Hirshfeld analysis and molecular docking with the RDR enzyme of 2-(5-chloro-2-oxoindolin-3-ylidene)-N-methylhydrazinecarbothioamide

The title isatin thiosemicarbazone derivative is an intermediate in the synthetic pathway of HIV-1 reverse transcriptase inhibitors. A molecular docking evaluation of the title compound with the ribonucleoside diphosphate reductase (RDR) enzyme was carried out.


Chemical context
Methods for the synthesis of isatin derivatives were first reported in the first half of the 19th century (Erdmann, 1841a,b;Laurent, 1841), while for thiosemicarbazone derivatives one of the first reports can be traced back to the early 1900's (Freund & Schander, 1902). Initially, thiosemicarbazone chemistry was not related to the pharmacological sciences. This has changed since the discovery that in vitro assays of sulfur-containing compounds showed that they are effective for Mycobacterium tuberculosis growth inhibition (Domagk et al., 1946). In the 1950's, the synthesis of isatinthiosemicarbazone derivatives was reported (Campaigne & Archer, 1952) and in vitro assays indicated such compounds to be active against Cruzain, Falcipain-2 and Rhodesian (Chiyanzu et al., 2003). Nowadays, many isatin-thiosemicarbazone derivatives employed in medicinal chemistry. For example, 1-[(2-methylbenzimidazol-1-yl) methyl]-2-oxo-indolin-3-ylidene]amino]thiourea is an in vitro and in silico ISSN 2056-9890 Chikungunya virus inhibitor (Mishra et al., 2016). The title compound (I), 5-chloroisatin-4-methylthiosemicarbazone, is an intermediate in the synthetic pathway of HIV-1 (human immunodeficiency virus type 1) RT (reverse transcriptase) inhibitor synthesis (Meleddu et al., 2017); a new crystal structure determination is reported here, the original work having been published by Qasem Ali et al. (2012). Thus, the crystal structure determination of isatin-thiosemicarbazonebased molecules is an intensive research area in medicinal chemistry and the main focus of our work.

Structural commentary
The present analysis of the title compound (I), measured at 200 K, is very similar to that measured by Qasem Ali et al. (2012) at 100 K. There is one intramolecular hydrogen bond, N3-H3NÁ Á ÁO1 (Table 1), with an S(6) graph-set motif (Fig. 1).

Supramolecular features
In the crystal, molecules are linked by N1-H1NÁ Á ÁO1 i hydrogen bonds, forming chains propagating along the a-axis direction. The chains are linked by N4-H4NÁ Á ÁS ii hydrogen bonds, forming a three-dimensional supramolecular structure (Fig. 2, Table 1). The three-dimensional framework is reinforced by C6-H6Á Á Á iii interactions, as shown in Fig. 2 (see also Table 1). The crystal structure determined in this work and that of the originally published article (Qasem Ali et al., 2012) Table 1 Hydrogen-bond geometry (Å , ).

Figure 2
A view along the a axis of the crystal packing of the title compound (I) (this work). Details of the N-HÁ Á ÁO and N-HÁ Á ÁS hydrogen bonds (dashed lines) and the C-HÁ Á Á interactions (blue arrows) are given in Table 1. H atoms not involved in these interactions have been omitted for clarity.

Figure 1
The molecular structure of the title compound (I) (this work), showing the atom labelling and displacement ellipsoids drawn at the 50% probability level. The intramolecular hydrogen bond [graph-set motif S(6)] is shown as a dashed line (see Table 1).

