| Literature DB >> 34898800 |
Aravind R Nesaragi1, Ravindra R Kamble1, Swati R Hoolageri1, Ahmedraza Mavazzan1, Suresh F Madar1, Ashish Anand2, Shrinivas D Joshi3.
Abstract
Since 2019, the infection of SARS-CoV-2 has been spreading worldwide and caused potentially lethal health problems. In view of this, the present study explores the most commodious and environmentally benign synthetic protocol for the synthesis of tetrahydrobenzo[b]pyran and pyrano[2,3-d]pyrimidinones as SARS-CoV-2 inhibitors via three-component cycloaddition of aromatic aldehyde, malononitrile, and dimedone/barbituric acid in water. Lemon peel from juice factory waste, namely, lemon (Citrus limon), sweet lemon (C. limetta), and Kaffir lime or Citron (C. hystrix), effectually utilized to obtain WELPSA, WESLPSA, and WEKLPSA, respectively, for the synthesis of title compounds. The catalyst was characterized by scanning electron microscope (SEM) and energy-dispersive x-ray spectroscopy (EDX). The concentration of sodium, potassium, calcium, and magnesium in the catalyst (WELPSA) was determined using atomic absorption spectrometry (AAS). The current approach manifests numerous notable advantages that include ease of preparation, handling and benignity of the catalyst, low cost, green reaction conditions, facile workup, excellent yields (93%-97%) with extreme purity, and recyclability of the catalyst. Compounds were docked on the crystal structure of SARS-CoV-2 (PDB: 6M3M). The consensus score obtained in the range 2.47-4.63 suggests that docking study was optimistic indicating the summary of all forces of interaction between ligands and the protein.Entities:
Keywords: Covid‐19; WELPSA; atomic absorption spectrometry; pyrano[2,3‐d]pyrimidinones; tetrahydrobenzo[b]pyrans
Year: 2021 PMID: 34898800 PMCID: PMC8646655 DOI: 10.1002/aoc.6469
Source DB: PubMed Journal: Appl Organomet Chem ISSN: 0268-2605 Impact factor: 4.072
Most affected countries due to coronavirus
| Country | Total cases (in millions) | Average cases/day | Total deaths (in millions) | Number of waves |
|---|---|---|---|---|
| United States | 35.2 | 85,866 | 0.613 | 3 |
| India | 31.77 | 40,794 | 0.425 | 3 |
| Brazil | 20 | 35,120 | 0.557 | 3 |
| Russia | 6.23 | 511,265 | 0.157 | 3 |
| France | 6.15 | 22,289 | 0.112 | 3 |
| United Kingdom | 5.9 | 25,722 | 0.130 | 3 |
| Turkey | 5.77 | 22,083 | 0.052 | 3 |
| Argentina | 4.95 | 11,183 | 0.106 | 2 |
| Colombia | 4.8 | 81,658 | 0.121 | 3 |
| Spain | 4.5 | 22,990 | 0.082 | 4 |
FIGURE 1Preparation of WELPSA
FIGURE 2SEM images of LPA for WELPSA (a), SLPA for WESLPSA (b), and KLPA for WEKLPSA (c)
FIGURE 3EDX spectrum of WELPSA LPA for WELPSA (a), SLPA for WESLPSA (b), and KLPA for WEKLPSA (c)
Results of determination of concentrations of metal cations in WELPSA
| Atom | Wave length λmax | Absorbance au | Concentration μg/ml |
|---|---|---|---|
| Sodium | 589.00 | 0.107 | 0.35 |
| Potassium | 766.5 | 1.004 | 0.87 |
| Calcium | 422.70 | 0.082 | 0.45 |
| Magnesium | 285.2 | 0.0002 | 0.25 |
FIGURE 4Optimization of the catalyst
Optimization of reaction conditions for the compound 5a at room temperature
| Entry | Catalyst Volume (mL) | Solvent | Time (h) | Yield (%) |
|---|---|---|---|---|
| 1 | 3 | DMF | 20 | 15 |
| 2 | 3 | Acetone | 16 | 32 |
| 3 | 3 | DMSO | 15 | 28 |
| 4 | 3 | Ethanol | 14 | 70 |
| 5 | 3 | Methanol | 15 | 70 |
| 6 | 3 | Ethanol:H2O (1:1) | 12 | 78 |
| 7 | 3 | THF:H2O (1:1) | 14 | 65 |
| 8 | 3 | DCM | 13 | 68 |
| 9 | 3 | Acetonitrile | 13 | 56 |
| 10 | 3 | Dioxane:H2O (1:1) | 17 | 68 |
| 11 | 3 | Ethanol:H2O (1:2) | 12 | 80 |
| 12 | 3 | PEG‐400 | 18 | 70 |
| 13 | 3 | Ethanol:H2O (2:1) | 17 | 72 |
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| 15 | 3 | Toluene | 15 | 35 |
SCHEME 1Strategic depiction to synthesize tetrahydrobenzo[b]pyrans 5a–j and pyrano[2,3‐d]pyrimidinones 6k–t
Optimization of reaction conditions with different methods to furnish compound 5a
| Method | Time | Yield (%) |
|---|---|---|
| Grinding | 4 h | 70 |
| Conventional heating | 6 h | 88 |
| Room temperature | 10 h | 88 |
| Microwave | 3 min | 96 |
Comparison of WELPSA with identical reaction conditions in presence of analogous catalysts to furnish the compound 5a at room temperature
| Entry no. | Catalyst | Solvent | Yield (%) |
|---|---|---|---|
| 1 | ‐ | H2O | Trace |
| 2 | Na2CO3 | H2O | 80 |
| 3 | K2CO3 | H2O | 78 |
| 4 | CaCO3 | H2O | Trace |
| 5 | MgCO3 | H2O | Trace |
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Synthesized library of compounds and their yields
| Entry | Aldehyde | Product | Conventional | Microwave | ||
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| Time (h) | Yield (%) | Time (min) | Yield (%) | |||
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| 10 | 88 | 3 | 96 |
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| 9 | 85 | 3 | 95 |
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| 12 | 86 | 4 | 95 |
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| 10 | 85 | 3 | 96 |
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| 11 | 88 | 4 | 95 |
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| 10 | 86 | 4 | 96 |
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| 9 | 85 | 3 | 96 |
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| 10 | 85 | 4 | 96 |
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| 9 | 86 | 4 | 94 |
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| 10 | 85 | 3 | 93 |
