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Amado D, Chaves OA, Cruz PF, Loureiro RJS, Almeida ZL, Jesus CSH, Serpa C, Brito RMM. Folding Kinetics and Volume Variation of the β-Hairpin Peptide Chignolin upon Ultrafast pH-Jumps. J Phys Chem B 2024; 128:4898-4910. [PMID: 38733339 DOI: 10.1021/acs.jpcb.3c08271] [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: 05/13/2024]
Abstract
In-depth characterization of fundamental folding steps of small model peptides is crucial for a better understanding of the folding mechanisms of more complex biomacromolecules. We have previously reported on the folding/unfolding kinetics of a model α-helix. Here, we study folding transitions in chignolin (GYDPETGTWG), a short β-hairpin peptide previously used as a model to study conformational changes in β-sheet proteins. Although previously suggested, until now, the role of the Tyr2-Trp9 interaction in the folding mechanism of chignolin was not clear. In the present work, pH-dependent conformational changes of chignolin were characterized by circular dichroism (CD), nuclear magnetic resonance (NMR), ultrafast pH-jump coupled with time-resolved photoacoustic calorimetry (TR-PAC), and molecular dynamics (MD) simulations. Taken together, our results present a comprehensive view of chignolin's folding kinetics upon local pH changes and the role of the Tyr2-Trp9 interaction in the folding process. CD data show that chignolin's β-hairpin formation displays a pH-dependent skew bell-shaped curve, with a maximum close to pH 6, and a large decrease in β-sheet content at alkaline pH. The β-hairpin structure is mainly stabilized by aromatic interactions between Tyr2 and Trp9 and CH-π interactions between Tyr2 and Pro4. Unfolding of chignolin at high pH demonstrates that protonation of Tyr2 is essential for the stability of the β-hairpin. Refolding studies were triggered by laser-induced pH-jumps and detected by TR-PAC. The refolding of chignolin from high pH, mainly due to the protonation of Tyr2, is characterized by a volume expansion (10.4 mL mol-1), independent of peptide concentration, in the microsecond time range (lifetime of 1.15 μs). At high pH, the presence of the deprotonated hydroxyl (tyrosinate) hinders the formation of the aromatic interaction between Tyr2 and Trp9 resulting in a more disorganized and dynamic tridimensional structure of the peptide. This was also confirmed by comparing MD simulations of chignolin under conditions mimicking neutral and high pH.
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Affiliation(s)
- Daniela Amado
- CQC-IMS, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Otávio A Chaves
- CQC-IMS, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Pedro F Cruz
- CQC-IMS, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Rui J S Loureiro
- CQC-IMS, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Zaida L Almeida
- CQC-IMS, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Catarina S H Jesus
- CQC-IMS, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Carlos Serpa
- CQC-IMS, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Rui M M Brito
- CQC-IMS, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
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2
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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.
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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
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Tököli A, Mag B, Bartus É, Wéber E, Szakonyi G, Simon MA, Czibula Á, Monostori É, Nyitray L, Martinek TA. Proteomimetic surface fragments distinguish targets by function. Chem Sci 2020; 11:10390-10398. [PMID: 34094300 PMCID: PMC8162404 DOI: 10.1039/d0sc03525d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 09/09/2020] [Indexed: 11/21/2022] Open
Abstract
The fragment-centric design promises a means to develop complex xenobiotic protein surface mimetics, but it is challenging to find locally biomimetic structures. To address this issue, foldameric local surface mimetic (LSM) libraries were constructed. Protein affinity patterns, ligand promiscuity and protein druggability were evaluated using pull-down data for targets with various interaction tendencies and levels of homology. LSM probes based on H14 helices exhibited sufficient binding affinities for the detection of both orthosteric and non-orthosteric spots, and overall binding tendencies correlated with the magnitude of the target interactome. Binding was driven by two proteinogenic side chains and LSM probes could distinguish structurally similar proteins with different functions, indicating limited promiscuity. Binding patterns displayed similar side chain enrichment values to those for native protein-protein interfaces implying locally biomimetic behavior. These analyses suggest that in a fragment-centric approach foldameric LSMs can serve as useful probes and building blocks for undruggable protein interfaces.
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Affiliation(s)
- Attila Tököli
- Department of Medical Chemistry, University of Szeged Dóm tér 8 H6720 Szeged Hungary
| | - Beáta Mag
- Department of Medical Chemistry, University of Szeged Dóm tér 8 H6720 Szeged Hungary
| | - Éva Bartus
- Department of Medical Chemistry, University of Szeged Dóm tér 8 H6720 Szeged Hungary
- MTA-SZTE Biomimetic Systems Research Group, University of Szeged Dóm tér 8 H6720 Szeged Hungary
| | - Edit Wéber
- Department of Medical Chemistry, University of Szeged Dóm tér 8 H6720 Szeged Hungary
| | - Gerda Szakonyi
- Institute of Pharmaceutical Analysis, University of Szeged Somogyi u. 4. H6720 Szeged Hungary
| | - Márton A Simon
- Department of Biochemistry, Eötvös Loránd University Pázmány Péter sétány 1/C H1077 Budapest Hungary
| | - Ágnes Czibula
- Lymphocyte Signal Transduction Laboratory, Institute of Genetics, Biological Research Centre Temesvári krt. 62 H6726 Szeged Hungary
| | - Éva Monostori
- Lymphocyte Signal Transduction Laboratory, Institute of Genetics, Biological Research Centre Temesvári krt. 62 H6726 Szeged Hungary
| | - László Nyitray
- Department of Biochemistry, Eötvös Loránd University Pázmány Péter sétány 1/C H1077 Budapest Hungary
| | - Tamás A Martinek
- Department of Medical Chemistry, University of Szeged Dóm tér 8 H6720 Szeged Hungary
- MTA-SZTE Biomimetic Systems Research Group, University of Szeged Dóm tér 8 H6720 Szeged Hungary
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Bartáček J, Váňa J, Drabina P, Svoboda J, Kocúrik M, Sedlák M. Recoverable polystyrene-supported palladium catalyst for construction of all-carbon quaternary stereocenters via asymmetric 1,4-addition of arylboronic acids to cyclic enones. REACT FUNCT POLYM 2020. [DOI: 10.1016/j.reactfunctpolym.2020.104615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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5
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Mantsyzov AB, Sokolov MN, Ivantcova PM, Bräse S, Polshakov VI, Kudryavtsev KV. Interplay of Pyrrolidine Units with Homo/Hetero Chirality and CF 3-Aryl Substituents on Secondary Structures of β-Proline Tripeptides in Solution. J Org Chem 2020; 85:8865-8871. [PMID: 32526142 DOI: 10.1021/acs.joc.0c00598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
All possible variants of β-proline functionalized tripeptides consisting of homo/hetero chiral monomeric all-cis 5-arylpyrrolidine-2,4-dicarboxylate units were synthesized for the first time by a nonpeptidic coupling method based on 1,3-dipolar cycloaddition chemistry of azomethine ylides. Secondary structures of β-proline tripeptides in solution were determined using the NMR spectroscopy data. o-(Trifluoromethyl)phenyl substituent contributes to stereoselectivity of 1,3-dipolar cycloaddition and structural features of β-proline tripeptides. A β-proline CF3-tripeptide with alternating absolute chirality between adjacent pyrrolidine units mimics natural PPII helix secondary structure.
