1
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Albani S, Costanzi E, Hoang GL, Kuzikov M, Frings M, Ansari N, Demitri N, Nguyen TT, Rizzi V, Schulz JB, Bolm C, Zaliani A, Carloni P, Storici P, Rossetti G. Unexpected Single-Ligand Occupancy and Negative Cooperativity in the SARS-CoV-2 Main Protease. J Chem Inf Model 2024; 64:892-904. [PMID: 38051605 PMCID: PMC10865365 DOI: 10.1021/acs.jcim.3c01497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/20/2023] [Accepted: 11/20/2023] [Indexed: 12/07/2023]
Abstract
Many homodimeric enzymes tune their functions by exploiting either negative or positive cooperativity between subunits. In the SARS-CoV-2 Main protease (Mpro) homodimer, the latter has been suggested by symmetry in most of the 500 reported protease/ligand complex structures solved by macromolecular crystallography (MX). Here we apply the latter to both covalent and noncovalent ligands in complex with Mpro. Strikingly, our experiments show that the occupation of both active sites of the dimer originates from an excess of ligands. Indeed, cocrystals obtained using a 1:1 ligand/protomer stoichiometry lead to single occupation only. The empty binding site exhibits a catalytically inactive geometry in solution, as suggested by molecular dynamics simulations. Thus, Mpro operates through negative cooperativity with the asymmetric activity of the catalytic sites. This allows it to function with a wide range of substrate concentrations, making it resistant to saturation and potentially difficult to shut down, all properties advantageous for the virus' adaptability and resistance.
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Affiliation(s)
- Simone Albani
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich 52425, Germany
- Faculty
of Mathematics, Computer Science and Natural Sciences, RWTH Aachen, Aachen 52062, Germany
| | - Elisa Costanzi
- Elettra–Sincrotrone
Trieste S.C.p.A., SS 14 – km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Gia Linh Hoang
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
| | - Maria Kuzikov
- Fraunhofer
Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, Frankfurt 60590, Germany
- Constructor University, School of Science, Campus Ring 1, Bremen 28759, Germany
| | - Marcus Frings
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, Aachen 52074, Germany
| | - Narjes Ansari
- Atomistic
Simulations, Italian Institute of Technology, Via Enrico Melen, 83, 16152 Genova, Italy
| | - Nicola Demitri
- Elettra–Sincrotrone
Trieste S.C.p.A., SS 14 – km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Toan T. Nguyen
- Key
Laboratory for Multiscale Simulation of Complex Systems, and Department
of Theoretical Physics, Faculty of Physics, University of Science, Vietnam National University – Hanoi, 334 Nguyen Trai Street, Thanh Xuan, Hanoi 11400, Vietnam
| | - Valerio Rizzi
- School
of Pharmaceutical Sciences, University of
Geneva, Rue Michel Servet 1, 1206 Genève, Switzerland
| | - Jörg B. Schulz
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
- Department
of Neurology, Medical Faculty, RWTH Aachen
University, Aachen 52074, Germany
| | - Carsten Bolm
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, Aachen 52074, Germany
| | - Andrea Zaliani
- Fraunhofer
Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee 114, Hamburg 22525, Germany
- Fraunhofer
Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, Frankfurt 60590, Germany
| | - Paolo Carloni
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich 52425, Germany
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
- Key
Laboratory for Multiscale Simulation of Complex Systems, and Department
of Theoretical Physics, Faculty of Physics, University of Science, Vietnam National University – Hanoi, 334 Nguyen Trai Street, Thanh Xuan, Hanoi 11400, Vietnam
| | - Paola Storici
- Elettra–Sincrotrone
Trieste S.C.p.A., SS 14 – km 163, 5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Giulia Rossetti
- Institute
for Neuroscience and Medicine (INM-9), Forschungszentrum
Jülich, Jülich 52425, Germany
- JARA-Brain
Institute Molecular Neuroscience and Neuroimaging, Research Center Jülich GmbH, Jülich 52425, Germany
- RWTH
Aachen University, Aachen 52056, Germany
- Department
of Neurology, Medical Faculty, RWTH Aachen
University, Aachen 52074, Germany
- Jülich
Supercomputing Center (JSC), Forschungszentrum
Jülich, Jülich 52425, Germany
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2
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Pachota M, Grzywa R, Iwanejko J, Synowiec A, Iwan D, Kamińska K, Skoreński M, Bielecka E, Szczubialka K, Nowakowska M, Mackereth CD, Wojaczyńska E, Sieńczyk M, Pyrć K. Novel inhibitors of HSV-1 protease effective in vitro and in vivo. Antiviral Res 2023; 213:105604. [PMID: 37054954 DOI: 10.1016/j.antiviral.2023.105604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/06/2023] [Accepted: 04/10/2023] [Indexed: 04/15/2023]
Abstract
Herpes simplex virus type 1 (HSV-1) is a widespread human pathogen known to cause infections of diverse severity, ranging from mild ulceration of mucosal and dermal tissues to life-threatening viral encephalitis. In most cases, standard treatment with acyclovir is sufficient to manage the disease progression. However, the emergence of ACV-resistant strains drives the need for new therapeutics and molecular targets. HSV-1 VP24 is a protease indispensable for the assembly of mature virions and, as such, constitutes an interesting target for the therapy. In this study, we present novel compounds, KI207M and EWDI/39/55BF, that block the activity of VP24 protease and consequently inhibit HSV-1 infection in vitro and in vivo. The inhibitors were shown to prevent the egress of viral capsids from the cell nucleus and suppress the cell-to-cell spread of the infection. They were also proven effective against ACV-resistant HSV-1 strains. Considering their low toxicity and high antiviral potency, the novel VP24 inhibitors could provide an alternative for treating ACV-resistant infections or a drug to be used in combined, highly effective therapy.
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Affiliation(s)
- Magdalena Pachota
- Virogenetics Laboratory of Virology, Małopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Kraków, Poland; Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Renata Grzywa
- Department of Organic and Medicinal Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspianskiego 27, 50-370, Wrocław, Poland
| | - Jakub Iwanejko
- Department of Physical and Quantum Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspianskiego 27, 50-370, Wrocław, Poland
| | - Aleksandra Synowiec
- Virogenetics Laboratory of Virology, Małopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Kraków, Poland
| | - Dominika Iwan
- Department of Physical and Quantum Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspianskiego 27, 50-370, Wrocław, Poland
| | - Karolina Kamińska
- Department of Physical and Quantum Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspianskiego 27, 50-370, Wrocław, Poland
| | - Marcin Skoreński
- Department of Organic and Medicinal Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspianskiego 27, 50-370, Wrocław, Poland
| | - Ewa Bielecka
- Laboratory of Proteolysis and Post-translational Modification of Proteins, Małopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Kraków, Poland
| | - Krzysztof Szczubialka
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Kraków, Poland
| | - Maria Nowakowska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Kraków, Poland
| | - Cameron D Mackereth
- Univ. Bordeaux, Inserm U1212, CNRS UMR 5320, ARNA Laboratory, IECB, 33706, Pessac, France
| | - Elżbieta Wojaczyńska
- Department of Physical and Quantum Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspianskiego 27, 50-370, Wrocław, Poland.
| | - Marcin Sieńczyk
- Department of Organic and Medicinal Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspianskiego 27, 50-370, Wrocław, Poland.
| | - Krzysztof Pyrć
- Virogenetics Laboratory of Virology, Małopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Kraków, Poland.
