1
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Petersen ME, Brant MG, Lasalle M, Fung VKC, Rojas AH, Wong J, Das S, Barnscher SD, Rich JR, Winters GC. Structure-Activity Relationships of Bis-Intercalating Peptides and Their Application as Antibody-Drug Conjugate Payloads. J Med Chem 2023. [PMID: 37307297 DOI: 10.1021/acs.jmedchem.3c00760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Synthetic analogs based on the DNA bis-intercalating natural product peptides sandramycin and quinaldopeptin were investigated as antibody drug conjugate (ADC) payloads. Synthesis, biophysical characterization, and in vitro potency of 34 new analogs are described. Conjugation of an initial drug-linker derived from a novel bis-intercalating peptide produced an ADC that was hydrophobic and prone to aggregation. Two strategies were employed to improve ADC physiochemical properties: addition of a solubilizing group in the linker and the use of an enzymatically cleavable hydrophilic mask on the payload itself. All ADCs showed potent in vitro cytotoxicity in high antigen expressing cells; however, masked ADCs were less potent than payload matched unmasked ADCs in lower antigen expressing cell lines. Two pilot in vivo studies were conducted using stochastically conjugated DAR4 anti-FRα ADCs, which showed toxicity even at low doses, and site-specific conjugated (THIOMAB) DAR2 anti-cMet ADCs that were well tolerated and highly efficacious.
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Affiliation(s)
- Mark E Petersen
- ADC Therapeutic Development, Zymeworks Inc., Vancouver, BC V5T 1G4, Canada
| | - Michael G Brant
- ADC Therapeutic Development, Zymeworks Inc., Vancouver, BC V5T 1G4, Canada
| | - Manuel Lasalle
- ADC Therapeutic Development, Zymeworks Inc., Vancouver, BC V5T 1G4, Canada
| | - Vincent K C Fung
- ADC Therapeutic Development, Zymeworks Inc., Vancouver, BC V5T 1G4, Canada
| | | | - Jodi Wong
- ADC Therapeutic Development, Zymeworks Inc., Vancouver, BC V5T 1G4, Canada
| | - Samir Das
- ADC Therapeutic Development, Zymeworks Inc., Vancouver, BC V5T 1G4, Canada
| | - Stuart D Barnscher
- ADC Therapeutic Development, Zymeworks Inc., Vancouver, BC V5T 1G4, Canada
| | - Jamie R Rich
- ADC Therapeutic Development, Zymeworks Inc., Vancouver, BC V5T 1G4, Canada
| | - Geoffrey C Winters
- Technical and Manufacturing Operations, Zymeworks Inc., Vancouver, BC V5T 1G4, Canada
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2
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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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3
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Leko M, Filippova P, Dorosh M, Rustler K, Bruckdorfer T, Burov S. 2-Chlorotrityl Chloride and 4-Methylbenzhydryl Bromide Resin Loading Using the Mixture of Organic Solvents: A “Greener” Alternative to Dichloromethane and N,N-Dimethylformamide. Org Process Res Dev 2021. [DOI: 10.1021/acs.oprd.1c00356] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Maria Leko
- Cytomed JSC, Orlovo-Denisovsky pr. 14A, 197375 St. Petersburg, Russia
| | - Polina Filippova
- Cytomed JSC, Orlovo-Denisovsky pr. 14A, 197375 St. Petersburg, Russia
| | - Marina Dorosh
- Cytomed JSC, Orlovo-Denisovsky pr. 14A, 197375 St. Petersburg, Russia
| | - Karin Rustler
- Iris Biotech, Adalbert-Zoellner-Str. 1, 95615 Marktredwitz, Germany
| | | | - Sergey Burov
- Cytomed JSC, Orlovo-Denisovsky pr. 14A, 197375 St. Petersburg, Russia
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4
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Pal R, Chakraborty J, Mukhopadhyay TK, Kanungo A, Saha R, Chakraborty A, Patra D, Datta A, Dutta S. Substituent effect of benzyl moiety in nitroquinoxaline small molecules upon DNA binding: Cumulative destacking of DNA nucleobases leading to histone eviction. Eur J Med Chem 2021; 229:113995. [PMID: 34802835 DOI: 10.1016/j.ejmech.2021.113995] [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: 09/27/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 11/29/2022]
Abstract
Cooperative disruption of Watson-Crick hydrogen bonds, as well as base-destacking, is shown to be triggered by a quinoxaline-based small molecule consisting of an N,N-dimethylaminopropyl tether, and a para-substituted benzyl moiety. This events lead to superstructure formation and DNA condensation as evident from biophysical experiments and classical molecular dynamics simulations. The DNA superstructure formation by mono-quinoxaline derivatives is highly entropically favored and predominantly driven by hydrophobic interactions. Furthermore, oversupercoiling of DNA and base-destacking cumulatively induces histone eviction from in-vitro assembled nucleosomes at lower micromolar concentrations implicating biological relevance. The DNA structural modulation and histone eviction capacity of the benzyl para-substituents are in the order: -I > -CF3> -Br > -Me > -OMe > -OH, which is largely