Table 1

Figures at a glance

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Figure 5

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Figure 10

Figure S1

Figure S2

Table 1

Ligand Name	Interacting residues	Type of bond	H-bond distance (Å)	H-bond donor-acceptor angles	Docking score (kcal/mol)
ATP	LYS459	Hydrogen	2.21	178.94˚	-6.9
	ASP669		1.92	150.76˚
	SER715		2.16	143.33˚
GTP	ASP668		2.03	137.82˚	-7.3
GTP	CYS714		2.2	139.85˚	-7.3
CTP	SER604		1.98	137.14˚	-6.5
	TYR610		1.97	130.22˚
	SER666		2.15	125.40˚
UTP	THR609		2.39	110.0˚	-6.6
UTP	ASN613		2.07	154.47˚	-6.6

Table 1: Interaction of NTPs with JEV NS5 RdRp residues

FIGURE 1

Figure 1: Interactions of NTPs with JEV NS5 at the RdRp active site. Only docking poses with the highest docking scores are shown for the representation of each ligand

FIGURE 2

Figure 2: A) System setup for NAMD simulations. JEV NS5 protein (ribbon), water (red) and small organic probe molecules (blue licorice structures), and B) binding hotspots at the RdRp domain (Table S2: Site 2- Solution 1). More details on the hotspot identification process are presented under supplementary data (Table S1)

FIGURE 3

Figure 3: Hotspot (pharmacophore) distribution of JEV NS5 protein. More details on the druggability analysis are presented under supplementary data (Table S1)

FIGURE 4

Figure 4: Potential drug molecule structures and their corresponding ZINC IDs

FIGURE 5

Figure 5: A) Binding affinities of all the NTPs, and screened compounds; B) Superimposition of docked poses of the screened compounds at the RdRp domain

FIGURE 6

Figure 6: Protein backbone RMSD plot of JEV NS5 protein apo-structure (blue), NS5 complexed with ATP (red), and ZINC 9367 (green). Inset: The initial frame (yellow: ligand, blue: protein) and end frame (red: ligand, grey: protein) of JEV NS5 complexed with ATP (red box) and ZINC 9367 (green box) in a 100 ns simulation.

FIGURE 7

Figure 7: Protein backbone RMSF plot of JEV NS5 protein apo-structure (blue), NS5 complexed with ATP (red), and ZINC 9367 (green) over the trajectory of each system in a 100 ns simulation

FIGURE 8

Figure 8: A) Histogram of JEV NS5-ATP interactions throughout the simulation. B) A schematic diagram of ATP atom interactions with the JEV NS5 protein residues. Interactions that occur more than 20.0% of the entire simulation time in the trajectory are shown.

FIGURE 9

Figure 9: A) Histogram of JEV NS5-ZINC 9367 interactions throughout the simulation. B) A schematic diagram of ZINC 9367 atom interactions with the JEV NS5 protein residues. Interactions that occur more than 20.0% of the entire simulation time in the trajectory are shown

FIGURE 10

Figure 10: MM-GBSA free binding energy of ATP (blue) and ZINC 9367 (red) complexed with JEV NS5 protein. The free energy of binding (ΔG_Bind) is shown in kcal/mol

FIGURE S1

Figure S1: Structural superposition of JEV NS5 RdRp domains: 4K6M apo-structure (blue) and ATP-bound crystal structure 4HDH (green). The RMSD for 4HDH relative to the 4K6M structure is 6.5540 Å. The original substrate ATP (4HDH) is shown in orange. The RMSD for docked ATP (red) and ZINC 9367 (purple) was 4.1093 Å and 11.9828 Å respectively compared to the reference original substrate ATP

FIGURE S2

Figure S2: JEV NS5 protein (PDB: 4K6M chain A) information. Total number of residues = 893. Alpha-helical (red cylinders) and beta-strand (blue arrows) regions connected by loops (black lines) are shown