1
|
Polo-Megías D, Cano-Muñoz M, Berruezo AG, Laumond G, Moog C, Conejero-Lara F. Investigating vulnerability of the conserved SARS-CoV-2 spike's heptad repeat 2 as target for fusion inhibitors using chimeric miniproteins. Int J Biol Macromol 2024; 262:130132. [PMID: 38354919 DOI: 10.1016/j.ijbiomac.2024.130132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 02/09/2024] [Accepted: 02/10/2024] [Indexed: 02/16/2024]
Abstract
Inhibition of SARS-CoV-2 membrane fusion is a highly desired target to combat COVID-19. The interaction between the spike's heptad repeat (HR) regions 1 (HR1) and 2 (HR2) is a crucial step during the fusion process and these highly conserved HR regions constitute attractive targets for fusion inhibitors. However, the relative importance of each subregion of the long HR1-HR2 interface for viral inhibition remains unclear. Here, we designed, produced, and characterized a series of chimeric miniproteins that mimic two different half subdomains of HR1. The proteins were designed as single polypeptide chains that spontaneously fold into antiparallel trimeric helical bundles aimed at structurally imitate the molecular surface of each HR1 half subregion. All the miniproteins folded stably as helical structures and could bind complementary HR2 peptides with moderate affinity. However, only the miniproteins mimicking the N-terminal HR1 half subdomain, but not those imitating C-terminal one, could inhibit cell infection by SARS-COV-2 real viruses in cell cultures. Most interestingly, the inhibitory activity of the miniproteins correlated with their structural stability, but not with their relative binding affinity for HR2 peptides. These results are highly relevant for designing more focused and active fusion inhibitors targeting the highly conserved HR2 region of the Spike.
Collapse
Affiliation(s)
- Daniel Polo-Megías
- Departamento de Química Física, Instituto de Biotecnología y Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Mario Cano-Muñoz
- Departamento de Química Física, Instituto de Biotecnología y Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Alberto G Berruezo
- Departamento de Química Física, Instituto de Biotecnología y Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Géraldine Laumond
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1109, Institut Thématique Interdisciplinaire (ITI) de Médecine de Précision de Strasbourg, Transplantex NG, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, F-67000 Strasbourg, France
| | - Christiane Moog
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1109, Institut Thématique Interdisciplinaire (ITI) de Médecine de Précision de Strasbourg, Transplantex NG, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, F-67000 Strasbourg, France; Vaccine Research Institute (VRI), F-94000 Créteil, France
| | - Francisco Conejero-Lara
- Departamento de Química Física, Instituto de Biotecnología y Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
| |
Collapse
|
2
|
Reza D, Balo R, Otero JM, Fletcher AM, García-Fandino R, Sánchez-Pedregal VM, Davies SG, Estévez RJ, Estévez JC. β-Peptides incorporating polyhydroxylated cyclohexane β-amino acid: synthesis and conformational study. Org Biomol Chem 2023; 21:8535-8547. [PMID: 37840474 DOI: 10.1039/d3ob00906h] [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: 10/17/2023]
Abstract
We describe the synthesis of trihydroxylated cyclohexane β-amino acids from (-)-shikimic acid, in their cis and trans configuration, and the incorporation of the trans isomer into a trans-2-aminocyclohexanecarboxylic acid peptide chain. Subsequently, the hydroxyl groups were partially or totally deprotected. The structural study of the new peptides by FTIR, CD, solution NMR and DFT calculations revealed that they all fold into a 14-helix secondary structure, similarly to the homooligomer of trans-2-aminocyclohexanecarboxylic acid. This means that the high degree of substitution of the cyclohexane ring of the new residue is compatible with the adoption of a stable helical secondary structure and opens opportunities for the design of more elaborate peptidic foldamers with oriented polar substituents at selected positions of the cycloalkane residues.
Collapse
Affiliation(s)
- David Reza
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica. Universidade de Santiago de Compostela, c/Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain.
| | - Rosalino Balo
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica. Universidade de Santiago de Compostela, c/Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain.
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - José M Otero
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica. Universidade de Santiago de Compostela, c/Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain.
| | - Ai M Fletcher
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Rebeca García-Fandino
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica. Universidade de Santiago de Compostela, c/Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain.
- Departamento de Química Orgánica, Universidade de Santiago de Compostela, Avda. das Ciencias s/n, 15782 Santiago de Compostela, Spain
| | - Víctor M Sánchez-Pedregal
- Departamento de Química Orgánica, Universidade de Santiago de Compostela, Avda. das Ciencias s/n, 15782 Santiago de Compostela, Spain
| | - Stephen G Davies
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Ramón J Estévez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica. Universidade de Santiago de Compostela, c/Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain.
- Departamento de Química Orgánica, Universidade de Santiago de Compostela, Avda. das Ciencias s/n, 15782 Santiago de Compostela, Spain
| | - Juan C Estévez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica. Universidade de Santiago de Compostela, c/Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain.
- Departamento de Química Orgánica, Universidade de Santiago de Compostela, Avda. das Ciencias s/n, 15782 Santiago de Compostela, Spain
| |
Collapse
|
3
|
Sang P, Cai J. Unnatural helical peptidic foldamers as protein segment mimics. Chem Soc Rev 2023; 52:4843-4877. [PMID: 37401344 PMCID: PMC10389297 DOI: 10.1039/d2cs00395c] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Indexed: 07/05/2023]
Abstract
Unnatural helical peptidic foldamers have attracted considerable attention owing to their unique folding behaviours, diverse artificial protein binding mechanisms, and promising applications in chemical, biological, medical, and material fields. Unlike the conventional α-helix consisting of molecular entities of native α-amino acids, unnatural helical peptidic foldamers are generally comprised of well-defined backbone conformers with unique and unnatural structural parameters. Their folded structures usually arise from unnatural amino acids such as N-substituted glycine, N-substituted-β-alanine, β-amino acid, urea, thiourea, α-aminoxy acid, α-aminoisobutyric acid, aza-amino acid, aromatic amide, γ-amino acid, as well as sulfono-γ-AA amino acid. They can exhibit intriguing and predictable three-dimensional helical structures, generally featuring superior resistance to proteolytic degradation, enhanced bioavailability, and improved chemodiversity, and are promising in mimicking helical segments of various proteins. Although it is impossible to include every piece of research work, we attempt to highlight the research progress in the past 10 years in exploring unnatural peptidic foldamers as protein helical segment mimics, by giving some representative examples and discussing the current challenges and future perspectives. We expect that this review will help elucidate the principles of structural design and applications of existing unnatural helical peptidic foldamers in protein segment mimicry, thereby attracting more researchers to explore and generate novel unnatural peptidic foldamers with unique structural and functional properties, leading to more unprecedented and practical applications.
Collapse
Affiliation(s)
- Peng Sang
- Tianjian Laboratory of Advanced Biomedical Sciences, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China.
