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Zhang H, Sun Y, Saha S, Saha LK, Pongor LS, Dhall A, Pommier Y. Genome-wide Mapping of Topoisomerase Binding Sites Suggests Topoisomerase 3α (TOP3A) as a Reader of Transcription-Replication Conflicts (TRC). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.17.599352. [PMID: 38948815 PMCID: PMC11212928 DOI: 10.1101/2024.06.17.599352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Both transcription and replication can take place simultaneously on the same DNA template, potentially leading to transcription-replication conflicts (TRCs) and topological problems. Here we asked which topoisomerase(s) is/are the best candidate(s) for sensing TRC. Genome-wide topoisomerase binding sites were mapped in parallel for all the nuclear topoisomerases (TOP1, TOP2A, TOP2B, TOP3A and TOP3B). To increase the signal to noise ratio (SNR), we used ectopic expression of those topoisomerases in H293 cells followed by a modified CUT&Tag method. Although each topoisomerase showed distinct binding patterns, all topoisomerase binding signals positively correlated with gene transcription. TOP3A binding signals were suppressed by DNA replication inhibition. This was also observed but to a lesser extent for TOP2A and TOP2B. Hence, we propose the involvement of TOP3A in sensing both head-on TRCs (HO-TRCs) and co-directional TRCs (CD-TRCs). In which case, the TOP3A signals appear concentrated within the promoters and first 20 kb regions of the 5' -end of genes, suggesting the prevalence of TRCs and the recruitment of TOP3A in the 5'-regions of transcribed and replicated genes.
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Affiliation(s)
- Hongliang Zhang
- Laboratory of Molecular Pharmacology and Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Yilun Sun
- Laboratory of Molecular Pharmacology and Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Sourav Saha
- Laboratory of Molecular Pharmacology and Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Liton Kumar Saha
- Laboratory of Molecular Pharmacology and Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Lorinc S Pongor
- Laboratory of Molecular Pharmacology and Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Anjali Dhall
- Laboratory of Molecular Pharmacology and Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Yves Pommier
- Laboratory of Molecular Pharmacology and Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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Santos MB, de Azevedo Teotônio Cavalcanti M, de Medeiros E Silva YMS, Dos Santos Nascimento IJ, de Moura RO. Overview of the New Bioactive Heterocycles as Targeting Topoisomerase Inhibitors Useful Against Colon Cancer. Anticancer Agents Med Chem 2024; 24:236-262. [PMID: 38038012 DOI: 10.2174/0118715206269722231121173311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 10/14/2023] [Accepted: 10/24/2023] [Indexed: 12/02/2023]
Abstract
Colorectal cancer (CRC) is the third most common cancer globally, with high mortality. Metastatic CRC is incurable in most cases, and multiple drug therapy can increase patients' life expectancy by 2 to 3 years. Efforts are being made to understand the relationship between topoisomerase enzymes and colorectal cancer. Some studies have shown that higher expression of these enzymes is correlated to a poor prognosis for this type of cancer. One of the primary drugs used in the treatment of CRC is Irinotecan, which can be used in monotherapy or, more commonly, in therapeutic schemes such as FOLFIRI (Fluorouracil, Leucovorin, and Irinotecan) and CAPIRI (Capecitabine and Irinotecan). Like Camptothecin, Irinotecan and other compounds have a mechanism of action based on the formation of a ternary complex with topoisomerase I and DNA providing damage to it, therefore leading to cell death. Thus, this review focused on the principal works published in the last ten years that demonstrate a correlation between the inhibition of different isoforms of topoisomerase and in vitro cytotoxic activity against CRC by natural products, semisynthetic and synthetic compounds of pyridine, quinoline, acridine, imidazoles, indoles, and metal complexes. The results revealed that natural compounds, semisynthetic and synthetic derivatives showed potential in vitro cytotoxicity against several colon cancer cell lines, and this activity was often accompanied by the ability to inhibit both isoforms of topoisomerase (I and II), highlighting that these enzymes can be promising targets for the development of new chemotherapy against CRC. Pyridine analogs were considered the most promising for this study, while the evaluation of the real potential of natural products was limited by the lack of information in their work. Moreover, the complexes, although promising, presented as the main limitation the lack of selectivity.
