| Literature DB >> 36033106 |
Lilia Adjissi1, Nadjib Chafai1, Khalissa Benbouguerra1, Imene Kirouani1, Abdelkader Hellal1, Houdheifa Layaida1, Meriem Elkolli2, Chawki Bensouici3, Salah Chafaa1.
Abstract
Three hydrazone derivatives have been synthesized using condensation reaction of 4-hydrazinylbenzoic acid with three aromatic aldehydes namely: thiophene-2-carbaldehyde, thiophene-3-carbaldehyde and 2-furaldehyde in ethanol at 78 °C reflux. The synthesized molecules have been characterized using spectroscopic and physicochemical methods including UV-Vis, IR, 1H NMR, 13C NMR, 15N NMR and melting point determination. Optimized molecular structures, UV-Vis and IR spectra modeling, the reactivity, the stability and some quantum chemical parameters of the synthesized molecules were modeled utilizing density functional theory (DFT). The obtained theoretical results were found in good agreement with the experimental results. On the other hand, the antioxidant and antibacterial activities of the molecules under study were evaluated to better understand the associated mechanisms of action specifically. Also, predicted ADME-T and pharmacokinetic parameters indicated that these compounds showed good oral bioavailability. Finally, molecular docking has been used to predict the inhibitory activity of the studied hydrazone derivatives on the SARS-CoV-2 main protease (Mpro).Entities:
Keywords: Antibacterial; Antioxidant; DFT; Hydrazones; SARS-CoV-2; Synthesis
Year: 2022 PMID: 36033106 PMCID: PMC9395430 DOI: 10.1016/j.molstruc.2022.134005
Source DB: PubMed Journal: J Mol Struct ISSN: 0022-2860 Impact factor: 3.841
Fig. 1Synthetic rout of the studied hydrazone derivatives.
Fig. 6Optimized molecular structures and frontier molecular orbitals density distributions of HYDZ-1, HYDZ-2 and HYDZ-3.
Fig. 2Crystal structure of SARS-CoV-2 main protease.
Fig. 3Theoretical and experimental UV–Vis spectra of HYDZ-1, HYDZ-2 and HYDZ-3.
Fig. 4Experimental and calculated IR spectra of HYDZ-1, HYDZ-2 and HYDZ-3.
Experimental and theoretical frequencies of selected vibrations of HYDZ-1, HYDZ-2 and HYDZ-3.
| Compounds | HYDZ-1 | HYDZ-2 | HYDZ-3 | ||||||
|---|---|---|---|---|---|---|---|---|---|
| Assignement | Experimental frequencies (cm–1) | Calculated frequencies (cm–1) | Experimental frequencies (cm–1) | Calculated frequencies (cm–1) | Experimental frequencies (cm–1) | Calculated frequencies (cm–1) | |||
| Unscaled | Scaled | Unscaled | Scaled | Unscaled | Scaled | ||||
| (N-H) | 3311 | 3497 | 3362 | 3313 | 3516 | 3380 | 3312 | 3498 | 3362 |
| ν(C—H)Ar | 3276 | 3248 | 3314 | 3282 | 3238 | 3113 | 3277 | 3244 | 3118 |
| ν(C—H)Alph | 2930 | 3029 | 2912 | 2954 | 3153 | 3031 | 2975 | 3049 | 2931 |
| ν(C = O) | 1661 | 1773 | 1704 | 1654 | 1774 | 1705 | 1650 | 1773 | 1704 |
| ν(C = N) | 1593 | 1646 | 1582 | 1593 | 1651 | 1587 | 1590 | 1643 | 1579 |
| ν(C—N) | 1273 | 1295 | 1245 | 1268 | 1291 | 1241 | 1272 | 1296 | 1245 |
| (N—N) | 1138 | 1193 | 1146 | 1150 | 1097 | 1054 | 1162 | 1218 | 1170 |
| ν(C—O) | 1090 | 1091 | 1048 | 1091 | 1090 | 1047 | 1095 | 1102 | 1059 |
| ν(C-S) | 852 | 858 | 824 | 852 | 823 | 791 | – | – | – |
| 762 | 701 | 673 | 771 | 652 | 626 | 734 | 743 | 714 | |
| 685 | 642 | 617 | 627 | 442 | 424 | 674 | 500 | 480 | |
ν: stretching, ρout: out of plane bending.
Fig. 5Correlation diagrams between the theoretical and experimental wavenumbers of HYDZ-1, HYDZ-2 and HYDZ-3.
