1
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Scala MC, Marchetti M, Superti F, Agamennone M, Campiglia P, Sala M. Rational Design of Novel Peptidomimetics against Influenza A Virus: Biological and Computational Studies. Int J Mol Sci 2023; 24:14268. [PMID: 37762571 PMCID: PMC10531517 DOI: 10.3390/ijms241814268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/08/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Effective therapy against the influenza virus is still an unmet goal. Drugs with antiviral effects exist, but the appearance of resistant viruses pushes towards the discovery of drugs with different mechanisms of action. New anti-influenza molecules should target a good candidate, as a new anti-influenza molecule could be an inhibitor of the influenza A virus hemagglutinin (HA), which plays a key role during the early phases of infection. In previous work, we identified two tetrapeptide sequences, SLDC (1) and SKHS (2), derived from bovine lactoferrin (bLf) C-lobe fragment 418-429, which were able to bind HA and inhibit cell infection at picomolar concentration. Considering the above, the aim of this study was to synthesize a new library of peptidomimetics active against the influenza virus. In order to test their ability to bind HA, we carried out a preliminary screening using biophysical assays such as surface plasmon resonance (SPR) and orthogonal immobilization-free microscale thermophoresis (MST). Biological and computational studies on the most interesting compounds were carried out. The methods applied allowed for the identification of a N-methyl peptide, S(N-Me)LDC, which, through high affinity binding of influenza virus hemagglutinin, was able to inhibit virus-induced hemagglutination and cell infection at picomolar concentration. This small sequence, with high activity, represents a good starting point for the design of new peptidomimetics and small molecules.
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Affiliation(s)
- Maria Carmina Scala
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy; (M.C.S.); (P.C.)
| | - Magda Marchetti
- National Centre for Innovative Technologies in Public Health, National Institute of Health, Viale Regina Elena, 299, 00161 Rome, Italy; (M.M.); or (F.S.)
| | - Fabiana Superti
- National Centre for Innovative Technologies in Public Health, National Institute of Health, Viale Regina Elena, 299, 00161 Rome, Italy; (M.M.); or (F.S.)
- Association for Research on Integrative Oncology Therapies (ARTOI) Foundation, Via Ludovico Micara, 73, 00165 Rome, Italy
| | - Mariangela Agamennone
- Department of Pharmacy, University “G. d’Annunzio” of Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy;
| | - Pietro Campiglia
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy; (M.C.S.); (P.C.)
| | - Marina Sala
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy; (M.C.S.); (P.C.)
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2
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Lindman J, Yadav A, Gising J, Larhed M. Two-Chamber Aminocarbonylation of Aryl Bromides and Triflates Using Amino Acids as Nucleophiles. J Org Chem 2023; 88:12978-12985. [PMID: 37639573 PMCID: PMC10507664 DOI: 10.1021/acs.joc.3c00972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Indexed: 08/31/2023]
Abstract
A palladium(0)-catalyzed aminocarbonylation reaction employing molybdenum hexacarbonyl as a carbon monoxide precursor for the production of N-capped amino acids using aryl and heteroaryl bromides and triflates is reported. The carbon monoxide is formed ex situ through the use of a two-chamber system, where carbon monoxide generated in one chamber is free to diffuse over and be consumed in the other palladium-catalyzed reaction chamber. Using this method, two series of aryl bromides and aryl triflates were utilized to synthesize 21 N-capped amino acids in isolated yields between 40 and 91%.
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Affiliation(s)
- Jens Lindman
- Department of Medicinal Chemistry, Uppsala University, Husargatan 3, SE-751
23 Uppsala, Sweden
| | - Anubha Yadav
- Department of Medicinal Chemistry, Uppsala University, Husargatan 3, SE-751
23 Uppsala, Sweden
| | - Johan Gising
- Department of Medicinal Chemistry, Uppsala University, Husargatan 3, SE-751
23 Uppsala, Sweden
| | - Mats Larhed
- Department of Medicinal Chemistry, Uppsala University, Husargatan 3, SE-751
23 Uppsala, Sweden
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3
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Todaro B, Ottalagana E, Luin S, Santi M. Targeting Peptides: The New Generation of Targeted Drug Delivery Systems. Pharmaceutics 2023; 15:1648. [PMID: 37376097 DOI: 10.3390/pharmaceutics15061648] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/22/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Peptides can act as targeting molecules, analogously to oligonucleotide aptamers and antibodies. They are particularly efficient in terms of production and stability in physiological environments; in recent years, they have been increasingly studied as targeting agents for several diseases, from tumors to central nervous system disorders, also thanks to the ability of some of them to cross the blood-brain barrier. In this review, we will describe the techniques employed for their experimental and in silico design, as well as their possible applications. We will also discuss advancements in their formulation and chemical modifications that make them even more stable and effective. Finally, we will discuss how their use could effectively help to overcome various physiological problems and improve existing treatments.
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Affiliation(s)
- Biagio Todaro
- NEST Laboratory, Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Elisa Ottalagana
- NEST Laboratory, Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy
- Fondazione Pisana per la Scienza, Via Ferruccio Giovannini 13, San Giuliano Terme, 56017 Pisa, Italy
| | - Stefano Luin
- NEST Laboratory, Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy
- NEST, Istituto Nanoscienze-CNR and Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Melissa Santi
- NEST, Istituto Nanoscienze-CNR and Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy
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4
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Abstract
Peptides have traditionally been perceived as poor drug candidates due to unfavorable characteristics mainly regarding their pharmacokinetic behavior, including plasma stability, membrane permeability and circulation half-life. Nonetheless, in recent years, general strategies to tackle those shortcomings have been established, and peptides are subsequently gaining increasing interest as drugs due to their unique ability to combine the advantages of antibodies and small molecules. Macrocyclic peptides are a special focus of drug development efforts due to their ability to address so called ‘undruggable’ targets characterized by large and flat protein surfaces lacking binding pockets. Here, the main strategies developed to date for adapting peptides for clinical use are summarized, which may soon help usher in an age highly shaped by peptide-based therapeutics. Nonetheless, limited membrane permeability is still to overcome before peptide therapeutics will be broadly accepted.
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5
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Thurston R, Zantop V, Park KS, Maid H, Seitz A, Heinrich MR. pH-Dependent Conformational Switching of Amide Bonds─from Full trans to Full cis and Vice Versa. Org Lett 2022; 24:3488-3492. [PMID: 35544347 DOI: 10.1021/acs.orglett.2c00938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Strategies enabling the pH-dependent conformational switching of amide bonds from trans to cis, and vice versa, are yet limited in the sense that, in a suitable pH range, one rotamer may be stabilized to a large extent while the complementary pH range only leads to a mixture of isomers. By exploiting the effects of steric demand and the interaction of the amide carbonyl with a positive charge, we herein present the first examples for reversible pH-dependent switching from full trans to full cis.
