1
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Ivanova E, Osipova M, Vasilieva T, Eremkin A, Markova S, Zazhivihina E, Smirnova S, Mitrasov Y, Nasakin O. The Recycling of Substandard Rocket Fuel N,N-Dimethylhydrazine via the Involvement of Its Hydrazones Derived from Glyoxal, Acrolein, Metacrolein, Crotonaldehyde, and Formaldehyde in Organic Synthesis. Int J Mol Sci 2023; 24:17196. [PMID: 38139025 PMCID: PMC10742919 DOI: 10.3390/ijms242417196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/05/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
"Heptil" (unsymmetrical dimethylhydrazine-UDMH) is extensively employed worldwide as a propellant for rocket engines. However, UDMH constantly loses its properties as a result of its continuous and uncontrolled absorption of moisture, which cannot be rectified. This situation threatens its long-term usability. UDMH is an exceedingly toxic compound (Hazard Class 1), which complicates its transportation and disposal. Incineration is currently the only method used for its disposal, but this process generates oxidation by-products that are even more toxic than the original UDMH. A more benign approach involves its immediate reaction with a formalin solution to form 1,1-dimethyl-2-methylene hydrazone (MDH), which is significantly less toxic by an order of magnitude. MDH can then be polymerized under acidic conditions, and the resulting product can be burned, yielding substantial amounts of nitrogen oxides. This review seeks to shift the focus of MDH from incineration towards its application in the synthesis of relatively non-toxic and readily available analogs of various pharmaceutical substances. We aim to bring the attention of the international chemical community to the distinctive properties of MDH, as well as other hydrazones (such as glyoxal, acrolein, crotonal, and meta-crolyl), wherein each structural fragment can initiate unique transformations that have potential applications in molecular design, pharmaceutical research, and medicinal chemistry.
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Affiliation(s)
- Elizaveta Ivanova
- Organic and Pharmaceutical Chemistry Department, Ulyanov Chuvash State University, Moskovsky Prospect, 15, 428015 Cheboksary, Russia; (E.I.); (M.O.); (T.V.); (A.E.); (S.M.); (E.Z.); (S.S.)
| | - Margarita Osipova
- Organic and Pharmaceutical Chemistry Department, Ulyanov Chuvash State University, Moskovsky Prospect, 15, 428015 Cheboksary, Russia; (E.I.); (M.O.); (T.V.); (A.E.); (S.M.); (E.Z.); (S.S.)
| | - Tatyana Vasilieva
- Organic and Pharmaceutical Chemistry Department, Ulyanov Chuvash State University, Moskovsky Prospect, 15, 428015 Cheboksary, Russia; (E.I.); (M.O.); (T.V.); (A.E.); (S.M.); (E.Z.); (S.S.)
| | - Alexey Eremkin
- Organic and Pharmaceutical Chemistry Department, Ulyanov Chuvash State University, Moskovsky Prospect, 15, 428015 Cheboksary, Russia; (E.I.); (M.O.); (T.V.); (A.E.); (S.M.); (E.Z.); (S.S.)
| | - Svetlana Markova
- Organic and Pharmaceutical Chemistry Department, Ulyanov Chuvash State University, Moskovsky Prospect, 15, 428015 Cheboksary, Russia; (E.I.); (M.O.); (T.V.); (A.E.); (S.M.); (E.Z.); (S.S.)
| | - Ekaterina Zazhivihina
- Organic and Pharmaceutical Chemistry Department, Ulyanov Chuvash State University, Moskovsky Prospect, 15, 428015 Cheboksary, Russia; (E.I.); (M.O.); (T.V.); (A.E.); (S.M.); (E.Z.); (S.S.)
| | - Svetlana Smirnova
- Organic and Pharmaceutical Chemistry Department, Ulyanov Chuvash State University, Moskovsky Prospect, 15, 428015 Cheboksary, Russia; (E.I.); (M.O.); (T.V.); (A.E.); (S.M.); (E.Z.); (S.S.)
| | - Yurii Mitrasov
- Organic and Pharmaceutical Chemistry Department, Yakovlev Chuvash State Pedagogical University, K. Marx Street, 38, 428000 Cheboksary, Russia;
| | - Oleg Nasakin
- Organic and Pharmaceutical Chemistry Department, Ulyanov Chuvash State University, Moskovsky Prospect, 15, 428015 Cheboksary, Russia; (E.I.); (M.O.); (T.V.); (A.E.); (S.M.); (E.Z.); (S.S.)
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2
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Yoshida S, Sako Y, Nikaido E, Ueda T, Kozono I, Ichihashi Y, Nakahashi A, Onishi M, Yamatsu Y, Kato T, Nishikawa J, Tachibana Y. Peptide-to-Small Molecule: Discovery of Non-Covalent, Active-Site Inhibitors of β-Herpesvirus Proteases. ACS Med Chem Lett 2023; 14:1558-1566. [PMID: 37974946 PMCID: PMC10641906 DOI: 10.1021/acsmedchemlett.3c00359] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/21/2023] [Accepted: 10/24/2023] [Indexed: 11/19/2023] Open
Abstract
Viral proteases, the key enzymes that regulate viral replication and assembly, are promising targets for antiviral drug discovery. Herpesvirus proteases are enzymes with no crystallographically confirmed noncovalent active-site binders, owing to their shallow and polar substrate-binding pockets. Here, we applied our previously reported "Peptide-to-Small Molecule" strategy to generate novel inhibitors of β-herpesvirus proteases. Rapid selection with a display technology was used to identify macrocyclic peptide 1 bound to the active site of human cytomegalovirus protease (HCMVPro) with high affinity, and pharmacophore queries were defined based on the results of subsequent intermolecular interaction analyses. Membrane-permeable small molecule 19, designed de novo according to this hypothesis, exhibited enzyme inhibitory activity (IC50 = 10-6 to 10-7 M) against β-herpesvirus proteases, and the design concept was proved by X-ray cocrystal analysis.
