BIAdb: A curated database of benzylisoquinoline alkaloids
© Singla et al; licensee BioMed Central Ltd. 2010
Received: 8 December 2009
Accepted: 5 March 2010
Published: 5 March 2010
Benzylisoquinoline is the structural backbone of many alkaloids with a wide variety of structures including papaverine, noscapine, codeine, morphine, apomorphine, berberine, protopine and tubocurarine. Many benzylisoquinoline alkaloids have been reported to show therapeutic properties and to act as novel medicines. Thus it is important to collect and compile benzylisoquinoline alkaloids in order to explore their usage in medicine.
We extract information about benzylisoquinoline alkaloids from various sources like PubChem, KEGG, KNApSAcK and manual curation from literature. This information was processed and compiled in order to create a comprehensive database of benzylisoquinoline alkaloids, called BIAdb. The current version of BIAdb contains information about 846 unique benzylisoquinoline alkaloids, with multiple entries in term of source, function leads to total number of 2504 records. One of the major features of this database is that it provides data about 627 different plant species as a source of benzylisoquinoline and 114 different types of function performed by these compounds. A large number of online tools have been integrated, which facilitate user in exploring full potential of BIAdb. In order to provide additional information, we give external links to other resources/databases. One of the important features of this database is that it is tightly integrated with Drugpedia, which allows managing data in fixed/flexible format.
A database of benzylisoquinoline compounds has been created, which provides comprehensive information about benzylisoquinoline alkaloids. This database will be very useful for those who are working in the field of drug discovery based on natural products. This database will also serve researchers working in the field of synthetic biology, as developing medicinally important alkaloids using synthetic process are one of important challenges. This database is available from http://crdd.osdd.net/raghava/biadb/.
Alkaloids are naturally occurring secondary metabolites, low molecular weight, and nitrogen containing compounds that are found in more than 20% of plant species . A plant contains more than 0.01% of alkaloids is called alkaloid plants [2–4]. They show pharmacological effects and are being commonly used as medicines (e.g., analgesic as morphine). Alkaloids are biologically significant and can act as stimulators, inhibitors and growth terminators [5, 6]. They also have anti-microbial and anti-parasitic properties [7–14]. Alkaloids can alter DNA, selectively deform cells and cause locoism. Nowadays, non-natural alkaloids are growing rapidly as a result of bioorganic and stereochemistry research. Pharmacological research and the drug industry rapidly advance and promote the most promising new molecules for possible production applications .
Alkaloids can be classified on the basis of biological activities, chemical structure and biosynthetic pathways. Following are few of major classes of alkaloids; (i) Pyrrolidine: is an organic compound with the molecular formula C4H9N; (ii) Quinoline: is a heterocyclic aromatic organic compound with formula C9H7N; (iii) Benzylisoquinoline: is a heterocyclic aromatic organic compound & structural isomer of quinoline; (iv) Indole: is an aromatic heterocyclic organic compound (v) Terpenoid: a diverse class of naturally occurring organic chemicals. The benzylisoquinoline alkaloid (BIA) is a diverse category of alkaloids including berberine, morphine, sanguinarine, hydrastine and many more. Alkaloids belonging to this class are found to be pharmacologically active and show potential therapeutic properties. Recent studies suggested that these alkaloids could be considered as novel medicines . For example, the magnoflorine has been reported to protect HDL during oxidant stress [16–18]. A recent report stated that anti-microbial agent berberine had cholesterol-lowering activity . Tetrandrine (TET) is a bis-benzylisoquinoline alkaloid, which is identified as an active ingredient in Radix Stephanae tetrandrae (a Chinese medicinal herb). It has been used traditionally for the treatment of congestive circulatory disorder and inflammatory diseases .
Best of authors' knowledge there is no databases of BIA molecules, which are very important from medicine point of view. In order to facilitate researchers working in the field of drug discovery/design, we made a systematic attempt in this study to collect and compile BIA molecules. This database is user-friendly and equipped with powerful computational tools like Jmol . BIAdb also has provision for searching the chemical compounds against this database on the basis of structural similarity.
