Synthesis, spectroscopic, topological, hirshfeld surface analysis, and anti-covid-19 molecular docking investigation of isopropyl 1-benzoyl-4-(benzoyloxy)-2,6-diphenyl-1,2,5,6-tetrahydropyridine-3-carboxylate.

Isopropyl 1-benzoyl-4-(benzoyloxy)-2,6-diphenyl-1,2,5,6-tetrahydropyridine-3-carboxylate (IDPC) was synthesized and characterized via spectroscopic (FT-IR and NMR) techniques. Hirshfeld surface and topological analyses were conducted to study structural and molecular properties. The energy gap (Eg), frontier orbital energies (EHOMO, ELUMO) and reactivity parameters (like chemical hardness and global hardness) were calculated using density functional theory with B3LYP/6-311++G (d,p) level of theory. Molecular docking of IDPC at the active sites of SARS-COVID receptors was investigated. IDPC molecule crystallized in the centrosymmetric triclinic ( P 1 ¯ ) space group. The topological and Hirshfeld surface analysis revealed that covalent, non-covalent and intermolecular H-bonding interactions, and electron delocalization exist in the molecular framework. Higher binding score (-6.966 kcal/mol) of IDPC at the active site of SARS-COVID main protease compared to other proteases suggests that IDPC has the potential of blocking polyprotein maturation. H-bonding and π-cationic and interactions of the phenyl ring and carbonyl oxygen of the ligand indicate the effective inhibiting potential of the compound against the virus.

Introduction

Heterocyclic compounds are planar rings of carbon atoms containing at least one heteroatom such as O, N, P and/or S in their structures 1,2. They are of interest to scientists and researchers because of their applications in different areas of materials and pharmaceutical research 3,4,5,6. Nitrogen heterocyclic compounds are important building blocks in the many bioactive natural products and commercial drugs. Piperidine-based heterocyclic amines are widely used as a building block in organic synthesis and drug discovery. Its compounds show a variety of biological activities viz; anticancer, antimicrobial, analgesic and anti-inflammatory agents. Piperidine and pyridine components are the most common heterocyclic fragments present in FDA approved drugs [7]. Instead of having a secondary amine group in the piperidine ring, the ring nitrogen substituted by alkyl, aryl, and carbonyl groups [8], acetyl or benzoyl group possesses more biological activity 9,10. Substituted piperidin-4-one molecules normally acquire a chair conformation; however, the conformation may differ from the others depending on the phenyl ring substitutions 11,12,13,14.

Their use as medicinal/pharmaceutical agents is well reported 15,16. Some of the derivatives have been reported for their ability to inhibit tuberculosis [17], influenza [18] and Severe Acute Respiratory Syndrome-Coronavirus Disease (SARS-COVID or SARS-CoV-2) 19,20. With the outbreak of a new coronavirus in 2019 (COVID-19), there have been more than 281 million confirmed cases and about 5.4 million deaths recorded all over the world [21] as at the 3rd of January 2022. The devastating effects from this pandemic was felt by individuals, governments and businesses, this led to an urgent development of vaccines as no cure was found. As at the 3rd of January 2022, a total of 8.69 million vaccine doses have been administered [21]. However, with different controversies surrounding the use of vaccines [22], the search for drugs that can combat the disease is ongoing. Although, Veklury (remdesivir) has been approved by the United States of America's Food and Drug Administration (USA-FDA) [23], the World Health Organization (WHO) raised some reservations on its use for the treatment of COVID infections [24]. The main protease (Mpro) also known as the 3-Chromotrypsin-like protease (3CLpro), RNA dependent RNA polymerase (RdRp), human Angiotensin-Converting Enzyme 2 (ACE-2) and Papain-like protease (PLpro) are enzymes of coronaviruses 25,26. The Mpro/3Cpro is crucial in polyprotein maturation process and therefore may serve as a therapeutic target in the search for SARS-CoV2 drugs 27,28. PLpro is very important in RNA virus polyproteins maturation and disruption of host immune responses [29]. SARS-CoV2 uses ACE-2 as an access into the host cell [30] while RdRp regulates viral replication [31]. Formulating antiviral drugs that can inhibit these enzymes is, therefore, very important in the development of effective SARS-CoV-2 drugs. In this regard, drugs like Baicalin, Baicalein and Perampanel analogue 5 have been reported to be effective against SARS-CoV-2 infection by inhibiting Mpro and PLpro activity via catalytic binding on the enzymes 31,32,33, Remdesivir has been approved by the FDA for its action against SARS-CoV-2 via its ability to inhibit RdRp 34,35. Angiotensin converting enzyme inhibitors (ACEIs) such as benazepril and angiotensin receptor blockers (ARBs) such as irbesartan were recommended for the treatment of SARS-CoV-2 infections by acting as ACE-2 inhibitors [36]. However, a lot of concerns have been raised with most of these drugs, from contraindications to disturbing side effects 37,38, even with the FDA-approved remdesivir 37,40. Therefore, there is need to continually search for novel drugs that could combat SARS-CoV-2 effectively and safely.

