{"entity": "researcher", "timestamp": "2026-07-15T16:21:24.516Z", "family": "Das", "given": "Rabindra Nath", "initials": "RN", "orcid": "0000-0001-6347-2169", "affiliations": ["Department of Chemistry, Ume\u00e5 University, 90187, Ume\u00e5, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/fec8d8bcbe8648258cfbab86693c77c6.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/fec8d8bcbe8648258cfbab86693c77c6"}}, "publications": [{"entity": "publication", "iuid": "e84df26075a4401cac144c75bbbf1de9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e84df26075a4401cac144c75bbbf1de9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e84df26075a4401cac144c75bbbf1de9"}}, "title": "Design, Synthesis, and Biophysical Characterization of Pyridine Bis\u2010Quinazoline Derivatives as Selective G\u2010Quadruplex DNA Stabilizers", "authors": [{"family": "Nath Das", "given": "Rabindra", "initials": "R", "orcid": "0000-0001-6347-2169", "researcher": {"href": "https://publications.scilifelab.se/researcher/fec8d8bcbe8648258cfbab86693c77c6.json"}}, {"family": "Chorell", "given": "Erik", "initials": "E", "orcid": "0000-0003-2523-1940", "researcher": {"href": "https://publications.scilifelab.se/researcher/ada783ae0a824621a3b8e1024aae13a4.json"}}], "type": "journal-article", "published": "2025-04-09", "journal": {"title": "Chem. Eur. J.", "issn": "0947-6539", "volume": "31", "issue": "21", "issn-l": "0947-6539"}, "abstract": null, "doi": "10.1002/chem.202404689", "pmid": null, "labels": {"Chemical Biology Consortium Sweden": "Service"}, "xrefs": [], "notes": [], "created": "2025-04-23T09:42:14.931Z", "modified": "2025-10-17T13:04:26.742Z"}, {"entity": "publication", "iuid": "ef5dff07e6294aa286365ab35e19436b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ef5dff07e6294aa286365ab35e19436b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ef5dff07e6294aa286365ab35e19436b"}}, "title": "Enhanced mitochondrial G-quadruplex formation impedes replication fork progression leading to mtDNA loss in human cells.", "authors": [{"family": "Doimo", "given": "Mara", "initials": "M", "orcid": "0000-0002-6771-5233", "researcher": {"href": "https://publications.scilifelab.se/researcher/644b7aaefa12496890f4fbfe884afdb2.json"}}, {"family": "Chaudhari", "given": "Namrata", "initials": "N"}, {"family": "Abrahamsson", "given": "Sanna", "initials": "S"}, {"family": "L'H\u00f4te", "given": "Valentin", "initials": "V", "orcid": "0000-0001-5168-2943", "researcher": {"href": "https://publications.scilifelab.se/researcher/12fee9d8747648fab64338de0ebbd9aa.json"}}, {"family": "Nguyen", "given": "Tran V H", "initials": "TVH"}, {"family": "Berner", "given": "Andreas", "initials": "A", "orcid": "0000-0001-7864-8403", "researcher": {"href": "https://publications.scilifelab.se/researcher/49b5bb87e1eb44c8bc70f60dfd0ebf0e.json"}}, {"family": "Ndi", "given": "Mama", "initials": "M"}, {"family": "Abrahamsson", "given": "Alva", "initials": "A"}, {"family": "Das", "given": "Rabindra Nath", "initials": "RN", "orcid": "0000-0001-6347-2169", "researcher": {"href": "https://publications.scilifelab.se/researcher/fec8d8bcbe8648258cfbab86693c77c6.json"}}, {"family": "Aasumets", "given": "Koit", "initials": "K"}, {"family": "Goffart", "given": "Steffi", "initials": "S", "orcid": "0000-0001-8491-1458", "researcher": {"href": "https://publications.scilifelab.se/researcher/3e72dc810f3245b390f721a088f01765.json"}}, {"family": "Pohjoism\u00e4ki", "given": "Jaakko L O", "initials": "JLO", "orcid": "0000-0002-1185-3610", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3dec32b253440eab477911e81ec3c1f.json"}}, {"family": "L\u00f3pez", "given": "Marcela D\u00e1vila", "initials": "MD"}, {"family": "Chorell", "given": "Erik", "initials": "E", "orcid": "0000-0003-2523-1940", "researcher": {"href": "https://publications.scilifelab.se/researcher/ada783ae0a824621a3b8e1024aae13a4.json"}}, {"family": "Wanrooij", "given": "Sjoerd", "initials": "S", "orcid": "0000-0001-6126-4382", "researcher": {"href": "https://publications.scilifelab.se/researcher/84c9ac1e1b8f4cf68ae25766bc8dfa0e.json"}}], "type": "journal