101
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Herzog K, Bracco P, Onoda A, Hayashi T, Hoffmann K, Schallmey A. Enzyme-substrate complex structures of CYP154C5 shed light on its mode of highly selective steroid hydroxylation. ACTA ACUST UNITED AC 2014; 70:2875-89. [PMID: 25372679 DOI: 10.1107/s1399004714019129] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 08/25/2014] [Indexed: 01/06/2023]
Abstract
CYP154C5 from Nocardia farcinica is a bacterial cytochrome P450 monooxygenase active on steroid molecules. The enzyme has recently been shown to exhibit exclusive regioselectivity and stereoselectivity in the conversion of various pregnans and androstans, yielding 16α-hydroxylated steroid products. This makes the enzyme an attractive candidate for industrial application in steroid hormone synthesis. Here, crystal structures of CYP154C5 in complex with four different steroid molecules were solved at resolutions of up to 1.9 Å. These are the first reported P450 structures from the CYP154 family in complex with a substrate. The active site of CYP154C5 forms a flattened hydrophobic channel with two opposing polar regions, perfectly resembling the size and polarity distribution of the steroids and thus resulting in highly specific steroid binding with Kd values in the range 10-100 nM. Key enzyme-substrate interactions were identified that accounted for the exclusive regioselectivity and stereoselectivity of the enzyme. Additionally, comparison of the four CYP154C5-steroid structures revealed distinct structural differences, explaining the observed variations in kinetic data obtained for this P450 with the steroids pregnenolone, dehydroepiandrosterone, progesterone, androstenedione, testosterone and nandrolone. This will facilitate the generation of variants with improved activity or altered selectivity in the future by means of protein engineering.
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Affiliation(s)
- Konrad Herzog
- Junior Professorship for Biocatalysis, Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Paula Bracco
- Junior Professorship for Biocatalysis, Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Akira Onoda
- Department of Applied Chemistry, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takashi Hayashi
- Department of Applied Chemistry, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kurt Hoffmann
- Institute of Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Anett Schallmey
- Junior Professorship for Biocatalysis, Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
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102
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Hutton JA, Goncalves V, Brannigan JA, Paape D, Wright MH, Waugh TM, Roberts SM, Bell AS, Wilkinson AJ, Smith DF, Leatherbarrow RJ, Tate EW. Structure-based design of potent and selective Leishmania N-myristoyltransferase inhibitors. J Med Chem 2014; 57:8664-70. [PMID: 25238611 PMCID: PMC4211304 DOI: 10.1021/jm5011397] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Inhibitors
of LeishmaniaN-myristoyltransferase
(NMT), a potential target for the
treatment of leishmaniasis, obtained from a high-throughput screen,
were resynthesized to validate activity. Crystal structures bound
to Leishmania major NMT were obtained,
and the active diastereoisomer of one of the inhibitors was identified.
On the basis of structural insights, enzyme inhibition was increased
40-fold through hybridization of two distinct binding modes, resulting
in novel, highly potent Leishmania donovani NMT inhibitors with good selectivity over the human enzyme.
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Affiliation(s)
- Jennie A Hutton
- Department of Chemistry, Imperial College London , London SW7 2AZ, U.K
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103
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Burlein C, Bahnck C, Bhatt T, Murphy D, Lemaire P, Carroll S, Miller MD, Lai MT. Development of a sensitive amplified luminescent proximity homogeneous assay to monitor the interactions between pTEFb and Tat. Anal Biochem 2014; 465:164-71. [PMID: 25132562 DOI: 10.1016/j.ab.2014.08.007] [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: 06/09/2014] [Revised: 08/03/2014] [Accepted: 08/06/2014] [Indexed: 12/31/2022]
Abstract
The viral transactivator protein (Tat) plays an essential role in the replication of human immunodeficiency type 1 virus (HIV-1) by recruiting the host positive transcription elongation factor (pTEFb) to the RNA polymerase II transcription machinery to enable an efficient HIV-1 RNA elongation process. Blockade of the interaction between Tat and pTEFb represents a novel strategy for developing a new class of antiviral agents. In this study, we developed a homogeneous assay in AlphaLISA (amplified luminescent proximity homogeneous assay) format using His-tagged pTEFb and biotinylated Tat to monitor the interaction between Tat and pTEFb. On optimizing the assay conditions, the signal-to-background ratio was found to be greater than 10-fold. The assay was validated with untagged Tat and peptides known to compete with Tat for pTEFb binding. The Z' of the assay is greater than 0.5, indicating that the assay is robust and can be easily adapted to a high-throughput screening format. Furthermore, the affinity between Tat and pTEFb was determined to be approximately 20 pM, and only 7% of purified Tat was found to be active in forming tertiary complex with pTEFb. Development of this assay should facilitate the discovery of a new class of antiviral agents providing HIV-1 patients with broader treatment choices.
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Affiliation(s)
- Christine Burlein
- Department of In Vitro Pharmacology, Merck Research Laboratories, West Point, PA 19486, USA
| | - Carolyn Bahnck
- Department of In Vitro Pharmacology, Merck Research Laboratories, West Point, PA 19486, USA
| | - Triveni Bhatt
- Department of In Vitro Pharmacology, Merck Research Laboratories, West Point, PA 19486, USA
| | - Dennis Murphy
- Department of In Vitro Pharmacology, Merck Research Laboratories, West Point, PA 19486, USA
| | - Peter Lemaire
- Department of In Vitro Pharmacology, Merck Research Laboratories, West Point, PA 19486, USA
| | - Steve Carroll
- Department of In Vitro Pharmacology, Merck Research Laboratories, West Point, PA 19486, USA
| | - Michael D Miller
- Antiviral Research, Merck Research Laboratories, West Point, PA 19486, USA
| | - Ming-Tain Lai
- Antiviral Research, Merck Research Laboratories, West Point, PA 19486, USA.
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104
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Burch JD, Lau K, Barker JJ, Brookfield F, Chen Y, Chen Y, Eigenbrot C, Ellebrandt C, Ismaili MHA, Johnson A, Kordt D, MacKinnon CH, McEwan PA, Ortwine DF, Stein DB, Wang X, Winkler D, Yuen PW, Zhang Y, Zarrin AA, Pei Z. Property- and structure-guided discovery of a tetrahydroindazole series of interleukin-2 inducible T-cell kinase inhibitors. J Med Chem 2014; 57:5714-27. [PMID: 24918870 DOI: 10.1021/jm500550e] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Interleukin-2 inducible T-cell kinase (ITK), a member of the Tec family of tyrosine kinases, plays a major role in T-cell signaling downstream of the T-cell receptor (TCR), and considerable efforts have been directed toward discovery of ITK-selective inhibitors as potential treatments of inflammatory disorders such as asthma. Using a previously disclosed indazole series of inhibitors as a starting point, and using X-ray crystallography and solubility forecast index (SFI) as guides, we evolved a series of tetrahydroindazole inhibitors with improved potency, selectivity, and pharmaceutical properties. Highlights include identification of a selectivity pocket above the ligand plane, and identification of appropriate lipophilic substituents to occupy this space. This effort culminated in identification of a potent and selective ITK inhibitor (GNE-9822) with good ADME properties in preclinical species.
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Affiliation(s)
- Jason D Burch
- Genentech Inc. , 1 DNA Way, South San Francisco, California 94080, United States
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105
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Ligand efficiency metrics considered harmful. J Comput Aided Mol Des 2014; 28:699-710. [DOI: 10.1007/s10822-014-9757-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 05/26/2014] [Indexed: 10/25/2022]
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106
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Tipton KF, Armstrong RN, Bakker BM, Bairoch A, Cornish-Bowden A, Halling PJ, Hofmeyr JH, Leyh TS, Kettner C, Raushel FM, Rohwer J, Schomburg D, Steinbeck C. Standards for Reporting Enzyme Data: The STRENDA Consortium: What it aims to do and why it should be helpful. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.pisc.2014.02.012] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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107
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A structural biology approach enables the development of antimicrobials targeting bacterial immunophilins. Antimicrob Agents Chemother 2013; 58:1458-67. [PMID: 24366729 DOI: 10.1128/aac.01875-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Macrophage infectivity potentiators (Mips) are immunophilin proteins and essential virulence factors for a range of pathogenic organisms. We applied a structural biology approach to characterize a Mip from Burkholderia pseudomallei (BpML1), the causative agent of melioidosis. Crystal structure and nuclear magnetic resonance analyses of BpML1 in complex with known macrocyclics and other derivatives led to the identification of a key chemical scaffold. This scaffold possesses inhibitory potency for BpML1 without the immunosuppressive components of related macrocyclic agents. Biophysical characterization of a compound series with this scaffold allowed binding site specificity in solution and potency determinations for rank ordering the set. The best compounds in this series possessed a low-micromolar affinity for BpML1, bound at the site of enzymatic activity, and inhibited a panel of homologous Mip proteins from other pathogenic bacteria, without demonstrating toxicity in human macrophages. Importantly, the in vitro activity of BpML1 was reduced by these compounds, leading to decreased macrophage infectivity and intracellular growth of Burkholderia pseudomallei. These compounds offer the potential for activity against a new class of antimicrobial targets and present the utility of a structure-based approach for novel antimicrobial drug discovery.
