Bromodomain Inhibition Blocks Inflammation-Induced Cardiac Dysfunction and SARS-CoV2 Infection (preprint)

Cardiac injury and dysfunction occur in COVID-19 patients and increase the risk of mortality. Causes are ill defined, but could be direct cardiac infection and/or ‘cytokine-storm’ induced dysfunction. To identify mechanisms and discover cardio-protective drugs, we use a state-of-the-art pipeline combining human cardiac organoids with high throughput phosphoproteomics and single nuclei RNA sequencing. We identify that ‘cytokine-storm’ induced diastolic dysfunction can be caused by a cocktail of interferon gamma, interleukin 1β and poly(I:C) and also human COVID-19 serum. Bromodomain protein 4 (BRD4) is activated along with pathology driving fibrotic and induced nitric oxide synthase genes. BRD inhibitors fully recover function in hCO and totally prevent death in a cytokine-storm mouse model. BRD inhibition decreases transcription of multiple genes, including fibrotic, induced nitric oxide synthase and ACE2, and prevention of cardiac infection with SARS-CoV2. Thus, BRD inhibitors are promising candidates to prevent COVID-19 mediated cardiac damage.Funding: We acknowledge grant and fellowship support from the National Health and Medical Research Council of Australia (J.E.H., M.J.S., C.R.E., T.B.), Heart Foundation of Australia (J.E.H.), QIMR Berghofer Medical Research Institute (J.E.H.), The Stafford Fox Foundation (E.R.P.), the Royal Children’s Hospital Foundation (E.R.P.), Australian Research Council Strategic Initiative in Stem Cell Science (Stem Cells Australia) (E.R.P. and J.E.H.) and the Medical Research Future Fund (MRFF9200008) (J.E.H., T.B., M.J.S., K.P.A.MD., C.R.E., E.R.P.). M.J.S. is supported by Health and Medical Research Council of Australia Program (APP1132519) and Investigator (APP1173958) grants. A.S. is also supported by Investigator grant (APP1173880). The Murdoch Children’s Research Institute is supported by the Victorian Government’s Operational Infrastructure Support Program. This project received support from Dynomics Inc. J.E.H. is supported by a Snow Medical Fellowship. Conflict of Interest: R.J.M., J.E.H., G.A.Q.-R., D.M.T. and E.R.P. are listed as co-inventors on pending patents held by The University of Queensland and QIMR Berghofer Medical Research Institute that relate to cardiac organoid maturation and putative cardiac regeneration therapeutics. J.E.H. is a coinventor on licensed patents held by the University of Goettingen. R.J.M, E.R.P., D.M.T., B.G. and J.E.H. are co-founders, scientific advisors and stockholders in Dynomics Inc. D.M.T. and B.G. are employees of Dynomics Inc. /Dynomics Pty Ltd. QIMR Berghofer Medical Research Institute has filed a patent on the use of BRD inhibitors. Ethical Approval: Animal work was approved by the QIMR Berghofer Medical Research Institute Animal Ethics Committee. Ethical approval for the use of human embryonic stem cells (hESCs) was obtained from QIMR Berghofer’s Ethics Committee and was carried out in accordance with the National Health and Medical Research Council of Australia (NHMRC) regulations. Procedures complied with standards set under Australian guidelines for animal welfare and experiments were subject to Monash University animal welfare ethics review (Approval #MARP/2019/13606).

Discovery of drugs to treat cytokine storm-induced cardiac dysfunction using human cardiac organoids (preprint)

SARS-CoV2 infection leads to cardiac injury and dysfunction in 20-30% of hospitalized patients1 and higher rates of mortality in patients with pre-existing cardiovascular disease2,3. Inflammatory factors released as part of the cytokine storm are thought to play a critical role in cardiac dysfunction in severe COVID-19 patients4. Here we use human cardiac organoids combined with high sensitivity phosphoproteomics and single nuclei RNA sequencing to identify inflammatory targets inducing cardiac dysfunction. This state-of-the-art pipeline allowed rapid deconvolution of mechanisms and identification of putative therapeutics. We identify a novel interferon-{gamma} driven BRD4 (bromodomain protein 4)-fibrosis/iNOS axis as a key intracellular mediator of inflammation-induced cardiac dysfunction. This axis is therapeutically targetable using BRD4 inhibitors, which promoted full recovery of function in human cardiac organoids and prevented severe inflammation and death in a cytokine-storm mouse model. The BRD inhibitor INCB054329 was the most efficacious, and is a prime candidate for drug repurposing to attenuate cardiac dysfunction and improve COVID-19 mortality in humans.

