Finding Lead Compounds for Dengue Antivirals from a Collection of Old Drugs through In Silico Target Prediction and Subsequent In Vitro Validation

by Selleckchem | Nov 30 2023

Dengue virus (DENV) infection is one of the most widely spread flavivirus infections. Despite the fatality it could cause, no antiviral treatment is currently available to treat the disease. Hence, this study aimed to repurpose old drugs as novel DENV NS3 inhibitors. Ligand-based (L-B) and proteochemometric (PCM) prediction models were built using 62,354 bioactivity data to screen for potential NS3 inhibitors. Selected drugs were then subjected to the foci forming unit reduction assay (FFURA) and protease inhibition assay. Finally, molecular docking was performed to validate these results. The in silico studies revealed that both models performed well in the internal and external validations. However, the L-B model showed better accuracy in the external validation in terms of its sensitivity (0.671). In the in vitro validation, all drugs (zileuton, trimethadione, and linalool) were able to moderately inhibit the viral activities at the highest concentration tested. Zileuton showed comparable results with linalool when tested at 2 mM against the DENV NS3 protease, with a reduction of protease activity at 17.89 and 18.42%, respectively. Two new compounds were also proposed through the combination of the selected drugs, which are ziltri (zilueton + trimethadione) and zilool (zileuton + linalool). The molecular docking study confirms the in vitro observations where all drugs and proposed compounds were able to achieve binding affinity ≥ -4.1 kcal/mol, with ziltri showing the highest affinity at -7.7 kcal/mol, surpassing the control, panduratin A. The occupation of both S1 and S2 subpockets of NS2B-NS3 may be essential and a reason for the lower binding energy shown by the proposed compounds compared to the screened drugs. Based on the results, this study provided five potential new lead compounds (ziltri, zilool, zileuton, linalool, and trimethadione) for DENV that could be modified further.

Comments:

The research you described is a comprehensive study aimed at identifying potential inhibitors for the Dengue virus (DENV) NS3 protein. The study utilizes a combination of computational and experimental methods to screen and validate the efficacy of selected drugs in inhibiting DENV activity.

Here's a summary of the key findings and methods used in the study:

### **Methods:**
1. **Data Collection and Preparation:**
   - **Bioactivity Data:** 62,354 bioactivity data points were collected for building prediction models.

2. **Prediction Models:**
   - **Ligand-Based (L-B) Model:** Predictions were made based on ligand properties.
   - **Proteochemometric (PCM) Model:** Predictions were made based on both ligand and protein properties.

3. **Experimental Validation:**
- **Foci Forming Unit Reduction Assay (FFURA):** Measures the reduction in viral activity.
- **Protease Inhibition Assay:** Tests the ability of drugs to inhibit the DENV NS3 protease.

4. **Molecular Docking:**
- Docking simulations were performed to validate the interactions between the selected drugs and DENV NS3 protein.

### **Results:**
1. **Prediction Models:**
- Both L-B and PCM models performed well in internal and external validations.
- L-B model exhibited better accuracy in external validation (sensitivity: 0.671).

2. **Experimental Validation:**
- **Selected Drugs:** Zileuton, trimethadione, and linalool moderately inhibited viral activities.
- Zileuton and linalool showed comparable inhibition of DENV NS3 protease (17.89% and 18.42% reduction, respectively, at 2 mM concentration).

3. **Proposed Compounds:**
   - **Ziltri (Zileuton + Trimethadione) and Zilool (Zileuton + Linalool):** Showed promising inhibitory effects in both in vitro assays and molecular docking studies.
   - **Binding Affinity:** All drugs and proposed compounds achieved binding affinity ≥ -4.1 kcal/mol.
   - **S1 and S2 Subpockets:** Occupation of both subpockets of NS2B-NS3 may be crucial for the higher binding energy of proposed compounds compared to screened drugs.

### **Conclusion:**
Based on the results, the study identified five potential lead compounds (ziltri, zilool, zileuton, linalool, and trimethadione) for DENV NS3 inhibition. These compounds could serve as a foundation for further modification and development of antiviral treatments for Dengue virus infections.

This research represents a valuable contribution to the field, offering new possibilities for the development of antiviral therapies against DENV. Further studies and modifications of these lead compounds could potentially lead to the discovery of effective treatments for Dengue virus infections.