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108
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Kwiatkowska A, Couture F, Levesque C, Ly K, Desjardins R, Beauchemin S, Prahl A, Lammek B, Neugebauer W, Dory YL, Day R. Design, synthesis, and structure-activity relationship studies of a potent PACE4 inhibitor. J Med Chem 2013; 57:98-109. [PMID: 24350995 DOI: 10.1021/jm401457n] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
PACE4 plays an important role in the progression of prostate cancer and is an attractive target for the development of novel inhibitor-based tumor therapies. We previously reported the design and synthesis of a novel, potent, and relatively selective PACE4 inhibitor known as a Multi-Leu (ML) peptide. In the present work, we examined the ML peptide through detailed structure-activity relationship studies. A variety of ML-peptide analogues modified at the P8-P5 positions with leucine isomers (Nle, DLeu, and DNle) or substituted at the P1 position with arginine mimetics were tested for their inhibitory activity, specificity, stability, and antiproliferative effect. By incorporating d isomers at the P8 position or a decarboxylated arginine mimetic, we obtained analogues with an improved stability profile and excellent antiproliferative properties. The DLeu or DNle residue also has improved specificity toward PACE4, whereas specificity was reduced for a peptide modified with the arginine mimetic, such as 4-amidinobenzylamide.
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Affiliation(s)
- Anna Kwiatkowska
- Institut de Pharmacologie de Sherbrooke, Department of Surgery/Urology Division, Université de Sherbrooke , 3001 12th Avenue North, Sherbrooke, Québec, J1H 5N4, Canada
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109
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Salas-Sarduy E, Cabrera-Muñoz A, Cauerhff A, González-González Y, Trejo SA, Chidichimo A, Chávez-Planes MDLA, Cazzulo JJ. Antiparasitic effect of a fraction enriched in tight-binding protease inhibitors isolated from the Caribbean coral Plexaura homomalla. Exp Parasitol 2013; 135:611-22. [DOI: 10.1016/j.exppara.2013.09.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 09/17/2013] [Accepted: 09/22/2013] [Indexed: 01/13/2023]
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110
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Bhattarai S, Liou K, Oh TJ. Hydroxylation of long chain fatty acids by CYP147F1, a new cytochrome P450 subfamily protein from Streptomyces peucetius. Arch Biochem Biophys 2013; 539:63-9. [DOI: 10.1016/j.abb.2013.09.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 09/09/2013] [Accepted: 09/11/2013] [Indexed: 10/26/2022]
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111
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Desmolaris, a novel factor XIa anticoagulant from the salivary gland of the vampire bat (Desmodus rotundus) inhibits inflammation and thrombosis in vivo. Blood 2013; 122:4094-106. [PMID: 24159172 DOI: 10.1182/blood-2013-08-517474] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The identity of vampire bat saliva anticoagulant remained elusive for almost a century. Sequencing the salivary gland genes from the vampire bat Desmodus rotundus identified Desmolaris as a novel 21.5-kDa naturally deleted (Kunitz 1-domainless) form of tissue factor pathway inhibitor. Recombinant Desmolaris was expressed in HEK293 cells and characterized as a slow, tight, and noncompetitive inhibitor of factor (F) XIa by a mechanism modulated by heparin. Desmolaris also inhibits FXa with lower affinity, independently of protein S. In addition, Desmolaris binds kallikrein and reduces bradykinin generation in plasma activated with kaolin. Truncated and mutated forms of Desmolaris determined that Arg32 in the Kunitz-1 domain is critical for protease inhibition. Moreover, Kunitz-2 and the carboxyl-terminus domains mediate interaction of Desmolaris with heparin and are required for optimal inhibition of FXIa and FXa. Notably, Desmolaris (100 μg/kg) inhibited FeCl3-induced carotid artery thrombus without impairing hemostasis. These results imply that FXIa is the primary in vivo target for Desmolaris at antithrombotic concentrations. Desmolaris also reduces the polyphosphate-induced increase in vascular permeability and collagen- and epinephrine-mediated thromboembolism in mice. Desmolaris emerges as a novel anticoagulant targeting FXIa under conditions in which the coagulation activation, particularly the contact pathway, plays a major pathological role.
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112
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Wadsworth JM, Clarke DJ, McMahon SA, Lowther JP, Beattie AE, Langridge-Smith PRR, Broughton HB, Dunn TM, Naismith JH, Campopiano DJ. The chemical basis of serine palmitoyltransferase inhibition by myriocin. J Am Chem Soc 2013; 135:14276-85. [PMID: 23957439 DOI: 10.1021/ja4059876] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Sphingolipids (SLs) are essential components of cellular membranes formed from the condensation of L-serine and a long-chain acyl thioester. This first step is catalyzed by the pyridoxal-5'-phosphate (PLP)-dependent enzyme serine palmitoyltransferase (SPT) which is a promising therapeutic target. The fungal natural product myriocin is a potent inhibitor of SPT and is widely used to block SL biosynthesis despite a lack of a detailed understanding of its molecular mechanism. By combining spectroscopy, mass spectrometry, X-ray crystallography, and kinetics, we have characterized the molecular details of SPT inhibition by myriocin. Myriocin initially forms an external aldimine with PLP at the active site, and a structure of the resulting co-complex explains its nanomolar affinity for the enzyme. This co-complex then catalytically degrades via an unexpected 'retro-aldol-like' cleavage mechanism to a C18 aldehyde which in turn acts as a suicide inhibitor of SPT by covalent modification of the essential catalytic lysine. This surprising dual mechanism of inhibition rationalizes the extraordinary potency and longevity of myriocin inhibition.
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Affiliation(s)
- John M Wadsworth
- School of Chemistry, The University of Edinburgh , Edinburgh, Scotland, EH9 3JJ, United Kingdom
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113
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Howe AYM, Venkatraman S. The Discovery and Development of Boceprevir: A Novel, First-generation Inhibitor of the Hepatitis C Virus NS3/4A Serine Protease. J Clin Transl Hepatol 2013; 1:22-32. [PMID: 26357603 PMCID: PMC4548358 DOI: 10.14218/jcth.2013.002xx] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 02/22/2013] [Accepted: 02/25/2013] [Indexed: 12/11/2022] Open
Abstract
An estimated 2-3% of the world's population is infected with hepatitis C virus (HCV), making it a major global health problem. Consequently, over the past 15 years, there has been a concerted effort to understand the pathophysiology of HCV infection and the molecular virology of replication, and to utilize this knowledge for the development of more effective treatments. The virally encoded non-structural serine protease (NS3) is required to process the HCV polyprotein and release the individual proteins that form the viral RNA replication machinery. Given its critical role in the replication of HCV, the NS3 protease has been recognized as a potential drug target for the development of selective HCV therapies. In this review, we describe the key scientific discoveries that led to the approval of boceprevir, a first-generation, selective, small molecule inhibitor of the NS3 protease. We highlight the early studies that reported the crystal structure of the NS3 protease, its role in the processing of the HCV polyprotein, and the structural requirements critical for substrate cleavage. We also consider the novel attributes of the NS3 protease-binding pocket that challenged development of small molecule inhibitors, and the studies that ultimately yielded milligram quantities of this enzyme in a soluble, tractable form suitable for inhibitor screening programs. Finally, we describe the discovery of boceprevir, from the early chemistry studies, through the development of high-throughput assays, to the phase III clinical development program that ultimately provided the basis for approval of this drug. This latest phase in the development of boceprevir represents the culmination of a major global effort to understand the pathophysiology of HCV and develop small molecule inhibitors for the NS3 protease.
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114
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Avrutina O, Fittler H, Glotzbach B, Kolmar H, Empting M. Between two worlds: a comparative study on in vitro and in silico inhibition of trypsin and matriptase by redox-stable SFTI-1 variants at near physiological pH. Org Biomol Chem 2013; 10:7753-62. [PMID: 22903577 DOI: 10.1039/c2ob26162f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A comparative study on in vitro and in silico inhibition of trypsin and matriptase by derivatives of the sunflower trypsin inhibitor-1 at near physiological pH is reported. Besides wild-type bicyclic SFTI-1, monocyclic variants possessing native cystine as well as redox-stable triazolyl side-chain macrocyclization motifs were studied for the first time in matriptase inhibition assays. Interestingly, monocyclic SFTI-1[1,14] demonstrated higher potency against this pharmacologically relevant protease compared to its bicyclic counterpart. Structural analysis of binding/inhibition of investigated SFTI-1 derivatives was performed using a combination of molecular dynamics simulations and docking experiments. In silico data were in good accordance with in vitro results, indicating the importance of the terminal inhibitor regions for the affinity towards matriptase. Presented work gives new perspectives for the optimization of the SFTI-1 framework towards in vivo applications.
