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Ghosh U, Kumar V, Singh G, Kanti Chakraborty T. Conformation Based in silico Studies of Cyclic Tetrapeptides with βγ Fused Turns as Thrombin Inhibitors. ChemistrySelect 2023. [DOI: 10.1002/slct.202204761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Affiliation(s)
- Uttam Ghosh
- Department of Organic Chemistry Indian Institute of Science Bengaluru 560012 India
| | - Vikash Kumar
- CSIR-Central Drug Research Institute Lucknow 226031 India
| | - Gajendra Singh
- CSIR-Central Drug Research Institute Lucknow 226031 India
- School of Life Sciences Central University of Rajasthan Bandar Sindri Ajmer 305817 Rajasthan India
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2
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Legrand B, Maillard LT. α,β-Unsaturated γ-Peptide Foldamers. Chempluschem 2021; 86:629-645. [PMID: 33856125 DOI: 10.1002/cplu.202100045] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/31/2021] [Indexed: 01/01/2023]
Abstract
Despite their concomitant emergence in the 1990s, γ-peptide foldamers have not developed as fast as β-peptide foldamers and to date, only a few γ-oligomer structures have been reported, and with sparse applications. Among these examples, sequences containing α,β-unsaturated γ-amino acids have recently drawn attention since the Z/E configurations of the double bond provide opposite planar restrictions leading to divergent conformational behaviors, from helix to extended structures. In this Review, we give a comprehensive overview of the developments of γ-peptide foldamers containing α,β-unsaturated γ-amino acids with examples of applications for health and catalysis, as well as materials science.
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Affiliation(s)
- Baptiste Legrand
- Institut des Biomolécules Max Mousseron, IBMM, University of Montpellier, ENSCM, CNRS, Montpellier, France., 15 Av. Charles Flahault BP 14 491, 34093, Montpellier Cedex 5, France
| | - Ludovic T Maillard
- Institut des Biomolécules Max Mousseron, IBMM, University of Montpellier, ENSCM, CNRS, Montpellier, France., 15 Av. Charles Flahault BP 14 491, 34093, Montpellier Cedex 5, France
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3
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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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4
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Jwad R, Weissberger D, Hunter L. Strategies for Fine-Tuning the Conformations of Cyclic Peptides. Chem Rev 2020; 120:9743-9789. [PMID: 32786420 DOI: 10.1021/acs.chemrev.0c00013] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cyclic peptides are promising scaffolds for drug development, attributable in part to their increased conformational order compared to linear peptides. However, when optimizing the target-binding or pharmacokinetic properties of cyclic peptides, it is frequently necessary to "fine-tune" their conformations, e.g., by imposing greater rigidity, by subtly altering certain side chain vectors, or by adjusting the global shape of the macrocycle. This review systematically examines the various types of structural modifications that can be made to cyclic peptides in order to achieve such conformational control.
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Affiliation(s)
- Rasha Jwad
- Department of Chemistry, College of Science, Al-Nahrain University, Baghdad, Iraq
| | - Daniel Weissberger
- School of Chemistry, University of New South Wales (UNSW) Sydney, New South Wales 2052, Australia
| | - Luke Hunter
- School of Chemistry, University of New South Wales (UNSW) Sydney, New South Wales 2052, Australia
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5
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Merritt HI, Sawyer N, Arora PS. Bent Into Shape: Folded Peptides to Mimic Protein Structure and Modulate Protein Function. Pept Sci (Hoboken) 2020; 112:e24145. [PMID: 33575525 PMCID: PMC7875438 DOI: 10.1002/pep2.24145] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 12/11/2019] [Indexed: 12/16/2022]
Abstract
Protein secondary and tertiary structure mimics have served as model systems to probe biophysical parameters that guide protein folding and as attractive reagents to modulate protein interactions. Here we review contemporary methods to reproduce loop, helix, sheet and coiled-coil conformations in short peptides.
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Affiliation(s)
| | | | - Paramjit S. Arora
- Department of Chemistry New York University, New York, New York 10003, United States
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6
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Malde AK, Hill TA, Iyer A, Fairlie DP. Crystal Structures of Protein-Bound Cyclic Peptides. Chem Rev 2019; 119:9861-9914. [DOI: 10.1021/acs.chemrev.8b00807] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Alpeshkumar K. Malde
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Timothy A. Hill
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Abishek Iyer
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David P. Fairlie
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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7
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Wesche F, Adihou H, Wichelhaus TA, Bode HB. Synthesis and SAR of the antistaphylococcal natural product nematophin from Xenorhabdus nematophila. Beilstein J Org Chem 2019; 15:535-541. [PMID: 30873237 PMCID: PMC6404511 DOI: 10.3762/bjoc.15.47] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 02/13/2019] [Indexed: 12/12/2022] Open
Abstract
The repeated and improper use of antibiotics had led to an increased number of multiresistant bacteria. Therefore, new lead structures are needed. Here, the synthesis and an expanded structure-activity relationship of the simple and antistaphylococcal amide nematophin from Xenorhabdus nematophila and synthetic derivatives are described. Moreover, the synthesis of intrinsic fluorescent derivatives, incorporating azaindole moieties was achieved for the first time.
