1
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Georg M, Laping LA, Billo V, Gatto B, Friedhoff P, Göttlich R. Secondary 3-Chloropiperidines: Powerful Alkylating Agents. ChemistryOpen 2024; 13:e202300181. [PMID: 38088585 PMCID: PMC11164021 DOI: 10.1002/open.202300181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/15/2023] [Indexed: 06/11/2024] Open
Abstract
In previous works, we demonstrated that tertiary 3-chloropiperidines are potent chemotherapeutics, alkylating the DNA through the formation of bicyclic aziridinium ions. Herein, we report the synthesis of novel secondary 3-chloropiperidine analogues. The synthesis incorporates a new procedure to monochlorinate unsaturated primary amines utilizing N-chlorosuccinimide, while carefully monitoring the temperature to prevent dichlorination. Furthermore, we successfully isolated highly strained bicyclic aziridines by treating the secondary 3-chloropiperidines with a sufficient amount of base. We conclude this work with a DNA cleavage assay as a proof of principle, comparing our previously known substrates to the novel compounds. In this, the secondary 3-chloropiperidine as well as the isolated bicyclic aziridine, proved to be more effective than their tertiary counterpart.
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Affiliation(s)
- Mats Georg
- Institute of Organic ChemistryJustus Liebig University GiessenHeinrich-Buff-Ring 1735392GiessenGermany
| | - Lina Alexandra Laping
- Institute of Organic ChemistryJustus Liebig University GiessenHeinrich-Buff-Ring 1735392GiessenGermany
| | - Veronica Billo
- Institute of Organic ChemistryJustus Liebig University GiessenHeinrich-Buff-Ring 1735392GiessenGermany
- Department of Pharmaceutical and Pharmacological SciencesUniversity of PadovaPadovaItaly
| | - Barbara Gatto
- Department of Pharmaceutical and Pharmacological SciencesUniversity of PadovaPadovaItaly
| | - Peter Friedhoff
- Institute of BiochemistryJustus Liebig University GiessenHeinrich-Buff-Ring 1735392GiessenGermany
| | - Richard Göttlich
- Institute of Organic ChemistryJustus Liebig University GiessenHeinrich-Buff-Ring 1735392GiessenGermany
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2
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Velema WA, Lu Z. Chemical RNA Cross-Linking: Mechanisms, Computational Analysis, and Biological Applications. JACS AU 2023; 3:316-332. [PMID: 36873678 PMCID: PMC9975857 DOI: 10.1021/jacsau.2c00625] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/23/2022] [Accepted: 12/23/2022] [Indexed: 06/18/2023]
Abstract
In recent years, RNA has emerged as a multifaceted biomolecule that is involved in virtually every function of the cell and is critical for human health. This has led to a substantial increase in research efforts to uncover the many chemical and biological aspects of RNA and target RNA for therapeutic purposes. In particular, analysis of RNA structures and interactions in cells has been critical for understanding their diverse functions and druggability. In the last 5 years, several chemical methods have been developed to achieve this goal, using chemical cross-linking combined with high-throughput sequencing and computational analysis. Applications of these methods resulted in important new insights into RNA functions in a variety of biological contexts. Given the rapid development of new chemical technologies, a thorough perspective on the past and future of this field is provided. In particular, the various RNA cross-linkers and their mechanisms, the computational analysis and challenges, and illustrative examples from recent literature are discussed.
