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de Araujo AD, Lim J, Wu KC, Hoang HN, Nguyen HT, Fairlie DP. Landscaping macrocyclic peptides: stapling hDM2-binding peptides for helicity, protein affinity, proteolytic stability and cell uptake. RSC Chem Biol 2022; 3:895-904. [PMID: 35866171 PMCID: PMC9257625 DOI: 10.1039/d1cb00231g] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 05/19/2022] [Indexed: 12/25/2022] Open
Abstract
Surveying macrocycles for mimicking a helical tumor suppressor protein, resisting breakdown by proteases, and entering cancer cells.
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Affiliation(s)
- Aline D. de Araujo
- Division of Chemistry and Structural Biology, ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Junxian Lim
- Division of Chemistry and Structural Biology, ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Kai-Chen Wu
- Division of Chemistry and Structural Biology, ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Huy N. Hoang
- Division of Chemistry and Structural Biology, ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Huy T. Nguyen
- Division of Chemistry and Structural Biology, ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David P. Fairlie
- Division of Chemistry and Structural Biology, ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
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2
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Fischer NH, Fumi E, Oliveira MT, Thulstrup PW, Diness F. Tuning peptide structure and function through fluorobenzene stapling. Chemistry 2021; 28:e202103788. [PMID: 34897848 DOI: 10.1002/chem.202103788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Indexed: 11/09/2022]
Abstract
Cyclic peptides are promising next-generation therapeutics with improved biological stability and activity. A catalyst-free stapling method for cysteine-containing peptides was developed. This enables fine-tuning of the macrocycle by using the appropriate regioisomers of fluorobenzene linkers. Stapling was performed on the unprotected linear peptide or, more conveniently, directly on-resin after peptide synthesis. NMR spectroscopy and circular dichroism studies demonstrate that the type of stapling can tune the secondary structures of the peptides. The method was applied to a set of potential agonists for melanocortin receptors, generating a library of macrocyclic potent ligands with ortho , meta or para relationships between the thioethers. Their small but significant difference in potency and efficacy demonstrates how the method allows facile fine-tuning of macrocyclic peptides towards biological targets from the same linear precursor.
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Affiliation(s)
| | - Erik Fumi
- University of Copenhagen: Kobenhavns Universitet, Department of Chemistry, DENMARK
| | | | - Peter W Thulstrup
- University of Copenhagen: Kobenhavns Universitet, Department of Chemistry, DENMARK
| | - Frederik Diness
- University of Copenhagen, Department of Chemistry, Universitetsparken 5, DK2100, Copenhagen, DENMARK
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3
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Small and Simple, yet Sturdy: Conformationally Constrained Peptides with Remarkable Properties. Int J Mol Sci 2021; 22:ijms22041611. [PMID: 33562633 PMCID: PMC7915549 DOI: 10.3390/ijms22041611] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 12/20/2022] Open
Abstract
The sheer size and vast chemical space (i.e., diverse repertoire and spatial distribution of functional groups) underlie peptides’ ability to engage in specific interactions with targets of various structures. However, the inherent flexibility of the peptide chain negatively affects binding affinity and metabolic stability, thereby severely limiting the use of peptides as medicines. Imposing conformational constraints to the peptide chain offers to solve these problems but typically requires laborious structure optimization. Alternatively, libraries of constrained peptides with randomized modules can be screened for specific functions. Here, we present the properties of conformationally constrained peptides and review rigidification chemistries/strategies, as well as synthetic and enzymatic methods of producing macrocyclic peptides. Furthermore, we discuss the in vitro molecular evolution methods for the development of constrained peptides with pre-defined functions. Finally, we briefly present applications of selected constrained peptides to illustrate their exceptional properties as drug candidates, molecular recognition probes, and minimalist catalysts.
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4
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Malde AK, Hill TA, Iyer A, Fairlie DP. Crystal Structures of Protein-Bound Cyclic Peptides. Chem Rev 2019; 119:9861-9914. [DOI: 10.1021/acs.chemrev.8b00807] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Alpeshkumar K. Malde
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Timothy A. Hill
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Abishek Iyer
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David P. Fairlie
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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5
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Schumann NC, Bruning J, Marshall AC, Abell AD. The role of N-terminal heterocycles in hydrogen bonding to α-chymotrypsin. Bioorg Med Chem Lett 2019; 29:396-399. [PMID: 30579793 DOI: 10.1016/j.bmcl.2018.12.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/11/2018] [Accepted: 12/14/2018] [Indexed: 01/14/2023]
Abstract
A series of dipeptide aldehydes containing different N-terminal heterocycles was prepared and assayed in vitro against α-chymotrypsin to ascertain the importance of the heterocycle in maintaining a β-strand geometry while also providing a hydrogen bond donor equivalent to the backbone amide nitrogen of the surrogate amino acid. The dipeptide containing a pyrrole constraint (10) was the most potent inhibitor, with >30-fold improved activity over dipeptides which lacked a nitrogen hydrogen bond donor (namely thiophene 11, furan 12 and pyridine 13). Molecular docking studies of 10 bound to α-chymotrypsin demonstrates a hydrogen bond between the pyrrole nitrogen donor and the backbone carbonyl of Gly216 located in the S3 pocket which is proposed to be critical for overall binding.
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Affiliation(s)
- Nicholas C Schumann
- School of Chemistry & Physics, The University of Adelaide, North Terrace, Adelaide, SA 5005, Australia
| | - John Bruning
- School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, SA 5005, Australia
| | - Andrew C Marshall
- School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, SA 5005, Australia
| | - Andrew D Abell
- School of Chemistry & Physics, The University of Adelaide, North Terrace, Adelaide, SA 5005, Australia; ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP) and Institute of Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide, South Australia 5005, Australia.
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6
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Agbowuro AA, Huston WM, Gamble AB, Tyndall JDA. Proteases and protease inhibitors in infectious diseases. Med Res Rev 2017; 38:1295-1331. [PMID: 29149530 DOI: 10.1002/med.21475] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 09/10/2017] [Accepted: 10/17/2017] [Indexed: 12/31/2022]
Abstract
There are numerous proteases of pathogenic organisms that are currently targeted for therapeutic intervention along with many that are seen as potential drug targets. This review discusses the chemical and biological makeup of some key druggable proteases expressed by the five major classes of disease causing agents, namely bacteria, viruses, fungi, eukaryotes, and prions. While a few of these enzymes including HIV protease and HCV NS3-4A protease have been targeted to a clinically useful level, a number are yet to yield any clinical outcomes in terms of antimicrobial therapy. A significant aspect of this review discusses the chemical and pharmacological characteristics of inhibitors of the various proteases discussed. A total of 25 inhibitors have been considered potent and safe enough to be trialed in humans and are at different levels of clinical application. We assess the mechanism of action and clinical performance of the protease inhibitors against infectious agents with their developmental strategies and look to the next frontiers in the use of protease inhibitors as anti-infective agents.
