Viruses manipulate cellular metabolism and macromolecule recycling processes like autophagy. Dysregulated metabolism might lead to excessive inflammatory and autoimmune responses as observed in severe and long COVID-19 patients. Here we show that SARS-CoV-2 modulates cellular metabolism and reduces autophagy. Accordingly, compound-driven induction of autophagy limits SARS-CoV-2 propagation. In detail, SARS-CoV-2-infected cells show accumulation of key metabolites, activation of autophagy inhibitors (AKT1, SKP2) and reduction of proteins responsible for autophagy initiation (AMPK, TSC2, ULK1), membrane nucleation, and phagophore formation (BECN1, VPS34, ATG14), as well as autophagosome-lysosome fusion (BECN1, ATG14 oligomers). Consequently, phagophore-incorporated autophagy markers LC3B-II and P62 accumulate, which we confirm in a hamster model and lung samples of COVID-19 patients. Single-nucleus and single-cell sequencing of patient-derived lung and mucosal samples show differential transcriptional regulation of autophagy and immune genes depending on cell type, disease duration, and SARS-CoV-2 replication levels. Targeting of autophagic pathways by exogenous administration of the polyamines spermidine and spermine, the selective AKT1 inhibitor MK-2206, and the BECN1-stabilizing anthelmintic drug niclosamide inhibit SARS-CoV-2 propagation in vitro with IC50 values of 136.7, 7.67, 0.11, and 0.13 μM, respectively. Autophagy-inducing compounds reduce SARS-CoV-2 propagation in primary human lung cells and intestinal organoids emphasizing their potential as treatment options against COVID-19.

21Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses an acute threat to public health 22 and the world economy, especially because no approved specific drugs or vaccines are available. 23Pharmacological modulation of metabolism-dependent cellular pathways such as autophagy reduced 24 propagation of highly pathogenic Middle East respiratory syndrome (MERS)-CoV. 25Here we show that SARS-CoV-2 infection limits autophagy by interfering with multiple metabolic 26 pathways and that compound-driven interventions aimed at autophagy induction reduce SARS-CoV-2 27 propagation in vitro. In-depth analyses of autophagy signaling and metabolomics indicate that SARS-28 CoV-2 reduces glycolysis and protein translation by limiting activation of AMP-protein activated kinase 29 (AMPK) and mammalian target of rapamycin complex 1 (mTORC1). Infection also downregulates 30 autophagy-inducing spermidine, and facilitates AKT1/SKP2-dependent degradation of autophagy-31 initiating Beclin-1 (BECN1). Targeting of these pathways by exogenous administration of spermidine, 32AKT inhibitor MK-2206, and the Beclin-1 stabilizing, antihelminthic drug niclosamide inhibited SARS- 33CoV-2 propagation by 85, 88, and >99%, respectively. In sum, SARS-CoV-2 infection causally diminishes 34 autophagy. A clinically approved and well-tolerated autophagy-inducing compound shows potential 35 for evaluation as a treatment against SARS-CoV-2. 36 37 38 (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.The copyright holder for this preprint this version posted April 15, 2020. . https://doi.org/10.1101 3 The current pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses an 39 imminent threat to global health. As of 15 April 2020, 1,878,489 individuals were infected in >200 40 countries, with >119,000 fatalities (1). SARS-CoV-2 infections cause CoV-associated disease 19 (COVID-41 19), which can lead to severe atypical pneumonia in humans (2). Currently, there are no approved 42 therapeutics or vaccines available. The development and licensing of new FDA-approved drugs takes 43 years, which is problematic given the urgent need for effective therapies against novel, rapidly 44 emergent diseases like COVID-19. Antiviral drug screenings are commonly based on testing FDA-45 approved compound libraries against cellular and viral components (3). However, these undirected 46 approaches lack functional insights into how the drugs affect virus propagation. Risk evaluations for 47 drug repurposing and development of new therapeutics would benefit from rational drug design 48 founded on known SARS-CoV-2-host interactions. 49 Compound-based targeting of cellular proteins that are essential for the virus life cycle has led to the 50 discovery of broadly reactive drugs against a range of CoVs (3-6). As virus propagation strongly 51 depends on energy and catabolic substrates of host cells, drug target identification should consider 52 the metabolism of infected cells (3)....