Case Study on finding inhibitors for DENV NS-3 Helicase

Team Members : B.Sonali Patro - BT18CME004

Vijay Mukesh Parmar - BT18CME012

Saloni Pramod Lal Gupta - BT18CME103

Objective :To find the best inhibitor by determining the binding affinity of similar inhibitors towards DENV NS-3 Helicase.

Softwares :

1. Perl Software : It’s a supporting software which enables us to dock multiple ligands simultaneously.
2. Auto-Dock Vina : It’s an open-source programme for molecular docking.
3. Zinc Database : It is a database which enables us to screen molecules based on various parameters.
4. Auto-Dock Tool, Chimera : Visualisation Software.

Theory

Why Dengue Virus ?

Dengue virus is the cause for Dengue fever, which can be fatal.

The DENV genome is about 11000 bases of positive-sense, single stranded RNA (ssRNA) that codes for three structural proteins (capsid protein C, membrane protein M, envelope protein E) and seven nonstructural proteins (NS1, NS2a, NS2b, NS3, NS4a, NS4b, NS5).

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Why DENV NS-3 Helicase ?

The seven DENV non-structural proteins are essential in the virus life-cycle.

NS-3 is a multifunctional protein that possess serine protease helicase (DENV NS-3 Helicase), RNA - stimulated nucleoside triphosphatase (Helicase), and RNA 5’ triphosphatase (RTPase) activities which are essential for viral RNA replication and capping.

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Virtual Screening

After deciding the receptor as DENV NS-3 Helicase, we researched through the papers to find the potential candidates and, then we found similar inhibitors using Zinc Database.

Molecular Docking - Receptor Preparation.

Step 1 : Read Molecule

Step 2: Removing the selected atoms (yellow in colour)

Step 3 : Delete water molecules, because it might affect docking.

Step 4: Add Kollman Charges

Step 5: Choose the macromolecule from Grid

Step 6: Select Grid Box having appropriate dimensions.

Step 7: Save the perl script

Step 8: Save the data related to grid box, total number of configurations taken of an inhibitor and energy range

Step 9: File name of the Inhibitors should be saved in a text document.

Step 10: Call the ligand.txt using Command Prompt.

Step 11 : Analysed the binding sites and obtained the results (this is for one inhibitor)

Results

Binding sites of selected inhibitor in the receptor

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Additional Findings :

We were also able to find the best binding site as majority (6 out of 10 ) inhibitors docked to this particular binding site.

DECREASING ORDER OF BINDING AFFINITY OF INHIBITORS TOWARDS THE RECEPTOR

Conclusion

1. We came to a conclusion that inhibitor, 2-(3,4 dimethoxyphenyl-4-methyl-N-[5-(trifluoromethyl)-4H-1,2,4-triazol-3-yl]thiazole-5-carboxamide) or ZINC29389407 has the highest binding affinity to the receptor DENV NS-3 Helicase .
2. We predict that receptor attached to this inhibitor might reduce replication of the RNA. Hence, help in treating the disease