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Affiliation(s)
| | - Wilhelmina M Huston
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
| | - Allan B Gamble
- School of Pharmacy, University of Otago, Dunedin, New Zealand
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7
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Marshall GR, Ballante F. Limiting Assumptions in the Design of Peptidomimetics. Drug Dev Res 2017; 78:245-267. [DOI: 10.1002/ddr.21406] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Garland R. Marshall
- Department of Biochemistry and Molecular Biophysics; Washington University School of Medicine; St. Louis Missouri 63110
| | - Flavio Ballante
- Department of Biochemistry and Molecular Biophysics; Washington University School of Medicine; St. Louis Missouri 63110
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8
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Zhang L, Navaratna T, Thurber GM. A Helix-Stabilizing Linker Improves Subcutaneous Bioavailability of a Helical Peptide Independent of Linker Lipophilicity. Bioconjug Chem 2016; 27:1663-72. [PMID: 27327034 DOI: 10.1021/acs.bioconjchem.6b00209] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Stabilized peptides address several limitations to peptide-based imaging agents and therapeutics such as poor stability and low affinity due to conformational flexibility. There is also active research in developing these compounds for intracellular drug targeting, and significant efforts have been invested to determine the effects of helix stabilization on intracellular delivery. However, much less is known about the impact on other pharmacokinetic parameters such as plasma clearance and bioavailability. We investigated the effect of different fluorescent helix-stabilizing linkers with varying lipophilicity on subcutaneous (sc) bioavailability using the glucagon-like peptide-1 (GLP-1) receptor ligand exendin as a model system. The stabilized peptides showed significantly higher protease resistance and increased bioavailability independent of linker hydrophilicity, and all subcutaneously delivered conjugates were able to successfully target the islets of Langerhans with high specificity. The lipophilic peptide variants had slower absorption and plasma clearance than their respective hydrophilic conjugates, and the absolute bioavailability was also lower likely due to the longer residence times in the skin. Their ease and efficiency make double-click helix stabilization chemistries a useful tool for increasing the bioavailability of peptide therapeutics, many of which suffer from rapid in vivo protease degradation. Helix stabilization using linkers of varying lipophilicity can further control sc absorption and clearance rates to customize plasma pharmacokinetics.
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Affiliation(s)
- Liang Zhang
- Department of Chemical Engineering, and ‡Department of Biomedical Engineering University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Tejas Navaratna
- Department of Chemical Engineering, and ‡Department of Biomedical Engineering University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Greg M Thurber
- Department of Chemical Engineering, and ‡Department of Biomedical Engineering University of Michigan , Ann Arbor, Michigan 48109, United States
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9
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Strisovsky K. Why cells need intramembrane proteases - a mechanistic perspective. FEBS J 2016; 283:1837-45. [DOI: 10.1111/febs.13638] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 12/19/2015] [Accepted: 12/24/2015] [Indexed: 01/01/2023]
Affiliation(s)
- Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; Prague Czech Republic
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10
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Page MJ, Lourenço AL, David T, LeBeau AM, Cattaruzza F, Castro HC, VanBrocklin HF, Coughlin SR, Craik CS. Non-invasive imaging and cellular tracking of pulmonary emboli by near-infrared fluorescence and positron-emission tomography. Nat Commun 2015; 6:8448. [PMID: 26423607 PMCID: PMC4593073 DOI: 10.1038/ncomms9448] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 08/21/2015] [Indexed: 12/22/2022] Open
Abstract
Functional imaging of proteolytic activity is an emerging strategy to quantify disease and response to therapy at the molecular level. We present a new peptide-based imaging probe technology that advances these goals by exploiting enzymatic activity to deposit probes labelled with near-infrared (NIR) fluorophores or radioisotopes in cell membranes of disease-associated proteolysis. This strategy allows for non-invasive detection of protease activity in vivo and ex vivo by tracking deposited probes in tissues. We demonstrate non-invasive detection of thrombin generation in a murine model of pulmonary embolism using our protease-activated peptide probes in microscopic clots within the lungs with NIR fluorescence optical imaging and positron-emission tomography. Thrombin activity is imaged deep in tissue and tracked predominantly to platelets within the lumen of blood vessels. The modular design of our probes allows for facile investigation of other proteases, and their contributions to disease by tailoring the protease activation and cell-binding elements. Functional imaging of proteolytic activity is an emerging strategy to guide patient diagnosis and monitor clinical outcome. Here the authors present a peptide-based probe to detect and localize thrombin activity ex vivo and non-invasively in mouse models of wounding and pulmonary thrombosis.
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Affiliation(s)
- Michael J Page
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158-2517, USA
| | - André L Lourenço
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158-2517, USA.,CAPES Foundation, Ministry of Education of Brazil, Brasília DF 70040-020, Brazil.,LABiEMol, Postgraduate Program in Pathology, Universidade Federal Fluminense, Niterói, Rio de Janeiro RJ 23230-060, Brazil
| | - Tovo David
- Cardiovascular Research Institute, University of California, San Francisco, California 94158-9001, USA
| | - Aaron M LeBeau
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158-2517, USA
| | - Fiore Cattaruzza
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158-2517, USA
| | - Helena C Castro
- LABiEMol, Postgraduate Program in Pathology, Universidade Federal Fluminense, Niterói, Rio de Janeiro RJ 23230-060, Brazil
| | - Henry F VanBrocklin
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, California 94107, USA
| | - Shaun R Coughlin
- Cardiovascular Research Institute, University of California, San Francisco, California 94158-9001, USA
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158-2517, USA
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11
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The membrane anchor of the transcriptional activator SREBP is characterized by intrinsic conformational flexibility. Proc Natl Acad Sci U S A 2015; 112:12390-5. [PMID: 26392539 DOI: 10.1073/pnas.1513782112] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Regulated intramembrane proteolysis (RIP) is a conserved mechanism crucial for numerous cellular processes, including signaling, transcriptional regulation, axon guidance, cell adhesion, cellular stress responses, and transmembrane protein fragment degradation. Importantly, it is relevant in various diseases including Alzheimer's disease, cardiovascular diseases, and cancers. Even though a number of structures of different intramembrane proteases have been solved recently, fundamental questions concerning mechanistic underpinnings of RIP and therapeutic interventions remain. In particular, this includes substrate recognition, what properties render a given substrate amenable for RIP, and how the lipid environment affects the substrate cleavage. Members of the sterol regulatory element-binding protein (SREBP) family of transcription factors are critical regulators of genes involved in cholesterol/lipid homeostasis. After site-1 protease cleavage of the inactive SREBP transmembrane precursor protein, RIP of the anchor intermediate by site-2 protease generates the mature transcription factor. In this work, we have investigated the labile anchor intermediate of SREBP-1 using NMR spectroscopy. Surprisingly, NMR chemical shifts, site-resolved solvent exposure, and relaxation studies show that the cleavage site of the lipid-signaling protein intermediate bears rigid α-helical topology. An evolutionary conserved motif, by contrast, interrupts the secondary structure ∼9-10 residues C-terminal of the scissile bond and acts as an inducer of conformational flexibility within the carboxyl-terminal transmembrane region. These results are consistent with molecular dynamics simulations. Topology, stability, and site-resolved dynamics data suggest that the cleavage of the α-helical substrate in the case of RIP may be associated with a hinge motion triggered by the molecular environment.