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Affiliation(s)
- Frank Wesche
- Molekulare Biotechnologie, Goethe University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.,present address: Respiratory, Inflammation and Autoimmunity, Innovative Medicines and Early Development, Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal 43183, Sweden
| | - Hélène Adihou
- Molekulare Biotechnologie, Goethe University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.,present address: Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development, Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal 43183, Sweden.,present address: AstraZeneca MPI Satellite Unit, Abteilung Chemische Biologie, Max Planck Institut für Molekulare Physiologie, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Thomas A Wichelhaus
- Institut für Medizinische Mikrobiologie und Krankenhaushygiene, Universitätsklinikum Frankfurt, Paul-Ehrlich-Str. 40, D-60596 Frankfurt am Main, Germany
| | - Helge B Bode
- Molekulare Biotechnologie, Goethe University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 15, D-60438 Frankfurt am Main, Germany
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8
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Chen X, Zhang L, Wu Y, Wang L, Ma C, Xi X, Bininda-Emonds ORP, Shaw C, Chen T, Zhou M. Evaluation of the bioactivity of a mastoparan peptide from wasp venom and of its analogues designed through targeted engineering. Int J Biol Sci 2018; 14:599-607. [PMID: 29904274 PMCID: PMC6001651 DOI: 10.7150/ijbs.23419] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 02/21/2018] [Indexed: 12/15/2022] Open
Abstract
Mastoparan is a typical cationic and amphipathic tetradecapeptide found in wasp venom and exhibits potent biological activities. Yet, compared with other insect-derived peptides, such as melittin from the bee venom, this family have been underrated. Herein, we evaluated the biological activities of mastoparan-C (MP-C), which was identified from the venom of the European Hornet (Vespa crabro), and rationally designed two analogues (a skeleton-based cyclization by two cysteine residues and an N-terminal extension via tat-linked) for enhancing the stability of the biological activity and membrane permeability, respectively. Three peptides possessed broadly efficacious inhibiting capacities towards common pathogens, resistant strains, as well as microbial biofilm. Although, cyclized MP-C showed longer half-life time than the parent peptide, the lower potency of antimicrobial activity and higher degree of haemolysis were observed. The tat-linked MP-C exhibited more potent anticancer activity than the parent peptide, but it also loses the specificity. The study revealed that MP-C is good candidate for developing antimicrobial agents and the targeted-design could improve the stability and transmembrane delivery, but more investigation would be needed to adjust the side effects brought from the design.
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Affiliation(s)
- Xiaoling Chen
- Natural Drug Discovery Group, School of Pharmacy, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Luyao Zhang
- Natural Drug Discovery Group, School of Pharmacy, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Yue Wu
- Natural Drug Discovery Group, School of Pharmacy, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Lei Wang
- Natural Drug Discovery Group, School of Pharmacy, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Chengbang Ma
- Natural Drug Discovery Group, School of Pharmacy, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Xinping Xi
- Natural Drug Discovery Group, School of Pharmacy, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Olaf R P Bininda-Emonds
- AG Systematik und Evolutionsbiologie, IBU-Faculty V, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Chris Shaw
- Natural Drug Discovery Group, School of Pharmacy, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Tianbao Chen
- Natural Drug Discovery Group, School of Pharmacy, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Mei Zhou
- Natural Drug Discovery Group, School of Pharmacy, Queen's University Belfast, Belfast, Northern Ireland, UK
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9
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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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10
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Gogineni V, Hamann MT. Marine natural product peptides with therapeutic potential: Chemistry, biosynthesis, and pharmacology. Biochim Biophys Acta Gen Subj 2018; 1862:81-196. [PMID: 28844981 PMCID: PMC5918664 DOI: 10.1016/j.bbagen.2017.08.014] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 08/07/2017] [Accepted: 08/09/2017] [Indexed: 12/21/2022]
Abstract
The oceans are a uniquely rich source of bioactive metabolites, of which sponges have been shown to be among the most prolific producers of diverse bioactive secondary metabolites with valuable therapeutic potential. Much attention has been focused on marine bioactive peptides due to their novel chemistry and diverse biological properties. As summarized in this review, marine peptides are known to exhibit various biological activities such as antiviral, anti-proliferative, antioxidant, anti-coagulant, anti-hypertensive, anti-cancer, antidiabetic, antiobesity, and calcium-binding activities. This review focuses on the chemistry and biology of peptides isolated from sponges, bacteria, cyanobacteria, fungi, ascidians, and other marine sources. The role of marine invertebrate microbiomes in natural products biosynthesis is discussed in this review along with the biosynthesis of modified peptides from different marine sources. The status of peptides in various phases of clinical trials is presented, as well as the development of modified peptides including optimization of PK and bioavailability.
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Affiliation(s)
- Vedanjali Gogineni
- Department of BioMolecular Sciences, Division of Medicinal Chemistry, School of Pharmacy, The University of Mississippi, University, MS, United States.
| | - Mark T Hamann
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy and Public Health Sciences, Medical University of South Carolina, Charleston, SC, United States.
