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Mravic M, He L, Kratochvil HT, Hu H, Nick SE, Bai W, Edwards A, Jo H, Wu Y, DiMaio D, DeGrado WF. De novo-designed transmembrane proteins bind and regulate a cytokine receptor. Nat Chem Biol 2024; 20:751-760. [PMID: 38480980 PMCID: PMC11142920 DOI: 10.1038/s41589-024-01562-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 01/25/2024] [Indexed: 05/30/2024]
Abstract
Transmembrane (TM) domains as simple as a single span can perform complex biological functions using entirely lipid-embedded chemical features. Computational design has the potential to generate custom tool molecules directly targeting membrane proteins at their functional TM regions. Thus far, designed TM domain-targeting agents have been limited to mimicking the binding modes and motifs of natural TM interaction partners. Here, we demonstrate the design of de novo TM proteins targeting the erythropoietin receptor (EpoR) TM domain in a custom binding topology competitive with receptor homodimerization. The TM proteins expressed in mammalian cells complex with EpoR and inhibit erythropoietin-induced cell proliferation. In vitro, the synthetic TM domain complex outcompetes EpoR homodimerization. Structural characterization reveals that the complex involves the intended amino acids and agrees with our designed molecular model of antiparallel TM helices at 1:1 stoichiometry. Thus, membrane protein TM regions can now be targeted in custom-designed topologies.
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Affiliation(s)
- Marco Mravic
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA.
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Li He
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Huong T Kratochvil
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA
- Department of Chemistry, University of North Carolina Chapel Hill, Chapel Hill, NC, USA
| | - Hailin Hu
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Sarah E Nick
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA
| | - Weiya Bai
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Anne Edwards
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Hyunil Jo
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA
| | - Yibing Wu
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA
| | - Daniel DiMaio
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, USA.
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA.
- Yale Cancer Center, New Haven, CT, USA.
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA.
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2
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Mravic M, He L, Kratochvil H, Hu H, Nick SE, Bai W, Edwards A, Jo H, Wu Y, DiMaio D, DeGrado WF. Designed Transmembrane Proteins Inhibit the Erythropoietin Receptor in a Custom Binding Topology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.13.526773. [PMID: 36824741 PMCID: PMC9949092 DOI: 10.1101/2023.02.13.526773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Transmembrane (TM) domains as simple as a single span can perform complex biological functions using entirely lipid-embedded chemical features. Computational design has potential to generate custom tool molecules directly targeting membrane proteins at their functional TM regions. Thus far, designed TM domain-targeting agents have been limited to mimicking binding modes and motifs of natural TM interaction partners. Here, we demonstrate the design of de novo TM proteins targeting the erythropoietin receptor (EpoR) TM domain in a custom binding topology competitive with receptor homodimerization. The TM proteins expressed in mammalian cells complex with EpoR and inhibit erythropoietin-induced cell proliferation. In vitro, the synthetic TM domain complex outcompetes EpoR homodimerization. Structural characterization reveals that the complex involves the intended amino acids and agrees with our designed molecular model of antiparallel TM helices at 1:1 stoichiometry. Thus, membrane protein TM regions can now be targeted in custom designed topologies.
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3
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Zhang B, Peng Y, Wang Y, Wang X. Exploring the trimerization process of a transmembrane helix with an ionizable residue by molecular dynamics simulations: a case study of transmembrane domain 5 of LMP-1. Phys Chem Chem Phys 2022; 24:7084-7092. [PMID: 35262149 DOI: 10.1039/d2cp00102k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The oligomerization of membrane proteins is an important biological process that plays a critical role in the initialization of membrane protein receptor signaling. Unveiling how transmembrane segments oligomerize is critical for understanding the mechanism of membrane receptor signaling activation. Owing to the complicated membrane environment and the extraordinary dynamic properties of the ionizable residues in the transmembrane segment, it is extremely challenging to thoroughly understand the oligomerization process of the transmembrane domain. In this study, transmembrane domain 5 (TMD5) of latent membrane protein-1 from Epstein-Barr virus was used as a prototype model to investigate the trimerization process of the transmembrane segment with ionizable residues. The trimerization process of TMD5 was rebuilt and investigated via conventional molecular dynamics simulations and constant-pH molecular dynamics simulations. When TMD5s approached each other, the tilting angles of the TMD5 monomer decreased. TMD5s formed stable trimers until two interacting sites (D150s and Q139s) along each transmembrane helix were created to lock the TMD5s. The pKa values of D150 shifted toward neutral states in the membrane environment. When TMD5s were monomers, the pKa shift of D150 was mainly influenced by its microenvironment in the lipid bilayer. When TMD5s were moving close to each other, protein-protein interactions became the main contributing factor for the pKa shift of D150s. Overall, this work elucidates the behavior of the TMD5 helix and the pKa shift of ionizable residue D150 in the process of TMD5 oligomerization. This study may provide insight into the development of agents for targeting the oligomerization of membrane proteins.