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, Tampa, FL 33620, USA.
| |
Collapse
|
4
|
Polo-Megías D, Cano-Muñoz M, Berruezo AG, Laumond G, Moog C, Conejero-Lara F. Exploring Highly Conserved Regions of SARS-CoV-2 Spike S2 Subunit as Targets for Fusion Inhibition Using Chimeric Proteins. Int J Mol Sci 2022; 23:ijms232415511. [PMID: 36555153 PMCID: PMC9778920 DOI: 10.3390/ijms232415511] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 11/23/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
Since the beginning of the COVID-19 pandemic, considerable efforts have been made to develop protective vaccines against SARS-CoV-2 infection. However, immunity tends to decline within a few months, and new virus variants are emerging with increased transmissibility and capacity to evade natural or vaccine-acquired immunity. Therefore, new robust strategies are needed to combat SARS-CoV-2 infection. The viral spike composed of S1 and S2 subunits mediates viral attachment and membrane fusion to infect the host cell. In this process, interaction between the highly conserved heptad repeat 1 and 2 regions (HR1 and HR2) of S2 is crucial and for this reason; these regions are promising targets to fight SARS-CoV-2. Here, we describe the design and characterization of chimeric proteins that structurally imitate the S2 HR1 region in a trimeric coiled-coil conformation. We biophysically characterized the proteins and determined their capacity to bind the HR2 region, as well as their inhibitory activity of SARS-CoV-2 infection in vitro. HR1 mimetic proteins showed conformational heterogeneity and a propensity to form oligomers. Moreover, their structure is composed of subdomains with varied stability. Interestingly, the full HR1 proteins showed high affinity for HR2-derived peptides and SARS-CoV-2 inhibitory activity, whereas smaller proteins mimicking HR1 subdomains had a decreased affinity for their complementary HR2 region and did not inhibit the virus. The results provide insight into effective strategies to create mimetic proteins with broad inhibitory activity and therapeutic potential against SARS-CoV-2.
Collapse
Affiliation(s)
- Daniel Polo-Megías
- Departamento de Química Física, Instituto de Biotecnología y Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Mario Cano-Muñoz
- Departamento de Química Física, Instituto de Biotecnología y Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Alberto G Berruezo
- Departamento de Química Física, Instituto de Biotecnología y Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Géraldine Laumond
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1109, Institut Thématique Interdisciplinaire (ITI) de Médecine de Précision de Strasbourg, Transplantex NG, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, F-67000 Strasbourg, France
| | - Christiane Moog
- Laboratoire d'ImmunoRhumatologie Moléculaire, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1109, Institut Thématique Interdisciplinaire (ITI) de Médecine de Précision de Strasbourg, Transplantex NG, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, F-67000 Strasbourg, France
- Vaccine Research Institute (VRI), F-94000 Créteil, France
| | - Francisco Conejero-Lara
- Departamento de Química Física, Instituto de Biotecnología y Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| |
Collapse
|
5
|
Huhmann S, Nyakatura EK, Rohrhofer A, Moschner J, Schmidt B, Eichler J, Roth C, Koksch B. Systematic Evaluation of Fluorination as Modification for Peptide-Based Fusion Inhibitors against HIV-1 Infection. Chembiochem 2021; 22:3443-3451. [PMID: 34605595 PMCID: PMC9297971 DOI: 10.1002/cbic.202100417] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 10/04/2021] [Indexed: 01/01/2023]
Abstract
With the emergence of novel viruses, the development of new antivirals is more urgent than ever. A key step in human immunodeficiency virus type 1 (HIV-1) infection is six-helix bundle formation within the envelope protein subunit gp41. Selective disruption of bundle formation by peptides has been shown to be effective; however, these drugs, exemplified by T20, are prone to rapid clearance from the patient. The incorporation of non-natural amino acids is known to improve these pharmacokinetic properties. Here, we evaluate a peptide inhibitor in which a critical Ile residue is replaced by fluorinated analogues. We characterized the influence of the fluorinated analogues on the biophysical properties of the peptide. Furthermore, we show that the fluorinated peptides can block HIV-1 infection of target cells at nanomolar levels. These findings demonstrate that fluorinated amino acids are appropriate tools for the development of novel peptide therapeutics.
Collapse
Affiliation(s)
- Susanne Huhmann
- Freie Universität BerlinDepartment of Biology, Chemistry and PharmacyInstitute of Chemistry and BiochemistryArnimallee 2014195BerlinGermany
| | - Elisabeth K. Nyakatura
- Freie Universität BerlinDepartment of Biology, Chemistry and PharmacyInstitute of Chemistry and BiochemistryArnimallee 2014195BerlinGermany
- Antibody Engineering Tri-Institutional Therapeutics Discovery Institute417 East 68th Street, 19 Floor North, P: 646-888-2003New YorkNY 10021USA
| | - Anette Rohrhofer
- Institute of Clinical Microbiology and HygieneRegensburg University HospitalFranz-Josef-Strauß-Allee 1193053RegensburgGermany
| | - Johann Moschner
- Freie Universität BerlinDepartment of Biology, Chemistry and PharmacyInstitute of Chemistry and BiochemistryArnimallee 2014195BerlinGermany
| | - Barbara Schmidt
- Institute of Clinical Microbiology and HygieneRegensburg University HospitalFranz-Josef-Strauß-Allee 1193053RegensburgGermany
| | - Jutta Eichler
- Friedrich-Alexander-Universität Erlangen-NürnbergDepartment Chemie und PharmazieNikolaus-Fiebiger-Str. 1091058ErlangenGermany
| | - Christian Roth
- Max Planck Institute of Colloids and InterfacesBiomolecular SystemsArnimallee 2214195BerlinGermany
| | - Beate Koksch
- Freie Universität BerlinDepartment of Biology, Chemistry and PharmacyInstitute of Chemistry and BiochemistryArnimallee 2014195BerlinGermany
| |
Collapse
|
6
|
Conformational flexibility of the conserved hydrophobic pocket of HIV-1 gp41. Implications for the discovery of small-molecule fusion inhibitors. Int J Biol Macromol 2021; 192:90-99. [PMID: 34619276 DOI: 10.1016/j.ijbiomac.2021.09.198] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/24/2021] [Accepted: 09/29/2021] [Indexed: 11/21/2022]
Abstract
During HIV-1 infection, the envelope glycoprotein subunit gp41 folds into a six-helix bundle structure (6HB) formed by the interaction between its N-terminal (NHR) and C-terminal (CHR) heptad-repeats, promoting viral and cell membranes fusion. A highly preserved, hydrophobic pocket (HP) on the NHR surface is crucial in 6HB formation and, therefore, HP-binding compounds constitute promising therapeutics against HIV-1. Here, we investigated the conformational and dynamic properties of the HP using a rationally designed single-chain protein (named covNHR) that mimics the gp41 NHR structure. We found that the fluorescent dye 8-anilino-naphtalene-1-sulfonic acid (ANS) binds specifically to the HP, suggesting that ANS derivatives may constitute lead compounds to inhibit 6HB formation. ANS shows different binding modes to the HP, depending on the occupancy of other NHR pockets. Moreover, in presence of a CHR peptide bound to the N-terminal pockets in gp41, two ANS molecules can occupy the HP showing cooperative behavior. This binding mode was assessed using molecular docking and molecular dynamics simulations. The results show that the HP is conformationally flexible and connected allosterically to other NHR regions, which strongly influence the binding of potential ligands. These findings could guide the development of small-molecule HIV-1 inhibitors targeting the HP.
