Structure and surface analyses of a newly synthesized acyl thiourea derivative along with its in silico and in vitro investigations for RNR, DNA binding, urease inhibition and radical scavenging activities

Abstract

N-((4-Acetylphenyl)carbamothioyl)-2,4-dichlorobenzamide (4) was synthesized by the treatment of 2,4-dichlorobenzoyl chloride with potassium thiocyanate in a 1 : 1 molar ratio in dry acetone to afford the 2,4-dichlorobenzoyl isothiocyanate in situ which on reaction with acetyl aniline furnished (4) in good yield and high purity. The compound was confirmed by FTIR, ¹H-NMR, and ¹³C-NMR and single crystal X-ray diffraction studies. The planar rings were situated at a dihedral angle of 33.32(6)°. The molecules, forming S(6) ring motifs with the intramolecular N-H⋯O hydrogen bonds, were linked through intermolecular C-H⋯O and N-H⋯S hydrogen bonds, enclosing R₂ ²(8) ring motifs, into infinite double chains along [101]. C-H⋯π and π⋯π interactions with an inter-centroid distance of 3.694 (1) Å helped to consolidate a three-dimensional architecture. Hirshfeld surface (HS) analysis further indicated that the most important contributions for the crystal packing were from H⋯C/C⋯H (20.9%), H⋯H (20.5%), H⋯Cl/Cl⋯H (19.4%), H⋯O/O⋯H (13.8%) and H⋯S/S⋯H (8.9%) interactions. Thus C-H⋯π (ring), π⋯π, van der Waals interactions and hydrogen bonding played the major roles in the crystal packing. The electronic structure and computed DFT (density functional theory) parameters identified the reactivity profile of compound (4). In silico binding of (4) with RNA indicated the formation of a stable protein-ligand complex via hydrogen bonding, while DNA docking studies inferred (4) as a potent groove binder. The experimentally observed hypochromic change (57.2%) in the UV-visible spectrum of (4) in the presence of varying DNA concentrations together with the evaluated binding parameters (K _b; 7.9 × 10⁴ M^-1, ΔG; -28.42 kJ mol^-1) indicated spontaneous interaction of (4) with DNA via groove binding and hence supported the findings obtained through docking analysis. This compound also showed excellent urease inhibition activity in both in silico and vitro studies with an IC₅₀ value of 0.0389 ± 0.0017 μM. However, the radical scavenging efficiency of (4) was found to be modest in comparison to vitamin C.

Fig. 1. The molecular architecture of the title novel thiourea molecule (4).

Scheme 1. Synthetic scheme for acyl thiourea derivative (4).

Fig. 2. (A) Crystal structure of (4) with the atoms numbering scheme; the thermal ellipsoids are drawn at the 50% probability level, (B) crystal's partial packing viewed down the b-axis. The dashed lines () showed N–H⋯O (intramolecular) and C–H⋯O, N–H⋯S (intermolecular) hydrogen bonds. For clarity, the nonbonding H-atoms were omitted.

Fig. 3. (A) 3-D view of HS of (4) mapped over d_norm in the range of −0.3442 to 1.6171 a.u., (B) 3-D view of HS of (4) mapped over electrostatic potential energy ranging from −0.0500—0.0500 a.u. {at the Hartree–Fock (HF) level of theory (basis set; STO-3 G)}.The blue and red regions represent positive (hydrogen-bond donors) and negative (hydrogen-bond acceptors) potentials, respectively, (C) HS of (4) plotted over shape-index.

Fig. 4. Two-dimensional fingerprint plots for (4), showing (a) all interactions, and described into (b) H⋯C/C⋯H, (c) H⋯H, (d) H⋯Cl/Cl⋯H, (e) H⋯O/O⋯ H, (f) H⋯S/S⋯H, (g) Cl⋯Cl, (h) S⋯C/C⋯S, (i) C⋯C, (j) O⋯C/C⋯O, (k) H⋯N/N⋯H, (l) C⋯Cl/Cl⋯C, (m) N⋯Cl/Cl⋯N, (n) S⋯Cl/Cl⋯S, (o) O⋯O, (p) N⋯C/C⋯N and (r) N⋯O/O⋯N interactions. The d_i and d_e values are the closest internal and external distances (in Å) from given points on the HS contacts.

Fig. 5. The HS images with the d_norm function plotted on the surface for (a) H⋯C/C⋯H, (b) H⋯H, (c) H⋯Cl/Cl⋯H, (d) H⋯O/O⋯H and (e) H⋯S/S⋯H interactions.

Fig. 6. Optimized structure of (4) along with bonding molecular orbital (HOMO), anti-bonding molecular orbital (LUMO).

Fig. 7. Top: crystallographic structure of ribonucleotide reductase (RNR), black clouds indicating activation loop. Bottom: most probable 2D and 3D interactions of (4) within activation loop of RNR protein.

Fig. 8. Left upper and left bottom: docked conformation of (4) indicating DNA groove binding mode. Right: 2D conformation.

Fig. 9. Top: crystallographic structure of jack bean urease. Bottom: 3D and 2D conformation of (4) docked with urease.

Fig. 10. (a) UV-visible spectral responses of (4) and (4)–DNA adduct. Changes in the peak intensity and peak shift are represented by the direction of arrows. (b) A_o − A/A_ovs. 1/[DNA] graph for binding constant calculation.

Fig. 11. Percent free radical scavenging activity of (4) and reference scavenger for DPPH radical.