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Affiliation(s)
- Shuhei Yoshida
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Yusuke Sako
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Eiji Nikaido
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Taichi Ueda
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Iori Kozono
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Yusuke Ichihashi
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Atsufumi Nakahashi
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Motoyasu Onishi
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Yukiko Yamatsu
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Teruhisa Kato
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Junichi Nishikawa
- PeptiDream
Inc., 3-25-23 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-0821, Japan
| | - Yuki Tachibana
- Pharmaceutical
Research Division, Shionogi Pharmaceutical
Research Center, 3-1-1 Futaba-cho, Toyonaka, Osaka 561-0825, Japan
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3
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Botta L, Cesarini S, Zippilli C, Bizzarri BM, Fanelli A, Saladino R. Multicomponent reactions in the synthesis of antiviral compounds. Curr Med Chem 2021; 29:2013-2050. [PMID: 34620058 DOI: 10.2174/0929867328666211007121837] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 07/16/2021] [Accepted: 08/18/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Multicomponent reactions are one-pot processes for the synthesis of highly functionalized hetero-cyclic and hetero-acyclic compounds, often endowed with biological activity. OBJECTIVE Multicomponent reactions are considered green processes with high atom economy. In addition, they present advantages compared to the classic synthetic methods such as high efficiency and low wastes production. METHOD In these reactions two or more reagents are combined together in the same flask to yield a product containing almost all the atoms of the starting materials. RESULTS The scope of this review is to present an overview of the application of multicomponent reactions in the synthesis of compounds endowed with antiviral activity. The syntheses are classified depending on the viral target. CONCLUSION Multicomponent reactions can be applied to all the stages of the drug discovery and development process making them very useful in the search for new agents active against emerging (viral) pathogens.
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Affiliation(s)
- Lorenzo Botta
- Department Biological and Ecological Sciences, University of Tuscia, Viterbo. Italy
| | - Silvia Cesarini
- Department Biological and Ecological Sciences, University of Tuscia, Viterbo. Italy
| | - Claudio Zippilli
- Department Biological and Ecological Sciences, University of Tuscia, Viterbo. Italy
| | | | - Angelica Fanelli
- Department Biological and Ecological Sciences, University of Tuscia, Viterbo. Italy
| | - Raffaele Saladino
- Department Biological and Ecological Sciences, University of Tuscia, Viterbo. Italy
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4
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Yuan WY, Chen X, Liu NN, Wen YN, Yang B, Andrei G, Snoeck R, Xiang YH, Wu YW, Jiang Z, Schols D, Zhang ZY, Wu QP. Synthesis, Anti-Varicella-Zoster Virus and Anti-Cytomegalovirus Activity of 4,5-Disubstituted 1,2,3-(1H)-Triazoles. Med Chem 2019; 15:801-812. [PMID: 30411688 DOI: 10.2174/1573406414666181109095239] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 10/05/2018] [Accepted: 10/30/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Clinical drugs for herpesvirus exhibit high toxicity and suffer from significant drug resistance. The development of new, effective, and safe anti-herpesvirus agents with different mechanisms of action is greatly required. OBJECTIVE Novel inhibitors against herpesvirus with different mechanisms of action from that of clinical drugs. METHODS A series of novel 5-(benzylamino)-1H-1,2,3-triazole-4-carboxamides were efficiently synthesized and EC50 values against Human Cytomegalovirus (HCMV), Varicella-Zoster Virus (VZV) and Herpes Simplex Virus (HSV) were evaluated in vitro. RESULTS Some compounds present antiviral activity. Compounds 5s and 5t are potent against both HCMV and VZV. Compounds 5m, 5n, 5s, and 5t show similar EC50 values against both TK+ and TK- VZV strains. CONCLUSION 5-(Benzylamino)-1H-1, 2,3-triazole-4-carboxamides are active against herpesviruses and their activity is remarkably affected by the nature and the position of substituents in the benzene ring. The results indicate that these derivatives are independent of the viral thymidine kinase (TK) for activation, which is indispensable for current drugs. Their mechanisms of action may differ from those of the clinic anti-herpesvirus drugs.
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Affiliation(s)
- Wei-Yuan Yuan
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Xue Chen
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Ning-Ning Liu
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Yi-Ning Wen
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Bei Yang
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Graciela Andrei
- Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, Leuven B-3000, Belgium
| | - Robert Snoeck
- Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, Leuven B-3000, Belgium
| | - Yu-Hong Xiang
- School of Chemistry, Capital Normal University, Beijing 100048, China
| | - Yong-Wei Wu
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Zhen Jiang
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Dominique Schols
- Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, Leuven B-3000, Belgium
| | - Zhuo-Yong Zhang
- School of Chemistry, Capital Normal University, Beijing 100048, China
| | - Qin-Pei Wu
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
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5
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Abstract
The article discusses the basic properties of fluorine atom that have made it so useful in drug development. It presents several examples of therapeutically useful drugs acting against many life-threatening diseases along with the mechanism as to how fluorine influences the drug activity. It has been pointed out that fluorine, due to its ability to increase the lipophilicity of the molecule, greatly affects the hydrophobic interaction between the drug molecule and the receptor. Because of its small size, it hardly produces any steric effect, rather due to electronic properties enters into electrostatic and hydrogen-bond interactions. Thus, it greatly affects the drug-receptor interaction and leads to increase the activity of the drugs.
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Affiliation(s)
- Satya Prakash Gupta
- Department of Pharmaceutical Technology, Meerut Institute of Engineering and Technology, Meerut 250005, India
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6
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Dev D, Chandra J, Palakurthy NB, Thalluri K, Kalita T, Mandal B. Benzoxazole and Benzothiazole Synthesis from Carboxylic Acids in Solution and on Resin by Using Ethyl 2-Cyano-2-(2-nitrobenzenesulfonyloxyimino)acetate and para
-Toluenesulfonic Acid. ASIAN J ORG CHEM 2016. [DOI: 10.1002/ajoc.201500527] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Dharm Dev
- Department of Chemistry; Indian Institute of Technology Guwahati; North Guwahati- 781039 India
| | - Jyoti Chandra
- Department of Chemistry; Indian Institute of Technology Guwahati; North Guwahati- 781039 India
| | - Nani Babu Palakurthy
- Department of Chemistry; Indian Institute of Technology Guwahati; North Guwahati- 781039 India
| | - Kishore Thalluri
- Department of Chemistry; Indian Institute of Technology Guwahati; North Guwahati- 781039 India
| | - Tapasi Kalita
- Department of Chemistry; Indian Institute of Technology Guwahati; North Guwahati- 781039 India
| | - Bhubaneswar Mandal
- Department of Chemistry; Indian Institute of Technology Guwahati; North Guwahati- 781039 India
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7
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Nenajdenko VG, Muzalevskiy VM, Shastin AV. Polyfluorinated ethanes as versatile fluorinated C2-building blocks for organic synthesis. Chem Rev 2015; 115:973-1050. [PMID: 25594605 DOI: 10.1021/cr500465n] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Valentine G Nenajdenko
- Department of Chemistry, Moscow State University , Leninskie Gory, Moscow 119992, Russia
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8
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Gable J, Acker TM, Craik CS. Current and potential treatments for ubiquitous but neglected herpesvirus infections. Chem Rev 2014; 114:11382-412. [PMID: 25275644 PMCID: PMC4254030 DOI: 10.1021/cr500255e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Indexed: 02/07/2023]
Affiliation(s)
- Jonathan
E. Gable
- Department
of Pharmaceutical Chemistry, University
of California, San Francisco, 600 16th Street, San Francisco, California 94158-2280, United States
- Graduate
Group in Biophysics, University of California,
San Francisco, 600 16th
Street, San Francisco, California 94158-2280, United States
| | - Timothy M. Acker
- Department
of Pharmaceutical Chemistry, University
of California, San Francisco, 600 16th Street, San Francisco, California 94158-2280, United States
| | - Charles S. Craik
- Department
of Pharmaceutical Chemistry, University
of California, San Francisco, 600 16th Street, San Francisco, California 94158-2280, United States
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9
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Substrate derived peptidic α-ketoamides as inhibitors of the malarial protease PfSUB1. Bioorg Med Chem Lett 2014; 24:4486-4489. [PMID: 25129616 DOI: 10.1016/j.bmcl.2014.07.086] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Revised: 07/25/2014] [Accepted: 07/30/2014] [Indexed: 01/19/2023]
Abstract
Peptidic α-ketoamides have been developed as inhibitors of the malarial protease PfSUB1. The design of inhibitors was based on the best known endogenous PfSUB1 substrate sequence, leading to compounds with low micromolar to submicromolar inhibitory activity. SAR studies were performed indicating the requirement of an aspartate mimicking the P1' substituent and optimal P1-P4 length of the non-prime part. The importance of each of the P1-P4 amino acid side chains was investigated, revealing crucial interactions and size limitations.