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Affiliation(s)
- Alexey B Mantsyzov
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Lomonosovsky Ave 31/5, Moscow, 119992, Russian Federation
| | - Mikhail N Sokolov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russian Federation
| | - Polina M Ivantcova
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russian Federation
| | - Stefan Bräse
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, Karlsruhe, 76131, Germany.,Institute of Biological and Chemical Systems - Functional Molecular Systems, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen, D-76344, Germany
| | - Vladimir I Polshakov
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Lomonosovsky Ave 31/5, Moscow, 119992, Russian Federation
| | - Konstantin V Kudryavtsev
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russian Federation.,Pirogov Russian National Research Medical University, Ostrovityanova Street 1, 117997, Moscow, Russian Federation
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6
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John-White M, Gardiner J, Johanesen P, Lyras D, Dumsday G. β-Aminopeptidases: Insight into Enzymes without a Known Natural Substrate. Appl Environ Microbiol 2019; 85:e00318-19. [PMID: 31126950 PMCID: PMC6643246 DOI: 10.1128/aem.00318-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 05/08/2019] [Indexed: 02/05/2023] Open
Abstract
β-Aminopeptidases have the unique capability to hydrolyze N-terminal β-amino acids, with varied preferences for the nature of β-amino acid side chains. This unique capability makes them useful as biocatalysts for synthesis of β-peptides and to kinetically resolve β-peptides and amides for the production of enantiopure β-amino acids. To date, six β-aminopeptidases have been discovered and functionally characterized, five from Gram-negative bacteria and one from a fungus, Aspergillus Here we report on the purification and characterization of an additional four β-aminopeptidases, one from a Gram-positive bacterium, Mycolicibacterium smegmatis (BapAMs), one from a yeast, Yarrowia lipolytica (BapAYlip), and two from Gram-negative bacteria isolated from activated sludge identified as Burkholderia spp. (BapABcA5 and BapABcC1). The genes encoding β-aminopeptidases were cloned, expressed in Escherichia coli, and purified. The β-aminopeptidases were produced as inactive preproteins that underwent self-cleavage to form active enzymes comprised of two different subunits. The subunits, designated α and β, appeared to be tightly associated, as the active enzyme was recovered after immobilized-metal affinity chromatography (IMAC) purification, even though only the α-subunit was 6-histidine tagged. The enzymes were shown to hydrolyze chromogenic substrates with the N-terminal l-configurations β-homo-Gly (βhGly) and β3-homo-Leu (β3hLeu) with high activities. These enzymes displayed higher activity with H-βhGly-p-nitroanilide (H-βhGly-pNA) than previously characterized enzymes from other microorganisms. These data indicate that the new β-aminopeptidases are fully functional, adding to the toolbox of enzymes that could be used to produce β-peptides. Overexpression studies in Pseudomonas aeruginosa also showed that the β-aminopeptidases may play a role in some cellular functions.IMPORTANCE β-Aminopeptidases are unique enzymes found in a diverse range of microorganisms that can utilize synthetic β-peptides as a sole carbon source. Six β-aminopeptidases have been previously characterized with preferences for different β-amino acid substrates and have demonstrated the capability to catalyze not only the degradation of synthetic β-peptides but also the synthesis of short β-peptides. Identification of other β-aminopeptidases adds to this toolbox of enzymes with differing β-amino acid substrate preferences and kinetics. These enzymes have the potential to be utilized in the sustainable manufacture of β-amino acid derivatives and β-peptides for use in biomedical and biomaterial applications. This is important, because β-amino acids and β-peptides confer increased proteolytic resistance to bioactive compounds and form novel structures as well as structures similar to α-peptides. The discovery of new enzymes will also provide insight into the biological importance of these enzymes in nature.
