1
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Holland DC, Schroder WA, Calcott MJ, Kaemmerer E, Avery VM, Ekins MG, Carroll AR. Cyclotheonellazoles D-I, Potent Elastase Inhibitory Thiazole-Containing Cyclic Peptides from Theonella sp. (2131). JOURNAL OF NATURAL PRODUCTS 2023; 86:2216-2227. [PMID: 37609780 DOI: 10.1021/acs.jnatprod.3c00633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Six new thiazole-containing cyclic peptides, the cyclotheonellazoles D-I (1-6), were isolated from the Australian marine sponge Theonella sp. (2131) with their structures assigned by comprehensive 1D and 2D NMR spectroscopic and MS spectrometric analyses, Marfey's derivatization studies, and comparison with time-dependent density functional theory (TDDFT) calculated ECD data. The Type 2 azole-homologated peptides herein comprise up to five nonproteinogenic amino acids, including the protease transition state mimic α-keto-β-amino acid residue 3-amino-4-methyl-2-oxohexanoic acid (Amoha), while 1-3 also contain a terminal hydantoin residue not previously found in cyclotheonellazoles. The keramamides A (7) and L (8) were reisolated affording expanded exploration of their biological activities. The peptides were examined for protease inhibitory activities against two mammalian serine proteases (elastase and chymotrypsin) and SARS-CoV-2 3-chymotrypsin-like protease (3CLpro), a validated antiviral therapeutic target for COVID-19. Peptides 1-6 and keramamide A (7) displayed potent nanomolar inhibition of elastase (IC50 16.0 to 61.8 nM), while 7 also contained modest inhibition of chymotrypsin and SARS-CoV-2 3CLpro (IC50 0.73 and 1.1 μM, respectively). The cyclotheonellazoles D-E (1-3) do not affect the viability of human breast, ovarian, and colon cancer cells (>100 μM), with the cytotoxicity previously reported for keramamide L (8) not replicated (inactive >20 μM).
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Affiliation(s)
- Darren C Holland
- School of Environment and Science, Griffith University, Gold Coast, Queensland 4222, Australia
- Griffith Institute for Drug Discovery, Griffith University,Nathan, Queensland 4111, Australia
| | - Wayne A Schroder
- School of Environment and Science, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Mark J Calcott
- School of Biological Sciences, Victoria University of Wellington, Wellington 6102, New Zealand
| | - Elke Kaemmerer
- Discovery Biology, Griffith University, Nathan, Queensland 4111, Australia
| | - Vicky M Avery
- School of Environment and Science, Griffith University, Gold Coast, Queensland 4222, Australia
- Griffith Institute for Drug Discovery, Griffith University,Nathan, Queensland 4111, Australia
- Discovery Biology, Griffith University, Nathan, Queensland 4111, Australia
| | - Merrick G Ekins
- Queensland Museum, South Brisbane BC, Queensland 4101, Australia
| | - Anthony R Carroll
- School of Environment and Science, Griffith University, Gold Coast, Queensland 4222, Australia
- Griffith Institute for Drug Discovery, Griffith University,Nathan, Queensland 4111, Australia
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2
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Tokuhiro Y, Yoshikawa K, Murayama S, Nanjo T, Takemoto Y. Highly Stereoselective, Organocatalytic Mannich-type Addition of Glyoxylate Cyanohydrin: A Versatile Building Block for the Asymmetric Synthesis of β-Amino-α-ketoacids. ACS Catal 2022. [DOI: 10.1021/acscatal.2c00950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yusuke Tokuhiro
- Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida,
Sakyo-ku, Kyoto 606-8501, Japan
| | - Kosuke Yoshikawa
- Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida,
Sakyo-ku, Kyoto 606-8501, Japan
| | - Sei Murayama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida,
Sakyo-ku, Kyoto 606-8501, Japan
| | - Takeshi Nanjo
- Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida,
Sakyo-ku, Kyoto 606-8501, Japan
| | - Yoshiji Takemoto
- Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida,
Sakyo-ku, Kyoto 606-8501, Japan
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3
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de Almeida Barros R, Meriño-Cabrera Y, Vital CE, da Silva Júnior NR, de Oliveira CN, Lessa Barbosa S, Marques Gonçalves Assis JV, Ramos HJ, de Almeida Oliveira MG. Small peptides inhibit gut trypsin-like proteases and impair Anticarsia gemmatalis (Lepidoptera: Noctuidae) survival and development. PEST MANAGEMENT SCIENCE 2021; 77:1714-1723. [PMID: 33200876 DOI: 10.1002/ps.6191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 09/02/2020] [Accepted: 11/17/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Anticarsia gemmatalis larvae are key defoliating pests of soybean plants. Inorganic insecticides, harmful to the environment and human health, are the main molecules used in the control of this pest. To apply more sustainable management methods, organic molecules with high specificities, such as proteinaceous protease inhibitors, have been sought. Thus, molecular docking studies, kinetics assays, and biological tests were performed to evaluate the inhibitory activity of two peptides (GORE1 and GORE2) rationally designed to inhibit trypsin-like enzymes, which are the main proteases of A. gemmatalis midgut. RESULTS The molecular docking simulations revealed critical hydrogen bonding patterns of the peptides with key active site residues of trypsin-like proteases of A. gemmatalis and other Lepidopteran insects. The negative values of binding energy indicate that hydrogen bonds potentiate the tight binding of the peptides with trypsin-like proteases, predicting an effective inhibition. The inhibition's rate constants (Ki) were 0.49 and 0.10 mM for GORE1 and GORE2, resulting in effective inhibition of the activity trypsin on the L-BApNA substrate in the in vitro tests, indicating that the peptide GORE2 has higher inhibitory capacity on the A. gemmatalis trypsins. In addition, the two peptides were determined to be reversible competitive inhibitors. The in vivo test demonstrated that the peptides harm the survival and development of A. gemmatalis larvae. CONCLUSION These results suggest that these peptides are potential candidates in the management of A. gemmatalis larvae and provide baseline information for the design of new trypsin-like inhibitors based on peptidomimetic tools. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Rafael de Almeida Barros
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Brazil
- Instituto de Biotecnologia Aplicada à Agropecuária, BIOAGRO-UFV, Viçosa, Brazil
| | - Yaremis Meriño-Cabrera
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Brazil
- Instituto de Biotecnologia Aplicada à Agropecuária, BIOAGRO-UFV, Viçosa, Brazil
| | - Camilo E Vital
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Brazil
- Instituto de Biotecnologia Aplicada à Agropecuária, BIOAGRO-UFV, Viçosa, Brazil
- Center of Analysis of Biomolecules, NuBioMol, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Neilier R da Silva Júnior
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Brazil
- Instituto de Biotecnologia Aplicada à Agropecuária, BIOAGRO-UFV, Viçosa, Brazil
| | - Cauê N de Oliveira
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Brazil
- Instituto de Biotecnologia Aplicada à Agropecuária, BIOAGRO-UFV, Viçosa, Brazil
| | - Samuel Lessa Barbosa
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Brazil
