1
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Miura T, Lee KJ, Katoh T, Suga H. In Vitro Selection of Macrocyclic l-α/d-α/β/γ-Hybrid Peptides Targeting IFN-γ/IFNGR1 Protein-Protein Interaction. J Am Chem Soc 2024. [PMID: 38888290 DOI: 10.1021/jacs.4c01979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Nonproteinogenic amino acids, including d-α-, β-, and γ-amino acids, present in bioactive peptides play pivotal roles in their biochemical activities and proteolytic stabilities. d-α-Amino acids (dαAA) are widely used building blocks that can enhance the proteolytic stability. Cyclic β2,3-amino acids (cβAA), for instance, can fold peptides into rigid secondary structures, improving the binding affinity and proteolytic stability. Cyclic γ2,4-amino acids (cγAA) are recently highlighted as rigid residues capable of preventing the proteolysis of flanking residues. Simultaneous incorporation of all dαAA, cβAA, and cγAA into a peptide is expected to yield l-α/d-α/β/γ-hybrid peptides with improved stability and potency. Despite challenges in the ribosomal incorporation of multiple nonproteinogenic amino acids, our engineered tRNAPro1E2 successfully reaches such a difficulty. Here, we report the ribosomal synthesis of macrocyclic l-α/d-α/β/γ-hybrid peptide libraries and their application to in vitro selection against interferon gamma receptor 1 (IFNGR1). One of the resulting l-α/d-α/β/γ-hybrid peptides, IB1, exhibited remarkable inhibitory activity against the IFN-γ/IFNGR1 protein-protein interaction (PPI) (IC50 = 12 nM), primarily attributed to the presence of a cβAA in the sequence. Additionally, cγAAs and dαAAs in the resulting peptides contributed to their serum stability. Furthermore, our peptides effectively inhibit IFN-γ/IFNGR1 PPI at the cellular level (best IC50 = 0.75 μM). Altogether, our platform expands the chemical space available for exploring peptides with high activity and stability, thereby enhancing their potential for drug discovery.
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Affiliation(s)
- Takashi Miura
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kang Ju Lee
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayuki Katoh
- 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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2
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Xia T, Wu W, Wu X, Qu J, Chen Y. Cobalt-Catalyzed Enantioselective Reductive α-Chloro-Carbonyl Addition of Ketimine to Construct the β-Tertiary Amino Acid Analogues. Angew Chem Int Ed Engl 2024; 63:e202318991. [PMID: 38252658 DOI: 10.1002/anie.202318991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 01/24/2024]
Abstract
β-Tertiary amino acid derivatives constitute one of the most frequently occurring units in natural products and bioactive molecules. However, the efficient asymmetric synthesis of this motif still remains a significant challenge. Herein, we disclose a cobalt-catalyzed enantioselective reductive addition reaction of ketimine using α-chloro carbonyl compound as a radical precursor, providing expedient access to a diverse array of enantioenriched β-quaternary amino acid analogues. This protocol exhibits outstanding enantioselectivity and broad substrate scope with excellent functional group tolerance. Preliminary mechanism studies rule out the possibility of Reformatsky-type addition and confirm the involvement of radical species in stereoselective addition process. The synthetic utility has been demonstrated through the rapid assembly of iterative amino acid units and oligopeptide, showcasing its versatile platform for late-stage modification of drug candidates.
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Affiliation(s)
- Tingting Xia
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Wenwen Wu
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Xianqing Wu
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Jingping Qu
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Yifeng Chen
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
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3
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Lu L, Chen S, Kong W, Gao B, Li Y, Zhu L, Yin G. Enantioselective Synthesis of β-Aminoboronic Acids via Borylalkylation of Enamides. J Am Chem Soc 2024. [PMID: 38853359 DOI: 10.1021/jacs.4c03700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Aminoboronic acids represent a class of significant compounds that have attracted significant attention in the fields of drug discovery and organic synthesis. Despite notable progress in their synthesis, the efficient construction of chiral β-aminoboronic acids with alkyl side chains remains a challenging endeavor. Here, we introduce an unprecedented nickel-catalyzed asymmetric borylalkylation of enamides, employing a simple chiral diamine ligand, readily available B2pin2, and alkyl halides as coupling partners. This reaction serves as an efficient platform for assembling a diverse range of β-aminoboronic acid derivatives with flexible alkyl side chains, displaying exceptional regio-, stereo-, and enantioselectivities. Moreover, this transformation exhibits a broad substrate scope and remarkable tolerance toward various functional groups. Theoretical calculations demonstrate that the benzyl group on the ligand is the key to the high enantiocontrol in this transformation. Additionally, we exemplify the practical application of this strategy through the concise synthesis of complex bioactive molecules.
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Affiliation(s)
- Liguo Lu
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Shuhan Chen
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, Hubei Engineering University, Wuhan, Hubei 430072, P. R. China
| | - Weiyu Kong
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Ben Gao
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Yangyang Li
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Lei Zhu
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, Hubei Engineering University, Wuhan, Hubei 430072, P. R. China
| | - Guoyin Yin
- The Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 430072, P. R. China
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4
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Lyu X, Jung H, Kim D, Chang S. Enantioselective Access to β-Amino Carbonyls via Ni-Catalyzed Formal Olefin Hydroamidation. J Am Chem Soc 2024; 146:14745-14753. [PMID: 38742738 DOI: 10.1021/jacs.4c02497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
We herein describe a Ni-catalyzed formal hydroamidation of readily available α,β-unsaturated carbonyl compounds to afford valuable chiral β-amino acid derivatives (up to >99:1 e.r.) using dioxazolones as a robust amino source. A wide range of alkyl-substituted olefins conjugated to esters, amides, thioesters, and ketones were successfully amidated at the β-position with excellent enantioselectivity for the first time. Combined experimental and computational mechanistic studies supported our working hypothesis that this unconventional β-amidation of unsaturated carbonyl substrates can be attributed to the polar-matched migratory olefin insertion of an (amido)(Cl)NiII intermediate, in situ generated from the dioxazolone precursor.
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Affiliation(s)
- Xiang Lyu
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, South Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, South Korea
| | - Hoimin Jung
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, South Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, South Korea
| | - Dongwook Kim
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, South Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, South Korea
| | - Sukbok Chang
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, South Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, South Korea
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5
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Just D, Palivec V, Bártová K, Bednárová L, Pazderková M, Císařová I, Martinez-Seara H, Jahn U. Foldamers controlled by functional triamino acids: structural investigation of α/γ-hybrid oligopeptides. Commun Chem 2024; 7:114. [PMID: 38796536 PMCID: PMC11128005 DOI: 10.1038/s42004-024-01201-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 05/14/2024] [Indexed: 05/28/2024] Open
Abstract
Peptide-like foldamers controlled by normal amide backbone hydrogen bonding have been extensively studied, and their folding patterns largely rely on configurational and conformational constraints induced by the steric properties of backbone substituents at appropriate positions. In contrast, opportunities to influence peptide secondary structure by functional groups forming individual hydrogen bond networks have not received much attention. Here, peptide-like foldamers consisting of alternating α,β,γ-triamino acids 3-amino-4-(aminomethyl)-2-methylpyrrolidine-3-carboxylate (AAMP) and natural amino acids glycine and alanine are reported, which were obtained by solution phase peptide synthesis. They form ordered secondary structures, which are dominated by a three-dimensional bridged triazaspiranoid-like hydrogen bond network involving the non-backbone amino groups, the backbone amide hydrogen bonds, and the relative configuration of the α,β,γ-triamino and α-amino acid building blocks. This additional stabilization leads to folding in both nonpolar organic as well as in aqueous environments. The three-dimensional arrangement of the individual foldamers is supported by X-ray crystallography, NMR spectroscopy, chiroptical methods, and molecular dynamics simulations.
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Affiliation(s)
- David Just
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Vladimír Palivec
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Kateřina Bártová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Markéta Pazderková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Ivana Císařová
- Department of Inorganic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030/8, 12843, Prague 2, Czech Republic
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic.
| | - Ullrich Jahn
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic.
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6
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Sigal M, Matsumoto S, Beattie A, Katoh T, Suga H. Engineering tRNAs for the Ribosomal Translation of Non-proteinogenic Monomers. Chem Rev 2024; 124:6444-6500. [PMID: 38688034 PMCID: PMC11122139 DOI: 10.1021/acs.chemrev.3c00894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/21/2024] [Accepted: 04/10/2024] [Indexed: 05/02/2024]
Abstract
Ribosome-dependent protein biosynthesis is an essential cellular process mediated by transfer RNAs (tRNAs). Generally, ribosomally synthesized proteins are limited to the 22 proteinogenic amino acids (pAAs: 20 l-α-amino acids present in the standard genetic code, selenocysteine, and pyrrolysine). However, engineering tRNAs for the ribosomal incorporation of non-proteinogenic monomers (npMs) as building blocks has led to the creation of unique polypeptides with broad applications in cellular biology, material science, spectroscopy, and pharmaceuticals. Ribosomal polymerization of these engineered polypeptides presents a variety of challenges for biochemists, as translation efficiency and fidelity is often insufficient when employing npMs. In this Review, we will focus on the methodologies for engineering tRNAs to overcome these issues and explore recent advances both in vitro and in vivo. These efforts include increasing orthogonality, recruiting essential translation factors, and creation of expanded genetic codes. After our review on the biochemical optimizations of tRNAs, we provide examples of their use in genetic code manipulation, with a focus on the in vitro discovery of bioactive macrocyclic peptides containing npMs. Finally, an analysis of the current state of tRNA engineering is presented, along with existing challenges and future perspectives for the field.
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Affiliation(s)
- Maxwell Sigal
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Satomi Matsumoto
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Adam Beattie
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayuki Katoh
- 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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7
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Miura T, Malla TR, Brewitz L, Tumber A, Salah E, Lee KJ, Terasaka N, Owen CD, Strain-Damerell C, Lukacik P, Walsh MA, Kawamura A, Schofield CJ, Katoh T, Suga H. Cyclic β 2,3-amino acids improve the serum stability of macrocyclic peptide inhibitors targeting the SARS-CoV-2 main protease. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2024; 97:uoae018. [PMID: 38828441 PMCID: PMC11141402 DOI: 10.1093/bulcsj/uoae018] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/10/2024] [Accepted: 02/10/2024] [Indexed: 06/05/2024]
Abstract
Due to their constrained conformations, cyclic β2,3-amino acids (cβAA) are key building blocks that can fold peptides into compact and rigid structures, improving peptidase resistance and binding affinity to target proteins, due to their constrained conformations. Although the translation efficiency of cβAAs is generally low, our engineered tRNA, referred to as tRNAPro1E2, enabled efficient incorporation of cβAAs into peptide libraries using the flexible in vitro translation (FIT) system. Here we report on the design and application of a macrocyclic peptide library incorporating 3 kinds of cβAAs: (1R,2S)-2-aminocyclopentane carboxylic acid (β1), (1S,2S)-2-aminocyclohexane carboxylic acid (β2), and (1R,2R)-2-aminocyclopentane carboxylic acid. This library was applied to an in vitro selection against the SARS-CoV-2 main protease (Mpro). The resultant peptides, BM3 and BM7, bearing one β2 and two β1, exhibited potent inhibitory activities with IC50 values of 40 and 20 nM, respectively. BM3 and BM7 also showed remarkable serum stability with half-lives of 48 and >168 h, respectively. Notably, BM3A and BM7A, wherein the cβAAs were substituted with alanine, lost their inhibitory activities against Mpro and displayed substantially shorter serum half-lives. This observation underscores the significant contribution of cβAA to the activity and stability of peptides. Overall, our results highlight the potential of cβAA in generating potent and highly stable macrocyclic peptides with drug-like properties.