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10
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Gable JE, Lee GM, Jaishankar P, Hearn BR, Waddling CA, Renslo AR, Craik CS. Broad-spectrum allosteric inhibition of herpesvirus proteases. Biochemistry 2014; 53:4648-60. [PMID: 24977643 PMCID: PMC4108181 DOI: 10.1021/bi5003234] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Herpesviruses
rely on a homodimeric protease for viral capsid maturation.
A small molecule, DD2, previously shown to disrupt dimerization of
Kaposi’s sarcoma-associated herpesvirus protease (KSHV Pr)
by trapping an inactive monomeric conformation and two analogues generated
through carboxylate bioisosteric replacement (compounds 2 and 3) were shown to inhibit the associated proteases
of all three human herpesvirus (HHV) subfamilies (α, β,
and γ). Inhibition data reveal that compound 2 has
potency comparable to or better than that of DD2 against the tested
proteases. Nuclear magnetic resonance spectroscopy and a new application
of the kinetic analysis developed by Zhang and Poorman [Zhang, Z.
Y., Poorman, R. A., et al. (1991) J. Biol. Chem. 266, 15591–15594] show DD2, compound 2, and compound 3 inhibit HHV proteases by dimer disruption. All three compounds
bind the dimer interface of other HHV proteases in a manner analogous
to binding of DD2 to KSHV protease. The determination and analysis
of cocrystal structures of both analogues with the KSHV Pr monomer
verify and elaborate on the mode of binding for this chemical scaffold,
explaining a newly observed critical structure–activity relationship.
These results reveal a prototypical chemical scaffold for broad-spectrum
allosteric inhibition of human herpesvirus proteases and an approach
for the identification of small molecules that allosterically regulate
protein activity by targeting protein–protein interactions.
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Affiliation(s)
- Jonathan E Gable
- Department of Pharmaceutical Chemistry, University of California , San Francisco, California 94158-2280, United States
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11
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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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12
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Heravi MM, Javanmardi N, Oskooie HA, Baghernejad B, Heidari M, Bamoharram FF. Heteropolyacid as a New, Green and Recyclable Catalyst for the Synthesis of 2-Aryl Benzoxazole under Solvent-Free Conditions. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.200900087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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13
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Skoreński M, Oleksyszyn J, Sieńczyk M. A convenient method for the one-step synthesis of phosphonic peptides. Tetrahedron Lett 2013. [DOI: 10.1016/j.tetlet.2013.07.049] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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14
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Craik CS, Shahian T. A screening strategy for trapping the inactive conformer of a dimeric enzyme with a small molecule inhibitor. Methods Mol Biol 2012; 928:119-131. [PMID: 22956137 PMCID: PMC3739972 DOI: 10.1007/978-1-62703-008-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is the etiological agent of Kaposi's sarcoma (KS), the most common cancer in AIDS patients. All herpesviruses express a conserved dimeric serine protease that is required for generating infectious virions and is therefore of pharmaceutical interest. Given the past challenges of developing drug-like active-site inhibitors to this class of proteases, small-molecules targeting allosteric sites are of great value. In light of evidence supporting a strong structural linkage between the dimer interface and the protease active site, we have focused our efforts on the dimer interface for identifying dimer disrupting inhibitors. Here, we describe a high throughput screening approach for identifying small molecule dimerization inhibitors of KSHV protease. The helical mimetic, small molecule library used, as well as general strategies for selecting compound libraries for this application will also be discussed. This methodology can be applicable to other systems where an alpha helical moiety plays a dominant role at the interaction site of interest, and in vitro assays to monitor function are in place.
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Affiliation(s)
- Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
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15
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Lee GM, Shahian T, Baharuddin A, Gable JE, Craik CS. Enzyme inhibition by allosteric capture of an inactive conformation. J Mol Biol 2011; 411:999-1016. [PMID: 21723875 DOI: 10.1016/j.jmb.2011.06.032] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 06/15/2011] [Accepted: 06/16/2011] [Indexed: 10/18/2022]
Abstract
All members of the human herpesvirus protease (HHV Pr) family are active as weakly associating dimers but inactive as monomers. A small-molecule allosteric inhibitor of Kaposi's sarcoma-associated herpesvirus protease (KSHV Pr) traps the enzyme in an inactive monomeric state where the C-terminal helices are unfolded and the hydrophobic dimer interface is exposed. NMR titration studies demonstrate that the inhibitor binds to KSHV Pr monomers with low micromolar affinity. A 2.0-Å-resolution X-ray crystal structure of a C-terminal truncated KSHV Pr-inhibitor complex locates the binding pocket at the dimer interface and displays significant conformational perturbations at the active site, 15 Å from the allosteric site. NMR and CD data suggest that the small molecule inhibits human cytomegalovirus protease via a similar mechanism. As all HHV Prs are functionally and structurally homologous, the inhibitor represents a class of compounds that may be developed into broad-spectrum therapeutics that allosterically regulate enzymatic activity by disrupting protein-protein interactions.
