1
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Jiang Z, Huang YH, Kaas Q, Craik DJ, Wang CK. Structure and Activity of Reconstructed Pseudo-Ancestral Cyclotides. ChemMedChem 2024; 19:e202400124. [PMID: 38632079 DOI: 10.1002/cmdc.202400124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/17/2024] [Accepted: 04/17/2024] [Indexed: 04/19/2024]
Abstract
Cyclotides are cyclic peptides that are promising scaffolds for the design of drug candidates and chemical tools. However, despite there being hundreds of reported cyclotides, drug design studies have commonly focussed on a select few prototypic examples. Here, we explored whether ancestral sequence reconstruction could be used to generate new cyclotides for further optimization. We show that the reconstructed 'pseudo-ancestral' sequences, named Ancy-m (for the ancestral cyclotide of the Möbius sub-family) and Ancy-b (for the bracelet sub-family), have well-defined structures like their extant members, comprising the core structural feature of a cyclic cystine knot. This motif underpins efforts to re-engineer cyclotides for agrochemical and therapeutic applications. We further show that the reconstructed sequences are resistant to temperatures approaching boiling, bind to phosphatidyl-ethanolamine lipid bilayers at micromolar affinity, and inhibit the growth of insect cells at inhibitory concentrations in the micromolar range. Interestingly, the Ancy-b cyclotide had a higher oxidative folding yield than its comparator cyclotide cyO2, which belongs to the bracelet cyclotide subfamily known to be notoriously difficult to fold. Overall, this study provides new cyclotide sequences not yet found naturally that could be valuable starting points for the understanding of cyclotide evolution and for further optimization as drug leads.
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Affiliation(s)
- Zhihao Jiang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Quentin Kaas
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Conan K Wang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Qld, 4072, Australia
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2
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Tian S, de Veer SJ, Durek T, Wang CK, Craik DJ. Nucleation of a key beta-turn promotes cyclotide oxidative folding. J Biol Chem 2024; 300:107125. [PMID: 38432638 PMCID: PMC10999817 DOI: 10.1016/j.jbc.2024.107125] [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: 11/07/2023] [Revised: 02/05/2024] [Accepted: 02/19/2024] [Indexed: 03/05/2024] Open
Abstract
Cyclotides are plant-derived peptides characterized by a head-to-tail cyclic backbone and a cystine knot motif comprised of three disulfide bonds. Formation of this motif via in vitro oxidative folding can be challenging and can result in misfolded isomers with nonnative disulfide connectivities. Here, we investigated the effect of β-turn nucleation on cyclotide oxidative folding. Two types of β-turn mimics were grafted into kalata B1, individually replacing each of the four β-turns in the folded cyclotide. Insertion of d-Pro-Gly into loop 5 was beneficial to the folding of both cyclic kB1 and a linear form of the peptide. The linear grafted analog folded four-times faster in aqueous conditions than cyclic kB1 in optimized conditions. Additionally, the cyclic analogue folded without the need for redox agents by transitioning through a native-like intermediate that was on-pathway to product formation. Kalata B1 is from the Möbius subfamily of cyclotides. Grafting d-Pro-Gly into loop 5 of cyclotides from two other subfamilies also had a beneficial effect on folding. Our findings demonstrate the importance of a β-turn nucleation site for cyclotide oxidative folding, which could be adopted as a chemical strategy to improve the in vitro folding of diverse cystine-rich peptides.
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Affiliation(s)
- Sixin Tian
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Simon J de Veer
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Thomas Durek
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Conan K Wang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia.
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3
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Lander A, Kong Y, Jin Y, Wu C, Luk LYP. Deciphering the Synthetic and Refolding Strategy of a Cysteine-Rich Domain in the Tumor Necrosis Factor Receptor (TNF-R) for Racemic Crystallography Analysis and d-Peptide Ligand Discovery. ACS BIO & MED CHEM AU 2024; 4:68-76. [PMID: 38404743 PMCID: PMC10885103 DOI: 10.1021/acsbiomedchemau.3c00060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 02/27/2024]
Abstract
Many cell-surface receptors are promising targets for chemical synthesis because of their critical roles in disease development. This synthetic approach enables investigations by racemic protein crystallography and ligand discovery by mirror-image methodologies. However, due to their complex nature, the chemical synthesis of a receptor can be a significant challenge. Here, we describe the chemical synthesis and folding of a central, cysteine-rich domain of the cell-surface receptor tumor necrosis factor 1 which is integral to binding of the cytokine TNF-α, namely, TNFR-1 CRD2. Racemic protein crystallography at 1.4 Å confirmed that the native binding conformation was preserved, and TNFR-1 CRD2 maintained its capacity to bind to TNF-α (KD ≈ 7 nM). Encouraged by this discovery, we carried out mirror-image phage display using the enantiomeric receptor mimic and identified a d-peptide ligand for TNFR-1 CRD2 (KD = 1 μM). This work demonstrated that cysteine-rich domains, including the central domains, can be chemically synthesized and used as mimics for investigations.
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Affiliation(s)
- Alexander
J. Lander
- School
of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, U.K.
| | - Yifu Kong
- Department
of Chemistry, College of Chemistry and Chemical Engineering, The MOE
Key Laboratory of Spectrochemical Analysis and Instrumentation, State
Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Fujian Province 361005, China
| | - Yi Jin
- Manchester
Institute of Biotechnology, University of
Manchester, Manchester M1 7DN, U.K.
| | - Chuanliu Wu
- Department
of Chemistry, College of Chemistry and Chemical Engineering, The MOE
Key Laboratory of Spectrochemical Analysis and Instrumentation, State
Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Fujian Province 361005, China
| | - Louis Y. P. Luk
- School
of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, U.K.
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4
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Gou F, Shi D, Kou B, Li Z, Yan X, Wu X, Jiang YB. One-Pot Cyclization to Large Peptidomimetic Macrocycles by In Situ-Generated β-Turn-Enforced Folding. J Am Chem Soc 2023; 145:9530-9539. [PMID: 37037798 DOI: 10.1021/jacs.2c11684] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Macrocycles have been targets of extensive synthetic efforts for decades because of their potent molecular recognition and self-assembly capabilities. Yet, efficient syntheses of macrocyclic molecules via irreversible covalent bonds remain challenging. Here, we report an efficient approach to large peptidomimetic macrocycles by using the in situ-generated β-turn structural motifs afforded in the amidothiourea moieties from the early steps of the reaction of 2 molecules of bilateral amino acid-based acylhydrazine with 2 molecules of diisothiocyanate. Four chiral and achiral peptidomimetic large macrocycles were successfully synthesized in high yields of 45-63% in a feasible one-pot reaction under sub-molar concentration conditions and were purified by simple filtration. X-ray crystallographic characterization of three macrocycles reveals an important feature that their four β-turn structures, each maintained by four 10-membered intramolecular hydrogen bonds, alternatively network the four aromatic arms. This affords an interesting conformation switching mode upon anion binding. Binding of SO42- to 1L or 1D that contains 4 alanine residues (with the lowest steric hinderance among the macrocycles) leads to an inside-out structural change of the host macrocycle, as confirmed by the X-ray crystal structure of 1L-SO42- and 1D-SO42- complexes, accompanied by an inversion of the CD signals. On the basis of the strong sulfate affinity of the macrocycles, we succeeded in the removal of sulfate anions from water via a macrocycle-mediated liquid-liquid extraction method. Our synthetic protocol can be easily extended to other macrocycles of varying arms and/or chiral amino acid residues; thus, a variety of structurally and functionally diverse macrocycles are expected to be readily made.