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Affiliation(s)
- Marietta John-White
- CSIRO Manufacturing, Clayton, Victoria, Australia
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | | | - Priscilla Johanesen
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Dena Lyras
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
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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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Restriction of Human Cytomegalovirus Infection by Galectin-9. J Virol 2019; 93:JVI.01746-18. [PMID: 30487283 DOI: 10.1128/jvi.01746-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 10/31/2018] [Indexed: 12/24/2022] Open
Abstract
Human cytomegalovirus (HCMV) is a ubiquitous human herpesvirus. While HCMV infection is generally asymptomatic in the immunocompetent, it can have devastating consequences in those with compromised or underdeveloped immune systems, including transplant recipients and neonates. Galectins are a widely expressed protein family that have been demonstrated to modulate both antiviral immunity and regulate direct host-virus interactions. The potential for galectins to directly modulate HCMV infection has not previously been studied, and our results reveal that galectin-9 (Gal-9) can potently inhibit HCMV infection. Gal-9-mediated inhibition of HCMV was dependent upon its carbohydrate recognition domains and thus dependent on glycan interactions. Temperature shift studies revealed that Gal-9 specific inhibition was mediated primarily at the level of virus-cell fusion and not binding. Additionally, we found that during reactivation of HCMV in hematopoietic stem cell transplant (HSCT) patients soluble Gal-9 is upregulated. This study provides the first evidence for Gal-9 functioning as a potent antiviral defense effector molecule against HCMV infection and identifies it as a potential clinical candidate to restrict HCMV infections.IMPORTANCE Human cytomegalovirus (HCMV) continues to cause serious and often life-threatening disease in those with impaired or underdeveloped immune systems. This virus is able to infect and replicate in a wide range of human cell types, which enables the virus to spread to other individuals in a number of settings. Current antiviral drugs are associated with a significant toxicity profile, and there is no vaccine; these factors highlight a need to identify additional targets for the development of anti-HCMV therapies. We demonstrate for the first time that secretion of a member of the galectin family of proteins, galectin-9 (Gal-9), is upregulated during natural HCMV-reactivated infection and that this soluble cellular protein possesses a potent capacity to block HCMV infection by inhibiting virus entry into the host cell. Our findings support the possibility of harnessing the antiviral properties of Gal-9 to prevent HCMV infection and disease.
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Jian JH, Hsu CL, Syu JF, Kuo TS, Tsai MK, Wu PY, Wu HL. Access to β 2-Amino Acids via Enantioselective 1,4-Arylation of β-Nitroacrylates Catalyzed by Chiral Rhodium Catalysts. J Org Chem 2018; 83:12184-12191. [PMID: 30153730 DOI: 10.1021/acs.joc.8b00586] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The highly enantioselective conjugate addition of a variety of arylboronic acids to β-nitroacrylates is reported to provide optically active α-aryl β-nitropropionates in up to 70% yields and >99.5% ee's, which are useful building blocks for preparing chiral β2-amino acids. The applicability of this transformation is demonstrated by converting 3aa into the β2-amino acid 5 and transforming 3ap to β-amino ester 7 via reduction and reductive N-alkylation. The latter compound is a precursor for preparing ent-ipatasertib.
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Affiliation(s)
- Jia-Hong Jian
- Department of Chemistry , National Taiwan Normal University , No. 88, Section 4, Tingzhou Road , Taipei 11677 , Taiwan
| | - Chih-Lung Hsu
- Department of Chemistry , National Taiwan Normal University , No. 88, Section 4, Tingzhou Road , Taipei 11677 , Taiwan
| | - Jin-Fong Syu
- Department of Chemistry , National Taiwan Normal University , No. 88, Section 4, Tingzhou Road , Taipei 11677 , Taiwan
| | - Ting-Shen Kuo
- Department of Chemistry , National Taiwan Normal University , No. 88, Section 4, Tingzhou Road , Taipei 11677 , Taiwan
| | - Ming-Kang Tsai
- Department of Chemistry , National Taiwan Normal University , No. 88, Section 4, Tingzhou Road , Taipei 11677 , Taiwan
| | - Ping-Yu Wu
- Oleader Technologies, Co., Ltd. , 1F., No. 8, Aly. 29, Ln. 335, Chenggong Rd. , Hukou Township, 30345 Hsinchu , Taiwan
| | - Hsyueh-Liang Wu
- Department of Chemistry , National Taiwan Normal University , No. 88, Section 4, Tingzhou Road , Taipei 11677 , Taiwan
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Plumridge A, Katz AM, Calvey GD, Elber R, Kirmizialtin S, Pollack L. Revealing the distinct folding phases of an RNA three-helix junction. Nucleic Acids Res 2018; 46:7354-7365. [PMID: 29762712 PMCID: PMC6101490 DOI: 10.1093/nar/gky363] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/17/2018] [Accepted: 04/24/2018] [Indexed: 01/08/2023] Open
Abstract
Remarkable new insight has emerged into the biological role of RNA in cells. RNA folding and dynamics enable many of these newly discovered functions, calling for an understanding of RNA self-assembly and conformational dynamics. Because RNAs pass through multiple structures as they fold, an ensemble perspective is required to visualize the flow through fleetingly populated sets of states. Here, we combine microfluidic mixing technology and small angle X-ray scattering (SAXS) to measure the Mg-induced folding of a small RNA domain, the tP5abc three helix junction. Our measurements are interpreted using ensemble optimization to select atomically detailed structures that recapitulate each experimental curve. Structural ensembles, derived at key stages in both time-resolved studies and equilibrium titrations, reproduce the features of known intermediates, and more importantly, offer a powerful new structural perspective on the time-progression of folding. Distinct collapse phases along the pathway appear to be orchestrated by specific interactions with Mg ions. These key interactions subsequently direct motions of the backbone that position the partners of tertiary contacts for later bonding, and demonstrate a remarkable synergy between Mg and RNA across numerous time-scales.
