| Literature DB >> 35782313 |
Abstract
Synthesis of a new series of spiropyrazole derivatives using microwaves irradiation with high yield in minutes was achieved through a cycloaddition reaction of nitrile imines and arylidenes of 5-bromo-indan-1-one. The structure of the new spiropyrazoles was assured based on their available spectral analyses and the comparison of the extracted data with the literature reports. Molecular docking simulations of all new synthesized spiropyrazole derivatives into leucyl-tRNA synthetase editing domain of Candida albicans (Pdb: 2WFC) indicated that about seven spiropyrazole derivatives can fit deeply in the active site via the formation of stable complexes. In addition, the docking study was utilized to tested the ability of these spiropyrazoles to inhibit COVID-19 through the interaction with COVID-19 main protease (Pdb: 6LU7). The results were surprising which revealed high docking score ranging from -7.764 to -5.9464 kcal/mol. Moreover, the nitrogen atom of pyrazole, Br atom and the C=O group of indanone are essential parts in the binding mode of almost the active derivatives. The results of the docking study are a glimmer of hope to complete the study on these compounds and examine them in the laboratory to ensure their effectiveness as antimicrobials and antiviral, especially Covid-19. Moreover, pharmacokinetics and physicochemical properties were studied.Entities:
Keywords: Antimicrobial; COVID-19; Hydrazonoyl halides; Microwaves; Spiropyrazoles
Year: 2022 PMID: 35782313 PMCID: PMC9232256 DOI: 10.1016/j.molstruc.2022.133581
Source DB: PubMed Journal: J Mol Struct ISSN: 0022-2860 Impact factor: 3.841
Scheme 1Synthesis of spiropyrazoles 6a,b under microwaves irradiation.
Fig. 11H NMR spectrum of spiropyrazole 6b.
Scheme 2Synthesis of spiropyrazoles 10a-h under microwaves irradiation.
Fig. 2The 13C NMR spectrum of spiropyrazole 10d.
Scheme 3Synthesis of spiropyrazoles 14a,b under microwaves irradiation.
Docking results of the new synthesized derivatives 6a-b and 10a-h with the receptors of (2WFC) for microbes.
| Compd. | Ligand moiety | Receptor site | Interacting residues(Type of interaction) | Distance (oA) | E (kcal/mol) | Docking score (kcal/mol) |
|---|---|---|---|---|---|---|
| 6a | 6-ring | CD LYS 407 (A) | pi-H | 3.81 | -0.9 | - 4.5946 |
| 6b | – | – | – | – | – | - 5.7907 |
| 10a | – | – | – | – | – | -4.9668 |
| 10b | O 156-ring | NZ LYS 407 (A)CD LYS 407 (A) | H-donorpi-H | 3.062.80 | -8.6-0.9 | -3.8321 |
| 10c | O 15N 216-ring | NZ LYS 483 (A)NZ LYS 407 (A)N LEU 317 (A) | H-acceptorH-acceptorpi-H | 2.703.724.17 | -5.3-1.3-1.8 | -6.4628 |
| 10d | 6-ring6-ring | N LEU 317 (A)CD LYS 407 (A) | pi-Hpi-H | 4.644.01 | -0.6-0.8 | -3.8721 |
| 10e | – | – | – | – | – | -3.2041 |
| 10f | CL 54O 15N 216-ring | O THR 413 (A)NZ LYS 483 (A)NZ LYS 407 (A)N LEU 317 (A) | H-donorH-acceptorH-acceptorpi-H | 3.392.633.704.13 | -1.4-5.0-1.4-2.2 | -4.1968 |
| 10g | BR 16O 556-ring | OG1 THR 321 (A)NZ LYS 483 (A)CA THR 316 (A) | H-donorH-acceptorpi-H | 3.41 2.823.87 | -0.9-6.8-0.7 | -5.6246 |
| 10h | BR 16O 156-ring | OG1 THR 321 (A)NZ LYS 483 (A)CA THR 316 (A) | H-donorH-acceptorpi-H | 3.402.773.91 | -0.8-7.4-0.6 | -4.8742 |
| 14a | O 60 | N THR 409 (A) | H-acceptor | 2.80 | -1.7 | -4.1252 |
| 14b | O 59O 606-ring | CA VAL 403 (A)N LEU 404 (A)CB SER 419 (A) | H-acceptorH-acceptorpi-H | 3.253.083.86 | -0.8-1.0-0.8 | -6.2704 |
Fig. 3The 2D docked model and contact performance of derivatives 10c, 10h and 14b into the active site of 2WFG.