guided by the polarity of benzyl para-substituent and the resulting molecular topology. The most hydrophobic derivative 3c with para-iodo benzyl moiety causes maximal disruption of base pairing and generation of superstructures. Both these events gradually diminish as the polarity of the benzyl para-substituent increases. On the other hand, quinoxaline derivatives having heterocyclic ring instead of benzyl ring, or in the absence of N,N-dimethylamino head-group, is incapable of inducing any DNA structural change and histone eviction. Further, the quinoxaline compounds displayed potent anticancer activities against different cancer cell lines which directly correlates with the hydrophobic effects of the benzyl para-substituents. Overall, the present study provides new insights into the mechanistic approach of DNA structural modulation driven histone eviction guided by the hydrophobicity of synthesized compounds leading to cellular cytotoxicity towards cancer cells.
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Affiliation(s)
- Ritesh Pal
- Organic and Medicinal Chemistry Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Jeet Chakraborty
- Organic and Medicinal Chemistry Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India
| | - Titas Kumar Mukhopadhyay
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A and 2B Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India
| | - Ajay Kanungo
- Organic and Medicinal Chemistry Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India
| | - Rimita Saha
- Organic and Medicinal Chemistry Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Amit Chakraborty
- Organic and Medicinal Chemistry Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India
| | - Dipendu Patra
- Organic and Medicinal Chemistry Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Ayan Datta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A and 2B Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India.
| | - Sanjay Dutta
- Organic and Medicinal Chemistry Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, 700032, West Bengal, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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5
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Ng-Choi I, Figueras E, Oliveras À, Feliu L, Planas M. Solid-Phase Synthesis of Biaryl Cyclic Lipopeptides Derived from Arylomycins. ACS OMEGA 2020; 5:23401-23412. [PMID: 32954193 PMCID: PMC7496001 DOI: 10.1021/acsomega.0c03352] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 08/12/2020] [Indexed: 06/11/2023]
Abstract
An efficient approach for the solid-phase synthesis of N-methylated tailed biaryl cyclic lipopeptides based on the structure of arylomycins was established. Each of these analogues incorporates an N-terminal linear lipopeptide attached to a biaryl cyclic tripeptide containing a Phe-Tyr, a Tyr-Tyr, or a His-Tyr linkage. This methodology first involved an intramolecular Suzuki-Miyaura arylation of a linear peptidyl resin incorporating the corresponding halogenated amino acid at the N-terminus and a boronotyrosine at the C-terminus. After N-methylation of the resulting biaryl cyclic peptidyl resin, the N-methylated lipopeptidyl tail was then assembled. The biaryl cyclic lipopeptides were purified and characterized.
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6
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Koike K, Nagano M, Ebihara M, Hirayama T, Tsuji M, Suga H, Nagasawa H. Design, Synthesis, and Conformation-Activity Study of Unnatural Bridged Bicyclic Depsipeptides as Highly Potent Hypoxia Inducible Factor-1 Inhibitors and Antitumor Agents. J Med Chem 2020; 63:4022-4046. [PMID: 32202785 DOI: 10.1021/acs.jmedchem.9b02039] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
By carrying out structural modifications based on the bicyclic peptide structure of echinomycin, we successfully synthesized various powerful antitumor derivatives. The ring conformation in the obtained compounds was restricted by cross-linking with an unnatural bond. The prepared derivatives were demonstrated to strongly suppress the hypoxia inducible factor (HIF)-1 transcriptional activation and hypoxia induction of HIF-1 protein expression. Particularly, alkene-bridged derivative 12 exhibited remarkably potent cytotoxicity (IC50 = 0.22 nM on the MCF-7 cell line) and HIF-1 inhibition (IC50 = 0.09 nM), which considerably exceeded those of echinomycin. Conformational analyses and molecular modeling studies revealed that the biological activities were enhanced following restriction of the conformation by cross-linking through a metabolically stable and rigid bridge bond. In addition, we proposed a new globular conformation stabilized by intramolecular π stacking that can contribute to the biological effects of bicyclic depsipeptides. The developments presented in the current study serve as a useful guide to expand the chemical space of peptides in drug discovery.