- Instituto de Biotecnologia Aplicada à Agropecuária, BIOAGRO-UFV, Viçosa, Brazil
| | - João V Marques Gonçalves Assis
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Brazil
- Instituto de Biotecnologia Aplicada à Agropecuária, BIOAGRO-UFV, Viçosa, Brazil
| | - Humberto Jo Ramos
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Brazil
- Instituto de Biotecnologia Aplicada à Agropecuária, BIOAGRO-UFV, Viçosa, Brazil
- Center of Analysis of Biomolecules, NuBioMol, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Maria G de Almeida Oliveira
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Brazil
- Instituto de Biotecnologia Aplicada à Agropecuária, BIOAGRO-UFV, Viçosa, Brazil
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4
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Diversity, molecular mechanisms and structure-activity relationships of marine protease inhibitors-A review. Pharmacol Res 2021; 166:105521. [PMID: 33662574 DOI: 10.1016/j.phrs.2021.105521] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 02/24/2021] [Accepted: 02/25/2021] [Indexed: 11/23/2022]
Abstract
Marine habitats are well-known for their diverse life forms that are potential sources of novel bioactive compounds. Evidence from existing studies suggests that these compounds contribute significantly to the field of pharmaceuticals, nutraceuticals, and cosmeceuticals. The isolation of natural compounds from a marine environment with protease inhibitory activity has gained importance due to drug discovery potential. Despite the increasing research endeavours focusing on protease inhibitors' design and characterization, many of these compounds have failed to reach final phases of clinical trials. As a result, the search for new sources for the development of protease inhibitors remains pertinent. This review focuses on the diverse marine protease inhibitors and their structure-activity relationships. Furthermore, the potential of marine protease inhibitors in drug discovery and molecular mechanism inhibitor binding are critically discussed.
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5
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Kaysser L. Built to bind: biosynthetic strategies for the formation of small-molecule protease inhibitors. Nat Prod Rep 2019; 36:1654-1686. [DOI: 10.1039/c8np00095f] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The discovery and characterization of natural product protease inhibitors has inspired the development of numerous pharmaceutical agents.
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Affiliation(s)
- Leonard Kaysser
- Department of Pharmaceutical Biology
- University of Tübingen
- 72076 Tübingen
- Germany
- German Centre for Infection Research (DZIF)
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6
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Abstract
This review discusses the chemistry of cyclic azole-homologated peptides (AHPs) from the marine sponges, Theonella swinhoei, other Theonella species, Calyx spp. and Plakina jamaicensis. The origin, distribution of AHPs and molecular structure elucidations of AHPs are described followed by their biosynthesis, bioactivity, and synthetic efforts towards their total synthesis. Reports of partial and total synthesis of AHPs extend beyond peptide coupling reactions and include creative construction of the non-proteinogenic amino acid components, mainly the homologated heteroaromatic and α-keto-β-amino acids. A useful conclusion is drawn regarding AHPs: despite their rarity, exotic structures and the potent protease inhibitory properties of some members, their synthesis is under-developed and beckons solutions for outstanding problems towards their efficient assembly.
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Affiliation(s)
- Tadeusz F Molinski
- Department of Chemistry and Biochemistry, and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Dr 0358, La Jolla, California 92093, USA.
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7
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Biologically active cyclic polypeptides with fragments of β-amino acid derivatives isolated from marine organisms (review). Chem Heterocycl Compd (N Y) 2011. [DOI: 10.1007/s10593-011-0774-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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8
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Adang AEP, Hermkens PHH, Linders JTM, Ottenheijm HCJ, van Staveren CJ. Case histories of peptidomimetics: Progression from peptides to drugs. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19941130202] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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9
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Faure S, Hjelmgaard T, Roche SP, Aitken DJ. Passerini reaction-amine deprotection-acyl migration peptide assembly: efficient formal synthesis of cyclotheonamide C. Org Lett 2010; 11:1167-70. [PMID: 19203293 DOI: 10.1021/ol900048r] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A short, convergent, formal total synthesis of cyclotheonamide C is described. The key linear pentapeptide intermediate is assembled at the same time as the elaboration of the alpha-hydroxyhomoarginine (H-hArg) residue via a three-component Passerini reaction-amine deprotection-O,N-acyl migration strategy.
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Affiliation(s)
- Sophie Faure
- Laboratoire de Synthèse et Etude de Systèmes d'Intérêt Biologique, SEESIB (UMR 6504-CNRS), Université Blaise Pascal-Clermont-Ferrand 2, 24 avenue des Landais, 63177 Aubière Cedex, France.
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10
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Roche SP, Faure S, El Blidi L, Aitken DJ. Total Synthesis of Cyclotheonamide C by Use of an α-Keto Cyanophosphorane Methodology for Peptide Assembly. European J Org Chem 2008. [DOI: 10.1002/ejoc.200800591] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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11
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Hashizume H, Nishimura Y. Cyclic Lipopeptide Antibiotics. BIOACTIVE NATURAL PRODUCTS (PART O) 2008. [DOI: 10.1016/s1572-5995(08)80016-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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12
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Kamoune L, De Borggraeve WM, Gielens C, Voet A, Robeyns K, De Maeyer M, Van Meervelt L, Compernolle F, Hoornaert G. Design, Synthesis and Evaluation of Serine Protease Inhibitor Analogues. European J Org Chem 2007. [DOI: 10.1002/ejoc.200700180] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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13
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Sellanes D, Manta E, Serra G. Toward the Total Synthesis of Scleritodermin A: Preparation of the C(1)-N(15) Fragment. Tetrahedron Lett 2007; 48:1827-1830. [PMID: 18320006 DOI: 10.1016/j.tetlet.2007.01.034] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The synthesis of the C(1)-N(15) fragment of the marine natural product Scleritodermin A has been accomplished through a short and stereocontrolled sequence. Highlights of this route include the synthesis of the novel ACT fragment and the formation of the alpha-keto amide linkage by the use of a highly activated alpha, beta-ketonitrile.