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12
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Zhang L, Navaratna T, Liao J, Thurber GM. Dual-purpose linker for alpha helix stabilization and imaging agent conjugation to glucagon-like peptide-1 receptor ligands. Bioconjug Chem 2015; 26:329-37. [PMID: 25594741 DOI: 10.1021/bc500584t] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Peptides display many characteristics of efficient imaging agents such as rapid targeting, fast background clearance, and low non-specific cellular uptake. However, poor stability, low affinity, and loss of binding after labeling often preclude their use in vivo. Using glucagon-like peptide-1 receptor (GLP-1R) ligands exendin and GLP-1 as a model system, we designed a novel α-helix-stabilizing linker to simultaneously address these limitations. The stabilized and labeled peptides showed an increase in helicity, improved protease resistance, negligible loss or an improvement in binding affinity, and excellent in vivo targeting. The ease of incorporating azidohomoalanine in peptides and efficient reaction with the dialkyne linker enable this technique to potentially be used as a general method for labeling α helices. This strategy should be useful for imaging beta cells in diabetes research and in developing and testing other peptide targeting agents.
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Affiliation(s)
- Liang Zhang
- Department of Chemical Engineering, ‡Department of Biomedical Engineering, University of Michigan , Ann Arbor, Michigan 48109, United States
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13
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Belfrage AK, Gising J, Svensson F, Åkerblom E, Sköld C, Sandström A. Efficient and Selective Palladium-Catalysed C-3 Urea Couplings to 3,5-Dichloro-2(1H)-pyrazinones. European J Org Chem 2015. [DOI: 10.1002/ejoc.201403405] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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14
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Hill TA, Shepherd NE, Diness F, Fairlie DP. Constraining cyclic peptides to mimic protein structure motifs. Angew Chem Int Ed Engl 2014; 53:13020-41. [PMID: 25287434 DOI: 10.1002/anie.201401058] [Citation(s) in RCA: 306] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 04/02/2013] [Indexed: 12/18/2022]
Abstract
Many proteins exert their biological activities through small exposed surface regions called epitopes that are folded peptides of well-defined three-dimensional structures. Short synthetic peptide sequences corresponding to these bioactive protein surfaces do not form thermodynamically stable protein-like structures in water. However, short peptides can be induced to fold into protein-like bioactive conformations (strands, helices, turns) by cyclization, in conjunction with the use of other molecular constraints, that helps to fine-tune three-dimensional structure. Such constrained cyclic peptides can have protein-like biological activities and potencies, enabling their uses as biological probes and leads to therapeutics, diagnostics and vaccines. This Review highlights examples of cyclic peptides that mimic three-dimensional structures of strand, turn or helical segments of peptides and proteins, and identifies some additional restraints incorporated into natural product cyclic peptides and synthetic macrocyclic peptidomimetics that refine peptide structure and confer biological properties.
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Affiliation(s)
- Timothy A Hill
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072 (Australia)
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15
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Hill TA, Shepherd NE, Diness F, Fairlie DP. Fixierung cyclischer Peptide: Mimetika von Proteinstrukturmotiven. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201401058] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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16
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Rigden DJ, Xu Q, Chang Y, Eberhardt RY, Finn RD, Rawlings ND. The first structure in a family of peptidase inhibitors reveals an unusual Ig-like fold. F1000Res 2014; 2:154. [PMID: 24555072 PMCID: PMC3901451 DOI: 10.12688/f1000research.2-154.v2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/19/2013] [Indexed: 12/03/2022] Open
Abstract
We report the crystal structure solution of the Intracellular Protease Inhibitor (IPI) protein from
Bacillus subtilis, which has been reported to be an inhibitor of the intracellular subtilisin Isp1 from the same organism. The structure of IPI is a variant of the all-beta, immunoglobulin (Ig) fold. It is possible that IPI is important for protein-protein interactions, of which inhibition of Isp1 is one. The intracellular nature of ISP is questioned, because an alternative ATG codon in the
ipi gene would produce a protein with an N-terminal extension containing a signal peptide. It is possible that alternative initiation exists, producing either an intracellular inhibitor or a secreted form that may be associated with the cell surface. Homologues of the IPI protein from other species are multi-domain proteins, containing signal peptides and domains also associated with the bacterial cell-surface. The cysteine peptidase inhibitors chagasin and amoebiasin also have Ig-like folds, but their topology differs significantly from that of IPI, and they share no recent common ancestor. A model of IPI docked to Isp1 shows similarities to other subtilisin:inhibitor complexes, particularly where the inhibitor interacts with the peptidase active site.
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Affiliation(s)
- Daniel J Rigden
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Qingping Xu
- Joint Center for Structural Genomics, La Jolla CA, 92037, USA ; Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park CA, 94025, USA
| | | | - Ruth Y Eberhardt
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK ; European Molecular Biology Laboratory, European Bioinformatics Institute,Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Robert D Finn
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn VA, 20147, USA
| | - Neil D Rawlings
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK ; European Molecular Biology Laboratory, European Bioinformatics Institute,Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
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17
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Strisovsky K. Structural and mechanistic principles of intramembrane proteolysis--lessons from rhomboids. FEBS J 2013; 280:1579-603. [PMID: 23432912 DOI: 10.1111/febs.12199] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 02/11/2013] [Accepted: 02/18/2013] [Indexed: 02/03/2023]
Abstract
Intramembrane proteases cleave membrane proteins in their transmembrane helices to regulate a wide range of biological processes. They catalyse hydrolytic reactions within the hydrophobic environment of lipid membranes where water is normally excluded. How? Do the different classes of intramembrane proteases share any mechanistic principles? In this review these questions will be discussed in view of the crystal structures of prokaryotic members of the three known catalytic types of intramembrane proteases published over the past 7 years. Rhomboids, the intramembrane serine proteases that are the best understood family, will be the initial area of focus, and the principles that have arisen from a number of structural and biochemical studies will be considered. The site-2 metalloprotease and GXGD-type aspartyl protease structures will then be discussed, with parallels drawn and differences highlighted between these enzymes and the rhomboids. Despite the significant advances achieved so far, to obtain a detailed understanding of the mechanism of any intramembrane protease, high-resolution structural information on the substrate-enzyme complex is required. This remains a major challenge for the field.
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Affiliation(s)
- Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
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18
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Kang CW, Sun Y, Del Valle JR. Substituted imidazo[1,2-a]pyridines as β-strand peptidomimetics. Org Lett 2012; 14:6162-5. [PMID: 23210770 DOI: 10.1021/ol302850n] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
New conformationally extended dipeptide surrogates based on an imidazo[1,2-a]pyridine scaffold are described. Efficient synthesis and incorporation into host peptides affords structures with native side-chain functionality and hydrogen bonding elements on one face of the backbone. Structural analysis by NMR suggests that model peptidomimetics adopt a β-strand-like conformation in solution.
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Affiliation(s)
- Chang Won Kang
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, United States
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19
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Fontana A, de Laureto PP, Spolaore B, Frare E. Identifying disordered regions in proteins by limited proteolysis. Methods Mol Biol 2012; 896:297-318. [PMID: 22821533 DOI: 10.1007/978-1-4614-3704-8_20] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Limited proteolysis experiments can be successfully used to detect sites of disorder in otherwise folded globular proteins. The approach relies on the fact that the proteolysis of a polypeptide substrate requires its binding in an extended conformation at the protease's active site and thus an enhanced backbone flexibility or local unfolding of the site of proteolytic attack. A striking correlation was found between sites of limited proteolysis and sites of enhanced chain flexibility of the polypeptide chain, this last evaluated by the crystallographically determined B-factor. In numerous cases, it has been shown that limited proteolysis occurs at chain regions characterized by missing electron density and thus being disordered. Therefore, limited proteolysis is a simple and reliable experimental technique that can detect sites of disorder in proteins, thus complementing the results that can be obtained by the use of other physicochemical and computational approaches.
