1
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Li Y, Wu M, Fu Y, Xue J, Yuan F, Qu T, Rissanou AN, Wang Y, Li X, Hu H. Therapeutic stapled peptides: Efficacy and molecular targets. Pharmacol Res 2024; 203:107137. [PMID: 38522761 DOI: 10.1016/j.phrs.2024.107137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/06/2024] [Accepted: 03/06/2024] [Indexed: 03/26/2024]
Abstract
Peptide stapling, by employing a stable, preformed alpha-helical conformation, results in the production of peptides with improved membrane permeability and enhanced proteolytic stability, compared to the original peptides, and provides an effective solution to accelerate the rapid development of peptide drugs. Various reviews present peptide stapling chemistries, anchoring residues and one- or two-component cyclization, however, therapeutic stapled peptides have not been systematically summarized, especially focusing on various disease-related targets. This review highlights the latest advances in therapeutic peptide drug development facilitated by the application of stapling technology, including different stapling techniques, synthetic accessibility, applicability to biological targets, potential for solving biological problems, as well as the current status of development. Stapled peptides as therapeutic drug candidates have been classified and analysed mainly by receptor- and ligand-based stapled peptide design against various diseases, including cancer, infectious diseases, inflammation, and diabetes. This review is expected to provide a comprehensive reference for the rational design of stapled peptides for different diseases and targets to facilitate the development of therapeutic peptides with enhanced pharmacokinetic and biological properties.
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Affiliation(s)
- Yulei Li
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China.
| | - Minghao Wu
- School of Medicine, Shanghai University, 99 Shangda Road, Shanghai 200444, China
| | - Yinxue Fu
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China
| | - Jingwen Xue
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China
| | - Fei Yuan
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China
| | - Tianci Qu
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China
| | - Anastassia N Rissanou
- Theoretical & Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, Athens 11635, Greece
| | - Yilin Wang
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, 131 Dong'an Road, Shanghai 200032, China
| | - Xiang Li
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, China.
| | - Honggang Hu
- School of Medicine, Shanghai University, 99 Shangda Road, Shanghai 200444, China.
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2
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Sharma S, Anand A, Singh R, Singh RK, Verma S. Peptide-triggered IL-12 and IFN-γ mediated immune response in CD4 + T-cells against Leishmania donovani infection. Chem Commun (Camb) 2024; 60:4092-4095. [PMID: 38511970 DOI: 10.1039/d3cc05946d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Leishmania donovani are intracellular, human blood parasites that cause visceral leishmaniasis or kala-azar. Cell-penetrating peptides (CPPs) have been shown to modulate intracellular processes and cargo delivery, whereas host defense peptides (HDPs) promote proliferation of both naïve and antigen activated CD4+ T-cells. We report newly designed tripeptides that were able to trigger proinflammatory cytokine (IL-12 and IFN-γ) secretion by CD4+CD44+ T-cells in response to Leishmania donovani infection. These peptides can be used to induce antigen specific TH1 responses to combat obstacles of cytotoxicity and drug resistance associated with current anti-leishmanial drugs. Furthermore, these peptides can also be used as adjuvants to develop an effective immunoprophylactic approach for immunity restoration against visceral leishmaniasis.
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Affiliation(s)
- Swati Sharma
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India.
| | - Anshul Anand
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India.
| | - Rajan Singh
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India.
| | - Rakesh K Singh
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India.
| | - Sandeep Verma
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India.
- Gangwal School of Medical Sciences and Technology, Indian Institute of Technology Kanpur, Kanpur 208016, India
- Mehta Family Center for Engineering in Medicine, IIT Kanpur, Kanpur 208016, India
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3
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Li J, Tan YS, Verma CS. Dissecting the geometric and hydrophobic constraints of stapled peptides. Proteins 2024. [PMID: 38196284 DOI: 10.1002/prot.26662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/01/2023] [Accepted: 12/27/2023] [Indexed: 01/11/2024]
Abstract
Stapled peptides are a promising class of molecules with potential as highly specific probes of protein-protein interactions and as therapeutics. Hydrocarbon stapling affects the peptide properties through the interplay of two factors: enhancing the overall hydrophobicity and constraining the conformational flexibility. By constructing a series of virtual peptides, we study the role of each factor in modulating the structural properties of a hydrocarbon-stapled peptide PM2, which has been shown to enter cells, engage its target Mouse Double Minute 2 (MDM2), and activate p53. Hamiltonian replica exchange molecular dynamics (HREMD) simulations suggest that hydrocarbon stapling favors helical populations of PM2 through a combination of the geometric constraints and the enhanced hydrophobicity of the peptide. To further understand the conformational landscape of the stapled peptides along the binding pathway, we performed HREMD simulations by restraining the peptide at different distances from MDM2. When the peptide approaches MDM2, the binding pocket undergoes dehydration which appears to be greater in the presence of the stapled peptide compared with the linear peptide. In the binding pocket, the helicity of the stapled peptide is increased due to the favorable interactions between the peptide residues as well as the staple and the microenvironment of the binding pocket, contributing to enhanced affinity. The dissection of the multifaceted mechanism of hydrocarbon stapling into individual factors not only deepens fundamental understanding of peptide stapling, but also provides guidelines for the design of new stapled peptides.
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Affiliation(s)
- Jianguo Li
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Singapore Eye Research Institute, Singapore, Singapore
| | - Yaw Sing Tan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Chandra S Verma
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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4
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Shao C, Jian Q, Li B, Zhu Y, Yu W, Li Z, Shan A. Ultrashort All-Hydrocarbon Stapled α-Helix Amphiphile as a Potent and Stable Antimicrobial Compound. J Med Chem 2023; 66:11414-11427. [PMID: 37531494 DOI: 10.1021/acs.jmedchem.3c00856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
Abstract
The ravaging effect of drug-resistant bacteria has heightened the need for the development of membrane-soluble antimicrobial peptides (AMPs). However, their potential for clinical use is hindered by issues such as poor biocompatibility, salt sensitivity, and proteolytic lability. In this study, a series of ultrashort stapled cyclization heptapeptides were obtained by inserting all-hydrocarbon staples. StRRL with the highest therapeutic index (TI = 36.3) was selected after evaluating its antibacterial and toxic activity. Furthermore, stRRL demonstrated exceptional performance in high-protease and high-salt environments, making it an effective weapon against bacteria like Escherichia coli in a mouse peritonitis-sepsis model. The membrane lytic mechanism of stRRL, which operates from outside to inside, gives it a low drug-resistant tendency. This suggests that stRRL has the potential to replace antibiotics as a powerful candidate in tackling bacterial infection. In conclusion, the ultrashort all-hydrocarbon stapled antimicrobial amphiphiles inaugurated a novel entrance to the advancements of highly stable peptide compounds.
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Affiliation(s)
- Changxuan Shao
- Laboratory of Molecular Nutrition and Immunity. College of Animal Science and Technology, Northeast Agricultural University, Harbin, Heilongjiang 150030, P. R. China
| | - Qiao Jian
- Laboratory of Molecular Nutrition and Immunity. College of Animal Science and Technology, Northeast Agricultural University, Harbin, Heilongjiang 150030, P. R. China
| | - Bowen Li
- Laboratory of Molecular Nutrition and Immunity. College of Animal Science and Technology, Northeast Agricultural University, Harbin, Heilongjiang 150030, P. R. China
| | - Yongjie Zhu
- Laboratory of Molecular Nutrition and Immunity. College of Animal Science and Technology, Northeast Agricultural University, Harbin, Heilongjiang 150030, P. R. China
| | - Weikang Yu
- Laboratory of Molecular Nutrition and Immunity. College of Animal Science and Technology, Northeast Agricultural University, Harbin, Heilongjiang 150030, P. R. China
| | - Zhongyu Li
- Laboratory of Molecular Nutrition and Immunity. College of Animal Science and Technology, Northeast Agricultural University, Harbin, Heilongjiang 150030, P. R. China
| | - Anshan Shan
- Laboratory of Molecular Nutrition and Immunity. College of Animal Science and Technology, Northeast Agricultural University, Harbin, Heilongjiang 150030, P. R. China
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5
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You Y, Liu H, Zhu Y, Zheng H. Rational design of stapled antimicrobial peptides. Amino Acids 2023; 55:421-442. [PMID: 36781451 DOI: 10.1007/s00726-023-03245-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 01/30/2023] [Indexed: 02/15/2023]
Abstract
The global increase in antimicrobial drug resistance has dramatically reduced the effectiveness of traditional antibiotics. Structurally diverse antibiotics are urgently needed to combat multiple-resistant bacterial infections. As part of innate immunity, antimicrobial peptides have been recognized as the most promising candidates because they comprise diverse sequences and mechanisms of action and have a relatively low induction rate of resistance. However, because of their low chemical stability, susceptibility to proteases, and high hemolytic effect, their usage is subject to many restrictions. Chemical modifications such as D-amino acid substitution, cyclization, and unnatural amino acid modification have been used to improve the stability of antimicrobial peptides for decades. Among them, a side-chain covalent bridge modification, the so-called stapled peptide, has attracted much attention. The stapled side-chain bridge stabilizes the secondary structure, induces protease resistance, and increases cell penetration and biological activity. Recent progress in computer-aided drug design and artificial intelligence methods has also been used in the design of stapled antimicrobial peptides and has led to the successful discovery of many prospective peptides. This article reviews the possible structure-activity relationships of stapled antimicrobial peptides, the physicochemical properties that influence their activity (such as net charge, hydrophobicity, helicity, and dipole moment), and computer-aided methods of stapled peptide design. Antimicrobial peptides under clinical trial: Pexiganan (NCT01594762, 2012-05-07). Omiganan (NCT02576847, 2015-10-13).
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Affiliation(s)
- YuHao You
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, People's Republic of China
| | - HongYu Liu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, People's Republic of China
| | - YouZhuo Zhu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, People's Republic of China
| | - Heng Zheng
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, People's Republic of China.
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6
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Ma L, Ouyang H, Su A, Zhang Y, Pang D, Zhang T, Sun R, Wang W, Xie Z, Lv D. AbSE Workflow: Rapid Identification of the Coding Sequence and Linear Epitope of the Monoclonal Antibody at the Single-cell Level. ACS Synth Biol 2022; 11:1856-1864. [PMID: 35503752 DOI: 10.1021/acssynbio.2c00018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Monoclonal antibody (mAb) has been widely used in immunity research and disease diagnosis and therapy. Antibody sequence and epitope are the prerequisites and basis of mAb applications, which determine the properties of antibodies and make the preparation of antibody-based molecules controllable and reliable. Here, we present the antibody sequence and epitope identification (AbSE) workflow, a time-saving and cost-effective route for rapid determination of antibody sequence and linear epitope of mAb even at the single-cell level. The feasibility and accuracy of the AbSE workflow were demonstrated through the identification and validation of the coding sequence and epitope of antihuman serum albumin (antiHSA) mAb. It can be inferred that the AbSE workflow is a powerful and universal approach for paired antibody-epitope sequence identification. It may characterize antibodies not only on a single hybridoma cell but also on any other antibody-secreting cells.
