1
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Wootton JM, Tam JKF, Unsworth WP. Cascade ring expansion reactions for the synthesis of medium-sized rings and macrocycles. Chem Commun (Camb) 2024; 60:4999-5009. [PMID: 38655659 DOI: 10.1039/d4cc01303d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
This Feature Article discusses recent advances in the development of cascade ring expansion reactions for the synthesis of medium-sized rings and macrocycles. Cascade ring expansion reactions have much potential for use in the synthesis of biologically important medium-sized rings and macrocycles, most notably as they don't require high dilution conditions, which are commonly used in established end-to-end macrocyclisation methods. Operation by cascade ring expansion method can allow large ring products to be accessed via rearrangements that proceed exclusively by normal-sized ring cyclisation steps. Ensuring that there is adequate thermodynamic driving force for ring expansion is a key challenge when designing such methods, especially for the expansion of normal-sized rings into medium-sized rings. This Article is predominantly focused on methods developed in our own laboratory, with selected works by other groups also discussed. Thermodynamic considerations, mechanism, reaction design, route planning and future perspective for this field are all covered.
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Affiliation(s)
- Jack M Wootton
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.
| | - Jerry K F Tam
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.
| | - William P Unsworth
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.
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2
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Sighel D, Battistini G, Rosatti EF, Vigna J, Pavan M, Belli R, Peroni D, Alessandrini F, Longhi S, Pancher M, Rorbach J, Moro S, Quattrone A, Mancini I. Streptogramin A derivatives as mitochondrial translation inhibitors to suppress glioblastoma stem cell growth. Eur J Med Chem 2023; 246:114979. [PMID: 36495628 DOI: 10.1016/j.ejmech.2022.114979] [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: 06/09/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 12/04/2022]
Abstract
New therapeutic strategies for glioblastoma treatment, especially tackling the tumour's glioblastoma stem cell (GSC) component, are an urgent medical need. Recently, mitochondrial translation inhibition has been shown to affect GSC growth, clonogenicity, and self-renewal capability, therefore becoming an attractive therapeutic target. The combination of streptogramins B and A antibiotics quinupristin/dalfopristin (Q/D), which inhibits mitochondrial ribosome function, affects GSCs more effectively in vitro than the standard of care temozolomide. Here, docking calculations based on the cryo-EM structure of the Q/D-bound mitochondrial ribosome have been used to develop a series of streptogramin A derivatives. We obtained twenty-two new and known molecules starting from the dalfopristin and virginiamycin M1 scaffolds. A structure-activity relationship refinement was performed to evaluate the capability of these compounds to suppress GSC growth and inhibit mitochondrial translation, either alone or in combination with quinupristin. Finally, quantitative ultra HPLC-mass spectrometry allowed us to assess the cell penetration of some of these derivatives. Among all, the fluorine derivatives of dalfopristin and virginiamycin M1, (16R)-1e and (16R)-2e, respectively, and flopristin resulted in being more potent than the corresponding lead compounds and penetrating to a greater extent into the cells. We, therefore, propose these three compounds for further evaluation in vivo as antineoplastic agents.
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Affiliation(s)
- Denise Sighel
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Povo, Trento, Italy.
| | - Giulia Battistini
- Laboratory of Bioorganic Chemistry, Department of Physics, University of Trento, Via Sommarive 14, 38123, Povo, Trento, Italy
| | - Emanuele Filiberto Rosatti
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Povo, Trento, Italy
| | - Jacopo Vigna
- Laboratory of Bioorganic Chemistry, Department of Physics, University of Trento, Via Sommarive 14, 38123, Povo, Trento, Italy
| | - Matteo Pavan
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via F. Marzolo 5, 35131, Padova, Italy
| | - Romina Belli
- Mass Spectrometry and Proteomics Core Facility, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Povo, Trento, Italy
| | - Daniele Peroni
- Mass Spectrometry and Proteomics Core Facility, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Povo, Trento, Italy
| | - Federica Alessandrini
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Povo, Trento, Italy
| | - Sara Longhi
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Povo, Trento, Italy
| | - Michael Pancher
- High Throughput Screening (HTS) and Validation Core Facility, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Povo, Trento, Italy
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Biomedicum, Solnavägen 9, 171 65, Solna, Stockholm, Sweden
| | - Stefano Moro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via F. Marzolo 5, 35131, Padova, Italy
| | - Alessandro Quattrone
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123, Povo, Trento, Italy
| | - Ines Mancini
- Laboratory of Bioorganic Chemistry, Department of Physics, University of Trento, Via Sommarive 14, 38123, Povo, Trento, Italy.