Experimental 1H NMR and 13C NMR chemical shifts (δ in ppm) of HYDZ-1, HYDZ-2 and HYDZ-3.
| HYDZ-1 | HYDZ-2 | HYDZ-3 | |||
|---|---|---|---|---|---|
| 1H NMR | 13C NMR | 1H NMR | 13C NMR | 1H NMR | 13C NMR |
| 7.01 | 111.54 | 7.09 | 111.54 | 6.85 | 110.73 |
| 7.10 | 120.84 | 7.53 | 120.55 | 6.74 | 111.60 |
| 7.30 | 127.13 | 7.58 | 125.12 | 7.06 | 112.42 |
| 7.55 | 128.17 | 7.73 | 125.16 | 7.75 | 120.87 |
| 7.83 | 128.30 | 7.82 | 127.61 | 7.83 | 129.98 |
| 8.15 | 131.69 | 8.01 | 131.64 | 7.85 | 131.66 |
| 10.75 | 134.93 | 10.64 | 135.63 | 10.75 | 144.22 |
| 12.73 | 140.71 | 11.91 | 138.82 | 12.29 | 149.07 |
Global chemical reactivity descriptors for HYDZ-1, HYDZ-2 and HYDZ-3 calculated by DFT method at B3LYP/6–311++G(d,p).
| Quantum chemical descriptors | HYDZ-1 | HYDZ-2 | HYDZ-3 |
|---|---|---|---|
| −30,521.49432 | −30,521.364 | −21,732.7029 | |
| −5.70487 | −5.9002 | −5.6689 | |
| −2.061263 | −1.8198 | −1.9548 | |
| 3.6436 | 4.0804 | 3.7141 | |
| 4.4728 | 5.5653 | 4.4565 | |
| 1.8218 | 2.0402 | 1.8570 | |
| 0.5489 | 0.4901 | 0.5385 | |
| 3.8830 | 3.860 | 3.8118 | |
| 4.1382 | 3.6515 | 3.9122 |
Atomic NBO charges of HYDZ-1, HYDZ-2 and HYDZ-3 calculated by DFT method at B3LYP/6–311++G(d,p).
| HYDZ-1 | HYDZ-2 | HYDZ-3 | |||
|---|---|---|---|---|---|
| Symbol | NBO Charge | Symbol | NBO Charge | Symbol | NBO Charge |
| C1 | −0.2196900 | −0.3600700 | 0.2420600 | ||
| C2 | −0.2457100 | 0.4482700 | −0.4609100 | ||
| C3 | −0.2439300 | −0.1716300 | −0.2562800 | ||
| S4 | 0.4259500 | −0.3762300 | 0.1305300 | ||
| C5 | −0.3827100 | −0.2621100 | −0.2944000 | ||
| C6 | 0.0257600 | 0.0447000 | 0.0077900 | ||
| H7 | 0.2199800 | −0.2430600 | −0.2448700 | ||
| H8 | 0.2267800 | −0.1258000 | −0.1250500 | ||
| C9 | −0.2444200 | 0.1904000 | 0.1872100 | ||
| C10 | −0.1249300 | −0.2055000 | −0.2061700 | ||
| C11 | 0.1877300 | −0.2491000 | −0.2489400 | ||
| C12 | −0.2062300 | −0.1409600 | −0.1402900 | ||
| C13 | −0.2489400 | 0.7855200 | 0.7850000 | ||
| C14 | −0.1400200 | −0.6124800 | −0.6127000 | ||
| C15 | 0.7850000 | −0.6979600 | −0.6977500 | ||
| O16 | −0.6126400 | −0.4033300 | −0.3762900 | ||
| O17 | −0.6977300 | −0.2401700 | −0.2366500 | ||
| N18 | −0.3780000 | 0.1945300 | 0.2305500 | ||
| N19 | −0.2395200 | 0.2300800 | 0.2286600 | ||
| H20 | 0.2303400 | 0.2295300 | 0.2028600 | ||
| H21 | 0.2286700 | 0.2257700 | 0.2253900 | ||
| H22 | 0.2028800 | 0.2331300 | 0.4836000 | ||
| H23 | 0.2253700 | 0.2283000 | 0.3559200 | ||
| H24 | 0.4836100 | 0.2029600 | 0.2308000 | ||
| H25 | 0.3553200 | 0.2248100 | 0.2238900 | ||
| H26 | 0.2289000 | 0.4834000 | 0.1978500 | ||
| H27 | 0.1581900 | 0.3670100 | 0.1681800 | ||
Fig. 7Molecular electrostatic potential maps of HYDZ-1, HYDZ-2 and HYDZ-3.
The antibacterial inhibition diameters in mm.
| Strains | Diameter of the inhibition zones (mm) | |||
|---|---|---|---|---|
| HYDZ-1 | HYDZ-2 | HYDZ-3 | GM | |
| 14±2.08 | 7 ± 0.57 | <5 | 20 | |
| <5 | <5 | <5 | 30 | |
| <5 | <5 | <5 | 25 | |
| <5 | <5 | <5 | 22 | |
*GM : gentamicine.
