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Petrillo N, Dinh K, Vogt KA, Ma S. Catalytic Mechanism of Human T-Cell Leukemia Virus Type 1 Protease Investigated by Combined QM/MM Molecular Dynamics Simulations. J Chem Inf Model 2023. [PMID: 37289654 DOI: 10.1021/acs.jcim.3c00440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Combined quantum mechanical and molecular mechanical (QM/MM) molecular dynamics simulations were performed to investigate the catalytic mechanism of human T-cell leukemia virus type 1 (HTLV-1) protease, a retroviral aspartic protease that is a potential therapeutic target for curing HTLV-1-associated diseases. To elucidate the proteolytic cleavage mechanism, we determined the two-dimensional free energy surfaces of the HTLV-1 protease-catalyzed reactions through various possible pathways. The free energy simulations suggest that the catalytic reactions of the HTLV-1 protease occur in the following sequential steps: (1) a proton is transferred from the lytic water to Asp32', followed by the nucleophilic addition of the resulting hydroxyl to the carbonyl carbon of the scissile bond, forming a tetrahedral oxyanion intermediate, and (2) a proton is transferred from Asp32 to the peptide nitrogen of the scissile bond, leading to the spontaneous breakage of the scissile bond. The rate-limiting step of this catalytic process is the proton transfer from Asp32 to the peptide nitrogen of the scissile bond, with a free energy of activation of 21.1 kcal/mol. This free energy barrier is close to the experimentally determined free energy of activation (16.3 kcal/mol) calculated from the measured catalytic rate constant (kcat). This mechanistic study provides detailed dynamic and structural information that will facilitate the design of mechanism-based inhibitors for the treatment of HTLV-1-associated diseases.
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Affiliation(s)
- Natalie Petrillo
- Department of Chemistry, Jess and Mildred Fisher College of Science and Mathematics, Towson University, 8000 York Road, Towson, Maryland 21252, United States
| | - Kim Dinh
- Department of Chemistry, Jess and Mildred Fisher College of Science and Mathematics, Towson University, 8000 York Road, Towson, Maryland 21252, United States
| | - Kimberly A Vogt
- Department of Chemistry, Jess and Mildred Fisher College of Science and Mathematics, Towson University, 8000 York Road, Towson, Maryland 21252, United States
| | - Shuhua Ma
- Department of Chemistry, Jess and Mildred Fisher College of Science and Mathematics, Towson University, 8000 York Road, Towson, Maryland 21252, United States
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2
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Mótyán JA, Kassay N, Matúz K, Tőzsér J. Different Mutation Tolerance of Lentiviral (HIV-1) and Deltaretroviral (BLV and HTLV) Protease Precursors. Viruses 2022; 14:v14091888. [PMID: 36146695 PMCID: PMC9505669 DOI: 10.3390/v14091888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/17/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
The bovine leukemia virus (BLV) and the human T-lymphothropic viruses (HTLVs) are members of the deltaretrovirus genus of Retroviridae family. An essential event of the retroviral life cycle is the processing of the polyproteins by the viral protease (PR); consequently, these enzymes became important therapeutic targets of the anti-retroviral drugs. As compared to human immunodeficiency viruses (HIVs), the deltaretroviruses have a different replication strategy, as they replicate predominantly in the DNA form, by forcing the infected cell to divide, unlike HIV-1, which replicates mainly by producing a vast number of progeny virions and by reinfection. Due to bypassing the error-prone reverse transcription step of replication, the PRs of deltaretroviruses did not undergo such extensive evolution as HIV PRs and remained more highly conserved. In this work, we studied the abilities of wild-type and modified BLV, HTLV (type 1, 2 and 3), and HIV-1 PRs (fused to an N-terminal MBP tag) for self-processing. We designed a cleavage site mutant MBP-fused BLV PR precursor as well, this recombinant enzyme was unable for self-proteolysis, the MBP fusion tag decreased its catalytic efficiency but showed an unusually low Ki for the IB-268 protease inhibitor. Our results show that the HTLV and BLV deltaretrovirus PRs exhibit lower mutation tolerance as compared to HIV-1 PR, and are less likely to retain their activity upon point mutations at various positions, indicating a higher flexibility of HIV-1 PR in tolerating mutations under selective pressure.
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Affiliation(s)
- János András Mótyán
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Correspondence: (J.A.M.); (J.T.); Tel.: +36-52-512-900 (J.A.M. & J.T.)
| | - Norbert Kassay
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, 4032 Debrecen, Hungary
| | - Krisztina Matúz
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - József Tőzsér
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Correspondence: (J.A.M.); (J.T.); Tel.: +36-52-512-900 (J.A.M. & J.T.)
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3
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Fló M, Carrión F, Olivero-Deibe N, Bianchi S, Portela M, Rammauro F, Alvarez B, Pritsch O. Kinetics of Bovine leukemia virus aspartic protease reveals its dimerization and conformational change. PLoS One 2022; 17:e0271671. [PMID: 35867649 PMCID: PMC9307154 DOI: 10.1371/journal.pone.0271671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 07/05/2022] [Indexed: 11/28/2022] Open
Abstract
The retropepsin (PR) of the Bovine leukemia virus (BLV) plays, as in other retroviruses, a crucial role in the transition from the non-infective viral particle to the infective virion by processing the polyprotein Gag. PR is expressed as an immature precursor associated with Gag, after an occasional −1 ribosomal frameshifting event. Self-hydrolysis of PR at specific N- and C-terminal sites releases the monomer that dimerizes giving rise to the active protease. We designed a strategy to express BLV PR in E. coli as a fusion protein with maltose binding protein, with a six-histidine tag at its N-terminal end, and bearing a tobacco etch virus protease hydrolysis site. This allowed us to obtain soluble and mature recombinant PR in relatively good yields, with exactly the same amino acid composition as the native protein. As PR presents relative promiscuity for the hydrolysis sites we designed four fluorogenic peptide substrates based on Förster resonance energy transfer (FRET) in order to characterize the activity of the recombinant enzyme. These substrates opened the way to perform kinetic studies, allowing us to characterize the dimer-monomer equilibrium. Furthermore, we obtained kinetic evidence for the existence of a conformational change that enables the interaction with the substrate. These results constitute a starting point for the elucidation of the kinetic properties of BLV-PR, and may be relevant not only to improve the chemical warfare against this virus but also to better understand other viral PRs.
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Affiliation(s)
- Martín Fló
- Laboratorio de Inmunovirología, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Departamento de Inmunobiología, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
- * E-mail: (OP); (MF)
| | - Federico Carrión
- Laboratorio de Inmunovirología, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | | | - Sergio Bianchi
- Laboratorio de Inmunovirología, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Laboratorio de Biomarcadores Moleculares, Departamento de Fisiopatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Madelón Portela
- Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo, Facultad de Ciencias, Montevideo, Uruguay
| | - Florencia Rammauro
- Laboratorio de Inmunovirología, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Departamento de Inmunobiología, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Beatriz Alvarez
- Laboratorio de Enzimología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Otto Pritsch
- Laboratorio de Inmunovirología, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Departamento de Inmunobiología, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
- * E-mail: (OP); (MF)
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4
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Awahara C, Oku D, Furuta S, Kobayashi K, Teruya K, Akaji K, Hattori Y. The Effects of Side-Chain Configurations of a Retro-Inverso-Type Inhibitor on the Human T-Cell Leukemia Virus (HTLV)-1 Protease. Molecules 2022; 27:1646. [PMID: 35268749 PMCID: PMC8911550 DOI: 10.3390/molecules27051646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/26/2022] [Accepted: 02/28/2022] [Indexed: 11/16/2022] Open
Abstract
In this study, the effects of side-chain configurations of D-Ile residues of a retro-inverso (RI)-type inhibitor on the human T-cell leukemia virus type 1 (HTLV-1) protease containing a hydroxyethylamine dipeptide isostere were clarified. Prior to evaluation using the RI-type inhibitor, the effects of side-chain configurations of Ile residues of the substrate peptide on the HTLV-1 protease were examined to estimate the influence of side-chain configurations on enzyme activity. Based on the estimation of the influence of side-chain configurations on protease affinity, the RI-type inhibitors containing a D-allo-Ile residue in the corresponding substrate sequence, instead of a D-Ile residue, were synthesized via 9-fluorenylmethoxycarbonyl-based solid-phase peptide synthesis. Refolded recombinant HTLV-1 protease (1-116, L40I) was used for the simple and short evaluation of the inhibitory activities of the synthesized RI-type inhibitors. The results clearly indicated that mimicking the whole topology, comprising both the main- and side-chain structures of the parent inhibitor, is effective for the design of potent RI-modified protease inhibitors.
