Medicinal Plants Database and Three Dimensional Structure of the Chemical Compounds from Medicinal Plants in Indonesia

During this era of new drug designing, medicinal plants had become a very interesting object of further research. Pharmacology screening of active compound of medicinal plants would be time consuming and costly. Molecular docking is one of the in silico method which is more efficient compare to in vitro or in vivo method for its capability of finding the active compound in medicinal plants. In this method, three-dimensional structure becomes very important in the molecular docking methods, so we need a database that provides information on three-dimensional structures of chemical compounds from medicinal plants in Indonesia. Therefore, this study will prepare a database which provides information of the three dimensional structures of chemical compounds of medicinal plants. The database will be prepared by using MySQL format and is designed to be placed in http://herbaldb.farmasi.ui.ac.id website so that eventually this database can be accessed quickly and easily by users via the Internet.

💡 Research Summary

The paper presents the design and implementation of an online database that integrates information on Indonesian medicinal plants and three‑dimensional (3D) structures of their chemical constituents. Recognizing Indonesia’s status as a megabiodiversity hotspot with thousands of plant species possessing pharmacological activity, the authors aim to facilitate in‑silico drug discovery, particularly molecular docking, by providing ready‑to‑use 3D ligand structures.

The methodology proceeds through five main stages. First, an extensive literature survey of scientific journals, books, and web resources identified 3,825 medicinal plant species, compiling their scientific names, local names, parts used, and other metadata. Second, the chemical compounds reported for these plants were retrieved from public repositories such as PubChem and KNApSAcK. When only 2‑D images (e.g., GIF) were available, the authors redrew the structures using Symyx Draw to generate .mol files. Third, the 2‑D structures were converted to 3‑D conformations using the VEGAZZ program, with additional processing in PyMOL and format conversion to .mol2 via OpenBabel, ensuring compatibility with docking software. Fourth, all data were organized into a relational MySQL schema, illustrated by an entity‑relationship diagram that links Species, Compound, Content, and User tables. Finally, a web front‑end was built with PHP and HTML, offering pages for home, species details, compound details, file uploads, search results, FAQs, and user management. User roles (administrator, expert, contributor, general visitor) control data entry, editing, and deletion, while a comment system enables community feedback.

At the time of writing, the prototype hosts 3,825 plant records, 16,244 local‑name entries, 12,980 species‑compound relationships, and 1,412 3‑D structures in .mol and .mol2 formats. The site (http://herbaldb.farmasi.ui.ac.id) is publicly accessible, with English language support to reach an international audience. The authors emphasize the “open system” nature of the platform: data can be added, modified, or removed by authorized users, and expert verification is required before entries are marked as validated.

The discussion acknowledges several strengths: (1) integration of multiple public chemical databases; (2) automation of the 2‑D to 3‑D conversion pipeline; (3) provision of searchable metadata (species name, synonyms, local names, compound name, usage keywords); and (4) a community‑driven validation workflow. However, limitations are also noted. The reliance on literature for initial compound lists may miss recently discovered or unpublished metabolites. The 3‑D generation tools (VEGAZZ, OpenBabel) may not fully capture stereochemistry, potentially affecting docking accuracy. Security aspects of the PHP implementation (e.g., protection against SQL injection, safe file upload handling) are not detailed, raising concerns for a public web service. Scalability is another issue: as the database expands to tens of thousands of compounds, indexing, query optimization, and server load balancing will become critical.

In conclusion, the study delivers the first publicly available Indonesian medicinal plant database that couples taxonomic information with downloadable 3‑D ligand structures. By lowering the barrier to obtain high‑quality ligand geometries, the platform can accelerate virtual screening and structure‑based drug design efforts focused on Indonesian flora. Future work should concentrate on (i) systematic expert validation of entries, (ii) incorporation of quantum‑chemical geometry optimization to improve stereochemical fidelity, (iii) development of robust security measures, (iv) provision of RESTful APIs for seamless integration with external docking pipelines, and (v) continuous enrichment of the dataset through community contributions and collaborations with phytochemistry laboratories. With these enhancements, the database has the potential to become a cornerstone resource for both academic researchers and pharmaceutical developers seeking novel bioactive compounds from Indonesia’s rich botanical heritage.