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11
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Anjum K, Abbas SQ, Shah SAA, Akhter N, Batool S, Hassan SSU. Marine Sponges as a Drug Treasure. Biomol Ther (Seoul) 2016; 24:347-62. [PMID: 27350338 PMCID: PMC4930278 DOI: 10.4062/biomolther.2016.067] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 04/28/2016] [Accepted: 05/19/2016] [Indexed: 12/22/2022] Open
Abstract
Marine sponges have been considered as a drug treasure house with respect to great potential regarding their secondary metabolites. Most of the studies have been conducted on sponge's derived compounds to examine its pharmacological properties. Such compounds proved to have antibacterial, antiviral, antifungal, antimalarial, antitumor, immunosuppressive, and cardiovascular activity. Although, the mode of action of many compounds by which they interfere with human pathogenesis have not been clear till now, in this review not only the capability of the medicinal substances have been examined in vitro and in vivo against serious pathogenic microbes but, the mode of actions of medicinal compounds were explained with diagrammatic illustrations. This knowledge is one of the basic components to be known especially for transforming medicinal molecules to medicines. Sponges produce a different kind of chemical substances with numerous carbon skeletons, which have been found to be the main component interfering with human pathogenesis at different sites. The fact that different diseases have the capability to fight at different sites inside the body can increase the chances to produce targeted medicines.
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Affiliation(s)
- Komal Anjum
- Ocean College, Zhejiang University, Hangzhou 310058,
China
| | - Syed Qamar Abbas
- Faculty of Pharmacy, Gomal University D.I.Khan, K.P.K. 29050,
Pakistan
| | | | - Najeeb Akhter
- Ocean College, Zhejiang University, Hangzhou 310058,
China
| | - Sundas Batool
- Department of Molecular Biology, University of Heidelberg,
Germany
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12
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Fukuhara K, Takada K, Okada S, Matsunaga S. Nazumazoles D-F, Cyclic Pentapeptides That Inhibit Chymotrypsin, from the Marine Sponge Theonella swinhoei. JOURNAL OF NATURAL PRODUCTS 2016; 79:1694-1697. [PMID: 27213234 DOI: 10.1021/acs.jnatprod.6b00261] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Nazumazoles D-F (1-3) were isolated from the marine sponge Theonella swinhoei. The compounds gave extremely broad peaks by reversed-phase HPLC using an ODS column. HPLC using a gel permeation column was instrumental for the separation of the three compounds. Their planar structures were determined by interpretation of NMR data to be cyclic pentapeptides. Nazumazoles D-F contained one residue each of α-keto-l-norvaline (l-Knv) {or α-keto-d-leucine (l-Kle)}, l-alanyloxazole (l-Aox), d-Abu (or d-Ser), N-α-CHO-β-l-Dpr, and cis-4-methyl-l-proline. The absolute configuration of each amino acid residue was determined by Marfey's method in combination with conversion of the α-keto-β-amino acid to the α-amino acid by oxidation. Nazumazoles D-F are not cytotoxic against P388 cells at 50 μM, but inhibit chymotrypsin.
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Affiliation(s)
- Kazuya Fukuhara
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo , Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kentaro Takada
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo , Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shigeru Okada
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo , Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shigeki Matsunaga
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo , Bunkyo-ku, Tokyo 113-8657, Japan
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13
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De Risi C, Pollini GP, Zanirato V. Recent Developments in General Methodologies for the Synthesis of α-Ketoamides. Chem Rev 2016; 116:3241-305. [DOI: 10.1021/acs.chemrev.5b00443] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Carmela De Risi
- Dipartimento
di Scienze Chimiche e Farmaceutiche, Università degli Studi di Ferrara, Via Fossato di Mortara 17, 44121 Ferrara, Italy
| | - Gian Piero Pollini
- Istituto Universitario
di Studi Superiori “IUSS−Ferrara 1391”, Via delle Scienze 41/b, 44121 Ferrara, Italy
| | - Vinicio Zanirato
- Dipartimento
di Scienze Chimiche e Farmaceutiche, Università degli Studi di Ferrara, Via Fossato di Mortara 17, 44121 Ferrara, Italy
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14
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Lee SH, Kyung H, Yokota R, Goto T, Oe T. Hydroxyl Radical-Mediated Novel Modification of Peptides: N-Terminal Cyclization through the Formation of α-Ketoamide. Chem Res Toxicol 2014; 28:59-70. [DOI: 10.1021/tx500332y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Seon Hwa Lee
- Department of Bio-analytical
Chemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Hyunsook Kyung
- Department of Bio-analytical
Chemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Ryo Yokota
- Department of Bio-analytical
Chemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Takaaki Goto
- Department of Bio-analytical
Chemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Tomoyuki Oe
- Department of Bio-analytical
Chemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
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15
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Hill TA, Shepherd NE, Diness F, Fairlie DP. Constraining cyclic peptides to mimic protein structure motifs. Angew Chem Int Ed Engl 2014; 53:13020-41. [PMID: 25287434 DOI: 10.1002/anie.201401058] [Citation(s) in RCA: 292] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 04/02/2013] [Indexed: 12/18/2022]
Abstract
Many proteins exert their biological activities through small exposed surface regions called epitopes that are folded peptides of well-defined three-dimensional structures. Short synthetic peptide sequences corresponding to these bioactive protein surfaces do not form thermodynamically stable protein-like structures in water. However, short peptides can be induced to fold into protein-like bioactive conformations (strands, helices, turns) by cyclization, in conjunction with the use of other molecular constraints, that helps to fine-tune three-dimensional structure. Such constrained cyclic peptides can have protein-like biological activities and potencies, enabling their uses as biological probes and leads to therapeutics, diagnostics and vaccines. This Review highlights examples of cyclic peptides that mimic three-dimensional structures of strand, turn or helical segments of peptides and proteins, and identifies some additional restraints incorporated into natural product cyclic peptides and synthetic macrocyclic peptidomimetics that refine peptide structure and confer biological properties.