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Affiliation(s)
- Fei Gou
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, and Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Xiamen University, Xiamen 361005, China
| | - Di Shi
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, and Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Xiamen University, Xiamen 361005, China
| | - Bohan Kou
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, and Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Xiamen University, Xiamen 361005, China
| | - Zhao Li
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, and Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Xiamen University, Xiamen 361005, China
| | - Xiaosheng Yan
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, and Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Xiamen University, Xiamen 361005, China
- School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
| | - Xin Wu
- School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Yun-Bao Jiang
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, and Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Xiamen University, Xiamen 361005, China
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5
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Lander AJ, Jin Y, Luk LYP. D-Peptide and D-Protein Technology: Recent Advances, Challenges, and Opportunities. Chembiochem 2023; 24:e202200537. [PMID: 36278392 PMCID: PMC10805118 DOI: 10.1002/cbic.202200537] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/23/2022] [Indexed: 11/08/2022]
Abstract
Total chemical protein synthesis provides access to entire D-protein enantiomers enabling unique applications in molecular biology, structural biology, and bioactive compound discovery. Key enzymes involved in the central dogma of molecular biology have been prepared in their D-enantiomeric forms facilitating the development of mirror-image life. Crystallization of a racemic mixture of L- and D-protein enantiomers provides access to high-resolution X-ray structures of polypeptides. Additionally, D-enantiomers of protein drug targets can be used in mirror-image phage display allowing discovery of non-proteolytic D-peptide ligands as lead candidates. This review discusses the unique applications of D-proteins including the synthetic challenges and opportunities.
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Affiliation(s)
- Alexander J. Lander
- School of ChemistryCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUK
| | - Yi Jin
- Manchester Institute of BiotechnologyThe University of ManchesterManchesterM1 7DNUK
| | - Louis Y. P. Luk
- School of ChemistryCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUK
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6
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Zhao D, Zhao Y, He X, Ayers PW, Liu S. Efficient and accurate density-based prediction of macromolecular polarizabilities. Phys Chem Chem Phys 2023; 25:2131-2141. [PMID: 36562468 DOI: 10.1039/d2cp04690c] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Accurately and efficiently predicting macromolecules' polarizabilities is an open problem. In this work, we employ a few simple density-based quantities from the information-theoretic approach (ITA) to predict polarizability of proteins. We first build quantitative structure/property relationships between molecular polarizabilities and ITA quantities. We then verify the broad applicability of ITA quantities for polarizability prediction for inorganic, organic, and biological systems with both localized and delocalized electronic structure. As a proof-of-concept application, we predict the molecular polarizabilities of complex proteins. Based on the linear regression equations for 20 natural amino acid residues, 400 dipeptides, and 8000 tripeptides, one then predicts the molecular polarizability of a larger peptide or even a protein once the molecular wavefunction is obtained. Because it is extremely costly to determine the wavefunction for a macromolecule like a protein, we propose to combine the ITA with the linear-scaling generalized energy-based fragmentation (GEBF) method to predict the macromolecular polarizability. In GEBF, the total molecular polarizability is obtained as a linear combination of the corresponding quantities from a series of small subsystems. We can predict them based on the subsystem wavefunction and linear regression equations rather than compute them from the nearly-intractable coupled-perturbed Hartree-Fock or Kohn-Sham equations for the whole macromolecule. Computational results showcase that the GEBF-ITA protocol should be an inexpensive yet accurate theoretical tool for predicting macromolecular polarizabilities.
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Affiliation(s)
- Dongbo Zhao
- Institute of Biomedical Research, Yunnan University, Kunming 650500, Yunnan, P. R. China
| | - Yilin Zhao
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ONL8S 4M1, Canada.
| | - Xin He
- Qingdao Institute for Theoretical and Computational Sciences, Shandong University, Qingdao 266237, Shandong, P. R. China
| | - Paul W Ayers
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ONL8S 4M1, Canada.
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599-3420, USA. .,Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
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7
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Chen JL, Li B, Ma B, Su XC. Distinct stereospecific effect of chiral tether between a tag and protein on the rigidity of paramagnetic tag. JOURNAL OF BIOMOLECULAR NMR 2022; 76:107-119. [PMID: 35841475 DOI: 10.1007/s10858-022-00399-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
Flexibility between the paramagnetic tag and its protein conjugates is a common yet unresolved issue in the applications of paramagnetic NMR spectroscopy in biological systems. The flexibility greatly attenuates the magnetic anisotropy and compromises paramagnetic effects especially for pseudocontact shift and residual dipolar couplings. Great efforts have been made to improve the rigidity of paramagnetic tag in the protein conjugates, however, the effect of local environment vicinal to the protein ligation site on the paramagnetic effects remains poorly understood. In the present work, the stereospecific effect of chiral tether between the protein and a tag on the paramagnetic effects produced by the tag attached via a D- and L-type linker between the protein and paramagnetic metal chelating moiety was assessed. The remarkable chiral effect of the D- and L-type tether between the tag and the protein on the rigidity of paramagnetic tag is disclosed in a number of protein-tag-Ln complexes. The chiral tether formed between the D-type tag and L-type protein surface minimizes the effect of the local environment surrounding the ligation site on the averaging of paramagnetic tag, which is helpful to preserve the rigidity of a paramagnetic tag in the protein conjugates.
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Affiliation(s)
- Jia-Liang Chen
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Bin Li
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Bo Ma
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China.
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8
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Nguyen NGT, Nguyen XT, Nguyen NH, Luu TXT, Dao XT. Ground solid permanganate oxidative coupling of thiols into symmetrical/unsymmetrical disulfides: selective and improved process. J Sulphur Chem 2022. [DOI: 10.1080/17415993.2022.2083914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
| | - Xuan-Triet Nguyen
- Faculty of Chemistry, University of Science, Ho Chi Minh City, Vietnam
| | - Ngoc-Huy Nguyen
- Faculty of Chemistry, University of Science, Ho Chi Minh City, Vietnam
| | - Thi Xuan Thi Luu
- Faculty of Chemistry, University of Science, Ho Chi Minh City, Vietnam
- Department of Chemistry, Vietnam National University, Ho Chi Minh City, Vietnam
| | - Xuan-Tien Dao
- Faculty of Chemistry, University of Science, Ho Chi Minh City, Vietnam
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9
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Kremsmayr T, Aljnabi A, Blanco-Canosa JB, Tran HNT, Emidio NB, Muttenthaler M. On the Utility of Chemical Strategies to Improve Peptide Gut Stability. J Med Chem 2022; 65:6191-6206. [PMID: 35420805 PMCID: PMC9059125 DOI: 10.1021/acs.jmedchem.2c00094] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Inherent susceptibility
of peptides to enzymatic degradation in
the gastrointestinal tract is a key bottleneck in oral peptide drug
development. Here, we present a systematic analysis of (i) the gut
stability of disulfide-rich peptide scaffolds, orally administered
peptide therapeutics, and well-known neuropeptides and (ii) medicinal
chemistry strategies to improve peptide gut stability. Among a broad
range of studied peptides, cyclotides were the only scaffold class
to resist gastrointestinal degradation, even when grafted with non-native
sequences. Backbone cyclization, a frequently applied strategy, failed
to improve stability in intestinal fluid, but several site-specific
alterations proved efficient. This work furthermore highlights the
importance of standardized gut stability test conditions and suggests
defined protocols to facilitate cross-study comparison. Together,
our results provide a comparative overview and framework for the chemical
engineering of gut-stable peptides, which should be valuable for the
development of orally administered peptide therapeutics and molecular
probes targeting receptors within the gastrointestinal tract.
