Design and synthesis of new tripeptide-type SARS-CoV 3CL protease inhibitors containing an electrophilic arylketone moiety

Abstract

We describe here the design, synthesis and biological evaluation of a series of molecules toward the development of novel peptidomimetic inhibitors of SARS-CoV 3CL(pro). A docking study involving binding between the initial lead compound 1 and the SARS-CoV 3CL(pro) motivated the replacement of a thiazole with a benzothiazole unit as a warhead moiety at the P1' site. This modification led to the identification of more potent derivatives, including 2i, 2k, 2m, 2o, and 2p, with IC(50) or K(i) values in the submicromolar to nanomolar range. In particular, compounds 2i and 2p exhibited the most potent inhibitory activities, with K(i) values of 4.1 and 3.1 nM, respectively. The peptidomimetic compounds identified through this process are attractive leads for the development of potential therapeutic agents against SARS. The structural requirements of the peptidomimetics with potent inhibitory activities against SARS-CoV 3CL(pro) may be summarized as follows: (i) the presence of a benzothiazole warhead at the S1'-position; (ii) hydrogen bonding capabilities at the cyclic lactam of the S1-site; (iii) appropriate stereochemistry and hydrophobic moiety size at the S2-site and (iv) a unique folding conformation assumed by the phenoxyacetyl moiety at the S4-site.

Graphical abstract

Figure 1

Structure of a lead compound 1 (A) and their molecular stimulated representation (B).

Scheme 1

Solid-phase synthesis of dipeptidic 9. Reagents and conditions: (a) Fmoc-R¹-OH, DIC, DMAP/DMF; (b) 20% piperidine/DMF; (c) Fmoc-Val-OH, DIC, DMAP, HOBt/DMF; (d) 20% piperidine/DMF; (e) R(Acyl)-Cl, Et₃N or R(Acyl)-OH, DIC, HOBt/DMF; (f) TFA/H₂O. Note: The substituents R (acyl) and R¹ are indicated in Table 1, Table 2, Table 3.

Scheme 2

Synthetic outline for the preparation of title compounds 2, 3 and 5. Reagents and conditions: (a) HN(OMe)Me, EDC·HCl, HOBT, Et₃N/DMF; (b) n-BuLi, THF, −78 °C (if R² = thiazole, 4,5-dimethylthiazole or benzothiazole) or LDA, THF, −78 °C (if R² = 5-arylated thiazoles); (c) TFA/H₂O; (d) 9, HBTU, DIPEA/DMF followed by HPLC purification. Note: The substituents R(acyl), R¹ and R² are indicated in Table 1, Table 2, Table 3.

Scheme 3

Synthetic outline for the preparation of imidazole type compounds 4. Reagents and conditions: (a) HN(OMe)Me, EDC·HCl, HOBT, Et₃N/DMF; (b) thiazole, n-BuLi, THF, −78 °C; (c) TsCl, Et₃N, THF; (d) TFA/H₂O; (e) 9, HBTU, DIPEA/DMF followed by HPLC purification. Note: The substituents R(acyl) and R¹ are indicated in Table 2.

Figure 2

Molecular dynamics stimulated pose of compound 2o, (yellow stick) bound to SARS-CoV 3CLpro (PDB ID: 1WOF (green stick) with blue molecular surface); with lead compound 1 (red stick); (A) overlapped view of 2o with an original vinyl ester (green stick) and lead 1 (red stick); (B) contacted residues with hydrogen bonding interactions (dotted lines).