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Affiliation(s)
- Timothy A Hill
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072 (Australia)
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16
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Hill TA, Shepherd NE, Diness F, Fairlie DP. Fixierung cyclischer Peptide: Mimetika von Proteinstrukturmotiven. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201401058] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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17
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Abou-Hussein DR, Badr JM, Youssef DTA. Dragmacidoside: a new nucleoside from the Red Sea sponge Dragmacidon coccinea. Nat Prod Res 2014; 28:1134-41. [PMID: 24831420 DOI: 10.1080/14786419.2014.915828] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Chemical investigation of the Red Sea sponge Dragmacidon coccinea led to the isolation of a new nucleoside, dragmacidoside (1), along with eight known compounds: adenosine (2), inosine (3), deoxycytidine (4), methyl-α-d-glucopyranoside (5), clionasterol (6), stigmasterol (7), campesterol (8) and brassicasterol (9). The compounds were isolated from chloroform and ethyl acetate fractions of the methanolic extract of the sponge, and their structures were established based on various spectroscopic data including MS, 1D and 2D NMR (COSY, HSQC and HMBC). Biological testing revealed that the chloroform fraction possesses significant anti-inflammatory activity in the carrageenan-induced hind paw oedema in rats.
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Affiliation(s)
- Dina R Abou-Hussein
- a Department of Natural Products and Alternative Medicine , Faculty of Pharmacy, King Abdulaziz University , Jeddah 21589 , Saudi Arabia
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18
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Schlippe YVG, Hartman MCT, Josephson K, Szostak JW. In vitro selection of highly modified cyclic peptides that act as tight binding inhibitors. J Am Chem Soc 2012; 134:10469-77. [PMID: 22428867 PMCID: PMC3384292 DOI: 10.1021/ja301017y] [Citation(s) in RCA: 178] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
There is a great demand for the discovery of new therapeutic
molecules
that combine the high specificity and affinity of biologic drugs with
the bioavailability and lower cost of small molecules. Small, natural-product-like
peptides hold great promise in bridging this gap; however, access
to libraries of these compounds has been a limitation. Since ribosomal
peptides may be subjected to in vitro selection techniques,
the generation of extremely large libraries (>1013)
of
highly modified macrocyclic peptides may provide a powerful alternative
for the generation and selection of new useful bioactive molecules.
Moreover, the incorporation of many non-proteinogenic amino acids
into ribosomal peptides in conjunction with macrocyclization should
enhance the drug-like features of these libraries. Here we show that
mRNA-display, a technique that allows the in vitro selection of peptides, can be applied to the evolution of macrocyclic
peptides that contain a majority of unnatural amino acids. We describe
the isolation and characterization of two such unnatural cyclic peptides
that bind the protease thrombin with low nanomolar affinity, and we
show that the unnatural residues in these peptides are essential for
the observed high-affinity binding. We demonstrate that the selected
peptides are tight-binding inhibitors of thrombin, with Kiapp values in the low nanomolar range. The
ability to evolve highly modified macrocyclic peptides in the laboratory
is the first crucial step toward the facile generation of useful molecular
reagents and therapeutic lead molecules that combine the advantageous
features of biologics with those of small-molecule drugs.
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Affiliation(s)
- Yollete V Guillen Schlippe
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA
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19
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Gersch M, Kreuzer J, Sieber SA. Electrophilic natural products and their biological targets. Nat Prod Rep 2012; 29:659-82. [DOI: 10.1039/c2np20012k] [Citation(s) in RCA: 193] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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20
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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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21
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Synthesis and biological evaluation of α-ketoamides as inhibitors of the Dengue virus protease with antiviral activity in cell-culture. Bioorg Med Chem 2011; 19:4067-74. [PMID: 21641807 DOI: 10.1016/j.bmc.2011.05.015] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Revised: 05/10/2011] [Accepted: 05/10/2011] [Indexed: 11/21/2022]
Abstract
The development of small molecule inhibitors of the viral protease is of considerable interest for the treatment of emergent flaviviral diseases such as Dengue or West Nile fever. Until today little progress has been made in finding drug-like compounds that inhibit the protease and provide a starting point for lead optimization. We describe here the initial steps of a drug discovery effort that focused on the styryl pharmacophore, combined with a ketoamide function to serve as electrophilic trap for the catalytic serine. This resulted in a fragment-like lead compound with reasonable target affinity and good ligand efficiency, which was extensively modified to explore structure-activity relationships. Selected compounds were cross-tested against the West Nile virus protease and thrombin, indicating that selectivity for one or more flaviviral proteases can be achieved. Finally, the antiviral activity of several protease inhibitors was confirmed in a cell-culture model of Dengue virus replication. The SAR presented here may serve as starting point for further drug discovery efforts with the aim of targeting flaviviral proteases.
