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Marine Cyclic Peptides: Antimicrobial Activity and Synthetic Strategies. Mar Drugs 2022; 20:md20060397. [PMID: 35736200 PMCID: PMC9230156 DOI: 10.3390/md20060397] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/06/2022] [Accepted: 06/13/2022] [Indexed: 01/29/2023] Open
Abstract
Oceans are a rich source of structurally unique bioactive compounds from the perspective of potential therapeutic agents. Marine peptides are a particularly interesting group of secondary metabolites because of their chemistry and wide range of biological activities. Among them, cyclic peptides exhibit a broad spectrum of antimicrobial activities, including against bacteria, protozoa, fungi, and viruses. Moreover, there are several examples of marine cyclic peptides revealing interesting antimicrobial activities against numerous drug-resistant bacteria and fungi, making these compounds a very promising resource in the search for novel antimicrobial agents to revert multidrug-resistance. This review summarizes 174 marine cyclic peptides with antibacterial, antifungal, antiparasitic, or antiviral properties. These natural products were categorized according to their sources—sponges, mollusks, crustaceans, crabs, marine bacteria, and fungi—and chemical structure—cyclic peptides and depsipeptides. The antimicrobial activities, including against drug-resistant microorganisms, unusual structural characteristics, and hits more advanced in (pre)clinical studies, are highlighted. Nocathiacins I–III (91–93), unnarmicins A (114) and C (115), sclerotides A (160) and B (161), and plitidepsin (174) can be highlighted considering not only their high antimicrobial potency in vitro, but also for their promising in vivo results. Marine cyclic peptides are also interesting models for molecular modifications and/or total synthesis to obtain more potent compounds, with improved properties and in higher quantity. Solid-phase Fmoc- and Boc-protection chemistry is the major synthetic strategy to obtain marine cyclic peptides with antimicrobial properties, and key examples are presented guiding microbiologist and medicinal chemists to the discovery of new antimicrobial drug candidates from marine sources.
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Manne S, Sharma A, Sazonovas A, El-Faham A, de la Torre BG, Albericio F. Understanding OxymaPure as a Peptide Coupling Additive: A Guide to New Oxyma Derivatives. ACS OMEGA 2022; 7:6007-6023. [PMID: 35224362 PMCID: PMC8867806 DOI: 10.1021/acsomega.1c06342] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
An in silico study, using the GALAS algorithm available in ACD/PhysChem Suite, was performed to calculate the pK a(s) of various oximes with potential application as peptide coupling additives. Among the known oximes and predicted structures, OxymaPure is superior based on the pK a values calculated, confirming the results described in the literature and validating this algorithm for further use in that field. Among the nondescribed oximes, based on pK a calculation, ethyl 2-(hydroxyimino)-2-nitroacetate seems to be a potential candidate to be used as an additive during peptide coupling.
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Affiliation(s)
- Srinivasa
Rao Manne
- Peptide
Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Westville, Durban 4000, South Africa
| | - Anamika Sharma
- Peptide
Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Westville, Durban 4000, South Africa
- KwaZulu-Natal
Research Innovation and Sequencing Platform (KRISP), School of Laboratory
Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South
Africa
- Department
of Chemistry, Prayoga Institute of Education
Research (PIER), Bangalore 560082, India
| | - Andrius Sazonovas
- Advanced
Chemistry Development, Inc. (ACD/Labs), 8 King Street East, Suite 107, Toronto, Ontario M5C 1B5, Canada
| | - Ayman El-Faham
- Department
of Chemistry, Faculty of Science, Alexandria
University, P.O. Box 426,
Ibrahimia, Alexandria 21321, Egypt
| | - Beatriz G. de la Torre
- Peptide
Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Westville, Durban 4000, South Africa
- KwaZulu-Natal
Research Innovation and Sequencing Platform (KRISP), School of Laboratory
Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South
Africa
| | - Fernando Albericio
- Peptide
Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Westville, Durban 4000, South Africa
- Institute
for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain
- CIBER-BBN,
Networking Centre on Bioengineering, Biomaterials and Nanomedicine,
and Department of Organic Chemistry, University
of Barcelona, Martí
i Franqués 1-11, 08028 Barcelona, Spain