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Affiliation(s)
- Olga Avrutina
- Clemens-Schöpf Institute of Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Petersenstr. 22, 64287 Darmstadt, Germany
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115
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Hsu-Kim H, Kucharzyk KH, Zhang T, Deshusses MA. Mechanisms regulating mercury bioavailability for methylating microorganisms in the aquatic environment: a critical review. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:2441-56. [PMID: 23384298 DOI: 10.1021/es304370g] [Citation(s) in RCA: 401] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Mercury is a potent neurotoxin for humans, particularly if the metal is in the form of methylmercury. Mercury is widely distributed in aquatic ecosystems as a result of anthropogenic activities and natural earth processes. A first step toward bioaccumulation of methylmercury in aquatic food webs is the methylation of inorganic forms of the metal, a process that is primarily mediated by anaerobic bacteria. In this Review, we evaluate the current state of knowledge regarding the mechanisms regulating microbial mercury methylation, including the speciation of mercury in environments where methylation occurs and the processes that control mercury bioavailability to these organisms. Methylmercury production rates are generally related to the presence and productivity of methylating bacteria and also the uptake of inorganic mercury to these microorganisms. Our understanding of the mechanisms behind methylation is limited due to fundamental questions related to the geochemical forms of mercury that persist in anoxic settings, the mode of uptake by methylating bacteria, and the biochemical pathway by which these microorganisms produce and degrade methylmercury. In anoxic sediments and water, the geochemical forms of mercury (and subsequent bioavailability) are largely governed by reactions between Hg(II), inorganic sulfides, and natural organic matter. These interactions result in a mixture of dissolved, nanoparticulate, and larger crystalline particles that cannot be adequately represented by conventional chemical equilibrium models for Hg bioavailability. We discuss recent advances in nanogeochemistry and environmental microbiology that can provide new tools and unique perspectives to help us solve the question of how microorganisms methylate mercury. An understanding of the factors that cause the production and degradation of methylmercury in the environment is ultimately needed to inform policy makers and develop long-term strategies for controlling mercury contamination.
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Affiliation(s)
- Heileen Hsu-Kim
- Department of Civil and Environmental Engineering, Duke University , 121 Hudson Hall, Box 90287, Durham, North Carolina 27708, USA.
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116
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Higashi S, Hirose T, Takeuchi T, Miyazaki K. Molecular design of a highly selective and strong protein inhibitor against matrix metalloproteinase-2 (MMP-2). J Biol Chem 2013; 288:9066-76. [PMID: 23395821 DOI: 10.1074/jbc.m112.441758] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Synthetic inhibitors of matrix metalloproteinases (MMPs), designed previously, as well as tissue inhibitors of metalloproteinases (TIMPs) lack enzyme selectivity, which has been a major obstacle for developing inhibitors into safe and effective MMP-targeted drugs. Here we designed a fusion protein named APP-IP-TIMP-2, in which the ten amino acid residue sequence of APP-derived MMP-2 selective inhibitory peptide (APP-IP) is added to the N terminus of TIMP-2. The APP-IP and TIMP-2 regions of the fusion protein are designed to interact with the active site and the hemopexin-like domain of MMP-2, respectively. The reactive site of the TIMP-2 region, which has broad specificity against MMPs, is blocked by the APP-IP adduct. The recombinant APP-IP-TIMP-2 showed strong inhibitory activity toward MMP-2 (Ki(app) = 0.68 pm), whereas its inhibitory activity toward MMP-1, MMP-3, MMP-7, MMP-8, MMP-9, or MT1-MMP was six orders of magnitude or more weaker (IC50 > 1 μm). The fusion protein inhibited the activation of pro-MMP-2 in the concanavalin A-stimulated HT1080 cells, degradation of type IV collagen by the cells, and the migration of stimulated cells. Compared with the decapeptide APP-IP (t½ = 30 min), APP-IP-TIMP-2 (t½ ≫ 96 h) showed a much longer half-life in cultured tumor cells. Therefore, the fusion protein may be a useful tool to evaluate contributions of proteolytic activity of MMP-2 in various pathophysiological processes. It may also be developed as an effective anti-tumor drug with restricted side effects.
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Affiliation(s)
- Shouichi Higashi
- Department of Genome System Science, Graduate School of Nanobioscience, Yokohama City University, 641-12, Maioka-cho, Totsuka-ku, Yokohama 244-0813, Japan.
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117
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Janocha S, Zapp J, Hutter M, Kleser M, Bohlmann J, Bernhardt R. Resin Acid Conversion with CYP105A1: An Enzyme with Potential for the Production of Pharmaceutically Relevant Diterpenoids. Chembiochem 2013; 14:467-73. [DOI: 10.1002/cbic.201200729] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Indexed: 11/08/2022]
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118
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Lee HJ, Schaefer G, Heffron TP, Shao L, Ye X, Sideris S, Malek S, Chan E, Merchant M, La H, Ubhayakar S, Yauch RL, Pirazzoli V, Politi K, Settleman J. Noncovalent wild-type-sparing inhibitors of EGFR T790M. Cancer Discov 2012; 3:168-81. [PMID: 23229345 DOI: 10.1158/2159-8290.cd-12-0357] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
UNLABELLED Approximately half of EGFR-mutant non-small cell lung cancer (NSCLC) patients treated with small-molecule EGFR kinase inhibitors develop drug resistance associated with the EGF receptor (EGFR) T790M "gatekeeper" substitution, prompting efforts to develop covalent EGFR inhibitors, which can effectively suppress EGFR T790M in preclinical models. However, these inhibitors have yet to prove clinically efficacious, and their toxicity in skin, reflecting activity against wild-type EGFR, may limit dosing required to effectively suppress EGFR T790M in vivo. While profiling sensitivity to various kinase inhibitors across a large cancer cell line panel, we identified indolocarbazole compounds, including a clinically well-tolerated FLT3 inhibitor, as potent and reversible inhibitors of EGFR T790M that spare wild-type EGFR. These findings show the use of broad cancer cell profiling of kinase inhibitor efficacy to identify unanticipated novel applications, and they identify indolocarbazole compounds as potentially effective EGFR inhibitors in the context of T790M-mediated drug resistance in NSCLC. SIGNIFICANCE EGFR-mutant lung cancer patients who respond to currently used EGFR kinase inhibitors invariably develop drug resistance, which is associated with the EGFR T790M resistance mutation in about half these cases. We unexpectedly identified a class of reversible potent inhibitors of EGFR T790M that do not inhibit wild-type EGFR, revealing a promising therapeutic strategy to overcome T790M-associated drug-resistant lung cancers.
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Affiliation(s)
- Ho-June Lee
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, California 94080, USA
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119
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HLA-DO acts as a substrate mimic to inhibit HLA-DM by a competitive mechanism. Nat Struct Mol Biol 2012; 20:90-8. [PMID: 23222639 PMCID: PMC3537886 DOI: 10.1038/nsmb.2460] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 10/25/2012] [Indexed: 12/03/2022]
Abstract
MHCII proteins bind peptide antigens in endosomal compartments of antigen-presenting cells. The non-classical MHCII protein HLA-DM chaperones peptide-free MHCII against inactivation and catalyzes peptide exchange on loaded MHCII. Another non-classical MHCII protein, HLA-DO, binds HLA-DM and influences the repertoire of peptides presented by MHCII proteins. However, the mechanism by which HLA-DO functions is unclear. Here we use x-ray crystallography, enzyme kinetics and mutagenesis approaches to investigate human HLA-DO structure and function. In complex with HLA-DM, HLA-DO adopts a classical MHCII structure, with alterations near the alpha subunit 310 helix. HLA-DO binds to HLA-DM at the same sites implicated in MHCII interaction, and kinetic analysis demonstrates that HLA-DO acts as a competitive inhibitor. These results show that HLA-DO inhibits HLA-DM function by acting as a substrate mimic and place constraints on possible functional roles for HLA-DO in antigen presentation.
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120
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Unique thrombin inhibition mechanism by anophelin, an anticoagulant from the malaria vector. Proc Natl Acad Sci U S A 2012; 109:E3649-58. [PMID: 23223529 DOI: 10.1073/pnas.1211614109] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Anopheles mosquitoes are vectors of malaria, a potentially fatal blood disease affecting half a billion humans worldwide. These blood-feeding insects include in their antihemostatic arsenal a potent thrombin inhibitor, the flexible and cysteine-less anophelin. Here, we present a thorough structure-and-function analysis of thrombin inhibition by anophelin, including the 2.3-Å crystal structure of the human thrombin·anophelin complex. Anophelin residues 32-61 are well-defined by electron density, completely occupying the long cleft between the active site and exosite I. However, in striking contrast to substrates, the D50-R53 anophelin tetrapeptide occupies the active site cleft of the enzyme, whereas the upstream residues A35-P45 shield the regulatory exosite I, defining a unique reverse-binding mode of an inhibitor to the target proteinase. The extensive interactions established, the disruption of thrombin's active site charge-relay system, and the insertion of residue R53 into the proteinase S(1) pocket in an orientation opposed to productive substrates explain anophelin's remarkable specificity and resistance to proteolysis by thrombin. Complementary biophysical and functional characterization of point mutants and truncated versions of anophelin unambiguously establish the molecular mechanism of action of this family of serine proteinase inhibitors (I77). These findings have implications for the design of novel antithrombotics.
