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Gordon CP. The renascence of continuous-flow peptide synthesis - an abridged account of solid and solution-based approaches. Org Biomol Chem 2019; 16:180-196. [PMID: 29255827 DOI: 10.1039/c7ob02759a] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Within a decade of Merrifield's seminal description of solid-phase peptide synthesis, the synergies between solid-phase approaches and flow synthesis were noted by a number of groups. However, despite the various advantages flow brings to peptide synthesis, throughout the 1990s and 2000s, interest in the technique was overshadowed by microwave assisted approaches. However, the current expansion of flow technologies has reinvigorated interest in both solid-phase and solution-phase continuous-flow approaches for assembling peptides. This perspective traces the introduction and evolution of continuous-flow solid-phase synthesis from a practical aspect with a particular focus on solid supports, acylation protocols, and racemisation suppression. Practical aspects of solution-phase continuous-flow peptide synthesis are also considered with an evaluation of microreactor systems, coupling protocols, and fragment-based approaches for assembly of extended peptide units.
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Affiliation(s)
- Christopher P Gordon
- School of Science and Health, Western Sydney University, Locked Bag, 1797, Penrith South, DC, Australia.
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2
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Wang QM, Johnson RB, Cohen JD, Voy GT, Richardson JM, Jungheim LN. Development of a Continuous Fluorescence Assay for Rhinovirus 14 3C Protease Using Synthetic Peptides. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029700800402] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Rhinovirus 3C protease is an attractive target for therapeutic intervention owing to its important role in virion maturation and infectivity. In order to facilitate the identification of potential 3C protease inhibitors, we have developed a continuous fluorescence assay using 5-[(2-aminoethyl)amino]naphthalene-1-sulphonic acid (Edans) as a fluorescent donor and 4-(4-dimethylaminophenylazo)benzoic acid (Dabcyl) as a quenching acceptor. Several fluorogenic peptide substrates for 3C protease were synthesized by both solution chemistry and solid phase peptide synthesis. One of the synthetic Edans/Dabcyl substrates, with an amino acid sequence derived from the 2C/3A site of the virus polyprotein, yielded a 24-fold increase in fluorescence intensity after 3C cleavage. Data regarding substrate cleavage kinetics, assay sensitivity and optimization are presented. The application of this assay to the evaluation of 3C protease inhibitors is also shown.
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Affiliation(s)
- QM Wang
- Infectious Diseases Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - RB Johnson
- Infectious Diseases Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - JD Cohen
- Infectious Diseases Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - GT Voy
- Infectious Diseases Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - JM Richardson
- Infectious Diseases Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - LN Jungheim
- Infectious Diseases Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
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3
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Abstract
The recent approval by the regulatory authorities in the United States of several HIV proteinase inhibitors as therapeutics for the treatment of AIDS confirms that virus proteinases are valid molecular targets in the search for new antiviral drugs. This review summarizes the available approaches that can be taken to discover virus proteinase inhibitors and reviews the current status of our knowledge with respect to virus proteinases in viruses of clinical significance other than HIV. The major focus is on proteinases identified in the viruses that cause the common cold, hepatitis C virus and the herpesviruses.
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Affiliation(s)
- J. S. Mills
- Molecular Virology Department, Roche Research Centre, 40 Broadwater Road, Welwyn Garden City, Herts AL7 3AY, UK
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4
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Sudo K, Yamaji K, Kawamura K, Nishijima T, Kojima N, Aibe K, Shimotohno K, Shimizu Y. High-throughput screening of low molecular weight NS3-NS4A protease inhibitors using a fluorescence resonance energy transfer substrate. Antivir Chem Chemother 2006; 16:385-92. [PMID: 16329285 DOI: 10.1177/095632020501600605] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Hepatitis C virus (HCV) NS3-NS4A protease is an attractive target for anti-HCV agents because of its important role in replication. An optimized fluorescence resonance energy transfer (FRET) substrate for NS3-NS4A protease, based on the sequence of the NS5A-5B cleavage site, was designed and synthesized. High-throughput screening of in-house compound libraries was performed using a FRET substrate FS10 (MOCAcDKIVPC-SMSYK-Dnp) and MBP-NS3-NS4A fusion protein. Several hit compounds were found, including YZ-9577 (2-oxido-1,2,5-oxadiazole-3,4-diyl) bis (phenylmethanone) with potent inhibitory activity (IC50=1.6 microM) and good selectivity against other human serine proteases.
