101
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Tajimi T, Wakui N, Yanagisawa K, Yoshikawa Y, Ohue M, Akiyama Y. Computational prediction of plasma protein binding of cyclic peptides from small molecule experimental data using sparse modeling techniques. BMC Bioinformatics 2018; 19:527. [PMID: 30598072 PMCID: PMC6311893 DOI: 10.1186/s12859-018-2529-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Cyclic peptide-based drug discovery is attracting increasing interest owing to its potential to avoid target protein depletion. In drug discovery, it is important to maintain the biostability of a drug within the proper range. Plasma protein binding (PPB) is the most important index of biostability, and developing a computational method to predict PPB of drug candidate compounds contributes to the acceleration of drug discovery research. PPB prediction of small molecule drug compounds using machine learning has been conducted thus far; however, no study has investigated cyclic peptides because experimental information of cyclic peptides is scarce. RESULTS First, we adopted sparse modeling and small molecule information to construct a PPB prediction model for cyclic peptides. As cyclic peptide data are limited, applying multidimensional nonlinear models involves concerns regarding overfitting. However, models constructed by sparse modeling can avoid overfitting, offering high generalization performance and interpretability. More than 1000 PPB data of small molecules are available, and we used them to construct a prediction models with two enumeration methods: enumerating lasso solutions (ELS) and forward beam search (FBS). The accuracies of the prediction models constructed by ELS and FBS were equal to or better than those of conventional non-linear models (MAE = 0.167-0.174) on cross-validation of a small molecule compound dataset. Moreover, we showed that the prediction accuracies for cyclic peptides were close to those for small molecule compounds (MAE = 0.194-0.288). Such high accuracy could not be obtained by a simple method of learning from cyclic peptide data directly by lasso regression (MAE = 0.286-0.671) or ridge regression (MAE = 0.244-0.354). CONCLUSION In this study, we proposed a machine learning techniques that uses low-dimensional sparse modeling to predict the PPB value of cyclic peptides computationally. The low-dimensional sparse model not only exhibits excellent generalization performance but also improves interpretation of the prediction model. This can provide common an noteworthy knowledge for future cyclic peptide drug discovery studies.
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Affiliation(s)
- Takashi Tajimi
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 W8-76 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Naoki Wakui
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 W8-76 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.,Middle Molecule IT-based Drug Discovery Laboratory (MIDL), Tokyo Institute of Technology, RGBT2-A-1C 3-25-10 Tonomachi, Kawasaki-ku, Kawasaki city, Kanagawa, 210-0821, Japan
| | - Keisuke Yanagisawa
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 W8-76 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Yasushi Yoshikawa
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 W8-76 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.,Middle Molecule IT-based Drug Discovery Laboratory (MIDL), Tokyo Institute of Technology, RGBT2-A-1C 3-25-10 Tonomachi, Kawasaki-ku, Kawasaki city, Kanagawa, 210-0821, Japan
| | - Masahito Ohue
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 W8-76 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.,Middle Molecule IT-based Drug Discovery Laboratory (MIDL), Tokyo Institute of Technology, RGBT2-A-1C 3-25-10 Tonomachi, Kawasaki-ku, Kawasaki city, Kanagawa, 210-0821, Japan
| | - Yutaka Akiyama
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, 2-12-1 W8-76 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan. .,Middle Molecule IT-based Drug Discovery Laboratory (MIDL), Tokyo Institute of Technology, RGBT2-A-1C 3-25-10 Tonomachi, Kawasaki-ku, Kawasaki city, Kanagawa, 210-0821, Japan. .,Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan.
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102
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Chen Y. Recent Advances in Methylation: A Guide for Selecting Methylation Reagents. Chemistry 2018; 25:3405-3439. [DOI: 10.1002/chem.201803642] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Yantao Chen
- Medicinal Chemistry, Cardiovascular, Renal and Metabolism, IMED Biotech UnitAstraZeneca Gothenburg Sweden
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103
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Witek J, Wang S, Schroeder B, Lingwood R, Dounas A, Roth HJ, Fouché M, Blatter M, Lemke O, Keller B, Riniker S. Rationalization of the Membrane Permeability Differences in a Series of Analogue Cyclic Decapeptides. J Chem Inf Model 2018; 59:294-308. [PMID: 30457855 DOI: 10.1021/acs.jcim.8b00485] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cyclization and selected backbone N-methylations are found to be often necessary but not sufficient conditions for peptidic drugs to have a good bioavailability. Thus, the design of cyclic peptides with good passive membrane permeability and good solubility remains a challenge. The backbone scaffold of a recently published series of cyclic decapeptides with six selected backbone N-methylations was designed to favor the adoption of a closed conformation with β-turns and four transannular hydrogen bonds. Although this conformation was indeed adopted by the peptides as determined by NMR measurements, substantial differences in the membrane permeability were observed. In this work, we aim to rationalize the impact of discrete side chain modifications on membrane permeability for six of these cyclic decapeptides. The thermodynamic and kinetic properties were investigated using molecular dynamics simulations and Markov state modeling in water and chloroform. The study highlights the influence that side-chain modifications can have on the backbone conformation. Peptides with a d-proline in the β-turns were more likely to adopt, even in water, the closed conformation with transannular hydrogen bonds, which facilitates transition through the membrane. The population of the closed conformation in water was found to correlate positively with PAMPA log Pe.
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Affiliation(s)
- Jagna Witek
- Laboratory of Physical Chemistry , ETH Zürich , Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland
| | - Shuzhe Wang
- Laboratory of Physical Chemistry , ETH Zürich , Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland
| | - Benjamin Schroeder
- Laboratory of Physical Chemistry , ETH Zürich , Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland
| | - Robin Lingwood
- Laboratory of Physical Chemistry , ETH Zürich , Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland
| | - Andreas Dounas
- Laboratory of Physical Chemistry , ETH Zürich , Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland
| | - Hans-Jörg Roth
- Novartis Institutes for BioMedical Research , Novartis Pharma AG, Novartis Campus , 4056 Basel , Switzerland
| | - Marianne Fouché
- Novartis Institutes for BioMedical Research , Novartis Pharma AG, Novartis Campus , 4056 Basel , Switzerland
| | - Markus Blatter
- Novartis Institutes for BioMedical Research , Novartis Pharma AG, Novartis Campus , 4056 Basel , Switzerland
| | - Oliver Lemke
- Department of Biology, Chemistry, Pharmacy , Freie Universität Berlin , Takustrasse 3 , 14195 Berlin , Germany
| | - Bettina Keller
- Department of Biology, Chemistry, Pharmacy , Freie Universität Berlin , Takustrasse 3 , 14195 Berlin , Germany
| | - Sereina Riniker
- Department of Biology, Chemistry, Pharmacy , Freie Universität Berlin , Takustrasse 3 , 14195 Berlin , Germany
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104
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Chopra G, Chopra N, Kaur D. Elucidating the intermolecular hydrogen bonding interaction of proline with amides—quantum chemical calculations. Struct Chem 2018. [DOI: 10.1007/s11224-018-1235-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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105
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Ongpipattanakul C, Nair SK. Molecular Basis for Autocatalytic Backbone N-Methylation in RiPP Natural Product Biosynthesis. ACS Chem Biol 2018; 13:2989-2999. [PMID: 30204409 DOI: 10.1021/acschembio.8b00668] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
N-methylation of nucleic acids, proteins, and peptides is a chemical modification with significant impact on biological regulation. Despite the simplicity of the structural change, N-methylation can influence diverse functions including epigenetics, protein complex formation, and microtubule stability. While there are limited examples of N-methylation of the α-amino group of bacterial and eukaryotic proteins, there are no examples of catalysts that carry out post-translation methylation of backbone amides in proteins or peptides. Recent studies have identified enzymes that catalyze backbone N-methylation on a peptide substrate, a reaction with little biochemical precedent, in a family of ribosomally synthesized natural products produced in basidiomycetes. Here, we describe the crystal structures of Dendrothele bispora dbOphMA, a methyltransferase that catalyzes multiple N-methylations on the peptide backbone. We further carry out biochemical studies of this catalyst to determine the molecular details that promote this unusual chemical transformation. The structural and biochemical framework described here could facilitate biotechnological applications of catalysts for the rapid production of backbone N-methylated peptides.
