On a path toward a broad-spectrum anti-viral: inhibition of HIV-1 and coronavirus replication by SR kinase inhibitor harmine

Author:

Dahal Subha1ORCID,Clayton Kiera2,Cabral Tyler1,Cheng Ran1,Jahanshahi Shahrzad13,Ahmed Choudhary1,Koirala Amrit45,Villasmil Ocando Alonso6,Malty Ramy37,Been Terek1,Hernandez Javier3,Mangos Maria3,Shen David1,Babu Mohan7,Calarco John8,Chabot Benoit9,Attisano Liliana3,Houry Walid A.310,Cochrane Alan1ORCID

Affiliation:

1. Department of Molecular Genetics, University of Toronto , Toronto, Ontario, Canada

2. Department of Pathology, University of Massachusetts Medical School , Worcester, Massachusetts, USA

3. Department of Biochemistry, University of Toronto , Toronto, Ontario, Canada

4. Department of Molecular and Cellular Biology, Baylor College of Medicine , Houston, Texas, USA

5. Dan L. Duncan Cancer Comprehensive Center, Baylor College of Medicine , Houston, Texas, USA

6. Ragon Institute of MGH, MIT and Harvard , Cambridge, Massachusetts, USA

7. Research and Innovation Centre, Department of Biochemistry, University of Regina , Regina, Saskatchewan, Canada

8. Department of Cell and Systems Biology, University of Toronto , Toronto, Ontario, Canada

9. Department of Microbiology and Infectious Diseases, Université de Sherbrooke , Sherbrooke, Quebec, Canada

10. Department of Chemistry, University of Toronto , Toronto, Ontario, Canada

Abstract

ABSTRACT RNA processing plays a key role in gene expression, allowing for increased protein diversity and functional complexity. Consequently, modulating RNA processing can impact gene function. Given HIV-1’s reliance on host RNA processing machinery for viral protein production/replication, modulators of this process could serve as novel anti-virals to complement and/or enhance existing therapies. In this study, screening of several serine-arginine-rich (SR) kinase inhibitors for their impact on HIV-1 gene expression identified harmine as an inhibitor of HIV-1 gene expression in several cell lines and primary CD4 + T cells/macrophages at low micromolar concentrations with limited cell toxicity. Harmine induced a loss of viral structural protein expression associated with reduced HIV-1 unspliced and singly-spliced HIV-1 RNA levels but limited impact on multiply spliced RNAs. Although harmine is a known inhibitor of both DYRK1A and monoaminoxidase A (MAO A), neither DYRK1A depletion nor other MAO A inhibitors had any effect on HIV-1 expression. However, the compound altered the expression of several other SR kinases in primary CD4 + T cells, increasing CLK1 and reducing CLK2 kinase levels, effects known to regulate HIV-1 expression. Harmine was also unique among the SR kinase inhibitors tested for its ability to suppress replication of a seasonal coronavirus, human coronavirus (HCoV)-229E, and multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants, reducing viral protein expression and virus release. Harmine acts post-entry, arresting virus replication even after the onset of viral protein production. At doses required to suppress HIV-1 replication, harmine had limited impact on the host transcriptome, alternative splicing, or alterative polyadenylation as assessed by RNA-Seq. Together, our study demonstrates the feasibility of targeting host RNA processing to inhibit a range of viruses with minimal impact on the host cell. IMPORTANCE This study highlights the crucial role RNA processing plays in regulating viral gene expression and replication. By targeting SR kinases, we identified harmine as a potent inhibitor of HIV-1 as well as coronavirus (HCoV-229E and multiple SARS-CoV-2 variants) replication. Harmine inhibits HIV-1 protein expression and reduces accumulation of HIV-1 RNAs in both cell lines and primary CD4 + T cells. Harmine also suppresses coronavirus replication post-viral entry by preferentially reducing coronavirus sub-genomic RNA accumulation. By focusing on host factors rather than viral targets, our study offers a novel approach to combating viral infections that is effective against a range of unrelated viruses. Moreover, at doses required to inhibit virus replication, harmine had limited toxicity and minimal effect on the host transcriptome. These findings support the viability of targeting host cellular processes as a means of developing broad-spectrum anti-virals.

Funder

Canadian Foundation for AIDS Research

Gouvernement du Canada | Canadian Institutes of Health Research

PRiME fellowship

Publisher

American Society for Microbiology

Subject

Virology,Insect Science,Immunology,Microbiology

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