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3
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Liang X, Yoo M, Schempp T, Maejima S, Krische MJ. Ruthenium-Catalyzed Butadiene-Mediated Crotylation and Oxazaborolidine-Catalyzed Vinylogous Mukaiyama Aldol Reaction for The Synthesis of C1-C19 and C23-C35 of Neaumycin B. Angew Chem Int Ed Engl 2022; 61:e202214786. [PMID: 36322115 PMCID: PMC9772151 DOI: 10.1002/anie.202214786] [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: 10/07/2022] [Indexed: 11/07/2022]
Abstract
Neaumycin B is a femtomolar inhibitor of U87 human glioblastoma. Using a newly developed anti-diastereoselective ruthenium-catalyzed butadiene-mediated crotylation of primary alcohol proelectrophiles via hydrogen auto-transfer, as well as a novel variant of the catalytic asymmetric vinylogous Mukaiyama aldol (VMA) reaction applicable to linear aliphatic aldehydes and terminally methylated dienyl ketene acetals, preparation of the key C1-C19 and C23-C35 substructures of neaumycin B is achieved in 12 and 7 steps (LLS), respectively.
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Affiliation(s)
- Xinting Liang
- University of Texas at Austin, Department of Chemistry, 105 E 24th St. (A5300), Austin, TX 78712-1167 (USA)
| | - Minjin Yoo
- University of Texas at Austin, Department of Chemistry, 105 E 24th St. (A5300), Austin, TX 78712-1167 (USA)
| | - Tabitha Schempp
- University of Texas at Austin, Department of Chemistry, 105 E 24th St. (A5300), Austin, TX 78712-1167 (USA)
| | - Saki Maejima
- University of Texas at Austin, Department of Chemistry, 105 E 24th St. (A5300), Austin, TX 78712-1167 (USA)
| | - Michael J. Krische
- University of Texas at Austin, Department of Chemistry, 105 E 24th St. (A5300), Austin, TX 78712-1167 (USA)
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4
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Ruthenium‐Catalyzed Butadiene‐Mediated Crotylation and Oxazaborolidine‐Catalyzed Vinylogous Mukaiyama Aldol Reaction for The Synthesis of C1–C19 and C23–C35 of Neaumycin B. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202214786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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5
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Mansour A, Gagosz F. Expedited Total Synthesis of (±)-Brevianamide A via the Strategic Use of Gold(I) Catalysis. Org Lett 2022; 24:7200-7204. [PMID: 36170661 DOI: 10.1021/acs.orglett.2c02971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two concise and complementary routes to the polycyclic alkaloid (±)-brevianamide A from readily available amino acid building blocks are presented. Key to the synthesis is the strategic use of a gold(I)-catalyzed cascade process that quickly assembles the characteristic pseudoindoxyl motif of the natural product along with the two adjacent quaternary centers in a single step. This sequence, which exemplifies the structural complexity that can be achieved with gold catalysis, allowed for the shortest and highest-yield synthesis of (±)-brevianamide A to date (four steps LLS, 14% overall yield).
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Affiliation(s)
- Ali Mansour
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, K1N 6N5 Ottawa, Ontario, Canada
| | - Fabien Gagosz
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, K1N 6N5 Ottawa, Ontario, Canada
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6
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Abstract
Being able to effectively target RNA with potent ligands will open up a large number of potential therapeutic options. The knowledge on how to achieve this is ever expanding but an important question that remains open is what chemical matter is suitable to achieve this goal. The high flexibility of an RNA as well as its more limited chemical diversity and featureless binding sites can be difficult to target selectively but can be addressed by well-designed cyclic peptides. In this review we will provide an overview of reported cyclic peptide ligands for therapeutically relevant RNA targets and discuss the methods used to discover them. We will also provide critical insights into the properties required for potent and selective interaction and suggestions on how to assess these parameters. The use of cyclic peptides to target RNA is still in its infancy but the lessons learned from past examples can be adopted for the development of novel potent and selective ligands.