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Affiliation(s)
- Willem A. Velema
- Institute
for Molecules and Materials, Radboud University, Nijmegen 6500 HC, The Netherlands
| | - Zhipeng Lu
- Department
of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90033, United States
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3
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Carraro C, Bonaguro L, Schulte-Schrepping J, Horne A, Oestreich M, Warnat-Herresthal S, Helbing T, De Franco M, Haendler K, Mukherjee S, Ulas T, Gandin V, Goettlich R, Aschenbrenner AC, Schultze JL, Gatto B. Decoding mechanism of action and sensitivity to drug candidates from integrated transcriptome and chromatin state. eLife 2022; 11:e78012. [PMID: 36043458 PMCID: PMC9433094 DOI: 10.7554/elife.78012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Omics-based technologies are driving major advances in precision medicine, but efforts are still required to consolidate their use in drug discovery. In this work, we exemplify the use of multi-omics to support the development of 3-chloropiperidines, a new class of candidate anticancer agents. Combined analyses of transcriptome and chromatin accessibility elucidated the mechanisms underlying sensitivity to test agents. Furthermore, we implemented a new versatile strategy for the integration of RNA- and ATAC-seq (Assay for Transposase-Accessible Chromatin) data, able to accelerate and extend the standalone analyses of distinct omic layers. This platform guided the construction of a perturbation-informed basal signature predicting cancer cell lines' sensitivity and to further direct compound development against specific tumor types. Overall, this approach offers a scalable pipeline to support the early phases of drug discovery, understanding of mechanisms, and potentially inform the positioning of therapeutics in the clinic.
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Affiliation(s)
- Caterina Carraro
- Department of Pharmaceutical and Pharmacological Sciences, University of PadovaPadovaItaly
| | - Lorenzo Bonaguro
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of BonnBonnGermany
| | - Jonas Schulte-Schrepping
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of BonnBonnGermany
| | - Arik Horne
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of BonnBonnGermany
| | - Marie Oestreich
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
| | - Stefanie Warnat-Herresthal
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of BonnBonnGermany
| | - Tim Helbing
- Institute of Organic Chemistry, Justus Liebig University GiessenGiessenGermany
| | - Michele De Franco
- Department of Pharmaceutical and Pharmacological Sciences, University of PadovaPadovaItaly
| | - Kristian Haendler
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
- PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of BonnBonnGermany
- Institute of Human Genetics, University of LübeckLübeckGermany
| | - Sach Mukherjee
- Statistics and Machine Learning, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
- MRC Biostatistics Unit, University of CambridgeCambridgeUnited Kingdom
| | - Thomas Ulas
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of BonnBonnGermany
- PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of BonnBonnGermany
| | - Valentina Gandin
- Department of Pharmaceutical and Pharmacological Sciences, University of PadovaPadovaItaly
| | - Richard Goettlich
- Institute of Organic Chemistry, Justus Liebig University GiessenGiessenGermany
| | - Anna C Aschenbrenner
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of BonnBonnGermany
- PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of BonnBonnGermany
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical CenterNijmegenNetherlands
| | - Joachim L Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of BonnBonnGermany
- PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of BonnBonnGermany
| | - Barbara Gatto
- Department of Pharmaceutical and Pharmacological Sciences, University of PadovaPadovaItaly
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4
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Sosic A, Olivato G, Carraro C, Göttlich R, Fabris D, Gatto B. In Vitro Evaluation of Bis-3-Chloropiperidines as RNA Modulators Targeting TAR and TAR-Protein Interaction. Int J Mol Sci 2022; 23:ijms23020582. [PMID: 35054766 PMCID: PMC8776071 DOI: 10.3390/ijms23020582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/01/2022] [Accepted: 01/04/2022] [Indexed: 12/04/2022] Open
Abstract
After a long limbo, RNA has gained its credibility as a druggable target, fully earning its deserved role in the next generation of pharmaceutical R&D. We have recently probed the trans-activation response (TAR) element, an RNA stem–bulge–loop domain of the HIV-1 genome with bis-3-chloropiperidines (B-CePs), and revealed the compounds unique behavior in stabilizing TAR structure, thus impairing in vitro the chaperone activity of the HIV-1 nucleocapsid (NC) protein. Seeking to elucidate the determinants of B-CePs inhibition, we have further characterized here their effects on the target TAR and its NC recognition, while developing quantitative analytical approaches for the study of multicomponent RNA-based interactions.
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Affiliation(s)
- Alice Sosic
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Francesco Marzolo 5, 35131 Padova, Italy; (A.S.); (G.O.); (C.C.)
| | - Giulia Olivato
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Francesco Marzolo 5, 35131 Padova, Italy; (A.S.); (G.O.); (C.C.)
| | - Caterina Carraro
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Francesco Marzolo 5, 35131 Padova, Italy; (A.S.); (G.O.); (C.C.)
| | - Richard Göttlich
- Institute of Organic Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany;
| | - Dan Fabris
- Department of Chemistry, University of Connecticut, 55 North Eagleville Rd., Storrs, CT 06269, USA;
| | - Barbara Gatto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Francesco Marzolo 5, 35131 Padova, Italy; (A.S.); (G.O.); (C.C.)