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Affiliation(s)
- Ryan Thurston
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Pharmaceutical Chemistry, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Viviane Zantop
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Pharmaceutical Chemistry, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Kristen Sodam Park
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Pharmaceutical Chemistry, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Harald Maid
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Organic Chemistry II, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Anke Seitz
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Pharmaceutical Chemistry, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Markus R Heinrich
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Pharmaceutical Chemistry, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
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6
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Horvat G, Tarana S, Vidović N, Cindro N, Speranza G, Tomišić V. Thermodynamic and MD studies of anion complexation by cyclopentaleucine in acetonitrile and dimethyl sulfoxide. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Kerbs A, Mindt M, Schwardmann L, Wendisch VF. Sustainable Production of N-methylphenylalanine by Reductive Methylamination of Phenylpyruvate Using Engineered Corynebacterium glutamicum. Microorganisms 2021; 9:microorganisms9040824. [PMID: 33924554 PMCID: PMC8070496 DOI: 10.3390/microorganisms9040824] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 12/17/2022] Open
Abstract
N-alkylated amino acids occur widely in nature and can also be found in bioactive secondary metabolites such as the glycopeptide antibiotic vancomycin and the immunosuppressant cyclosporine A. To meet the demand for N-alkylated amino acids, they are currently produced chemically; however, these approaches often lack enantiopurity, show low product yields and require toxic reagents. Fermentative routes to N-alkylated amino acids like N-methyl-l-alanine or N-methylantranilate, a precursor of acridone alkaloids, have been established using engineered Corynebacterium glutamicum, which has been used for the industrial production of amino acids for decades. Here, we describe metabolic engineering of C. glutamicum for de novo production of N-methylphenylalanine based on reductive methylamination of phenylpyruvate. Pseudomonas putida Δ-1-piperideine-2-carboxylate reductase DpkA containing the amino acid exchanges P262A and M141L showed comparable catalytic efficiencies with phenylpyruvate and pyruvate, whereas the wild-type enzyme preferred the latter substrate over the former. Deletion of the anthranilate synthase genes trpEG and of the genes encoding branched-chain amino acid aminotransferase IlvE and phenylalanine aminotransferase AroT in a strain engineered to overproduce anthranilate abolished biosynthesis of l-tryptophan and l-phenylalanine to accumulate phenylpyruvate. Upon heterologous expression of DpkAP262A,M141L, N-methylphenylalanine production resulted upon addition of monomethylamine to the medium. In glucose-based minimal medium, an N-methylphenylalanine titer of 0.73 ± 0.05 g L−1, a volumetric productivity of 0.01 g L−1 h−1 and a yield of 0.052 g g−1 glucose were reached. When xylose isomerase gene xylA from Xanthomonas campestris and the endogenous xylulokinase gene xylB were expressed in addition, xylose as sole carbon source supported production of N-methylphenylalanine to a titer of 0.6 ± 0.04 g L−1 with a volumetric productivity of 0.008 g L−1 h−1 and a yield of 0.05 g g−1 xylose. Thus, a fermentative route to sustainable production of N-methylphenylalanine by recombinant C. glutamicum has been established.
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Affiliation(s)
- Anastasia Kerbs
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, 33615 Bielefeld, Germany; (A.K.); (L.S.)
| | - Melanie Mindt
- BU Bioscience, Wagenigen University and Research, 6700AA Wageningen, The Netherlands;
| | - Lynn Schwardmann
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, 33615 Bielefeld, Germany; (A.K.); (L.S.)
| | - Volker F. Wendisch
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, 33615 Bielefeld, Germany; (A.K.); (L.S.)
- Correspondence: ; Tel.: +49-521-106-5611
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8
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Ludwig BS, Kessler H, Kossatz S, Reuning U. RGD-Binding Integrins Revisited: How Recently Discovered Functions and Novel Synthetic Ligands (Re-)Shape an Ever-Evolving Field. Cancers (Basel) 2021; 13:1711. [PMID: 33916607 PMCID: PMC8038522 DOI: 10.3390/cancers13071711] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/22/2021] [Accepted: 03/29/2021] [Indexed: 12/19/2022] Open
Abstract
Integrins have been extensively investigated as therapeutic targets over the last decades, which has been inspired by their multiple functions in cancer progression, metastasis, and angiogenesis as well as a continuously expanding number of other diseases, e.g., sepsis, fibrosis, and viral infections, possibly also Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2). Although integrin-targeted (cancer) therapy trials did not meet the high expectations yet, integrins are still valid and promising targets due to their elevated expression and surface accessibility on diseased cells. Thus, for the future successful clinical translation of integrin-targeted compounds, revisited and innovative treatment strategies have to be explored based on accumulated knowledge of integrin biology. For this, refined approaches are demanded aiming at alternative and improved preclinical models, optimized selectivity and pharmacological properties of integrin ligands, as well as more sophisticated treatment protocols considering dose fine-tuning of compounds. Moreover, integrin ligands exert high accuracy in disease monitoring as diagnostic molecular imaging tools, enabling patient selection for individualized integrin-targeted therapy. The present review comprehensively analyzes the state-of-the-art knowledge on the roles of RGD-binding integrin subtypes in cancer and non-cancerous diseases and outlines the latest achievements in the design and development of synthetic ligands and their application in biomedical, translational, and molecular imaging approaches. Indeed, substantial progress has already been made, including advanced ligand designs, numerous elaborated pre-clinical and first-in-human studies, while the discovery of novel applications for integrin ligands remains to be explored.
