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Skoreński M, Sieńczyk M. Anti-herpesvirus agents: a patent and literature review (2003 to present). Expert Opin Ther Pat 2014; 24:925-41. [PMID: 25010889 DOI: 10.1517/13543776.2014.927442] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
INTRODUCTION The standard therapy used to treat herpesvirus infections is based on the application of DNA polymerase inhibitors such as ganciclovir or aciclovir. Unfortunately, all of these compounds exhibit relatively high toxicity and the mutation of herpesviruses results in the appearance of new drug-resistant strains. Consequently, there is a great need for the development of new, effective and safe anti-herpesvirus agents that employ different patterns of therapeutic action at various stages of the virus life cycle. AREAS COVERED Patents and patent applications concerning the development of anti-herpesvirus agents displaying different mechanisms of action that have been published since 2003 are reviewed. In addition, major discoveries in this field that have been published in academic papers have also been included. EXPERT OPINION Among all the anti-herpesvirus agents described in this article, the inhibitors of viral serine protease seem to present one of the most effective/promising therapeutics. Unfortunately, the practical application of these antiviral agents has not yet been proven in any clinical trials. Nevertheless, the dynamic and extensive work on this subject gives hope that a new class of anti-herpesvirus agents aimed at the enzymatic activity of herpesvirus serine protease may be developed.
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Affiliation(s)
- Marcin Skoreński
- Wroclaw University of Technology, Division of Medicinal Chemistry and Microbiology, Faculty of Chemistry , Wybrzeze Wyspianskiego 27, 50-370 Wroclaw , Poland +48 71 320 24 39 ; +48 71 320 24 27 ;
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LaPlante SR, Nar H, Lemke CT, Jakalian A, Aubry N, Kawai SH. Ligand bioactive conformation plays a critical role in the design of drugs that target the hepatitis C virus NS3 protease. J Med Chem 2013; 57:1777-89. [PMID: 24144444 DOI: 10.1021/jm401338c] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A ligand-focused strategy employed NMR, X-ray, modeling, and medicinal chemistry to expose the critical role that bioactive conformation played in the design of a variety of drugs that target the HCV protease. The bioactive conformation (bound states) were determined for key inhibitors identified along our drug discovery pathway from the hit to clinical compounds. All adopt similar bioactive conformations for the common core derived from the hit peptide DDIVPC. A carefully designed SAR analysis, based on the advanced inhibitor 1 in which the P1 to P3 side chains and the N-terminal Boc were sequentially truncated, revealed a correlation between affinity and the relative predominance of the bioactive conformation in the free state. Interestingly, synergistic conformation effects on potency were also noted. Comparisons with clinical and recently marketed drugs from the pharmaceutical industry showed that all have the same core and similar bioactive conformations. This suggested that the variety of appendages discovered for these compounds also properly satisfy the bioactive conformation requirements and allowed for a large variety of HCV protease drug candidates to be designed.
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Affiliation(s)
- Steven R LaPlante
- Department of Chemistry, Boehringer-Ingelheim (Canada) Ltd., Research and Development , Laval, Québec H7S 2G5, Canada
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Sabit H, Dahan A, Sun J, Provoda CJ, Lee KD, Hilfinger JH, Amidon GL. Cytomegalovirus protease targeted prodrug development. Mol Pharm 2013; 10:1417-24. [PMID: 23485093 PMCID: PMC3616455 DOI: 10.1021/mp3007067] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Human cytomegalovirus (HCMV) is a
prevalent virus that infects
up to 90% of the population. The goal of this research is to determine
if small molecular prodrug substrates can be developed for a specific
HCMV encoded protease and thus achieve site-specific activation. HCMV
encodes a 256 amino acid serine protease that is responsible for capsid
assembly, an essential process for herpes virus production. The esterase
activity of the more stable HCMV A143T/A144T protease mutant was evaluated
with model p-nitrophenol (ONp) esters, Boc-Xaa-ONp
(Ala, Leu, Ile, Val, Gln, Phe at the Xaa position). We demonstrate
that the A143T/A144T mutant has esterase activity toward specific
small ester compounds, e.g., Boc-l-Ala-ONp. Mono amino acid
and dipeptide prodrugs of ganciclovir (GCV) were also synthesized
and evaluated for hydrolysis by the A143T/A144T protease mutant in
solution. Hydrolysis of these prodrugs was also evaluated in Caco-2
cell homogenates, human liver microsomes (HLMs), and rat and human
plasma. For the selectivity potential of the prodrugs, the hydrolysis
ratio was evaluated as a percentage of prodrug hydrolyzed by the HCMV
protease over the percentages of prodrug hydrolyses by Caco-2 cell
homogenates, HLMs, and human/rat plasma. A dipeptide prodrug of ganciclovir,
Ac-l-Gln-l-Ala-GCV, emerged as a potential selective
prodrug candidate. The results of this research demonstrate that targeting
prodrugs for activation by a specific protease encoded by the infectious
HCMV pathogen may be achievable.