- Correspondence:
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5
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Helbing T, Georg M, Stöhr F, Carraro C, Becker J, Gatto B, Göttlich R. Understanding the Alkylation Mechanism of 3‐Chloropiperidines – NMR Kinetic Studies and Isolation of Bicyclic Aziridinium Ions. European J Org Chem 2021. [DOI: 10.1002/ejoc.202101072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Tim Helbing
- Institute of Organic Chemistry Justus Liebig University Giessen Heinrich-Buff-Ring 17 35392 Giessen Germany
| | - Mats Georg
- Institute of Organic Chemistry Justus Liebig University Giessen Heinrich-Buff-Ring 17 35392 Giessen Germany
| | - Fabian Stöhr
- Institute of Organic Chemistry Justus Liebig University Giessen Heinrich-Buff-Ring 17 35392 Giessen Germany
- Institute of Inorganic and Analytical Chemistry Justus Liebig University Giessen Heinrich-Buff-Ring 17 35392 Giessen Germany
| | - Caterina Carraro
- Department of Pharmaceutical and Pharmacological Sciences University of Padova Via Francesco Marzolo 5 35131 Padova Italy
| | - Jonathan Becker
- Institute of Inorganic and Analytical Chemistry Justus Liebig University Giessen Heinrich-Buff-Ring 17 35392 Giessen Germany
| | - Barbara Gatto
- Department of Pharmaceutical and Pharmacological Sciences University of Padova Via Francesco Marzolo 5 35131 Padova Italy
| | - Richard Göttlich
- Institute of Organic Chemistry Justus Liebig University Giessen Heinrich-Buff-Ring 17 35392 Giessen Germany
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6
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Sosic A, Göttlich R, Fabris D, Gatto B. B-CePs as cross-linking probes for the investigation of RNA higher-order structure. Nucleic Acids Res 2021; 49:6660-6672. [PMID: 34125908 PMCID: PMC8266612 DOI: 10.1093/nar/gkab468] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 05/13/2021] [Accepted: 05/19/2021] [Indexed: 11/12/2022] Open
Abstract
Elucidating the structure of RNA and RNA ensembles is essential to understand biological functions. In this work, we explored the previously uncharted reactivity of bis-chloropiperidines (B-CePs) towards RNA. We characterized at the molecular level the different adducts induced by the fast reacting compound B-CeP 1 with RNA. Following an approach based on solution thermal melting coupled with ESI mass spectrometry (STHEM-ESI), we proved the ability of B-CePs to induce inter-molecular cross-links between guanines in double stranded RNA. These results open the possibility of using B-CePs as structural probes for investigating higher-order structures, such as the kissing loop complex established by the dimerization initiation site (DIS) of the HIV-1 genome. We confirmed the potential of B-CePs to reveal the identity of RNA structures involved in long-range interactions, expecting to benefit the characterization of samples that are not readily amenable to traditional high-resolution techniques, and thus promoting the elucidation of pertinent RNA systems associated with old and new diseases.
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Affiliation(s)
- Alice Sosic
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy
| | - Richard Göttlich
- Institute of Organic Chemistry, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Dan Fabris
- Departments of Chemistry and Biological Sciences, University at Albany-SUNY, Albany, NY, 12222, USA
| | - Barbara Gatto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy
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7
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Bis-3-Chloropiperidines Targeting TAR RNA as A Novel Strategy to Impair the HIV-1 Nucleocapsid Protein. Molecules 2021; 26:molecules26071874. [PMID: 33810333 PMCID: PMC8038054 DOI: 10.3390/molecules26071874] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/16/2021] [Accepted: 03/22/2021] [Indexed: 11/16/2022] Open
Abstract
Specific RNA sequences regulate functions essential to life. The Trans-Activation Response element (TAR) is an RNA stem-bulge-loop structure involved in several steps of HIV-1 replication. In this work, we show how RNA targeting can inhibit HIV-1 nucleocapsid (NC), a highly conserved protein known to catalyze nucleic acid melting and strand transfers during reverse transcription. Our RNA targeting strategy consists of the employment of bis-3-chloropiperidines (B-CePs) to impair RNA melting through bifunctional alkylation. Specific interactions between B-CePs and TAR RNA were analytically investigated by gel electrophoresis and mass spectrometry, allowing the elucidation of B-CePs' recognition of TAR, and highlighting an RNA-directed mechanism of protein inhibition. We propose that B-CePs can freeze TAR tridimensional conformation, impairing NC-induced dynamics and finally inhibiting its functions in vitro.