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Affiliation(s)
- Thomas Kremsmayr
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Währinger Straße 38, Vienna 1090, Austria
| | - Aws Aljnabi
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Währinger Straße 38, Vienna 1090, Austria
| | - Juan B Blanco-Canosa
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, Barcelona 08034, Spain
| | - Hue N T Tran
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Nayara Braga Emidio
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Markus Muttenthaler
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Währinger Straße 38, Vienna 1090, Austria.,Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4072, Australia
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10
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Protocols for measuring the stability and cytotoxicity of cyclotides. Methods Enzymol 2022; 663:19-40. [PMID: 35168789 DOI: 10.1016/bs.mie.2021.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Cyclotides are plant host-defense peptides that have a wide range of biological activities and have diverse potential applications in medicine and agriculture. These 27-37 amino acid peptides have a head-to-tail cyclic backbone and are built around a cystine knot core, which makes them exceptionally stable. This stability and their amenability to sequence modifications has made cyclotides attractive scaffolds in drug design, and many synthetic cyclotides have now been designed and synthesized to test their efficacy as leads for a wide range of diseases, including infectious disease, cancer, pain and multiple sclerosis. Additionally, some natural cyclotides are selectively toxic to certain cancer cell lines, opening their potential as anticancer agents, and others have insecticidal activity, with applications in crop protection. With these applications in mind, there is a need to be able to measure cyclotides in pharmaceutical or agrichemical formulations and in biological media such as blood serum, as well as to assess their potential persistence in the environment when used as agrichemical agents. This chapter describes protocols for quantifying cyclotides in biological fluids, measuring their stability, and assessing their relative cytotoxicity on various types of cells.
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11
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Huang YH, Du Q, Jiang Z, King GJ, Collins BM, Wang CK, Craik DJ. Enabling Efficient Folding and High-Resolution Crystallographic Analysis of Bracelet Cyclotides. Molecules 2021; 26:5554. [PMID: 34577034 PMCID: PMC8467136 DOI: 10.3390/molecules26185554] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/05/2021] [Accepted: 09/09/2021] [Indexed: 11/23/2022] Open
Abstract
Cyclotides have attracted great interest as drug design scaffolds because of their unique cyclic cystine knotted topology. They are classified into three subfamilies, among which the bracelet subfamily represents the majority and comprises the most bioactive cyclotides, but are the most poorly utilized in drug design applications. A long-standing challenge has been the very low in vitro folding yields of bracelets, hampering efforts to characterize their structures and activities. Herein, we report substantial increases in bracelet folding yields enabled by a single point mutation of residue Ile-11 to Leu or Gly. We applied this discovery to synthesize mirror image enantiomers and used quasi-racemic crystallography to elucidate the first crystal structures of bracelet cyclotides. This study provides a facile strategy to produce bracelet cyclotides, leading to a general method to easily access their atomic resolution structures and providing a basis for development of biotechnological applications.
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Affiliation(s)
- Yen-Hua Huang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; (Y.-H.H.); (Q.D.); (Z.J.); (B.M.C.); (C.K.W.)
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Qingdan Du
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; (Y.-H.H.); (Q.D.); (Z.J.); (B.M.C.); (C.K.W.)
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Zhihao Jiang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; (Y.-H.H.); (Q.D.); (Z.J.); (B.M.C.); (C.K.W.)
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Gordon J. King
- The Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Brett M. Collins
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; (Y.-H.H.); (Q.D.); (Z.J.); (B.M.C.); (C.K.W.)
| | - Conan K. Wang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; (Y.-H.H.); (Q.D.); (Z.J.); (B.M.C.); (C.K.W.)
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; (Y.-H.H.); (Q.D.); (Z.J.); (B.M.C.); (C.K.W.)
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
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12
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de Veer SJ, White AM, Craik DJ. Sunflower Trypsin Inhibitor-1 (SFTI-1): Sowing Seeds in the Fields of Chemistry and Biology. Angew Chem Int Ed Engl 2020; 60:8050-8071. [PMID: 32621554 DOI: 10.1002/anie.202006919] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Indexed: 12/24/2022]
Abstract
Nature-derived cyclic peptides have proven to be a vast source of inspiration for advancing modern pharmaceutical design and synthetic chemistry. The focus of this Review is sunflower trypsin inhibitor-1 (SFTI-1), one of the smallest disulfide-bridged cyclic peptides found in nature. SFTI-1 has an unusual biosynthetic pathway that begins with a dual-purpose albumin precursor and ends with the production of a high-affinity serine protease inhibitor that rivals other inhibitors much larger in size. Investigations on the molecular basis for SFTI-1's rigid structure and adaptable function have planted seeds for thought that have now blossomed in several different fields. Here we survey these applications to highlight the growing potential of SFTI-1 as a versatile template for engineering inhibitors, a prototypic peptide for studying inhibitory mechanisms, a stable scaffold for grafting bioactive peptides, and a model peptide for evaluating peptidomimetic motifs and platform technologies.
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Affiliation(s)
- Simon J de Veer
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Andrew M White
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia
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13
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Veer SJ, White AM, Craik DJ. Der Sonnenblumen‐Trypsin‐Inhibitor 1 (SFTI‐1) in der Chemie und Biologie. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006919] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Simon J. Veer
- Institute for Molecular Bioscience, ARC Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane QLD 4072 Australien
| | - Andrew M. White
- Institute for Molecular Bioscience, ARC Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane QLD 4072 Australien
| | - David J. Craik
- Institute for Molecular Bioscience, ARC Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane QLD 4072 Australien
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14
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Handley TNG, Wang CK, Harvey PJ, Lawrence N, Craik DJ. Cyclotide Structures Revealed by NMR, with a Little Help from X‐ray Crystallography. Chembiochem 2020; 21:3463-3475. [DOI: 10.1002/cbic.202000315] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/08/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Thomas N. G. Handley
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
| | - Conan K. Wang
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
| | - Peta J. Harvey
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
| | - Nicole Lawrence
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
| | - David J. Craik
- Institute for Molecular Bioscience Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science The University of Queensland Brisbane Queensland 4072 Australia
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15
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Wang CK, Amiss AS, Weidmann J, Craik DJ. Structure-activity analysis of truncated albumin-binding domains suggests new lead constructs for potential therapeutic delivery. J Biol Chem 2020; 295:12143-12152. [PMID: 32647013 PMCID: PMC7443490 DOI: 10.1074/jbc.ra120.014168] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/09/2020] [Indexed: 12/13/2022] Open
Abstract
Rapid clearance by renal filtration is a major impediment to the translation of small bioactive biologics into drugs. To extend serum t1/2, a commonly used approach is to attach drug leads to the G-related albumin-binding domain (ABD) to bind albumin and evade clearance. Despite the success of this approach in extending half-lives of a wide range of biologics, it is unclear whether the existing constructs are optimized for binding and size; any improvements along these lines could lead to improved drugs. Characterization of the biophysics of binding of an ABD to albumin in solution could shed light on this question. Here, we examine the binding of an ABD to human serum albumin using isothermal titration calorimetry and assess the structural integrity of the ABD using CD, NMR, and molecular dynamics. A structure-activity analysis of truncations of the ABD suggests that downsized variants could replace the full-length domain. Reducing size could have the benefit of reducing potential immunogenicity problems. We further showed that one of these variants could be used to design a bifunctional molecule with affinity for albumin and a serum protein involved in cholesterol metabolism, PCSK9, demonstrating the potential utility of these fragments in the design of cholesterol-lowering drugs. Future work could extend these in vitro binding studies to other ABD variants to develop therapeutics. Our study presents new understanding of the solution structural and binding properties of ABDs, which has implications for the design of next-generation long-lasting therapeutics.
