51
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Lee D, Lee S, Choi J, Song YK, Kim MJ, Shin DS, Bae MA, Kim YC, Park CJ, Lee KR, Choi JH, Seo J. Interplay among Conformation, Intramolecular Hydrogen Bonds, and Chameleonicity in the Membrane Permeability and Cyclophilin A Binding of Macrocyclic Peptide Cyclosporin O Derivatives. J Med Chem 2021; 64:8272-8286. [PMID: 34096287 DOI: 10.1021/acs.jmedchem.1c00211] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A macrocyclic peptide scaffold with well-established structure-property relationship is desirable for tackling undruggable targets. Here, we adopted a natural macrocycle, cyclosporin O (CsO) and its derivatives (CP1-3), and evaluated the impact of conformation on membrane permeability, cyclophilin A (CypA) binding, and the pharmacokinetic (PK) profile. In nonpolar media, CsO showed a similar conformation to cyclosporin A (CsA), a well-known chameleonic macrocycle, but less chameleonic behavior in a polar environment. The weak chameleonicity of CsO resulted in decreased membrane permeability; however, the more rigid conformation of CsO was not detrimental to its PK profile. CsO exhibited a higher plasma concentration than CsA, which resulted from minimal CypA binding and lower accumulation in red blood cells and moderate oral bioavailability (F = 12%). Our study aids understanding of CsO, a macrocyclic peptide that is less explored than CsA but with greater potential for diversity generation and rational design.
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Affiliation(s)
- Dongjae Lee
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Sungjin Lee
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Jieun Choi
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Yoo-Kyung Song
- Laboratory of Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang 28116, Republic of Korea
| | - Min Ju Kim
- Laboratory of Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang 28116, Republic of Korea
| | - Dae-Seop Shin
- Bio Platform Technology Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
| | - Myung Ae Bae
- Bio Platform Technology Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
| | - Yong-Chul Kim
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Chin-Ju Park
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Kyeong-Ryoon Lee
- Laboratory of Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang 28116, Republic of Korea
| | - Jun-Ho Choi
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Jiwon Seo
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
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Adaligil E, Song A, Hallenbeck KK, Cunningham CN, Fairbrother WJ. Ribosomal Synthesis of Macrocyclic Peptides with β 2- and β 2,3-Homo-Amino Acids for the Development of Natural Product-Like Combinatorial Libraries. ACS Chem Biol 2021; 16:1011-1018. [PMID: 34008946 DOI: 10.1021/acschembio.1c00062] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The development of large, natural-product-like, combinatorial macrocyclic peptide libraries is essential in the quest to develop therapeutics for "undruggable" cellular targets. Herein we report the ribosomal synthesis of macrocyclic peptides containing one or more β2-homo-amino acids (β2haa) to enable their incorporation into mRNA display-based selection libraries. We confirmed the compatibility of 14 β2-homo-amino acids, (S)- and (R)-stereochemistry, for single incorporation into a macrocyclic peptide with low to high translation efficiency. Interestingly, N-methylation of the backbone amide of β2haa prevented the incorporation of this amino acid subclass by the ribosome. Additionally, we designed and incorporated several α,β-disubstituted β2,3-homo-amino acids (β2,3haa) with different R-groups on the α- and β-carbons of the same amino acid. Incorporation of these β2,3haa enables increased diversity in a single position of a macrocyclic peptide without significantly increasing the overall molecular weight, which is an important consideration for passive cell permeability. We also successfully incorporated multiple (S)-β2hAla into a single macrocycle with other non-proteinogenic amino acids, confirming that this class of β-amino acid is suitable for development of large scale macrocyclic peptide libraries.
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Affiliation(s)
- Emel Adaligil
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Aimin Song
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Kenneth K. Hallenbeck
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Christian N. Cunningham
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Wayne J. Fairbrother
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
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53
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Wang W, Khojasteh SC, Su D. Biosynthetic Strategies for Macrocyclic Peptides. Molecules 2021; 26:3338. [PMID: 34206124 PMCID: PMC8199541 DOI: 10.3390/molecules26113338] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/22/2021] [Accepted: 05/23/2021] [Indexed: 11/28/2022] Open
Abstract
Macrocyclic peptides are predominantly peptide structures bearing one or more rings and spanning multiple amino acid residues. Macrocyclization has become a common approach for improving the pharmacological properties and bioactivity of peptides. A variety of ribosomal-derived and non-ribosomal synthesized cyclization approaches have been established. The biosynthesis of backbone macrocyclic peptides using seven new emerging methodologies will be discussed with regard to the features and strengths of each platform rather than medicinal chemistry tools. The mRNA display variant, known as the random nonstandard peptide integrated discovery (RaPID) platform, utilizes flexible in vitro translation (FIT) to access macrocyclic peptides containing nonproteinogenic amino acids (NAAs). As a new discovery approach, the ribosomally synthesized and post-translationally modified peptides (RiPPs) method involves the combination of ribosomal synthesis and the phage screening platform together with macrocyclization chemistries to generate libraries of macrocyclic peptides. Meanwhile, the split-intein circular ligation of peptides and proteins (SICLOPPS) approach relies on the in vivo production of macrocyclic peptides. In vitro and in vivo peptide library screening is discussed as an advanced strategy for cyclic peptide selection. Specifically, biosynthetic bicyclic peptides are highlighted as versatile and attractive modalities. Bicyclic peptides represent another type of promising therapeutics that allow for building blocks with a heterotrimeric conjugate to address intractable challenges and enable multimer complexes via linkers. Additionally, we discuss the cell-free chemoenzymatic synthesis of macrocyclic peptides with a non-ribosomal catalase known as the non-ribosomal synthetase (NRPS) and chemo-enzymatic approach, with recombinant thioesterase (TE) domains. Novel insights into the use of peptide library tools, activity-based two-hybrid screening, structure diversification, inclusion of NAAs, combinatorial libraries, expanding the toolbox for macrocyclic peptides, bicyclic peptides, chemoenzymatic strategies, and future perspectives are presented. This review highlights the broad spectrum of strategy classes, novel platforms, structure diversity, chemical space, and functionalities of macrocyclic peptides enabled by emerging biosynthetic platforms to achieve bioactivity and for therapeutic purposes.
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Affiliation(s)
| | | | - Dian Su
- Drug Metabolism and Disposition, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA; (W.W.); (S.C.K.)
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Improvement on Permeability of Cyclic Peptide/Peptidomimetic: Backbone N-Methylation as A Useful Tool. Mar Drugs 2021; 19:md19060311. [PMID: 34072121 PMCID: PMC8229464 DOI: 10.3390/md19060311] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/22/2021] [Accepted: 05/24/2021] [Indexed: 12/14/2022] Open
Abstract
Peptides have a three-dimensional configuration that can adopt particular conformations for binding to proteins, which are well suited to interact with larger contact surface areas on target proteins. However, low cell permeability is a major challenge in the development of peptide-related drugs. In recent years, backbone N-methylation has been a useful tool for manipulating the permeability of cyclic peptides/peptidomimetics. Backbone N-methylation permits the adjustment of molecule’s conformational space. Several pathways are involved in the drug absorption pathway; the relative importance of each N-methylation to total permeation is likely to differ with intrinsic properties of cyclic peptide/peptidomimetic. Recent studies on the permeability of cyclic peptides/peptidomimetics using the backbone N-methylation strategy and synthetic methodologies will be presented in this review.
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Kerbs A, Mindt M, Schwardmann L, Wendisch VF. Sustainable Production of N-methylphenylalanine by Reductive Methylamination of Phenylpyruvate Using Engineered Corynebacterium glutamicum. Microorganisms 2021; 9:microorganisms9040824. [PMID: 33924554 PMCID: PMC8070496 DOI: 10.3390/microorganisms9040824] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 12/17/2022] Open
Abstract
N-alkylated amino acids occur widely in nature and can also be found in bioactive secondary metabolites such as the glycopeptide antibiotic vancomycin and the immunosuppressant cyclosporine A. To meet the demand for N-alkylated amino acids, they are currently produced chemically; however, these approaches often lack enantiopurity, show low product yields and require toxic reagents. Fermentative routes to N-alkylated amino acids like N-methyl-l-alanine or N-methylantranilate, a precursor of acridone alkaloids, have been established using engineered Corynebacterium glutamicum, which has been used for the industrial production of amino acids for decades. Here, we describe metabolic engineering of C. glutamicum for de novo production of N-methylphenylalanine based on reductive methylamination of phenylpyruvate. Pseudomonas putida Δ-1-piperideine-2-carboxylate reductase DpkA containing the amino acid exchanges P262A and M141L showed comparable catalytic efficiencies with phenylpyruvate and pyruvate, whereas the wild-type enzyme preferred the latter substrate over the former. Deletion of the anthranilate synthase genes trpEG and of the genes encoding branched-chain amino acid aminotransferase IlvE and phenylalanine aminotransferase AroT in a strain engineered to overproduce anthranilate abolished biosynthesis of l-tryptophan and l-phenylalanine to accumulate phenylpyruvate. Upon heterologous expression of DpkAP262A,M141L, N-methylphenylalanine production resulted upon addition of monomethylamine to the medium. In glucose-based minimal medium, an N-methylphenylalanine titer of 0.73 ± 0.05 g L−1, a volumetric productivity of 0.01 g L−1 h−1 and a yield of 0.052 g g−1 glucose were reached. When xylose isomerase gene xylA from Xanthomonas campestris and the endogenous xylulokinase gene xylB were expressed in addition, xylose as sole carbon source supported production of N-methylphenylalanine to a titer of 0.6 ± 0.04 g L−1 with a volumetric productivity of 0.008 g L−1 h−1 and a yield of 0.05 g g−1 xylose. Thus, a fermentative route to sustainable production of N-methylphenylalanine by recombinant C. glutamicum has been established.
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Affiliation(s)
- Anastasia Kerbs
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, 33615 Bielefeld, Germany; (A.K.); (L.S.)
| | - Melanie Mindt
- BU Bioscience, Wagenigen University and Research, 6700AA Wageningen, The Netherlands;
| | - Lynn Schwardmann
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, 33615 Bielefeld, Germany; (A.K.); (L.S.)
| | - Volker F. Wendisch
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, 33615 Bielefeld, Germany; (A.K.); (L.S.)