Collapse
|
7
|
Outlaw VK, Cheloha RW, Jurgens EM, Bovier FT, Zhu Y, Kreitler DF, Harder O, Niewiesk S, Porotto M, Gellman SH, Moscona A. Engineering Protease-Resistant Peptides to Inhibit Human Parainfluenza Viral Respiratory Infection. J Am Chem Soc 2021; 143:5958-5966. [PMID: 33825470 DOI: 10.1021/jacs.1c01565] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The lower respiratory tract infections affecting children worldwide are in large part caused by the parainfluenza viruses (HPIVs), particularly HPIV3, along with human metapneumovirus and respiratory syncytial virus, enveloped negative-strand RNA viruses. There are no vaccines for these important human pathogens, and existing treatments have limited or no efficacy. Infection by HPIV is initiated by viral glycoprotein-mediated fusion between viral and host cell membranes. A viral fusion protein (F), once activated in proximity to a target cell, undergoes a series of conformational changes that first extend the trimer subunits to allow insertion of the hydrophobic domains into the target cell membrane and then refold the trimer into a stable postfusion state, driving the merger of the viral and host cell membranes. Lipopeptides derived from the C-terminal heptad repeat (HRC) domain of HPIV3 F inhibit infection by interfering with the structural transitions of the trimeric F assembly. Clinical application of this strategy, however, requires improving the in vivo stability of antiviral peptides. We show that the HRC peptide backbone can be modified via partial replacement of α-amino acid residues with β-amino acid residues to generate α/β-peptides that retain antiviral activity but are poor protease substrates. Relative to a conventional α-lipopeptide, our best α/β-lipopeptide exhibits improved persistence in vivo and improved anti-HPIV3 antiviral activity in animals.
Collapse
Affiliation(s)
- Victor K Outlaw
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Ross W Cheloha
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Eric M Jurgens
- Department of Pediatrics, Columbia University Vagelos College of Physicians & Surgeons, New York, New York 10032, United States
| | - Francesca T Bovier
- Department of Pediatrics, Columbia University Vagelos College of Physicians & Surgeons, New York, New York 10032, United States.,Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Caserta, 81100, Italy.,Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians & Surgeons, New York, New York 10032, United States
| | - Yun Zhu
- Department of Pediatrics, Columbia University Vagelos College of Physicians & Surgeons, New York, New York 10032, United States.,Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians & Surgeons, New York, New York 10032, United States.,Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing 100045, China
| | - Dale F Kreitler
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Olivia Harder
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Stefan Niewiesk
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Matteo Porotto
- Department of Pediatrics, Columbia University Vagelos College of Physicians & Surgeons, New York, New York 10032, United States.,Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Caserta, 81100, Italy.,Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians & Surgeons, New York, New York 10032, United States
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Anne Moscona
- Department of Pediatrics, Columbia University Vagelos College of Physicians & Surgeons, New York, New York 10032, United States.,Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians & Surgeons, New York, New York 10032, United States.,Department of Microbiology & Immunology, Columbia University Vagelos College of Physicians & Surgeons, New York, New York 10032, United States.,Department of Physiology & Cellular Biophysics, Columbia University Vagelos College of Physicians & Surgeons, New York, New York 10032, United States
| |
Collapse
|
8
|
Jurado S, Moog C, Cano-Muñoz M, Schmidt S, Laumond G, Ruocco V, Standoli S, Polo-Megías D, Conejero-Lara F, Morel B. Probing Vulnerability of the gp41 C-Terminal Heptad Repeat as Target for Miniprotein HIV Inhibitors. J Mol Biol 2020; 432:5577-5592. [PMID: 32822695 DOI: 10.1016/j.jmb.2020.08.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/09/2020] [Accepted: 08/10/2020] [Indexed: 12/20/2022]
Abstract
One of the therapeutic strategies in HIV neutralization is blocking membrane fusion. In this process, tight interaction between the N-terminal and C-terminal heptad-repeat (NHR and CHR) regions of gp41 is essential to promote membranes apposition and merging. We have previously developed single-chain proteins (named covNHR) that accurately mimic the complete gp41 NHR region in its trimeric conformation. They tightly bind CHR-derived peptides and show a potent and broad HIV inhibitory activity in vitro. However, the extremely high binding affinity (sub-picomolar) is not in consonance with their inhibitory activity (nanomolar), likely due to partial or temporal accessibility of their target in the virus. Here, we have designed and characterized two single-chain covNHR miniproteins each encompassing one of the two halves of the NHR region and containing two of the four sub-pockets of the NHR crevice. The two miniproteins fold as trimeric helical bundles as expected but while the C-terminal covNHR (covNHR-C) miniprotein is highly stable, the N-terminal counterpart (covNHR-N) shows only marginal stability that could be improved by engineering an internal disulfide bond. Both miniproteins bind their respective complementary CHR peptides with moderate (micromolar) affinity. Moreover, the covNHR-N miniproteins can access their target in the context of trimeric native envelope proteins and show significant inhibitory activity for several HIV pseudoviruses. In contrast, covNHR-C cannot bind its target sequence and neither inhibits HIV, indicating a higher vulnerability of C-terminal part of CHR. These results may guide the development of novel HIV inhibitors targeting the gp41 CHR region.
Collapse
Affiliation(s)
- Samuel Jurado
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Christiane Moog
- INSERM U1109, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Mario Cano-Muñoz
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Sylvie Schmidt
- INSERM U1109, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Géraldine Laumond
- INSERM U1109, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Valentina Ruocco
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Sara Standoli
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Daniel Polo-Megías
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Francisco Conejero-Lara
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
| | - Bertrand Morel
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
| |
Collapse
|
9
|
Outlaw VK, Kreitler DF, Stelitano D, Porotto M, Moscona A, Gellman SH. Effects of Single α-to-β Residue Replacements on Recognition of an Extended Segment in a Viral Fusion Protein. ACS Infect Dis 2020; 6:2017-2022. [PMID: 32692914 PMCID: PMC8019249 DOI: 10.1021/acsinfecdis.0c00385] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Partial replacement of α-amino acid residues with β-amino acid residues has been established as a strategy for preserving target-engagement by helix-forming polypeptides while altering other properties. The impact of β-residue incorporation within polypeptides that adopt less regular conformations, however, has received less attention. The C-terminal heptad repeat (HRC) domains of fusion glycoproteins from pathogenic paramyxoviruses contain a segment that must adopt an extended conformation in order to coassemble with the N-terminal heptad repeat (HRN) domain in the postfusion state and drive a merger of the viral envelope with a target cell membrane. Here, we examine the impact of single α-to-β substitutions within this extended N-terminal segment of an engineered HRC peptide designated VIQKI. Stabilities of hexameric coassemblies formed with the native human parainfluenza virus 3 (HPIV3) HRN have been evaluated, the structures of five coassemblies have been determined, and antiviral efficacies have been measured. Many sites within the extended segment show functional tolerance of α-to-β substitution. These results offer a basis for future development of paramyxovirus infection inhibitors with novel biological activity profiles, possibly including resistance to proteolysis.