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Affiliation(s)
- Alex Plumridge
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
| | - Andrea M Katz
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
| | - George D Calvey
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
| | - Ron Elber
- Department of Chemistry and Institute for Computational Engineering and Sciences (ICES) University of Texas at Austin, Austin, TX, USA
| | - Serdal Kirmizialtin
- Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
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Sussman F, Sánchez-Pedregal VM, Estévez JC, Balo R, Jiménez-Barbero J, Ardá A, Gimeno A, Royo M, Villaverde MC, Estévez RJ. Environmental Effects Determine the Structure of Potential β-Amino Acid Based Foldamers. Chemistry 2018; 24:10625-10629. [DOI: 10.1002/chem.201801953] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 05/24/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Fredy Sussman
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS); Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - Víctor M. Sánchez-Pedregal
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS); Departamento de Química Orgánica; Universidade de Santiago de Compostela; 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; 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; 15782 Santiago de Compostela Spain
| | - Jesús Jiménez-Barbero
- Molecular Recognition & Host-Pathogen Interactions Unit; CIC bioGUNE; Bizkaia Technology Park, Building 801A 48170 Derio Spain
- Ikerbasque; Basque Foundation for Science; Maria Diaz de Haro 13 48009 Bilbao Spain
- Department of Organic Chemistry II, Faculty of Science & Technology; University of the Basque Country; 48940 Leioa Spain
| | - Ana Ardá
- Molecular Recognition & Host-Pathogen Interactions Unit; CIC bioGUNE; Bizkaia Technology Park, Building 801A 48170 Derio Spain
| | - Ana Gimeno
- Molecular Recognition & Host-Pathogen Interactions Unit; CIC bioGUNE; Bizkaia Technology Park, Building 801A 48170 Derio Spain
| | - Miriam Royo
- Combinatorial Chemistry Unit; Barcelona Science Park; Baldiri Reixac 10 08028 Barcelona Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN); Barcelona Science Park; Baldiri Reixac 10 08028 Barcelona Spain
| | - M. Carmen Villaverde
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS); Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - Ramón J. Estévez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS); Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
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12
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Paikar A, Debnath M, Podder D, Sasmal S, Haldar D. Synthesis and structural investigation of 2-aminomethyl-3-(4-methoxy-phenyl)-propionic acid containing a peptide analogue of the amyloidogenic AS(6–7) sequence: inhibition of fibril formation. Org Biomol Chem 2017; 15:4218-4225. [DOI: 10.1039/c7ob00797c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The incorporation of a β-amino acid, namely 2-aminomethyl-3-(4-methoxy-phenyl)-propionic acid, inhibits amyloid-like fibril formation.
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Affiliation(s)
- Arpita Paikar
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- Mohanpur
- India
| | - Mintu Debnath
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- Mohanpur
- India
| | - Debasish Podder
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- Mohanpur
- India
| | - Supriya Sasmal
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- Mohanpur
- India
| | - Debasish Haldar
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- Mohanpur
- India
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13
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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.
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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
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14
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Archer RM, Hutchby M, Winn CL, Fossey JS, Bull SD. A chiral ligand mediated aza-conjugate addition strategy for the enantioselective synthesis of β-amino esters that contain hydrogenolytically sensitive functionality. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.08.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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15
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Ganesh Kumar M, Gopi HN. γ- and β-Peptide Foldamers from Common Multifaceted Building Blocks: Synthesis and Structural Characterization. Org Lett 2015; 17:4738-41. [DOI: 10.1021/acs.orglett.5b02263] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mothukuri Ganesh Kumar
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, India
| | - Hosahudya N. Gopi
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, India
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16
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Fisher BF, Guo L, Dolinar BS, Guzei IA, Gellman SH. Heterogeneous H-bonding in a foldamer helix. J Am Chem Soc 2015; 137:6484-7. [PMID: 25974390 DOI: 10.1021/jacs.5b03382] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Structural characterization of new α/γ-peptide foldamers containing the cyclically constrained γ-amino acid I is described. Crystallographic and 2D NMR analysis shows that γ residue I promotes the formation of a 12/10-helical secondary structure in α/γ-peptides. This helix contains two different types of internal H-bond, and the data show that the 12-atom C═O(i) → H-N(i+3) H-bond is more favorable than the 10-atom C═O(i) → H-N(i-1) H-bond. Several foldamer helices featuring topologically distinct H-bonds have been discovered, but our findings are the first to show that such H-bonds may differ in their favorability.
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Affiliation(s)
- Brian F Fisher
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Li Guo
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Brian S Dolinar
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ilia A Guzei
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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17
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Jadhav SV, Misra R, Gopi HN. Foldamers to Nanotubes: Influence of Amino Acid Side Chains in the Hierarchical Assembly of α,γ4-Hybrid Peptide Helices. Chemistry 2014; 20:16523-8. [DOI: 10.1002/chem.201404961] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Indexed: 12/28/2022]
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18
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Ahmed S, Sprules T, Kaur K. Structural similarity between β(3)-peptides synthesized from β(3)-homo-amino acids and aspartic acid monomers. Biopolymers 2014; 102:359-67. [PMID: 24852341 DOI: 10.1002/bip.22510] [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: 03/14/2014] [Revised: 05/09/2014] [Accepted: 05/16/2014] [Indexed: 11/11/2022]
Abstract
Formation of stable secondary structures by oligomers that mimic natural peptides is a key asset for enhanced biological response. Here we show that oligomeric β(3)-hexapeptides synthesized from L-aspartic acid monomers (β(3)-peptides 1, 5a, and 6) or homologated β(3)-amino acids (β(3)-peptide 2), fold into similar stable 14-helical secondary structures in solution, except that the former form right-handed 14-helix and the later form left-handed 14-helix. β(3)-Peptides from L-Asp monomers contain an additional amide bond in the side chains that provides opportunities for more hydrogen bonding. However, based on the NMR solution structures, we found that β(3)-peptide from L-Asp monomers (1) and from homologated amino acids (2) form similar structures with no additional side-chain interactions. These results suggest that the β(3)-peptides derived from L-Asp are promising peptide-mimetics that can be readily synthesized using L-Asp monomers as well as the right-handed 14-helical conformation of these β(3)-peptides (such as 1 and 6) may prove beneficial in the design of mimics for right-handed α-helix of α-peptides.
