substantially increased past few years, which can be characterized using chemoinformatics approaches. We other groups explored libraries containing up to 26,500 compounds. This study aimed analyze contents, diversity, coverage space additives and, from here on, components. approach components addressed this is database more than 70,000 compounds, including those predicted via

Language: Английский

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Towards Decoding Hepatotoxicity of Approved Drugs through Navigation of Multiverse and Consensus Chemical Spaces

Biomolecules, Journal Year: 2023, Volume and Issue: 13(1), P. 176 - 176

Published: Jan. 14, 2023

Drug-induced liver injury (DILI) is the principal reason for failure in developing drug candidates. It most common to withdraw from market after a has been approved clinical use. In this context, data animal models, function tests, and chemical properties could complement each other understand DILI events better prevent them. Since space concept improves decision-making design related prediction of structure–property relationships, side effects, polypharmacology activity (uniquely mentioning recent advances), it an attractive approach combining different phenomena influencing (e.g., individual “chemical spaces”) exploring all simultaneously integrated analysis DILI-relevant space. However, currently, no systematic methods allow fusion collection spaces collect types on unique representation, namely “consensus space.” This study first report that implements consider criteria facilitate DILI-related events. particular, highlights importance analyzing together vitro topology, bond order, atom types, presence rings, ring sizes, aromaticity compounds encoded RDKit fingerprints). These be aimed at improving understanding

Language: Английский

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