Collapse
Affiliation(s)
- Victor K. Outlaw
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, 53706, United States
| | - Dale F. Kreitler
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, 53706, United States
| | - Debora Stelitano
- Department of Pediatrics, Columbia University Medical Center, New York, New York, 10032, United States
- Center for Host–Pathogen Interaction, Columbia University Medical Center, New York, New York, 10032, United States
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 81100 Caserta, Italy
| | - Matteo Porotto
- Department of Pediatrics, Columbia University Medical Center, New York, New York, 10032, United States
- Center for Host–Pathogen Interaction, Columbia University Medical Center, New York, New York, 10032, United States
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 81100 Caserta, Italy
| | - Anne Moscona
- Department of Pediatrics, Columbia University Medical Center, New York, New York, 10032, United States
- Center for Host–Pathogen Interaction, Columbia University Medical Center, New York, New York, 10032, United States
- Department of Microbiology & Immunology, Columbia University Medical Center, New York, New York, 10032, United States
- Department of Physiology & Cellular Biophysics, Columbia University Medical Center, New York, New York, 10032, United States
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, 53706, United States
| |
Collapse
|
10
|
Jurado S, Cano-Muñoz M, Polo-Megías D, Conejero-Lara F, Morel B. Thermodynamic dissection of the interface between HIV-1 gp41 heptad repeats reveals cooperative interactions and allosteric effects. Arch Biochem Biophys 2020; 688:108401. [PMID: 32376316 DOI: 10.1016/j.abb.2020.108401] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/03/2020] [Accepted: 04/27/2020] [Indexed: 11/27/2022]
Abstract
HIV-1 glycoprotein 41 (gp41) mediates fusion between virus and target cells by folding into a fusion active state, in which the C-terminal heptad repeat (CHR) regions associate externally to the N-terminal heptad repeat (NHR) trimer and form a very stable six-helix bundle coiled-coil structure. Therefore, interfering with the NHR-CHR interaction of gp41 is a promising therapeutic approach against HIV-1. However, a full understanding of the molecular and mechanistic details of this interaction is still incomplete. Here, we use single-chain, chimeric proteins (named covNHR) that reproduce accurately the CHR-NHR interactions to analyze the binding thermodynamics of several peptides with different length from the CHR region. The results indicate that cooperative binding involving two or more pockets of the NHR groove is necessary to obtain relevant affinities and that the binding energy is broadly distributed along the interface, underlining a crucial role of a middle pocket to achieve tight binding. In contrast, targeting only the deep hydrophobic pocket is insufficient to achieve significant affinity. Moreover, calorimetry experiments in combination with limited proteolysis performed using a mutant with occluded binding in the N-terminal pocket reveal the existence of an allosteric communication between the different regions. This study is the first detailed thermodynamic dissection of the NHR-CHR interaction in gp41 and contributes therefore to a better understanding of HIV fusion. These results are relevant for the development of potential fusion inhibitors.
Collapse
Affiliation(s)
- Samuel Jurado
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Mario Cano-Muñoz
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Daniel Polo-Megías
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Francisco Conejero-Lara
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
| | - Bertrand Morel
- Departamento de Química Física, Instituto de Biotecnología e Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
| |
Collapse
|
11
|
Sadek J, Wuo MG, Rooklin D, Hauenstein A, Hong SH, Gautam A, Wu H, Zhang Y, Cesarman E, Arora PS. Modulation of virus-induced NF-κB signaling by NEMO coiled coil mimics. Nat Commun 2020; 11:1786. [PMID: 32286300 PMCID: PMC7156456 DOI: 10.1038/s41467-020-15576-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 03/12/2020] [Indexed: 01/07/2023] Open
Abstract
Protein-protein interactions featuring intricate binding epitopes remain challenging targets for synthetic inhibitors. Interactions of NEMO, a scaffolding protein central to NF-κB signaling, exemplify this challenge. Various regulators are known to interact with different coiled coil regions of NEMO, but the topological complexity of this protein has limited inhibitor design. We undertook a comprehensive effort to block the interaction between vFLIP, a Kaposi’s sarcoma herpesviral oncoprotein, and NEMO using small molecule screening and rational design. Our efforts reveal that a tertiary protein structure mimic of NEMO is necessary for potent inhibition. The rationally designed mimic engages vFLIP directly causing complex disruption, protein degradation and suppression of NF-κB signaling in primary effusion lymphoma (PEL). NEMO mimic treatment induces cell death and delays tumor growth in a PEL xenograft model. Our studies with this inhibitor reveal the critical nexus of signaling complex stability in the regulation of NF-κB by a viral oncoprotein. NF-κB signalling involves the scaffold protein NEMO, which can be bound by the oncoprotein vFLIP to promote cell survival and oncogenic transformation. Here the authors rationally engineer a tertiary protein mimic of NEMO to disrupt the vFLIP-NEMO interaction to induce cell death.
Collapse
Affiliation(s)
- Jouliana Sadek
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Michael G Wuo
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - David Rooklin
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Arthur Hauenstein
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Seong Ho Hong
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Archana Gautam
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029-5674, USA
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, NY, 10003, USA.,NYU-ECNU Center for Computational Chemistry, New York University-Shanghai, 200122, Shanghai, China
| | - Ethel Cesarman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, 10065, USA.
| | - Paramjit S Arora
- Department of Chemistry, New York University, New York, NY, 10003, USA.
| |
Collapse
|
12
|
Andrei SA, Thijssen V, Brunsveld L, Ottmann C, Milroy LG. A study on the effect of synthetic α-to-β 3-amino acid mutations on the binding of phosphopeptides to 14-3-3 proteins. Chem Commun (Camb) 2020; 55:14809-14812. [PMID: 31763628 DOI: 10.1039/c9cc07982c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Here we describe the synthesis of a series of α,β-phosphopeptides, based on the phosphoepitope site on YAP1 (yes-associated protein 1), and the biochemical, biophysical and structural characterization of their binding to 14-3-3 proteins. The impact of systematic mono- and di-substitution of α → β3 amino acid residues around the phosphoserine residue are discussed. Our results confirm the important role played by the +2 proline residue in the thermodynamics and structure of the phosphoepitope/14-3-3 interaction.
Collapse
Affiliation(s)
- Sebastian A Andrei
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands.
| | | | | | | | | |
Collapse
|
13
|
Cheloha RW, Woodham AW, Bousbaine D, Wang T, Liu S, Sidney J, Sette A, Gellman SH, Ploegh HL. Recognition of Class II MHC Peptide Ligands That Contain β-Amino Acids. THE JOURNAL OF IMMUNOLOGY 2019; 203:1619-1628. [PMID: 31391235 DOI: 10.4049/jimmunol.1900536] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 07/05/2019] [Indexed: 12/12/2022]
Abstract
Proteins are composed of α-amino acid residues. This consistency in backbone structure likely serves an important role in the display of an enormous diversity of peptides by class II MHC (MHC-II) products, which make contacts with main chain atoms of their peptide cargo. Peptides that contain residues with an extra carbon in the backbone (derived from β-amino acids) have biological properties that differ starkly from those of their conventional counterparts. How changes in the structure of the peptide backbone affect the loading of peptides onto MHC-II or recognition of the resulting complexes by TCRs has not been widely explored. We prepared a library of analogues of MHC-II-binding peptides derived from OVA, in which at least one α-amino acid residue was replaced with a homologous β-amino acid residue. The latter contain an extra methylene unit in the peptide backbone but retain the original side chain. We show that several of these α/β-peptides retain the ability to bind tightly to MHC-II, activate TCR signaling, and induce responses from T cells in mice. One α/β-peptide exhibited enhanced stability in the presence of an endosomal protease relative to the index peptide. Conjugation of this backbone-modified peptide to a camelid single-domain Ab fragment specific for MHC-II enhanced its biological activity. Our results suggest that backbone modification offers a method to modulate MHC binding and selectivity, T cell stimulatory capacity, and susceptibility to processing by proteases such as those found within endosomes where Ag processing occurs.