Spectroscopic techniques like Fourier Transform Infrared (FTIR), Nuclear Magnetic Resonance (NMR) and Mass Spectroscopy are helpful in establishing the structures of molecules 41,42,43,44,45. Density Functional Theory (DFT) has been used solely and/or in conjunction with experimental methods for understanding the bonding and structural properties, characterization and applications of molecules 46,47,48,49,50. Molecular docking helps to ascertain the interaction of molecules (ligands) with receptors and has been a useful technique in drug design and discovery 51,52,53,54.

Spectroscopic application of organic systems has been associated with their structural features like asymmetric charge distribution, π-electron rich structure, donor-acceptor groups and low band gap 55,56,57,58. The distribution of charge density, localized atomic orbitals and electron localization which influence molecular stability, chemical reactivity and drug-like properties can be effectively studied using topological analyses such as atoms in molecule (AIM), molecular electrostatic potential (MESP), reduced density gradient (RDG), electron localization function (ELF) and localized orbital locator (LOL) maps 59,60,61,62. Similarly, biological and anti-COVID-19 investigations of drug candidates with benzoyl, benzoyloxy, carboxylate and pyridine moieties using in-vitro and in-silico approaches have been recently reported 63,64,65,66,67,68 which motivates the present study of molecular and anti-SARS-CoV-2 properties of isopropyl 1-benzoyl-4-(benzoyloxy)-2,6-diphenyl-1,2,5,6-tetrahydropyridine-3-carboxylate (IDPC). Therefore, this work reports the synthesis, characterization, topological (AIM, RDG, ELF, LOL and MESP) analysis and DFT calculations on the structural properties of IDPC. The inhibitory potentials of IDPC against SARS-COV-2 enzymes were also investigated via extra precision (XP) molecular docking technique.

Synthesis of IDPC [Scheme 1]

IDPC was synthesized by Mannich condensation of benzaldehyde with isopropyl acetoacetate. 0.01 mol of Isopropyl acetoacetate, 0.02 mol of benzaldehyde and 0.01 mol of ammonium acetate were put in a round bottom flask (500 ml). Ethanol was added (25 ml), warmed for about 10 min and allowed to crystallize. The product was filtered, with the solid product recovered, washed (cold water), dried (25 °C) and recrystallized from ethanol/ether to give 3-isopropyl-2,6-diphenylpiperidin-4-one carboxylate (3-IDC). A mixture of 3-IDC (3.37 g, 100 mmol) and benzoyl chloride (2 ml, 100 mmol) triethylamine (2 ml, 200 mmol) and benzene (50 ml) was refluxed for 6 h under monitoring with TLC. The solvent was washed with 2 M hydrochloric acid (10 ml) followed by water. Solvent was removed under vacuum and the residue was recrystallized from ethanol. Yield of product was 2.65 g (70%) [69].

Synthetic Scheme of IDPC.

FTIR (cm) (KBr): 1731, 1708, 1700 cm−1 [carbonyl groups and one amide carbonyl group], 1708 cm−1 [ester carbonyl of hydroxyl group, C-4], 1731 cm−1 [ester carbonyl group, C-3], 1700 cm−1 [amide carbonyl group], 1640 cm−1 [aromatic C=C stretch] (Table S1); H NMR (CDCl ): 6.83–8.11 [aromatic protons, m], 0.61, 0.99 [methyl protons of COOiPr at C-2, d, d (6.3)], 4.76 [methine protons of COOiPr at C-2, m], 6.89 [H5a, m], 3.12 (H5e, d (18.3)), 2.99 [H5a, dd (7.2, 2.1)], 5.7 [H2a, broad]; C NMR (CDCl ): 126.3–137.8 [aromatic carbons], 164.5 [ester carbonyl at C-4], 171.4, 68.5, 21.4, 20.98 [CO, methine and methyl groups of COOiPr at C-2], 56.4 [C-6], 31.4 [C-5], 138.7 [C-4], 120.1 [C-3], 53 [C-2].