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Affiliation(s)
- Beatrice S. Ludwig
- Department of Nuclear Medicine, University Hospital Klinikum Rechts der Isar and Central Institute for Translational Cancer Research (TranslaTUM), Technical University Munich, 81675 Munich, Germany;
| | - Horst Kessler
- Department of Chemistry, Institute for Advanced Study, Technical University Munich, 85748 Garching, Germany;
| | - Susanne Kossatz
- Department of Nuclear Medicine, University Hospital Klinikum Rechts der Isar and Central Institute for Translational Cancer Research (TranslaTUM), Technical University Munich, 81675 Munich, Germany;
- Department of Chemistry, Institute for Advanced Study, Technical University Munich, 85748 Garching, Germany;
| | - Ute Reuning
- Clinical Research Unit, Department of Obstetrics and Gynecology, University Hospital Klinikum Rechts der Isar, Technical University Munich, 81675 Munich, Germany
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9
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Ghaffari S, Kazemi F. Highly Efficient Synthesis of
N
‐Alkyl‐α‐amino Acid Methyl Esters by Microwave Irradiation. ChemistrySelect 2021. [DOI: 10.1002/slct.202100114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Saeedeh Ghaffari
- Department of Chemistry Institute of Advanced Studies in Basic Sciences (IASBS) Zanjan 45195-1159 Iran
- Department of Chemistry, College of Sciences Shiraz University Shiraz 71946-84795 Iran
| | - Foad Kazemi
- Department of Chemistry Institute of Advanced Studies in Basic Sciences (IASBS) Zanjan 45195-1159 Iran
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10
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Evans BJ, King AT, Katsifis A, Matesic L, Jamie JF. Methods to Enhance the Metabolic Stability of Peptide-Based PET Radiopharmaceuticals. Molecules 2020; 25:molecules25102314. [PMID: 32423178 PMCID: PMC7287708 DOI: 10.3390/molecules25102314] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/11/2020] [Accepted: 05/13/2020] [Indexed: 12/28/2022] Open
Abstract
The high affinity and specificity of peptides towards biological targets, in addition to their favorable pharmacological properties, has encouraged the development of many peptide-based pharmaceuticals, including peptide-based positron emission tomography (PET) radiopharmaceuticals. However, the poor in vivo stability of unmodified peptides against proteolysis is a major challenge that must be overcome, as it can result in an impractically short in vivo biological half-life and a subsequently poor bioavailability when used in imaging and therapeutic applications. Consequently, many biologically and pharmacologically interesting peptide-based drugs may never see application. A potential way to overcome this is using peptide analogues designed to mimic the pharmacophore of a native peptide while also containing unnatural modifications that act to maintain or improve the pharmacological properties. This review explores strategies that have been developed to increase the metabolic stability of peptide-based pharmaceuticals. It includes modifications of the C- and/or N-termini, introduction of d- or other unnatural amino acids, backbone modification, PEGylation and alkyl chain incorporation, cyclization and peptide bond substitution, and where those strategies have been, or could be, applied to PET peptide-based radiopharmaceuticals.
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Affiliation(s)
- Brendan J. Evans
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; (B.J.E.); (A.T.K.)
| | - Andrew T. King
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; (B.J.E.); (A.T.K.)
| | - Andrew Katsifis
- Department of Molecular Imaging, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia;
| | - Lidia Matesic
- Australian Nuclear Science and Technology Organisation (ANSTO), Lucas Heights, NSW 2234, Australia;
| | - Joanne F. Jamie
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; (B.J.E.); (A.T.K.)
- Correspondence: ; Tel.: +61-2-9850-8283
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11
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Abstract
Macrocyclic peptides are a unique class of molecules that display a relatively constrained peptidic backbone as compared to their linear counterparts leading to the defined 3-D orientation of the constituent amino acids (pharmacophore). Although they are attractive candidates for lead discovery owing to the unique conformational features, their peptidic backbone is susceptible to proteolytic cleavage in various biological fluids that compromise their efficacy. In this chapter we review the various classical and contemporary chemical and biological approaches that have been utilized to combat the metabolic instability of macrocyclic peptides. We note that any chemical modification that helps in providing either local or global conformational rigidity to these macrocyclic peptides aids in improving their metabolic stability typically by slowing the cleavage kinetics by the proteases.
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Affiliation(s)
- Bhavesh Khatri
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | | | - Jayanta Chatterjee
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.
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Räder AFB, Weinmüller M, Reichart F, Schumacher-Klinger A, Merzbach S, Gilon C, Hoffman A, Kessler H. Orally Active Peptides: Is There a Magic Bullet? Angew Chem Int Ed Engl 2018; 57:14414-14438. [DOI: 10.1002/anie.201807298] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Andreas F. B. Räder
- Technische Universität München; Department Chemie; Institute for Advanced Study; Lichtenbergstrasse 4 85748 Garching Germany
| | - Michael Weinmüller
- Technische Universität München; Department Chemie; Institute for Advanced Study; Lichtenbergstrasse 4 85748 Garching Germany
| | - Florian Reichart
- Technische Universität München; Department Chemie; Institute for Advanced Study; Lichtenbergstrasse 4 85748 Garching Germany
| | | | - Shira Merzbach
- The Hebrew University of Jerusalem; Institutes of Chemistry and Drug Research; Israel
| | - Chaim Gilon
- The Hebrew University of Jerusalem; Institutes of Chemistry and Drug Research; Israel
| | - Amnon Hoffman
- The Hebrew University of Jerusalem; Institutes of Chemistry and Drug Research; Israel
| | - Horst Kessler
- Technische Universität München; Department Chemie; Institute for Advanced Study; Lichtenbergstrasse 4 85748 Garching Germany
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13
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Räder AFB, Weinmüller M, Reichart F, Schumacher-Klinger A, Merzbach S, Gilon C, Hoffman A, Kessler H. Oral aktive Peptide: Gibt es ein Patentrezept? Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807298] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Andreas F. B. Räder
- Technische Universität München; Department Chemie; Institute for Advanced Study; Lichtenbergstraße 4 85748 Garching Deutschland
| | - Michael Weinmüller
- Technische Universität München; Department Chemie; Institute for Advanced Study; Lichtenbergstraße 4 85748 Garching Deutschland
| | - Florian Reichart
- Technische Universität München; Department Chemie; Institute for Advanced Study; Lichtenbergstraße 4 85748 Garching Deutschland
| | | | - Shira Merzbach
- Hebrew University of Jerusalem; Institutes of Chemistry and Drug Research; Israel
| | - Chaim Gilon
- Hebrew University of Jerusalem; Institutes of Chemistry and Drug Research; Israel
| | - Amnon Hoffman
- Hebrew University of Jerusalem; Institutes of Chemistry and Drug Research; Israel
| | - Horst Kessler
- Technische Universität München; Department Chemie; Institute for Advanced Study; Lichtenbergstraße 4 85748 Garching Deutschland
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14
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Escobar L, Díaz-Moscoso A, Ballester P. Conformational selectivity and high-affinity binding in the complexation of N-phenyl amides in water by a phenyl extended calix[4]pyrrole. Chem Sci 2018; 9:7186-7192. [PMID: 30288237 PMCID: PMC6149442 DOI: 10.1039/c8sc03034k] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 07/31/2018] [Indexed: 12/14/2022] Open
Abstract
We report the synthesis of a tetrapyridinium phenyl extended calix[4]pyrrole receptor that shows high binding affinity and selectivity for the complexation of the cis-conformers of N-phenyl amides in water.
We describe the synthesis of a tetrapyridinium phenyl extended calix[4]pyrrole that is soluble in neutral water solution at mM concentrations. We show that, in pure water, the synthesized calix[4]pyrrole receptor selectively binds the cis-(E) conformers of secondary N-phenyl-amides and tertiary N-methyl-N-phenyl-formamide with binding affinities larger than 103 M–1. The conformational selectivity is remarkable owing to the energetic preference of amides to adopt the trans-(Z) conformation in solution. In this respect, we used two binding models for the mathematical analyses of the titration data and calculated apparent and intrinsic binding constants. The combined action of hydrogen bonding and the hydrophobic effect that operates in the binding of the amides in water is responsible for the large affinities displayed by the receptor.