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Affiliation(s)
- Angelo Fontana
- CRIBI Biotechnology Centre, University of Padua, Padua, Italy.
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20
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Loughlin WA, Tyndall JDA, Glenn MP, Hill TA, Fairlie DP. Update 1 of: Beta-Strand Mimetics. Chem Rev 2011; 110:PR32-69. [DOI: 10.1021/cr900395y] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Wendy A. Loughlin
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - Joel D. A. Tyndall
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - Matthew P. Glenn
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - Timothy A. Hill
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - David P. Fairlie
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
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21
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Madala PK, Tyndall JDA, Nall T, Fairlie DP. Update 1 of: Proteases Universally Recognize Beta Strands In Their Active Sites. Chem Rev 2011; 110:PR1-31. [DOI: 10.1021/cr900368a] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Praveen K. Madala
- Centre for Drug Design and Development, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2005, 105 (3), 973−1000; Published (Web) Feb. 16, 2005. Updates to the text appear in red type
| | - Joel D. A. Tyndall
- Centre for Drug Design and Development, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2005, 105 (3), 973−1000; Published (Web) Feb. 16, 2005. Updates to the text appear in red type
| | - Tessa Nall
- Centre for Drug Design and Development, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2005, 105 (3), 973−1000; Published (Web) Feb. 16, 2005. Updates to the text appear in red type
| | - David P. Fairlie
- Centre for Drug Design and Development, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2005, 105 (3), 973−1000; Published (Web) Feb. 16, 2005. Updates to the text appear in red type
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22
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Örtqvist P, Gising J, Ehrenberg AE, Vema A, Borg A, Karlén A, Larhed M, Danielson UH, Sandström A. Discovery of achiral inhibitors of the hepatitis C virus NS3 protease based on 2(1H)-pyrazinones. Bioorg Med Chem 2010; 18:6512-25. [DOI: 10.1016/j.bmc.2010.06.101] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Revised: 06/21/2010] [Accepted: 06/29/2010] [Indexed: 10/19/2022]
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23
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Ranatunga S, Liyanage W, Del Valle JR. Synthesis and conformational analysis of bicyclic extended dipeptide surrogates. J Org Chem 2010; 75:5113-25. [PMID: 20593836 PMCID: PMC2914495 DOI: 10.1021/jo1008433] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Regio- and diastereoselective reactions of a homoproline enolate enable the synthesis of novel extended dipeptide surrogates. Bicyclic carbamate 9 and fused beta-lactam scaffold 11 were prepared from L-pyroglutamic acid via substrate-controlled electrophilic azidation. Synthesis of orthogonally protected hexahydropyrrolizine, hexahydropyrrolizinone, and hexahydropyrroloazepinone dipeptide surrogates relied on allylation of proline derivative 5, followed by Curtius rearrangement to introduce the N-terminal carbamate group. A total of six azabicycloalkane derivatives were evaluated for conformational mimicry of extended dipeptides by a combination of X-ray diffraction and molecular modeling. Analysis of putative backbone dihedral angles and N- to C-terminal dipeptide distances indicate that compounds (alpha'S)-14b and 21 approximate the conformation of dipeptides found in beta-sheets, while tripeptide mimic 28 is also highly extended in the solid state. Structural data suggest that ring size and relative stereochemistry have a profound effect on the ability of these scaffolds to act as beta-strand mimetics and should inform the design of related conformational probes.
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24
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Löser R, Abbenante G, Madala PK, Halili M, Le GT, Fairlie DP. Noncovalent Tripeptidyl Benzyl- and Cyclohexyl-Amine Inhibitors of the Cysteine Protease Caspase-1. J Med Chem 2010; 53:2651-5. [DOI: 10.1021/jm901790w] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Reik Löser
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Giovanni Abbenante
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Praveen K. Madala
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Maria Halili
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Giang T. Le
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David P. Fairlie
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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25
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Chandrasekhar S, Sudhakar A, Kiran MU, Babu BN, Jagadeesh B. β-Strand mimetics: formation of bend-strands in oligomers of enantiomeric β-amino acids. Tetrahedron Lett 2008. [DOI: 10.1016/j.tetlet.2008.10.031] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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26
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Van Damme P, Vandekerckhove J, Gevaert K. Disentanglement of protease substrate repertoires. Biol Chem 2008; 389:371-81. [PMID: 18208357 DOI: 10.1515/bc.2008.043] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Identification of protease substrates and detailed characterization of processed sites are essential for understanding the biological function of proteases. Because of inherent complexity reasons, this however remains a formidable analytical challenge, illustrated by the fact that the majority of the more than 500 human proteases are uncharacterized to date. Recently, in addition to conventional genetic and biochemical approaches, diverse quantitative peptide-centric proteomics approaches, some of which selectively recover N-terminal peptides, have emerged. These latter proteomic technologies in particular allow the identification of natural protease substrates and delineation of cleavage sites in a complex, natural background of thousands of different proteins. We here review current biochemical, genetic and proteomic methods for global analysis of substrates of proteases and discuss selected applications.