article", "published": "2023-08-11", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "issn-l": "0305-1048", "volume": "51", "issue": "14", "pages": "7392-7408"}, "abstract": "Mitochondrial DNA (mtDNA) replication stalling is considered an initial step in the formation of mtDNA deletions that associate with genetic inherited disorders and aging. However, the molecular details of how stalled replication forks lead to mtDNA deletions accumulation are still unclear. Mitochondrial DNA deletion breakpoints preferentially occur at sequence motifs predicted to form G-quadruplexes (G4s), four-stranded nucleic acid structures that can fold in guanine-rich regions. Whether mtDNA G4s form in vivo and their potential implication for mtDNA instability is still under debate. In here, we developed new tools to map G4s in the mtDNA of living cells. We engineered a G4-binding protein targeted to the mitochondrial matrix of a human cell line and established the mtG4-ChIP method, enabling the determination of mtDNA G4s under different cellular conditions. Our results are indicative of transient mtDNA G4 formation in human cells. We demonstrate that mtDNA-specific replication stalling increases formation of G4s, particularly in the major arc. Moreover, elevated levels of G4 block the progression of the mtDNA replication fork and cause mtDNA loss. We conclude that stalling of the mtDNA replisome enhances mtDNA G4 occurrence, and that G4s not resolved in a timely manner can have a negative impact on mtDNA integrity.", "doi": "10.1093/nar/gkad535", "pmid": "37351621", "labels": {"Clinical Genomics Gothenburg": "Collaborative", "Clinical Genomics": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC10415151"}, {"db": "pii", "key": "7205764"}], "notes": [], "created": "2023-11-30T22:29:50.813Z", "modified": "2023-11-30T22:31:20.606Z"}, {"entity": "publication", "iuid": "83bfe5d1d31a4dd282c21d70ba3a05f7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/83bfe5d1d31a4dd282c21d70ba3a05f7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/83bfe5d1d31a4dd282c21d70ba3a05f7"}}, "title": "Macrocyclization of bis-indole quinolines for selective stabilization of G-quadruplex DNA structures.", "authors": [{"family": "Das", "given": "Rabindra Nath", "initials": "RN", "orcid": "0000-0001-6347-2169", "researcher": {"href": "https://publications.scilifelab.se/researcher/fec8d8bcbe8648258cfbab86693c77c6.json"}}, {"family": "Andr\u00e9asson", "given": "M\u00e5ns", "initials": "M", "orcid": "0000-0001-8089-2333", "researcher": {"href": "https://publications.scilifelab.se/researcher/7345c9c952d84801ad8334e3742ab7ec.json"}}, {"family": "Kumar", "given": "Rajendra", "initials": "R", "orcid": "0000-0002-7268-9519", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ba57d44c650444aa51a030541d3bba7.json"}}, {"family": "Chorell", "given": "Erik", "initials": "E", "orcid": "0000-0003-2523-1940", "researcher": {"href": "https://publications.scilifelab.se/researcher/ada783ae0a824621a3b8e1024aae13a4.json"}}], "type": "journal article", "published": "2020-09-16", "journal": {"title": "Chem. Sci.", "issn": "2041-6520", "volume": "11", "issue": "38", "pages": "10529-10537", "issn-l": null}, "abstract": "The recognition of G-quadruplex (G4) DNA structures as important regulatory elements in biological mechanisms, and the connection between G4s and the evolvement of different diseases, has sparked interest in developing small organic molecules targeting G4s. However, such compounds often lack drug-like properties and selectivity. Here, we describe the design and synthesis of a novel class of macrocyclic bis-indole quinolines based on their non-macrocyclic lead compounds. The effects of the macrocyclization on the ability to interact with G4 DNA structures were investigated using biophysical assays and molecular dynamic simulations. Overall, this revealed compounds with potent abilities to interact with and stabilize G4 structures and a clear selectivity for both G4 DNA over dsDNA and for parallel/hybrid