Dynamics Insight of Dodonaea viscosa Phytochemicals as a Potent Inhibitor Targeting Dengue Virus NS5 Methyltransferase ^†

Abstract

The dengue virus is globally widespread and has a high infection and fatality rate. Currently, no medication is available. So, this study aims to screen for promising inhibitors from Dodonaea viscosa by targeting NS5 methyltransferase (crucial in RNA capping) of the dengue virus. The compounds were screened from Dodonaea viscosa, and docking analysis was performed with the NS5 methyltransferase (PDB ID: 6KR2). Based on the docking investigation, the top five compounds were selected, having a score range of −7.164 to −5.837 Kcal/Mol, comparably higher than the control (Qunine; −3.050 Kcal/Mol), and examined. Among these selected compounds, Quercetin (PubChem ID; 5280343) revealed highly promising activity and was further analyzed for stability over 100 ns simulation. The ADME of the selected compound was examined and found to have favourable activity. Moreover, the compound can be used for therapeutic development to combat dengue infection.

1. Introduction

Dengue virus (DENV) is an emerging ongoing public health concern [1]. Dengue is a mosquito-borne flavivirus specifically transmitted by the Aedes mosquito, and it is found to cause trouble in many parts of the world. Still, tropical and subtropical areas are specific places of concern regarding the spread of the disease. The Aedes mosquito, specifically Aedes aegypti and Aedes albopictus, is the vector that spreads dengue fever. The disease is more prevalent in places with high mosquito populations and inadequate sanitation because the virus is transmitted by the bite of an infected mosquito [2,3]. Approximately one million cases of DENV infections are reported annually, with four antigenically distinct serotypes (DENV1-4) being the cause [1,4]. DENV can be asymptomatic, but it can also have a broad range of clinical symptoms, from moderate flu-like syndrome to severe illness types that could lead to hypovolemic shock. The major symptoms of the disease are high fever, headaches, muscle, etc. In severe cases, it may also lead to death due to complications like multiple organ failure, internal bleeding, etc. [2,5,6]. It harbours 10–11 kb of genomes, followed by their structural and non-structural proteins. Interestingly, among the non-structural proteins, NS5 is crucial as it occurs in both cases, such as replication via RNA-dependent RNA polymerase (RdRp) and protecting the genome via methyltransferase enzyme (MTase). The methyltransferase is mainly involved in the cap of the genome and enables particle translation, which makes it an ideal candidate for therapeutic development [4,7,8]. There is no specific treatment available and to combat this infection; the design of promising drugs and medicines is necessary. Researchers are currently using advanced computational approaches and other steps to find promising inhibitors and therapeutic designs [9,10,11,12,13,14].

Dodonaea viscosa is a well-known plant with multiple bioactivities, and its activity towards the dengue virus has not yet been explored [15]. Therefore, the active phytochemicals from Dodonaea viscosa were examined via a docking and dynamics approach to identify a possible inhibitor targeting NS5 methyltransferase. The possible inhibitors were further analyzed for their drug-like features.

2. Materials and Methods

2.1. Target and Ligands Preparation

The target structures were collected via the PDB database and were further prepared using the Protein preparation wizard, followed by a set of parameters to improve structure quality [16]. The phytochemicals of Dodonaea viscosa were collected from a different database and compiled, and duplicates were removed. The 2D structure of these phytochemicals was downloaded from the PubChem Databases [17,18]. Furthermore, these compounds were examined via the QikProp module, and the compound having a STAR value of 0 (indicates promising activity) was further utilized. The selected phytochemical was prepared using the LigPrep module, according to the default parameters [19,20].

2.2. Grid Generation and Docking Investigation

The grid box within the target was generated via the Receptor Grid Generation application and based on the X, Y, and Z coordinates. Further, using the Glide module, the docking investigation was performed with the prepared ligand and the target (on the active site) followed by XP (Extra precision) methods [19,21]. The top identified compounds were discussed, respectively. Additionally, the drug-like, i.e., ADME attributes of the selected phytochemical were examined via QikProp (Version 12.8) [20].

2.3. Molecular Dynamics Simulation

The simulation investigation was accomplished via Desmond version 2.0 (academic version) [22]. The system was prepared by employing the TIP3P water model with a simulation box size of 10 Å × 10 Å × 10 Å, followed by force field 2005. Further, the system was neutralized, and energy-minimized, as previously reported [23]. The simulations were computed considering the OPLS 2005 force field along with the periodic boundary in the NPT ensemble system, and the simulations were accomplished over 100 ns [22,23]. Moreover, all other parameters were kept as reported previously, and the simulated docked complex trajectories were analyzed accordingly [24,25].

3. Results and Discussion

3.1. Target and Ligand Retrieval and Their Preparation

The NS5 methyltransferase (PDB ID: 6KR2) structure was collected from the PDB database and prepared via the protein preparation wizard. The phytochemicals belonging to Dodonaea viscosa were retrieved from IMPPAT [26], the Dr. Duke Library [27], and the KNApSAcK [28] database, and a total of 134 phytochemicals were collected. Moreover, the duplicates within the collected phytochemicals were removed, and 58 were uniquely identified. The QikProp module was applied, and based on a STAR value of 0, of the 58 phytochemicals, 28 lie within the selection criteria [20]. Finally, these phytochemicals were prepared via the LigPrep module.

