Phospholipidosis is a shared mechanism underlying the in vitro antiviral activity of many repurposed drugs against SARS-CoV-2

Repurposing drugs as treatments for COVID-19 has drawn much attention. A common strategy has been to screen for established drugs, typically developed for other indications, that are antiviral in cells or organisms. Intriguingly, most of the drugs that have emerged from these campaigns, though diverse in structure, share a common physical property: cationic amphiphilicity. Provoked by the similarity of these repurposed drugs to those inducing phospholipidosis, a well-known drug side effect, we investigated phospholipidosis as a mechanism for antiviral activity. We tested 23 cationic amphiphilic drugs—including those from phenotypic screens and others that we ourselves had found—for induction of phospholipidosis in cell culture. We found that most of the repurposed drugs, which included hydroxychloroquine, azithromycin, amiodarone, and four others that have already progressed to clinical trials, induced phospholipidosis in the same concentration range as their antiviral activity; indeed, there was a strong monotonic correlation between antiviral efficacy and the magnitude of the phospholipidosis. Conversely, drugs active against the same targets that did not induce phospholipidosis were not antiviral. Phospholipidosis depends on the gross physical properties of drugs, and does not reflect specific target-based activities, rather it may be considered a confound in early drug discovery. Understanding its role in infection, and detecting its effects rapidly, will allow the community to better distinguish between drugs and lead compounds that more directly impact COVID-19 from the large proportion of molecules that manifest this confounding effect, saving much time, effort and cost. One Sentence Summary Drug-induced phospholipidosis is a single mechanism that may explain the in vitro efficacy of a wide-variety of therapeutics repurposed for COVID-19. ### Competing Interest Statement B.F., A.F., H.S., L.U., F.M, & F.P are employees of Novartis. A.C.K. is a founder and advisor to Tectonic Therapeutic, Inc., and the Institute for Protein Innovation. K.M.S. has consulting agreements for the following companies, which involve monetary and/or stock compensation: Black Diamond Therapeutics, BridGene Biosciences, Denali Therapeutics, Dice Molecules, eFFECTOR Therapeutics, Erasca, Genentech/Roche, Janssen Pharmaceuticals, Kumquat Biosciences, Kura Oncology, Merck, Mitokinin, Petra Pharma, Revolution Medicines, Type6 Therapeutics, Venthera, Wellspring Biosciences. The Krogan Laboratory has received research support from Vir Biotechnology and F. Hoffmann-La Roche. N.J.K. has consulting agreements with Maze Therapeutics and Interline Therapeutics and is a shareholder of Tenaya Therapeutics. The Garcia-Sastre Laboratory has received research support from Pfizer, Senhwa Biosciences, and 7Hills Pharma; and A.G.-S. has consulting agreements for the following companies involving cash and/or stock: Vivaldi Biosciences, Contrafect, 7Hills Pharma, Avimex, Valneva, Accurius, and Esperovax. * Terminology : COVID-19 : Coronavirus Disease 2019 SAR : structure-activity relationship CAD : cationic amphiphilic drug DIPL : drug-induced phospholipidosis HCQ : hydroxychloroquine Tc : Tanimoto coefficient EthD-2 : Ethidium homodimer-2