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Affiliation(s)
- Sunit Pal
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Peter 't Hart
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology, Dortmund, Germany
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7
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Bellotto O, Semeraro S, Bandiera A, Tramer F, Pavan N, Marchesan S. Polymer Conjugates of Antimicrobial Peptides (AMPs) with d-Amino Acids (d-aa): State of the Art and Future Opportunities. Pharmaceutics 2022; 14:pharmaceutics14020446. [PMID: 35214178 PMCID: PMC8879212 DOI: 10.3390/pharmaceutics14020446] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 12/15/2022] Open
Abstract
In recent years, antimicrobial peptides (AMPs) have enjoyed a renaissance, as the world is currently facing an emergency in terms of severe infections that evade antibiotics’ treatment. This is due to the increasing emergence and spread of resistance mechanisms. Covalent conjugation with polymers is an interesting strategy to modulate the pharmacokinetic profile of AMPs and enhance their biocompatibility profile. It can also be an effective approach to develop active coatings for medical implants and devices, and to avoid biofilm formation on their surface. In this concise review, we focus on the last 5 years’ progress in this area, pertaining in particular to AMPs that contain d-amino acids, as well as their role, and the advantages that may arise from their introduction into AMPs.
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Affiliation(s)
- Ottavia Bellotto
- Chemical and Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy; (O.B.); (S.S.)
| | - Sabrina Semeraro
- Chemical and Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy; (O.B.); (S.S.)
| | - Antonella Bandiera
- Life Sciences Department, University of Trieste, 34127 Trieste, Italy; (A.B.); (F.T.)
| | - Federica Tramer
- Life Sciences Department, University of Trieste, 34127 Trieste, Italy; (A.B.); (F.T.)
| | - Nicola Pavan
- Medical, Surgical and Health Sciences Department, University of Trieste, 34127 Trieste, Italy;
| | - Silvia Marchesan
- Chemical and Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy; (O.B.); (S.S.)
- Correspondence:
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8
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Xu F, Smith MW. A general approach to 2,2-disubstituted indoxyls: total synthesis of brevianamide A and trigonoliimine C. Chem Sci 2021; 12:13756-13763. [PMID: 34760160 PMCID: PMC8549782 DOI: 10.1039/d1sc03533a] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 09/15/2021] [Indexed: 12/11/2022] Open
Abstract
The indoxyl unit is a common structural motif in alkaloid natural products and bioactive compounds. Here, we report a general method that transforms readily available 2-substituted indoles into 2,2-disubstituted indoxyls via nucleophile coupling with a 2-alkoxyindoxyl intermediate and showcase its utility in short total syntheses of the alkaloids brevianamide A (7 steps) and trigonoliimine C (6 steps). The developed method is operationally simple and demonstrates broad scope in terms of nucleophile identity and indole substitution, tolerating 2-alkyl substituents and free indole N-H groups, elements beyond the scope of most prior approaches. Spirocyclic indoxyl products are also accessible via intramolecular nucleophilic trapping.
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Affiliation(s)
- Fan Xu
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas Texas 75390 USA
| | - Myles W Smith
- Department of Biochemistry, UT Southwestern Medical Center 5323 Harry Hines Blvd Dallas Texas 75390 USA
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9
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Jiang ZK, Hu XX, Xiao LL, Ren YR, Shakhtina AN, Lukianov DA, Osterman IA, Sergiev PV, Dontsova OA, Wang H, Wu G, You XF, Sun CH. Beilunmycin, a new virginiamycins antibiotic from mangrove-derived Streptomyces sp. 2BBP-J2 and the antibacterial activity by inhibiting protein translation. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2021; 23:992-1000. [PMID: 32924591 DOI: 10.1080/10286020.2020.1810669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 08/02/2020] [Indexed: 06/11/2023]
Abstract
One new virginiamycin derivative, 'beilunmycin' (1), and three known virginiamycin antibiotics, 16-hydroxy-virginiamycin M1 (2), virginiamycin M2 (3), and virginiamycin M1 (4), were isolated from the culture of a mangrove-derived endophytic Streptomyces sp. 2BBP-J2. The structures were characterized on the basis of their spectroscopic data, and the absolute configuration of 1 was established by ECD calculations. Compounds 1-4 exhibited antibacterial activities against Gram-positive bacteria, with MIC values in the range of 0.5-16 μg/ml. All the compounds demonstrated strong protein translation-stalling activity, with minimal concentrations detected with pDualrep2 in the range of 1.9-5.9 nmol.