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3
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Viral proteases as therapeutic targets. Mol Aspects Med 2022; 88:101159. [PMID: 36459838 PMCID: PMC9706241 DOI: 10.1016/j.mam.2022.101159] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 11/30/2022]
Abstract
Some medically important viruses-including retroviruses, flaviviruses, coronaviruses, and herpesviruses-code for a protease, which is indispensable for viral maturation and pathogenesis. Viral protease inhibitors have become an important class of antiviral drugs. Development of the first-in-class viral protease inhibitor saquinavir, which targets HIV protease, started a new era in the treatment of chronic viral diseases. Combining several drugs that target different steps of the viral life cycle enables use of lower doses of individual drugs (and thereby reduction of potential side effects, which frequently occur during long term therapy) and reduces drug-resistance development. Currently, several HIV and HCV protease inhibitors are routinely used in clinical practice. In addition, a drug including an inhibitor of SARS-CoV-2 main protease, nirmatrelvir (co-administered with a pharmacokinetic booster ritonavir as Paxlovid®), was recently authorized for emergency use. This review summarizes the basic features of the proteases of human immunodeficiency virus (HIV), hepatitis C virus (HCV), and SARS-CoV-2 and discusses the properties of their inhibitors in clinical use, as well as development of compounds in the pipeline.
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4
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Preußke N, Lipfert M, Rothemund S, Leippe M, Sönnichsen FD. Designed Trp-Cage Proteins with Antimicrobial Activity and Enhanced Stability. Biochemistry 2021; 60:3187-3199. [PMID: 34613690 DOI: 10.1021/acs.biochem.1c00567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
α-Helical antimicrobial peptides (αAMPs) are among the potential candidates for new anti-infectives to tackle the global crisis in antibiotic resistance, but they suffer from low bioavailability due to high susceptibility to enzymatic degradation. Here, we describe a strategy to increase the resistance of αAMPs against proteases. Fusing the 12-residue αAMP KR-12 with a Trp-cage domain induces an α-helical structure in the otherwise unfolded KR-12 moiety in solution. The resulting antimicrobial Trp-cage exhibits higher proteolytic resistance due to its stable fold as evidenced by correlating sequence-resolved digest data with structural analyses. In addition, the antimicrobial Trp-cage displays increased activity against bacteria in the presence of physiologically relevant concentrations of NaCl, while the hemolytic activity remains negligible. In contrast to previous strategies, the presented approach is not reliant on artificial amino acids and is therefore applicable to biosynthetic procedures. Our study aims to improve the pharmacokinetics of αAMPs to facilitate their use as therapeutics.
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Affiliation(s)
- Nils Preußke
- Otto Diels Institute for Organic Chemistry, Kiel University, Otto-Hahn-Platz 3-5, 24118 Kiel, Germany.,Zoological Institute, Kiel University, Am Botanischen Garten 3-9, 24118 Kiel, Germany
| | - Matthias Lipfert
- Otto Diels Institute for Organic Chemistry, Kiel University, Otto-Hahn-Platz 3-5, 24118 Kiel, Germany
| | - Sven Rothemund
- Faculty of Medicine, University of Leipzig, Liebigstraße 21, 04103 Leipzig, Germany
| | - Matthias Leippe
- Zoological Institute, Kiel University, Am Botanischen Garten 3-9, 24118 Kiel, Germany
| | - Frank D Sönnichsen
- Otto Diels Institute for Organic Chemistry, Kiel University, Otto-Hahn-Platz 3-5, 24118 Kiel, Germany
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5
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Nguyen D, Abdullin D, Heubach CA, Pfaffeneder T, Nguyen A, Heine A, Reuter K, Diederich F, Schiemann O, Klebe G. Entschlüsselung der ligandeninduzierten Verdrehung eines homodimeren Enzyms mit Hilfe der gepulsten Elektron‐Elektron‐Doppelresonanz‐Spektroskopie. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202108179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Dzung Nguyen
- Institut für Pharmazeutische Chemie Philipps-Universität Marburg Marbacher Weg 8 35032 Marburg Deutschland
| | - Dinar Abdullin
- Institut für Physikalische und Theoretische Chemie Rheinische Friedrich-Wilhelms-Universität Bonn Wegelerstr. 12 53115 Bonn Deutschland
| | - Caspar A. Heubach
- Institut für Physikalische und Theoretische Chemie Rheinische Friedrich-Wilhelms-Universität Bonn Wegelerstr. 12 53115 Bonn Deutschland
| | - Toni Pfaffeneder
- Laboratorium für Organische Chemie ETH Zürich Vladimir-Prelog-Weg 3, HCI 8093 Zürich Schweiz
| | - Andreas Nguyen
- Institut für Pharmazeutische Chemie Philipps-Universität Marburg Marbacher Weg 8 35032 Marburg Deutschland
| | - Andreas Heine
- Institut für Pharmazeutische Chemie Philipps-Universität Marburg Marbacher Weg 8 35032 Marburg Deutschland
| | - Klaus Reuter
- Institut für Pharmazeutische Chemie Philipps-Universität Marburg Marbacher Weg 8 35032 Marburg Deutschland
| | - François Diederich
- Laboratorium für Organische Chemie ETH Zürich Vladimir-Prelog-Weg 3, HCI 8093 Zürich Schweiz
| | - Olav Schiemann
- Institut für Physikalische und Theoretische Chemie Rheinische Friedrich-Wilhelms-Universität Bonn Wegelerstr. 12 53115 Bonn Deutschland
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie Philipps-Universität Marburg Marbacher Weg 8 35032 Marburg Deutschland
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6
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Precursors of Viral Proteases as Distinct Drug Targets. Viruses 2021; 13:v13101981. [PMID: 34696411 PMCID: PMC8537868 DOI: 10.3390/v13101981] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/25/2021] [Accepted: 09/28/2021] [Indexed: 12/16/2022] Open
Abstract
Viral proteases are indispensable for successful virion maturation, thus making them a prominent drug target. Their enzyme activity is tightly spatiotemporally regulated by expression in the precursor form with little or no activity, followed by activation via autoprocessing. These cleavage events are frequently triggered upon transportation to a specific compartment inside the host cell. Typically, precursor oligomerization or the presence of a co-factor is needed for activation. A detailed understanding of these mechanisms will allow ligands with non-canonical mechanisms of action to be designed, which would specifically modulate the initial irreversible steps of viral protease autoactivation. Binding sites exclusive to the precursor, including binding sites beyond the protease domain, can be exploited. Both inhibition and up-regulation of the proteolytic activity of viral proteases can be detrimental for the virus. All these possibilities are discussed using examples of medically relevant viruses including herpesviruses, adenoviruses, retroviruses, picornaviruses, caliciviruses, togaviruses, flaviviruses, and coronaviruses.