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Affiliation(s)
- Diver Sellanes
- Cátedra de Química Farmacéutica, Departamento de Química Orgánica, Facultad de Química, UDELAR, Av. General Flores 2124, C. C. 1157, Montevideo, Uruguay
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14
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Almond CSD, Chen EA, Berman MR, Less JR, Baldwin JT, Linde-Feucht SR, Hoke TR, Pearson GD, Jenkins K, Duncan BW, Zuckerman BD. High-Risk Medical Devices, Children and the FDA: Regulatory Challenges Facing Pediatric Mechanical Circulatory Support Devices. ASAIO J 2007; 53:4-7. [PMID: 17237642 DOI: 10.1097/01.mat.0000247958.84788.3a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Pediatric mechanical circulatory support is a critical unmet need in the United States. Infant- and child-sized ventricular assist devices are currently being developed largely through federal contracts and grants through the National Heart, Lung, and Blood Institute (NHLBI). Human testing and marketing of high-risk devices for children raises epidemiologic and regulatory issues that will need to be addressed. Leaders from the US Food and Drug Administration (FDA), NHLBI, academic pediatric community, and industry convened in January 2006 for the first FDA Workshop on the Regulatory Process for Pediatric Mechanical Circulatory Support Devices. The purpose was to provide the pediatric community with an overview of the federal regulatory process for high-risk medical devices and to review the challenges specific to the development and regulation of pediatric mechanical circulatory support devices. Pediatric mechanical circulatory support present significant epidemiologic, logistic, and financial challenges to industry, federal regulators, and the pediatric community. Early interactions with the FDA, shared appreciation of challenges, and careful planning will be critical to avoid unnecessary delays in making potentially life-saving devices available for children. Collaborative efforts to address these challenges are warranted.
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Affiliation(s)
- Christopher S D Almond
- Department of Cardiology, Children's Hospital Boston, Harvard Medical School, Boston, Massachusetts 02115, USA
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15
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Staas DD, Savage KL, Sherman VL, Shimp HL, Lyle TA, Tran LO, Wiscount CM, McMasters DR, Sanderson PEJ, Williams PD, Lucas BJ, Krueger JA, Lewis SD, White RB, Yu S, Wong BK, Kochansky CJ, Anari MR, Yan Y, Vacca JP. Discovery of potent, selective 4-fluoroproline-based thrombin inhibitors with improved metabolic stability. Bioorg Med Chem 2006; 14:6900-16. [PMID: 16870455 DOI: 10.1016/j.bmc.2006.06.040] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2006] [Revised: 06/10/2006] [Accepted: 06/19/2006] [Indexed: 11/18/2022]
Abstract
Previous reports from our laboratories described potent tripeptide thrombin inhibitors which incorporate heterocycle-substituted chlorophenyl groups in the P1 position. Using these as lead compounds for further optimization, we identified sites of metabolism and designed analogs with 4-fluoroproline in P2 and cyclopropane-containing side chains in P3 as an approach to reducing metabolism and improving their oral pharmacokinetic performance. The large (300-fold) difference in potency between analogs containing (4R)- and (4S)-4-fluoroproline was rationalized by analyzing inhibitor-enzyme interactions in crystal structures of related compounds and by molecular modeling which indicated that the more potent (4R)-4-fluoroproline isomer stabilizes a proline ring conformation that is preferred for binding to the enzyme. An optimal compound from this work, 41, exhibits high potency in a coagulation assay in human plasma (2xAPTT=190 nM), excellent selectivity versus the digestive enzyme trypsin (K(i)=3300 nM), and excellent oral bioavailability in dogs with moderate clearance (F=100%, CL=12 mL/min/kg).
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Affiliation(s)
- Donnette D Staas
- Department of Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486, USA.
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16
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Stauffer KJ, Williams PD, Selnick HG, Nantermet PG, Newton CL, Homnick CF, Zrada MM, Lewis SD, Lucas BJ, Krueger JA, Pietrak BL, Lyle EA, Singh R, Miller-Stein C, White RB, Wong B, Wallace AA, Sitko GR, Cook JJ, Holahan MA, Stranieri-Michener M, Leonard YM, Lynch JJ, McMasters DR, Yan Y. 9-hydroxyazafluorenes and their use in thrombin inhibitors. J Med Chem 2005; 48:2282-93. [PMID: 15801822 DOI: 10.1021/jm049423s] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Optimization of a previously reported thrombin inhibitor, 9-hydroxy-9-fluorenylcarbonyl-l-prolyl-trans-4-aminocyclohexylmethylamide (1), by replacing the aminocyclohexyl P1 group provided a new lead structure, 9-hydroxy-9-fluorenylcarbonyl-l-prolyl-2-aminomethyl-5-chlorobenzylamide (2), with improved potency (K(i) = 0.49 nM for human thrombin, 2x APTT = 0.37 microM in human plasma) and pharmacokinetic properties (F = 39%, iv T(1/2) = 13 h in dogs). An effective strategy for reducing plasma protein binding of 2 and improving efficacy in an in vivo thrombosis model in rats was to replace the lipophilic fluorenyl group in P3 with an azafluorenyl group. Systematic investigation of all possible azafluorenyl P3 isomers and azafluorenyl-N-oxide analogues of 2 led to the identification of an optimal compound, 3-aza-9-hydroxyfluoren-9(R)-ylcarbonyl-l-prolyl-2-aminomethyl-5-chlorobenzylamide (19b), with high potency (K(i) = 0.40 nM, 2x APTT = 0.18 microM), excellent pharmacokinetic properties (F = 55%, T(1/2) = 14 h in dogs), and complete efficacy in the in vivo thrombosis model in rats (inhibition of FeCl(3)-induced vessel occlusions in six of six rats receiving an intravenous infusion of 10 microg/kg/min of 19b). The stereochemistry of the azafluorenyl group in 19b was determined by X-ray crystallographic analysis of its N-oxide derivative (23b) bound in the active site of human thrombin.
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Affiliation(s)
- Kenneth J Stauffer
- Department of Medicinal Chemistry, Biological Chemistry, Pharmacology, Drug Metabolism, and Molecular Systems, Merck Research Laboratories, West Point, Pennsylvania 19486, USA.
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17
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Morrissette MM, Stauffer KJ, Williams PD, Lyle TA, Vacca JP, Krueger JA, Lewis SD, Lucas BJ, Wong BK, White RB, Miller-Stein C, Lyle EA, Wallace AA, Leonard YM, Welsh DC, Lynch JJ, McMasters DR. Low molecular weight thrombin inhibitors with excellent potency, metabolic stability, and oral bioavailability. Bioorg Med Chem Lett 2004; 14:4161-4. [PMID: 15261262 DOI: 10.1016/j.bmcl.2004.06.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2004] [Accepted: 06/09/2004] [Indexed: 11/24/2022]
Abstract
Modification of lead compound 1 by reducing lipophilicity in the P3 group produced a series of low molecular weight thrombin inhibitors with excellent potency in functional assays, metabolic stability, and oral bioavailability. These modifications led to the identification of two optimized compounds, 14 and 16.