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Affiliation(s)
- Takashi Miura
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tika R Malla
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Lennart Brewitz
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Anthony Tumber
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Eidarus Salah
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Kang Ju Lee
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Naohiro Terasaka
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - C David Owen
- Harwell Science & Innovation Campus, Diamond Light Source, Didcot, Oxfordshire, OX11 0DE, United Kingdom
- Harwell Science & Innovation Campus, Research Complex at Harwell, Didcot, OX11 0FA, United Kingdom
| | - Claire Strain-Damerell
- Harwell Science & Innovation Campus, Diamond Light Source, Didcot, Oxfordshire, OX11 0DE, United Kingdom
- Harwell Science & Innovation Campus, Research Complex at Harwell, Didcot, OX11 0FA, United Kingdom
| | - Petra Lukacik
- Harwell Science & Innovation Campus, Diamond Light Source, Didcot, Oxfordshire, OX11 0DE, United Kingdom
- Harwell Science & Innovation Campus, Research Complex at Harwell, Didcot, OX11 0FA, United Kingdom
| | - Martin A Walsh
- Harwell Science & Innovation Campus, Diamond Light Source, Didcot, Oxfordshire, OX11 0DE, United Kingdom
- Harwell Science & Innovation Campus, Research Complex at Harwell, Didcot, OX11 0FA, United Kingdom
| | - Akane Kawamura
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
- Chemistry—School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Christopher J Schofield
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Takayuki Katoh
- 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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8
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Kovalenko V, Rudzińska-Szostak E, Ślepokura K, Berlicki Ł. Scalable Synthesis of All Stereoisomers of 2-Aminocyclopentanecarboxylic Acid─A Toolbox for Peptide Foldamer Chemistry. J Org Chem 2024; 89:4760-4767. [PMID: 38544408 PMCID: PMC11002926 DOI: 10.1021/acs.joc.3c02991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 03/07/2024] [Accepted: 03/15/2024] [Indexed: 04/06/2024]
Abstract
Although the construction of peptides with well-defined three-dimensional structures and predictable functions, including biological activity, using conformationally constrained β-amino acids has been shown to be a very successful strategy, their broad application is limited by access to the appropriate building blocks. In particular, trans- and cis-stereoisomers of 2-aminocyclopentanecarboxylic acid (ACPC) are of high interest. The scalable synthesis of all four stereoisomers of Fmoc derivatives of ACPC is presented with NMR-based analysis methods for their enantiomeric purity.
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Affiliation(s)
- Vitaly Kovalenko
- Department
of Bioorganic Chemistry, Wrocław University
of Science and Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Ewa Rudzińska-Szostak
- Department
of Bioorganic Chemistry, Wrocław University
of Science and Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Katarzyna Ślepokura
- Faculty
of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Łukasz Berlicki
- Department
of Bioorganic Chemistry, Wrocław University
of Science and Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
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9
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Katoh T, Suga H. Fine-tuning the tRNA anticodon arm for multiple/consecutive incorporations of β-amino acids and analogs. Nucleic Acids Res 2024:gkae219. [PMID: 38572748 DOI: 10.1093/nar/gkae219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/27/2024] [Accepted: 03/17/2024] [Indexed: 04/05/2024] Open
Abstract
Ribosomal incorporation of β-amino acids into nascent peptides is much less efficient than that of the canonical α-amino acids. To overcome this, we have engineered a tRNA chimera bearing T-stem of tRNAGlu and D-arm of tRNAPro1, referred to as tRNAPro1E2, which efficiently recruits EF-Tu and EF-P. Using tRNAPro1E2 indeed improved β-amino acid incorporation. However, multiple/consecutive incorporations of β-amino acids are still detrimentally poor. Here, we attempted fine-tuning of the anticodon arm of tRNAPro1E2 aiming at further enhancement of β-amino acid incorporation. By screening various mutations introduced into tRNAPro1E2, C31G39/C28G42 mutation showed an approximately 3-fold enhancement of two consecutive incorporation of β-homophenylglycine (βPhg) at CCG codons. The use of this tRNA made it possible for the first time to elongate up to ten consecutive βPhg's. Since the enhancement effect of anticodon arm mutations differs depending on the codon used for β-amino acid incorporation, we optimized anticodon arm sequences for five codons (CCG, CAU, CAG, ACU and UGG). Combination of the five optimal tRNAs for these codons made it possible to introduce five different kinds of β-amino acids and analogs simultaneously into model peptides, including a macrocyclic scaffold. This strategy would enable ribosomal synthesis of libraries of macrocyclic peptides containing multiple β-amino acids.
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Affiliation(s)
- Takayuki Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - 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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10
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Cramer J, Pero B, Jiang X, Bosko C, Silbermann M, Rabbani S, Wilke S, Nemli DD, Ernst B, Peczuh MW. Does size matter? - Comparing pyranoses with septanoses as ligands of the bacterial lectin FimH. Eur J Med Chem 2024; 268:116225. [PMID: 38367495 PMCID: PMC10964925 DOI: 10.1016/j.ejmech.2024.116225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 01/27/2024] [Accepted: 02/07/2024] [Indexed: 02/19/2024]
Abstract
The pharmacological modulation of disease-relevant carbohydrate-protein interactions represents an underexplored area of medicinal chemistry. One particular challenge in the design of glycomimetic compounds is the inherent instability of the glycosidic bond toward enzymatic cleavage. This problem has traditionally been approached by employing S-, N-, or C-glycosides with reduced susceptibility toward glycosidases. The application of ring-extended glycomimetics is an innovative approach to circumvent this issue. On the example of the bacterial adhesin FimH, it was explored how design principles from pyranose glycomimetics transfer to analogous septanose structures. A series of ring-extended FimH antagonists exhibiting the well-proven pharmacophore necessary for targeting the tyrosine-gate of FimH was synthesized. The resulting septanoses were evaluated for their affinity to the conformationally rigid isolated lectin domain of FimH (FimHLD), as well as a structurally flexible full-length FimH (FimHFL) construct. Some elements of potent mannoside-based FimH antagonists could be successfully transferred to septanose-based ligands, ultimately resulting in a 32-fold increase in binding affinity. Interestingly, the canonical ca. 100-fold loss of binding affinity between FimHLD and FimHFL is partly mitigated by the more flexible septanose antagonists, hinting at potentially differing interaction features of the flexible glycomimetics with intermediately populated states during the conformational transition of FimHFL.
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Affiliation(s)
- Jonathan Cramer
- Molecular Pharmacy Group, Department of Pharmaceutical Sciences, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland; Institute for Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Bryant Pero
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, U3060, Storrs, CT, 06269, USA
| | - Xiaohua Jiang
- Molecular Pharmacy Group, Department of Pharmaceutical Sciences, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Cristin Bosko
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, U3060, Storrs, CT, 06269, USA
| | - Marleen Silbermann
- Molecular Pharmacy Group, Department of Pharmaceutical Sciences, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Said Rabbani
- Molecular Pharmacy Group, Department of Pharmaceutical Sciences, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Sebastian Wilke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Dilara D Nemli
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Beat Ernst
- Molecular Pharmacy Group, Department of Pharmaceutical Sciences, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Mark W Peczuh
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, U3060, Storrs, CT, 06269, USA.
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11
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Patil MD, Ghosh KK, RajanBabu TV. Cobalt-Catalyzed Enantioselective Hydroboration of α-Substituted Acrylates. J Am Chem Soc 2024; 146:6604-6617. [PMID: 38431968 DOI: 10.1021/jacs.3c12020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2024]
Abstract
Even though metal-catalyzed enantioselective hydroborations of alkenes have attracted enormous attention, few preparatively useful reactions of α-alkyl acrylic acid derivatives are known, and most use rhodium catalysts. No examples of asymmetric hydroboration of the corresponding α-arylacrylic acid esters are known. In our continuing efforts to search for new applications of earth-abundant cobalt catalysts for broadly applicable organic transformations, we have identified 2-(2-diarylphosphinophenyl)oxazoline ligands and mild reaction conditions for efficient and highly regio- and enantioselective hydroboration of α-alkyl- and α-aryl- acrylates, giving β-borylated propionates. Since the C-B bonds in these compounds can be readily replaced by C-O, C-N, and C-C bonds, these intermediates could serve as valuable chiral synthons, some from feedstock carbon sources, for the synthesis of propionate-bearing motifs including polyketides and related molecules. Two-step syntheses of "Roche" ester from methyl methacrylate (79%; er 99:1), arguably the most widely used chiral fragment in polyketide synthesis, and tropic acid esters (∼80% yield; er ∼93:7), which are potential intermediates for several medicinally important classes of compounds, illustrate the power of the new methods. Mechanistic studies confirm the requirement of a cationic Co(I) species [(L)Co]+as the viable catalyst in these reactions and rule out the possibility of a [L]Co-H-initiated route, which has been well-established in related hydroborations of other classes of alkenes. A mechanism involving an oxidative migration of a boryl group to the β-carbon of an η4-coordinated acrylate-cobalt complex is proposed as a plausible route.
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Affiliation(s)
- Manoj D Patil
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States
| | - Kiron Kumar Ghosh
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States
| | - T V RajanBabu
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States
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12
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Pavlovic B, Heubel C, Kurz M, Oehl E, Waldvogel SR, Méndez M, Ruf S. Single step synthesis of β- and γ- aryl-substituted ß- and γ-amino acid derivatives by electrochemistry. Bioorg Med Chem Lett 2024; 100:129614. [PMID: 38199329 DOI: 10.1016/j.bmcl.2024.129614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/18/2023] [Accepted: 01/06/2024] [Indexed: 01/12/2024]
Abstract
Electrochemical transformations are a subject of increasing interest in early drug discovery due to its ability to assemble complex scaffolds under rather mild reaction conditions. In this context, we became interested in electrochemical decarboxylative cross-coupling (DCC) protocols of redox-active esters (RAEs) and halo(hetero)arenes. Starting with the one-step electrochemical synthesis of novel methylamino-substituted heterocycles we recognized the potential of this methodology to deliver a novel approach to β- and γ- amino acids by starting from the corresponding RAEs. Our work finally resulted in the delivery of novel and highly valuable trifunctional building blocks based on ß- and γ-amino-acid scaffolds.