- Correspondence: ; Tel.: +49-521-106-5611
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Abstract
Since the introduction of insulin almost a century ago, more than 80 peptide drugs have reached the market for a wide range of diseases, including diabetes, cancer, osteoporosis, multiple sclerosis, HIV infection and chronic pain. In this Perspective, we summarize key trends in peptide drug discovery and development, covering the early efforts focused on human hormones, elegant medicinal chemistry and rational design strategies, peptide drugs derived from nature, and major breakthroughs in molecular biology and peptide chemistry that continue to advance the field. We emphasize lessons from earlier approaches that are still relevant today as well as emerging strategies such as integrated venomics and peptide-display libraries that create new avenues for peptide drug discovery. We also discuss the pharmaceutical landscape in which peptide drugs could be particularly valuable and analyse the challenges that need to be addressed for them to reach their full potential.
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57
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Comeau C, Ries B, Stadelmann T, Tremblay J, Poulet S, Fröhlich U, Côté J, Boudreault PL, Derbali RM, Sarret P, Grandbois M, Leclair G, Riniker S, Marsault É. Modulation of the Passive Permeability of Semipeptidic Macrocycles: N- and C-Methylations Fine-Tune Conformation and Properties. J Med Chem 2021; 64:5365-5383. [PMID: 33750117 DOI: 10.1021/acs.jmedchem.0c02036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Incorporating small modifications to peptidic macrocycles can have a major influence on their properties. For instance, N-methylation has been shown to impact permeability. A better understanding of the relationship between permeability and structure is of key importance as peptidic drugs are often associated with unfavorable pharmacokinetic profiles. Starting from a semipeptidic macrocycle backbone composed of a tripeptide tethered head-to-tail with an alkyl linker, we investigated two small changes: peptide-to-peptoid substitution and various methyl placements on the nonpeptidic linker. Implementing these changes in parallel, we created a collection of 36 compounds. Their permeability was then assessed in parallel artificial membrane permeability assay (PAMPA) and Caco-2 assays. Our results show a systematic improvement in permeability associated with one peptoid position in the cycle, while the influence of methyl substitution varies on a case-by-case basis. Using a combination of molecular dynamics simulations and NMR measurements, we offer hypotheses to explain such behavior.
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Affiliation(s)
- Christian Comeau
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Quebec, Canada J1H5N4
| | - Benjamin Ries
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Thomas Stadelmann
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Jacob Tremblay
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Quebec, Canada J1H5N4
| | - Sylvain Poulet
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Quebec, Canada J1H5N4
| | - Ulrike Fröhlich
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Quebec, Canada J1H5N4
| | - Jérôme Côté
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Quebec, Canada J1H5N4
| | - Pierre-Luc Boudreault
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Quebec, Canada J1H5N4
| | - Rabeb Mouna Derbali
- Faculté de pharmacie, Université de Montréal, C.P. 6128, succursale Centre-ville, Montréal, Quebec, Canada H3C 3J7
| | - Philippe Sarret
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Quebec, Canada J1H5N4
| | - Michel Grandbois
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Quebec, Canada J1H5N4
| | - Grégoire Leclair
- Faculté de pharmacie, Université de Montréal, C.P. 6128, succursale Centre-ville, Montréal, Quebec, Canada H3C 3J7
| | - Sereina Riniker
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Éric Marsault
- Département de Pharmacologie-Physiologie, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Quebec, Canada J1H5N4
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58
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Brueckner AC, Deng Q, Cleves AE, Lesburg CA, Alvarez JC, Reibarkh MY, Sherer EC, Jain AN. Conformational Strain of Macrocyclic Peptides in Ligand-Receptor Complexes Based on Advanced Refinement of Bound-State Conformers. J Med Chem 2021; 64:3282-3298. [PMID: 33724820 DOI: 10.1021/acs.jmedchem.0c02159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Macrocyclic peptides are an important modality in drug discovery, but molecular design is limited due to the complexity of their conformational landscape. To better understand conformational propensities, global strain energies were estimated for 156 protein-macrocyclic peptide cocrystal structures. Unexpectedly large strain energies were observed when the bound-state conformations were modeled with positional restraints. Instead, low-energy conformer ensembles were generated using xGen that fit experimental X-ray electron density maps and gave reasonable strain energy estimates. The ensembles featured significant conformational adjustments while still fitting the electron density as well or better than the original coordinates. Strain estimates suggest the interaction energy in protein-ligand complexes can offset a greater amount of strain for macrocyclic peptides than for small molecules and non-peptidic macrocycles. Across all molecular classes, the approximate upper bound on global strain energies had the same relationship with molecular size, and bound-state ensembles from xGen yielded favorable binding energy estimates.
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Affiliation(s)
- Alexander C Brueckner
- Computational & Structural Chemistry, Merck & Co Inc, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Qiaolin Deng
- Computational & Structural Chemistry, Merck & Co Inc, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Ann E Cleves
- Bioengineering and Therapeutic Sciences, University of California San Francisco, Box 0128, San Francisco, California 94158, United States
| | - Charles A Lesburg
- Computational and Structural Chemistry, Merck and Co Inc, 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Juan C Alvarez
- Computational and Structural Chemistry, Merck and Co Inc, 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Mikhail Y Reibarkh
- Analytical Research and Development, Merck & Co Inc, 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Edward C Sherer
- Analytical Research and Development, Merck & Co Inc, 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Ajay N Jain
- Bioengineering and Therapeutic Sciences, University of California San Francisco, Box 0128, San Francisco, California 94158, United States
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Arancillo M, Taechalertpaisarn J, Liang X, Burgess K. Piptides: New, Easily Accessible Chemotypes For Interactions With Biomolecules. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Maritess Arancillo
- Department of Chemistry Texas A & M University Box 30012 College Station TX 77842 USA
| | | | - Xiaowen Liang
- Center for Infectious and Inflammatory Diseases Institute of Biosciences and Technology Texas A&M Health Science Center Houston TX 77030 USA
| | - Kevin Burgess
- Department of Chemistry Texas A & M University Box 30012 College Station TX 77842 USA
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60
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Arancillo M, Taechalertpaisarn J, Liang X, Burgess K. Piptides: New, Easily Accessible Chemotypes For Interactions With Biomolecules. Angew Chem Int Ed Engl 2021; 60:6653-6659. [PMID: 33319463 PMCID: PMC7940574 DOI: 10.1002/anie.202015203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/07/2020] [Indexed: 12/22/2022]
Abstract
Small molecule probe development is pivotal in biomolecular science. Research described here was undertaken to develop a non-peptidic chemotype, piptides, that is amenable to convenient, iterative solid-phase syntheses, and useful in biomolecular probe discovery. Piptides can be made from readily accessible pip acid building blocks and have good proteolytic and pH stabilities. An illustrative application of piptides against a protein-protein interaction (PPI) target was explored. The Exploring Key Orientations (EKO) strategy was used to evaluate piptide candidates for this. A library of only 14 piptides contained five members that disrupted epidermal growth factor (EGF) and its receptor, EGFR, at low micromolar concentrations. These piptides also caused apoptotic cell death, and antagonized EGF-induced phosphorylation of intracellular tyrosine residues in EGFR.
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Affiliation(s)
- Maritess Arancillo
- Department of Chemistry, Texas A & M University, Box 30012, College Station, TX, 77842, USA
| | - Jaru Taechalertpaisarn
- Department of Chemistry, Texas A & M University, Box 30012, College Station, TX, 77842, USA
| | - Xiaowen Liang
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, 77030, USA
| | - Kevin Burgess
- Department of Chemistry, Texas A & M University, Box 30012, College Station, TX, 77842, USA
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61
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Damjanovic J, Miao J, Huang H, Lin YS. Elucidating Solution Structures of Cyclic Peptides Using Molecular Dynamics Simulations. Chem Rev 2021; 121:2292-2324. [PMID: 33426882 DOI: 10.1021/acs.chemrev.0c01087] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein-protein interactions are vital to biological processes, but the shape and size of their interfaces make them hard to target using small molecules. Cyclic peptides have shown promise as protein-protein interaction modulators, as they can bind protein surfaces with high affinity and specificity. Dozens of cyclic peptides are already FDA approved, and many more are in various stages of development as immunosuppressants, antibiotics, antivirals, or anticancer drugs. However, most cyclic peptide drugs so far have been natural products or derivatives thereof, with de novo design having proven challenging. A key obstacle is structural characterization: cyclic peptides frequently adopt multiple conformations in solution, which are difficult to resolve using techniques like NMR spectroscopy. The lack of solution structural information prevents a thorough understanding of cyclic peptides' sequence-structure-function relationship. Here we review recent development and application of molecular dynamics simulations with enhanced sampling to studying the solution structures of cyclic peptides. We describe novel computational methods capable of sampling cyclic peptides' conformational space and provide examples of computational studies that relate peptides' sequence and structure to biological activity. We demonstrate that molecular dynamics simulations have grown from an explanatory technique to a full-fledged tool for systematic studies at the forefront of cyclic peptide therapeutic design.
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Affiliation(s)
- Jovan Damjanovic
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Jiayuan Miao
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - He Huang
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Yu-Shan Lin
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
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62
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Pursuing Orally Bioavailable Hepcidin Analogues via Cyclic N-Methylated Mini-Hepcidins. Biomedicines 2021; 9:biomedicines9020164. [PMID: 33567510 PMCID: PMC7915682 DOI: 10.3390/biomedicines9020164] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/20/2021] [Accepted: 02/02/2021] [Indexed: 11/20/2022] Open
Abstract
The peptide hormone hepcidin is one of the key regulators of iron absorption, plasma iron levels, and tissue iron distribution. Hepcidin functions by binding to and inducing the internalisation and subsequent lysosomal degradation of ferroportin, which reduces both iron absorption in the gut and export of iron from storage to ultimately decrease systemic iron levels. The key interaction motif in hepcidin has been localised to the highly conserved N-terminal region, comprising the first nine amino acid residues, and has led to the development of mini-hepcidin analogs that induce ferroportin internalisation and have improved drug-like properties. In this work, we have investigated the use of head-to-tail cyclisation and N-methylation of mini-hepcidin as a strategy to increase oral bioavailability by reducing proteolytic degradation and enhancing membrane permeability. We found that backbone cyclisation and N-methylation was well-tolerated in the mini-hepcidin analogues, with the macrocylic analogues often surpassing their linear counterparts in potency. Both macrocyclisation and backbone N-methylation were found to improve the stability of the mini-hepcidins, however, there was no effect on membrane-permeabilizing activity.