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Smajlagic I, Carlson B, Dudding T. Brønsted Acid Organocatalyzed Three-Component Hydroamidation Reactions of Vinyl Ethers. J Org Chem 2021; 86:4171-4181. [PMID: 33626274 DOI: 10.1021/acs.joc.0c03017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydroamidation of carbon-carbon double bonds is an attractive strategy for installing nitrogen functionality into molecular scaffolds and, with it, increasing molecular complexity. To date, metal-based approaches have dominated this area of chemical synthesis, despite the drawbacks of air and moisture sensitivity, limited functional group tolerance, toxicity, and/or high cost often associated with using metals. Here, in offering an alternative solution, we disclose an operationally simple, metal-free, one-pot, regioselective, multicomponent synthetic procedure for the hydroamidation of carbon-carbon double bonds. This method features mild reaction conditions and utilizes isocyanides and vinyl ethers for the rapid and modular synthesis of privileged α-oxygenated amide scaffolds. In unraveling the mechanistic underpinning of this non-metal-based reactivity, we present kinetic solvent isotope effect studies, variable time normalization analysis, and density functional theory computations offering insight into the mechanism of this multistep catalytic hydroamidation process.
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Affiliation(s)
- Ivor Smajlagic
- Department of Chemistry, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON L2S 3A1, Canada
| | - Brenden Carlson
- Department of Chemistry, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON L2S 3A1, Canada
| | - Travis Dudding
- Department of Chemistry, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON L2S 3A1, Canada
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El-Faham A, Albericio F, Manne SR, de la Torre BG. OxymaPure Coupling Reagents: Beyond Solid-Phase Peptide Synthesis. SYNTHESIS-STUTTGART 2020. [DOI: 10.1055/s-0040-1706296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
AbstractOxymaPure [ethyl 2-cyano-2-(hydroxyimino)acetate] is an exceptional reagent with which to suppress racemization and enhance coupling efficiency during amide bond formation. The tremendous popularity of OxymaPure has led to the development of several Oxyma-based reagents. OxymaPure and its derived reagents are widely used in solid- and solution-phase peptide chemistry. This review summarizes the recent developments and applications of OxymaPure and Oxyma-based reagents in peptide chemistry, in particular in solution-phase chemistry. Moreover, the side reaction associated with OxymaPure is also discussed.1 Introduction2 Oxyma-Based Coupling Reagents2.1 Aminium/Uronium Salts of OxymaPure2.2 Phosphonium Salts of OxymaPure2.3 Oxyma-Based Phosphates2.4 Sulfonate Esters of OxymaPure2.5 Benzoate Esters of OxymaPure2.6 Carbonates of OxymaPure Derivatives3 OxymaPure Derivatives4 Other Oxime-Based Additives and Coupling Reagents5 Side Reactions Using OxymaPure Derivatives6 Conclusion7 List of Abbreviations
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Affiliation(s)
- Ayman El-Faham
- Department of Chemistry, College of Science, King Saud University
- Department of Chemistry, Faculty of Science, Alexandria University,
| | - Fernando Albericio
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal
- Department of Chemistry, College of Science, King Saud University
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC)
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, and Department of Organic Chemistry, University of Barcelona
| | - Srinivasa Rao Manne
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal
| | - Beatriz G. de la Torre
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal
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Michigami K, Sakaguchi T, Takemoto Y. Catalytic Dehydrative Peptide Synthesis with gem-Diboronic Acids. ACS Catal 2019. [DOI: 10.1021/acscatal.9b03894] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Kenichi Michigami
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Tatsuhiko Sakaguchi
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Yoshiji Takemoto
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
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Rajadurai R, Padmanabhan R, Ananthan S. Synthesis, characterization and complexation studies of bis-oxy biphenyl based novel diamides. ARAB J CHEM 2019. [DOI: 10.1016/j.arabjc.2014.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Langille NF, Horne DB. Discovery and Development of AMG 333: A TRPM8 Antagonist for Migraine. ACS SYMPOSIUM SERIES 2019. [DOI: 10.1021/bk-2019-1332.ch006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Neil F. Langille
- Pivotal Drug Substance Synthetic Technologies, Amgen, Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Daniel B. Horne
- Discovery Research, Amgen, Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States
