A Chemographic Audit of Anti-Coronavirus Structure-Activity Information from Public Databases (ChEMBL)

Horvath, Dragos; Orlov, Alexey A.; Osolodkin, Dmitry I.; Marcou, Gilles; Ишмухаметов, А. А.; Varnek, Alexandre

doi:10.26434/chemrxiv.12104010.v1

“…It is also highlighted that the concept of chemical space has had recent applications in Alzheimer's disease and in emerging diseases such as COVID-19. Particularly for COVID-19, chemical space visualization proved to be a fast way to analyze and describe the huge chemical space of known antiviral compounds [71,72]. For instance, GTM is one of the methods used to represent the chemical space of compounds obtained from medicinal chemistry efforts against coronaviruses (CoVs) [72].…”

Section: Meta-analysis Of Applications Of Chemical Spacementioning

confidence: 99%

“…Particularly for COVID-19, chemical space visualization proved to be a fast way to analyze and describe the huge chemical space of known antiviral compounds [71,72]. For instance, GTM is one of the methods used to represent the chemical space of compounds obtained from medicinal chemistry efforts against coronaviruses (CoVs) [72]. In particular, GTMs helped highlight the structural relationship between antivirals of different categories, predict their polypharmacological profiles, and emphasize frequently encountered chemotypes.…”

Section: Meta-analysis Of Applications Of Chemical Spacementioning

confidence: 99%

Approaches for enhancing the analysis of chemical space for drug discovery

Saldívar-González

¹

,

Medina-Franco

²

2022

Expert Opinion on Drug Discovery

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Chemical space is a powerful, general, and practical conceptual framework in drug discovery and other areas in chemistry that addresses the diversity of molecules and it has various applications. Moreover, chemical space is a cornerstone of chemoinformatics as a scientific discipline. In response to the increase in the set of chemical compounds in databases, generators of chemical structures, and tools to calculate molecular descriptors, novel approaches to generate visual representations of chemical space in low dimensions are emerging and evolving. Such approaches include a wide range of commercial and free applications, software, and open-source methods. Herein, the current state of chemical space in drug design and discovery is reviewed. The topics discussed herein include advances for efficient navigation in chemical space, the use of this concept in assessing the diversity of different data sets, exploring structure-property/activity relationships for one or multiple endpoints, and compound library design. Recent advances in methodologies for generating visual representations of chemical space have been highlighted, thereby emphasizing open-source methods. It is concluded that quantitative and qualitative generation and analysis of chemical space require novel approaches for handling the increasing number of molecules and their information available in chemical databases (including emerging ultra-large libraries). In addition, it is of utmost importance to note that chemical space is a conceptual framework that goes beyond visual representation in low dimensions. However, the graphical representation of chemical space has several practical applications in drug discovery and beyond.

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“…In independent work, GTM was used to visualize a large library of 40 million fragment-like molecules [ 65 ] and the entire ZINC database of purchasable compounds, relative to 1.6 million biologically relevant molecules in ChEMBL [ 66 ]. A similar chemography approach using GTM was implemented to navigate the chemical space of 800 million organic molecules and identify "anti-CoV" regions [ 67 ]. More recently, GTM was used as a framework to visualize interactively the chemical space of a large database of natural products (COCONUT, vide supra) and ChEMBL [ 22 ].…”

Section: Resources For the Visualization Of Chemical Spacementioning

confidence: 99%

Progress on open chemoinformatic tools for expanding and exploring the chemical space

Medina-Franco

¹

,

Sánchez-Cruz

²

,

López-López

³

et al. 2021

J Comput Aided Mol Des

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The concept of chemical space is a cornerstone in chemoinformatics, and it has broad conceptual and practical applicability in many areas of chemistry, including drug design and discovery. One of the most considerable impacts is in the study of structure–property relationships where the property can be a biological activity or any other characteristic of interest to a particular chemistry discipline. The chemical space is highly dependent on the molecular representation that is also a cornerstone concept in computational chemistry. Herein, we discuss the recent progress on chemoinformatic tools developed to expand and characterize the chemical space of compound data sets using different types of molecular representations, generate visual representations of such spaces, and explore structure–property relationships in the context of chemical spaces. We emphasize the development of methods and freely available tools focusing on drug discovery applications. We also comment on the general advantages and shortcomings of using freely available and easy-to-use tools and discuss the value of using such open resources for research, education, and scientific dissemination.

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Approaches for enhancing the analysis of chemical space for drug discovery

Saldívar-González

¹

,

Medina-Franco

²

2022

Preprint

View full text Add to dashboard Cite

Chemical space is a powerful, general, and practical conceptual framework in drug discovery and other areas in chemistry that addresses the diversity of molecules and it has various applications. Moreover, chemical space is a cornerstone of chemoinformatics as a scientific discipline. In response to the increase in the set of chemical compounds in databases, generators of chemical structures, and tools to calculate molecular descriptors, novel approaches to generate visual representations of chemical space in low dimensions are emerging and evolving. Such approaches include a wide range of commercial and free applications, software, and open-source methods. Herein, the current state of chemical space in drug design and discovery is reviewed. The topics discussed herein include advances for efficient navigation in chemical space, the use of this concept in assessing the diversity of different data sets, exploring structure-property/activity relationships for one or multiple endpoints, and compound library design. Recent advances in methodologies for generating visual representations of chemical space have been highlighted, thereby emphasizing open-source methods. It is concluded that quantitative and qualitative generation and analysis of chemical space require novel approaches for handling the increasing number of molecules and their information available in chemical databases (including emerging ultra-large libraries). In addition, it is of utmost importance to note that chemical space is a conceptual framework that goes beyond visual representation in low dimensions. However, the graphical representation of chemical space has several practical applications in drug discovery and beyond.

show abstract

A Chemographic Audit of Anti-Coronavirus Structure-Activity Information from Public Databases (ChEMBL)

Cited by 4 publications

References 26 publications

Approaches for enhancing the analysis of chemical space for drug discovery

Approaches for enhancing the analysis of chemical space for drug discovery

Progress on open chemoinformatic tools for expanding and exploring the chemical space

Approaches for enhancing the analysis of chemical space for drug discovery

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