Dynamics of the N-terminal domain of SARS-CoV-2 nucleocapsid protein drives dsRNA melting in a counterintuitive tweezer-like mechanism (preprint)

The N protein of betacoronaviruses is responsible for nucleocapsid assembly and other essential regulatory functions. Its N-terminal domain (NTD) interacts and melts the double-stranded transcriptional regulatory sequences (dsTRS), regulating the discontinuous subgenome transcription process. Here, we used molecular dynamics (MD) simulations to study the binding of SARS-CoV-2 N-NTD to non-specific (NS) and TRS dsRNAs. We probed dsRNAs Watson and Crick (WC) base-pairing over 25 replicas of 100 ns MD simulations, showing that only one N-NTD of dimeric N is enough to destabilize dsRNAs, initiating melting. N-NTD dsRNA destabilizing activity was more efficient for dsTRS than dsNS. N-NTD dynamics, especially a tweezer-like motion of {beta}2-{beta}3 and * 2-{beta}5 loops, played a key role in WC base-pairing destabilization. Based on experimental information available in the literature, we constructed kinetics models for N-NTD-mediated dsRNA melting. Our results support a 1:1 stoichiometry (N-NTD:dsRNA), matching MD simulations and raising different possibilities for N-NTD action: (i) two N-NTDs of dimeric N would act independently, increasing efficiency; (ii) two N-NTDs of dimeric N would bind to two different RNA sites, bridging distant regions of the genome; and (iii) monomeric N would be active, opening up the possibility of a regulatory dissociation event.

An hACE2 peptide mimic blocks SARS-CoV-2 Pulmonary Cell Infection (preprint)

In the light of the recent accumulated knowledge on SARS-CoV-2 and its mode of human cells invasion, the binding of viral spike glycoprotein to human Angiotensin Converting Enzyme 2 (hACE2) receptor plays a central role in cell entry. We designed a series of peptides mimicking the N-terminal helix of hACE2 protein which contains most of the contacting residues at the binding site and have a high helical folding propensity in aqueous solution. Our best peptide mimic binds to the virus spike protein with high affinity and is able to block SARS-CoV-2 human pulmonary cell infection with an inhibitory concentration (IC50) in the nanomolar range. This first in class blocking peptide mimic represents a powerful tool that might be used in prophylactic and therapeutic approaches to fight the coronavirus disease 2019 (COVID-19). In BriefHelical peptide mimicking H1 helix of hACE2 and composed of only natural amino acids binds to SARS-CoV-2 spike protein with high affinity and blocks human pulmonary cells infection with IC50 in the nM range. HighlightsA peptide mimic of hACE2 designed from H1 helix and composed of only natural amino acids show high helical folding propensity in aqueous media. This peptide mimic binds to virus spike RBD with high affinity (sub-nM range). This peptide mimic blocks SARS-CoV-2 pulmonary cells infection with an IC50 in the nM range. This peptide mimic is devoid of toxicity on pulmonary cells.

A negative feedback model to explain regulation of SARS-CoV-2 replication and transcription (preprint)

BackgroundCoronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although a preliminary understanding of the replication and transcription mechanisms of SARS-CoV-2 has recently emerged, their regulation remains unclear. ResultsBased on reanalysis of public data, we propose a negative feedback model to explain the regulation of replication and transcription in--but not limited to--SARS-CoV-2. The key step leading to new discoveries was the identification of the cleavage sites of nsp15--an RNA uridylate-specific endoribonuclease, encoded by CoVs. According to this model, nsp15 regulates the synthesis of subgenomic RNAs (sgRNAs) and genomic RNAs (gRNAs) by cleaving transcription regulatory sequences in the body. The expression level of nsp15 determines the relative proportions of sgRNAs and gRNAs, which in turn change the expression level of nps15 to reach equilibrium between the replication and transcription of CoVs. ConclusionsThe replication and transcription of CoVs are regulated by a negative feedback mechanism that influences the persistence of CoVs in hosts. Our findings enrich fundamental knowledge in the field of gene expression and its regulation, and provide new clues for future studies. One important clue is that nsp15 may be an important and ideal target for the development of drugs (e.g. uridine derivatives) against CoVs.