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Affiliation(s)
- Kota Koike
- Laboratory of Pharmaceutical and Medicinal Chemistry, Gifu Pharmaceutical University, Gifu-city, Gifu 501-1196, Japan
| | - Masanobu Nagano
- Department of Chemistry, The University of Tokyo, Bunkyoku, Tokyo 113-0033, Japan
| | - Masahiro Ebihara
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Gifu-city, Gifu 501-1193, Japan
| | - Tasuku Hirayama
- Laboratory of Pharmaceutical and Medicinal Chemistry, Gifu Pharmaceutical University, Gifu-city, Gifu 501-1196, Japan
| | - Mieko Tsuji
- Laboratory of Pharmaceutical and Medicinal Chemistry, Gifu Pharmaceutical University, Gifu-city, Gifu 501-1196, Japan
| | - Hiroaki Suga
- Department of Chemistry, The University of Tokyo, Bunkyoku, Tokyo 113-0033, Japan
| | - Hideko Nagasawa
- Laboratory of Pharmaceutical and Medicinal Chemistry, Gifu Pharmaceutical University, Gifu-city, Gifu 501-1196, Japan
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7
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Affiliation(s)
- Varsha J. Thombare
- School of ChemistryThe University of MelbourneVictoria3010 Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of MelbourneVictoria3010 Australia
| | - Craig A. Hutton
- School of ChemistryThe University of MelbourneVictoria3010 Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of MelbourneVictoria3010 Australia
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8
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Lu Y, Wang L, Wang X, Xi T, Liao J, Wang Z, Jiang F. Design, combinatorial synthesis and biological evaluations of novel 3-amino-1′-((1-aryl-1 H -1,2,3-triazol-5-yl)methyl)-2′-oxospiro[benzo[ a ] pyrano[2,3- c ]phenazine-1,3′-indoline]-2-carbonitrile antitumor hybrid molecules. Eur J Med Chem 2017; 135:125-141. [DOI: 10.1016/j.ejmech.2017.04.040] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 04/12/2017] [Accepted: 04/14/2017] [Indexed: 01/11/2023]
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9
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Peptides, Peptidomimetics, and Polypeptides from Marine Sources: A Wealth of Natural Sources for Pharmaceutical Applications. Mar Drugs 2017; 15:md15040124. [PMID: 28441741 PMCID: PMC5408270 DOI: 10.3390/md15040124] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 04/11/2017] [Accepted: 04/18/2017] [Indexed: 01/07/2023] Open
Abstract
Nature provides a variety of peptides that are expressed in most living species. Evolutionary pressure and natural selection have created and optimized these peptides to bind to receptors with high affinity. Hence, natural resources provide an abundant chemical space to be explored in peptide-based drug discovery. Marine peptides can be extracted by simple solvent extraction techniques. The advancement of analytical techniques has made it possible to obtain pure peptides from natural resources. Extracted peptides have been evaluated as possible therapeutic agents for a wide range of diseases, including antibacterial, antifungal, antidiabetic and anticancer activity as well as cardiovascular and neurotoxin activity. Although marine resources provide thousands of possible peptides, only a few peptides derived from marine sources have reached the pharmaceutical market. This review focuses on some of the peptides derived from marine sources in the past ten years and gives a brief review of those that are currently in clinical trials or on the market.
