Structural Investigations on Novel Non-Nucleoside Inhibitors of Human Norovirus Polymerase

Figure 1. Chemical structures of previously reported inhibitors of norovirus RdRp [16].

Figure 2. Micromolar inhibitors of norovirus RdRp previously identified by our group through a docking-based virtual screening approach [18].

Figure 3. Summary of the planned structural modifications to the scaffolds of hit compounds 1–5.

Figure 4. Previously proposed binding mode for 5 (carbon atoms in purple) to the human norovirus RdRp, overlapped with the co-crystallized ligand PPNDS (atoms in grey) [18,19]. The binding site area is represented as green molecular surface. Human norovirus RdRp is represented as green ribbon, with carbon atoms in green. Black dashed lines represent non-bonded interactions (e.g., hydrogen bonds, electrostatic interactions) between the ligand and the amino acid residues of the protein.

Figure 5. Proposed binding mode for 1 (carbon atoms in purple) and 1e,f (carbon atoms in lilac) to the human norovirus RdRp (PDB ID 4LQ3). The binding site area is represented as green molecular surface. Human norovirus RdRp is represented as green ribbon, with carbon atoms in green. Black dashed lines represent non-bonded interactions (e.g., hydrogen bonds, electrostatic interactions) between the ligand and the amino acid residues of the protein.

Figure 6. Proposed binding mode for 2 (carbon atoms in purple) and 2g,h (carbon atoms in lilac) to the human norovirus RdRp (PDB ID 4LQ3). The binding site area is represented as green molecular surface. Human norovirus RdRp is represented as green ribbon, with carbon atoms in green. Black dashed lines represent non-bonded interactions (e.g., hydrogen bonds, electrostatic interactions) between the ligand and the amino acid residues of the protein.

Figure 7. Proposed binding mode for 3 (carbon atoms in purple), 3a–d and 3f (carbon atoms in lilac) to the human norovirus RdRp (PDB ID 4LQ3). The binding site area is represented as green molecular surface. Human norovirus RdRp is represented as green ribbon, with carbon atoms in green. Black dashed lines represent non-bonded interactions (e.g., hydrogen bonds, electrostatic interactions) between the ligand and the amino acid residues of the protein.

Figure 8. Proposed binding mode for 4 (carbon atoms in purple) and 4a–c (carbon atoms in lilac) to the human norovirus RdRp (PDB ID 4LQ3). The binding site area is represented as green molecular surface. Human norovirus RdRp is represented as green ribbon, with carbon atoms in green. Black dashed lines represent non-bonded interactions (e.g., hydrogen bonds, electrostatic interactions) between the ligand and the amino acid residues of the protein.

Figure 9. Proposed binding mode for 5 (carbon atoms in purple), 5a and 64 (carbon atoms in lilac) to the human norovirus RdRp (PDB ID 4LQ3). The binding site area is represented as green molecular surface. Human norovirus RdRp is represented as green ribbon, with carbon atoms in green. Black dashed lines represent non-bonded interactions (e.g., hydrogen bonds, electrostatic interactions) between the ligand and the amino acid residues of the protein.

Scheme 1. Preparation of 1 and its novel target analogues 1a–f. Reagents and conditions: (i) H2SO4, MeOH, reflux, o.n. (88%); (ii) NH2NH2*H2O, EtOH, reflux, o.n. (94%); (iii) NH4SCN, EtOH, HCl, reflux, o.n. (58%); (iv) 10% aq. NaOH, reflux, o.n. (72%); (v) K2CO3, Me2CO, r.t., o.n. (72–99%); (vi) Pyr, EtOH, reflux, o.n. (53–71%); (vii) m-CPBA, DCM, r.t., o.n. (34%); (viii) Nb(OEt)5, 30% aq. H2O2, MeOH, 45 °C, 2 h (87%).

Scheme 2. Preparation of 2 and novel target analogues 2a–h and 3a–f. Reagents and conditions: (i) AcOH, 130 °C, o.n. (83–93%); (ii) H2, Pd/C, THF, r.t., o.n. (74–99%); (iii) Pyr, THF, r.t., o.n. or anhydrous DCM, Et3N, r.t., o.n. (36–59%); (iv) H2SO4, MeOH, reflux, o.n. (89%); (v) a. diethyl chlorophosphate, Et3N, anhydrous DCM, 0 °C, 2h (65%), b. TMSBr, Pyr, anhydrous DCM, 0 °C to r.t., 56h (32%); (vi) H2SO4, MeOH, reflux, o.n. or MeI, K2CO3, Me2CO, reflux, 4h (84–99%); (vii) NH2NH2*H2O, EtOH, reflux, o.n. (58–96%); (viii) EtOH, reflux, o.n. (47–88%); (ix) diethylchlorophoshpate, Et3N, anhydrous DCM, 0 °C to r.t., o.n. (67–99%); (x) TMSBr, Pyr, anhydrous DCM, 0 °C to r.t., o.n. (54–95%).

Scheme 3. Preparation of novel analogues 4a–c and 5a. Reagents and conditions: (i) Pd(PPh3)4, K2CO3, H2O, EtOH, PhMe, reflux, o.n. (32–63%); (ii) ß-alanine, AcOH, 100 °C, o.n. (29–67%); (iii) a. diethyl chlorophosphate, Et3N, anhydrous DCM, 0 °C, 5h (89%), b. TMSBr, anhydrous DCM, 0 °C to r.t., 24 h (49%); (iv) Pyr, anhydrous DCM, 0 °C to r.t., 20 h (quant.); (v) H2, Pd/C, THF, r.t., 24 h (97%); (vi) HCl, NaNO2, SnCl2, H2O, 0 °C, 3 h (77%); (vii) ethyl malonyl chloride, Et3N, THF, -10 °C to r.t., 3 h (56%); (viii) 1M NaOH/EtOH, EtOH, r.t., 30 min (73%); (ix) AcOH, 120 °C, 3 h (72%); (x) a. diethyl chlorophosphate, Et3N, anhydrous DCM, 0 °C, o.n. (66%), b. TMSBr, anhydrous DCM, 0 °C to r.t., 3 h (58%).