HAMdb: a database of human autophagy modulators with specific pathway and disease information

Abstract

Autophagy is an important homeostatic cellular recycling mechanism responsible for degrading unnecessary or dysfunctional cellular organelles and proteins in all living cells. In addition to its vital homeostatic role, this degradation pathway also involves in various human disorders, including metabolic conditions, neurodegenerative diseases, cancers and infectious diseases. Therefore, the comprehensive understanding of autophagy process, autophagy-related modulators and corresponding pathway and disease information will be of great help for identifying the new autophagy modulators, potential drug candidates, new diagnostic and therapeutic targets. In recent years, some autophagy databases providing structural and functional information were developed, but the specific databases covering autophagy modulator (proteins, chemicals and microRNAs)-related target, pathway and disease information do not exist. Hence, we developed an online resource, Human Autophagy Modulator Database (HAMdb, http://hamdb.scbdd.com), to provide researchers related pathway and disease information as many as possible. HAMdb contains 796 proteins, 841 chemicals and 132 microRNAs. Their specific effects on autophagy, physicochemical information, biological information and disease information were manually collected and compiled. Additionally, lots of external links were available for more information covering extensive biomedical knowledge. HAMdb provides a user-friendly interface to query, search, browse autophagy modulators and their comprehensive related information. HAMdb will help researchers understand the whole autophagy process and provide detailed information about related diseases. Furthermore, it can give hints for the identification of new diagnostic and therapeutic targets and the discovery of new autophagy modulators. In a word, we hope that HAMdb has the potential to promote the autophagy research in pharmacological and pathophysiological area.

Rapamycin protects against aristolochic acid nephropathy in mice by potentiating mammalian target of rapamycin‑mediated autophagy

“…Autophagy is a method of cellular adaptation that prevents cell death resulting from external stimulation. During this process, damaged organelles, including the mitochondria and endoplasmic reticulum, are removed ( 11 , 25 ). Therefore, the present study determined whether rapamycin could modulate the renal activity of mTOR in a mouse AAN model, thereby activating renal autophagy and protecting against AA-induced renal damage.…”

Autophagy and Tumor Database: ATdb, a novel database connecting autophagy and tumor

“…THANATOS is a comprehensive database of PTMs associated with the regulation of autophagy ( 9 ). HAMdb archived the specific effects of proteins, chemicals and microRNA on autophagy and disease information ( 18 ). ATD annotated the genes and chemicals influencing autophagy and human diseases ( 19 ).…”

“…Autophagy Database and HADb (Human Autophagy Database) ( 16 , 17 ) published in 2011 provided the glossary of ATGs and proteins. To elucidate the modulators and regulators of autophagy, ARN (Autophagy Regulatory Network), ncRDeathDB, THANATOS, HAMdb (Human Autophagy Modulator Database) and ACDB (Autophagic Compound Database) were also established ( 8–11 , 18 ). Moreover, ATD (Autophagy To Disease) annotated the genes and chemicals, which are implicated in autophagy-associated human diseases ( 19 ).…”

Mechanisms of Action of Autophagy Modulators Dissected by Quantitative Systems Pharmacology Analysis

“…Pharmacological modulation of autophagy has great therapeutic potential and attracted a great deal of attention in the past two decades [18]. A variety of autophagy-focused databases have been developed to provide annotation information for autophagy-related proteins (such as Autophagy Database [84]), the interactions of autophagy components (e.g., Autophagy Regulatory Network [85], THANATOS [86]), and autophagy-modulating small molecules (e.g., AutophagySMDB [87], HAMdb [88]). These resources contain extensive data on autophagy that enables systems-level analyses of its regulation.…”