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Affiliation(s)
- Petra Van Damme
- Department of Medical Protein Research, Flanders Interuniversity Institute for Biotechnology (VIB), B-9000 Ghent, Belgium
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27
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Stoermer MJ, Chappell KJ, Liebscher S, Jensen CM, Gan CH, Gupta PK, Xu WJ, Young PR, Fairlie DP. Potent Cationic Inhibitors of West Nile Virus NS2B/NS3 Protease With Serum Stability, Cell Permeability and Antiviral Activity. J Med Chem 2008; 51:5714-21. [DOI: 10.1021/jm800503y] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Martin J. Stoermer
- Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia, School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Keith J. Chappell
- Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia, School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Susann Liebscher
- Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia, School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Christina M. Jensen
- Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia, School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Chun H. Gan
- Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia, School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Praveer K. Gupta
- Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia, School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Wei-Jun Xu
- Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia, School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Paul R. Young
- Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia, School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - David P. Fairlie
- Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia, School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
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28
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Löser R, Frizler M, Schilling K, Gütschow M. Azadipeptidnitrile – hochpotente und proteolysestabile Inhibitoren Papain-ähnlicher Cysteinproteasen. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200705858] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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29
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Löser R, Frizler M, Schilling K, Gütschow M. Azadipeptide Nitriles: Highly Potent and Proteolytically Stable Inhibitors of Papain-Like Cysteine Proteases. Angew Chem Int Ed Engl 2008; 47:4331-4. [DOI: 10.1002/anie.200705858] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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30
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Tyndall JDA, Pattenden LK, Reid RC, Hu SH, Alewood D, Alewood PF, Walsh T, Fairlie DP, Martin JL. Crystal Structures of Highly Constrained Substrate and Hydrolysis Products Bound to HIV-1 Protease. Implications for the Catalytic Mechanism. Biochemistry 2008; 47:3736-44. [DOI: 10.1021/bi7023157] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Joel D. A. Tyndall
- National School of Pharmacy, University of Otago, P.O. Box 913, Dunedin 9054, New Zealand, Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane QLD 4072, Australia, and Centre for Molecular Biotechnology, Queensland University of Technology, Brisbane QLD 4001, Australia
| | - Leonard K. Pattenden
- National School of Pharmacy, University of Otago, P.O. Box 913, Dunedin 9054, New Zealand, Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane QLD 4072, Australia, and Centre for Molecular Biotechnology, Queensland University of Technology, Brisbane QLD 4001, Australia
| | - Robert C. Reid
- National School of Pharmacy, University of Otago, P.O. Box 913, Dunedin 9054, New Zealand, Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane QLD 4072, Australia, and Centre for Molecular Biotechnology, Queensland University of Technology, Brisbane QLD 4001, Australia
| | - Shu-Hong Hu
- National School of Pharmacy, University of Otago, P.O. Box 913, Dunedin 9054, New Zealand, Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane QLD 4072, Australia, and Centre for Molecular Biotechnology, Queensland University of Technology, Brisbane QLD 4001, Australia
| | - Dianne Alewood
- National School of Pharmacy, University of Otago, P.O. Box 913, Dunedin 9054, New Zealand, Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane QLD 4072, Australia, and Centre for Molecular Biotechnology, Queensland University of Technology, Brisbane QLD 4001, Australia
| | - Paul F. Alewood
- National School of Pharmacy, University of Otago, P.O. Box 913, Dunedin 9054, New Zealand, Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane QLD 4072, Australia, and Centre for Molecular Biotechnology, Queensland University of Technology, Brisbane QLD 4001, Australia
| | - Terry Walsh
- National School of Pharmacy, University of Otago, P.O. Box 913, Dunedin 9054, New Zealand, Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane QLD 4072, Australia, and Centre for Molecular Biotechnology, Queensland University of Technology, Brisbane QLD 4001, Australia
| | - David P. Fairlie
- National School of Pharmacy, University of Otago, P.O. Box 913, Dunedin 9054, New Zealand, Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane QLD 4072, Australia, and Centre for Molecular Biotechnology, Queensland University of Technology, Brisbane QLD 4001, Australia
| | - Jennifer L. Martin
- National School of Pharmacy, University of Otago, P.O. Box 913, Dunedin 9054, New Zealand, Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane QLD 4072, Australia, and Centre for Molecular Biotechnology, Queensland University of Technology, Brisbane QLD 4001, Australia
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31
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Quantitative measurement of protease ligand conformation. J Comput Aided Mol Des 2008; 22:105-9. [DOI: 10.1007/s10822-008-9173-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2007] [Accepted: 01/05/2008] [Indexed: 10/22/2022]
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32
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Harrison RS, Sharpe PC, Singh Y, Fairlie DP. Amyloid peptides and proteins in review. Rev Physiol Biochem Pharmacol 2007; 159:1-77. [PMID: 17846922 DOI: 10.1007/112_2007_0701] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Amyloids are filamentous protein deposits ranging in size from nanometres to microns and composed of aggregated peptide beta-sheets formed from parallel or anti-parallel alignments of peptide beta-strands. Amyloid-forming proteins have attracted a great deal of recent attention because of their association with over 30 diseases, notably neurodegenerative conditions like Alzheimer's, Huntington's, Parkinson's, Creutzfeldt-Jacob and prion disorders, but also systemic diseases such as amyotrophic lateral sclerosis (Lou Gehrig's disease) and type II diabetes. These diseases are all thought to involve important conformational changes in proteins, sometimes termed misfolding, that usually produce beta-sheet structures with a strong tendency to aggregate into water-insoluble fibrous polymers. Reasons for such conformational changes in vivo are still unclear. Intermediate aggregated state(s), rather than precipitated insoluble polymeric aggregates, have recently been implicated in cellular toxicity and may be the source of aberrant pathology in amyloid diseases. Numerous in vitro studies of short and medium length peptides that form amyloids have provided some clues to amyloid formation, with an alpha-helix to beta-sheet folding transition sometimes implicated as an intermediary step leading to amyloid formation. More recently, quite a few non-pathological amyloidogenic proteins have also been identified and physiological properties have been ascribed, challenging previous implications that amyloids were always disease causing. This article summarises a great deal of current knowledge on the occurrence, structure, folding pathways, chemistry and biology associated with amyloidogenic peptides and proteins and highlights some key factors that have been found to influence amyloidogenesis.
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Affiliation(s)
- R S Harrison
- Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, QLD 4072, Brisbane, Australia
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33
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Larsen KS, Østergaard H, Bjelke JR, Olsen OH, Rasmussen HB, Christensen L, Kragelund BB, Stennicke HR. Engineering the substrate and inhibitor specificities of human coagulation Factor VIIa. Biochem J 2007; 405:429-38. [PMID: 17456045 PMCID: PMC2267294 DOI: 10.1042/bj20061901] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The remarkably high specificity of the coagulation proteases towards macromolecular substrates is provided by numerous interactions involving the catalytic groove and remote exosites. For FVIIa [activated FVII (Factor VII)], the principal initiator of coagulation via the extrinsic pathway, several exosites have been identified, whereas only little is known about the specificity dictated by the active-site architecture. In the present study, we have profiled the primary P4-P1 substrate specificity of FVIIa using positional scanning substrate combinatorial libraries and evaluated the role of the selective active site in defining specificity. Being a trypsin-like serine protease, FVIIa had P1 specificity exclusively towards arginine and lysine residues. In the S2 pocket, threonine, leucine, phenylalanine and valine residues were the most preferred amino acids. Both S3 and S4 appeared to be rather promiscuous, however, with some preference for aromatic amino acids at both positions. Interestingly, a significant degree of interdependence between the S3 and S4 was observed and, as a consequence, the optimal substrate for FVIIa could not be derived directly from a subsite-directed specificity screen. To evaluate the role of the active-site residues in defining specificity, a series of mutants of FVIIa were prepared at position 239 (position 99 in chymotrypsin), which is considered to be one of the most important residues for determining P2 specificity of the trypsin family members. This was confirmed for FVIIa by marked changes in primary substrate specificity and decreased rates of antithrombin III inhibition. Interestingly, these changes do not necessarily coincide with an altered ability to activate Factor X, demonstrating that inhibitor and macromolecular substrate selectivity may be engineered separately.
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Affiliation(s)
- Katrine S Larsen
- Haemostasis Biochemistry, Novo Nordisk A/S, Novo Nordisk Park, DK-2760 Måløv, Denmark.