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63
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Cardoso P, Glossop H, Meikle TG, Aburto-Medina A, Conn CE, Sarojini V, Valery C. Molecular engineering of antimicrobial peptides: microbial targets, peptide motifs and translation opportunities. Biophys Rev 2021; 13:35-69. [PMID: 33495702 PMCID: PMC7817352 DOI: 10.1007/s12551-021-00784-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 01/07/2021] [Indexed: 02/07/2023] Open
Abstract
The global public health threat of antimicrobial resistance has led the scientific community to highly engage into research on alternative strategies to the traditional small molecule therapeutics. Here, we review one of the most popular alternatives amongst basic and applied research scientists, synthetic antimicrobial peptides. The ease of peptide chemical synthesis combined with emerging engineering principles and potent broad-spectrum activity, including against multidrug-resistant strains, has motivated intense scientific focus on these compounds for the past decade. This global effort has resulted in significant advances in our understanding of peptide antimicrobial activity at the molecular scale. Recent evidence of molecular targets other than the microbial lipid membrane, and efforts towards consensus antimicrobial peptide motifs, have supported the rise of molecular engineering approaches and design tools, including machine learning. Beyond molecular concepts, supramolecular chemistry has been lately added to the debate; and helped unravel the impact of peptide self-assembly on activity, including on biofilms and secondary targets, while providing new directions in pharmaceutical formulation through taking advantage of peptide self-assembled nanostructures. We argue that these basic research advances constitute a solid basis for promising industry translation of rationally designed synthetic peptide antimicrobials, not only as novel drugs against multidrug-resistant strains but also as components of emerging antimicrobial biomaterials. This perspective is supported by recent developments of innovative peptide-based and peptide-carrier nanobiomaterials that we also review.
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Affiliation(s)
- Priscila Cardoso
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia
- School of Science, RMIT University, Melbourne, Australia
| | - Hugh Glossop
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | | | | | | | | | - Celine Valery
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia
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64
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Sasikumar PG, Ramachandra M. Peptide and peptide-inspired checkpoint inhibitors: Protein fragments to cancer immunotherapy. MEDICINE IN DRUG DISCOVERY 2020. [DOI: 10.1016/j.medidd.2020.100073] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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65
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Talhami A, Swed A, Hess S, Ovadia O, Greenberg S, Schumacher-Klinger A, Rosenthal D, Shalev DE, Hurevich M, Lazarovici P, Hoffman A, Gilon C. Cyclizing Painkillers: Development of Backbone-Cyclic TAPS Analogs. Front Chem 2020; 8:532577. [PMID: 33282822 PMCID: PMC7689096 DOI: 10.3389/fchem.2020.532577] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 10/07/2020] [Indexed: 12/02/2022] Open
Abstract
Painkillers are commonly used medications. Native peptide painkillers suffer from various pharmacological disadvantages, while small molecule painkillers like morphine are highly addictive. We present a general approach aimed to use backbone-cyclization to develop a peptidomimetic painkiller. Backbone-cyclization was applied to transform the linear peptide Tyr-Arg-Phe-Sar (TAPS) into an active backbone-cyclic peptide with improved drug properties. We designed and synthesized a focused backbone-cyclic TAPS library with conformational diversity, in which the members of the library have the generic name TAPS c(n-m) where n and m represent the lengths of the alkyl chains on the nitrogens of Gly and Arg, respectively. We used a combined screening approach to evaluate the pharmacological properties and the potency of the TAPS c(n-m) library. We focused on an in vivo active compound, TAPS c(2-6), which is metabolically stable and has the potential to become a peripheral painkiller being a full μ opioid receptor functional agonist. To prepare a large quantity of TAPS c(2-6), we optimized the conditions of the on-resin reductive alkylation step to increase the efficiency of its SPPS. NMR was used to determine the solution conformation of the peptide lead TAPS c(2-6).
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Affiliation(s)
- Alaa Talhami
- Department of Organic Chemistry, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Avi Swed
- School of Pharmacy, Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shmuel Hess
- Meytav Technologies Incubator, Kiryat Shmona, Israel
| | - Oded Ovadia
- School of Pharmacy, Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sarit Greenberg
- School of Pharmacy, Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Adi Schumacher-Klinger
- School of Pharmacy, Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - David Rosenthal
- Department of Organic Chemistry, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Deborah E Shalev
- Department of Pharmaceutical Engineering, Azrieli College of Engineering Jerusalem, Jerusalem, Israel.,Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mattan Hurevich
- Department of Organic Chemistry, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Philip Lazarovici
- School of Pharmacy, Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amnon Hoffman
- School of Pharmacy, Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Chaim Gilon
- Department of Organic Chemistry, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
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66
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Buckton LK, Rahimi MN, McAlpine SR. Cyclic Peptides as Drugs for Intracellular Targets: The Next Frontier in Peptide Therapeutic Development. Chemistry 2020; 27:1487-1513. [PMID: 32875673 DOI: 10.1002/chem.201905385] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 08/26/2020] [Indexed: 12/18/2022]
Abstract
Developing macrocyclic peptides that can reach intracellular targets is a significant challenge. This review discusses the most recent strategies used to develop cell permeable cyclic peptides that maintain binding to their biological target inside the cell. Macrocyclic peptides are unique from small molecules because traditional calculated physical properties are unsuccessful for predicting cell membrane permeability. Peptide synthesis and experimental membrane permeability is the only strategy that effectively differentiates between cell permeable and cell impermeable molecules. Discussed are chemical strategies, including backbone N-methylation and stereochemical changes, which have produced molecular scaffolds with improved cell permeability. However, these improvements often come at the expense of biological activity as chemical modifications alter the peptide conformation, frequently impacting the compound's ability to bind to the target. Highlighted is the most promising approach, which involves side-chain alterations that improve cell permeability without impact binding events.
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Affiliation(s)
- Laura K Buckton
- Department of Chemistry, University of New South Wales, Sydney, Gate 2 High Street, SEB 701, Kensington, NSW, 2052, Australia
| | - Marwa N Rahimi
- Department of Chemistry, University of New South Wales, Sydney, Gate 2 High Street, SEB 701, Kensington, NSW, 2052, Australia
| | - Shelli R McAlpine
- Department of Chemistry, University of New South Wales, Sydney, Gate 2 High Street, SEB 701, Kensington, NSW, 2052, Australia
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67
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Salaverri N, Mas-Ballesté R, Marzo L, Alemán J. Visible light mediated photocatalytic [2 + 2] cycloaddition/ring-opening rearomatization cascade of electron-deficient azaarenes and vinylarenes. Commun Chem 2020; 3:132. [PMID: 36703325 PMCID: PMC9814732 DOI: 10.1038/s42004-020-00378-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 09/04/2020] [Indexed: 01/29/2023] Open
Abstract
The broad presence of azaarene moieties in natural products has promoted the development of new functionalization reactions, giving access to larger libraries of bioactive compounds. The light promoted [2 + 2] photocycloaddition reaction to generate cyclobutanes has been extensively studied in photochemistry. In particular, De Mayo reported the [2 + 2] cycloaddition followed by retroaldol condensation between enols of 1,3-dicarbonyls and double bonds to synthesize 1,5-dicarbonyls. Herein, we describe the [2 + 2] photocycloaddition followed by a ring-opening rearomatization reaction between electron-deficient 2-methylene-azaarenes and double bonds, taking advantage of the ability of these heterocyclic derivatives to form the corresponding pseudo-enamine intermediate. The procedure shows a high functional group tolerance either on the double bond or the heteroarene side and allows the presence of different electron-withdrawing groups. In addition, the wide applicability of this reaction has been demonstrated through the late-stage derivatization of several natural products. Photochemical studies, together with theoretical calculations, support a mechanism involving the photosensitization of the pseudo-enamine intermediate.
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Affiliation(s)
- Noelia Salaverri
- grid.5515.40000000119578126Organic Chemistry Department, Módulo 2, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Rubén Mas-Ballesté
- grid.5515.40000000119578126Inorganic Chemistry Department, Módulo 7, Universidad Autónoma de Madrid, 28049 Madrid, Spain ,grid.5515.40000000119578126Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Madrid, Spain
| | - Leyre Marzo
- grid.5515.40000000119578126Organic Chemistry Department, Módulo 2, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - José Alemán
- grid.5515.40000000119578126Organic Chemistry Department, Módulo 2, Universidad Autónoma de Madrid, 28049 Madrid, Spain ,grid.5515.40000000119578126Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Madrid, Spain
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68
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Xu F, Mejia EGD, Chen H, Rebecca K, Pan M, He R, Yao Y, Wang L, Ju X. Assessment of the DPP-IV inhibitory activity of a novel octapeptide derived from rapeseed using Caco-2 cell monolayers and molecular docking analysis. J Food Biochem 2020; 44:e13406. [PMID: 32734634 DOI: 10.1111/jfbc.13406] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/19/2020] [Accepted: 07/07/2020] [Indexed: 12/11/2022]
Abstract
The Octapeptide ELHQEEPL, which was identified from the rapeseed protein napin showed prominent Dipeptidyl peptidase-IV (DPP-IV) inhibitory activity. The objective of this study was to investigate the DPP-IV inhibitory activity and transepithelial transport of ELHQEEPL in an approaching intestinal condition using Caco-2 cell monolayers. ELHQEEPL and its degraded fragments EL, HQEEP, and methylated ELHQEEPL were transported across Caco-2 cell monolayers through different pathways. Compared with the nonbiological enzyme inhibition test, the in vitro experiment on Caco-2 cell monolayers showed that the IC50 value of DPP-IV inhibition increased by 43.11% for ELHQEEPL. There was no significant change in DPP-IV gene expression in the Caco-2 cell monolayers upon treatment with ELHQEEPL. Furthermore, molecular docking predicted that the weaker binding between inhibitory peptide and enzyme for the degradation products from ELHQEEPL during transepithelial transport greatly limited its role in inhibiting DPP-IV. PRACTICAL APPLICATIONS: The DPP-IV inhibitory activity of ELHQEEPL was confirmed using Caco-2 cell monolayers as a novel assessment tool, although its potency was reduced by metabolic degradation. In general, this study reported the use of Caco-2 cell monolayers as a tool for comprehensively studying peptides as sources of DPP-IV inhibitors. A Caco-2 cell-based approach with molecular docking can be adapted for the investigation of intestinal absorption and activity attenuation of food peptides being considered for enzymatic action. Moreover, since the Caco-2 cells express a wide range of enzymes, this method can be used for screening for other active food peptides such as for the inhibitors of ACE and a-glucosidase.