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10
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Lu Y, Yan Y, Wang L, Wang X, Gao J, Xi T, Wang Z, Jiang F. Design, facile synthesis and biological evaluations of novel pyrano[3,2- a ]phenazine hybrid molecules as antitumor agents. Eur J Med Chem 2017; 127:928-943. [DOI: 10.1016/j.ejmech.2016.10.068] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 10/24/2016] [Accepted: 10/25/2016] [Indexed: 12/18/2022]
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11
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Vrettos EI, Sayyad N, Mavrogiannaki EM, Stylos E, Kostagianni AD, Papas S, Mavromoustakos T, Theodorou V, Tzakos AG. Unveiling and tackling guanidinium peptide coupling reagent side reactions towards the development of peptide-drug conjugates. RSC Adv 2017. [DOI: 10.1039/c7ra06655d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Discovery of uncharted guanidinium peptide coupling reagent side reactions during peptide-drug conjugates synthesis.
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Affiliation(s)
- Eirinaios I. Vrettos
- Section of Organic Chemistry and Biochemistry
- Department of Chemistry
- University of Ioannina
- Ioannina GR-45110
- Greece
| | - Nisar Sayyad
- Section of Organic Chemistry and Biochemistry
- Department of Chemistry
- University of Ioannina
- Ioannina GR-45110
- Greece
| | - Eftychia M. Mavrogiannaki
- Section of Organic Chemistry and Biochemistry
- Department of Chemistry
- University of Ioannina
- Ioannina GR-45110
- Greece
| | - Evgenios Stylos
- Section of Organic Chemistry and Biochemistry
- Department of Chemistry
- University of Ioannina
- Ioannina GR-45110
- Greece
| | - Androniki D. Kostagianni
- Section of Organic Chemistry and Biochemistry
- Department of Chemistry
- University of Ioannina
- Ioannina GR-45110
- Greece
| | - Serafim Papas
- Section of Organic Chemistry and Biochemistry
- Department of Chemistry
- University of Ioannina
- Ioannina GR-45110
- Greece
| | - Thomas Mavromoustakos
- Section of Organic Chemistry and Biochemistry
- Department of Chemistry
- University of Ioannina
- Ioannina GR-45110
- Greece
| | - Vassiliki Theodorou
- Section of Organic Chemistry and Biochemistry
- Department of Chemistry
- University of Ioannina
- Ioannina GR-45110
- Greece
| | - Andreas G. Tzakos
- Section of Organic Chemistry and Biochemistry
- Department of Chemistry
- University of Ioannina
- Ioannina GR-45110
- Greece
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12
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Mahata T, Kanungo A, Ganguly S, Modugula EK, Choudhury S, Pal SK, Basu G, Dutta S. The Benzyl Moiety in a Quinoxaline-Based Scaffold Acts as a DNA Intercalation Switch. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201511881] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Tridib Mahata
- Department of Organic and Medicinal Chemistry; CSIR-Indian Institute of Chemical Biology; 4 Raja S. C. Mullick Road Kolkata 700032 WB India
| | - Ajay Kanungo
- Department of Organic and Medicinal Chemistry; CSIR-Indian Institute of Chemical Biology; 4 Raja S. C. Mullick Road Kolkata 700032 WB India
| | - Sudakshina Ganguly
- Department of Biophysics; Bose Institute; P-1/12 CIT Scheme VIIM Kolkata 700054 India
| | - Eswar Kalyan Modugula
- Department of Biophysics; Bose Institute; P-1/12 CIT Scheme VIIM Kolkata 700054 India
| | - Susobhan Choudhury
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III SaltLake; Kolkata 700 098 India
| | - Samir Kumar Pal
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III SaltLake; Kolkata 700 098 India
| | - Gautam Basu
- Department of Biophysics; Bose Institute; P-1/12 CIT Scheme VIIM Kolkata 700054 India
| | - Sanjay Dutta
- Department of Organic and Medicinal Chemistry; CSIR-Indian Institute of Chemical Biology; 4 Raja S. C. Mullick Road Kolkata 700032 WB India
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13