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Affiliation(s)
- Hairat Sabit
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 40850, USA
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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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Lazic A, Goetz DH, Nomura AM, Marnett AB, Craik CS. Substrate modulation of enzyme activity in the herpesvirus protease family. J Mol Biol 2007; 373:913-23. [PMID: 17870089 PMCID: PMC2078331 DOI: 10.1016/j.jmb.2007.07.073] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2007] [Revised: 07/21/2007] [Accepted: 07/26/2007] [Indexed: 11/23/2022]
Abstract
The herpesvirus proteases are an example in which allosteric regulation of an enzyme activity is achieved through the formation of quaternary structure. Here, we report a 1.7 A resolution structure of Kaposi's sarcoma-associated herpesvirus protease in complex with a hexapeptide transition state analogue that stabilizes the dimeric state of the enzyme. Extended substrate binding sites are induced upon peptide binding. In particular, 104 A2 of surface are buried in the newly formed S4 pocket when tyrosine binds at this site. The peptide inhibitor also induces a rearrangement of residues that stabilizes the oxyanion hole and the dimer interface. Concomitant with the structural changes, an increase in catalytic efficiency of the enzyme results upon extended substrate binding. A nearly 20-fold increase in kcat/KM results upon extending the peptide substrate from a tetrapeptide to a hexapeptide exclusively due to a KM effect. This suggests that the mechanism by which herpesvirus proteases achieve their high specificity is by using extended substrates to modulate both the structure and activity of the enzyme.
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Affiliation(s)
- Ana Lazic
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158-2517, USA
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6
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Exploiting Ligand and Receptor Adaptability in Rational Drug Design Using Dynamics and Structure-Based Strategies. Top Curr Chem (Cham) 2006. [DOI: 10.1007/128_2006_087] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
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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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Affiliation(s)
- Liang Tong
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA.
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Buisson M, Valette E, Hernandez JF, Baudin F, Ebel C, Morand P, Seigneurin JM, Arlaud GJ, Ruigrok RW. Functional determinants of the Epstein-Barr virus protease. J Mol Biol 2001; 311:217-28. [PMID: 11469870 DOI: 10.1006/jmbi.2001.4854] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Herpesvirus proteases are essential for the production of progeny virus. They cleave the assembly protein that fills the immature capsid in order to make place for the viral DNA. The recombinant protease of the human gamma-herpesvirus Epstein-Barr virus (EBV) was expressed in Escherichia coli and purified. Circular dichroism indicated that the protein was properly folded with a secondary structure content similar to that of other herpesvirus proteases. Gel filtration and sedimentation analysis indicated a fast monomer-dimer equilibrium of the protease with a K(d) of about 60 microM. This value was not influenced by glycerol but was lowered to 1.7 microM in the presence of 0.5 M sodium citrate. We also developed an HPLC-based enzymatic assay using a 20 amino acid residue synthetic peptide substrate derived from one of the viral target sequences for the protease. We found that conditions that stabilised the dimer also led to a higher enzymatic activity. Through sequential deletion of amino acid residues from either side of the cleavage site, the minimal peptide substrate for the protease was determined as P5-P2'. This minimal sequence is shorter than that for other herpesvirus proteases. The implications of our findings are discussed with reference to the viral life-cycle. These results are the first ever published on the EBV protease and represent a first step towards the development of protease inhibitors.
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Affiliation(s)
- M Buisson
- Laboratoire de Virologie, Hôpital Michallon, Grenoble Cedex 9, 38043, France
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Martinez A, Castro A, Gil C, Perez C. Recent strategies in the development of new human cytomegalovirus inhibitors. Med Res Rev 2001; 21:227-44. [PMID: 11301412 DOI: 10.1002/med.1008] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Human cytomegalovirus (HCMV) is one of the most common opportunistic infections in immunucompromised individuals, such as AIDS patients and organ transplant recipients, and is the most frequent congenital viral infection in humans. Despite a reduction of the incidence of AIDS-related opportunistic infections in patients under highly active antiretroviral treatment, attention should be paid to the HCMV risk factor in these individuals. Furthermore, HCMV may have an important role in atherosclerosis. Existing antiviral treatments for the HCMV infection suffer from poor bioavailability, toxicity, and limited effectiveness, mainly due to the development of drug resistance. Fortunately there are novel and potentially very effective new compounds undergoing pre-clinical and clinical evaluation. This review provides an overview in the last five years of new HCMV inhibitors (chemical structures, SAR, and new mechanisms of action) with the aim to provide new clues for the development of future drugs against this opportunistic virus.
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Affiliation(s)
- A Martinez
- Instituto de Química Médica (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain.
