Valproate-coenzyme A conjugate blocks opening of receptor binding domains in the spike trimer of SARS-CoV-2 through an allosteric mechanism
The receptor-binding domains (RBDs) of the SARS-CoV-2 spike trimer exhibit ''up'' and ''down'' conformations often targeted by neutralizing antibodies. Only in the “up” configuration can RBDs bind to the ACE2 receptor of the host cell and initiate the process...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-01-01
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| Series: | Computational and Structural Biotechnology Journal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037023000144 |
| _version_ | 1797384132429348864 |
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| author | Federica Maschietto Tianyin Qiu Jimin Wang Yuanjun Shi Brandon Allen George P. Lisi Elias Lolis Victor S. Batista |
| author_facet | Federica Maschietto Tianyin Qiu Jimin Wang Yuanjun Shi Brandon Allen George P. Lisi Elias Lolis Victor S. Batista |
| author_sort | Federica Maschietto |
| collection | DOAJ |
| description | The receptor-binding domains (RBDs) of the SARS-CoV-2 spike trimer exhibit ''up'' and ''down'' conformations often targeted by neutralizing antibodies. Only in the “up” configuration can RBDs bind to the ACE2 receptor of the host cell and initiate the process of viral multiplication. Here, we identify a lead compound (3-oxo-valproate-coenzyme A conjugate or Val-CoA) that stabilizes the spike trimer with RBDs in the down conformation. Val-CoA interacts with three R408 residues, one from each RBD, which significantly reduces the inter-subunit R408-R408 distance by ∼ 13 Å and closes the central pore formed by the three RBDs. Experimental evidence is presented that R408 is part of a triggering mechanism that controls the prefusion to postfusion state transition of the spike trimer. By stabilizing the RBDs in the down configuration, this and other related compounds can likely attenuate viral transmission. The reported findings for binding of Val-CoA to the spike trimer suggest a new approach for the design of allosteric antiviral drugs that do not have to compete for specific virus-receptor interactions but instead hinder the conformational motion of viral membrane proteins essential for interaction with the host cell. Here, we introduce an approach to target the spike protein by identifying lead compounds that stabilize the RBDs in the trimeric “down” configuration. When these compounds trimerize monomeric RBD immunogens as co-immunogens, they could also induce new types of non-ACE2 blocking antibodies that prevent local cell-to-cell transmission of the virus, providing a novel approach for inhibition of SARS-CoV-2. |
| first_indexed | 2024-03-08T21:31:09Z |
| format | Article |
| id | doaj.art-5916798c559645fa85848f4bb9e34d7b |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-03-08T21:31:09Z |
| publishDate | 2023-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-5916798c559645fa85848f4bb9e34d7b2023-12-21T07:30:45ZengElsevierComputational and Structural Biotechnology Journal2001-03702023-01-012110661076Valproate-coenzyme A conjugate blocks opening of receptor binding domains in the spike trimer of SARS-CoV-2 through an allosteric mechanismFederica Maschietto0Tianyin Qiu1Jimin Wang2Yuanjun Shi3Brandon Allen4George P. Lisi5Elias Lolis6Victor S. Batista7Department of Chemistry, Yale University, New Haven, CT 06520-8449, USADepartment of Chemistry, Yale University, New Haven, CT 06520-8449, USADepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA; Corresponding authors.Department of Chemistry, Yale University, New Haven, CT 06520-8449, USADepartment of Chemistry, Yale University, New Haven, CT 06520-8449, USADepartment of Molecular and Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USADepartment of Pharmacology, Yale University, New Haven, CT 06520-8066, USADepartment of Chemistry, Yale University, New Haven, CT 06520-8449, USA; Corresponding authors.The receptor-binding domains (RBDs) of the SARS-CoV-2 spike trimer exhibit ''up'' and ''down'' conformations often targeted by neutralizing antibodies. Only in the “up” configuration can RBDs bind to the ACE2 receptor of the host cell and initiate the process of viral multiplication. Here, we identify a lead compound (3-oxo-valproate-coenzyme A conjugate or Val-CoA) that stabilizes the spike trimer with RBDs in the down conformation. Val-CoA interacts with three R408 residues, one from each RBD, which significantly reduces the inter-subunit R408-R408 distance by ∼ 13 Å and closes the central pore formed by the three RBDs. Experimental evidence is presented that R408 is part of a triggering mechanism that controls the prefusion to postfusion state transition of the spike trimer. By stabilizing the RBDs in the down configuration, this and other related compounds can likely attenuate viral transmission. The reported findings for binding of Val-CoA to the spike trimer suggest a new approach for the design of allosteric antiviral drugs that do not have to compete for specific virus-receptor interactions but instead hinder the conformational motion of viral membrane proteins essential for interaction with the host cell. Here, we introduce an approach to target the spike protein by identifying lead compounds that stabilize the RBDs in the trimeric “down” configuration. When these compounds trimerize monomeric RBD immunogens as co-immunogens, they could also induce new types of non-ACE2 blocking antibodies that prevent local cell-to-cell transmission of the virus, providing a novel approach for inhibition of SARS-CoV-2.http://www.sciencedirect.com/science/article/pii/S2001037023000144Valproic acidValproateVPA3-oxo-VPAVPA-CoASpike protein |
| spellingShingle | Federica Maschietto Tianyin Qiu Jimin Wang Yuanjun Shi Brandon Allen George P. Lisi Elias Lolis Victor S. Batista Valproate-coenzyme A conjugate blocks opening of receptor binding domains in the spike trimer of SARS-CoV-2 through an allosteric mechanism Computational and Structural Biotechnology Journal Valproic acid Valproate VPA 3-oxo-VPA VPA-CoA Spike protein |
| title | Valproate-coenzyme A conjugate blocks opening of receptor binding domains in the spike trimer of SARS-CoV-2 through an allosteric mechanism |
| title_full | Valproate-coenzyme A conjugate blocks opening of receptor binding domains in the spike trimer of SARS-CoV-2 through an allosteric mechanism |
| title_fullStr | Valproate-coenzyme A conjugate blocks opening of receptor binding domains in the spike trimer of SARS-CoV-2 through an allosteric mechanism |
| title_full_unstemmed | Valproate-coenzyme A conjugate blocks opening of receptor binding domains in the spike trimer of SARS-CoV-2 through an allosteric mechanism |
| title_short | Valproate-coenzyme A conjugate blocks opening of receptor binding domains in the spike trimer of SARS-CoV-2 through an allosteric mechanism |
| title_sort | valproate coenzyme a conjugate blocks opening of receptor binding domains in the spike trimer of sars cov 2 through an allosteric mechanism |
| topic | Valproic acid Valproate VPA 3-oxo-VPA VPA-CoA Spike protein |
| url | http://www.sciencedirect.com/science/article/pii/S2001037023000144 |
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