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Affiliation(s)
- Feiran Xu
- National Engineering Laboratory for Cereal Fermentation Technology, State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
- Department of Food Science and Human Nutrition, Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Elvira Gonzalez de Mejia
- Department of Food Science and Human Nutrition, Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Hong Chen
- Department of Food Science and Human Nutrition, Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Kowalski Rebecca
- Department of Food Science and Human Nutrition, Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Mengmeng Pan
- College of Food Science and Engineering, Collaborative Innovation Center for Modern Grain Circulation and Safety, Key Laboratory of Grains and Oils Quality Control and Processing, Nanjing University of Finance and Economics, Nanjing, People's Republic of China
| | - Rong He
- College of Food Science and Engineering, Collaborative Innovation Center for Modern Grain Circulation and Safety, Key Laboratory of Grains and Oils Quality Control and Processing, Nanjing University of Finance and Economics, Nanjing, People's Republic of China
| | - Yijun Yao
- National Engineering Laboratory for Cereal Fermentation Technology, State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
- College of Food Science and Engineering, Collaborative Innovation Center for Modern Grain Circulation and Safety, Key Laboratory of Grains and Oils Quality Control and Processing, Nanjing University of Finance and Economics, Nanjing, People's Republic of China
| | - Lifeng Wang
- College of Food Science and Engineering, Collaborative Innovation Center for Modern Grain Circulation and Safety, Key Laboratory of Grains and Oils Quality Control and Processing, Nanjing University of Finance and Economics, Nanjing, People's Republic of China
| | - Xingrong Ju
- National Engineering Laboratory for Cereal Fermentation Technology, State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China
- College of Food Science and Engineering, Collaborative Innovation Center for Modern Grain Circulation and Safety, Key Laboratory of Grains and Oils Quality Control and Processing, Nanjing University of Finance and Economics, Nanjing, People's Republic of China
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69
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Liu T, Zhu N, Zhong C, Zhu Y, Gou S, Chang L, Bao H, Liu H, Zhang Y, Ni J. Effect of N-methylated and fatty acid conjugation on analogs of antimicrobial peptide Anoplin. Eur J Pharm Sci 2020; 152:105453. [PMID: 32649983 DOI: 10.1016/j.ejps.2020.105453] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 06/15/2020] [Accepted: 07/02/2020] [Indexed: 12/20/2022]
Abstract
With the increment of drug-resistant bacteria and the slow development of novel antibiotics, antimicrobial peptides have gained increasing attention as a potential antibiotic alternative. They not only displayed a broad-spectrum antimicrobial activity but also were difficult to induce resistance development because of their unique membrane-lytic activity. Herein, to improve the limitations of Anoplin, the N-methyl amino acids were first used to replace the amino acids of Anoplin at sensitive enzymatic cleave sites (Leu, Ile, Lys and Arg). Afterward, the N-methylated analogs M3.6/M4.7/M5.7 with high stability were screened out and further modified by N-terminal fatty acid conjugation to develop new antimicrobial peptide analogs with both potent antimicrobial activity and high proteolytic stability, and 12 new Anoplin analogs Cn-M3.6/M4.7/M5.7 (n = 8,10,12,14) were designed and synthesized. Our results showed that compared with native Anoplin, the stability of these N-methylated lipopeptides against trypsin and chymotrypsin degradation were increased by 104-106 times. Besides, they still possessed potent antimicrobial activity under physiological salts and serum environment. Among them, the new designed analogs C12-M3.6/M4.7/M5.7 showed the optimal antimicrobial activity, synergy and additive effects were also observed when they were combined with traditional antibiotics polymyxin B, rifampin, and kanamycin. Moreover, they could effectively inhibit the formation of biofilms by P. aeruginosa and S. aureus. The antimicrobial mechanism studied revealed that these N-methylated lipopeptides could display a rapid bactericidal effect by destroying the bacterial cell membrane. Notably, no detectable resistance of these new designed peptides was developed after continuous cultured with E. coli for 20 passages. In summary, we have designed a new class of antimicrobial peptide analogs with potent antimicrobial activity and high proteolytic stability through N-methyl amino acids substitution and N-terminal fatty acid conjugation. This study also provides new ideas and methods for the modification of antimicrobial peptides in the future.
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Affiliation(s)
- Tianqi Liu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Ningyi Zhu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Chao Zhong
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China; Key Laboratory of Preclinical Study for New Drugs of Gansu Province School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yuewen Zhu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Sanhu Gou
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Linlin Chang
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China; Key Laboratory of Preclinical Study for New Drugs of Gansu Province School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Hexin Bao
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Hui Liu
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Yun Zhang
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Jingman Ni
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China; Key Laboratory of Preclinical Study for New Drugs of Gansu Province School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China.
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70
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Ding Y, Ting JP, Liu J, Al-Azzam S, Pandya P, Afshar S. Impact of non-proteinogenic amino acids in the discovery and development of peptide therapeutics. Amino Acids 2020; 52:1207-1226. [PMID: 32945974 PMCID: PMC7544725 DOI: 10.1007/s00726-020-02890-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 09/05/2020] [Indexed: 12/14/2022]
Abstract
With the development of modern chemistry and biology, non-proteinogenic amino acids (NPAAs) have become a powerful tool for developing peptide-based drug candidates. Drug-like properties of peptidic medicines, due to the smaller size and simpler structure compared to large proteins, can be changed fundamentally by introducing NPAAs in its sequence. While peptides composed of natural amino acids can be used as drug candidates, the majority have shown to be less stable in biological conditions. The impact of NPAA incorporation can be extremely beneficial in improving the stability, potency, permeability, and bioavailability of peptide-based therapies. Conversely, undesired effects such as toxicity or immunogenicity should also be considered. The impact of NPAAs in the development of peptide-based therapeutics is reviewed in this article. Further, numerous examples of peptides containing NPAAs are presented to highlight the ongoing development in peptide-based therapeutics.
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Affiliation(s)
- Yun Ding
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA
| | - Joey Paolo Ting
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA
| | - Jinsha Liu
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA
| | - Shams Al-Azzam
- Professional Scientific Services, Eurofins Lancaster Laboratories, Lancaster, PA, 17605, USA
| | - Priyanka Pandya
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA
| | - Sepideh Afshar
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA.
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71
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Jwad R, Weissberger D, Hunter L. Strategies for Fine-Tuning the Conformations of Cyclic Peptides. Chem Rev 2020; 120:9743-9789. [PMID: 32786420 DOI: 10.1021/acs.chemrev.0c00013] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cyclic peptides are promising scaffolds for drug development, attributable in part to their increased conformational order compared to linear peptides. However, when optimizing the target-binding or pharmacokinetic properties of cyclic peptides, it is frequently necessary to "fine-tune" their conformations, e.g., by imposing greater rigidity, by subtly altering certain side chain vectors, or by adjusting the global shape of the macrocycle. This review systematically examines the various types of structural modifications that can be made to cyclic peptides in order to achieve such conformational control.
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Affiliation(s)
- Rasha Jwad
- Department of Chemistry, College of Science, Al-Nahrain University, Baghdad, Iraq
| | - Daniel Weissberger
- School of Chemistry, University of New South Wales (UNSW) Sydney, New South Wales 2052, Australia
| | - Luke Hunter
- School of Chemistry, University of New South Wales (UNSW) Sydney, New South Wales 2052, Australia
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72
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Brayden D, Hill T, Fairlie D, Maher S, Mrsny R. Systemic delivery of peptides by the oral route: Formulation and medicinal chemistry approaches. Adv Drug Deliv Rev 2020; 157:2-36. [PMID: 32479930 DOI: 10.1016/j.addr.2020.05.007] [Citation(s) in RCA: 123] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 02/07/2023]
Abstract
In its 33 years, ADDR has published regularly on the po5tential of oral delivery of biologics especially peptides and proteins. In the intervening period, analysis of the preclinical and clinical trial failures of many purported platform technologies has led to reflection on the true status of the field and reigning in of expectations. Oral formulations of semaglutide, octreotide, and salmon calcitonin have completed Phase III trials, with oral semaglutide being approved by the FDA in 2019. The progress made with oral peptide formulations based on traditional permeation enhancers is against a background of low and variable oral bioavailability values of ~1%, leading to a current perception that only potent peptides with a viable cost of synthesis can be realistically considered. Desirable features of candidates should include a large therapeutic index, some stability in the GI tract, a long elimination half-life, and a relatively low clearance rate. Administration in nanoparticle formats have largely disappointed, with few prototypes reaching clinical trials: insufficient particle loading, lack of controlled release, low epithelial particle uptake, and lack of scalable synthesis being the main reasons for discontinuation. Disruptive technologies based on engineered devices promise improvements, but scale-up and toxicology aspects are issues to address. In parallel, medicinal chemists are synthesizing stable hydrophobic macrocyclic candidate peptides of lower molecular weight and with potential for greater oral bioavailability than linear peptides, but perhaps without the same requirement for elaborate drug delivery systems. In summary, while there have been advances in understanding the limitations of peptides for oral delivery, low membrane permeability, metabolism, and high clearance rates continue to hamper progress.
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73
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O'Reilly C, O'Sullivan Ó, Cotter PD, O'Connor PM, Shanahan F, Cullen A, Rea MC, Hill C, Coulter I, Ross RP. Encapsulated cyclosporine does not change the composition of the human microbiota when assessed ex vivo and in vivo. J Med Microbiol 2020; 69:854-863. [PMID: 31958048 DOI: 10.1099/jmm.0.001130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Introduction. Management of steroid-refractory ulcerative colitis has predominantly involved treatment with systemic cyclosporine A (CyA) and infliximab.Aim. The purpose of this study was to assess the effect of using a colon-targeted delivery system CyA formulation on the composition and functionality of the gut microbiota.Methodology. Ex vivo faecal fermentations from six healthy control subjects were treated with coated minispheres (SmPill) with (+) or without (-) CyA and compared with a non-treated control in a model colon system. In addition, the in vivo effect of the SmPill+CyA formulation was investigated by analysing the gut microbiota in faecal samples collected before the administration of SmPill+CyA and after 7 consecutive days of administration from eight healthy subjects who participated in a pilot study.Results. Analysis of faecal samples by 16S rRNA gene sequencing indicated little variation in the diversity or relative abundance of the microbiota composition before or after treatment with SmPill minispheres with or without CyA ex vivo or with CyA in vivo. Short-chain fatty acid profiles were evaluated using gas chromatography, showing an increase in the concentration of n-butyrate (P=0.02) and acetate (P=0.32) in the faecal fermented samples incubated in the presence of SmPill minispheres with or without CyA. This indicated that increased acetate and butyrate production was attributed to a component of the coated minispheres rather than an effect of CyA on the microbiota. Butyrate and acetate levels also increased significantly (P=0.05 for both) in the faecal samples of healthy individuals following 7 days' treatment with SmPill+CyA in the pilot study.Conclusion. SmPill minispheres with or without CyA at the clinically relevant doses tested here have negligible direct effects on the gut microbiota composition. Butyrate and acetate production increased, however, in the presence of the beads in an ex vivo model system as well as in vivo in healthy subjects. Importantly, this study also demonstrates the relevance and value of using ex vivo colon models to predict the in vivo impact of colon-targeted drugs directly on the gut microbiota.