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106
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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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107
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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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108
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109
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Hsieh WH, Liaw J. Applications of cyclic peptide nanotubes (cPNTs). J Food Drug Anal 2018; 27:32-47. [PMID: 30648586 PMCID: PMC9298616 DOI: 10.1016/j.jfda.2018.09.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 09/12/2018] [Indexed: 12/31/2022] Open
Abstract
Self-assembled cyclic peptide nanotubes (cPNTs) have recently drawn particular attention as one of the most intriguing nanostructures in the field of nanotechnology. Given their unique features including high surface area, increased drug loading, environmental stability, enhanced permeation, and modifiable drug release, these hollow tubular structures can be constructed with cyclic di-, tri-, tetra-, hexa-, octa-, and decapeptides with various amino acid sequences, enantiomers, and functionalized side chains and can be applied for antiviral and antibacterial drugs, drug delivery and gene delivery vectors, organic electronic devices, and ionic or molecular channels. Recent publications have presented promising results regarding the use of cPNTs as drugs or biomedical devices. However, there is an urgent need for the further in vivo nanotoxicity and safety testing of these nanotubes to evaluate their suitability in different fields.
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Affiliation(s)
- Wei-Hsien Hsieh
- Department of Biotechnology and Pharmaceutical Technology, Yuanpei University of Medical Technology, Hsinchu, Taiwan
| | - Jiahorng Liaw
- Department of Pharmaceutics, School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan.
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110
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Peraro L, Kritzer JA. Emerging Methods and Design Principles for Cell-Penetrant Peptides. Angew Chem Int Ed Engl 2018; 57:11868-11881. [PMID: 29740917 PMCID: PMC7184558 DOI: 10.1002/anie.201801361] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/24/2018] [Indexed: 12/12/2022]
Abstract
Biomolecules such as antibodies, proteins, and peptides are important tools for chemical biology and leads for drug development. They have been used to inhibit a variety of extracellular proteins, but accessing intracellular proteins has been much more challenging. In this review, we discuss diverse chemical approaches that have yielded cell-penetrant peptides and identify three distinct strategies: masking backbone amides, guanidinium group patterning, and amphipathic patterning. We summarize a growing number of large data sets, which are starting to reveal more specific design guidelines for each strategy. We also discuss advantages and disadvantages of current methods for quantifying cell penetration. Finally, we provide an overview of best-odds approaches for applying these new methods and design principles to optimize cytosolic penetration for a given bioactive peptide.
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Affiliation(s)
- Leila Peraro
- Department of Chemistry, Tufts University, Medford, Massachusetts, 02155, USA
| | - Joshua A Kritzer
- Department of Chemistry, Tufts University, Medford, Massachusetts, 02155, USA
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111
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Ermondi G, Vallaro M, Camacho-Leal M, Potter T, Visentin S, Caron G. Charged cyclic hexapeptides: Updating molecular descriptors for permeability purposes. Eur J Pharm Sci 2018; 122:85-93. [DOI: 10.1016/j.ejps.2018.06.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 06/16/2018] [Accepted: 06/19/2018] [Indexed: 10/28/2022]
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112
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Szałaj N, Lu L, Benediktsdottir A, Zamaratski E, Cao S, Olanders G, Hedgecock C, Karlén A, Erdélyi M, Hughes D, Mowbray SL, Brandt P. Boronic ester-linked macrocyclic lipopeptides as serine protease inhibitors targeting Escherichia coli type I signal peptidase. Eur J Med Chem 2018; 157:1346-1360. [DOI: 10.1016/j.ejmech.2018.08.086] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/22/2018] [Accepted: 08/29/2018] [Indexed: 12/22/2022]
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113
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One-step process for production of N-methylated amino acids from sugars and methylamine using recombinant Corynebacterium glutamicum as biocatalyst. Sci Rep 2018; 8:12895. [PMID: 30150644 PMCID: PMC6110843 DOI: 10.1038/s41598-018-31309-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/02/2018] [Indexed: 02/07/2023] Open
Abstract
N-methylated amino acids are found in Nature in various biological compounds. N-methylation of amino acids has been shown to improve pharmacokinetic properties of peptide drugs due to conformational changes, improved proteolytic stability and/or higher lipophilicity. Due to these characteristics N-methylated amino acids received increasing interest by the pharmaceutical industry. Syntheses of N-methylated amino acids by chemical and biocatalytic approaches are known, but often show incomplete stereoselectivity, low yields or expensive co-factor regeneration. So far a one-step fermentative process from sugars has not yet been described. Here, a one-step conversion of sugars and methylamine to the N-methylated amino acid N-methyl-l-alanine was developed. A whole-cell biocatalyst was derived from a pyruvate overproducing C. glutamicum strain by heterologous expression of the N-methyl-l-amino acid dehydrogenase gene from Pseudomonas putida. As proof-of-concept, N-methyl-l-alanine titers of 31.7 g L−1 with a yield of 0.71 g per g glucose were achieved in fed-batch cultivation. The C. glutamicum strain producing this imine reductase enzyme was engineered further to extend this green chemistry route to production of N-methyl-l-alanine from alternative feed stocks such as starch or the lignocellulosic sugars xylose and arabinose.
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114
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Kaminker* R, Anastasaki A, Gutekunst WR, Luo Y, Lee S, Hawker* CJ. Tuning of protease resistance in oligopeptides through N-alkylation. Chem Commun (Camb) 2018; 54:9631-9634. [PMID: 30095837 PMCID: PMC6141190 DOI: 10.1039/c8cc04407d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
N-Methylation of amino acids is an effective way to create protease resistance in both natural and synthetic peptides. However, alkyl substituents other than N-methyl have not been extensively studied. Here, we prepare and examine a series of N-substituted peptides in which the size and length of the alkyl group is modulated. These design insights provide a unique and modular handle for tuning proteolysis in oligopeptides.
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Affiliation(s)
- R. Kaminker*
- Materials Research Laboratory, University of California, Santa Barbara, California 93106, United States. ;
| | - A. Anastasaki
- Materials Research Laboratory, University of California, Santa Barbara, California 93106, United States. ;
| | - W. R. Gutekunst
- Materials Research Laboratory, University of California, Santa Barbara, California 93106, United States. ;
| | - Y. Luo
- Materials Research Laboratory, University of California, Santa Barbara, California 93106, United States. ;
| | - S. Lee
- Materials Research Laboratory, University of California, Santa Barbara, California 93106, United States. ;
| | - C. J. Hawker*
- Materials Research Laboratory, University of California, Santa Barbara, California 93106, United States. ;
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United Sates
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115
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116
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Peraro L, Kritzer JA. Neue Methoden und Designprinzipien für zellgängige Peptide. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201801361] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Leila Peraro
- Department of Chemistry Tufts University Medford Massachusetts 02155 USA
| | - Joshua A. Kritzer
- Department of Chemistry Tufts University Medford Massachusetts 02155 USA
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117
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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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118
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Slough DP, McHugh SM, Lin YS. Understanding and designing head-to-tail cyclic peptides. Biopolymers 2018; 109:e23113. [PMID: 29528114 PMCID: PMC6135719 DOI: 10.1002/bip.23113] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 02/23/2018] [Accepted: 02/26/2018] [Indexed: 01/30/2023]
Abstract
Cyclic peptides (CPs) are an exciting class of molecules with a variety of applications. However, design strategies for CP therapeutics, for example, are generally limited by a poor understanding of their sequence-structure relationships. This knowledge gap often leads to a trial-and-error approach for designing CPs for a specific purpose, which is both costly and time-consuming. Herein, we describe the current experimental and computational efforts in understanding and designing head-to-tail CPs along with their respective challenges. In addition, we provide several future directions in the field of computational CP design to improve its accuracy, efficiency and applicability. These advances, combined with experimental techniques, shall ultimately provide a better understanding of these interesting molecules and a reliable working platform to rationally design CPs with desired characteristics.