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Weiss HM, Wirz B, Schweitzer A, Amstutz R, Rodriguez Perez MI, Andres H, Metz Y, Gardiner J, Seebach D. ADME Investigations of Unnatural Peptides: Distribution of a14C-Labeledβ3-Octaarginine in Rats. Chem Biodivers 2007; 4:1413-37. [PMID: 17638323 DOI: 10.1002/cbdv.200790121] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The highly positively charged, cell-penetrating beta3-octaarginine has been prepared with a radioactive label by acetylation at the N-terminus with a doubly (14)C-labeled acetyl group ((14)CH3-(14)CO). With the radioactive compound, an ADME study (Absorption, Distribution, Metabolism, Excretion) was performed in male rats following an intravenous or oral dose of 1 mg/kg. Sampling was carried out after periods ranging from 5 min to 4 d or 7 d for blood/excretia and quantitative whole-body autoradioluminography (QWBA), respectively. After p.o. dosing, no systemic exposure to peptide-related radioactivity was observed, and the dose was completely excreted in the feces within 24 h suggesting the absence of relevant absorption; less than 3% of the i.v. dose was excreted from the animals within 4 d. Blood levels, after i.v. dosing, dropped within 4 d to less than 2% of Cmax and decreased afterwards only very slowly. No metabolites were observed in the systemic circulation. QWBA Data indicated that the distribution of the acetyl-beta-octaarginine-related radioactivity in the organs and tissues shifted over time. Notably, after 7 d, the highest concentration was measured in the lymph nodes, and the largest amount was found in the liver. A comparison with the results of two previous ADME investigations of beta-peptides (cf. Table 1) reveals that the distribution of the compounds within the animals is structure-dependent, and that there is a full range from oral availability with rather rapid excretion (of a tetrapeptide) to essentially complete lack of both oral absorption and excretion after i.v. administration (of a highly charged octapeptide). A discussion is presented about the in vivo stability and 'drug-ability' of peptides. In general, beta-peptides bearing proteinogenic side chains are compared with peptides consisting entirely of D-alpha-amino acid residues (the enantiomers of the 'natural' building blocks), and suggestions are made regarding a possible focus of future biomedical investigations with beta-peptides.
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Affiliation(s)
- H Markus Weiss
- Drug Metabolism and Pharmacokinetics, Novartis Pharma AG, Postfach, CH-4002 Basel
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Le GT, Abbenante G, Madala PK, Hoang HN, Fairlie DP. Organic Azide Inhibitors of Cysteine Proteases. J Am Chem Soc 2006; 128:12396-7. [PMID: 16984172 DOI: 10.1021/ja0637649] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cysteine proteases are crucial regulatory enzymes in human physiology and disease. Inhibitors are usually designed with reactive electrophiles to covalently bond to the catalytic cysteinyl sulfur, and consequently they also indiscriminately interact with biological thiolates and other nucleophiles, leading to toxic side effects in vivo. Here we describe an alternative to using reactive electrophiles, demonstrating the use of a much less reactive azidomethylene substituent (-CH2-N3) that confers potent inhibition of cysteine proteases. This new approach resulted in potent, reversible, competitive inhibitors of caspase-1 (IC50 < 10 nM), with significant advantages over aldehydes such as high stability in vitro to thiols (10 mM dithiothreitol (pH 7.2), 20 mM glutathione (pH 7.2, 9, 11)) and aqueous media, as well as some highly desirable druglike features. It was also demonstrated that azides can be incorporated into inhibitors of other caspases (e.g. 3, 8) and cathepsins (e.g. K, S, B), indicating the versatility of this valuable new approach to cysteine protease inhibition.
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Affiliation(s)
- Giang Thanh Le
- Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
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36
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Srivastava V, Saxena HO, Shanker K, Kumar JK, Luqman S, Gupta MM, Khanuja SPS, Negi AS. Synthesis of gallic acid based naphthophenone fatty acid amides as cathepsin D inhibitors. Bioorg Med Chem Lett 2006; 16:4603-8. [PMID: 16797987 DOI: 10.1016/j.bmcl.2006.06.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2006] [Revised: 05/23/2006] [Accepted: 06/05/2006] [Indexed: 02/08/2023]
Abstract
Gallic acid, one of the most abundant plant phenolic acids, has been modified to cathepsin D protease inhibitors. The strategy of modification was proposed basing on some previously reported structure and activity relationship (SAR) studies. The synthesized naphthophenone fatty acid amide derivatives have been evaluated for in vitro cathepsin D inhibition activity. Two of them have shown significant inhibition activity with IC(50) values of 0.06 and 0.14 microM, respectively, as compared against pepstatin (0.0023 microM), the most potent inhibitor known so far. The study revealed that such attempts on gallic acid based pharmacophores might result in potent inhibitors of cathepsin D.
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Affiliation(s)
- Vandana Srivastava
- Central Institute of Medicinal and Aromatic Plants, PO CIMAP, Lucknow, India
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37
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López-Lira F, Rosales-León L, Martínez VM, Ruiz Ordaz BH. The role of β2-glycoprotein I (β2GPI) in the activation of plasminogen. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:815-23. [PMID: 16480936 DOI: 10.1016/j.bbapap.2005.12.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2005] [Revised: 12/21/2005] [Accepted: 12/22/2005] [Indexed: 10/25/2022]
Abstract
Beta2-glycoprotein I (beta2GPI) is a glycoprotein of unknown physiological function. It is the main target antigen for antiphospholipid antibodies in patients with antiphospholipid syndrome (APS). beta2GPI binds with high affinity to the atherogenic lipoprotein Lp(a) which shares structural homology with plasminogen, a key molecule in the fibrinolytic system. Impaired fibrinolysis has been described in APS. The present work reports the interaction between beta2GPI and Glu-Plasminogen which may explain the recently described proteolytic effect of plasmin on beta2GPI. In the process of Glu-Plasminogen activation, we found an increase in plasmin generation both at fibrin and cellular surface level as a function of the concentration of beta2GPI added, suggesting an important role as a cofactor in the trimolecular complex beta2GPI-Plasminogen-tPA. This phenomenon represents a novel regulatory step both in the positive feedback mechanism for extrinsic fibrinolysis and in antithrombotic regulation. IgG anti-beta2GPI antibodies recognized the beta2GPI at the endothelial surface inducing its activation with an increase of ICAM-I and a decrease in the expression of thrombomodulin favoring a pro-thrombotic state in the vascular endothelium. The interference in the plasmin conversion by anti-beta2GPI antibodies could generate thrombosis as observed in APS.
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Affiliation(s)
- Francisco López-Lira
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, UNAM, Ciudad Universitaria 04510, México, D.F., Mexico
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38
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Tyndall JDA, Nall T, Fairlie DP. Proteases universally recognize beta strands in their active sites. Chem Rev 2005; 105:973-99. [PMID: 15755082 DOI: 10.1021/cr040669e] [Citation(s) in RCA: 301] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Joel D A Tyndall
- Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia.
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Tyndall JDA, Pfeiffer B, Abbenante G, Fairlie DP. Over One Hundred Peptide-Activated G Protein-Coupled Receptors Recognize Ligands with Turn Structure. Chem Rev 2005; 105:793-826. [PMID: 15755077 DOI: 10.1021/cr040689g] [Citation(s) in RCA: 176] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Joel D A Tyndall
- Center for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
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40
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Affiliation(s)
- Wendy A Loughlin
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia.
