3.1 X-ray crystallography
The molecular structure of the titled compound is shown in Fig. 1 The compound consists of a sulphonamide moiety sandwiched between a para-nitro phenyl moiety and hydroxy pyrrolidone carboxylic acid in a slightly distorted tetrahedral. The S1-N1 (1.628 (2) Å) bond length indicates the formation of the titled compound. This is similar to the reported value of 1.636 in the work of Murthy et al [63]. The aromatic ring is disubstituted at para positions with nitro and sulphonyl groups. The N2-C4 and S1-C1 bonds are 1.472 (4) and 1.774 (3) Å respectively. The pyrrolidine ring is on the other hand is trisubstituted by carboxylic acid, hydroxyl, and sulphonyl groups. The bond lengths of O4-C11 and O3-C11 are 1.331 and 1.200 Å respectively. As expected, the length of C = O (O3-C11) is shorter than that of C-OH (O4-C11). The angles around the slightly distorted tetrahedron range from a narrower O1-S1-N1 (106.21 (13)) to a slightly larger O1-S1-C1 (107.57 (13)). The sulphonamide is stabilized by the torsion angles of O2-S1-N1-C10 (-51.5 (2)˚) and O1-S1-NI-C7 (39.9 (2)˚). The molecular aggregation structure of the solid-state structure of the compound shows the presence of two types of intermolecular hydrogen bonding interactions, the Carboxyl-O4-H4—O5(Hydroxyl) and N4-H4—O3
\(D-H\cdots A\)
|
\(D-H\)
|
\(H\cdots A\)
|
\(D\cdots A\)
|
\(D-H\cdots A\)
|
Table 2
Hydrogen bond geometry of the title compound (Å, °)
O4\(-\)H4\(\cdots\)05a
|
0.80(5)
|
1.88(5)
|
2.668(3)
|
168(5)
|
N4\(-\)H4\(\cdots\)O3a
|
0.88(5)
|
2.04(5)
|
2.888(2)
|
164(5)
|
Symmetry codes: (i) 1-x, 1-y, -z (ii) -1 + x, y, z (iii) 1-x, -y, 1-z (iv) 1-x, 1-y, 1-z (v) |
3.2 Non Covalent Index Nci
The stability of HNPCA can be determined based on its molecular interactions which can be analyzed using the RDG based on NCI. The NCI isosurface was generated using the B3LYP optimized geometry and this is illustrated in Fig. 3. The blue-green-red isosurfaces color are classified according to the strength and type of interaction whereby blue indicates strong attractive interactions, green indicates van der Waal interaction and red indicates a strong repulsion[64]. Therefore, the presence of the green and red isosurfaces in Fig. 3 indicates the presence of van der Waals interaction as well as steric interactions [65]. In addition to the NCI isosurface, the 2D NCI scatter plot is displayed in Fig. 4. The spikes in the RDG region where λ2 ≈ 0 and ρ ≈ 0, suggest that HPNCA consists of van der Waals interactions (-0.02 to 0 a. u.) mainly corresponding to the intramolecular O•••H interactions. Spikes are also observed in the positive region (0 to 0.04 a. u.) indicating steric hindrance arising from the aromatic ring as well as the pyrrolidine ring. The absence of blue coloured spikes confirms that HNPCA does not exhibit any conventional intramolecular hydrogen bond within the structure but engages in intermolecular hydrogen bond.