3.2. Grid Generation and Docking Investigation

Identifying the active site within the target can help bind the ligands properly. The grid box was generated, followed by the X (128.77), Y (24.14), and Z (233.8) coordinates, followed by their bounded ligands (Figure 1). Further, all 28 promising ligands were utilized for the docking analysis via the Glide Module, considering XP methods. The investigation revealed several instances of promising phytochemical activity towards the NS5 methyltransferase [8], and among them, the top five were selected (

Table 1. The docking scores of the top compounds along with the control and NS5 methyltransferase (PDB ID: 6KR2).

Sl. No.	PubChem ID	Name	Docking Score (Kcal/Mol)
1	5280343	Quercetin	−7.164
2	440833	Leucocianidol	−6.839
3	5281654	Isorhamnetin	−6.392
4	5320462	Penduletin	−5.850
5	5280863	kaempferol	−5.837
	3034034	Quinine (Control)	−3.050

) and discussed, with docking scores varying from −5.837 to −7.164 Kcal/Mol, which are comparably higher than Quinine’s (PubChem ID; 3034034) −3.050 Kcal/Mol.

Based on the molecular interactions and their generated docking scores, Quercetin shows five (GLU149, GLY148, LYS 181, ARG84, and GLY86), Leucocianidol shows four (GLU149, GLY148, ASP146, and GLY86), Isorhamnetin shows four (GLU149, GLY148, GLY86, and GLY85), Penduletin shows three (GLU149, GLY148, and GLY86), kaempferol shows three (GLU149, GLY148, and GLY86), and Quinine (Control) shows two (GLY86 and ASP146) hydrogen bonds (Figure 2A–F). Apart from the h bond activity of the top phytochemicals towards the NS5 methyltransferase, it also shows four hydrophobic interactions (ILE147, CYS82, TRP87, and VAL55) in Quercetin (Figure 2A), four (ILE147, CYS82, TRP87, and VAL55) in Leucocianidol (Figure 2B), four (VAL55, CYS82, TRP87, and ILE147) in Isorhamnetin (Figure 2C), five (VAL55, CYS82, TRP87, VAL132, and ILE147) in Penduletin (Figure 2D), four (VAL55, CYS82, TRP87, and ILE147) in Kaempferol (Figure 2E), and similarly four (VAL55, CYS82, TRP87, and ILE147) in Quinine (Figure 2F). Moreover, Quinine shows HIE110 as a Pi-cation, followed by GLU111 and GLU149 as salt bridges. Of the overall activity among the screened compounds towards the NS5 methyltransferase, Quercetin, shows remarkable activity and was further examined via simulation to analyze its stability. Additionally, the drug-like properties of these top molecules were examined via QikProp, as shown in

Table 2. Assessments of drug-like properties of top phytochemicals.

Name	#Stars	CNS	mol MW	RuleOfFive
Quercetin	0	−2	302.24	0
Leucocianidol	0	−2	306.271	1
Isorhamnetin	0	−2	316.267	0
Penduletin	0	−1	344.32	0
Kaempferol	0	−2	286.24	0
Quinine (Control)	0	−1	324.422	0
Range	0 to 5	−2 (inactive), +2 (active)	130.0 to 725.0	Maximum 4

. The overall property assessments revealed the significant features of the top phytochemicals, followed by Quinine as a control. The assessments and findings show that the identified phytochemicals can help combat dengue infection.

3.3. Molecular Dynamics Simulation

The simulation examination of Quercetin with the NS5 methyltransferase complex was analyzed over 100 ns. The RMSD of the Quercetin with the NS5 methyltransferase complex shows stability within the range of 1 to 7 Å from 0 to 100 ns, followed by minor fluctuation (Figure 3A). The overall residue activity throughout the simulation was examined based on the RMSF, which revealed that the NS5 methyltransferase with Quercetin shows fluctuation mostly in the range of 0.8 to 4.0 Å, followed by some variation for a few residues exceeding 6.4 Å. Moreover, the higher fluctuation in the graph is represented by its high flexibility (Figure 3B). The interaction analysis of Quercetin with NS5 methyltransferase represents the strong molecular connection followed by the type of interaction such as hydrogen bonds and hydrophobic, ionic, and water bridges, and the bar diagram represents the value under 0.8 leading to the interaction being maintained approximately 80% of the time [22]. The interaction revelaed GLY 83, ARG84, GLY85, and GLY86 as the hydrogen bonds, LYS29, ASP79, GLY81, SER88, GLY109, ASP146, GLU149, and ARG212 as the water bridges, and LYS61 and LYS 181 as the hydrophobic interactions (Figure 3C). The overall examination of the docked complex’s stability revealed stable activity followed by the steps of the trajectory analysis [23].

4. Conclusions

Due to the unavailability of specific drugs for dengue infection, this study aimed to find promising compounds from Dodonaea viscosa for dengue infection by targeting its NS5 methyltransferase. Based on the overall investigation followed by docking, drug-like properties and dynamics investigation, Quercetin was found to have the most promising inhibitor activity compared to the control used, i.e., Quinine, followed by their binding and stability towards the target. The identified compounds can potentially lead to a reduction in dengue infection.