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121
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Bell SG, Zhou R, Yang W, Tan ABH, Gentleman AS, Wong LL, Zhou W. Investigation of the Substrate Range of CYP199A4: Modification of the Partition between Hydroxylation and Desaturation Activities by Substrate and Protein Engineering. Chemistry 2012; 18:16677-88. [DOI: 10.1002/chem.201202776] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Indexed: 11/08/2022]
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122
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Hanan EJ, van Abbema A, Barrett K, Blair WS, Blaney J, Chang C, Eigenbrot C, Flynn S, Gibbons P, Hurley CA, Kenny JR, Kulagowski J, Lee L, Magnuson SR, Morris C, Murray J, Pastor RM, Rawson T, Siu M, Ultsch M, Zhou A, Sampath D, Lyssikatos JP. Discovery of Potent and Selective Pyrazolopyrimidine Janus Kinase 2 Inhibitors. J Med Chem 2012; 55:10090-107. [DOI: 10.1021/jm3012239] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | | | | | | | | | | | | | - Sean Flynn
- Argenta,
8/9 Spire Green Centre,
Flex Meadow, Harlow, Essex CM19 5TR, United Kingdom
| | | | - Christopher A. Hurley
- Argenta,
8/9 Spire Green Centre,
Flex Meadow, Harlow, Essex CM19 5TR, United Kingdom
| | | | - Janusz Kulagowski
- Argenta,
8/9 Spire Green Centre,
Flex Meadow, Harlow, Essex CM19 5TR, United Kingdom
| | | | | | - Claire Morris
- Argenta,
8/9 Spire Green Centre,
Flex Meadow, Harlow, Essex CM19 5TR, United Kingdom
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123
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de Leon-Boenig G, Bowman KK, Feng JA, Crawford T, Everett C, Franke Y, Oh A, Stanley M, Staben ST, Starovasnik MA, Wallweber HJA, Wu J, Wu LC, Johnson AR, Hymowitz SG. The crystal structure of the catalytic domain of the NF-κB inducing kinase reveals a narrow but flexible active site. Structure 2012; 20:1704-14. [PMID: 22921830 DOI: 10.1016/j.str.2012.07.013] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 07/20/2012] [Accepted: 07/23/2012] [Indexed: 11/18/2022]
Abstract
The NF-κB inducing kinase (NIK) regulates the non-canonical NF-κB pathway downstream of important clinical targets including BAFF, RANKL, and LTβ. Despite numerous genetic studies associating dysregulation of this pathway with autoimmune diseases and hematological cancers, detailed molecular characterization of this central signaling node has been lacking. We undertook a systematic cloning and expression effort to generate soluble, well-behaved proteins encompassing the kinase domains of human and murine NIK. Structures of the apo NIK kinase domain from both species reveal an active-like conformation in the absence of phosphorylation. ATP consumption and peptide phosphorylation assays confirm that phosphorylation of NIK does not increase enzymatic activity. Structures of murine NIK bound to inhibitors possessing two different chemotypes reveal conformational flexibility in the gatekeeper residue controlling access to a hydrophobic pocket. Finally, a single amino acid difference affects the ability of some inhibitors to bind murine and human NIK with the same affinity.
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Affiliation(s)
- Gladys de Leon-Boenig
- Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
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124
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Venkataraman H, Beer SBAD, Geerke DP, Vermeulen NPE, Commandeur JNM. Regio- and Stereoselective Hydroxylation of Optically Active α-Ionone Enantiomers by Engineered Cytochrome P450 BM3 Mutants. Adv Synth Catal 2012. [DOI: 10.1002/adsc.201200067] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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125
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Bell SG, Yang W, Dale A, Zhou W, Wong LL. Improving the affinity and activity of CYP101D2 for hydrophobic substrates. Appl Microbiol Biotechnol 2012; 97:3979-90. [DOI: 10.1007/s00253-012-4278-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 06/24/2012] [Accepted: 06/29/2012] [Indexed: 11/28/2022]
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126
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Collin N, Assumpção TCF, Mizurini DM, Gilmore DC, Dutra-Oliveira A, Kotsyfakis M, Sá-Nunes A, Teixeira C, Ribeiro JMC, Monteiro RQ, Valenzuela JG, Francischetti IMB. Lufaxin, a novel factor Xa inhibitor from the salivary gland of the sand fly Lutzomyia longipalpis blocks protease-activated receptor 2 activation and inhibits inflammation and thrombosis in vivo. Arterioscler Thromb Vasc Biol 2012; 32:2185-98. [PMID: 22796577 DOI: 10.1161/atvbaha.112.253906] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVE Blood-sucking arthropods' salivary glands contain a remarkable diversity of antihemostatics. The aim of the present study was to identify the unique salivary anticoagulant of the sand fly Lutzomyia longipalpis, which remained elusive for decades. METHODS AND RESULTS Several L. longipalpis salivary proteins were expressed in human embryonic kidney 293 cells and screened for inhibition of blood coagulation. A novel 32.4-kDa molecule, named Lufaxin, was identified as a slow, tight, noncompetitive, and reversible inhibitor of factor Xa (FXa). Notably, Lufaxin's primary sequence does not share similarity to any physiological or salivary inhibitors of coagulation reported to date. Lufaxin is specific for FXa and does not interact with FX, Dansyl-Glu-Gly-Arg-FXa, or 15 other enzymes. In addition, Lufaxin blocks prothrombinase and increases both prothrombin time and activated partial thromboplastin time. Surface plasmon resonance experiments revealed that FXa binds Lufaxin with an equilibrium constant ≈3 nM, and isothermal titration calorimetry determined a stoichiometry of 1:1. Lufaxin also prevents protease-activated receptor 2 activation by FXa in the MDA-MB-231 cell line and abrogates edema formation triggered by injection of FXa in the paw of mice. Moreover, Lufaxin prevents FeCl(3)-induced carotid artery thrombus formation and prolongs activated partial thromboplastin time ex vivo, implying that it works as an anticoagulant in vivo. Finally, salivary gland of sand flies was found to inhibit FXa and to interact with the enzyme. CONCLUSIONS Lufaxin belongs to a novel family of slow-tight FXa inhibitors, which display antithrombotic and anti-inflammatory activities. It is a useful tool to understand FXa structural features and its role in prohemostatic and proinflammatory events.
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Affiliation(s)
- Nicolas Collin
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20892, USA
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127
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Dossetter AG, Beeley H, Bowyer J, Cook CR, Crawford JJ, Finlayson JE, Heron NM, Heyes C, Highton AJ, Hudson JA, Jestel A, Kenny PW, Krapp S, Martin S, MacFaul PA, McGuire TM, Gutierrez PM, Morley AD, Morris JJ, Page KM, Ribeiro LR, Sawney H, Steinbacher S, Smith C, Vickers M. (1R,2R)-N-(1-Cyanocyclopropyl)-2-(6-methoxy-1,3,4,5-tetrahydropyrido[4,3-b]indole-2-carbonyl)cyclohexanecarboxamide (AZD4996): A Potent and Highly Selective Cathepsin K Inhibitor for the Treatment of Osteoarthritis. J Med Chem 2012; 55:6363-74. [DOI: 10.1021/jm3007257] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Howard Beeley
- AstraZeneca R&D, Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG, U.K
| | - Jonathan Bowyer
- AstraZeneca R&D, Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG, U.K
| | - Calum R. Cook
- AstraZeneca R&D, Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG, U.K
| | - James J. Crawford
- AstraZeneca R&D, Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG, U.K
| | | | - Nicola M. Heron
- AstraZeneca R&D, Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG, U.K
| | - Christine Heyes
- AstraZeneca R&D, Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG, U.K
| | - Adrian J. Highton
- AstraZeneca R&D, Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG, U.K
| | - Julian A. Hudson
- AstraZeneca R&D, Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG, U.K
| | - Anja Jestel
- Proteros Biostructures, Am Klopferspitz 19, D-82152 Martinsried, Germany
| | - Peter W. Kenny
- AstraZeneca R&D, Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG, U.K
| | - Stephan Krapp
- Proteros Biostructures, Am Klopferspitz 19, D-82152 Martinsried, Germany
| | - Scott Martin
- AstraZeneca R&D, Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG, U.K
| | - Philip A. MacFaul
- AstraZeneca R&D, Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG, U.K
| | - Thomas M. McGuire
- AstraZeneca R&D, Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG, U.K
| | | | - Andrew D. Morley
- AstraZeneca R&D, Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG, U.K
| | - Jeffrey J. Morris
- AstraZeneca R&D, Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG, U.K
| | - Ken M. Page
- AstraZeneca R&D, Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG, U.K
| | | | - Helen Sawney
- AstraZeneca R&D, Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG, U.K
| | - Stefan Steinbacher
- Proteros Biostructures, Am Klopferspitz 19, D-82152 Martinsried, Germany
| | - Caroline Smith
- AstraZeneca R&D, Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG, U.K
| | - Madeleine Vickers
- AstraZeneca R&D, Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG, U.K
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128
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Menon V, Rao M. A low-molecular-mass aspartic protease inhibitor from a novel Penicillium sp.: implications in combating fungal infections. Microbiology (Reading) 2012; 158:1897-1907. [DOI: 10.1099/mic.0.058511-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Vishnu Menon
- Division of Biochemical Sciences, National Chemical Laboratory, Pune 411 008, India
| | - Mala Rao
- Division of Biochemical Sciences, National Chemical Laboratory, Pune 411 008, India
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129
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Tzoupis H, Leonis G, Megariotis G, Supuran CT, Mavromoustakos T, Papadopoulos MG. Dual Inhibitors for Aspartic Proteases HIV-1 PR and Renin: Advancements in AIDS–Hypertension–Diabetes Linkage via Molecular Dynamics, Inhibition Assays, and Binding Free Energy Calculations. J Med Chem 2012; 55:5784-96. [DOI: 10.1021/jm300180r] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Haralambos Tzoupis
- Institute of Organic and Pharmaceutical
Chemistry, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens 11635, Greece
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimioupolis
Zographou, Athens 15771, Greece
| | - Georgios Leonis
- Institute of Organic and Pharmaceutical
Chemistry, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens 11635, Greece
| | - Grigorios Megariotis
- Institute of Organic and Pharmaceutical
Chemistry, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens 11635, Greece
- School of Chemical Engineering, National Technical University of Athens, 9 Heroon Polytechniou
Street, Athens 15780, Greece
| | - Claudiu T. Supuran
- Department of Chemistry, University of Florence, Via della Lastruccia 3, Rm
18, 50019 Sesto Fiorentino (Florence), Italy
| | - Thomas Mavromoustakos
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimioupolis
Zographou, Athens 15771, Greece
| | - Manthos G. Papadopoulos
- Institute of Organic and Pharmaceutical
Chemistry, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens 11635, Greece
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130
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Urscher M, More SS, Alisch R, Vince R, Deponte M. Tight-binding inhibitors efficiently inactivate both reaction centers of monomeric Plasmodium falciparum glyoxalase 1. FEBS J 2012; 279:2568-78. [DOI: 10.1111/j.1742-4658.2012.08640.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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131
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Bell SG, Yang W, Tan ABH, Zhou R, Johnson EOD, Zhang A, Zhou W, Rao Z, Wong LL. The crystal structures of 4-methoxybenzoate bound CYP199A2 and CYP199A4: structural changes on substrate binding and the identification of an anion binding site. Dalton Trans 2012; 41:8703-14. [PMID: 22695988 DOI: 10.1039/c2dt30783a] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The crystal structures of the 4-methoxybenzoate bound forms of cytochrome P450 enzymes CYP199A2 and CYP199A4 from the Rhodopseudomonas palustris strains CGA009 and HaA2 have been solved. The structures of these two enzymes, which share 86% sequence identity, are very similar though some differences are found on the proximal surface. In these structures the enzymes have a closed conformation, in contrast to the substrate-free form of CYP199A2 where an obvious substrate access channel is observed. The switch from an open to a closed conformation arises from pronounced residue side-chain movements and alterations of ion pair and hydrogen bonding interactions at the entrance of the access channel. A chloride ion bound just inside the protein surface caps the entrance to the active site and protects the substrate and the heme from the external solvent. In both structures the substrate is held in place via hydrophobic and hydrogen bond interactions. The methoxy group is located over the heme iron, accounting for the high activity and selectivity of these enzymes for oxidative demethylation of the substrate. Mutagenesis studies on CYP199A4 highlight the involvement of hydrophobic (Phe185) and hydrophilic (Arg92, Ser95 and Arg243) amino acid residues in the binding of para-substituted benzoates by these enzymes.