Spectral characterization

FT-IR details of the IDPC was recorded in the region of 4000–400 cm−1 on AVATAR 330 FTIR Thermo Nicolet Spectrometer in KBr pellets at Annamalai University, Annamalai Nagar, Tamil Nadu, India. 1D and 2D NMR spectra were recorded on a Bruker AV 300 NMR spectrometer operating at 300.13 MHz for 1H and 75.47 MHz for 13C. For 1H NMR spectrum, 10 mg of IDPC was dissolved in 0.5 ml of CDCl3. For recording 2D spectra 50 ml of IDPC was dissolved in 0.5 ml of CDCl3. X-ray crystallography analysis confirmed the structure of the compound [69].

Computational details

IDPC was optimized with DFT method at the B3LYP/6–311++G (d,p) level of theory [70] with Gaussian 09 software [71] with the aid of the Chemcraft visualization program [72]. The nature and types of H-bonding were examined with atoms in molecule (AIM), electron localization function (ELF), localized orbital locator (LOL) and reduced density gradient (RDG) analysis using Multiwfn software [73]. The isosurface maps were visualized using VMD software package [74]. The reactivity of the title molecule was predicted by using the energy gap between the HOMO and LUMO orbitals via DFT approach [75]. Further, the molecular electrostatic potential map (MESP) surface has been computed at the same level of theory using GaussView [76]. IDPC was docked into the active sites of SARS COVID-19 Mpro, 6W63 (resolutions 2.10 Å), PLpro, 7JRN (resolution 2.48 Å), RdRp receptor, 7BV2 (resolution 2.50 Å) and ACE2 receptor, 6M18 (resolution 2.90 Å). The receptors were downloaded from the Protein Data Bank website [77]. The co-crystallized ligands accompanying the receptors were re-docked for docking validation and for comparison. The receptors and IDPC were prepared using the Protein Preparation Wizard and LigPrep, respectively in the Maestro/Schrodinger suite 78,79. The site maps were generated [80] before extra precision (XP) docking of the compounds and co-crystallized ligands in the active sites of the receptors (6W63: x = -20.71, y = -16.36, z = -27.59; 7JRN: x = 9.99, y = -10.18, z = 31.72; 7BV2: x = 106.81, y = 111.26, z = 99.09; 6M18: x = 127.74, y = 127.33, z = 135.64) using Glide [81].

Results and discussion

Assignment of proton and 13C signals

In the 1H NMR spectrum, as expected two doublets and one multiplet for isopropyl moiety of an ester group observed at 0.61, 0.89 and 4.76 ppm, and they are conveniently assigned to isopropyl group (Fig. S1). Two doublet of doublets at 2.98 and 3.12 ppm with coupling constant 7.2 Hz and 18 Hz are assigned to methylene protons at C-5 and it was confirmed by HOMOCOSY spectrum. Also, coupling between the two methyl protons (δ 0.61 and 0.89 ppm) and the methine proton of the isopropyl was observed as cross peaks in the 1H–1H COSY spectrum. The signals due to benzylic protons at C-2/C-6 are broadened and deshielded as a result of restricted rotation about N–C=O bond. Thus, the more de-shielded broad signal 6.89 ppm was assigned to H-6 proton, while the other at 5.7 ppm due to H-2 protons.

Individual carbon signals were assigned with the help of DEPT-135 and HSQC spectra. In the 13C NMR spectrum, signals observed at 171.4, 164.5, 162.7, 138.8, 137.8, 136.5, 129.0 and 120.1 ppm are assigned to quaternary carbons, which is confirmed by DEPT spectrum The above signals are missing in the DEPT spectrum. In the above, the C-13 signals at 171.4, 164.5 and 162.7 ppm are assigned conveniently to the ester carbonyl at C-3, C-4 and amide carbonyl groups, respectively. C-13 signals at 138.8 and 120.1 ppm are assigned to C-4 and C-3 respectively based on similar reported values [82].

Remaining quaternary signals are due to ipso carbons of the phenyl groups at C-2, C-6 and benzoyl group. In the HSQC spectrum, cross peaks 2.98/31.4 and 3.15/31.4 shows the correlation between methylenic protons with C-5. Hence the C-13 signal at 31.4 ppm is unambiguously assigned to C-5. C-13 signals at 20.9, 21.4 and 68.4 ppm are due to isopropyl group of the ester at C-3. The cross peak at 5.7/53.0 and 6.7/54.6 reveals the correlation between H-2 proton with C-2 and H-6 with C-6. Hence the C-13 resonance at 53.0 and 54.6 ppm are assigned to C-2 and C-6. Other C-13 resonances from 126.3 to 133.9 ppm are assigned to aromatic carbons (see Supplementary Information, Figs. S2 – S5).