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Affiliation(s)
- Chiyuki Awahara
- Department of Medicinal Chemistry, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan; (C.A.); (D.O.); (S.F.); (K.K.)
| | - Daiki Oku
- Department of Medicinal Chemistry, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan; (C.A.); (D.O.); (S.F.); (K.K.)
| | - Saki Furuta
- Department of Medicinal Chemistry, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan; (C.A.); (D.O.); (S.F.); (K.K.)
| | - Kazuya Kobayashi
- Department of Medicinal Chemistry, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan; (C.A.); (D.O.); (S.F.); (K.K.)
| | - Kenta Teruya
- Department of Neurochemistry, Tohoku University Graduate School of Medicine, Aoba-ku, Sendai 980-8575, Japan;
| | - Kenichi Akaji
- Department of Medicinal Chemistry, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan; (C.A.); (D.O.); (S.F.); (K.K.)
| | - Yasunao Hattori
- Center for Instrumental Analysis, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan
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5
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Lockbaum GJ, Henes M, Talledge N, Rusere LN, Kosovrasti K, Nalivaika EA, Somasundaran M, Ali A, Mansky LM, Yilmaz NK, Schiffer CA. Inhibiting HTLV-1 Protease: A Viable Antiviral Target. ACS Chem Biol 2021; 16:529-538. [PMID: 33619959 PMCID: PMC8126997 DOI: 10.1021/acschembio.0c00975] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Human T-cell lymphotropic virus type 1 (HTLV-1) is a retrovirus that can cause severe paralytic neurologic disease and immune disorders as well as cancer. An estimated 20 million people worldwide are infected with HTLV-1, with prevalence reaching 30% in some parts of the world. In stark contrast to HIV-1, no direct acting antivirals (DAAs) exist against HTLV-1. The aspartyl protease of HTLV-1 is a dimer similar to that of HIV-1 and processes the viral polyprotein to permit viral maturation. We report that the FDA-approved HIV-1 protease inhibitor darunavir (DRV) inhibits the enzyme with 0.8 μM potency and provides a scaffold for drug design against HTLV-1. Analogs of DRV that we designed and synthesized achieved submicromolar inhibition against HTLV-1 protease and inhibited Gag processing in viral maturation assays and in a chronically HTLV-1 infected cell line. Cocrystal structures of these inhibitors with HTLV-1 protease highlight opportunities for future inhibitor design. Our results show promise toward developing highly potent HTLV-1 protease inhibitors as therapeutic agents against HTLV-1 infections.
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Affiliation(s)
- Gordon J. Lockbaum
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Mina Henes
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Nathaniel Talledge
- Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota – Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Linah N. Rusere
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Klajdi Kosovrasti
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Ellen A. Nalivaika
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Mohan Somasundaran
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Akbar Ali
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Louis M. Mansky
- Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota – Twin Cities, Minneapolis, Minnesota 55455, United States
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, United States
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6
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Kassay N, Mótyán JA, Matúz K, Golda M, Tőzsér J. Biochemical Characterization, Specificity and Inhibition Studies of HTLV-1, HTLV-2, and HTLV-3 Proteases. Life (Basel) 2021; 11:life11020127. [PMID: 33562087 PMCID: PMC7915765 DOI: 10.3390/life11020127] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 01/03/2023] Open
Abstract
The human T-lymphotropic viruses (HTLVs) are causative agents of severe diseases including adult T-cell leukemia. Similar to human immunodeficiency viruses (HIVs), the viral protease (PR) plays a crucial role in the viral life-cycle via the processing of the viral polyproteins. Thus, it is a potential target of anti-retroviral therapies. In this study, we performed in vitro comparative analysis of human T-cell leukemia virus type 1, 2, and 3 (HTLV-1, -2, and -3) proteases. Amino acid preferences of S4 to S1′ subsites were studied by using a series of synthetic oligopeptide substrates representing the natural and modified cleavage site sequences of the proteases. Biochemical characteristics of the different PRs were also determined, including catalytic efficiencies and dependence of activity on pH, temperature, and ionic strength. We investigated the effects of different HIV-1 PR inhibitors (atazanavir, darunavir, DMP-323, indinavir, ritonavir, and saquinavir) on enzyme activities, and inhibitory potentials of IB-268 and IB-269 inhibitors that were previously designed against HTLV-1 PR. Comparative biochemical analysis of HTLV-1, -2, and -3 PRs may help understand the characteristic similarities and differences between these enzymes in order to estimate the potential of the appearance of drug-resistance against specific HTLV-1 PR inhibitors.
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Affiliation(s)
- Norbert Kassay
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (N.K.); (K.M.); (M.G.)
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, 4032 Debrecen, Hungary
| | - János András Mótyán
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (N.K.); (K.M.); (M.G.)
- Correspondence: (J.A.M.); (J.T.); Tel.: +36-52-512-900 (J.A.M. & J.T.)
| | - Krisztina Matúz
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (N.K.); (K.M.); (M.G.)
| | - Mária Golda
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (N.K.); (K.M.); (M.G.)
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, 4032 Debrecen, Hungary
| | - József Tőzsér
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (N.K.); (K.M.); (M.G.)
- Correspondence: (J.A.M.); (J.T.); Tel.: +36-52-512-900 (J.A.M. & J.T.)
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7
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Gazda LD, Joóné Matúz K, Nagy T, Mótyán JA, Tőzsér J. Biochemical characterization of Ty1 retrotransposon protease. PLoS One 2020; 15:e0227062. [PMID: 31917798 PMCID: PMC6952103 DOI: 10.1371/journal.pone.0227062] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 12/10/2019] [Indexed: 01/08/2023] Open
Abstract
Ty1 is one of the many transposons in the budding yeast Saccharomyces cerevisiae. The life-cycle of Ty1 shows numerous similarities with that of retroviruses, e.g. the initially synthesized polyprotein precursor undergoes proteolytic processing by the protease. The retroviral proteases have become important targets of current antiretroviral therapies due to the critical role of the limited proteolysis of Gag-Pol polyprotein in the replication cycle and they therefore belong to the most well-studied enzymes. Comparative analyses of retroviral and retroviral-like proteases can help to explore the key similarities and differences which may help understanding how resistance is developed against protease inhibitors, but the available information about the structural and biochemical characteristics of retroviral-like, and especially retrotransposon, proteases is limited. To investigate the main characteristics of Ty1 retrotransposon protease of Saccharomyces cerevisiae, untagged and His6-tagged forms of Ty1 protease were expressed in E. coli. After purification of the recombinant proteins, activity measurements were performed using synthetic oligopeptide and fluorescent recombinant protein substrates, which represented the wild-type and the modified forms of naturally occurring cleavage sites of the protease. We investigated the dependence of enzyme activity on different reaction conditions (pH, temperature, ionic strength, and urea concentration), and determined enzyme kinetic parameters for the studied substrates. Inhibitory potentials of 10 different protease inhibitors were also tested. Ty1 protease was not inhibited by the inhibitors which have been designed against human immunodeficiency virus type 1 protease and are approved as antiretroviral therapeutics. A quaternary structure of homodimeric Ty1 protease was proposed based on homology modeling, and this structure was used to support interpretation of experimental results and to correlate some structural and biochemical characteristics with that of other retroviral proteases.
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Affiliation(s)
- Lívia Diána Gazda
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Krisztina Joóné Matúz
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Tibor Nagy
- Department of Applied Chemistry, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - János András Mótyán
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- * E-mail: (JAM); (JT)
| | - József Tőzsér
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- * E-mail: (JAM); (JT)
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8
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Maldonado JO, Cao S, Zhang W, Mansky LM. Distinct Morphology of Human T-Cell Leukemia Virus Type 1-Like Particles. Viruses 2016; 8:v8050132. [PMID: 27187442 PMCID: PMC4885087 DOI: 10.3390/v8050132] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 04/15/2016] [Accepted: 04/21/2016] [Indexed: 02/06/2023] Open
Abstract
The Gag polyprotein is the main retroviral structural protein and is essential for the assembly and release of virus particles. In this study, we have analyzed the morphology and Gag stoichiometry of human T-cell leukemia virus type 1 (HTLV-1)-like particles and authentic, mature HTLV-1 particles by using cryogenic transmission electron microscopy (cryo-TEM) and scanning transmission electron microscopy (STEM). HTLV-1-like particles mimicked the morphology of immature authentic HTLV-1 virions. Importantly, we have observed for the first time that the morphology of these virus-like particles (VLPs) has the unique local feature of a flat Gag lattice that does not follow the curvature of the viral membrane, resulting in an enlarged distance between the Gag lattice and the viral membrane. Other morphological features that have been previously observed with other retroviruses include: (1) a Gag lattice with multiple discontinuities; (2) membrane regions associated with the Gag lattice that exhibited a string of bead-like densities at the inner leaflet; and (3) an arrangement of the Gag lattice resembling a railroad track. Measurement of the average size and mass of VLPs and authentic HTLV-1 particles suggested a consistent range of size and Gag copy numbers in these two groups of particles. The unique local flat Gag lattice morphological feature observed suggests that HTLV-1 Gag could be arranged in a lattice structure that is distinct from that of other retroviruses characterized to date.
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Affiliation(s)
- José O Maldonado
- Institute for Molecular Virology & DDS-PhD Dual Degree Program, 18-242 Moos Tower, 515 Delaware Street SE, Minneapolis, MN 55455, USA.
| | - Sheng Cao
- Institute for Molecular Virology, 18-242 Moos Tower, 515 Delaware Street SE, Minneapolis, MN 55455, USA.
| | - Wei Zhang
- Institute for Molecular Virology & Characterization Facility, 18-242 Moos Tower, 515 Delaware Street SE, Minneapolis, MN 55455, USA.
| | - Louis M Mansky
- Institute for Molecular Virology, 18-242 Moos Tower, 515 Delaware Street SE, Minneapolis, MN 55455, USA.