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Loughlin WA, Tyndall JDA, Glenn MP, Hill TA, Fairlie DP. Update 1 of: Beta-Strand Mimetics. Chem Rev 2011; 110:PR32-69. [DOI: 10.1021/cr900395y] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Wendy A. Loughlin
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - Joel D. A. Tyndall
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - Matthew P. Glenn
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - Timothy A. Hill
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - David P. Fairlie
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
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Marsault E, Peterson ML. Macrocycles Are Great Cycles: Applications, Opportunities, and Challenges of Synthetic Macrocycles in Drug Discovery. J Med Chem 2011; 54:1961-2004. [DOI: 10.1021/jm1012374] [Citation(s) in RCA: 591] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Eric Marsault
- Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke Québec, J1H5N4, Canada
| | - Mark L. Peterson
- Tranzyme Pharma Inc., 3001 12e Avenue Nord, Sherbrooke, Québec, J1H5N4, Canada
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Wang Y, Niu L, Li Y, Mao X, Yang Y, Wang C. Single molecule studies of cyclic peptides using molecular matrix at liquid/solid interface by scanning tunneling microscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:16305-16311. [PMID: 20593799 DOI: 10.1021/la101467s] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
We report in this work the single molecule studies of cyclic peptide, cyclosporine A (CsA), using a molecular network formed by star-shaped oligofluorene (StOF-COOH(3)) at the liquid/solid interface by scanning tunneling microscopy (STM). Individual cyclosporine A can be identified and resolved in the molecular network, and the high-resolution STM images of CsA show polygon-like characteristics with a diameter of approximately 1.7 nm. Furthermore, the complex of CsA and Mg(2+) has also been observed to adsorb inside of the molecular matrix. The STM results reveal two adsorption characteristics for the CsA-Mg(2+) complex, which is suggestive of asymmetrical configurations of the complex. The difference in binding energy between the two observed adsorption configurations is estimated to be 1.88 kJ·mol(-1). These results help set the stage for studying the fine structures and functions of various cyclic peptides at the liquid/solid interface.
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Affiliation(s)
- Yibing Wang
- National Center for Nanoscience and Technology, Beijing 100190, PR China
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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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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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Schaschke N, Sommerhoff CP. Upgrading a natural product: inhibition of human beta-tryptase by cyclotheonamide analogues. ChemMedChem 2010; 5:367-70. [PMID: 20077463 DOI: 10.1002/cmdc.200900484] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Norbert Schaschke
- Fakultät für Chemie, Universität Bielefeld, Universitätsstr. 25, 33615 Bielefeld, Germany.
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Abstract
A convergent synthesis of alpha-ketoamide inhibitors of Pin1 is described. An alpha-hydroxyorthothioester derivative of Ser was reacted directly with an amine synthon. The reaction was catalyzed by HgO and HgCl(2) to form alpha-hydroxyamide. Thus, hydrolysis and coupling were combined in one step with 80% yield. Two diastereomers of a phospho-Ser-Pro alpha-ketoamide analogue were synthesized. The IC(50) values of 100 and 200 microM were surprisingly weak for Pin1 peptidyl prolyl isomerase.
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Affiliation(s)
- Guoyan G Xu
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, USA
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29
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Stoermer MJ, Leung D, Young PR, Fairlie DP. Base-Sensitivity of Arginine Alpha-Ketoamide Inhibitors of Serine Proteases. Aust J Chem 2009. [DOI: 10.1071/ch09150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Serine protease enzymes use a serine hydroxyl group to catalyze hydrolysis of polypeptides. They are important in immunity, blood clotting, digestion, and as therapeutic or diagnostic targets for cancer, diabetes, stroke, inflammatory diseases, and viral infections. Their inhibitors typically possess an electrophile that reacts with the nucleophilic hydroxyl group of the catalytic serine. The α-ketoamide is a valuable electrophile in inhibitor discovery as it permits synthetic elaboration to both sides, unlike other electrophiles. Here we show that an α-ketoamide is unstable above pH 7 when adjacent to the C-terminus of arginine – the guanidine side chain condenses with the α-ketoamide at the keto group rather than the amide carbonyl to form a six-membered hemiaminal rather than a seven-membered lactam.