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Mahata T, Kanungo A, Ganguly S, Modugula EK, Choudhury S, Pal SK, Basu G, Dutta S. The Benzyl Moiety in a Quinoxaline-Based Scaffold Acts as a DNA Intercalation Switch. Angew Chem Int Ed Engl 2016; 55:7733-6. [DOI: 10.1002/anie.201511881] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 02/09/2016] [Indexed: 01/28/2023]
Affiliation(s)
- Tridib Mahata
- Department of Organic and Medicinal Chemistry; CSIR-Indian Institute of Chemical Biology; 4 Raja S. C. Mullick Road Kolkata 700032 WB India
| | - Ajay Kanungo
- Department of Organic and Medicinal Chemistry; CSIR-Indian Institute of Chemical Biology; 4 Raja S. C. Mullick Road Kolkata 700032 WB India
| | - Sudakshina Ganguly
- Department of Biophysics; Bose Institute; P-1/12 CIT Scheme VIIM Kolkata 700054 India
| | - Eswar Kalyan Modugula
- Department of Biophysics; Bose Institute; P-1/12 CIT Scheme VIIM Kolkata 700054 India
| | - Susobhan Choudhury
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III SaltLake; Kolkata 700 098 India
| | - Samir Kumar Pal
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III SaltLake; Kolkata 700 098 India
| | - Gautam Basu
- Department of Biophysics; Bose Institute; P-1/12 CIT Scheme VIIM Kolkata 700054 India
| | - Sanjay Dutta
- Department of Organic and Medicinal Chemistry; CSIR-Indian Institute of Chemical Biology; 4 Raja S. C. Mullick Road Kolkata 700032 WB India
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14
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Kaneda M, Sueyoshi K, Teruya T, Ohno H, Fujii N, Oishi S. Total synthesis of odoamide, a novel cyclic depsipeptide, from an Okinawan marine cyanobacterium. Org Biomol Chem 2016; 14:9093-9104. [DOI: 10.1039/c6ob01583b] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Odoamide, a highly potent cytotoxic cyclic depsipeptide was synthesized.
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Affiliation(s)
- Masato Kaneda
- Graduate School of Pharmaceutical Sciences
- Kyoto University
- Sakyo-ku
- Japan
| | | | | | - Hiroaki Ohno
- Graduate School of Pharmaceutical Sciences
- Kyoto University
- Sakyo-ku
- Japan
| | - Nobutaka Fujii
- Graduate School of Pharmaceutical Sciences
- Kyoto University
- Sakyo-ku
- Japan
| | - Shinya Oishi
- Graduate School of Pharmaceutical Sciences
- Kyoto University
- Sakyo-ku
- Japan
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15
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Shan Y, Dong J, Pan X, Zhang L, Zhang J, Dong Y, Wang M. Expanding the structural diversity of Bcr-Abl inhibitors: Dibenzoylpiperazin incorporated with 1H-indazol-3-amine. Eur J Med Chem 2015; 104:139-47. [DOI: 10.1016/j.ejmech.2015.09.034] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 09/27/2015] [Accepted: 09/28/2015] [Indexed: 12/18/2022]
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16
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Vippila MR, Ly PK, Cuny GD. Synthesis and Antiproliferative Activity Evaluation of the Disulfide-Containing Cyclic Peptide Thiochondrilline C and Derivatives. JOURNAL OF NATURAL PRODUCTS 2015; 78:2398-2404. [PMID: 26444379 DOI: 10.1021/acs.jnatprod.5b00428] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Thiochondrilline C (4) was previously isolated from Verrucisispora sp. and reported to have moderate cytotoxicity against human lung adenocarcinoma cells. Herein, we report the synthesis of thiochondrilline C by N-terminal peptide extension, oxidative disulfide bond formation, and heterocycle installation as key steps. Antiproliferative activities for the prepared natural product and several derivatives against the NCI 60 cancer cell line panel are also described. Derivative 22 was identified as a moderately potent antiproliferative agent (50% growth inhibition (GI50) = 0.2-12.2 μM) with leukemia (average GI50 = 1.8 ± 0.1 μM) and colon (average GI50 = 2.4 ± 0.3 μM) cells being most sensitive.