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Synthetic studies towards Pseudoxylallemycin B, an antibiotic active against gram-negative bacteria: Total synthesis of 3-epi-Pseudoxylallemycin B. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.06.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Huang T, Toro M, Lee R, Hui DS, Edwards JL. Multi-functional derivatization of amine, hydroxyl, and carboxylate groups for metabolomic investigations of human tissue by electrospray ionization mass spectrometry. Analyst 2018; 143:3408-3414. [PMID: 29915825 DOI: 10.1039/c8an00490k] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Metabolomics, the study of small molecules involved in cellular processes, offers the potential to reveal insights into the pathophysiology of disease states. Analysis of metabolites by electrospray mass spectrometry is complicated by their structural diversity. Amine, hydroxyl, and carboxylate groups all affect signal responses differently based on their polarity and proton affinity. This heterogeneity of signal response, sensitivity, and resistance to competing ionization complicates metabolite quantitation. Such limitations can be mitigated by a dual derivatization scheme. In this work, primary amine and hydroxyl groups are tagged with a linear acyl chloride head containing a tertiary amine tail, followed by carboxylate groups coupled to a linear amine tag with a tertiary amine tail. This tagging scheme increases analyte proton affinity and hydrophobicity. In the case of carboxylate groups, the inherent anionic charge is inverted to a cationic charge. This dual tagging is completed within 2.5 hours, diminishes adduct formation, and improves sensitivity by >75-fold. The average limit of detection for 23 metabolites was 38 nM and the R2 was 0.97. This process was used to investigate metabolite changes from human tissue. Examination of diabetic and non-diabetic human tissue showed marked changes in both energy metabolites and amino acids. Further examination of the tissue showed that HbA1C value is inversely correlated with fumarate levels. This technique potentially allows for the analysis of virtually all metabolites in a single analytical run. Thus, it may lead to a more complete picture of metabolic dysfunction in human disease.
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Affiliation(s)
- Tianjiao Huang
- Department of Chemistry, Saint Louis University, 3501 Laclede Ave, St louis MO, USA.
| | - Maria Toro
- Department of Chemistry, Saint Louis University, 3501 Laclede Ave, St louis MO, USA. and Department of Chemistry, Duke University, Durham, NC, USA
| | - Richard Lee
- Cardiovascular Comprehensive Care Center, Saint Louis University, 3635 Vista Ave, St louis MO, USA
| | - Dawn S Hui
- Cardiovascular Comprehensive Care Center, Saint Louis University, 3635 Vista Ave, St louis MO, USA
| | - James L Edwards
- Department of Chemistry, Saint Louis University, 3501 Laclede Ave, St louis MO, USA.
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Reszka P, Schulz R, Methling K, Lalk M, Bednarski PJ. Synthesis, enzymatic evaluation, and docking studies of fluorogenic caspase 8 tetrapeptide substrates. ChemMedChem 2010; 5:103-17. [PMID: 19918833 DOI: 10.1002/cmdc.200900356] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The synthesis, enzymatic evaluation, and molecular modeling studies of new fluorogenic tetrapeptide-based substrates selective for caspase 8, having the general structure Ac-IETD-AXX, are described. Various fluorescent reporter groups (AXX), i.e., 3- and 4-substituted coumarins and quinolin-2(1H)-ones were synthesized by von Pechmann condensation. They were subsequently coupled with the caspase-8-selective tetrapeptide Ac-IETD-OH under newly developed synthetic conditions to give the desired substrates in good yields and in high enantiomeric purity. Based on K(M) and V(max) values, the new compounds proved to be excellent substrates for recombinant human caspase 8. In contrast, the K(M) values for the same compounds as substrates for human caspase 3 were approximately 10-20-fold higher. Molecular modeling studies based on the X-ray crystal structures of both human caspases 3 and 8 revealed that there is sufficient room within both active sites to accommodate substrates with moderately bulky substituents in the 3- and 4-positions of the fluorogenic coumarins and quinolin-2(1H)-ones. Automated docking of the substrates into the active sites of both human caspases 3 and 8 with the program AutoDock 3 gave structures similar to the published crystallographic structures for the same tetrapeptide bound to caspase 8 in the form of an irreversible inhibitor. The calculated binding energies for the new substrates to either caspase 3 or 8 showed little difference between the substrates, consistent with the K(M) data. In addition, the calculated binding energies (DeltaG) to caspase 8 were considerably more negative than those to caspase 3, also consistent with the K(M) data. A possible molecular interaction that might explain the selectivity of the IETD tetrapeptide motif for caspase 8 over caspase 3 is discussed.