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Affiliation(s)
- Kenji Sudo
- Institute for Drug Discovery Research, Yamanouchi Pharmaceutical Co. Ltd., Ibaraki, Japan
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5
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Abstract
Viruses of the family Herpesviridae are responsible for a diverse set of human diseases. The available treatments are largely ineffective, with the exception of a few drugs for treatment of herpes simplex virus (HSV) infections. For several members of this DNA virus family, advances have been made recently in the biochemistry and structural biology of the essential viral protease, revealing common features that may be possible to exploit in the development of a new class of anti-herpesvirus agents. The herpesvirus proteases have been identified as belonging to a unique class of serine protease, with a Ser-His-His catalytic triad. A new, single domain protein fold has been determined by X-ray crystallography for the proteases of at least three different herpesviruses. Also unique for serine proteases, dimerization has been shown to be required for activity of the cytomegalovirus and HSV proteases. The dimerization requirement seriously impacts methods needed for productive, functional analysis and inhibitor discovery. The conserved functional and catalytic properties of the herpesvirus proteases lead to common considerations for this group of proteases in the early phases of inhibitor discovery. In general, classical serine protease inhibitors that react with active site residues do not readily inactivate the herpesvirus proteases. There has been progress however, with activated carbonyls that exploit the selective nucleophilicity of the active site serine. In addition, screening of chemical libraries has yielded novel structures as starting points for drug development. Recent crystal structures of the herpesvirus proteases now allow more direct interpretation of ligand structure-activity relationships. This review first describes basic functional aspects of herpesvirus protease biology and enzymology. Then we discuss inhibitors identified to date and the prospects for their future development.
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Affiliation(s)
- L Waxman
- Department of Antiviral Research, Merck Research Laboratories, West Point, PA 19486, USA
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6
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Bonneau PR, Hasani F, Plouffe C, Malenfant E, LaPlante SR, Guse I, Ogilvie WW, Plante R, Davidson WC, Hopkins JL, Morelock MM, Cordingley MG, Déziel R. Inhibition of Human Cytomegalovirus Protease by Monocyclic β-Lactam Derivatives: Kinetic Characterization Using a Fluorescent Probe. J Am Chem Soc 1999. [DOI: 10.1021/ja983905+] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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7
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Grahn S, Ullmann D, Jakubke H. Design and synthesis of fluorogenic trypsin peptide substrates based on resonance energy transfer. Anal Biochem 1998; 265:225-31. [PMID: 9882396 DOI: 10.1006/abio.1998.2902] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
An assay based on new internally quenched fluorogenic peptide substrates with the general structure 4-(4-dimethylaminophenylazo)benzoic acid (DABCYL)-Gly-Pro-Ala-Xaa-Leu-Ala-Ile-Gly-5-(2-aminoethylamino++ +)naphtha lene-1-sulfonic acid (EDANS), where Xaa = Arg, Lys, has been developed to measure proteolytic activity of trypsin and similar proteases. The kinetic parameters for the tryptic hydrolysis of DABCYL-Gly-Pro-Ala-Arg-Leu-Ala-Ile-Gly-EDANS are Km = 34 microM, kcat = 40 s-1, and kcat/Km = 1.17 x 10(6) M-1 s-1. The substrates offer two advantages over common substrates. First they are very sensitive. Applications to chemically modified trypsin and engineered variants show the ability to detect traces of proteolytic activity. In addition, these substrates are adapted to the S'-specificity of the investigated protease. These features and the prospect of miniaturization makes the assay suitable for applications to high-throughput screening.