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9
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Laco GS. HIV-1 protease substrate-groove: Role in substrate recognition and inhibitor resistance. Biochimie 2015; 118:90-103. [PMID: 26300060 DOI: 10.1016/j.biochi.2015.08.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 08/18/2015] [Indexed: 11/17/2022]
Abstract
A key target in the treatment of HIV-1/AIDS has been the viral protease. Here we first studied in silico the evolution of protease resistance. Primary active site resistance mutations were found to weaken interactions between protease and both inhibitor and substrate P4-P4' residues. We next studied the effects of secondary resistance mutations, often distant from the active site, on protease binding to inhibitors and substrates. Those secondary mutations contributed to the rise of multi-drug resistance while also enhancing viral replicative capacity. Here many secondary resistance mutations were found in the HIV-1 protease substrate-grooves, one on each face of the symmetrical protease dimer. The protease active site binds substrate P4-P4' residues, while the substrate-groove allows the protease to bind residues P12-P5/P5'-P12', for a total of twenty-four residues. The substrate-groove secondary resistance mutations were found to compensate for the loss of interactions between the inhibitor resistant protease active site and substrate P4-P4' residues, due to primary resistance mutations, by increasing interactions with substrate P12-P5/P5'-P12' residues. In vitro experiments demonstrated that a multi-drug resistant protease with substrate-groove resistance mutations was slower than wild-type protease in cleaving a peptide substrate, which did not allow for substrate-groove interactions, while it had similar activity as wild-type protease when using a Gag polyprotein in which cleavage-site P12-P5/P5'-P12' residues could be bound by the protease substrate-grooves. When the Gag MA/CA cleavage site P12-P5/P5'-P12' residues were mutated the multi-drug resistant protease cleaved the mutant Gag significantly slower, indicating the importance of the protease S-grooves in binding to substrate.
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Affiliation(s)
- Gary S Laco
- Laboratory of Computational and Molecular Biochemistry, The Roskamp Institute, Sarasota, FL, USA.
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10
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Characterizing the protonation states of the catalytic residues in apo and substrate-bound human T-cell leukemia virus type 1 protease. Comput Biol Chem 2015; 56:61-70. [PMID: 25889320 DOI: 10.1016/j.compbiolchem.2015.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 03/22/2015] [Accepted: 04/03/2015] [Indexed: 11/23/2022]
Abstract
Human T-cell leukemia virus type 1 (HTLV-1) protease is an attractive target when developing inhibitors to treat HTLV-1 associated diseases. To study the catalytic mechanism and design novel HTLV-1 protease inhibitors, the protonation states of the two catalytic aspartic acid residues must be determined. Free energy simulations have been conducted to study the proton transfer reaction between the catalytic residues of HTLV-1 protease using a combined quantum mechanical and molecular mechanical (QM/MM) molecular dynamics simulation. The free energy profiles for the reaction in the apo-enzyme and in an enzyme - substrate complex have been obtained. In the apo-enzyme, the two catalytic residues are chemically equivalent and are expected to be both unprotonated. Upon substrate binding, the catalytic residues of HTLV-1 protease evolve to a singly protonated state, in which the OD1 of Asp32 is protonated and forms a hydrogen bond with the OD1 of Asp32', which is unprotonated. The HTLV-1 protease-substrate complex structure obtained from this simulation can serve as the Michaelis complex structure for further mechanistic studies of HTLV-1 protease while providing a receptor structure with the correct protonation states for the active site residues toward the design of novel HTLV-1 protease inhibitors through virtual screening.
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11
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Teruya K, Tanaka T, Kawakami T, Akaji K, Aimoto S. Epimerization in peptide thioester condensation. J Pept Sci 2012; 18:669-77. [DOI: 10.1002/psc.2452] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 08/06/2012] [Accepted: 08/17/2012] [Indexed: 11/09/2022]
Affiliation(s)
- Kenta Teruya
- Institute for Protein Research; Osaka University; 3-2, Yamadaoka Suita Osaka 565-0871 Japan
- Department of Chemistry, Graduate School of Medical Science; Kyoto Prefectural University of Medicine; Kita-ku Kyoto 603-8334 Japan
| | - Takeyuki Tanaka
- Department of Life Science, Graduate School of Science and Technology; Kobe University; 1-1 Rokkodai-cho Nada-ku Kobe 657-8501 Japan
| | - Toru Kawakami
- Institute for Protein Research; Osaka University; 3-2, Yamadaoka Suita Osaka 565-0871 Japan
| | - Kenichi Akaji
- Institute for Protein Research; Osaka University; 3-2, Yamadaoka Suita Osaka 565-0871 Japan
- Department of Medicinal Chemistry; Kyoto Pharmaceutical University; Yamashina-ku Kyoto 607-8412 Japan
| | - Saburo Aimoto
- Institute for Protein Research; Osaka University; 3-2, Yamadaoka Suita Osaka 565-0871 Japan
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12
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Demir A, Oguariri RM, Magis A, Ostrov DA, Imamichi T, Dunn BM. Kinetic characterization of newly discovered inhibitors of various constructs of human T-cell leukemia virus-1 (HTLV-1) protease and their effect on HTLV-1-infected cells. Antivir Ther 2012; 17:883-92. [PMID: 22436331 DOI: 10.3851/imp2090] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2011] [Indexed: 10/28/2022]
Abstract
BACKGROUND Human T-cell leukemia virus-1 (HTLV-1) was the first identified human retrovirus and was shown to be associated with diseases such as adult T-cell leukemia lymphoma and tropical spastic paraparesis/HTLV-1 associated myelopathy. Retroviral proteases (PRs) are essential for viral replication by processing viral Gag and Gag-(Pro)-Pol polyproteins during maturation. Full-length HTLV-1 PR is 125 residues long; whether the C-terminal region is required for catalytic activity is still controversial. In this study, we characterized the effect of C-terminal amino acids of HTLV-1 PR for PR activity and examined the binding of compounds identified by in silico screening. One compound showed inhibition against the virus in infected cells. METHODS Truncated (116-, 121- and 122-residue) forms of HTLV-1 PR were prepared and proteins from expression of the genes were purified. In silico screening was performed by docking small molecules into the active site of HTLV-1 PR. The kinetic constants k(cat), K(m), k(cat)/K(m) and inhibition constants K(i) for inhibitors identified by the computational screening were determined. Western blot and ELISA analyses were used to determine the effect of the most potent PR inhibitors on HTLV-1 protein processing in infected cells. RESULTS The constructs showed similar catalytic efficiency constants (k(cat)/K(m)); thus HTLV-1 PR C-terminal amino acids are not essential for full activity. Computational screening revealed new PR inhibitors and some were shown to be inhibitory in enzyme assays. In HTLV-1-infected cells, one of the small molecules inhibited HTLV-1 gag cleavage and decreased the amount of HTLV-1 p19 produced in the cells. CONCLUSIONS We have identified an HTLV-1 PR inhibitor that is biologically functional. Inhibitor screening will continue to develop possible drugs for therapy of HTLV-1 infection.
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Affiliation(s)
- Ahu Demir
- University of Florida College of Medicine Biochemistry and Molecular Biology, Gainesville, FL, USA
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13
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Kumada HO, Nguyen JT, Kakizawa T, Hidaka K, Kimura T, Hayashi Y, Kiso Y. Development of [Ile40]HTLV-I protease inhibition assay using novel fluorogenic and chromogenic substrate. J Pept Sci 2011; 17:569-75. [DOI: 10.1002/psc.1375] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 03/09/2011] [Accepted: 03/11/2011] [Indexed: 11/07/2022]
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14
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Sayer JM, Agniswamy J, Weber IT, Louis JM. Autocatalytic maturation, physical/chemical properties, and crystal structure of group N HIV-1 protease: relevance to drug resistance. Protein Sci 2011; 19:2055-72. [PMID: 20737578 DOI: 10.1002/pro.486] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The mature protease from Group N human immunodeficiency virus Type 1 (HIV-1) (PR1(N)) differs in 20 amino acids from the extensively studied Group M protease (PR1(M)) at positions corresponding to minor drug-resistance mutations (DRMs). The first crystal structure (1.09 Å resolution) of PR1(N) with the clinical inhibitor darunavir (DRV) reveals the same overall structure as PR1(M), but with a slightly larger inhibitor-binding cavity. Changes in the 10s loop and the flap hinge propagate to shift one flap away from the inhibitor, whereas L89F and substitutions in the 60s loop perturb inhibitor-binding residues 29-32. However, kinetic parameters of PR1(N) closely resemble those of PR1(M), and calorimetric results are consistent with similar binding affinities for DRV and two other clinical PIs, suggesting that minor DRMs coevolve to compensate for the detrimental effects of drug-specific major DRMs. A miniprecursor (TFR 1-61-PR1(N)) comprising the transframe region (TFR) fused to the N-terminus of PR1(N) undergoes autocatalytic cleavage at the TFR/PR1(N) site concomitant with the appearance of catalytic activity characteristic of the dimeric, mature enzyme. This cleavage is inhibited at an equimolar ratio of precursor to DRV (∼6 μM), which partially stabilizes the precursor dimer from a monomer. However, cleavage at L34/W35 within the TFR, which precedes the TFR 1-61/PR1(N) cleavage at pH ≤ 5, is only partially inhibited. Favorable properties of PR1(N) relative to PR1(M) include its suitability for column fractionation by size under native conditions and >10-fold higher dimer dissociation constant (150 nM). Exploiting these properties may facilitate testing of potential dimerization inhibitors that perturb early precursor processing steps.