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Affiliation(s)
- Stephen G Bell
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford, OX1 3QR, UK.
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132
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Kulagowski JJ, Blair W, Bull RJ, Chang C, Deshmukh G, Dyke HJ, Eigenbrot C, Ghilardi N, Gibbons P, Harrison TK, Hewitt PR, Liimatta M, Hurley CA, Johnson A, Johnson T, Kenny JR, Bir Kohli P, Maxey RJ, Mendonca R, Mortara K, Murray J, Narukulla R, Shia S, Steffek M, Ubhayakar S, Ultsch M, van Abbema A, Ward SI, Waszkowycz B, Zak M. Identification of Imidazo-Pyrrolopyridines as Novel and Potent JAK1 Inhibitors. J Med Chem 2012; 55:5901-21. [DOI: 10.1021/jm300438j] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Janusz J. Kulagowski
- Departments
of Medicinal Chemistry and ‡Computer Aided Drug Design, Argenta, 8/9 Spire Green Centre, Harlow CM19 5TR, United
Kingdom
- Departments of Biochemical and Cellular Pharmacology, ∥Discovery Chemistry, ⊥Drug Metabolism
and Pharmacokinetics, #Immunology, and ○Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080,
United States
| | - Wade Blair
- Departments
of Medicinal Chemistry and ‡Computer Aided Drug Design, Argenta, 8/9 Spire Green Centre, Harlow CM19 5TR, United
Kingdom
- Departments of Biochemical and Cellular Pharmacology, ∥Discovery Chemistry, ⊥Drug Metabolism
and Pharmacokinetics, #Immunology, and ○Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080,
United States
| | - Richard J. Bull
- Departments
of Medicinal Chemistry and ‡Computer Aided Drug Design, Argenta, 8/9 Spire Green Centre, Harlow CM19 5TR, United
Kingdom
- Departments of Biochemical and Cellular Pharmacology, ∥Discovery Chemistry, ⊥Drug Metabolism
and Pharmacokinetics, #Immunology, and ○Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080,
United States
| | - Christine Chang
- Departments
of Medicinal Chemistry and ‡Computer Aided Drug Design, Argenta, 8/9 Spire Green Centre, Harlow CM19 5TR, United
Kingdom
- Departments of Biochemical and Cellular Pharmacology, ∥Discovery Chemistry, ⊥Drug Metabolism
and Pharmacokinetics, #Immunology, and ○Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080,
United States
| | - Gauri Deshmukh
- Departments
of Medicinal Chemistry and ‡Computer Aided Drug Design, Argenta, 8/9 Spire Green Centre, Harlow CM19 5TR, United
Kingdom
- Departments of Biochemical and Cellular Pharmacology, ∥Discovery Chemistry, ⊥Drug Metabolism
and Pharmacokinetics, #Immunology, and ○Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080,
United States
| | - Hazel J. Dyke
- Departments
of Medicinal Chemistry and ‡Computer Aided Drug Design, Argenta, 8/9 Spire Green Centre, Harlow CM19 5TR, United
Kingdom
- Departments of Biochemical and Cellular Pharmacology, ∥Discovery Chemistry, ⊥Drug Metabolism
and Pharmacokinetics, #Immunology, and ○Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080,
United States
| | - Charles Eigenbrot
- Departments
of Medicinal Chemistry and ‡Computer Aided Drug Design, Argenta, 8/9 Spire Green Centre, Harlow CM19 5TR, United
Kingdom
- Departments of Biochemical and Cellular Pharmacology, ∥Discovery Chemistry, ⊥Drug Metabolism
and Pharmacokinetics, #Immunology, and ○Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080,
United States
| | - Nico Ghilardi
- Departments
of Medicinal Chemistry and ‡Computer Aided Drug Design, Argenta, 8/9 Spire Green Centre, Harlow CM19 5TR, United
Kingdom
- Departments of Biochemical and Cellular Pharmacology, ∥Discovery Chemistry, ⊥Drug Metabolism
and Pharmacokinetics, #Immunology, and ○Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080,
United States
| | - Paul Gibbons
- Departments
of Medicinal Chemistry and ‡Computer Aided Drug Design, Argenta, 8/9 Spire Green Centre, Harlow CM19 5TR, United
Kingdom
- Departments of Biochemical and Cellular Pharmacology, ∥Discovery Chemistry, ⊥Drug Metabolism
and Pharmacokinetics, #Immunology, and ○Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080,
United States
| | - Trevor K. Harrison
- Departments
of Medicinal Chemistry and ‡Computer Aided Drug Design, Argenta, 8/9 Spire Green Centre, Harlow CM19 5TR, United
Kingdom
- Departments of Biochemical and Cellular Pharmacology, ∥Discovery Chemistry, ⊥Drug Metabolism
and Pharmacokinetics, #Immunology, and ○Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080,
United States
| | - Peter R. Hewitt
- Departments
of Medicinal Chemistry and ‡Computer Aided Drug Design, Argenta, 8/9 Spire Green Centre, Harlow CM19 5TR, United
Kingdom
- Departments of Biochemical and Cellular Pharmacology, ∥Discovery Chemistry, ⊥Drug Metabolism
and Pharmacokinetics, #Immunology, and ○Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080,
United States
| | - Marya Liimatta
- Departments
of Medicinal Chemistry and ‡Computer Aided Drug Design, Argenta, 8/9 Spire Green Centre, Harlow CM19 5TR, United
Kingdom
- Departments of Biochemical and Cellular Pharmacology, ∥Discovery Chemistry, ⊥Drug Metabolism
and Pharmacokinetics, #Immunology, and ○Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080,
United States
| | - Christopher A. Hurley
- Departments
of Medicinal Chemistry and ‡Computer Aided Drug Design, Argenta, 8/9 Spire Green Centre, Harlow CM19 5TR, United
Kingdom
- Departments of Biochemical and Cellular Pharmacology, ∥Discovery Chemistry, ⊥Drug Metabolism
and Pharmacokinetics, #Immunology, and ○Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080,
United States
| | - Adam Johnson
- Departments
of Medicinal Chemistry and ‡Computer Aided Drug Design, Argenta, 8/9 Spire Green Centre, Harlow CM19 5TR, United
Kingdom
- Departments of Biochemical and Cellular Pharmacology, ∥Discovery Chemistry, ⊥Drug Metabolism
and Pharmacokinetics, #Immunology, and ○Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080,
United States
| | - Tony Johnson
- Departments
of Medicinal Chemistry and ‡Computer Aided Drug Design, Argenta, 8/9 Spire Green Centre, Harlow CM19 5TR, United
Kingdom
- Departments of Biochemical and Cellular Pharmacology, ∥Discovery Chemistry, ⊥Drug Metabolism
and Pharmacokinetics, #Immunology, and ○Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080,
United States
| | - Jane R. Kenny
- Departments
of Medicinal Chemistry and ‡Computer Aided Drug Design, Argenta, 8/9 Spire Green Centre, Harlow CM19 5TR, United
Kingdom
- Departments of Biochemical and Cellular Pharmacology, ∥Discovery Chemistry, ⊥Drug Metabolism
and Pharmacokinetics, #Immunology, and ○Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080,
United States
| | - Pawan Bir Kohli
- Departments
of Medicinal Chemistry and ‡Computer Aided Drug Design, Argenta, 8/9 Spire Green Centre, Harlow CM19 5TR, United
Kingdom
- Departments of Biochemical and Cellular Pharmacology, ∥Discovery Chemistry, ⊥Drug Metabolism
and Pharmacokinetics, #Immunology, and ○Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080,
United States
| | - Robert J. Maxey
- Departments
of Medicinal Chemistry and ‡Computer Aided Drug Design, Argenta, 8/9 Spire Green Centre, Harlow CM19 5TR, United
Kingdom
- Departments of Biochemical and Cellular Pharmacology, ∥Discovery Chemistry, ⊥Drug Metabolism
and Pharmacokinetics, #Immunology, and ○Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080,
United States
| | - Rohan Mendonca
- Departments
of Medicinal Chemistry and ‡Computer Aided Drug Design, Argenta, 8/9 Spire Green Centre, Harlow CM19 5TR, United
Kingdom
- Departments of Biochemical and Cellular Pharmacology, ∥Discovery Chemistry, ⊥Drug Metabolism
and Pharmacokinetics, #Immunology, and ○Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080,
United States
| | - Kyle Mortara
- Departments
of Medicinal Chemistry and ‡Computer Aided Drug Design, Argenta, 8/9 Spire Green Centre, Harlow CM19 5TR, United
Kingdom
- Departments of Biochemical and Cellular Pharmacology, ∥Discovery Chemistry, ⊥Drug Metabolism
and Pharmacokinetics, #Immunology, and ○Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080,
United States
| | - Jeremy Murray
- Departments