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Affiliation(s)
- Lerong Ma
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, Jilin Province, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - HongSheng Ouyang
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, Jilin Province, College of Animal Sciences, Jilin University, Changchun 130062, China
- Chongqing Research Institute, Jilin University, Chongqing 401123, China
- Chongqing Jitang Biotechnology Research Institute Co., Ltd., Chongqing 401123, China
- Shenzhen Kingsino Technology Co., Ltd., Shenzhen 518100, China
| | - Ang Su
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, Jilin Province, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Yuanzhu Zhang
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, Jilin Province, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Daxin Pang
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, Jilin Province, College of Animal Sciences, Jilin University, Changchun 130062, China
- Chongqing Research Institute, Jilin University, Chongqing 401123, China
- Chongqing Jitang Biotechnology Research Institute Co., Ltd., Chongqing 401123, China
| | - Tao Zhang
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, Jilin Province, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Ruize Sun
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, Jilin Province, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Wentao Wang
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, Jilin Province, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Zicong Xie
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, Jilin Province, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Dongmei Lv
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, Jilin Province, College of Animal Sciences, Jilin University, Changchun 130062, China
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7
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Methodological advances in the design of peptide-based vaccines. Drug Discov Today 2022; 27:1367-1380. [DOI: 10.1016/j.drudis.2022.03.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/02/2021] [Accepted: 03/07/2022] [Indexed: 12/11/2022]
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8
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Luong HX, Bui HTP, Tung TT. Application of the All-Hydrocarbon Stapling Technique in the Design of Membrane-Active Peptides. J Med Chem 2022; 65:3026-3045. [PMID: 35112864 DOI: 10.1021/acs.jmedchem.1c01744] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The threats of drug resistance and new emerging pathogens have led to an urgent need to develop alternative treatment therapies. Recently, considerable research efforts have focused on membrane-active peptides (MAPs), a category of peptides in drug discovery with antimicrobial, anticancer, and cell penetration activities that have demonstrated their potential to be multifunctional agents. Nonetheless, natural MAPs have encountered various disadvantages, which mainly include poor bioavailability, the lack of a secondary structure in short peptides, and high production costs for long peptide sequences. Hence, an "all-hydrocarbon stapling system" has been applied to these peptides and proven to effectively stabilize the helical conformations, improving proteolytic resistance and increasing both the potency and the cell permeability. In this review, we summarized and categorized the advances made using this powerful technique in the development of stapled MAPs. Furthermore, outstanding issues and suggestions for future design within each subcategory were thoroughly discussed.
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Affiliation(s)
- Huy Xuan Luong
- Faculty of Pharmacy, PHENIKAA University, Hanoi 12116, Vietnam.,PHENIKAA Institute for Advanced Study (PIAS), PHENIKAA University, Hanoi 12116, Vietnam
| | | | - Truong Thanh Tung
- Faculty of Pharmacy, PHENIKAA University, Hanoi 12116, Vietnam.,PHENIKAA Institute for Advanced Study (PIAS), PHENIKAA University, Hanoi 12116, Vietnam
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9
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Farooq Z, Howell LA, McCormick PJ. Probing GPCR Dimerization Using Peptides. Front Endocrinol (Lausanne) 2022; 13:843770. [PMID: 35909575 PMCID: PMC9329873 DOI: 10.3389/fendo.2022.843770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 06/10/2022] [Indexed: 11/13/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are the largest class of membrane proteins and the most common and extensively studied pharmacological target. Numerous studies over the last decade have confirmed that GPCRs do not only exist and function in their monomeric form but in fact, have the ability to form dimers or higher order oligomers with other GPCRs, as well as other classes of receptors. GPCR oligomers have become increasingly attractive to investigate as they have the ability to modulate the pharmacological responses of the receptors which in turn, could have important functional roles in diseases, such as cancer and several neurological & neuropsychiatric disorders. Despite the growing evidence in the field of GPCR oligomerisation, the lack of structural information, as well as targeting the 'undruggable' protein-protein interactions (PPIs) involved in these complexes, has presented difficulties. Outside the field of GPCRs, targeting PPIs has been widely studied, with a variety of techniques being investigated; from small-molecule inhibitors to disrupting peptides. In this review, we will demonstrate several physiologically relevant GPCR dimers and discuss an array of strategies and techniques that can be employed when targeting these complexes, as well as provide ideas for future development.
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Affiliation(s)
- Zara Farooq
- Centre for Endocrinology, William Harvey Research Institute, Bart’s and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, United Kingdom
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, Mile End Road, London, United Kingdom
| | - Lesley A. Howell
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, Mile End Road, London, United Kingdom
| | - Peter J. McCormick
- Centre for Endocrinology, William Harvey Research Institute, Bart’s and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, United Kingdom
- *Correspondence: Peter J. McCormick,
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10
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Peptide Multimerization as Leads for Therapeutic Development. Biologics 2021. [DOI: 10.3390/biologics2010002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Multimerization of peptide structures has been a logical evolution in their development as potential therapeutic molecules. The multivalent properties of these assemblies have attracted much attention from researchers in the past and the development of more complex branching dendrimeric structures, with a wide array of biocompatible building blocks is revealing previously unseen properties and activities. These branching multimer and dendrimer structures can induce greater effect on cellular targets than monomeric forms and act as potent antimicrobials, potential vaccine alternatives and promising candidates in biomedical imaging and drug delivery applications. This review aims to outline the chemical synthetic innovations for the development of these highly complex structures and highlight the extensive capabilities of these molecules to rival those of natural biomolecules.
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11
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Helton LG, Rideout HJ, Herberg FW, Kennedy EJ. Leucine rich repeat kinase 2 (
LRRK2
) peptide modulators: Recent advances and future directions. Pept Sci (Hoboken) 2021. [DOI: 10.1002/pep2.24251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Leah G. Helton
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy University of Georgia Athens Georgia USA
| | - Hardy J. Rideout
- Center for Clinical, Experimental Surgery, and Translational Research Biomedical Research Foundation of the Academy of Athens Athens Greece
| | - Friedrich W. Herberg
- Department of Biochemistry Institute for Biology, University of Kassel Kassel Germany
| | - Eileen J. Kennedy
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy University of Georgia Athens Georgia USA
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12
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Vu QN, Young R, Sudhakar HK, Gao T, Huang T, Tan YS, Lau YH. Cyclisation strategies for stabilising peptides with irregular conformations. RSC Med Chem 2021; 12:887-901. [PMID: 34263169 PMCID: PMC8230030 DOI: 10.1039/d1md00098e] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 04/12/2021] [Indexed: 11/21/2022] Open
Abstract
Cyclisation is a common synthetic strategy for enhancing the therapeutic potential of peptide-based molecules. While there are extensive studies on peptide cyclisation for reinforcing regular secondary structures such as α-helices and β-sheets, there are remarkably few reports of cyclising peptides which adopt irregular conformations in their bioactive target-bound state. In this review, we highlight examples where cyclisation techniques have been successful in stabilising irregular conformations, then discuss how the design of cyclic constraints for irregularly structured peptides can be informed by existing β-strand stabilisation approaches, new computational design techniques, and structural principles extracted from cyclic peptide library screening hits. Through this analysis, we demonstrate how existing peptide cyclisation techniques can be adapted to address the synthetic design challenge of stabilising irregularly structured binding motifs.
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Affiliation(s)
- Quynh Ngoc Vu
- School of Chemistry, Eastern Ave, The University of Sydney NSW 2006 Australia
| | - Reginald Young
- School of Chemistry, Eastern Ave, The University of Sydney NSW 2006 Australia
| | | | - Tianyi Gao
- School of Chemistry, Eastern Ave, The University of Sydney NSW 2006 Australia
| | - Tiancheng Huang
- School of Chemistry, Eastern Ave, The University of Sydney NSW 2006 Australia
| | - Yaw Sing Tan
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR) 30 Biopolis Street, #07-01, Matrix Singapore 138671 Singapore
| | - Yu Heng Lau
- School of Chemistry, Eastern Ave, The University of Sydney NSW 2006 Australia
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13
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Stocks BB, Bird GH, Walensky LD, Melanson JE. Characterizing Native and Hydrocarbon-Stapled Enfuvirtide Conformations with Ion Mobility Mass Spectrometry and Hydrogen-Deuterium Exchange. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:753-761. [PMID: 33534566 DOI: 10.1021/jasms.0c00453] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The number of approved peptide therapeutics, as well as those in development, has been increasing in recent years. Frequently, the biological activity of such peptides is elicited through the adoption of secondary structural elements upon interaction with their cellular target. However, many therapeutic peptides are unstructured in solution and accordingly exhibit a poor bioavailability due to rapid proteolysis in vivo. To combat this degradation, numerous naturally occurring peptides with therapeutic properties contain stabilizing features, such as N-to-C cyclization or disulfide bonds. Recently, hydrocarbon stapling via non-native amino acid substitution followed by ring-closing metathesis has been shown to induce a dramatic stabilization of α-helical peptides. Identifying the ideal staple location along the peptide backbone is a critical developmental step, and methods to streamline this optimization are needed. Mass spectrometry-based methods such as ion mobility (IM) and hydrogen-deuterium exchange (HDX) can detect multiple discrete peptide conformations, a significant advantage over bulk spectroscopic techniques. In this study we use IM-MS and HDX-MS to demonstrate that the native 36-residue enfuvirtide peptide is highly dynamic in solution and the conformational ensemble populated by stabilized constructs depends heavily on the staple location. Further, our measurements yielded results that correlate well with the average α-helical content measured by circular dichroism. The MS-based approaches described herein represent sensitive and potentially high-throughput methods for characterizing and identifying optimally stapled peptides.