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Affiliation(s)
- Bo Zhang
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China. .,Department of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Yinghua Peng
- State Key Laboratory for Molecular Biology of Special Economic Animal, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, Jilin, 130112, China
| | - Yibo Wang
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China.
| | - Xiaohui Wang
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China. .,Department of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, China.,Beijing National Laboratory for Molecular Sciences, Beijing, 100190, China
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Zhang B, Jin Y, Zhang L, Wang H, Wang X. Pentamidine Ninety Years on: the Development and Applications of Pentamidine and its Analogs. Curr Med Chem 2022; 29:4602-4609. [PMID: 35289252 DOI: 10.2174/0929867329666220314121446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/25/2021] [Accepted: 01/07/2022] [Indexed: 11/22/2022]
Abstract
Pentamidine, an FDA-approved human drug for many protozoal infections, was initially synthesized in the late 1930s and first reported to be curative for parasitosis in the 1940s. After ninety years of sometimes quiet growth, pentamidine and its derivatives have gone far beyond antibacterial agents, including but not limited to the ligands of DNA minor groove, modulators of PPIs (protein-protein interactions) of the transmembrane domain 5 of lateral membrane protein 1, and the blockers of the SARS-CoV-2 3a channel. This mini review highlights the development and applications of pentamidine and its analogs, aiming to provide insights for further developing pentamidine derivatives in the following decades.
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Affiliation(s)
- Bo Zhang
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, China;
- Department of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui, China
| | - Yushan Jin
- Department of Immunology and Department of Cell & Systems Biology, University of Toronto, Toronto, M5S 3G3, Canada
| | - Lei Zhang
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, China
| | - Hongshuang Wang
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, China
| | - Xiaohui Wang
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, China;
- Department of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui, China
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5
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Wang Y, Zhang B, Lin C, Liu Y, Yang M, Peng Y, Wang X. Dissecting Role of Charged Residue from Transmembrane Domain 5 of Latent Membrane Protein 1 via In Silico Simulations and Wet-Lab Experiments. J Phys Chem B 2021; 125:2124-2133. [PMID: 33595309 DOI: 10.1021/acs.jpcb.0c10708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Charged residues are frequently found in the transmembrane segments of membrane proteins, which reside in the hydrophobic bilayer environment. Charged residues are critical for the function of membrane protein. However, studies of their role in protein oligomerization are limited. By taking the fifth transmembrane domain (TMD5) of latent membrane protein 1 from the Epstein-Barr virus as a prototype model, in silico simulations and wet-lab experiments were performed to investigate how the charged states affect transmembrane domain oligomerization. Molecular dynamics (MD) simulations showed that the D150-protonated TMD5 trimer was stable, whereas unprotonated D150 created bends in the helices which distort the trimeric structure. D150 was mutated to asparagine to mimic the protonated D150 in TMD5, and the MD simulations of different D150N TMD5 trimers supported that the protonation state of D150 was critical for the trimerization of TMD5. In silico mutations found that D150N TMD5 preferred to interact with TMD5 to form the heterotrimer (1 D150N TMD5:2 protonated TMD5s) rather than the heterotrimer (2 D150N TMD5s:1 protonated TMD5). D150R TMD5 interacted with TMD5 to form the heterotrimer (1 D150R TMD5:2 protonated TMD5). These in silico results imply that D150N TMD5 and D150R TMD5 peptides may be probes for disrupting TMD5 trimerization, which was supported by the dominant-negative ToxR assay in bacterial membranes. In all, this study elucidates the role of charged residues at the membrane milieu in membrane protein oligomerization and provides insight into the development of oligomerization-regulating peptides for modulating transmembrane domain lateral interactions.
