Sandacrabins - Structurally Unique Antiviral RNA Polymerase Inhibitors from a Rare Myxobacterium

Abstract

Structure elucidation and total synthesis of five unprecedented terpenoid-alkaloids, the sandacrabins, are reported, alongside with the first description of their producing organism Sandaracinus defensii MSr10575, which expands the Sandaracineae family by only its second member. The genome sequence of S. defensii as presented in this study was utilized to identify enzymes responsible for sandacrabin formation, whereby dimethylbenzimidazol, deriving from cobalamin biosynthesis, was identified as key intermediate. Biological activity profiling revealed that all sandacrabins except congener A exhibit potent antiviral activity against the human pathogenic coronavirus HCoV229E in the three digit nanomolar range. Investigation of the underlying mode of action discloses that the sandacrabins inhibit the SARS-CoV-2 RNA-dependent RNA polymerase complex, highlighting them as structurally distinct non-nucleoside RNA synthesis inhibitors. The observed segregation between cell toxicity at higher concentrations and viral inhibition opens the possibility for their medicinal chemistry optimization towards selective inhibitors.

Keywords: antiviral agents; natural products; structure elucidation; supercritical fluids; terpenoids.

Figure 1

Phylogenetic classification of S. defensii MSr10575 as well as BGCs found in its genome using AntiSmash.

Figure 2

Structural formulae of sandacrabin A, B and C and the respective methods used for their purification.

Figure 3

A Key NMR correlations used for structure elucidation. COSY correlations: bold line. HMBC correlations: arrows. Dashed orange line: symmetry axis of sandacrabin B and C. B Prominent MSⁿ fragments of sandacrabin B and C.

Figure 4

A GTP‐cyclohydrolase type reaction catalyzed by RIB 1‐like enzymes. B Putative sandacrabin biosynthesis starting from DMB. Carbon atoms are color‐coded highlighting their position in the respective educts and products. C Synthesis of sandacrabin B and C (lower part), as well as their mono‐farneslyated derivatives sandacrabin D and E (upper part).

Figure 5

A Antiviral activities of Sandacrabin B and C against HCoV229E displayed as reduction in viral replication (orange) with simultaneous determination of the cell viability of Huh‐7.5 host cells (black). Mean values and standard deviation of triplicate measurements normalized to solvent control are given. Application window between cytotoxicity and antiviral activity as is marked in green. B Sandacrabin‐dependent inhibition of RNA synthesis catalyzed by SARS‐CoV‐2 RdRp complex represented as reduction in RNA synthesis products corresponding to the full template length. Respective curves for the positive controls can be found in the supporting information.