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Affiliation(s)
- Conan K. Wang
- Institute for Molecular Bioscience and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Anna S. Amiss
- Institute for Molecular Bioscience and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Joachim Weidmann
- Institute for Molecular Bioscience and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - David J. Craik
- Institute for Molecular Bioscience and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
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16
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Cheng B, Li Y, Zhang X, Duan S, Li H, He Y, Li Y, Wang T, Zhai H. Two Reaction Modes of Pyridinium 1,4-Zwitterionic Thiolates with Sulfenes: Synthesis of 3H-1,2-Dithiole 2,2-Dioxides, 1,9a-Dihydropyrido[2,1-c][1,4]thiazines, and Indolizines. Org Lett 2020; 22:5817-5821. [DOI: 10.1021/acs.orglett.0c01888] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Bin Cheng
- Institute of Marine Biomedicine/Hoffmann Institute of Advanced Materials, Shenzhen Polytechnic, Shenzhen 518055, China
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Yuntong Li
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Xinping Zhang
- Institute of Marine Biomedicine/Hoffmann Institute of Advanced Materials, Shenzhen Polytechnic, Shenzhen 518055, China
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Shengguo Duan
- Department of Chemistry, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Hui Li
- Institute of Marine Biomedicine/Hoffmann Institute of Advanced Materials, Shenzhen Polytechnic, Shenzhen 518055, China
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Yixuan He
- Institute of Marine Biomedicine/Hoffmann Institute of Advanced Materials, Shenzhen Polytechnic, Shenzhen 518055, China
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Yun Li
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Taimin Wang
- Institute of Marine Biomedicine/Hoffmann Institute of Advanced Materials, Shenzhen Polytechnic, Shenzhen 518055, China
| | - Hongbin Zhai
- Institute of Marine Biomedicine/Hoffmann Institute of Advanced Materials, Shenzhen Polytechnic, Shenzhen 518055, China
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
- State Key Laboratory of Chemical Oncogenomics, Shenzhen Engineering Laboratory of Nano Drug Slow-Release, Peking University Shenzhen Graduate School, Shenzhen 518055, China
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17
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Morimoto J, Kim J, Kuroda D, Nagatoishi S, Tsumoto K, Sando S. Per-Residue Program of Multiple Backbone Dihedral Angles of β-Peptoids via Backbone Substitutions. J Am Chem Soc 2020; 142:2277-2284. [PMID: 31917919 DOI: 10.1021/jacs.9b10496] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Unique folded structures of natural and synthetic oligomers are the most fundamental basis for their unique functions. N-Substituted β-peptides, or β-peptoids, are synthetic oligomers with great potential to fold into diverse three-dimensional structures because of the existence of four rotatable bonds in a monomer with highly modular synthetic accessibility. However, the existence of the four rotatable bonds poses a challenge for conformational control of β-peptoids. Here, we report a strategy for per-residue programming of two dihedral angles of β-peptoids, which is useful for restricting the conformational space of the oligomers. The oligomer was found to form a unique loop conformation that is stabilized by the backbone rotational restrictions. Circular dichroism and NMR spectroscopic analyses and X-ray crystallographic analysis of the oligomer are presented. The strategy would significantly facilitate the discovery of many more unique folded structures of β-peptoids.
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Affiliation(s)
- Jumpei Morimoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku , Tokyo 113-8656 , Japan
| | - Jungyeon Kim
- Department of Chemistry and Biotechnology, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku , Tokyo 113-8656 , Japan
| | - Daisuke Kuroda
- Department of Chemistry and Biotechnology, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku , Tokyo 113-8656 , Japan.,Department of Bioengineering, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku , Tokyo 113-8656 , Japan
| | - Satoru Nagatoishi
- Institute of Medical Science , The University of Tokyo , 4-6-1 Shirokanedai , Minato-ku , Tokyo 108-8639 , Japan
| | - Kouhei Tsumoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku , Tokyo 113-8656 , Japan.,Department of Bioengineering, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku , Tokyo 113-8656 , Japan.,Institute of Medical Science , The University of Tokyo , 4-6-1 Shirokanedai , Minato-ku , Tokyo 108-8639 , Japan
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku , Tokyo 113-8656 , Japan.,Department of Bioengineering, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku , Tokyo 113-8656 , Japan
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18
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Li CY, Yap K, Swedberg JE, Craik DJ, de Veer SJ. Binding Loop Substitutions in the Cyclic Peptide SFTI-1 Generate Potent and Selective Chymase Inhibitors. J Med Chem 2020; 63:816-826. [PMID: 31855419 DOI: 10.1021/acs.jmedchem.9b01811] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chymase is a serine protease that is predominantly expressed by mast cells and has key roles in immune defense and the cardiovascular system. This enzyme has also emerged as a therapeutic target for cardiovascular disease due to its ability to remodel cardiac tissue and generate angiotensin II. Here, we used the nature-derived cyclic peptide sunflower trypsin inhibitor-1 (SFTI-1) as a template for designing novel chymase inhibitors. The key binding contacts of SFTI-1 were optimized by combining a peptide substrate library screen with structure-based design, which yielded several variants with potent activity. The lead variant was further modified by replacing the P1 Tyr residue with para-substituted Phe derivatives, generating new inhibitors with improved potency (Ki = 1.8 nM) and higher selectivity over closely related enzymes. Several variants were shown to block angiotensin I cleavage in vitro, highlighting their potential for further development and future evaluation as pharmaceutical leads.
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Affiliation(s)
- Choi Yi Li
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Kuok Yap
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Joakim E Swedberg
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - David J Craik
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Simon J de Veer
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia
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19
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Abstract
This Review explores the class of plant-derived macrocyclic peptides called cyclotides. We include an account of their discovery, characterization, and distribution in the plant kingdom as well as a detailed analysis of their sequences and structures, biosynthesis and chemical synthesis, biological functions, and applications. These macrocyclic peptides are around 30 amino acids in size and are characterized by their head-to-tail cyclic backbone and cystine knot motif, which render them to be exceptionally stable, with resistance to thermal or enzymatic degradation. Routes to their chemical synthesis have been developed over the past two decades, and this capability has facilitated a wide range of mutagenesis and structure-activity relationship studies. In turn, these studies have both led to an increased understanding of their mechanisms of action as well as facilitated a range of applications in agriculture and medicine, as ecofriendly crop protection agents, and as drug leads or scaffolds for pharmaceutical design. Our overall objective in this Review is to provide readers with a comprehensive overview of cyclotides that we hope will stimulate further work on this fascinating family of peptides.
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Affiliation(s)
- Simon J de Veer
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Meng-Wei Kan
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - David J Craik
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
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20
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Henriques ST, Peacock H, Benfield AH, Wang CK, Craik DJ. Is the Mirror Image a True Reflection? Intrinsic Membrane Chirality Modulates Peptide Binding. J Am Chem Soc 2019; 141:20460-20469. [PMID: 31765148 DOI: 10.1021/jacs.9b11194] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Peptides with pharmaceutical activities are attractive drug leads, and knowledge of their mode-of-action is essential for translation into the clinic. Comparison of native and enantiomeric peptides has long been used as a powerful approach to discriminate membrane- or receptor-mediated modes-of-action on the basis of the assumption that interactions with cell membranes are independent of peptide chirality. Here, we revisit this paradigm with the cyclotide kalata B1, a drug scaffold with intrinsic membrane-binding activity whose enantiomer is less potent than native peptide. To investigate this chirality dependence, we compared peptide-lipid binding using mirror image model membranes. We synthesized phospholipids with non-natural chirality and demonstrate that native kalata B1 binds with higher affinity to phospholipids with chirality found in eukaryotic membranes. This study shows for the first time that the chiral environment of lipid bilayers can modulate the function of membrane-active peptides and challenges the view that peptide-lipid interactions are achiral.