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Affiliation(s)
- Yibo Wang
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin China, 130022
| | - Bo Zhang
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin China, 130022.,Department of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui China, 230026
| | - Cong Lin
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin China, 130022
| | - Ying Liu
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, Jilin China, 130112
| | - Min Yang
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, Jilin China, 130112
| | - Yinghua Peng
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, Jilin China, 130112
| | - Xiaohui Wang
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin China, 130022.,Department of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui China, 230026
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Targeting the transmembrane domain 5 of latent membrane protein 1 using small molecule modulators. Eur J Med Chem 2021; 214:113210. [PMID: 33550183 DOI: 10.1016/j.ejmech.2021.113210] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 01/14/2021] [Accepted: 01/14/2021] [Indexed: 12/16/2022]
Abstract
Protein-protein interactions (PPIs) play a critical role in living cells and represent promising targets for the drug discovery and life sciences communities. However, lateral transmembrane PPIs are difficult targets for small-molecule inhibitor development given less structural information is known and fewer ligand discovery methods have been explored compared to soluble proteins. In this study, the interactions of the transmembrane domain 5 (TMD-5) of latent membrane protein 1 (LMP-1) of Epstein-Barr virus (EBV) were disrupted by pentamidine derivatives to curb the committed step of EBV infection. A pentamidine derivative 2 with a 7-atom di-amide linker had the best activity whilst switching the amide regiochemistry in the linker influenced membrane permeability and abolished anti TMD-5 activity. Molecular dynamics simulations were performed to understand the interaction between pentamidine derivatives and TMD-5, and to rationalise the observed structure-activity relationships. This study explicitly demonstrated that the interaction of small molecule with lipid should be considered alongside interaction with the protein target when designing small molecules targeting the PPIs of TMDs. In all, this study provides proof of concept for the rational design of small molecules targeting transmembrane PPIs.
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7
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Oligomerization analysis as a tool to elucidate the mechanism of EBV latent membrane protein 1 inhibition by pentamidine. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183380. [DOI: 10.1016/j.bbamem.2020.183380] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/27/2020] [Accepted: 05/28/2020] [Indexed: 01/06/2023]
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Barreto CAV, Baptista SJ, Preto AJ, Matos-Filipe P, Mourão J, Melo R, Moreira I. Prediction and targeting of GPCR oligomer interfaces. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 169:105-149. [PMID: 31952684 DOI: 10.1016/bs.pmbts.2019.11.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
GPCR oligomerization has emerged as a hot topic in the GPCR field in the last years. Receptors that are part of these oligomers can influence each other's function, although it is not yet entirely understood how these interactions work. The existence of such a highly complex network of interactions between GPCRs generates the possibility of alternative targets for new therapeutic approaches. However, challenges still exist in the characterization of these complexes, especially at the interface level. Different experimental approaches, such as FRET or BRET, are usually combined to study GPCR oligomer interactions. Computational methods have been applied as a useful tool for retrieving information from GPCR sequences and the few X-ray-resolved oligomeric structures that are accessible, as well as for predicting new and trustworthy GPCR oligomeric interfaces. Machine-learning (ML) approaches have recently helped with some hindrances of other methods. By joining and evaluating multiple structure-, sequence- and co-evolution-based features on the same algorithm, it is possible to dilute the issues of particular structures and residues that arise from the experimental methodology into all-encompassing algorithms capable of accurately predict GPCR-GPCR interfaces. All these methods used as a single or a combined approach provide useful information about GPCR oligomerization and its role in GPCR function and dynamics. Altogether, we present experimental, computational and machine-learning methods used to study oligomers interfaces, as well as strategies that have been used to target these dynamic complexes.
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Affiliation(s)
- Carlos A V Barreto
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Salete J Baptista
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, CTN, LRS, Portugal
| | - António José Preto
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Pedro Matos-Filipe
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Joana Mourão
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Rita Melo
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, CTN, LRS, Portugal
| | - Irina Moreira
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Science and Technology Faculty, University of Coimbra, Coimbra, Portugal.
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