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Affiliation(s)
- Sahar Ahmed
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada, T6G 2E1; Department of Pharmacognosy and Medicinal Chemistry, Faculty of Pharmacy, Taibah University, Al-Madinah Al-munawarah, 41477, Kingdom of Saudi Arabia
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19
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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]
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21
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Kudryavtsev KV, Ivantcova PM, Churakov AV, Wiedmann S, Luy B, Muhle-Goll C, Zefirov NS, Bräse S. Alternierende asymmetrische Selbstinduktion in funktionalisierten Pyrrolidin-Oligomeren. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201302862] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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22
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Kudryavtsev KV, Ivantcova PM, Churakov AV, Wiedmann S, Luy B, Muhle-Goll C, Zefirov NS, Bräse S. Alternating Asymmetric Self-Induction in Functionalized Pyrrolidine Oligomers. Angew Chem Int Ed Engl 2013; 52:12736-40. [DOI: 10.1002/anie.201302862] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2013] [Revised: 07/24/2013] [Indexed: 01/25/2023]
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23
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Borst EM, Ständker L, Wagner K, Schulz TF, Forssmann WG, Messerle M. A peptide inhibitor of cytomegalovirus infection from human hemofiltrate. Antimicrob Agents Chemother 2013; 57:4751-60. [PMID: 23856778 PMCID: PMC3811406 DOI: 10.1128/aac.00854-13] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 07/10/2013] [Indexed: 12/18/2022] Open
Abstract
Naturally occurring substances with antimicrobial activity can serve as a starting point for the rational design of new drugs to treat infectious diseases. Here, we screened a library of peptides derived from human hemofiltrate for inhibitory effects on human cytomegalovirus (CMV) infection. We isolated a previously unknown derivative of the neutrophil-activating peptide 2, which we termed CYVIP, for CMV-inhibiting peptide. The peptide blocked infection with human and mouse CMV as well as with herpes simplex virus type 1 in different cell types. We found that CYVIP interferes with virus attachment to the cell surface, and structure-activity relationship studies revealed that positively charged lysine and arginine residues of CYVIP are essential for its inhibitory activity. The N-terminal 29 amino acids of the peptide were sufficient for inhibition, and substitution with an acidic residue further improved its activity. The target structure of CYVIP on the cell surface seems to be the sulfate residues of heparan sulfate proteoglycans, which are known to serve as herpesvirus attachment receptors. Our data suggest that O-sulfation of heparan sulfate is required for binding of CYVIP, and furthermore, that the initial interaction of CMV particles with cells takes place preferentially via 6-O-linked sulfate groups. These findings about CYVIP's mode of action lay the basis for further development of antivirals interfering with attachment of CMV to cells, a crucial step of the infection cycle.
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Affiliation(s)
| | - Ludger Ständker
- Center of Pharmacology and Clinic of Immunology, Research Group of Peptide Chemistry
| | | | - Thomas F. Schulz
- Department of Virology
- German Centre for Infection Research, Hannover Medical School, Hannover, Germany
| | - Wolf-Georg Forssmann
- Center of Pharmacology and Clinic of Immunology, Research Group of Peptide Chemistry
| | - Martin Messerle
- Department of Virology
- German Centre for Infection Research, Hannover Medical School, Hannover, Germany
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24
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Inhibition of α-helix-mediated protein-protein interactions using designed molecules. Nat Chem 2013; 5:161-73. [PMID: 23422557 DOI: 10.1038/nchem.1568] [Citation(s) in RCA: 572] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 01/07/2013] [Indexed: 12/21/2022]
Abstract
Inhibition of protein-protein interactions (PPIs) represents a significant challenge because it is unclear how they can be effectively and selectively targeted using small molecules. Achieving this goal is critical given the defining role of these interactions in biological processes. A rational approach to inhibitor design based on the secondary structure at the interface is the focus of much research, and different classes of designed ligands have emerged, some of which effectively and selectively disrupt targeted PPIs. This Review discusses the relevance of PPIs and, in particular, the importance of α-helix-mediated PPIs to chemical biology and drug discovery with a focus on designing inhibitors, including constrained peptides, foldamers and proteomimetic-derived ligands. In doing so, key challenges and major advances in developing generic approaches for the elaboration of PPI inhibitors are highlighted. The challenges faced in developing such ligands as drug leads--and how criteria applied to these may differ from conventional small-molecule drugs--are summarized.
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25
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Jadhav SV, Bandyopadhyay A, Gopi HN. Protein secondary structure mimetics: crystal conformations of α/γ4-hybrid peptide12-helices with proteinogenic side chains and their analogy with α- and β-peptide helices. Org Biomol Chem 2013; 11:509-14. [DOI: 10.1039/c2ob26805a] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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26
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One-pot efficient synthesis of N(α)-urethane-protected β- and γ-amino acids. Amino Acids 2012; 44:1085-91. [PMID: 23250684 PMCID: PMC3569585 DOI: 10.1007/s00726-012-1443-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 12/01/2012] [Indexed: 11/11/2022]
Abstract
1-[(4-Methylphenyl)oxy]pyrrolidine-2,5-dione and 1-[(4-methylphenyl)oxy]piperidine-2,6-dione react in a Lossen-type reaction with primary alcohols in the presence of triethylamine to furnish corresponding Nα-urethane-protected β-alanine and γ-aminopropionic acid (GABA), respectively, with excellent yields and purities, in an essentially “one-pot” procedure.
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27
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Heck T, Geueke B, Kohler HPE. Bacterialβ-Aminopeptidases: Structural Insights and Applications for Biocatalysis. Chem Biodivers 2012; 9:2388-409. [DOI: 10.1002/cbdv.201200305] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Indexed: 12/12/2022]
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28
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Interplay between human cytomegalovirus and intrinsic/innate host responses: a complex bidirectional relationship. Mediators Inflamm 2012; 2012:607276. [PMID: 22701276 PMCID: PMC3371353 DOI: 10.1155/2012/607276] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 03/22/2012] [Indexed: 02/07/2023] Open
Abstract
The interaction between human cytomegalovirus (HCMV) and its host is a complex process that begins with viral attachment and entry into host cells, culminating in the development of a specific adaptive response that clears the acute infection but fails to eradicate HCMV. We review the viral and cellular partners that mediate early host responses to HCMV with regard to the interaction between structural components of virions (viral glycoproteins) and cellular receptors (attachment/entry receptors, toll-like receptors, and other nucleic acid sensors) or intrinsic factors (PML, hDaxx, Sp100, viperin, interferon inducible protein 16), the reactions of innate immune cells (antigen presenting cells and natural killer cells), the numerous mechanisms of viral immunoevasion, and the potential exploitation of events that are associated with early phases of virus-host interplay as a therapeutic strategy.