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13
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De Franceschi I, Badi N, Du Prez FE. Telechelic sequence-defined oligoamides: their step-economical synthesis, depolymerization and use in polymer networks. Chem Sci 2024; 15:2805-2816. [PMID: 38404375 PMCID: PMC10882489 DOI: 10.1039/d3sc04820a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 01/13/2024] [Indexed: 02/27/2024] Open
Abstract
The application of sequence-defined macromolecules in material science remains largely unexplored due to their challenging, low yielding and time-consuming synthesis. This work first describes a step-economical method for synthesizing unnatural sequence-defined oligoamides through fluorenylmethyloxycarbonyl chemistry. The use of a monodisperse soluble support enables homogeneous reactions at elevated temperature (up to 65 °C), leading to rapid coupling times (<10 min) and improved synthesis protocols. Moreover, a one-pot procedure for the two involved iterative steps is demonstrated via an intermediate quenching step, eliminating the need for in-between purification. The protocol is optimized using γ-aminobutyric acid (GABA) as initial amino acid, and the unique ability of the resulting oligomers to depolymerize, with the formation of cyclic γ-butyrolactame, is evidenced. Furthermore, in order to demonstrate the versatility of the present protocol, a library of 17 unnatural amino acid monomers is synthesized, starting from the readily available GABA-derivative 4-amino-2-hydroxybutanoic acid, and then used to create multifunctional tetramers. Notably, the obtained tetramers show higher thermal stability than a similar thiolactone-based sequence-defined macromolecule, which enables its exploration within a material context. To that end, a bidirectional growth approach is proposed as a greener alternative that reduces the number of synthetic steps to obtain telechelic sequence-defined oligoamides. The latter are finally used as macromers for the preparation of polymer networks. We expect this strategy to pave the way for the further exploration of sequence-defined macromolecules in material science.
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Affiliation(s)
- Irene De Franceschi
- Polymer Chemistry Research Group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University 9000 Ghent Belgium
| | - Nezha Badi
- Polymer Chemistry Research Group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University 9000 Ghent Belgium
| | - Filip E Du Prez
- Polymer Chemistry Research Group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University 9000 Ghent Belgium
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14
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Ahmed N, Asif S, Arfan M, Mahmood Q, Islam A, Gatasheh MK, Zia M. Synthesis and Characterization of Short α and β-Mixed Peptides with Excellent Anti-Lipase Activities. Molecules 2024; 29:765. [PMID: 38398517 PMCID: PMC10892623 DOI: 10.3390/molecules29040765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 02/25/2024] Open
Abstract
Obesity is a source of significant pathologies and deadly diseases, including heart disease, diabetes, and cancer. One of the most intriguing strategies in the hunt for new anti-obesity medications is the inhibition of pancreatic lipase (PL). This study presents a novel application of short α and β-mixed peptides as pancreatic lipase inhibitors. These peptides were synthesized in the solution phase and characterized using FTIR and 1H-NMR. L-proline is present in a high percentage of natural anti-lipase peptides and was used as a β-amino acid in this study to enhance anti-lipase activity and proteolytic stability. Moreover, L-α-proline was converted to β-amino acid derivatives using the Arndt-Eistert method with the advantage of stereo control at the α-carbon. The synthesized peptides with anti-lipase activity are N-Boc-β-Pro-Gly-OBz (93%), N-Boc-O-Bz-Tyr-β-Pro-β-Pro-Gly-OBz (92%), N-Boc-O-Bz-Tyr-β-Pro-COOH (91%), N-Boc-Phe-β-Pro-OCH3 (90%), and N-Boc-O-Bz-Tyr-β-Pro-OCH3 (89%). These peptides may function as lead molecules for further modification to more significant molecules, which can help control obesity.
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Grants
- RSP2024R393 King Saud University
- 9ebfe58b5d63cfdf,0fc4036025155e1a,3a852f3e85a2433b,ffc04817768e29d8,1eae9545a3244bed,db5d8742b53a782c,fc9of098bf237c77,8ce5883758852285 Qaiser Mahmood
- 0bb1baa309ebdbb0,6a5aa5d7ed313e53,61843063f3444df7,58875d947b81e726,615b239e803be0b0,45e50be7ef0245f1,c5d9a4fe383b609e,0ceab0ce3ca2061e Amjad Islam
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Affiliation(s)
- Naeem Ahmed
- Department of Chemistry, School of Natural Sciences, National University of Sciences and Technology, Islamabad 44000, Pakistan;
| | - Sabahat Asif
- Department of Chemistry and Chemical Engineering, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences (LUMS), Lahore 54792, Pakistan;
| | - Muhammad Arfan
- Department of Chemistry, School of Natural Sciences, National University of Sciences and Technology, Islamabad 44000, Pakistan;
| | - Qaiser Mahmood
- Chemistry and Chemical Engineering Guangdong Laboratory, Shantou 515031, China;
| | - Amjad Islam
- Key Laboratory for Preparation and Application of Ordered Structured Materials of Guangdong Province, College of Chemistry and Chemical Engineering, Shantou University, Shantou 515063, China;
| | - Mansour K. Gatasheh
- Department of Biochemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia;
| | - Muhammad Zia
- Department of Biotechnology, Quaid-i-Azam University, Islamabad 45320, Pakistan;
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15
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Anwar K, Capaldo L, Wan T, Noël T, Gómez-Suárez A. Modular synthesis of congested β 2,2-amino acids via the merger of photocatalysis and oxidative functionalisations. Chem Commun (Camb) 2024; 60:1456-1459. [PMID: 38223935 DOI: 10.1039/d3cc06172h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
A two-step protocol for the modular synthesis of β2- and α-quaternary β2,2-amino acid derivatives is reported. The key steps are a photocatalytic hydroalkylation reaction, followed by an oxidative functionalisation to access N-protected β-amino acids, esters, and amides. This strategy can be effectively scaled up via continuous-flow technology.
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Affiliation(s)
- Khadijah Anwar
- Organic Chemistry, Bergische Universität Wuppertal, Gaußstr. 20, 42119, Wuppertal, Germany.
| | - Luca Capaldo
- Flow Chemistry Group, Van't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, Amsterdam 1098 XH, The Netherlands
| | - Ting Wan
- Flow Chemistry Group, Van't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, Amsterdam 1098 XH, The Netherlands
| | - Timothy Noël
- Flow Chemistry Group, Van't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, Amsterdam 1098 XH, The Netherlands
| | - Adrián Gómez-Suárez
- Organic Chemistry, Bergische Universität Wuppertal, Gaußstr. 20, 42119, Wuppertal, Germany.
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16
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Qin Y, Wang Y, Deng R, Pei Z, Xiong HY, Wang T, Zhang G. Straightforward Access to Free β 2,3,3 -Amino Acids through One Pot C-H Activation/C-C Cleavage. Chemistry 2024:e202304254. [PMID: 38236073 DOI: 10.1002/chem.202304254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 01/19/2024]
Abstract
The first synthesis of unnatural β2,3,3 -amino acids with a spirocyclic backbone by one-pot protocol has been presented. This reaction features wide functional group tolerance and feasibility of post-functionalization of natural products and biologically important molecules. Novel dipeptide and tripeptide structures were assembled using this newly developed β2,3,3 -amino acid in high efficiency. The combination of C-H activation and C-C cleavage for the synthesis of β-amino acids would trigger more promising synthetic routes for this compound.
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Affiliation(s)
- Yibo Qin
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng, 475004, P.R. China
| | - Yaping Wang
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng, 475004, P.R. China
| | - Ruwendan Deng
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng, 475004, P.R. China
| | - Zengkai Pei
- Tianjin Kailiqi Biopharma Technology Co., Ltd, Tianjin, 300190, P.R. China
| | - Heng-Ying Xiong
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng, 475004, P.R. China
| | - Teng Wang
- College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Guangwu Zhang
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng, 475004, P.R. China
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17
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Li C, Jin K. Chemical Strategies towards the Development of Effective Anticancer Peptides. Curr Med Chem 2024; 31:1839-1873. [PMID: 37170992 DOI: 10.2174/0929867330666230426111157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/28/2023] [Accepted: 02/24/2023] [Indexed: 05/13/2023]
Abstract
Cancer is increasingly recognized as one of the primary causes of death and has become a multifaceted global health issue. Modern medical science has made significant advancements in the diagnosis and therapy of cancer over the past decade. The detrimental side effects, lack of efficacy, and multidrug resistance of conventional cancer therapies have created an urgent need for novel anticancer therapeutics or treatments with low cytotoxicity and drug resistance. The pharmaceutical groups have recognized the crucial role that peptide therapeutic agents can play in addressing unsatisfied healthcare demands and how these become great supplements or even preferable alternatives to biological therapies and small molecules. Anticancer peptides, as a vibrant therapeutic strategy against various cancer cells, have demonstrated incredible anticancer potential due to high specificity and selectivity, low toxicity, and the ability to target the surface of traditional "undruggable" proteins. This review will provide the research progression of anticancer peptides, mainly focusing on the discovery and modifications along with the optimization and application of these peptides in clinical practice.
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Affiliation(s)
- Cuicui Li
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmacy, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Kang Jin
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmacy, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
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18
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Jaber S, Nemska V, Iliev I, Ivanova E, Foteva T, Georgieva N, Givechev I, Tanev D, Naydenova E, Danalev D. Synthesis, antiproliferative and antimicrobial activities of (KLAKLAK) 2-NH 2 analogue containing nor-Leu and its conjugates with a second pharmacophore. BIOTECHNOL BIOTEC EQ 2023. [DOI: 10.1080/13102818.2022.2162965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Sirine Jaber
- Department of Biotechnology, Faculty of Chemical and System Engineering, University of Chemical Technology and Metallurgy, Sofia, Bulgaria
| | - Veronica Nemska
- Department of Biotechnology, Faculty of Chemical and System Engineering, University of Chemical Technology and Metallurgy, Sofia, Bulgaria
| | - Ivan Iliev
- Department of Pathology, Institute of Experimental Morphology, Pathology and Anthropology with Museum, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Elena Ivanova
- Department of Pathology, Institute of Experimental Morphology, Pathology and Anthropology with Museum, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Tsvetelina Foteva
- Department of Biotechnology, Faculty of Chemical and System Engineering, University of Chemical Technology and Metallurgy, Sofia, Bulgaria
| | - Nelly Georgieva
- Department of Biotechnology, Faculty of Chemical and System Engineering, University of Chemical Technology and Metallurgy, Sofia, Bulgaria
| | | | | | - Emilia Naydenova
- Department of Organic Chemistry, Faculty of Chemical Technologies, University of Chemical Technology and Metallurgy, Sofia, Bulgaria
| | - Dancho Danalev
- Department of Biotechnology, Faculty of Chemical and System Engineering, University of Chemical Technology and Metallurgy, Sofia, Bulgaria
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19
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Marković V, Shaik JB, Ożga K, Ciesiołkiewicz A, Lizandra Perez J, Rudzińska-Szostak E, Berlicki Ł. Peptide foldamer-based inhibitors of the SARS-CoV-2 S protein-human ACE2 interaction. J Enzyme Inhib Med Chem 2023; 38:2244693. [PMID: 37605435 PMCID: PMC10446788 DOI: 10.1080/14756366.2023.2244693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/07/2023] [Accepted: 07/31/2023] [Indexed: 08/23/2023] Open
Abstract
The entry of the SARS-CoV-2 virus into a human host cell begins with the interaction between the viral spike protein (S protein) and human angiotensin-converting enzyme 2 (hACE2). Therefore, a possible strategy for the treatment of this infection is based on inhibiting the interaction of the two abovementioned proteins. Compounds that bind to the SARS-CoV-2 S protein at the interface with the alpha-1/alpha-2 helices of ACE2 PD Subdomain I are of particular interest. We present a stepwise optimisation of helical peptide foldamers containing trans-2-aminocylopentanecarboxylic acid residues as the folding-inducing unit. Four rounds of optimisation led to the discovery of an 18-amino-acid peptide with high affinity for the SARS-CoV-2 S protein (Kd = 650 nM) that inhibits this protein-protein interaction with IC50 = 1.3 µM. Circular dichroism and nuclear magnetic resonance studies indicated the helical conformation of this peptide in solution.