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Affiliation(s)
- L Escobar
- Institute of Chemical Research of Catalonia (ICIQ) , The Barcelona Institute of Science and Technology (BIST) , Av. Països Catalans, 16 , 43007-Tarragona , Spain . .,Universitat Rovira i Virgili , Departament de Química Analítica i Química Orgànica , c/Marcel·li Domingo, 1 , 43007-Tarragona , Spain
| | - A Díaz-Moscoso
- Institute of Chemical Research of Catalonia (ICIQ) , The Barcelona Institute of Science and Technology (BIST) , Av. Països Catalans, 16 , 43007-Tarragona , Spain .
| | - P Ballester
- Institute of Chemical Research of Catalonia (ICIQ) , The Barcelona Institute of Science and Technology (BIST) , Av. Països Catalans, 16 , 43007-Tarragona , Spain . .,ICREA , Pg. Lluís Companys, 23 , 08018-Barcelona , Spain
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15
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Improving oral bioavailability of cyclic peptides by N-methylation. Bioorg Med Chem 2018; 26:2766-2773. [DOI: 10.1016/j.bmc.2017.08.031] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/16/2017] [Accepted: 08/18/2017] [Indexed: 01/19/2023]
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16
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Szloszár A, Mándity IM, Fülöp F. Sustainable synthesis of N-methylated peptides in a continuous-flow fixed bed reactor. J Flow Chem 2018. [DOI: 10.1007/s41981-018-0002-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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17
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Wałęsa R, Broda MA. The influence of solvent on conformational properties of peptides with Aib residue-a DFT study. J Mol Model 2017; 23:349. [PMID: 29164349 PMCID: PMC5698364 DOI: 10.1007/s00894-017-3508-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 10/24/2017] [Indexed: 12/30/2022]
Abstract
The conformational propensities of the Aib residue on the example of two model peptides Ac-Aib-NHMe (1) and Ac-Aib-NMe2 (2), were studied by B3LYP and M06-2X functionals, in the gas phase and in the polar solvents. To verify the reliability of selected functionals, we also performed MP2 calculations for the tested molecules in vacuum. Polarizable continuum models (PCM and SMD) were used to estimate the solvent effect. Ramachandran maps were calculated to find all energy minima. Noncovalent intramolecular interactions due to hydrogen-bonds and dipole attractions between carbonyl groups are responsible for the relative stabilities of the conformers. In order to verify the theoretical results, the available conformations of similar X-ray structures from the Cambridge Crystallographic Data Center (CCDC) were analyzed. The results of the calculations show that both derivatives with the Aib residue in the gas phase prefer structures stabilized by intramolecular N-H⋯O hydrogen bonds, i.e., C5 and C7 conformations, while polar solvent promotes helical conformation with φ, ψ values equal to +/-60°, +/-40°. In addition, in the case of molecule 2, the helical conformation is the only one available in the polar environment. This result is fully consistent with the X-ray data. Graphical abstract Effect of solvent on the Ramachandran maps of the model peptides with Aib residue.
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Affiliation(s)
- Roksana Wałęsa
- Faculty of Chemistry, University of Opole, 48, Oleska St., 45-052 Opole, Poland
| | - Małgorzata A. Broda
- Faculty of Chemistry, University of Opole, 48, Oleska St., 45-052 Opole, Poland
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Srinivasadesikan V, Lu CH, Ramachandran B, Lee SL. Effects of Microsolvation on the Electronic Properties of Sarcosine: A Computational Study. ChemistrySelect 2017. [DOI: 10.1002/slct.201701430] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Venkatesan Srinivasadesikan
- Department of Chemistry and Biochemistry; National Chung Cheng University; Taiwan
- Centre of Excellence in Advanced Materials, Division of Chemistry, Vignan's Foundation for Science; Technology and Research University (VFSTRU), Vadlamudi; Guntur 522 213, Andhra Pradesh India
| | - Chih-Hung Lu
- Department of Chemistry and Biochemistry; National Chung Cheng University; Taiwan
| | - Balajee Ramachandran
- Department of chemistry; University of Southern California, California; United States 90089
| | - Shyi-Long Lee
- Department of Chemistry and Biochemistry; National Chung Cheng University; Taiwan
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19
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Naoum JN, Chandra K, Shemesh D, Gerber RB, Gilon C, Hurevich M. DMAP-assisted sulfonylation as an efficient step for the methylation of primary amine motifs on solid support. Beilstein J Org Chem 2017; 13:806-816. [PMID: 28546838 PMCID: PMC5433225 DOI: 10.3762/bjoc.13.81] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/11/2017] [Indexed: 11/23/2022] Open
Abstract
Several multistep strategies were developed to ensure single methylation of amines on solid support. These strategies rely on the introduction of the o-NBS protecting/activating group as a key step. We found that the state-of-the-art strategies fail for the methylation of several primary amine motifs, largely due to inefficient sulfonylation. Here we show that using the superior nucleophilic base DMAP instead of the commonly used base collidine as a sulfonylation additive is essential for the introduction of the o-NBS group to these amine motifs. DFT calculations provide an explanation by showing that the energy barrier of the DMAP intermediate is significantly lower than the one of the collidine. We demonstrate that using DMAP as a sole additive in the sulfonylation step results in an overall effective and regioselective N-methylation. The method presented herein proved highly efficient in solid-phase synthesis of a somatostatin analogue bearing three Nα-methylation sites that could not be synthesized using the previously described state-of-the-art methods.
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Affiliation(s)
- Johnny N Naoum
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Koushik Chandra
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Dorit Shemesh
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond Safra Campus, Givat Ram, Jerusalem, 91904, Israel
- Fritz Haber Research Center, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - R Benny Gerber
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond Safra Campus, Givat Ram, Jerusalem, 91904, Israel
- Fritz Haber Research Center, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Chaim Gilon
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Mattan Hurevich
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond Safra Campus, Givat Ram, Jerusalem, 91904, Israel
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20
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Hemmaragala NM, Abrahamse H, George BP. Effect of GNP functionalisation and multiple
N
‐methylation of
β
‐amyloid residue (32–37) on Gram‐positive bacterium. IET Nanobiotechnol 2017; 11:377-382. [DOI: 10.1049/iet-nbt.2016.0083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | - Heidi Abrahamse
- Laser Research CentreFaculty of Health SciencesUniversity of JohannesburgP.O. Box 17011Doornfontein 2028South Africa
| | - Blassan P. George
- Laser Research CentreFaculty of Health SciencesUniversity of JohannesburgP.O. Box 17011Doornfontein 2028South Africa
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21
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22
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23
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Wałęsa R, Man D, Engel G, Siodłak D, Kupka T, Ptak T, Broda MA. The Impact of Model Peptides on Structural and Dynamic Properties of Egg Yolk Lecithin Liposomes - Experimental and DFT Studies. Chem Biodivers 2015; 12:1007-24. [DOI: 10.1002/cbdv.201400179] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Indexed: 12/21/2022]
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24
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Md. Abdur Rauf S, Arvidsson PI, Albericio F, Govender T, Maguire GEM, Kruger HG, Honarparvar B. The effect of N-methylation of amino acids (Ac-X-OMe) on solubility and conformation: a DFT study. Org Biomol Chem 2015; 13:9993-10006. [DOI: 10.1039/c5ob01565k] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
N-Methylation of amino acid derivatives (Ac-X-OMe, X = Gly, Val, Leu, Ile, Phe, Met, Cys, Ser, Asp and His) leads to an increase in aqueous solubility, lipophilicity and lowering of the cis/trans amide conformational energy barrier (EA).