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Affiliation(s)
- S Grahn
- Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Talstrasse 33, Leipzig, 04103, Germany
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8
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Bonneau PR, Plouffe C, Pelletier A, Wernic D, Poupart MA. Design of fluorogenic peptide substrates for human cytomegalovirus protease based on structure-activity relationship studies. Anal Biochem 1998; 255:59-65. [PMID: 9448842 DOI: 10.1006/abio.1997.2445] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Human cytomegalovirus (HCMV) protease is a slow-processing enzyme in vitro and its characterization would be facilitated if more efficiently cleaved substrates were available. Here we describe the development of improved fluorogenic peptide substrates for this protease and demonstrate that its indolent nature can be overcome by appropriate modifications within existing substrates. Prior structure-activity studies have indicated that replacement of the Val-Val-Asn sequence corresponding to the P4-P2 residues of the maturation site of the enzyme by the optimized Tbg-Tbg-Asn(NMe2) sequence conferred significant binding to inhibitors (Tbg, t-butylglycine). Incorporation of this improved sequence in a variety of substrates invariably led to improved kinetic parameters compared to homologues containing the natural sequence only. For example, the substrate o-aminobenzoyl-Tbg-Tbg-Asn (NMe2)-Ala decreases Ser-Ser-Arg-Leu-Tyr(3-NO2)Arg-OH (2) displayed a kcat/K(m) value of 15,940 M-1 s-1 i.e., more than 60-fold greater than that of the equivalent, nonoptimized substrate 1 under identical conditions. This improved sequence also permitted the development of a sensitive 7-amino-4-methylcoumarin fluorogenic substrate 3 which represents the shortest HCMV protease substrate to date. The kinetic and photometric advantages of these various substrates are discussed along with specific applications.
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Affiliation(s)
- P R Bonneau
- Department of Biological Sciences, Bio-Méga Research Division, Boehringer Ingelheim (Canada) Ltd., Laval, Québec, Canada
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Ogilvie W, Bailey M, Poupart MA, Abraham A, Bhavsar A, Bonneau P, Bordeleau J, Bousquet Y, Chabot C, Duceppe JS, Fazal G, Goulet S, Grand-Maître C, Guse I, Halmos T, Lavallée P, Leach M, Malenfant E, O'Meara J, Plante R, Plouffe C, Poirier M, Soucy F, Yoakim C, Déziel R. Peptidomimetic inhibitors of the human cytomegalovirus protease. J Med Chem 1997; 40:4113-35. [PMID: 9406601 DOI: 10.1021/jm970104t] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The development of peptidomimetic inhibitors of the human cytomegalovirus (HCMV) protease showing sub-micromolar potency in an enzymatic assay is described. Selective substitution of the amino acid residues of these inhibitors led to the identification of tripeptide inhibitors showing improvements in inhibitor potency of 27-fold relative to inhibitor 39 based upon the natural tetrapeptide sequence. Small side chains at P1 were well tolerated by this enzyme, a fact consistent with previous observations. The S2 binding pocket of HCMV protease was very permissive, tolerating lipophilic and basic residues. The substitutions tried at P3 indicated that a small increase in inhibitor potency could be realized by the substitution of a tert-leucine residue for valine. Substitutions of the N-terminal capping group did not significantly affect inhibitor potency. Pentafluoroethyl ketones, alpha,alpha-difluoro-beta-keto amides, phosphonates and alpha-keto amides were all effective substitutions for the activated carbonyl component and gave inhibitors which were selective for HCMV protease. A slight increase in potency was observed by lengthening the P1' residue of the alpha-keto amide series of inhibitors. This position also tolerated a variety of groups making this a potential site for future modifications which could modulate the physicochemical properties of these molecules.