Determination of the antioxidant activity of the examined hydrazone derivatives by DPPH, ABTS, CUPRAC, FRAP and Phenantroline assays.
| Compounds | DPPHIC50 mMa | ABTSIC50 mMa | CUPRACA0.50 mMa | FRAPA0.50 mMa | PhenanthrolineA0.50 mMa |
|---|---|---|---|---|---|
| 87.91±3.34 | 8.29±0.32 | 49.23±1.2 | 41.12±0.40 | 11.49±1.45 | |
| 143.07±1.30 | 7.46±0.39 | 31.59±0.30 | 77.40±0.30 | 14.06±0.87 | |
| 38.33±0.81 | 1.27±0.10 | 30.95±1.05 | 56.38±0.49 | 15.89±1.12 | |
| 24.28±1.28 | 7.67±0.40 | 17.97±0.66 | N.T | 4.31±0.03 | |
| 70.9 ± 6.6 | 8.24±0.13 | 16.62±0.79 | N.T | 4.20±0.06 | |
| N.T | N.T | N.T | 15.39±1.10 | N.T |
aValues expressed are means ± S.D. of three parallel measurements. (p<0.05). N.T: not tested.
bReferences.
Calculated physicochemical and pharmacokinetic parameters (ADME-T) of the synthesized compounds, which important for a good oral bioavailability.
| Compounds | miLogP<5 | solubility | TPSA (oA) <500 | MW | nON<10 | nOHNH<5 | MV | vio | Toxicity risks | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Mut | Tumo | Irr | R,E | ||||||||||
| HYDZ-1 | 4.57 | −3.17 | 61.69 | 246.29 | 4 | 2 | 208.83 | 0 | No | No | No | No | |
| HYDZ-2 | 4.26 | −3.06 | 61.69 | 246.29 | 4 | 2 | 208.83 | 0 | No | No | No | No | |
| HYDZ-3 | 3.93 | −2.84 | 74.83 | 230.22 | 5 | 2 | 199.68 | 0 | No | No | No | No | |
| Chloroquine* | 4.01 | -4.06 | 28.16 | 319.88 | 3 | 1 | 313.12 | 1 | Yes | No | Yes | No | |
| Hydroxychl-oroquine* | 3.08 | -3.55 | 48.38 | 335.88 | 4 | 2 | 321.38 | 0 | Yes | No | No | No | |
*: Drugs Reference, Topological polar surface area (TPSA); Number of rotatable bonds (n-rotb); Molecular weight (MW); Molecular volume (MV); Logarithm of partition coefficient between n-octanol and water (miLogP); Number of hydrogen bond donors (n-OHNH); Number of hydrogen bond acceptors (n-ON); Lipinski's violation (vio) (Mut) mutagenic (Tumo): tumorigenic (Irr) : irritant (R.E) reproductive effective.
Energy distribution of the investigated hydrazones between van der Waals forces, hydrogen bonding and electrostatic interactions.
| Compounds | Total energy | vdW | H-Bond | Elec | ||
|---|---|---|---|---|---|---|
| Mpro—HYDZ-1 | −89.90 | −70.17 | −17.17 | −2.56 | ||
| Mpro-HYDZ-2 | −85.66 | −60.75 | −22.03 | −2.88 | ||
| Mpro-HYDZ-3 | −84.82 | −71.07 | −13.07 | −0.69 | ||
| Chloroquine | -83.91 | −74.41 | −9.5 | 0 | ||
| Hydroxychloroquine | -82.27 | −67.02 | −15.25 | 0 | ||
Drugs Reference, H-bonds: hydrogen bonding, vdW: van der Waals forces and Elec: electrostatic interactions.
Fig. 8Best docked poses visualization of HYDZ-1, HYDZ-2 and HYDZ-3 with SARS-CoV-2 main protease.
Fig. 93D and 2D Binding-interaction diagrams of HYDZ-1, HYDZ-2, HYDZ-3, Chloroquine and Hydroxychloroquine with SARS-CoV-2 main protease.
Molecular docking results interactions and distance of the investigated inhibitors with SARS-CoV-2 main protease.
| Compounds | Amino acid Interactions | Distance (Å) | Type of the interaction |
|---|---|---|---|
| - LEU141 | 6.35 | Hydrogen bond | |
| - ARG 217, THY 304 | 5.44, 3.83 | Hydrogen bond | |
| - CYS145, GLY143, SER144,SER 144, HIS163 | 3.55, 3.41, 3.93, 3.36, 4.57. | Hydrogen bond | |
| - ASN 142 | 4.12 | Hydrogen bond | |
| - GLY143, SER 144, CYS 145 | 2.95, 4.28, 3.07 | Hydrogen bond |
: Drugs Reference.
Fig. 10Ligands interaction with their molecular surface maps inside the active site pocket.
Comparison of the binding energy of HYDZ-1, HYDZ-2 and HYDZ-3 with these of some drugs.
| Compounds | Binding energy in Kcal/mol |
|---|---|
| HYDZ-1 | - 89.90 |
| HYDZ-2 | −85.66 |
| HYDZ-3 | - 84.82 |
| Chloroquine | - 83.91 |
| Hydroxychloroquine | - 82.27 |
: Drugs Reference.