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Affiliation(s)
- Violeta Marković
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Jeelan Basha Shaik
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Katarzyna Ożga
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Agnieszka Ciesiołkiewicz
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Juan Lizandra Perez
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Ewa Rudzińska-Szostak
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
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20
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Liu N, Feng J, Chen X, Luo Y, Lv T, Wu Q, Zhu D. Reshaping the Substrate Binding Pocket of β-Amino Acid Dehydrogenase for the Synthesis of Aromatic β-Amino Acids. Org Lett 2023; 25:8469-8473. [PMID: 37972311 DOI: 10.1021/acs.orglett.3c03366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
By reshaping the substrate-binding pocket of β-amino acid dehydrogenase (β-AADH), some variants were obtained with up to 2560-fold enhanced activity toward the model substrates (S)-β-homophenylalanine and (R)-β-phenylalanine. A few aromatic β-amino acids were prepared with >99% ee and high isolated yields via either kinetic resolution of racemates or reductive amination of the corresponding β-keto acids. This work expands the catalytic capability of β-AADHs and highlights their practical application in the synthesis of pharmaceutically relevant β-amino acids.
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Affiliation(s)
- Na Liu
- National Engineering Research Center of Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology, Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, National Center of Technology Innovation for Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Jinhui Feng
- National Engineering Research Center of Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology, Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, National Center of Technology Innovation for Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xi Chen
- National Engineering Research Center of Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology, Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, National Center of Technology Innovation for Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yuyang Luo
- National Engineering Research Center of Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology, Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, National Center of Technology Innovation for Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- School of Biotechnology, Key Lab of Industrial Fermentation Microbiology of the Ministry of Education, State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Tong Lv
- National Engineering Research Center of Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology, Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, National Center of Technology Innovation for Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Qiaqing Wu
- National Engineering Research Center of Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology, Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, National Center of Technology Innovation for Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Dunming Zhu
- National Engineering Research Center of Industrial Enzymes, Tianjin Engineering Research Center of Biocatalytic Technology, Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, National Center of Technology Innovation for Synthetic Biology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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21
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Brown SM, Mayer-Bacon C, Freeland S. Xeno Amino Acids: A Look into Biochemistry as We Do Not Know It. Life (Basel) 2023; 13:2281. [PMID: 38137883 PMCID: PMC10744825 DOI: 10.3390/life13122281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/18/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
Would another origin of life resemble Earth's biochemical use of amino acids? Here, we review current knowledge at three levels: (1) Could other classes of chemical structure serve as building blocks for biopolymer structure and catalysis? Amino acids now seem both readily available to, and a plausible chemical attractor for, life as we do not know it. Amino acids thus remain important and tractable targets for astrobiological research. (2) If amino acids are used, would we expect the same L-alpha-structural subclass used by life? Despite numerous ideas, it is not clear why life favors L-enantiomers. It seems clearer, however, why life on Earth uses the shortest possible (alpha-) amino acid backbone, and why each carries only one side chain. However, assertions that other backbones are physicochemically impossible have relaxed into arguments that they are disadvantageous. (3) Would we expect a similar set of side chains to those within the genetic code? Many plausible alternatives exist. Furthermore, evidence exists for both evolutionary advantage and physicochemical constraint as explanatory factors for those encoded by life. Overall, as focus shifts from amino acids as a chemical class to specific side chains used by post-LUCA biology, the probable role of physicochemical constraint diminishes relative to that of biological evolution. Exciting opportunities now present themselves for laboratory work and computing to explore how changing the amino acid alphabet alters the universe of protein folds. Near-term milestones include: (a) expanding evidence about amino acids as attractors within chemical evolution; (b) extending characterization of other backbones relative to biological proteins; and (c) merging computing and laboratory explorations of structures and functions unlocked by xeno peptides.
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22
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Tanaka N, Zhu JL, Valencia OL, Schull CR, Scheidt KA. Cooperative Carbene Photocatalysis for β-Amino Ester Synthesis. J Am Chem Soc 2023. [PMID: 37906227 DOI: 10.1021/jacs.3c09875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
β-Amino acids are useful building blocks of bioactive molecules, including peptidomimetics and pharmaceutical compounds. The current limited accessibility to β2,2-type amino acids which bear an α-quaternary center has limited their use in chemical synthesis and biological investigations. Disclosed herein is the development of a new N-heterocyclic carbene/photocatalyzed aminocarboxylation of olefins, affording β2,2-amino esters with high regioselectivity. The generation of nitrogen-centered radicals derived from simple imides via a sequence of deprotonation and single-electron oxidation allows for the subsequent addition to geminal-disubstituted olefins regioselectively. The intermediate tertiary radicals then cross-couple with a stabilized azolium-based radical generated in situ to efficiently construct the quaternary centers. Mechanistic studies, including Stern-Volmer fluorescence quenching experiments, support the proposed catalytic cycle.
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Affiliation(s)
- Nao Tanaka
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Joshua L Zhu
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Oniya L Valencia
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Cullen R Schull
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Karl A Scheidt
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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23
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D'Accolti M, Bellotti D, Dzień E, Leonetti C, Leveraro S, Albanese V, Marzola E, Guerrini R, Caselli E, Rowińska-Żyrek M, Remelli M. Impact of C- and N-terminal protection on the stability, metal chelation and antimicrobial properties of calcitermin. Sci Rep 2023; 13:18228. [PMID: 37880318 PMCID: PMC10600247 DOI: 10.1038/s41598-023-45437-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/19/2023] [Indexed: 10/27/2023] Open
Abstract
The main limitation to the use of antimicrobial peptides (AMPs) as regular drugs, against antibiotic and antifungal resistance, mainly relates to their rapid degradation by proteolytic enzymes. The introduction of suitable structural changes in the peptide chain can make the peptide less susceptible to the action of proteases, thus overcoming this problem. To improve the plasma stability of calcitermin, a metal-chelating AMP present in the human respiratory tract and investigated in the present study, C- and/or N- terminal modifications have been introduced in the native sequence. Evaluation of peptide stability has been performed to determine the half-life times in human plasma of both native calcitermin and its derivatives. However, the protection of the peptide termini can also affect its metal coordination behaviour. Thus, the characterization of Zn2+ and Cu2+ complexes has been performed by means of several techniques, including potentiometry, high-resolution mass spectrometry, UV-Vis, circular dichroism and EPR. On the basis of the obtained results, it was possible to compare the biological activity of the studied systems, taking into account both the metal-binding ability and the peptide stability to search for a link among them. A significant result of this study is that the N-terminal protection increases the calcitermin half-life over seven times and the formation of metal complexes confers resistance towards degradation almost doubling its half-life.
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Affiliation(s)
- Maria D'Accolti
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, L. Borsari 46, 44121, Ferrara, Italy
| | - Denise Bellotti
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, L. Borsari 46, 44121, Ferrara, Italy.
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383, Wrocław, Poland.
| | - Emilia Dzień
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383, Wrocław, Poland
| | - Carlotta Leonetti
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, L. Borsari 46, 44121, Ferrara, Italy
| | - Silvia Leveraro
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, L. Borsari 46, 44121, Ferrara, Italy
| | - Valentina Albanese
- Department of Environmental and Prevention Sciences, University of Ferrara, L. Borsari 46, 44121, Ferrara, Italy
| | - Erika Marzola
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, L. Borsari 46, 44121, Ferrara, Italy
| | - Remo Guerrini
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, L. Borsari 46, 44121, Ferrara, Italy
| | - Elisabetta Caselli
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, L. Borsari 46, 44121, Ferrara, Italy
| | | | - Maurizio Remelli
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, L. Borsari 46, 44121, Ferrara, Italy
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24
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Wegner U, Matthes F, von Wirén N, Lemke I, Bode R, Vorbrodt HM, Rauter M, Kunze G. Enhancing a Sphaerobacter thermophilus ω-transaminase for kinetic resolution of β- and γ-amino acids. AMB Express 2023; 13:117. [PMID: 37864072 PMCID: PMC10589169 DOI: 10.1186/s13568-023-01623-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/03/2023] [Indexed: 10/22/2023] Open
Abstract
Sphaerobacter thermophilus synthesizes an ω-transaminase (ω-TA) that allows the production of enantiomerically pure β-amino acids. To obtain ω-TA variants with a higher activity and more favorable properties for industrial use, we modified critical amino acid residues either in the catalytic center or in a previously proposed signature motif critical for aromatic β-amino acid ω-TAs. Seventeen different variants of this enzyme were generated and their activity was examined with four β-amino acids and one γ-amino acid, and compared with the wildtype's activity. Among all variants, seven showed up to ninefold higher activity with at least one of the tested substrates. For most of these seven variants, the temperature optimum was even lower as in the wild type enzyme, with keeping a high temperature stability, making them more valuable for industrial purposes. Our results indicate that for the production of enantiomerically pure β-amino acids replacement of critical amino acid residues in the proposed signature motif of ω-TAs is a more effective strategy than modifying their catalytic center. Another finding was, that the proposed motif is not only suitable for aromatic amino acid ω-TAs, because some of the variants have a higher activity with β-alanine or β-leucine than with aromatic β-amino acids.
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Affiliation(s)
- Uwe Wegner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466, Seeland, OT Gatersleben, Germany
| | - Falko Matthes
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466, Seeland, OT Gatersleben, Germany
| | - Nicolaus von Wirén
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466, Seeland, OT Gatersleben, Germany
| | - Ina Lemke
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466, Seeland, OT Gatersleben, Germany
| | - Rüdiger Bode
- Institute of Microbiology, University of Greifswald, Jahnstr. 15, 17487, Greifswald, Germany
| | - H-Matthias Vorbrodt
- Orgentis Chemicals GmbH, Bahnhofstr. 3-5, 06466, Seeland, OT Gatersleben, Germany
| | - Marion Rauter
- Orgentis Chemicals GmbH, Bahnhofstr. 3-5, 06466, Seeland, OT Gatersleben, Germany
| | - Gotthard Kunze
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466, Seeland, OT Gatersleben, Germany.
