Design and Identification of Lead Compounds Targeting Nipah G Attachment Glycoprotein by In Silico Approaches

Nipah virus (NiV) caused several outbreaks in Asian countries, including the latest one from the Kerala state of India. There is no drug available against NiV till now, despite its urgent requirement. There are reports about the anti-influenza viral drug Favipiravir, which has positively affected the Nipah virus in vitro models. In the current work, we have provided a computational screening for NiV inhibitors. Twenty-two designed compounds from favipiravir and Nipah glycoprotein, 3D11, were chosen and performed molecular docking to analyse the various conformations and interactions with the amino acids; further, their physicochemical and ADMET properties were also computed. The compound 5_Favipiravir have an excellent docking score (-6.16 kcal/mol), followed by compound 4_Favipiravir and 19_Favipiravir with docking score of -5.50 and -5.38 kcal/mol respectively. The three compounds had the respective heterocyclic moieties such as pyrazole, imidazole and pyrazinone. All the twenty-two designed compounds obey the Lipinski rule of five, which infer that they will not have problems with oral bioavailability. Thus, it is concluded that the incorporated heterocyclic groups in favipiravir can add to the anti-Nipah activity; hence it can act as future leads for the treatment for the disease caused by Nipah virus. Original Research Article James et al.; JPRI, 33(40A): 156-169, 2021; Article no.JPRI.72296 157


INTRODUCTION
Nipah virus (NiV) is an evolving virus that can cause severe respiratory disease and deadly encephalitis in humans, including paramyxovirus (Henipavirus, Paramyxovirinae subfamily, family Paramyxoviridae, the order of Mononegavirales). Several significant individual outbreaks occurred in the twenty-first century beginning in Bangladesh and India in 2001 [1]. Similar explosions were also reported in two villages in the Philippines in 2014. In Kerala, a southern Indian state, the latest uprising started in May 2018 [2,3].
Therapy is limited to treatment and support. In preventing hospital-acquired infections, standard infection prevention procedures and barrier nursing strategies are critical as NiV encephalitis can be transmitted from person to person. Ribavirin, a hepatitis C antiviral drug, has also proved helpful in vitro, but to date, human trials have not been completed with doubt regarding the clinical usefulness of ribavirin [4,5]. Ribavirin is a therapy that is approved or tolerated for a variety of viral infections [6]. In vitro experiments showed that ribavirin acts against replication of Hendra and Nipah viruses [7,8].
Furthermore, it was earlier demonstrated that anti-malarial drug chloroquine blocks the essential proteolytic processing required to develop the structure and function of Hendra F glycoprotein virus and chloroquine [9] and, not surprisingly, was later shown to inhibit Nipah and Hendra infection in cell culture [10]. There have been two experiments in hamsters and one in non-human primates (African Green Monkey (A Green monkey)) that only delayed treatment with ribavirin but not prevented death following infection by Nipah Virus [11,12]. The use in the post-exposure therapy in ferret models of a human monoclonal antibody targeting Nipah G glycoprotein has been tested and has proved to be effective [13,14].
The chemical modification of the pyrazine analogue initially screened for in vitro antiinfluenza virus activity in cells discovered Favipiravir [15]. Favipiravir inhibits influenza viral RNA polymerase [16] and is a versatile and effective inhibitor that works against all subtypes and strains of the flu virus, including those susceptible or immune to neuraminidase and M2 inhibitors on the market. Antiviral activities against other RNA viruses were also demonstrated by Favipiravir [17]. These data indicate that favipiravir is potent medicine for treating influenza virus infections and various RNA viruses.
Favipiravir disrupted the viral genome in the centre of the replication process in a drug additive test. Antiviral favipiravir action was attenuated by purine nucleosides or purine bases, suggesting that favipiravir interacts with purine nucleosides instead of pyrimidine nucleosides [16].
Nowadays, computer-aided drug design is one of the essential techniques of rational drug design. The in silico study involves different computational methods which help to reduce the time and cost of the drug discovery process [18]. The high-throughput automated screening method is time-consuming, as more compounds must be trialled. Structure-based drug design is helpful to find out the new lead compound, which is active against the target. This process required a lesser number of compounds that may take into the trial [19].
In continuation of the in silico studies conducted earlier [20,21], in this study, we have designed 22 compounds of favipiravir containing pyrazine as the moiety and other heterocyclic rings to identify novel inhibitors of NiV using different in silico methods. Molecular docking, physicochemical properties and ADMET properties were determined by using Schrodinger software. The comparison of in silico results was made with standard drug favipiravir.