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Affiliation(s)
- Bradley B Stocks
- Metrology, National Research Council Canada, 1200 Montreal Road, Ottawa, Ontario K1A 0R6, Canada
| | - Gregory H Bird
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
| | - Loren D Walensky
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
| | - Jeremy E Melanson
- Metrology, National Research Council Canada, 1200 Montreal Road, Ottawa, Ontario K1A 0R6, Canada
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14
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Bluntzer MTJ, O'Connell J, Baker TS, Michel J, Hulme AN. Designing stapled peptides to inhibit
protein‐protein
interactions: An analysis of successes in a rapidly changing field. Pept Sci (Hoboken) 2020. [DOI: 10.1002/pep2.24191] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
| | | | | | - Julien Michel
- EaStChem School of Chemistry The University of Edinburgh Edinburgh UK
| | - Alison N. Hulme
- EaStChem School of Chemistry The University of Edinburgh Edinburgh UK
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15
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Chen CW, Saubi N, Joseph-Munné J. Design Concepts of Virus-Like Particle-Based HIV-1 Vaccines. Front Immunol 2020; 11:573157. [PMID: 33117367 PMCID: PMC7561392 DOI: 10.3389/fimmu.2020.573157] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/31/2020] [Indexed: 01/04/2023] Open
Abstract
Prophylactic vaccines remain the best approach for controlling the human immunodeficiency virus-1 (HIV-1) transmission. Despite the limited efficacy of the RV144 trial in Thailand, there is still no vaccine candidate that has been proven successful. Consequently, great efforts have been made to improve HIV-1 antigens design and discover delivery platforms for optimal immune elicitation. Owing to immunogenic, structural, and functional diversity, virus-like particles (VLPs) could act as efficient vaccine carriers to display HIV-1 immunogens and provide a variety of HIV-1 vaccine development strategies as well as prime-boost regimes. Here, we describe VLP-based HIV-1 vaccine candidates that have been enrolled in HIV-1 clinical trials and summarize current advances and challenges according to preclinical results obtained from five distinct strategies. This mini-review provides multiple perspectives to help in developing new generations of VLP-based HIV-1 vaccine candidates with better capacity to elicit specific anti-HIV immune responses.
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Affiliation(s)
- Chun-Wei Chen
- Microbiology Department, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Narcís Saubi
- Microbiology Department, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain.,EAVI2020 European AIDS Vaccine Initiative H2020 Research Programme, London, United Kingdom
| | - Joan Joseph-Munné
- Microbiology Department, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain.,EAVI2020 European AIDS Vaccine Initiative H2020 Research Programme, London, United Kingdom.,Microbiology Department, Hospital Universitari de la Vall d'Hebron, Barcelona, Spain
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16
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Targeting the Respiratory Syncytial Virus N 0-P Complex with Constrained α-Helical Peptides in Cells and Mice. Antimicrob Agents Chemother 2020; 64:AAC.00717-20. [PMID: 32660994 PMCID: PMC7508628 DOI: 10.1128/aac.00717-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 06/30/2020] [Indexed: 02/07/2023] Open
Abstract
Respiratory syncytial virus (RSV) is the main cause of severe respiratory infection in young children worldwide, and no therapies have been approved for the treatment of RSV infection. Data from recent clinical trials of fusion or L polymerase inhibitors for the treatment of RSV-infected patients revealed the emergence of escape mutants, highlighting the need for the discovery of inhibitors with novel mechanisms of action. Here we describe stapled peptides derived from the N terminus of the phosphoprotein (P) that act as replication inhibitors. Respiratory syncytial virus (RSV) is the main cause of severe respiratory infection in young children worldwide, and no therapies have been approved for the treatment of RSV infection. Data from recent clinical trials of fusion or L polymerase inhibitors for the treatment of RSV-infected patients revealed the emergence of escape mutants, highlighting the need for the discovery of inhibitors with novel mechanisms of action. Here we describe stapled peptides derived from the N terminus of the phosphoprotein (P) that act as replication inhibitors. We demonstrate that these peptides inhibit RSV replication in vitro and in vivo by preventing the formation of the N0-P complex. The present strategy provides a novel means of targeting RSV replication with constrained macrocyclic peptides or small molecules and is broadly applicable to other viruses of the Mononegavirales order.
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17
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Li X, Chen S, Zhang WD, Hu HG. Stapled Helical Peptides Bearing Different Anchoring Residues. Chem Rev 2020; 120:10079-10144. [DOI: 10.1021/acs.chemrev.0c00532] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Xiang Li
- School of Pharmacy, Second Military Medical University, Shanghai, China
- Insititute of Translational Medicine, Shanghai University, Shanghai, China
| | - Si Chen
- School of Medicine, Shanghai University, Shanghai, China
| | - Wei-Dong Zhang
- School of Pharmacy, Second Military Medical University, Shanghai, China
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hong-Gang Hu
- Insititute of Translational Medicine, Shanghai University, Shanghai, China
- Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
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18
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Sevy AM, Gilchuk IM, Brown BP, Bozhanova NG, Nargi R, Jensen M, Meiler J, Crowe JE. Computationally Designed Cyclic Peptides Derived from an Antibody Loop Increase Breadth of Binding for Influenza Variants. Structure 2020; 28:1114-1123.e4. [PMID: 32610044 DOI: 10.1016/j.str.2020.04.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/12/2020] [Accepted: 04/06/2020] [Indexed: 01/12/2023]
Abstract
The influenza hemagglutinin (HA) glycoprotein is the target of many broadly neutralizing antibodies. However, influenza viruses can rapidly escape antibody recognition by mutation of hypervariable regions of HA that overlap with the binding epitope. We hypothesized that by designing peptides to mimic antibody loops, we could enhance breadth of binding to HA antigenic variants by reducing contact with hypervariable residues on HA that mediate escape. We designed cyclic peptides that mimic the heavy-chain complementarity-determining region 3 (CDRH3) of anti-influenza broadly neutralizing antibody C05 and show that these peptides bound to HA molecules with <100 nM affinity, comparable with that of the full-length parental C05 IgG. In addition, these peptides exhibited increased breadth of recognition to influenza H4 and H7 subtypes by eliminating clashes between the hypervariable antigenic regions and the antibody CDRH1 loop. This approach can be used to generate antibody-derived peptides against a wide variety of targets.
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Affiliation(s)
- Alexander M Sevy
- Chemical & Physical Biology Program, Vanderbilt University, Nashville, TN 37235, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA; Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Iuliia M Gilchuk
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Benjamin P Brown
- Chemical & Physical Biology Program, Vanderbilt University, Nashville, TN 37235, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Nina G Bozhanova
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Rachel Nargi
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Mattie Jensen
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jens Meiler
- Chemical & Physical Biology Program, Vanderbilt University, Nashville, TN 37235, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA.
| | - James E Crowe
- Chemical & Physical Biology Program, Vanderbilt University, Nashville, TN 37235, USA; Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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19
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Bird GH, Fu A, Escudero S, Godes M, Opoku-Nsiah K, Wales TE, Cameron MD, Engen JR, Danial NN, Walensky LD. Hydrocarbon-Stitched Peptide Agonists of Glucagon-Like Peptide-1 Receptor. ACS Chem Biol 2020; 15:1340-1348. [PMID: 32348108 DOI: 10.1021/acschembio.0c00308] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Glucagon-like peptide 1 (GLP-1) is a natural peptide agonist of the GLP-1 receptor (GLP-1R) found on pancreatic β-cells. Engagement of the receptor stimulates insulin release in a glucose-dependent fashion and increases β-cell mass, two ideal features for pharmacologic management of type 2 diabetes. Thus, intensive efforts have focused on developing GLP-1-based peptide agonists of GLP-1R for therapeutic application. A primary challenge has been the naturally short half-life of GLP-1 due to its rapid proteolytic degradation in vivo. Whereas mutagenesis and lipidation strategies have yielded clinical agents, we developed an alternative approach to preserving the structure and function of GLP-1 by all-hydrocarbon i, i + 7 stitching. This particular "stitch" is especially well-suited for reinforcing and protecting the structural fidelity of GLP-1. Lead constructs demonstrate striking proteolytic stability and potent biological activity in vivo. Thus, we report a facile approach to generating alternative GLP-1R agonists for glycemic control.
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Affiliation(s)
- Gregory H. Bird
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
- Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
| | - Accalia Fu
- Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston Massachusetts 02215, United States
- Department of Cell Biology, Harvard Medical School, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Silvia Escudero
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
- Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
| | - Marina Godes
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
- Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
| | - Kwadwo Opoku-Nsiah
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
- Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
| | - Thomas E. Wales
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Michael D. Cameron
- DMPK Core, Department of Molecular Medicine, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - John R. Engen
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Nika N. Danial
- Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston Massachusetts 02215, United States
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
- Department of Medicine, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Loren D. Walensky
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
- Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, United States
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20
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Tornesello AL, Tagliamonte M, Tornesello ML, Buonaguro FM, Buonaguro L. Nanoparticles to Improve the Efficacy of Peptide-Based Cancer Vaccines. Cancers (Basel) 2020; 12:E1049. [PMID: 32340356 PMCID: PMC7226445 DOI: 10.3390/cancers12041049] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/24/2020] [Accepted: 04/20/2020] [Indexed: 12/11/2022] Open
Abstract
Nanoparticles represent a potent antigen presentation and delivery system to elicit an optimal immune response by effector cells targeting tumor-associated antigens expressed by cancer cells. Many types of nanoparticles have been developed, such as polymeric complexes, liposomes, micelles and protein-based structures such as virus like particles. All of them show promising results for immunotherapy approaches. In particular, the immunogenicity of peptide-based cancer vaccines can be significantly potentiated by nanoparticles. Indeed, nanoparticles are able to enhance the targeting of antigen-presenting cells (APCs) and trigger cytokine production for optimal T cell response. The present review summarizes the categories of nanoparticles and peptide cancer vaccines which are currently under pre-clinical evaluation.