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29
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Otero JM, Fernández F, Estévez JC, Nash R, Estévez RJ. A Nitro Sugar-Mediated Stereocontrolled Synthesis of β2-Amino Acids: Synthesis of a Polyhydroxylated trans-2-Aminocyclohexanecarboxylic Acid. European J Org Chem 2012. [DOI: 10.1002/ejoc.201200103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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30
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Geibel B, Merschky M, Rether C, Schmuck C. Artificial Enzyme Mimics. Supramol Chem 2012. [DOI: 10.1002/9780470661345.smc159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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31
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Vaz E, Dames SA, Geyer M, Brunsveld L. Positional screening and NMR structure determination of side-chain-to-side-chain cyclized β3-peptides. Org Biomol Chem 2012; 10:1365-73. [DOI: 10.1039/c1ob06422c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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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.
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Affiliation(s)
- Matthew T Weinstock
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112-5650, USA
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33
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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.
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Affiliation(s)
- Melissa D Boersma
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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Segman-Magidovich S, Lee MR, Vaiser V, Struth B, Gellman SH, Rapaport H. Sheet-Like Assemblies of Charged Amphiphilic α/β-Peptides at the Air-Water Interface. Chemistry 2011; 17:14857-66. [DOI: 10.1002/chem.201101775] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Indexed: 11/10/2022]
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Affiliation(s)
- W Seth Horne
- University of Pittsburgh, Department of Chemistry,
219 Parkman Ave., Pittsburgh, PA 15260, USA
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36
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Abstract
INTRODUCTION Cytomegalovirus (CMV) is a ubiquitous pathogen that establishes a lifelong asymptomatic infection in healthy individuals. Infection of immunesuppressed individuals causes serious illness. Transplant and AIDS patients are highly susceptible to CMV leading to life-threatening end-organ disease. Another vulnerable population is the developing fetus in utero, where congenital infection can result in surviving newborns with long-term developmental problems. There is no vaccine licensed for CMV and current antivirals suffer from complications associated with prolonged treatment. These include drug toxicity and emergence of resistant strains. There is an obvious need for new antivirals. Candidate intervention strategies are tested in controlled preclinical animal models but species specificity of human CMV precludes the direct study of the virus in an animal model. AREAS COVERED This review explores the current status of CMV antivirals and development of new drugs. This includes the use of animal models and the development of new improved models such as humanized animal CMV and bioluminescent imaging of virus in animals in real time. EXPERT OPINION Various new CMV antivirals are in development, some with greater spectrum of activity against other viruses. Although the greatest need is in the setting of transplant patients, there remains an unmet need for a safe antiviral strategy against congenital CMV. This is especially important as an effective CMV vaccine remains an elusive goal. In this regard, greater emphasis should be placed on suitable preclinical animal models and greater collaboration between industry and academia.
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Affiliation(s)
- Alistair McGregor
- University of Minnesota Medical School, Center for Infectious Diseases and Microbiology Translational Research, 2001 6th Street SE, MN 55455, USA.
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Estieu-Gionnet K, Guichard G. Stabilized helical peptides: overview of the technologies and therapeutic promises. Expert Opin Drug Discov 2011; 6:937-63. [PMID: 22646216 DOI: 10.1517/17460441.2011.603723] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Helical structures in proteins and naturally occurring peptides play a major role in a variety of biological processes by mediating interactions with proteins and other macromolecules such as nucleic acids and lipid membranes. The use of short synthetic peptides encompassing helical segments to modulate or disrupt such interactions, when associated with human diseases, represents great pharmacological interest. AREAS COVERED Multiple chemical approaches have been developed to increase the conformational and metabolic stabilities of helical peptides and to improve their biomedical potential. After a brief overview of these technologies and the most recent developments, this review will focus on the main therapeutic areas and targets and will discuss their promise. EXPERT OPINION Potential benefits associated with increased helix stability extend beyond simple affinity enhancement. Some peptidomimetic helices are being endowed with features desirable for cellular activity such as increased resistance to proteolysis and/or cell permeability. Recent advances in the field of peptide and related peptidomimetic helices are not just conceptual, but are likely to be of practical utility in the process of optimizing peptides as clinical candidates, and developing medium-size therapeutics.
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Affiliation(s)
- Karine Estieu-Gionnet
- Institut Européen de Chimie et Biologie , Université de Bordeaux, CNRS UMR 5248, CBMN, 2 rue R. Escarpit, 33607 Pessac , France
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Sawada T, Gellman SH. Structural mimicry of the α-helix in aqueous solution with an isoatomic α/β/γ-peptide backbone. J Am Chem Soc 2011; 133:7336-9. [PMID: 21520956 PMCID: PMC3141811 DOI: 10.1021/ja202175a] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Artificial mimicry of α-helices offers a basis for development of protein-protein interaction antagonists. Here we report a new type of unnatural peptidic backbone, containing α-, β-, and γ-amino acid residues in an αγααβα repeat pattern, for this purpose. This unnatural hexad has the same number of backbone atoms as a heptad of α residues. Two-dimensional NMR data clearly establish the formation of an α-helix-like conformation in aqueous solution. The helix formed by our 12-mer α/β/γ-peptide is considerably more stable than the α-helix formed by an analogous 14-mer α-peptide, presumably because of the preorganized β and γ residues employed.
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Affiliation(s)
- Tomohisa Sawada
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
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39
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Declerck V, Aitken DJ. A refined synthesis of enantiomerically pure 2-aminocyclobutanecarboxylic acids. Amino Acids 2011; 41:587-95. [DOI: 10.1007/s00726-011-0918-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2011] [Accepted: 04/12/2011] [Indexed: 11/24/2022]
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40
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Abstract
Human cytomegalovirus continues to impact adversely on the outcome of solid organ and stem cell transplantation and remains a major cause of congenital abnormalities. In the absence of a vaccine, antiviral drugs have been the mainstay of therapy. Although very few anticytomegalovirus drugs are currently licensed, there are multiple opportunities within the viral life cycle for drug development. In this article we summarize some of the key new antiviral agents undergoing preclinical and clinical development against a range of targets in the viral life cycle, highlighting those where further development is warranted or being undertaken.