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Affiliation(s)
- Jane M Sayer
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland 20892-0520, USA
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15
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A comparative study of HIV-1 and HTLV-I protease structure and dynamics reveals a conserved residue interaction network. J Mol Model 2011; 17:2693-705. [PMID: 21279524 DOI: 10.1007/s00894-011-0971-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Accepted: 01/11/2011] [Indexed: 12/14/2022]
Abstract
The two retroviruses human T-lymphotropic virus type I (HTLV-I) and human immunodeficiency virus type 1 (HIV-1) are the causative agents of severe and fatal diseases including adult T-cell leukemia and the acquired immune deficiency syndrome (AIDS). Both viruses code for a protease that is essential for replication and therefore represents a key target for drugs interfering with viral infection. The retroviral proteases from HIV-1 and HTLV-I share 31% sequence identity and high structural similarities. Yet, their substrate specificities and inhibition profiles differ substantially. In this study, we performed all-atom molecular dynamics (MD) simulations for both enzymes in their ligand-free states and in complex with model substrates in order to compare their dynamic behaviors and enhance our understanding of the correlation between sequence, structure, and dynamics in this protein family. We found extensive similarities in both local and overall protein dynamics, as well as in the energetics of their interactions with model substrates. Interestingly, those residues that are important for strong ligand binding are frequently not conserved in sequence, thereby offering an explanation for the differences in binding specificity. Moreover, we identified an interaction network of contacts between conserved residues that interconnects secondary structure elements and serves as a scaffold for the protein fold. This interaction network is conformationally stable over time and may provide an explanation for the highly similar dynamic behavior of the two retroviral proteases, even in the light of their rather low overall sequence identity.
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16
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Nguyen JT, Kato K, Kumada HO, Hidaka K, Kimura T, Kiso Y. Maintaining potent HTLV-I protease inhibition without the P3-cap moiety in small tetrapeptidic inhibitors. Bioorg Med Chem Lett 2011; 21:1832-7. [PMID: 21316958 DOI: 10.1016/j.bmcl.2011.01.048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 01/11/2011] [Accepted: 01/12/2011] [Indexed: 10/18/2022]
Abstract
The human T cell lymphotropic/leukemia virus type 1 (HTLV-I) causes adult T cell lymphoma/leukemia. The virus is also responsible for chronic progressive myelopathy and several inflammatory diseases. To stop the manufacturing of new viral components, in our previous reports, we derived small tetrapeptidic HTLV-I protease inhibitors with an important amide-capping moiety at the P(3) residue. In the current study, we removed the P(3)-cap moiety and, with great difficulty, optimized the P(3) residue for HTLV-I protease inhibition potency. We discovered a very potent and small tetrapeptidic HTLV-I protease inhibitor (KNI-10774a, IC(50)=13 nM).
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Affiliation(s)
- Jeffrey-Tri Nguyen
- Department of Medicinal Chemistry, Center for Frontier Research in Medicinal Science, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto, Japan
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17
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Li C, Li X, Lu W. Total chemical synthesis of human T-cell leukemia virus type 1 protease via native chemical ligation. Biopolymers 2010; 94:487-94. [PMID: 20593478 DOI: 10.1002/bip.21375] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Human T-cell leukemia virus 1 (HTLV-1) protease, a member of the aspartic acid protease family, plays critical roles in the pathogenesis of the virus and is an attractive viral target for therapeutic intervention. HTLV-1 protease consists of 125 amino acid residues and functions as a homodimer stabilized in part by a four-stranded beta-sheet comprising the N- and C-termini. Compared with many other viral proteases such as HIV-1 protease, HTLV-1 protease is elongated by an extra 10 amino acid residue "tail" at the C-terminus. The structural and functional role of the extra C-terminal residues in the catalysis of HTLV-1 protease has been a subject of debate for years. Using the native chemical ligation technique pioneered by Kent and coworkers, we chemically synthesized a full-length HTLV protease and a C-terminally truncated form encompassing residues 1-116. Enzyme kinetic analysis using three different peptide substrates indicated that truncation of the C-terminal tail lowered the turnover number of the viral enzyme by a factor of 2 and its catalytic efficiency by roughly 10-fold. Our findings differ from the two extreme views that the C-terminal tail of HTLV-1 protease is either fully dispensable or totally required for enzyme dimerization and/or catalysis.
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Affiliation(s)
- Changqing Li
- Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
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18
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Satoh T, Li M, Nguyen JT, Kiso Y, Gustchina A, Wlodawer A. Crystal structures of inhibitor complexes of human T-cell leukemia virus (HTLV-1) protease. J Mol Biol 2010; 401:626-41. [PMID: 20600105 PMCID: PMC2918672 DOI: 10.1016/j.jmb.2010.06.052] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Revised: 06/22/2010] [Accepted: 06/23/2010] [Indexed: 10/19/2022]
Abstract
Human T-cell leukemia virus type 1 (HTLV-1) is a retrovirus associated with several serious diseases, such as adult T-cell leukemia and tropical spastic paraparesis/myelopathy. For a number of years, the protease (PR) encoded by HTLV-1 has been a target for designing antiviral drugs, but that effort was hampered by limited available structural information. We report a high-resolution crystal structure of HTLV-1 PR complexed with a statine-containing inhibitor, a significant improvement over the previously available moderate-resolution structure. We also report crystal structures of the complexes of HTLV-1 PR with five different inhibitors that are more compact and more potent. A detailed study of structure-activity relationships was performed to interpret in detail the influence of the polar and hydrophobic interactions between the inhibitors and the protease.
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Affiliation(s)
- Tadashi Satoh
- Protein Structure Section, Macromolecular Crystallography Laboratory, NCI at Frederick, Frederick, MD 21702, USA
| | - Mi Li
- Protein Structure Section, Macromolecular Crystallography Laboratory, NCI at Frederick, Frederick, MD 21702, USA
- Basic Research Program, SAIC-Frederick, Frederick, MD, USA
| | - Jeffrey-Tri Nguyen
- Department of Medicinal Chemistry, Center for Frontier Research in Medicinal Science, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan
| | - Yoshiaki Kiso
- Department of Medicinal Chemistry, Center for Frontier Research in Medicinal Science, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan
| | - Alla Gustchina
- Protein Structure Section, Macromolecular Crystallography Laboratory, NCI at Frederick, Frederick, MD 21702, USA
| | - Alexander Wlodawer
- Protein Structure Section, Macromolecular Crystallography Laboratory, NCI at Frederick, Frederick, MD 21702, USA
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19
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Louis JM, Ishima R, Aniana A, Sayer JM. Revealing the dimer dissociation and existence of a folded monomer of the mature HIV-2 protease. Protein Sci 2010; 18:2442-53. [PMID: 19798742 DOI: 10.1002/pro.261] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Purification and in vitro protein-folding schemes were developed to produce monodisperse samples of the mature wild-type HIV-2 protease (PR2), enabling a comprehensive set of biochemical and biophysical studies to assess the dissociation of the dimeric protease. An E37K substitution in PR2 significantly retards autoproteolytic cleavage during expression. Furthermore, it permits convenient measurement of the dimer dissociation of PR2(E37K) (elevated K(d) approximately 20 nM) by enzyme kinetics. Differential scanning calorimetry reveals a T(m) of 60.5 for PR2 as compared with 65.7 degrees C for HIV-1 protease (PR1). Consistent with weaker binding of the clinical inhibitor darunavir (DRV) to PR2, the T(m) of PR2 increases by 14.8 degrees C in the presence of DRV as compared with 22.4 degrees C for PR1. Dimer interface mutations, such as a T26A substitution in the active site (PR2(T26A)) or a deletion of the C-terminal residues 96-99 (PR2(1-95)), drastically increase the K(d) (>10(5)-fold). PR2(T26A) and PR2(1-95) consist predominantly of folded monomers, as determined by nuclear magnetic resonance (NMR) and size-exclusion chromatography coupled with multiangle light scattering and refractive index measurements (SMR), whereas wild-type PR2 and its active-site mutant PR2(D25N) are folded dimers. Addition of twofold excess active-site inhibitor promotes dimerization of PR2(T26A) but not of PR2(1-95), indicating that subunit interactions involving the C-terminal residues are crucial for dimer formation. Use of SMR and NMR with PR2 facilitates probing for potential inhibitors that restrict protein folding and/or dimerization and, thus, may provide insights for the future design of inhibitors to circumvent drug resistance.
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Affiliation(s)
- John M Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland 20892-0520, USA.
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20
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Analysis and characterization of dimerization inhibition of a multi-drug-resistant human immunodeficiency virus type 1 protease using a novel size-exclusion chromatographic approach. Biochem J 2009; 419:497-506. [PMID: 19149765 DOI: 10.1042/bj20082068] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Active-site inhibitors of HIV-1 PR (protease) block viral replication by preventing viral maturation. However, HIV-1 often develops resistance to active-site inhibitors through multiple mutations in PR and therefore recent efforts have focused on inhibiting PR dimerization as an alternative approach. Dimerization inhibitors have been identified using kinetic analysis, but additional characterization of the effect of these inhibitors on PR by physical methods has been difficult. In the present study, we identified a PR(MDR) (multi-drug-resistant HIV-1 PR) that was highly resistant to autoproteolysis. Using this PR and a novel size-exclusion chromatographic approach that incorporated fluorescence and MS detection, we were able to demonstrate inhibition of dimerization using P27 (peptide 27), a peptide dimerization inhibitor of PR previously identified on the basis of kinetic analysis. Incubation of PR(MDR) with P27, or other dimerization inhibitors, led to a dose- and time-dependent formation of PR monomers based on the change in elution time by size exclusion and its similar elution time to engineered forms of monomeric PR, namely PR(T26A) and glutathionylated PR. In contrast, incubation of PR(MDR) with a potent active-site inhibitor did not change the elution time for the PR(MDR) dimer. The monomeric PR induced by P27 had fluorescent characteristics which were consistent with unfolded PR. Structure-activity studies identified the active regions of P27 and experiments were performed to examine the effect of other dimerization inhibitors on PR. The present study is the first characterization of dimerization inhibition of PR(MDR), a prime target for these inhibitors, using a novel size-exclusion chromatographic approach.