G4 topologies, which could be attributed to the macrocyclic structure. Moreover, we obtained knowledge about the structure-activity relationship of importance for the macrocyclic design and how structural modifications could be made to construct improved macrocyclic compounds. Thus, the macrocyclization of G4 ligands can serve as a basis for the optimization of research tools to study G4 biology and potential therapeutics targeting G4-related diseases.", "doi": "10.1039/d0sc03519j", "pmid": "34094311", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [{"db": "pii", "key": "d0sc03519j"}, {"db": "pmc", "key": "PMC8162405"}], "notes": [], "created": "2020-11-24T20:27:43.691Z", "modified": "2025-10-17T13:03:56.637Z"}, {"entity": "publication", "iuid": "81f8017172254c37a519f7c4ef21984f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/81f8017172254c37a519f7c4ef21984f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/81f8017172254c37a519f7c4ef21984f"}}, "title": "The Relation Between Position and Chemical Composition of Bis-Indole Substituents Determines Their Interactions with G-Quadruplex DNA.", "authors": [{"family": "Prasad", "given": "Bagineni", "initials": "B", "orcid": "0000-0002-8498-1250", "researcher": {"href": "https://publications.scilifelab.se/researcher/6eaf800ddfd04f5aaa7b29802fe433d2.json"}}, {"family": "Das", "given": "Rabindra Nath", "initials": "RN", "orcid": "0000-0001-6347-2169", "researcher": {"href": "https://publications.scilifelab.se/researcher/fec8d8bcbe8648258cfbab86693c77c6.json"}}, {"family": "Jamroskovic", "given": "Jan", "initials": "J", "orcid": "0000-0001-6871-7663", "researcher": {"href": "https://publications.scilifelab.se/researcher/154847e2f84f4336a07e219fac6db2f9.json"}}, {"family": "Kumar", "given": "Rajendra", "initials": "R", "orcid": "0000-0002-7268-9519", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ba57d44c650444aa51a030541d3bba7.json"}}, {"family": "Hedenstr\u00f6m", "given": "Mattias", "initials": "M"}, {"family": "Sabouri", "given": "Nasim", "initials": "N", "orcid": "0000-0002-4541-7702", "researcher": {"href": "https://publications.scilifelab.se/researcher/4bdc688dc85a4932acfdfffad8bfc443.json"}}, {"family": "Chorell", "given": "Erik", "initials": "E", "orcid": "0000-0003-2523-1940", "researcher": {"href": "https://publications.scilifelab.se/researcher/ada783ae0a824621a3b8e1024aae13a4.json"}}], "type": "journal article", "published": "2020-08-03", "journal": {"title": "Chemistry", "issn": "1521-3765", "volume": "26", "issue": "43", "pages": "9561-9572", "issn-l": "0947-6539"}, "abstract": "G-quadruplex (G4) DNA structures are linked to fundamental biological processes and human diseases, which has triggered the development of compounds that affect these DNA structures. However, more knowledge is needed about how small molecules interact with G4 DNA structures. This study describes the development of a new class of bis-indoles (3,3-diindolyl-methyl derivatives) and detailed studies of how they interact with G4 DNA using orthogonal assays, biophysical techniques, and computational studies. This revealed compounds that strongly bind and stabilize G4 DNA structures, and detailed binding interactions which for example, show that charge variance can play a key role in G4 DNA binding. Furthermore, the structure-activity relationships generated opened the possibilities to replace or introduce new substituents on the core structure, which is of key importance to optimize compound properties or introduce probes to further expand the possibilities of these compounds as tailored research tools to study G4 biology.", "doi": "10.1002/chem.202000579", "pmid": "32187406", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC7497243"}], "notes": [], "created": "2020-03-30T11:43:49.969Z", "modified": "2025-10-17T13:03:56.658Z"}, {"entity": "publication", "iuid": "1472dc974e934876920eaee93787c313", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1472dc974e934876920eaee93787c313.