Development of iminosugar-based glycosidase inhibitors as drug candidates for SARS-CoV-2 virus via molecular modelling and in vitro studies

Figures & data

Figure 1. Selected glycosidase inhibitors that underwent clinical trials for various medical indications.

Scheme 1. Synthesis of deoxynojirimycin (DNJ)-derived α-glucosidase inhibitors. Reagents and conditions: a) R¹CHO, H₂ (1–4.2 atm), 10% Pd/C, 70–91%; b) H₂ (1–4.2 atm), 10% Pd/C, 70–100%; c) n-BuBr, K₂CO₃, DMF, 80 °C, 69%; d) MeLi, –40 °C, Et₂O, 100%; e) TBTH, AIBN, PhH, 80 °C, 88%; f) p-TsOH, MeOH, 95%; g) PPh₃, I₂, imidazole, THF, 88%; h) 74, K₂CO₃, DMF, 80 °C, 86%; i) H₂ (4 atm), Pd(OH)₂/C, HCl, MeOH, 98%. Ad = adamantane-1-yl.

Figure 2. Structures and protonation states of the initial set of molecules at pH 7.00 ± 2.00, as predicted by the Epik module.

Figure 3. Binding interactions of small molecules with the binding site of endoplasmic reticulum (ER) α-glucosidase II (5DL0).

Table 1. Docking scores of the investigated compounds after docking (left) and refining (right) as well as the previously reported data on α-glucosidase inhibitors.

Docking			Refined scores
Compound	Docking score	XP GScore	Compound	Docking score	XP GScore	Inhibitory activity
IHVR-19029 12	−10.379	−10.382	IHVR-19029 12	−11.154	−11.158	IC50 = 27.8 μM (pig liver)^43
1	−10.281	−10.285	8	−10.811	−10.855	IC50 = 41.3 μM (yeast)^46 IC50 = 9.88 mM (yeast)^37
13	−10.263	−10.267	13	−10.617	−10.621	43.0 % at 1 mM (yeast)^45
11	−10.042	−10.086	1	−10.468	−10.472	IC50 = 13 μM (rat liver)^44 12.7 % at 1 mM (yeast)^45
10	−9.713	−9.895	10	−10.091	−10.273	IC50 = 16.73 mM (yeast)^37
8	−9.637	−9.681	11	−10.042	−10.086	No literature data
2	−9.570	−9.582	2	−9.570	−9.582	Ki = 25 μM (yeast)^40 Ki = 21 μM (yeast)^41 Ki = 7.0 μM (pig liver)^39 IC50 = 16 μM (rat liver)^44
6	−9.073	−9.076	9	−9.542	−9.722	No activity (yeast)^37
5	−8.760	−8.773	6	−9.073	−9.076	18 % at 5 mM (yeast)^38
9	−8.652	−8.832	5	−8.760	−8.773	Ki = 2000 μM (yeast)^40
7	−8.610	−8.663	7	−8.610	−8.664	Ki = 19 μM (yeast)^40 Ki = 47 μM (yeast)^41 Ki > 5 mM (pig liver)^39

Figure 4. Structures and protonation states of the set of bicyclopentyl (BCP)-containing molecules at pH 7.00 ± 2.00, as predicted by the Epik module.

Figure 5. Interactions of ligands 26 (A) and 38 (B) at the binding site.

Figure 6. Presumed α-galactosidase A (GAL) inhibitors.

Figure 7. Non-iminosugar-type mannosidase inhibitors AR524 (71) and tamoxifen (72).

Scheme 2. Synthesis of deoxygalactonojirimycin (DGJ) and its analogues. Reagents and conditions: a) (R)-Pro (cat.), DMF, rt, 61%; b) H₂ (4.5 atm), 10% Pd/C, EtOH, 75%; c) HCl, MeOH, 70–90%; d) RCHO, H₂ (1–4 atm), 10% Pd/C, EtOH, 54–94%; e) (R)-Pro (cat.), DMF, 4 °C, 24 h, 60%; f) K₂CO₃, DMF, 80 °C, 95 : 96 = 2 : 1, 94% total yield; g) HCl, MeOH, 50%.

Scheme 3. Synthesis of pyrrolidine derivatives 41 and 42. Reagents and conditions: a) (R)-Pro (cat.), DMF, 4 °C, 48h, 98: 37%, 99: 33%; b) H₂ (4.5 atm), 10% Pd/C, EtOH; c) 3 M HCl, MeOH, 42: 43% over 2 steps, 41: 55% over 2 steps.

Scheme 4. Synthesis of azagalactofagomine (AGF) and its methylated derivative. Reagents and conditions: a) (S)-Pro, DMSO, H₂O, 53%; b) H₂ (1 atm), 10% Pd/C, MeOH, rt, 1 h; c) NaBH₃CN, AcOH, MeOH, rt, 30 min, 65% over 2 steps; d) 3 M HCl_(aq), MeOH, rt, 24 h, 40: 96%; 104: 100%; e) HCHO_(aq), H₂ (1 atm), Pd(OH)₂/C, EtOAc, AcOH, rt, 6 h, 84%.

Scheme 5. Synthesis of (–)-swainsonine (3). Reagents and conditions: a) (R)-Pro (cat.), DMF, 66%; b) H₂, Pd/C (10%), MeOH; c) CbzCl, Et₃N, THF (71% over 2 steps).

Figure 8. Dependence of the percentage of inhibition on concentration (A) and log c (B) of 76.

Table 2. IC₅₀ values of the yeast α-glucosidase inhibitors.

Compound	IC50/µM
1	≫500
2	54
8	≫500
22	218
75	572
76	70
77	67

Figure 9. Dependence of the percentage of inhibition on concentration (A) and log c (B) of 41.

Table 3. IC₅₀ values of the human α-galactosidase inhibitors.

Compound	IC50/µM
4	0.17
40	≫100
41	1.0
42	5.0
53	59.3
87	5.1
88	24.4
89	≫100
93	≫100
94	≫100
104	≫100

Figure 10. Anti-SARS-CoV-2 activities and cytotoxicities for α-glucosidase II inhibitors: 77 (A), 22 (B), 76 (C) and 1 (D).

Figure 11. Interactions of ligands 1, 76, 22, and 77 in the binding site of α-glucosidase II.

Figure 12. Antiviral activities and cell viabilities of mannosidase inhibitors: (−)-swainsonine (3, A), 71 (B), and tamoxifen (72, C).

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