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Affiliation(s)
- Matthew M Morrissette
- Department of Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486, USA.
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18
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Maryanoff BE. Inhibitors of Serine Proteases as Potential Therapeutic Agents: The Road from Thrombin to Tryptase to Cathepsin G†. J Med Chem 2004; 47:769-87. [PMID: 14761180 DOI: 10.1021/jm030493t] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bruce E Maryanoff
- Drug Discovery, Johnson & Johnson Pharmaceutical Research & Development, Spring House, Pennsylvania 19477-0776, USA.
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19
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Chen JJ, Deshpande SV. Rapid synthesis of α-ketoamides using microwave irradiation–simultaneous cooling method. Tetrahedron Lett 2003. [DOI: 10.1016/j.tetlet.2003.09.180] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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20
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Sanderson PEJ, Cutrona KJ, Savage KL, Naylor-Olsen AM, Bickel DJ, Bohn DL, Clayton FC, Krueger JA, Lewis SD, Lucas BJ, Lyle EA, Wallace AA, Welsh DC, Yan Y. 3-amino-4-sulfonylpyridinone acetamide and related pyridothiadiazine thrombin inhibitors. Bioorg Med Chem Lett 2003; 13:1441-4. [PMID: 12668008 DOI: 10.1016/s0960-894x(03)00154-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We describe a series of highly potent and efficacious thrombin inhibitors based on a 3-amino-4-sulfonylpyridinone acetamide template. The functionally dense sulfonyl group stabilizes the aminopyridinone, conformationally constrains the 4-substituent, and forms a hydrogen bond to the insertion loop tyrosine OH. We also describe a related series of fused bicyclic dihydrothiadiazinedioxide derivatives, of which one had improved pharmacokinetics in dogs after oral dosing.
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Affiliation(s)
- Philip E J Sanderson
- Department of Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486, USA.
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21
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Sanderson PEJ, Stanton MG, Dorsey BD, Lyle TA, McDonough C, Sanders WM, Savage KL, Naylor-Olsen AM, Krueger JA, Lewis SD, Lucas BJ, Lynch JJ, Yan Y. Azaindoles: moderately basic P1 groups for enhancing the selectivity of thrombin inhibitors. Bioorg Med Chem Lett 2003; 13:795-8. [PMID: 12617893 DOI: 10.1016/s0960-894x(03)00017-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Starting from a 2-amino-6-methylpyridine P1 group and following a strategy of enlarging it whilst reducing its polarity, we have developed a series of potent, moderately basic azaindoles which are intrinsically much more selective for thrombin versus trypsin. Certain pyrazinone acetamide azaindole derivatives have pharmacokinetic parameters after oral administration to dogs, or efficacy in vitro, comparable to an optimized pyrazinone acetamide 2-amino-6-methylpyridine derivative.
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Affiliation(s)
- Philip E J Sanderson
- Department of Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486, USA.
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22
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Sanderson PEJ, Cutrona KJ, Dyer DL, Krueger JA, Kuo LC, Lewis SD, Lucas BJ, Yan Y. Small, low nanomolar, noncovalent thrombin inhibitors lacking a group to fill the 'distal binding pocket'. Bioorg Med Chem Lett 2003; 13:161-4. [PMID: 12482415 DOI: 10.1016/s0960-894x(02)00946-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Use of a chlorophenoxyacetamide P1 group with a pyridinone acetamide P2/P3 gave an exceptionally potent thrombin inhibitor (K(i)=40 pM). Truncation of the molecule at the N-terminus gave unique, low nanomolar, non-covalent thrombin inhibitors which do not have a group to fill thrombin's 'distal binding pocket'. A co-crystal structure indicates the importance of an intramolecular hydrogen bond between the P1 side chain and P1/P2 amide link in this series.
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Affiliation(s)
- Philip E J Sanderson
- Department of Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486, USA.
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23
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Edrada RA, Ebel R, Supriyono A, Wray V, Schupp P, Steube K, van Soest R, Proksch P. Swinhoeiamide A, a new highly active calyculin derivative from the marine sponge Theonella swinhoei. JOURNAL OF NATURAL PRODUCTS 2002; 65:1168-1172. [PMID: 12193024 DOI: 10.1021/np020049d] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Analysis of the Papua New Guinean sponge Theonella swinhoei afforded a new calyculinamide-related congener for which we propose the name swinhoeiamide A (1). The structure of the new compound was unambiguously established on the basis of NMR spectroscopic ((1)H, (13)C, COSY, HMBC) and mass spectrometric (FABMS) data. Swinhoeiamide A exhibited insecticidal activity toward neonate larvae of the polyphagous pest insect Spodoptera littoralis when incorporated in an artificial diet offered to the larvae in a chronic feeding bioassay (ED(50) 2.11 ppm, LD(50) 2.98 ppm). Furthermore, it was found to be fungicidal against Candida albicans and Aspergillus fumigatus (MIC 1.2 and 1.0 microg/mL, respectively).
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Affiliation(s)
- Ru Angelie Edrada
- Institut für Pharmazeutische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, Geb. 26.23, Germany
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24
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Owens TD, Semple JE. Atom-economical synthesis of the N(10)-C(17) fragment of cyclotheonamides via a novel Passerini reaction-deprotection-acyl migration strategy. Org Lett 2001; 3:3301-4. [PMID: 11594819 DOI: 10.1021/ol0165239] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text]. A novel variant of the atom-economical Passerini reaction between suitably protected argininal, dipeptide isonitrile, and proline components afforded adduct 13. Orthogonal N-deprotection of 13 led, via a smooth O- to N-acyl migration, to 14, which constitutes the N(10)-C(17) fragment of the cyclotheonamide family of serine protease inhibitors. Each reaction in this three-step protocol proceeds in good yield and under very mild conditions.