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7
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Klebe G, Nguyen D, Abdullin D, Heubach CA, Pfaffeneder T, Nguyen A, Heine A, Reuter K, Diederich F, Schiemann O. Unraveling a ligand-induced twist of a homodimeric enzyme by pulsed electron-electron double resonance. Angew Chem Int Ed Engl 2021; 60:23419-23426. [PMID: 34387025 PMCID: PMC8597004 DOI: 10.1002/anie.202108179] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Indexed: 11/30/2022]
Abstract
Mechanistic insights into protein–ligand interactions can yield chemical tools for modulating protein function and enable their use for therapeutic purposes. For the homodimeric enzyme tRNA‐guanine transglycosylase (TGT), a putative virulence target of shigellosis, ligand binding has been shown by crystallography to transform the functional dimer geometry into an incompetent twisted one. However, crystallographic observation of both end states does neither verify the ligand‐induced transformation of one dimer into the other in solution nor does it shed light on the underlying transformation mechanism. We addressed these questions in an approach that combines site‐directed spin labeling (SDSL) with distance measurements based on pulsed electron–electron double resonance (PELDOR or DEER) spectroscopy. We observed an equilibrium between the functional and twisted dimer that depends on the type of ligand, with a pyranose‐substituted ligand being the most potent one in shifting the equilibrium toward the twisted dimer. Our experiments suggest a dissociation–association mechanism for the formation of the twisted dimer upon ligand binding.
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Affiliation(s)
- Gerhard Klebe
- Univ. of Marburg, Inst. Pharmaceut. Chem., Marbacher Weg 6, D35032, Marburg, GERMANY
| | - Dzung Nguyen
- Philipps-Universität Marburg: Philipps-Universitat Marburg, Pharmaceutical Chemistry, GERMANY
| | - Dinar Abdullin
- Universität Bonn: Rheinische Friedrich-Wilhelms-Universitat Bonn, Physical and Theoretical Chemistry, GERMANY
| | - Caspar A Heubach
- Universität Bonn: Rheinische Friedrich-Wilhelms-Universitat Bonn, Physical and Theoretical Chemistry, GERMANY
| | - Toni Pfaffeneder
- ETH-Zürich LOC: Eidgenossische Technische Hochschule Zurich Laboratorium fur Organische Chemie, Organic Chemistry, SWITZERLAND
| | - Andreas Nguyen
- Philipps-Universität Marburg: Philipps-Universitat Marburg, Pharmaceutical Chemistry, GERMANY
| | - Andreas Heine
- Philipps-Universität Marburg: Philipps-Universitat Marburg, Pharmaceutical Chemistry, GERMANY
| | - Klaus Reuter
- Philipps-Universität Marburg: Philipps-Universitat Marburg, Pharmaceutical Chemistry, GERMANY
| | - Francois Diederich
- ETH Zurich Department of Chemistry and Applied Biosciences: Eidgenossische Technische Hochschule Zurich Departement Chemie und Angewandte Biowissenschaften, Organic Chemistry, SWITZERLAND
| | - Olav Schiemann
- Universität Bonn: Rheinische Friedrich-Wilhelms-Universitat Bonn, Physical and Theoretical Chemistry, GERMANY
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8
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Ghassabian H, Falchi F, Timmoneri M, Mercorelli B, Loregian A, Palù G, Alvisi G. Divide et impera: An In Silico Screening Targeting HCMV ppUL44 Processivity Factor Homodimerization Identifies Small Molecules Inhibiting Viral Replication. Viruses 2021; 13:v13050941. [PMID: 34065234 PMCID: PMC8160850 DOI: 10.3390/v13050941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 12/19/2022] Open
Abstract
Human cytomegalovirus (HCMV) is a leading cause of severe diseases in immunocompromised individuals, including AIDS patients and transplant recipients, and in congenitally infected newborns. The utility of available drugs is limited by poor bioavailability, toxicity, and emergence of resistant strains. Therefore, it is crucial to identify new targets for therapeutic intervention. Among the latter, viral protein–protein interactions are becoming increasingly attractive. Since dimerization of HCMV DNA polymerase processivity factor ppUL44 plays an essential role in the viral life cycle, being required for oriLyt-dependent DNA replication, it can be considered a potential therapeutic target. We therefore performed an in silico screening and selected 18 small molecules (SMs) potentially interfering with ppUL44 homodimerization. Antiviral assays using recombinant HCMV TB4-UL83-YFP in the presence of the selected SMs led to the identification of four active compounds. The most active one, B3, also efficiently inhibited HCMV AD169 strain in plaque reduction assays and impaired replication of an AD169-GFP reporter virus and its ganciclovir-resistant counterpart to a similar extent. As assessed by Western blotting experiments, B3 specifically reduced viral gene expression starting from 48 h post infection, consistent with the inhibition of viral DNA synthesis measured by qPCR starting from 72 h post infection. Therefore, our data suggest that inhibition of ppUL44 dimerization could represent a new class of HCMV inhibitors, complementary to those targeting the DNA polymerase catalytic subunit or the viral terminase complex.
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Affiliation(s)
- Hanieh Ghassabian
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy; (H.G.); (M.T.); (B.M.); (A.L.); (G.P.)
| | | | - Martina Timmoneri
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy; (H.G.); (M.T.); (B.M.); (A.L.); (G.P.)
| | - Beatrice Mercorelli
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy; (H.G.); (M.T.); (B.M.); (A.L.); (G.P.)
| | - Arianna Loregian
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy; (H.G.); (M.T.); (B.M.); (A.L.); (G.P.)
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy; (H.G.); (M.T.); (B.M.); (A.L.); (G.P.)
| | - Gualtiero Alvisi
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy; (H.G.); (M.T.); (B.M.); (A.L.); (G.P.)
- Correspondence:
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9
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Tsurumi S, Watanabe T, Iwaisako Y, Suzuki Y, Nakano T, Fujimuro M. Kaposi's sarcoma-associated herpesvirus ORF17 plays a key role in capsid maturation. Virology 2021; 558:76-85. [PMID: 33735753 DOI: 10.1016/j.virol.2021.02.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 02/12/2021] [Accepted: 02/19/2021] [Indexed: 01/04/2023]
Abstract
Kaposi's sarcoma-associated herpesvirus is a human rhadinovirus of the gammaherpesvirus sub-family. Although herpesviruses are well-studied models of capsid formation and its processes, those of KSHV remain unknown. KSHV ORF17 encoding the viral protease precursor (ORF17-prePR) is thought to contribute to capsid formation; however, functional information is largely unknown. Here, we evaluated the role of ORF17 during capsid formation by generating ORF17-deficient and ORF17 protease-dead KSHV. Both mutants showed a decrease in viral production but not DNA replication. ORF17 R-mut, with a point-mutation at the restriction or release site (R-site) by which ORF17-prePR can be functionally cleaved into a protease (ORF17-PR) and an assembly region (ORF17-pAP/-AP), failed to play a role in viral production. Furthermore, wild type KSHV produced a mature capsid, whereas ORF17-deficient and protease-dead KSHV produced a B-capsid, (i.e., a closed body possessing a circular inner structure). Therefore, ORF17 and its protease function are essential for appropriate capsid maturation.
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Affiliation(s)
- Sayaka Tsurumi
- Department of Cell Biology, Kyoto Pharmaceutical University, 1 Misasagi-Shichono, Yamashina, Kyoto, 607-8412, Japan
| | - Tadashi Watanabe
- Department of Cell Biology, Kyoto Pharmaceutical University, 1 Misasagi-Shichono, Yamashina, Kyoto, 607-8412, Japan; Department of Virology, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara, Nakagami, Okinawa, 903-0215, Japan
| | - Yuki Iwaisako
- Department of Cell Biology, Kyoto Pharmaceutical University, 1 Misasagi-Shichono, Yamashina, Kyoto, 607-8412, Japan
| | - Youichi Suzuki
- Department of Microbiology and Infection Control, Osaka Medical College, 2-7 Daigaku-machi, Takatsuki, Osaka, 569-8686, Japan
| | - Takashi Nakano
- Department of Microbiology and Infection Control, Osaka Medical College, 2-7 Daigaku-machi, Takatsuki, Osaka, 569-8686, Japan
| | - Masahiro Fujimuro
- Department of Cell Biology, Kyoto Pharmaceutical University, 1 Misasagi-Shichono, Yamashina, Kyoto, 607-8412, Japan.