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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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Roche S, Faure S, Aitken D. Total Synthesis of Cyclotheonamide C using a Tandem Backbone-Extension-Coupling Methodology. Angew Chem Int Ed Engl 2008; 47:6840-2. [DOI: 10.1002/anie.200802005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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33
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Roche S, Faure S, Aitken D. Total Synthesis of Cyclotheonamide C using a Tandem Backbone-Extension-Coupling Methodology. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200802005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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34
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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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35
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Maryanoff BE, McComsey DF, Costanzo MJ, Yabut SC, Lu T, Player MR, Giardino EC, Damiano BP. Exploration of potential prodrugs of RWJ-445167, an oxyguanidine-based dual inhibitor of thrombin and factor Xa. Chem Biol Drug Des 2006; 68:29-36. [PMID: 16923023 DOI: 10.1111/j.1747-0285.2006.00408.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Compound 2 (RWJ-445167; 3DP-10017), a dual inhibitor of thrombin and factor Xa, was advanced into human clinical studies. However, its oral bioavailability in humans proved to be below acceptable limits. To address this issue, we explored a prodrug approach involving numerous guanidine derivatives. Prodrug candidates of classes A (carbamate derivatives), B (imidate derivatives), and C (alkyl and acyl derivatives), compounds 3-6, were synthesized and evaluated for anticoagulant activity at 2 h after oral administration to rats. In comparison to the parent drug (2), little worthwhile improvement was observed for the prodrug candidates.
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Affiliation(s)
- Bruce E Maryanoff
- Vascular Research Team, Johnson & Johnson Pharmaceutical Research & Development, Spring House, PA 19477-0776, USA.
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36
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Butenas S, Orfeo T, Kalafatis M, Mann KG. Peptidomimetic inhibitors for activated protein C: implications for hemophilia management. J Thromb Haemost 2006; 4:2411-6. [PMID: 17059471 DOI: 10.1111/j.1538-7836.2006.02226.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND Several clinical studies and experiments with transgenic mice have suggested that the severity of the bleeding phenotype in hemophilic patients is substantially reduced in association with impaired inactivation of factor (F) Va by activated protein C (APC) in the presence of the FV Leiden mutation. Experiments using a synthetic coagulation proteome model showed that the presence of FV Leiden significantly increased thrombin generation in the absence of FVIII or FIX. OBJECTIVE To test the effect of APC inhibition on thrombin generation in hemophilia. METHODS Prothrombinase and a synthetic coagulation proteome model of tissue factor-triggered thrombin generation were used. RESULTS Peptide-based APC inhibitors, which mimic the P4-P4' residues surrounding the APC cleavage site at Arg306 of FVa, were synthesized. These compounds are specific and reversible inhibitors of APC, with Ki values as low as 1-2 microM; most have insignificant affinity for FXa or thrombin. The affinity for APC is dependent upon the location and character of the protecting groups. Representatives of this group of compounds inhibit FVa inactivation by APC and prolong FVa functional activity in the prothrombinase complex. When evaluated in a synthetic coagulation proteome model, one inhibitor partially compensated for the absence of FVIII. CONCLUSIONS Synthetic APC inhibitors may be useful as adjuvants for hemophilia treatment.
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Affiliation(s)
- S Butenas
- Department of Biochemistry, University of Vermont, Colchester, VT 05446, USA.
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37
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Cotesta S, Stahl M. The environment of amide groups in protein–ligand complexes: H-bonds and beyond. J Mol Model 2005; 12:436-44. [PMID: 16344948 DOI: 10.1007/s00894-005-0067-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2005] [Accepted: 10/18/2005] [Indexed: 10/25/2022]
Abstract
A comprehensive structural analysis of interactions involving amide NH and C=O groups in protein-ligand complexes has been performed based on 3,275 published crystal structures (resolution < or =2.5 A). Most of the amide C=O and NH groups at the protein-ligand interface are highly buried within the binding site and involved in H-bonds with corresponding counter-groups. Small percentages of C=O and NH groups are solvated or embedded in hydrophobic environments. In particular, C=O groups show a higher propensity to be solvated or embedded in a hydrophobic environment than NH groups do. A small percentage of carbonyl groups is involved in weak hydrogen bonds with CH. Cases of dipolar interactions, involving carbonyl oxygen and electrophilic carbon atoms, such as amide, amidinium, guanidium groups, are also identified. A higher percentage of NH are in contact with aromatic carbons, interacting either through hydrogen bonds (preferably with the NH group pointing towards a ring carbon atom) or through stacking between amide plane and ring plane. Comprehensive studies such as the present one are thought to be important for future improvements in the molecular design area, in particular for the development of new scoring functions. [Figure: see text].
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Affiliation(s)
- Simona Cotesta
- Molecular Design, Pharmaceutical Division, F. Hoffmann-La Roche AG, Discovery technologies, Bldg. 092/2.10D, CH-4070, Basel, Switzerland.
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Abstract
Our bodies are made of molecules, and it is from molecules that we derive our strength and joys. The joys of molecules manifest themselves in many ways. These include beautiful colors, exquisite aromas, distinct tastes, psychological ups and downs, and intellectual inspirations, among other forms of stimulation, material or spiritual. In this Perspective, written on the occasion of the 2005 American Chemical Society Arthur C. Cope Award address, I recount some of the joys I have experienced and shared with my students during campaigns to synthesize some of Nature's most intriguing and complex molecules.