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Affiliation(s)
- Gregory M Lee
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158-2280, USA
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16
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Mlostoń G, Obijalska E, Heimgartner H. Synthesis of β-amino-α-trifluoromethyl alcohols and their applications in organic synthesis. J Fluor Chem 2010; 131:829-843. [PMID: 32287377 PMCID: PMC7125969 DOI: 10.1016/j.jfluchem.2010.05.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2010] [Revised: 05/21/2010] [Accepted: 05/29/2010] [Indexed: 11/26/2022]
Abstract
A comprehensive overview on methods applied for syntheses of β-amino-α-trifluoromethyl alcohols, including stereocontrolled variants, is presented. In addition, reported cases of the exploration of β-amino-α-trifluoromethyl alcohols for the preparation of trifluoromethylated peptidomimetics and other biologically active, fluorinated compounds are discussed. Attractive opportunities for their applications as organocatalysts are also presented.
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Affiliation(s)
- Grzegorz Mlostoń
- Department of Organic and Applied Chemistry, University of Łódź, Tamka 12, PL-91-403, Łódź, Poland
| | - Emilia Obijalska
- Department of Organic and Applied Chemistry, University of Łódź, Tamka 12, PL-91-403, Łódź, Poland
| | - Heinz Heimgartner
- Institute of Organic Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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17
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Abstract
A convergent synthesis of alpha-ketoamide inhibitors of Pin1 is described. An alpha-hydroxyorthothioester derivative of Ser was reacted directly with an amine synthon. The reaction was catalyzed by HgO and HgCl(2) to form alpha-hydroxyamide. Thus, hydrolysis and coupling were combined in one step with 80% yield. Two diastereomers of a phospho-Ser-Pro alpha-ketoamide analogue were synthesized. The IC(50) values of 100 and 200 microM were surprisingly weak for Pin1 peptidyl prolyl isomerase.
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Affiliation(s)
- Guoyan G Xu
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, USA
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18
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Kawai SH, Aubry N, Duceppe JS, Llinàs-Brunet M, LaPlante SR. Dimethylthiazolidine Carboxylic Acid as a Rigid P3 Unit in Inhibitors of Serine Proteases: Application to Two Targets. Chem Biol Drug Des 2009; 74:517-22. [DOI: 10.1111/j.1747-0285.2009.00870.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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19
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Shahian T, Lee GM, Lazic A, Arnold LA, Velusamy P, Roels CM, Guy RK, Craik CS. Inhibition of a viral enzyme by a small-molecule dimer disruptor. Nat Chem Biol 2009; 5:640-6. [PMID: 19633659 PMCID: PMC2752665 DOI: 10.1038/nchembio.192] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Accepted: 05/18/2009] [Indexed: 11/03/2022]
Abstract
Small molecule dimer disruptors that inhibit an essential dimeric protease of human Kaposi’s sarcoma-associated herpesvirus (KSHV) were identified by screening an α-helical mimetic library. Subsequently, a second generation of low micromolar inhibitors with improved potency and solubility was synthesized. Complementary methods including size exclusion chromatography and 1H-13C HSQC titration using selectively labeled 13C-Met samples revealed that monomeric protease is enriched in the presence of inhibitor. 1H-15N-HSQC titration studies mapped the inhibitor binding-site to the dimer interface, and mutagenesis studies targeting this region were consistent with a mechanism where inhibitor binding prevents dimerization through the conformational selection of a dynamic intermediate. These results validate the interface of herpesvirus proteases and other similar oligomeric interactions as suitable targets for the development of small molecule inhibitors.
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Affiliation(s)
- Tina Shahian
- Graduate Group in Biochemistry and Molecular Biology, University of California, San Francisco, California, USA
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20
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Lin W, Theberge CR, Henderson TJ, Zercher CK, Jasinski J, Butcher RJ. Stereoselective formation of a functionalized dipeptide isostere by zinc carbenoid-mediated chain extension. J Org Chem 2009; 74:645-51. [PMID: 19055379 PMCID: PMC2680025 DOI: 10.1021/jo801993k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The application of a zinc carbenoid-mediated chain-extension reaction to a functionalized peptide isostere is reported. The cleavage site of human CVM protease was utilized as a target for testing the synthetic methodology. The utility of this chain-extension reaction is demonstrated in the preparation of an amino acid-derived alpha-unsubstituted gamma-keto ester, which is incorporated into a framework that mimics a tetrapeptide. The identification of a suitable protecting group strategy facilitated the application of a tandem reaction for the incorporation of an alpha-side chain, and the use of an oxazolidinone auxiliary provided excellent diastereocontrol in a tandem chain-extension-aldol reaction. Stereoselectivity of the tandem chain-extension-aldol reaction was determined through application of a CAN-mediated oxidative cleavage reaction.
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Affiliation(s)
- Weimin Lin
- Department of Chemistry, University of New Hampshire, Durham, NH 03824
| | - Cory R. Theberge
- Department of Chemistry, University of New Hampshire, Durham, NH 03824
| | | | | | - Jerry Jasinski
- Department of Chemistry, Keene State College, 229 Main Street, Keene, NH 03435
| | - Ray J. Butcher
- Department of Chemistry, Howard University, 525 College Street NW, Washington DC 20059, USA
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21
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Regio- and π-facial selective Lewis acid interceded Diels–Alder reactions of α-dienyl-β-lactams: an indepth analysis. Tetrahedron 2008. [DOI: 10.1016/j.tet.2008.04.087] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Shao YM, Yang WB, Kuo TH, Tsai KC, Lin CH, Yang AS, Liang PH, Wong CH. Design, synthesis, and evaluation of trifluoromethyl ketones as inhibitors of SARS-CoV 3CL protease. Bioorg Med Chem 2008; 16:4652-60. [PMID: 18329272 PMCID: PMC7127754 DOI: 10.1016/j.bmc.2008.02.040] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2007] [Revised: 02/10/2008] [Accepted: 02/11/2008] [Indexed: 11/18/2022]
Abstract
A series of trifluoromethyl ketones as SARS-CoV 3CL protease inhibitors was developed. The inhibitors were synthesized in four steps from commercially available compounds. Three different amino acids were explored in the P1-position and in the P2–P4 positions varying amino acids and long alkyl chain were incorporated. All inhibitors were evaluated in an in vitro assay using purified enzyme and fluorogenic substrate peptide. One of the inhibitors showed a time-dependent inhibition, with a Ki value of 0.3 μM after 4 h incubation.