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10
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Targeting protein self-association in drug design. Drug Discov Today 2021; 26:1148-1163. [PMID: 33548462 DOI: 10.1016/j.drudis.2021.01.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/24/2020] [Accepted: 01/26/2021] [Indexed: 01/05/2023]
Abstract
Protein self-association is a universal phenomenon essential for stability and molecular recognition. Disrupting constitutive homomers constitutes an original and emerging strategy in drug design. Inhibition of homomeric proteins can be achieved through direct complex disruption, subunit intercalation, or by promoting inactive oligomeric states. Targeting self-interaction grants several advantages over active site inhibition because of the stimulation of protein degradation, the enhancement of selectivity, substoichiometric inhibition, and by-pass of compensatory mechanisms. This new landscape in protein inhibition is driven by the development of biophysical and biochemical tools suited for the study of homomeric proteins, such as differential scanning fluorimetry (DSF), native mass spectrometry (MS), Förster resonance energy transfer (FRET) spectroscopy, 2D nuclear magnetic resonance (NMR), and X-ray crystallography. In this review, we discuss the different aspects of this new paradigm in drug design.
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11
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Raza S, Abbas G, Azam SS. Screening Pipeline for Flavivirus Based Inhibitors for Zika Virus NS1. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020; 17:1751-1761. [PMID: 30990437 DOI: 10.1109/tcbb.2019.2911081] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In-silico pipeline is applied for identifying and designing novel inhibitors against ZIKV NS1 protein. Comparative molecular docking studies are performed to explore the binding of structurally diverse compounds to ZIKV NS1 by AutoDock/Vina and GOLD. The Zika virus (ZIKV) is a flavivirus, responsible for life-threatening infections and transmitted by Aedes mosquitoes in other organisms. It is associated with Guillain Barre Syndrome (GBS) and microcephaly. This epidemic increase in GBS and microcephaly convoyed the World Health Organization to affirm ZIKV a public health crisis. To combat the ZIKV infections, non-structural protein 1 (NS1), a major host-interaction molecule contributing towards replication, pathogenesis and immune evasion is targeted in the current study. For this purpose, a comprehensive study is required to develop potential novel antiviral inhibitors. Three compounds were identified through docking programs exhibiting properties which are non-toxic to human host and could inhibit the elusive ZIKV. Significant interaction with active site residues and H-bond interactions with the key residues were analyzed for these compounds using molecular dynamics simulation. Free energy calculation predicted higher affinity of Deoxycalyxin-A for ZIKV NS1. This study contributes towards fighting ZIKV infections and can help researchers in designing drug for the treatment of ZIKV.
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12
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Tang A, Caballero AR, Marquart ME, Bierdeman MA, O'Callaghan RJ. Mechanism of Pseudomonas aeruginosa Small Protease (PASP), a Corneal Virulence Factor. Invest Ophthalmol Vis Sci 2019; 59:5993-6002. [PMID: 30572344 PMCID: PMC6306078 DOI: 10.1167/iovs.18-25834] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose Pseudomonas aeruginosa is the leading cause of contact lens-associated bacterial keratitis. Secreted bacterial proteases have a key role in keratitis, including the P. aeruginosa small protease (PASP), a proven corneal virulence factor. We investigated the mechanism of PASP and its importance to corneal toxicity. Methods PASP, a serine protease, was tested for activity on various substrates. The catalytic triad of PASP was sought by bioinformatic analysis and site-directed mutagenesis. All mutant constructs were expressed in a P. aeruginosa PASP-deficient strain; the resulting proteins were purified using ion-exchange, gel filtration, or affinity chromatography; and the proteolytic activity was assessed by gelatin zymography and a fluorometric assay. The purified PASP proteins with single amino acid changes were injected into rabbit corneas to determine their pathological effects. Results PASP substrates were cleaved at arginine or lysine residues. Alanine substitution of PASP residues Asp-29, His-34, or Ser-47 eliminated protease activity, whereas PASP with substitution for Ser-59 (control) retained activity. Computer modeling and Western blot analysis indicated that formation of a catalytic triad required dimer formation, and zymography demonstrated the protease activity of the homodimer, but not the monomer. PASP with the Ser-47 mutation, but not with the control mutation, lacked corneal toxicity, indicating the importance of protease activity. Conclusions PASP is a secreted serine protease that can cleave proteins at arginine or lysine residues and PASP activity requires dimer or larger aggregates to create a functional active site. Most importantly, proteolytic PASP molecules demonstrated highly significant toxicity for the rabbit cornea.
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Affiliation(s)
- Aihua Tang
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi, United States
| | - Armando R Caballero
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi, United States
| | - Mary E Marquart
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi, United States
| | - Michael A Bierdeman
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi, United States
| | - Richard J O'Callaghan
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi, United States
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13
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GII.4 Norovirus Protease Shows pH-Sensitive Proteolysis with a Unique Arg-His Pairing in the Catalytic Site. J Virol 2019; 93:JVI.01479-18. [PMID: 30626675 DOI: 10.1128/jvi.01479-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 12/17/2018] [Indexed: 11/20/2022] Open
Abstract
Human noroviruses (NoVs) are the main cause of epidemic and sporadic gastroenteritis. Phylogenetically, noroviruses are divided into seven genogroups, with each divided into multiple genotypes. NoVs belonging to genogroup II and genotype 4 (GII.4) are globally most prevalent. Genetic diversity among the NoVs and the periodic emergence of novel strains present a challenge for the development of vaccines and antivirals to treat NoV infection. NoV protease is essential for viral replication and is an attractive target for the development of antivirals. The available structure of GI.1 protease provided a basis for the design of inhibitors targeting the active site of the protease. These inhibitors, although potent against the GI proteases, poorly inhibit the GII proteases, for which structural information is lacking. To elucidate the structural basis for this difference in the inhibitor efficiency, we determined the crystal structure of a GII.4 protease. The structure revealed significant changes in the S2 substrate-binding pocket, making it noticeably smaller, and in the active site, with the catalytic triad residues showing conformational changes. Furthermore, a conserved arginine is found inserted into the active site, interacting with the catalytic histidine and restricting substrate/inhibitor access to the S2 pocket. This interaction alters the relationships between the catalytic residues and may allow for a pH-dependent regulation of protease activity. The changes we observed in the GII.4 protease structure may explain the reduced potency of the GI-specific inhibitors against the GII protease and therefore must be taken into account when designing broadly cross-reactive antivirals against NoVs.IMPORTANCE Human noroviruses (NoVs) cause sporadic and epidemic gastroenteritis worldwide. They are divided into seven genogroups (GI to GVII), with each genogroup further divided into several genotypes. Human NoVs belonging to genogroup II and genotype 4 (GII.4) are the most prevalent. Currently, there are no vaccines or antiviral drugs available for NoV infection. The protease encoded by NoV is considered a valuable target because of its essential role in replication. NoV protease structures have only been determined for the GI genogroup. We show here that the structure of the GII.4 protease exhibits several significant changes from GI proteases, including a unique pairing of an arginine with the catalytic histidine that makes the proteolytic activity of GII.4 protease pH sensitive. A comparative analysis of NoV protease structures may provide a rational framework for structure-based drug design of broadly cross-reactive inhibitors targeting NoVs.
