Berbamine suppresses intestinal SARS-CoV-2 infection via a BNIP3-dependent autophagy blockade

Abstract

SARS-CoV-2, the causative virus of COVID-19, continues to threaten global public health. COVID-19 is a multi-organ disease, causing not only respiratory distress, but also extrapulmonary manifestations, including gastrointestinal symptoms with SARS-CoV-2 RNA shedding in stool long after respiratory clearance. Despite global vaccination and existing antiviral treatments, variants of concern are still emerging and circulating. Of note, new Omicron BA.5 sublineages both increasingly evade neutralizing antibodies and demonstrate an increased preference for entry via the endocytic entry route. Alternative to direct-acting antivirals, host-directed therapies interfere with host mechanisms hijacked by viruses, and enhance cell-mediated resistance with a reduced likelihood of drug resistance development. Here, we demonstrate that the autophagy-blocking therapeutic berbamine dihydrochloride robustly prevents SARS-CoV-2 acquisition by human intestinal epithelial cells via an autophagy-mediated BNIP3 mechanism. Strikingly, berbamine dihydrochloride exhibited pan-antiviral activity against Omicron subvariants BA.2 and BA.5 at nanomolar potency, providing a proof of concept for the potential for targeting autophagy machinery to thwart infection of current circulating SARS-CoV-2 subvariants. Furthermore, we show that autophagy-blocking therapies limited virus-induced damage to intestinal barrier function, affirming the therapeutic relevance of autophagy manipulation to avert the intestinal permeability associated with acute COVID-19 and post-COVID-19 syndrome. Our findings underscore that SARS-CoV-2 exploits host autophagy machinery for intestinal dissemination and indicate that repurposed autophagy-based antivirals represent a pertinent therapeutic option to boost protection and ameliorate disease pathogenesis against current and future SARS-CoV-2 variants of concern.

Dengue virus exploits autophagy vesicles and secretory pathways to promote transmission by human dendritic cells

“…Previous reports in human cell lines have demonstrated that LC3+ vesicles can be trafficked for secretion ( 46 , 69 ). In line with these reports, using the standardized autophagy reporter human cell line ( 26 , 50 , 70 ), we observed that fluorescently-labeled intracellular LC3+ vesicles can be released extracellularly ( Supplementary Figure 4 ). Markedly, subsequent immunophenotypical characterization of secreted vesicles by human DCs demonstrated that an average of 26% of the total population of CD9/CD81/CD63+ DC-derived EVs co-expressed the autophagy-associated LC3 marker ( Figures 7C, D ).…”

“…Human DCs are one of the first immune cells to encounter DENV upon a mosquito bite, and due to their migratory capacity and instruction of T cell responses they have been implicated in the facilitation of DENV systemic infection and dengue associated inflammation ( 11 – 14 ). We and others have shown that autophagosomes and autophagy pathways play key defensive or pro-viral roles during viral replication depending on the virus in question ( 26 , 38 , 41 , 46 , 50 ), however the role of autophagy pathways during DENV replication in primary human DCs remains unexplored. First, we confirmed that primary human DCs were infected with DENV-2/16681, as indicated by the presence of the early viral non-structural protein NS3 ( Figures 1A, B ) and viral dsRNA ( Figure 1C ), the latter of which forms as an intermediate during replication of the +ssRNA viral genome.…”

“…We have also recently shown that intrinsically enhanced autophagy correlates with superior antiviral T cell immunity during chronic HIV-1 infection ( 52 ). In the case of SARS-CoV-2, our research indicates that acidifying autophagy vesicles are usurped to promote viral entry ( 50 ), and additional reports indicate that the virus institutes a late block in autophagy flux to avoid autophagic degradation ( 53 ). For flaviviruses such as DENV, triggering of autophagy pathways have been variably associated with either a pro- or anti-viral role in different cellular models ( 18 , 20 , 41 , 42 ).…”

“…However, the impact of autophagy pathways and secretory vesicles on DENV replication and dissemination by human DCs remains elusive. Recently, research from our lab has highlighted the potential of targeting autophagy as a host-directed therapeutic strategy to intervene in replication and transmission of epidemic and pandemic viruses, namely HIV-1 and SARS-CoV-2 ( 26 , 50 ). IV-1 actively blocks autophagy post-entry in DCs ( 27 , 51 ), and autophagy-enhancing drugs decrease HIV-1 transmission by DCs thus underlining the antiviral functioning of autophagy ( 26 ).…”

Morphological and biochemical characteristics associated with autophagy in gastrointestinal diseases

“…Some studies showed that SARS-CoV-2 exploits host autophagy machinery for intestinal dissemination[ 23 , 24 ]. Furthermore, Cloherty et al [ 25 ] proofed that Berbamine, a selection of autophagy-blocking drugs, can suppress intestinal SARS-CoV-2 infection as well as prevent SARS-CoV-2-mediated disruption of the intestinal barrier via an autophagy-mediated BNIP3 mechanism. However, not all viruses have evolved such an escape mechanism.…”