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Affiliation(s)
- T D Owens
- Department of Medicinal Chemistry, Corvas International, Inc., 3030 Science Park Road, San Diego, California 92121, USA
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25
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Abstract
A large number of potent and selective therapeutic agents, useful for the treatment of several diseases, have been isolated from natural sources. For example, the most active thrombin inhibitors are those secreted by the salivary glands of leeches. One peculiar feature of these agents is the lack of any significant inhibitory cross-reaction with other serine proteinases. Hence, the knowledge of the exact mechanism of action of these molecules provides the basis for the development of new and efficient synthetic drugs. For this reason, many studies have been undertaken on the structure-activity relationships of natural thrombin inhibitors, and a large amount of detailed information has been obtained by the crystal structures of these inhibitors when complexed with thrombin. In this paper, we review natural and synthetic multisite thrombin inhibitors, whose structural aspects have been determined in detail. We also report here the approach used by us to develop a new class of synthetic, multisite directed thrombin inhibitors, named hirunorms, designed to mimic the distinctive binding mode of hirudin.
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Affiliation(s)
- A Lombardi
- Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Napoli Federico II, Italy
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26
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Sanderson PE, Lyle TA, Cutrona KJ, Dyer DL, Dorsey BD, McDonough CM, Naylor-Olsen AM, Chen IW, Chen Z, Cook JJ, Cooper CM, Gardell SJ, Hare TR, Krueger JA, Lewis SD, Lin JH, Lucas BJ, Lyle EA, Lynch JJ, Stranieri MT, Vastag K, Yan Y, Shafer JA, Vacca JP. Efficacious, orally bioavailable thrombin inhibitors based on 3-aminopyridinone or 3-aminopyrazinone acetamide peptidomimetic templates. J Med Chem 1998; 41:4466-74. [PMID: 9804686 DOI: 10.1021/jm980368v] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have addressed the key deficiency of noncovalent pyridinone acetamide thrombin inhibitor L-374,087 (1), namely, its modest half-lives in animals, by making a chemically stable 3-alkylaminopyrazinone bioisostere for its 3-sulfonylaminopyridinone core. Compound 3 (L-375,378), the closest aminopyrazinone analogue of 1, has comparable selectivity and slightly decreased efficacy but significantly improved pharmacokinetics in rats, dogs, and monkeys to 1. We have developed an efficient and versatile synthesis of 3, and this compound has been chosen for further preclinical and clinical development.
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Affiliation(s)
- P E Sanderson
- Departments of Antiviral Research, Biological Chemistry, Drug Metabolism, Medicinal Chemistry, Molecular Design and Diversity, Pharmacology, Merck Research Laboratories, West Point, Pennsylvania 19486, USA
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27
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Clark DP, Carroll J, Naylor S, Crews P. An Antifungal Cyclodepsipeptide, Cyclolithistide A, from the Sponge Theonella swinhoei. J Org Chem 1998. [DOI: 10.1021/jo980758p] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dale P. Clark
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California 95064, and Biomedical Mass Spectrometry Facility and Molecular Biology, Mayo Clinic, Department of Biochemistry, Rochester, Minnesota 55905
| | - Jennifer Carroll
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California 95064, and Biomedical Mass Spectrometry Facility and Molecular Biology, Mayo Clinic, Department of Biochemistry, Rochester, Minnesota 55905
| | - Stephen Naylor
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California 95064, and Biomedical Mass Spectrometry Facility and Molecular Biology, Mayo Clinic, Department of Biochemistry, Rochester, Minnesota 55905
| | - Phillip Crews
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California 95064, and Biomedical Mass Spectrometry Facility and Molecular Biology, Mayo Clinic, Department of Biochemistry, Rochester, Minnesota 55905
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28
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Naylor-Olsen AM, Ponticello GS, Lewis SD, Mulichak AM, Chen Z, Habecker CN, Phillips BT, Sanders WM, Tucker TJ, Shafer JA, Vacca JP. Identification and SAR for a selective, nonpeptidyl thrombin inhibitor. Bioorg Med Chem Lett 1998; 8:1697-702. [PMID: 9873418 DOI: 10.1016/s0960-894x(98)00296-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A novel, nonpeptidyl thrombin inhibitor, L-636,619 (1), was identified via topological similarity searching over the Merck Corporate Sample Database. X-ray crystallographic studies determined the geometry for ligand binding to the enzyme. Chemical modification of the P1 and P3 segments of the ligand resulted in enhanced potency and improvement in the chemical stability of the lead. Analog 9 proved to be the most interesting lead from this structurally novel series.
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Affiliation(s)
- A M Naylor-Olsen
- Department of Molecular Design and Diversity, Merck Research Laboratories, West Point, PA 19486, USA
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29
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Nakao Y, Oku N, Matsunaga S, Fusetani N. Cyclotheonamides E2 and E3, new potent serine protease inhibitors from the marine sponge of the genus Theonella. JOURNAL OF NATURAL PRODUCTS 1998; 61:667-670. [PMID: 9599274 DOI: 10.1021/np970544n] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Two new potent serine protease inhibitors, cyclotheonamides E2 (3) and E3 (4), have been isolated from a marine sponge of the genus Theonella. Their structures were determined by interpretation of spectral data and chemical degradation studies. They are closely related to the previously reported cyclotheonamide E, from which they differ in the N-acyl group of the alanyl side chain. Cyclotheonamides E, E2, and E3 were more active against thrombin than against trypsin.
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Affiliation(s)
- Y Nakao
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
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30
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Sanderson PE, Cutrona KJ, Dorsey BD, Dyer DL, McDonough CM, Naylor-Olsen AM, Chen IW, Chen Z, Cook JJ, Gardell SJ, Krueger JA, Lewis SD, Lin JH, Lucas BJ, Lyle EA, Lynch JJ, Stranieri MT, Vastag K, Shafer JA, Vacca JP. L-374,087, an efficacious, orally bioavailable, pyridinone acetamide thrombin inhibitor. Bioorg Med Chem Lett 1998; 8:817-22. [PMID: 9871547 DOI: 10.1016/s0960-894x(98)00117-6] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Replacement of the amidinopiperidine P1 group of 3-benzylsulfonylamino-6-methyl-2-pyridinone acetamide thrombin inhibitor L-373,890 (2) with a mildly basic 5-linked 2-amino-6-methylpyridine results in an equipotent compound L-374,087 (5, Ki = 0.5 nM). Compound 5 is highly selective for thrombin over trypsin, is efficacious in the rat ferric chloride model of arterial thrombosis and is orally bioavailable in dogs and cynomolgus monkeys. The structural basis for the critical importance of both methyl groups in 5 was confirmed by X-ray crystallography.