Conformation analysis

The introduction of the benzoyl group to heterocyclic nitrogen can adopt either a coplanar or perpendicular orientation to the reference plane of the piperidine ring system 83,84. π-electron orbital of the amide carbonyl group overlaps with the orbital of the lone pair of electrons on the nitrogen thereby stabilizing the planar conformation. Also, the benzylic protons are broadened instead of getting splitting in their signals as observed in the parent piperidone. This suggests the existence of limited rotation about N–C=O group brought about by high energy barrier. Despite this, only one set of signals for the ring proton was observed instead of two set of signals corresponding to two rotamers Figure 1 arising out of limited rotation 82,83. In IDPC, benzylic proton at C-2 shows a broad signal while benzylic proton at C-6 merged with aromatic protons (refer proton NMR spectrum). Ring methylene protons at C-5 appear as doublet of doublet.

Figure 1

IDPC molecule occurs in a state of equilibrium between half boat conformations.

By comparing the parent piperidone with substituted nitrogen in the heterocyclic ring makes the ring protons to de-shield significantly. By comparing the coupling constant of parent wit N-substituted compound more substituted rigid chair conformation is not possible. Therefore, it is noteworthy that the decreased coupling constant value in IDPC may be due to increased electronegativity of nitrogen. Thus, IDPC exists in equilibrium between half boat conformations as seen in Figure 1.

Optimized parameters

The structure of IDPC optimized with DFT method at the B3LYP/6–311++G (d,p) level of theory is presented (Figure 2 ). The geometric parameters (bond lengths and angles) were obtained. The experimental bond lengths and angles from X-ray analysis [63] were compared with those obtained with DFT calculation. There is a close agreement between them (Table S2). This infers that DFT calculations can be used for structural elucidation of hypothetical molecules prior synthesis.

Figure 2

Optimized structure of IDPC.

Atoms in molecule (AIM) analysis

The “atoms in molecules” (AIM) is a quantum chemistry model for characterizing the chemical bond of a system based on a topological charge density approach. This method gives the information about the presence of strong and weak hydrogen bonds. This analysis of electron density (ρ) at different characteristic points is developed by Bader 85,86. So, to understand the non-covalent interactions existing within the studied molecule, AIM analysis was performed. This analysis was used to search all the bond critical points (BCP) using Multiwfn software [73] and the geometrical structure is shown [Figure 3 ]. From the AIM method, the energetic, geometrical and topological parameters are determined here as descriptors of hydrogen bonding proprieties. Table 1 summarized the calculated values obtained at BCP for IDPC. The electron density ρ(r), its Laplacian ∇2ρ(r), kinetic energy density G(r), potential V(r), total energy density H(r) and the total energy E interactions are used to measure the strength and the nature of the bond at BCPs [87]. In addition, the topological parameters ∇2ρ(r), H(r) and the ratio │V│/G allows to classify the nature of the chemical interactions into three types [88]: when the ∇2ρ(r) > 0, H(r) < 0 and │V│/G > 2, the type of interaction is shared-shared (SS), covalent. The type shared-closed (SC), transit or intermediate is indicated by ∇2ρ(r) > 0, H(r) < 0 and 1 < │V│/G < 2. Whereas for ∇2ρ(r) > 0, H(r) < 0 and │V│/G < 1, the interaction is closed-closed (CC), ionic, van der Waals... Inspection of the Table indicates that the Laplacians ∇2ρ(r) and the total energy densities H(r) of all interactions are positive. The ratios │V│/G < 1 in all cases, indicating a pure ionic, van der Waals interactions (CC). The values of energy interactions of the C–H⋯O types are less than 50 kJ/mol (12 kcal/mol). These results prove that the hydrogen bonds existing within IDPC are considered weak.

Figure 3

AIM representation of bond critical points within the IDPC.

Table 1

Calculated topological parameters of IDPC.