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41
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Nall TA, Chappell KJ, Stoermer MJ, Fang NX, Tyndall JDA, Young PR, Fairlie DP. Enzymatic Characterization and Homology Model of a Catalytically Active Recombinant West Nile Virus NS3 Protease. J Biol Chem 2004; 279:48535-42. [PMID: 15322074 DOI: 10.1074/jbc.m406810200] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
West Nile Virus (WNV) is a mosquito-borne flavivirus with a rapidly expanding global distribution. Infection causes severe neurological disease and fatalities in both human and animal hosts. The West Nile viral protease (NS2B-NS3) is essential for post-translational processing in host-infected cells of a viral polypeptide precursor into structural and functional viral proteins, and its inhibition could represent a potential treatment for viral infections. This article describes the design, expression, and enzymatic characterization of a catalytically active recombinant WNV protease, consisting of a 40-residue component of cofactor NS2B tethered via a noncleavable nonapeptide (G4SG4) to the N-terminal 184 residues of NS3. A chromogenic assay using synthetic para-nitroanilide (pNA) hexapeptide substrates was used to identify optimal enzyme-processing conditions (pH 9.5, I <0.1 m, 30% glycerol, 1 mm CHAPS), preferred substrate cleavage sites, and the first competitive inhibitor (Ac-FASGKR-H, IC50 approximately 1 microm). A putative three-dimensional structure of WNV protease, created through homology modeling based on the crystal structures of Dengue-2 and Hepatitis C NS3 viral proteases, provides some valuable insights for structure-based design of potent and selective inhibitors of WNV protease.
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Affiliation(s)
- Tessa A Nall
- Centre for Drug Design and Development, Institute for Molecular Bioscience, Univeristy of Queensland, Brisbane, Australia
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42
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Deaton DN, Kumar S. Cathepsin K Inhibitors: Their Potential as Anti-Osteoporosis Agents. PROGRESS IN MEDICINAL CHEMISTRY 2004; 42:245-375. [PMID: 15003723 DOI: 10.1016/s0079-6468(04)42006-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Affiliation(s)
- David N Deaton
- Medicinal Chemistry Department, GlaxoSmithKline Inc., 5 Moore Drive, Research Triangle Park, NC 27709, USA
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43
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Mak CC, Brik A, Lerner DL, Elder JH, Morris GM, Olson AJ, Wong CH. Design and synthesis of broad-based mono- and bi- cyclic inhibitors of FIV and HIV proteases. Bioorg Med Chem 2003; 11:2025-40. [PMID: 12670654 DOI: 10.1016/s0968-0896(03)00054-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Based on the substrate transition state and our strategy to tackle the problem of drug resistance, a series of HIV/FIV protease (HIV /FIV PR) monocyclic inhibitors incorporating a 15- or 17-membered macrocycle with an equivalent P3 or P3' group and a unique unnatural amino acid, (2R, 3S)-3-amino-2-hydroxy-4-phenylbutyric acid, have been designed and synthesized. In addition, based on the structure of TL3 with small P3/P3' group, we have synthesized two conformationally restricted bicyclic inhibitors containing the macrocycle, which mimic the P1/P1'-P3/P3' tripeptide [Phe-Val-Ala] of TL3. We have found that the contribution of the macrocycle in our monocyclic inhibitors is important to the overall activity, but the ring size does not affect the activity to a significant extent. Several inhibitors that were developed in this work, exhibit low nanomolar inhibitory activity against the wild-type HIV/FIV PR and found to be highly effective against some drug-resistant as well as TL3-resistant mutants of HIV PRs. Compound 15, in particular, is the most effective cyclic inhibitor in hand to inhibit FIV replication in tissue culture at a concentration of 1.0 micro g/mL (1.2 microM).
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Affiliation(s)
- Chi Ching Mak
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550North Torrey Pines Road, La Jolla, CA 92037, USA.
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44
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Franco OL, Grossi de Sá MF, Sales MP, Mello LV, Oliveira AS, Rigden DJ. Overlapping binding sites for trypsin and papain on a Kunitz-type proteinase inhibitor from Prosopis juliflora. Proteins 2002; 49:335-41. [PMID: 12360523 DOI: 10.1002/prot.10228] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Proteinase inhibitors are among the most promising candidates for expression by transgenic plants and consequent protection against insect predation. However, some insects can respond to the threat of the proteinase inhibitor by the production of enzymes insensitive to inhibition. Inhibitors combining more than one favorable activity are therefore strongly favored. Recently, a known small Kunitz trypsin inhibitor from Prosopis juliflora (PTPKI) has been shown to possess unexpected potent cysteine proteinase inhibitory activity. Here we show, by enzyme assay and gel filtration, that, unlike other Kunitz inhibitors with dual activities, this inhibitor is incapable of simultaneous inhibition of trypsin and papain. These data are most readily interpreted by proposing overlapping binding sites for the two enzymes. Molecular modeling and docking experiments favor an interaction mode in which the same inhibitor loop that interacts in a canonical fashion with trypsin can also bind into the papain catalytic site cleft. Unusual residue substitutions at the proposed interface can explain the relative rarity of twin trypsin/papain inhibition. Other changes seem responsible for the relative low affinity of PTPKI for trypsin. The predicted coincidence of trypsin and papain binding sites, once confirmed, would facilitate the search, by phage display for example, for mutants highly active against both proteinases.
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Affiliation(s)
- Octávio L Franco
- Embrapa Recursos Genéticos e Biotecnologia, Cenargen, Brasília, Brazil
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45
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Radisky ES, Koshland DE. A clogged gutter mechanism for protease inhibitors. Proc Natl Acad Sci U S A 2002; 99:10316-21. [PMID: 12142461 PMCID: PMC124911 DOI: 10.1073/pnas.112332899] [Citation(s) in RCA: 116] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2002] [Indexed: 11/18/2022] Open
Abstract
A classical peptide inhibitor of serine proteases that is hydrolyzed approximately 10(7) times more slowly than a good substrate is shown to form an acyl-enzyme intermediate rapidly. Despite this quick first step, further reaction is slowed dramatically because of tight and oriented binding of the cleaved peptide, preventing acyl-enzyme hydrolysis and favoring the reverse reaction. Moreover, this mechanism appears to be common to a large class of tight-binding serine protease inhibitors that mimic good substrates. The arrest of enzymatic reaction at the intermediate stage allowed us to determine that the consensus nucleophilic attack angle is close to 90 degrees in the reactive Michaelis complexes.
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Affiliation(s)
- Evette S Radisky
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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46
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Rigden DJ, Mosolov VV, Galperin MY. Sequence conservation in the chagasin family suggests a common trend in cysteine proteinase binding by unrelated protein inhibitors. Protein Sci 2002; 11:1971-7. [PMID: 12142451 PMCID: PMC2373688 DOI: 10.1110/ps.0207202] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2002] [Revised: 05/13/2002] [Accepted: 05/21/2002] [Indexed: 10/27/2022]
Abstract
The recently described inhibitor of cysteine proteinases from Trypanosoma cruzi, chagasin, was found to have close homologs in several eukaryotes, bacteria and archaea, the first protein inhibitors of cysteine proteases in prokaryotes. These previously uncharacterized 110-130 residue-long proteins share a well-conserved sequence motif that corresponds to two adjacent beta-strands and the short loop connecting them. Chagasin-like proteins also have other conserved, mostly aromatic, residues, and share the same predicted secondary structure. These proteins adopt an all-beta fold with eight predicted beta-strands of the immunoglobulin type. The phylogenetic distribution of the chagasins generally correlates with the presence of papain-like cysteine proteases. Previous studies have uncovered similar trends in cysteine proteinase binding by two unrelated inhibitors, stefin and p41, that belong to the cystatin and thyroglobulin families, respectively. A hypothetical model of chagasin-cruzipain interaction suggests that chagasin may dock to the cruzipain active site in a similar manner with the conserved NPTTG motif of chagasin forming a loop that is similar to the wedge structures formed at the active sites of papain and cathepsin L by stefin and p41.