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25
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Yu Z, Kreitler DF, Chiu YTT, Xu R, Bruchs AT, Bingman CA, Gellman SH. Harnessing Aromatic-Histidine Interactions through Synergistic Backbone Extension and Side Chain Modification. Angew Chem Int Ed Engl 2023; 62:e202308100. [PMID: 37587780 PMCID: PMC10668598 DOI: 10.1002/anie.202308100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/31/2023] [Accepted: 08/14/2023] [Indexed: 08/18/2023]
Abstract
Peptide engineering efforts have delivered drugs for diverse human diseases. Side chain alteration is among the most common approaches to designing new peptides for specific applications. The peptide backbone can be modified as well, but this strategy has received relatively little attention. Here we show that new and favorable contacts between a His side chain on a target protein and an aromatic side chain on a synthetic peptide ligand can be engineered by rational and coordinated side chain modification and backbone extension. Side chain modification alone was unsuccessful. Binding measurements, high-resolution structural studies and pharmacological outcomes all support the synergy between backbone and side chain modification in engineered ligands of the parathyroid hormone receptor-1, which is targeted by osteoporosis drugs. These results should motivate other structure-based designs featuring coordinated side chain modification and backbone extension to enhance the engagement of peptide ligands with target proteins.
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Affiliation(s)
- Zhen Yu
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Dale F Kreitler
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York, 11973, USA
| | - Yin Ting T Chiu
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Ruiwen Xu
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Austin T Bruchs
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
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26
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Quintavalla A, Carboni D, Simeone M, Lombardo M. Stereoselective Synthesis of α-Disubstituted β-Homoprolines. Org Lett 2023; 25:7067-7071. [PMID: 37729003 PMCID: PMC10546376 DOI: 10.1021/acs.orglett.3c02891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Indexed: 09/22/2023]
Abstract
An efficient enantioselective synthesis of chiral α-disubstituted β-homoprolines was developed, starting with the stereodivergent allylation of chiral N-tert-butanesulfinyl imines derived from 4-bromobutanal with indium or zinc and using well-established and reliable synthetic transformations. This methodology allows the easy introduction of different substituents at the α-position of the pyrrolidine scaffold and is characterized by the possibility of switching the absolute configuration of the newly formed stereocenter either by changing the configuration of the tert-butanesufinamide chiral auxiliary or by using a different stereodivergent allylation protocol with the same auxiliary.
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Affiliation(s)
- Arianna Quintavalla
- Alma
Mater Studiorum - University of Bologna, Department of Chemistry “G. Ciamician”, via P. Gobetti 85, 40129 Bologna, Italy
- Center
for Chemical Catalysis - C3, Alma Mater
Studiorum - Università di Bologna, via P. Gobetti 85, 40129 Bologna, Italy
| | - Davide Carboni
- Alma
Mater Studiorum - University of Bologna, Department of Chemistry “G. Ciamician”, via P. Gobetti 85, 40129 Bologna, Italy
- Center
for Chemical Catalysis - C3, Alma Mater
Studiorum - Università di Bologna, via P. Gobetti 85, 40129 Bologna, Italy
| | - Maria Simeone
- Alma
Mater Studiorum - University of Bologna, Department of Chemistry “G. Ciamician”, via P. Gobetti 85, 40129 Bologna, Italy
| | - Marco Lombardo
- Alma
Mater Studiorum - University of Bologna, Department of Chemistry “G. Ciamician”, via P. Gobetti 85, 40129 Bologna, Italy
- Center
for Chemical Catalysis - C3, Alma Mater
Studiorum - Università di Bologna, via P. Gobetti 85, 40129 Bologna, Italy
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27
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Lim D, Lee W, Hong J, Gong J, Choi J, Kim J, Lim S, Yoo SH, Lee Y, Lee HS. Versatile Post-synthetic Modifications of Helical β-Peptide Foldamers Derived from a Thioether-Containing Cyclic β-Amino Acid. Angew Chem Int Ed Engl 2023; 62:e202305196. [PMID: 37309575 DOI: 10.1002/anie.202305196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/30/2023] [Accepted: 06/12/2023] [Indexed: 06/14/2023]
Abstract
We introduce a novel cyclic β-amino acid, trans-(3S,4R)-4-aminotetrahydrothiophene-3-carboxylic acid (ATTC), as a versatile building block for designing peptide foldamers with controlled secondary structures. We synthesized and characterized a series of β-peptide hexamers containing ATTC using various techniques, including X-ray crystallography, circular dichroism, and NMR spectroscopy. Our findings reveal that ATTC-containing foldamers can adopt 12-helical conformations similar to their isosteres and offer the possibility of fine-tuning their properties via post-synthetic modifications. In particular, chemoselective conjugation strategies demonstrate that ATTC provides unique post-synthetic modification opportunities, which expand their potential applications across diverse research areas. Collectively, our study highlights the versatility and utility of ATTC as an alternative to previously reported cyclic β-amino acid building blocks in both structural and functional aspects, paving the way for future research in the realm of peptide foldamers and beyond.
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Affiliation(s)
- Danim Lim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Center for Multiscale Chiral Architectures (CMCA), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Wonchul Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Center for Multiscale Chiral Architectures (CMCA), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Current address: Department of Chemistry, Institute for Molecular Science and Fusion Technology, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon, Gangwon, 24341, Republic of Korea
| | - Jungwoo Hong
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Center for Multiscale Chiral Architectures (CMCA), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jintaek Gong
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Center for Multiscale Chiral Architectures (CMCA), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Current address: Department of Chemistry Education, Sunchon National University, 255 Jungang-ro, Suncheon-si, Jeollanam-do, 57922, Republic of Korea
| | - Jonghoon Choi
- Center for Multiscale Chiral Architectures (CMCA), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
- Current address: Department of Chemistry Education, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju, 61186, Republic of Korea
| | - Jaewook Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Center for Multiscale Chiral Architectures (CMCA), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Seolhee Lim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Sung Hyun Yoo
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Center for Multiscale Chiral Architectures (CMCA), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Yunho Lee
- Center for Multiscale Chiral Architectures (CMCA), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Hee-Seung Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Center for Multiscale Chiral Architectures (CMCA), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
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28
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Katoh T, Suga H. Translation initiation with exotic amino acids using EF-P-responsive artificial initiator tRNA. Nucleic Acids Res 2023; 51:8169-8180. [PMID: 37334856 PMCID: PMC10450175 DOI: 10.1093/nar/gkad496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 05/10/2023] [Accepted: 06/17/2023] [Indexed: 06/21/2023] Open
Abstract
Translation initiation using noncanonical initiator substrates with poor peptidyl donor activities, such as N-acetyl-l-proline (AcPro), induces the N-terminal drop-off-reinitiation event. Thereby, the initiator tRNA drops-off from the ribosome and the translation reinitiates from the second amino acid to yield a truncated peptide lacking the N-terminal initiator substrate. In order to suppress this event for the synthesis of full-length peptides, here we have devised a chimeric initiator tRNA, referred to as tRNAiniP, whose D-arm comprises a recognition motif for EF-P, an elongation factor that accelerates peptide bond formation. We have shown that the use of tRNAiniP and EF-P enhances the incorporation of not only AcPro but also d-amino, β-amino and γ-amino acids at the N-terminus. By optimizing the translation conditions, e.g. concentrations of translation factors, codon sequence and Shine-Dalgarno sequence, we could achieve complete suppression of the N-terminal drop-off-reinitiation for the exotic amino acids and enhance the expression level of full-length peptide up to 1000-fold compared with the use of the ordinary translation conditions.
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Affiliation(s)
- Takayuki Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - 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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29
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Costa L, Sousa E, Fernandes C. Cyclic Peptides in Pipeline: What Future for These Great Molecules? Pharmaceuticals (Basel) 2023; 16:996. [PMID: 37513908 PMCID: PMC10386233 DOI: 10.3390/ph16070996] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/06/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023] Open
Abstract
Cyclic peptides are molecules that are already used as drugs in therapies approved for various pharmacological activities, for example, as antibiotics, antifungals, anticancer, and immunosuppressants. Interest in these molecules has been growing due to the improved pharmacokinetic and pharmacodynamic properties of the cyclic structure over linear peptides and by the evolution of chemical synthesis, computational, and in vitro methods. To date, 53 cyclic peptides have been approved by different regulatory authorities, and many others are in clinical trials for a wide diversity of conditions. In this review, the potential of cyclic peptides is presented, and general aspects of their synthesis and development are discussed. Furthermore, an overview of already approved cyclic peptides is also given, and the cyclic peptides in clinical trials are summarized.
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Affiliation(s)
- Lia Costa
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal;
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Edifício do Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4050-208 Matosinhos, Portugal
| | - Emília Sousa
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal;
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Edifício do Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4050-208 Matosinhos, Portugal
| | - Carla Fernandes
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal;
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Edifício do Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4050-208 Matosinhos, Portugal
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30
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Zhao S, Zhang Y, Xu Z, Wang H, Xu L, Wu Y, Zeng X, Luo X. A low-fouling electrochemical biosensor for biomarker detection in serum based on designed α/β-peptides with anti-enzymolysis and antifouling capabilities. Anal Chim Acta 2023; 1263:341244. [PMID: 37225330 DOI: 10.1016/j.aca.2023.341244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/16/2023] [Accepted: 04/20/2023] [Indexed: 05/26/2023]
Abstract
The zwitterionic peptides, especially those composed of glutamic (E) and lysine (K) groups have drawn enormous attention as antifouling biomaterials owing to their strong hydration capability and biocompatibility. However, the susceptibility of α-amino acid K to the proteolytic enzymes in human serum limited the broad application of such peptides in biological media. Herein, a new multifunctional peptide with favorable stability in human serum was designed, and it was composed of three sections with immobilizing, recognizing and antifouling capabilities, respectively. The antifouling section was composed of alternating E and K amino acids, but the enzymolysis-susceptive amino acid α-K was replaced by the unnatural β-K. Compared with the conventional peptide composed of all α-amino acids, the α/β-peptide exhibited significantly enhanced stability and longer antifouling performance in human serum and blood. The electrochemical biosensor based on the α/β-peptide showed a favorable sensitivity to its target IgG, with a quite wide linear range from 100 pg mL-1 to 10 μg mL-1 and a low detection limit (33.7 pg mL-1, S/N = 3), and it was promising for the detection of IgG in complex human serum. The tactic of designing antifouling α/β-peptides offered an efficient way to develop low-fouling biosensors with robust operation in complex body fluids.
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Affiliation(s)
- Shuju Zhao
- State Key Laboratory Base of Eco-chemical Engineering, Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science & Technology, Qingdao, 266042, China
| | - Yuxi Zhang
- State Key Laboratory Base of Eco-chemical Engineering, Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science & Technology, Qingdao, 266042, China
| | - Zhenying Xu
- State Key Laboratory Base of Eco-chemical Engineering, Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science & Technology, Qingdao, 266042, China
| | - Hao Wang
- State Key Laboratory Base of Eco-chemical Engineering, Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science & Technology, Qingdao, 266042, China
| | - Liang Xu
- State Key Laboratory Base of Eco-chemical Engineering, Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science & Technology, Qingdao, 266042, China
| | - Yumin Wu
- State Key Laboratory Base of Eco-chemical Engineering, Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science & Technology, Qingdao, 266042, China
| | - Xianghua Zeng
- State Key Laboratory Base of Eco-chemical Engineering, Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science & Technology, Qingdao, 266042, China.
| | - Xiliang Luo
- State Key Laboratory Base of Eco-chemical Engineering, Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science & Technology, Qingdao, 266042, China.