Interactions types	∇2ρ(r) (a.u)	ρ (r) (a.u)	G(r) (a.u)	V(r) (a.u)	H(r) (a.u)	ε	Einteractions kJ/mol
C30–H31⋯O48	0.0349	0.0107	0.0077	-0.0066	0.0011	0.0732	-8.66
C9–H10⋯O47	0.0332	0.0102	0.0071	-0.0059	0.0012	0.0279	-7.75
C9–H10⋯H16	0.0495	0.0121	0.0100	-0.0077	0.0023	1.4900	-10.11
C33–O45⋯O46	0.0475	0.0117	0.0106	-0.0092	0.0014	0.8222	-12.08
C35–H37⋯C53	0.0075	0.0028	0.0015	-0.0012	0.0003	1.1146	-1.58
C14–H15⋯H60	0.0137	0.0043	0.0028	-0.0022	0.0006	0.6896	-2.89
C12–H13⋯C51	0.0567	0.0159	0.0121	-0.0100	0.0021	1.8909	-13.13

Reduced density gradient (RDG) analysis

The reduced density gradient (Eq. 1) is derived from the first derivative of the density. The RDG and its first derivative S, describes the deviation from a homogenous electron distribution [89].

It is used to identify covalent bonds and other non-covalent interactions by plotting ρ(r) against sign λ2. Non-bonding interactions occur when λ2 is positive while bonding interactions occur when λ2 is negative. The top of the plot indicates strong interaction while the bottom indicates weak interaction of the molecular system. The RDG analysis here was performed using Multiwfn 3.7 software [73]. The interactions represented via RDG isosurface enclosing their real space, where the hydrogen bond interactions, vdW interactions and steric effect are represented by the blue, green and red regions, respectively (Figs. 4 a and b). In Figure 4a, the red regions at the centre of the three aromatic rings indicate the effect of steric repulsion in IDPC while the green colour isosurface represents non-covalent interactions. The intermolecular distance of 2.65Å has about 31% from the Hirshfeld surface and it is consistent with H∙∙∙π interactions. The blue colour in the RDG isosurface indicates the strong attraction of IDPC. The RDG, hence, predicts the possible H-bonding, covalent and non-covalent interactions between the IDPC and SARS-COVID receptors mainly via the π-bonds and the heteroatoms.

Figure 4

(a) RDG graph and (b) RDG scatter map of the IDPC where the hydrogen bond interactions, vdW interactions and steric effect are represented by the blue, green and red regions, respectively.

ELF and LOL maps

The Electron Localization Function (ELF) and Localized Orbital Locator (LOL) topological analyses were employed in rationalizing the chemical content of the molecule. Their values usually range between 0 and 1. The red colour legend indicates the upper limit values close to 1; white indicates values that exceed the upper limit; black depicts values below the lower limit; and blue indicates values below 0.5. Values of ELF close to unity indicates great localization of electron suggesting a nonbonding electron pair, covalent bond or inner shells of the atom involved while values <0.5 depict electron delocalization 90,91. The LOL also explains the localization of orbitals, where small LOL value essentially appears at the boundary region and large values appear at the inner region of the localized orbitals. The colour-shaded ELF and LOL maps of IDPC are reported in Figure 5 (a) and (b), respectively. The red region around the hydrogen atoms in the ELF and LOL maps indicates high electron localization due to covalent bond or lone-pair of electrons while the light blue and deep blue colour in the inner regions of the nitrogen (N43) and phenyl carbon atoms signifies remarkable delocalization of electron cloud [90]. Additional information about the localization of atomic orbitals was obtained for the hydrogen and carbon atoms in the LOL topological analysis. In the LOL map, the inner white region in the H orbitals (H27, H54, H62 and H64) indicates that the electron density in that region exceeds the upper boundary of the colour legend [92]. Also, significant localization of bonding orbitals was observed between the sp2-hybridized carbon atoms (for instance, C61 and C69), indicating well-localized covalently bonded orbitals.

Figure 5

(a) ELF and (b) LOL maps of the IDPC.

