DrugDevCovid19

Tracking the relevant researches of CADD drug development against COVID-19

Neomycin

ID MW HBD HBA
8378  614.6137
RB NOA Rings logP
16194-8.99

Function

DrugBank ID:

DB00452


Description:

A component of neomycin that is produced by Streptomyces fradiae. On hydrolysis it yields neamine and neobiosamine B. (From Merck Index, 11th ed) [DrugBank]

Targets:

16S ribosomal RNA (Enteric bacteria and other eubacteria); 30S ribosomal protein S12 (Escherichia coli (strain K12)); C-X-C chemokine receptor type 4 (Humans) [DrugBank]

Pharmacodynamics:

Framycetin is used for the treatment of bacterial eye infections such as conjunctivitis. Framycetin is an antibiotic. It is not active against fungi, viruses and most kinds of anaerobic bacteria. Framycetin works by binding to the bacterial 30S ribosomal subunit, causing misreading of t-RNA, leaving the bacterium unable to synthesize proteins vital to its growth. Framycetin is useful primarily in infections involving aerobic bacteria bacteria. [DrugBank]

Structures

SMILES:

NC[C@@H]1O[C@H](O[C@@H]2[C@@H](CO)O[C@@H](O[C@@H]3[C@@H](O)[C@H](N)C[C@H](N)[C@H]3O[C@H]3O[C@H](CN)[C@@H](O)[C@H](O)[C@H]3N)[C@@H]2O)[C@H](N)[C@@H](O)[C@@H]1O

2D structures:  

3D structures:  

Docking in target protein

Receptor: Mpro

Docking Site: Catalytic pocket

Ligand: Neomycin

Vina score: -6.7

Off-target analysis based on ligand similarity (Homo sapiens)

Step 1 - Target prediction for Neomycin: SwissTargetPrediction

Tips: Click on the link to jump to the 'SwissTargetPrediction' webserver. Select the species of 'Homo sapiens', and then paste the SMILES of Neomycin in the SMILES input box.

Step 2 - Blind docking for Neomycin: CB-Dock

Tips: Click on the link to jump to the 'CB-Dock' webserver. Upload the structure file of target predicted by 'SwissTargetPrediction' and the 2D/3D structure file of Neomycin to perform blind docking.