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8
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Carraro C, Helbing T, Francke A, Zuravka I, Sosic A, De Franco M, Gandin V, Gatto B, Göttlich DR. Appended Aromatic Moieties in Flexible Bis-3-chloropiperidines Confer Tropism against Pancreatic Cancer Cells. ChemMedChem 2021; 16:860-868. [PMID: 33200541 PMCID: PMC7984046 DOI: 10.1002/cmdc.202000814] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Indexed: 12/24/2022]
Abstract
Nitrogen mustards (NMs) are an old but still largely diffused class of anticancer drugs. However, spreading mechanisms of resistance undermine their efficacy and therapeutic applicability. To expand their antitumour value, we developed bis-3-chloropiperidines (B-CePs), a new class of mustard-based alkylating agent, and we recently reported the striking selectivity for BxPC-3 pancreatic tumour cells of B-CePs bearing aromatic moieties embedded in the linker. In this study, we demonstrate that such tropism is shared by bis-3-chloropiperidines bearing appended aromatic groups in flexible linkers, whereas esters substituted by aliphatic groups or by efficient DNA-interacting groups are potent but nonselective cytotoxic agents. Besides, we describe how the critical balance between water stability and DNA reactivity can affect the properties of bis-3-chloropiperidines. Together, these findings support the exploitation of B-CePs as potential antitumour clinical candidates.
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Affiliation(s)
- Caterina Carraro
- Department of Pharmaceutical and Pharmacological SciencesUniversity of PadovaVia Francesco Marzolo 535131PadovaItaly
| | - Tim Helbing
- Institute of Organic ChemistryJustus Liebig University GiessenHeinrich-Buff-Ring 1735392GiessenGermany
| | - Alexander Francke
- Institute of Organic ChemistryJustus Liebig University GiessenHeinrich-Buff-Ring 1735392GiessenGermany
| | - Ivonne Zuravka
- Institute of Organic ChemistryJustus Liebig University GiessenHeinrich-Buff-Ring 1735392GiessenGermany
| | - Alice Sosic
- Department of Pharmaceutical and Pharmacological SciencesUniversity of PadovaVia Francesco Marzolo 535131PadovaItaly
| | - Michele De Franco
- Department of Pharmaceutical and Pharmacological SciencesUniversity of PadovaVia Francesco Marzolo 535131PadovaItaly
| | - Valentina Gandin
- Department of Pharmaceutical and Pharmacological SciencesUniversity of PadovaVia Francesco Marzolo 535131PadovaItaly
| | - Barbara Gatto
- Department of Pharmaceutical and Pharmacological SciencesUniversity of PadovaVia Francesco Marzolo 535131PadovaItaly
| | - D. Richard Göttlich
- Institute of Organic ChemistryJustus Liebig University GiessenHeinrich-Buff-Ring 1735392GiessenGermany
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9
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Srivastava V, Wani MY, Al-Bogami AS, Ahmad A. Piperidine based 1,2,3-triazolylacetamide derivatives induce cell cycle arrest and apoptotic cell death in Candida auris. J Adv Res 2020; 29:121-135. [PMID: 33842010 PMCID: PMC8020347 DOI: 10.1016/j.jare.2020.11.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/18/2020] [Accepted: 11/03/2020] [Indexed: 12/23/2022] Open
Abstract