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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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LaPlante SR, Cameron DR, Aubry N, Lefebvre S, Kukolj G, Maurice R, Thibeault D, Lamarre D, Llinàs-Brunet M. Solution structure of substrate-based ligands when bound to hepatitis C virus NS3 protease domain. J Biol Chem 1999; 274:18618-24. [PMID: 10373473 DOI: 10.1074/jbc.274.26.18618] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The interactions of the NS3 protease domain with inhibitors that are based on N-terminal cleavage products of peptide substrates were studied by NMR methods. Transferred nuclear Overhauser effect experiments showed that these inhibitors bind the protease in a well defined, extended conformation. Protease-induced line-broadening studies helped identify the segments of inhibitors which come into contact with the protease. A comparison of the NMR data of the free and protease-bound states suggests that these ligands undergo rigidification upon complexation. This work provides the first structure of an inhibitor when bound to NS3 protease and should be valuable for designing more potent inhibitors.
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Affiliation(s)
- S R LaPlante
- Departments of Chemistry and Biological Sciences, Boehringer Ingelheim (Canada) Ltd., Bio-Méga Research Division, Laval, Québec H7S 2G5, Canada.
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LaPlante SR, Bonneau PR, Aubry N, Cameron DR, Déziel R, Grand-Maître C, Plouffe C, Tong L, Kawai SH. Characterization of the Human Cytomegalovirus Protease As an Induced-Fit Serine Protease and the Implications to the Design of Mechanism-Based Inhibitors. J Am Chem Soc 1999. [DOI: 10.1021/ja983904h] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Steven R. LaPlante
- Contribution from the Departments of Chemistry and Biological Sciences, Boehringer Ingelheim (Canada) Ltd., Bio-Méga Research Division, Laval, Quebec H7S 2G5, Canada
| | - Pierre R. Bonneau
- Contribution from the Departments of Chemistry and Biological Sciences, Boehringer Ingelheim (Canada) Ltd., Bio-Méga Research Division, Laval, Quebec H7S 2G5, Canada
| | - Norman Aubry
- Contribution from the Departments of Chemistry and Biological Sciences, Boehringer Ingelheim (Canada) Ltd., Bio-Méga Research Division, Laval, Quebec H7S 2G5, Canada
| | - Dale R. Cameron
- Contribution from the Departments of Chemistry and Biological Sciences, Boehringer Ingelheim (Canada) Ltd., Bio-Méga Research Division, Laval, Quebec H7S 2G5, Canada
| | - Robert Déziel
- Contribution from the Departments of Chemistry and Biological Sciences, Boehringer Ingelheim (Canada) Ltd., Bio-Méga Research Division, Laval, Quebec H7S 2G5, Canada
| | - Chantal Grand-Maître
- Contribution from the Departments of Chemistry and Biological Sciences, Boehringer Ingelheim (Canada) Ltd., Bio-Méga Research Division, Laval, Quebec H7S 2G5, Canada
| | - Céline Plouffe
- Contribution from the Departments of Chemistry and Biological Sciences, Boehringer Ingelheim (Canada) Ltd., Bio-Méga Research Division, Laval, Quebec H7S 2G5, Canada
| | - Liang Tong
- Contribution from the Departments of Chemistry and Biological Sciences, Boehringer Ingelheim (Canada) Ltd., Bio-Méga Research Division, Laval, Quebec H7S 2G5, Canada
| | - Stephen H. Kawai
- Contribution from the Departments of Chemistry and Biological Sciences, Boehringer Ingelheim (Canada) Ltd., Bio-Méga Research Division, Laval, Quebec H7S 2G5, Canada
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LaPlante SR, Cameron DR, Aubry N, Bonneau PR, Déziel R, Grand-Maître C, Ogilvie WW, Kawai SH. Die Konformation eines an die humane Cytomegalievirus-Protease gebundenen Peptidylmethylketon-Inhibitors. Angew Chem Int Ed Engl 1998. [DOI: 10.1002/(sici)1521-3757(19981002)110:19<2858::aid-ange2858>3.0.co;2-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Tong L, Qian C, Massariol MJ, Déziel R, Yoakim C, Lagacé L. Conserved mode of peptidomimetic inhibition and substrate recognition of human cytomegalovirus protease. NATURE STRUCTURAL BIOLOGY 1998; 5:819-26. [PMID: 9731777 DOI: 10.1038/1860] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Human cytomegalovirus (HCMV) protease belongs to a new class of serine proteases, with a unique polypeptide backbone fold. The crystal structure of the protease in complex with a peptidomimetic inhibitor (based on the natural substrates and covering the P4 to P1' positions) has been determined at 2.7 A resolution. The inhibitor is bound in an extended conformation, forming an anti-parallel beta-sheet with the protease. The P3 and P1 side chains are less accessible to solvent, whereas the P4 and P2 side chains are more exposed. The inhibitor binding mode shows significant similarity to those observed for peptidomimetic inhibitors or substrates of other classes of serine proteases (chymotrypsin and subtilisin). HCMV protease therefore represents example of convergent evolution. In addition, large conformational differences relative to the structure of the free enzyme are observed, which may be important for inhibitor binding.
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Affiliation(s)
- L Tong
- Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut 06877, USA.
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