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Todorov P, Georgieva S, Trapella C, Chakarov K, Tchekalarova J, Pechlivanova D, Cheshmedzhieva D, Fantinati A, Illuminati D. Synthesis, characterization, and biological study of new synthetic opioid hemorphin-4 peptides containing sterically restricted nonnatural amino acids. Arch Pharm (Weinheim) 2024:e2400052. [PMID: 38578075 DOI: 10.1002/ardp.202400052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 02/25/2024] [Accepted: 02/29/2024] [Indexed: 04/06/2024]
Abstract
Some new hemorphin-4 analogs with structures of Xxx-Pro-Trp-Thr-NH2 and Tyr-Yyy-Trp-Thr-NH2, where Xxx is 2-amino-3-(4-hydroxy-2,6-dimethylphenyl)propanoic acid or 2-amino-3-(4-dibenzylamino-2,6-dimethylphenyl)propanoic acid, and Yyy is (2S,4S)-4-amino-pyrrolidine-2-carboxylic acid, were synthesized and characterized by electrochemical and spectral analyses. In vivo anticonvulsant and antinociceptive activities of peptide derivatives were studied after intracerebroventricular injection in mice. The therapeutic effects of the modified peptides on seizures and pain in mice were evaluated to provide valuable insights into the potential applications of the novel compounds. Electrochemical characterization showed that the compounds behave as weak protolytes and that they are in a soluble, stable molecular form at physiological pH values. The antioxidant activity of the peptides was evaluated with voltammetric analyses, which were confirmed by applying the 2,2-Diphenyl-1-picrylhydrazyl method. The compounds showed satisfactory results regarding their structural stability, reaching the desired centers for the manifestation of biological activity without hydrolysis processes at 37°C and physiological pH. Dm-H4 and H4-P1 exhibited 100% and 83% potency to suppress the psychomotor seizures in the 6-Hz test compared to 67% activity of H4. Notably, only the H4-P1 had efficacy in blocking the tonic component in the maximal electroshock test with a potency comparable to H4. All investigated peptides containing unnatural conformationally restricted amino acids showed antinociceptive effects. The analogs Db-H4 and H4-P1 showed the most pronounced and long-lasting effect in both experimental models of pain induced by thermal and chemical stimuli. Dm-H4 produced a dose-dependent thermal antinociception and H4-P2 inhibited only formalin-induced pain behavior.
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Affiliation(s)
- Petar Todorov
- Department of Organic Chemistry, University of Chemical Technology and Metallurgy, Sofia, Bulgaria
| | - Stela Georgieva
- Department of Analytical Chemistry, University of Chemical Technology and Metallurgy, Sofia, Bulgaria
| | - Claudio Trapella
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
| | - Kalin Chakarov
- Department of Organic Chemistry, University of Chemical Technology and Metallurgy, Sofia, Bulgaria
- Department of Analytical Chemistry, University of Chemical Technology and Metallurgy, Sofia, Bulgaria
| | - Jana Tchekalarova
- Institute of Neurobiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Daniela Pechlivanova
- Institute of Neurobiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
- Faculty of Medicine, Sofia University "St. Kliment Ohridski" 1, Sofia, Bulgaria
| | - Diana Cheshmedzhieva
- Faculty of Chemistry and Pharmacy, Sofia University "St. Kliment Ohridski", Sofia, Bulgaria
| | - Anna Fantinati
- Department of Environmental and Prevention Sciences, University of Ferrara, Ferrara, Italy
| | - Davide Illuminati
- Department of Life Science, University of Modena and Reggio Emilia, Modena, Italy
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Groff D, Carlos NA, Chen R, Hanson JA, Liang S, Armstrong S, Li X, Zhou S, Steiner A, Hallam TJ, Yin G. Development of an E. coli strain for cell-free ADC manufacturing. Biotechnol Bioeng 2021; 119:162-175. [PMID: 34655229 PMCID: PMC9297987 DOI: 10.1002/bit.27961] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/19/2021] [Accepted: 08/30/2021] [Indexed: 12/22/2022]
Abstract
Recent advances in cell‐free protein synthesis have enabled the folding and assembly of full‐length antibodies at high titers with extracts from prokaryotic cells. Coupled with the facile engineering of the Escherichia coli translation machinery, E. coli based in vitro protein synthesis reactions have emerged as a leading source of IgG molecules with nonnatural amino acids incorporated at specific locations for producing homogeneous antibody–drug conjugates (ADCs). While this has been demonstrated with extract produced in batch fermentation mode, continuous extract fermentation would facilitate supplying material for large‐scale manufacturing of protein therapeutics. To accomplish this, the IgG‐folding chaperones DsbC and FkpA, and orthogonal tRNA for nonnatural amino acid production were integrated onto the chromosome with high strength constitutive promoters. This enabled co‐expression of all three factors at a consistently high level in the extract strain for the duration of a 5‐day continuous fermentation. Cell‐free protein synthesis reactions with extract produced from cells grown continuously yielded titers of IgG containing nonnatural amino acids above those from extract produced in batch fermentations. In addition, the quality of the synthesized IgGs and the potency of ADC produced with continuously fermented extract were indistinguishable from those produced with the batch extract. These experiments demonstrate that continuous fermentation of E. coli to produce extract for cell‐free protein synthesis is feasible and helps unlock the potential for cell‐free protein synthesis as a platform for biopharmaceutical production.
