Computational design and engineering of self-assembling multivalent microproteins with therapeutic potential against SARS-CoV-2
Abstract Multivalent drugs targeting homo-oligomeric viral surface proteins, such as the SARS-CoV-2 trimeric spike (S) protein, have the potential to elicit more potent and broad-spectrum therapeutic responses than monovalent drugs by synergistically engaging multiple binding sites on viral targets....
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| Format: | Article |
| Language: | English |
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BMC
2024-02-01
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| Series: | Journal of Nanobiotechnology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12951-024-02329-3 |
| _version_ | 1797273415651950592 |
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| author | Qin Qin Xinyi Jiang Liyun Huo Jiaqiang Qian Hongyuan Yu Haixia Zhu Wenhao Du Yuhui Cao Xing Zhang Qiang Huang |
| author_facet | Qin Qin Xinyi Jiang Liyun Huo Jiaqiang Qian Hongyuan Yu Haixia Zhu Wenhao Du Yuhui Cao Xing Zhang Qiang Huang |
| author_sort | Qin Qin |
| collection | DOAJ |
| description | Abstract Multivalent drugs targeting homo-oligomeric viral surface proteins, such as the SARS-CoV-2 trimeric spike (S) protein, have the potential to elicit more potent and broad-spectrum therapeutic responses than monovalent drugs by synergistically engaging multiple binding sites on viral targets. However, rational design and engineering of nanoscale multivalent protein drugs are still lacking. Here, we developed a computational approach to engineer self-assembling trivalent microproteins that simultaneously bind to the three receptor binding domains (RBDs) of the S protein. This approach involves four steps: structure-guided linker design, molecular simulation evaluation of self-assembly, experimental validation of self-assembly state, and functional testing. Using this approach, we first designed trivalent constructs of the microprotein miniACE2 (MP) with different trimerization scaffolds and linkers, and found that one of the constructs (MP-5ff) showed high trimerization efficiency, good conformational homogeneity, and strong antiviral neutralizing activity. With its trimerization unit (5ff), we then engineered a trivalent nanobody (Tr67) that exhibited potent and broad neutralizing activity against the dominant Omicron variants, including XBB.1 and XBB.1.5. Cryo-EM complex structure confirmed that Tr67 stably binds to all three RBDs of the Omicron S protein in a synergistic form, locking them in the “3-RBD-up” conformation that could block human receptor (ACE2) binding and potentially facilitate immune clearance. Therefore, our approach provides an effective strategy for engineering potent protein drugs against SARS-CoV-2 and other deadly coronaviruses. Graphical Abstract |
| first_indexed | 2024-03-07T14:43:05Z |
| format | Article |
| id | doaj.art-cb4440e424064ccc862abc37f57d7d0d |
| institution | Directory Open Access Journal |
| issn | 1477-3155 |
| language | English |
| last_indexed | 2024-03-07T14:43:05Z |
| publishDate | 2024-02-01 |
| publisher | BMC |
| record_format | Article |
| series | Journal of Nanobiotechnology |
| spelling | doaj.art-cb4440e424064ccc862abc37f57d7d0d2024-03-05T20:09:49ZengBMCJournal of Nanobiotechnology1477-31552024-02-0122112010.1186/s12951-024-02329-3Computational design and engineering of self-assembling multivalent microproteins with therapeutic potential against SARS-CoV-2Qin Qin0Xinyi Jiang1Liyun Huo2Jiaqiang Qian3Hongyuan Yu4Haixia Zhu5Wenhao Du6Yuhui Cao7Xing Zhang8Qiang Huang9State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan UniversityState Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan UniversityState Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan UniversityState Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan UniversityACROBiosystems IncState Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan UniversityState Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan UniversityACROBiosystems IncACROBiosystems IncState Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan UniversityAbstract Multivalent drugs targeting homo-oligomeric viral surface proteins, such as the SARS-CoV-2 trimeric spike (S) protein, have the potential to elicit more potent and broad-spectrum therapeutic responses than monovalent drugs by synergistically engaging multiple binding sites on viral targets. However, rational design and engineering of nanoscale multivalent protein drugs are still lacking. Here, we developed a computational approach to engineer self-assembling trivalent microproteins that simultaneously bind to the three receptor binding domains (RBDs) of the S protein. This approach involves four steps: structure-guided linker design, molecular simulation evaluation of self-assembly, experimental validation of self-assembly state, and functional testing. Using this approach, we first designed trivalent constructs of the microprotein miniACE2 (MP) with different trimerization scaffolds and linkers, and found that one of the constructs (MP-5ff) showed high trimerization efficiency, good conformational homogeneity, and strong antiviral neutralizing activity. With its trimerization unit (5ff), we then engineered a trivalent nanobody (Tr67) that exhibited potent and broad neutralizing activity against the dominant Omicron variants, including XBB.1 and XBB.1.5. Cryo-EM complex structure confirmed that Tr67 stably binds to all three RBDs of the Omicron S protein in a synergistic form, locking them in the “3-RBD-up” conformation that could block human receptor (ACE2) binding and potentially facilitate immune clearance. Therefore, our approach provides an effective strategy for engineering potent protein drugs against SARS-CoV-2 and other deadly coronaviruses. Graphical Abstracthttps://doi.org/10.1186/s12951-024-02329-3SARS-CoV-2Protein therapeuticsMicroproteinNanobodyComputational designCryo-EM |
| spellingShingle | Qin Qin Xinyi Jiang Liyun Huo Jiaqiang Qian Hongyuan Yu Haixia Zhu Wenhao Du Yuhui Cao Xing Zhang Qiang Huang Computational design and engineering of self-assembling multivalent microproteins with therapeutic potential against SARS-CoV-2 Journal of Nanobiotechnology SARS-CoV-2 Protein therapeutics Microprotein Nanobody Computational design Cryo-EM |
| title | Computational design and engineering of self-assembling multivalent microproteins with therapeutic potential against SARS-CoV-2 |
| title_full | Computational design and engineering of self-assembling multivalent microproteins with therapeutic potential against SARS-CoV-2 |
| title_fullStr | Computational design and engineering of self-assembling multivalent microproteins with therapeutic potential against SARS-CoV-2 |
| title_full_unstemmed | Computational design and engineering of self-assembling multivalent microproteins with therapeutic potential against SARS-CoV-2 |
| title_short | Computational design and engineering of self-assembling multivalent microproteins with therapeutic potential against SARS-CoV-2 |
| title_sort | computational design and engineering of self assembling multivalent microproteins with therapeutic potential against sars cov 2 |
| topic | SARS-CoV-2 Protein therapeutics Microprotein Nanobody Computational design Cryo-EM |
| url | https://doi.org/10.1186/s12951-024-02329-3 |
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