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21
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Kádas J, Boross P, Weber IT, Bagossi P, Matúz K, Tözsér J. C-terminal residues of mature human T-lymphotropic virus type 1 protease are critical for dimerization and catalytic activity. Biochem J 2008; 416:357-64. [PMID: 18636969 PMCID: PMC2778851 DOI: 10.1042/bj20071132] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
HTLV-1 [HTLV (human T-cell lymphotrophic virus) type 1] is associated with a number of human diseases. HTLV-1 protease is essential for virus replication, and similarly to HIV-1 protease, it is a potential target for chemotherapy. The primary sequence of HTLV-1 protease is substantially longer compared with that of HIV-1 protease, and the role of the ten C-terminal residues is controversial. We have expressed C-terminally-truncated forms of HTLV-1 protease with and without N-terminal His tags. Removal of five of the C-terminal residues caused a 4-40-fold decrease in specificity constants, whereas the removal of an additional five C-terminal residues rendered the protease completely inactive. The addition of the N-terminal His tag dramatically decreased the activity of HTLV-1 protease forms. Pull-down experiments carried out with His-tagged forms, gel-filtration experiments and dimerization assays provided the first unequivocal experimental results for the role of the C-terminal residues in dimerization of the enzyme. There is a hydrophobic tunnel on the surface of HTLV-1 protease close to the C-terminal ends that is absent in the HIV-1 protease. This hydrophobic tunnel can accommodate the extra C-terminal residues of HTLV-1 protease, which was predicted to stabilize the dimer of the full-length enzyme and provides an alternative target site for protease inhibition.
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Affiliation(s)
- János Kádas
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, Medical and Health Science Center, University of Debrecen H-4012, Hungary
| | - Péter Boross
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, Medical and Health Science Center, University of Debrecen H-4012, Hungary
| | - Irene T. Weber
- Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, Georgia 30303
| | - Péter Bagossi
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, Medical and Health Science Center, University of Debrecen H-4012, Hungary
| | - Krisztina Matúz
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, Medical and Health Science Center, University of Debrecen H-4012, Hungary
| | - József Tözsér
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, Medical and Health Science Center, University of Debrecen H-4012, Hungary
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22
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Amino acid preferences of retroviral proteases for amino-terminal positions in a type 1 cleavage site. J Virol 2008; 82:10111-7. [PMID: 18701588 DOI: 10.1128/jvi.00418-08] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The specificities of the proteases of 11 retroviruses were studied using a series of oligopeptides with amino acid substitutions in the P1, P3, and P4 positions of a naturally occurring type 1 cleavage site (Val-Ser-Gln-Asn-Tyr downward arrowPro-Ile-Val-Gln) in human immunodeficiency virus type 1 (HIV-1). Previously, the substrate specificity of the P2 site was studied for the same representative set of retroviral proteases, which included at least one member from each of the seven genera of the family Retroviridae (P. Bagossi, T. Sperka, A. Fehér, J. Kádas, G. Zahuczky, G. Miklóssy, P. Boross, and J. Tözsér, J. Virol. 79:4213-4218, 2005). Our enzyme set comprised the proteases of HIV-1, HIV-2, equine infectious anemia virus, avian myeloblastosis virus (AMV), Mason-Pfizer monkey virus, mouse mammary tumor virus (MMTV), Moloney murine leukemia virus, human T-lymphotropic virus type 1, bovine leukemia virus, walleye dermal sarcoma virus, and human foamy virus. Molecular models were used to interpret the similarities and differences in specificity between these retroviral proteases. The results showed that the retroviral proteases had similar preferences (Phe and Tyr) for the P1 position in this sequence context, but differences were found for the P3 and P4 positions. Importantly, the sizes of the P3 and P4 residues appear to be a major contributor for specificity. The substrate specificities correlated well with the phylogenetic tree of the retroviruses. Furthermore, while the specificities of some enzymes belonging to different genera appeared to be very similar (e.g., those of AMV and MMTV), the specificities of the primate lentiviral proteases substantially differed from that observed for a nonprimate lentiviral protease.
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23
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Synthesis and activity of tetrapeptidic HTLV-I protease inhibitors possessing different P3-cap moieties. Bioorg Med Chem 2008; 16:5795-802. [PMID: 18400502 DOI: 10.1016/j.bmc.2008.03.055] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2008] [Revised: 03/21/2008] [Accepted: 03/22/2008] [Indexed: 11/24/2022]
Abstract
The causative agent behind adult T-cell leukemia and tropical spastic paraparesis/HTLV-I-associated myelopathy is the human T-cell leukemia virus type 1 (HTLV-I). Tetrapeptidic HTLV-I protease inhibitors were designed on a previously reported potent inhibitor KNI-10516, with modifications at the P(3)-cap moieties. All the inhibitors showed high HIV-1 protease inhibitory activity (over 98% inhibition at 50nM) and most exhibited highly potent inhibition against HTLV-I protease (IC(50) values were less than 100nM).
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24
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Sperka T, Miklóssy G, Tie Y, Bagossi P, Zahuczky G, Boross P, Matúz K, Harrison RW, Weber IT, Tözsér J. Bovine leukemia virus protease: comparison with human T-lymphotropic virus and human immunodeficiency virus proteases. J Gen Virol 2007; 88:2052-2063. [PMID: 17554040 DOI: 10.1099/vir.0.82704-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Bovine leukemia virus (BLV) is a valuable model system for understanding human T-lymphotropic virus 1 (HTLV-1); the availability of an infectious BLV clone, together with animal-model systems, will help to explore anti-HTLV-1 strategies. Nevertheless, the specificity and inhibitor sensitivity of the BLV protease (PR) have not been characterized in detail. To facilitate such studies, a molecular model for the enzyme was built. The specificity of the BLV PR was studied with a set of oligopeptides representing naturally occurring cleavage sites in various retroviruses. Unlike HTLV-1 PR, but similar to the human immunodeficiency virus 1 (HIV-1) enzyme, BLV PR was able to hydrolyse the majority of the peptides, mostly at the same position as did their respective host PRs, indicating a broad specificity. When amino acid residues of the BLV PR substrate-binding sites were replaced by equivalent ones of the HIV-1 PR, many substitutions resulted in inactive protein, indicating a great sensitivity to mutations, as observed previously for the HTLV-1 PR. The specificity of the enzyme was studied further by using a series of peptides containing amino acid substitutions in a sequence representing a naturally occurring HTLV-1 PR cleavage site. Also, inhibitors of HIV-1 PR, HTLV-1 PR and other retroviral proteases were tested on the BLV PR. Interestingly, the BLV PR was more susceptible than the HTLV-1 PR to the inhibitors tested. Therefore, despite the specificity differences, in terms of mutation intolerance and inhibitor susceptibility of the PR, BLV and the corresponding animal-model systems may provide good models for testing of PR inhibitors that target HTLV-1.
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Affiliation(s)
- Tamás Sperka
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, Medical and Health Science Center, University of Debrecen, Hungary
| | - Gabriella Miklóssy
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, Medical and Health Science Center, University of Debrecen, Hungary
| | - Yunfeng Tie
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
| | - Péter Bagossi
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, Medical and Health Science Center, University of Debrecen, Hungary
| | - Gábor Zahuczky
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, Medical and Health Science Center, University of Debrecen, Hungary
| | - Péter Boross
- Department of Biology, Georgia State University, Atlanta, GA, USA
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, Medical and Health Science Center, University of Debrecen, Hungary
| | - Krisztina Matúz
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, Medical and Health Science Center, University of Debrecen, Hungary
| | - Robert W Harrison
- Department of Computer Science, Georgia State University, Atlanta, GA, USA
- Department of Biology, Georgia State University, Atlanta, GA, USA
| | - Irene T Weber
- Department of Biology, Georgia State University, Atlanta, GA, USA
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
| | - József Tözsér
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, Medical and Health Science Center, University of Debrecen, Hungary
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25
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Kimura T, Nguyen JT, Maegawa H, Nishiyama K, Arii Y, Matsui Y, Hayashi Y, Kiso Y. Chipping at large, potent human T-cell leukemia virus type 1 protease inhibitors to uncover smaller, equipotent inhibitors. Bioorg Med Chem Lett 2007; 17:3276-80. [PMID: 17448657 DOI: 10.1016/j.bmcl.2007.04.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2007] [Revised: 03/20/2007] [Accepted: 04/04/2007] [Indexed: 11/30/2022]
Abstract
The human T-cell leukemia virus type 1 (HTLV-I) causes adult T-cell leukemia and several severe chronic diseases. HTLV-I protease (PR) inhibition stops the propagation of the virus. Herein, truncation studies were performed on potent octapeptidic HTLV-I PR inhibitor KNI-10161 to derive small hexapeptide KNI-10127 with some loss in activity. After performing residue-substitution studies on compound KNI-10127, HTLV-I PR inhibitory activity was recovered in inhibitor KNI-10166.