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Affiliation(s)
- Zhong-Ke Jiang
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xin-Xin Hu
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Lan-Lin Xiao
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Yi-Ru Ren
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Anna N Shakhtina
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Dmitrii A Lukianov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 143025, Russia
| | - Ilya A Osterman
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119992, Russia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 143025, Russia
| | - Petr V Sergiev
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119992, Russia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 143025, Russia
| | - Olga A Dontsova
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119992, Russia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 143025, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 119992, Russia
| | - Hao Wang
- School of Pharmacy, Minzu University of China, Beijing 100081, China
- Key Laboratory of Ethnomedicine (Minzu University of China), Ministry of Education, Beijing 100081, China
| | - Gang Wu
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xue-Fu You
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Cheng-Hang Sun
- Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
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10
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Cai L, Seiple IB, Li Q. Modular Chemical Synthesis of Streptogramin and Lankacidin Antibiotics. Acc Chem Res 2021; 54:1891-1908. [PMID: 33792282 DOI: 10.1021/acs.accounts.0c00894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Continued, rapid development of antimicrobial resistance has become worldwide health crisis and a burden on the global economy. Decisive and comprehensive action is required to slow down the spread of antibiotic resistance, including increased investment in antibiotic discovery, sustainable policies that provide returns on investment for newly launched antibiotics, and public education to reduce the overusage of antibiotics, especially in livestock and agriculture. Without significant changes in the current antibiotic pipeline, we are in danger of entering a post-antibiotic era.In this Account, we summarize our recent efforts to develop next-generation streptogramin and lankacidin antibiotics that overcome bacterial resistance by means of modular chemical synthesis. First, we describe our highly modular, scalable route to four natural group A streptogramins antibiotics in 6-8 steps from seven simple chemical building blocks. We next describe the application of this route to the synthesis of a novel library of streptogramin antibiotics informed by in vitro and in vivo biological evaluation and high-resolution cryo-electron microscopy. One lead compound showed excellent inhibitory activity in vitro and in vivo against a longstanding streptogramin-resistance mechanism, virginiamycin acetyltransferase. Our results demonstrate that the combination of rational design and modular chemical synthesis can revitalize classes of antibiotics that are limited by naturally arising resistance mechanisms.Second, we recount our modular approaches toward lankacidin antibiotics. Lankacidins are a group of polyketide natural products with activity against several strains of Gram-positive bacteria but have not been deployed as therapeutics due to their chemical instability. We describe a route to several diastereomers of 2,18-seco-lankacidinol B in a linear sequence of ≤8 steps from simple building blocks, resulting in a revision of the C4 stereochemistry. We next detail our modular synthesis of several diastereoisomers of iso-lankacidinol that resulted in the structural reassignment of this natural product. These structural revisions raise interesting questions about the biosynthetic origin of lankacidins, all of which possessed uniform stereochemistry prior to these findings. Finally, we summarize the ability of several iso- and seco-lankacidins to inhibit the growth of bacteria and to inhibit translation in vitro, providing important insights into structure-function relationships for the class.
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Affiliation(s)
- Lingchao Cai
- Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-Forest Biomass, Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Key Lab of Biomass-Based Green Fuels and Chemicals, Nanjing Forestry University, Nanjing 210037, Jiangsu China
| | - Ian B. Seiple
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California 94158, United States
| | - Qi Li
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
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11
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Herlé B, Späth G, Schreyer L, Fürstner A. Total Synthesis of Mycinolide IV and Path‐Scouting for Aldgamycin N. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Bart Herlé
- Max-Planck-Institut für Kohlenforschung 45470 Mülheim/Ruhr Germany
| | - Georg Späth
- Max-Planck-Institut für Kohlenforschung 45470 Mülheim/Ruhr Germany
| | - Lucas Schreyer
- Max-Planck-Institut für Kohlenforschung 45470 Mülheim/Ruhr Germany
| | - Alois Fürstner
- Max-Planck-Institut für Kohlenforschung 45470 Mülheim/Ruhr Germany
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12
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Herlé B, Späth G, Schreyer L, Fürstner A. Total Synthesis of Mycinolide IV and Path-Scouting for Aldgamycin N. Angew Chem Int Ed Engl 2021; 60:7893-7899. [PMID: 33448619 PMCID: PMC8048839 DOI: 10.1002/anie.202016475] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/13/2021] [Indexed: 12/19/2022]
Abstract
Proof-of-concept is provided that a large estate of 16-membered macrolide antibiotics can be reached by a "unified" approach. The key building block was formed on scale by an asymmetric vinylogous Mukaiyama aldol reaction; its alkene terminus was then converted either into the corresponding methyl ketone by Wacker oxidation or into a chain-extended aldehyde by catalyst-controlled branch-selective asymmetric hydroformylation. These transformations ultimately opened access to two structurally distinct series of macrolide targets. Notable late-stage maneuvers comprise a rare example of a ruthenium-catalyzed redox isomerization of an 1,3-enyne-5-ol into a 1,3-diene-5-one derivative, as well as the elaboration of a tertiary propargylic alcohol into an acyloin by trans-hydrostannation/Chan-Lam-type coupling. Moreover, this case study illustrates the underutilized possibility of forging complex macrolactone rings by transesterification under essentially neutral conditions.
