This repository hosts the research paper:
“Molecular Docking Studies of Phytochemicals Against RNA-dependent RNA Polymerase of Mucormycosis”
The study performs in silico screening of antifungal phytochemicals targeting the RNA-dependent RNA polymerase (RdRp) of Rhizopus oryzae, with the aim of identifying potential antifungal drug candidates.
Mucormycosis is a high-mortality fungal infection, particularly in immunocompromised individuals. Current treatment options are limited. RdRp is a conserved and functionally critical enzyme, making it a strong therapeutic target.
- Protein modelling: RdRp sequence retrieved from NCBI; 3D structure generated via SWISS-MODEL
- Ligand dataset: ~1000 antifungal phytochemicals from PubChem
- Drug-likeness filtering: SwissADME (Lipinski’s Rule of Five)
- Toxicity prediction: ProTox-II (LD50, hepatotoxicity, carcinogenicity, etc.)
- Molecular docking: PyRx (AutoDock Vina) with UFF energy minimisation
- Molecular weight ≤ 500 Da
- LogP ≤ 5
- H-bond donors ≤ 5
- H-bond acceptors ≤ 10
- 1000 → 209 compounds shortlisted after ADME screening
| Compound | Binding Affinity (kcal/mol) |
|---|---|
| Dregamine | -11.1 |
| Alantolactone | -9.5 |
| Isoalantolactone | -9.5 |
| Solasodine | -9.5 |
- More negative binding energy indicates stronger ligand–protein interaction
- Interaction types include hydrogen bonding, alkyl, π-alkyl, and electrostatic interactions
- Dregamine is the most promising candidate based on binding affinity and pharmacokinetic profile
- Several compounds were excluded due to toxicity despite good docking scores
- In silico screening significantly reduces the search space for experimental validation
- PyRx / AutoDock Vina
- SwissADME
- ProTox-II
- SWISS-MODEL
- PubChem / NCBI
- No experimental (in vitro / in vivo) validation
- Protein structure derived via homology modelling
- Toxicity predictions are computational
- Molecular dynamics simulations
- Experimental validation
- Lead optimisation
- Extension to additional targets
Jha et al., Molecular Docking Studies of Phytochemicals Against RNA-dependent RNA Polymerase of Mucormycosis, Journal of Diseases and Medicinal Plants, 2022