Construction and content
Number of unique BIA molecules from different data sources
NUMBER OF ENTRIES
KEGG (COMPOUNDS & DRUGS)
Comparative Toxicogenomics Database (CTD)
Other Sources (literature search)
The BIAdb database contains the following fields for each benzylisoquinoline alkaloid entry; (1) name; (2) PubChemID; 3) KEGG ID; (4) source; (5) type; (6) function; (7) molecular weight; (8)exact mass; (9) molecular formula; (10) XLogP; (11) Topological Polar Surface Area (TPSA); (12) IUPAC name; (13) H-bond donors; (14) H-bond acceptors; (15) number of rotatable bonds; (16) canonical smile; (17) isomeric smile; (18) structure (sdf, mol, pdb) file;(19) pubmed web-link; and (20) link to Drugpedia.
Organization of Data
The whole data of BIA's compounds was organized in four different ways, these are physio-chemical properties, sources, functions and clustering of whole data was done using standalone version of LibraryMCS software. The organization of data on the basis of physio-chemical properties can be retrieve through the browse option provided in the web server. The data has been organized according to the different ranges of the molecular weight, XLogP, TPSA of BIA's.
The whole data was clustered using the standalone LibraryMCS v0.7 from ChemAxon. LibraryMCS clusters a set of chemical structures on a structural basis. Structures that share a common substructure are clustered together. The clustering program identifies the common substructure, and it is always the largest one among all substructures found in the structure set. Such substructure is called the Maximum Common Substructure (MCS). The clustering technique applied in LibraryMCS is hierarchical, that is, clusters of input structures are grouped into second level clusters, and then these second level clusters are grouped again and so on, until a termination condition is reached.
The matching parameters for clustering were atom type, bond type, charge, hybridization and isotopes, minimum cluster size. Performance of LibraryMCS software depends upon various factors like average structure size, diversity, minimal required MCS size and atom/bond constraints.
Number of compounds in 14 Top level clusters obtained from LibraryMCS
Number of Compounds in each cluster
Apart from the data collected about benzylisoquinoline alkaloids, a variety of tools has been implemented within the database to enhance the scope of database. Following are the main web tools integrated in BIAdb.
Keyword Search and Advanced search
A simple text search tool is provided for searching on selected fields of database. The advance search option has been incorporated separately for intensive search. Using this option, users can search BIA's compounds within a range of value of physiochemical properties and retrieve corresponding results.
The browsing tool provides the options to the user to select particular range of compounds on the basis of their physio-chemical properties like molecular weight, XLogP and TPSA.
Structure visualization and similarity Search
Online submission tool
BIAdb also has the facility to add more entries related to benzylisoquinoline alkaloids by the users. The user can add new compound information with in specified fields (the fields with star are mandatory) and entries will be then added to the database after proper validation.
Web Interface and Application
LAMP (Linux-Apache-Mysql-PHP), an open source software has been used to create the database. PHP, HTML and CSS technologies have been used to build the dynamic web interface. MySQL, a relational database management system (RDBMS), works at the backend. Server-side scripting makes use of PHP. The whole software system runs on IBM SAS x3800 machine under Red Hat Enterprise Linux 5 environment using Apache httpd server. PHP and MySQL combination is quite efficient and powerful for database management.
BIAdb is a comprehensive information portal of benzylisoquinoline alkaloids. User can search important information regarding the BIA's and can also view the structures of the compounds. This database will definitely be of great use for researchers. BIAdb is developed keeping in mind the general user requirement. Thus searching and exploring the database is easy and convenient. Further, this information can be used to design analogs of BIA's, which can act as potential drug candidates.
BIAdb is a webserver of an important class of alkaloids called benzylisoquinoliones which facilitate users to do extensive search. This database encapsulates important information about BIA's compounds regarding their source and medicinal values. The structure search facility will be helpful for users in finding compounds similar to BIA's. The online submission facility will be helpful for expanding this database. This resource will be helpful for those working in the field of drug designing to explore their role as potential drug molecules.
Limitations and future prospects
Our major limitation in developing the database is that the information about benzylisoquinoline alkaloids is very less and too scattered. Lot of literature search is required to further expand the database. In order to maintain the database dynamically without losing any information about BIA's, we make the multiple records in term of different source and function performed by a compounds. In near future, we are hopeful of expanding the database both qualitatively as well as quantitatively to cover the synthesis pathways of these BIA's and to include the synthetic parts available to shorten the synthesis process and to increase the yield. This database will be updated manually as soon as enough data will be available.
Availability and requirements
List of abbreviations used
Comparative Toxicogenomics Database
Hypertext Preprocessor language
Hypertext Markup Language
Cascading Style Sheet.
The authors are thankful to Council of scientific and Industrial Research (CSIR) and Department of Biotechnology, Government of India, for financial assistance.
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