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Affiliation(s)
- Bart Herlé
- Max-Planck-Institut für Kohlenforschung45470Mülheim/RuhrGermany
| | - Georg Späth
- Max-Planck-Institut für Kohlenforschung45470Mülheim/RuhrGermany
| | - Lucas Schreyer
- Max-Planck-Institut für Kohlenforschung45470Mülheim/RuhrGermany
| | - Alois Fürstner
- Max-Planck-Institut für Kohlenforschung45470Mülheim/RuhrGermany
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13
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Fostier CR, Monlezun L, Ousalem F, Singh S, Hunt JF, Boël G. ABC-F translation factors: from antibiotic resistance to immune response. FEBS Lett 2020; 595:675-706. [PMID: 33135152 DOI: 10.1002/1873-3468.13984] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 12/24/2022]
Abstract
Energy-dependent translational throttle A (EttA) from Escherichia coli is a paradigmatic ABC-F protein that controls the first step in polypeptide elongation on the ribosome according to the cellular energy status. Biochemical and structural studies have established that ABC-F proteins generally function as translation factors that modulate the conformation of the peptidyl transferase center upon binding to the ribosomal tRNA exit site. These factors, present in both prokaryotes and eukaryotes but not in archaea, use related molecular mechanisms to modulate protein synthesis for heterogenous purposes, ranging from antibiotic resistance and rescue of stalled ribosomes to modulation of the mammalian immune response. Here, we review the canonical studies characterizing the phylogeny, regulation, ribosome interactions, and mechanisms of action of the bacterial ABC-F proteins, and discuss the implications of these studies for the molecular function of eukaryotic ABC-F proteins, including the three human family members.
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Affiliation(s)
- Corentin R Fostier
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Laura Monlezun
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Farès Ousalem
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Shikha Singh
- Department of Biological Sciences, 702A Sherman Fairchild Center, Columbia University, New York, NY, USA
| | - John F Hunt
- Department of Biological Sciences, 702A Sherman Fairchild Center, Columbia University, New York, NY, USA
| | - Grégory Boël
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
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14
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Abstract
Streptogramins are antibiotics produced by several species of Streptomyces bacteria that are used in both human and veterinary medicine. Group A streptogramins comprise 23-membered macrocyclic polyketide/nonribosomal peptide hybrids for which several innovative, fully synthetic routes have been developed. Herein we describe in detail our scalable routes to natural group A streptogramins and compare these routes to other reported syntheses.
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Affiliation(s)
- Qi Li
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California 94158, United States
| | - Ian B Seiple
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California 94158, United States
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15
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Sušnik P, Koert U. Studies Towards the Synthesis of Pristinamycin II
A. ChemistrySelect 2020. [DOI: 10.1002/slct.202003411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Peter Sušnik
- Fachbereich Chemie Philipps-Universität Marburg Hans-Meerwein Strasse 4 35032 Marburg Germany
| | - Ulrich Koert
- Fachbereich Chemie Philipps-Universität Marburg Hans-Meerwein Strasse 4 35032 Marburg Germany
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16
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Lawer A, Epton RG, Stephens TC, Palate KY, Lodi M, Marotte E, Lamb KJ, Sangha JK, Lynam JM, Unsworth WP. Evaluating the Viability of Successive Ring-Expansions Based on Amino Acid and Hydroxyacid Side-Chain Insertion. Chemistry 2020; 26:12674-12683. [PMID: 32432817 PMCID: PMC7589337 DOI: 10.1002/chem.202002164] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Indexed: 01/20/2023]
Abstract
The outcome of ring-expansion reactions based on amino/hydroxyacid side-chain insertion is strongly dependent on ring size. This manuscript, which builds upon our previous work on Successive Ring Expansion (SuRE) methods, details efforts to better define the scope and limitations of these reactions on lactam and β-ketoester ring systems with respect to ring size and additional functionality. The synthetic results provide clear guidelines as to which substrate classes are more likely to be successful and are supported by computational results, using a density functional theory (DFT) approach. Calculating the relative Gibbs free energies of the three isomeric species that are formed reversibly during ring expansion enables the viability of new synthetic reactions to be correctly predicted in most cases. The new synthetic and computational results are expected to support the design of new lactam- and β-ketoester-based ring-expansion reactions.