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Affiliation(s)
- Przemysław Reszka
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, University of Greifswald, F.-L.-Jahn Strasse 17, 17487 Greifswald, Germany
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Ghosh AK, Xu CX. A convergent synthesis of the proposed structure of antitumor depsipeptide stereocalpin A. Org Lett 2009; 11:1963-6. [PMID: 19354233 DOI: 10.1021/ol900412u] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The total synthesis of the proposed structure of anticancer agent stereocalpin A is described. The synthesis features a diastereoselective synthesis of a 5-hydroxy-2,4-dimethyl-3-oxooctanoic acid unit with asymmetric anti- and syn-aldol reactions as the key steps. Initial cycloamidation led to complete epimerization at the C-11 stereocenter due to unique steric constraints in the 12-membered depsipeptide ring. A late-stage methylation strategy led to the synthesis of the proposed structure of stereocalpin A.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, USA.
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Richard JA, Jean L, Schenkels C, Massonneau M, Romieu A, Renard PY. Self-cleavable chemiluminescent probes suitable for protease sensing. Org Biomol Chem 2009; 7:2941-57. [DOI: 10.1039/b905725k] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Stasiak M, Słomczyńska U, Olma A, Leplawy MT. Chemistry of alpha-hydroxymethylserine: problems and solutions. J Pept Sci 2008; 14:1163-72. [PMID: 18646253 DOI: 10.1002/psc.1054] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Further improvements related to the synthesis of peptides containing HmS are presented. Efficient synthetic protocols have been developed to synthesize "difficult" sequences containing a C-terminal HmS residue, MeA-HmS or consecutive HmS. Preparative methods for orthogonal N- and/or C-protected HmS(Ipr) derivatives are described. Their compatibility with standard solution or solid-phase peptide chemistry protocols allows synthetic flexibility toward HmS-containing peptides. In the synthesis of the sterically hindered dipeptides with the C-terminal HmS(Ipr) residue, HATU proves the highest efficiency, as compared with the fluoride and PyBroP/DMAP coupling methods. The HATU method also outperforms the fluoride activation in the solid-phase assembly of HmS homosequence. Specific protocols are described to overcome an undesired cyclization to diketopiperazines that occurs during the removal of Fmoc from dipeptides with the C-terminal HmS(Ipr) or HmS residues, thus precluding their C-->N elongation. The successful protocols involve: (i) the 2+1 condensation using mixed anhydride activation yielding the desired product with the highest optical integrity or (ii) use of the 2-chlorotrityl resin as a solid support sterically suppressing the undesired cleavage due to diketopiperazine formation. The latter approach allows the mild conditions of peptide cleavage from solid support, preserving the isopropylidene protection and minimizing the undesired N-->O-acyl migration that was observed under prolonged acid treatment used for cleaving the HmS peptide from the Wang resin.
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Affiliation(s)
- Marcin Stasiak
- Institute of Organic Chemistry, Technical University, Zeromskiego 116, 90-924 Łódź, Poland
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Vogel S, Kaufmann D, Pojarová M, Müller C, Pfaller T, Kühne S, Bednarski PJ, Angerer EV. Aroyl hydrazones of 2-phenylindole-3-carbaldehydes as novel antimitotic agents. Bioorg Med Chem 2008; 16:6436-47. [DOI: 10.1016/j.bmc.2008.04.071] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2007] [Revised: 04/25/2008] [Accepted: 04/30/2008] [Indexed: 11/30/2022]
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