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Affiliation(s)
- Daniel J Rigden
- National Centre of Genetic Resources and Biotechnology, Cenargen/Embrapa, S.A.I.N. Parque Rural, Final W5 Norte, 70770-900 Brasília, Brazil.
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47
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Melo FR, Rigden DJ, Franco OL, Mello LV, Ary MB, Grossi de Sá MF, Bloch C. Inhibition of trypsin by cowpea thionin: characterization, molecular modeling, and docking. Proteins 2002; 48:311-9. [PMID: 12112698 DOI: 10.1002/prot.10142] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Higher plants produce several families of proteins with toxic properties, which act as defense compounds against pests and pathogens. The thionin family represents one family and comprises low molecular mass cysteine-rich proteins, usually basic and distributed in different plant tissues. Here, we report the purification and characterization of a new thionin from cowpea (Vigna unguiculata) with proteinase inhibitory activity. Cowpea thionin inhibits trypsin, but not chymotrypsin, binding with a stoichiometry of 1:1 as shown with the use of mass spectrometry. Previous annotations of thionins as proteinase inhibitors were based on their erroneous identification as homologues of Bowman-Birk family inhibitors. Molecular modeling experiments were used to propose a mode of docking of cowpea thionin with trypsin. Consideration of the dynamic properties of the cowpea thionin was essential to arrive at a model with favorable interface characteristics comparable with structures of trypsin-inhibitor complexes determined by X-ray crystallography. In the final model, Lys11 occupies the S1 specificity pocket of trypsin as part of a canonical style interaction.
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Affiliation(s)
- Francislete R Melo
- Departamento de Biologia Celular, Universidade de Brasília, Brasília-DF, Brasil.
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48
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Reid RC, Kelso MJ, Scanlon MJ, Fairlie DP. Conformationally constrained macrocycles that mimic tripeptide beta-strands in water and aprotic solvents. J Am Chem Soc 2002; 124:5673-83. [PMID: 12010040 DOI: 10.1021/ja0256461] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The beta-strand conformation is unknown for short peptides in aqueous solution, yet it is a fundamental building block in proteins and the crucial recognition motif for proteolytic enzymes that enable formation and turnover of all proteins. To create a generalized scaffold as a peptidomimetic that is pre-organized in a beta-strand, we individually synthesized a series of 15-22-membered macrocyclic analogues of tripeptides and analyzed their structures. Each cycle is highly constrained by two trans amide bonds and a planar aromatic ring with a short nonpeptidic linker between them. A measure of this ring strain is the restricted rotation of the component tyrosinyl aromatic ring (DeltaG(rot) 76.7 kJ mol(-1) (16-membered ring), 46.1 kJ mol(-1) (17-membered ring)) evidenced by variable temperature proton NMR spectra (DMF-d(7), 200-400 K). Unusually large amide coupling constants ((3)J(NH-CHalpha) 9-10 Hz) corresponding to large dihedral angles were detected in both protic and aprotic solvents for these macrocycles, consistent with a high degree of structure in solution. The temperature dependence of all amide NH chemical shifts (Deltadelta/T 7-12 ppb/deg) precluded the presence of transannular hydrogen bonds that define alternative turn structures. Whereas similar sized conventional cyclic peptides usually exist in solution as an equilibrium mixture of multiple conformers, these macrocycles adopt a well-defined beta-strand structure even in water as revealed by 2-D NMR spectral data and by a structure calculation for the smallest (15-membered) and most constrained macrocycle. Macrocycles that are sufficiently constrained to exclusively adopt a beta-strand-mimicking structure in water may be useful pre-organized and generic templates for the design of compounds that interfere with beta-strand recognition in biology.
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Affiliation(s)
- Robert C Reid
- Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
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49
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Abstract
Peptide recognition by G-protein coupled receptors (GPCRs) is reviewed with an emphasis on the indirect approach used to determine the receptor-bound conformation of peptide ligands. This approach was developed in response to the lack of detailed structural information available for these receptors. Recent advances in the structural determination of rhodopsin (the GPCR of the visual system) by crystallography have provided a scaffold for homology modeling of the inactive state of a wide variety of GPCRs that interact with peptide messages. Additionally, the ability to mutate GPCRs and assay compounds of similar chemical structure to test a common binding site on the receptor provides a firm experimental basis for structure-activity studies. Recognition motifs, common in other well-studied systems such as proteolytic enzymes and major histocompatibility class receptors (MHC) are reviewed briefly to provide a basis of comparison. Finally, the development of true peptidomimetics is contrasted with nonpeptide ligands, discovered through combinatorial chemistry. In many systems, the evidence suggests that the peptide ligands bind at the interface between the transmembrane segments and the extracellular loops, while nonpeptide antagonists bind within the transmembrane segments. Plausible models of GPCRs and the mechanism by which they activate G-proteins on binding peptides are beginning to emerge.
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Affiliation(s)
- G R Marshall
- Center for Computational Biology, 700 S. Euclid Avenue, Washington University, St. Louis, MO 63110, USA.
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50
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Franco OL, Rigden DJ, Melo FR, Grossi-De-Sá MF. Plant alpha-amylase inhibitors and their interaction with insect alpha-amylases. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:397-412. [PMID: 11856298 DOI: 10.1046/j.0014-2956.2001.02656.x] [Citation(s) in RCA: 248] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Insect pests and pathogens (fungi, bacteria and viruses) are responsible for severe crop losses. Insects feed directly on the plant tissues, while the pathogens lead to damage or death of the plant. Plants have evolved a certain degree of resistance through the production of defence compounds, which may be aproteic, e.g. antibiotics, alkaloids, terpenes, cyanogenic glucosides or proteic, e.g. chitinases, beta-1,3-glucanases, lectins, arcelins, vicilins, systemins and enzyme inhibitors. The enzyme inhibitors impede digestion through their action on insect gut digestive alpha-amylases and proteinases, which play a key role in the digestion of plant starch and proteins. The natural defences of crop plants may be improved through the use of transgenic technology. Current research in the area focuses particularly on weevils as these are highly dependent on starch for their energy supply. Six different alpha-amylase inhibitor classes, lectin-like, knottin-like, cereal-type, Kunitz-like, gamma-purothionin-like and thaumatin-like could be used in pest control. These classes of inhibitors show remarkable structural variety leading to different modes of inhibition and different specificity profiles against diverse alpha-amylases. Specificity of inhibition is an important issue as the introduced inhibitor must not adversely affect the plant's own alpha-amylases, nor the nutritional value of the crop. Of particular interest are some bifunctional inhibitors with additional favourable properties, such as proteinase inhibitory activity or chitinase activity. The area has benefited from the recent determination of many structures of alpha-amylases, inhibitors and complexes. These structures highlight the remarkable variety in structural modes of alpha-amylase inhibition. The continuing discovery of new classes of alpha-amylase inhibitor ensures that exciting discoveries remain to be made. In this review, we summarize existing knowledge of insect alpha-amylases, plant alpha-amylase inhibitors and their interaction. Positive results recently obtained for transgenic plants and future prospects in the area are reviewed.
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Affiliation(s)
- Octávio L Franco
- Centro Nacional de Recursos Genéticos e Biotecnologia, Cenargen/Embrapa, Brasília-DF, Brazil.
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