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Affiliation(s)
- P E Sanderson
- Department of Biological Chemistry, Merck Research Laboratories, West Point, PA 19486, USA
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31
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Lewis SD, Lucas BJ, Brady SF, Sisko JT, Cutrona KJ, Sanderson PE, Freidinger RM, Mao SS, Gardell SJ, Shafer JA. Characterization of the two-step pathway for inhibition of thrombin by alpha-ketoamide transition state analogs. J Biol Chem 1998; 273:4843-54. [PMID: 9478925 DOI: 10.1074/jbc.273.9.4843] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The interaction of thrombin with several potent and selective alpha-ketoamide transition state analogs was characterized. L-370, 518 (H-N-Me-D-Phe-Pro-t-4-aminocyclohexylglycyl N-methylcarboxamide) a potent (Ki = 90 pM) and selective (>10(4)-fold versus trypsin) ketoamide thrombin inhibitor was shown to bind thrombin via a two-step reaction wherein the initially formed thrombin-inhibitor complex (EI1) rearranges to a more stable, final complex (EI2). A novel sequential stopped-flow analysis showed that k-1, the rate constant for dissociation of EI1, was comparable to k2, the rate constant for conversion of EI1 to EI2 (0.049 and 0.035 s-1, respectively) indicating that formation of the initial complex EI1 is partially rate controlling. Replacement of the N-terminal methylamino group in L-370,518 with a hydrogen (L-372,051) resulted in a 44-fold loss in potency (Ki = 4 nM) largely due to an increase in k-1. Consequently in the reaction of L-372,051 with thrombin formation of EI1 was not rate controlling. Replacement of the P1' N-methylcarboxamide group of L-370,518 with an azetidylcarboxamido (L-372,228) produced a 58-fold increase in the value of the equilibrium constant (K-1) for dissociation of EI1. Nevertheless, L-372,228 was a 2-fold more potent thrombin inhibitor (Ki = 40 pM) than L-370,518 due to its 16-fold higher k2 and 10-fold lower k-2 values. The desketoamide analogs of L-370,518 and L-372,051, namely L-371,912 and L-372,011, inhibited thrombin via a one-step process. The Ki value for L-371,912 and the K-1 value for its alpha-ketoamide analog, L-370,518, were similar (5 and 14 nM, respectively). Likewise, the Ki value for L-372,011 and the K-1 value for its alpha-ketoamide analog, L-372,051, were similar (330 and 285 nM, respectively). These observations are consistent with the view that the alpha-ketoamides L-370,518 and L-372,051 form initial complexes with thrombin that are similar to the complexes formed by their desketoamide analogs, and in a second step the alpha-ketoamides react with the active site serine residue of thrombin to form a more stable hemiketal adduct.
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Affiliation(s)
- S D Lewis
- Department of Biological Chemistry, Merck Research Laboratories, West Point, Pennsylvania 19486, USA
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32
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Nilsson T, Sjöling-Ericksson A, Deinum J. The mechanism of binding of low-molecular-weight active site inhibitors to human alpha-thrombin. JOURNAL OF ENZYME INHIBITION 1998; 13:11-29. [PMID: 9879511 DOI: 10.3109/14756369809035824] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The thrombin inhibitors argatroban, efegatran, NAPAP, CH 1091, CH 248, inogatran and melagatran have been characterised with respect to their mechanism of binding to human alpha-thrombin. Stopped-flow spectrophotometry was used to follow thrombin-catalysed hydrolysis of the chromogenic substrate S-2238 in the presence of inhibitors. The rate of onset or decay of inhibition was evaluated using progress curve analysis. It was possible to obtain apparent association and dissociation rate constants from the dependence of the rates on the inhibitor concentrations. Inhibition constants calculated from the association and dissociation rate constants were in good agreement with those calculated from steady-state rates. The binding of 6 inhibitors was also monitored directly using stopped-flow spectrofluorimetry when two kinetic components were found with all inhibitors. The faster component accounted for the largest part of the change in the intrinsic fluorescence of thrombin induced by inhibitor binding and was dependent on the inhibitor concentration. The slower component was independent of the concentration of the inhibitor. The concentration dependence of the faster component was linear with the compounds argatroban, NAPAP, CH 1091 and melagatran and hyperbolic with the compounds CH 248 and inogatran. The values of the apparent second-order rate constants at pH 7.4 and 37 degrees C range from slow to rapid binding in the interval 16-78 x 10(6) M-1 s-1, which is somewhat higher than 1-34 x 10(6)M-1 s-1 obtained from progress curve analysis of the onset of inhibition. The present results support a mechanism that includes rearrangement of a weak initial thrombin-inhibitor complex towards a tighter complex. Moreover, at least one additional step is required in the mechanism. In this model, the rate-limiting step for the binding of the inhibitor at concentrations in the nanomolar range depends on the primary interaction between the inhibitor and native thrombin.
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Affiliation(s)
- T Nilsson
- Department of Biochemistry and Biophysics, University of Göteborg, Sweden
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33
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Lai MT, Di Cera E, Shafer JA. Kinetic pathway for the slow to fast transition of thrombin. Evidence of linked ligand binding at structurally distinct domains. J Biol Chem 1997; 272:30275-82. [PMID: 9374513 DOI: 10.1074/jbc.272.48.30275] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The kinetic pathway for the Na+-induced slow --> fast transition of thrombin was characterized. The slow form was shown to consist of two conformers in a 3:1 ratio (ES2:ES1) at 5 degrees C, pH 7.4, Gamma/2 0.3. ES2 binds Na+ 3 orders of magnitude faster than does ES1. The small molecule active site-directed inhibitor L-371,912, and the exosite I binding ligand hirugen, like Na+, bind selectively to ES2 and induce the slow --> fast conversion of thrombin. The slow --> fast transition is limited by the rate of conversion of ES1 to ES2 (k approximately 28 s-1 at 5 degrees C). Replacement of Arg-221a or Lys-224 at the Na+ binding site with Ala appears to selectively alter the slow form and reduce the apparent affinity of the mutants for Na+ and L-371,912. This replacement, however, has little effect on the affinity for the inhibitor in the presence of saturating concentrations of Na+. The kinetically linked ligand binding at the Na+ binding site, exosite I, and the active site of thrombin characterized in the present study indicates the basis for the plasticity of this important enzyme, and suggests the possibility that the substrate specificity and, therefore, the procoagulant and anticoagulant activities of thrombin may be subject to allosteric regulation by as yet unidentified physiologically important effectors.