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Affiliation(s)
- Sónia Troeira Henriques
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia.,School of Biomedical Sciences, Faculty of Health, Institute of Health & Biomedical Innovation , Queensland University of Technology , Translational Research Institute , Brisbane , Queensland 4102 , Australia
| | - Hayden Peacock
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Aurélie H Benfield
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia.,School of Biomedical Sciences, Faculty of Health, Institute of Health & Biomedical Innovation , Queensland University of Technology , Translational Research Institute , Brisbane , Queensland 4102 , Australia
| | - Conan K Wang
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - David J Craik
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
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21
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Huang YH, Du Q, Craik DJ. Cyclotides: Disulfide-rich peptide toxins in plants. Toxicon 2019; 172:33-44. [DOI: 10.1016/j.toxicon.2019.10.244] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/30/2019] [Accepted: 10/30/2019] [Indexed: 12/27/2022]
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22
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23
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Wang CK, Craik DJ. Toward Structure Determination of Disulfide-Rich Peptides Using Chemical Shift-Based Methods. J Phys Chem B 2019; 123:1903-1912. [PMID: 30730741 DOI: 10.1021/acs.jpcb.8b10649] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Disulfide-rich peptides are a class of molecules for which NMR spectroscopy has been the primary tool for structural characterization. Here, we explore whether the process can be achieved by using structural information encoded in chemical shifts. We examine (i) a representative set of five cyclic disulfide-rich peptides that have high-resolution NMR and X-ray structures and (ii) a larger set of 100 disulfide-rich peptides from the PDB. Accuracy of the calculated structures was dependent on the methods used for searching through conformational space and for identifying native conformations. Although Hα chemical shifts could be predicted reasonably well using SHIFTX, agreement between predicted and experimental chemical shifts was sufficient for identifying native conformations for only some peptides in the representative set. Combining chemical shift data with the secondary structure information and potential energy calculations improved the ability to identify native conformations. Additional use of sparse distance restraints or homology information to restrict the search space also improved the resolution of the calculated structures. This study demonstrates that abbreviated methods have potential for elucidation of peptide structures to high resolution and further optimization of these methods, e.g., improvement in chemical shift prediction accuracy, will likely help transition these methods into the mainstream of disulfide-rich peptide structural biology.
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Affiliation(s)
- Conan K Wang
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - David J Craik
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
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24
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Ramalho SD, Wang CK, King GJ, Byriel KA, Huang YH, Bolzani VS, Craik DJ. Synthesis, Racemic X-ray Crystallographic, and Permeability Studies of Bioactive Orbitides from Jatropha Species. JOURNAL OF NATURAL PRODUCTS 2018; 81:2436-2445. [PMID: 30345754 DOI: 10.1021/acs.jnatprod.8b00447] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Orbitides are small cyclic peptides with a diverse range of therapeutic bioactivities. They are produced by many plant species, including those of the Jatropha genus. Here, the objective was to provide new structural information on orbitides to complement the growing knowledge base on orbitide sequences and activities by focusing on three Jatropha orbitides: ribifolin (1), pohlianin C (7), and jatrophidin (12). To determine three-dimensional structures, racemic crystallography, an emerging structural technique that enables rapid crystallization of biomolecules by combining equal amounts of the two enantiomers, was used. The high-resolution structure of ribifolin (0.99 Å) was elucidated from its racemate and showed it was identical to the structure crystallized from its l-enantiomer only (1.35 Å). Racemic crystallography was also used to elucidate high-resolution structures of pohlianin C (1.20 Å) and jatrophidin (1.03 Å), for which there was difficulty forming crystals without using racemic mixtures. The structures were used to interpret membrane permeability data in PAMPA and a Caco-2 cell assay, showing they had poor permeability. Overall, the results show racemic crystallography can be used to obtain high-resolution structures of orbitides and is useful when enantiopure samples are difficult to crystallize or solution structures from NMR are of low resolution.
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Affiliation(s)
- Suelem D Ramalho
- Institute of Chemistry , São Paulo State University-UNESP , Araraquara , São Paulo 14800-060 , Brazil
| | - Conan K Wang
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Gordon J King
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Karl A Byriel
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Yen-Hua Huang
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Vanderlan S Bolzani
- Institute of Chemistry , São Paulo State University-UNESP , Araraquara , São Paulo 14800-060 , Brazil
| | - David J Craik
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
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25
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A structural perspective of plant antimicrobial peptides. Biochem J 2018; 475:3359-3375. [PMID: 30413680 DOI: 10.1042/bcj20180213] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 10/12/2018] [Accepted: 10/14/2018] [Indexed: 12/26/2022]
Abstract
Among the numerous strategies plants have developed to fend off enemy attack, antimicrobial peptides (AMPs) stand out as one of the most prominent defensive barriers that grant direct and durable resistance against a wide range of pests and pathogens. These small proteins are characterized by a compact structure and an overall positive charge. AMPs have an ancient origin and widespread occurrence in the plant kingdom but show an unusually high degree of variation in their amino acid sequences. Interestingly, there is a strikingly conserved topology among the plant AMP families, suggesting that the defensive properties of these peptides are not determined by their primary sequences but rather by their tridimensional structure. To explore and expand this idea, we here discuss the role of AMPs for plant defense from a structural perspective. We show how specific structural properties, such as length, charge, hydrophobicity, polar angle and conformation, are essential for plant AMPs to act as a chemical shield that hinders enemy attack. Knowledge on the topology of these peptides is facilitating the isolation, classification and even structural redesign of AMPs, thus allowing scientists to develop new peptides with multiple agronomical and pharmacological potential.
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26
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Wu B, Murray JK, Andrews KL, Sham K, Long J, Aral J, Ligutti J, Amagasu S, Liu D, Zou A, Min X, Wang Z, Ilch CP, Kornecook TJ, Lin MHJ, Be X, Miranda LP, Moyer BD, Biswas K. Discovery of Tarantula Venom-Derived NaV1.7-Inhibitory JzTx-V Peptide 5-Br-Trp24 Analogue AM-6120 with Systemic Block of Histamine-Induced Pruritis. J Med Chem 2018; 61:9500-9512. [DOI: 10.1021/acs.jmedchem.8b00736] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Xiaoshan Min
- Therapeutic Discovery, Amgen Research, Amgen Inc., 1120 Veterans Blvd, South San Francisco, California 94080, United States
| | - Zhulun Wang
- Therapeutic Discovery, Amgen Research, Amgen Inc., 1120 Veterans Blvd, South San Francisco, California 94080, United States
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27
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Kent SBH. Racemic & quasi-racemic protein crystallography enabled by chemical protein synthesis. Curr Opin Chem Biol 2018; 46:1-9. [DOI: 10.1016/j.cbpa.2018.03.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/14/2018] [Accepted: 03/17/2018] [Indexed: 12/12/2022]
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28
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Chen C, Gao S, Qu Q, Mi P, Tao A, Li YM. Chemical synthesis and structural analysis of guanylate cyclase C agonist linaclotide. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2018.01.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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29
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Racemic X-ray structure of L-type calcium channel antagonist Calciseptine prepared by total chemical synthesis. Sci China Chem 2018. [DOI: 10.1007/s11426-017-9198-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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30
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Cardoso MH, Oshiro KG, Rezende SB, Cândido ES, Franco OL. The Structure/Function Relationship in Antimicrobial Peptides: What Can we Obtain From Structural Data? THERAPEUTIC PROTEINS AND PEPTIDES 2018; 112:359-384. [DOI: 10.1016/bs.apcsb.2018.01.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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31
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Johnstone TC, Nolan EM. Determination of the Molecular Structures of Ferric Enterobactin and Ferric Enantioenterobactin Using Racemic Crystallography. J Am Chem Soc 2017; 139:15245-15250. [PMID: 28956921 PMCID: PMC5748154 DOI: 10.1021/jacs.7b09375] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Enterobactin is a secondary metabolite produced by Enterobacteriaceae for acquiring iron, an essential metal nutrient. The biosynthesis and utilization of enterobactin permits many Gram-negative bacteria to thrive in environments where low soluble iron concentrations would otherwise preclude survival. Despite extensive work carried out on this celebrated molecule since its discovery over 40 years ago, the ferric enterobactin complex has eluded crystallographic structural characterization. We report the successful growth of single crystals containing ferric enterobactin using racemic crystallization, a method that involves cocrystallization of a chiral molecule with its mirror image. The structures of ferric enterobactin and ferric enantioenterobactin obtained in this work provide a definitive assignment of the stereochemistry at the metal center and reveal secondary coordination sphere interactions. The structures were employed in computational investigations of the interactions of these complexes with two enterobactin-binding proteins, which illuminate the influence of metal-centered chirality on these interactions. This work highlights the utility of small-molecule racemic crystallography for obtaining elusive structures of coordination complexes.