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31
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Crotti S, Menicatti M, Pallecchi M, Bartolucci G. Tandem mass spectrometry approaches for recognition of isomeric compounds mixtures. MASS SPECTROMETRY REVIEWS 2023; 42:1244-1260. [PMID: 34841547 DOI: 10.1002/mas.21757] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 10/27/2021] [Accepted: 10/27/2021] [Indexed: 06/07/2023]
Abstract
The present review aims to collect the published literature pertaining the recognition of isobaric compounds (isomers or stereoisomers) using the features of tandem mass spectrometry (MS) experiments without any chromatographic separation or chemical modification (derivatization or isotopic enrichment) of the analytes. MS/MS methods possess high selectivity, wide dynamic range and high throughput capabilities. Generally, tandem MS has limited capability for distinguishing isomers that fragment similarly. However, some MS/MS methods have been developed and positively applied to isomers discrimination. Among the literature on this topic, the applications that fit on the review subject can be summarized as follow: (1) chiral discrimination by the kinetic method, (2) the use energy-resolved tandem mass spectra and the survival yield (SY) representation, (3) the kinetics evaluation of the ion-molecule interaction and (4) the postprocessing mathematical algorithm to resolve the isomers in MS/MS signal.
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Affiliation(s)
- Sara Crotti
- Fondazione Istituto di Ricerca Pediatrica Città della Speranza, Padova, Italy
| | - Marta Menicatti
- Dipartimento Neurofarba, Università di Firenze, Florence, Italy
| | - Marco Pallecchi
- Dipartimento Neurofarba, Università di Firenze, Florence, Italy
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32
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do Amaral SC, Xavier LP, Vasconcelos V, Santos AV. Cyanobacteria: A Promising Source of Antifungal Metabolites. Mar Drugs 2023; 21:359. [PMID: 37367684 DOI: 10.3390/md21060359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/23/2023] [Accepted: 05/27/2023] [Indexed: 06/28/2023] Open
Abstract
Cyanobacteria are a rich source of secondary metabolites, and they have received a great deal of attention due to their applicability in different industrial sectors. Some of these substances are known for their notorious ability to inhibit fungal growth. Such metabolites are very chemically and biologically diverse. They can belong to different chemical classes, including peptides, fatty acids, alkaloids, polyketides, and macrolides. Moreover, they can also target different cell components. Filamentous cyanobacteria have been the main source of these compounds. This review aims to identify the key features of these antifungal agents, as well as the sources from which they are obtained, their major targets, and the environmental factors involved when they are being produced. For the preparation of this work, a total of 642 documents dating from 1980 to 2022 were consulted, including patents, original research, review articles, and theses.
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Affiliation(s)
- Samuel Cavalcante do Amaral
- Laboratory of Biotechnology of Enzymes and Biotransformation, Biological Sciences Institute, Federal University of Pará, Belém 66075-110, Brazil
| | - Luciana Pereira Xavier
- Laboratory of Biotechnology of Enzymes and Biotransformation, Biological Sciences Institute, Federal University of Pará, Belém 66075-110, Brazil
| | - Vítor Vasconcelos
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, University of Porto, 4450-208 Matosinhos, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Edifício FC4, 4169-007 Porto, Portugal
| | - Agenor Valadares Santos
- Laboratory of Biotechnology of Enzymes and Biotransformation, Biological Sciences Institute, Federal University of Pará, Belém 66075-110, Brazil
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33
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Todaro B, Ottalagana E, Luin S, Santi M. Targeting Peptides: The New Generation of Targeted Drug Delivery Systems. Pharmaceutics 2023; 15:1648. [PMID: 37376097 DOI: 10.3390/pharmaceutics15061648] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/22/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Peptides can act as targeting molecules, analogously to oligonucleotide aptamers and antibodies. They are particularly efficient in terms of production and stability in physiological environments; in recent years, they have been increasingly studied as targeting agents for several diseases, from tumors to central nervous system disorders, also thanks to the ability of some of them to cross the blood-brain barrier. In this review, we will describe the techniques employed for their experimental and in silico design, as well as their possible applications. We will also discuss advancements in their formulation and chemical modifications that make them even more stable and effective. Finally, we will discuss how their use could effectively help to overcome various physiological problems and improve existing treatments.
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Affiliation(s)
- Biagio Todaro
- NEST Laboratory, Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Elisa Ottalagana
- NEST Laboratory, Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy
- Fondazione Pisana per la Scienza, Via Ferruccio Giovannini 13, San Giuliano Terme, 56017 Pisa, Italy
| | - Stefano Luin
- NEST Laboratory, Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy
- NEST, Istituto Nanoscienze-CNR and Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Melissa Santi
- NEST, Istituto Nanoscienze-CNR and Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy
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34
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Zebrowski P, Röser K, Chrenko D, Pospíšil J, Waser M. Enantioselective β-Selective Addition of Isoxazolidin-5-ones to Allenoates Catalyzed by Quaternary Ammonium Salts. SYNTHESIS-STUTTGART 2023; 55:1706-1713. [PMID: 38855403 PMCID: PMC7616069 DOI: 10.1055/a-1948-5493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
The enantioselective addition of isoxazolidin-5-ones to the β-carbon of allenoates has been carried out by using a novel spirobiindane-based quaternary ammonium salt catalyst. This protocol, which proceeds under classical liquid-solid phase-transfer conditions, gives access to unprecedented highly functionalized β2,2-amino acid derivatives with good enantioselectivities and in high yields, and further manipulations of these products have been carried out as well.
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Affiliation(s)
- Paul Zebrowski
- Institute of Organic Chemistry, Johannes Kepler University Linz, Altenbergerstrasse 69, 4040 Linz, Austria
| | - Katharina Röser
- Institute of Organic Chemistry, Johannes Kepler University Linz, Altenbergerstrasse 69, 4040 Linz, Austria
| | - Daniel Chrenko
- Department of Chemical Biology, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Jiří Pospíšil
- Department of Chemical Biology, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
- Laboratory of Growth Regulators, Palacký University & Institute of Experimental Botany AS CR, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Mario Waser
- Institute of Organic Chemistry, Johannes Kepler University Linz, Altenbergerstrasse 69, 4040 Linz, Austria
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Baiula M, Anselmi M, Musiani F, Ghidini A, Carbone J, Caligiana A, Maurizio A, Spampinato S, Gentilucci L. Design, Pharmacological Characterization, and Molecular Docking of Minimalist Peptidomimetic Antagonists of α 4β 1 Integrin. Int J Mol Sci 2023; 24:ijms24119588. [PMID: 37298541 DOI: 10.3390/ijms24119588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/17/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Integrin receptors mediate cell-cell interactions via the recognition of cell-adhesion glycoproteins, as well as via the interactions of cells with proteins of the extracellular matrix, and upon activation they transduce signals bi-directionally across the cell membrane. In the case of injury, infection, or inflammation, integrins of β2 and α4 families participate in the recruitment of leukocytes, a multi-step process initiated by the capturing of rolling leukocytes and terminated by their extravasation. In particular, α4β1 integrin is deeply involved in leukocyte firm adhesion preceding extravasation. Besides its well-known role in inflammatory diseases, α4β1 integrin is also involved in cancer, being expressed in various tumors and showing an important role in cancer formation and spreading. Hence, targeting this integrin represents an opportunity for the treatment of inflammatory disorders, some autoimmune diseases, and cancer. In this context, taking inspiration from the recognition motives of α4β1 integrin with its natural ligands FN and VCAM-1, we designed minimalist α/β hybrid peptide ligands, with our approach being associated with a retro strategy. These modifications are expected to improve the compounds' stability and bioavailability. As it turned out, some of the ligands were found to be antagonists, being able to inhibit the adhesion of integrin-expressing cells to plates coated with the natural ligands without inducing any conformational switch and any activation of intracellular signaling pathways. An original model structure of the receptor was generated using protein-protein docking to evaluate the bioactive conformations of the antagonists via molecular docking. Since the experimental structure of α4β1 integrin is still unknown, the simulations might also shed light on the interactions between the receptor and its native protein ligands.
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Affiliation(s)
- Monica Baiula
- Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Michele Anselmi
- Department of Chemistry "G. Ciamician", University of Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale Fanin 40, 40126 Bologna, Italy
| | - Alessia Ghidini
- Department of Chemistry "G. Ciamician", University of Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Jacopo Carbone
- Department of Chemistry "G. Ciamician", University of Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Alberto Caligiana
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Andrea Maurizio
- Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Santi Spampinato
- Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Luca Gentilucci
- Department of Chemistry "G. Ciamician", University of Bologna, Via Selmi 2, 40126 Bologna, Italy
- Health Sciences & Technologies (HST) CIRI, University of Bologna, 40064 Ozzano Emilia, Italy
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36
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Wei J, Ning LW, Li Y. Diastereoselective addition of 2-alkoxy-2-fluoroacetate to N-(tert‑butylsulfinyl)imines: Synthesis of α-alkoxy-α-fluoro-β-amino acids. J Fluor Chem 2023. [DOI: 10.1016/j.jfluchem.2023.110118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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37
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Allen MA, Volosheniuk M, Nicol EA, Schwan AL, Beauchemin AM. Cope-Type Hydroamination of Vinylboronates. Org Lett 2023; 25:3045-3048. [PMID: 37097727 DOI: 10.1021/acs.orglett.3c00857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Aminoboronic acid derivatives can serve as versatile synthetic intermediates and pharmacophores but remain difficult to synthesize. Herein we report a synthesis of the β-aminoboronic acid motif via anti-Markovnikov hydroamination of vinylboronates. This reaction benefits from the activating effect of the boronate substituent and forms novel BON-containing heterocycles, oxazaborolidine zwitterions. A computational study is included to help determine the effects of alkene boron substitution. Derivatization reactions also support the synthetic utility of the oxazaborolidine adducts.