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Affiliation(s)
- Shah Md. Abdur Rauf
- Catalysis and Peptide Research Unit
- School of Health Sciences
- University of KwaZulu-Natal
- Durban 4001
- South Africa
| | - Per I. Arvidsson
- Catalysis and Peptide Research Unit
- School of Health Sciences
- University of KwaZulu-Natal
- Durban 4001
- South Africa
| | - Fernando Albericio
- Catalysis and Peptide Research Unit
- School of Health Sciences
- University of KwaZulu-Natal
- Durban 4001
- South Africa
| | - Thavendran Govender
- Catalysis and Peptide Research Unit
- School of Health Sciences
- University of KwaZulu-Natal
- Durban 4001
- South Africa
| | - Glenn E. M. Maguire
- Catalysis and Peptide Research Unit
- School of Health Sciences
- University of KwaZulu-Natal
- Durban 4001
- South Africa
| | - Hendrik G. Kruger
- Catalysis and Peptide Research Unit
- School of Health Sciences
- University of KwaZulu-Natal
- Durban 4001
- South Africa
| | - Bahareh Honarparvar
- Catalysis and Peptide Research Unit
- School of Health Sciences
- University of KwaZulu-Natal
- Durban 4001
- South Africa
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25
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Kim Y, Komoda E, Miyashita M, Miyagawa H. Continuous stimulation of the plant immune system by the peptide elicitor PIP-1 is required for phytoalexin biosynthesis in tobacco cells. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:5781-8. [PMID: 24881999 DOI: 10.1021/jf501679p] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The peptide elicitor PIP-1 (YGIHTH-nh2) induced various defense responses in tobacco cells. Types of defense responses induced by PIP-1 were different based on its concentration range: oxidative burst (an early response) was induced at low micromolar levels, but phytoalexin production (a late response) required about 10-50-fold higher concentrations than those required for oxidative burst. We assumed that rapid decreases in the PIP-1 concentration due to enzymatic hydrolysis in the culture media could cause this difference. To examine the potential impact of such degradation particularly on induction of phytoalexin biosynthesis, we designed a degradation-resistant analogue, MePIP-1, in which the amide bond between the fifth and sixth residues was N-methylated. MePIP-1 was considerably more stable than PIP-1 and induced significant phytoalexin production upon treatment at low micromolar levels. Further investigation of the mechanism of action of MePIP-1 showed a requirement of continuous elicitor stimulation for 3-6 h for the phytoalexin production, which is likely to be regulated by long-lasting MAP kinase activation.
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Affiliation(s)
- Yonghyun Kim
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University , Kyoto 606-8502, Japan
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26
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Farahani MD, Honarparvar B, Albericio F, Maguire GEM, Govender T, Arvidsson PI, Kruger HG. Proline N-oxides: modulators of the 3D conformation of linear peptides through “NO-turns”. Org Biomol Chem 2014; 12:4479-90. [DOI: 10.1039/c4ob00433g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Konar AD. The unique crystallographic signature of a β-turn mimic nucleated by N-methylated phenylalanine and Aib as corner residue: conformational and self-assembly studies. CrystEngComm 2013. [DOI: 10.1039/c3ce41448e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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Amijee H, Bate C, Williams A, Virdee J, Jeggo R, Spanswick D, Scopes DIC, Treherne JM, Mazzitelli S, Chawner R, Eyers CE, Doig AJ. The N-methylated peptide SEN304 powerfully inhibits Aβ(1-42) toxicity by perturbing oligomer formation. Biochemistry 2012; 51:8338-52. [PMID: 23025847 DOI: 10.1021/bi300415v] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Oligomeric forms of β-amyloid (Aβ) have potent neurotoxic activity and are the primary cause of neuronal injury and cell death in Alzheimer's disease (AD). Compounds that perturb oligomer formation or structure may therefore be therapeutic for AD. We previously reported that d-[(chGly)-(Tyr)-(chGly)-(chGly)-(mLeu)]-NH(2) (SEN304) is able to inhibit Aβ aggregation and toxicity, shown primarily by thioflavin T fluorescence and MTT (Kokkoni, N. et al. (2006) N-Methylated peptide inhibitors of β-amyloid aggregation and toxicity. Optimisation of inhibitor structure. Biochemistry 45, 9906-9918). Here we extensively characterize how SEN304 affects Aβ(1-42) aggregation and toxicity, using biophysical assays (thioflavin T, circular dichroism, SDS-PAGE, size exclusion chromatography, surface plasmon resonance, traveling wave ion mobility mass spectrometry, electron microscopy, ELISA), toxicity assays in cell culture (MTT and lactate dehydrogenase in human SH-SHY5Y cells, mouse neuronal cell death and synaptophysin) and long-term potentiation in a rat hippocampal brain slice. These data, with dose response curves, show that SEN304 is a powerful inhibitor of Aβ(1-42) toxicity, particularly effective at preventing Aβ inhibition of long-term potentiation. It can bind directly to Aβ(1-42), delay β-sheet formation and promote aggregation of toxic oligomers into a nontoxic form, with a different morphology that cannot bind thioflavin T. SEN304 appears to work by inducing aggregation, and hence removal, of Aβ oligomers. It is therefore a promising lead compound for Alzheimer's disease.