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Affiliation(s)
| | | | - Yu-Shan Lin
- Department of Chemistry, Tufts University, Medford, Massachusetts, 02155, United States
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119
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Li XN, Rao T, Xu YF, Hu KR, Zhu ZP, Li HF, Kang D, Shao YH, Shen BY, Yin XX, Xie L, Wang GJ, Liang Y. Pharmacokinetic and pharmacodynamic evidence for developing an oral formulation of octreotide against gastric mucosal injury. Acta Pharmacol Sin 2018; 39:1373-1385. [PMID: 29188801 DOI: 10.1038/aps.2017.159] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 10/18/2017] [Indexed: 12/30/2022] Open
Abstract
Among the somatostatin analogues, octreotide (OCT) is the most commonly used in clinic via intravenous or subcutaneous injection to treat various diseases caused by increased secretion of growth hormone, gastrin or insulin. In order to assesse the feasibility of developing oral formulations of OCT, we conducted systematical pharmacokinetic and pharmacodynamic analyses of OCT in several animal models. The pharmacokinetic studies in rats showed that intragastric administration of OCT had extremely low bioavailability (<0.5%), but it could specifically distribute to the gastric mucosa due to the high expression of somatostatin receptor 2 (SSTR2) in the rat stomach. The pharmacodynamic studies revealed that intragastric administration of OCT dose-dependently protected against gastric mucosal injury (GMI) in mice with WIRS-induced mouse gastric ulcers, which were comparable to those achieved by intravenous injection of OCT, and this effect was markedly attenuated by co-administration of CYN-154806, an antagonist of SSTR2. In pyloric ligation-induced ulcer mice, we further demonstrated that OCT significantly reduced the secretion of gastric acid via down-regulating the level of gastrin, which was responsible for the protective effect of OCT against GMI. Overall, we have provided pharmacokinetic and pharmacodynamic evidence for the feasibility of developing an oral formulation of OCT. Most importantly, the influence of SSTR2 on the pharmacokinetics and pharmacodynamics of OCT suggested that an oral formulation of OCT might be applicable for other clinical indications, including neuroendocrine neoplasms and pituitary adenoma due to the overexpression of SSTR2 on these tumor cells.
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120
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Schumacher-Klinger A, Fanous J, Merzbach S, Weinmüller M, Reichart F, Räder AFB, Gitlin-Domagalska A, Gilon C, Kessler H, Hoffman A. Enhancing Oral Bioavailability of Cyclic RGD Hexa-peptides by the Lipophilic Prodrug Charge Masking Approach: Redirection of Peptide Intestinal Permeability from a Paracellular to Transcellular Pathway. Mol Pharm 2018; 15:3468-3477. [PMID: 29976060 DOI: 10.1021/acs.molpharmaceut.8b00466] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrophilic peptides constitute most of the active peptides. They mostly permeate via tight junctions (paracellular pathway) in the intestine. This permeability mechanism restricts the magnitude of their oral absorption and bioavailability. We hypothesized that concealing the hydrophilic residues of the peptide using the lipophilic prodrug charge masking approach (LPCM) can improve the bioavailability of hydrophilic peptides. To test this hypothesis, a cyclic N-methylated hexapeptide containing Arg-Gly-Asp (RGD) and its prodrug derivatives, masking the Arg and Asp charged side chains, were synthesized. The library was evaluated for intestinal permeability in vitro using the Caco-2 model. Further investigation of metabolic stability ex vivo models in rat plasma, brush border membrane vesicles (BBMVs), and isolated CYP3A4 microsomes and pharmacokinetic studies was performed on a selected peptide and its prodrug (peptide 12). The parent drug analogues were found to have a low permeability rate in vitro, corresponding to atenolol, a marker for paracellular permeability. Moreover, palmitoyl carnitine increased the Papp of peptide 12 by 4-fold, indicating paracellular permeability. The Papp of the prodrug derivatives was much higher than that of their parent peptides. For instance, the Papp of the prodrug 12P was 20-fold higher than the Papp of peptide 12 in the apical to basolateral (AB) direction. Whereas the permeability in the opposite direction (BA of the Caco-2 model) was significantly faster than the Papp AB, indicating the involvement of an efflux system. These results were corroborated when verapamil, a P-gp inhibitor, was added to the Caco-2 model and increased the Papp AB of prodrug 12P by 3-fold. The prodrug 12P was stable in the BBMVs environment, yet degraded quickly (less than 5 min) in the plasma into the parent peptide 12. Pharmacokinetic studies in rats showed an increase in the bioavailability of peptide 12 > 70-fold (from 0.58 ± 0.11% to 43.8 ± 14.9%) after applying the LPCM method to peptide 12 and converting it to the prodrug 12P. To conclude, the LPCM approach converted the absorption mechanism of the polar peptides from a paracellular to transcellular pathway that tremendously affects their oral bioavailability. The LPCM method provides a solution for the poor bioavailability of RGD cyclohexapeptides and paves the way for other active hydrophilic and charged peptides with poor oral bioavailability.
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Affiliation(s)
- Adi Schumacher-Klinger
- Institute for Drug Research, School of Pharmacy, Faculty of Medicine , The Hebrew University of Jerusalem , P.O. Box 12065, Jerusalem 91120 , Israel
| | - Joseph Fanous
- Institute for Drug Research, School of Pharmacy, Faculty of Medicine , The Hebrew University of Jerusalem , P.O. Box 12065, Jerusalem 91120 , Israel
| | - Shira Merzbach
- Institute for Drug Research, School of Pharmacy, Faculty of Medicine , The Hebrew University of Jerusalem , P.O. Box 12065, Jerusalem 91120 , Israel
| | - Michael Weinmüller
- Institute for Advanced Study and Center of Integrated Protein Science, Department Chemie , Technische Universität München , Lichtenbergstrasse 4 , 85748 Garching , Germany
| | - Florian Reichart
- Institute for Advanced Study and Center of Integrated Protein Science, Department Chemie , Technische Universität München , Lichtenbergstrasse 4 , 85748 Garching , Germany
| | - Andreas F B Räder
- Institute for Advanced Study and Center of Integrated Protein Science, Department Chemie , Technische Universität München , Lichtenbergstrasse 4 , 85748 Garching , Germany
| | - Agata Gitlin-Domagalska
- Institute of Chemistry , The Hebrew University of Jerusalem, Edmond Safra Campus, Givat Ram Campus, The Hebrew University , Jerusalem 91904 , Israel
| | - Chaim Gilon
- Institute of Chemistry , The Hebrew University of Jerusalem, Edmond Safra Campus, Givat Ram Campus, The Hebrew University , Jerusalem 91904 , Israel
| | - Horst Kessler
- Institute for Advanced Study and Center of Integrated Protein Science, Department Chemie , Technische Universität München , Lichtenbergstrasse 4 , 85748 Garching , Germany
| | - Amnon Hoffman
- Institute for Drug Research, School of Pharmacy, Faculty of Medicine , The Hebrew University of Jerusalem , P.O. Box 12065, Jerusalem 91120 , Israel
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121
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122
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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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123
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Katoh T, Passioura T, Suga H. Advances in in vitro genetic code reprogramming in 2014-2017. Synth Biol (Oxf) 2018; 3:ysy008. [PMID: 32995516 PMCID: PMC7445766 DOI: 10.1093/synbio/ysy008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 04/27/2018] [Accepted: 05/21/2018] [Indexed: 11/16/2022] Open
Abstract
To date, various genetic code manipulation methods have been developed to introduce non-proteinogenic amino acids into peptides by translation. However, the number of amino acids that can be used simultaneously remains limited even using these methods. Additionally, the scope of amino acid substrates that are compatible with ribosomal translation systems is also limited. For example, difficult substrates such as d-amino acids and β-amino acids are much less efficiently incorporated into peptides than l-α-amino acids. Here, we focus on three recently developed methodologies that address these issues: (i) artificial division of codon boxes to increase the number of available amino acids, (ii) orthogonal ribosomal translation systems to ‘duplicate’ the codon table and (iii) development of novel artificial tRNAs that enhance incorporation of difficult amino acid substrates.