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Affiliation(s)
- Dan Groff
- Sutro Biopharma, Inc., San Francisco, California, USA
| | - Nina A Carlos
- Sutro Biopharma, Inc., San Francisco, California, USA
| | - Rishard Chen
- Sutro Biopharma, Inc., San Francisco, California, USA
| | | | | | | | - Xiaofan Li
- Sutro Biopharma, Inc., San Francisco, California, USA
| | - Sihong Zhou
- Sutro Biopharma, Inc., San Francisco, California, USA
| | - Alex Steiner
- Sutro Biopharma, Inc., San Francisco, California, USA
| | | | - Gang Yin
- Sutro Biopharma, Inc., San Francisco, California, USA
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Li Z, Yu B. HFIP-Promoted de Novo Synthesis of Biologically Relevant Nonnatural α-Arylated Amino Esters and Dipeptide Mimetics. Chemistry 2019; 25:16528-16532. [PMID: 31617627 DOI: 10.1002/chem.201904395] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/15/2019] [Indexed: 01/24/2023]
Abstract
Amino acids are fundamental building blocks, which have been extensively used in drug design and organic synthesis. However, nonnatural amino acids are relatively less studied. In this work, the authors report the first HFIP-promoted de novo synthesis of nonnatural α-arylated amino esters and dipeptide mimetics (27 examples, up to 99 % yield) from readily available amines, ethyl glyoxylate and electron-rich arenes under mild conditions, in which one C-C bond, one C-N bond and one chiral center were established simultaneously. The reaction was also performed on a gram scale, giving compound 4 a in 96 % yield. In addition, this protocol was successfully applied to the late-stage elaboration of drug molecules, such as tranylcypromine (TCP or PCPA) and troxipide. Interestingly, compound 4 h inactivated histone lysine specific demethylase 1 (LSD1) potently with an IC50 value of 0.296 μm. To the best of our knowledge, compound 4 h is the first LSD1 inhibitor derived from nonnatural α-arylated amino esters, and therefore could be used as a hit compound for the development of new LSD1 inhibitors. The synthesized nonnatural α-arylated amino esters and dipeptide mimetics as unique building blocks may have potential synthetic utilities.
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Affiliation(s)
- Zhonghua Li
- Scientific Research Center & Laboratory Animal Center, Henan University of Chinese Medicine, 156 Jinshui East Road, 450046, Zhengzhou, Henan, P. R. China
| | - Bin Yu
- School of Pharmaceutical Sciences, Zhengzhou University, 100 Science Avenue, 450001, Zhengzhou, Henan, P. R. China.,State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210023, P. R. China
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Ruckthong L, Stuckey JA, Pecoraro VL. How Outer Coordination Sphere Modifications Can Impact Metal Structures in Proteins: A Crystallographic Evaluation. Chemistry 2019; 25:6773-6787. [PMID: 30861211 PMCID: PMC6510599 DOI: 10.1002/chem.201806040] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Indexed: 11/06/2022]
Abstract
A challenging objective of de novo metalloprotein design is to control of the outer coordination spheres of an active site to fine tune metal properties. The well-defined three stranded coiled coils, TRI and CoilSer peptides, are used to address this question. Substitution of Cys for Leu yields a thiophilic site within the core. Metals such as HgII , PbII , and AsIII result in trigonal planar or trigonal pyramidal geometries; however, spectroscopic studies have shown that CdII forms three-, four- or five-coordinate CdII S3 (OH2 )x (in which x=0-2) when the outer coordination spheres are perturbed. Unfortunately, there has been little crystallographic examination of these proteins to explain the observations. Here, the high-resolution X-ray structures of apo- and mercurated proteins are compared to explain the modifications that lead to metal coordination number and geometry variation. It reveals that Ala substitution for Leu opens a cavity above the Cys site allowing for water excess, facilitating CdII S3 (OH2 ). Replacement of Cys by Pen restricts thiol rotation, causing a shift in the metal-binding plane, which displaces water, forming CdII S3 . Residue d-Leu, above the Cys site, reorients the side chain towards the Cys layer, diminishing the space for water accommodation yielding CdII S3 , whereas d-Leu below opens more space, allowing for equal CdII S3 (OH2 ) and CdII S3 (OH2 )2 . These studies provide insights into how to control desired metal geometries in metalloproteins by using coded and non-coded amino acids.