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Affiliation(s)
- Mirelly Barbosa Santos
- Postgraduate Program in Pharmaceutical Sciences, State University of Paraíba, Campina Grande, 58429-500, Brazil
- Drug Development and Synthesis Laboratory, Department of Pharmacy, State University of Paraíba, Campina Grande, 58429-500, Brazil
| | - Misael de Azevedo Teotônio Cavalcanti
- Postgraduate Program in Pharmaceutical Sciences, State University of Paraíba, Campina Grande, 58429-500, Brazil
- Drug Development and Synthesis Laboratory, Department of Pharmacy, State University of Paraíba, Campina Grande, 58429-500, Brazil
| | - Yvnni Maria Sales de Medeiros E Silva
- Postgraduate Program in Pharmaceutical Sciences, State University of Paraíba, Campina Grande, 58429-500, Brazil
- Drug Development and Synthesis Laboratory, Department of Pharmacy, State University of Paraíba, Campina Grande, 58429-500, Brazil
| | - Igor José Dos Santos Nascimento
- Postgraduate Program in Pharmaceutical Sciences, State University of Paraíba, Campina Grande, 58429-500, Brazil
- Drug Development and Synthesis Laboratory, Department of Pharmacy, State University of Paraíba, Campina Grande, 58429-500, Brazil
- Departament of Pharmacy, Cesmac University Center, Maceió, Brazil
| | - Ricardo Olimpio de Moura
- Postgraduate Program in Pharmaceutical Sciences, State University of Paraíba, Campina Grande, 58429-500, Brazil
- Drug Development and Synthesis Laboratory, Department of Pharmacy, State University of Paraíba, Campina Grande, 58429-500, Brazil
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Schöffski P, Wang CC, Schöffski MP, Wozniak A. Current Role of Topoisomerase I Inhibitors for the Treatment of Mesenchymal Malignancies and Their Potential Future Use as Payload of Sarcoma-Specific Antibody-Drug Conjugates. Oncol Res Treat 2023; 47:18-41. [PMID: 38016427 PMCID: PMC10860894 DOI: 10.1159/000535491] [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: 07/24/2023] [Accepted: 11/19/2023] [Indexed: 11/30/2023]
Abstract
BACKGROUND Topoisomerase I is an enzyme that plays a crucial part in DNA replication and transcription by the relaxation of supercoiled double-stranded DNA. Topoisomerase I inhibitors bind to the topoisomerase I cleavage complex, thereby stabilizing it and preventing the religation of the DNA strands, leading to DNA damage, cell cycle arrest, and apoptosis. Various topoisomerase I inhibitors have been evaluated in solid tumors, and irinotecan and topotecan have been approved for the treatment of epithelial malignancies. None of them have been approved for sarcoma, a diverse group of rare solid tumors with an unmet need for effective treatments. SUMMARY Topoisomerase I inhibitors have been evaluated in preclinical studies as single agents or in combination in solid tumors, some of which have included sarcomas where activity was observed. Clinical trials evaluating topoisomerase I inhibitors for the treatment of sarcoma have shown limited efficacy as monotherapy. In combination with other cytotoxic agents, topoisomerase I inhibitors have become part of clinical routine in selected sarcoma subtypes. Regimens such as irinotecan/vincristine/temozolomide are used in relapsed rhabdomyosarcoma, irinotecan/temozolomide and vincristine/topotecan/cyclophosphamide are commonly given in refractory Ewing sarcoma, and topotecan/carboplatin showed some activity in advanced soft tissue sarcoma. This review provides an overview of key studies with topoisomerase I inhibitors for the treatment of sarcoma. Topoisomerase I inhibitors are currently also being assessed as "payloads" for antibody-drug conjugates (ADCs), allowing for the targeting of specific antigen-expressing tumor cells and the delivery of the inhibitor directly to the tumor cells with the potential of enhancing therapeutic efficacy while minimizing systemic toxicity. Here, we also provide a brief overview on topoisomerase I-ADCs. KEY MESSAGE Topoisomerase I inhibitors are an important component of some systemic therapies for selected sarcomas and have potent cytotoxic properties and pharmacological characteristics that make them relevant candidates as payloads for the development of sarcoma-specific ADCs. ADCs are antibody-based targeted agents allowing for efficient and specific delivery of a given drug to the tumor cell. Topoisomerase I-ADCs are a novel targeted delivery approach which may have the potential to improve the therapeutic index of topoisomerase I inhibitors in the treatment of sarcoma and warrants investigation in a broad variety of mesenchymal malignancies.