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Affiliation(s)
- Takayuki Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,JST, PRESTO, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Toby Passioura
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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124
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Wesche F, Adihou H, Kaiser A, Wurglics M, Schubert-Zsilavecz M, Kaiser M, Bode HB. Combined Approach of Backbone Amide Linking and On-Resin N-Methylation for the Synthesis of Bioactive and Metabolically Stable Peptides. J Med Chem 2018; 61:3930-3938. [DOI: 10.1021/acs.jmedchem.7b01809] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Frank Wesche
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe University Frankfurt, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Hélène Adihou
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe University Frankfurt, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Astrid Kaiser
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Mario Wurglics
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Manfred Schubert-Zsilavecz
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Marcel Kaiser
- Parasite Chemotherapy, Swiss Tropical and Public Health Institute, Socinstrasse 57, CH-4051 Basel, Switzerland
- University of Basel, Petersplatz 1, CH-4003 Basel, Switzerland
| | - Helge B. Bode
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe University Frankfurt, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Strasse 15, D-60438 Frankfurt am Main, Germany
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125
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Designing macrocyclic disulfide-rich peptides for biotechnological applications. Nat Chem Biol 2018; 14:417-427. [DOI: 10.1038/s41589-018-0039-y] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 12/18/2017] [Indexed: 12/21/2022]
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126
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Durek T, Cromm PM, White AM, Schroeder CI, Kaas Q, Weidmann J, Ahmad Fuaad A, Cheneval O, Harvey PJ, Daly NL, Zhou Y, Dellsén A, Österlund T, Larsson N, Knerr L, Bauer U, Kessler H, Cai M, Hruby VJ, Plowright AT, Craik DJ. Development of Novel Melanocortin Receptor Agonists Based on the Cyclic Peptide Framework of Sunflower Trypsin Inhibitor-1. J Med Chem 2018; 61:3674-3684. [PMID: 29605997 DOI: 10.1021/acs.jmedchem.8b00170] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Ultrastable cyclic peptide frameworks offer great potential for drug design due to their improved bioavailability compared to their linear analogues. Using the sunflower trypsin inhibitor-1 (SFTI-1) peptide scaffold in combination with systematic N-methylation of the grafted pharmacophore led to the identification of novel subtype selective melanocortin receptor (MCR) agonists. Multiple bicyclic peptides were synthesized and tested toward their activity at MC1R and MC3-5R. Double N-methylated compound 18 showed a p Ki of 8.73 ± 0.08 ( Ki = 1.92 ± 0.34 nM) and a pEC50 of 9.13 ± 0.04 (EC50 = 0.75 ± 0.08 nM) at the human MC1R and was over 100 times more selective for MC1R. Nuclear magnetic resonance structural analysis of 18 emphasized the role of peptide bond N-methylation in shaping the conformation of the grafted pharmacophore. More broadly, this study highlights the potential of cyclic peptide scaffolds for epitope grafting in combination with N-methylation to introduce receptor subtype selectivity in the context of peptide-based drug discovery.
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Affiliation(s)
- Thomas Durek
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Philipp M Cromm
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia.,Institute for Advanced Study and Center of Integrated Protein Science, Department Chemie , Technische Universität München , Lichtenbergstrasse 4 , 85747 Garching , Germany
| | - Andrew M White
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Christina I Schroeder
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Quentin Kaas
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Joachim Weidmann
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Abdullah Ahmad Fuaad
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Olivier Cheneval
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Peta J Harvey
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Norelle L Daly
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia
| | - Yang Zhou
- Department of Chemistry and Biochemistry , University of Arizona , Tucson , Arizona 85721 , United States
| | - Anita Dellsén
- Mechanistic Biology & Profiling, Discovery Sciences, IMED Biotech Unit , AstraZeneca , Gothenburg 43183 Sweden
| | - Torben Österlund
- Discovery Biology, Discovery Sciences, IMED Biotech Unit , AstraZeneca , Gothenburg 43183 Sweden.,Drug Safety and Metabolism, IMED Biotech Unit , AstraZeneca , Gothenburg 43183 Sweden
| | - Niklas Larsson
- Discovery Biology, Discovery Sciences, IMED Biotech Unit , AstraZeneca , Gothenburg 43183 Sweden
| | - Laurent Knerr
- Medicinal Chemistry, Cardiovascular and Metabolic Diseases, IMED Biotech Unit , AstraZeneca , Gothenburg 43183 Sweden
| | - Udo Bauer
- Medicinal Chemistry, Cardiovascular and Metabolic Diseases, IMED Biotech Unit , AstraZeneca , Gothenburg 43183 Sweden
| | - Horst Kessler
- Institute for Advanced Study and Center of Integrated Protein Science, Department Chemie , Technische Universität München , Lichtenbergstrasse 4 , 85747 Garching , Germany
| | - Minying Cai
- Department of Chemistry and Biochemistry , University of Arizona , Tucson , Arizona 85721 , United States
| | - Victor J Hruby
- Department of Chemistry and Biochemistry , University of Arizona , Tucson , Arizona 85721 , United States
| | - Alleyn T Plowright
- Medicinal Chemistry, Cardiovascular and Metabolic Diseases, IMED Biotech Unit , AstraZeneca , Gothenburg 43183 Sweden
| | - David J Craik
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , QLD 4072 , Australia
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127
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Shin MK, Hyun YJ, Lee JH, Lim HS. Comparison of Cell Permeability of Cyclic Peptoids and Linear Peptoids. ACS COMBINATORIAL SCIENCE 2018; 20:237-242. [PMID: 29481042 DOI: 10.1021/acscombsci.7b00194] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Cyclic peptoids are emerging as an attractive class of peptidomimetics. Compared to their linear counterparts, cyclic peptoids should have increased conformational rigidity and preorganized structures, enabling them to bind more tightly to target proteins without major entropy penalty. Because cyclic peptoids lack the amide protons in their backbones like linear peptoids, it is perceived that cyclic peptoids are seemingly cell permeable as much as linear peptoids. However, no systematic investigation for cell permeability of cyclic peptoids has been reported yet. Here, we, for the first time, demonstrate that cyclic peptoids are far more cell permeable than linear counterparts irrespective of their size and side chains. This study highlights that cyclic peptoids, along with combinatorial library and high-throughput screening technologies, will serve as a rich source of protein binding molecules, particularly targeting intracellular proteins, given their excellent cell permeability in addition to their conformational rigidity and proteolytic stability.