Global reactivity descriptors and electrostatic potential (MESP) maps

The electrostatic interactions and the reactivity of IDPC were obtained from the frontier molecular orbitals (EHOMO and ELUMO) [93]. The HOMO of IDPC is distributed over the 2,6-diphenyl moiety to the tetrahydropyridine group, with an energy of -2.04 eV while the LUMO is distributed across the benzoyl ring, with an energy of -6.51 eV, making the energy band gap (ΔE) of IDPC to be 4.47 eV (Figure 6 ). It shows that there is intramolecular charge transfer within the molecule. Other properties (reactivity descriptors) are presented (Table 2 ), with chemical hardness, softness, chemical potential and global electrophilicity being 2.235, 0.224, -4.275 and 4.089 eV respectively. The global electrophilicity gives us the electron flow between donor-acceptor species. The high electrophilicity index value of 4.089 eV shows that the IDPC will act as an electrophile in biological responses. The chemical hardness value 2.235 eV for IDPC reveals that the molecule is not as hard as benzene whose chemical hardness is 3.2943 eV [59]. The molecular electrostatic potential (MESP) map shows the electrophilic and nucleophilic regions on the molecular structure as a result of asymmetric charge distribution [94]. The red region is the highly negative electrostatic potential surface depicting areas where a positive charge (electrophile) will likely attack while the blue region (positive electrostatic potential) is the local reactive site that is susceptible to nucleophilic attack (Figure 7 ) [95]. Highly negative electrostatic potential is essentially localized around the oxygen of carbonyl groups of the benzoyl, benzoyloxy and isopropyl carboxylate moieties indicating that they are local nucleophilic sites. The yellow map on the phenyl rings indicates their negative electrostatic potential and possible π-π stacking interactions with the receptor's aromatic active sites. The electrophilic centres (positive electrostatic potentials) are located mainly over the phenyl hydrogen. The hydropyridinyl nitrogen is relatively electrostatically neutral indicating that it may not be involved in either nucleophilic or electrophilic attack. The MESP, therefore, indicates the carbonyl oxygen as the local binding site for possible interactions with the electrophilic regions (active sites) of the SARS-COVID receptors.

Figure 6

Frontier molecular orbital's image of IDPC.

Table 2

The frontier molecular orbitals of IDPC.

Quantum Parameters	DFT/B3LYP/6–31++G (d, p)
EHOMO (eV)	-6.51
ELUMO (eV)	-2.04
EHOMO+1 (eV)	-6.74
ELUMO-1 (eV)	-1.19
ΔEHOMO-LUMO (eV)	4.47
ΔEHOMO-1-LUMO+1 (eV)	5.55
I	6.51
A	2.04
χ	4.28
η	2.24
μ	-4.28
ω	4.09
S	0.22

Figure 7

Molecular electrostatic surface of the IDPC.

Vibrational assignments

The theoretical vibrational analysis of IDPC was conducted at DFT/B3LYP/6–311++G (d,p) level of theory. The absence of imaginary frequency in the vibrational modes confirms that the optimized geometry corresponds to a minimum [96]. Since a molecule of IDPC is a nonlinear polyatomic system with 72 atoms, 210 normal vibrational modes were obtained. The calculated IR and Raman spectra are depicted in Figure 8 with pure Lorentzian band shape. The computed wavenumbers, scaled frequency and their intensity of IR and Raman data are compared and listed in Table S3. The IR frequencies were corrected using scaled quantum mechanics (SQM) for good comparison with experimental data (Table S3) [97]. The vibrational frequencies were scaled by 0.983 and 0.958 for wavenumbers 4000–1700 and <1700 cm−1, respectively 98,99. Although there is a difference in intensity between the normal vibrational modes, a good agreement is observed between the calculated vibrational frequencies of the IR and the Raman spectra. The computed vibrational modes aid the assignment of the characteristic vibration like C–H, C=O, C–O and C=C bonds. These essential normal vibrational modes of IDPC are both IR- and Raman-active though with different intensities, indicating their change in dipole moment and polarizability on absorption of appropriate energy 100,101. The vibrational frequencies between 2978 – 3175 cm−1 are assigned the C–H stretch. The C=O stretching vibration is easy to assign as it usually appears around 1700 cm−1. The three C=O stretching vibrations observed at 1749, 1735 and 1706 cm−1 could be assigned to the carbonyl groups of the benzoyloxy, isopropyl carboxylate and benzoyl moieties. The C–O stretch of the ester functional was obtained at 1122, 1098, 1034 and 915 cm−1. The aromatic C=C stretch was observed over a range of vibrational frequencies (for instance, 1609, 1607 and 1605 cm−1). The computed and the experimental wavenumbers are in good agreement (see Supplementary Information, Fig. S6).

Figure 8

Theoritical (a) IR and (b) Raman spectra of the IDPC compound.