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Affiliation(s)
| | - Richard SB Milne
- Medical Research Council Centre for Medical Molecular Virology, Division of Infection & Immunity, Department of Infection, University College Medical School (Royal Free Campus), Rowland Hill Street, Hampstead, London NW3 2QG, UK
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Mercorelli B, Lembo D, Palù G, Loregian A. Early inhibitors of human cytomegalovirus: state-of-art and therapeutic perspectives. Pharmacol Ther 2011; 131:309-29. [PMID: 21570424 PMCID: PMC7112563 DOI: 10.1016/j.pharmthera.2011.04.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Accepted: 04/05/2011] [Indexed: 12/31/2022]
Abstract
Human cytomegalovirus (HCMV) infection is associated with severe morbidity and mortality in immunocompromised individuals, mainly transplant recipients and AIDS patients, and is the most frequent cause of congenital malformations in newborn children. To date, few drugs are licensed for the treatment of HCMV infections, most of which target the viral DNA polymerase and suffer from many drawbacks, including long-term toxicity, low potency, and poor bioavailability. In addition, the emergence of drug-resistant viral strains is becoming an increasing problem for disease management. Finally, none of the current anti-HCMV drugs have been approved for the treatment of congenital infections. For all these reasons, there is still a strong need for new anti-HCMV drugs with novel mechanisms of action. The first events of the virus replication cycle, including attachment, entry, immediate-early gene expression, and immediate-early functions—in particular that of Immediate-Early 2 protein—represent attractive targets for the development of novel antiviral compounds. Such inhibitors would block not only the expression of viral immediate-early proteins, which play a key role in the pathogenesis of HCMV infection, but also the host immunomodulation and the changes to cell physiology induced by the first events of virus infection. This review describes the current knowledge on the initial phases of HCMV replication, their validation as potential novel antiviral targets, and the development of compounds that block such processes.
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Affiliation(s)
- Beatrice Mercorelli
- Department of Histology, Microbiology and Medical Biotechnologies, University of Padova, 35121 Padova, Italy
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42
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Choi SH, Guzei IA, Spencer LC, Gellman SH. Crystallographic characterization of 12-helical secondary structure in β-peptides containing side chain groups. J Am Chem Soc 2011; 132:13879-85. [PMID: 20828159 DOI: 10.1021/ja1062532] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Helices are the most extensively studied secondary structures formed by β-peptide foldamers. Among the five known β-peptide helices, the 12-helix is particularly interesting because the internal hydrogen bond orientation and macrodipole are analogous to those of α-peptide helices (α-helix and 3(10)-helix). The β-peptide 12-helix is defined by i, i+3 C═O···H-N backbone hydrogen bonds and promoted by β-residues with a five-membered ring constraint. The 12-helical scaffold has been used to generate β-peptides with specific biological functions, for which diverse side chains must be properly placed along the backbone and, upon folding, properly arranged in space. Only two crystal structures of 12-helical β-peptides have previously been reported, both for homooligomers of trans-2-aminocyclopentanecarboxylic acid (ACPC). Here we report five additional crystal structures of 12-helical β-peptides, all containing residues that bear side chains. Four of the crystallized β-peptides include trans-4,4-dimethyl-2-aminocyclopentanecarboxylic acid (dm-ACPC) residues, and the fifth contains a β(3)-hPhe residue. These five β-peptides adopt fully folded 12-helical conformations in the solid state. The new crystal structures, along with previously reported data, allow a detailed characterization of the 12-helical conformation; average backbone torsion angles of β-residues and helical parameters are derived. These structural parameters are found to be similar to those for i, i+3 C═O···H-N hydrogen-bonded helices formed by other peptide backbones generated from α- and/or β-amino acids. The similarity between the conformational behavior of dm-ACPC and ACPC is consistent with previous NMR-based conclusions that 4,4-disubstituted ACPC derivatives are compatible with 12-helical folding. In addition, our data show how a β(3)-residue is accommodated in the 12-helix, thus enhancing understanding of the diverse conformational behavior of this flexible class of β-amino acids.
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Affiliation(s)
- Soo Hyuk Choi
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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43
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Abstract
Enveloped viruses penetrate their cell targets following the merging of their membrane with that of the cell. This fusion process is catalyzed by one or several viral glycoproteins incorporated on the membrane of the virus. These envelope glycoproteins (EnvGP) evolved in order to combine two features. First, they acquired a domain to bind to a specific cellular protein, named "receptor." Second, they developed, with the help of cellular proteins, a function of finely controlled fusion to optimize the replication and preserve the integrity of the cell, specific to the genus of the virus. Following the activation of the EnvGP either by binding to their receptors and/or sometimes the acid pH of the endosomes, many changes of conformation permit ultimately the action of a specific hydrophobic domain, the fusion peptide, which destabilizes the cell membrane and leads to the opening of the lipidic membrane. The comprehension of these mechanisms is essential to develop medicines of the therapeutic class of entry inhibitor like enfuvirtide (Fuzeon) against human immunodeficiency virus (HIV). In this chapter, we will summarize the different envelope glycoprotein structures that viruses develop to achieve membrane fusion and the entry of the virus. We will describe the different entry pathways and cellular proteins that viruses have subverted to allow infection of the cell and the receptors that are used. Finally, we will illustrate more precisely the recent discoveries that have been made within the field of the entry process, with a focus on the use of pseudoparticles. These pseudoparticles are suitable for high-throughput screenings that help in the development of natural or artificial inhibitors as new therapeutics of the class of entry inhibitors.