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Affiliation(s)
- Anna Lucia Tornesello
- Molecular Biology and Viral Oncology Unit, Istituto Nazionale Tumori IRCCS “Fondazione G. Pascale”, via Mariano Semmola, 80131 Napoli, Italy; (M.L.T.); (F.M.B.)
| | - Maria Tagliamonte
- Innovative Immunological Models, Istituto Nazionale Tumori IRCCS “Fondazione G. Pascale”, via Mariano Semmola, 80131 Napoli, Italy;
| | - Maria Lina Tornesello
- Molecular Biology and Viral Oncology Unit, Istituto Nazionale Tumori IRCCS “Fondazione G. Pascale”, via Mariano Semmola, 80131 Napoli, Italy; (M.L.T.); (F.M.B.)
| | - Franco M. Buonaguro
- Molecular Biology and Viral Oncology Unit, Istituto Nazionale Tumori IRCCS “Fondazione G. Pascale”, via Mariano Semmola, 80131 Napoli, Italy; (M.L.T.); (F.M.B.)
| | - Luigi Buonaguro
- Innovative Immunological Models, Istituto Nazionale Tumori IRCCS “Fondazione G. Pascale”, via Mariano Semmola, 80131 Napoli, Italy;
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21
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Anananuchatkul T, Chang IV, Miki T, Tsutsumi H, Mihara H. Construction of a Stapled α-Helix Peptide Library Displayed on Phage for the Screening of Galectin-3-Binding Peptide Ligands. ACS OMEGA 2020; 5:5666-5674. [PMID: 32226843 PMCID: PMC7097893 DOI: 10.1021/acsomega.9b03461] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 02/24/2020] [Indexed: 06/10/2023]
Abstract
A stapled α-helix peptide library was designed and constructed using a chemically modified phage display system for screening stapled-peptide ligands against target proteins. The α-helix peptide library, with two cysteine residues on the opposite side of the randomized face, was modified with a rigid hydrocarbon staple linker on a phage. The stapled α-helix peptide phage library was screened against galectin-3 (Gal-3), a cancer-related galactose-binding protein. The obtained stapled peptides showed a high binding affinity (K d = 0.45 μM) despite being nonsugar ligands. The stapled modification played important roles in stabilizing the α-helical structure that contributed to the high binding affinity to Gal-3. In addition, the best stapled peptide ligands showed specific binding to Gal-3 among various carbohydrate-binding proteins. Thus, the designed α-helix peptide phage library with a constrained structure by the staple linker will advance the discovery of peptide ligands with improved specificity and affinity.
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22
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Coco D, Leanza S, Guerra F. Total Pancreatectomy: Indications, Advantages and Disadvantages - A Review. MÆDICA 2020; 14:391-396. [PMID: 32153671 DOI: 10.26574/maedica.2019.14.4.391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Background: Total pancreatectomy is an obligatory surgical procedure in locally advanced or centrally located pancreatic neoplasms to achieve complete tumour clearance. Owing to sound understanding of tumour biology and evolution in intervention technique and improved postoperative care, nowadays the indications of total pancreatectomy have taken a significant change. Aim: To review the indications of total pancreatectomy and its advantages and disadvantages under current perspectives. Method: Major databases, including PubMed, EMBASE, Science Citation Index Expanded, Scopus and the Cochrane Library, were searched for studies of total pancreatectomy and the results reported by various authors were summarized. Results: The indications of total pancreatectomy in subjects diagnosed with chronic pancreatitis were classified into four subgroups, including "Tumour", "Trouble", "Technical difficulties" and "Therapy-refractory pain". Today, total pancreatectomy has more specific and different indications than before. Currently, IPMN (intraductal papillary mucinous neoplasm) seems to have the most essential indication quantitatively. Morbidity and mortality related to total pancreatectomy are more profoundly decreased than before due to improvements in the operative techniques and post-operative managements. Some of the metabolic disorders are reported as major disadvantages of total pancreatectomy. Conclusion: Despite the disadvantages of total pancreatectomy, it remains an inevitable procedure for subjects with chronic pancreatitis, improvements in operative techniques and postoperative management ensuring long-term survival, a better quality of life, and diminished mortality and morbidity rates.
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Affiliation(s)
- Danilo Coco
- Department of General Surgery, Ospedali Riuniti Marche Nord, Pesaro, Italy
| | - Silvana Leanza
- Department of General Surgery Carlo Urbani Hospital, Jesi, Italy
| | - Francesco Guerra
- Department of General Surgery, Ospedali Riuniti Marche Nord, Pesaro, Italy
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23
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Pinto D, Fenwick C, Caillat C, Silacci C, Guseva S, Dehez F, Chipot C, Barbieri S, Minola A, Jarrossay D, Tomaras GD, Shen X, Riva A, Tarkowski M, Schwartz O, Bruel T, Dufloo J, Seaman MS, Montefiori DC, Lanzavecchia A, Corti D, Pantaleo G, Weissenhorn W. Structural Basis for Broad HIV-1 Neutralization by the MPER-Specific Human Broadly Neutralizing Antibody LN01. Cell Host Microbe 2019; 26:623-637.e8. [PMID: 31653484 PMCID: PMC6854463 DOI: 10.1016/j.chom.2019.09.016] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/29/2019] [Accepted: 09/27/2019] [Indexed: 11/24/2022]
Abstract
Potent and broadly neutralizing antibodies (bnAbs) are the hallmark of HIV-1 protection by vaccination. The membrane-proximal external region (MPER) of the HIV-1 gp41 fusion protein is targeted by the most broadly reactive HIV-1 neutralizing antibodies. Here, we examine the structural and molecular mechansims of neutralization by anti-MPER bnAb, LN01, which was isolated from lymph-node-derived germinal center B cells of an elite controller and exhibits broad neutralization breadth. LN01 engages both MPER and the transmembrane (TM) region, which together form a continuous helix in complex with LN01. The tilted TM orientation allows LN01 to interact simultaneously with the peptidic component of the MPER epitope and membrane via two specific lipid binding sites of the antibody paratope. Although LN01 carries a high load of somatic mutations, most key residues interacting with the MPER epitope and lipids are germline encoded, lending support for the LN01 epitope as a candidate for lineage-based vaccine development. bNAb LN01 neutralizes 92% of a 118-strain virus panel LN01 targets the HIV-1 gp41 MPER, the TM region, and lipids LN01-complexed MPER forms a continuous helix with TM Most LN01 paratope residues interacting with MPER-TM and lipids are germline encoded
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Affiliation(s)
- Dora Pinto
- Institute for Research in Biomedicine, Bellinzona 6500, Ticino, Switzerland
| | - Craig Fenwick
- Swiss Vaccine Research Institute, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Christophe Caillat
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38000 Grenoble, France
| | - Chiara Silacci
- Institute for Research in Biomedicine, Bellinzona 6500, Ticino, Switzerland
| | - Serafima Guseva
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38000 Grenoble, France
| | - François Dehez
- LPCT, UMR 7019 Université de Lorraine CNRS, 54500 Vandœuvre-lès-Nancy, France; Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, LPCT, UMR 7019 Universiteé de Lorraine CNRS, Vandœuvre-lès-Nancy 54500, France
| | - Christophe Chipot
- LPCT, UMR 7019 Université de Lorraine CNRS, 54500 Vandœuvre-lès-Nancy, France; Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, LPCT, UMR 7019 Universiteé de Lorraine CNRS, Vandœuvre-lès-Nancy 54500, France; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Sonia Barbieri
- Institute for Research in Biomedicine, Bellinzona 6500, Ticino, Switzerland
| | - Andrea Minola
- Humabs Biomed SA, Vir Biotechnology, 6500 Bellinzona, Ticino, Switzerland
| | - David Jarrossay
- Institute for Research in Biomedicine, Bellinzona 6500, Ticino, Switzerland
| | - Georgia D Tomaras
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Paris Diderot University, Sorbonne Paris Cité, Paris 75013, France
| | | | - Agostino Riva
- Department of Biomedical and Clinical Sciences, Luigi Sacco University Hospital, Università di Milano, 20157 Milan, Italy; III Division of Infectious Diseases, ASST Fatebenefratelli-Sacco, 20157 Milan, Italy
| | - Maciej Tarkowski
- Department of Biomedical and Clinical Sciences, Luigi Sacco University Hospital, Università di Milano, 20157 Milan, Italy
| | - Olivier Schwartz
- Institut Pasteur, Virus & Immunity Unit, CNRS UMR 3569, Paris 75015, France; Vaccine Research Institute, 94000 Créteil, France
| | - Timothée Bruel
- Institut Pasteur, Virus & Immunity Unit, CNRS UMR 3569, Paris 75015, France; Vaccine Research Institute, 94000 Créteil, France
| | - Jérémy Dufloo
- Institut Pasteur, Virus & Immunity Unit, CNRS UMR 3569, Paris 75015, France; Vaccine Research Institute, 94000 Créteil, France; Paris Diderot University, Sorbonne Paris Cité, Paris 75013, France
| | - Michael S Seaman
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - David C Montefiori
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | | | - Davide Corti
- Humabs Biomed SA, Vir Biotechnology, 6500 Bellinzona, Ticino, Switzerland.
| | - Giuseppe Pantaleo
- Swiss Vaccine Research Institute, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland; Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland.
| | - Winfried Weissenhorn
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38000 Grenoble, France.
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24
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Su CTT, Koh DWS, Gan SKE. Reviewing HIV-1 Gag Mutations in Protease Inhibitors Resistance: Insights for Possible Novel Gag Inhibitor Designs. Molecules 2019; 24:molecules24183243. [PMID: 31489889 PMCID: PMC6767625 DOI: 10.3390/molecules24183243] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/03/2019] [Accepted: 09/04/2019] [Indexed: 12/31/2022] Open
Abstract
HIV protease inhibitors against the viral protease are often hampered by drug resistance mutations in protease and in the viral substrate Gag. To overcome this drug resistance and inhibit viral maturation, targeting Gag alongside protease rather than targeting protease alone may be more efficient. In order to successfully inhibit Gag, understanding of its drug resistance mutations and the elicited structural changes on protease binding needs to be investigated. While mutations on Gag have already been mapped to protease inhibitor resistance, there remain many mutations, particularly the non-cleavage mutations, that are not characterized. Through structural studies to unravel how Gag mutations contributes to protease drug resistance synergistically, it is thus possible to glean insights to design novel Gag inhibitors. In this review, we discuss the structural role of both novel and previously reported Gag mutations in PI resistance, and how new Gag inhibitors can be designed.
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Affiliation(s)
- Chinh Tran-To Su
- Antibody & Product Development Lab, Bioinformatics Institute, A*STAR, Singapore 138671, Singapore
| | - Darius Wen-Shuo Koh
- Antibody & Product Development Lab, Bioinformatics Institute, A*STAR, Singapore 138671, Singapore
| | - Samuel Ken-En Gan
- Antibody & Product Development Lab, Bioinformatics Institute, A*STAR, Singapore 138671, Singapore.
- p53 Laboratory, A*STAR, Singapore 138648, Singapore.
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Combadière B, Beaujean M, Chaudesaigues C, Vieillard V. Peptide-Based Vaccination for Antibody Responses Against HIV. Vaccines (Basel) 2019; 7:vaccines7030105. [PMID: 31480779 PMCID: PMC6789779 DOI: 10.3390/vaccines7030105] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/29/2019] [Accepted: 08/30/2019] [Indexed: 12/14/2022] Open
Abstract
HIV-1 is responsible for a global pandemic of 35 million people and continues to spread at a rate of >2 million new infections/year. It is widely acknowledged that a protective vaccine would be the most effective means to reduce HIV-1 spread and ultimately eliminate the pandemic, whereas a therapeutic vaccine might help to mitigate the clinical course of the disease and to contribute to virus eradication strategies. However, despite more than 30 years of research, we do not have a vaccine capable of protecting against HIV-1 infection or impacting on disease progression. This, in part, denotes the challenge of identifying immunogens and vaccine modalities with a reduced risk of failure in late stage development. However, progress has been made in epitope identification for the induction of broadly neutralizing antibodies. Thus, peptide-based vaccination has become one of the challenges of this decade. While some researchers reconstitute envelope protein conformation and stabilization to conserve the epitope targeted by neutralizing antibodies, others have developed strategies based on peptide-carrier vaccines with a similar goal. Here, we will review the major peptide-carrier based approaches in the vaccine field and their application and recent development in the HIV-1 field.
