Active site prediction
We found the 58 pocket and pocket 1 is the largest area coverage of 732.092 and highest volume 822.046 (Figure 2). The binding pocket and the amino acid residues are presented in S3.
Binding affinity and interaction
Molecular docking was performed of 90 ligands to derive their binding affinity against the prepared Nipah virus attachment glycoprotein. Binding affinity scores were distributed between -2.1 to -6.5 kcal/mol (Figure 3). The binding scores are available in S4.
Top four (4) ligands were selected for further study based on better binding affinity by comparing them to the control ligand (Table 1). The control ligand (CID:24139), CID:11096158, CID:11861102, CID:6971258, and CID:102601745 had a binding affinity of -5.8, -6.4, -6.4, -6.2, and -6.2 kcal/mol, respectively (Table 1).
Table1. List of binding affinity predicted by Autodock vina of top 4 compounds and control (CID24139) along with compound ID, IUPAC chemical name and 2D structure.
Compound ID
|
Chemical Name (IUPAC)
|
2D structure
|
Binding affinity (kcal/mol)
|
CID: 11096158
|
N-[2,4,5-trihydroxy-6-(hydroxymethyl)oxan-3-yl]acetamide
|
|
-6.4
|
CID: 11861102
|
N-[2,4,5-trihydroxy-6-(hydroxymethyl)oxan-3-yl]acetamide
|
|
-6.4
|
Amb35795905
|
N/A
|
|
-6.2
|
CID: 102601745
|
2-acetamido-2-deoxy-D-gluco-hexopyranose
|
|
-6.2
|
CID: 24139 (Control)
|
2-acetamido-2-deoxy-beta-D-gluco-hexopyranose
|
|
-5.8
|
Binding Interaction of the Selected Ligands
The binding interaction of the selected ligands with the desired protein was visualized with BIOVIA Discovery Studio. The interacting residues of control ligand (CID:24139), CID:11096158, CID:11861102, CID:6971258, and CID:102601745 was showing in the Table 2.
Table 2. Nonbonding interactions of selected top five compounds along with control ligands against the attachment glycoprotein (pose predicted by AutoDock Vina).
ID
|
Amino acid
|
Distance (Å)
|
Bond category
|
Bond types
|
CID: 24139 (Control)
|
ASN557
|
2.72
|
Hydrogen Bond
|
Conventional Hydrogen Bond
|
ILE217
|
2.19
|
Hydrogen Bond
|
Conventional Hydrogen Bond
|
CID: 11096158
|
GLN559
|
2.69
|
Hydrogen Bond
|
Conventional Hydrogen Bond
|
ASN557
|
2.87
|
Hydrogen Bond
|
Conventional Hydrogen Bond
|
GLU579
|
2.13
|
Hydrogen Bond
|
Conventional Hydrogen Bond
|
CID: 11861102
|
GLN559
|
2.69
|
Hydrogen Bond
|
Conventional Hydrogen Bond
|
CYS216
|
2.95
|
Hydrogen Bond
|
Conventional Hydrogen Bond
|
ILE217
|
2.02
|
Hydrogen Bond
|
Conventional Hydrogen Bond
|
CID: 102601745
|
GLN559
|
2.74
|
Hydrogen Bond
|
Conventional Hydrogen Bond
|
CYS216
|
2.77
|
Hydrogen Bond
|
Conventional Hydrogen Bond
|
ILE217
|
2.31
|
Hydrogen Bond
|
Conventional Hydrogen Bond
|
Amb35795905
|
GLU579
|
2.57389
|
Hydrogen Bond
|
Conventional Hydrogen Bond
|
ILE217
|
2.21994
|
Hydrogen Bond
|
Conventional Hydrogen Bond
|
GLU579
|
2.70235
|
Hydrogen Bond
|
Conventional Hydrogen Bond
|
All the selected ligands (CID:11096158, CID:11861102, Amb35795905, and CID:102601745) formed complexes with the attachment glycoprotein using three conventional hydrogen bonds. For CID: 11096158 (Pubchem CID), the interaction took place in GLN559 (2.69 Å), ASN557 (2.87 Å) and GLU579 (2.13 Å) amino acids. The compound 11861102 (Pubchem CID) was stabilized by GLN559 (2.69 Å), CYS216 (2.95 Å) and ILE217 (2.02 Å) residue interactions. In the case of compound Amb35795905, the complex was formed by GLN559 (2.57 Å), ILE217 (2.21 Å), and GLU579 (2.70 Å) interactions. The interactions are shown in Table 2 and Figure 4.
The control compound CID24139 formed two conventional hydrogen bonds with the protein at ASN557 and ILE217 residues at 2.72 Å and 2.19 Å respectively. Finally, in the case of 102601745 (Pubchem CID), the interactions were observed in GLN559 (2.74 Å), CYS216 (2.77 Å) and ILE217 (2.31 Å) residues. The interactions are shown in Table 2 and Figure 5.
Pharmacokinetic and Toxicity properties
Important pharmacokinetic properties of the selected four compounds were calculated using the SwissADME server. Physicochemical parameters such as molecular weight, rotatable bonds, H bond acceptor, H bond donors, GI absorption, drug-likeness (Lipinski/RO5) etc were enumerated and listed in Table 3. The selected compounds have encouraging pharmacokinetic properties. Toxicity properties such as AMES toxicity, LD50, hepatotoxicity etc were estimated using the pkCSM server (Table 3). All the selected compounds had desirable non-toxic properties.
Table 3. Pharmacokinetic properties of the selected compounds.