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Boukadida C, Fritz M, Blumen B, Fogeron ML, Penin F, Martin A. NS2 proteases from hepatitis C virus and related hepaciviruses share composite active sites and previously unrecognized intrinsic proteolytic activities. PLoS Pathog 2018; 14:e1006863. [PMID: 29415072 PMCID: PMC5819835 DOI: 10.1371/journal.ppat.1006863] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 02/20/2018] [Accepted: 01/08/2018] [Indexed: 12/17/2022] Open
Abstract
Over the recent years, several homologues with varying degrees of genetic relatedness to hepatitis C virus (HCV) have been identified in a wide range of mammalian species. HCV infectious life cycle relies on a first critical proteolytic event of its single polyprotein, which is carried out by nonstructural protein 2 (NS2) and allows replicase assembly and genome replication. In this study, we characterized and evaluated the conservation of the proteolytic mode of action and regulatory mechanisms of NS2 across HCV and animal hepaciviruses. We first demonstrated that NS2 from equine, bat, rodent, New and Old World primate hepaciviruses also are cysteine proteases. Using tagged viral protein precursors and catalytic triad mutants, NS2 of equine NPHV and simian GBV-B, which are the most closely and distantly related viruses to HCV, respectively, were shown to function, like HCV NS2 as dimeric proteases with two composite active sites. Consistent with the reported essential role for NS3 N-terminal domain (NS3N) as HCV NS2 protease cofactor via NS3N key hydrophobic surface patch, we showed by gain/loss of function mutagenesis studies that some heterologous hepacivirus NS3N may act as cofactors for HCV NS2 provided that HCV-like hydrophobic residues are conserved. Unprecedently, however, we also observed efficient intrinsic proteolytic activity of NS2 protease in the absence of NS3 moiety in the context of C-terminal tag fusions via flexible linkers both in transiently transfected cells for all hepaciviruses studied and in the context of HCV dicistronic full-length genomes. These findings suggest that NS3N acts as a regulatory rather than essential cofactor for hepacivirus NS2 protease. Overall, unique features of NS2 including enzymatic function as dimers with two composite active sites and additional NS3-independent proteolytic activity are conserved across hepaciviruses regardless of their genetic distances, highlighting their functional significance in hepacivirus life cycle. Despite remarkable progress in the development of therapeutic options, more than 70 million individuals are chronically infected by hepatitis C virus (HCV) worldwide and major challenges in basic and translational research remain. Phylogenetically-related HCV homologues have recently been identified in the wild in several mammalian species, whose host restriction and potential for zoonosis remain largely unknown. We comparatively characterized the functions and properties of nonstructural proteins 2 (NS2) from several animal hepaciviruses and HCV. We demonstrated that NS2 from animal hepaciviruses, like HCV NS2, are cysteine proteases, which function as dimers with two composite active sites to ensure a key proteolytic event of the single viral polyprotein at the NS2/NS3 junction. In addition to the activation of HCV NS2 protease by NS3 N-terminal domain, our data revealed a novel NS3-independent substrate specificity and efficient intrinsic proteolytic activity of NS2. The conservation of its properties and peculiar mode of action among distantly related hepaciviruses supports an important regulatory role for NS2 protein in the life cycle of these viruses. It also strengthens the value of animal, notably rodent hepaciviruses for the development of surrogate, immunocompetent models of HCV infection to address HCV-associated pathogenesis and vaccine strategies.
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Affiliation(s)
- Célia Boukadida
- Institut Pasteur, Unité de Génétique Moléculaire des Virus à ARN, Paris, France
- CNRS UMR 3569, Paris, France
- Université Paris Diderot–Sorbonne Paris Cité, Paris, France
| | - Matthieu Fritz
- Institut Pasteur, Unité de Génétique Moléculaire des Virus à ARN, Paris, France
- CNRS UMR 3569, Paris, France
- Université Paris Diderot–Sorbonne Paris Cité, Paris, France
| | - Brigitte Blumen
- Institut Pasteur, Unité de Génétique Moléculaire des Virus à ARN, Paris, France
- CNRS UMR 3569, Paris, France
- Université Paris Diderot–Sorbonne Paris Cité, Paris, France
| | - Marie-Laure Fogeron
- Institut de Biologie et Chimie des Protéines, Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, Lyon, France
| | - François Penin
- Institut de Biologie et Chimie des Protéines, Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, Lyon, France
| | - Annette Martin
- Institut Pasteur, Unité de Génétique Moléculaire des Virus à ARN, Paris, France
- CNRS UMR 3569, Paris, France
- Université Paris Diderot–Sorbonne Paris Cité, Paris, France
- * E-mail:
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15
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Shen Q, Zhang C, Liu H, Liu Y, Cao J, Zhang X, Liang Y, Zhao M, Lai L. De novo design of helical peptides to inhibit tumor necrosis factor-α by disrupting its trimer formation. MEDCHEMCOMM 2016. [DOI: 10.1039/c5md00549c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Helical peptide TNFα inhibitors were designed by targeting their dimer structure.
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Affiliation(s)
- Qi Shen
- Center for Quantitative Biology
- Peking University
- Beijing 100871
- China
| | - Changsheng Zhang
- BNLMS
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, and Peking-Tsinghua Center for Life Sciences
- Peking University
- Beijing 100871
- China
| | - Hongbo Liu
- BNLMS
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, and Peking-Tsinghua Center for Life Sciences
- Peking University
- Beijing 100871
- China
| | - Yuting Liu
- BNLMS
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
- China
| | - Junyue Cao
- School of Life Sciences
- Peking University
- Beijing 100871
- China
| | - Xiaolin Zhang
- Center for Quantitative Biology
- Peking University
- Beijing 100871
- China
| | - Yuan Liang
- BNLMS
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
- China
| | - Meiping Zhao
- BNLMS
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
- China
| | - Luhua Lai
- Center for Quantitative Biology
- Peking University
- Beijing 100871
- China
- BNLMS
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16
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Soner S, Ozbek P, Garzon JI, Ben-Tal N, Haliloglu T. DynaFace: Discrimination between Obligatory and Non-obligatory Protein-Protein Interactions Based on the Complex's Dynamics. PLoS Comput Biol 2015; 11:e1004461. [PMID: 26506003 PMCID: PMC4623975 DOI: 10.1371/journal.pcbi.1004461] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 07/08/2015] [Indexed: 12/31/2022] Open
Abstract
Protein-protein interfaces have been evolutionarily-designed to enable transduction between the interacting proteins. Thus, we hypothesize that analysis of the dynamics of the complex can reveal details about the nature of the interaction, and in particular whether it is obligatory, i.e., persists throughout the entire lifetime of the proteins, or not. Indeed, normal mode analysis, using the Gaussian network model, shows that for the most part obligatory and non-obligatory complexes differ in their decomposition into dynamic domains, i.e., the mobile elements of the protein complex. The dynamic domains of obligatory complexes often mix segments from the interacting chains, and the hinges between them do not overlap with the interface between the chains. In contrast, in non-obligatory complexes the interface often hinges between dynamic domains, held together through few anchor residues on one side of the interface that interact with their counterpart grooves in the other end. In automatic analysis, 117 of 139 obligatory (84.2%) and 203 of 246 non-obligatory (82.5%) complexes are correctly classified by our method: DynaFace. We further use DynaFace to predict obligatory and non-obligatory interactions among a set of 300 putative protein complexes. DynaFace is available at: http://safir.prc.boun.edu.tr/dynaface.