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Affiliation(s)
- Behazine Combadière
- Sorbonne University, UPMC Univ Paris 06, INSERM, U1135, CNRS, ERL 8255, Center of Immunology and Infectious Diseases (CIMI-Paris), 91 Boulevard de l'Hôpital, F-75013 Paris, France.
| | - Manon Beaujean
- Sorbonne University, UPMC Univ Paris 06, INSERM, U1135, CNRS, ERL 8255, Center of Immunology and Infectious Diseases (CIMI-Paris), 91 Boulevard de l'Hôpital, F-75013 Paris, France
| | - Chloé Chaudesaigues
- Sorbonne University, UPMC Univ Paris 06, INSERM, U1135, CNRS, ERL 8255, Center of Immunology and Infectious Diseases (CIMI-Paris), 91 Boulevard de l'Hôpital, F-75013 Paris, France
| | - Vincent Vieillard
- Sorbonne University, UPMC Univ Paris 06, INSERM, U1135, CNRS, ERL 8255, Center of Immunology and Infectious Diseases (CIMI-Paris), 91 Boulevard de l'Hôpital, F-75013 Paris, France
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26
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Cholesterol-conjugated stapled peptides inhibit Ebola and Marburg viruses in vitro and in vivo. Antiviral Res 2019; 171:104592. [PMID: 31473342 DOI: 10.1016/j.antiviral.2019.104592] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 08/22/2019] [Accepted: 08/25/2019] [Indexed: 02/07/2023]
Abstract
Filoviridae currently includes five official and one proposed genera. Genus Ebolavirus includes five established and one proposed ebolavirus species for Bombali virus (BOMV), Bundibugyo virus (BDBV), Ebola virus (EBOV), Reston virus (RESTV), Sudan virus (SUDV) and Taï Forest virus (TAFV), and genus Marburgvirus includes a single species for Marburg virus (MARV) and Ravn virus (RAVV). Ebola virus (EBOV) has emerged as a significant public health concern since the 2013-2016 Ebola Virus Disease outbreak in Western Africa. Currently, there are no therapeutics approved and the need for Ebola-specific therapeutics remains a gap. In search for anti-Ebola therapies we tested the idea of using inhibitory properties of peptides corresponding to the C-terminal heptad-repeat (HR2) domains of class I fusion proteins against EBOV infection. The fusion protein GP2 of EBOV belongs to class I, suggesting that a similar strategy to HIV may be applied to inhibit EBOV infection. The serum half-life of peptides was expanded by cholesterol conjugation to allow daily dosing. The peptides were further constrained to stabilize a helical structure to increase the potency of inhibition. The EC50s of lead peptides were in low micromolar range, as determined by a high-content imaging test of EBOV-infected cells. Lead peptides were tested in an EBOV lethal mouse model and efficacy of the peptides were determined following twice-daily administration of peptides for 9 days. The most potent peptide was able to protect mice from lethal challenge of mouse-adapted Ebola virus. These data show that engineered peptides coupled with cholesterol can inhibit viral production, protect mice against lethal EBOV infection, and may be used to build novel therapeutics against EBOV.
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27
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Guarracino DA, Riordan JA, Barreto GM, Oldfield AL, Kouba CM, Agrinsoni D. Macrocyclic Control in Helix Mimetics. Chem Rev 2019; 119:9915-9949. [DOI: 10.1021/acs.chemrev.8b00623] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Danielle A. Guarracino
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
| | - Jacob A. Riordan
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
| | - Gianna M. Barreto
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
| | - Alexis L. Oldfield
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
| | - Christopher M. Kouba
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
| | - Desiree Agrinsoni
- Department of Chemistry, The College of New Jersey, Ewing, New Jersey 08628, United States
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Computational Analysis of Dengue Virus Envelope Protein (E) Reveals an Epitope with Flavivirus Immunodiagnostic Potential in Peptide Microarrays. Int J Mol Sci 2019; 20:ijms20081921. [PMID: 31003530 PMCID: PMC6514720 DOI: 10.3390/ijms20081921] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 04/15/2019] [Accepted: 04/16/2019] [Indexed: 01/14/2023] Open
Abstract
The mosquito-borne viral disease caused by the Dengue virus is an expanding global threat. Diagnosis in low-resource-settings and epidemiological surveillance urgently requires new immunoprobes for serological tests. Structure-based epitope prediction is an efficient method to design diagnostic peptidic probes able to reveal specific antibodies elicited in response to infections in patients’ sera. In this study, we focused on the Dengue viral envelope protein (E); computational analyses ranging from extensive Molecular Dynamics (MD) simulations and energy-decomposition-based prediction of potentially immunoreactive regions identified putative epitope sequences. Interestingly, one such epitope showed internal dynamic and energetic properties markedly different from those of other predicted sequences. The epitope was thus synthesized as a linear peptide, modified for chemoselective immobilization on microarrays and used in a serological assay to discriminate Dengue-infected individuals from healthy controls. The synthetic epitope probe showed a diagnostic performance comparable to that of the full antigen in terms of specificity and sensitivity. Given the high level of sequence identity among different flaviviruses, the epitope was immune-reactive towards Zika-infected sera as well. The results are discussed in the context of the quest for new possible structure-dynamics-based rules for the prediction of the immunoreactivity of selected antigenic regions with potential pan-flavivirus immunodiagnostic capacity.
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29
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Ali AM, Atmaj J, Van Oosterwijk N, Groves MR, Dömling A. Stapled Peptides Inhibitors: A New Window for Target Drug Discovery. Comput Struct Biotechnol J 2019; 17:263-281. [PMID: 30867891 PMCID: PMC6396041 DOI: 10.1016/j.csbj.2019.01.012] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 01/28/2019] [Accepted: 01/29/2019] [Indexed: 12/11/2022] Open
Abstract
Protein-protein interaction (PPI) is a hot topic in clinical research as protein networking has a major impact in human disease. Such PPIs are potential drugs targets, leading to the need to inhibit/block specific PPIs. While small molecule inhibitors have had some success and reached clinical trials, they have generally failed to address the flat and large nature of PPI surfaces. As a result, larger biologics were developed for PPI surfaces and they have successfully targeted PPIs located outside the cell. However, biologics have low bioavailability and cannot reach intracellular targets. A novel class -hydrocarbon-stapled α-helical peptides that are synthetic mini-proteins locked into their bioactive structure through site-specific introduction of a chemical linker- has shown promise. Stapled peptides show an ability to inhibit intracellular PPIs that previously have been intractable with traditional small molecule or biologics, suggesting that they offer a novel therapeutic modality. In this review, we highlight what stapling adds to natural-mimicking peptides, describe the revolution of synthetic chemistry techniques and how current drug discovery approaches have been adapted to stabilize active peptide conformations, including ring-closing metathesis (RCM), lactamisation, cycloadditions and reversible reactions. We provide an overview on the available stapled peptide high-resolution structures in the protein data bank, with four selected structures discussed in details due to remarkable interactions of their staple with the target surface. We believe that stapled peptides are promising drug candidates and open the doors for peptide therapeutics to reach currently "undruggable" space.
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Affiliation(s)
| | | | | | | | - Alexander Dömling
- Department of Drug Design, University of Groningen, Antonius Deusinglaan1, 9700AD Groningen, the Netherlands
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30
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Roy S, Ghosh P, Ahmed I, Chakraborty M, Naiya G, Ghosh B. Constrained α-Helical Peptides as Inhibitors of Protein-Protein and Protein-DNA Interactions. Biomedicines 2018; 6:E118. [PMID: 30567318 PMCID: PMC6315407 DOI: 10.3390/biomedicines6040118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/13/2018] [Accepted: 09/14/2018] [Indexed: 02/06/2023] Open
Abstract
Intracellular regulatory pathways are replete with protein-protein and protein-DNA interactions, offering attractive targets for therapeutic interventions. So far, most drugs are targeted toward enzymes and extracellular receptors. Protein-protein and protein-DNA interactions have long been considered as "undruggable". Protein-DNA interactions, in particular, present a difficult challenge due to the repetitive nature of the B-DNA. Recent studies have provided several breakthroughs; however, a design methodology for these classes of inhibitors is still at its infancy. A dominant motif of these macromolecular interactions is an α-helix, raising possibilities that an appropriate conformationally-constrained α-helical peptide may specifically disrupt these interactions. Several methods for conformationally constraining peptides to the α-helical conformation have been developed, including stapling, covalent surrogates of hydrogen bonds and incorporation of unnatural amino acids that restrict the conformational space of the peptide. We will discuss these methods and several case studies where constrained α-helices have been used as building blocks for appropriate molecules. Unlike small molecules, the delivery of these short peptides to their targets is not straightforward as they may possess unfavorable cell penetration and ADME properties. Several methods have been developed in recent times to overcome some of these problems. We will discuss these issues and the prospects of this class of molecules as drugs.
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Affiliation(s)
- Siddhartha Roy
- Department of Biophysics, Bose Institute, P1/12 CIT Scheme VII M, Kolkata 700054, India.
| | - Piya Ghosh
- Department of Biophysics, Bose Institute, P1/12 CIT Scheme VII M, Kolkata 700054, India.
| | - Israr Ahmed
- Department of Biophysics, Bose Institute, P1/12 CIT Scheme VII M, Kolkata 700054, India.
| | - Madhumita Chakraborty
- Department of Biophysics, Bose Institute, P1/12 CIT Scheme VII M, Kolkata 700054, India.
| | - Gitashri Naiya
- Department of Biophysics, Bose Institute, P1/12 CIT Scheme VII M, Kolkata 700054, India.
| | - Basusree Ghosh
- Department of Biophysics, Bose Institute, P1/12 CIT Scheme VII M, Kolkata 700054, India.
