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)....

The stress response is an essential mechanism for maintaining homeostasis, and its disruption is implicated in several psychiatric disorders. On the cellular level, stress activates, among other mechanisms, autophagy that regulates homeostasis through protein degradation and recycling. Secretory autophagy is a recently described pathway in which autophagosomes fuse with the plasma membrane rather than with lysosomes. Here, we demonstrate that glucocorticoid-mediated stress enhances secretory autophagy via the stress-responsive co-chaperone FK506-binding protein 51. We identify the matrix metalloproteinase 9 (MMP9) as one of the proteins secreted in response to stress. Using cellular assays and in vivo microdialysis, we further find that stress-enhanced MMP9 secretion increases the cleavage of pro-brain-derived neurotrophic factor (proBDNF) to its mature form (mBDNF). BDNF is essential for adult synaptic plasticity and its pathway is associated with major depression and posttraumatic stress disorder. These findings unravel a cellular stress adaptation mechanism that bears the potential of opening avenues for the understanding of the pathophysiology of stress-related disorders.

Due to its important roles in oncogenic signaling, AKT has been subjected to extensive drug discovery efforts leading to small molecule inhibitors investigated in advanced clinical trials. To better understand how these drugs exert their therapeutic effects at the molecular level, we combined chemoproteomic target affinity profiling using kinobeads and phosphoproteomics to analyze the five clinical AKT inhibitors AZD5363 (Capivasertib), GSK2110183 (Afuresertib), GSK690693, Ipatasertib, and MK-2206 in BT-474 breast cancer cells. Kinobead profiling identified between four and 29 nM targets for these compounds and showed that AKT1 and AKT2 were the only common targets. Similarly, measuring the response of the phosphoproteome to the same inhibitors identified ∼1700 regulated phosphorylation sites, 276 of which were perturbed by all five compounds. This analysis expanded the known AKT signaling network by 119 phosphoproteins that may represent direct or indirect targets of AKT. Within this new network, 41 regulated phosphorylation sites harbor the AKT substrate motif, and recombinant kinase assays validated 16 as novel AKT substrates. These included CEP170 and FAM83H, suggesting a regulatory function of AKT in mitosis and cytoskeleton organization. In addition, a specific phosphorylation pattern on the ULK1-FIP200-ATG13-VAPB complex was found to determine the active state of ULK1, leading to elevated autophagy in response to AKT inhibition.

Disturbed activation or regulation of the stress response through the hypothalamic-pituitary-adrenal (HPA) axis is a fundamental component of multiple stress-related diseases, including psychiatric, metabolic, and immune disorders. The FK506 binding protein 51 (FKBP5) is a negative regulator of the glucocorticoid receptor (GR), the main driver of HPA axis regulation, and FKBP5 polymorphisms have been repeatedly linked to stress-related disorders in humans. However, the specific role of Fkbp5 in the paraventricular nucleus of the hypothalamus (PVN) in shaping HPA axis (re)activity remains to be elucidated. We here demonstrate that the deletion of Fkbp5 in Sim1+ neurons dampens the acute stress response and increases GR sensitivity. In contrast, Fkbp5 overexpression in the PVN results in a chronic HPA axis over-activation, and a PVN-specific rescue of Fkbp5 expression in full Fkbp5 KO mice normalizes the HPA axis phenotype. Single-cell RNA sequencing revealed the cell-type-specific expression pattern of Fkbp5 in the PVN and showed that Fkbp5 expression is specifically upregulated in Crh+ neurons after stress. Finally, Crh-specific Fkbp5 overexpression alters Crh neuron activity, but only partially recapitulates the PVN-specific Fkbp5 overexpression phenotype. Together, the data establish the central and cell-type-specific importance of Fkbp5 in the PVN in shaping HPA axis regulation and the acute stress response.

Highlights d FKBP5 and MRs, but not GRs, exhibit similar hippocampal expression patterns d MRs, rather than GRs, regulate FKBP5 expression in hippocampal neurons at baseline d Inhibition and deletion of MRs decrease hippocampal Fkbp5 mRNA levels in vivo d Forebrain MR deletion leads to GR hypersensitivity during acute stress

Subtype selectivity represents ac hallenge in many drug discovery campaigns.Atypical example is the FK506 binding protein 51 (FKBP51), whichh as emerged as an attractive drug target. The most advanced FKBP51 ligands of the SAFit class are highly selective vs.F KBP52 but poorly discriminate against the homologs and off-targets FKBP12 and FKBP12.6. During am acrocyclization pilot study,w eo bserved that many of these macrocyclic analogs have unanticipated and unprecedented preference for FKBP51 over FKBP12 and FKBP12.6. Structural studies revealed that these macrocycles bind with anew binding mode featuring atransient conformation, which is disfavored for the small FKBPs.Using aconformation-sensitive assayweshow that this binding mode occurs in solution and is characteristic for this new class of compounds.T he discovered macrocycles are non-immunosuppressive,e ngage FKBP51 in cells,a nd blockt he cellular effect of FKBP51 on IKKa.O ur findings provide an ew chemical scaffold for improved FKBP51 ligands and the structural basis for enhanced selectivity.

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