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Affiliation(s)
- Hozefa Amijee
- Senexis Limited, Babraham Research Campus, Cambridge CB22 3AT, UK
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29
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Pedersen SL, Tofteng AP, Malik L, Jensen KJ. Microwave heating in solid-phase peptide synthesis. Chem Soc Rev 2012; 41:1826-44. [DOI: 10.1039/c1cs15214a] [Citation(s) in RCA: 214] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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30
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Kisseljova K, Baudy-Floc'h M, Kuznetsov A, Järv J. Nβ-methylation changes the recognition pattern of aza-β3-amino acid containing peptidomimetic substrates by protein kinase A. Org Med Chem Lett 2011; 1:16. [PMID: 22373236 PMCID: PMC3305904 DOI: 10.1186/2191-2858-1-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Accepted: 11/08/2011] [Indexed: 11/30/2022] Open
Abstract
The protein kinase A (PKA)-catalyzed phosphorylation of peptide substrate RRASVA analogs, containing Nβ-Me-aza-β3-amino acid residues in all subsequent positions, was studied. This work follows along the lines of our previous research of the phosphorylation of aza-β3-analogs of RRASVA (the shortest active substrate of PKA) and allows characterizing the influence of Nβ-methylation of aza-β3-amino acid residues on substrate recognition by PKA on substrate binding and phosphorylation steps. It was found that the effect of Nβ-methylation was dependent upon the position of the structure alteration. Moreover, the presence of a single Nβ-methylation site in the substrate changed the recognition pattern of this series of peptidomimetics, strongly affecting the phosphorylation step. Structure modeling of aza-β3- and Nβ-Me-aza-β3-containing substrates revealed that Nβ-methylation of aza-β3-moieties changed the peptide bond geometry from trans- to cis-configuration in -CO-NMe- fragments, with an exception for the N-terminally methylated Nβ-Me-aza-β3-RRRASVA (with the N-terminal amino group not participating in the peptide bond) and RRAS-Nβ-Me-aza-β3-VA. As has been shown in literature, this conformational preference of the backbone has a significant influence on the flexibility of the peptide substrate chain. Following our results, this property seems to have significant influence on the recognition of the amino acid side groups by the enzyme binding site, and in the case of PKA this structural modification was decisive for the phosphate transfer step of the catalytic process.
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Affiliation(s)
- Ksenija Kisseljova
- Institute of Chemistry, University of Tartu, 14A Ravila Street, 50411 Tartu, Estonia.
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31
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Tal-Gan Y, Freeman NS, Klein S, Levitzki A, Gilon C. Metabolic stability of peptidomimetics: N-methyl and aza heptapeptide analogs of a PKB/Akt inhibitor. Chem Biol Drug Des 2011; 78:887-92. [PMID: 21824328 DOI: 10.1111/j.1747-0285.2011.01207.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Linear peptides suffer from poor pharmacokinetic and pharmacodynamic properties. Peptidomimetics are designed to overcome these pharmacological drawbacks while maintaining the biological effects of the parent peptides. Aza-peptides, in which an alpha carbon is replaced with nitrogen, are promising peptidomimetic analogs; however, little is known about the stability of these analogs toward enzymatic degradation. We performed systematic aza and N-methyl scans of a PKB/Akt inhibitor, PTR6154. We evaluated the stability of the aza-scan and N-methyl scan libraries toward enzymatic degradation by trypsin/chymotrypsin. Our results indicate that the modification site is important for metabolic stability and that aza-peptides have a more global effect than N-methylation, affecting cleavage sites distant from the modification site.
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Affiliation(s)
- Yftah Tal-Gan
- Institute of Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
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32
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Fang WJ, Bennett MA, Aldrich JV. Deletion of Ac-NMePhe(1) from [NMePhe(1) ]arodyn under acidic conditions, part 1: effects of cleavage conditions and N-terminal functionality. Biopolymers 2011; 96:97-102. [PMID: 20560149 PMCID: PMC3412617 DOI: 10.1002/bip.21496] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Peptides containing N-methylamino acids can exhibit improved pharmacodynamic and pharmacokinetic profiles compared to nonmethylated peptides, and therefore interest in these N-methylated peptides has been increasing in recent years. Arodyn (Ac[Phe¹,²,³,Arg⁴,D-Ala⁸]Dyn A(1-11)NH₂) is an acetylated dynorphin A(Dyn A) analog that is a potent and selective κ opioid receptor antagonist (Bennett et al., J Med Chem 2002, 45, 5617), and its analog [NMePhe¹]arodyn shows even higher affinity and selectivity for κ opioid receptors (Bennett et al., J Pept Res 2005, 65, 322). During the synthesis of [NMePhe¹]arodyn analogs, the arodyn-(2-11) derivatives were obtained as major products. Analysis indicated that Ac-NMePhe was lost from the completed peptide sequence during acidic cleavage of the peptides from the resin and that the acetyl group played an important role in this side reaction. Different cleavage conditions were evaluated to minimize this side reaction and maximize the yield of pure [NMePhe¹]arodyn analogs. Modifications to the N-terminus of the peptides to prevent the side reaction were also explored. The incorporation of a heteroatom-containing group such as methoxycarbonyl as the N-terminal functionality prevented this side reaction, while the incorporation of a bulky acyl group could not. Substituting NMePhe with the conformationally constrained analog Tic (1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid) also prevented the side reaction.
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Affiliation(s)
- Wei-Jie Fang
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66045, USA
| | - Marco A. Bennett
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD 21201, USA
| | - Jane V. Aldrich
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66045, USA
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33
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In vitro ADMET and physicochemical investigations of poly-N-methylated peptides designed to inhibit Aβ aggregation. Bioorg Med Chem 2010; 18:5896-902. [DOI: 10.1016/j.bmc.2010.06.087] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Revised: 06/24/2010] [Accepted: 06/28/2010] [Indexed: 11/23/2022]
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34
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Doedens L, Opperer F, Cai M, Beck JG, Dedek M, Palmer E, Hruby VJ, Kessler H. Multiple N-methylation of MT-II backbone amide bonds leads to melanocortin receptor subtype hMC1R selectivity: pharmacological and conformational studies. J Am Chem Soc 2010; 132:8115-28. [PMID: 20496895 PMCID: PMC2895553 DOI: 10.1021/ja101428m] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Multiple N-methylation is a novel technology to improve bioavailability of peptides and increase receptor subtype selectivity. This technique has been applied here to the superpotent but nonselective cyclic peptide MT-II. A library of all possible 31 backbone N-methylated derivatives has been synthesized and tested for binding and activation at melanocortin receptor subtypes 1, 3, 4, and 5. It turned out that selectivity is improved with every introduced N-methyl group, resulting in several N-methylated selective and potent agonists for the hMC1R. The most potent of these derivatives is N-methylated on four out of five amide bonds in the cyclic structure. Its solution structure indicates a strongly preferred backbone conformation that resembles other alpha-MSH analogs but possesses much less flexibility and in addition distinct differences in the spatial arrangement of individual amino acid side chains.