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31
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Di Costanzo L, Dutta S, Burley SK. Amino acid modifications for conformationally constraining naturally occurring and engineered peptide backbones: Insights from the Protein Data Bank. Biopolymers 2018; 109:e23230. [PMID: 30368772 DOI: 10.1002/bip.23230] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 05/23/2018] [Accepted: 05/24/2018] [Indexed: 01/08/2023]
Abstract
Extensive efforts invested in understanding the rules of protein folding are now being applied, with good effect, in de novo design of proteins/peptides. For proteins containing standard α-amino acids alone, knowledge derived from experimentally determined three-dimensional (3D) structures of proteins and biologically active peptides are available from the Protein Data Bank (PDB), and the Cambridge Structural Database (CSD). These help predict and design protein structures, with reasonable confidence. However, our knowledge of 3D structures of biomolecules containing backbone modified amino acids is still evolving. A major challenge in de novo protein/peptide design concerns the engineering of conformationally constrained molecules with specific structural elements and chemical groups appropriately positioned for biological activity. This review explores four classes of amino acid modifications that constrain protein/peptide backbone structure. Systematic analysis of peptidic molecule structures (eg, bioactive peptides, inhibitors, antibiotics, and designed molecules), containing these backbone-modified amino acids, found in the PDB and CSD are discussed. The review aims to provide structure-function insights that will guide future design of proteins/peptides.
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Affiliation(s)
- Luigi Di Costanzo
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ, U.S.A
| | - Shuchismita Dutta
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ, U.S.A.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, U.S.A
| | - Stephen K Burley
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ, U.S.A.,Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, U.S.A.,RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, U.S.A.,Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, U.S.A
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32
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Abstract
A large array of broadly neutralizing antibodies (bnAbs) against HIV have been isolated and described, particularly in the last decade. This continually expanding array of bnAbs has crucially led to the identification of novel epitopes on the HIV envelope protein via which antibodies can block a broad range of HIV strains. Moreover, these studies have produced high-resolution understanding of these sites of vulnerability on the envelope protein. They have also clarified the mechanisms of action of bnAbs and provided detailed descriptions of B cell ontogenies from which they arise. However, it is still not possible to predict which HIV-infected individuals will go onto develop breath nor is it possible to induce neutralization breadth by immunization in humans. This review aims to discuss the major insights gained so far and also to evaluate the requirement to continue isolating and characterizing new bnAbs. While new epitopes may remain to be uncovered, a clearer probable benefit of further bnAb characterization is a greater understanding of key decision points in bnAb development within the anti-HIV immune response. This in turn may lead to new insights into how to trigger bnAbs by immunization and more clearly define the challenges to using bnAbs as therapeutic agents.
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Affiliation(s)
- Laura E McCoy
- Division of Infection and Immunity, University College London, London, UK.
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33
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HIV-1 Vaccines Based on Antibody Identification, B Cell Ontogeny, and Epitope Structure. Immunity 2018; 48:855-871. [DOI: 10.1016/j.immuni.2018.04.029] [Citation(s) in RCA: 225] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 04/26/2018] [Accepted: 04/26/2018] [Indexed: 12/12/2022]
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34
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Cornillie SP, Bruno BJ, Lim CS, Cheatham TE. Computational Modeling of Stapled Peptides toward a Treatment Strategy for CML and Broader Implications in the Design of Lengthy Peptide Therapeutics. J Phys Chem B 2018. [DOI: 10.1021/acs.jpcb.8b01014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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35
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Mandal A, Pal D, Agrahari V, Trinh HM, Joseph M, Mitra AK. Ocular delivery of proteins and peptides: Challenges and novel formulation approaches. Adv Drug Deliv Rev 2018; 126:67-95. [PMID: 29339145 DOI: 10.1016/j.addr.2018.01.008] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 12/21/2017] [Accepted: 01/10/2018] [Indexed: 12/12/2022]
Abstract
The impact of proteins and peptides on the treatment of various conditions including ocular diseases over the past few decades has been advanced by substantial breakthroughs in structural biochemistry, genetic engineering, formulation and delivery approaches. Formulation and delivery of proteins and peptides, such as monoclonal antibodies, aptamers, recombinant proteins and peptides to ocular tissues poses significant challenges owing to their large size, poor permeation and susceptibility to degradation. A wide range of advanced drug delivery systems including polymeric controlled release systems, cell-based delivery and nanowafers are being exploited to overcome the challenges of frequent administration to ocular tissues. The next generation systems integrated with new delivery technologies are anticipated to generate improved efficacy and safety through the expansion of the therapeutic target space. This review will highlight recent advances in formulation and delivery strategies of protein and peptide based biopharmaceuticals. We will also describe the current state of proteins and peptides based ocular therapy and future therapeutic opportunities.
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36
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McLoughlin NM, Mueller C, Grossmann TN. The Therapeutic Potential of PTEN Modulation: Targeting Strategies from Gene to Protein. Cell Chem Biol 2018; 25:19-29. [DOI: 10.1016/j.chembiol.2017.10.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 10/05/2017] [Accepted: 10/23/2017] [Indexed: 01/04/2023]
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37
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Zhang R, Verkoczy L, Wiehe K, Munir Alam S, Nicely NI, Santra S, Bradley T, Pemble CW, Zhang J, Gao F, Montefiori DC, Bouton-Verville H, Kelsoe G, Larimore K, Greenberg PD, Parks R, Foulger A, Peel JN, Luo K, Lu X, Trama AM, Vandergrift N, Tomaras GD, Kepler TB, Moody MA, Liao HX, Haynes BF. Initiation of immune tolerance-controlled HIV gp41 neutralizing B cell lineages. Sci Transl Med 2017; 8:336ra62. [PMID: 27122615 DOI: 10.1126/scitranslmed.aaf0618] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 03/28/2016] [Indexed: 01/09/2023]
Abstract
Development of an HIV vaccine is a global priority. A major roadblock to a vaccine is an inability to induce protective broadly neutralizing antibodies (bnAbs). HIV gp41 bnAbs have characteristics that predispose them to be controlled by tolerance. We used gp41 2F5 bnAb germline knock-in mice and macaques vaccinated with immunogens reactive with germline precursors to activate neutralizing antibodies. In germline knock-in mice, bnAb precursors were deleted, with remaining anergic B cells capable of being activated by germline-binding immunogens to make gp41-reactive immunoglobulin M (IgM). Immunized macaques made B cell clonal lineages targeted to the 2F5 bnAb epitope, but 2F5-like antibodies were either deleted or did not attain sufficient affinity for gp41-lipid complexes to achieve the neutralization potency of 2F5. Structural analysis of members of a vaccine-induced antibody lineage revealed that heavy chain complementarity-determining region 3 (HCDR3) hydrophobicity was important for neutralization. Thus, gp41 bnAbs are controlled by immune tolerance, requiring vaccination strategies to transiently circumvent tolerance controls.
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Affiliation(s)
- Ruijun Zhang
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Laurent Verkoczy
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA. Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA. Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA. Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - S Munir Alam
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA. Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA. Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Nathan I Nicely
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sampa Santra
- Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Todd Bradley
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA. Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Charles W Pemble
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jinsong Zhang
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Feng Gao
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA. Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - David C Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA. Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | | | - Garnett Kelsoe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA. Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kevin Larimore
- Fred Hutchinson Cancer Research Center, University of Washington, Seattle, WA 98109, USA
| | - Phillip D Greenberg
- Fred Hutchinson Cancer Research Center, University of Washington, Seattle, WA 98109, USA
| | - Robert Parks
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Andrew Foulger
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jessica N Peel
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kan Luo
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xiaozhi Lu
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ashley M Trama
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Nathan Vandergrift
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA. Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Georgia D Tomaras
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA. Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Thomas B Kepler
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - M Anthony Moody
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA. Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA. Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hua-Xin Liao
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA. Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA.
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA. Department of Pathology, Duke University School of Medicine, Durham, NC 27710, USA. Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA.
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38
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Quach K, LaRochelle J, Li XH, Rhoades E, Schepartz A. Unique arginine array improves cytosolic localization of hydrocarbon-stapled peptides. Bioorg Med Chem 2017; 26:1197-1202. [PMID: 29150077 DOI: 10.1016/j.bmc.2017.11.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Revised: 10/30/2017] [Accepted: 11/03/2017] [Indexed: 11/19/2022]
Abstract
We have previously reported that miniature proteins containing a distinct array of 5 arginine residues on a folded α-helix - a penta-arg motif - traffic with high efficiency from endosomes into the cytosol and nucleus of mammalian cells. Here we evaluate whether a penta-arg motif can improve the intracellular trafficking of an otherwise impermeant hydrocarbon-stapled peptide, SAH-p53-4Rho. We prepared a panel of SAH-p53-4Rho variants containing penta-arg sequences with different spacings and axial arrangement and evaluated their overall uptake (as judged by flow cytometry) and their intracellular access (as determined by fluorescence correlation spectroscopy, FCS). One member of this panel reached the cytosol extremely well, matching the level achieved by SAH-p53-8Rho, a previously reported and highly permeant hydrocarbon-stapled peptide. Notably, we found no relationship between cellular uptake as judged by flow cytometry and cytosolic access as determined by FCS. This result reiterates that overall uptake and endosomal release represent fundamentally different biological processes. To determine cytosolic and/or nuclear access, one must measure concentration directly using a quantitative and non-amplified tool such as FCS. As has been observed for highly cell permeant miniature proteins such as ZF5.3, optimal penetration of hydrocarbon-stapled peptides into the cell cytosol results when the penta-arg motif is located within more (as opposed to less) structured regions.
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Affiliation(s)
- Kim Quach
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, United States
| | - Jonathan LaRochelle
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8107, United States
| | - Xiao-Han Li
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, United States
| | - Elizabeth Rhoades
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8107, United States
| | - Alanna Schepartz
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, United States; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8107, United States.
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39
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Ouyang Y, Yin Q, Li W, Li Z, Kong D, Wu Y, Hong K, Xing H, Shao Y, Jiang S, Ying T, Ma L. Escape from humoral immunity is associated with treatment failure in HIV-1-infected patients receiving long-term antiretroviral therapy. Sci Rep 2017; 7:6222. [PMID: 28740221 PMCID: PMC5524822 DOI: 10.1038/s41598-017-05594-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 05/31/2017] [Indexed: 01/22/2023] Open
Abstract
Interindividual heterogeneity in the disease progression of HIV-1-infected patients receiving long-term antiretroviral therapy suggests that some host-related factors may have limited treatment efficacy. To understand the nature of factors contributing to treatment failure, we performed a retrospective cohort study of 45 chronically HIV-1-infected individuals sharing a similar demographics and route of infection, compared the differences between virologically suppressed (VS) and treatment failure (TF) patients with respect to clinical, immunological and virological characteristics. We found that the baseline diversity of HIV-1 env quasispecies was the major difference between VS and TF group, and higher baseline diversity in TF patients. We further predicted TF-related env mutations using a selection pressure-based approach, followed by an analysis of these mutations based on the available three-dimensional structures of gp120/gp41 or their complexes with neutralizing antibodies. Notably, almost all of the identified residues could be mapped to the epitopes of known HIV-1 neutralizing antibodies, especially the epitopes of broadly neutralizing antibodies, and these mutations tended to compromise antibody-antigen interactions. These results indicate that the escape of HIV-1 from host humoral immunity may play a direct role in TF in long-term antiretroviral-experienced patients and that based on env gene sequence of the viruses in the patients.