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Affiliation(s)
- M T Lai
- Department of Biological Chemistry, Merck Research Laboratories, West Point, Pennsylvania 19486, USA
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34
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Bastiaans HMM, van der Baan JL, Ottenheijm HCJ. Flexible and Convergent Total Synthesis of Cyclotheonamide B. J Org Chem 1997. [DOI: 10.1021/jo961447m] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Harold M. M. Bastiaans
- Leiden/Amsterdam Center for Drug Research, Division of Medicinal Chemistry, Department of Pharmacochemistry, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands, Department of Chemistry, Vrije Universiteit, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands, and N.V. Organon, Scientific Development Group, P.O. Box 20, 5340 BH Oss, The Netherlands
| | - Juul L. van der Baan
- Leiden/Amsterdam Center for Drug Research, Division of Medicinal Chemistry, Department of Pharmacochemistry, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands, Department of Chemistry, Vrije Universiteit, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands, and N.V. Organon, Scientific Development Group, P.O. Box 20, 5340 BH Oss, The Netherlands
| | - Harry C. J. Ottenheijm
- Leiden/Amsterdam Center for Drug Research, Division of Medicinal Chemistry, Department of Pharmacochemistry, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands, Department of Chemistry, Vrije Universiteit, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands, and N.V. Organon, Scientific Development Group, P.O. Box 20, 5340 BH Oss, The Netherlands
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35
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36
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McDonnell PA, Caldwell GW, Leo GC, Podlogar BL, Maryanoff BE. NMR three-dimensional solution structure of the serine protease inhibitor cyclotheonamide A. Biopolymers 1997. [DOI: 10.1002/(sici)1097-0282(199703)41:3<349::aid-bip10>3.0.co;2-f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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37
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Greco MN, Maryanoff BE. Macrocyclic inhibitors of serine proteases. ACTA ACUST UNITED AC 1997. [DOI: 10.1016/s1874-5113(97)80004-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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38
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Synthesis, evaluation, and crystallographic analysis of L-371,912: A potent and selective active-site thrombin inhibitor. Bioorg Med Chem Lett 1997. [DOI: 10.1016/s0960-894x(96)00583-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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39
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Transformation of the marine natural product cyclotheonamide A by aqueous base. X-ray analysis of a novel ligand complexed with human α-thrombin. Tetrahedron Lett 1996. [DOI: 10.1016/0040-4039(96)00658-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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40
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Ganesh V, Lee AY, Clardy J, Tulinsky A. Comparison of the structures of the cyclotheonamide A complexes of human alpha-thrombin and bovine beta-trypsin. Protein Sci 1996; 5:825-35. [PMID: 8732754 PMCID: PMC2143408 DOI: 10.1002/pro.5560050504] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Thrombin, a trypsin-like serine protease present in blood, plays a central role in the regulation of thrombosis and hemostasis. A cyclic pentapeptide, cyclotheonamide A (CtA), isolated from sponges of the genus Theonella, inhibits thrombin, trypsin, and certain other serine proteases. Enzyme inhibition data for CtA indicate that it is a moderate inhibitor of alpha-thrombin (K(i) = 1.0 nM), but substantially more potent toward trypsin (K(i) = 0.2 nM). The comparative study of the crystal structures of the CtA complexes of alpha-thrombin and beta-trypsin reported here focuses on structure-function relationships in general and the enhanced specificity of trypsin, in particular. The crystal structures of the CtA complexes of thrombin and trypsin were solved and refined at 1.7 and 2.0 A resolution, respectively. The structures show that CtA occupies the active site with the Pro-Arg motif positioned in the S2 and S1 binding sites. The alpha-keto group of CtA is involved in a tetrahedral intermediate hemiketal structure with Ser 195 OG of the catalytic triad and is positioned within bonding distance from, and orthogonal to, the re-face of the carbonyl of the arginine of CtA. As in other productive binding modes of serine proteases, the Ser 214-Gly 216 segment runs in a twisted antiparallel beta-strand manner with respect to the diaminopropionic acid (Dpr)-Arg segment of CtA. The Tyr 60A-Thr 60I insertion loop of thrombin makes a weak aromatic stacking interaction with the v-Tyr of CtA through Trp 60D. The Glu 39 Tyr and Leu 41 Phe substitutions in trypsin produce an enhanced aromatic interaction with D-Phe of CtA, which also leads to different orientations of the side chains of D-Phe and the v-Tyr. The comparison of the CtA complexes of thrombin and trypsin shows that the gross structural features of both in the active site region are the same, whereas the differences observed are mainly due to minor insertions and substitutions. In trypsin, the substitution of Ile 174-Arg 175 by Gly 174-Gln 175 makes the S3 aryl site more polar because the Arg 175 side chain is directed away from thrombin and into the solvent, whereas Gln 175 is not. Because the site is occupied by the Dpr group of CtA, the occupancy of the S3 site is better in trypsin than in thrombin. In trypsin, the D-Phe side chain of CtA fits between Tyr 39 and Phe 41 in a favorable manner, whereas in thrombin, these residues are Glu 39 and Leu 41. The higher degree of specificity for trypsin is most likely the result of these substitutions and the absence of the fairly rigid Tyr 60A-Thr 60I insertion loop of thrombin, which narrows access to the active site and forces less favorable orientations for the D-Phe and v-Tyr residues.
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Affiliation(s)
- V Ganesh
- Department of Chemistry, Michigan State University, East Lansing 48824-1322, USA
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41
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Jingen D, Yasumasa H, Takayuki S. A new synthesis of cyclotheonamide B via guanidination of ornithine. Tetrahedron Lett 1996. [DOI: 10.1016/0040-4039(96)00270-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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42
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Krishnan R, Tulinsky A, Vlasuk GP, Pearson D, Vallar P, Bergum P, Brunck TK, Ripka WC. Synthesis, structure, and structure-activity relationships of divalent thrombin inhibitors containing an alpha-keto-amide transition-state mimetic. Protein Sci 1996; 5:422-33. [PMID: 8868478 PMCID: PMC2143369 DOI: 10.1002/pro.5560050303] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A new class of divalent thrombin inhibitors is described that contains an alpha-keto-amide transition-state mimetic linking an active site binding group and a group that binds to the fibrinogen-binding exosite. The X-ray crystallographic structure of the most potent member of this new class, CVS995, shows many features in common with other divalent thrombin inhibitors and clearly defines the transition-state-like binding of the alpha-keto-amide group. The structure of the active site part of the inhibitor shows a network of water molecules connecting both the side-chain and backbone atoms of thrombin and the inhibitor. Direct peptide analogues of the new transition-state-containing divalent thrombin inhibitors were compared using in vitro assays of thrombin inhibition. There was no direct correlation between the binding constants of the peptides and their alpha-keto-amide counterparts. The most potent alpha-keto-amide inhibitor, CVS995, with a Ki = 1 pM, did not correspond to the most potent divalent peptide and contained a single amino acid deletion in the exosite binding region with respect to the equivalent region of the natural thrombin inhibitor hirudin. The interaction energies of the active site, transition state, and exosite binding regions of these new divalent thrombin inhibitors are not additive.