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Affiliation(s)
- Seren Soner
- Department of Computer Engineering and Polymer Research Center, Bogazici University, Istanbul, Turkey
| | - Pemra Ozbek
- Department of Bioengineering, Marmara University, Istanbul, Turkey
| | - Jose Ignacio Garzon
- Departments of Biochemistry and Molecular Biophysics and Systems Biology and Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America
| | - Nir Ben-Tal
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Turkan Haliloglu
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, Istanbul, Turkey
- * E-mail:
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17
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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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18
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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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19
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Uversky VN, Davé V, Iakoucheva LM, Malaney P, Metallo SJ, Pathak RR, Joerger AC. Pathological unfoldomics of uncontrolled chaos: intrinsically disordered proteins and human diseases. Chem Rev 2014; 114:6844-79. [PMID: 24830552 PMCID: PMC4100540 DOI: 10.1021/cr400713r] [Citation(s) in RCA: 196] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute University of South Florida, Tampa, Florida 33612, United States
- Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 22254, Saudi Arabia
| | - Vrushank Davé
- Department of Pathology and Cell Biology , Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, United States
| | - Lilia M. Iakoucheva
- Department of Psychiatry, University of California San Diego, La Jolla, California 92093, United States
| | - Prerna Malaney
- Department of Pathology and Cell Biology , Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Steven J. Metallo
- Department of Chemistry, Georgetown University, Washington, District of Columbia 20057, United States
| | - Ravi Ramesh Pathak
- Department of Pathology and Cell Biology , Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Andreas C. Joerger
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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20
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Huber K, Ghosh S, Hardy JA. Inhibition of caspase-9 by stabilized peptides targeting the dimerization interface. Biopolymers 2012; 98:451-65. [PMID: 23203690 PMCID: PMC3544179 DOI: 10.1002/bip.22080] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 03/29/2012] [Accepted: 04/04/2012] [Indexed: 11/09/2022]
Abstract
Caspases comprise a family of dimeric cysteine proteases that control apoptotic programmed cell death and are therefore critical in both organismal development and disease. Specific inhibition of individual caspases has been repeatedly attempted, but has not yet been attained. Caspase-9 is an upstream or initiator caspase that is regulated differently from all other caspases, as interaction with natural inhibitor X-linked inhibitor of apoptosis protein (XIAP)-baculovirus inhibitory repeat 3 (BIR3) occurs at the dimer interface maintaining caspase-9 in an inactive monomeric state. One route to caspase-9-specific inhibition is to mimic this interaction, which has been localized to the α5 helix of XIAP-BIR3. We have developed three types of stabilized peptides derived from the α5 helix, using incorporation of aminoisobutyric acid, the avian pancreatic polypeptide (aPP)-scaffold or aliphatic staples. The stabilized peptides are helical in solution and achieve up to 32 μM inhibition, indicating that this allosteric site at the caspase-9 dimerization interface is regulatable with low-molecular weight synthetic ligands and is thus a druggable site. The most potent peptides against caspase-9 activity are the aPP-scaffolded peptides. Other caspases, which are not regulated by dimerization, should not be inactivated by these peptides. Given that all of the peptides attain helical structures but cannot recapitulate the high-affinity inhibition of the intact BIR3 domain, it has become clear that interactions of caspase-9 with the BIR3 exosite are essential for high-affinity binding. These results explain why the full XIAP-BIR3 domain is required for maximal inhibition and suggest a path forward for achieving allosteric inhibition at the dimerization interface using peptides or small molecules.
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Affiliation(s)
- Kristen Huber
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003
| | | | - Jeanne A. Hardy
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003
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21
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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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22
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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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23
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Affiliation(s)
- Christopher J Farady
- Graduate Group in Biophysics, University of California-San Francisco, San Francisco, CA 94143-2240, USA
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24
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Shen A. Allosteric regulation of protease activity by small molecules. MOLECULAR BIOSYSTEMS 2010; 6:1431-43. [PMID: 20539873 DOI: 10.1039/c003913f] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Proteases regulate a plethora of biological processes. Because they irreversibly cleave peptide bonds, the activity of proteases is strictly controlled. While there are many ways to regulate protease activity, an emergent mechanism is the modulation of protease function by small molecules acting at allosteric sites. This mode of regulation holds the potential to allow for the specific and temporal control of a given biological process using small molecules. These compounds also serve as useful tools for studying protein dynamics and function. This review highlights recent advances in identifying and characterizing natural and synthetic small molecule allosteric regulators of proteases and discusses their utility in studies of protease function, drug discovery and protein engineering.
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Affiliation(s)
- Aimee Shen
- Department of Pathology, Stanford School of Medicine, Stanford, California 94305, USA.
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25
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Current and Novel Inhibitors of HIV Protease. Viruses 2009; 1:1209-39. [PMID: 21994591 PMCID: PMC3185513 DOI: 10.3390/v1031209] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2009] [Revised: 12/07/2009] [Accepted: 12/07/2009] [Indexed: 12/25/2022] Open
Abstract
The design, development and clinical success of HIV protease inhibitors represent one of the most remarkable achievements of molecular medicine. This review describes all nine currently available FDA-approved protease inhibitors, discusses their pharmacokinetic properties, off-target activities, side-effects, and resistance profiles. The compounds in the various stages of clinical development are also introduced, as well as alternative approaches, aiming at other functional domains of HIV PR. The potential of these novel compounds to open new way to the rational drug design of human viruses is critically assessed.
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26
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Huber KL, Olson KD, Hardy JA. Robust production of a peptide library using methodological synchronization. Protein Expr Purif 2009; 67:139-47. [PMID: 19457455 PMCID: PMC2758701 DOI: 10.1016/j.pep.2009.05.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Revised: 05/05/2009] [Accepted: 05/08/2009] [Indexed: 01/26/2023]
Abstract
Peptide libraries have proven to be useful in applications such as substrate profiling, drug candidate screening and identifying protein-protein interaction partners. However, issues of fidelity, peptide length, and purity have been encountered when peptide libraries are chemically synthesized. Biochemically produced libraries, on the other hand, circumvent many of these issues due to the fidelity of the protein synthesis machinery. Using thioredoxin as an expression partner, a stably folded peptide scaffold (avian pancreatic polypeptide) and a compatible cleavage site for human rhinovirus 3C protease, we report a method that allows robust expression of a genetically encoded peptide library, which yields peptides of high purity. In addition, we report the use of methodological synchronization, an experimental design created for the production of a library, from initial cloning to peptide characterization, within a 5-week period of time. Total peptide yields ranged from 0.8% to 16%, which corresponds to 2-70 mg of pure peptide. Additionally, no correlation was observed between the ability to be expressed or overall yield of peptide-fusions and the intrinsic chemical characteristics of the peptides, indicating that this system can be used for a wide variety of peptide sequences with a range of chemical characteristics.
