About:
BioPhytMol is a manually curated drug discovery resource on natural
products, both plant extracts and phytomolecules that have been reported to show
anti-mycobacterial properties. The data has been collected from published
literature and other public resources. Currently, the resource has a total of
2582 entries that includes 188 plant families (comprised of 692 genera and 808
species) and 633 active phytomolecules identified against 25 target mycobacteria.
BioPhytMol has an extensive search tool which can be easily used to perform
systematic search based on classification of the compounds to complex queries.
A structure similarity tool has also been incorporated in the resource where
a user can draw his/her chemical structure or load structure files (sdf, mol,
mol2) that can be used to search against known anti-tuberculosis drugs, nutraceutical, FDA
approved drugs and BioPhytMol phytomolecules itself. The user can perform 'substructure search', 'superstructure search' and an 'exact search'. A separate browse option has been provided for easy navigation.
| Field Name | Full Description of Field |
| Compound ID | A unique identifier for a particular
record |
| Compound Structure | Detailed 2D and 3D structure of the
phytomolecule |
| Plant source and common name | Information of the source
from where the biophytmolecule was derived and its corresponding common name |
| Source Family | Family of the plant source |
| Origin | Location of the plant source |
| Plant part used | Part of the plant used for conducting
experiments |
| Extract | Information on prepared extract |
| Target bacteria | Bacterial Strains against which the
activity of the phytomolecule/plant extract has been checked |
| Assay/Test done | Name of the assay used to measure the
activity of the active phytomolecule identified |
| Positive control used | Concentration of the Reference controls used in the assay |
| Inhibition [%] | Mycobacterial growth percent inhibition |
| Activity [MIC] | Minimum Inhibitory Concentration value (in µg/ml) |
| Activity | In terms of dilution |
| Activity | Zone of inhibition (in mm) |
| Active Compound Identified | Name of the compound
identified in the plant source |
| PubChem ID | ID of the active compound identified present in PubChem database |
| Ethnomedicinal Information | Medicinal value of the plant
source |
| PubMed ID | ID of the reference paper of PubMed database, from where the data has been extracted (if available) |
| Extract Preparation | Steps followed for preparing the extract |
| Chemical Classification | Classification assigned to the active compound identified |
| Media/Broth Used | Information on the type of medium used
to culture mycobacteria |
| Cytotoxicity Assay | Information of assay used to test cytotoxicity |
| Molecular Weight | The molecular weight of the active compound identified |
| SMILES | Representation of the active compound identified in SMILES format |
| XLogP | Octanol/water partition coefficient of the active compound identified |
| PSA | Polar surface area of the active compound identified |
| H-bond Donor | No. of electronegative atoms in the active compound identified |
| H-bond Acceptor | No. of electropositive atoms in the active compound identified |
| No. of Rotatable Bond Count | No. of single bonds between heavy atoms in the active compound identified |
| No. of Rings | No. of cycles in the active compound identified |
| No. of N | No. of Nitrogen atoms in the active compound identified |
| No. of O | No. of Oxygen atoms in the active compound identified |
| No. of S | No. of Sulphur atoms in the active compound identified |
| Reference 1, 2 and 3 | Provides information of the reference source from where the data has been collected |
Frequently Asked Questions:
- What is BioPhytMol ?
Ans. BioPhytMol is a manually curated drug discovery resource on natural products, both extracts and compounds that have been reported to show anti-mycobacterial properties. The data has been collected from published literature and other public resources.
- Why to search BioPhytMol?
Ans. BioPhytMol has been developed to facilitate searching of compounds and plant extracts that have been reported to show anti-mycobacterial properties.
Exploring natural product space may provide a valuable source of new, less-toxic, inexpensive, safer, accessible and reliable drugs.
- Can I search BioPhytMol for a molecule of interest?
Ans. BioPhytMol has different search features that can be used to look for a molecule of interest. If the compound name is known, you can directly search for the compound from the homepage.
If you have the SMILES, SDF, MOL or MOL2 format of the compound, you can use the BioPhytMol structure search form.
- How can I get the compounds/extracts having their MIC within a range?
Ans.You can use the query builder. The query builder example shows how to find the compounds that have their MIC within a range.
- Can I find out which compounds have the least MIC?
Ans.You can Browse BioPhytMol by MIC (Defined) and sort the list by the 'Activity MIC (µg/ml)' header to get the compounds with least MIC.
- Can I download the structure (2D/3D) of molecule of my interest?
Ans. Every record in the resource (containing an active compound identified) has the option to download 2D and 3D structures in SDF and MOL format. You can find the download option just below the image of the compound.
- Can I search molecule having activity against particular mycobacteria?
Ans. You can go to Browse by Target Bacteria page and click from a choice of 25 target mycobacteria currently available in BioPhytMol to know an active phytomolecule or plant extract and its activity against that particular mycobacteria.
- Can I search similar compounds from BioPhytMol using SMILES of my structure?
Ans. You can use the structure search form to do such job. You can perform a substructure, superstructure and an exact structure search on BioPhytMol compounds using your SMILES.
An example has been provided on the help page.
- Can I enter details of a new compound not available in BioPhytMol ?
Ans. You can go to the submission page in order to submit data. For submission, you should be a registered sysborg member with a valid screen name and password.
Ans. If you find any errors in the resource, please contact any one of the team members present in the Contact us page.