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Affiliation(s)
- Catherine O'Reilly
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland.,APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Órla O'Sullivan
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Paul D Cotter
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Paula M O'Connor
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Fergus Shanahan
- School of Medicine, University College Cork, Cork, Ireland.,APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Alan Cullen
- Sublimity Therapeutics Holdco Limited (formerly known as Sigmoid Pharma Limited), DCU Alpha Innovation Campus, Old Finglas Road, Dublin, Ireland
| | - Mary C Rea
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Ivan Coulter
- Sublimity Therapeutics Holdco Limited (formerly known as Sigmoid Pharma Limited), DCU Alpha Innovation Campus, Old Finglas Road, Dublin, Ireland
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
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74
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Muhl C, Zengerling L, Groß J, Eckhardt P, Opatz T, Besenius P, Barz M. Insight into the synthesis of N-methylated polypeptides. Polym Chem 2020. [DOI: 10.1039/d0py01055c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The ring-opening polymerization of α-substituted N-methylated N-carboxy anhydrides is reported. The polymerization was tested using various amino acids and initiators, and was found to be limited by the steric demand of N-methylated compared to conventional amino acids.
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Affiliation(s)
- Christian Muhl
- Department of Chemistry
- Johannes Gutenberg University Mainz
- 55099 Mainz
- Germany
| | - Lydia Zengerling
- Department of Chemistry
- Johannes Gutenberg University Mainz
- 55099 Mainz
- Germany
| | - Jonathan Groß
- Department of Chemistry
- Johannes Gutenberg University Mainz
- 55099 Mainz
- Germany
| | - Paul Eckhardt
- Department of Chemistry
- Johannes Gutenberg University Mainz
- 55099 Mainz
- Germany
| | - Till Opatz
- Department of Chemistry
- Johannes Gutenberg University Mainz
- 55099 Mainz
- Germany
| | - Pol Besenius
- Department of Chemistry
- Johannes Gutenberg University Mainz
- 55099 Mainz
- Germany
| | - Matthias Barz
- Department of Chemistry
- Johannes Gutenberg University Mainz
- 55099 Mainz
- Germany
- Leiden Academic Center for Drug Research (LACDR)
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75
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Chen Y. Advances in the Synthesis of Methylated Products through Indirect Approaches. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201901240] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yantao Chen
- Medicinal Chemistry, Research and Early DevelopmentCardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca 43183 Gothenburg Sweden
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76
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Paul B, Maji M, Panja D, Kundu S. Tandem Transformation of Aldoximes to N‐Methylated Amides Using Methanol. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201900962] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Bhaskar Paul
- Department of ChemistryIndian Institute of Technology Kanpur Kanpur, Uttar Pradesh India
| | - Milan Maji
- Department of ChemistryIndian Institute of Technology Kanpur Kanpur, Uttar Pradesh India
| | - Dibyajyoti Panja
- Department of ChemistryIndian Institute of Technology Kanpur Kanpur, Uttar Pradesh India
| | - Sabuj Kundu
- Department of ChemistryIndian Institute of Technology Kanpur Kanpur, Uttar Pradesh India
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77
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Ibeji CU. Molecular dynamics and DFT study on the structure and dynamics of N-terminal domain HIV-1 capsid inhibitors. MOLECULAR SIMULATION 2019. [DOI: 10.1080/08927022.2019.1674850] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Collins U. Ibeji
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Department of Pure and Industrial Chemistry, University of Nigeria, Nsukka, Nigeria
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Jing X, Jin K. A gold mine for drug discovery: Strategies to develop cyclic peptides into therapies. Med Res Rev 2019; 40:753-810. [PMID: 31599007 DOI: 10.1002/med.21639] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/05/2019] [Accepted: 09/26/2019] [Indexed: 12/19/2022]
Abstract
As a versatile therapeutic modality, peptides attract much attention because of their great binding affinity, low toxicity, and the capability of targeting traditionally "undruggable" protein surfaces. However, the deficiency of cell permeability and metabolic stability always limits the success of in vitro bioactive peptides as drug candidates. Peptide macrocyclization is one of the most established strategies to overcome these limitations. Over the past decades, more than 40 cyclic peptide drugs have been clinically approved, the vast majority of which are derived from natural products. The de novo discovered cyclic peptides on the basis of rational design and in vitro evolution, have also enabled the binding with targets for which nature provides no solutions. The current review summarizes different classes of cyclic peptides with diverse biological activities, and presents an overview of various approaches to develop cyclic peptide-based drug candidates, drawing upon series of examples to illustrate each strategy.
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Affiliation(s)
- Xiaoshu Jing
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Kang Jin
- Department of Medicinal Chemistry, School of Pharmacy, Shandong University, Jinan, Shandong, China
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79
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Lupien LE, Dunkley EM, Maloy MJ, Lehner IB, Foisey MG, Ouellette ME, Lewis LD, Pooler DB, Kinlaw WB, Baures PW. An Inhibitor of Fatty Acid Synthase Thioesterase Domain with Improved Cytotoxicity against Breast Cancer Cells and Stability in Plasma. J Pharmacol Exp Ther 2019; 371:171-185. [PMID: 31300609 PMCID: PMC7184194 DOI: 10.1124/jpet.119.258947] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 07/01/2019] [Indexed: 12/12/2022] Open
Abstract
It is well recognized that many cancers are addicted to a constant supply of fatty acids (FAs) and exhibit brisk de novo FA synthesis. Upregulation of a key lipogenic enzyme, fatty acid synthase (FASN), is a near-universal feature of human cancers and their precursor lesions, and has been associated with chemoresistance, tumor metastasis, and diminished patient survival. FASN inhibition has been shown to be effective in killing cancer cells, but progress in the field has been hindered by off-target effects and poor pharmaceutical properties of candidate compounds. Our initial hit (compound 1) was identified from a high-throughput screening effort by the Sanford-Burnham Center for Chemical Genomics using purified FASN thioesterase (FASN-TE) domain. Despite being a potent inhibitor of purified FASN-TE, compound 1 proved highly unstable in mouse plasma and only weakly cytotoxic to breast cancer (BC) cells in vitro. An iterative process of synthesis, cytotoxicity testing, and plasma stability assessment was used to identify a new lead (compound 41). This lead is more cytotoxic against multiple BC cell lines than tetrahydro-4-methylene-2S-octyl-5-oxo-3R-furancarboxylic acid (the literature standard for inhibiting FASN), is stable in mouse plasma, and shows negligible cytotoxic effects against nontumorigenic mammary epithelial cells. Compound 41 also has drug-like physical properties based on Lipinski's rules and is, therefore, a valuable new lead for targeting fatty acid synthesis to exploit the requirement of tumor cells for fatty acids. SIGNIFICANCE STATEMENT: An iterative process of synthesis and biological testing was used to identify a novel thioesterase domain FASN inhibitor that has drug-like properties, is more cytotoxic to breast cancer cells than the widely used tetrahydro-4-methylene-2S-octyl-5-oxo-3R-furancarboxylic acid, and has negligible effects on the growth and proliferation of noncancerous mammary epithelial cells. Our studies have confirmed the value of using potent and selective FASN inhibitors in the treatment of BC cells and have shown that the availability of exogenous lipoproteins may impact both cancer cell FA metabolism and survival.
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Affiliation(s)
- Leslie E Lupien
- Division of Endocrinology and Metabolism, Department of Medicine, Norris Cotton Cancer Center (W.B.K.) and Section of Clinical Pharmacology & The Clinical Pharmacology Shared Resource (L.D.L., D.B.P.), The Geisel School of Medicine (L.E.L., W.B.K.), and Program in Experimental and Molecular Medicine, Dartmouth-Hitchcock Medical Center (L.E.L.), Dartmouth College, Lebanon, New Hampshire; and Department of Chemistry, Keene State College, Keene, New Hampshire (E.M.D., M.J.M., I.B.L., M.G.F., M.E.O., P.W.B.)
| | - Evan M Dunkley
- Division of Endocrinology and Metabolism, Department of Medicine, Norris Cotton Cancer Center (W.B.K.) and Section of Clinical Pharmacology & The Clinical Pharmacology Shared Resource (L.D.L., D.B.P.), The Geisel School of Medicine (L.E.L., W.B.K.), and Program in Experimental and Molecular Medicine, Dartmouth-Hitchcock Medical Center (L.E.L.), Dartmouth College, Lebanon, New Hampshire; and Department of Chemistry, Keene State College, Keene, New Hampshire (E.M.D., M.J.M., I.B.L., M.G.F., M.E.O., P.W.B.)
| | - Margaret J Maloy
- Division of Endocrinology and Metabolism, Department of Medicine, Norris Cotton Cancer Center (W.B.K.) and Section of Clinical Pharmacology & The Clinical Pharmacology Shared Resource (L.D.L., D.B.P.), The Geisel School of Medicine (L.E.L., W.B.K.), and Program in Experimental and Molecular Medicine, Dartmouth-Hitchcock Medical Center (L.E.L.), Dartmouth College, Lebanon, New Hampshire; and Department of Chemistry, Keene State College, Keene, New Hampshire (E.M.D., M.J.M., I.B.L., M.G.F., M.E.O., P.W.B.)
| | - Ian B Lehner
- Division of Endocrinology and Metabolism, Department of Medicine, Norris Cotton Cancer Center (W.B.K.) and Section of Clinical Pharmacology & The Clinical Pharmacology Shared Resource (L.D.L., D.B.P.), The Geisel School of Medicine (L.E.L., W.B.K.), and Program in Experimental and Molecular Medicine, Dartmouth-Hitchcock Medical Center (L.E.L.), Dartmouth College, Lebanon, New Hampshire; and Department of Chemistry, Keene State College, Keene, New Hampshire (E.M.D., M.J.M., I.B.L., M.G.F., M.E.O., P.W.B.)