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Affiliation(s)
- Timothy C. Johnstone
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Elizabeth M. Nolan
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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32
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Yan B, Ye L, Xu W, Liu L. Recent advances in racemic protein crystallography. Bioorg Med Chem 2017; 25:4953-4965. [DOI: 10.1016/j.bmc.2017.05.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/03/2017] [Accepted: 05/09/2017] [Indexed: 10/19/2022]
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33
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Sable R, Durek T, Taneja V, Craik DJ, Pallerla S, Gauthier T, Jois S. Constrained Cyclic Peptides as Immunomodulatory Inhibitors of the CD2:CD58 Protein-Protein Interaction. ACS Chem Biol 2016; 11:2366-74. [PMID: 27337048 DOI: 10.1021/acschembio.6b00486] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The interaction between the cell-cell adhesion proteins CD2 and CD58 plays a crucial role in lymphocyte recruitment to inflammatory sites, and inhibitors of this interaction have potential as immunomodulatory drugs in autoimmune diseases. Peptides from the CD2 adhesion domain were designed to inhibit CD2:CD58 interactions. To improve the stability of the peptides, β-sheet epitopes from the CD2 region implicated in CD58 recognition were grafted into the cyclic peptide frameworks of sunflower trypsin inhibitor and rhesus theta defensin. The designed multicyclic peptides were evaluated for their ability to modulate cell-cell interactions in three different cell adhesion assays, with one candidate, SFTI-a, showing potent activity in the nanomolar range (IC50: 51 nM). This peptide also suppresses the immune responses in T cells obtained from mice that exhibit the autoimmune disease rheumatoid arthritis. SFTI-a was resistant to thermal denaturation, as judged by circular dichroism spectroscopy and mass spectrometry, and had a half-life of ∼24 h in human serum. Binding of this peptide to CD58 was predicted by molecular docking studies and experimentally confirmed by surface plasmon resonance experiments. Our results suggest that cyclic peptides from natural sources are promising scaffolds for modulating protein-protein interactions that are typically difficult to target with small-molecule compounds.
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Affiliation(s)
- Rushikesh Sable
- Basic
Pharmaceutical Sciences, School of Pharmacy, University of Louisiana at Monroe, Monroe, Louisiana 71201, United States
| | - Thomas Durek
- The
University of Queensland, Institute for Molecular Bioscience, Brisbane, Queensland 4072, Australia
| | - Veena Taneja
- Department
of Immunology, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - David J. Craik
- The
University of Queensland, Institute for Molecular Bioscience, Brisbane, Queensland 4072, Australia
| | - Sandeep Pallerla
- Basic
Pharmaceutical Sciences, School of Pharmacy, University of Louisiana at Monroe, Monroe, Louisiana 71201, United States
| | - Ted Gauthier
- LSU-Ag
Center, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Seetharama Jois
- Basic
Pharmaceutical Sciences, School of Pharmacy, University of Louisiana at Monroe, Monroe, Louisiana 71201, United States
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34
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Pan M, Gao S, Zheng Y, Tan X, Lan H, Tan X, Sun D, Lu L, Wang T, Zheng Q, Huang Y, Wang J, Liu L. Quasi-Racemic X-ray Structures of K27-Linked Ubiquitin Chains Prepared by Total Chemical Synthesis. J Am Chem Soc 2016; 138:7429-35. [PMID: 27268299 DOI: 10.1021/jacs.6b04031] [Citation(s) in RCA: 157] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Quasi-racemic crystallography has been used to determine the X-ray structures of K27-linked ubiquitin (Ub) chains prepared through total chemical synthesis. Crystal structures of K27-linked di- and tri-ubiquitins reveal that the isopeptide linkages are confined in a unique buried conformation, which provides the molecular basis for the distinctive function of K27 linkage compared to the other seven Ub chains. K27-linked di- and triUb were found to adopt different structural conformations in the crystals, one being symmetric whereas the other triangular. Furthermore, bioactivity experiments showed that the ovarian tumor family de-ubiquitinase 2 significantly favors K27-linked triUb than K27-linked diUb. K27-linked triUb represents the so-far largest chemically synthesized protein (228 amino acids) that has been crystallized to afford a high-resolution X-ray structure.