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| 9 | 86 | 2 | 95 |
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| 10 | 85 | 3 | 94 |
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| 12 | 86 | 3 | 95 |
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| 9 | 86 | 4 | 93 |
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| 9 | 85 | 3 | 93 |
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| 10 | 84 | 4 | 94 |
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| 9 | 86 | 4 | 95 |
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| 10 | 84 | 3 | 96 |
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| 9 | 85 | 3 | 94 |
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| 10 | 85 | 4 | 95 |
FIGURE 5WELPSA recyclability
SCHEME 2Plausible mechanism for the emergence of tetrahydrobenzo[b]pyrans 5a–j
FIGURE 6ORTEP projection and packing diagram of compound 5b
FIGURE 7Docked view of all the compounds at the active site of the enzyme PDB ID: 6M3M
Comparison of different catalysts with WELPSA to synthesize 6k
| Entry | Catalyst | Solvent | Yield (%) |
|---|---|---|---|
| 1 | [H2‐DABCO][H2PO4]2 | EtOH: H2O (2:1) | 95[
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| 2 | DAHP | EtOH: H2O (1:1) | 81[
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| EtOH: H2O (1:1) | 80[
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| 4 | CaHPO4 | EtOH: H2O (1:4) | 89[
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| 5 | WELPSA | H2O | 95 |
Present work.
FIGURE 8Docked view of compound 6t at the active site of the enzyme PDB: 6M3M
FIGURE 9Docked view of compound 6s at the active site of the enzyme PDB: 6M3M
FIGURE 10Docked view of standard compound at the active site of the enzyme PDB: 6M3M
FIGURE 11(a) Hydrophobic amino acids surrounded to compounds 6t (green color) and 6s (cyan color). (b) Hydrophilic amino acids surrounded to compounds 6t and 6s
Surflex docking score (kcal/mol) of the derivatives (PDB: 6M3M)
| Compounds | C score | Crash score | Polar score | D score | PMF score | G score | Chem score |
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| 4.63 | −0.96 | 2.35 | −77.045 | −16.464 | 56.781 | −20.449 |
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| 4.20 | −1.77 | 1.52 | −87.274 | −41.520 | −173.307 | −20.901 |
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| 4.20 | −1.78 | 1.32 | −87.722 | −40.355 | −169.099 | −20.619 |
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| 4.15 | −1.21 | 0.00 | −79.879 | −25.823 | −180.695 | −16.327 |
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| 3.41 | −0.85 | 1.07 | −75.076 | −72.023 | −142.250 | −10.396 |
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| 3.35 | −0.72 | 1.06 | −59.901 | −52.284 | −124.598 | −18.614 |
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| 3.19 | −0.34 | 2.28 | −52.992 | −51.624 | −94.862 | −15.137 |
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| 3.11 | −0.56 | 2.90 | −62.976 | −38.091 | −118.028 | −17.606 |
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| 2.82 | −0.38 | 2.24 | −60.489 | −48.862 | −83.674 | −13.883 |
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| 2.55 | −0.19 | 2.33 | −45.733 | −45.110 | −81.876 | −14.852 |
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| 2.53 | −0.18 | 2.32 | −46.210 | −46.136 | −82.774 | −14.903 |
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| 2.52 | −1.13 | 1.62 | −64.990 | −26.241 | −133.274 | −11.213 |
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| 2.47 | −0.37 | 3.32 | −37.905 | −28.625 | −72.868 | −15.046 |
CScore (consensus score): This is an integration of the number of popular scoring functions for assessing the affinity of synthesized compounds docked into the active site of the protein, and this is the total score.
Crash score: It indicates the unsuitable penetration into the docking pocket. Crash scores nearer to 0 are favorable. The negative numbers illustrate the penetration.
Polar score: The polar score is a measure of polar interactions to the total score and is useful for excluding docking results that make no hydrogen bonds.
D score: It reveals the charge and van der Waals interactions between the receptor and the reported compounds.
PMF score: This indicates the Helmholtz free energies of interactions between the receptor and the atom pairs of the synthesized molecule or the reference compound (potential of mean force, PMF).
G score: It is a measure of H‐bond between the external (compound–protein) and internal (compound–compound).
Chem score: This indicates the H‐bonding, lipophilic contact, and rotational entropy, along with an intercept term.
Comparison of different catalysts with WELPSA to synthesize 5a
| Entry | Catalyst | Solvent | Yield (%) |
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| 1 | ZnONPs | EtOH: H2O (1:1) | 86[
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| 2 | Fe3O4@SiO2@BenzIm‐Fc[Cl]/NiCl2 | EtOH: H2O (4:2) | 95[
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| 3 | [H2‐DABCO][H2PO4]2 | EtOH: H2O (2:1) | 90[
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| 4 | RHPrBPCl nanocomposite | H2O | 90[
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| 5 | Glutamic acid | EtOH | 90[
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| 6 | CaHPO4 | EtOH: H2O (1:4) | 91[
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| 8 | WELPSA | H2O | 96 |
Present work.