| | - Maxwell G Foisey
- Division of Endocrinology and Metabolism, Department of Medicine, Norris Cotton Cancer Center (W.B.K.) and Section of Clinical Pharmacology & The Clinical Pharmacology Shared Resource (L.D.L., D.B.P.), The Geisel School of Medicine (L.E.L., W.B.K.), and Program in Experimental and Molecular Medicine, Dartmouth-Hitchcock Medical Center (L.E.L.), Dartmouth College, Lebanon, New Hampshire; and Department of Chemistry, Keene State College, Keene, New Hampshire (E.M.D., M.J.M., I.B.L., M.G.F., M.E.O., P.W.B.)
| | - Maddison E Ouellette
- Division of Endocrinology and Metabolism, Department of Medicine, Norris Cotton Cancer Center (W.B.K.) and Section of Clinical Pharmacology & The Clinical Pharmacology Shared Resource (L.D.L., D.B.P.), The Geisel School of Medicine (L.E.L., W.B.K.), and Program in Experimental and Molecular Medicine, Dartmouth-Hitchcock Medical Center (L.E.L.), Dartmouth College, Lebanon, New Hampshire; and Department of Chemistry, Keene State College, Keene, New Hampshire (E.M.D., M.J.M., I.B.L., M.G.F., M.E.O., P.W.B.)
| | - Lionel D Lewis
- Division of Endocrinology and Metabolism, Department of Medicine, Norris Cotton Cancer Center (W.B.K.) and Section of Clinical Pharmacology & The Clinical Pharmacology Shared Resource (L.D.L., D.B.P.), The Geisel School of Medicine (L.E.L., W.B.K.), and Program in Experimental and Molecular Medicine, Dartmouth-Hitchcock Medical Center (L.E.L.), Dartmouth College, Lebanon, New Hampshire; and Department of Chemistry, Keene State College, Keene, New Hampshire (E.M.D., M.J.M., I.B.L., M.G.F., M.E.O., P.W.B.)
| | - Darcy Bates Pooler
- Division of Endocrinology and Metabolism, Department of Medicine, Norris Cotton Cancer Center (W.B.K.) and Section of Clinical Pharmacology & The Clinical Pharmacology Shared Resource (L.D.L., D.B.P.), The Geisel School of Medicine (L.E.L., W.B.K.), and Program in Experimental and Molecular Medicine, Dartmouth-Hitchcock Medical Center (L.E.L.), Dartmouth College, Lebanon, New Hampshire; and Department of Chemistry, Keene State College, Keene, New Hampshire (E.M.D., M.J.M., I.B.L., M.G.F., M.E.O., P.W.B.)
| | - William B Kinlaw
- Division of Endocrinology and Metabolism, Department of Medicine, Norris Cotton Cancer Center (W.B.K.) and Section of Clinical Pharmacology & The Clinical Pharmacology Shared Resource (L.D.L., D.B.P.), The Geisel School of Medicine (L.E.L., W.B.K.), and Program in Experimental and Molecular Medicine, Dartmouth-Hitchcock Medical Center (L.E.L.), Dartmouth College, Lebanon, New Hampshire; and Department of Chemistry, Keene State College, Keene, New Hampshire (E.M.D., M.J.M., I.B.L., M.G.F., M.E.O., P.W.B.)
| | - Paul W Baures
- Division of Endocrinology and Metabolism, Department of Medicine, Norris Cotton Cancer Center (W.B.K.) and Section of Clinical Pharmacology & The Clinical Pharmacology Shared Resource (L.D.L., D.B.P.), The Geisel School of Medicine (L.E.L., W.B.K.), and Program in Experimental and Molecular Medicine, Dartmouth-Hitchcock Medical Center (L.E.L.), Dartmouth College, Lebanon, New Hampshire; and Department of Chemistry, Keene State College, Keene, New Hampshire (E.M.D., M.J.M., I.B.L., M.G.F., M.E.O., P.W.B.)
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Abstract
Approximately 75% of all disease-relevant human proteins, including those involved in intracellular protein-protein interactions (PPIs), are undruggable with the current drug modalities (i.e., small molecules and biologics). Macrocyclic peptides provide a potential solution to these undruggable targets because their larger sizes (relative to conventional small molecules) endow them the capability of binding to flat PPI interfaces with antibody-like affinity and specificity. Powerful combinatorial library technologies have been developed to routinely identify cyclic peptides as potent, specific inhibitors against proteins including PPI targets. However, with the exception of a very small set of sequences, the vast majority of cyclic peptides are impermeable to the cell membrane, preventing their application against intracellular targets. This Review examines common structural features that render most cyclic peptides membrane impermeable, as well as the unique features that allow the minority of sequences to enter the cell interior by passive diffusion, endocytosis/endosomal escape, or other mechanisms. We also present the current state of knowledge about the molecular mechanisms of cell penetration, the various strategies for designing cell-permeable, biologically active cyclic peptides against intracellular targets, and the assay methods available to quantify their cell-permeability.
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Affiliation(s)
- Patrick G. Dougherty
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, Ohio 43210, United States
| | - Ashweta Sahni
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, Ohio 43210, United States
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Avenue, Columbus, Ohio 43210, United States
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81
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The Entrapment of Somatostatin in a Lipid Formulation: Retarded Release and Free Radical Reactivity. Molecules 2019; 24:molecules24173085. [PMID: 31450691 PMCID: PMC6749267 DOI: 10.3390/molecules24173085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 08/19/2019] [Accepted: 08/22/2019] [Indexed: 11/25/2022] Open
Abstract
The natural peptide somatostatin has hormonal and cytostatic effects exerted by the binding to specific receptors in various tissues. Therapeutic uses are strongly prevented by its very short biological half-life of 1–2 min due to enzymatic hydrolysis, therefore encapsulation methodologies are explored to overcome the need for continuous infusion regimes. Multilamellar liposomes made of natural phosphatidylcholine were used for the incorporation of a mixture of somatostatin and sorbitol dissolved in citrate buffer at pH = 5. Lyophilization and reconstitution of the suspension were carried out, showing the flexibility of this preparation. Full characterization of this suspension was obtained as particle size, encapsulation efficiency and retarded release properties in aqueous medium and human plasma. Liposomal somatostatin incubated at 37 °C in the presence of Fe(II) and (III) salts were used as a biomimetic model of drug-cell membrane interaction, evidencing the free radical processes of peroxidation and isomerization that transform the unsaturated fatty acid moieties of the lipid vesicles. This study offers new insights into a liposomal delivery system and highlights molecular reactivity of sulfur-containing drugs with its carrier or biological membranes for pharmacological applications.
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82
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Sarojini V, Cameron AJ, Varnava KG, Denny WA, Sanjayan G. Cyclic Tetrapeptides from Nature and Design: A Review of Synthetic Methodologies, Structure, and Function. Chem Rev 2019; 119:10318-10359. [PMID: 31418274 DOI: 10.1021/acs.chemrev.8b00737] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Small cyclic peptides possess a wide range of biological properties and unique structures that make them attractive to scientists working in a range of areas from medicinal to materials chemistry. However, cyclic tetrapeptides (CTPs), which are important members of this family, are notoriously difficult to synthesize. Various synthetic methodologies have been developed that enable access to natural product CTPs and their rationally designed synthetic analogues having novel molecular structures. These methodologies include the use of reversible protecting groups such as pseudoprolines that restrict conformational freedom, ring contraction strategies, on-resin cyclization approaches, and optimization of coupling reagents and reaction conditions such as temperature and dilution factors. Several fundamental studies have documented the impacts of amino acid configurations, N-alkylation, and steric bulk on both synthetic success and ensuing conformations. Carefully executed retrosynthetic ring dissection and the unique structural features of the linear precursor sequences that result from the ring dissection are crucial for the success of the cyclization step. Other factors that influence the outcome of the cyclization step include reaction temperature, solvent, reagents used as well as dilution levels. The purpose of this review is to highlight the current state of affairs on naturally occurring and rationally designed cyclic tetrapeptides, including strategies investigated for their syntheses in the literature, the conformations adopted by these molecules, and specific examples of their function. Using selected examples from the literature, an in-depth discussion of the synthetic techniques and reaction parameters applied for the successful syntheses of 12-, 13-, and 14-membered natural product CTPs and their novel analogues are presented, with particular focus on the cyclization step. Selected examples of the three-dimensional structures of cyclic tetrapeptides studied by NMR, and X-ray crystallography are also included.
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Affiliation(s)
- Vijayalekshmi Sarojini
- School of Chemical Sciences and the Centre for Green Chemical Science , University of Auckland , Auckland 1142 , New Zealand.,The MacDiarmid Institute for Advanced Materials and Nanotechnology , Wellington 6140 , New Zealand
| | - Alan J Cameron
- School of Chemical Sciences and the Centre for Green Chemical Science , University of Auckland , Auckland 1142 , New Zealand
| | - Kyriakos G Varnava
- School of Chemical Sciences and the Centre for Green Chemical Science , University of Auckland , Auckland 1142 , New Zealand
| | | | - Gangadhar Sanjayan
- Division of Organic Chemistry , CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road , Pune 411 008 , India
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83
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Tsiamantas C, Kwon S, Douat C, Huc I, Suga H. Optimizing aromatic oligoamide foldamer side-chains for ribosomal translation initiation. Chem Commun (Camb) 2019; 55:7366-7369. [PMID: 31172994 DOI: 10.1039/c9cc03547h] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The tolerance of ribosomal peptide translation for helical aromatic oligoamide foldamers appended as initiators has been investigated. Small cationic foldamer side-chains were shown to expand the range of foldamer-peptide hybrids that can be produced by the ribosome to more rigid sequences.
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Affiliation(s)
- Christos Tsiamantas
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
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84
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Velkov T, Swarbrick JD, Hussein MH, Schneider-Futschik EK, Hoyer D, Li J, Karas JA. The impact of backbone N-methylation on the structure-activity relationship of Leu 10 -teixobactin. J Pept Sci 2019; 25:e3206. [PMID: 31389086 DOI: 10.1002/psc.3206] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/29/2019] [Accepted: 07/03/2019] [Indexed: 11/07/2022]
Abstract
Antimicrobial resistance is a serious threat to global human health; therefore, new anti-infective therapeutics are required. The cyclic depsi-peptide teixobactin exhibits potent antimicrobial activity against several Gram-positive pathogens. To study the natural product's mechanism of action and improve its pharmacological properties, efficient chemical methods for preparing teixobactin analogues are required to expedite structure-activity relationship studies. Described herein is a synthetic route that enables rapid access to analogues. Furthermore, our new N-methylated analogues highlight that hydrogen bonding along the N-terminal tail is likely to be important for antimicrobial activity.
