Profiling Chemobiological Connection between Natural Product and Target Space Based on Systematic Analysis DOI Open Access

Disheng Wang,

Xue Li,

Yicheng Miao

et al.

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(14), P. 11265 - 11265

Published: July 10, 2023

Natural products provide valuable starting points for new drugs with unique chemical structures. Here, we retrieve and join the LOTUS natural product database ChEMBL interaction to explore relations rhythm between features of biotarget spaces. Our analysis revealed biogenic pathways species taxonomy. Nitrogen-containing were more likely achieve high activity have a higher potential become candidate compounds. An apparent trend existed in target space originating from different biological sources. Highly active alkaloids related targets neurodegenerative or neural diseases. Oligopeptides polyketides mainly associated protein phosphorylation HDAC receptors. Fatty acids readily intervened various physiological processes involving prostanoids leukotrienes. We also used FusionDTA, deep learning model, predict affinity all 622 therapeutic drug targets, exploring products. data exploration provided global perspective on gaps chemobiological compounds through systematic prediction their space, which can be design repurposing.

Language: Английский

Molecular similarity: Theory, applications, and perspectives DOI Creative Commons

Kenneth López‐Pérez,

Juan F. Avellaneda-Tamayo, Lexin Chen

et al.

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

Citations

12
How Do Microbial Metabolites Interact with Their Protein Targets? DOI

Mario Astigarraga,

Andrés Sánchez-Ruiz,

Aminata Diop-Aw

et al.

Journal of Chemical Information and Modeling, Journal Year: 2025, Volume and Issue: 65(1), P. 201 - 213

Published: Jan. 2, 2025

The design of drugs and nutraceutics that mimic microbial metabolites is an emerging drug modality in medicinal chemistry attempts to modulate the myriad interactions these molecules establish with host proteins. Understanding how interact their target proteins key perform a rational metabolite mimetic for therapeutic usage. In present work, we address this question by analyzing functional groups they display set more than 71K protein–metabolite from PDB. Significant differences group distributions, chemical features, co-occurrences are observed distinct subsets molecules. same true distributions interaction types. By correlating both data sets, able explain patterns terms patterns. These results will shed light on novel purposes.

Language: Английский

Citations

1
Chemical Multiverse and Diversity of Food Chemicals DOI Creative Commons
Juan F. Avellaneda-Tamayo, Ana L. Chávez‐Hernández, Diana L. Prado‐Romero

et al.

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

Citations

5
Multidisciplinary approach combining food metabolomics and epidemiology identifies meglutol as an important bioactive metabolite in tempe, an Indonesian fermented food DOI Creative Commons
Marvin Nathanael Iman, Danielle E. Haslam, Liming Liang

et al.

Food Chemistry, Journal Year: 2024, Volume and Issue: 446, P. 138744 - 138744

Published: Feb. 16, 2024

Language: Английский

Citations

4
Prediction, Discovery, and Characterization of Plant- and Food-Derived Health-Beneficial Bioactive Peptides DOI Open Access
Martin Kussmann

Nutrients, Journal Year: 2022, Volume and Issue: 14(22), P. 4810 - 4810

Published: Nov. 14, 2022

Nature may have the answer to many of our questions about human, animal, and environmental health. Natural bioactives, especially when harvested from sustainable plant food sources, provide a plethora molecular solutions nutritionally actionable, chronic conditions. The spectrum these conditions, such as metabolic, immune, gastrointestinal disorders, has changed with prolonged human life span, which should be matched an appropriately extended health would in turn favour more care: “adding years adding years”. To date, bioactive peptides been undervalued underexploited ingredients drugs. future translational science on peptides—and natural bioactives general—is being built (a) systems-level rather than reductionist strategies for understanding their interdependent, at times synergistic, functions; (b) leverage artificial intelligence prediction discovery, thereby significantly reducing time idea concept finished consumers patients. This new strategy follows path benefit definition via design and, eventually, validation production.

Language: Английский

Citations

11
Identifying and Filling the Chemobiological Gaps of Gut Microbial Metabolites DOI

Cristian Orgaz,

Andrés Sánchez-Ruiz, Gonzalo Colmenarejo

et al.