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Affiliation(s)
- Min-Kyung Shin
- Department of Chemistry and Division of Advanced Material Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
| | - Yu-Jung Hyun
- Department of Chemistry and Division of Advanced Material Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
| | - Ji Hoon Lee
- New Drug Development Center, Daegu Gyeongbuk Medical Innovation Foundation, Daegu 41061, South Korea
| | - Hyun-Suk Lim
- Department of Chemistry and Division of Advanced Material Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
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128
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Kheirabadi M, Creech GS, Qiao JX, Nirschl DS, Leahy DK, Boy KM, Carter PH, Eastgate MD. Leveraging a "Catch-Release" Logic Gate Process for the Synthesis and Nonchromatographic Purification of Thioether- or Amine-Bridged Macrocyclic Peptides. J Org Chem 2018. [PMID: 29537839 DOI: 10.1021/acs.joc.7b03124] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Macrocyclic peptides containing N-alkylated amino acids have emerged as a promising therapeutic modality, capable of modulating protein-protein interactions and an intracellular delivery of hydrophilic payloads. While multichannel automated solid-phase peptide synthesis (SPPS) is a practical approach for peptide synthesis, the requirement for slow and inefficient chromatographic purification of the product peptides is a significant limitation to exploring these novel compounds. Herein, we invent a "catch-release" strategy for the nonchromatographic purification of macrocyclic peptides. A traceless catch process is enabled by the invention of a dual-functionalized N-terminal acetate analogue, which serves as a handle for capture onto a purification resin and as a leaving group for macrocyclization. Displacement by a C-terminal nucleophilic side chain thus releases the desired macrocycle from the purification resin. By design, this catch/release process is a logic test for the presence of the key components required for cyclization, thus removing impurities which lack the required functionality, such as common classes of peptide impurities, including hydrolysis fragments and truncated sequences. The method was shown to be highly effective with three libraries of macrocyclic peptides, containing macrocycles of 5-20 amino acids, with either thioether- or amine-based macrocyclic linkages; in this latter class, the reported method represents an enabling technology. In all cases, the catch-release protocol afforded significant enrichment of the target peptides purity, in many cases completely obviating the need for chromatography. Importantly, we have adapted this process for automation on a standard multichannel peptide synthesizer, achieving an efficient and completely integrated synthesis and purification platform for the preparation of these important molecules.
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Affiliation(s)
- Mahboubeh Kheirabadi
- Chemical and Synthetic Development , Bristol-Myers Squibb , One Squibb Drive , New Brunswick , New Jersey 08903 , United States
| | - Gardner S Creech
- Chemical and Synthetic Development , Bristol-Myers Squibb , One Squibb Drive , New Brunswick , New Jersey 08903 , United States
| | - Jennifer X Qiao
- Discovery Chemistry , Bristol-Myers Squibb , Princeton , New Jersey 08543 , United States
| | - David S Nirschl
- Discovery Chemistry , Bristol-Myers Squibb , Princeton , New Jersey 08543 , United States
| | - David K Leahy
- Chemical and Synthetic Development , Bristol-Myers Squibb , One Squibb Drive , New Brunswick , New Jersey 08903 , United States
| | - Kenneth M Boy
- Discovery Chemistry , Bristol-Myers Squibb , Wallingford , Connecticut 06492 , United States
| | - Percy H Carter
- Discovery Chemistry , Bristol-Myers Squibb , Princeton , New Jersey 08543 , United States
| | - Martin D Eastgate
- Chemical and Synthetic Development , Bristol-Myers Squibb , One Squibb Drive , New Brunswick , New Jersey 08903 , United States
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129
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Sharma A, Kumar A, Abdel Monaim SAH, Jad YE, El-Faham A, de la Torre BG, Albericio F. N-methylation in amino acids and peptides: Scope and limitations. Biopolymers 2018. [PMID: 29528112 DOI: 10.1002/bip.23110] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Active pharmaceutical ingredients (APIs) can be divided into two types, namely chemical and biological entities. Traditionally, the former has been associated with the so-called small molecules. The revival of peptides in pharmaceutical industry results from their importance in many biological roles. However, low metabolic stability and the lack of oral availability of most peptides is the main drawback for peptide to fulfill that paradigmatic situation. In this regard, efforts are being channeled into addressing this issue by introducing restrictions into the flexible peptide backbone, mainly through N-methyl amino acids (NMAAs) or development of small cyclic peptides. In many cases, both the above restrictions are combined with the aim to enhance oral availability. The synthesis of NMAAs is complex and their introduction into the peptide chain brings additional synthetic challenges and also sometimes leads to side-reactions. Here we discuss the most efficient methods for the synthesis of NMAAs (either in solution or in solid phase) and also their introduction into peptide sequences. Special attention is also given to the detection of side reactions and the most efficient way to prevent them.
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Affiliation(s)
- Anamika Sharma
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, 4001, South Africa
| | - Ashish Kumar
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, 4001, South Africa.,School of Chemistry and Physics, University of KwaZulu-Natal, Westville, Durban, 4001, South Africa
| | - Shimaa A H Abdel Monaim
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, 4001, South Africa
| | - Yahya E Jad
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, 4001, South Africa
| | - Ayman El-Faham
- Department of Chemistry, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia.,Department of Chemistry, Faculty of Science, Alexandria University, Ibrahimia, Alexandria, 21321, Egypt
| | - Beatriz G de la Torre
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, 4001, South Africa.,KRISP, College of Health Sciences, University of KwaZulu-Natal, Westville, Durban, 4001, South Africa
| | - Fernando Albericio
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, 4001, South Africa.,School of Chemistry and Physics, University of KwaZulu-Natal, Westville, Durban, 4001, South Africa.,Department of Chemistry, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia.,Department of Organic Chemistry, University of Barcelona, Martí i Franqués 1-11, Barcelona, 08028, Spain.,CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, Baldiri Reixac 10, Barcelona, 08028, Spain
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130
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Wang CK, Swedberg JE, Harvey PJ, Kaas Q, Craik DJ. Conformational Flexibility Is a Determinant of Permeability for Cyclosporin. J Phys Chem B 2018; 122:2261-2276. [DOI: 10.1021/acs.jpcb.7b12419] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Conan K. Wang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Joakim E. Swedberg
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Peta J. Harvey
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Quentin Kaas
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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131
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Lundy TA, Mori S, Garneau-Tsodikova S. Engineering Bifunctional Enzymes Capable of Adenylating and Selectively Methylating the Side Chain or Core of Amino Acids. ACS Synth Biol 2018; 7:399-404. [PMID: 29393631 DOI: 10.1021/acssynbio.7b00426] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nonribosomal peptides (NRPs) are known sources of therapeutics. Some nonribosomal peptide synthetase assembly lines contain unique functional interrupted adenylation (A) domains, where nature has combined two different functional domains into one bifunctional enzyme. Most often these interrupted A domains contain a part of a methylation (M) domain embedded in their sequence. Herein, we aimed to emulate nature and create fully functional interrupted A domains by inserting two different noncognate M domains, KtzH(MH) and TioS(M3S), into a naturally occurring uninterrupted A domain, Ecm6(A1T1). We evaluated the engineered enzymes, Ecm6(A1aMHA1bT1) and Ecm6(A1aM3SA1bT1), by a series of radiometric assays and found that not only do they maintain A domain activity, but also they gain the site-specific methylation patterns observed in the parent M domain donors. These findings provide an exciting proof-of-concept for generating interrupted A domains as future tools to modify NRPs and increase the diversity and activity of potential therapeutics.