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Affiliation(s)
- Mohana Rao Vippila
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston , Science and Research Building 2, Room 549A, Houston, Texas 77204, United States
| | - Phuong Kim Ly
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston , Science and Research Building 2, Room 549A, Houston, Texas 77204, United States
| | - Gregory D Cuny
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston , Science and Research Building 2, Room 549A, Houston, Texas 77204, United States
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17
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Sable GA, Lim D. Solid-Phase Synthesis of Triostin A Using a Symmetrical Bis(diphenylmethyl) Linker System. J Org Chem 2015; 80:7486-94. [DOI: 10.1021/acs.joc.5b01055] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ganesh A. Sable
- Department
of Chemistry, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul, Republic of Korea
| | - Dongyeol Lim
- Department
of Chemistry, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul, Republic of Korea
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18
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Chen H, Liu C, Chen D, Madrid K, Peng S, Dong X, Zhang M, Gu Y. Bacteria-Targeting Conjugates Based on Antimicrobial Peptide for Bacteria Diagnosis and Therapy. Mol Pharm 2015; 12:2505-16. [DOI: 10.1021/acs.molpharmaceut.5b00053] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Haiyan Chen
- Department of Biomedical Engineering, School of Engineering, State Key Laboratory of Natural Medicines, and ‡School of Pharmacy, China Pharmaceutical University, 24 Tongjia Lane, Gulou
District, Nanjing 210009, China
| | - Cuicui Liu
- Department of Biomedical Engineering, School of Engineering, State Key Laboratory of Natural Medicines, and ‡School of Pharmacy, China Pharmaceutical University, 24 Tongjia Lane, Gulou
District, Nanjing 210009, China
| | - Dan Chen
- Department of Biomedical Engineering, School of Engineering, State Key Laboratory of Natural Medicines, and ‡School of Pharmacy, China Pharmaceutical University, 24 Tongjia Lane, Gulou
District, Nanjing 210009, China
| | - Kyle Madrid
- Department of Chemistry, University of California, 900 University Avenue, Riverside, California 92521, United States
| | - Shuwen Peng
- Department of Biomedical Engineering, School of Engineering, State Key Laboratory of Natural Medicines, and ‡School of Pharmacy, China Pharmaceutical University, 24 Tongjia Lane, Gulou
District, Nanjing 210009, China
| | | | - Min Zhang
- Department of Biomedical Engineering, School of Engineering, State Key Laboratory of Natural Medicines, and ‡School of Pharmacy, China Pharmaceutical University, 24 Tongjia Lane, Gulou
District, Nanjing 210009, China
| | - Yueqing Gu
- Department of Biomedical Engineering, School of Engineering, State Key Laboratory of Natural Medicines, and ‡School of Pharmacy, China Pharmaceutical University, 24 Tongjia Lane, Gulou
District, Nanjing 210009, China
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19
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Camunas-Soler J, Manosas M, Frutos S, Tulla-Puche J, Albericio F, Ritort F. Single-molecule kinetics and footprinting of DNA bis-intercalation: the paradigmatic case of Thiocoraline. Nucleic Acids Res 2015; 43:2767-79. [PMID: 25690887 PMCID: PMC4357703 DOI: 10.1093/nar/gkv087] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
DNA bis-intercalators are widely used in molecular biology with applications ranging from DNA imaging to anticancer pharmacology. Two fundamental aspects of these ligands are the lifetime of the bis-intercalated complexes and their sequence selectivity. Here, we perform single-molecule optical tweezers experiments with the peptide Thiocoraline showing, for the first time, that bis-intercalation is driven by a very slow off-rate that steeply decreases with applied force. This feature reveals the existence of a long-lived (minutes) mono-intercalated intermediate that contributes to the extremely long lifetime of the complex (hours). We further exploit this particularly slow kinetics to determine the thermodynamics of binding and persistence length of bis-intercalated DNA for a given fraction of bound ligand, a measurement inaccessible in previous studies of faster intercalating agents. We also develop a novel single-molecule footprinting technique based on DNA unzipping and determine the preferred binding sites of Thiocoraline with one base-pair resolution. This fast and radiolabelling-free footprinting technique provides direct access to the binding sites of small ligands to nucleic acids without the need of cleavage agents. Overall, our results provide new insights into the binding pathway of bis-intercalators and the reported selectivity might be of relevance for this and other anticancer drugs interfering with DNA replication and transcription in carcinogenic cell lines.