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Affiliation(s)
- K C Nicolaou
- Department of Chemistry and Skaggs Institute for Chemical Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
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Costanzo MJ, Almond HR, Hecker LR, Schott MR, Yabut SC, Zhang HC, Andrade-Gordon P, Corcoran TW, Giardino EC, Kauffman JA, Lewis JM, de Garavilla L, Haertlein BJ, Maryanoff BE. In-depth study of tripeptide-based alpha-ketoheterocycles as inhibitors of thrombin. Effective utilization of the S1' subsite and its implications to structure-based drug design. J Med Chem 2005; 48:1984-2008. [PMID: 15771442 DOI: 10.1021/jm0303857] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Thrombin inhibitors are potentially useful in medicine for their anticoagulant and antithrombotic effects. We synthesized and evaluated diverse heterocycle-activated ketones based on the d-Phe-Pro-Arg, and related thrombin active-site recognition motifs, as candidate inhibitors. The peptide-based alpha-ketoheterocycles were typically prepared by either an imidate or a Weinreb amide route (Schemes 1 and 2), the latter of which proved to be more general. Test compounds were generally assayed for inhibition of human alpha-thrombin and bovine trypsin. From a structure-based design standpoint, the heterocycle allows one to explore and adjust interactions within the S1' subsite of thrombin. The preferred alpha-ketoheterocycle is a pi-rich 2-substituted azole with at least two heteroatoms proximal to the carbon bearing the keto group, and a preferred thrombin inhibitor is 2-ketobenzothiazole 3, with a potent K(i) value of 0.2 nM and ca. 15-fold selectivity over trypsin. 2-Ketobenzothiazole 13 exhibited exceedingly potent thrombin inhibition (K(i) = 0.000 65 nM; slow tight binding). Several alpha-ketoheterocycles had thrombin K(i) values in the range 0.1-400 nM. The "Arg" unit in the alpha-ketoheterocycles can be sensitive to stereomutation under mildy basic conditions. For example, 2-ketothiazoles 4 and 59 readily epimerize at pH 7.4, although they are fairly stable stereochemically at pH 3-4; thus, suitable conditions had to be selected for the enzymatic assays. Lead d-Phe-Pro-Arg 2-benzothiazoles 3, 4, and 68 displayed good selectivity for thrombin over other key coagulation enzymes (e.g., factor Xa, plasmin, protein Ca, uPA, tPA, and streptokinase); however, their selectivity for thrombin over trypsin was modest (<25-fold). Compounds 3, 4, and 68 exhibited potent in vitro antithrombotic activity as measured by inhibition of gel-filtered platelet aggregation induced by alpha-thrombin (IC(50) = 30-40 nM). They also proved to be potent anticoagulant/antithrombotic agents in vivo on intravenous administration, as determined in the canine arteriovenous shunt (ED(50) = 0.45-0.65 mg/kg) and the rabbit deep vein thrombosis (ED(50) = 0.1-0.4 mg/kg) models. Intravenous administration of 3, and several analogues, to guinea pigs caused hypotension and electrocardiogram abnormalities. Such cardiovascular side effects were also observed with some nonguanidine inhibitors and inhibitors having recognition motifs other than d-Phe-Pro-Arg. 2-Benzothiazolecarboxylates 4 and 68 exhibited significantly diminished cardiovascular side effects, and benzothiazolecarboxylic acid 4 had the best profile with respect to therapeutic index. The X-ray crystal structures of the ternary complexes 3-thrombin-hirugen and 4-thrombin-hirugen depict novel interactions in the S(1)' region, with the benzothiazole ring forming a hydrogen bond with His-57 and an aromatic stacking interaction with Trp-60D of thrombin's insertion loop. The benzothiazole ring of 3 displaces the Lys-60F side chain into a U-shaped gauche conformation, whereas the benzothiazole carboxylate of 4 forms a salt bridge with the side chain of Lys-60F such that it adopts an extended anti conformation. Since 3 has a 10-fold greater affinity for thrombin than does 4, any increase in binding energy resulting from this salt bridge is apparently offset by perturbations across the enzyme (viz. Figure 4). The increased affinity and selectivity of 2-ketobenzothiazole inhibitors, such as 3, may be primarily due to the aromatic stacking interaction with Trp-60D. However, energy contour calculations with the computer program GRID also indicate a favorable interaction between the benzothiazole sulfur atom and a hydrophobic patch on the surface of thrombin.
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Affiliation(s)
- Michael J Costanzo
- Drug Discovery, Johnson & Johnson Pharmaceutical Research & Development, Spring House, Pennsylvania 19477-0776, USA
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Sipkema D, Franssen MCR, Osinga R, Tramper J, Wijffels RH. Marine sponges as pharmacy. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2005; 7:142-62. [PMID: 15776313 PMCID: PMC7087563 DOI: 10.1007/s10126-004-0405-5] [Citation(s) in RCA: 199] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2004] [Accepted: 08/24/2004] [Indexed: 05/04/2023]
Abstract
Marine sponges have been considered as a gold mine during the past 50 years, with respect to the diversity of their secondary metabolites. The biological effects of new metabolites from sponges have been reported in hundreds of scientific papers, and they are reviewed here. Sponges have the potential to provide future drugs against important diseases, such as cancer, a range of viral diseases, malaria, and inflammations. Although the molecular mode of action of most metabolites is still unclear, for a substantial number of compounds the mechanisms by which they interfere with the pathogenesis of a wide range of diseases have been reported. This knowledge is one of the key factors necessary to transform bioactive compounds into medicines. Sponges produce a plethora of chemical compounds with widely varying carbon skeletons, which have been found to interfere with pathogenesis at many different points. The fact that a particular disease can be fought at different points increases the chance of developing selective drugs for specific targets.