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Affiliation(s)
- W Ogilvie
- Bio-Méga Research Division, Boehringer Ingelheim Ltd., Laval, Québec, Canada
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10
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Flynn DL, Abood NA, Holwerda BC. Recent advances in antiviral research: identification of inhibitors of the herpesvirus proteases. Curr Opin Chem Biol 1997; 1:190-6. [PMID: 9667847 DOI: 10.1016/s1367-5931(97)80009-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Major advances have been reported in the last two years regarding the molecular biology and structural properties of the herpesvirus proteases. X-ray diffraction studies have enabled several groups to solve the structure of the human cytomegalovirus protease. Fluorescence-based substrate assays have also been recently reported. These substrates exhibit sufficient kinetic and sensitivity properties to enable high-throughput screening efforts dedicated toward the discovery of protease inhibitors. Three classes of inhibitors have been reported recently: nonpeptidic aryl trifluoromethylketones; alternate substrate inhibitors (benzoxazinones/azalactones); and thiol-modifying inhibitors. The thiol-modifying class offers a unique opportunity to discover inhibitors specific to the human cytomegalovirus protease, as this protease requires reduced cysteine residues for its enzymatic activity.
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Affiliation(s)
- D L Flynn
- Searle Research and Development, Department of Medicinal Chemistry, 800 N Lindbergh Blvd, St Louis, MO 63167, USA.
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11
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Abstract
Herpesvirus proteases have emerged as targets for the development of novel antiviral drugs. These enzymes, which are necessary for the replication of all herpesviruses, are serine proteases, but possess a unique structure as revealed by solution of the crystal structure of human cytomegalovirus protease. Many of the biochemical properties of these enzymes are now explained by the structure. Conventional serine protease inhibitors are not potent inhibitors of these enzymes and therefore the search for potent inhibitors possessing necessary features of an effective antiviral will require novel approaches. The three-dimensional structure serves as a milestone for continued endeavors towards this goal.
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Affiliation(s)
- B C Holwerda
- Searle Research and Development, St. Louis, MO 63198, USA.
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12
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Levine LM, Michener ML, Toth MV, Holwerda BC. Measurement of specific protease activity utilizing fluorescence polarization. Anal Biochem 1997; 247:83-8. [PMID: 9126375 DOI: 10.1006/abio.1997.2047] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A fluorescence polarization assay was designed to measure proteolytic cleavage of a specific peptide substrate for human cytomegalovirus protease. The peptide substrate was derivatized by biotinylation of a gamma-aminobutyric acid-modified amino-terminus and labeled with 5-(4,6-dichlorotriazinyl)aminofluorescein at the carboxy-terminus. Incubation of this substrate with recombinant human cytomegalovirus protease and subsequent addition of egg white avidin produced a polarization signal that was proportional to the relative amounts of cleaved and uncleaved substrate. The uncleaved substrate produced a high polarization value upon binding to avidin, whereas the cleaved, low-molecular-weight fluorescently tagged peptide that cannot bind to avidin produced a low polarization value. The inhibitory activity of a 3,4-dichloroisocoumarin against the protease was evaluated by comparing the change in polarization with a noninhibited control. The fluorescence polarization protease assay does not suffer from interference due to the presence of absorptive interferants making this a convenient, homogenous assay for high throughput screening.
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Affiliation(s)
- L M Levine
- Monsanto Corporate Research, St. Louis, Missouri, USA
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13
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Tigue NJ, Matharu PJ, Roberts NA, Mills JS, Kay J, Jupp R. Cloning, expression and characterization of the proteinase from human herpesvirus 6. J Virol 1996; 70:4136-41. [PMID: 8648756 PMCID: PMC190303 DOI: 10.1128/jvi.70.6.4136-4141.1996] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
After the U53 gene encoding the proteinase from human herpesvirus 6 (HHV-6) was sequenced, it was expressed in Escherichia coli, and the activity of the purified, recombinant HHV-6 proteinase was characterized quantitatively by using synthetic peptide substrates mimicking the release and maturation cleavage sites in the polyprotein precursors of HHV-6, human cytomegalovirus (CMV), murine CMV, and Epstein-Barr virus. Despite sharing 40% identity with other betaherpesvirus proteinases such as human CMV proteinase, the one-chain HHV-6 enzyme was distinguished from these two-chain proteinases by the absence of an internal autocatalytic cleavage site.
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Affiliation(s)
- N J Tigue
- Department of Molecular and Medical Biosciences, University of Wales College of Cardiff, United Kingdom
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