Introduction: The fungal pathogen Candida auris, is a serious threat to public health and is associated with bloodstream infections causing high mortality particularly in patients with serious medical problems. As this pathogen is generally resistant to all the available classes of antifungals, there is a constant demand for novel antifungal drugs with new mechanisms of antifungal action. Objective: Therefore, in this study we synthesised six novel piperidine based 1,2,3-triazolylacetamide derivatives (pta1-pta6) and tested their antifungal activity and mechanism of action against clinical C. auris isolates. Methods: Antifungal susceptibility testing was done to estimate MIC values of piperidine derivatives following CLSI recommended guidelines. MUSE Cell Analyzer was used to check cell viability and cell cycle arrest in C. auris after exposure to piperidine derivatives using different kits. Additionally, fluorescence microscopy was done to check the effect of test compound on C. auris membrane integrity and related apoptotic assays were performed to confirm cellular apoptosis using different apoptosis markers. Results: Out of the six derivatives; pta1, pta2 and pta3 showed highest active with MIC values from 0.24 to 0.97 μg/mL and MFC ranging from 0.97 to 3.9 μg/mL. Fungicidal behaviour of these compounds was confirmed by cell count and viability assay. Exposure to test compounds at sub-inhibitory and inhibitory concentrations resulted in disruption of C. auris plasma membrane. Further in-depth studies showed that these derivatives were able to induce apoptosis and cell cycle arrest in S-phase. Furthermore, the compounds demonstrated lower toxicity profile. Conclusion: Present study suggests that the novel derivatives (pta1-pta3) induce apoptotic cell death and cell cycle arrest in C. auris and could be potential candidates against C. auris infections.
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Affiliation(s)
- Vartika Srivastava
- Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - Mohmmad Younus Wani
- University of Jeddah, College of Science, Department of Chemistry, Jeddah 21589, Saudi Arabia
| | - Abdullah Saad Al-Bogami
- University of Jeddah, College of Science, Department of Chemistry, Jeddah 21589, Saudi Arabia
| | - Aijaz Ahmad
- Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa.,Infection Control Unit, Charlotte Maxeke Johannesburg Academic Hospital, National Health Laboratory Service, Johannesburg 2193, South Africa
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10
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Helbing T, Carraro C, Francke A, Sosic A, De Franco M, Gandin V, Göttlich R, Gatto B. Aromatic Linkers Unleash the Antiproliferative Potential of 3-Chloropiperidines Against Pancreatic Cancer Cells. ChemMedChem 2020; 15:2040-2051. [PMID: 32744774 PMCID: PMC7692949 DOI: 10.1002/cmdc.202000457] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Indexed: 12/27/2022]
Abstract
In this study, we describe the synthesis and biological evaluation of a set of bis-3-chloropiperidines (B-CePs) containing rigid aromatic linker structures. A modification of the synthetic strategy also enabled the synthesis of a pilot tris-3-chloropiperidine (Tri-CeP) bearing three reactive meta-chloropiperidine moieties on the aromatic scaffold. A structure-reactivity relationship analysis of B-CePs suggests that the arrangement of the reactive units affects the DNA alkylating activity, while also revealing correlations between the electron density of the aromatic system and the reactivity with biologically relevant nucleophiles, both on isolated DNA and in cancer cells. Interestingly, all aromatic 3-chloropiperidines exhibited a marked cytotoxicity and tropism for 2D and 3D cultures of pancreatic cancer cells. Therefore, the new aromatic 3-chloropiperidines appear to be promising contenders for further development of mustard-based anticancer agents aimed at pancreatic cancers.