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Affiliation(s)
- Tony Velkov
- Department of Pharmacology and Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - James D Swarbrick
- Department of Pharmacology and Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Maytham H Hussein
- Department of Pharmacology and Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Elena K Schneider-Futschik
- Department of Pharmacology and Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
- Lung Health Research Centre, Department of Pharmacology and Therapeutics, The University of Melbourne, Parkville, Victoria, Australia
| | - Daniel Hoyer
- Department of Pharmacology and Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, Australia
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California
| | - Jian Li
- Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - John A Karas
- Department of Pharmacology and Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
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85
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Liras S, Mcclure KF. Permeability of Cyclic Peptide Macrocycles and Cyclotides and Their Potential as Therapeutics. ACS Med Chem Lett 2019; 10:1026-1032. [PMID: 31312403 DOI: 10.1021/acsmedchemlett.9b00149] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/14/2019] [Indexed: 12/15/2022] Open
Abstract
Macrocycles have emerged as a viable approach for the modulation of tough targets in drug discovery. In this Innovations article we discuss recent progress toward the design of cell permeable and orally bioavailable peptide macrocycles and cyclotides and provide a perspective for their potential as therapeutics. We highlight design concepts that may be broadly relevant to drug discovery efforts beyond the rule of five.
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Affiliation(s)
- Spiros Liras
- Biogen Inc., 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Kim F. Mcclure
- Pinteon Therapeutics, 1188 Centre Street, Newton Centre, Massachusetts 02549, United States
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86
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Mindt M, Heuser M, Wendisch VF. Xylose as preferred substrate for sarcosine production by recombinant Corynebacterium glutamicum. BIORESOURCE TECHNOLOGY 2019; 281:135-142. [PMID: 30818264 DOI: 10.1016/j.biortech.2019.02.084] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/17/2019] [Accepted: 02/18/2019] [Indexed: 06/09/2023]
Abstract
The aim of this work was to study the fermentative production of the N-methylated amino acid sarcosine by C. glutamicum. Characterization of the imine reductase DpkA from Pseudomonas putida revealed that it catalyses N-methylamination of glyoxylate to sarcosine. Heterologous expression of dpkA in a C. glutamicum strain engineered for glyoxylate overproduction enabled fermentative production of sarcosine from sugars and monomethylamine. Glucose-based fermentation reached sarcosine production titers of 2.4 ± 0.1 g L-1. Sarcosine production based on the second generation feedstocks xylose and arabinose led to higher product titers of 2.7 ± 0.1 g L-1 and 3.4 ± 0.3 g L-1, respectively, than glucose-based production. Optimization of production conditions with xylose and potassium acetate blends increased sarcosine titers to 8.7 ± 0.2 g L-1 with a yield of 0.25 g g-1. This is the first example in which a C. glutamicum process using lignocellulosic pentoses is superior to glucose-based production.
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Affiliation(s)
- Melanie Mindt
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Maria Heuser
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany.
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87
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Saavedra CJ, Carro C, Hernández D, Boto A. Conversion of “Customizable Units” into N-Alkyl Amino Acids and Generation of N-Alkyl Peptides. J Org Chem 2019; 84:8392-8410. [DOI: 10.1021/acs.joc.9b00114] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Carlos J. Saavedra
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Spain
- BIOSIGMA, Antonio Domı́nguez Alfonso 16, 38003-Sta. Cruz de Tenerife, Tenerife, Spain
| | - Carmen Carro
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Spain
- BIOSIGMA, Antonio Domı́nguez Alfonso 16, 38003-Sta. Cruz de Tenerife, Tenerife, Spain
| | - Dácil Hernández
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Spain
| | - Alicia Boto
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Spain
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88
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Leroux M, Vorherr T, Lewis I, Schaefer M, Koch G, Karaghiosoff K, Knochel P. Late-Stage Functionalization of Peptides and Cyclopeptides Using Organozinc Reagents. Angew Chem Int Ed Engl 2019; 58:8231-8234. [PMID: 30946517 DOI: 10.1002/anie.201902454] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/01/2019] [Indexed: 12/26/2022]
Abstract
We report a new late-stage functionalization of small peptides and cyclopeptides relying on the Negishi cross-coupling of readily prepared iodotyrosine- or iodophenylalanine-containing peptides with aryl-, heteroaryl-, and alkylzinc pivalates or halides. In silico and in vitro determinations of membrane permeability parameters of the modified cyclopeptides showed that in most cases, the solubility was improved by the introduction of polar pyridyl units while the cell-membrane permeability was maintained.
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Affiliation(s)
- Marcel Leroux
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, Haus F, 81377, München, Germany
| | | | - Ian Lewis
- Novartis Pharma AG, 4002, Basel, Switzerland
| | | | - Guido Koch
- Novartis Pharma AG, 4002, Basel, Switzerland
| | - Konstantin Karaghiosoff
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, Haus F, 81377, München, Germany
| | - Paul Knochel
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, Haus F, 81377, München, Germany
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89
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Leroux M, Vorherr T, Lewis I, Schaefer M, Koch G, Karaghiosoff K, Knochel P. Spätphasenfunktionalisierung von Peptiden und Cyclopeptiden mithilfe von Organozinkreagenzien. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201902454] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Marcel Leroux
- Department Chemie Ludwig-Maximilians-Universität München Butenandtstraße 5–13, Haus F 81377 München Deutschland
| | | | - Ian Lewis
- Novartis Pharma AG 4002 Basel Schweiz
| | | | | | - Konstantin Karaghiosoff
- Department Chemie Ludwig-Maximilians-Universität München Butenandtstraße 5–13, Haus F 81377 München Deutschland
| | - Paul Knochel
- Department Chemie Ludwig-Maximilians-Universität München Butenandtstraße 5–13, Haus F 81377 München Deutschland
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90
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Deprey K, Becker L, Kritzer J, Plückthun A. Trapped! A Critical Evaluation of Methods for Measuring Total Cellular Uptake versus Cytosolic Localization. Bioconjug Chem 2019; 30:1006-1027. [PMID: 30882208 PMCID: PMC6527423 DOI: 10.1021/acs.bioconjchem.9b00112] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Biomolecules have many properties that make them promising for intracellular therapeutic applications, but delivery remains a key challenge because large biomolecules cannot easily enter the cytosol. Furthermore, quantification of total intracellular versus cytosolic concentrations remains demanding, and the determination of delivery efficiency is thus not straightforward. In this review, we discuss strategies for delivering biomolecules into the cytosol and briefly summarize the mechanisms of uptake for these systems. We then describe commonly used methods to measure total cellular uptake and, more selectively, cytosolic localization, and discuss the major advantages and drawbacks of each method. We critically evaluate methods of measuring "cell penetration" that do not adequately distinguish total cellular uptake and cytosolic localization, which often lead to inaccurate interpretations of a molecule's cytosolic localization. Finally, we summarize the properties and components of each method, including the main caveats of each, to allow for informed decisions about method selection for specific applications. When applied correctly and interpreted carefully, methods for quantifying cytosolic localization offer valuable insight into the bioactivity of biomolecules and potentially the prospects for their eventual development into therapeutics.
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Affiliation(s)
- Kirsten Deprey
- Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155, United States
| | - Lukas Becker
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Joshua Kritzer
- Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155, United States
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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91
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Rahimi MN, Foster HG, Farazi SN, Chapman R, McAlpine SR. Polymer mediated transport of the Hsp90 inhibitor LB76, a polar cyclic peptide, produces an Hsp90 cellular phenotype. Chem Commun (Camb) 2019; 55:4515-4518. [PMID: 30920570 DOI: 10.1039/c9cc00890j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
LB76 is a cyclic peptide that shows great promise as a selective heat shock protein 90 (Hsp90) inhibitor. However despite strong binding to and inhibition of Hsp90 in cell lysate its polar structure prevents it from crossing the cell membrane. We have developed a pH responsive polymer nanoparticle that effectively encapsulates LB76 from solution without need for purification. The nanoparticle releases the molecule upon crossing the cell membrane. Treatment of human colon cancer HCT116 cells with nanoparticles laden with LB76 produces the typical phenotype associated with Hsp90 inhibition, providing evidence of a therapeutically active payload.
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Affiliation(s)
- Marwa N Rahimi
- School of Chemistry, University of New South Wales, Gate 2 High street, Dalton 219, Sydney, Australia.
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92
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Lundy TA, Mori S, Garneau-Tsodikova S. Probing the limits of interrupted adenylation domains by engineering a trifunctional enzyme capable of adenylation, N-, and S-methylation. Org Biomol Chem 2019; 17:1169-1175. [PMID: 30644493 DOI: 10.1039/c8ob02996b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The adenylation (A) domains found in nonribosomal peptide synthetases (NRPSs) exhibit tremendous plasticity. Some A domains have been shown to display the ability to contain within them the catalytic portion of an auxiliary domain, most commonly that of a methyltransferase (M) enzyme. This unique feature of A domains interrupted by M domains allows them to possess bifunctionality, where they can both adenylate and methylate an amino acid substrate. Additionally, these types of inserted M domains are able to selectively carry out either backbone or side chain methylation of amino acids. Interruptions with M domains are naturally found to occur either between the a2-a3 or the a8-a9 of the ten conserved motifs of A domains. Herein, we set out to answer the following question: Can one A domain support two different M domain interruptions occurring in two different locations (a2-a3 and a8-a9) of the A domain and possess the ability to adenylate an amino acid and methylate it on both its side chain and backbone? To answer this question we added a backbone methylating M3S domain from TioS(A3aM3SA3b) between the a8-a9 region of a mono-interrupted A domain, TioN(AaMNAb), that already contained a side chain methylating MN domain between its a2-a3 region. We evaluated the di-interrupted A domain TioN(AMNAM3SA) with a series of radiometric and mass spectrometry assays and found that this engineered enzyme was indeed capable of all three activities. These findings show that production of an active trifunctional di-interrupted A domain is possible and represents an exciting new avenue for future nonribosomal peptide (NRP) derivatization.
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Affiliation(s)
- Taylor A Lundy
- University of Kentucky, Department of Pharmaceutical Sciences, College of Pharmacy, Lexington, KY 40536-0596, USA.