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Affiliation(s)
- Leela Ruckthong
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Department of Chemistry, Faculty of Science, King Mongkut's University of Technology, Thonburi (KMUTT), Bang Mod, Thung Khru, Bangkok, 10140, Thailand
| | - Jeanne A Stuckey
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Vincent L Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
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Gubbens J, Kim SJ, Yang Z, Johnson AE, Skach WR. In vitro incorporation of nonnatural amino acids into protein using tRNA(Cys)-derived opal, ochre, and amber suppressor tRNAs. RNA 2010; 16:1660-72. [PMID: 20581130 PMCID: PMC2905763 DOI: 10.1261/rna.2024810] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Accepted: 05/12/2010] [Indexed: 05/25/2023]
Abstract
Amber suppressor tRNAs are widely used to incorporate nonnatural amino acids into proteins to serve as probes of structure, environment, and function. The utility of this approach would be greatly enhanced if multiple probes could be simultaneously incorporated at different locations in the same protein without other modifications. Toward this end, we have developed amber, opal, and ochre suppressor tRNAs derived from Escherichia coli, and yeast tRNA(Cys) that incorporate a chemically modified cysteine residue with high selectivity at the cognate UAG, UGA, and UAA stop codons in an in vitro translation system. These synthetic tRNAs were aminoacylated in vitro, and the labile aminoacyl bond was stabilized by covalently attaching a fluorescent dye to the cysteine sulfhydryl group. Readthrough efficiency (amber > opal > ochre) was substantially improved by eRF1/eRF3 inhibition with an RNA aptamer, thus overcoming an intrinsic hierarchy in stop codon selection that limits UGA and UAA termination suppression in higher eukaryotic translation systems. This approach now allows concurrent incorporation of two different modified amino acids at amber and opal codons with a combined apparent readthrough efficiency of up to 25% when compared with the parent protein lacking a stop codon. As such, it significantly expands the possibilities for incorporating nonnative amino acids for protein structure/function studies.
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Affiliation(s)
- Jacob Gubbens
- Department of Biochemistry and Molecular Biology, Oregon Health and Sciences University, Portland, OR 97231, USA
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Abstract
A shuttle system has been developed to genetically encode unnatural amino acids in mammalian cells using aminoacyl-tRNA synthetases (aaRSs) evolved in E. coli. A pyrrolysyl-tRNA synthetase (PylRS) mutant was evolved in E. coli that selectively aminoacylates a cognate nonsense suppressor tRNA with a photocaged lysine derivative. Transfer of this orthogonal tRNA-aaRS pair into mammalian cells made possible the selective incorporation of this unnatural amino acid into proteins.
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Affiliation(s)
- Peng R. Chen
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute 10550 Torry Pines Road, La Jolla, CA 92037 (USA)
| | - Dan Groff
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute 10550 Torry Pines Road, La Jolla, CA 92037 (USA)
| | - Jiantao Guo
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute 10550 Torry Pines Road, La Jolla, CA 92037 (USA)
| | - Weijia Ou
- Genomics Institute of the Novartis Research Foundation 10675 John Jay Hopkins Drive, San Diego, CA 92121 (USA)
| | - Susan Cellitti
- Genomics Institute of the Novartis Research Foundation 10675 John Jay Hopkins Drive, San Diego, CA 92121 (USA)
| | - Bernhard H. Geierstanger
- Genomics Institute of the Novartis Research Foundation 10675 John Jay Hopkins Drive, San Diego, CA 92121 (USA)
| | - Peter G. Schultz
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute 10550 Torry Pines Road, La Jolla, CA 92037 (USA)
- Genomics Institute of the Novartis Research Foundation 10675 John Jay Hopkins Drive, San Diego, CA 92121 (USA)
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