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Affiliation(s)
- François-Loic Cosset
- Université de Lyon, UCB-Lyon1, IFR128, Lyon, France,INSERM, U758, Lyon, France,Ecole Normale Supérieure de Lyon, Lyon, France
| | - Dimitri Lavillette
- Université de Lyon, UCB-Lyon1, IFR128, Lyon, France,INSERM, U758, Lyon, France,Ecole Normale Supérieure de Lyon, Lyon, France
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44
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Araghi RR, Koksch B. A helix-forming αβγ-chimeric peptide with catalytic activity: a hybrid peptide ligase. Chem Commun (Camb) 2011; 47:3544-6. [DOI: 10.1039/c0cc03760e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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45
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Prichard MN, Kern ER. The search for new therapies for human cytomegalovirus infections. Virus Res 2010; 157:212-21. [PMID: 21095209 DOI: 10.1016/j.virusres.2010.11.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 11/11/2010] [Accepted: 11/12/2010] [Indexed: 12/19/2022]
Abstract
Ganciclovir (GCV), the therapy of choice for human cytomegalovirus (CMV) infections and foscarnet, a drug used to treat GCV-resistant CMV infections was approved more than twenty years ago. Although cidofovir and a prodrug of GCV have since been added to the armamentarium, a highly effective drug without significant toxicities has yet to be approved. Such a therapeutic agent is required for treatment of immunocompromised hosts and infants, which bear the greatest burden of disease. The modest antiviral activity of existing drugs is insufficient to completely suppress viral replication, which results in the selection of drug-resistant variants that remain pathogenic, continue to replicate, and contribute to disease. Sustained efforts, largely in the biotech industry and academia, have identified highly active lead compounds that have progressed into clinical studies with varying levels of success. A few of these compounds inhibit new molecular targets, remain effective against isolates that have developed resistance to existing therapies, and promise to augment existing therapies. Some of the more promising drugs will be discussed with an emphasis on those progressing to clinical studies. Their antiviral activity both in vitro and in vivo, spectrum of antiviral activity, and mechanism of action will be reviewed to provide an update on the progress of potential new therapies for CMV infections.
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Affiliation(s)
- Mark N Prichard
- Department of Pediatrics, University of Alabama School of Medicine, Birmingham, AL 35233-1711, USA.
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46
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Fernandes C, Faure S, Pereira E, Théry V, Declerck V, Guillot R, Aitken DJ. 12-Helix folding of cyclobutane beta-amino acid oligomers. Org Lett 2010; 12:3606-9. [PMID: 20704401 DOI: 10.1021/ol101267u] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The hexamer and octamer of trans-2-aminocyclobutane carboxylic acid were prepared and their conformational preferences studied experimentally and using molecular modeling. All observations suggest a marked preference for the folding of these oligomers into a well-defined 12-helical conformation, in both solution and the solid state.
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Affiliation(s)
- Carlos Fernandes
- Clermont Université, Université Blaise Pascal, Laboratoire SEESIB (UMR 6504 - CNRS), 24 avenue des Landais, 63177 Aubière cedex, France
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47
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Iriondo-Alberdi J, Laxmi-Reddy K, Bouguerne B, Staedel C, Huc I. Cellular Internalization of Water-Soluble Helical Aromatic Amide Foldamers. Chembiochem 2010; 11:1679-85. [DOI: 10.1002/cbic.201000256] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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48
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The glycoprotein B disintegrin-like domain binds beta 1 integrin to mediate cytomegalovirus entry. J Virol 2010; 84:10026-37. [PMID: 20660204 DOI: 10.1128/jvi.00710-10] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Cellular integrins were identified as human cytomegalovirus (HCMV) entry receptors and signaling mediators in both fibroblasts and endothelial cells. The goal of these studies was to determine the mechanism by which HCMV binds to cellular integrins to mediate virus entry. HCMV envelope glycoprotein B (gB) has sequence similarity to the integrin-binding disintegrin-like domain found in the ADAM (a disintegrin and metalloprotease) family of proteins. To test the ability of this region to bind to cellular integrins, we generated a recombinant soluble version of the gB disintegrin-like domain (gB-DLD). The gB-DLD protein bound to human fibroblasts in a specific, dose-dependent and saturable manner that required the expression of an intact beta1 integrin ectodomain. Furthermore, a physical association between gB-DLD and beta1 integrin was demonstrated through in vitro pull-down assays. The function of this interaction was shown by the ability of cell-bound gB-DLD to efficiently block HCMV entry and the infectivity of multiple in vivo target cells. Additionally, rabbit polyclonal antibodies raised against gB-DLD neutralized HCMV infection. Mimicry of the ADAM family disintegrin-like domain by HCMV gB represents a novel mechanism for integrin engagement by a virus and reveals a unique therapeutic target for HCMV neutralization. The strong conservation of the DLD across beta- and gammaherpesviruses suggests that integrin recognition and utilization may be a more broadly conserved feature throughout the Herpesviridae.
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Bautista AD, Appelbaum JS, Craig CJ, Michel J, Schepartz A. Bridged beta(3)-peptide inhibitors of p53-hDM2 complexation: correlation between affinity and cell permeability. J Am Chem Soc 2010; 132:2904-6. [PMID: 20158215 DOI: 10.1021/ja910715u] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Beta-peptides possess several features that are desirable in peptidomimetics; they are easily synthesized, fold into stable secondary structures in physiologic buffers, and resist proteolysis. They can also bind to a diverse array of proteins to inhibit their interactions with alpha-helical ligands. beta-peptides are usually not cell-permeable, however, and this feature limits their utility as research tools and potential therapeutics. Appending an Arg(8) sequence to a beta-peptide improves uptake but adds considerable mass. We previously reported that embedding a small cationic patch within a PPII, alpha-, or beta-peptide helix improves uptake without the addition of significant mass. In another mass-neutral strategy, Verdine, Walensky, and others have reported that insertion of a hydrocarbon bridge between the i and i + 4 positions of an alpha-helix also increases cell uptake. Here we describe a series of beta-peptides containing diether and hydrocarbon bridges and compare them on the basis of cell uptake and localization, affinities for hDM2, and 14-helix structure. Our results highlight the relative merits of the cationic-patch and hydrophobic-bridge strategies for improving beta-peptide uptake and identify a surprising correlation between uptake efficiency and hDM2 affinity.
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Affiliation(s)
- Arjel D Bautista
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, USA
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50
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Heck T, Reimer A, Seebach D, Gardiner J, Deniau G, Lukaszuk A, Kohler HPE, Geueke B. β-Aminopeptidase-Catalyzed Biotransformations of β2-Dipeptides: Kinetic Resolution and Enzymatic Coupling. Chembiochem 2010; 11:1129-36. [DOI: 10.1002/cbic.200900757] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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