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Affiliation(s)
- Taylor A. Lundy
- Department of Pharmaceutical
Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Shogo Mori
- Department of Pharmaceutical
Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical
Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536-0596, United States
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132
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Slough DP, Yu H, McHugh SM, Lin YS. Toward accurately modeling N-methylated cyclic peptides. Phys Chem Chem Phys 2018; 19:5377-5388. [PMID: 28155950 DOI: 10.1039/c6cp07700e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cyclic peptides have unique properties and can target protein surfaces specifically and potently. N-Methylation provides a promising way to further optimize the pharmacokinetic and structural profiles of cyclic peptides. The capability to accurately model structures adopted by N-methylated cyclic peptides would facilitate rational design of this interesting and useful class of molecules. We apply molecular dynamics simulations with advanced enhanced sampling methods to efficiently characterize the structural ensembles of N-methylated cyclic peptides, while simultaneously evaluating the overall performance of several simulation force fields. We find that one of the residue-specific force fields, RSFF2, is able to recapitulate experimental structures of the N-methylated cyclic peptide benchmarks tested here when the correct amide isomers are used as initial configurations and enforced during the simulations. Thus, using our simulation approach, it is possible to accurately and efficiently predict the structures of N-methylated cyclic peptides if sufficient information is available to determine the correct amide cis/trans configuration. Moreover, our results suggest that, upon further optimization of RSFF2 to more reliably predict cis/trans isomers, molecular dynamics simulations will be able to de novo predict N-methylated cyclic peptides in the near future, strongly motivating such continued optimization.
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Affiliation(s)
- Diana P Slough
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, USA.
| | - Hongtao Yu
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, USA.
| | - Sean M McHugh
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, USA.
| | - Yu-Shan Lin
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, USA.
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133
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Erak M, Bellmann-Sickert K, Els-Heindl S, Beck-Sickinger AG. Peptide chemistry toolbox - Transforming natural peptides into peptide therapeutics. Bioorg Med Chem 2018; 26:2759-2765. [PMID: 29395804 DOI: 10.1016/j.bmc.2018.01.012] [Citation(s) in RCA: 174] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/09/2018] [Accepted: 01/18/2018] [Indexed: 01/27/2023]
Abstract
The development of solid phase peptide synthesis has released tremendous opportunities for using synthetic peptides in medicinal applications. In the last decades, peptide therapeutics became an emerging market in pharmaceutical industry. The need for synthetic strategies in order to improve peptidic properties, such as longer half-life, higher bioavailability, increased potency and efficiency is accordingly rising. In this mini-review, we present a toolbox of modifications in peptide chemistry for overcoming the main drawbacks during the transition from natural peptides to peptide therapeutics. Modifications at the level of the peptide backbone, amino acid side chains and higher orders of structures are described. Furthermore, we are discussing the future of peptide therapeutics development and their impact on the pharmaceutical market.
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Affiliation(s)
- Miloš Erak
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Bruederstrasse 34, 04103 Leipzig, Germany
| | - Kathrin Bellmann-Sickert
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Bruederstrasse 34, 04103 Leipzig, Germany
| | - Sylvia Els-Heindl
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Bruederstrasse 34, 04103 Leipzig, Germany
| | - Annette G Beck-Sickinger
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Bruederstrasse 34, 04103 Leipzig, Germany.
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134
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Buckton LK, McAlpine SR. Improving the Cell Permeability of Polar Cyclic Peptides by Replacing Residues with Alkylated Amino Acids, Asparagines, and d-Amino Acids. Org Lett 2018; 20:506-509. [DOI: 10.1021/acs.orglett.7b03363] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Laura K. Buckton
- School of Chemistry, University of New South Wales, Sydney NSW 2051, Australia
| | - Shelli R. McAlpine
- School of Chemistry, University of New South Wales, Sydney NSW 2051, Australia
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135
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Verma H, Khatri B, Chakraborti S, Chatterjee J. Increasing the bioactive space of peptide macrocycles by thioamide substitution. Chem Sci 2018; 9:2443-2451. [PMID: 29732120 PMCID: PMC5909342 DOI: 10.1039/c7sc04671e] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 01/19/2018] [Indexed: 12/23/2022] Open
Abstract
We show that substituting a single atom, O to S (amide to thioamide), in a peptide bond results in global restriction of the conformational flexibility in peptide macrocycles with minimal perturbation of the parent conformation. The van der Waals interactions between the C 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 S group and the surrounding atoms are the major driving force in inducing the conformational restriction, resulting in well-defined structures of these cyclic peptides with static 3-D presentation of the pharmacophores. Utilizing this property of thioamides, we report the development of a superactive antagonist of pro-angiogenic αvβ3, αvβ5 and α5β1 integrins, which are responsible for cancer cell proliferation and survival. Using simple thio-scanning and spatial screening of a non-efficacious and conformationally flexible cyclic peptide, we could achieve a more than 105 fold enhancement in its efficacy in cellulo via a single O to S substitution. The developed peptide shows better efficacy in inhibiting the pro-angiogenic integrins than the drug candidate cilengitide, with a significantly enhanced serum half-life of 36 h compared to that of cilengitide (12 h). The long shelf-life, absence of non-specific toxicity and resistance to degradation of the thioamidated macrocyclic peptides in human serum suggest the promise of thioamides in markedly improving the affinity, efficacy and pharmacology of peptide macrocycles.
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Affiliation(s)
- Hitesh Verma
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
| | - Bhavesh Khatri
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
| | - Sohini Chakraborti
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
| | - Jayanta Chatterjee
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India . .,NMR Research Centre , Indian Institute of Science , Bangalore 560012 , India
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136
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Zong G, Sun X, Bhakta R, Whisenhunt L, Hu Z, Wang F, Shi WQ. New insights into structure-activity relationship of ipomoeassin F from its bioisosteric 5-oxa/aza analogues. Eur J Med Chem 2018; 144:751-757. [PMID: 29291442 PMCID: PMC5800971 DOI: 10.1016/j.ejmech.2017.11.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 11/03/2017] [Accepted: 11/08/2017] [Indexed: 10/18/2022]
Abstract
Ipomoeassin F, a plant-derived macrolide, exhibited single-digit nanomolar growth inhibition activity against many cancer cell lines. In this report, a series of 5-oxa/aza analogues was prepared and screened for cytotoxicity. Replacement of 5-CH2 with O/NH simplified the synthesis and led to only a small activity loss. N-methylation almost completely restored the potency. Further studies with additional 5-oxa analogues suggested, for the first time, that size and flexibility of the ring also significantly influence the bioactivity of ipomoeassin F.
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Affiliation(s)
- Guanghui Zong
- Department of Chemistry and Biochemistry, J. William Fulbright College of Arts & Science, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Xianwei Sun
- Department of Chemistry and Biochemistry, J. William Fulbright College of Arts & Science, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Rima Bhakta
- Department of Chemistry and Biochemistry, J. William Fulbright College of Arts & Science, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Lucas Whisenhunt
- Department of Chemistry and Biochemistry, J. William Fulbright College of Arts & Science, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Zhijian Hu
- Department of Chemistry and Biochemistry, J. William Fulbright College of Arts & Science, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Feng Wang
- Department of Chemistry and Biochemistry, J. William Fulbright College of Arts & Science, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Wei Q Shi
- Department of Chemistry and Biochemistry, J. William Fulbright College of Arts & Science, University of Arkansas, Fayetteville, AR, 72701, USA.