Molecular docking
Finally, for an interaction between the 5-chloroisatin-4methylthiosemicarbazone (this work) and a biological target, the ribonucleoside diphosphate reductase (RDR), a lock-andkey supramolecular analysis was carried out (Chen, 2015). The RDR enzyme was selected for this work due its importance in cell proliferation. It catalyzes the conversion of ribonucleotides to deoxyribonucleotides, which is the rate-limiting step for DNA synthesis. In addition, a thiosemicarbazone derivative, the 3-amino-pyridine-2-carboxaldehyde thiosemicarbazone, shows RDR inhibition and biological activity is suggested by its coordination with the Fe ions of the enzyme   The semi-empirical equilibrium energy of the title compound (this work) was obtained using the PM6 Hamiltonian (Stewart, 2013), but the experimental bond lengths were conserved. The crystal structure of the RDR enzyme (PDB code: 1W68) was downloaded from the Protein Data Bank (Strand et al., 2004). The calculated parameters were: heat of formation = 98.697 kcal mol À1 , gradient normal = 0.68005, HOMO = À8.934 eV, LUMO = À1.598 eV and energy gap = 7.336 eV. The title compound (I) and the active site of the selected enzyme matches and structure-activity relation-ship can be assumed by the following observed intermolecular interactions: Cl1Á Á ÁH-C(LYS140) = 2.538 Å , Cg(aromatic ring)Á Á ÁH-C(SER71) = 2.714 Å , H5Á Á ÁO-C(GLU200) = 1.663 Å , Fe1Á Á ÁO1 = 2.567 Å and Fe2Á Á ÁO1 = 2.511 Å . The in silico evaluation suggests through the graphical representation the bridging O1 atom connecting the two Fe III metal centers by intermolecular interactions (Fig. 6).

Comparison with a related structure
Isatin-thiosemicarbazone derivatives have molecular structural features in common, viz. nearly a planar geometry as a result of the sp 2 -hybridized C and N atoms of the main fragment. For a comparison with the title compound [5-chloroisatin-4-methylthiosemicarbazone (I); this work], 5-chloroisatin-thiosemicarbazone, (II), was selected (de Bittencourt et al., 2014) as both structures have the same main entity. The molecular structural difference is the substitution of one H atom of the amine group of (II) by a methyl group in the title compound (I). Although the molecular basis for the two compounds is the same, there are significant differences in the crystal packing. For compound (I), the unit cell is chiral and the molecules are linked by hydrogen bonding into a threedimensional network (Figs. 2 and 7a), while for compound (II) the unit cell is centrosymmetric and the hydrogen bonding is observed in a planar arrangement, with the molecules stacked along the [001] direction (Fig. 7b). The terminal methyl group in (I) decreases the possibility of H-atom contacts with S and O acceptors, while in compound (II), the presence of the terminal unsubstituted amine increases the chances for hydrogen bonding, as suggested by the Hirshfeld surface analysis, d norm , for the two molecules (Fig. 3a,b). The Hirshfeld surface two-dimensional fingerprint plot shows that the contribution of the HÁ Á ÁS intermolecular interaction to the crystal cohesion amounts to 12.0% in the title compound (I), while for the 5-chloroisatin-thiosemicarbazone (II) it amounts to 17.2% (Fig. 5a,b). The relationship between thio-

Synthesis and crystallization
The starting materials are commercially available and were used without further purification. The synthesis of the title compound was adapted from a previously reported procedure (Freund & Schander, 1902). In an acetic acid-catalyzed reaction, a mixture of 5-cloroisatin (3 mmol) and 4-methyl-3thiosemicarbazide (3 mmol) in ethanol (40 ml) was stirred and refluxed for 5 h. On cooling, a solid was obtained which was filtered off. Yellow prismatic crystals of the title compound were grown in tetrahydrofuran by slow evaporation of the solvent.

Refinement
Crystal data, data collection and structure refinement details for the title compound (I) are summarized in Table 2. The NH H atoms were located in difference-Fourier maps and freely refined. The C-bound H atoms were positioned with idealized geometry and refined using a riding model: C-H = 0.95-0.98 Å with U iso (H) = 1.5U eq (C-methyl) and 1.2U eq (C) for other H atoms. The absolute structure of the molecule in the crystal was determined by resonant scattering [Flack parameter = 0.006 (9)   program(s) used to solve structure: SHELXT2014 (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2016 (Sheldrick, 2015b); molecular graphics: Mercury (Macrae et al., 2008), DIAMOND (Brandenburg, 2006), GOLD (Chen, 2015), MOPAC (Stewart, 2013) and Crystal Explorer (Wolff et al., 2012); software used to prepare material for publication: SHELXL2016 (Sheldrick, 2015b), publCIF (Westrip, 2010) and enCIFer (Allen et al., 2004).  (9) Special details Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.