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Affiliation(s)
- Tim Helbing
- Institute of Organic ChemistryJustus Liebig University GiessenHeinrich-Buff-Ring 1735392GiessenGermany
| | - Caterina Carraro
- Department of Pharmaceutical and Pharmacological SciencesUniversity of PadovaVia Francesco Marzolo 535131PadovaItaly
| | - Alexander Francke
- Institute of Organic ChemistryJustus Liebig University GiessenHeinrich-Buff-Ring 1735392GiessenGermany
| | - Alice Sosic
- Department of Pharmaceutical and Pharmacological SciencesUniversity of PadovaVia Francesco Marzolo 535131PadovaItaly
| | - Michele De Franco
- Department of Pharmaceutical and Pharmacological SciencesUniversity of PadovaVia Francesco Marzolo 535131PadovaItaly
| | - Valentina Gandin
- Department of Pharmaceutical and Pharmacological SciencesUniversity of PadovaVia Francesco Marzolo 535131PadovaItaly
| | - Richard Göttlich
- Institute of Organic ChemistryJustus Liebig University GiessenHeinrich-Buff-Ring 1735392GiessenGermany
| | - Barbara Gatto
- Department of Pharmaceutical and Pharmacological SciencesUniversity of PadovaVia Francesco Marzolo 535131PadovaItaly
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11
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Sadanandan S, Gupta DK. Changing stereoselectivity and regioselectivity in copper( i)-catalyzed 5- exo cyclization by chelation and rigidity in aminoalkyl radicals: synthesis towards diverse bioactive N-heterocycles. NEW J CHEM 2020. [DOI: 10.1039/c9nj05166j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Chelation, rigidity and carbon-radical positions in aminoalkyl precursors disturb the usual 2,4-trans diastereoselectivity and 5-exo mode in Cu(i)-catalyzed ATRC.
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12
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Carraro C, Francke A, Sosic A, Kohl F, Helbing T, De Franco M, Fabris D, Göttlich R, Gatto B. Behind the Mirror: Chirality Tunes the Reactivity and Cytotoxicity of Chloropiperidines as Potential Anticancer Agents. ACS Med Chem Lett 2019; 10:552-557. [PMID: 30996795 PMCID: PMC6466835 DOI: 10.1021/acsmedchemlett.8b00580] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 02/13/2019] [Indexed: 12/18/2022] Open
Abstract
![]()
The
pressing demand for sustainable antitumor drugs prompted us
to investigate 3-chloropiperidines as potential mustard-based anticancer
agents. In this study, an explorative set of variously decorated monofunctional
3-chloropiperidines (M-CePs) was efficiently synthesized through a
fast and affordable route providing high yields of pure racemates
and enantiomers. Consistently with their reactivity, M-CePs were demonstrated
to alkylate DNA in vitro. On a panel of carcinoma
cell lines, M-CePs exhibited low nanomolar cytotoxicity indexes, which
showed their remarkable activity against pancreatic cancer cells and
in all cases performed strikingly better than the chlorambucil control.
Very interestingly, stereochemistry modulated the activity of M-CePs
in unexpected ways, pointing to additional molecular mechanisms of
action beyond the direct damage of genomic DNA. This encouraging combination
of efficacy and sustainability suggests they are valid candidates
for anticancer agent development.
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Affiliation(s)
- Caterina Carraro
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Francesco Marzolo 5, 35131 Padova, Italy
| | - Alexander Francke
- Institute of Organic Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Alice Sosic
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Francesco Marzolo 5, 35131 Padova, Italy
| | - Franziska Kohl
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Francesco Marzolo 5, 35131 Padova, Italy
| | - Tim Helbing
- Institute of Organic Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Michele De Franco
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Francesco Marzolo 5, 35131 Padova, Italy
| | - Daniele Fabris
- Departments of Chemistry and Biological Sciences, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Richard Göttlich
- Institute of Organic Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Barbara Gatto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Francesco Marzolo 5, 35131 Padova, Italy
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13
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Sosic A, Zuravka I, Schmitt NK, Miola A, Göttlich R, Fabris D, Gatto B. Direct and Topoisomerase II Mediated DNA Damage by Bis-3-chloropiperidines: The Importance of Being an Earnest G. ChemMedChem 2017; 12:1471-1479. [PMID: 28724198 DOI: 10.1002/cmdc.201700368] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 07/19/2017] [Indexed: 01/19/2023]
Abstract
Bis-3-chloropiperidines are a new class of DNA-active compounds capable of alkylating nucleobases and inducing strand cleavage. In this study, we investigated the reactivity of these mustard-based agents with both single- and double-stranded DNA constructs. Polyacrylamide gel electrophoresis (PAGE) and electrospray ionization mass spectrometry (ESI-MS) were used to obtain valuable insight into their mechanism at the molecular level and to investigate their time- and concentration-dependent activity. The results revealed the preferential formation of mono- and bifunctional adducts at nucleophilic guanine sites. In a stepwise fashion, alkylation was followed by depurination and subsequent strand scission at the ensuing apurinic site. We demonstrated that the covalent modifications introduced by this new class of compounds can inhibit the activity of essential DNA-processing proteins, such as topoisomerase IIα, thereby suggesting that bis-3-chloropiperidines may have excellent anticancer potential.