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Affiliation(s)
- Tooru Kimura
- Department of Medicinal Chemistry, Center for Frontier Research in Medicinal Science and 21st Century COE Program, Kyoto Pharmaceutical University, Kyoto 607-8412, Japan
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26
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Kontijevskis A, Wikberg JES, Komorowski J. Computational proteomics analysis of HIV-1 protease interactome. Proteins 2007; 68:305-12. [PMID: 17427231 DOI: 10.1002/prot.21415] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
HIV-1 protease is a small homodimeric enzyme that ensures maturation of HIV virions by cleaving the viral precursor Gag and Gag-Pol polyproteins into structural and functional elements. The cleavage sites in the viral polyproteins share neither sequence homology nor binding motif and the specificity of the HIV-1 protease is therefore only partially understood. Using an extensive data set collected from 16 years of HIV proteome research we have here created a general and predictive rule-based model for HIV-1 protease specificity based on rough sets. We demonstrate that HIV-1 protease specificity is much more complex than previously anticipated, which cannot be defined based solely on the amino acids at the substrate's scissile bond or by any other single substrate amino acid position only. Our results show that the combination of at least three particular amino acids is needed in the substrate for a cleavage event to occur. Only by combining and analyzing massive amounts of HIV proteome data it was possible to discover these novel and general patterns of physico-chemical substrate cleavage determinants. Our study is an example how computational biology methods can advance the understanding of the viral interactomes.
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27
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Kontijevskis A, Prusis P, Petrovska R, Yahorava S, Mutulis F, Mutule I, Komorowski J, Wikberg JES. A look inside HIV resistance through retroviral protease interaction maps. PLoS Comput Biol 2007; 3:e48. [PMID: 17352531 PMCID: PMC1817660 DOI: 10.1371/journal.pcbi.0030048] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2006] [Accepted: 01/24/2007] [Indexed: 11/19/2022] Open
Abstract
Retroviruses affect a large number of species, from fish and birds to mammals and humans, with global socioeconomic negative impacts. Here the authors report and experimentally validate a novel approach for the analysis of the molecular networks that are involved in the recognition of substrates by retroviral proteases. Using multivariate analysis of the sequence-based physiochemical descriptions of 61 retroviral proteases comprising wild-type proteases, natural mutants, and drug-resistant forms of proteases from nine different viral species in relation to their ability to cleave 299 substrates, the authors mapped the physicochemical properties and cross-dependencies of the amino acids of the proteases and their substrates, which revealed a complex molecular interaction network of substrate recognition and cleavage. The approach allowed a detailed analysis of the molecular-chemical mechanisms involved in substrate cleavage by retroviral proteases.
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Affiliation(s)
- Aleksejs Kontijevskis
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
- Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden
| | - Peteris Prusis
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Ramona Petrovska
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Sviatlana Yahorava
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Felikss Mutulis
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Ilze Mutule
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Jan Komorowski
- Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden
| | - Jarl E. S Wikberg
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
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Naka H, Teruya K, Bang JK, Aimoto S, Tatsumi T, Konno H, Nosaka K, Akaji K. Evaluations of substrate specificity and inhibition at PR/p3 cleavage site of HTLV-1 protease. Bioorg Med Chem Lett 2006; 16:3761-4. [PMID: 16682197 DOI: 10.1016/j.bmcl.2006.04.056] [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: 03/22/2006] [Revised: 04/08/2006] [Accepted: 04/18/2006] [Indexed: 10/24/2022]
Abstract
Core sequences necessary for substrate recognition and its inhibition at the PR/p3 site of HTLV-1 protease were clarified for the first time. From the cleavage rates of peptides containing a part of the PR/p3 site, a heptapeptide was found to be the minimal sequence required for substrate recognition. The use of synthetic inhibitors containing hydroxyethylamine dipeptide isostere indicated that a tetrapeptide sequence was necessary to achieve potent inhibition.
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Affiliation(s)
- Hiromi Naka
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
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30
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Mitchell MS, Tözsér J, Princler G, Lloyd PA, Auth A, Derse D. Synthesis, processing, and composition of the virion-associated HTLV-1 reverse transcriptase. J Biol Chem 2005; 281:3964-71. [PMID: 16368688 DOI: 10.1074/jbc.m507660200] [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] [Indexed: 11/06/2022] Open
Abstract
It is not known whether the low infectivity and low virion-associated polymerase activity of human T-cell lymphotropic virus type-1 (HTLV-1) are due to the quantity or quality of the reverse transcriptase (RT), because the protein has not yet been fully characterized. We have developed anti-RT antibodies and constructed HTLV-1 expression plasmids that express truncated or hemagglutinin-tagged Pol polyproteins to examine the maturation and composition of HTLV-1 RT. We detected virion-associated proteins corresponding to RT-integrase (IN) (pr98) and RT (p62) as well as smaller proteins containing the polymerase (p49) or RNase H domains. We have identified the amino acid sequences in the Pol polyprotein that are cleaved by HTLV-1 protease to yield RT and IN. We have also identified the cleavage sites within RT that give rise to the p49 polymerase fragment. Immunoprecipitation of an epitope-tagged p62 subunit coprecipitated p49, indicating that the HTLV-1 RT complex can exist as a p62/p49 heterodimer analogous to the RT of HIV-1 (p66/p51).
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31
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Li M, Laco GS, Jaskolski M, Rozycki J, Alexandratos J, Wlodawer A, Gustchina A. Crystal structure of human T cell leukemia virus protease, a novel target for anticancer drug design. Proc Natl Acad Sci U S A 2005; 102:18332-7. [PMID: 16352712 PMCID: PMC1317974 DOI: 10.1073/pnas.0509335102] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The successful development of a number of HIV-1 protease (PR) inhibitors for the treatment of AIDS has validated the utilization of retroviral PRs as drug targets and necessitated their detailed structural study. Here we report the structure of a complex of human T cell leukemia virus type 1 (HTLV-1) PR with a substrate-based inhibitor bound in subsites P5 through P5'. Although HTLV-1 PR exhibits an overall fold similar to other retroviral PRs, significant structural differences are present in several loop areas, which include the functionally important flaps, previously considered to be structurally highly conserved. Potential key residues responsible for the resistance of HTLV-1 PR to anti-HIV drugs are identified. We expect that the knowledge accumulated during the development of anti-HIV drugs, particularly in overcoming drug resistance, will help in designing a novel class of antileukemia drugs targeting HTLV-1 PR and in predicting their drug-resistance profile. The structure presented here can be used as a starting point for the development of such anticancer therapies.
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Affiliation(s)
- Mi Li
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
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32
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Bagossi P, Sperka T, Fehér A, Kádas J, Zahuczky G, Miklóssy G, Boross P, Tözsér J. Amino acid preferences for a critical substrate binding subsite of retroviral proteases in type 1 cleavage sites. J Virol 2005; 79:4213-8. [PMID: 15767422 PMCID: PMC1061542 DOI: 10.1128/jvi.79.7.4213-4218.2005] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2004] [Accepted: 10/31/2004] [Indexed: 11/20/2022] Open
Abstract
The specificities of the proteases of 11 retroviruses representing each of the seven genera of the family Retroviridae were studied using a series of oligopeptides with amino acid substitutions in the P2 position of a naturally occurring type 1 cleavage site (Val-Ser-Gln-Asn-Tyr Pro-Ile-Val-Gln; the arrow indicates the site of cleavage) in human immunodeficiency virus type 1 (HIV-1). This position was previously found to be one of the most critical in determining the substrate specificity differences of retroviral proteases. Specificities at this position were compared for HIV-1, HIV-2, equine infectious anemia virus, avian myeloblastosis virus, Mason-Pfizer monkey virus, mouse mammary tumor virus, Moloney murine leukemia virus, human T-cell leukemia virus type 1, bovine leukemia virus, human foamy virus, and walleye dermal sarcoma virus proteases. Three types of P2 preferences were observed: a subgroup of proteases preferred small hydrophobic side chains (Ala and Cys), and another subgroup preferred large hydrophobic residues (Ile and Leu), while the protease of HIV-1 preferred an Asn residue. The specificity distinctions among the proteases correlated well with the phylogenetic tree of retroviruses prepared solely based on the protease sequences. Molecular models for all of the proteases studied were built, and they were used to interpret the results. While size complementarities appear to be the main specificity-determining features of the S2 subsite of retroviral proteases, electrostatic contributions may play a role only in the case of HIV proteases. In most cases the P2 residues of naturally occurring type 1 cleavage site sequences of the studied proteases agreed well with the observed P2 preferences.
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Affiliation(s)
- Péter Bagossi
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary
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33
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Maegawa H, Kimura T, Arii Y, Matsui Y, Kasai S, Hayashi Y, Kiso Y. Identification of peptidomimetic HTLV-I protease inhibitors containing hydroxymethylcarbonyl (HMC) isostere as the transition-state mimic. Bioorg Med Chem Lett 2005; 14:5925-9. [PMID: 15501070 DOI: 10.1016/j.bmcl.2004.09.034] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2004] [Accepted: 09/03/2004] [Indexed: 11/26/2022]
Abstract
Towards the development of chemotherapy for the infection by human T-cell leukemia virus type I (HTLV-I), we have established evaluation systems for HTLV-I protease (PR) inhibitors using both recombinant and chemically synthesized HTLV-I PRs. Newly synthesized substrate-based inhibitors containing hydroxymethylcarbonyl (HMC) isostere showed potent anti-HTLV-I PR activity.
