De novo Design of SARS-CoV-2 Main Protease Inhibitors

Abstract

The COVID-19 pandemic prompted many scientists to investigate remedies against SARS-CoV-2 and related viruses that are likely to appear in the future. As the main protease of the virus, M^Pro, is highly conserved among coronaviruses, it has emerged as a prime target for developing inhibitors. Using a combination of virtual screening and molecular modeling, we identified small molecules that were easily accessible and could be quickly diversified. Biochemical assays confirmed a class of pyridones as low micromolar noncovalent inhibitors of the viral main protease.

Key words

viral main protease - small-molecule inhibitor - SARS-CoV-2 - coronavirus - molecular modeling

Publication History

Received: 13 July 2021

Accepted after revision: 10 August 2021

Accepted Manuscript online:
10 August 2021

Article published online:
05 October 2021

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• 12 Procedures a-d for the synthesis of compound 28: (a) To a mixture of 5‑bromo-2-hydroxypyridine (25) (522 mg, 3.00 mmol), K₂CO₃ (1.24 g, 9.00 mmol) in acetone (30 mL) was added 2-chloro-N-cyclohexylacetamide (5a) (738 mg, 4.20 mmol) at room temperature and the mixture was stirred at 50 °C for 18 hours. The suspension was treated with hexanes (50 mL), filtered and washed portionwisely with water (100 mL). The remaining solid was dried and recrystallized from acetone/hexanes to give intermediate 26 as an off-white solid (716 mg, 76%): R _f 0.31 (hexanes:EtOAc, 1:2); ¹H-NMR (400 MHz, CDCl₃): δ = 7.56 (1H, d, ⁴ J 2.6 Hz), 7.41 (1H, dd, ³ J 9.7 Hz, ⁴ J 2.7 Hz), 6.62 (1H, d, ³ J 5.8 Hz), 6.52 (1H, d, ³ J 9.7 Hz), 4.45 (2H, s), 3.65–3.74 (1H, m), 1.83–1.87 (2H, m), 1.65–1.71 (2H, m), 1.54–1.61 (1H, m), 1.28–1.39 (2H, m), 1.11–1.21 (3H, m); ¹³C‑NMR (101 MHz, CDCl₃): δ = 165.6, 161.4, 143.7, 138.1, 121.9, 99.0, 54.0, 48.8, 32.8, 25.6, 24.7; APCI-HRMS: m/z calcd. for [C₁₃H₁₈BrN₂O₂]⁺ 315.0526 found 315.0529 [M+H]⁺. (b) A mixture of intermediate 26 (94.0 mg, 0.300 mmol), 4-fluorophenylboronic acid (105 mg, 0.750 mmol), Na₂CO₃ (127 mg, 1.20 mmol), Pd(PPh₃)₄ (17.3 mg, 15.0 µmol, 5.00 mol%) was evacuated for 10 minutes under high vacuum and backfilled with N₂at room temperature. The mixture was treated with PhMe:EtOH:H₂O (1.9 mL, 0.74 mL, 0.26 mL) and stirred at 75 °C for 3 hours in a pre-heated sand bath. The mixture was treated with water and extracted with CH₂Cl₂. The combined organic layers were dried over Na₂SO₄, filtered and concentrated in vacuo. Precipitation from hexanes gives intermediate 27 as a white solid (85.3 mg, 87%): R _f 0.26 (hexanes:EtOAc, 1:2, UV); ¹H-NMR (400 MHz, CDCl₃): δ = 7.64 (1H, dd, ³ J 9.4 Hz, ⁴ J 2.6 Hz), 7.59 (1H, d, ⁴ J 2.4 Hz), 7.36–7.40 (2H, m), 7.09–7.13 (2H, m), 6.82 (1H, d, ³ J 6.7 Hz), 6.71 (1H, d, ³ J 9.4 Hz), 4.57 (2H, s), 3.67–3.76 (1H, m), 1.85–1.89 (2H, m), 1.66–1.71 (2H, m), 1.55–1.60 (1H, m), 1.28–1.36 (2H, m), 1.14–1.24 (3H, m); ¹³C‑NMR (101 MHz, CDCl₃): δ = 166.1, 162.6 (¹ J _CF 247 Hz), 162.2, 140.4, 135.4, 132.3 (⁴ J _CF 3.7 Hz), 127.8 (³ J _CF 8.1 Hz), 120.9, 120.5, 116.2 (² J _CF 22 Hz), 54.6, 48.7, 32.8, 25.6, 24.7; ¹⁹F-NMR (377 MHz, CDCl₃): δ = –114.66; APCI-HRMS: m/z calcd. for [C₁₉H₂₂FN₂O₂]⁺ 329.1660 found 329.1660 [M+H]⁺. (c) To a solution of intermediate 27 (32.8 mg, 0.100 mmol) in glacial acetic acid (1.0 mL) was added dropwise bromine (8.00 µL, 0.150 mmol) at room temperature. The orange mixture was stirred at 60 °C for 18 hours. When cooled to room temperature the mixture was treated with aqueous saturated Na₂S₂O₃ and adjusted to pH 7 with aqueous saturated NaHCO₃. The suspension was filtered and washed extensively with water. The filter cake was dried in vacuo and purified by column chromatography over silica gel with eluent 100% hexanes to hexanes:EtOAc 90:10 to 75:25 to 60:40 to 50:50 to give 2-(3-bromo-5-(4-fluorophenyl)-2-oxopyridin-1(2H)-yl)-N-cyclohexyl­acetamide (27.0 mg, 66%): R _f 0.30 (hexanes:EtOAc, 1:1, UV); ¹H‑NMR (400 MHz, CDCl₃): δ = 8.03 (1H, d, ⁴ J 2.4 Hz), 7.64 (1H, d, ⁴ J 2.3 Hz), 7.36–7.39 (2H, m), 7.09–7.13 (2H, m), 6.73 (1H, d, ³ J 8.1 Hz), 4.63 (2H, s), 3.67–3.76 (1H, m), 1.85–1.89 (2H, m), 1.67–1.72 (2H, m), 1.56–1.61 (1H, m), 1.28–1.38 (2H, m), 1.15–1.24 (3H, m); ¹³C‑NMR (101 MHz, CDCl₃): δ = 165.5, 162.8 (¹ J _CF 248 Hz), 158.6, 142.3, 135.1, 131.3 (⁴ J _CF 3.3 Hz), 128.0 (³ J _CF 8.8 Hz), 120.6, 116.3 (² J _CF 21 Hz), 55.0, 49.0, 32.8, 25.5, 24.8; ¹⁹F-NMR (377 MHz, CDCl₃): δ = – 13.99; APCI-HRMS: m/z calcd. for [C₁₉H₂₁BrFN₂O₂]⁺ 407.0765 found 407.0767 [M+H]⁺. (d) A solution of 2-(3-bromo-5-(4-fluorophenyl)-2-oxopyridin-1(2H)-yl)-N-cyclohexylacetamide (12.7 mg, 30.0 µmol) in dry DMF (0.30 mL) was treated with CuCN (8.40 mg, 90.0 µmol) at room temperature. The mixture was deareated by N₂ sparging for five minutes at room temperature and heated at 120 °C for 20 hours. The mixture was treated with water and extracted with EtOAc. The combined organic layers were washed with brine, dried over Na₂SO₄, filtered and concentrated in vacuo. Purification by column chromatography over silica gel with eluent 100% CH₂Cl₂ to 95:5 CH₂Cl₂:MeOH gives 2-(3-cyano-5-(4-fluorophenyl)-2-oxopyridin-1(2H)-yl)-N-cyclo­hexylacetamide (28) as a white solid (3.70 mg, 34%): R _f 0.21 (hexanes:EtOAc, 1:1, UV); ¹H-NMR (400 MHz, CDCl₃): δ = 8.07 (1H, d, ⁴ J 2.6 Hz), 7.87 (1H, d, ⁴ J 2.7 Hz), 7.34–7.41 (2H, m), 7.11–7.19 (2H, m), 6.40 (1H, d, ³ J 7.9 Hz), 4.62 (2H, s), 3.67–3.77 (1H, m), 1.85–1.94 (2H, m), 1.67–1.72 (2H, m), 1.58–1.64 (1H, m), 1.28–1.40 (2H, m), 1.13–1.26 (3H, m); ¹³C-NMR (101 MHz, CDCl₃): δ = 164.5, 163.0 (¹ J _CF 248 Hz), 159.2, 147.2, 141.0, 130.5 (⁴ J _CF 3.4 Hz), 128.1 (³ J _CF 8.3 Hz), 119.9, 116.6 (² J _CF 22 Hzs), 105.6, 53.7, 49.3, 32.9, 25.5, 24.8; ¹⁹F-NMR (377 MHz, CDCl₃): δ = –113.03; APCI-HRMS: m/z calcd. for [C₂₀H₂₁FN₃O₂]⁺ 354.1612 found 354.1609 [M+H]⁺. Further details can be found in the Supporting Information.