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Affiliation(s)
- Alice Sosic
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Francesco Marzolo 5, 35131, Padova, Italy
| | - Ivonne Zuravka
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Francesco Marzolo 5, 35131, Padova, Italy.,Institute of Organic Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Nina-Katharina Schmitt
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Francesco Marzolo 5, 35131, Padova, Italy
| | - Angelica Miola
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Francesco Marzolo 5, 35131, Padova, Italy
| | - Richard Göttlich
- Institute of Organic Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Dan Fabris
- Departments of Chemistry and Biological Sciences, University at Albany - SUNY, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Barbara Gatto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Francesco Marzolo 5, 35131, Padova, Italy
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Ars‐legendi‐Fakultätenpreis: R. Göttlich, N. Graulich, S. Schindler / Preis der Berlin‐Brandenburgischen Akademie der Wissenschaften: D. Rauh. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602742] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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15
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Ars‐legendi‐Fakultätenpreis: R. Göttlich, N. Graulich, S. Schindler / Preis der Berlin‐Brandenburgischen Akademie der Wissenschaften: D. Rauh. Angew Chem Int Ed Engl 2016; 55:5893. [DOI: 10.1002/anie.201602742] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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16
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Zuravka I, Sosic A, Gatto B, Göttlich R. Synthesis and evaluation of a bis-3-chloropiperidine derivative incorporating an anthraquinone pharmacophore. Bioorg Med Chem Lett 2015; 25:4606-9. [PMID: 26342869 DOI: 10.1016/j.bmcl.2015.08.042] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 08/15/2015] [Accepted: 08/18/2015] [Indexed: 12/18/2022]
Abstract
With the aim to attain an alkylating agent with enhanced DNA-affinity, we have successfully synthesised lysine-linked bis-3-chloropiperidine 1 bearing an anthraquinone moiety known to bind double-stranded DNA. Consistent with our expectations, compound 1 appears to intercalate into the DNA double helix, which can be observed by conformational changes of plasmid DNA suggesting alkylation and intercalation-induced DNA unwinding. The results of this work can provide a meaningful starting point for investigating the molecular mechanism of action of this novel DNA alkylating conjugate 1 with improved affinity for DNA.
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Affiliation(s)
- Ivonne Zuravka
- Institute of Organic Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany; Dipartimento di Scienze del Farmaco, Università di Padova, via Marzolo 5, 35131 Padova, Italy
| | - Alice Sosic
- Dipartimento di Scienze del Farmaco, Università di Padova, via Marzolo 5, 35131 Padova, Italy
| | - Barbara Gatto
- Dipartimento di Scienze del Farmaco, Università di Padova, via Marzolo 5, 35131 Padova, Italy.
| | - Richard Göttlich
- Institute of Organic Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany.
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Bis-3-chloropiperidines containing bridging lysine linkers: Influence of side chain structure on DNA alkylating activity. Bioorg Med Chem 2015; 23:1241-50. [PMID: 25693786 DOI: 10.1016/j.bmc.2015.01.050] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 01/27/2015] [Accepted: 01/28/2015] [Indexed: 02/02/2023]
Abstract
A series of bis-3-chloropiperidines containing lysine linkers was synthesised as DNA alkylating model compounds by using a bidirectional synthetic strategy. These novel piperidine mustard based agents have been evaluated for their alkylating properties towards nucleic acids and were shown to alkylate and cleave DNA with strong preference for guanine residues. Our studies reveal that the introduction of aromatic groups in the side chain of the lysine linker has an impact on DNA alkylating activity. Analysis by ESI mass spectrometry enabled the verification of the reactive aziridinium ion formation. Overall, the results confirm our recently proposed reaction mechanism of bis-3-chloropiperidines.
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