Hirshfeld surface analysis

Hirshfeld surface analysis produces an excellent graphical depiction. Hirshfeld's surface and fingerprint plots are suitable for analysing the inputs of neighbouring atoms' interactions and the precision of molecular structure 102,103. Hirshfeld surfaces (HS) were generated using Crystal Explorer 17.5 software to illustrate the critical interactions inside the crystal of the IDPC molecule. Hirshfeld analysis for the IDPC utilizing the d with an adjacent molecule beyond the surface, as illustrated in Figure 9 . The red region represents the more prominent interaction between oxygen (O) and hydrogen (H) atoms [49]. Also, C–C and H–H interactions are seen on the Hirshfeld surfaces. Hirshfeld surfaces for d , d , d , shape index, and curvedness of IDPC compound were illustrated in Figure 10 . The intramolecular diameter of the closest nucleus from the point beyond the region of surface values ranges from -0.1327 to 2.5293. The normalized distance of the title structure's contact surface d value is between -0.1327 and 1.5982. The red areas on the d and d surfaces of the IDPC molecule represent π∙∙∙C–H interactions. The interatomic interactions engaged in the high hydrogen bonding and interatomic interactions are depicted by the red patch on the surface. The IDPC molecule has intermolecular hydrogen bonding, resulting in a red colour spot area on the d diagram. The 2D fingerprint plots in Figure 11 (i) depict the title molecule's 100 percent weak intermolecular interactions (d Vs d ). Figure 11(ii) depicted the 2D Fingerprint plots of the major intercontact and proportion of various intermolecular interactions contributed to the Hirshfeld surfaces. (a) H⋯H (63.1 %), (b) C⋯H/H⋯C (18.3 %), (c) H⋯O/O⋯H (13.5 %), (d) C⋯C (3.1 %), (e) O⋯C/C⋯O (1.2 %) and (f) O⋯O (0.8 %) in IDPC compound.

Figure 9

Hirshfeld analysis mapped with dnorm and showing adjacent molecule outside the surface for the IDPC.

Figure 10

Hirshfeld surface for IDPC with di, de, dnorm, shape index, curvedness and fragment patch.

Figure 11

(i) 2D fingerprint plots of the Hirshfeld surface contact contributing 100 percent of IDPC (ii) 2D Fingerprint plots of the significant intercontact and percentage of various intermolecular contacts contributed to the Hirshfeld surfaces (a) H⋯H (63.1 %), (b) C⋯H/H⋯C (18.3 %), (c) H⋯O/O⋯H (13.5 %), (d) C⋯C (3.1 %), (e) O⋯C/C⋯O (1.2 %) and (f) O⋯O (0.8 %) in IDPC compound.

Molecular docking discussion

IDPC was docked against four SARS-COVID (Mpro, PLpro, ACE2 and RdRp) receptors, with binding affinities recorded (Table 3 ). For the Mpro receptor 6W63, IDPC had higher binding affinity (–6.966 kcal mol-1 for 6W63) than the co-crystallized ligand (−6.722 kcal mol-1). IDPC showed a pi-cationic interaction with HIP via its phenyl ring and hydrogen bond interaction with GLN 189 via its carbonyl oxygen group (Figure 12 a) while its co-crystallized ligand (X77) showed hydrogen bond interactions with ASN 142 (via carbonyl oxygen), GLU 166 (via carbonyl oxygen) and THR 25 via its amino hydrogen (Figure 12b). The compounds showed hydrogen bond interaction with the receptors, this was also observed in previous work 25,104.

Table 3

Docking results of IDPC molecule and various SARS-COVID receptors, as well as their co-crystallized compounds.

Receptor type	Receptors	Molecule	XP Docking score (kcalmol−1)
Mpro	6W63	IDPC	-6.966
		Co-ligand Image 1	-6.722
PLpro	7JRN	IDPC	-4.141
		Co-ligand Image 2	-6.915
RdRp	7BV2	IDPC	-4.847
		Co-ligand Image 3	-5.396
ACE2	6M18	IDPC	-3.658
		Co-ligand Image 4	-4.933

Figure 12

Docking interactions with 6W63 (a) IDPC (b) Co-ligand N-(4-tert-butylphenyl)-N-[(1R)-2-(cyclohexylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-1H-imidazole-4-carboxamide (X77).

For the PLpro receptor, 7JRN, IDPC had binding affinity lower (−4.141 kcal mol-1) than the co-crystallized ligand (−6.915 kcal mol-1). IDPC showed a pi-pi stacking interaction with TYR 268 via its phenyl ring, hydrogen bond interactions with TYR 268 and ARG 166 via its carbonyl oxygen groups (Figure 13 a) while its co-crystallized ligand (TTT) showed hydrogen bond interaction with GLN 269 via its carbonyl oxygen, pi-pi stacking interactions with TYR 268 via its naphthalene and benzamide rings (Figure 13b).

Figure 13

Docking interactions with 7JRN (a) IDPC (b) Co-ligand, 5-amino-2-methyl-N-[(1R)-1-naphthalen-1-ylethyl]benzamide (TTT).