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Affiliation(s)
- Aggie Lawer
- Department of ChemistryUniversity of YorkYorkYO10 5DDUK
| | - Ryan G. Epton
- Department of ChemistryUniversity of YorkYorkYO10 5DDUK
| | | | | | - Mahendar Lodi
- Department of ChemistryUniversity of YorkYorkYO10 5DDUK
| | - Emilie Marotte
- ENSICAEN6 Boulevard Maréchal Juin, CS 4505314050Caen Cedex 04France
| | - Katie J. Lamb
- Department of ChemistryUniversity of YorkYorkYO10 5DDUK
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17
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Blair DJ, Burke MD. Modular synthesis enables molecular ju-jitsu in the fight against antibiotic resistance. Nature 2020; 586:32-33. [DOI: 10.1038/d41586-020-02565-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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18
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Synthetic group A streptogramin antibiotics that overcome Vat resistance. Nature 2020; 586:145-150. [PMID: 32968273 PMCID: PMC7546582 DOI: 10.1038/s41586-020-2761-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 08/19/2020] [Indexed: 11/08/2022]
Abstract
Natural products serve as chemical blueprints for the majority of antibiotics in our clinical arsenal. The evolutionary process by which these molecules arise is inherently accompanied by the co-evolution of resistance mechanisms that shorten the clinical lifetime of any given class1. Virginiamycin acetyltransferases (Vats) are resistance proteins that provide protection against streptogramins2, potent Gram-positive antibiotics that inhibit the bacterial ribosome3. Due to the challenge of selectively modifying the chemically complex, 23-membered macrocyclic scaffold of group A streptogramins, analogs that overcome Vat resistance have not been previously accessed2. Here we report the design, synthesis, and antibacterial evaluation of group A streptogramin antibiotics with unprecedented structural variability. Using cryo-electron microscopy and forcefield-based refinement, we characterize the binding of eight analogs to the bacterial ribosome at high resolution, revealing new binding interactions that extend into the peptidyl tRNA binding site and towards synergistic binders that occupy the nascent peptide exit tunnel (NPET). One of these analogs has excellent activity against several streptogramin-resistant strains of S. aureus, exhibits decreased acetylation rates in vitro, and is effective at lowering bacterial load in a mouse model of infection. Our results demonstrate that the combination of rational design and modular chemical synthesis can revitalize classes of antibiotics that are limited by naturally arising resistance mechanisms.
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19
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Cai L, Yao Y, Yeon SK, Seiple IB. Modular Approaches to Lankacidin Antibiotics. J Am Chem Soc 2020; 142:15116-15126. [PMID: 32786797 DOI: 10.1021/jacs.0c06648] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Lankacidins are a class of polyketide natural products isolated from Streptomyces spp. that show promising antimicrobial activity. Owing to their complex molecular architectures and chemical instability, structural assignment and derivatization of lankacidins are challenging tasks. Herein we describe three fully synthetic approaches to lankacidins that enable access to new structural variability within the class. We use these routes to systematically generate stereochemical derivatives of both cyclic and acyclic lankacidins. Additionally, we access a new series of lankacidins bearing a methyl group at the C4 position, a modification intended to increase chemical stability. In the course of this work, we discovered that the reported structures for two natural products of the lankacidin class were incorrect, and we determine the correct structures of 2,18-seco-lankacidinol B and iso-lankacidinol. We also evaluate the ability of several iso- and seco-lankacidins to inhibit the growth of bacteria and to inhibit translation in vitro. This work grants insight into the rich chemical complexity of this class of antibiotics and provides an avenue for further structural derivatization.