Journal of Chemical Information and Modeling, Journal Year: 2024, Volume and Issue: 64(17), P. 6778 - 6798

Published: Aug. 21, 2024

Human gut microbial metabolites are currently undergoing much research due to their involvement in multiple biological processes that important for health, including immunity, metabolism, nutrition, and the nervous system. Metabolites exert effect through interaction with host bacterial proteins, suggesting use of "metabolite-mimetic" molecules as drugs nutraceutics. In present work, we retrieve analyze full set published interactions these compounds human microbiome-relevant proteins find patterns structure, chemical class, target origins. addition, virtual screening expand (more than 4-fold) interactions, validate them retrospective analyses, bioinformatic tools prioritize based on relevance. this way, fill many chemobiological gaps observed data. By providing expect speed up clarification space by reliable predictions fast, focused experimental testing.

Language: Английский

Citations

2
Analysis of metabolites in human gut: illuminating the design of gut-targeted drugs DOI Creative Commons

Alberto Gil-Pichardo,

Andrés Sánchez-Ruiz, Gonzalo Colmenarejo

et al.

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

Published: Oct. 13, 2023

Abstract Gut-targeted drugs provide a new drug modality besides that of oral, systemic molecules, could tap into the growing knowledge gut metabolites bacterial or host origin and their involvement in biological processes health through interaction with targets (bacterial host, too). Understanding properties can guidance for design gut-targeted drugs. In present work we analyze large set metabolites, both shared serum only gut, compare them oral We find patterns specific these two subsets be used to targeting gut. addition, develop openly share Super Learner model predict permanence, order aid molecules appropriate profiles remain resulting putatively reduced secondary effects better pharmacokinetics.

Language: Английский

Citations

4
Identifying and Filling the Chemobiological Gaps of Gut Microbial Metabolites DOI Creative Commons

Cristian Orgaz,

Andrés Sánchez-Ruiz, Gonzalo Colmenarejo

et al.

Published: June 12, 2024

Human gut microbial metabolites are currently undergoing much research due to their involvement in multiple biological processes important for health, including immunity, metabolism, nutrition, and the nervous system. Metabolites exert effect through interaction with host bacterial proteins, suggesting use of “metabolite-mimetic” molecules as drugs nutraceutics. In present work, we retrieve analyze full set published interactions these compounds human microbiome-relevant find patterns structure, chemical class, target origins. addition, virtual screening expand (> 4-fold) interactions, validate them retrospective analyses, bioinformatic tools prioritize based on relevance. this way, fill many chemobiological gaps observed data. By providing expect speed up clarification space compounds, by reliable predictions fast, focused experimental testing.

Language: Английский

Citations

1
Quimioinformática, Inteligencia Artificial y la Química de Alimentos DOI Creative Commons
Juan F. Avellaneda-Tamayo, Andrés Sánchez-Ruiz,

Biljana Savic

et al.

Deleted Journal, Journal Year: 2024, Volume and Issue: 27

Published: June 12, 2024

La Quimioinformática y la Inteligencia Artificial (IA) son disciplinas con métodos que, actualmente, contribuyen al desarrollo de varias áreas del conocimiento Química, por medio almacenamiento, organización, búsqueda datos químicos, el procesamiento modelado, para generar información a nivel molecular las relaciones estructura-propiedad los compuestos químicos existentes determinar propiedades nuevos, partir diseño base en un perfil deseado. Todas estas técnicas se han utilizado Química Alimentos, lo que objetivo este artículo es analizar bases Quimioinformáticos IA su aplicación estudio alimentos.

Citations

1
Analysis of Metabolites in Human Gut: Illuminating the Design of Gut-Targeted Drugs DOI Creative Commons

Alberto Gil-Pichardo,

Andrés Sánchez-Ruiz, Gonzalo Colmenarejo

et al.

Published: Aug. 21, 2023

Gut-targeted drugs provide a new drug modality besides that of oral, systemic molecules, could tap from the growing knowledge gut metabolites bacterial or host origin and their involvement in biological processes health through interaction with targets (bacterial host, too). Understanding properties can hints for design gut-targeted drugs. In present work we analyze large set metabolites, both shared serum only gut, compare them oral We find patterns specific these two subsets be used to targeting gut. addition, develop openly share Super Learner model predict permanence, order aid molecules appropriate profiles remain resulting putatively reduced secondary effects distribution issues.

Language: Английский

Citations

1