For RdRp receptor (7BV2), IDPC had a lower binding affinity of -4.847 kcal mol-1 than the co-crystallized ligand, F86 (−5.396 kcal mol-1). IDPC showed a pi-cationic interaction with ARG 349 via its phenyl ring, hydrogen bond interactions with ARG 349 and PHE 396 via its carbonyl oxygen groups (Figure 14 a) while its co-crystallized ligand (F86) showed hydrogen bond interactions with PHE 396, VAL 675, GLU 350 and ARG 349 via its hydroxyl and amino hydrogen groups and a salt bridge with ARG 349 via its phosphate oxygen (Figure 14b). The formation of hydrogen bond and pi-cationic interactions was also observed in the work of Gajjar et al [104] and Singh et al [105].

Figure 14

Docking interactions with 7VB2 (a) IDPC (b) Co-ligand, [(2∼{R},3∼{S},4∼{R},5∼{R})-5-(4-azanylpyrrolo [2,1-f][1,2,4]triazin-7-yl)-5-cyano-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate (F86).

For ACE2 receptor (6M18), IDPC had a lower binding affinity of -3.658 kcal mol-1 than the co-crystallized ligand, NAG (−4.933 kcal mol-1). IDPC showed a pi-cationic interaction with LYS 575 via its phenyl ring, hydrogen bond interactions with LYS 575 and SER 489 via its carbonyl oxygen groups (Figure 15 a) while its co-crystallized ligand (NAG) showed hydrogen bond interactions with GLN 556 via hydroxyl groups and ASP 270 via its amino hydrogen group (Figure 15b). Hydrogen bond interactions of ACE2 inhibitors with receptors have also been reported 106,107. The results revealed that IDPC shows tendency to inhibit COVID by binding to the active sites of the receptors, with the best anti-COVID activity observed with the Mpro. Similar to IDPC, the co-crystallized ligands interact with the receptors via heteroatoms and/or π-structure. This may be as a result of some carbonyl and/or aromatic functional similarities the co-crystallized ligands share with IDPC. The low values observed in the PLpro, RdRp and ACE2 receptors shows that IDPC could inhibit polyprotein maturation and consequently, abolish infectivity [108].

Figure 15

Docking interactions with 6M18 (a) IDPC (b) Co-ligand (2-acetamido-2-deoxy-beta-D-glucopyranose).

Conclusion

The synthesis and characterization (via x-ray crystallography, FT-IR and NMR) of IDPC is hereby reported. Geometrical parameters, normal vibrational modes, molecular properties (EHOMO, ELUMO, energy gap) and reactivity descriptors were calculated using density functional theory. X-ray crystallographic data agreed with optimized geometrical parameters. The assignment of calculated vibrational frequencies was achieved using scaled quantum mechanics force field. The selected experimental FT-IR wavenumbers for major vibrations (C–H, C=O, C=C and C–O) were consistent with the calculated vibrational modes. The frontier orbital energies and the low energy gap indicate intramolecular charge transfer tendency and good bioactivity of the compound. Topological (AIM, RDG, ELF, LOL, MESP) and Hirshfeld analyses confirm the presence of H-bonding, covalent and noncovalent interactions and electron delocalization in the molecule. Molecular docking of IDPC on four SARS-COVID proteins was achieved. Strong binding affinity observed between the active sites of the Mpro receptor and IDPC ligand was mainly attributed to H-bonding and π-cationic interactions via the phenyl ring and the carbonyl oxygen groups resulting into good anti-COVID potentials of the compound by blocking polyprotein maturation.

Declarations

Author contribution statement

Arulraj Ramalingam: Conceived and designed the experiments; Performed the experiments; Contributed reagents, materials, analysis tools or data; Wrote the paper.

Murugavel Kuppusamy: Conceived and designed the experiments; Contributed reagents, materials, analysis tools or data; Wrote the paper.

Sivakumar Sambandam, Mouna Medimagh, Amirthaganesan Shanmugasundaram, Noureddine Issaoui: Analyzed and interpreted the data; Contributed reagents, materials, analysis tools or data.

Oluwatoba Emmanuel Oyeneyin: Performed the experiments; Analyzed and interpreted the data; Contributed reagents, materials, analysis tools or data, Wrote the paper.

Nathanael Damilare Ojo: Analyzed and interpreted the data; Wrote the paper.

Funding statement

This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.

Data availability statement

Data included in article/supplementary material/referenced in article.

Declaration of interests statement

The authors declare no conflict of interest.

Additional information

No additional information is available for this paper.

Uncited reference

[39].