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Affiliation(s)
- Yabo Ouyang
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention, Beijing, China and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China.,Beijing You'an Hospital, Capital Medical University, Beijing, China and Beijing Institute of Hepatology, Beijing, China
| | - Qianqian Yin
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention, Beijing, China and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Wei Li
- Key Laboratory of Medical Molecular Virology of MOE/MOH, School of Basic Medical Sciences, Fudan University, Shanghai, China.,Protein Interactions Section, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Zhenpeng Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention, Beijing, China and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Desheng Kong
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention, Beijing, China and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Yanling Wu
- Key Laboratory of Medical Molecular Virology of MOE/MOH, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Kunxue Hong
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention, Beijing, China and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Hui Xing
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention, Beijing, China and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Yiming Shao
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention, Beijing, China and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology of MOE/MOH, School of Basic Medical Sciences, Fudan University, Shanghai, China. .,Lindsley F. Kimball Research Institute, New York Blood Center, New York, USA.
| | - Tianlei Ying
- Key Laboratory of Medical Molecular Virology of MOE/MOH, School of Basic Medical Sciences, Fudan University, Shanghai, China.
| | - Liying Ma
- State Key Laboratory of Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention (NCAIDS), Chinese Center for Disease Control and Prevention, Beijing, China and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China.
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40
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Gourlay L, Peri C, Bolognesi M, Colombo G. Structure and Computation in Immunoreagent Design: From Diagnostics to Vaccines. Trends Biotechnol 2017; 35:1208-1220. [PMID: 28739221 DOI: 10.1016/j.tibtech.2017.06.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 06/28/2017] [Accepted: 06/30/2017] [Indexed: 11/26/2022]
Abstract
Novel immunological tools for efficient diagnosis and treatment of emerging infections are urgently required. Advances in the diagnostic and vaccine development fields are continuously progressing, with reverse vaccinology and structural vaccinology (SV) methods for antigen identification and structure-based antigen (re)design playing increasingly relevant roles. SV, in particular, is predicted to be the front-runner in the future development of diagnostics and vaccines targeting challenging diseases such as AIDS and cancer. We review state-of-the-art methodologies for structure-based epitope identification and antigen design, with specific applicative examples. We highlight the implications of such methods for the engineering of biomolecules with improved immunological properties, potential diagnostic and/or therapeutic uses, and discuss the perspectives of structure-based rational design for the production of advanced immunoreagents.
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Affiliation(s)
- Louise Gourlay
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Claudio Peri
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Via Mario Bianco, 9, 20131, Milan, Italy
| | - Martino Bolognesi
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, 20133, Milan, Italy; Centro di Ricerca Pediatrica Romeo ed Enrica Invernizzi, Università di Milano, Milan, Italy.
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Via Mario Bianco, 9, 20131, Milan, Italy.
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41
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Gori A, Bolognesi M, Colombo G, Gourlay LJ. Structural Vaccinology for Melioidosis Vaccine Design and Immunodiagnostics. CURRENT TROPICAL MEDICINE REPORTS 2017. [DOI: 10.1007/s40475-017-0117-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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42
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Peraro L, Zou Z, Makwana KM, Cummings AE, Ball HL, Yu H, Lin YS, Levine B, Kritzer JA. Diversity-Oriented Stapling Yields Intrinsically Cell-Penetrant Inducers of Autophagy. J Am Chem Soc 2017; 139:7792-7802. [PMID: 28414223 PMCID: PMC5473019 DOI: 10.1021/jacs.7b01698] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
Autophagy
is an essential pathway by which cellular and foreign
material are degraded and recycled in eukaryotic cells. Induction
of autophagy is a promising approach for treating diverse human diseases,
including neurodegenerative disorders and infectious diseases. Here,
we report the use of a diversity-oriented stapling approach to produce
autophagy-inducing peptides that are intrinsically cell-penetrant.
These peptides induce autophagy at micromolar concentrations in vitro,
have aggregate-clearing activity in a cellular model of Huntington’s
disease, and induce autophagy in vivo. Unexpectedly, the solution
structure of the most potent stapled peptide, DD5-o, revealed an α-helical
conformation in methanol, stabilized by an unusual (i,i+3) staple which cross-links two d-amino
acids. We also developed a novel assay for cell penetration that reports
exclusively on cytosolic access and used it to quantitatively compare
the cell penetration of DD5-o and other autophagy-inducing peptides.
These new, cell-penetrant autophagy inducers and their molecular details
are critical advances in the effort to understand and control autophagy.
More broadly, diversity-oriented stapling may provide a promising
alternative to polycationic sequences as a means for rendering peptides
more cell-penetrant.
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Affiliation(s)
- Leila Peraro
- Department of Chemistry, Tufts University , Medford, Massachusetts 02155, United States
| | | | - Kamlesh M Makwana
- Department of Chemistry, Tufts University , Medford, Massachusetts 02155, United States
| | - Ashleigh E Cummings
- Department of Chemistry, Tufts University , Medford, Massachusetts 02155, United States
| | | | - Hongtao Yu
- Department of Chemistry, Tufts University , Medford, Massachusetts 02155, United States
| | - Yu-Shan Lin
- Department of Chemistry, Tufts University , Medford, Massachusetts 02155, United States
| | | | - Joshua A Kritzer
- Department of Chemistry, Tufts University , Medford, Massachusetts 02155, United States
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43
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Rujas E, Insausti S, García-Porras M, Sánchez-Eugenia R, Tsumoto K, Nieva JL, Caaveiro JMM. Functional Contacts between MPER and the Anti-HIV-1 Broadly Neutralizing Antibody 4E10 Extend into the Core of the Membrane. J Mol Biol 2017; 429:1213-1226. [PMID: 28300601 DOI: 10.1016/j.jmb.2017.03.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 03/06/2017] [Accepted: 03/06/2017] [Indexed: 12/18/2022]
Abstract
The exceptional breadth of broadly neutralizing antibodies (bNAbs) against the membrane-proximal external region (MPER) of the transmembrane protein gp41 makes this class of antibodies an ideal model to design HIV vaccines. From a practical point of view, however, the preparation of vaccines eliciting bNAbs is still a major roadblock that limits their clinical application. Fresh mechanistic insights are necessary to develop more effective strategies. In particular, the function of the unusually long complementarity-determining region three of the heavy chain (CDRH3) of 4E10, an anti-MPER bNAb, is an open question that fascinates researchers in the field. Residues comprising the apex region are dispensable for engagement of the epitope in solution; still, their single mutation profoundly impairs the neutralization capabilities of the antibody. Since this region is very hydrophobic, it has been proposed that the apex is essential for anchoring the antibody to the viral membrane where MPER resides. Herein, we have critically examined this idea using structural, biophysical, biochemical, and cell-based approaches. Our results demonstrate that the apex region is not just a "greasy" spot merely increasing the affinity of the antibody for the membrane. We demonstrate the three-dimensional engagement of the apex region of the CDRH3 with the conglomerate of gp41 epitope and membrane lipids as a means of effective binding and neutralization of the virus. This mechanism of recognition suggests a standard route of antibody ontogeny. Therefore, we need to focus our efforts on recreating a more realistic MPER/lipid immunogen in order to generate more effective anti-HIV-1 vaccines.
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Affiliation(s)
- Edurne Rujas
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country, P.O. Box 644, Bilbao 48080, Spain; Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Sara Insausti
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country, P.O. Box 644, Bilbao 48080, Spain
| | - Miguel García-Porras
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country, P.O. Box 644, Bilbao 48080, Spain
| | - Rubén Sánchez-Eugenia
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country, P.O. Box 644, Bilbao 48080, Spain
| | - Kouhei Tsumoto
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - José L Nieva
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country, P.O. Box 644, Bilbao 48080, Spain.
| | - Jose M M Caaveiro
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan; Laboratory of Global Healthcare, School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan.
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44
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Rujas E, Caaveiro JMM, Insausti S, García-Porras M, Tsumoto K, Nieva JL. Peripheral Membrane Interactions Boost the Engagement by an Anti-HIV-1 Broadly Neutralizing Antibody. J Biol Chem 2017; 292:5571-5583. [PMID: 28213514 DOI: 10.1074/jbc.m117.775429] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 02/16/2017] [Indexed: 12/16/2022] Open
Abstract
The 4E10 antibody displays an extreme breadth of HIV-1 neutralization and therefore constitutes a suitable model system for structure-guided vaccine design and immunotherapeutics against AIDS. In this regard, the relevance of autoreactivity with membrane lipids for the biological function of this antibody is still a subject of controversy. To address this dispute, herein we have compared the membrane partitioning ability of the 4E10 antibody and several of its variants, which were mutated at the region of the paratope surface in contact with the membrane interface. We first employed a physical separation approach (vesicle flotation) and subsequently carried out quantitative fluorescence measurements in an intact system (spectroscopic titration), using 4E10 Fab labeled with a polarity-sensitive fluorescent probe. Moreover, recognition of epitope peptide in membrane was demonstrated by photo-cross-linking assays using a Fab that incorporated the genetically encoded unnatural amino acid p-benzoylphenylalanine. The experimental data ruled out that the proposed stereospecific recognition of viral lipids was necessary for the function of the antibody. In contrast, our data suggest that nonspecific electrostatic interactions between basic residues of 4E10 and acidic phospholipids in the membranes contribute to the observed biological function. Moreover, the energetics of membrane partitioning indicated that 4E10 behaves as a peripheral membrane protein, tightening the binding to the ligand epitope inserted in the viral membrane. The implications of these findings for the natural production and biological function of this antibody are discussed.
