REVIEW | doi:10.20944/preprints202004.0012.v1
Subject: Chemistry, General & Theoretical Chemistry Keywords: chemoinformatics; chemical space; database; LANaPD; molecular diversity; drug discovery; natural sources
Online: 2 April 2020 (04:47:13 CEST)
Around the World, the number of compound databases of natural products in the public domain is rising. This is in line with the increasing synergistic combination of natural product research and chemoinformatics. Towards this global endeavor, countries in Latin America are assembling, curating, and analyzing the contents and diversity of natural products available in their geographical regions. In this manuscript we collect and analyze the efforts that countries in Latin America have made so far to build natural product databases. We further encourage the scientific community in particular in Latin America, to continue their efforts to building quality natural product databases and, whenever possible, to make them publicly accessible. It is proposed that all compound collections could be assembled into a unified resource called LANaPD: Latin America Natural Products Database. Opportunities and challenges to build, distribute, and maintain LANaPD are also discussed
REVIEW | doi:10.20944/preprints202208.0230.v1
Subject: Chemistry, General & Theoretical Chemistry Keywords: chemoinformatics; compound databases; chemical space; diversity; drug discovery; openscience; pseudo-natural product
Online: 12 August 2022 (08:39:40 CEST)
Natural products (NPs) are a rich source of structurally novel molecules, and the chemical space they encompass is far from being fully explored. Over history, NPs have represented a significant source of bioactive molecules and have served as a source of inspiration for developing many drugs on the market. On the other hand, computer-aided drug design (CADD) has contributed to drug discovery research, mitigating costs and time. In this sense, compound databases represent a fundamental element for the CADD. This work reviews the progress toward developing compound databases of natural origin, particularly databases developed in Latin America, and their practical applications in the drug discovery area. We also survey the computational methods, emphasizing chemoinformatic approaches to profile natural product databases.
ARTICLE | doi:10.20944/preprints202008.0690.v1
Subject: Chemistry, General & Theoretical Chemistry Keywords: Theopapuamides A-D; Virtual Screening; Chemoinformatics; Conceptual DFT; Computational Peptidology; Bioavailability; Bioactivity Scores; ADMET
Online: 31 August 2020 (03:57:38 CEST)
This work presents the results of a computational study of the chemical reactivity and bioactivity properties of the members of the Theopapuamides A-D family of marine peptides by making use of our own proposed methodology named Computational Peptidology (CP) that has been successfully considered in previous studies of this kind of molecular systems. CP allowed for the determination of the global and local descriptors that come from Conceptual Density Functional Theory (CDFT) that can give an idea of the chemical reactivity properties of the marine natural products under study which are already known to be related to their bioactivity. At the same time, the validity of the procedure based on the adoption of the KID (Koopmans in DFT) technique as well as the MN12SX/Def2TZVP/H2O model chemistry has been successfully verified. Together with several Chemoinformatic tools that can be used for the improvement of process of Virtual Screening, some additional properties of these marine peptides were identified related to their ability to behave as useful drugs. With the further object of analyzing their bioactivity some parameters of usefulness for future QSAR studies, their predicted biological targets and the the ADMET (Absorption, Distribution, Metabolism, Excretion and Toxicity) parameters related to the Theopapuamides A-D pharmacokinetics are also reported.
ARTICLE | doi:10.20944/preprints201811.0627.v1
Subject: Chemistry, General & Theoretical Chemistry Keywords: chemical space; chemical data set; chemoinformatics; consensus diversity plot; drug discovery; molecular diversity; visualization
Online: 30 November 2018 (10:06:15 CET)
Compound databases of natural products have a major impact on drug discovery projects and other areas of research. The number of databases in the public domain with compounds from natural origin is increasing. Several countries have initiatives in place to construct and maintain compound databases that are representative of their diversity. Examples are Brazil, France, Panama and recently Vietnam. Herein, we discuss the first version of BIOFACQUIM, a novel compound database with natural products isolated and characterized in Mexico. We discuss its construction, curation, and a complete chemoinformatic characterization of the content and coverage in chemical space. It is reported the profile of physicochemical properties, scaffold content, and diversity, as well as structural diversity based on molecular fingerprints. BIOFACQUIM is freely available.
REVIEW | doi:10.20944/preprints201807.0116.v1
Subject: Chemistry, Medicinal Chemistry Keywords: chemical space; chemoinformatics; data mining; databases; DNMT inhibitors; drug discovery; epi-informatics; molecular modeling; similarity searching; virtual screening
Online: 6 July 2018 (10:04:44 CEST)
Naturally occurring small molecules include a large variety of natural products from different sources that have confirmed activity against epigenetic targets. In this work we review chemoinformatic, molecular modeling and other computational approaches that have been used to uncover natural products as inhibitors of DNA metiltransferases, a major family of epigenetic targets with significant potential for the treatment of cancer and several other diseases. Examples of these computational approaches include docking, similarity-based virtual screening, and pharmacophore modeling. It is also commented the chemoinformatic-based exploration of the chemical space of naturally occurring compounds as epigenetic modulators which may have significant implications in epigenetic drug discovery and nutriepigenetics.