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Affiliation(s)
- Lingchao Cai
- Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-Forest Biomass, Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jinagsu Key Lab of Biomass-Based Green Fuels and Chemicals, Nanjing Forestry University, Nanjing, 210037 Jiangsu, China.,Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California at San Francisco, San Francisco, California 94158, United States
| | - Yanmin Yao
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California at San Francisco, San Francisco, California 94158, United States
| | - Seul Ki Yeon
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California at San Francisco, San Francisco, California 94158, United States
| | - Ian B Seiple
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California at San Francisco, San Francisco, California 94158, United States
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20
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Liu K, Huigens RW. Instructive Advances in Chemical Microbiology Inspired by Nature's Diverse Inventory of Molecules. ACS Infect Dis 2020; 6:541-562. [PMID: 31842540 PMCID: PMC7346871 DOI: 10.1021/acsinfecdis.9b00413] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Natural product antibiotics have played an essential role in the treatment of bacterial infection in addition to serving as useful tools to explore the intricate biology of bacteria. Our current arsenal of antibiotics operate through the inhibition of well-defined bacterial targets critical for replication and growth. Pathogenic bacteria effectively utilize a diversity of mechanisms that lead to acquired resistance and/or innate tolerance toward antibiotic therapies, which can result in devastating consequences to human life. Several research groups have established innovative programs that work at the chemistry-biology interface to develop new molecules that aim to define and address concerns related to antibiotic resistance and tolerance. In this Review, we present recent progress by select research groups that highlight a diversity of integrated chemical biology and medicinal chemistry approaches aimed at the development and utilization of chemical tools that have led to promising new microbiological insights that may lead to significant clinical advances regarding the treatment of pathogenic bacteria.
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Affiliation(s)
- Ke Liu
- 1345 Center Drive, Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Robert W. Huigens
- 1345 Center Drive, Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
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21
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Hernandez LW, Sarlah D. Empowering Synthesis of Complex Natural Products. Chemistry 2019; 25:13248-13270. [DOI: 10.1002/chem.201901808] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 06/08/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Lucas W. Hernandez
- Department of Chemistry University of Illinois at Urbana-Champaign 600 South Mathews Avenue 270 RAL, Box 107-5 Urbana IL 61801 USA
| | - David Sarlah
- Department of Chemistry University of Illinois at Urbana-Champaign 600 South Mathews Avenue 270 RAL, Box 107-5 Urbana IL 61801 USA
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22
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Abstract
Modular, fully synthetic routes to structurally complex natural products provide useful avenues to access chemical diversity. Herein we report a concise route to virginiamycin M2, a member of the group A streptogramin class of natural products that inhibits bacterial protein synthesis. Our approach features a longest linear sequence of six steps from 7 simple building blocks, and is the shortest and highest yielding synthesis of any member of the streptogramin class reported to date. We believe this route will enable access to unexplored structural diversity and may serve as a useful tool to improve the therapeutic potential of the streptogramin class of antibiotics.
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Affiliation(s)
- Qi Li
- Department of Pharmaceutical Chemistry and Cardiovascular Reseach Institute, University of California, San Francisco, San Francisco, California 94158, United States
| | - Ian B Seiple
- Department of Pharmaceutical Chemistry and Cardiovascular Reseach Institute, University of California, San Francisco, San Francisco, California 94158, United States
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23
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Abstract
This review describes a selection of macrocyclic natural products and structurally modified analogs containing peptidic and non-peptidic elements as structural features that potentially modulate cellular permeability. Examples range from exclusively peptidic structures like cyclosporin A or phepropeptins to compounds with mostly non-peptidic character, such as telomestatin or largazole. Furthermore, semisynthetic approaches and synthesis platforms to generate general and focused libraries of compounds at the interface of cyclic peptides and non-peptidic macrocycles are discussed.
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24
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Goethe O, Heuer A, Ma X, Wang Z, Herzon SB. Antibacterial properties and clinical potential of pleuromutilins. Nat Prod Rep 2019; 36:220-247. [PMID: 29979463 DOI: 10.1039/c8np00042e] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Covering: up to 2018Pleuromutilins are a clinically validated class of antibiotics derived from the fungal diterpene (+)-pleuromutilin (1). Pleuromutilins inhibit bacterial protein synthesis by binding to the peptidyl transferase center (PTC) of the ribosome. In this review we summarize the biosynthesis and recent total syntheses of (+)-pleuromutilin (1). We review the mode of interaction of pleuromutilins with the bacterial ribosome, which involves binding of the C14 extension and the tricyclic core to the P and A sites of the PTC, respectively. We provide an overview of existing clinical agents, and discuss the three primary modes of bacterial resistance (mutations in ribosomal protein L3, Cfr methylation, and efflux). Finally we collect structure-activity relationships from publicly available reports, and close with some forward looking statements regarding future development.
