Crystal structure, Hirshfeld analysis and a molecular docking study of a new inhibitor of the Hepatitis B virus (HBV): ethyl 5-methyl-1,1-dioxo-2-{[5-(pentan-3-yl)-1,2,4-oxadiazol-3-yl]methyl}-2H-1,2,6-thiadiazine-4-carboxylate

The title compound, a new inhibitor of the Hepatitis B virus (HBV), was prepared via alkylation of 3-(chloromethyl)-5-(pentan-3-yl)-1,2,4-oxadiazole in anhydrous dioxane in the presence of triethylamine.

Single-crystal X-ray diffraction analysis and different spectroscopic techniques confirm the assigned chemical structure of the title compound. Molecular docking simulations were also carried out.

Supramolecular features
In the crystal, molecules are linked by C-HÁ Á ÁN hydrogen bonds, forming chains propagating along the b-axis direction (Table 1 and Fig. 4). There are no other significant intermolecular interactions present in the crystal. Synthesis of 2H-1,2,6-thiadiazine 1,1-dioxide via intermolecular cyclization of sulfamide with the corresponding 1,3-diketone.

Figure 2
Synthesis of the title compound 3.

Figure 3
The molecular structure of compound 3, with atom labelling. Displacement ellipsoids are drawn at the 50% probability level.

Figure 4
A partial view along the a axis of the crystal packing of compound 3. Hydrogen bonds (

Hirshfeld surface analysis
The Hirshfeld surface analysis (Spackman & Jayatilaka, 2009) and the associated two-dimensional fingerprint plots (McKinnon et al., 2007) were performed with Crystal-Explorer17 (Turner et al., 2017). The molecular Hirshfeld surfaces were obtained using a standard (high) surface resolution with the three-dimensional d norm surface (Fig. 5), mapped over a fixed colour scale of À0.484 (red) to 1.652 (blue). There are four red spots in the d norm surface indicating the regions of donor-acceptor interactions or short contacts. A list of short contacts in the crystal of compound 3 are given in Table 2. The intermolecular interactions in the crystal of the title compound are shown on the two-dimensional fingerprint plots presented in Fig. 6. The contribution of the OÁ Á ÁH/HÁ Á ÁO contacts, corresponding to the C-HÁ Á ÁO interactions, is represented by a pair of sharp spikes. The interactions appear in the middle of the scattered points in the two-dimensional fingerprint plot with a contribution to the overall Hirshfeld surface of 27.5% (Fig. 6c). The fingerprint plots indicate that the principal contributions are from HÁ Á ÁH (48.7%; Fig. 6b

Molecular docking evaluation
The title molecule (3) was investigated as a potential system that can interact effectively with the capsid of the Hepatitis B virus (HBV). We performed molecular modelling of the interaction of title molecule with core HBV proteins including 5E0I, 5GMZ, 5WRE and 5T2P. The crystal structures of these proteins were obtained at high resolution (1.5-2 Å ), all necessary information about the crystal structures being downloaded from the Protein Data bank (Berman et al., 2000; accessed on 24 July 2019). The pharmacophore model was generated by using the The Hirshfeld surface of compound 3, mapped over d norm , with a fixed colour scale of À0.484 to 1.652 a.u. Table 1 Hydrogen-bond geometry (Å , ).

Table 2
Short contacts (Å ) in the crystal of compound 3.
Symmetry codes: (i) Àx + 1, y À 1 2 , Àz + 1 2 ; (ii) x À 1 2 , Ày + 1 2 , Àz + 1; (iii) Àx + 1, Ày + 1, Àz + 1; (iv) Àx + 1 2 , y À 1 2 , z; (v) Àx + 3 2 , y À 1 2 , z.  Langer, 2005; accessed on 24 July 2019). All of the abovementioned protein structures contain six chains (designated as A, B, C, D, E, F). The docking poses of ligands (reference molecules) were extracted from the obtained crystallographic data. For the correct choice of appropriate chain and poses for molecular modelling (docking), all the reference ligands were re-docked. According to our calculations, the minimal values of the residual mean-square deviations (r.m.s.d.) for the geometry were obtained for poses in the D chains (r.m.s.d. < 1 Å ). Hence, the active-site selection and corresponding pharmacophore analyses were performed for the D chains of the above-mentioned proteins. The most significant information is collected in Table 3. As can be seen from Table 3, our system demonstrated rather large values of binding affinity for all the proteins. The corresponding graphical representation describes the pharmacophore environment of the ligands (Fig. 7, left) and poses in proteins (Fig. 7, right). The red lines designate hydrogenbond acceptors, while yellow lines designated hydrophobic interactions.
It should be noted that the geometrical configuration of the title molecule (as ligand immersed to protein) essentially depends on the pharmacophore surroundings. The most significant geometrical parameters (torsion angles) obtained from the docking procedure are compared with results of the non-empirical calculations and X-ray data in Table 4. The calculated structure of the title compound is illustrated in Fig. 8. The ab initio calculations were performed by using density functional theory with M062x functional and cc-pVDZ basis set.
The obtained data demonstrate significant geometrical relaxation associated with immersion of the molecule in a protein.   Table 4 Torsion angles ( ) comparison for X-ray, ab initio and docking data.  Calculated docking poses for the complex 'title molecule-protein'.

Figure 8
Calculated structure of the title compound.
with the NTCP gene (Sun et al., 2016) was developed in our laboratories for identification of viral entry inhibitors able to prevent development of resistant HBV forms (Ivachtchenko et al., 2019b). Compound 3 demonstrated 80% inhibition of HBV replication (in 10 mM concentration) in this model and could be considered to be a promising candidate for the development of a potent anti-HBV medicine capable of preventing the development of resistant HBV forms (Donkers et al., 2017).

Refinement
Crystal data, data collection and structure refinement details are summarized in Table 5. H atoms were included in calculated positions and treated as riding on their parent C atom: C-H = 0.93-0.98 Å with U iso (H) = 1.5U eq (C-methyl) and 1.2U eq (C) for other H atoms.