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Identification of Novel Antagonists for Rab38 Protein by Homology Modeling and Virtual Screening
Aboubakr Haredi Abdelmonsef, Ramasree Dulapalli, Thirupathi Dasari
1Department of Chemistry, University College of Science, Osmania University, Hyderabad 500007, Telangana, India.. India.
Background:
The Rab family proteins are involved in membrane trafficking, cell growth and differentiation. Rab38 is implicated in the biogenesis of melanosomes that help in the synthesis, storage and transport of melanin pigments. The Rab38 protein is overexpressed at the RNA level in melanoma cancer.
Aim And Objective:
The protein Rab38 is targeted for identification of novel antagonists as cancer drug candidates.
Materials And Methods:
The 3D structure of Rab38 was generated using homology modelling method. The 3D model was validated. The active site was identified by using standard computational prediction tools like CASTp, efindsite and SiteMap. The study of protein-protein docking was performed between Rab38 and its natural substrate BLOC-3 using patchDock server tool. Virtual screening protocols were carried out using glide module. Various informatics tools like 1) Schrodinger Suite 2) Modeller 3) Accelrys Discovery Studio 4) PyMOL 5) SPDBV etc. are applied for the identification of novel inhibitors of Rab38.
Results:
The residues from SER35 to LEU63 of Rab38 protein are important for binding to ligands. The nineteen docked structures were obtained as an output of virtual screening. The compounds obtained show good glide score, and a common binding pattern at the active site.
Conclusion:
The benzosulfonamide and heterocyclic nitrogen moieties may be considered as pharmacophores for designing new anticancer leads with better docking score and admissible ADME properties. Our study helps in the identification of potential inhibitors against Rab38 and melanoma cancer.
Insights
Researchers identified potential new cancer drugs by computationally targeting the Rab38 protein, which is overexpressed in melanoma. This study focused on finding novel inhibitors for Rab38 to combat melanoma cancer.
Area of Science:
- Computational drug discovery
- Molecular biology
- Cancer research
Background:
- Rab proteins regulate membrane trafficking, cell growth, and differentiation.
- Rab38 is crucial for melanosome biogenesis and is overexpressed in melanoma.
- Melanoma is a significant form of skin cancer.
Purpose of the Study:
- To identify novel antagonists of the Rab38 protein as potential cancer drug candidates.
- To computationally screen for compounds that inhibit Rab38 activity.
Main Methods:
- Homology modeling was used to generate the 3D structure of Rab38.
- Active site identification and protein-protein docking were performed using computational tools.
- Virtual screening was employed to identify potential inhibitors of Rab38.
Main Results:
- Key residues (SER35 to LEU63) important for ligand binding were identified.
- Nineteen docked structures with favorable binding at the active site were obtained.
- Compounds showed good glide scores, indicating potential inhibitory activity.
Conclusions:
- Benzosulfonamide and heterocyclic nitrogen moieties are promising pharmacophores for designing Rab38 inhibitors.
- The identified compounds represent potential leads for developing new anticancer drugs against melanoma.
- This study aids in discovering inhibitors for Rab38, targeting melanoma cancer.
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