| Literature DB >> 35919373 |
Shaghayegh Saeedi1, Abbas Rahmati1, Zahra Chavoshpour-Natanzi1.
Abstract
A novel series of fused pyrazolo[5',1':2,3]imidazo[1,5-c]quinazolin-6(5H)-ones were synthesized and their affinity against the COVID-19 main protease was investigated using molecular docking study and compared to that of some used standard clinical drugs. These compounds were obtained in good to excellent yields from 63 to 91% in the presence of 30 mol% catalyst in ethanol at reflux for 2 h through an efficient one-pot three-component reaction including an intramolecular rearrangement and a cyclization through intramolecular nucleophilic reaction. The results of in silico studies showed that electronegativity, resonance effects, hydrophobic interaction, halogen and hydrogen bonding had significant effects on the performance of these compounds as an inhibitor ligand. Also, these results indicated the proper affinity of these compounds against the COVID-19 main protease with excellent binding energies (especially 4r = -8.77, 4q = -8.73 and 4m = -8.63) in comparison to remdesivir, chloroquine, hydroxychloroquine, molnupiravir and nirmatrelvir drugs. This journal is © The Royal Society of Chemistry.Entities:
Year: 2022 PMID: 35919373 PMCID: PMC9264878 DOI: 10.1039/d2ra03179e
Source DB: PubMed Journal: RSC Adv ISSN: 2046-2069 Impact factor: 4.036
Fig. 1The structure of SARS-CoV-2 Mpro. Ribbon representation of SARS-CoV-2 Mpro (PDB ID: 6LU7) (the substrate-binding pocket with the transparent surface is shown).
Scheme 1Synthesis of compound 4j using 5-chloroisatin, 3-amino-4-bromo-1H-pyrazole, and tert-butyl isocyanide.
Effects of various catalysts and different amounts of CeCl3·7H2O on the yield of compound 4ja
| Entry | Catalyst (mol%) | Yield (%) |
|---|---|---|
| 1 | — | 0 |
| 2 | AcOH (30) | 44 |
| 3 | ZnCl2 (30) | 32 |
| 4 | Sc (OTf)3 (30) | 51 |
| 5 | NH2SO3H (30) | 60 |
| 6 |
| 70 |
| 7 | MgCl2 (30) | 37 |
| 8 | MeSO3H (30) | 31 |
| 9 | H2SO4 (30) | 32 |
| 10 | CeCl3·7H2O (20) | 65 |
| 11 | CeCl3·7H2O (30) | 75 |
| 12 | CeCl3·7H2O (40) | 75 |
| 13 | CeCl3·7H2O (50) | 75 |
Reaction conditions: 5-chloroisatin (1 mmol), 3-amino-4-bromo-1H-pyrazole (1 mmol), tert-butyl isocyanide (1 mmol) and ethanol (3 mL), reaction time: 24 h.
The results of optimization of reaction conditions for compound 4j synthesisa
| Entry | Solvent | Temperature (°C) | Time (h) | Yield |
|---|---|---|---|---|
| 1 | Ethanol | Reflux | 24 | 75 |
| 2 | Water | Reflux | 24 | 50 |
| 3 | Methanol | Reflux | 24 | 61 |
| 4 | DMSO | 100 | 24 | 52 |
| 5 | DMF | 100 | 24 | 52 |
| 6 | Dioxane | 100 | 24 | 28 |
| 7 | THF | Reflux | 24 | 40 |
| 8 | Acetonitrile | Reflux | 24 | 38 |
| 9 | Ethyl acetate | Reflux | 24 | 30 |
| 10 | Chloroform | Reflux | 24 | 0 |
| 11 | Toluene | 100 | 24 | 0 |
| 12 | Solvent-free | 100 | 24 | 0 |
| 13 | Ethanol | RT | 24 | 0 |
| 14 | Ethanol | 40 | 24 | 0 |
| 15 | Ethanol | 60 | 24 | 34 |
| 16 | Ethanol | Reflux | 24 | 75 |
| 17 | Ethanol | Reflux | 10 | 75 |
| 18 | Ethanol | Reflux | 2 | 75 |
| 19 | Ethanol | Reflux | 1.5 | 60 |
| 20 | Ethanol | Reflux | 1 | 41 |
Reaction conditions: 5-chloroisatin (1 mmol), 3-amino-4-bromo-1H-pyrazole (1 mmol), tert-butyl isocyanide (1 mmol), solvent (3 mL).
Isolated yield in the presence of CeCl3·7H2O catalyst (30 mol%).
Scheme 2The structure of pyrazolo[5′,1′:2,3]imidazo[1,5-c]quinazolin-6(5H)-one derivatives synthesized under optimized reaction conditions in this work.
The yields of synthesized products (4a–4u) using different derivatives of isatin, 3-aminopyrazole and isocyanide in the presence of CeCl3·7H2O catalysta
| Entry | Pyrazole | Isatin | Isocyanide | Product | Yield (%) |
|---|---|---|---|---|---|
| 1 |
|
|
| 4a | 78 |
| 2 |
|
|
| 4b | 76 |
| 3 |
|
|
| 4c | 80 |
| 4 |
|
|
| 4d | 77 |
| 5 |
|
|
| 4e | 75 |
| 6 |
|
|
| 4f | 82 |
| 7 |
|
|
| 4g | 74 |
| 8 |
|
|
| 4h | 73 |
| 9 |
|
|
| 4i | 74 |
| 10 |
|
|
| 4j | 77 |
| 11 |
|
|
| 4k | 79 |
| 12 |
|
|
| 4l | 81 |
| 13 |
|
|
| 4m | 81 |
| 14 |
|
|
| 4n | 82 |
| 15 |
|
|
| 4o | 80 |
| 16 |
|
|
| 4p | 81 |
| 17 |
|
|
| 4q | 75 |
| 18 |
|
|
| 4r | 79 |
| 19 |
|
|
| 4s | 75 |
| 20 |
|
|
| 4t | 74 |
| 21 |
|
|
| 4u | 63 |
Isolated yield in the presence of CeCl3·7H2O catalyst (30 mol%).