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Affiliation(s)
- Kristen L Huber
- Chemistry Department, University of Massachusetts at Amherst, Amherst, MA 01003, USA
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27
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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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28
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Lim MD, Craik CS. Using specificity to strategically target proteases. Bioorg Med Chem 2009; 17:1094-100. [PMID: 18434168 PMCID: PMC2663002 DOI: 10.1016/j.bmc.2008.03.068] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2007] [Revised: 03/18/2008] [Accepted: 03/24/2008] [Indexed: 01/05/2023]
Abstract
Proteases are a family of naturally occurring enzymes in the body whose dysregulation has been implicated in numerous diseases and cancers. Their ability to selectively and catalytically turnover substrate adds both signal amplification and functionality as parameters for the detection of disease. This review will focus on the development of activity-based methodologies to characterize proteases, and in particular, the use of positional scanning, synthetic combinatorial libraries (PS-SCL's), and substrate activity screening (SAS) assays. The use of these approaches to better understand a protease's natural substrate will be discussed as well as the technologies that emerged.
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Affiliation(s)
- Mark D Lim
- Department of Pharmaceutical Chemistry, University of California, School of Pharmacy, 513 Parnassus Avenue Room S-926, San Francisco, CA 94158, USA
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29
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Abstract
This review provides an overview of the development of viral protease inhibitors as antiviral drugs. We concentrate on HIV-1 protease inhibitors, as these have made the most significant advances in the recent past. Thus, we discuss the biochemistry of HIV-1 protease, inhibitor development, clinical use of inhibitors, and evolution of resistance. Since many different viruses encode essential proteases, it is possible to envision the development of a potent protease inhibitor for other viruses if the processing site sequence and the catalytic mechanism are known. At this time, interest in developing inhibitors is limited to viruses that cause chronic disease, viruses that have the potential to cause large-scale epidemics, or viruses that are sufficiently ubiquitous that treating an acute infection would be beneficial even if the infection was ultimately self-limiting. Protease inhibitor development is most advanced for hepatitis C virus (HCV), and we also provide a review of HCV NS3/4A serine protease inhibitor development, including combination therapy and resistance. Finally, we discuss other viral proteases as potential drug targets, including those from Dengue virus, cytomegalovirus, rhinovirus, and coronavirus.
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Affiliation(s)
- Hans-Georg Kräusslich
- Hygiene Institute Department of Virology, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 324, Heidelberg, 69120 Germany
| | - Ralf Bartenschlager
- Hygiene Institute Department of Virology, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 324, Heidelberg, 69120 Germany
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30
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Tian RR, Liao QJ, Chen X. Prevention and treatment of KSHV-associated diseases with antiviral drugs. Virol Sin 2008. [DOI: 10.1007/s12250-008-2995-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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31
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Singh VK, Patel AK, Moir AJ, Jagannadham MV. Indicain, a dimeric serine protease from Morus indica cv. K2. PHYTOCHEMISTRY 2008; 69:2110-2119. [PMID: 18561962 DOI: 10.1016/j.phytochem.2008.05.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2007] [Revised: 05/06/2008] [Accepted: 05/07/2008] [Indexed: 05/26/2023]
Abstract
A high molecular mass serine protease has been purified to homogeneity from the latex of Morus indica cv. K2 by the combination of techniques of ammonium sulfate precipitation, hydrophobic interaction chromatography, and size-exclusion chromatography. The protein is a dimer with a molecular mass of 134.5 kDa and with two monomeric subunits of 67.2 kDa and 67.3 (MALDI-TOF), held by weak bonds susceptible to disruption on exposure to heat and very low pH. Isoelectric point of the enzyme is pH 4.8. The pH and temperature optima for caseinolytic activity were 8.5 and 80 degrees C, respectively. The extinction coefficient (epsilon280(1%)) of the enzyme was estimated as 41.24 and the molecular structure consists of 52 tryptophan, 198 tyrosine and 42 cysteine residues. The enzyme activity was inhibited by phenylmethylsulfonylflouride, chymostatin and mercuric chloride indicating the enzyme to be a serine protease. The enzyme is fairly stable and similar to subtilases in its stability toward pH, strong denaturants, temperature, and organic solvents. Polyclonal antibodies specific to enzyme and immunodiffusion studies reveal that the enzyme has unique antigenic determinants. The enzyme has activity towards broad range of substrates comparable to those of subtilisin like proteases. The N-terminal residues of indicain (T-T-N-S-W-D-F-I-G-F-P) exhibited considerable similarity to those of other known plant subtilases, especially with cucumisin, a well-characterized plant subtilase. This is the first report of purification and characterization of a subtilisin like dimeric serine protease from the latex of M. indica cv. K2. Owing to these unique properties the reported enzyme would find applications in food and pharma industry.
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Affiliation(s)
- Vijay Kumar Singh
- Molecular Biology Unit, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221 005, India
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32
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Affiliation(s)
- Abby M Hodges
- Department of Chemistry and Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8107, USA
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33
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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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34
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Casper C, Wald A. The use of antiviral drugs in the prevention and treatment of Kaposi sarcoma, multicentric Castleman disease and primary effusion lymphoma. Curr Top Microbiol Immunol 2006; 312:289-307. [PMID: 17089802 DOI: 10.1007/978-3-540-34344-8_11] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Kaposi sarcoma-associated herpesvirus [KSHV, also known as human herpesvirus 8 (HHV-8)] is the most recently identified member of the human herpesvirus family. Kaposi sarcoma (KS), primary effusion lymphoma, and multicentric Castleman disease are all associated with KSHV infection. Although the incidence of KS has declined dramatically in areas with access to highly active antiretroviral therapy, it remains the most common AIDS-associated malignancy in the developed world and is one of the most common cancers in developing nations. Current treatment options for KSHV-associated disease are ineffective, unavailable, or toxic to many affected persons. A growing body of basic science, preclinical, and observational data suggests that antiviral medications may play an important role in the prevention and treatment of KSHV-associated disease.
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Affiliation(s)
- C Casper
- University of Washington Virology Research Clinic, 600 Broadway, Suite 400, Seattle, WA 98122, USA.
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35
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Nomura AM, Marnett AB, Shimba N, Dötsch V, Craik CS. Induced structure of a helical switch as a mechanism to regulate enzymatic activity. Nat Struct Mol Biol 2006; 12:1019-20. [PMID: 16244665 DOI: 10.1038/nsmb1006] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2005] [Accepted: 09/19/2005] [Indexed: 11/09/2022]
Abstract
Herpesviruses encode a protease that is activated by homodimerization at high enzyme concentrations during lytic replication. The homodimer contains two active sites, which are distal from the dimer interface. Assignment of backbone NMR resonances and engineering of a redox switch show that two helices position a loop containing catalytic residues within each active site.