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Affiliation(s)
- Man Pan
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University , Beijing 100084, China
| | - Shuai Gao
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University , Beijing 100084, China
| | - Yong Zheng
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University , Beijing 100084, China
| | - Xiaodan Tan
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University , Beijing 100084, China
| | - Huan Lan
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University , Beijing 100084, China
| | - Xianglong Tan
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University , Beijing 100084, China
| | - Demeng Sun
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University , Beijing 100084, China
| | - Lining Lu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University , Beijing 100084, China
| | - Tian Wang
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University , Beijing 100084, China
| | - Qingyun Zheng
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University , Beijing 100084, China
| | - Yichao Huang
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University , Beijing 100084, China
| | - Jiawei Wang
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing 100084, China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University , Beijing 100084, China
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35
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Yeung H, Squire CJ, Yosaatmadja Y, Panjikar S, López G, Molina A, Baker EN, Harris PWR, Brimble MA. Radiation Damage and Racemic Protein Crystallography Reveal the Unique Structure of the GASA/Snakin Protein Superfamily. Angew Chem Int Ed Engl 2016; 55:7930-3. [DOI: 10.1002/anie.201602719] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Ho Yeung
- School of Biological Sciences; The University of Auckland; 3A Symonds St Auckland Central 1010 New Zealand
| | - Christopher J. Squire
- School of Biological Sciences; The University of Auckland; 3A Symonds St Auckland Central 1010 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery; Thomas Building Level 2; 3A Symonds St Auckland Central 1010 New Zealand
| | - Yuliana Yosaatmadja
- School of Biological Sciences; The University of Auckland; 3A Symonds St Auckland Central 1010 New Zealand
| | - Santosh Panjikar
- Australian Synchrotron; 800 Blackburn Road Clayton Victoria 3168 Australia
| | - Gemma López
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA); Universidad Politécnica de Madrid (UPM); Campus Montegancedo, M-40 (Km 38) 28223-Pozuelo de Alarcón Madrid Spain
| | - Antonio Molina
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA); Universidad Politécnica de Madrid (UPM); Campus Montegancedo, M-40 (Km 38) 28223-Pozuelo de Alarcón Madrid Spain
| | - Edward N. Baker
- School of Biological Sciences; The University of Auckland; 3A Symonds St Auckland Central 1010 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery; Thomas Building Level 2; 3A Symonds St Auckland Central 1010 New Zealand
| | - Paul W. R. Harris
- School of Chemical Sciences; The University of Auckland; 23 Symonds St Auckland Central 1010 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery; Thomas Building Level 2; 3A Symonds St Auckland Central 1010 New Zealand
| | - Margaret A. Brimble
- School of Chemical Sciences; The University of Auckland; 23 Symonds St Auckland Central 1010 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery; Thomas Building Level 2; 3A Symonds St Auckland Central 1010 New Zealand
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36
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Yeung H, Squire CJ, Yosaatmadja Y, Panjikar S, López G, Molina A, Baker EN, Harris PWR, Brimble MA. Radiation Damage and Racemic Protein Crystallography Reveal the Unique Structure of the GASA/Snakin Protein Superfamily. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602719] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ho Yeung
- School of Biological Sciences; The University of Auckland; 3A Symonds St Auckland Central 1010 New Zealand
| | - Christopher J. Squire
- School of Biological Sciences; The University of Auckland; 3A Symonds St Auckland Central 1010 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery; Thomas Building Level 2; 3A Symonds St Auckland Central 1010 New Zealand
| | - Yuliana Yosaatmadja
- School of Biological Sciences; The University of Auckland; 3A Symonds St Auckland Central 1010 New Zealand
| | - Santosh Panjikar
- Australian Synchrotron; 800 Blackburn Road Clayton Victoria 3168 Australia
| | - Gemma López
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA); Universidad Politécnica de Madrid (UPM); Campus Montegancedo, M-40 (Km 38) 28223-Pozuelo de Alarcón Madrid Spain
| | - Antonio Molina
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA); Universidad Politécnica de Madrid (UPM); Campus Montegancedo, M-40 (Km 38) 28223-Pozuelo de Alarcón Madrid Spain
| | - Edward N. Baker
- School of Biological Sciences; The University of Auckland; 3A Symonds St Auckland Central 1010 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery; Thomas Building Level 2; 3A Symonds St Auckland Central 1010 New Zealand
| | - Paul W. R. Harris
- School of Chemical Sciences; The University of Auckland; 23 Symonds St Auckland Central 1010 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery; Thomas Building Level 2; 3A Symonds St Auckland Central 1010 New Zealand
| | - Margaret A. Brimble
- School of Chemical Sciences; The University of Auckland; 23 Symonds St Auckland Central 1010 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery; Thomas Building Level 2; 3A Symonds St Auckland Central 1010 New Zealand
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37
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Wang CK, King GJ, Conibear AC, Ramos MC, Chaousis S, Henriques ST, Craik DJ. Mirror Images of Antimicrobial Peptides Provide Reflections on Their Functions and Amyloidogenic Properties. J Am Chem Soc 2016; 138:5706-13. [PMID: 27064294 DOI: 10.1021/jacs.6b02575] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Enantiomeric forms of BTD-2, PG-1, and PM-1 were synthesized to delineate the structure and function of these β-sheet antimicrobial peptides. Activity and lipid-binding assays confirm that these peptides act via a receptor-independent mechanism involving membrane interaction. The racemic crystal structure of BTD-2 solved at 1.45 Å revealed a novel oligomeric form of β-sheet antimicrobial peptides within the unit cell: an antiparallel trimer, which we suggest might be related to its membrane-active form. The BTD-2 oligomer extends into a larger supramolecular state that spans the crystal lattice, featuring a steric-zipper motif that is common in structures of amyloid-forming peptides. The supramolecular structure of BTD-2 thus represents a new mode of fibril-like assembly not previously observed for antimicrobial peptides, providing structural evidence linking antimicrobial and amyloid peptides.
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Affiliation(s)
- Conan K Wang
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, Queensland 4072, Australia
| | - Gordon J King
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, Queensland 4072, Australia
| | - Anne C Conibear
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, Queensland 4072, Australia
| | - Mariana C Ramos
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, Queensland 4072, Australia
| | - Stephanie Chaousis
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, Queensland 4072, Australia
| | - Sónia Troeira Henriques
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, Queensland 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, Queensland 4072, Australia
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38
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Salveson PJ, Spencer RK, Nowick JS. X-ray Crystallographic Structure of Oligomers Formed by a Toxic β-Hairpin Derived from α-Synuclein: Trimers and Higher-Order Oligomers. J Am Chem Soc 2016; 138:4458-67. [PMID: 26926877 PMCID: PMC4825732 DOI: 10.1021/jacs.5b13261] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
Oligomeric
assemblies of the protein α-synuclein are thought
to cause neurodegeneration in Parkinson’s disease and related
synucleinopathies. Characterization of α-synuclein oligomers
at high resolution is an outstanding challenge in the field of structural
biology. The absence of high-resolution structures of oligomers formed
by α-synuclein impedes understanding the synucleinopathies at
the molecular level. This paper reports the X-ray crystallographic
structure of oligomers formed by a peptide derived from residues 36–55
of α-synuclein. The peptide 1a adopts a β-hairpin
structure, which assembles in a hierarchical fashion. Three β-hairpins
assemble to form a triangular trimer. Three copies of the triangular
trimer assemble to form a basket-shaped nonamer. Two nonamers pack
to form an octadecamer. Molecular modeling suggests that full-length
α-synuclein may also be able to assemble in this fashion. Circular
dichroism spectroscopy demonstrates that peptide 1a interacts
with anionic lipid bilayer membranes, like oligomers of full-length
α-synuclein. LDH and MTT assays demonstrate that peptide 1a is toxic toward SH-SY5Y cells. Comparison of peptide 1a to homologues suggests that this toxicity results from
nonspecific interactions with the cell membrane. The oligomers formed
by peptide 1a are fundamentally different than the proposed
models of the fibrils formed by α-synuclein and suggest that
α-Syn36–55, rather than the NAC, may nucleate
oligomer formation.
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Affiliation(s)
- Patrick J Salveson
- Department of Chemistry, University of California Irvine , Irvine, California 92697-2025, United States
| | - Ryan K Spencer
- Department of Chemistry, University of California Irvine , Irvine, California 92697-2025, United States
| | - James S Nowick
- Department of Chemistry, University of California Irvine , Irvine, California 92697-2025, United States
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39
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Jorda J, Sawaya MR, Yeates TO. Progress in low-resolution ab initio phasing with CrowdPhase. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:446-53. [PMID: 26960132 PMCID: PMC4784676 DOI: 10.1107/s2059798316003405] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 02/26/2016] [Indexed: 11/21/2022]
Abstract
New developments in CrowdPhase, a collaborative online game for tackling the low-resolution phase problem, are presented. The new features address several crystallographic issues and extend the reach of CrowdPhase to a broader range of experimental data sets. Ab initio phasing by direct computational methods in low-resolution X-ray crystallography is a long-standing challenge. A common approach is to consider it as two subproblems: sampling of phase space and identification of the correct solution. While the former is amenable to a myriad of search algorithms, devising a reliable target function for the latter problem remains an open question. Here, recent developments in CrowdPhase, a collaborative online game powered by a genetic algorithm that evolves an initial population of individuals with random genetic make-up (i.e. random phases) each expressing a phenotype in the form of an electron-density map, are presented. Success relies on the ability of human players to visually evaluate the quality of these maps and, following a Darwinian survival-of-the-fittest concept, direct the search towards optimal solutions. While an initial study demonstrated the feasibility of the approach, some important crystallographic issues were overlooked for the sake of simplicity. To address these, the new CrowdPhase includes consideration of space-group symmetry, a method for handling missing amplitudes, the use of a map correlation coefficient as a quality metric and a solvent-flattening step. Performances of this installment are discussed for two low-resolution test cases based on bona fide diffraction data.