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137
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Siow A, Opiyo G, Kavianinia I, Li FF, Furkert DP, Harris PWR, Brimble MA. Total Synthesis of the Highly N-Methylated Acetylene-Containing Anticancer Peptide Jahanyne. Org Lett 2018; 20:788-791. [PMID: 29337569 DOI: 10.1021/acs.orglett.7b03925] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The first total synthesis of the highly N-methylated acetylene-containing lipopeptide jahanyne, an apoptosis-inducing natural product from marine cyanobacteria, is reported. A late-stage solution-phase coupling enabled introduction of the C-terminal ketone pyrrolidine moiety. A modified Fmoc solid-phase synthesis strategy was adopted to effectively couple multiple sterically hindered N-methylated amino acids while suppressing epimerization. The total synthesis has enabled confirmation of the proposed absolute configuration of natural jahanyne.
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Affiliation(s)
- Andrew Siow
- School of Biological Sciences, The University of Auckland , 3A Symonds Street, Auckland 1010, New Zealand
| | - George Opiyo
- School of Chemical Sciences, The University of Auckland , 23 Symonds Street, Auckland 1010, New Zealand
| | - Iman Kavianinia
- School of Biological Sciences, The University of Auckland , 3A Symonds Street, Auckland 1010, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland , 3A Symonds Street, Auckland 1010, New Zealand
| | - Freda F Li
- School of Chemical Sciences, The University of Auckland , 23 Symonds Street, Auckland 1010, New Zealand
| | - Daniel P Furkert
- School of Chemical Sciences, The University of Auckland , 23 Symonds Street, Auckland 1010, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland , 3A Symonds Street, Auckland 1010, New Zealand
| | - Paul W R Harris
- School of Biological Sciences, The University of Auckland , 3A Symonds Street, Auckland 1010, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland , 3A Symonds Street, Auckland 1010, New Zealand
| | - Margaret A Brimble
- School of Biological Sciences, The University of Auckland , 3A Symonds Street, Auckland 1010, New Zealand.,School of Chemical Sciences, The University of Auckland , 23 Symonds Street, Auckland 1010, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland , 3A Symonds Street, Auckland 1010, New Zealand
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138
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Li W, Hu K, Zhang Q, Wang D, Ma Y, Hou Z, Yin F, Li Z. N terminal N-methylation modulates chiral centre induced helical (CIH) peptides’ biophysical properties. Chem Commun (Camb) 2018; 54:1865-1868. [DOI: 10.1039/c7cc09201f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The effects of N-methylation on CIH peptides’ biophysical properties were systematically studied.
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Affiliation(s)
- Wenjun Li
- The Key Laboratory of Chemical Genomics School of Chemical Biology and Biotechnology
- Peking University Shenzhen Graduate School
- Shenzhen
- China
| | - Kuan Hu
- Beijing Institute of Nanoenergy and Nanosystems
- National Center for Nanoscience and Technology (NCNST)
- Chinese Academy of Sciences
- Beijing 100083
- China
| | - Qingzhou Zhang
- The Key Laboratory of Chemical Genomics School of Chemical Biology and Biotechnology
- Peking University Shenzhen Graduate School
- Shenzhen
- China
| | - Dongyuan Wang
- The Key Laboratory of Chemical Genomics School of Chemical Biology and Biotechnology
- Peking University Shenzhen Graduate School
- Shenzhen
- China
| | - Yue Ma
- The Key Laboratory of Chemical Genomics School of Chemical Biology and Biotechnology
- Peking University Shenzhen Graduate School
- Shenzhen
- China
| | - Zhanfeng Hou
- The Key Laboratory of Chemical Genomics School of Chemical Biology and Biotechnology
- Peking University Shenzhen Graduate School
- Shenzhen
- China
| | - Feng Yin
- The Key Laboratory of Chemical Genomics School of Chemical Biology and Biotechnology
- Peking University Shenzhen Graduate School
- Shenzhen
- China
| | - Zigang Li
- The Key Laboratory of Chemical Genomics School of Chemical Biology and Biotechnology
- Peking University Shenzhen Graduate School
- Shenzhen
- China
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139
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Kablaoui N, Vanase-Frawley M, Sciabola S. Hybrid peptide-small molecule oxytocin analogs are potent and selective agonists of the oxytocin receptor. Bioorg Med Chem Lett 2017; 28:415-419. [PMID: 29273395 DOI: 10.1016/j.bmcl.2017.12.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 12/04/2017] [Accepted: 12/13/2017] [Indexed: 10/18/2022]
Abstract
Oxytocin (OT) is a peptide hormone agonist of the oxytocin receptor (OTR) that has been proposed as a therapeutic to treat a number of social and emotional disorders in addition to its current clinical use to induce labor and treat postpartum bleeding. OT is administered intravenously and intranasally rather than orally, in part because its low passive permeability causes low oral bioavailability. Non-peptidic OTR agonists have also been reported, but none with the exquisite potency of the peptide based agonists. In this report, we describe the OTR agonist activity and exposed polarity of a set of truncated OT analogs as well as hybrid peptide-small molecule analogs of OT. Examples of both truncated analogs and peptide-small molecule hybrid analogs are potent and selective OTR agonists. Hybrid agonist 13, which is 232 Da smaller than OT, still retains subnanomolar potency, full agonist activity, and selectivity over V1a. While these compounds were designed to address the low permeability of OT and other full length analogs, we found that reduction in molecular weight and the removal or replacement of the three amino acid tail of OT did not have a significant effect on passive permeability.
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Affiliation(s)
- Natasha Kablaoui
- Pfizer Worldwide Research and Development, 610 Main Street, Cambridge, MA 02139, United States; Pfizer Worldwide Research and Development, Eastern Point Rd, Groton, CT 026340, United States.
| | - Michelle Vanase-Frawley
- Pfizer Worldwide Research and Development, 610 Main Street, Cambridge, MA 02139, United States; Pfizer Worldwide Research and Development, Eastern Point Rd, Groton, CT 026340, United States
| | - Simone Sciabola
- Pfizer Worldwide Research and Development, 610 Main Street, Cambridge, MA 02139, United States; Pfizer Worldwide Research and Development, Eastern Point Rd, Groton, CT 026340, United States
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140
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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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141
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Taylor RD, Rey-Carrizo M, Passioura T, Suga H. Identification of nonstandard macrocyclic peptide ligands through display screening. DRUG DISCOVERY TODAY. TECHNOLOGIES 2017; 26:17-23. [PMID: 29249238 DOI: 10.1016/j.ddtec.2017.10.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 10/23/2017] [Indexed: 11/25/2022]
Abstract
Techniques facilitating the synthesis and screening of very high diversity nonstandard macrocyclic peptide libraries have led to such compounds receiving increasing attention as potential drug candidates. Specifically, approaches which allow the use of non-proteinogenic amino acids are proving to be particularly effective, since they expand the accessible chemical space of the starting library and thus allow the identification of compounds with structural similarity to known drugs. This review focuses on mRNA display screening platforms for drug discovery and their combined use with genetic code reprogramming to identify novel macrocyclic peptides with high affinities for disease-related targets of interest.