of Medicinal Chemistry and ‡Computer Aided Drug Design, Argenta, 8/9 Spire Green Centre, Harlow CM19 5TR, United
Kingdom
- Departments of Biochemical and Cellular Pharmacology, ∥Discovery Chemistry, ⊥Drug Metabolism
and Pharmacokinetics, #Immunology, and ○Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080,
United States
| | - Raman Narukulla
- Departments
of Medicinal Chemistry and ‡Computer Aided Drug Design, Argenta, 8/9 Spire Green Centre, Harlow CM19 5TR, United
Kingdom
- Departments of Biochemical and Cellular Pharmacology, ∥Discovery Chemistry, ⊥Drug Metabolism
and Pharmacokinetics, #Immunology, and ○Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080,
United States
| | - Steven Shia
- Departments
of Medicinal Chemistry and ‡Computer Aided Drug Design, Argenta, 8/9 Spire Green Centre, Harlow CM19 5TR, United
Kingdom
- Departments of Biochemical and Cellular Pharmacology, ∥Discovery Chemistry, ⊥Drug Metabolism
and Pharmacokinetics, #Immunology, and ○Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080,
United States
| | - Micah Steffek
- Departments
of Medicinal Chemistry and ‡Computer Aided Drug Design, Argenta, 8/9 Spire Green Centre, Harlow CM19 5TR, United
Kingdom
- Departments of Biochemical and Cellular Pharmacology, ∥Discovery Chemistry, ⊥Drug Metabolism
and Pharmacokinetics, #Immunology, and ○Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080,
United States
| | - Savita Ubhayakar
- Departments
of Medicinal Chemistry and ‡Computer Aided Drug Design, Argenta, 8/9 Spire Green Centre, Harlow CM19 5TR, United
Kingdom
- Departments of Biochemical and Cellular Pharmacology, ∥Discovery Chemistry, ⊥Drug Metabolism
and Pharmacokinetics, #Immunology, and ○Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080,
United States
| | - Mark Ultsch
- Departments
of Medicinal Chemistry and ‡Computer Aided Drug Design, Argenta, 8/9 Spire Green Centre, Harlow CM19 5TR, United
Kingdom
- Departments of Biochemical and Cellular Pharmacology, ∥Discovery Chemistry, ⊥Drug Metabolism
and Pharmacokinetics, #Immunology, and ○Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080,
United States
| | - Anne van Abbema
- Departments
of Medicinal Chemistry and ‡Computer Aided Drug Design, Argenta, 8/9 Spire Green Centre, Harlow CM19 5TR, United
Kingdom
- Departments of Biochemical and Cellular Pharmacology, ∥Discovery Chemistry, ⊥Drug Metabolism
and Pharmacokinetics, #Immunology, and ○Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080,
United States
| | - Stuart I. Ward
- Departments
of Medicinal Chemistry and ‡Computer Aided Drug Design, Argenta, 8/9 Spire Green Centre, Harlow CM19 5TR, United
Kingdom
- Departments of Biochemical and Cellular Pharmacology, ∥Discovery Chemistry, ⊥Drug Metabolism
and Pharmacokinetics, #Immunology, and ○Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080,
United States
| | - Bohdan Waszkowycz
- Departments
of Medicinal Chemistry and ‡Computer Aided Drug Design, Argenta, 8/9 Spire Green Centre, Harlow CM19 5TR, United
Kingdom
- Departments of Biochemical and Cellular Pharmacology, ∥Discovery Chemistry, ⊥Drug Metabolism
and Pharmacokinetics, #Immunology, and ○Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080,
United States
| | - Mark Zak
- Departments
of Medicinal Chemistry and ‡Computer Aided Drug Design, Argenta, 8/9 Spire Green Centre, Harlow CM19 5TR, United
Kingdom
- Departments of Biochemical and Cellular Pharmacology, ∥Discovery Chemistry, ⊥Drug Metabolism
and Pharmacokinetics, #Immunology, and ○Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080,
United States
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133
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Eissenstat M, Guerassina T, Gulnik S, Afonina E, Silva AM, Ludtke D, Yokoe H, Yu B, Erickson J. Enamino-oxindole HIV protease inhibitors. Bioorg Med Chem Lett 2012; 22:5078-83. [PMID: 22749283 DOI: 10.1016/j.bmcl.2012.05.120] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 05/30/2012] [Accepted: 05/30/2012] [Indexed: 10/28/2022]
Abstract
We have designed and synthesized a series of HIV protease inhibitors (PIs) with enamino-oxindole substituents optimized to interact with the S2' subsite of the HIV protease binding pocket. Several of these inhibitors have sub-nanomolar K(i) and antiviral IC(50) in the low nM range against WT HIV and against a panel of multi-drug resistant (MDR) strains.
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134
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Mutations in HIV-1 gag and pol compensate for the loss of viral fitness caused by a highly mutated protease. Antimicrob Agents Chemother 2012; 56:4320-30. [PMID: 22644035 DOI: 10.1128/aac.00465-12] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
During the last few decades, the treatment of HIV-infected patients by highly active antiretroviral therapy, including protease inhibitors (PIs), has become standard. Here, we present results of analysis of a patient-derived, multiresistant HIV-1 CRF02_AG recombinant strain with a highly mutated protease (PR) coding sequence, where up to 19 coding mutations have accumulated in the PR. The results of biochemical analysis in vitro showed that the patient-derived PR is highly resistant to most of the currently used PIs and that it also exhibits very poor catalytic activity. Determination of the crystal structure revealed prominent changes in the flap elbow region and S1/S1' active site subsites. While viral loads in the patient were found to be high, the insertion of the patient-derived PR into a HIV-1 subtype B backbone resulted in reduction of infectivity by 3 orders of magnitude. Fitness compensation was not achieved by elevated polymerase (Pol) expression, but the introduction of patient-derived gag and pol sequences in a CRF02_AG backbone rescued viral infectivity to near wild-type (wt) levels. The mutations that accumulated in the vicinity of the processing sites spanning the p2/NC, NC/p1, and p6pol/PR proteins lead to much more efficient hydrolysis of corresponding peptides by patient-derived PR in comparison to the wt enzyme. This indicates a very efficient coevolution of enzyme and substrate maintaining high viral loads in vivo under constant drug pressure.
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135
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Becker GL, Lu Y, Hardes K, Strehlow B, Levesque C, Lindberg I, Sandvig K, Bakowsky U, Day R, Garten W, Steinmetzer T. Highly potent inhibitors of proprotein convertase furin as potential drugs for treatment of infectious diseases. J Biol Chem 2012; 287:21992-2003. [PMID: 22539349 DOI: 10.1074/jbc.m111.332643] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Optimization of our previously described peptidomimetic furin inhibitors was performed and yielded several analogs with a significantly improved activity. The most potent compounds containing an N-terminal 4- or 3-(guanidinomethyl)phenylacetyl residue inhibit furin with K(i) values of 16 and 8 pM, respectively. These analogs inhibit other proprotein convertases, such as PC1/3, PC4, PACE4, and PC5/6, with similar potency, whereas PC2, PC7, and trypsin-like serine proteases are poorly affected. Incubation of selected compounds with Madin-Darby canine kidney cells over a period of 96 h revealed that they exhibit great stability, making them suitable candidates for further studies in cell culture. Two of the most potent derivatives were used to inhibit the hemagglutinin cleavage and viral propagation of a highly pathogenic avian H7N1 influenza virus strain. The treatment with inhibitor 24 (4-(guanidinomethyl)phenylacetyl-Arg-Val-Arg-4-amidinobenzylamide) resulted in significantly delayed virus propagation compared with an inhibitor-free control. The same analog was also effective in inhibiting Shiga toxin activation in HEp-2 cells. This antiviral effect, as well as the protective effect against a bacterial toxin, suggests that inhibitors of furin or furin-like proprotein convertases could represent promising lead structures for future drug development, in particular for the treatment of infectious diseases.
