Bioguided Isolation of Cyclopenin Analogues as Potential SARS-CoV-2 Mpro Inhibitors from Penicillium citrinum TDPEF34

Abstract

SARS-CoV-2 virus mutations might increase its virulence, and thus the severity and duration of the ongoing pandemic. Global drug discovery campaigns have successfully developed several vaccines to reduce the number of infections by the virus. However, finding a small molecule pharmaceutical that is effective in inhibiting SARS-CoV-2 remains a challenge. Natural products are the origin of many currently used pharmaceuticals and, for this reason, a library of in-house fungal extracts were screened to assess their potential to inhibit the main viral protease M^pro in vitro. The extract of Penicillium citrinum, TDPEF34, showed potential inhibition and was further analysed to identify potential M^pro inhibitors. Following bio-guided isolation, a series of benzodiazepine alkaloids cyclopenins with good-to-moderate activity against SARS-CoV-2 M^pro were identified. The mode of enzyme inhibition of these compounds was predicted by docking and molecular dynamic simulation. Compounds 1 (isolated as two conformers of S- and R-isomers), 2, and 4 were found to have promising in vitro inhibitory activity towards M^pro, with an IC₅₀ values range of 0.36-0.89 µM comparable to the positive control GC376. The in silico investigation revealed compounds to achieve stable binding with the enzyme active site through multiple H-bonding and hydrophobic interactions. Additionally, the isolated compounds showed very good drug-likeness and ADMET properties. Our findings could be utilized in further in vitro and in vivo investigations to produce anti-SARS-CoV-2 drug candidates. These findings also provide critical structural information that could be used in the future for designing potent M^pro inhibitors.

Keywords: Mpro; Penicillium citrinum; SARS-CoV-2; cyclopenin; docking; molecular dynamic simulations.

Figure 1

Compounds isolated from the endophyte Penicillium citrinum TDPEF34.

Figure 2

Dose-response curves of compounds 1, 2, 4 and the positive control GC376.

Figure 3

Percentage inhibition of compound 1–11 and the positive control GC376 at 10 µM.

Figure 4

Docking scores and ΔG values of the isolated compounds (1–11). We set a cut-off at −7 kcal/mol (black dashed line).

Figure 5

Different binding modes of compounds 1–4 (A–C and E–G, respectively). The S-isomer of compound 1 (A,E) is cyan, while the R-isomer is brick red. Compound 3 has a brick red hue, while compound 4 has a cyan hue (C,G). The co-crystallized ligand (D,H) are shown in orange.

Figure 6

RMSDs of compounds 1–4 along with the free protein during the course of 100 ns.