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Affiliation(s)
- Yi-Ming Shao
- Genomics Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Taipei 11529, Taiwan
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23
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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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24
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Buisson M, Rivail L, Hernandez JF, Jamin M, Martinez J, Ruigrok RWH, Burmeister WP. Kinetics, inhibition and oligomerization of Epstein-Barr virus protease. FEBS Lett 2006; 580:6570-8. [PMID: 17118362 DOI: 10.1016/j.febslet.2006.11.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2006] [Accepted: 11/06/2006] [Indexed: 01/28/2023]
Abstract
Epstein-Barr virus (EBV) is an omnipresent human virus causing infectious mononucleosis and EBV associated cancers. Its protease is a possible target for antiviral therapy. We studied its dimerization and enzyme kinetics with two enzyme assays based either on the release of paranitroaniline or 7-amino-4-methylcoumarin from labeled pentapeptide (Ac-KLVQA) substrates. The protease is in a monomer-dimer equilibrium where only dimers are active. In absence of citrate the K(d) is 20 microM and drops to 0.2 microM in presence of 0.5M citrate. Citrate increases additionally the activity of the catalytic sites. The inhibitory constants of different substrate derived peptides and alpha-keto-amide based inhibitors, which have at best a K(i) of 4 microM, have also been evaluated.
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Affiliation(s)
- Marlyse Buisson
- Institut de Virologie Moléculaire et Structurale, FRE 2854 CNRS-UJF, BP181, 38042 Grenoble Cedex 9, France
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25
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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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26
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Fear G, Komarnytsky S, Raskin I. Protease inhibitors and their peptidomimetic derivatives as potential drugs. Pharmacol Ther 2006; 113:354-68. [PMID: 17098288 PMCID: PMC7112583 DOI: 10.1016/j.pharmthera.2006.09.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2006] [Accepted: 09/05/2006] [Indexed: 01/28/2023]
Abstract
Precise spatial and temporal regulation of proteolytic activity is essential to human physiology. Modulation of protease activity with synthetic peptidomimetic inhibitors has proven to be clinically useful for treating human immunodeficiency virus (HIV) and hypertension and shows potential for medicinal application in cancer, obesity, cardiovascular, inflammatory, neurodegenerative diseases, and various infectious and parasitic diseases. Exploration of natural inhibitors and synthesis of peptidomimetic molecules has provided many promising compounds performing successfully in animal studies. Several protease inhibitors are undergoing further evaluation in human clinical trials. New research strategies are now focusing on the need for improved comprehension of protease-regulated cascades, along with precise selection of targets and improved inhibitor specificity. It remains to be seen which second generation agents will evolve into approved drugs or complementary therapies.
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Affiliation(s)
- Georgie Fear
- Biotech Center, Rutgers University, 59 Dudley Road, New Brunswick, NJ 08901, USA.
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27
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Feroci M, Orsini M, Rossi L, Sotgiu G, Inesi A. An electrochemical alternative strategy to the synthesis of β-lactams. Electrochim Acta 2006. [DOI: 10.1016/j.electacta.2006.02.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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28
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Annedi SC, Biabani F, Poduch E, Mannargudi BM, Majumder K, Wei L, Khayat R, Tong L, Kotra LP. Engineering d-amino acid containing novel protease inhibitors using catalytic site architecture. Bioorg Med Chem 2005; 14:214-36. [PMID: 16198572 DOI: 10.1016/j.bmc.2005.08.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2005] [Revised: 08/02/2005] [Accepted: 08/02/2005] [Indexed: 11/30/2022]
Abstract
The mechanism of proteolysis by serine proteases is a reasonably well-understood process. Typically, a histidine residue acting as a general base deprotonates the catalytic serine residue and the hydrolytic water molecule. We disclose here, the use of an unnatural d-amino acid as a strategic residue in P1 position, designed de novo based on the architecture of the protease catalytic site to impede the catalytic histidine residue at the stage of acyl-enzyme intermediate. Several probe molecules containing d-homoserine or its derivatives at P1 position are evaluated. Compounds 1, 6, and 8-10 produced up to 57% loss of activity against chymotrypsin. More potent and specific inhibitors could be designed with structure optimization as this strategy is completely general and can be used to design inhibitors against any serine or cysteine protease.
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Affiliation(s)
- Subhash C Annedi
- Molecular Design and Information Technology Center, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Canada ON M5S 2S2
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29
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Zheltukhin VF, Dovbysh AI, Sadkova DN, Dobrynin AB, Kataeva ON, Litvinov IA, Alfonsov VA. Synthesis of stereoisomeric P—H-spirophosphoranes based on hydrobenzoin. Russ Chem Bull 2005. [DOI: 10.1007/s11172-006-0060-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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30
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Gerona-Navarro G, Pérez de Vega MJ, García-López MT, Andrei G, Snoeck R, De Clercq E, Balzarini J, González-Muñiz R. From 1-acyl-beta-lactam human cytomegalovirus protease inhibitors to 1-benzyloxycarbonylazetidines with improved antiviral activity. A straightforward approach to convert covalent to noncovalent inhibitors. J Med Chem 2005; 48:2612-21. [PMID: 15801851 DOI: 10.1021/jm0492812] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Starting from the structure of known beta-lactam covalent human cytomegalovirus (HCMV) protease inhibitors and from the knowledge of the residues implicated in the active site of this enzyme, we designed a series of phenylalanine-derived 2-azetidinones bearing a 4-carboxylate moiety that could be apt for additional interactions with the guanidine group of the Arg165/Arg166 residues of the viral protease. Some compounds within this series showed anti-HCMV activity at 10-50 muM, but rather high toxicity. The presence of aromatic 1-acyl groups and a certain hydrophobic character in the region of the 4-carboxylate were stringent requirements for anti-HCMV activity. To go a step ahead into the search for effective HCMV medicines, we then envisaged a series of noncovalent inhibitors by simple deletion of the carbonyl group in the beta-lactam derivatives to provide the corresponding azetidines. This led to low micromolar inhibitors of HCMV replication, with 17 and 27 being particularly promising lead compounds for further investigation, although their toxicity still needs to be lowered.
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31
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Geitmann M, Danielson UH. Studies of substrate-induced conformational changes in human cytomegalovirus protease using optical biosensor technology. Anal Biochem 2005; 332:203-14. [PMID: 15325287 DOI: 10.1016/j.ab.2004.06.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2004] [Indexed: 11/25/2022]
Abstract
The interaction between human cytomegalovirus (HCMV) protease and a peptide substrate was studied using a surface plasmon resonance (SPR)-based biosensor. Immobilization of the enzyme to the sensor chip surface by amine coupling resulted in an active enzyme with a higher catalytic efficiency than the enzyme in solution, primarily due to a lower K(m) value. The interaction between immobilized protease and substrate was characterized by a biphasic SPR signal. Rate constants for the formation of the initial enzyme-substrate complex could be determined from the sensorgrams. Simulated binding curves based on the determined k(cat) and the rate constants indicated that the complex binding signal did not originate from the accumulation of intermediates in the catalytic reaction. By chemical crosslinking of the immobilized HCMV protease, which was shown to limit the enzyme's structural flexibility, it was revealed that the obtained sensorgrams were composed of a signal caused by substrate binding and considerable structural alterations in the immobilized enzyme. Furthermore, HCMV protease was inactivated by chemical crosslinking, indicating that structural flexibility is essential for this enzyme. Parallel experiments with immobilized alpha-chymotrypsin revealed that it does not undergo similar conformational changes on peptide binding and that crosslinking did not inactivate the enzyme. The simultaneous detection of binding and conformational changes using optical biosensor technology is expected to be of importance for further characterization of the enzymatic properties of HCMV protease and for identification of inhibitors of this enzyme. It can also be of use for studies of other flexible proteins.