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Affiliation(s)
- Hikoichiro Maegawa
- Department of Medicinal Chemistry, Center for Frontier Research in Medicinal Science, Kyoto Pharmaceutical University, Yamashina-ku, Kyoto 607-8412, Japan
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34
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Bagossi P, Kádas J, Miklóssy G, Boross P, Weber IT, Tözsér J. Development of a microtiter plate fluorescent assay for inhibition studies on the HTLV-1 and HIV-1 proteinases. J Virol Methods 2004; 119:87-93. [PMID: 15158589 DOI: 10.1016/j.jviromet.2004.03.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2003] [Revised: 10/18/2003] [Accepted: 03/01/2004] [Indexed: 10/26/2022]
Abstract
The proteinase of human T-cell leukemia virus type-1 (HTLV-1), similar to the proteinase of human immunodeficiency virus type-1 (HIV-1), is a potential target for chemotherapy, since the virus is associated with a number of human diseases. A microtiter plate fluorescent assay was developed for the HTLV-1 and HIV-1 proteinases for direct comparison of the inhibition profiles of the enzymes. It was established that, except for Indinavir, none of the inhibitors designed against the HIV-1 proteinase were able to inhibit the HTLV-1 proteinase in the studied concentration range, while two reduced peptide bond-containing peptides having the sequence of HTLV-1 cleavage sites were inhibitors of the HTLV-1 proteinase. One of these was potent enough to be used for active site titration of the HTLV-1 proteinase.
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Affiliation(s)
- Péter Bagossi
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, Medical and Health Science Center, University of Debrecen, H4012 POB 6 Debrecen, Hungary
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35
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Kádas J, Weber IT, Bagossi P, Miklóssy G, Boross P, Oroszlan S, Tözsér J. Narrow substrate specificity and sensitivity toward ligand-binding site mutations of human T-cell Leukemia virus type 1 protease. J Biol Chem 2004; 279:27148-57. [PMID: 15102858 DOI: 10.1074/jbc.m401868200] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human T-cell leukemia virus type 1 (HTLV-1) is associated with a number of human diseases; therefore, its protease is a potential target for chemotherapy. To compare the specificity of HTLV-1 protease with that of human immunodeficiency virus type 1 (HIV-1) protease, oligopeptides representing naturally occurring cleavage sites in various retroviruses were tested. The number of hydrolyzed peptides as well as the specificity constants suggested a substantially broader specificity of the HIV protease. Amino acid residues of HTLV-1 protease substrate-binding sites were replaced by equivalent ones of HIV-1 protease. Most of the single and multiple mutants had altered specificity and a dramatically reduced folding and catalytic capability, suggesting that mutations are not well tolerated in HTLV-1 protease. The catalytically most efficient mutant was that with the flap residues of HIV-1 protease. The inhibition profile of the mutants was also determined for five inhibitors used in clinical practice and inhibitor analogs of HTLV-1 cleavage sites. Except for indinavir, the HIV-1 protease inhibitors did not inhibit wild type and most of the mutant HTLV-1 proteases. The wild type HTLV-1 protease was inhibited by the reduced peptide bond-containing substrate analogs, whereas the mutants showed various degrees of weakened binding capability. Most interesting, the enzyme with HIV-1-like residues in the flap region was the most sensitive to the HIV-1 protease inhibitors and least sensitive to the HTLV-1 protease inhibitors, indicating that the flap plays an important role in defining the specificity differences of retroviral proteases.
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Affiliation(s)
- János Kádas
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, Medical and Health Science Center, University of Debrecen, H-4012 Debrecen, P. O. Box 6, Hungary
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36
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Akaji K, Teruya K, Aimoto S. Solid-phase synthesis of HTLV-1 protease inhibitors containing hydroxyethylamine dipeptide isostere. J Org Chem 2003; 68:4755-63. [PMID: 12790579 DOI: 10.1021/jo030063a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An efficient method has been developed for the first solid-phase synthesis of HTLV-1 protease inhibitors that contain hydroxyethylamine isostere as a transition-state mimetic. The synthetic procedure was designed to allow the evaluation of stereostructure-activity relationships at the scissile site. All the possible configurations at the hydroxy- and side chain-bearing asymmetric centers of the isostere were constructed by an ester-derived asymmetric aldol reaction. Each inhibitor containing the isostere backbone was synthesized on solid support by using the newly developed succinate ester linker. The configuration at the hydroxy- and side chain-bearing asymmetric center showed remarkable effects on the inhibitory activity; the K(i) value changed with approximately 2 orders of magnitude. The described approach enables an efficient preparation of the inhibitors containing secondary alcohol as a transition-state mimetic.
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Affiliation(s)
- Kenichi Akaji
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan.
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37
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Shuker SB, Mariani VL, Herger BE, Dennison KJ. Understanding HTLV-I protease. CHEMISTRY & BIOLOGY 2003; 10:373-80. [PMID: 12770819 DOI: 10.1016/s1074-5521(03)00104-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Suzanne Beckham Shuker
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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38
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Davis DA, Brown CA, Newcomb FM, Boja ES, Fales HM, Kaufman J, Stahl SJ, Wingfield P, Yarchoan R. Reversible oxidative modification as a mechanism for regulating retroviral protease dimerization and activation. J Virol 2003; 77:3319-25. [PMID: 12584357 PMCID: PMC149757 DOI: 10.1128/jvi.77.5.3319-3325.2003] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Human immunodeficiency virus protease activity can be regulated by reversible oxidation of a sulfur-containing amino acid at the dimer interface. We show here that oxidation of this amino acid in human immunodeficiency virus type 1 protease prevents dimer formation. Moreover, we show that human T-cell leukemia virus type 1 protease can be similarly regulated through reversible glutathionylation of its two conserved cysteine residues. Based on the known three-dimensional structures and multiple sequence alignments of retroviral proteases, it is predicted that the majority of retroviral proteases have sulfur-containing amino acids at the dimer interface. The regulation of protease activity by the modification of a sulfur-containing amino acid at the dimer interface may be a conserved mechanism among the majority of retroviruses.
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Affiliation(s)
- David A Davis
- HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
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39
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Heidecker G, Hill S, Lloyd PA, Derse D. A novel protease processing site in the transframe protein of human T-cell leukemia virus type 1 PR76(gag-pro) defines the N terminus of RT. J Virol 2002; 76:13101-5. [PMID: 12438640 PMCID: PMC136720 DOI: 10.1128/jvi.76.24.13101-13105.2002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genomic RNA of human T-cell leukemia virus type 1 encodes three polyproteins, Gag, Gag-Pro, and Gag-Pro-Pol, which are translated as a result of no, one, and two frameshifts, respectively. In this report we demonstrate that the 77 residues encoded at the C terminus of the Gag-Pro precursor can be collectively detected as an 8-kDa transframe protein (TFP) in virions. Mutant viruses with a C-terminally truncated TFP (19, 32, or 50 residues) had essentially a wild-type phenotype in vitro. However, a virus mutant that encoded only the Gag and Gag-Pro-Pol polyproteins due to a mutation in the second frameshift site, and hence did not produce TFP, was noninfectious. Mutation analysis of the proteolytic cleavage site between PR and TFP revealed the presence of an additional site and the existence of a p1 peptide separating protease and TFP. While removal of the cleavage site at the PR-p1 junction had a modest effect on virus replication, mutation of the p1-TFP cleavage site led to noninfectious virus and the loss of reverse transcriptase activity. Determination of the amino-terminal sequence of a hemagglutinin-tagged RT demonstrated that the same site is used in processing the Gag-Pro-Pol precursor and thus defines the start of mature RT. Neither mutation alone or in combination caused changes in the amounts or processing patterns of the Gag polyprotein, indicating that protease is active independent of its C terminus.
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Affiliation(s)
- Gisela Heidecker
- Basic Research Laboratory, NCI-Frederick, Building 567, Room 154, Frederick, MD 21702-1201, USA.
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40
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Ha JJ, Gaul DA, Mariani VL, Ding YS, Ikeda RA, Shuker SB. HTLV-I protease cleavage of P19/24 substrates is not dependent on NaCl concentration. Bioorg Chem 2002; 30:138-44. [PMID: 12020138 DOI: 10.1006/bioo.2001.1230] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Understanding the factors that affect the activity of Human T-cell Leukemia Virus type I (HTLV-I) protease is essential for the discovery of inhibitors to be used for the treatment of HTLV-I infection, but little has been reported on the protease to date. Here we report the production of HTLV-I protease in purified yields greater than 150 mg/L, determination of its extinction coefficient, and determination of the optimum conditions for cleavage of the p19/24 substrates (DABCYL)-(GABA)-PQVL-Nph-VMH-(EDANS), (DABSYL)-(GABA)-PQVL-Nph-VMH-(EDANS), and (DABSYL)-(GABA)-PQVLPVMH-(EDANS). The highest activity was found at pH 5.2-5.3 and 37 degrees C. There was no effect on activity upon change in sodium chloride concentration from 0 to 1500 mM. The values of K(m) and k(cat) for cleavage of these substrates by the protease with and without the histidine tag were determined.