Collapse
Affiliation(s)
- Ross W Cheloha
- Boston Children's Hospital and Harvard Medical School, Boston, MA 02115
| | - Andrew W Woodham
- Boston Children's Hospital and Harvard Medical School, Boston, MA 02115
| | - Djenet Bousbaine
- Boston Children's Hospital and Harvard Medical School, Boston, MA 02115.,Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Tong Wang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Shi Liu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037; and
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037; and.,Department of Medicine, University of California San Diego, La Jolla, CA 92161
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706;
| | - Hidde L Ploegh
- Boston Children's Hospital and Harvard Medical School, Boston, MA 02115;
| |
Collapse
|
14
|
Yamamoto M, Du Q, Song J, Wang H, Watanabe A, Tanaka Y, Kawaguchi Y, Inoue JI, Matsuda Z. Cell-cell and virus-cell fusion assay-based analyses of alanine insertion mutants in the distal α9 portion of the JRFL gp41 subunit from HIV-1. J Biol Chem 2019; 294:5677-5687. [PMID: 30737278 DOI: 10.1074/jbc.ra118.004579] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 02/04/2019] [Indexed: 12/28/2022] Open
Abstract
Membrane fusion is the first essential step in HIV-1 replication. The gp41 subunit of HIV-1 envelope protein (Env), a class I fusion protein, achieves membrane fusion by forming a structure called a six-helix bundle composed of N- and C-terminal heptad repeats. We have recently shown that the distal portion of the α9 helix in the C-terminal heptad repeat of X4-tropic HXB2 Env plays a critical role in the late-stage membrane fusion and viral infection. Here, we used R5-tropic JRFL Env and constructed six alanine insertion mutants, 641+A to 646+A, in the further distal portion of α9 where several glutamine residues are conserved (the number corresponds to the position of the inserted alanine in JRFL Env). 644+A showed the most severe defect in syncytia formation. Decreased fusion pore formation activity, revealed by a dual split protein assay, was observed in all mutants except 641+A. Sequence analysis and substitution of inserted 644A with Gln revealed that the glutamine residue at position 644 that forms complex hydrogen-bond networks with other polar residues on the surface of the six-helix bundle is critical for cell-cell fusion. We also developed a split NanoLuc® (Nluc) reporter-based assay specific to the virus-cell membrane fusion step to analyze several of the mutants. Interestingly syncytia-competent mutants failed to display Nluc activities. In addition to defective fusion activity, a reduction of Env incorporation into virions may further contribute to differences in cell-cell and virus-cell fusions.
Collapse
Affiliation(s)
- Mizuki Yamamoto
- From the Research Center for Asian Infectious Diseases.,the Division of Cellular and Molecular Biology, and
| | - Qingling Du
- the Laboratory of Structural Virology and Immunology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100864, 100101 China, and
| | - Jiping Song
- the Laboratory of Structural Virology and Immunology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100864, 100101 China, and
| | - Hongyun Wang
- the Laboratory of Structural Virology and Immunology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100864, 100101 China, and
| | - Aya Watanabe
- From the Research Center for Asian Infectious Diseases.,the Division of Cellular and Molecular Biology, and
| | - Yuetsu Tanaka
- the Department of Immunology, Graduate School of Medicine, University of the Ryukyus, Okinawa 903-0215, Japan
| | - Yasushi Kawaguchi
- From the Research Center for Asian Infectious Diseases.,the Division of Molecular Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Jun-Ichiro Inoue
- From the Research Center for Asian Infectious Diseases, .,the Division of Cellular and Molecular Biology, and
| | - Zene Matsuda
- From the Research Center for Asian Infectious Diseases, .,the Laboratory of Structural Virology and Immunology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100864, 100101 China, and
| |
Collapse
|
15
|
de Lucio H, Gamo AM, Ruiz-Santaquiteria M, de Castro S, Sánchez-Murcia PA, Toro MA, Gutiérrez KJ, Gago F, Jiménez-Ruiz A, Camarasa MJ, Velázquez S. Improved proteolytic stability and potent activity against Leishmania infantum trypanothione reductase of α/β-peptide foldamers conjugated to cell-penetrating peptides. Eur J Med Chem 2017; 140:615-623. [DOI: 10.1016/j.ejmech.2017.09.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 08/30/2017] [Accepted: 09/18/2017] [Indexed: 02/06/2023]
|
16
|
Mándity IM, Nekkaa I, Paragi G, Fülöp F. Homochirality of β-Peptides: A Significant Biomimetic Property of Unnatural Systems. ChemistryOpen 2017; 6:492-496. [PMID: 28794942 PMCID: PMC5542748 DOI: 10.1002/open.201700078] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Indexed: 01/10/2023] Open
Abstract
Homochirality, an interesting phenomenon of life, is mainly an unresolved problem and was thought to be a property of living matter. Herein, we show that artificial β-peptides have the tendency toward homochiral diastereoselective chain elongation. Chain-length-dependent stereochemical discrimination was investigated in the synthesis of foldamers with various side chains and secondary structures. It was found that there is a strong tendency toward the synthesis of homochiral oligomers. The size of the side chain drastically influenced the selectivity of the stereodiscriminative chain-elongation reaction. It is noteworthy that water as the co-solvent increases the selectivity. Such behavior is a novel fundamental biomimetic property of foldamers with a potential of future industrial application.
Collapse
Affiliation(s)
- István M. Mándity
- Institute of Pharmaceutical ChemistryUniversity of SzegedEötvös u. 66720SzegedHungary
| | - Imane Nekkaa
- Institute of Pharmaceutical ChemistryUniversity of SzegedEötvös u. 66720SzegedHungary
| | - Gábor Paragi
- MTA-SZTE Supramolecular and Nanostructured Materials Research GroupDóm tér 86720SzegedHungary
| | - Ferenc Fülöp
- Institute of Pharmaceutical ChemistryUniversity of SzegedEötvös u. 66720SzegedHungary
- Research Group of Stereochemistry of the Hungarian Academy of SciencesDóm tér 86720SzegedHungary
| |
Collapse
|
17
|
Checco JW, Gellman SH. Iterative Nonproteinogenic Residue Incorporation Yields α/β-Peptides with a Helix-Loop-Helix Tertiary Structure and High Affinity for VEGF. Chembiochem 2017; 18:291-299. [PMID: 27897370 DOI: 10.1002/cbic.201600545] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Indexed: 12/12/2022]
Abstract
Inhibition of specific protein-protein interactions is attractive for a range of therapeutic applications, but the large and irregularly shaped contact surfaces involved in many such interactions make it challenging to design synthetic antagonists. Here, we describe the development of backbone-modified peptides containing both α- and β-amino acid residues (α/β-peptides) that target the receptor-binding surface of vascular endothelial growth factor (VEGF). Our approach is based on the Z-domain, which adopts a three-helix bundle tertiary structure. We show how a two-helix "mini-Z-domain" can be modified to contain β and other nonproteinogenic residues while retaining the target-binding epitope by using iterative unnatural residue incorporation. The resulting α/β-peptides are less susceptible to proteolysis than is their parent α-peptide, and some of these α/β-peptides match the full-length Z-domain in terms of affinity for receptor-recognition surfaces on the VEGF homodimer.