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Affiliation(s)
- Meredith A Allen
- Centre for Catalysis Research and Innovation, Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Myroslava Volosheniuk
- Centre for Catalysis Research and Innovation, Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Eric A Nicol
- Department of Chemistry, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Adrian L Schwan
- Department of Chemistry, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - André M Beauchemin
- Centre for Catalysis Research and Innovation, Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
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38
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Cui S, Zeng L. Amino amide assembly. Nat Chem 2023; 15:597-598. [PMID: 37055573 DOI: 10.1038/s41557-023-01182-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Affiliation(s)
- Sunliang Cui
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.
| | - Linwei Zeng
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
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Gattu R, Ramesh SS, Nadigar S, D CG, Ramesh S. Conjugation as a Tool in Therapeutics: Role of Amino Acids/Peptides-Bioactive (Including Heterocycles) Hybrid Molecules in Treating Infectious Diseases. Antibiotics (Basel) 2023; 12:antibiotics12030532. [PMID: 36978399 PMCID: PMC10044335 DOI: 10.3390/antibiotics12030532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 02/28/2023] [Accepted: 03/03/2023] [Indexed: 03/30/2023] Open
Abstract
Peptide-based drugs are gaining significant momentum in the modern drug discovery, which is witnessed by the approval of new drugs by the FDA in recent years. On the other hand, small molecules-based drugs are an integral part of drug development since the past several decades. Peptide-containing drugs are placed between small molecules and the biologics. Both the peptides as well as the small molecules (mainly heterocycles) pose several drawbacks as therapeutics despite their success in curing many diseases. This gap may be bridged by utilising the so called 'conjugation chemistry', in which both the partners are linked to one another through a stable chemical bond, and the resulting conjugates are found to possess attracting benefits, thus eliminating the stigma associated with the individual partners. Over the past decades, the field of molecular hybridisation has emerged to afford us new and efficient molecular architectures that have shown high promise in medicinal chemistry. Taking advantage of this and also considering our experience in this field, we present herein a review concerning the molecules obtained by the conjugation of peptides (amino acids) to small molecules (heterocycles as well as bioactive compounds). More than 125 examples of the conjugates citing nearly 100 references published during the period 2000 to 2022 having therapeutic applications in curing infectious diseases have been covered.
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Affiliation(s)
- Rohith Gattu
- Postgraduate Department of Chemistry, JSS College of Arts, Commerce and Science, Ooty Road, Mysuru 570025, Karnataka, India
| | - Sanjay S Ramesh
- Postgraduate Department of Chemistry, JSS College of Arts, Commerce and Science, Ooty Road, Mysuru 570025, Karnataka, India
| | - Siddaram Nadigar
- Postgraduate Department of Chemistry, JSS College of Arts, Commerce and Science, Ooty Road, Mysuru 570025, Karnataka, India
| | - Channe Gowda D
- Department of Studies in Chemistry, Manasagangotri, University of Mysore, Mysuru 570005, Karnataka, India
| | - Suhas Ramesh
- Postgraduate Department of Chemistry, JSS College of Arts, Commerce and Science, Ooty Road, Mysuru 570025, Karnataka, India
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40
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Ding D, Xu S, da Silva-Júnior EF, Liu X, Zhan P. Medicinal chemistry insights into antiviral peptidomimetics. Drug Discov Today 2023; 28:103468. [PMID: 36528280 DOI: 10.1016/j.drudis.2022.103468] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 12/06/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022]
Abstract
The (re)emergence of multidrug-resistant viruses and the emergence of new viruses highlight the urgent and ongoing need for new antiviral agents. The use of peptidomimetics as therapeutic drugs has often been associated with advantages, such as enhanced binding affinity, improved metabolic stability, and good bioavailability profiles. The development of novel antivirals is currently driven by strategies of converting peptides into peptidomimetic derivatives. In this review, we outline different structural modification design strategies for developing novel peptidomimetics as antivirals, involving N- or C-cap terminal structure modifications, pseudopeptides, amino acid modifications, inverse-peptides, cyclization, and molecular hybridization. We also present successful recent examples of peptidomimetic designs.
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Affiliation(s)
- Dang Ding
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Shujing Xu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | | | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
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41
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Chaurasiya A, Shome A, Chawla PA. Molecular docking analysis of peptide-based antiviral agents against SARS-CoV-2 main protease: an approach towards drug repurposing. EXPLORATION OF MEDICINE 2023. [DOI: 10.37349/emed.2023.00123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
Abstract
Aim:
Utilizing the therapeutic potentials of previously approved medications against a new target or pharmacological response is known as drug repurposing. The health and scientific communities are under continual pressure to discover new compounds with antiviral potential due to the rising reports of viral resistance and the occurrence and re-emergence of viral outbreaks. The use of antiviral peptides has emerged as an intriguing option in this search. Here, this article includes the current United States Food and Drug Administration (FDA)-approved antiviral peptides that might be enforced for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and carried out docking study of the viral protease inhibitors.
Methods:
In silico techniques like molecular docking was carried out using Autodock Vina software.
Results:
The molecular docking studies of peptide-based antiviral agents against SARS-CoV-2 [Protein Data Bank (PDB) ID: 7P35] using docking software AutoDockTools 1.5.6. Among all the docked ligands, compound velpatasvir showed interaction with residues ILE213, GLN256, LEU141, GLN189, GLU166, HIS41, CYS145, and ASN142, and displayed the highest docking score of –8.2 kcal/mol. This medication could be a novel treatment lead or candidate for treating SARS-CoV-2.
Conclusions:
To conclude, a docking study of peptide based antiviral compounds for their binding mode in the catalytic domain of SARS-CoV-2 receptor is reported. On molecular docking, the compounds have showed remarkable binding affinity with the amino acids of receptor chain A. The compounds occupied the same binding cavity as the reference compound maintaining the interactions with conserved amino acid residues essential for significant inhibitory potential, especially for compound velpatasvir with binding score of –8.2 kcal/mol.
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Affiliation(s)
- Abhishek Chaurasiya
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga 142001, India
| | - Abhimannu Shome
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga 142001, India
| | - Pooja A. Chawla
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga 142001, India
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42
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Verma NK, Dewangan RP, Harioudh MK, Ghosh JK. Introduction of a β-leucine residue instead of leucine 9 and glycine 10 residues in Temporin L for improved cell selectivity, stability and activity against planktonic and biofilm of methicillin resistant S. aureus. Bioorg Chem 2023; 134:106440. [PMID: 36870201 DOI: 10.1016/j.bioorg.2023.106440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/07/2023] [Accepted: 02/18/2023] [Indexed: 03/06/2023]
Abstract
Leucine and glycine residues, at the 9th and 10th positions of helical domain of naturally occurring antimicrobial peptide (AMP), Temporin L were substituted with an unnatural amino acid, β-leucine (homovaline) to improve its serum protease stability, haemolytic/cytotoxic properties and reduce the size to some extent. The designed analogue, L9βl-TL showed either equal or improved antimicrobial activity to TL against different microorganisms including the resistant strains. Interestingly, L9βl-TL also exhibited lower haemolytic and cytotoxic activities against human red blood cells and 3T3 cells, respectively. Moreover, L9βl-TL showed antibacterial activity in presence of 25% (v/v) human serum and showed resistance against proteolytic cleavage in presence of it that suggested the serum protease stability of the TL-analogue. L9βl-TL exhibited un-ordered secondary structures in both bacterial and mammalian membrane mimetic lipid vesicles as compared to the helical structures of TL in these environments. However, tryptophan fluorescence studies demonstrated more selective interaction of L9βl-TL with bacterial membrane mimetic lipid vesicles in comparison to non-selective interactions of TL with both kinds of lipid vesicles. Membrane depolarization studies with live MRSA and bacterial membrane-mimetic lipid vesicles suggested a membrane-disrupting mode of action of L9βl-TL. L9βl-TL showed faster bactericidal mechanism compared to TL against MRSA. Interestingly, L9βl-TL was found as more potent than TL either in inhibiting biofilm formation or in eradicating the mature biofilm formed by MRSA. Overall, the present work demonstrates a simple and useful strategy to design of an analogue of TL, with minimal modifications while maintaining its antimicrobial activity with lesser toxicity and higher stability which could be attempted for other AMPs as well.
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Affiliation(s)
- Neeraj Kumar Verma
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, India
| | - Rikeshwer Prasad Dewangan
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, India.
| | - Munesh Kumar Harioudh
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, India
| | - Jimut Kanti Ghosh
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, India.
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43
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Lamartina CW, Chartier CA, Lee S, Shah NH, Rovis T. Modular Synthesis of Unnatural Peptides via Rh(III)-Catalyzed Diastereoselective Three-Component Carboamidation Reaction. J Am Chem Soc 2023; 145:1129-1135. [PMID: 36576945 PMCID: PMC10580301 DOI: 10.1021/jacs.2c10793] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Herein we report a modular peptide ligation methodology that couples dioxazolones, arylboronic acids, and acrylamides to construct amide bonds in a diastereoselective manner under mild conditions, facilitated by Rh(III) catalysis. By converting the C-terminus of one peptide into a dioxazolone and the N-terminus of a second peptide into an acrylamide, the two pieces can be bridged by an arylboronic acid to construct unnatural phenylalanine, tyrosine, and tryptophan residues at the junction point with diastereoselectivity for their corresponding d-stereocenters. The reaction exhibits excellent functional group tolerance with a large substrate scope and is compatible with a wide array of protected amino acid residues that are utilized in Fmoc solid phase peptide synthesis. The methodology is applied to the synthesis of six diastereomeric proteasome inhibitor analogs, as well as the ligation of two 10-mer oligopeptides to construct a 21-mer polypeptide with an unnatural phenylalanine residue at the center.
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Affiliation(s)
| | - Cassandra A. Chartier
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Sumin Lee
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Neel H. Shah
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Tomislav Rovis
- Department of Chemistry, Columbia University, New York, New York 10027, United States
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44
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Pulcinella A, Bonciolini S, Lukas F, Sorato A, Noël T. Photocatalytic Alkylation of C(sp 3 )-H Bonds Using Sulfonylhydrazones. Angew Chem Int Ed Engl 2023; 62:e202215374. [PMID: 36394188 PMCID: PMC10108173 DOI: 10.1002/anie.202215374] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 11/18/2022]
Abstract
The ability to construct C(sp3 )-C(sp3 ) bonds from easily accessible reagents is a crucial, yet challenging endeavor for synthetic organic chemists. Herein, we report the realization of such a cross-coupling reaction, which combines N-sulfonyl hydrazones and C(sp3 )-H donors through a diarylketone-enabled photocatalytic hydrogen atom transfer and a subsequent fragmentation of the obtained alkylated hydrazide. This mild and metal-free protocol was employed to prepare a wide array of alkyl-alkyl cross-coupled products and is tolerant of a variety of functional groups. The application of this chemistry further provides a preparatively useful route to various medicinally-relevant compounds, such as homobenzylic ethers, aryl ethyl amines, β-amino acids and other moieties which are commonly encountered in approved pharmaceuticals, agrochemicals and natural products.