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Affiliation(s)
- Matthis Geitmann
- Department of Biochemistry, Uppsala University, BMC, Box 576, SE-751 23 Uppsala, Sweden
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32
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Gerona-Navarro G, Pérez de Vega MJ, García-López MT, Andrei G, Snoeck R, Balzarini J, De Clercq E, González-Muñiz R. Synthesis and anti-HCMV activity of 1-acyl-beta-lactams and 1-acylazetidines derived from phenylalanine. Bioorg Med Chem Lett 2004; 14:2253-6. [PMID: 15081019 DOI: 10.1016/j.bmcl.2004.02.010] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2003] [Revised: 12/30/2003] [Accepted: 02/03/2004] [Indexed: 11/25/2022]
Abstract
Different Phe-derived 1-acyl-beta-lactams, analogous to a series of 2-azetidinones acting as HCMV serine protease inhibitors, were synthesized. Some of these compounds were modest inhibitors of the HCMV replication. Interestingly, removal of the carbonyl group of the beta-lactam ring, most likely acting as the serine trap, resulted in an azetidine derivative with anti-HCMV activity comparable to that of the reference compound ganciclovir.
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33
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Bailey MD, Halmos T, Goudreau N, Lescop E, Llinàs-Brunet M. Novel Azapeptide Inhibitors of Hepatitis C Virus Serine Protease. J Med Chem 2004; 47:3788-99. [PMID: 15239657 DOI: 10.1021/jm049864b] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Azapeptides are known inhibitors of several serine and cysteine proteases. In seeking different classes of inhibitors for the HCV serine protease, a series of novel azapeptide-based inhibitors were investigated which incorporated noncleavable P1/P1' aza-amino acyl residues. Extensive SAR studies around the P1/P1' aza-amino acyl fragment resulted in the identification of potent and selective inhibitors. Using NMR studies, we have shown that this series of inhibitors bind in a noncovalent competitive fashion to the NS3 protease active site. The bound conformation of one of these new azapeptide-based inhibitors was determined using the transfer NOE technique. Incorporation of these new aza-amino acyl functionalities in the P1 position provided a handle to probe for new interactions in the S' region of the enzyme.
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Affiliation(s)
- Murray D Bailey
- Boehringer Ingelheim (Canada) Ltd. Research and Development, 2100 Cunard Street, Laval, Quebec, Canada H7S 2G5.
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34
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Khayat R, Batra R, Bebernitz GA, Olson MW, Tong L. Characterization of the monomer-dimer equilibrium of human cytomegalovirus protease by kinetic methods. Biochemistry 2004; 43:316-22. [PMID: 14717585 DOI: 10.1021/bi035170d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Herpesviruses encode a serine protease that is essential for the maturation of infectious virions. This protease has a unique polypeptide backbone fold and contains a novel Ser-His-His catalytic triad. It exists in a monomer-dimer equilibrium in solution, but only the dimer form of the enzyme is catalytically active. The stability of this dimer is affected by the presence of anti-chaotropic agents. Most of the reported Kd values for this dimer (between 0.6 and 6 microM) are inconsistent with the fact that the protease is routinely assayed at 20-50 nM concentrations, as only monomeric species would be expected with such Kd values. We have characterized the monomer-dimer equilibrium of HCMV protease using a new method, which observes the exchange between dimers of the wild-type enzyme and the active-site Ser132Ala mutant in a titration experiment. The Kd of the dimer was determined to be 8 microM and 31 nM in the absence or presence of anti-chaotropic agents (10% glycerol and 0.5 M Na2SO4), respectively. Detailed kinetic analysis also showed that, in addition to the 260-fold stabilization of the dimer, the anti-chaotropic agents produced a 7-fold enhancement in the catalytic activity of the dimer.
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Affiliation(s)
- Reza Khayat
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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35
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Marnett AB, Nomura AM, Shimba N, Ortiz de Montellano PR, Craik CS. Communication between the active sites and dimer interface of a herpesvirus protease revealed by a transition-state inhibitor. Proc Natl Acad Sci U S A 2004; 101:6870-5. [PMID: 15118083 PMCID: PMC406434 DOI: 10.1073/pnas.0401613101] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2003] [Indexed: 11/18/2022] Open
Abstract
Structurally diverse organophosphonate inhibitors targeting the active site of the enzyme were used to investigate the relationship of the active site and the dimer interface of wild-type protease in solution. Positional scanning synthetic combinatorial libraries revealed Kaposi's sarcoma-associated herpesvirus protease to be highly specific, even at sites distal to the peptide bond undergoing hydrolysis. Specificity results were used to synthesize a hexapeptide diphenylphosphonate inhibitor of Kaposi's sarcoma-associated herpesvirus protease. The transition state analog inhibitors covalently phosphonylate the active site serine, freezing the enzyme structure during catalysis. An NMR-based assay was developed to monitor the native monomer-dimer equilibrium in solution and was used to demonstrate the effect of protease inhibition on the quaternary structure of the enzyme. NMR, circular dichroism, and size exclusion chromatography analysis showed that active site inhibition strongly regulates the binding affinity of the monomer-dimer equilibrium at the spatially separate dimer interface of the protease, shifting the equilibrium to the dimeric form of the enzyme. Furthermore, inhibitor studies revealed that the catalytic cycles of the spatially separate active sites are independent. These results (i) provide direct evidence that peptide bond hydrolysis is integrally linked to the quaternary structure of the enzyme, (ii) establish a molecular mechanism of protease activation and stabilization during catalysis, and (iii) highlight potential implications of substoichiometric inhibition of the viral protease in developing herpesviral therapeutics.
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Affiliation(s)
- Alan B Marnett
- Program in Chemistry and Chemical Biology, Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA
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36
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Kuznetsova L, Ungureanu IM, Pepe A, Zanardi I, Wu X, Ojima I. Trifluoromethyl- and difluoromethyl-β-lactams as useful building blocks for the synthesis of fluorinated amino acids, dipeptides, and fluoro-taxoids. J Fluor Chem 2004. [DOI: 10.1016/j.jfluchem.2003.12.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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37
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Maryanoff BE. Inhibitors of Serine Proteases as Potential Therapeutic Agents: The Road from Thrombin to Tryptase to Cathepsin G†. J Med Chem 2004; 47:769-87. [PMID: 14761180 DOI: 10.1021/jm030493t] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bruce E Maryanoff
- Drug Discovery, Johnson & Johnson Pharmaceutical Research & Development, Spring House, Pennsylvania 19477-0776, USA.