Collapse
Affiliation(s)
- James W Checco
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin, 53706, USA
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin, 53706, USA
| |
Collapse
|
18
|
Gopalakrishnan R, Frolov AI, Knerr L, Drury WJ, Valeur E. Therapeutic Potential of Foldamers: From Chemical Biology Tools To Drug Candidates? J Med Chem 2016; 59:9599-9621. [PMID: 27362955 DOI: 10.1021/acs.jmedchem.6b00376] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Over the past decade, foldamers have progressively emerged as useful architectures to mimic secondary structures of proteins. Peptidic foldamers, consisting of various amino acid based backbones, have been the most studied from a therapeutic perspective, while polyaromatic foldamers have barely evolved from their nascency and remain perplexing for medicinal chemists due to their poor drug-like nature. Despite these limitations, this compound class may still offer opportunities to study challenging targets or provide chemical biology tools. The potential of foldamer drug candidates reaching the clinic is still a stretch. Nevertheless, advances in the field have demonstrated their potential for the discovery of next generation therapeutics. In this perspective, the current knowledge of foldamers is reviewed in a drug discovery context. Recent advances in the early phases of drug discovery including hit finding, target validation, and optimization and molecular modeling are discussed. In addition, challenges and focus areas are debated and gaps highlighted.
Collapse
Affiliation(s)
- Ranganath Gopalakrishnan
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca , Pepparedsleden 1, Mölndal, 431 83, Sweden.,AstraZeneca MPI Satellite Unit, Department of Chemical Biology, Max Planck Institute of Molecular Physiology , Dortmund 44202, Germany
| | - Andrey I Frolov
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca , Pepparedsleden 1, Mölndal, 431 83, Sweden
| | - Laurent Knerr
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca , Pepparedsleden 1, Mölndal, 431 83, Sweden
| | - William J Drury
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca , Pepparedsleden 1, Mölndal, 431 83, Sweden
| | - Eric Valeur
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca , Pepparedsleden 1, Mölndal, 431 83, Sweden
| |
Collapse
|
19
|
Watkins A, Wuo MG, Arora PS. Protein-Protein Interactions Mediated by Helical Tertiary Structure Motifs. J Am Chem Soc 2015; 137:11622-30. [PMID: 26302018 PMCID: PMC4577960 DOI: 10.1021/jacs.5b05527] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Indexed: 12/26/2022]
Abstract
The modulation of protein-protein interactions (PPIs) by means of creating or stabilizing secondary structure conformations is a rapidly growing area of research. Recent success in the inhibition of difficult PPIs by secondary structure mimetics also points to potential limitations, because often, specific cases require tertiary structure mimetics. To streamline protein structure-based inhibitor design, we have previously described the examination of protein complexes in the Protein Data Bank where α-helices or β-strands form critical contacts. Here, we examined coiled coils and helix bundles that mediate complex formation to create a platform for the discovery of potential tertiary structure mimetics. Though there has been extensive analysis of coiled coil motifs, the interactions between pre-formed coiled coils and globular proteins have not been systematically analyzed. This article identifies critical features of these helical interfaces with respect to coiled coil and other helical PPIs. We expect the analysis to prove useful for the rational design of modulators of this fundamental class of protein assemblies.
Collapse
Affiliation(s)
- Andrew
M. Watkins
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Michael G. Wuo
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Paramjit S. Arora
- Department of Chemistry, New York University, New York, New York 10003, United States
| |
Collapse
|
20
|
Mándity IM, Fülöp F. An overview of peptide and peptoid foldamers in medicinal chemistry. Expert Opin Drug Discov 2015; 10:1163-77. [PMID: 26289578 DOI: 10.1517/17460441.2015.1076790] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Foldamers are artificial self-organizing systems with various critical properties: i) a stable and designable secondary structure; ii) a larger molecular surface as compared with ordinary organic drug molecules; iii) appropriate control of the orientation of the side-chain functional groups; iv) resistance against proteolytic degradation, which leads to potentially increased oral bioavailability and a longer serum half-life relative to ordinary α-peptides; and v) the lower conformational freedom may result in increased receptor binding in comparison with the natural analogs. AREAS COVERED This article covers the general properties and types of foldamers. This includes highlighted examples of medicinal chemical applications, including antibacterial and cargo molecules, anti-Alzheimer compounds and protein-protein interaction modifiers. EXPERT OPINION Various new foldamers have been created with a range of structures and biological applications. Membrane-acting antibacterial foldamers have been introduced. A general property of these structures is their amphiphilic nature. The amphiphilicity can be stationary or induced by the membrane binding. Cell-penetrating foldamers have been described which serve as cargo molecules, and foldamers have been used as autophagy inducers. Anti-Alzheimer compounds too have been created and the greatest breakthrough was attained via the modification of protein-protein interactions. This can serve as the chemical and pharmaceutical basis for the relevance of foldamers in the future.
Collapse
Affiliation(s)
| | - Ferenc Fülöp
- a University of Szeged Institute of Pharmaceutical Chemistry , H-6720 Szeged, Eötvös u. 6, Hungary +36 62 545 768 ; +36 62 545 564 ; +36 62 545 705 ; ;
| |
Collapse
|
21
|
Cabrele C, Martinek TA, Reiser O, Berlicki Ł. Peptides Containing β-Amino Acid Patterns: Challenges and Successes in Medicinal Chemistry. J Med Chem 2014; 57:9718-39. [DOI: 10.1021/jm5010896] [Citation(s) in RCA: 182] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Chiara Cabrele
- Department
of Molecular Biology, University of Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria
| | - Tamás A. Martinek
- SZTE-MTA
Lendulet Foldamer Research Group, Institute of Pharmaceutical Analysis, University of Szeged, Somogyi u. 6., H-6720 Szeged, Hungary
| | - Oliver Reiser
- Institute
of Organic Chemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Łukasz Berlicki
- Department
of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| |
Collapse
|
22
|
Abstract
Virus-cell fusion is the primary means by which the human immunodeficiency virus-1 (HIV) delivers its genetic material into the human T-cell host. Fusion is mediated in large part by the viral glycoprotein 41 (gp41) which advances through four distinct conformational states: (i) native, (ii) pre-hairpin intermediate, (iii) fusion active (fusogenic), and (iv) post-fusion. The pre-hairpin intermediate is a particularly attractive step for therapeutic intervention given that gp41 N-terminal heptad repeat (NHR) and C-terminal heptad repeat (CHR) domains are transiently exposed prior to the formation of a six-helix bundle required for fusion. Most peptide-based inhibitors, including the FDA-approved drug T20, target the intermediate and there are significant efforts to develop small molecule alternatives. Here, we review current approaches to studying interactions of inhibitors with gp41 with an emphasis on atomic-level computer modeling methods including molecular dynamics, free energy analysis, and docking. Atomistic modeling yields a unique level of structural and energetic detail, complementary to experimental approaches, which will be important for the design of improved next generation anti-HIV drugs.