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Affiliation(s)
- Antonio Pulcinella
- Flow Chemistry Group, Van't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Stefano Bonciolini
- Flow Chemistry Group, Van't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Florian Lukas
- Flow Chemistry Group, Van't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Andrea Sorato
- Flow Chemistry Group, Van't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Timothy Noël
- Flow Chemistry Group, Van't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
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45
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Audzeyenka I, Szrejder M, Rogacka D, Angielski S, Saleem MA, Piwkowska A. β-Aminoisobutyric acid (L-BAIBA) is a novel regulator of mitochondrial biogenesis and respiratory function in human podocytes. Sci Rep 2023; 13:766. [PMID: 36641502 PMCID: PMC9840613 DOI: 10.1038/s41598-023-27914-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/10/2023] [Indexed: 01/15/2023] Open
Abstract
Podocytes constitute an external layer of the glomerular filtration barrier, injury to which is a hallmark of renal disease. Mitochondrial dysfunction often accompanies podocyte damage and is associated with an increase in oxidative stress and apoptosis. β-Aminoisobutyric acid (BAIBA) belongs to natural β-amino acids and is known to exert anti-inflammatory and antioxidant effects. BAIBA has been reported to be involved in regulating mitochondrial dynamics, but unknown is whether BAIBA influences podocyte bioenergetics. The present study showed that human podocytes express the BAIBA receptor, Mas-related G protein-coupled receptor type D (MRGPRD), which is sensitive to BAIBA stimulation. The treatment of podocytes with L-BAIBA significantly increased their respiratory parameters, such as basal and maximal respiration, adenosine triphosphate (ATP) production, and spare respiratory capacity. We also found that L-BAIBA altered mitochondrial quantity, size, and shape, promoting organelle elongation and branching. L-BAIBA significantly upregulated peroxisome proliferator activated receptor γ coactivator-1α (PGC-1α) and transcription factor A mitochondrial (TFAM), indicating an increase in mitochondrial biogenesis. Our results demonstrate a novel regulatory mechanism of mitochondrial dynamics in podocytes, which may be important for maintaining their functions in the renal filtration barrier and prompting further investigations of preventing or ameliorating mitochondrial damage in podocytes in pathological states.
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Affiliation(s)
- Irena Audzeyenka
- Laboratory of Molecular and Cellular Nephrology, Mossakowski Medical Research Institute, Polish Academy of Sciences, Wita Stwosza St. 63, 80-308, Gdansk, Poland. .,Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk, Poland.
| | - Maria Szrejder
- Laboratory of Molecular and Cellular Nephrology, Mossakowski Medical Research Institute, Polish Academy of Sciences, Wita Stwosza St. 63, 80-308, Gdansk, Poland
| | - Dorota Rogacka
- Laboratory of Molecular and Cellular Nephrology, Mossakowski Medical Research Institute, Polish Academy of Sciences, Wita Stwosza St. 63, 80-308, Gdansk, Poland.,Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk, Poland
| | - Stefan Angielski
- Laboratory of Molecular and Cellular Nephrology, Mossakowski Medical Research Institute, Polish Academy of Sciences, Wita Stwosza St. 63, 80-308, Gdansk, Poland
| | | | - Agnieszka Piwkowska
- Laboratory of Molecular and Cellular Nephrology, Mossakowski Medical Research Institute, Polish Academy of Sciences, Wita Stwosza St. 63, 80-308, Gdansk, Poland.,Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk, Poland
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46
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Targeting cancer through recently developed purine clubbed heterocyclic scaffolds: An overview. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.134967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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47
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Wegner U, Matthes F, von Wirén N, Hajirezaei MR, Bode R, Kunze G, Rauter M. A transaminase with β-activity from Variovorax boronicumulans for the production of enantiopure β-amino acids. Heliyon 2022; 9:e12729. [PMID: 36685366 PMCID: PMC9850050 DOI: 10.1016/j.heliyon.2022.e12729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/11/2022] [Accepted: 12/22/2022] [Indexed: 01/01/2023] Open
Abstract
Enantioselective transamination of amino acids is a great challenge in biotechnology as suitable enzymes with wide substrate spectrum are rare. Here, we present a new transaminase from Variovorax boronicumulans (VboTA, Variovorax boronicumulansω-transaminase) which is specific for β-amino acids. The amino acid sequence of VboTA is similar to an ω-transaminase from Variovorax paradoxus, for which a crystal-structure is available. This similarity is allowing us to classify VboTA as a fold type 1 ω-transaminase (ω-TA). Although both enzymes have a high sequence similarity (86% identities, 92% positives), there are differences in the active center, which allow VboTA to accept a broader substrate spectrum. Both enzymes have also a different temperature stability and temperature optimum. VboTA deaminates the D-form of aromatic β-amino acids, such as β-homophenylalanine and β-phenylalanine as well as aliphatic β-amino acids, such as β-homoalanine and β-leucine. The optimal reaction conditions turned out to be 32 °C and pH 9. Kinetic resolution lead to high enantiomeric excess of 86.6% to >99.9%, depending on the amino donor/acceptor pair. In contrast to many other ω-TAs, VboTA has a broad substrate spectrum and uses both aromatic or aliphatic amino acids. With γ-amino acids as substrates, VboTA showed no activity at all.
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Affiliation(s)
- Uwe Wegner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Seeland, Germany
| | - Falko Matthes
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Seeland, Germany
| | - Nicolaus von Wirén
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Seeland, Germany
| | - Mohammad-Reza Hajirezaei
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Seeland, Germany
| | - Rüdiger Bode
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8, D-17489 Greifswald, Germany
| | - Gotthard Kunze
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, D-06466 Seeland, Germany,Corresponding author.
| | - Marion Rauter
- Orgentis Chemicals GmbH, Bahnhofstr. 3-5, OT Gatersleben, D-06466 Seeland, Germany
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48
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Takyo M, Sato Y, Hirata N, Tsuchiya K, Ishida H, Kurohara T, Yanase Y, Ito T, Kanda Y, Yamamoto K, Misawa T, Demizu Y. Oligoarginine-Conjugated Peptide Foldamers Inhibiting Vitamin D Receptor-Mediated Transcription. ACS OMEGA 2022; 7:46573-46582. [PMID: 36570290 PMCID: PMC9774327 DOI: 10.1021/acsomega.2c05409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 11/16/2022] [Indexed: 06/17/2023]
Abstract
The vitamin D receptor (VDR) is a nuclear receptor, which is involved in several physiological processes, including differentiation and bone homeostasis. The VDR is a promising target for the development of drugs against cancer and bone-related diseases. To date, several VDR antagonists, which bind to the ligand binding domain of the VDR and compete with the endogenous agonist 1α,25(OH)D3, have been reported. However, these ligands contain a secosteroidal skeleton, which is chemically unstable and complicated to synthesize. A few VDR antagonists with a nonsecosteroidal skeleton have been reported. Alternative inhibitors against VDR transactivation that act via different mechanisms are desirable. Here, we developed peptide-based VDR inhibitors capable of disrupting the VDR-coactivator interaction. It was reported that helical SRC2-3 peptides strongly bound to the VDR and competed with the coactivator in vitro. Therefore, we designed and synthesized a series of SRC2-3 derivatives by the introduction of nonproteinogenic amino acids, such as β-amino acids, and by side-chain stapling to stabilize helical structures and provide resistance against digestive enzymes. In addition, conjugation with a cell-penetrating peptide increased the cell membrane permeability and was a promising strategy for intracellular VDR inhibition. The nona-arginine-conjugated peptides 24 with side-chain stapling and 25 with cyclic β-amino acids showed strong intracellular VDR inhibitory activity, resulting in suppression of the target gene expression and inhibition of the cell differentiation of HL-60 cells. Herein, the peptide design, structure-activity relationship (SAR) study, and biological evaluation of the peptides are described.
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Affiliation(s)
- Mami Takyo
- National
Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki, Kanagawa 210-9501, Japan
- Graduate
School of Medical Life Science, Yokohama
City University, 1-7-29
Yokohama, Yokohama, Kanagawa 230-0045, Japan
| | - Yumi Sato
- National
Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki, Kanagawa 210-9501, Japan
- Graduate
School of Medical Life Science, Yokohama
City University, 1-7-29
Yokohama, Yokohama, Kanagawa 230-0045, Japan
| | - Naoya Hirata
- National
Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki, Kanagawa 210-9501, Japan
| | - Keisuke Tsuchiya
- National
Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki, Kanagawa 210-9501, Japan
- Graduate
School of Pharmacy, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan
| | - Hiroaki Ishida
- Laboratory
of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machidashi, Tokyo 194-8543, Japan
| | - Takashi Kurohara
- National
Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki, Kanagawa 210-9501, Japan
| | - Yuta Yanase
- National
Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki, Kanagawa 210-9501, Japan
- Graduate
School of Medical Life Science, Yokohama
City University, 1-7-29
Yokohama, Yokohama, Kanagawa 230-0045, Japan
| | - Takahito Ito
- National
Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki, Kanagawa 210-9501, Japan
- Graduate
School of Medical Life Science, Yokohama
City University, 1-7-29
Yokohama, Yokohama, Kanagawa 230-0045, Japan
| | - Yasunari Kanda
- National
Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki, Kanagawa 210-9501, Japan
| | - Keiko Yamamoto
- Laboratory
of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machidashi, Tokyo 194-8543, Japan
| | - Takashi Misawa
- National
Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki, Kanagawa 210-9501, Japan
| | - Yosuke Demizu
- National
Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki, Kanagawa 210-9501, Japan
- Graduate
School of Medical Life Science, Yokohama
City University, 1-7-29
Yokohama, Yokohama, Kanagawa 230-0045, Japan
- Graduate
School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushimanaka, Kita-ku, Okayama 700-8530, Japan
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49
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Semghouli A, Remete AM, Kiss L. Synthesis of New β‐Amino Acid Scaffolds by Means of Ring‐Rearrangement Metathesis. ChemistrySelect 2022. [DOI: 10.1002/slct.202204244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Anas Semghouli
- Institute of Pharmaceutical Chemistry University of Szeged Eötvös u. 6 H-6720 Szeged Hungary
- Institute of Organic Chemistry Stereochemistry Research Group Research Centre for Natural Sciences Magyar tudósok krt. 2 H-1117 Budapest Hungary
| | - Attila M. Remete
- Institute of Pharmaceutical Chemistry University of Szeged Eötvös u. 6 H-6720 Szeged Hungary
| | - Loránd Kiss
- Institute of Organic Chemistry Stereochemistry Research Group Research Centre for Natural Sciences Magyar tudósok krt. 2 H-1117 Budapest Hungary
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50
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Wakabayashi R, Kawai M, Katoh T, Suga H. In Vitro Selection of Macrocyclic α/β 3-Peptides against Human EGFR. J Am Chem Soc 2022; 144:18504-18510. [PMID: 36173923 PMCID: PMC9563295 DOI: 10.1021/jacs.2c07624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Indexed: 11/30/2022]
Abstract
Here, we report ribosomal construction of thioether-macrocyclic α/β3-peptide libraries in which β-homoglycine, β-homoalanine, β-homophenylglycine, and β-homoglutamine are introduced by genetic code reprogramming. The libraries were applied to the RaPID (Random nonstandard Peptides Integrated Discovery) selection against human EGFR to obtain PPI (protein-protein interaction) inhibitors. The resulting peptides contained up to five β3-amino acid (β3AA) residues and exhibited outstanding binding affinity, PPI inhibitory activity, and proteolytic stability, which were attributed to the β3AAs included in the peptides. This showcase work has demonstrated that the use of such β3AAs enhances the drug-like properties of peptides, providing a unique platform for the discovery of de novo macrocycles against a protein of interest.
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Affiliation(s)
- Risa Wakabayashi
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Marina Kawai
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayuki Katoh
- 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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