Docking results of the new synthesized derivatives 6a-b, 10a-h and 14a-b with the receptors of (6lu7) for COVID-19.
| Compd. | Ligand moiety | Receptor site | Interacting residues(Type of interaction) | Distance (oA) | E (kcal/mol) | Docking score (kcal/mol) |
|---|---|---|---|---|---|---|
| 6a | O 15 | SG CYS 145 (A) | H-donor | 3.19 | - 1.0 | - 6.5155 |
| 6b | O 15C 25N 28 | SG CYS 145 (A)OE1 GLN 189 (A)N GLU 166 (A) | H-donorH-donorH-acceptor | 3.252.863.19 | -0.8-0.8-0.9 | - 6.6631 |
| 10a | BR 16C 18N 21 | O THR 26 (A)OE1 GLN 189 (A)N GLU 166 (A) | H-donorH-donorH-acceptor | 3.363.163.27 | -1.6-1.1-2.0 | -6.5876 |
| 10b | – | – | – | – | – | -6.3476 |
| 10c | 6-ring | N GLY 143 (A) | pi-H | 4.61 | -0.6 | -6.7045 |
| 10d | 6-ring | N GLY 143 (A) | pi-H | 4.56 | -0.7 | -6.9558 |
| 10e | BR 166-ring | O THR 26 (A)N GLY 143 (A) | H-donorpi-H | 3.804.27 | -0.5-0.7 | -6.7893 |
| 10f | BR 166-ring | O THR 26 (A)N GLY 143 (A) | H-donorpi-H | 3.844.53 | -0.4-1.1 | -5.9464 |
| 10g | 6-ring | N GLY 143 (A) | pi-H | 4.18 | -0.7 | -7.0122 |
| 10h | O 15 6-ring | SG CYS 145 (A)N GLY 143 (A) | H-donorpi-H | 3.844.14 | -0.7-0.7 | -7.2934 |
| 14a | BR 166-ring | O THR 26 (A)N GLY 143 (A) | H-donorpi-H | 3.64 4.12 | -0.6-1.2 | -7.764 |
| 14b | BR 16O 60 | O THR 26 (A)NE2 HIS 163 (A) | H-donorH-acceptor | 3.603.28 | -1.4-1.3 | -7.6202 |
Fig. 4The 2D docked model and contact performance of derivatives 6b, 14a and 14b into the active site of 6LU7.
Physiochemical and Pharmacokinetics properties for tested spiropyrazole derivatives 6a, 10c, 10g, 19h, 14a and 14b.
| Properties | Compounds | ||
|---|---|---|---|
| 6a | 10c | 10g | |
| Formula | C27H19BrN2OS | C30H23BrN2O2 | C29H20BrN3O3 |
| Molecular weight | 499.42 g/mol | 523.42 g/mol | 538.39 g/mol |
| Num. of heavy atoms | 32 | 35 | 36 |
| Num. of aromatic heavy atoms | 23 | 24 | 24 |
| Num. of rotatable bonds | 3 | 4 | 4 |
| Num. H-bond acceptor (HBA) | 2 | 3 | 4 |
| Num. H-bond donors (HBD) | 0 | 0 | 0 |
| Molar reactivity | 140.44 | 149.06 | 151.39 |
| Topological Polar Surface area (TPSA) | 60.91 Ų | 41.90 Ų | 78.49 Ų |
| Lipophilicity (Log P) | 3.90 | 4.14 | 3.18 |
| Water solubility (Log S) | -7.67 (InSoluble) | -7.90 (InSoluble) | -7.88 (inSoluble) |
| Pharmacokinetics (GI absorption) | High | High | High |
| Pharmacokinetics (BBB permeant) | No | Yes | No |
| Pharmacokinetics (CYP1A2, CYP2C19, CYP2C9, CYP2D6, CYP3A4 inhibitors) | No, No, Yes, No, No (respectively) | No, No, Yes, No, No (respectively) | No, Yes, Yes, No, No (respectively) |
| Druglikeness (Lipinski) | Yes; 1 violation: MLOGP>4.15 | No; 2 violations: MW>500, MLOGP>4.15 | |
Physiochemical and Pharmacokinetics properties for tested spiropyrazole derivatives 6a, 10c, 10g, 19h, 14a and 14b.
| Properties | Compounds | ||
|---|---|---|---|
| 10h | 14a | 14b | |
| Formula | C29H20BrN3O3 | C31H22BrN3O3 | C31H22BrN3O3 |
| Molecular weight | 538.39 g/mol | 564.43 g/mol | 564.43 g/mol |
| Num. of heavy atoms | 36 | 38 | 38 |
| Num. of aromatic heavy atoms | 24 | 24 | 24 |
| Num. of rotatable bonds | 4 | 5 | 5 |
| Num. H-bond acceptor (HBA) | 4 | 4 | 4 |
| Num. H-bond donors (HBD) | 0 | 0 | 0 |
| Molar reactivity | 151.39 | 161.32 | 161.32 |
| Topological Polar Surface area (TPSA) | 78.49 Ų | 78.49 Ų | 78.49 Ų |
| Lipophilicity (Log P) | 3.86 | 3.54 | 3.59 |
| Water solubility (Log S) | -7.88 (inSoluble) | -8.22 (inSoluble) | -8.22 (inSoluble) |
| Pharmacokinetics (GI absorption) | High | High | High |
| Pharmacokinetics (BBB permeant) | No | No | No |
| Pharmacokinetics (CYP1A2, CYP2C19, CYP2C9, CYP2D6, CYP3A4 inhibitors) | No, Yes, Yes, No, No (respectively) | No, No, Yes, No, No (respectively) | No, No, Yes, No, No (respectively) |
| Druglikeness (Lipinski) | No; 2 violations: MW>500, MLOGP>4.15 | No; 2 violations: MW>500, MLOGP>4.15 | No; 2 violations: MW>500, MLOGP>4.15 |