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Affiliation(s)
- Lucas Doedens
- Institute for Advanced Study and Center for Integrated Protein Science at the Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Florian Opperer
- Institute for Advanced Study and Center for Integrated Protein Science at the Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Minying Cai
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, 85721, U.S.A
| | - Johannes G. Beck
- Institute for Advanced Study and Center for Integrated Protein Science at the Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Matt Dedek
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, 85721, U.S.A
| | - Erin Palmer
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, 85721, U.S.A
| | - Victor J. Hruby
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, 85721, U.S.A
| | - Horst Kessler
- Institute for Advanced Study and Center for Integrated Protein Science at the Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
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35
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Tal-Gan Y, Freeman NS, Klein S, Levitzki A, Gilon C. Synthesis and structure–activity relationship studies of peptidomimetic PKB/Akt inhibitors: The significance of backbone interactions. Bioorg Med Chem 2010; 18:2976-85. [DOI: 10.1016/j.bmc.2010.02.031] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Revised: 02/12/2010] [Accepted: 02/18/2010] [Indexed: 10/19/2022]
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36
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Rodríguez H, Suarez M, Albericio F. A convenient microwave-enhanced solid-phase synthesis of short chain N
-methyl-rich peptides. J Pept Sci 2010; 16:136-40. [DOI: 10.1002/psc.1209] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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37
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Tulla-Puche J, Marcucci E, Prats-Alfonso E, Bayó-Puxan N, Albericio F. NMe Amide as a Synthetic Surrogate for the Thioester Moiety in Thiocoraline. J Med Chem 2009; 52:834-9. [DOI: 10.1021/jm800784k] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Judit Tulla-Puche
- Institute for Research in Biomedicine, Barcelona Science Park, 08028 Barcelona, Spain, Department of Organic Chemistry, University of Barcelona, 08028 Barcelona, Spain, CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, 08028 Barcelona, Spain
| | - Eleonora Marcucci
- Institute for Research in Biomedicine, Barcelona Science Park, 08028 Barcelona, Spain, Department of Organic Chemistry, University of Barcelona, 08028 Barcelona, Spain, CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, 08028 Barcelona, Spain
| | - Elisabet Prats-Alfonso
- Institute for Research in Biomedicine, Barcelona Science Park, 08028 Barcelona, Spain, Department of Organic Chemistry, University of Barcelona, 08028 Barcelona, Spain, CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, 08028 Barcelona, Spain
| | - Núria Bayó-Puxan
- Institute for Research in Biomedicine, Barcelona Science Park, 08028 Barcelona, Spain, Department of Organic Chemistry, University of Barcelona, 08028 Barcelona, Spain, CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, 08028 Barcelona, Spain
| | - Fernando Albericio
- Institute for Research in Biomedicine, Barcelona Science Park, 08028 Barcelona, Spain, Department of Organic Chemistry, University of Barcelona, 08028 Barcelona, Spain, CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, 08028 Barcelona, Spain
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38
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Linde Y, Ovadia O, Safrai E, Xiang Z, Portillo FP, Shalev DE, Haskell-Luevano C, Hoffman A, Gilon C. Structure-activity relationship and metabolic stability studies of backbone cyclization and N-methylation of melanocortin peptides. Biopolymers 2008; 90:671-82. [PMID: 18655141 DOI: 10.1002/bip.21057] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Backbone cyclization (BC) and N-methylation have been shown to enhance the activity and/or selectivity of biologically active peptides and improve metabolic stability and intestinal permeability. In this study, we describe the synthesis, structure-activity relationship (SAR) and intestinal metabolic stability of a backbone cyclic peptide library, BL3020, based on the linear alpha-Melanocyte stimulating hormone analog Phe-D-Phe-Arg-Trp-Gly. The drug lead, BL3020-1, selected from the BL3020 library (compound 1) has been shown to inhibit weight gain in mice following oral administration. Another member of the BL3020 library, BL3020-17, showed improved biological activity towards the mMC4R, in comparison to BL3020-1, although neither were selective for MC4R or MC5R. N-methylation, which restrains conformational freedom while increasing metabolic stability beyond that which is imparted by BC, was used to find analogs with increased selectivity. N-methylated backbone cyclic libraries were synthesized based on the BL3020 library. SAR studies showed that all the N-methylated backbone cyclic peptides demonstrated reduced biological activity and selectivity for all the analyzed receptors. N-methylation of active backbone cyclic peptides destabilized the active conformation or stabilized an inactive conformation, rendering the peptides biologically inactive. N-methylation of backbone cyclic peptides maintained stability to degradation by intestinal enzymes.
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Affiliation(s)
- Yaniv Linde
- Institute of Chemistry, Safra Campus, Givat Ram, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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39
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Monga V, Meena CL, Kaur N, Kumar S, Pawar C, Sharma SS, Jain R. Facile synthesis ofN-α-boc-1,2-dialkyl-l-histidines: Utility in the synthesis of thyrotropin-releasing hormone (trh) analogs and evaluation of the cns activity. J Heterocycl Chem 2008. [DOI: 10.1002/jhet.5570450608] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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40
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Malakoutikhah M, Teixidó M, Giralt E. Toward an Optimal Blood−Brain Barrier Shuttle by Synthesis and Evaluation of Peptide Libraries. J Med Chem 2008; 51:4881-9. [DOI: 10.1021/jm800156z] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Morteza Malakoutikhah
- Institut de Recerca Biomèdica (IRB Barcelona), Parc Científic de Barcelona, Baldiri Reixac 10, Barcelona, Spain, and Departament de Química Orgànica, Universitat de Barcelona, Martí i Franquès 1-11, Barcelona, Spain
| | - Meritxell Teixidó
- Institut de Recerca Biomèdica (IRB Barcelona), Parc Científic de Barcelona, Baldiri Reixac 10, Barcelona, Spain, and Departament de Química Orgànica, Universitat de Barcelona, Martí i Franquès 1-11, Barcelona, Spain
| | - Ernest Giralt
- Institut de Recerca Biomèdica (IRB Barcelona), Parc Científic de Barcelona, Baldiri Reixac 10, Barcelona, Spain, and Departament de Química Orgànica, Universitat de Barcelona, Martí i Franquès 1-11, Barcelona, Spain
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41
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Chatterjee J, Mierke DF, Kessler H. Conformational preference and potential templates of N-methylated cyclic pentaalanine peptides. Chemistry 2008; 14:1508-17. [PMID: 18080261 DOI: 10.1002/chem.200701029] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Systematic N-methylation of all peptide bonds in the cyclic pentapeptide cyclo(-D-Ala-Ala(4)-) has been performed yielding 30 different N-methylated derivatives, of which only seven displayed a single conformation on the NMR time scale. The conformation of these differentially N-methylated peptides was recently reported by us (J. Am. Chem. Soc. 2006, 128, 15 164-15 172). Here we present the conformational characterization of nine additional N-methylated peptides from the previous library which are not homogeneous but exist as a mixture in which at least one conformation is preferred by over 80 %. The structures of these peptides are investigated employing various 2D-NMR techniques, distance geometry calculations and further refined by molecular dynamics simulations in explicit DMSO. The comparison of the conformation of these nine peptides and the seven conformationally homogeneous peptides allow us to draw conclusions regarding the influence of N-methylation on the peptide backbone of cyclic pentapeptide of the class cyclo(-D-Ala-Ala(4)-). Here we present the different conformational classes of the peptides arising from the definitive pattern of N-methylation which can eventually serve as templates for the design of bioactive peptides.
