creators_name: Nanduri, Ravikanth
creators_name: Kalra, Rashi
creators_name: Bhagyaraj, Ella
creators_name: Chacko, Anuja P
creators_name: Ahuja, Nancy
creators_name: Tiwari, Drishti
creators_name: Kumar, Sumit
creators_name: Jain, Monika
creators_name: Parkesh, Raman
creators_name: Gupta, Pawan
type: article
datestamp: 2019-03-18 12:56:24
lastmod: 2019-12-12 09:53:16
metadata_visibility: show
title: AutophagySMDB: a curated database of small molecules that modulate protein targets regulating autophagy.
ispublished: pub
subjects: QR
keywords: Autophagy; autophagySMDB; database; drug target; small molecule
note: Copyright of this article belongs to T&F.
abstract: Macroautophagy/autophagy is a complex self-degradative mechanism responsible for clearance of non functional organelles and proteins. A range of factors influences the autophagic process, and disruptions in autophagy-related mechanisms lead to disease states, and further exacerbation of disease. Despite in-depth research into autophagy and its role in pathophysiological processes, the resources available to use it for therapeutic purposes are currently lacking. Herein we report the Autophagy Small Molecule Database (AutophagySMDB; http://www.autophagysmdb.org/ ) of small molecules and their cognate protein targets that modulate autophagy. Presently, AutophagySMDB enlists ~10,000 small molecules which regulate 71 target proteins. All entries are comprised of information such as EC50 (half maximal effective concentration), IC50 (half maximal inhibitory concentration), Kd (dissociation constant) and Ki (inhibition constant), IUPAC name, canonical SMILE, structure, molecular weight, QSAR (quantitative structure activity relationship) properties such as hydrogen donor and acceptor count, aromatic rings and XlogP. AutophagySMDB is an exhaustive, cross-platform, manually curated database, where either the cognate targets for small molecule or small molecules for a target can be searched. This database is provided with different search options including text search, advanced search and structure search. Various computational tools such as tree tool, cataloging tools, and clustering tools have also been implemented for advanced analysis. Data and the tools provided in this database helps to identify common or unique scaffolds for designing novel drugs or to improve the existing ones for autophagy small molecule therapeutics. The approach to multitarget drug discovery by identifying common scaffolds has been illustrated with experimental validation. Abbreviations: AMPK: AMP-activated protein kinase; ATG: autophagy related; AutophagySMDB: autophagy small molecule database; BCL2: BCL2, apoptosis regulator; BECN1: beclin 1; CAPN: calpain; MTOR: mechanistic target of rapamycin kinase; PPARG: peroxisome proliferator activated receptor gamma; SMILES: simplified molecular input line entry system; SQSTM1: sequestosome 1; STAT3: signal transducer and activator of transcription.
date: 2019-07-15
date_type: published
publication: Autophagy
volume: 15
number: 7
publisher: T&F
pagerange: 1280-1295
refereed: TRUE
issn: 1554-8635
official_url: https://www.tandfonline.com/doi/abs/10.1080/15548627.2019.1571717?journalCode=kaup20
citation:   Nanduri, Ravikanth and Kalra, Rashi and Bhagyaraj, Ella and Chacko, Anuja P and Ahuja, Nancy and Tiwari, Drishti and Kumar, Sumit and Jain, Monika and Parkesh, Raman and Gupta, Pawan  (2019) AutophagySMDB: a curated database of small molecules that modulate protein targets regulating autophagy.  Autophagy, 15 (7).  pp. 1280-1295.  ISSN 1554-8635