3.3 Hirshfeld Surface Analysis
The Hirshfeld surface contacts were mapped over dnorm using the method described in [66–68] and presented in Fig. 5a. The red regions are located mainly on the oxygen atoms and one of the H atoms of the aromatic ring of the compound, indicating stronger intermolecular hydrogen bonds with neighboring atoms. However, the light-colored regions indicate weaker and longer contacts other than hydrogen bonds [34; 69; 70]. Some of the significant intermolecular interactions within the crystal structure of HNPCA are shown in Fig. 5b and these include phenyl-C-H•••O(sulphonyl) in green dotted lines, pyrolidone-C-H•••O(Nitro) in red dotted lines and Phenyl-C•••O interactions in magenta. The fingerprint plots in Fig. 6, have been decomposed to analyze individual contributions and corroborate the results of the Hirshfeld surface analysis[54]. The fingerprint plots indicate that the most dominant interaction is the O•••H interactions (58.9%). The two sharp spikes correspond to the -OH group (O4-H) of the carboxylic group and the hydroxyl group (O5-H) of the pyrrolidine ring. The H•••H interaction contributes to 19.9% of the surface area of the fingerprint plot. All other interactions observed are less than 8.0% [C•••H (7.1%) > S•••H (0.2%) > O•••C (5.6%) > O•••O (4.1%) > O•••N (2.1%) > N•••H (2.0%) > C•••C (0.1%)].
3.4 Interaction Energy Calculations
The strength of intermolecular interactions can be estimated by calculating the interaction energies between pairs of molecules within the crystal of HNPCA and adding up the resulting four energy components comprising of the electrostatic (Eele), polarization (Epol), dispersion(Edis), and exchange repulsion (Erep) energies [71]. The energies were obtained by calculating the wave function of each pair of molecules or atoms at the B3LYP/6-31G(d,p) level of theory [67; 71]. Quantitative estimation of the strength and nature of the intermolecular interactions in HNPCA crystal with individual energy components (Eele, Epol, Edis, and Erep) as well as the sum of the energy components, Etot are presented in Table 3. The energy values show that the electrostatic component of the energy makes the most significant contribution to the total interaction energy profile in the crystal structure probably due to the intermolecular Vander Waal interactions resulting from the high level of H\(\cdots\)O/H\(\cdots\)O and H\(\cdots\)H intermolecular interactions. The dispersive interaction energy component of the total interaction energy is the second highest contributor to the total interaction energy and these probably result from the π\(\cdots\)π interaction of successive pairwise phenyl and pyrrolidone rings in the crystal lattice ([68; 72]. A graphical representation of the magnitude of the interaction energies is presented in Fig. 7(a)-(d) in the form of energy frameworks to show the supramolecular architecture using cylindrical poles joining the centroids of molecular pairs. The red, green, and blue color-coded frameworks in 7a, 7b, and 7c respectively represent Eele, Edis, and Etot, energy components for intermolecular interactions HNPCA crystal, while 7d is the annotated Etot energy. The magnitude of the cylindrical poles corroborates the results from the fingerprint plots indicating that the Eeleenergy component to the total interaction energy is significant and contributes substantially to the molecular packing in the crystal lattice.
N
|
Symop
|
R
|
Electron Density
|
Eele
|
E_pol
|
E_dis
|
E_rep
|
E_tot
|
Table 3
A summary of interaction energies (kJmol− 1) calculated for HNPCA
1
|
-x, y + 1/2, -z + 1/2
|
8.40
|
B3LYP/6-31G(d,p)
|
-21.9
|
-5.7
|
-22.8
|
17.9
|
-36.2
|
1
|
x, y, z
|
7.54
|
B3LYP/6-31G(d,p)
|
-82.5
|
-18.5
|
-33.8
|
97.3
|
-70.3
|
1
|
-x + 1/2, -y, z + 1/2
|
7.96
|
B3LYP/6-31G(d,p)
|
1.6
|
-4.0
|
-24.6
|
14.4
|
-13.8
|
0
|
x + 1/2, -y + 1/2, -z
|
7.47
|
B3LYP/6-31G(d,p)
|
-36.8
|
-8.3
|
-24.0
|
49.9
|
-35.1
|
1
|
x + 1/2, -y + 1/2, -z
|
7.24
|
B3LYP/6-31G(d,p)