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38
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Bianchi L, Dell'Erba C, Maccagno M, Mugnoli A, Novi M, Petrillo G, Sancassan F, Tavani C. α-Oxohydrazones as imine component in the synthesis of 4-functionalized azetidinones by the Staudinger reaction. Tetrahedron 2003. [DOI: 10.1016/j.tet.2003.10.072] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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39
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Marsilje TH, Hedrick MP, Desharnais J, Tavassoli A, Zhang Y, Wilson IA, Benkovic SJ, Boger DL. Design, synthesis, and biological evaluation of simplified alpha-keto heterocycle, trifluoromethyl ketone, and formyl substituted folate analogues as potential inhibitors of GAR transformylase and AICAR transformylase. Bioorg Med Chem 2003; 11:4487-501. [PMID: 13129585 DOI: 10.1016/s0968-0896(03)00456-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A series of simplified alpha-keto heterocycle, trifluoromethyl ketone, and formyl substituted folate analogues lacking the benzoylglutamate subunit were prepared and examined as potential inhibitors of glycinamide ribonucleotide transformylase (GAR Tfase) and aminoimidazole carboxamide transformylase (AICAR Tfase).
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Affiliation(s)
- Thomas H Marsilje
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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40
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de Oliveira CAF, Guimarães CRW, Barreiro G, de Alencastro RB. Investigation of the induced-fit mechanism and catalytic activity of the human cytomegalovirus protease homodimer via molecular dynamics simulations. Proteins 2003; 52:483-91. [PMID: 12910449 DOI: 10.1002/prot.10403] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Human cytomegalovirus (HCMV) is a highly species-specific DNA virus infecting up to 80% of the general population. The viral genome contains the open reading frame UL80, which encodes the full-length 80 kDa HCMV serine protease and its substrate. Full-length HCMV protease is composed of an N-terminal 256-amino-acid proteolytic domain, called assemblin, a linker region, and a C-terminal structural domain, the assembly protein precursor. Biochemical studies have shown that dimerization activates assemblin because of an induced stabilization of the oxyanion hole (Arg166). Thus, we performed here molecular dynamics (MD) simulations on HCMV protease models to study the induced-fit mechanism of the enzyme upon the binding of substrates and peptidyl inhibitors, and structural and energetic factors that are responsible for the catalytic activity of the enzyme dimer. Long and stable trajectories were obtained for the models of the monomeric and dimeric states, free in solution and bound to a peptidyl-activated carbonyl inhibitor, with very good agreement between theoretical and experimental results. Our results suggest that HCMV protease is indeed a novel example of serine protease that operates by an induced-fit mechanism. Also, in agreement with mutagenesis studies, our MD simulations suggest that the dimeric form is necessary to activate the enzyme because of an induced stabilization of the oxyanion hole.
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Affiliation(s)
- César Augusto Fernandes de Oliveira
- Physical Organic Chemistry Group, Departamento de Química Orgânica, Instituto de Química, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro, Brazil
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41
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Johansson A, Poliakov A, Akerblom E, Wiklund K, Lindeberg G, Winiwarter S, Danielson UH, Samuelsson B, Hallberg A. Acyl sulfonamides as potent protease inhibitors of the hepatitis C virus full-Length NS3 (protease-helicase/NTPase): a comparative study of different C-terminals. Bioorg Med Chem 2003; 11:2551-68. [PMID: 12757723 DOI: 10.1016/s0968-0896(03)00179-2] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Synthesis and inhibitory potencies of three types of protease inhibitors of the hepatitis C virus (HCV) full-length NS3 (protease-helicase/NTPase) are reported: (i) inhibitors comprising electrophilic serine traps (pentafluoroethyl ketones, alpha-keto acids, and alpha-ketotetrazoles), (ii) product-based inhibitors comprising a C-terminal carboxylate group, and (iii) previously unexplored inhibitors comprising C-terminal carboxylic acid bioisosteres (tetrazoles and acyl sulfonamides). Bioisosteric replacement with the tetrazole group provided inhibitors equally potent to the corresponding carboxylates, and substitution with the phenyl acyl sulfonamide group yielded more potent inhibitors. The hexapeptide inhibitors Suc-Asp-D-Glu-Leu-Ile-Cha-Nva-NHSO(2)Ph and Suc-Asp-D-Glu-Leu-Ile-Cha-ACPC-NHSO(2)Ph with K(i) values of 13.6 and 3.8 nM, respectively, were approximately 20 times more potent than the corresponding inhibitors with a C-terminal carboxylate and were comparable to the carboxylate-based inhibitor containing the native cysteine, Suc-Asp-D-Glu-Leu-Ile-Cha-Cys-OH (K(i)=28 nM). The acyl sulfonamide group constitutes a very promising C-terminal functionality that allows for prime site optimization.
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Affiliation(s)
- Anja Johansson
- Department of Medicinal Chemistry, Uppsala University, BMC, Box 574, SE-751 23 Uppsala, Sweden
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42
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Pause A, Kukolj G, Bailey M, Brault M, Dô F, Halmos T, Lagacé L, Maurice R, Marquis M, McKercher G, Pellerin C, Pilote L, Thibeault D, Lamarre D. An NS3 serine protease inhibitor abrogates replication of subgenomic hepatitis C virus RNA. J Biol Chem 2003; 278:20374-80. [PMID: 12646587 DOI: 10.1074/jbc.m210785200] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The hepatitis C virus (HCV) NS3 protease is essential for polyprotein maturation and viral propagation, and it has been proposed as a suitable target for antiviral drug discovery. An N-terminal hexapeptide cleavage product of a dodecapeptide substrate identified as a weak competitive inhibitor of the NS3 protease activity was optimized to a potent and highly specific inhibitor of the enzyme. The effect of this potent NS3 protease inhibitor was evaluated on replication of subgenomic HCV RNA and compared with interferon-alpha (IFN-alpha), which is currently used in the treatment of HCV-infected patients. Treatment of replicon-containing cells with the NS3 protease inhibitor or IFN-alpha showed a dose-dependent decrease in subgenomic HCV RNA that reached undetectable levels following a 14-day treatment. Kinetic studies in the presence of either NS3 protease inhibitor or IFN-alpha also revealed similar profiles in HCV RNA decay with half-lives of 11 and 14 h, respectively. The finding that an antiviral specifically targeting the NS3 protease activity inhibits HCV RNA replication further validates the NS3 enzyme as a prime target for drug discovery and supports the development of NS3 protease inhibitors as a novel therapeutic approach for HCV infection.