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Affiliation(s)
- Jayanta Chatterjee
- Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Organische Chemie II, Technische Universität München, Lichtenbergstrasse 4, Garching, Germany
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Biron E, Chatterjee J, Ovadia O, Langenegger D, Brueggen J, Hoyer D, Schmid HA, Jelinek R, Gilon C, Hoffman A, Kessler H. Improving oral bioavailability of peptides by multiple N-methylation: somatostatin analogues. Angew Chem Int Ed Engl 2008; 47:2595-9. [PMID: 18297660 DOI: 10.1002/anie.200705797] [Citation(s) in RCA: 273] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Eric Biron
- CIPS at Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747-Garching, Germany
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Biron E, Chatterjee J, Ovadia O, Langenegger D, Brueggen J, Hoyer D, Schmid H, Jelinek R, Gilon C, Hoffman A, Kessler H. Die Verbesserung der oralen Bioverfügbarkeit von Peptiden durch multiple N-Methylierung: Somatostatin-Analoga. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200705797] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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44
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Džolić Z, Margeta R, Vinković M, Štefanić Z, Kojić-Prodić B, Mlinarić-Majerski K, Žinić M. N-Methylation of adamantane-substituted oxalamide unit affects its conformational rigidity: A skew conformation of the oxalamide bridge. J Mol Struct 2008. [DOI: 10.1016/j.molstruc.2007.06.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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45
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Lu C, DesMarteau DD. Construction of N-1H,1H-perfluoroalkylated peptide bonds. Chem Commun (Camb) 2008:208-10. [DOI: 10.1039/b712617d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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46
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Rivera DG, Vercillo OE, Wessjohann LA. Rapid generation of macrocycles with natural-product-like side chains by multiple multicomponent macrocyclizations (MiBs). Org Biomol Chem 2008; 6:1787-95. [DOI: 10.1039/b715393g] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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47
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Mantey SA, Gonzalez N, Schumann M, Pradhan TK, Shen L, Coy DH, Jensen RT. Identification of Bombesin Receptor Subtype-Specific Ligands: Effect ofN-Methyl Scanning, Truncation, Substitution, and Evaluation of Putative Reported Selective Ligands. J Pharmacol Exp Ther 2006; 319:980-9. [PMID: 16943256 DOI: 10.1124/jpet.106.107011] [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: 11/22/2022] Open
Abstract
Mammalian bombesin (Bn) receptors include the gastrin-releasing peptide receptor, neuromedin B receptor, and bombesin receptor subtype 3 (BRS-3). These receptors are involved in a variety of physiological/pathologic processes, including thermoregulation, secretion, motility, chemotaxis, and mitogenic effects on both normal and malignant cells. Tumors frequently overexpress these receptors, and their presence is now used for imaging and receptor-mediated cytotoxicity. For these reasons, there is an increased need to develop synthetic, selective receptor subtype-specific ligands, especially agonists for these receptors. In this study, we used a number of strategies to identify useful receptor subtype-selective ligands, including synthesizing new analogs (N-methyl-substituted constrained analogs, truncations, and substitutions) in [d-Tyr(6),betaAla(11),Phe(13),Nle(14)]Bn(6-14), which has high affinity for all Bn receptors and is metabolically stable, as well as completely pharmacologically characterized analogs recently reported to be selective for these receptors in [Ca(2+)](i) assays. Affinities and potencies of each analog were determined for each human Bn receptor subtype. N-Methyl substitutions in positions 14, 12, 11, 10, 9, and 8 did not result in selective analogs, with the exception of position 11, which markedly decreased affinity/potency. N-Terminal truncations or position 12 substitutions did not increase selectivity as previously reported by others. Of the four shortened analogs of [d-Phe(6),betaAla(11),Phe(13),Nle(14)]Bn(6-14) reported to be potent selective BRS-3 ligands on [Ca(2+)](i) assays, only AcPhe,Trp,Ala,His(tauBzl),Nip,Gly,Arg-NH(2) had moderate selectivity for hBRS-3; however, it was less selective than previously reported Apa(11) analogs, demonstrating these are still the most selective BRS-3 analogs available. However, both of these analogs should be useful templates to develop more selective BRS-3 ligands.
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Affiliation(s)
- Samuel A Mantey
- DHHS/NIH, NIDDK, DDB, Bldg. 10, Rm. 9C103, 31 Center Drive, Bethesda, MD 20892, USA
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Zhang S, Govender T, Norström T, Arvidsson PI. An improved synthesis of Fmoc-N-methyl-alpha-amino acids. J Org Chem 2006; 70:6918-20. [PMID: 16095315 DOI: 10.1021/jo050916u] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A highly efficient and environmentally more benign synthesis of Fmoc-N-methyl-alpha-amino acids from the corresponding Fmoc-amino acid, via intermediate 5-oxazolidinones, has been developed by using Lewis acid catalysis for the reductive opening of the oxazolidinone ring.
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Affiliation(s)
- Suode Zhang
- Department of Chemistry, Organic Chemistry, Uppsala University Box 599, SE-751 24 Uppsala, Sweden
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Biron E, Chatterjee J, Kessler H. Optimized selective N-methylation of peptides on solid support. J Pept Sci 2006; 12:213-9. [PMID: 16189816 DOI: 10.1002/psc.711] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Peptides containing N(alpha)-methylamino acids exhibit interesting therapeutic profiles and are increasingly recognized as potentially useful therapeutics. Unfortunately, their synthesis is hampered by the high price and nonavailability of many N(alpha)-methylamino acids. An efficient and practical three-step procedure for selective N-methylation of peptides on solid support is described. The procedure was based on the well known solid-phase N-methylation of N(alpha)-arylsulfonyl peptides, which was improved by using dimethylsulfate and the less expensive DBU as base. Every step of the procedure, amine activation by an o-nitrobenzenesulfonyl group, selective N-methylation and removal of the sulfonamide group, was optimized in respect of time and economy. The described optimized three-step procedure is performed in 35 min without solvent changes, instead of 3 h. Tripeptides (Fmoc-Phe-MeXaa-Leu-OH) containing N-methylated common amino acids were also prepared using the optimized procedure to demonstrate its compatibility with these amino acids. The described procedure allows an efficient synthesis of N(alpha)-methylamino acid containing peptides in a very short time using Fmoc solid-phase peptide synthesis.
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Affiliation(s)
- Eric Biron
- Department Chemie, Lehrstuhl II für Organische Chemie, Technische Universität München, Germany
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