|
-4.6
|
-3.2
|
-18.3
|
11.4
|
-16.1
|
1
|
-x, y + 1/2, -z + 1/2
|
7.46
|
B3LYP/6-31G(d,p)
|
3.9
|
-3.0
|
-16.3
|
7.8
|
-7.5
|
0
|
-x + 1/2, -y, z + 1/2
|
10.25
|
B3LYP/6-31G(d,p)
|
-5.5
|
-1.3
|
-7.7
|
4.5
|
-10.6
|
3.5: Spectroscopic Studies
3.51: IR Spectra
The Infrared spectrum of the compound being investigated was recorded in the 4000 − 600 region using Bruker FT-IR spectrophotometer. The spectra of the compound (Figure S1)( shows an S-N stretching prevalent for benzenesulphonamide derivatives at 857 cm− 1(usually in the range of 947 − 836 cm-1) [73], and the band at 1355 cm− 1 was assigned to S = O indicating the formation of the benzenesulphonamide. Other characteristics bands present are; the C = O stretching of a carboxylic at 1745.19 cm− 1, N-O stretching for a nitro compound at 1524.70 cm− 1, O-H stretching at 3450 and 2700 cm− 1assigned to the OH of the alcohol and carboxylic acid respectively, C-H stretching at 2950 and 3100 cm− 1 for the aliphatic and aromatic carbons respectively. The simulated IR spectrum is provided in Figure S2 and describes a detailed vibrational analysis of HNPCA in the gas phase as performed based on potential energy distribution using VEDA 4 program.
3.52 H Nmr,c Nmr, And Dept
The H and 13C NMR of the named compound are presented in Figures S4 and S5 of the supplementary information. 1H NMR chemical shift at 8.38-8.41 are assigned to the protons present in the aromatic ring. The chemical shift at 8.08-8.11are assigned to the protons of the pyrrolidine ring. Also, the absence of a chemical shift for N-H at the upper field confirms the formation of the desired compounds. The 13C NMR like the 1H NMR agrees with the crystal structure of the compound gotten via X-ray diffraction studies of the compound’s crystal. The signal at 174.19 was assigned to C=O, signals between 150.28-123.79 were assigned to the six aromatic carbon atoms, while the signals from 69.21-39.00 were assigned to the four aliphatic carbons of the compound. The NMR values are corroborated by the calculated NMR values presented in Table S1 of the supplementary information. The DEPT analysis (Figure S6) showed that the compound had three tertiary carbons, six CH carbons, and two CH2 carbons. Although only four carbons appeared among the CH carbons, this was expected due to chemical equivalence in the para-substituted benzene ring. There was also no appearance of methyl carbon in the DEPT results. These observations are in agreement with the structure obtained from XRD analysis.
3.6 ADMET
Due to poor bioavailability, most orally administered drugs are unable to reach the target therapeutic site, resulting in failed clinical trials despite promising in vitro and in vivo efficacy [74]. Lipniski rule of five (MW ≤500, HBD ≤5, HBA ≤10, Log p ≤5, RBC ≤10) is a valid assessment of the oral bioavailability of a drug candidate [75]. A molecule that violates more than two categories is adjudged to elicit poor bioavailability. HNPCA was studied for Lipinski rule compliance and other properties that influence drug absorption, and the result is presented in Table 4. HNPCA showed total compliance in all calculated parameters except for TPSA (Veber rule: TPSA ≤140 Å2)[76], signaling a good bioavailability potential.
Table 4. ADMET calculation for HNPCA
|
MW
|
donor HB
|
accept HB
|
Log P
|
RBC
|
Rule of five
|
TPSA [Å2]
|
Bioavailability score
|
|
316.29
|
2
|
8
|
-0.61
|
4
|
0
|
149.11
|
0.56
|
Recommended values
|
≤500
|
≤5
|
≤10
|
≤5
|
≤10
|
Max 2
|
≤140
|
|
Abbreviations: MW- Molecular weight of the molecule, donorHB - approximated number of hydrogen bonds that would be donated by the solute to water molecules in an aqueous solution, acceptHB- approximated number of hydrogen bonds that would be accepted by the solute from water molecules in an aqueous solution, Rule of five- Number of violations of Lipinski rule, Log P- water partition coefficient, RBC - approximated number of rotatable bonds, TPSA – topological polar surface area.