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Affiliation(s)
- Anson M Nomura
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
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36
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Kritzer JA, Zutshi R, Cheah M, Ran FA, Webman R, Wongjirad TM, Schepartz A. Miniature Protein Inhibitors of the p53-hDM2 Interaction. Chembiochem 2006; 7:29-31. [PMID: 16397877 DOI: 10.1002/cbic.200500324] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Joshua A Kritzer
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06511, USA
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37
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Lee KN, Jackson KW, Christiansen VJ, Lee CS, Chun JG, McKee PA. Antiplasmin-cleaving enzyme is a soluble form of fibroblast activation protein. Blood 2005; 107:1397-404. [PMID: 16223769 DOI: 10.1182/blood-2005-08-3452] [Citation(s) in RCA: 129] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Circulating antiplasmin-cleaving enzyme (APCE) has a role in fibrinolysis and appears structurally similar to fibroblast activation protein (FAP), a cell-surface proteinase that promotes invasiveness of certain epithelial cancers. To explore this potential relationship, we performed comparative structure/function analyses of the 2 enzymes. APCE from human plasma and recombinant FAP (rFAP) exhibited identical pH optima of 7.5, extinction coefficients (in(280 nm)(1%)) of 20.2 and 20.5, common sequences of tryptic peptides, and cross-reactivity with FAP antibody. APCE and rFAP are homodimers with monomeric subunits of 97 and 93 kDa. Only homodimers appear to have enzymatic activity, with essentially identical kinetics toward Met-alpha2-antiplasmin (Met-alpha2AP) and peptide substrates. APCE and rFAP cleave both Pro3-Leu4 and Pro12-Asn13 bonds of Met-alpha2AP, but relative kcat/Km values for Pro12-Asn13 are about 16-fold higher than for Pro3-Leu4. APCE and rFAP demonstrate higher kcat/Km values toward a peptide modeled on P4-P4' sequence surrounding the Pro12-Asn13 primary cleavage site than for Z-Gly-Pro-AMC and Ala-Pro-AFC substrates. These data support APCE as a soluble derivative of FAP and Met-alpha2AP as its physiologic substrate. Conversion of Met-alpha2AP by membrane or soluble FAP to the more easily fibrin-incorporable form, Asn-alpha2AP, may increase plasmin inhibition within fibrin surrounding certain neoplasms and have an impact on growth and therapeutic susceptibility.
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Affiliation(s)
- Kyung N Lee
- W. K. Warren Medical Research Center, PO Box 26901, BSEB-306, Oklahoma City, OK 73190, USA.
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38
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Volkman HM, Rutledge SE, Schepartz A. Binding mode and transcriptional activation potential of high affinity ligands for the CBP KIX domain. J Am Chem Soc 2005; 127:4649-58. [PMID: 15796530 DOI: 10.1021/ja042761y] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We recently described a pair of ligands, PPKID4(P) (4(P)) and PPKID6(U) (6(U)), which present the alpha-helical functional epitope found on helix B of the CREB KID activation domain (KID(P)) on a pancreatic fold protein scaffold. 4(P) and 6(U) bind the natural target of KID(P), the KIX domain of the coactivator CBP, with equilibrium dissociation constants between 515 nM and 1.5 microM and compete effectively with KID(P) for binding to CBP KIX (KIX). Here we present a detailed investigation of the binding mode, orientation, and transcriptional activation potential of 4(P) and 6(U). Equilibrium binding experiments using a panel of well-characterized KIX variants support a model in which 4(P) binds KIX in a manner that closely resembles that of KID(P) but 6(U) binds an overlapping, yet distinct region of the protein. Equilibrium binding experiments using a judiciously chosen panel of 4(P) variants containing alanine or sarcosine substitutions along the putative alpha- or PPII helix of 4(P) support a model in which 4(P) folds into a pancreatic fold structure upon binding to KIX. Transcriptional activation assays performed in HEK293 cells using GAL4 DNA-binding domain fusion proteins indicate that 4(P) functions as a potent activator of p300/CBP-dependent transcription. Notably, 6(U) is a less potent transcriptional activator in this context than 4(P)despite the similarity of their affinities for CBP KIX. This final result suggests that thermodynamic affinity is an important, although not exclusive, criterion controlling the level of KIX-dependent transcriptional activation.
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Affiliation(s)
- Heather M Volkman
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA
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39
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Yang L, Schepartz A. Relationship between Folding and Function in a Sequence-Specific Miniature DNA-Binding Protein†. Biochemistry 2005; 44:7469-78. [PMID: 15895990 DOI: 10.1021/bi050121h] [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
Previously, we have described a miniature protein-based approach to the design of molecules that bind DNA or protein surfaces with high affinity and specificity. In this approach, the small, well-folded protein avian pancreatic polypeptide acts as a scaffold to present and stabilize an alpha-helical or PPII-helical recognition epitope. The first miniature protein designed in this way, a molecule called p007, presents the alpha-helical recognition epitope found on the bZIP protein GCN4 and binds DNA with nanomolar affinity and exceptional specificity. In this work we use alanine-scanning mutagenesis to explore the contributions of 29 p007 residues to DNA affinity, specificity, and secondary structure. Virtually every residue within the p007 alpha-helix, and most residues within the p007 PPII helix, contribute to both DNA affinity and specificity. These residues include those introduced to make specific and nonspecific DNA contacts, as well as those that complete the miniature protein core. Moreover, there exists a direct correlation between the affinity of a p007 variant for specific DNA and the ability of that variant to select for specific DNA over nonspecific DNA. Although we observe no correlation between alpha-helicity and affinity, we observe a limited correlation between alpha-helicity and sequence specificity that emphasizes the role of coupled binding/folding in the function of p007. Our results imply that formation of a highly evolved set of protein.DNA contacts in the context of a well-packed hydrophobic core, and not the extent of intrinsic alpha-helical structure, is the primary determinant of p007 function.
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Affiliation(s)
- Loretta Yang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
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40
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Schneider TL, Mathew RS, Rice KP, Tamaki K, Wood JL, Schepartz A. Increasing the Kinase Specificity of K252a by Protein Surface Recognition. Org Lett 2005; 7:1695-8. [PMID: 15844883 DOI: 10.1021/ol050179o] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[reaction: see text] Here we describe a miniature protein (1) that presents the cAMP-dependent protein kinase (PKA) recognition epitope found within the heat-stable Protein Kinase Inhibitor protein (PKI) and a miniature protein conjugate (1-K252a) in which 1 is joined covalently to the high-affinity but nonselective kinase inhibitor K252a. Miniature protein 1 recognizes PKA with an affinity that rivals that of PKI and, in the context of 1-K252a, leads to a dramatic increase in kinase specificity.
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Affiliation(s)
- Tanya L Schneider
- Department of Chemistry and Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8107, USA
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41
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Gemperli AC, Rutledge SE, Maranda A, Schepartz A. Paralog-selective ligands for bcl-2 proteins. J Am Chem Soc 2005; 127:1596-7. [PMID: 15700967 DOI: 10.1021/ja0441211] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
There is considerable current interest in molecules that bind intra- or extracellular protein surfaces and inhibit protein-protein interactions. Previously we have reported that miniature proteins based on pancreatic-fold polypeptides can recognize even shallow alpha-helix binding clefts with high affinity and selectivity against unrelated proteins. One such miniature protein, PPBH3-1, binds the anti-apoptotic protein paralogs Bcl-2 and Bcl-XL with nanomolar affinity and a DeltaDeltaG = 1.2 kcal.mol-1 preference for Bcl-XL. Here we describe the directed evolution of PPBH3-1 into two new miniature proteins, PPBH3-5 and PPBH3-6, whose paralog specificity is reversed relative to PPBH3-1. PPBH3-5 and PPBH3-6 bind Bcl-2 with nanomolar affinity and a DeltaDeltaG = 0.9-1.3 kcal.mol-1 preference for Bcl-2 over Bcl-XL. Experiments with Bcl-XL variants suggest that PPBH3-5 and PPBH3-6 achieve high paralog specificity by exploiting subtle structural or electrostatic differences in the Bcl-2 and Bcl-XL molecular landscapes. PPBH3-5 and PPBH3-6 may have unique applications as early examples of nonnatural ligands that interact selectively with Bcl-2 proteins.
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Affiliation(s)
- Anja C Gemperli
- Departments of Chemistry and Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
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