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Spratt AN, Gallazzi F, Quinn TP, Lorson CL, Sönnerborg A, Singh K. Coronavirus helicases: attractive and unique targets of antiviral drug-development and therapeutic patents. Expert Opin Ther Pat 2021; 31:339-350. [PMID: 33593200 PMCID: PMC8074651 DOI: 10.1080/13543776.2021.1884224] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Introduction: Coronaviruses encode a helicase that is essential for viral replication and represents an excellent antiviral target. However, only a few coronavirus helicase inhibitors have been patented. These patents include drug-like compound SSYA10-001, aryl diketo acids (ADK), and dihydroxychromones. Additionally, adamantane-derived bananins, natural flavonoids, one acrylamide derivative [(E)-3-(furan-2-yl)-N-(4-sulfamoylphenyl)acrylamide], a purine derivative (7-ethyl-8-mercapto-3-methyl-3,7-dihydro-1 H-purine-2,6-dione), and a few bismuth complexes. The IC50 of patented inhibitors ranges between 0.82 μM and 8.95 μM, depending upon the assays used. Considering the urgency of clinical interventions against Coronavirus Disease-19 (COVID-19), it is important to consider developing antiviral portfolios consisting of small molecules. Areas covered: This review examines coronavirus helicases as antiviral targets, and the potential of previously patented and experimental compounds to inhibit the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) helicase. Expert opinion: Small molecule coronavirus helicase inhibitors represent attractive pharmacological modalities for the treatment of coronaviruses such as SARS-CoV and SARS-CoV-2. Rightfully so, the current emphasis is focused upon the development of vaccines. However, vaccines may not work for everyone and broad-based adoption of vaccinations is an increasingly challenging societal endeavor. Therefore, it is important to develop additional pharmacological antivirals against the highly conserved coronavirus helicases to broadly protect against this and subsequent coronavirus epidemics.
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Affiliation(s)
- Austin N Spratt
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Fabio Gallazzi
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.,Department of Chemistry, University of Missouri, Columbia, MO, USA
| | - Thomas P Quinn
- cDepartment of Biochemistry, University of Missouri, Columbia, MO, USA
| | - Christian L Lorson
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.,dDepartment of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA
| | - Anders Sönnerborg
- eDivision of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Huddinge, Stockholm, Sweden.,fDepartment of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA
| | - Kamal Singh
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.,Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA.,Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Huddinge, Stockholm, Sweden.,gSanctum Therapeutics Corporation, Sunnyvale, CA, USA
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Yerukhimovich MM, Marohnic CC, Frick DN. Role of the Conserved DECH-Box Cysteine in Coupling Hepatitis C Virus Helicase-Catalyzed ATP Hydrolysis to RNA Unwinding. Biochemistry 2018; 57:6247-6255. [PMID: 30281972 DOI: 10.1021/acs.biochem.8b00796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DECH-box proteins are a subset of DExH/D-box superfamily 2 helicases possessing a conserved Asp-Glu-Cys-His motif in their ATP binding site. The conserved His helps position the Asp and Glu residues, which coordinate the divalent metal cation that connects the protein to ATP and activate the water molecule needed for ATP hydrolysis, but the role of the Cys is still unclear. This study uses site-directed mutants of the model DECH-box helicase encoded by the hepatitis C virus (HCV) to examine the role of the Cys in helicase action. Proteins lacking a Cys unwound DNA less efficiently than wild-type proteins did. For example, at low protein concentrations, a helicase harboring a Gly instead of the DECH-box Cys unwound DNA more slowly than the wild-type helicase did, but at higher protein concentrations, the two proteins unwound DNA at similar rates. All HCV proteins analyzed had similar affinities for ATP and nucleic acids and hydrolyzed ATP in the presence of RNA at similar rates. However, in the absence of RNA, all proteins lacking a DECH-box cysteine hydrolyzed ATP 10-15 times faster with higher Km values, and lower apparent affinities for metal ions, compared to those observed with wild-type proteins. These differences were observed with proteins isolated from HCV genotypes 2a and 1b, suggesting that this role is conserved. These data suggest the helicase needs Cys292 to bind ATP in a state where ATP is not hydrolyzed until RNA binds.
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Affiliation(s)
- Mark M Yerukhimovich
- Department of Chemistry & Biochemistry , University of Wisconsin-Milwaukee , Milwaukee , Wisconsin 53211 , United States
| | - Christopher C Marohnic
- Abbott Laboratories , 100 Abbott Park Road , Abbott Park , Illinois 60064 , United States
| | - David N Frick
- Department of Chemistry & Biochemistry , University of Wisconsin-Milwaukee , Milwaukee , Wisconsin 53211 , United States
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Büttner K, Nehring S, Hopfner KP. Structural basis for DNA duplex separation by a superfamily-2 helicase. Nat Struct Mol Biol 2007; 14:647-52. [PMID: 17558417 DOI: 10.1038/nsmb1246] [Citation(s) in RCA: 249] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2007] [Accepted: 04/06/2007] [Indexed: 11/08/2022]
Abstract
To reveal the mechanism of processive strand separation by superfamily-2 (SF2) 3'-->5' helicases, we determined apo and DNA-bound crystal structures of archaeal Hel308, a helicase that unwinds lagging strands and is related to human DNA polymerase theta. Our structure captures the duplex-unwinding reaction, shows that initial strand separation does not require ATP and identifies a prominent beta-hairpin loop as the unwinding element. Similar loops in hepatitis C virus NS3 helicase and RNA-decay factors support the idea that this duplex-unwinding mechanism is applicable to a broad subset of SF2 helicases. Comparison with ATP-bound SF2 enzymes suggests that ATP promotes processive unwinding of 1 base pair by ratchet-like transport of the 3' product strand. Our results provide a first structural framework for strand separation by processive SF2 3'-->5' helicases and reveal important mechanistic differences from SF1 helicases.
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Affiliation(s)
- Katharina Büttner
- Center for Integrated Protein Science, Gene Center and Department of Chemistry and Biochemistry, Ludwig-Maximilians-University Munich, Feodor-Lynen-Str. 25, 81377 Munich, Germany
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