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Affiliation(s)
- Patrick Schöffski
- Department of General Medical Oncology, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
- Department of Oncology, Laboratory of Experimental Oncology, KU Leuven, Leuven, Belgium
| | - Chao-Chi Wang
- Department of Oncology, Laboratory of Experimental Oncology, KU Leuven, Leuven, Belgium
| | | | - Agnieszka Wozniak
- Department of Oncology, Laboratory of Experimental Oncology, KU Leuven, Leuven, Belgium
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Sołek P, Czechowska E, Sowa-Kućma M, Stachowicz K, Kaczka P, Tabęcka-Łonczyńska A. Elucidating the molecular mechanisms underlying the induction of autophagy by antidepressant-like substances in C57BL/6J mouse testis model upon LPS challenge. Cell Commun Signal 2023; 21:251. [PMID: 37735683 PMCID: PMC10512556 DOI: 10.1186/s12964-023-01270-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/13/2023] [Indexed: 09/23/2023] Open
Abstract
The treatment of depression with pharmaceuticals is associated with many adverse side effects, including male fertility problems. The precise mechanisms by which these agents affect testicular cells remain largely unknown, but they are believed to induce cellular stress, which is sensed by the endoplasmic reticulum (ER) and the Golgi apparatus. These organelles are responsible for maintaining cellular homeostasis and regulating signal pathways that lead to autophagy or apoptosis. Therefore, in this study, we aimed to investigate the autophagy, ER, and Golgi stress-related pathways in mouse testis following treatment with antidepressant-like substances (ALS) and ALS combined with lipopolysaccharide (LPS). We found that most ALS and activated proteins are associated with the induction of apoptosis. However, when imipramine (IMI) was combined with NS-398 (a cyclooxygenase-2 inhibitor) after LPS administration, we observed a marked increase in the BECLIN1, Bcl-2, ATG16L, and LC3 expression, which are marker proteins of autophagosome formation. The expression of the BECN1 and ATG16L genes was also high compared to the control, indicating the induction of autophagy processes that may potentially protect mouse testicular cells from death and regulate metabolism in the testis. Our findings may provide a better understanding of the stress-related effects of specific ALS on the testis. Video Abstract.
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Affiliation(s)
- Przemysław Sołek
- Department of Biopharmacy, Medical University of Lublin, 4a Chodźki, 20-093, Lublin, Poland
| | - Ewelina Czechowska
- Department of Human Physiology, Institute of Medical Sciences, Medical College of Rzeszow University, 2a Kopisto, 35-959, Rzeszow, Poland
| | - Magdalena Sowa-Kućma
- Department of Human Physiology, Institute of Medical Sciences, Medical College of Rzeszow University, 2a Kopisto, 35-959, Rzeszow, Poland
| | - Katarzyna Stachowicz
- Maj Institute of Pharmacology Polish Academy of Sciences, 12 Smetna, 31-343, Krakow, Poland
| | - Piotr Kaczka
- PRO-NOO-BIOTICS Sp. z o.o., 39 Warszawska, 35-205, Rzeszow, Poland
| | - Anna Tabęcka-Łonczyńska
- Department of Biotechnology and Cell Biology, Medical College, University of Information Technology and Management in Rzeszow, 2 Sucharskiego, 35-225, Rzeszow, Poland.
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Dimethylmyricacene: An In Vitro and In Silico Study of a Semisynthetic Non-Camptothecin Derivative Compound, Targeting Human DNA Topoisomerase 1B. Cells 2022; 11:cells11213486. [DOI: 10.3390/cells11213486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 11/06/2022] Open
Abstract
Human topoisomerase 1B regulates the topological state of supercoiled DNA enabling all fundamental cell processes. This enzyme, which is the unique molecular target of the natural anticancer compound camptothecin, acts by nicking one DNA strand and forming a transient protein–DNA covalent complex. The interaction of human topoisomerase 1B and dimethylmyricacene, a compound prepared semisynthetically from myricanol extracted from Myrica cerifera root bark, was investigated using enzymatic activity assays and molecular docking procedures. Dimethylmyricacene was shown to inhibit both the cleavage and the religation steps of the enzymatic reaction, and cell viability of A-253, FaDu, MCF-7, HeLa and HCT-116 tumor cell lines.