Reaction Enumeration
In this method, numerous compounds can be generated as a derivative of the parent compound. There is a possibility to replace the substituent based on the chemical nature of the compounds. In this study, the hydrogen atom in the amino group of Favipiravir was replaced with aromatic monocyclic groups available in Schrodinger enumeration databases [22] (Table  1).

Ligand Preparation
All the ligands were neutralised, desalted, prevented from tautomers generation to retain a specific chirality by the Ligprep application tool in Schrodinger [23]. Only one structure was generated per ligand.

Protein Preparation
The specific Nipah protein 3D11 was imported from the protein data bank (PDB) [24] and processed by the Protein Preparation Wizard application tool in Schrodinger. Pre-processing of the protein was done by assigning bond orders by adding hydrogen, creating zero-order bonds to metals, creating disulphide bonds, filling the missing side chain and loops by using the prime module. All the water molecules were deleted beyond 5 Å, from the hetero groups. The hetero states of the ligand were maintained in the pH range 7±2.

Receptor Grid Generation
Grid generation specifies the 3D (X,Y,Z-axis) location where the ligand binds. A grid was generated for the minimised protein by using the tool Receptor Grid Generation in Schrodinger.

Ligand Docking
Ligand docking was performed by Glide-XP application in Schrodinger [25] .
In the Glide -XP panel, the receptor grid generated was uploaded, and the prepared ligands were imported as out.maegz file to the working panel. In the precision tab, XP (extra precision) was selected, and the method adopted was flexible docking in ligand sampling [24].

Physicochemical Properties
The physicochemical properties were calculated by QikProp application of Schrodinger software [26]. The prepared ligands were selected and incorporated into the Qikprop tool and processed. The properties Molecular weight, Log P, QPlogPo/w, donor-HB, accept-HB, which analyse Lipinski Rule of five [27] were assessed.

ADMET Properties
The ADMET properties were computed by the QikProp application of Schrodinger software [28]. The prepared ligand was selected and incorporated into the Qikprop tool and processed. The features such as QPPCaco, % Human oral absorption, QPlogKhsa, SASA, QPlogHERG was analysed.

Molecular Docking
In the present study, twenty-two designed compounds and Nipah glycoprotein, 3D11, were chosen and performed molecular docking to analyse the various conformations and interactions with the amino acids (Fig. 1). On further analysis of the results, thirteen favipiravir derivatives (5_Favipiravir, 4_Favipiravir, 19_Favipiravir, 8_Favipiravir, 15_Favipiravir, 12_Favipiravir, 18_Favipiravir, 20_Favipiravir, 22_Favipiravir, 1_Favipiravir, 3_Favipiravir, 6_Favipiravir, 21_Favipiravir) were found to have docking scores higher than the standard favipiravir, suggesting that they might have an

Binding of 5_Favipiravir with 3D11
The active amino acids in the protein 3D11, which made hydrophobic interaction with the 5_Favipiravir was found to be

Binding of 4_Favipiravir with 3D11
The docking score of 4_Favipiravir with 3D11 is -5.501 kcal/mol compared with the standard drug Favipiravir (-3.706 kcal/mol

Binding of 19_Favipiravir with 3D11
The compound 19_Favipiravir interacted with the protein 3D11 with the docking score of -5.38 kcal/mol. The respective active amino acids Tyr

Physicochemical Properties and Rule of Five Properties
All the compounds have their molecular weight below 500 ranging from 150-260. The calculated log P value of the compounds is below 5. The compounds under investigation possess hydrogen bond donors (˂5) and hydrogen bond acceptors (˂10) within the limit. Based on the experimental values (

In silico ADMET Studies
The results show that compounds have better scores for Caco-2 permeability, human oral absorption, Total solvent accessible surface area, human serum albumin binding (Table 5).

CONCLUSIONS
Twenty-two compounds were designed from the compound favipiravir and screened for their anti-Nipah activity by molecular docking and their ADMET properties were computed. The compound 5_Favipiravir have an excellent docking score, i.e., -6.16 kcal/mol, followed by compound 4_Favipiravir and 19_Favipiravir with docking score of -5.50 and -5.38 kcal/mol respectively. The three compounds had the respective heterocyclic moieties such as pyrazole, imidazole and pyrazinone. On further analysis of the results, thirteen favipiravir derivatives were found to have docking scores higher than the standard favipiravir, suggesting that they might have an excellent binding with the Nipah virus protein. All the twenty-two designed compounds obey the Lipinski rule of five, which infer that they will not have problems with oral bioavailability. Thus, it is concluded that the incorporated heterocyclic compounds can add to the anti-Nipah activity; hence it can act as future leads for the treatment for the disease caused by the Nipah virus.

CONSENT
It is not applicable.