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Affiliation(s)
- Joan Camunas-Soler
- Small Biosystems Lab, Departament de Física Fonamental, Facultat de Física, Universitat de Barcelona, 08028 Barcelona, Spain CIBER de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Maria Manosas
- Small Biosystems Lab, Departament de Física Fonamental, Facultat de Física, Universitat de Barcelona, 08028 Barcelona, Spain CIBER de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Silvia Frutos
- Small Biosystems Lab, Departament de Física Fonamental, Facultat de Física, Universitat de Barcelona, 08028 Barcelona, Spain CIBER de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Judit Tulla-Puche
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Fernando Albericio
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Felix Ritort
- Small Biosystems Lab, Departament de Física Fonamental, Facultat de Física, Universitat de Barcelona, 08028 Barcelona, Spain CIBER de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, 28029 Madrid, Spain
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20
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Fernández J, Marín L, Alvarez-Alonso R, Redondo S, Carvajal J, Villamizar G, Villar CJ, Lombó F. Biosynthetic modularity rules in the bisintercalator family of antitumor compounds. Mar Drugs 2014; 12:2668-99. [PMID: 24821625 PMCID: PMC4052310 DOI: 10.3390/md12052668] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 04/09/2014] [Accepted: 04/11/2014] [Indexed: 12/05/2022] Open
Abstract
Diverse actinomycetes produce a family of structurally and biosynthetically related non-ribosomal peptide compounds which belong to the chromodepsipeptide family. These compounds act as bisintercalators into the DNA helix. They give rise to antitumor, antiparasitic, antibacterial and antiviral bioactivities. These compounds show a high degree of conserved modularity (chromophores, number and type of amino acids). This modularity and their high sequence similarities at the genetic level imply a common biosynthetic origin for these pathways. Here, we describe insights about rules governing this modular biosynthesis, taking advantage of the fact that nowadays five of these gene clusters have been made public (thiocoraline, triostin, SW-163 and echinomycin/quinomycin). This modularity has potential application for designing and producing novel genetic engineered derivatives, as well as for developing new chemical synthesis strategies. These would facilitate their clinical development.
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Affiliation(s)
- Javier Fernández
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
| | - Laura Marín
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
| | - Raquel Alvarez-Alonso
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
| | - Saúl Redondo
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
| | - Juan Carvajal
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
| | - Germán Villamizar
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
| | - Claudio J Villar
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
| | - Felipe Lombó
- Research Group BITTEN, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), Universidad de Oviedo, C/Julián Clavería 7, Facultad de Medicina, Oviedo 33006, Spain.
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21
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Zamudio-Vázquez R, Albericio F, Tulla-Puche J, Fox KR. Thioester Bonds of Thiocoraline Can Be Replaced with NMe-Amide Bridges without Affecting Its DNA-Binding Properties. ACS Med Chem Lett 2014; 5:45-50. [PMID: 24900772 DOI: 10.1021/ml400323x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 11/04/2013] [Indexed: 11/30/2022] Open
Abstract
In the search for new drug candidates for DNA recognition, affinity and sequence selectivity are two of the most important features. NMe-azathiocoraline, a synthetic antitumor bisintercalator derived from the natural marine product thiocoraline, shows similar potency to the parent compound, as well as possessing enhanced stability. Analysis of the DNA-binding selectivity of NMe-azathiocoraline by DNase I footprinting using universal substrates with all 136 tetranucleotides and all possible symmetrical hexanucleotide sequences revealed that, although this ligand binds to all CpG steps with lower affinities than thiocoraline, it displays additional binding to AT-rich sites. Moreover, fluorescence melting studies showed a strong interaction of the synthetic molecule with CACGTG and weaker binding to ACATGT and AGATCT. These findings demonstrate that NMe-azathiocoraline has the same mode of action as thiocoraline, mimicking its DNA-binding selectivity despite the substitution of its thioester bonds by NMe-amide bridges.
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Affiliation(s)
- Rubí Zamudio-Vázquez
- Institute for Research in Biomedicine, Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Fernando Albericio
- Institute for Research in Biomedicine, Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain
- Department of Organic
Chemistry, Faculty of Chemistry, University of Barcelona, Martí
i Franquès 1-11, 08028 Barcelona, Spain
- School of Chemistry, University of KwaZulu-Natal, 4001 Durban, South Africa
| | - Judit Tulla-Puche
- Institute for Research in Biomedicine, Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Keith R. Fox
- Centre for Biological Sciences, Life Sciences Building
85, University of Southampton, Southampton SO17 1BJ, U.K
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