Properties
|
CID:11096158
|
CID:11861102
|
Amb35795905
|
CID:102601745
|
Physico-chemical Properties
|
MW (g/mol)
|
221.21
|
221.21
|
221.21
|
222.2
|
Heavy atoms
|
15
|
15
|
15
|
15
|
Arom. heavy atoms
|
0
|
0
|
0
|
0
|
Rotatable bonds
|
3
|
3
|
3
|
3
|
H-bond acceptors
|
6
|
6
|
6
|
6
|
H-bond donors
|
5
|
5
|
5
|
5
|
Lipophilicity
|
Consensus Log P
|
-1.79
|
-1.64
|
-1.74
|
-1.69
|
Water Solubility
|
Log S (ESOL)
|
-0.28
|
-0.28
|
-0.28
|
-0.29
|
Pharmacokinetics
|
GI absorption
|
Low
|
Low
|
Low
|
Low
|
BBB permeant
|
No
|
No
|
No
|
No
|
Druglikeness
|
Lipinski, Violation
|
0
|
0
|
0
|
0
|
Medicinal Chemistry
|
Synth. accessibility
|
3.79
|
3.79
|
3.79
|
3.79
|
Toxicity
|
AMES toxicity
|
No
|
No
|
No
|
No
|
Oral Rat Acute Toxicity (LD50)
|
1.706
|
1.706
|
1.706
|
1.706
|
Oral Rat Chronic Toxicity (LOAEL)
|
3.706
|
3.706
|
3.706
|
3.706
|
Hepatotoxicity
|
No
|
No
|
No
|
No
|
Skin Sensitization
|
No
|
No
|
No
|
No
|
MD simulation
Molecular Dynamics (MD) Simulation is a kind of computational process used for drug discovery from screening the bonding stability of protein-ligand complexes (Durrant and McCammon, 2011). The atoms and molecules are allowed to interact for a set amount of time, providing a perspective of the system's dynamic evolution. In this MD simulation, the Desmond tool was used to evaluate the trajectory output to illustrate the root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), protein-ligand contacts (P-L contact), and Ligand properties. (Incomplete)
RMSD analysis
In MD simulation, the root-mean-square deviation (RMSD) is typically used to determine if the simulation has equilibrated or not by calculating the mean value change by dislocation of atoms from a particular frame compared to a reference frame. RMSD is also known as the root-mean-square error (RMSE). In Figure 5 selected ligand compounds are compared with Apo-form and the control ligand CID24139. Apo is known as one of the acyl-chain properties (Chan et al., 2008). If Apo distance is comparatively like target ligand, then the ligand is considered as acceptable. CID102601745 (Amb33921182) and Amb35795905 compounds are acceptable in comparison to other compounds based on Apo distances (Figure 6). However, all protein–ligand complexes supported the combined screened potential compounds.
RMSF analysis
By generating information about RMSF, MD simulation not only offers the RMSD value of the protein–ligand complex structure, but it also gives information on protein heterogeneity and the steady state of macromolecules. The RMSF value is required for describing a protein since it offers information on the protein's local alterations as well as the protein chain. Based on Fluctuation, all protein–ligand complexes support the combined potential molecules in Figure 7. On the contrary, CID102601745(Amb33921182) compound displays less fluctuation compared to others. The overall fluctuations of selected legends are okay compared with Apo and control ligand. In comparison to Apo and control ligand, the overall fluctuations of selected legends are acceptable.
Protein–ligand contacts
Hydrogen bonding, ionic bonding, water bridges, and hydrophobic bonding all play a role in turning a molecule into an effective medicine.
NiV attachment glycoprotein (G) (Chain A) protein had protein–ligand interactions, and the MD trajectories of five substances were studied using the Desmond module's default parameters. These indicate how long it has interacted with bonds. In Figure 7, the bar diagram depicted that all compounds have the highest interaction fluctuation value in GLU_579 (amino acid). In Figure 8, CID102601745, Amb35795905, CID11906158, CID24139 (control) demonstrate that hydrogen and water bridge bond indicate maintaining interaction about 110%, 200%, 34%, 160% respectively. In contrast, CID11861102(Amb28974637) has three bonds (Hydrogen Bonds, Water bridges, Ionic) which are responsible for 150% interaction in GLU_579. Amb35795905 ligand maintains the highest interaction about 200% in GLU_579, where CID11906158 illustrates the lowest interaction in GLU_579 of about 34%.
Ligand properties
We used molecular dynamics (MD) simulation to investigate the stability of various ligand positions (Figure 9). In Figure 9(A), The shift in mean or average value from one frame to another with a range order of 1–3 or 0.1–0.3 nm is entirely acceptable, where a value greater than the desired range indicates a major conformational shift in the protein. According to this, CID102601745 maintains an appropriate distance when compared to the control ligand. Moving to the diagram of Figure 9(E), the line graph displayed the SASA value. The expansion of protein volume is indicated by a higher Solvent-Accessible Surface Area (SASA) value, and a minimal variation is expected across the simulation time. SASA can be altered by the binding of any tiny chemical, and this can have a significant impact on the protein structure. CID11906158(Amb22736116) shows much fluctuation compared to other ligands between 17ns 35ns and 60ns to 150ns. Similarly, Amb35795905 depicts around 375, between 130ns and 150ns where, CID11861102(Amb28974637) shows around 150 to 225, from 127ns to 150ns. On the contrary, CID102601745(Amb33921182) compound displays stabilisation compared with the control ligand.