Scheme 3Proposed mechanism for the formation of pyrazolo[5′,1′:2,3]imidazo[1,5-c]quinazolin-6(5H)-one derivatives using acid catalysts.
Scheme 4Tree possible products in this reaction.
Fig. 2Comparison of the stability of intermediate 6 and the final product in compound 4j based on the B3LYP/6-311++G(d,p) computational study.
Fig. 3View of the Mpro binding site (Cys145–His41) for compounds 4a–4f. Image of hydrophobic interaction, hydrogen and halogen bonds for ligands (yellow and green color indication H-bond and hydrophobic interaction, respectively) prepared by pymol software.
Fig. 4View of the Mpro binding site (Cys145–His41) for compounds 4g–4k. Image of hydrophobic interaction, hydrogen and halogen bonds for ligands (yellow, green and blue color indication H-bond, hydrophobic interaction and halogen bond, respectively) prepared by pymol software.
Molecular docking results for the interaction between Mpro and compounds 4a–4f
|
| ||||||
|---|---|---|---|---|---|---|
| Compound | R1 | R2 | Energy (kcal mol−1) | Hydrogen bond | Halogen bond | Hydrophobic interaction |
| 4a | Cl | — | −8.30 | THR26, ASN142, GLY143, CYS145 | — | THR25, PHE140, GLU166, VAL309, LEU310 |
| 4b | Br | — | −8.44 | THR26, ASN142, GLY143, CYS145 | — | THR25, PHE140, GLU166, VAL309, LEU310 |
| 4c | Me | — | −8.26 | THR26, ASN142, GLY143, CYS145 | — | THR25, PHE140, GLU166, VAL309, LEU310 |
| 4d | OMe | — | −8.05 | THR26, ASN142, GLY143, CYS145 | — | THR25, PHE140, GLU166, VAL309, LEU310 |
| 4e | — | — | −8.13 | THR26, ASN142, GLY143, CYS145 | — | THR25, PHE140, GLU166, VAL309 |
| 4f | Me | Me | −8.22 | SER144, HIS163, GLY143, CYS145 | — | THR25, PHE140, GLU166, VAL309 |
Molecular docking results for the interaction between Mpro and compounds 4g–4k
|
| |||||
|---|---|---|---|---|---|
| Compound | R | Energy (kcal mol−1) | Hydrogen bond | Halogen bond | Hydrophobic interaction |
| 4g | — | −7.96 | GLY143, SER144, CYS145 | — | PHE140, GLU166 |
| 4h | Me | −8.22 | GLY143, SER144, CYS145 | — | PHE140 |
| 4i | OMe | −7.90 | ASN142, GLY143, SER144, CYS145 | — | PHE140, GLU166 |
| 4j | Cl | −8.18 | GLY143, SER144, CYS145 | — | PHE140, GLU166 |
| 4k | Br | −8.28 | ASN142, GLY143, SER144, CYS145 | — | PHE140 |
Molecular docking results for the interaction between Mpro and compounds 4l–4p
|
| ||||||
|---|---|---|---|---|---|---|
| Compound | R1 | R2 | Energy (kcal mol−1) | Hydrogen bond | Halogen bond | Hydrophobic interaction |
| 4l | Cl | — | −8.51 | SER144, ASN142, GLY143, CYS145 | — | THR25, PHE140, GLU166 |
| 4m | Me | — | −8.63 | SER144, GLY143, CYS145 | — | THR25, PHE140, GLU166 |
| 4n | OMe | — | −8.39 | SER144, ASN142, GLY143, CYS145 | — | THR25, PHE140, GLU166 |
| 4o | — | — | −8.41 | HIS163, SER144, GLY143, CYS145 | — | THR25, THR26, GLU166, PHE140 |
| 4p | Me | Me | −7.62 | ASN142, GLY143 | — | LEU27, PHE140, GLU166, VAL309 |
Molecular docking results for the interaction between Mpro and compounds 4q–4u
|
| ||||||
|---|---|---|---|---|---|---|
| Compound | R1 | R2 | Energy (kcal mol−1) | Hydrogen bond | Halogen bond | Hydrophobic interaction |
| 4q | Cl | chx | −8.73 | ASN142, GLY143, SER144, CYS145 | THR26 | PHE140, GLU166 |
| 4r | Me | chx | −8.77 | HIS163, GLY143, SER144, CYS145 | THR26 | PHE140, GLU166 |
| 4s | OMe | chx | −8.51 | ASN142, GLY143, SER144, CYS145 | THR26 | PHE140, GLU166 |
| 4t | — | chx | −8.54 | HIS163, GLY143, SER144, CYS145 | THR26 | PHE140, GLU166 |
| 4u | I | 1,1,3,3-Tetramethylbutyl | −8.22 | ASN142, GLY143, SER144, CYS145 | — | PHE140, GLU166, VAL309 |
Molecular docking results for products and some drugs with Mpro
| Entry | Products and drugs | Energy | Energy |
|---|---|---|---|
| 1 | 4a–4u | −7.62 to −8.77 | — |
| 2 | Chloroquine | −7.09 | −5.75,[ |
| 3 | Hydroxychloroquine | −7.01 | −6.7,[ |
| 4 | Remdesivir | — | −7.22,[ |
| 5 | Molnupiravir | −7.53 | — |
| 6 | Nirmatrelvir | −8.91 | — |
Calculated in this work.
From other literature data.