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Affiliation(s)
- Julien Jorda
- UCLA-DOE, Institute for Genomics and Proteomics, 611 Charles Young Drive East, Los Angeles, CA 90095, USA
| | - Michael R Sawaya
- UCLA-DOE, Institute for Genomics and Proteomics, 611 Charles Young Drive East, Los Angeles, CA 90095, USA
| | - Todd O Yeates
- UCLA-DOE, Institute for Genomics and Proteomics, 611 Charles Young Drive East, Los Angeles, CA 90095, USA
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40
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Strömstedt AA, Kristiansen PE, Gunasekera S, Grob N, Skjeldal L, Göransson U. Selective membrane disruption by the cyclotide kalata B7: complex ions and essential functional groups in the phosphatidylethanolamine binding pocket. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1317-27. [PMID: 26878982 DOI: 10.1016/j.bbamem.2016.02.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 02/10/2016] [Accepted: 02/11/2016] [Indexed: 01/17/2023]
Abstract
The cyclic cystine knot plant peptides called cyclotides are active against a wide variety of organisms. This is primarily achieved through membrane binding and disruption, in part deriving from a high affinity for phosphatidylethanolamine (PE) lipids. Some cyclotides, such as kalata B7 (kB7), form complexes with divalent cations in a pocket associated with the tyrosine residue at position 15 (Tyr15). In the current work we explore the effect of cations on membrane leakage caused by cyclotides kB1, kB2 and kB7, and we identify a functional group that is essential for PE selectivity. The presence of PE-lipids in liposomes increased the membrane permeabilizing potency of the cyclotides, with the potency of kB7 increasing by as much as 740-fold. The divalent cations Mn(2+), Mg(2+) and Ca(2+) had no apparent effect on PE selectivity. However, amino acid substitutions in kB7 proved that Tyr15 is crucial for PE-selective membrane permeabilization on various liposome systems. Although the tertiary structure of kB7 was maintained, as reflected by the NMR solution structure, mutating Tyr into Ser at position 15 resulted in substantially reduced PE selectivity. Ala substitution at the same position produced a similar reduction in PE selectivity, while substitution with Phe maintained high selectivity. We conclude that the phenyl ring in Tyr15 is critical for the high PE selectivity of kB7. Our results suggest that PE-binding and divalent cation coordination occur in the same pocket without adverse effects of competitive binding for the phospholipid.
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Affiliation(s)
- Adam A Strömstedt
- Department of Medicinal Chemistry, Division of Pharmacognosy, Uppsala University, Box 574, SE 75123 Uppsala, Sweden
| | - Per Eugen Kristiansen
- Department of Molecular Biosciences, University of Oslo, Box 1041, 0316 Oslo, Norway
| | - Sunithi Gunasekera
- Department of Medicinal Chemistry, Division of Pharmacognosy, Uppsala University, Box 574, SE 75123 Uppsala, Sweden
| | - Nathalie Grob
- Department of Medicinal Chemistry, Division of Pharmacognosy, Uppsala University, Box 574, SE 75123 Uppsala, Sweden
| | - Lars Skjeldal
- Department of Chemistry, Biochemistry and Food Science, Norwegian University of Life Sciences, N-1432 Ås, Norway
| | - Ulf Göransson
- Department of Medicinal Chemistry, Division of Pharmacognosy, Uppsala University, Box 574, SE 75123 Uppsala, Sweden
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41
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Mandal K, Dhayalan B, Avital-Shmilovici M, Tokmakoff A, Kent SBH. Crystallization of Enantiomerically Pure Proteins from Quasi-Racemic Mixtures: Structure Determination by X-Ray Diffraction of Isotope-Labeled Ester Insulin and Human Insulin. Chembiochem 2016; 17:421-5. [DOI: 10.1002/cbic.201500600] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Kalyaneswar Mandal
- Department of Chemistry; University of Chicago; 929 East 57th Street Chicago IL 60637 USA
| | - Balamurugan Dhayalan
- Department of Chemistry; University of Chicago; 929 East 57th Street Chicago IL 60637 USA
| | | | - Andrei Tokmakoff
- Department of Chemistry; University of Chicago; 929 East 57th Street Chicago IL 60637 USA
| | - Stephen B. H. Kent
- Department of Chemistry; University of Chicago; 929 East 57th Street Chicago IL 60637 USA
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42
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Inhibition of tau aggregation using a naturally-occurring cyclic peptide scaffold. Eur J Med Chem 2016; 109:342-9. [DOI: 10.1016/j.ejmech.2016.01.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 01/06/2016] [Accepted: 01/07/2016] [Indexed: 11/24/2022]
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43
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Spaniol JM, Wheeler KA. Accessing Centnerszwer's quasiracemate – molecular shape controlled molecular recognition. RSC Adv 2016. [DOI: 10.1039/c6ra08131b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Reinvestigation of M. Centnerszwer's 1899 quasiracemate using tailor-made additives offers important insight to molecular shape directed supramolecular assemblies.
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44
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Wang CK, Swedberg JE, Northfield SE, Craik DJ. Effects of Cyclization on Peptide Backbone Dynamics. J Phys Chem B 2015; 119:15821-30. [DOI: 10.1021/acs.jpcb.5b11085] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Conan K. Wang
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Joakim E. Swedberg
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Susan E. Northfield
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David J. Craik
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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45
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Abstract
Interactions between polypeptide chains containing amino acid residues with opposite absolute configurations have long been a source of interest and speculation, but there is very little structural information for such heterochiral associations. The need to address this lacuna has grown in recent years because of increasing interest in the use of peptides generated from d amino acids (d peptides) as specific ligands for natural proteins, e.g., to inhibit deleterious protein-protein interactions. Coiled-coil interactions, between or among α-helices, represent the most common tertiary and quaternary packing motif in proteins. Heterochiral coiled-coil interactions were predicted over 50 years ago by Crick, and limited experimental data obtained in solution suggest that such interactions can indeed occur. To address the dearth of atomic-level structural characterization of heterochiral helix pairings, we report two independent crystal structures that elucidate coiled-coil packing between l- and d-peptide helices. Both structures resulted from racemic crystallization of a peptide corresponding to the transmembrane segment of the influenza M2 protein. Networks of canonical knobs-into-holes side-chain packing interactions are observed at each helical interface. However, the underlying patterns for these heterochiral coiled coils seem to deviate from the heptad sequence repeat that is characteristic of most homochiral analogs, with an apparent preference for a hendecad repeat pattern.
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46
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Shah SS, Karthik S, Singh NDP. Vis/NIR light driven mild and clean synthesis of disulfides in the presence of Cu2(OH)PO4 under aerobic conditions. RSC Adv 2015. [DOI: 10.1039/c5ra05138j] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A highly efficient one-pot strategy has been developed for the synthesis of disulfide in the presence of air under the irradiation of Vis/NIR light.
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Affiliation(s)
- Sk. Sheriff Shah
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- India
| | - S. Karthik
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- India
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