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Affiliation(s)
- Olivia Goethe
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA.
| | - Abigail Heuer
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA.
| | - Xiaoshen Ma
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA.
| | - Zhixun Wang
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA.
| | - Seth B Herzon
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA. and Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut 06520, USA
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25
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Stephens TC, Lawer A, French T, Unsworth WP. Iterative Assembly of Macrocyclic Lactones using Successive Ring Expansion Reactions. Chemistry 2018; 24:13947-13953. [PMID: 30011360 PMCID: PMC6334170 DOI: 10.1002/chem.201803064] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 07/12/2018] [Indexed: 12/27/2022]
Abstract
Macrocyclic lactones can be prepared from lactams and hydroxyacid derivatives via an efficient 3- or 4-atom iterative ring expansion protocol. The products can also be expanded using amino acid-based linear fragments, meaning that macrocycles with precise sequences of hydroxy- and amino acids can be assembled in high yields by "growing" them from smaller rings, using a simple procedure in which high dilution is not required. The method should significantly expedite the practical synthesis of diverse nitrogen containing macrolide frameworks.
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26
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Polikanov YS, Aleksashin NA, Beckert B, Wilson DN. The Mechanisms of Action of Ribosome-Targeting Peptide Antibiotics. Front Mol Biosci 2018; 5:48. [PMID: 29868608 PMCID: PMC5960728 DOI: 10.3389/fmolb.2018.00048] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 04/23/2018] [Indexed: 12/31/2022] Open
Abstract
The ribosome is one of the major targets in the cell for clinically used antibiotics. However, the increase in multidrug resistant bacteria is rapidly reducing the effectiveness of our current arsenal of ribosome-targeting antibiotics, highlighting the need for the discovery of compounds with new scaffolds that bind to novel sites on the ribosome. One possible avenue for the development of new antimicrobial agents is by characterization and optimization of ribosome-targeting peptide antibiotics. Biochemical and structural data on ribosome-targeting peptide antibiotics illustrates the large diversity of scaffolds, binding interactions with the ribosome as well as mechanism of action to inhibit translation. The availability of high-resolution structures of ribosomes in complex with peptide antibiotics opens the way to structure-based design of these compounds as novel antimicrobial agents.
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Affiliation(s)
- Yury S Polikanov
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States.,Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, IL, United States
| | - Nikolay A Aleksashin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, United States
| | - Bertrand Beckert
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
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27
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Zhu L, Hong R. Pursuing effective Gram-negative antibiotics: The chemical synthesis of negamycin. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.04.059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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28
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Peters DS, Romesberg FE, Baran PS. Scalable Access to Arylomycins via C-H Functionalization Logic. J Am Chem Soc 2018; 140:2072-2075. [PMID: 29381350 PMCID: PMC5817625 DOI: 10.1021/jacs.8b00087] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
Arylomycins
are a promising class of “latent” antibacterial
natural products currently in preclinical development. Access to analogues
within this family has previously required a lengthy route involving
multiple functional group manipulations that is costly and time-intensive
on scale. This study presents a simplified route predicated on simple
C–H functionalization logic that is enabled by a Cu-mediated
oxidative phenol coupling that mimics the putative biosynthesis. This
operationally simple macrocyclization is the largest of its
kind and can be easily performed on gram scale. The application of
this new route to a formal synthesis of the natural product and a
collection of new analogues along with their biological evaluation
is also reported.
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Affiliation(s)
- David S Peters
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Floyd E Romesberg
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Phil S Baran
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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29
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Padarti A, Kim D, Han H. Highly Stereoselective 2-Oxonia-Cope Rearrangement: A Platform Enabling At-Will Control of Regio-, Enantio-, and Diastereoselectivity in the Vinylogous Aldol Reactions of Aldehydes. Org Lett 2018; 20:756-759. [PMID: 29345942 DOI: 10.1021/acs.orglett.7b03895] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A distinctly different approach for the vinylogous aldolation of aldehydes is described, which exploits 2-oxonia-Cope rearrangement reactions between two readily available partners, a set of rationally designed chiral homoallylic alcohol synthons and aldehydes, under simple conditions. In these processes, chirality transfer from the former to the latter is nearly perfect, giving rise to excellent enantio- and diastereoselectivity without the regioselectivity issue associated with traditional vinylogous aldol reactions.
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Affiliation(s)
- Akhil Padarti
- Department of Chemistry, University of Texas at San Antonio , San Antonio, Texas 78249, United States
| | - Dongeun Kim
- Department of Chemistry, University of Texas at San Antonio , San Antonio, Texas 78249, United States
| | - Hyunsoo Han
- Department of Chemistry, University of Texas at San Antonio , San Antonio, Texas 78249, United States
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