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
ARTICLE | doi:10.20944/preprints201811.0574.v1
Subject: Chemistry, Medicinal Chemistry Keywords: activity cliff; activity landscape plotter; epigenetics; docking; drug discovery; D-tools; molecular dynamics; Epi-polypharmacology; SmART; structure-activity relationships
Online: 26 November 2018 (07:14:05 CET)
In this work we discuss the insights from activity landscape, docking and molecular dynamics towards the understanding of the structure-activity relationships of dual inhibitors of major epigenetic targets: lysine metiltransferase (G9a) and DNA metiltranferase 1 (DNMT1). The study was based on a novel data set of 50 published compounds with reported experimental activity for both targets. The activity landscape analysis revealed the presence of activity cliffs, e.g., pairs of compounds with high structure similarity but large activity difference. Activity cliffs were further rationalized at the molecular level by means of molecular docking and dynamics simulations that led to the identification of interactions with key residues involved in the dual activity or selectivity with the epigenetic targets.
ARTICLE | doi:10.20944/preprints202111.0125.v1
Subject: Chemistry, Medicinal Chemistry Keywords: artificial intelligence; de novo design; fragment-based drug discovery; HIV-1 inhibitors; pseudo natural products
Online: 8 November 2021 (09:23:49 CET)
The acquired immunodeficiency syndrome (AIDS) caused by the human immunodeficiency virus (HIV) continues to be a public health problem. In 2020, 680,000 people died from HIV-related causes, and 1.5 million people were infected. Antiretrovirals are only a way to control HIV infection but not to cure AIDS. As such, effective treatment must be developed to control AIDS. Developing a drug is not an easy task, and there is an enormous amount of work and economic resources invested. For this reason, it is highly convenient to employ computer-aided drug design methods, which can help generate and identify novel molecules. Using the de novo design, new novel molecules can be developed using fragments as building blocks. In this work, we develop a virtual-focused compound library of HIV-1 viral protease inhibitors from natural product fragments. Natural products are characterized by a large diversity of functional groups, many sp3 atoms, and chiral centers. Pseudo-natural products are a combination of natural products fragments that keep the desired structural characteristics from different natural products. An interactive version of chemical space visualization of virtual compounds focused on HIV-1 viral protease inhibitors from natural product fragments is freely available at https://figshare.com/s/ceb58d58e8f5585ce67e.
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.