phytochemdb: a platform for virtual screening and computer-aided drug designing

• Published in: Database : the journal of biological databases and curation 2022-01, Vol.2022 (2022)
• Main Authors: Mahmud, Shafi, Paul, Gobindo Kumar, Biswas, Suvro, Kazi, Taheruzzaman, Mahbub, Shafquat, Mita, Mohasana Akter, Afrose, Shamima, Islam, Ariful, Ahaduzzaman, Sheikh, Hasan, Robiul, Shimu, Sharmin Sultana, Promi, Maria Meha, Shehab, Mobasshir Noor, Rahman, Ekhtiar, Sujon, Khaled Mahmud, Alom, Wasim, Modak, Anik, Zaman, Shahriar, Uddin, Salah, Emran, Talha Bin, Islam, Sayeedul, Saleh, Abu
• Format: Article
• Language: English
• Subjects: Computers; Database Update; Databases, Factual; Drug Design; Phytochemicals - chemistry; Phytochemicals - pharmacology; Plants, Medicinal
• ISSN: 1758-0463; 1758-0463
• DOI: 10.1093/database/baac002

The phytochemicals of medicinal plants are regarded as a rich source of diverse chemical spaces that have been used as supplements and alternative medicines in the millennium. Even in this era of combinatorial chemical drugs, phytomedicines account for a large share of the statistics of newly approved drugs. In the field of computational aided and rational drug design, there is an urgent need to develop and build a useful phytochemical database management system with a user-friendly interface that allows proper data storage, retrieval and management. We showed 'phytochemdb', a manually managed database that compiles 525 plants and their corresponding 8093 phytochemicals, aiming to incorporate the activities of phytochemicals from medicinal plants. The database collects molecular formula, three-dimensional/two-dimensional structure, canonical SMILES, molecular weight, no. of heavy atoms, no. of aromatic heavy atoms, fraction Csp3, no. of rotatable bonds, no. of H-bond acceptors, no. of H-bond donors, molar refractivity, topological polar surface area, gastrointestinal absorption, Blood-Brain Barrier (BBB) permeant, P-gp substrate, CYP1A2 inhibitor, CYP2C19 inhibitor, CYP2C9 inhibitor, CYP2D6 inhibitor, CYP3A4 inhibitor, Log Kp, Ghose, Veber, Egan, Muegge, bioavailability scores, pan-assay interference compounds, Brenk, Leadlikeness, synthetic accessibility, iLOGP and Lipinski rule of five with the number of violations for each compound. It provides open contribution functions for the researchers who screen phytochemicals in the laboratory and have released their data. 'phytochemdb' is a comprehensive database that gathers most of the information about medicinal plants in one platform, which is considered to be very beneficial to the work of researchers on medicinal plants. 'phytochemdb' is available for free at https://phytochemdb.com/.