Abstract
Objective: Nowadays, There hasn’t any three-dimensional (3D) chemical structure database yet for biologically active compound in sponges from Indonesian origin. Therefore, this study aimed to create in silico a 3D-structure database of such compound and to evaluate the preferred software for this purpose. Methods: 2D- structure of selected compounds was established using MarvinSketch software. Conversion from 2D- into 3D-structures was evaluated by comparing MarvinSketch, OpenBabel and VegaZZ software packages. Visualization of the respective 3D-structures was perfomed by using PyMOL software. From 68 scientific articles, 212 chemical compounds were selected from 53 Indonesian sponge species. Results: The conversion of 2D-structures of the selected 212 chemical compound into 3D-structures lead to 7118 files, respectively consisting of 2508 files from the MarvinSketch, 1672 files from the OpenBabel and 1051 files from the VegaZZ software. The results based on the extention files were 1043 SDF, 1258 MOL and 2930 PDB format files of the three-dimensional structure. The valid and correct three-dimensional structure of chemical compound were 914 .sdf format files, 916 format .mol files and 72 .pdb format files. From the three-dimensional structures visualization, the database prefers established by using MarvinSketch with SDF or MOL format files since the results is consistent to literature and contain less number of errors.
Highlights
Ocean covered about 71% of the earth's surface and produced the largest source of bioactive compounds.[1]
The publication of new bioactive compounds from Indonesia's sponges and soft corals in 2000-2009 increased by about 300% compared to 1900-1999.4,7 Alkaloids, terpenoids, steroids and other types of new bioactive compounds were reported to be mostly derived from Indonesian sponges and soft corals.[7]
To support research in Indonesia, authors were interested in establishing the three-dimensional structure database of chemical compounds as a resource of the lead compounds required for the new drug development by in silico, especially from Indonesian sponges
Summary
Ocean covered about 71% of the earth's surface and produced the largest source of bioactive compounds.[1] Indonesia, the world's largest archipelago comprising about 17,508 islands and had a coastline of 81,000 km, was known as the richest country in the world regarding marine organisms biodiversity.[2,3] Since the 1950’s, research had shown marine organisms became the largest source of structural and active biological metabolites. It became the important field among the scientific community and have became an opportunity for drug discovery.[4]. To support research in Indonesia, authors were interested in establishing the three-dimensional structure database of chemical compounds as a resource of the lead compounds required for the new drug development by in silico, especially from Indonesian sponges
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