3.7 Molecular docking study
Molecular docking permits the prediction of molecular interaction between ligand-protein and has become a reliable tool in drug discovery. A docking study on HNPCA was done with selected protein targets; dihydropteroate synthase (5uoy), topoisomerase II DNA gyrase (5mmn), and a 2019-nCoV spike (6vsb). Dihydropteroate synthase (DHPS) catalyzes the transformation of 6-hydroxymethyl-7,8-dihydropterin pyrophosphate (DHPP) plus p-aminobenzoic acid (PABA) to 7,8-dihydropteroate, important folate intermediate in the folate biosynthetic pathway [77]. As a result, DHPS is an important antibacterial drug target and research on new inhibitors has intensified in recent times [78-80]. DNA gyrase is a type II topoisomerase that functions in DNA supercoils and replication, hence is investigated as a drug target for many agents, including antitumor and antibacterial [81]. The CoV spike (S) glycoprotein is a vital target for vaccines, and therapeutic antibodies [61]. HNPCA was docked in the active site of augmented protein targets using the intrinsic PyRx algorithm and obtained ligand-protein docked poses were visualized with Discovery Studio.
3.7.1 Binding affinity of HNPCA with the protein target
The binding energy of HNPCA with protein targets had been shown in Table 5. In the case of 5uoy and 5mmn, HNPCA interacted significantly with receptor site residues, thereby eliciting higher or comparable binding affinity with the native ligand, ciprofloxacin or gentamicin. This suggests that the compound could intercalate well with the studied antibacterial targets to demonstrate promising efficacy. A lower binding affinity was recorded with 6vsb, compared to the crystal ligand, remdesivir or dexamethasone, which have been indicated to reduce mortality in people with severe COVID-19 [82].
3.7.2 Bonding model HNPCA with protein target
H-bond is an important interaction stabilizing ligands with receptors. In the binding pocket of 5uoy, HNPCA demonstrated extensive H-bond between the COOH, OH, NO2, SO2-NR2 moieties and Thr62, Arg63, Glu60, Asn22, Arg255, His257, and Lys221 residues, Figure 8. In addition, a closer look showed a pi-bonding between the O=S=O group with His257. The extensive H-bonding may have conferred a higher binding affinity, indicating a reliable stability with protein target active site residues to impact promising antibacterial activity.
In the case of 5mmn, the NO2 group of HNPCA engaged in H-bond with Arg76, Gly77, Thr165, while the COOH group approached Asn46 in H-bond. Additional stability was supported by the phenyl ring, which had invested in Ile78 and Glu50 via pi-alkyl and pi-anion interactions. These key interactions providing stability encourage potential strong inhibitory efficacy against microbial strains, Figure 8.
On the other hand, the COOH, SO2, and NO2 groups established H-bond with Glu619, Thr618, Ser591, Thr553, and Asn536 amino acid residues in the binding cavity of 6vsb, while the phenyl group added stability by engaging in hydrophobic interaction with Val558, Figure 8.
Table 5. The binding energy of HNPCA with protein targets
Ligands
|
Protein
|
Binding energy (kcal/mol)
|
HNPCA
|
6vsb
|
-5.90
|
Dexamethasone
|
|
-6.90
|
Remdesivir
|
|
-7.40
|
Native ligand
|
|
-8.80
|
HNPCA
|
5uoy
|
-7.20
|
Ciprofloxacin
|
|
-7.10
|
Gentamicin
|
|
-6.80
|
Native ligand
|
|
-7.60
|
HNPCA
|
5mmn
|
-7.30
|
Ciprofloxacin
|
|
-7.40
|
Gentamicin
|
|
-7.20
|
Native ligand
|
|
-7.80
|