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Affiliation(s)
- Arnim Pause
- Department of Biological Sciences, Boehringer Ingelheim (Canada) Ltd., Research and Development, Laval, Québec H7S 2G5, Canada
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43
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Khayat R, Batra R, Qian C, Halmos T, Bailey M, Tong L. Structural and biochemical studies of inhibitor binding to human cytomegalovirus protease. Biochemistry 2003; 42:885-91. [PMID: 12549906 DOI: 10.1021/bi027045s] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Herpesvirus protease is required for the life cycle of the virus and is an attractive target for the design and development of new anti-herpes agents. The protease belongs to a new class of serine proteases, with a novel backbone fold and a unique Ser-His-His catalytic triad. Here we report the crystal structures of human cytomegalovirus protease in complex with two peptidomimetic inhibitors. The structures reveal a new hydrogen-bonding interaction between the main chain carbonyl of the P(5) residue and the main chain amide of amino acid 137 of the protease, which is important for the binding affinity of the inhibitor. Conformational flexibility was observed in the S(3) pocket of the enzyme, and this is supported by our characterization of several mutants in this pocket. One of the structures is at 2.5 A resolution, allowing us for the first time to locate ordered solvent molecules in the inhibitor complex. The presence of two solvent molecules in the active site may have implications for the design of new inhibitors against this enzyme. Favorable and stereospecific interactions have been established in the S(1)' pocket for one of these inhibitors.
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Affiliation(s)
- Reza Khayat
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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44
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Affiliation(s)
- Liang Tong
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA.
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45
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Powers JC, Asgian JL, Ekici OD, James KE. Irreversible inhibitors of serine, cysteine, and threonine proteases. Chem Rev 2002; 102:4639-750. [PMID: 12475205 DOI: 10.1021/cr010182v] [Citation(s) in RCA: 818] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- James C Powers
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA.
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46
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Alcaide B, Almendros P, Alonso JM, Aly MF, Pardo C, Sáez E, Torres MR. Efficient entry to highly functionalized beta-lactams by regio- and stereoselective 1,3-dipolar cycloaddition reaction of 2-azetidinone-tethered nitrones. Synthetic applications. J Org Chem 2002; 67:7004-13. [PMID: 12353993 DOI: 10.1021/jo025924e] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Racemic as well as optically pure 2-azetidinone-tethered nitrones, both cyclic and acyclic, were smoothly prepared from 4-oxoazetidine-2-carbaldehydes. The regio- and diastereoselectivities of the intermolecular 1,3-dipolar cycloaddition reactions of 2-azetidinone-tethered nitrones with substituted alkenes and alkynes were investigated. 2-Azetidinone-tethered nitrones on reacting with various dipolarophiles yielded isoxazolinyl-, isoxazolidinyl-, or fused polycyclic-beta-lactams, exhibiting good regio- and facial stereoselectivity in the most of the cases. In addition, some interesting transformations of these cycloadducts were performed, yielding aziridinyl beta-lactams or functionalized beta-alkoxycarbonyl gamma-lactams (derivatives of the aza analogue of paraconic acid).
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Affiliation(s)
- Benito Alcaide
- Departamento de Química Orgánica I, Facultad de Química, Universidad Complutense, 28040-Madrid,
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47
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Bräse S, Gil C, Knepper K. The recent impact of solid-phase synthesis on medicinally relevant benzoannelated nitrogen heterocycles. Bioorg Med Chem 2002; 10:2415-37. [PMID: 12057632 DOI: 10.1016/s0968-0896(02)00025-1] [Citation(s) in RCA: 241] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Benzoannelated heterocycles such as benzodiazepines and indoles can be prepared efficiently through cyclization on solid supports, although no single approach is currently universal for the preparation of all benzoannelated N-heterocycle chemistries. In this review, a number of synthetic strategies for the generation of benzoannelated nitrogen heterocycles using resin-bound substrates have been described. Classical heterocycle forming reactions such as the Fischer indole, the Bischler-Napieralski tetrahydroisoquinoline, the Pictet-Spengler tetrahydro-beta-carboline, the Tsuge, the Nenitzescu and the Richter cinnoline reaction are presented. In addition, the Heck, Sonogashira, Wittig, Diels-Alder, and olefin metathesis reactions have been also used. Multicomponent reactions such as the Grieco three-component assembly have been exploited for the synthesis of heterocycles. Cyclative cleavage from the solid support is particularly suitable for the synthesis of heterocycles while particular emphasis has been focused on the synthesis of libraries and the use of combinatorial chemistry techniques. In addition, the most relevant pharmacological properties of benzoannelated nitrogen heterocycles are included.
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Affiliation(s)
- Stefan Bräse
- Kekulé-Institut für Organische Chemie und Biochemie der Rheinischen Friedrich-Wilhelms-Universität Bonn, Gerhard-Domagk-Strasse 1, D-53121 Bonn, Germany.
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48
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Banfi L, Guanti G, Riva R, Basso A, Calcagno E. Short synthesis of protease inhibitors via modified Passerini condensation of N-Boc-α-aminoaldehydes. Tetrahedron Lett 2002. [DOI: 10.1016/s0040-4039(02)00728-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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49
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Khayat R, Batra R, Massariol MJ, Lagacé L, Tong L. Investigating the role of histidine 157 in the catalytic activity of human cytomegalovirus protease. Biochemistry 2001; 40:6344-51. [PMID: 11371196 DOI: 10.1021/bi010158b] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Herpesvirus proteases belong to a new class of serine proteases and contain a novel Ser-His-His catalytic triad, while classical serine proteases have an acidic residue as the third member. To gain a better understanding of the molecular basis for the functional role of the third-member His residue, we have carried out structural and biochemical investigations of human cytomegalovirus (HCMV) protease that bears mutations of the His157 third member. Kinetic studies showed that all the mutants have reduced catalytic activity. Structural studies revealed that a solvent molecule is hydrogen-bonded to the His63 second member and Ser134 in the H157A mutant, partly rescuing the activity of this mutant. This is confirmed by our kinetic and structural observations on the S134A/H157A double mutant, which showed further reductions in the catalytic activity. The structure of the H157A mutant is also in complex with the PMSF inhibitor. The H157E mutant has the best catalytic activity among the mutants; its structure, however, showed conformational readjustments of the His63 and Ser132 residues. The Ser132-His63 diad of HCMV protease has similar activity as the diads in classical serine proteases, whereas the contribution of the His157 third member to the catalysis is much smaller. Finally, structural comparisons revealed the presence of two conserved structural water molecules at the bottom of the S(1) pocket, suggesting a possible new direction for the design of HCMV protease inhibitors.
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Affiliation(s)
- R Khayat
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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50
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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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