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Affiliation(s)
- Detmer Sipkema
- Wageningen University, Food and Bioprocess Engineering Group, 8129, 6700 EV Wageningen, The Netherlands,
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41
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Ilies MA, Supuran CT, Scozzafava A. Therapeutic applications of serine protease inhibitors. Expert Opin Ther Pat 2005. [DOI: 10.1517/13543776.12.8.1181] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Toyota E, Sekizaki H, Takahashi YU, Itoh K, Tanizawa K. Amidino-Containing Schiff Base Copper(II) and Iron(III) Chelates as a Thrombin Inhibitor. Chem Pharm Bull (Tokyo) 2005; 53:22-6. [PMID: 15635223 DOI: 10.1248/cpb.53.22] [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] [Indexed: 11/22/2022]
Abstract
Four series of Schiff base copper(II) and iron(III) chelates were synthesized from 4-formyl-3-hydroxybenzamidine or 3-formyl-4-hydroxybenzamidine and various L- or D-amino acids. Their inhibitory activities for bovine alpha-thrombin (abbreviated as thrombin) were determined. The most potent thrombin inhibitor in this series is copper(II) chelate (1g') derived from 4-formyl-3-hydroxybenzamidine and D-Trp. Its Ki value, 2.7x10(-8) M, is comparable to that of Argatroban (MD-805), which is a clinically used compound. The iron(III) chelates derived from 4-formyl-3-hydroxybenzamidine and hydrophobic L-amino acids (Val, Ile, Leu, Phe, Trp, Met) also exhibited higher inhibitory potency. It appears that coordination geometry composed of metal ion, amidino group, amino acid side chain is well accommodated to the thrombin active site. From the Ki values of Schiff base metal chelates for thrombin, the structure-activity relationships between the chelates and active site of thrombin were discussed.
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Affiliation(s)
- Eiko Toyota
- Faculty of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Hokkaido, Japan
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Affiliation(s)
- Wendy A Loughlin
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia.
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44
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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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45
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Aitken DJ, Faure S, Roche S. Synthetic approaches to the southern part of cyclotheonamide C. Tetrahedron Lett 2003. [DOI: 10.1016/j.tetlet.2003.09.196] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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47
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Pearson ND, Eggleston DS, Haltiwanger RC, Hibbs M, Laver AJ, Kaura AC. Design and synthesis of conformationally restricted eight-Membered ring diketones as potential serine protease inhibitors. Bioorg Med Chem Lett 2002; 12:2359-62. [PMID: 12161133 DOI: 10.1016/s0960-894x(02)00461-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The design of conformationally restricted eight-membered ring diketones as transition state mimics of the mechanism of action of cyclotheonamides on serine proteases is described. Two target compounds are prepared from mutilin, derived from the natural product pleuromutilin. Compound 3 shows significant inhibition of plasmin and urokinase in enzyme rate assays, but an analogue 4 in which the amide moiety has been omitted does not. An X-ray crystal structure of the diketone 3 confirms the conformational predictions made by molecular modelling.
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Affiliation(s)
- Neil D Pearson
- GlaxoSmithKline Pharmaceuticals, New Frontiers Science Park North, Third Avenue, The Pinnacles, Harlow, Essex, UK
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48
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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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Murakami Y, Takei M, Shindo K, Kitazume C, Tanaka J, Higa T, Fukamachi H. Cyclotheonamide E4 and E5, new potent tryptase inhibitors from an Ircinia species of sponge. JOURNAL OF NATURAL PRODUCTS 2002; 65:259-261. [PMID: 11908961 DOI: 10.1021/np010304e] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Tryptase is a protease released from mast cells and is believed to contribute to the inflammatory process in allergic diseases including asthma. In the course of screening to find tryptase inhibitors, we isolated two new tryptase inhibitors, cyclotheonamide E4 (3) and E5 (4), from a marine sponge of the genus Ircinia. The structures of these molecules were determined by interpretation of 1H and 13C NMR spectra, and they were shown to be closely related to the previously reported cyclotheonamides E (1), E2, and E3 (2). These molecules contain two unusual amino acids, vinylogous tyrosine and alpha-ketohomoarginine, which are involved in strong activities against serine proteases. Cyclotheonamide E4 showed potent inhibitory activity against human tryptase (IC50 5.1 nM). Therefore, cyclotheonamide E4 may be useful as a therapeutic agent in the treatment of allergic diseases including asthma.
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Affiliation(s)
- Yasunobu Murakami
- Pharmaceutical Research Laboratory, Kirin Brewery Co., Ltd., 3, Miyahara-cho, Takasaki-shi, Gunma, 370-1295, Japan.
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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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