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93
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Vinogradov AA, Yin Y, Suga H. Macrocyclic Peptides as Drug Candidates: Recent Progress and Remaining Challenges. J Am Chem Soc 2019; 141:4167-4181. [PMID: 30768253 DOI: 10.1021/jacs.8b13178] [Citation(s) in RCA: 412] [Impact Index Per Article: 82.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Peptides as a therapeutic modality attract much attention due to their synthetic accessibility, high degree of specific binding, and the ability to target protein surfaces traditionally considered "undruggable". Unfortunately, at the same time, other pharmacological properties of a generic peptide, such as metabolic stability and cell permeability, are quite poor, which limits the success of de novo discovered biologically active peptides as drug candidates. Here, we review how macrocyclization as well as the incorporation of nonproteogenic amino acids and various conjugation strategies may be utilized to improve on these characteristics to create better drug candidates. We analyze recent progress and remaining challenges in improving individual pharmacological properties of bioactive peptides, and offer our opinion on interfacing these, often conflicting, considerations, to create balanced drug candidates as a potential way to make further progress in this area.
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Affiliation(s)
- Alexander A Vinogradov
- Department of Chemistry, Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-0033 , Japan
| | - Yizhen Yin
- 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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94
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Merlino F, Billard É, Yousif AM, Di Maro S, Brancaccio D, Abate L, Carotenuto A, Bellavita R, d'Emmanuele di Villa Bianca R, Santicioli P, Marinelli L, Novellino E, Hébert TE, Lubell WD, Chatenet D, Grieco P. Functional Selectivity Revealed by N-Methylation Scanning of Human Urotensin II and Related Peptides. J Med Chem 2019; 62:1455-1467. [PMID: 30615452 DOI: 10.1021/acs.jmedchem.8b01601] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In accordance with their common but also divergent physiological actions, human urotensin II (1) and urotensin II-related peptide (2) could stabilize specific urotensin II receptor (UTR) conformations, thereby activating different signaling pathways, a feature referred to as biased agonism or functional selectivity. Sequential N-methylation of the amides in the conserved core sequence of 1, 2, and fragment U-II4-11 (3) shed light on structural requirements involved in their functional selectivity. Thus, 18 N-methylated UTR ligands were synthesized and their biological profiles evaluated using in vitro competition binding assays, ex vivo rat aortic ring bioassays and BRET-based biosensor experiments. Biological activity diverged from that of the parent structures contingent on the location of amide methylation, indicating relevant hydrogen-bond interactions for the function of the endogenous peptides. Conformational analysis of selected N-methyl analogs indicated the importance of specific amide residues of 2 for the distinct pharmacology relative to 1 and 3.
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Affiliation(s)
- Francesco Merlino
- Department of Pharmacy , University of Naples "Federico II" , via D. Montesano 49 , Naples 80131 , Italy
| | - Étienne Billard
- INRS-Institut Armand-Frappier, Groupe de Recherche en Ingénierie des Peptides et en Pharmacothérapie (GRIPP) , Université du Québec , 531 Boulevard des Prairies , Ville de Laval , Québec H7V 1B7 , Canada
| | - Ali M Yousif
- Department of Pharmacy , University of Naples "Federico II" , via D. Montesano 49 , Naples 80131 , Italy
| | - Salvatore Di Maro
- Department of Pharmacy , University of Naples "Federico II" , via D. Montesano 49 , Naples 80131 , Italy
| | - Diego Brancaccio
- Department of Pharmacy , University of Naples "Federico II" , via D. Montesano 49 , Naples 80131 , Italy
| | - Luigi Abate
- Department of Pharmacy , University of Naples "Federico II" , via D. Montesano 49 , Naples 80131 , Italy
| | - Alfonso Carotenuto
- Department of Pharmacy , University of Naples "Federico II" , via D. Montesano 49 , Naples 80131 , Italy
| | - Rosa Bellavita
- Department of Pharmacy , University of Naples "Federico II" , via D. Montesano 49 , Naples 80131 , Italy
| | | | - Paolo Santicioli
- Department of Pharmacology , Menarini Ricerche , via Rismondo 12/A , Florence 50131 , Italy
| | - Luciana Marinelli
- Department of Pharmacy , University of Naples "Federico II" , via D. Montesano 49 , Naples 80131 , Italy
| | - Ettore Novellino
- Department of Pharmacy , University of Naples "Federico II" , via D. Montesano 49 , Naples 80131 , Italy
| | - Terence E Hébert
- Department of Pharmacology and Therapeutics , McGill University , Montréal , Québec H3A 1A3 , Canada
| | - William D Lubell
- Département de Chimie , Université de Montréal , C.P. 6128, Station Centre-ville , Montréal , Québec H3C 3J7 , Canada
| | - David Chatenet
- INRS-Institut Armand-Frappier, Groupe de Recherche en Ingénierie des Peptides et en Pharmacothérapie (GRIPP) , Université du Québec , 531 Boulevard des Prairies , Ville de Laval , Québec H7V 1B7 , Canada
| | - Paolo Grieco
- Department of Pharmacy , University of Naples "Federico II" , via D. Montesano 49 , Naples 80131 , Italy
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95
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Abstract
Macrocyclic peptides are a unique class of molecules that display a relatively constrained peptidic backbone as compared to their linear counterparts leading to the defined 3-D orientation of the constituent amino acids (pharmacophore). Although they are attractive candidates for lead discovery owing to the unique conformational features, their peptidic backbone is susceptible to proteolytic cleavage in various biological fluids that compromise their efficacy. In this chapter we review the various classical and contemporary chemical and biological approaches that have been utilized to combat the metabolic instability of macrocyclic peptides. We note that any chemical modification that helps in providing either local or global conformational rigidity to these macrocyclic peptides aids in improving their metabolic stability typically by slowing the cleavage kinetics by the proteases.
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Affiliation(s)
- Bhavesh Khatri
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | | | - Jayanta Chatterjee
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.
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96
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Tezgel Ö, Noinville S, Bennevault V, Illy N, Guégan P. An alternative approach to create N-substituted cyclic dipeptides. Polym Chem 2019. [DOI: 10.1039/c8py01552j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
N-Modified peptide backbones are promising peptidomimetics which offer several advantages in terms of improved biological activity and stability.
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Affiliation(s)
- Özgül Tezgel
- Sorbonne Université
- CNRS
- Institut Parisien de Chimie Moléculaire
- Equipe Chimie des Polymères
- F-75005 Paris
| | | | - Véronique Bennevault
- Sorbonne Université
- CNRS
- Institut Parisien de Chimie Moléculaire
- Equipe Chimie des Polymères
- F-75005 Paris
| | - Nicolas Illy
- Sorbonne Université
- CNRS
- Institut Parisien de Chimie Moléculaire
- Equipe Chimie des Polymères
- F-75005 Paris
| | - Philippe Guégan
- Sorbonne Université
- CNRS
- Institut Parisien de Chimie Moléculaire
- Equipe Chimie des Polymères
- F-75005 Paris
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97
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Abstract
This review describes a selection of macrocyclic natural products and structurally modified analogs containing peptidic and non-peptidic elements as structural features that potentially modulate cellular permeability. Examples range from exclusively peptidic structures like cyclosporin A or phepropeptins to compounds with mostly non-peptidic character, such as telomestatin or largazole. Furthermore, semisynthetic approaches and synthesis platforms to generate general and focused libraries of compounds at the interface of cyclic peptides and non-peptidic macrocycles are discussed.
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98
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Abstract
One of the most exciting facets of cyclic peptides is that they have the potential to be orally bioavailable, despite having physical properties well beyond the traditional "Rule-of-5" chemistry space (Lipinski et al., Adv Drug Deliv Rev. 23(1): 3-25, 1997). An important component of meeting this challenge is to design cyclic peptides with good intestinal permeability. Here we discuss the design principles for intestinal permeability that have been developed in recent year. These principles can be subdivided into three regimes: physical property guidelines, design strategies for the macrocyclic ring, and design strategies for side chains. The most important overall aims are to minimize solvent-exposed polarity while keeping size, flexibility, and lipophilicity within favorable ranges, thereby allowing peptide chemists to achieve intestinal permeability in addition to other important properties for their compounds, such as solubility and binding affinity. Here we describe a variety of design strategies that have been developed to help peptide chemists in this endeavor.
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99
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Kinsinger T, Kazmaier U. Mono-selective β-C–H arylation of N-methylated amino acids and peptides promoted by the 2-(methylthio)aniline directing group. Org Biomol Chem 2019; 17:5595-5600. [DOI: 10.1039/c9ob00966c] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
2-(Methylthio)aniline (MTA) directed C(sp3)–H functionalisations are efficient and straightforward protocols for the selective β-modification of N-methylated amino acids.
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Affiliation(s)
- Thorsten Kinsinger
- Institute of Organic Chemistry
- Saarland University
- 66041 Saarbrücken
- Germany
| | - Uli Kazmaier
- Institute of Organic Chemistry
- Saarland University
- 66041 Saarbrücken
- Germany
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100
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Duffy F, Maheshwari N, Buchete NV, Shields D. Computational Opportunities and Challenges in Finding Cyclic Peptide Modulators of Protein-Protein Interactions. Methods Mol Biol 2019; 2001:73-95. [PMID: 31134568 DOI: 10.1007/978-1-4939-9504-2_5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Peptide cyclization can improve stability, conformational constraint, and compactness. However, apart from beta-turn structures, which are well incorporated into cyclic peptides (CPs), many primary peptide structures and functions are markedly altered by cyclization. Accordingly, to mimic linear peptide interfaces with cyclic peptides, it can be beneficial to screen combinatorial cyclic peptide libraries. Computational methods have been developed to screen CPs, but face a number of challenges. Here, we review methods to develop in silico computational libraries, and the potential for screening naturally occurring libraries of CPs. The simplest and most rapid computational pharmacophore methods that estimate peptide three-dimensional structures to be screened versus targets are relatively easy to implement, and while the constraint on structure imposed by cyclization makes them more effective than the same approaches with linear peptides, there are a large number of limiting assumptions. In contrast, full molecular dynamics simulations of cyclic peptide structures not only are costly to implement, but also require careful attention to interpretation, so that not only is the computation time rate limiting, but the interpretation time is also rate limiting due to the analysis of the typically complex underlying conformational space of CPs. A challenge for the field of computational cyclic peptide screening is to bridge this gap effectively. Natural compound libraries of short cyclic peptides, and short cyclized regions of proteins, encoded in the genomes of many organisms present a potential treasure trove of novel functionality which may be screened via combined computational and experimental screening approaches.
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Affiliation(s)
- Fergal Duffy
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Nikunj Maheshwari
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | | | - Denis Shields
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland. .,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.
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