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Affiliation(s)
- R Krishnan
- Department of Chemistry, Michigan State University, East Lansing 48824-1322, USA
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43
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Brady SF, Sisko JT, Stauffer KJ, Colton CD, Qiu H, Lewis SD, Ng AS, Shafer JA, Bogusky MJ, Veber DF. Amide and alpha-keto carbonyl inhibitors of thrombin based on arginine and lysine: synthesis, stability and biological characterization. Bioorg Med Chem 1995; 3:1063-78. [PMID: 7582980 DOI: 10.1016/0968-0896(95)00105-p] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We report structure-activity investigations in a series of tripeptide amide inhibitors of thrombin, and the development of a series of highly potent active site directed alpha-keto carbonyl inhibitors having the side chain of lysine at P1. Compounds of this class are unstable by virtue of reactivity at the electrophilic carbonyl and racemization at the adjacent carbon (CH). Modifications of prototype alpha-keto-ester 8a have afforded analogs retaining nanomolar Ki. Optimal potency and stability have been realized in alpha-keto-amides 11b (Ki = 2.8 nM) and 11c (Ki = 0.25 nM).
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Affiliation(s)
- S F Brady
- Department of Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486, USA
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Håkansson K, Tulinsky A, Abelman MM, Miller TA, Vlasuk GP, Bergum PW, Lim-Wilby MS, Brunck TK. Crystallographic structure of a peptidyl keto acid inhibitor and human alpha-thrombin. Bioorg Med Chem 1995; 3:1009-17. [PMID: 7582975 DOI: 10.1016/0968-0896(95)00096-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The low molecular weight alpha-keto amide inhibitor CVS-1347, benzyl-SO2-Met(O2)-Pro-Arg(CO)((CONH)CH2)-phenyl, is a slow, tight binding inhibitor of alpha-thrombin amidolytic activity having a Ki = 1.28 x 10(-10) M. A complex between human alpha-thrombin and a hydrolysis product of CVS-1347 has been determined and refined using crystallography. The crystals belong to monoclinic space group C2 with cell dimensions of a = 71.08, b = 72.05 and c = 72.98 A and beta = 100.8 degrees. The structure was solved using isomorphous replacement methods and refined with resolution limits of (8.00-1.76) A to an R-value of 0.162. The Pro-Arg core of the inhibitor binds in the S2 and S1 subsites respectively, as is usually observed for Pro-Arg thrombin inhibitors. The Met(O2) side chain does not make any close contacts with the enzyme but influences the conformation of Glu192; the N-terminal benzylsulfonyl group makes an aromatic-aromatic contact with Trp215 in the hydrophobic part of the active site. The alpha-keto carboxylic acid of the proteolyzed inhibitor binds with the carboxylate group in the oxyanion hole, demonstrating that this region can accommodate an anion in a protease-peptide complex. The alpha-keto carbonyl group interacts closely with the two most important residues in the active site: the carbon atom is within a covalent bond distance of the active site Ser195 O gamma and the carbonyl oxygen is hydrogen bonded to His57.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- K Håkansson
- Department of Chemistry, Michigan State University, East Lansing 48824-1322, USA
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Maryanoff BE, Zhang HC, Greco MN, Glover KA, Kauffman JA, Andrade-Gordon P. Cyclotheonamide derivatives: synthesis and thrombin inhibition. Exploration of specific structure-function issues. Bioorg Med Chem 1995; 3:1025-38. [PMID: 7582977 DOI: 10.1016/0968-0896(95)00098-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Macrocyclic pentapeptide analogues (5-9) of the sponge natural product cyclotheonamide A (CtA, 3) were prepared by means of our convergent [3 + 2] synthetic protocol, in which a late-stage primary amine group is available for substitution (Maryanoff et al. Proc. Natl Acad. Sci. U.S.A. 1993, 90, 8048). These analogues, as well as CtA and cyclotheonamide B (CtB, 4), were examined for their ability to inhibit the serine protease alpha-thrombin, in comparison with suitable reference standards. We characterized Michaelis-Menten and slow-binding kinetics for the cyclotheonamide derivatives. An attempt was made to utilize the unoccupied hydrophobic S3 subsite of thrombin via analogues 5 and 6. Also, removal of the hydroxyphenyl group, which is thought to be involved in an aromatic stacking interaction with Trp60D of thrombin, was explored via analogue 9. The importance of the alpha-keto and olefin groups was examined via 7 and 8, respectively. The relationship of structure and function with the analogues proved to be less predictable than anticipated.
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Affiliation(s)
- B E Maryanoff
- R.W. Johnson Pharmaceutical Research Institute, Spring House, PA 19477, USA
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Ripka W, Brunck T, Stanssens P, LaRoche Y, Lauwereys M, Lambeir AM, Lasters I, DeMaeyer M, Vlasuk G, Levy O, Miller T, Webb T, Tamura S, Pearson D. Strategies in the Design of Inhibitors of Serine Proteases of the Coagulation Cascade - Factor Xa. Eur J Med Chem 1995. [DOI: 10.1016/s0223-5234(23)00116-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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Lee AY, Smitka TA, Bonjouklian R, Clardy J. Atomic structure of the trypsin-A90720A complex: a unified approach to structure and function. CHEMISTRY & BIOLOGY 1994; 1:113-7. [PMID: 9383379 DOI: 10.1016/1074-5521(94)90049-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND A90720A is a potent serine proteinase inhibitor produced by the terrestrial blue-green alga Microchaete loktakensis. Most of its structure has been defined by spectroscopic and degradative studies, but the configurations of several stereochemical centers are unknown, and its mode of inhibition of serine proteinases is not understood. We therefore examined the structure of the compound in a complex with trypsin. RESULTS We have crystallized the bovine trypsin-A90720A complex and determined its three-dimensional structure at 1.90 A resolution using single crystal X-ray diffraction. The structure of the bound inhibitor is clearly shown in the electron density. The structure defines the absolute stereostructure of A90720A, establishes its bound conformation and illuminates its mode of inhibition. CONCLUSIONS A90720A interacts with trypsin in a substrate-like manner through an extensive series of hydrogen bonds, hydrophobic interactions and steric complementarity. The compound uses a mixture of peptidal and nonpeptidal elements to imitate the canonical conformation of the exposed binding loop of 'small' proteinase inhibitors.
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Affiliation(s)
- A Y Lee
- Department of Chemistry, Baker Laboratory, Cornell University, Ithaca, NY 14853-1301, USA
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