Collapse
|
23
|
Jadhav SV, Misra R, Singh SK, Gopi HN. Efficient Access to Enantiopure γ4-Amino Acids with Proteinogenic Side-Chains and Structural Investigation of γ4-Asn and γ4-Ser in Hybrid Peptide Helices. Chemistry 2013; 19:16256-62. [DOI: 10.1002/chem.201302732] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Indexed: 01/09/2023]
|
24
|
Raj M, Bullock BN, Arora PS. Plucking the high hanging fruit: a systematic approach for targeting protein-protein interactions. Bioorg Med Chem 2013; 21:4051-7. [PMID: 23267671 PMCID: PMC3622812 DOI: 10.1016/j.bmc.2012.11.023] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 11/08/2012] [Accepted: 11/14/2012] [Indexed: 10/27/2022]
Abstract
Development of specific ligands for protein targets that help decode the complexities of protein-protein interaction networks is a key goal for the field of chemical biology. Despite the emergence of powerful in silico and experimental high-throughput screening strategies, the discovery of synthetic ligands that selectively modulate protein-protein interactions remains a challenge for bioorganic and medicinal chemists. This Perspective discusses emerging principles for the rational design of PPI inhibitors. Fundamentally, the approach seeks to adapt nature's protein recognition principles for the design of suitable secondary structure mimetics.
Collapse
Affiliation(s)
- Monika Raj
- Department of Chemistry, New York University, NY 10003, USA
| | | | | |
Collapse
|
25
|
Szolnoki É, Hetényi A, Mándity IM, Fülöp F, Martinek TA. Foldameric β-H18/20PMixed Helix Stabilized by Head-to-Tail Contacts: A Way to Higher-Order Structures. European J Org Chem 2013. [DOI: 10.1002/ejoc.201201633] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
26
|
Truncated and helix-constrained peptides with high affinity and specificity for the cFos coiled-coil of AP-1. PLoS One 2013; 8:e59415. [PMID: 23544065 PMCID: PMC3609778 DOI: 10.1371/journal.pone.0059415] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 02/14/2013] [Indexed: 01/20/2023] Open
Abstract
Protein-based therapeutics feature large interacting surfaces. Protein folding endows structural stability to localised surface epitopes, imparting high affinity and target specificity upon interactions with binding partners. However, short synthetic peptides with sequences corresponding to such protein epitopes are unstructured in water and promiscuously bind to proteins with low affinity and specificity. Here we combine structural stability and target specificity of proteins, with low cost and rapid synthesis of small molecules, towards meeting the significant challenge of binding coiled coil proteins in transcriptional regulation. By iteratively truncating a Jun-based peptide from 37 to 22 residues, strategically incorporating i→i+4 helix-inducing constraints, and positioning unnatural amino acids, we have produced short, water-stable, α-helical peptides that bind cFos. A three-dimensional NMR-derived structure for one peptide (24) confirmed a highly stable α-helix which was resistant to proteolytic degradation in serum. These short structured peptides are entropically pre-organized for binding with high affinity and specificity to cFos, a key component of the oncogenic transcriptional regulator Activator Protein-1 (AP-1). They competitively antagonized the cJun–cFos coiled-coil interaction. Truncating a Jun-based peptide from 37 to 22 residues decreased the binding enthalpy for cJun by ∼9 kcal/mol, but this was compensated by increased conformational entropy (TΔS ≤7.5 kcal/mol). This study demonstrates that rational design of short peptides constrained by α-helical cyclic pentapeptide modules is able to retain parental high helicity, as well as high affinity and specificity for cFos. These are important steps towards small antagonists of the cJun-cFos interaction that mediates gene transcription in cancer and inflammatory diseases.
Collapse
|
27
|
Abstract
We describe a general strategy for creating peptidic oligomers that have unnatural backbones but nevertheless adopt a conformation very similar to the α-helix. These oligomers contain both α- and β-amino acid residues (α/β-peptides). If the β content reaches 25-30% of the residue total, and the β residues are evenly distributed along the backbone, then substantial resistance to proteolytic degradation is often observed. These α/β-peptides can mimic the informational properties of α-helices involved in protein-protein recognition events, as documented in numerous crystal structures. Thus, these unnatural oligomers can be a source of antagonists of undesirable protein-protein interactions that are mediated by natural α-helices, or agonists of receptors for which the natural polypeptide ligands are α-helical. Successes include mimicry of BH3 domains found in proapoptotic proteins, which leads to ligands for antiapoptotic Bcl-2 family proteins, and mimicry of the gp41 CHR domain, which leads to inhibition of HIV infection in cell-based assays.
Collapse
Affiliation(s)
- Lisa M Johnson
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, USA
| | | |
Collapse
|
28
|
Lengyel GA, Horne WS. Design Strategies for the Sequence-Based Mimicry of Side-Chain Display in Protein β-Sheets by α/β-Peptides. J Am Chem Soc 2012; 134:15906-13. [DOI: 10.1021/ja306311r] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- George A. Lengyel
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - W. Seth Horne
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| |
Collapse
|
29
|
Fülöp L, Mándity IM, Juhász G, Szegedi V, Hetényi A, Wéber E, Bozsó Z, Simon D, Benkő M, Király Z, Martinek TA. A foldamer-dendrimer conjugate neutralizes synaptotoxic β-amyloid oligomers. PLoS One 2012; 7:e39485. [PMID: 22859942 PMCID: PMC3408453 DOI: 10.1371/journal.pone.0039485] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 05/21/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND AND AIMS Unnatural self-organizing biomimetic polymers (foldamers) emerged as promising materials for biomolecule recognition and inhibition. Our goal was to construct multivalent foldamer-dendrimer conjugates which wrap the synaptotoxic β-amyloid (Aβ) oligomers with high affinity through their helical foldamer tentacles. Oligomeric Aβ species play pivotal role in Alzheimer's disease, therefore recognition and direct inhibition of this undruggable target is a great current challenge. METHODS AND RESULTS Short helical β-peptide foldamers with designed secondary structures and side chain chemistry patterns were applied as potential recognition segments and their binding to the target was tested with NMR methods (saturation transfer difference and transferred-nuclear Overhauser effect). Helices exhibiting binding in the µM region were coupled to a tetravalent G0-PAMAM dendrimer. In vitro biophysical (isothermal titration calorimetry, dynamic light scattering, transmission electron microscopy and size-exclusion chromatography) and biochemical tests (ELISA and dot blot) indicated the tight binding between the foldamer conjugates and the Aβ oligomers. Moreover, a selective low nM interaction with the low molecular weight fraction of the Aβ oligomers was found. Ex vivo electrophysiological experiments revealed that the new material rescues the long-term potentiation from the toxic Aβ oligomers in mouse hippocampal slices at submicromolar concentration. CONCLUSIONS The combination of the foldamer methodology, the fragment-based approach and the multivalent design offers a pathway to unnatural protein mimetics that are capable of specific molecular recognition, and has already resulted in an inhibitor for an extremely difficult target.