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Sapio L, Naviglio S. Innovation through Tradition: The Current Challenges in Cancer Treatment. Int J Mol Sci 2022; 23:ijms23105296. [PMID: 35628105 PMCID: PMC9141447 DOI: 10.3390/ijms23105296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 05/05/2022] [Indexed: 12/01/2022] Open
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Soren BC, Babu Dasari J, Ottaviani A, Messina B, Andreotti G, Romeo A, Iacovelli F, Falconi M, Desideri A, Fiorani P. In Vitro and In Silico Characterization of an Antimalarial Compound with Antitumor Activity Targeting Human DNA Topoisomerase IB. Int J Mol Sci 2021; 22:7455. [PMID: 34299074 PMCID: PMC8306514 DOI: 10.3390/ijms22147455] [Citation(s) in RCA: 3] [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: 06/16/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 12/18/2022] Open
Abstract
Human DNA topoisomerase IB controls the topological state of supercoiled DNA through a complex catalytic cycle that consists of cleavage and religation reactions, allowing the progression of fundamental DNA metabolism. The catalytic steps of human DNA topoisomerase IB were analyzed in the presence of a drug, obtained by the open-access drug bank Medicines for Malaria Venture. The experiments indicate that the compound strongly and irreversibly inhibits the cleavage step of the enzyme reaction and reduces the cell viability of three different cancer cell lines. Molecular docking and molecular dynamics simulations suggest that the drug binds to the human DNA topoisomerase IB-DNA complex sitting inside the catalytic site of the enzyme, providing a molecular explanation for the cleavage-inhibition effect. For all these reasons, the aforementioned drug could be a possible lead compound for the development of an efficient anti-tumor molecule targeting human DNA topoisomerase IB.
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Affiliation(s)
- Bini Chhetri Soren
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (B.C.S.); (J.B.D.); (B.M.); (G.A.); (A.R.); (F.I.); (M.F.); (A.D.); (P.F.)
| | - Jagadish Babu Dasari
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (B.C.S.); (J.B.D.); (B.M.); (G.A.); (A.R.); (F.I.); (M.F.); (A.D.); (P.F.)
| | - Alessio Ottaviani
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (B.C.S.); (J.B.D.); (B.M.); (G.A.); (A.R.); (F.I.); (M.F.); (A.D.); (P.F.)
| | - Beatrice Messina
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (B.C.S.); (J.B.D.); (B.M.); (G.A.); (A.R.); (F.I.); (M.F.); (A.D.); (P.F.)
| | - Giada Andreotti
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (B.C.S.); (J.B.D.); (B.M.); (G.A.); (A.R.); (F.I.); (M.F.); (A.D.); (P.F.)
| | - Alice Romeo
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (B.C.S.); (J.B.D.); (B.M.); (G.A.); (A.R.); (F.I.); (M.F.); (A.D.); (P.F.)
| | - Federico Iacovelli
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (B.C.S.); (J.B.D.); (B.M.); (G.A.); (A.R.); (F.I.); (M.F.); (A.D.); (P.F.)
| | - Mattia Falconi
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (B.C.S.); (J.B.D.); (B.M.); (G.A.); (A.R.); (F.I.); (M.F.); (A.D.); (P.F.)
| | - Alessandro Desideri
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (B.C.S.); (J.B.D.); (B.M.); (G.A.); (A.R.); (F.I.); (M.F.); (A.D.); (P.F.)
| | - Paola Fiorani
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy; (B.C.S.); (J.B.D.); (B.M.); (G.A.); (A.R.); (F.I.); (M.F.); (A.D.); (P.F.)
- Institute of Translational Pharmacology, National Research Council, CNR, Via del Fosso del Cavaliere 100, 00133 Rome, Italy
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Ottaviani A, Iacovelli F, Fiorani P, Desideri A. Natural Compounds as Therapeutic Agents: The Case of Human Topoisomerase IB. Int J Mol Sci 2021; 22:4138. [PMID: 33923641 PMCID: PMC8073192 DOI: 10.3390/ijms22084138] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 11/25/2022] Open
Abstract
Natural products are widely used as source for drugs development. An interesting example is represented by natural drugs developed against human topoisomerase IB, a ubiquitous enzyme involved in many cellular processes where several topological problems occur due the formation of supercoiled DNA. Human topoisomerase IB, involved in the solution of such problems relaxing the DNA cleaving and religating a single DNA strand, represents an important target in anticancer therapy. Several natural compounds inhibiting or poisoning this enzyme are under investigation as possible new drugs. This review summarizes the natural products that target human topoisomerase IB that may be used as the lead compounds to develop new anticancer drugs. Moreover, the natural compounds and their derivatives that are in clinical trial are also commented on.
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Affiliation(s)
- Alessio Ottaviani
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, 00133 Rome, Italy; (F.I.); (P.F.); (A.D.)
| | - Federico Iacovelli
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, 00133 Rome, Italy; (F.I.); (P.F.); (A.D.)
| | - Paola Fiorani
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, 00133 Rome, Italy; (F.I.); (P.F.); (A.D.)
- Institute of Translational Pharmacology, National Research Council, CNR, Via Del Fosso del Cavaliere 100, 00133 Rome, Italy
| | - Alessandro Desideri
- Department of Biology, University of Rome Tor Vergata, Via Della Ricerca Scientifica, 00133 Rome, Italy; (F.I.); (P.F.); (A.D.)
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