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Affiliation(s)
- Rhys Dylan Taylor
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Matias Rey-Carrizo
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Toby Passioura
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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142
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Antimicrobial Electrospun Fibers of Polyester Loaded with Engineered Cyclic Gramicidin Analogues. FIBERS 2017. [DOI: 10.3390/fib5030034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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143
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Harner MJ, Mueller L, Robbins KJ, Reily MD. NMR in drug design. Arch Biochem Biophys 2017; 628:132-147. [DOI: 10.1016/j.abb.2017.06.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 06/02/2017] [Accepted: 06/06/2017] [Indexed: 02/09/2023]
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144
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Barnash KD, Lamb KN, James LI, Frye SV. Peptide Technologies in the Development of Chemical Tools for Chromatin-Associated Machinery. Drug Dev Res 2017. [DOI: 10.1002/ddr.21398] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kimberly D. Barnash
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy; University of North Carolina at Chapel Hill; Chapel Hill North Carolina 27599
| | - Kelsey N. Lamb
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy; University of North Carolina at Chapel Hill; Chapel Hill North Carolina 27599
| | - Lindsey I. James
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy; University of North Carolina at Chapel Hill; Chapel Hill North Carolina 27599
| | - Stephen V. Frye
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy; University of North Carolina at Chapel Hill; Chapel Hill North Carolina 27599
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145
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Abstract
INTRODUCTION The melanocortin system is a primordial and critical system for survival, involved in a wide variety of physiological functions. It includes melanocortin receptors (MCRs) and melanotropin ligands (MCLs). MCRs are important drug targets that can regulate several key physiological processes. Extensive efforts have been made to develop peptide and peptidomimetics targeting melanocortin receptors including MC1R, MC3R, MC4R and MC5R. Most research is focused on developing potent and selective melanotropins. However, developing bioavailable melanotropins remains challenging. Areas covered: Herein, the authors summarize promising strategies for developing bioavailable MCLs by using cyclized N-methylated melanotropins, and using cyclotide and tetrapeptide as templates. They discuss their unique advantages in oral availability and targeting MCRs in the central nervous system or in peripheral tissues. Finally, they discuss the observed differences in thepharmacology of MCRs between in vitro and in vivo tests. Expert opinion: N-methylated cyclized melanotropins have great potential to become bio- available drugs targeting MCRs in the brain, while MCR-grafted cyclotides tend to target MCRs in peripheral tissue. A better understanding of the biased signaling process is a new challenge and opportunity for the future discovery of bioavailable MCLs.
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Affiliation(s)
- Yang Zhou
- a Department of Chemistry and Biochemistry , University of Arizona , Tucson , AZ USA
| | - Minying Cai
- a Department of Chemistry and Biochemistry , University of Arizona , Tucson , AZ USA
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146
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Cyclic peptide natural products chart the frontier of oral bioavailability in the pursuit of undruggable targets. Curr Opin Chem Biol 2017; 38:141-147. [DOI: 10.1016/j.cbpa.2017.04.012] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 04/13/2017] [Accepted: 04/18/2017] [Indexed: 01/23/2023]
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147
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Nielsen DS, Shepherd NE, Xu W, Lucke AJ, Stoermer MJ, Fairlie DP. Orally Absorbed Cyclic Peptides. Chem Rev 2017; 117:8094-8128. [PMID: 28541045 DOI: 10.1021/acs.chemrev.6b00838] [Citation(s) in RCA: 266] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Peptides and proteins are not orally bioavailable in mammals, although a few peptides are intestinally absorbed in small amounts. Polypeptides are generally too large and polar to passively diffuse through lipid membranes, while most known active transport mechanisms facilitate cell uptake of only very small peptides. Systematic evaluations of peptides with molecular weights above 500 Da are needed to identify parameters that influence oral bioavailability. Here we describe 125 cyclic peptides containing four to thirty-seven amino acids that are orally absorbed by mammals. Cyclization minimizes degradation in the gut, blood, and tissues by removing cleavable N- and C-termini and by shielding components from metabolic enzymes. Cyclization also folds peptides into bioactive conformations that determine exposure of polar atoms to solvation by water and lipids and therefore can influence oral bioavailability. Key chemical properties thought to influence oral absorption and bioavailability are analyzed, including molecular weight, octanol-water partitioning, hydrogen bond donors/acceptors, rotatable bonds, and polar surface area. The cyclic peptides violated to different degrees all of the limits traditionally considered to be important for oral bioavailability of drug-like small molecules, although fewer hydrogen bond donors and reduced flexibility generally favored oral absorption.
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Affiliation(s)
- Daniel S Nielsen
- Division of Chemistry and Structural Biology, and ‡Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| | - Nicholas E Shepherd
- Division of Chemistry and Structural Biology, and ‡Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| | - Weijun Xu
- Division of Chemistry and Structural Biology, and ‡Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| | - Andrew J Lucke
- Division of Chemistry and Structural Biology, and ‡Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| | - Martin J Stoermer
- Division of Chemistry and Structural Biology, and ‡Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| | - David P Fairlie
- Division of Chemistry and Structural Biology, and ‡Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
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148
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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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149
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Asfaw H, Laqua K, Walkowska AM, Cunningham F, Martinez-Martinez MS, Cuevas-Zurita JC, Ballell-Pages L, Imming P. Design, synthesis and structure-activity relationship study of wollamide B; a new potential anti TB agent. PLoS One 2017; 12:e0176088. [PMID: 28423019 PMCID: PMC5397059 DOI: 10.1371/journal.pone.0176088] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 04/05/2017] [Indexed: 11/26/2022] Open
Abstract
Wollamide B is a cationic antimycobacterial cyclohexapeptide that exhibits activity against Mycobacterium bovis (M. bovis) (IC50 of 3.1 μM). Aiming to define its structural activity relationship (SAR), optimizing potency and pharmacokinetic properties, libraries of analogues were synthesized following a standard Fmoc-based solid phase peptide synthesis approach. The antimycobacterial activities of wollamide B and all the synthesized analogues were tested against Mycobacterium tuberculosis (Mtb) H37Rv. Parallely, in vitro drug metabolism and pharmacokinetic (ADME) profiling was done for the synthesized compounds to evaluate their drug likeness. Among the 25 synthesized wollamides five of them showed potent activities with MICs ≤ 3.1 μM and found to be nontoxic against human HepG2 cells up to 100 μM. The results of the in vitro ADME profiling revealed the remarkable plasma stability and very good aqueous solubility of the class in general while the metabolic stability was found to be moderate to low. Of particular note, compounds 7c (MIC = 1.1 μM) and 13c (0.6 μM) that exhibited good balance of antimycobacterial activity vs. optimal pharmacokinetic properties could be used as a new lead for further development.
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Affiliation(s)
- Henok Asfaw
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Katja Laqua
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Anna Maria Walkowska
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Fraser Cunningham
- Diseases of the Developing World, Medicines Development Campus, GlaxoSmithKline, Tres Cantos, Madrid, Spain
| | | | - Juan Carlos Cuevas-Zurita
- Diseases of the Developing World, Medicines Development Campus, GlaxoSmithKline, Tres Cantos, Madrid, Spain
| | - Lluís Ballell-Pages
- Diseases of the Developing World, Medicines Development Campus, GlaxoSmithKline, Tres Cantos, Madrid, Spain
| | - Peter Imming
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
- * E-mail:
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150
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Vorherr T, Lewis I, Berghausen J, Desrayaud S, Schaefer M. Modulation of Oral Bioavailability and Metabolism for Closely Related Cyclic Hexapeptides. Int J Pept Res Ther 2017. [PMID: 29527142 PMCID: PMC5838147 DOI: 10.1007/s10989-017-9590-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Abstract Recently, a variety of studies concerned with the permeability and oral bioavailability of cyclic peptides have been reported. In particular, strategies aiming at modifying peptides to maintain or to enhance solubility while enabling permeability constitute a significant challenge, but are of high interest to ensure a smooth drug discovery process. Current methodologies include N-methylation, matching of hydrogen bonding acceptors and donors across the macrocycle, and additional masking of polarity. In this study, we investigate further the pivotal effects of shielding on permeability and studied the metabolism of the corresponding peptides in more detail by comparing peptide concentrations in the portal versus the jugular vein in rats. Interestingly, minor changes in one particular side chain impacts both permeability and liver metabolism. Graphical Abstract ![]()
Electronic supplementary material The online version of this article (doi:10.1007/s10989-017-9590-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thomas Vorherr
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Ian Lewis
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Joerg Berghausen
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | | | - Michael Schaefer
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
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