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Affiliation(s)
- Edurne Rujas
- From the Biofisika Institute (Consejo Superior de Investigaciones Científicas, UPV/EHU), and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), 48080 Bilbao, Spain and.,the Department of Bioengineering, Graduate School of Engineering, University of Tokyo, Tokyo, 113-8656, Japan
| | - José M M Caaveiro
- the Department of Bioengineering, Graduate School of Engineering, University of Tokyo, Tokyo, 113-8656, Japan
| | - Sara Insausti
- From the Biofisika Institute (Consejo Superior de Investigaciones Científicas, UPV/EHU), and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), 48080 Bilbao, Spain and
| | - Miguel García-Porras
- From the Biofisika Institute (Consejo Superior de Investigaciones Científicas, UPV/EHU), and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), 48080 Bilbao, Spain and
| | - Kouhei Tsumoto
- the Department of Bioengineering, Graduate School of Engineering, University of Tokyo, Tokyo, 113-8656, Japan
| | - José L Nieva
- From the Biofisika Institute (Consejo Superior de Investigaciones Científicas, UPV/EHU), and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), 48080 Bilbao, Spain and
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45
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Rujas E, Caaveiro JMM, Partida-Hanon A, Gulzar N, Morante K, Apellániz B, García-Porras M, Bruix M, Tsumoto K, Scott JK, Jiménez MÁ, Nieva JL. Structural basis for broad neutralization of HIV-1 through the molecular recognition of 10E8 helical epitope at the membrane interface. Sci Rep 2016; 6:38177. [PMID: 27905530 PMCID: PMC5131266 DOI: 10.1038/srep38177] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 11/04/2016] [Indexed: 12/13/2022] Open
Abstract
The mechanism by which the HIV-1 MPER epitope is recognized by the potent neutralizing antibody 10E8 at membrane interfaces remains poorly understood. To solve this problem, we have optimized a 10E8 peptide epitope and analyzed the structure and binding activities of the antibody in membrane and membrane-like environments. The X-ray crystal structure of the Fab-peptide complex in detergents revealed for the first time that the epitope of 10E8 comprises a continuous helix spanning the gp41 MPER/transmembrane domain junction (MPER-N-TMD; Env residues 671–687). The MPER-N-TMD helix projects beyond the tip of the heavy-chain complementarity determining region 3 loop, indicating that the antibody sits parallel to the plane of the membrane in binding the native epitope. Biophysical, biochemical and mutational analyses demonstrated that strengthening the affinity of 10E8 for the TMD helix in a membrane environment, correlated with its neutralizing potency. Our research clarifies the molecular mechanisms underlying broad neutralization of HIV-1 by 10E8, and the structure of its natural epitope. The conclusions of our research will guide future vaccine-design strategies targeting MPER.
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Affiliation(s)
- Edurne Rujas
- Biophysics Unit (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country, P.O. Box 644, 48080 Bilbao, Spain.,Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Jose M M Caaveiro
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.,Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Angélica Partida-Hanon
- Institute of Physical Chemistry "Rocasolano" (IQFR-CSIC), Serrano 119, E-28006 Madrid, Spain
| | - Naveed Gulzar
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Koldo Morante
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.,Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Beatriz Apellániz
- Biophysics Unit (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country, P.O. Box 644, 48080 Bilbao, Spain
| | - Miguel García-Porras
- Biophysics Unit (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country, P.O. Box 644, 48080 Bilbao, Spain
| | - Marta Bruix
- Institute of Physical Chemistry "Rocasolano" (IQFR-CSIC), Serrano 119, E-28006 Madrid, Spain
| | - Kouhei Tsumoto
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.,Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Jamie K Scott
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada.,Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - M Ángeles Jiménez
- Institute of Physical Chemistry "Rocasolano" (IQFR-CSIC), Serrano 119, E-28006 Madrid, Spain
| | - José L Nieva
- Biophysics Unit (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country, P.O. Box 644, 48080 Bilbao, Spain
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46
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Bird GH, Mazzola E, Opoku-Nsiah K, Lammert MA, Godes M, Neuberg DS, Walensky LD. Biophysical determinants for cellular uptake of hydrocarbon-stapled peptide helices. Nat Chem Biol 2016; 12:845-52. [PMID: 27547919 PMCID: PMC5055751 DOI: 10.1038/nchembio.2153] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 05/23/2016] [Indexed: 12/23/2022]
Abstract
Hydrocarbon-stapled peptides are a class of bioactive alpha-helical ligands developed to dissect and target protein interactions. While there is consensus that stapled peptides can be effective chemical tools for investigating protein regulation, their broader utility for therapeutic modulation of intracellular interactions remains an active area of study. In particular, the design principles for generating cell-permeable stapled peptides are empiric, yet consistent intracellular access is essential to in vivo application. Here, we used an unbiased statistical approach to determine which biophysical parameters dictate the uptake of stapled-peptide libraries. We found that staple placement at the amphipathic boundary combined with optimal hydrophobic and helical content are the key drivers of cellular uptake, whereas excess hydrophobicity and positive charge at isolated amino acid positions can trigger membrane lysis at elevated peptide dosing. Our results provide a design roadmap for maximizing the potential to generate cell-permeable stapled peptides with on-mechanism cellular activity.
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Affiliation(s)
- Gregory H. Bird
- Department of Pediatric Oncology, Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215
| | - Emanuele Mazzola
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215
| | - Kwadwo Opoku-Nsiah
- Department of Pediatric Oncology, Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215
| | - Margaret A. Lammert
- Department of Pediatric Oncology, Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215
| | - Marina Godes
- Department of Pediatric Oncology, Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215
| | - Donna S. Neuberg
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215
| | - Loren D. Walensky
- Department of Pediatric Oncology, Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215
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47
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Stapled peptide design: principles and roles of computation. Drug Discov Today 2016; 21:1642-1653. [DOI: 10.1016/j.drudis.2016.06.012] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 05/11/2016] [Accepted: 06/13/2016] [Indexed: 12/23/2022]
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48
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Benjelloun F, Oruc Z, Thielens N, Verrier B, Champier G, Vincent N, Rochereau N, Girard A, Jospin F, Chanut B, Genin C, Cogné M, Paul S. First Membrane Proximal External Region–Specific Anti-HIV1 Broadly Neutralizing Monoclonal IgA1 Presenting Short CDRH3 and Low Somatic Mutations. THE JOURNAL OF IMMUNOLOGY 2016; 197:1979-88. [DOI: 10.4049/jimmunol.1600309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 07/03/2016] [Indexed: 11/19/2022]
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49
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Peraro L, Siegert TR, Kritzer JA. Conformational Restriction of Peptides Using Dithiol Bis-Alkylation. Methods Enzymol 2016; 580:303-32. [PMID: 27586339 DOI: 10.1016/bs.mie.2016.05.035] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Macrocyclic peptides are highly promising as inhibitors of protein-protein interactions. While many bond-forming reactions can be used to make cyclic peptides, most have limitations that make this chemical space challenging to access. Recently, a variety of cysteine alkylation reactions have been used in rational design and library approaches for cyclic peptide discovery and development. We and others have found that this chemistry is versatile and robust enough to produce a large variety of conformationally constrained cyclic peptides. In this chapter, we describe applications, methods, mechanistic insights, and troubleshooting for dithiol bis-alkylation reactions for the production of cyclic peptides. This method for efficient solution-phase macrocyclization is highly useful for the rapid production and screening of loop-based inhibitors of protein-protein interactions.
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Affiliation(s)
- L Peraro
- Tufts University, Medford, MA, United States
| | - T R Siegert
- Tufts University, Medford, MA, United States
| | - J A Kritzer
- Tufts University, Medford, MA, United States.
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50
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Gori A, Peri C, Quilici G, Nithichanon A, Gaudesi D, Longhi R, Gourlay L, Bolognesi M, Lertmemongkolchai G, Musco G, Colombo G. Flexible vs Rigid Epitope Conformations for Diagnostic- and Vaccine-Oriented Applications: Novel Insights from the Burkholderia pseudomallei BPSL2765 Pal3 Epitope. ACS Infect Dis 2016; 2:221-30. [PMID: 27623032 DOI: 10.1021/acsinfecdis.5b00118] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Peptides seldom retain stable conformations if separated from their native protein structure. In an immunological context, this potentially affects the development of selective peptide-based bioprobes and, from a vaccine perspective, poses inherent limits in the elicitation of cross-reactive antibodies by candidate epitopes. Here, a 1,4-disubstituted-1,2,3-triazole-mediated stapling strategy was used to stabilize the native α-helical fold of the Pal3 peptidic epitope from the protein antigen PalBp (BPSL2765) from Burkholderia pseudomallei, the etiological agent of melioidosis. Whereas Pal3 shows no propensity to fold outside its native protein context, the engineered peptide (Pal3H) forms a stable α-helix, as assessed by MD, NMR, and CD structural analyses. Importantly, Pal3H shows an enhanced ability to discriminate between melioidosis patient subclasses in immune sera reactivity tests, demonstrating the potential of the stapled peptide for diagnostic purposes. With regard to antibody elicitation and related bactericidal activities, the linear peptide is shown to elicit a higher response. On these bases, we critically discuss the implications of epitope structure engineering for diagnostic- and vaccine-oriented applications.
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Affiliation(s)
- Alessandro Gori
- Istituto di Chimica del Riconoscimento Molecolare,
Consiglio Nazionale delle Ricerche, Via Mario Bianco, 9, 20131, Milan, Italy
| | - Claudio Peri
- Istituto di Chimica del Riconoscimento Molecolare,
Consiglio Nazionale delle Ricerche, Via Mario Bianco, 9, 20131, Milan, Italy
| | - Giacomo Quilici
- Biomolecular NMR Laboratory,
Division of Genetics and Cell Biology, S. Raffaele Scientific Institute, 20132 Milan, Italy
| | - Arnone Nithichanon
- Center for Research and Development of
Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical
Sciences, Khon Kaen University, 40002, Khon Kaen, Thailand
| | - Davide Gaudesi
- Biomolecular NMR Laboratory,
Division of Genetics and Cell Biology, S. Raffaele Scientific Institute, 20132 Milan, Italy
| | - Renato Longhi
- Istituto di Chimica del Riconoscimento Molecolare,
Consiglio Nazionale delle Ricerche, Via Mario Bianco, 9, 20131, Milan, Italy
| | - Louise Gourlay
- Department of Biosciences, University of Milan, 20133, Milan, Italy
| | - Martino Bolognesi
- Department of Biosciences, University of Milan, 20133, Milan, Italy
- CNR-IBF and Cimaina,
c/o Department of Biosciences, University of Milan, 20133, Milan, Italy
| | - Ganjana Lertmemongkolchai
- Center for Research and Development of
Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical
Sciences, Khon Kaen University, 40002, Khon Kaen, Thailand
| | - Giovanna Musco
- Biomolecular NMR Laboratory,
Division of Genetics and Cell Biology, S. Raffaele Scientific Institute, 20132 Milan, Italy
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare,
Consiglio Nazionale delle Ricerche, Via Mario Bianco, 9, 20131, Milan, Italy
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