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Affiliation(s)
- Gero L Becker
- Institute of Pharmaceutical Chemistry, Philipps University, 35032 Marburg, Germany
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136
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Slow-tight binding inhibition of pepsin by an aspartic protease inhibitor from Streptomyces sp. MBR04. Int J Biol Macromol 2012; 51:165-74. [PMID: 22522047 DOI: 10.1016/j.ijbiomac.2012.04.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 04/03/2012] [Accepted: 04/04/2012] [Indexed: 11/20/2022]
Abstract
The present article reports a low molecular weight aspartic protease inhibitor from a Streptomyces sp. MBR04 exhibiting a two-step inhibition mechanism against pepsin. The kinetic interactions revealed a reversible, competitive, slow-tight binding inhibition with an IC(50) and K(i) values of 4.5 nM and 4 nM respectively. The conformational changes induced upon inhibitor binding to pepsin was monitored by far and near UV analysis, demonstrated that the inhibitor binds to the active site and causes inactivation. Chemical modification of the inhibitor with WRK and TNBS abolished the antiproteolytic activity of the inhibitor.
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137
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Conley NR, Dragulescu-Andrasi A, Rao J, Moerner WE. A selenium analogue of firefly D-luciferin with red-shifted bioluminescence emission. Angew Chem Int Ed Engl 2012; 51:3350-3. [PMID: 22344705 PMCID: PMC3494413 DOI: 10.1002/anie.201105653] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 01/18/2012] [Indexed: 01/16/2023]
Abstract
A selenium analogue of amino-D-luciferin, aminoseleno-D-luciferin, is synthesized and shown to be a competent substrate for the firefly luciferase enzyme. It has a red-shifted bioluminescence emission maximum at 600 nm and is suitable for bioluminescence imaging studies in living subjects.
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138
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Perera E, Rodríguez-Casariego J, Rodríguez-Viera L, Calero J, Perdomo-Morales R, Mancera JM. Lobster (Panulirus argus) hepatopancreatic trypsin isoforms and their digestion efficiency. THE BIOLOGICAL BULLETIN 2012; 222:158-170. [PMID: 22589406 DOI: 10.1086/bblv222n2p158] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
It is well known that crustaceans exhibit several isoforms of trypsin in their digestive system. Although the number of known crustacean trypsin isoforms continues increasing, especially those derived from cDNA sequences, the role of particular isoenzymes in digestion remains unknown. Among invertebrates, significant advances in the understanding of the role of multiple trypsins have been made only in insects. Since it has been demonstrated that trypsin isoenzyme patterns (phenotypes) in lobster differ in digestion efficiency, we used this crustacean as a model for assessing the biochemical basis of such differences. We demonstrated that the trypsin isoform known to be present in all individuals of Panulirus argus has a high catalytic efficiency (k(cat)/K(m) ) and is the most reactive toward native proteinaceous substrates, whereas one of the isoforms present in less efficient individuals has a lower k(cat) and a lower k(cat)/K(m), and it is less competent at digesting native proteins. A fundamental question in biology is how genetic differences produce different physiological performances. This work is the first to demonstrate that trypsin phenotypic variation in crustacean protein digestion relies on the biochemical properties of the different isoforms. Results are relevant for understanding trypsin polymorphism and protein digestion in lobster.
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Affiliation(s)
- Erick Perera
- Center for Marine Research, University of Havana, Cuba.
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139
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Modulation of glucokinase by glucose, small-molecule activator and glucokinase regulatory protein: steady-state kinetic and cell-based analysis. Biochem J 2012; 441:881-7. [PMID: 22044397 DOI: 10.1042/bj20110721] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
GK (glucokinase) is an enzyme central to glucose metabolism that displays positive co-operativity to substrate glucose. Small-molecule GKAs (GK activators) modulate GK catalytic activity and glucose affinity and are currently being pursued as a treatment for Type 2 diabetes. GK progress curves monitoring product formation are linear up to 1 mM glucose, but biphasic at 5 mM, with the transition from the lower initial velocity to the higher steady-state velocity being described by the rate constant kact. In the presence of a liver-specific GKA (compound A), progress curves at 1 mM glucose are similar to those at 5 mM, reflecting activation of GK by compound A. We show that GKRP (GK regulatory protein) is a slow tight-binding inhibitor of GK. Analysis of progress curves indicate that this inhibition is time dependent, with apparent initial and final Ki values being 113 and 12.8 nM respectively. When GK is pre-incubated with glucose and compound A, the inhibition observed by GKRP is time dependent, but independent of GKRP concentration, reflecting the GKA-controlled transition between closed and open GK conformations. These data are supported by cell-based imaging data from primary rat hepatocytes. This work characterizes the modulation of GK by a novel GKA that may enable the design of new and improved GKAs.
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140
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Alonso-del-Rivero M, Trejo SA, Reytor ML, Rodriguez-de-la-Vega M, Delfin J, Diaz J, González-González Y, Canals F, Chavez MA, Aviles FX. Tri-domain bifunctional inhibitor of metallocarboxypeptidases A and serine proteases isolated from marine annelid Sabellastarte magnifica. J Biol Chem 2012; 287:15427-38. [PMID: 22411994 DOI: 10.1074/jbc.m111.337261] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
This study describes a novel bifunctional metallocarboxypeptidase and serine protease inhibitor (SmCI) isolated from the tentacle crown of the annelid Sabellastarte magnifica. SmCI is a 165-residue glycoprotein with a molecular mass of 19.69 kDa (mass spectrometry) and 18 cysteine residues forming nine disulfide bonds. Its cDNA was cloned and sequenced by RT-PCR and nested PCR using degenerated oligonucleotides. Employing this information along with data derived from automatic Edman degradation of peptide fragments, the SmCI sequence was fully characterized, indicating the presence of three bovine pancreatic trypsin inhibitor/Kunitz domains and its high homology with other Kunitz serine protease inhibitors. Enzyme kinetics and structural analyses revealed SmCI to be an inhibitor of human and bovine pancreatic metallocarboxypeptidases of the A-type (but not B-type), with nanomolar K(i) values. SmCI is also capable of inhibiting bovine pancreatic trypsin, chymotrypsin, and porcine pancreatic elastase in varying measures. When the inhibitor and its nonglycosylated form (SmCI N23A mutant) were overproduced recombinantly in a Pichia pastoris system, they displayed the dual inhibitory properties of the natural form. Similarly, two bi-domain forms of the inhibitor (recombinant rSmCI D1-D2 and rSmCI D2-D3) as well as its C-terminal domain (rSmCI-D3) were also overproduced. Of these fragments, only the rSmCI D1-D2 bi-domain retained inhibition of metallocarboxypeptidase A but only partially, indicating that the whole tri-domain structure is required for such capability in full. SmCI is the first proteinaceous inhibitor of metallocarboxypeptidases able to act as well on another mechanistic class of proteases (serine-type) and is the first of this kind identified in nature.
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Affiliation(s)
- Maday Alonso-del-Rivero
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de la Habana, 10400 La Habana, Cuba
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141
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Conley NR, Dragulescu-Andrasi A, Rao J, Moerner WE. A Selenium Analogue of Firefly D-Luciferin with Red-Shifted Bioluminescence Emission. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201105653] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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142
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Bell SG, Yang W, Yorke JA, Zhou W, Wang H, Harmer J, Copley R, Zhang A, Zhou R, Bartlam M, Rao Z, Wong LL. Structure and function of CYP108D1 from Novosphingobium aromaticivorans DSM12444: an aromatic hydrocarbon-binding P450 enzyme. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:277-91. [PMID: 22349230 DOI: 10.1107/s090744491200145x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 01/12/2012] [Indexed: 11/11/2022]
Abstract
CYP108D1 from Novosphingobium aromaticivorans DSM12444 binds a range of aromatic hydrocarbons such as phenanthrene, biphenyl and phenylcyclohexane. Its structure, which is reported here at 2.2 Å resolution, is closely related to that of CYP108A1 (P450terp), an α-terpineol-oxidizing enzyme. The compositions and structures of the active sites of these two enzymes are very similar; the most significant changes are the replacement of Glu77 and Thr103 in CYP108A1 by Thr79 and Val105 in CYP108D1. Other residue differences lead to a larger and more hydrophobic access channel in CYP108D1. These structural features are likely to account for the weaker α-terpineol binding by CYP108D1 and, when combined with the presence of three hydrophobic phenylalanine residues in the active site, promote the binding of aromatic hydrocarbons. The haem-proximal surface of CYP108D1 shows a different charge distribution and topology to those of CYP101D1, CYP101A1 and CYP108A1, including a pronounced kink in the proximal loop of CYP108D1, which may result in poor complementarity with the [2Fe-2S] ferredoxins Arx, putidaredoxin and terpredoxin that are the respective redox partners of these three P450 enzymes. The unexpectedly low reduction potential of phenylcyclohexane-bound CYP108D1 (-401 mV) may also contribute to the low activity observed with these ferredoxins. CYP108D1 appears to function as an aromatic hydrocarbon hydroxylase that requires a different electron-transfer cofactor protein.