Collapse
Affiliation(s)
- Lívia Fülöp
- Department of Medical Chemistry, University of Szeged, Szeged, Hungary
| | - István M. Mándity
- Institute of Pharmaceutical Chemistry, University of Szeged, Szeged, Hungary
| | - Gábor Juhász
- Department of Medical Chemistry, University of Szeged, Szeged, Hungary
| | - Viktor Szegedi
- Bay Zoltán Foundation for Applied Research – BAYGEN, Szeged, Hungary
| | | | - Edit Wéber
- Institute of Pharmaceutical Chemistry, University of Szeged, Szeged, Hungary
| | - Zsolt Bozsó
- Department of Medical Chemistry, University of Szeged, Szeged, Hungary
| | - Dóra Simon
- Department of Medical Chemistry, University of Szeged, Szeged, Hungary
| | - Mária Benkő
- Department of Physical Chemistry and Materials Science, University of Szeged, Szeged, Hungary
| | - Zoltán Király
- Department of Physical Chemistry and Materials Science, University of Szeged, Szeged, Hungary
| | - Tamás A. Martinek
- Institute of Pharmaceutical Chemistry, University of Szeged, Szeged, Hungary
| |
Collapse
|
30
|
White BR, Carlson JCT, Kerns JL, Wagner CR. Protein interface remodeling in a chemically induced protein dimer. J Mol Recognit 2012; 25:393-403. [DOI: 10.1002/jmr.2196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Brian R. White
- Department of Medicinal Chemistry, College of Pharmacy; University of Minnesota; Minneapolis; MN; 55455; USA
| | - Jonathan C. T. Carlson
- Department of Medicinal Chemistry, College of Pharmacy; University of Minnesota; Minneapolis; MN; 55455; USA
| | - Jessie L. Kerns
- Department of Medicinal Chemistry, College of Pharmacy; University of Minnesota; Minneapolis; MN; 55455; USA
| | - Carston R. Wagner
- Department of Medicinal Chemistry, College of Pharmacy; University of Minnesota; Minneapolis; MN; 55455; USA
| |
Collapse
|
31
|
Haase HS, Peterson-Kaufman KJ, Lan Levengood SK, Checco JW, Murphy WL, Gellman SH. Extending foldamer design beyond α-helix mimicry: α/β-peptide inhibitors of vascular endothelial growth factor signaling. J Am Chem Soc 2012; 134:7652-5. [PMID: 22548447 PMCID: PMC3551614 DOI: 10.1021/ja302469a] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Diverse strategies have been explored to mimic the surface displayed by an α-helical segment of a protein, with the goal of creating inhibitors of helix-mediated protein-protein interactions. Many recognition surfaces on proteins, however, are topologically more complex and less regular than a single α-helix. We describe efforts to develop peptidic foldamers that bind to the irregular receptor-recognition surface of vascular endothelial growth factor (VEGF). Our approach begins with a 19-residue α-peptide previously reported by Fairbrother et al. (Biochemistry 1998, 37, 17754) to bind to this surface on VEGF. Systematic evaluation of α→β replacements throughout this 19-mer sequence enabled us to identify homologues that contain up to ~30% β residues, retain significant affinity for VEGF, and display substantial resistance to proteolysis. These α/β-peptides can block VEGF-stimulated proliferation of human umbilical vein endothelial cells.
Collapse
Affiliation(s)
- Holly S. Haase
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | | | | | - James W. Checco
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - William L. Murphy
- Department of Biomedical Engineering, University of Wisconsin, Madison, Wisconsin 53706
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| |
Collapse
|
32
|
Johnson LM, Mortenson DE, Yun HG, Horne WS, Ketas TJ, Lu M, Moore JP, Gellman SH. Enhancement of α-helix mimicry by an α/β-peptide foldamer via incorporation of a dense ionic side-chain array. J Am Chem Soc 2012; 134:7317-20. [PMID: 22524614 DOI: 10.1021/ja302428d] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We report a new method for preorganization of α/β-peptide helices, based on the use of a dense array of acidic and basic side chains. Previously we have used cyclically constrained β residues to promote α/β-peptide helicity; here we show that an engineered ion pair array can be comparably effective, as indicated by mimicry of the CHR domain of HIV protein gp41. The new design is effective in biochemical and cell-based infectivity assays; however, the resulting α/β-peptide is susceptible to proteolysis. This susceptibility was addressed via introduction of a few cyclic β residues near the cleavage site, to produce the most stable, effective α/β-peptide gp41 CHR analogue identified. Crystal structures of an α- and α/β-peptide (each involved in a gp41-mimetic helix bundle) that contain the dense acid/base residue array manifest disorder in the ionic side chains, but there is little side-chain disorder in analogous α- and α/β-peptide structures with a sparser ionic side-chain array. These observations suggest that dense arrays of complementary acidic and basic residues can provide conformational stabilization via Coulombic attractions that do not require entropically costly ordering of side chains.
Collapse
Affiliation(s)
- Lisa M Johnson
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, USA
| | | | | | | | | | | | | | | |
Collapse
|
33
|
Weinstock MT, Francis JN, Redman JS, Kay MS. Protease-resistant peptide design-empowering nature's fragile warriors against HIV. Biopolymers 2012; 98:431-42. [PMID: 23203688 PMCID: PMC3548907 DOI: 10.1002/bip.22073] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Revised: 03/05/2012] [Accepted: 04/04/2012] [Indexed: 01/29/2023]
Abstract
Peptides have great potential as therapeutic agents, but their use is often limited by susceptibility to proteolysis and their resulting in vivo fragility. In this review, we focus on peptidomimetic approaches to produce protease-resistant peptides with the potential for greatly improved clinical utility. We focus on the use of mirror-image (D-peptide) and ß-peptides as two leading approaches with distinct design principles and challenges. Application to the important and difficult problem of inhibiting HIV entry illustrates the current state-of-the-art in peptidomimetic technologies. We also summarize future directions for this field and highlight remaining obstacles to widespread use of protease-resistant peptides.
Collapse
Affiliation(s)
- Matthew T Weinstock
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112-5650, USA
| | | | | | | |
Collapse
|
34
|
Boersma MD, Haase HS, Peterson-Kaufman KJ, Lee EF, Clarke OB, Colman PM, Smith BJ, Horne WS, Fairlie WD, Gellman SH. Evaluation of diverse α/β-backbone patterns for functional α-helix mimicry: analogues of the Bim BH3 domain. J Am Chem Soc 2011; 134:315-23. [PMID: 22040025 DOI: 10.1021/ja207148m] [Citation(s) in RCA: 132] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Peptidic oligomers that contain both α- and β-amino acid residues, in regular patterns throughout the backbone, are emerging as structural mimics of α-helix-forming conventional peptides (composed exclusively of α-amino acid residues). Here we describe a comprehensive evaluation of diverse α/β-peptide homologues of the Bim BH3 domain in terms of their ability to bind to the BH3-recognition sites on two partner proteins, Bcl-x(L) and Mcl-1. These proteins are members of the anti-apoptotic Bcl-2 family, and both bind tightly to the Bim BH3 domain itself. All α/β-peptide homologues retain the side-chain sequence of the Bim BH3 domain, but each homologue contains periodic α-residue → β(3)-residue substitutions. Previous work has shown that the ααβαααβ pattern, which aligns the β(3)-residues in a 'stripe' along one side of the helix, can support functional α-helix mimicry, and the results reported here strengthen this conclusion. The present study provides the first evaluation of functional mimicry by ααβ and αααβ patterns, which cause the β(3)-residues to spiral around the helix periphery. We find that the αααβ pattern can support effective mimicry of the Bim BH3 domain, as manifested by the crystal structure of an α/β-peptide bound to Bcl-x(L), affinity for a variety of Bcl-2 family proteins, and induction of apoptotic signaling in mouse embryonic fibroblast extracts. The best αααβ homologue shows substantial protection from proteolytic degradation relative to the Bim BH3 α-peptide.
Collapse
Affiliation(s)
- Melissa D Boersma
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Affiliation(s)
- W Seth Horne
- University of Pittsburgh, Department of Chemistry,
219 Parkman Ave., Pittsburgh, PA 15260, USA
| |
Collapse
|