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Affiliation(s)
- Julie J Ha
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA
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41
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Teruya K, Kawakami T, Akaji K, Aimoto S. Total synthesis of [L40I, C90A, C109A]-human T-cell leukemia virus type 1 protease. Tetrahedron Lett 2002. [DOI: 10.1016/s0040-4039(02)00040-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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42
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Kapust RB, Tözsér J, Fox JD, Anderson DE, Cherry S, Copeland TD, Waugh DS. Tobacco etch virus protease: mechanism of autolysis and rational design of stable mutants with wild-type catalytic proficiency. Protein Eng Des Sel 2001; 14:993-1000. [PMID: 11809930 DOI: 10.1093/protein/14.12.993] [Citation(s) in RCA: 671] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Because of its stringent sequence specificity, the catalytic domain of the nuclear inclusion protease from tobacco etch virus (TEV) is a useful reagent for cleaving genetically engineered fusion proteins. However, a serious drawback of TEV protease is that it readily cleaves itself at a specific site to generate a truncated enzyme with greatly diminished activity. The rate of autoinactivation is proportional to the concentration of TEV protease, implying a bimolecular reaction mechanism. Yet, a catalytically active protease was unable to convert a catalytically inactive protease into the truncated form. Adding increasing concentrations of the catalytically inactive protease to a fixed amount of the wild-type enzyme accelerated its rate of autoinactivation. Taken together, these results suggest that autoinactivation of TEV protease may be an intramolecular reaction that is facilitated by an allosteric interaction between protease molecules. In an effort to create a more stable protease, we made amino acid substitutions in the P2 and P1' positions of the internal cleavage site and assessed their impact on the enzyme's stability and catalytic activity. One of the P1' mutants, S219V, was not only far more stable than the wild-type protease (approximately 100-fold), but also a more efficient catalyst.
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Affiliation(s)
- R B Kapust
- Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, PO Box B, Frederick, MD 21702-1201, USA
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43
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Hayashi Y, Kinoshita Y, Hidaka K, Kiso A, Uchibori H, Kimura T, Kiso Y. Analysis of amide bond formation with an alpha-hydroxy-beta-amino acid derivative, 3-amino-2-hydroxy-4-phenylbutanoic acid, as an acyl component: byproduction of homobislactone. J Org Chem 2001; 66:5537-44. [PMID: 11485480 DOI: 10.1021/jo010233o] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the synthesis of peptidomimetics containing alpha-hydroxy-beta-amino acid, the coupling of this N(beta)-protected beta-amino acid with amine components was generally performed without the protection of its alpha-hydroxyl group. However, the formation of dipeptides in low yield was often observed when sterically hindered amine components were used. Boc-Apns-OH [Apns: (2S,3S)-3-amino-2-hydroxy-4-phenylbutanoic acid, allophenylnorstatine] (6), which is one of such beta-amino acid derivatives, is intensively employed as a core structure in the development of HIV-1 protease inhibitors. There have been no precise studies, to date, that have examined amide bond formation with alpha-hydroxy-beta-amino acid derivatives as an acyl component. To determine the cause of this low-yield reaction, we studied the amide bond formation focusing on the activation step of N(beta)-protected alpha-hydroxy-beta-amino acid by using a model coupling reaction between 6 and H-Dmt-OR [Dmt: (R)-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid] (7). A significant amount of homobislactone 9 was formed through the activation of the carboxyl group of 6 to the benzotriazole-type active esters such as OBt and OAt. In addition, this homobislactone formation was markedly increased in the presence of a catalytic amount of a base, which exhibited good correlation with the low yield of the amide bond formation, suggesting that homobislactone formation is one major reason for the low yield of the amide bond formation. Moreover, homobislactones were also formed in other derivatives of the N(beta)-protected alpha-hydroxy-beta-amino acid, suggesting a common feature of this type of amino acids. The use of a strong activation method like EDC--HOAt without base addition enhanced amide bond formation, although a small amount of homobislactone may be formed during the coupling reaction.
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Affiliation(s)
- Y Hayashi
- Department of Medicinal Chemistry, Center for Frontier Research in Medicinal Science, Kyoto Pharmaceutical University, Yamashina-Ku, Kyoto 607-8412, Japan.
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44
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Agbuya PG, Sherman NE, Moen LK. Proteolytic processing of the human T-cell lymphotropic virus 1 reverse transcriptase: identification of the N-terminal cleavage site by mass spectrometry. Arch Biochem Biophys 2001; 392:93-102. [PMID: 11469799 DOI: 10.1006/abbi.2001.2432] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Human T-cell lymphotropic virus 1 (HTLV-1) is a type C human retrovirus, which is the causative agent of Adult T-cell Leukemia and other diseases. The reverse transcriptase of HTLV-1 (E.C. 2.7.7.49) is synthesized as part of a Gag--Pro--Pol precursor protein, and the mature Gag, Pro, and Pol proteins, including the reverse transcriptase, are created by proteolytic processing catalyzed by the viral protease. The location of the proteolytic cleavage site, which creates the N-terminus of mature HTLV-1 reverse transcriptase, has not been previously identified. By using sequence comparisons of several retroviral polymerases, as well as information about the location of the ribosomal frameshift, we tentatively identified this N-terminal processing site. PCR amplification was used to construct a clone, which spans a region of the pro--pol junction of HTLV-1, to produce a recombinant Pro--Pol protein spanning the locations of those cleavage sites proposed by others as well as the one identified by our sequence alignment. Cleavage of the recombinant Pro--Pol protein by HTLV-1 protease generated a 5.5-kDa fragment. Analysis of this fragment by capillary LC-MS and MS/MS revealed the N-terminal cleavage site to be between Leu(147)--Pro(148) of the pro ORF. This is the first physical identification of the authentic amino acid sequence of the reverse transcriptase of HTLV-1. The data reported here provides a basis for further investigation of the function and structural aspects of protein-nucleic interaction.
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Affiliation(s)
- P G Agbuya
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia, USA
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45
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Tözsér J, Zahuczky G, Bagossi P, Louis JM, Copeland TD, Oroszlan S, Harrison RW, Weber IT. Comparison of the substrate specificity of the human T-cell leukemia virus and human immunodeficiency virus proteinases. EUROPEAN JOURNAL OF BIOCHEMISTRY 2000; 267:6287-95. [PMID: 11012683 DOI: 10.1046/j.1432-1327.2000.01714.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Human T-cell leukemia virus type-1 (HTLV-1) is associated with a number of human diseases. Based on the therapeutic success of human immunodeficiency virus type 1 (HIV-1) PR inhibitors, the proteinase (PR) of HTLV-1 is a potential target for chemotherapy. To facilitate the design of potent inhibitors, the subsite specificity of HTLV-1 PR was characterized and compared to that of HIV-1 PR. Two sets of substrates were used that contained single amino-acid substitutions in peptides representing naturally occurring cleavage sites in HIV-1 and HTLV-1. The original HIV-1 matrix/capsid cleavage site substrate and most of its substituted peptides were not hydrolyzed by the HTLV-1 enzyme, except for those with hydrophobic residues at the P4 and P2 positions. On the other hand, most of the peptides representing the HTLV-1 capsid/nucleocapsid cleavage site were substrates of both enzymes. A large difference in the specificity of HTLV-1 and HIV-1 proteinases was demonstrated by kinetic measurements, particularly with regard to the S4 and S2 subsites, whereas the S1 subsite appeared to be more conserved. A molecular model of the HTLV-1 PR in complex with this substrate was built, based on the crystal structure of the S9 mutant of Rous sarcoma virus PR, in order to understand the molecular basis of the enzyme specificity. Based on the kinetics of shortened analogs of the HTLV-1 substrate and on analysis of the modeled complex of HTLV-1 PR with substrate, the substrate binding site of the HTLV-1 PR appeared to be more extended than that of HIV-1 PR. Kinetic results also suggested that the cleavage site between the capsid and nucleocapsid protein of HTLV-1 is evolutionarily optimized for rapid hydrolysis.
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Affiliation(s)
- J Tözsér
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Hungary.
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Zahuczky G, Boross P, Bagossi P, Emri G, Copeland TD, Oroszlan S, Louis JM, Tözsér J. Cloning of the bovine leukemia virus proteinase in Escherichia coli and comparison of its specificity to that of human T-cell leukemia virus proteinase. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1478:1-8. [PMID: 10719169 DOI: 10.1016/s0167-4838(99)00240-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The proteinase of bovine leukemia virus (BLV) was cloned into pMal-c2 vector with N-terminal or with N- as well as C-terminal flanking sequences, and expressed in fusion with maltose binding protein. The proteinase self-processed itself from the fusion protein during expression and formed inclusion bodies. The enzyme was purified from inclusion bodies by cation-exchange chromatography followed by gel filtration. Specificity of the enzyme was compared to that of human T-cell leukemia proteinase type 1. Although the two viruses belong to the same subfamily of retroviruses, the differences in their proteinase specificity, based on kinetics with oligopeptide substrates representing naturally occurring cleavage sites as well as on inhibition pattern, appear to be pronounced.
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Affiliation(s)
- G Zahuczky
- Department of Biochemistry and Molecular Biology, University Medical School of Debrecen, P.O. Box 6, H-4012, Debrecen, Hungary
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Fenyöfalvi G, Bagossi P, Copeland TD, Oroszlan S, Boross P, Tözsér J. Expression and characterization of human foamy virus proteinase. FEBS Lett 1999; 462:397-401. [PMID: 10622733 DOI: 10.1016/s0014-5793(99)01563-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The human foamy virus proteinase was expressed in fusion with maltose binding protein in Escherichia coli and purified. The specific activity of the fusion protein was similar to that of the processed enzyme. The kinetic constants on foamy virus cleavage site substrates were very low but comparable to those obtained with the gag-encoded avian proteinase on its own substrates. The proteinase showed preference for high ionic strength and a pH optimum of 6.6. None of the tested retroviral cleavage site peptides were substrates, however, some peptides representing cleavage sites in retrotransposons were properly processed by the enzyme.
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Affiliation(s)
- G Fenyöfalvi
- Department of Biochemistry and Molecular Biology, University Medical School of Debrecen, Hungary
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