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Affiliation(s)
- Stephen G Bell
- Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford,South Parks Road, Oxford OX1 3QR, England.
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143
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CYP264B1 from Sorangium cellulosum So ce56: a fascinating norisoprenoid and sesquiterpene hydroxylase. Appl Microbiol Biotechnol 2012; 95:123-33. [DOI: 10.1007/s00253-011-3727-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2011] [Revised: 10/28/2011] [Accepted: 11/14/2011] [Indexed: 10/14/2022]
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144
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Kuzmič P. Optimal design for the dose–response screening of tight-binding enzyme inhibitors. Anal Biochem 2011; 419:117-22. [DOI: 10.1016/j.ab.2011.06.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Revised: 05/26/2011] [Accepted: 06/07/2011] [Indexed: 10/17/2022]
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145
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Schneider EL, Lee MS, Baharuddin A, Goetz DH, Farady CJ, Ward M, Wang CI, Craik CS. A reverse binding motif that contributes to specific protease inhibition by antibodies. J Mol Biol 2011; 415:699-715. [PMID: 22154938 DOI: 10.1016/j.jmb.2011.11.036] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 11/12/2011] [Accepted: 11/18/2011] [Indexed: 10/14/2022]
Abstract
The type II transmembrane serine protease family consists of 18 closely related serine proteases that are implicated in multiple functions. To identify selective, inhibitory antibodies against one particular type II transmembrane serine protease, matriptase [MT-SP1 (membrane-type serine protease 1)], a phage display library was created with a natural repertoire of Fabs [fragment antigen binding (Fab)] from human naïve B cells. Fab A11 was identified with a 720 pM inhibition constant and high specificity for matriptase over other trypsin-fold serine proteases. A Trichoderma reesei system expressed A11 with a yield of ∼200 mg/L. The crystal structure of A11 in complex with matriptase has been determined and compared to the crystal structure of another antibody inhibitor (S4) in complex with matriptase. Previously discovered from a synthetic single-chain variable fragment library, S4 is also a highly selective and potent matriptase inhibitor. The crystal structures of the A11/matriptase and S4/matriptase complexes were solved to 2.1 Å and 1.5 Å, respectively. Although these antibodies, discovered from separate libraries, interact differently with the protease surface loops for their specificity, the structures reveal a similar novel mechanism of protease inhibition. Through the insertion of the H3 variable loop in a reverse orientation at the substrate-binding pocket, these antibodies bury a large surface area for potent inhibition and avoid proteolytic inactivation. This discovery highlights the critical role that the antibody scaffold plays in positioning loops to bind and inhibit protease function in a highly selective manner. Additionally, Fab A11 is a fully human antibody that specifically inhibits matriptase over other closely related proteases, suggesting that this approach could be useful for clinical applications.
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Affiliation(s)
- Eric L Schneider
- Department of Pharmaceutical Chemistry, University of California, San Francisco, Genentech Hall, San Francisco, CA 94143-2280, USA
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146
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Lu X, Zhou R, Sharma I, Li X, Kumar G, Swaminathan S, Tonge PJ, Tan DS. Stable analogues of OSB-AMP: potent inhibitors of MenE, the o-succinylbenzoate-CoA synthetase from bacterial menaquinone biosynthesis. Chembiochem 2011; 13:129-36. [PMID: 22109989 DOI: 10.1002/cbic.201100585] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Indexed: 12/15/2022]
Abstract
MenE, the o-succinylbenzoate (OSB)-CoA synthetase from bacterial menaquinone biosynthesis, is a promising new antibacterial target. Sulfonyladenosine analogues of the cognate reaction intermediate, OSB-AMP, have been developed as inhibitors of the MenE enzymes from Mycobacterium tuberculosis (mtMenE), Staphylococcus aureus (saMenE) and Escherichia coli (ecMenE). Both a free carboxylate and a ketone moiety on the OSB side chain are required for potent inhibitory activity. OSB-AMS (4) is a competitive inhibitor of mtMenE with respect to ATP (K(i) =5.4±0.1 nM) and a noncompetitive inhibitor with respect to OSB (K(i) =11.2±0.9 nM). These data are consistent with a Bi Uni Uni Bi Ping-Pong kinetic mechanism for these enzymes. In addition, OSB-AMS inhibits saMenE with K(i)(app) =22±8 nM and ecMenE with K(i)(OSB) =128±5 nM. Putative active-site residues, Arg222, which may interact with the OSB aromatic carboxylate, and Ser302, which may bind the OSB ketone oxygen, have been identified through computational docking of OSB-AMP with the unliganded crystal structure of saMenE. A pH-dependent interconversion of the free keto acid and lactol forms of the inhibitors is also described, along with implications for inhibitor design.
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Affiliation(s)
- Xuequan Lu
- Molecular Pharmacology and Chemistry Program and Tri-Institutional Research Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
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147
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The structure of a Burkholderia pseudomallei immunophilin-inhibitor complex reveals new approaches to antimicrobial development. Biochem J 2011; 437:413-22. [PMID: 21574961 DOI: 10.1042/bj20110345] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Mips (macrophage infectivity potentiators) are a subset of immunophilins associated with virulence in a range of micro-organisms. These proteins possess peptidylprolyl isomerase activity and are inhibited by drugs including rapamycin and tacrolimus. We determined the structure of the Mip homologue [BpML1 (Burkholderia pseudomallei Mip-like protein 1)] from the human pathogen and biowarfare threat B. pseudomallei by NMR and X-ray crystallography. The crystal structure suggests that key catalytic residues in the BpML1 active site have unexpected conformational flexibility consistent with a role in catalysis. The structure further revealed BpML1 binding to a helical peptide, in a manner resembling the physiological interaction of human TGFβRI (transforming growth factor β receptor I) with the human immunophilin FKBP12 (FK506-binding protein 12). Furthermore, the structure of BpML1 bound to the class inhibitor cycloheximide N-ethylethanoate showed that this inhibitor mimics such a helical peptide, in contrast with the extended prolyl-peptide mimicking shown by inhibitors such as tacrolimus. We suggest that Mips, and potentially other bacterial immunophilins, participate in protein-protein interactions in addition to their peptidylprolyl isomerase activity, and that some roles of Mip proteins in virulence are independent of their peptidylprolyl isomerase activity.
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148
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A Burkholderia pseudomallei macrophage infectivity potentiator-like protein has rapamycin-inhibitable peptidylprolyl isomerase activity and pleiotropic effects on virulence. Infect Immun 2011; 79:4299-307. [PMID: 21859853 DOI: 10.1128/iai.00134-11] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Macrophage infectivity potentiators (Mips) are a group of virulence factors encoded by pathogenic bacteria such as Legionella, Chlamydia, and Neisseria species. Mips are part of the FK506-binding protein (FKBP) family, whose members typically exhibit peptidylprolyl cis-trans isomerase (PPIase) activity which is inhibitable by the immunosuppressants FK506 and rapamycin. Here we describe the identification and characterization of BPSS1823, a Mip-like protein in the intracellular pathogen Burkholderia pseudomallei. Recombinant BPSS1823 protein has rapamycin-inhibitable PPIase activity, indicating that it is a functional FKBP. A mutant strain generated by deletion of BPSS1823 in B. pseudomallei exhibited a reduced ability to survive within cells and significant attenuation in vivo, suggesting that BPSS1823 is important for B. pseudomallei virulence. In addition, pleiotropic effects were observed with a reduction in virulence mechanisms, including resistance to host killing mechanisms, swarming motility, and protease production.
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149
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Earl STH, Richards R, Johnson LA, Flight S, Anderson S, Liao A, de Jersey J, Masci PP, Lavin MF. Identification and characterisation of Kunitz-type plasma kallikrein inhibitors unique to Oxyuranus sp. snake venoms. Biochimie 2011; 94:365-73. [PMID: 21843588 DOI: 10.1016/j.biochi.2011.08.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2011] [Accepted: 08/04/2011] [Indexed: 11/18/2022]
Abstract
As part of a wider study on Australian snake venom components, we have identified and characterised Kunitz-type protease inhibitors from the venoms of Oxyuranus scutellatus and Oxyuranus microlepidotus (Australian taipans) with plasma kallikrein inhibitory activity. Each inhibitor had a mass of 7 kDa and was purified from the venom as part of a protein complex. Mass spectrometry and N-terminal sequencing was employed to obtain amino acid sequence information for each inhibitor and a recombinant form of the O. scutellatus inhibitor, termed TSPI, was subsequently expressed and purified. TSPI was investigated for inhibition against a panel of 12 enzymes involved in haemostasis and estimates of the K(i) value determined for each enzyme. TSPI was found to be a broad spectrum inhibitor with most potent inhibitory activity observed against plasma kallikrein that corresponded to a K(i) of 0.057 ± 0.019 nM. TSPI also inhibited fibrinolysis in whole blood and prolonged the intrinsic clotting time. These inhibitors are also unique in that they appear to be found only in Oxyuranus sp. venoms.
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Affiliation(s)
- Stephen T H Earl
- The Queensland Institute of Medical Research, PO Royal Brisbane Hospital, Brisbane 4029, Australia
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150
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Tomita S, Shiraki K. Poly(acrylic acid) is a common noncompetitive inhibitor for cationic enzymes with high affinity and reversibility. ACTA ACUST UNITED AC 2011. [DOI: 10.1002/pola.24822] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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