BioPhytMol: a drug discovery community resource on anti-mycobacterial phytomolecules and plant extracts

Abstract

BackgroundTuberculosis (TB) is the second leading cause of death from a single infectious organism, demanding attention towards discovery of novel anti-tubercular compounds. Natural products or their derivatives have provided more than 50% of all existing drugs, offering a chemically diverse space for discovery of novel drugs.DescriptionBioPhytMol has been designed to systematically curate and analyze the anti-mycobacterial natural product chemical space. BioPhytMol is developed as a drug-discovery community resource with anti-mycobacterial phytomolecules and plant extracts. Currently, it holds 2582 entries including 188 plant families (692 genera and 808 species) from global flora, manually curated from literature. In total, there are 633 phytomolecules (with structures) curated against 25 target mycobacteria. Multiple analysis approaches have been used to prioritize the library for drug-like compounds, for both whole cell screening and target-based approaches. In order to represent the multidimensional data on chemical diversity, physiochemical properties and biological activity data of the compound library, novel approaches such as the use of circular graphs have been employed.ConclusionBioPhytMol has been designed to systematically represent and search for anti-mycobacterial phytochemical information. Extensive compound analyses can also be performed through web-application for prioritizing drug-like compounds. The resource is freely available online at http://ab-openlab.csir.res.in/biophytmol/.Graphical AbstractBioPhytMol: a drug discovery community resource on anti-mycobacterial phytomolecules and plant extracts generated using Crowdsourcing. The platform comprises of manually curated data on antimycobacterial natural products along with tools to perform structure similarity and visualization. The platform allows for prioritization of drug like natural products for antimycobacterial drug discovery.Electronic supplementary materialThe online version of this article (doi:10.1186/s13321-014-0046-2) contains supplementary material, which is available to authorized users.

Antimycobacterial activity of medicinal plants used by the Mayo people of Sonora, Mexico

“…Plant species with the best antimycobacterial activities studied here(R. precatoria, E. albomarginata and H. annuus) correspond to the families Leguminosae, Euphorbiaceae and Compositae, which is consistent with the findings published in the BioPhytMol database for antimycobacterial plants and compounds(Sharma et al, 2014), in which the 5 families Compositae, Leguminosae, Rutaceae, Lamiaceae and Euphorbiaceae are listed as having higher numbers of active plants. Additionally, some crude extracts of Aloysia sonorensis Moldenke (leaves), A. mexicana (shoots), Bursera laxiflora S. Watson (cortex), Citrus limetta Risso (leaves), C. alata (flowers and fruits), Datura discolor Bernh.…”

“…albomarginata was the second most active plant, with MICs of 250 µg/mL for extracts obtained with n-hexane, dichloromethane and EtOAc, and bactericidal activities of equal or higher concentrations ( showed 55% inhibition of Mtb growth, evaluated using a BACTEC 460 at 55 µg/mL (Graham et al, 2003;Sharma et al, 2014). Several steroidal and terpenoid compounds have been isolated from the Euphorbia genus: from the EtOAc fraction of a methanolic extract of shoots of Euphorbia microsciadia Boiss, the pentacyclic triterpenes betulinic acid, oleanolic acid and ursolic acid (Ayatollahi et al, 2011) were obtained, with Mtb antimycobacterial activity levels of 14-32 µg/mL for betulin, 12.5-25 µg/mL for ursolic acid and 25-50 µg/mL for oleanolic acid (Jiménez-Arellanes et al, 2013b).…”

Investigation of the anti-aging properties of allicin from <i>Allium sativum</i> L bulb extracts by a reverse docking approach

“…We used reference inhibitor reference for validating the docking results. The potential inhibitors were screened using DruLito based on Lipinski's rule [20]. The molecular docking result was analysed by LigPlus V.2.0 to understand the details of the interactions between ligands and the protein.…”

Updates in metabolomics tools and resources: 2014–2015

“…Each metabolite entry in TMDB contains an average of 24 separate data fields, such as compound structure, formula, molecular weight, name, CAS registry number, compound type, health benefits, reference literature, NMR, MS data, and the corresponding IDs from databases such as HMDB and PubMed. BioPhytMol database is a drug‐discovery community resource and database with anti‐mycobacterial phytomolecules and plant extracts that holds 2582 entries including collective information for 188 plant families (for 692 genera and 808 species) from global flora, that were manually curated from literature including 633 phytomolecules (with structures) curated against 25 target mycobacteria . The ESSential OIL DataBase (EssOilDB) is an electronic database designed to provide knowledge resource for plant essential oils that allows user queries on volatile profiles of native, invasive, normal, or stressed plants across taxonomic clades, geographical locations, and several other biotic and abiotic influences .…”