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1472dc974e934876920eaee93787c313"}}, "title": "A site-specific self-assembled light-up rotor probe for selective recognition and stabilization of c-MYC G-quadruplex DNA.", "authors": [{"family": "Deiana", "given": "Marco", "initials": "M", "orcid": "0000-0002-7815-4494", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9efbe74ca3940029d782d3ba645fa34.json"}}, {"family": "Chand", "given": "Karam", "initials": "K", "orcid": "0000-0001-7691-4392", "researcher": {"href": "https://publications.scilifelab.se/researcher/a20b7a82f4444b92b3ac1897e2fdb790.json"}}, {"family": "Jamroskovic", "given": "Jan", "initials": "J", "orcid": "0000-0001-6871-7663", "researcher": {"href": "https://publications.scilifelab.se/researcher/154847e2f84f4336a07e219fac6db2f9.json"}}, {"family": "Das", "given": "Rabindra Nath", "initials": "RN", "orcid": "0000-0001-6347-2169", "researcher": {"href": "https://publications.scilifelab.se/researcher/fec8d8bcbe8648258cfbab86693c77c6.json"}}, {"family": "Obi", "given": "Ikenna", "initials": "I", "orcid": "0000-0003-0364-8964", "researcher": {"href": "https://publications.scilifelab.se/researcher/e46c65e7b0e540b0a7c225d54c1502d7.json"}}, {"family": "Chorell", "given": "Erik", "initials": "E", "orcid": "0000-0003-2523-1940", "researcher": {"href": "https://publications.scilifelab.se/researcher/ada783ae0a824621a3b8e1024aae13a4.json"}}, {"family": "Sabouri", "given": "Nasim", "initials": "N", "orcid": "0000-0002-4541-7702", "researcher": {"href": "https://publications.scilifelab.se/researcher/4bdc688dc85a4932acfdfffad8bfc443.json"}}], "type": "journal article", "published": "2020-06-25", "journal": {"title": "Nanoscale", "issn": "2040-3372", "volume": "12", "issue": "24", "pages": "12950-12957", "issn-l": "2040-3364"}, "abstract": "Direct and unambiguous evidence of the formation of G-quadruplexes (G4s) in human cells have shown their implication in several key biological events and has emphasized their role as important targets for small-molecule cancer therapeutics. Here, we report on the first example of a self-assembled molecular-rotor G4-binder able to discriminate between an extensive panel of G4 and non-G4 structures and to selectively light-up (up to 64-fold), bind (nanomolar range), and stabilize the c-MYC promoter G4 DNA. In particular, association with the c-MYC G4 triggers the disassembly of its supramolecular state (disaggregation-induced emission, DIE) and induces geometrical restrictions (motion-induced change in emission, MICE) leading to a significant enhancement of its emission yield. Moreover, this optical reporter is able to selectively stabilize the c-MYC G4 and inhibit DNA synthesis. Finally, by using confocal laser-scanning microscopy (CLSM) we show the ability of this compound to localize primarily in the subnuclear G4-rich compartments of cancer cells. This work provides a benchmark for the future design and development of a new generation of smart sequence-selective supramolecular G4-binders that combine outstanding sensing and stability properties, to be utilized in anti-cancer therapy.", "doi": "10.1039/d0nr03404e", "pmid": "32525170", "labels": {"Swedish NMR Centre": "Service"}, "xrefs": [], "notes": [], "created": "2020-11-24T20:27:45.025Z", "modified": "2025-10-17T13:03:56.850Z"}, {"entity": "publication", "iuid": "4f91e593c9d848349f62c13e8004a3d6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4f91e593c9d848349f62c13e8004a3d6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4f91e593c9d848349f62c13e8004a3d6"}}, "title": "Quinazoline Ligands Induce Cancer Cell Death through Selective STAT3 Inhibition and G-Quadruplex Stabilization.", "authors": [{"family": "Jamroskovic", "given": "Jan", "initials": "J", "orcid": "0000-0001-6871-7663", "researcher": {"href": "https://publications.scilifelab.se/researcher/154847e2f84f4336a07e219fac6db2f9.json"}}, {"family": "Doimo", "given": "Mara", "initials": "M"}, {"family": "Chand", "given": "Karam", "initials": "K"}, {"family": "Obi", "given": "Ikenna", "initials": "I"}, {"family": "Kumar", "given": "Rajendra", "initials": "R", "orcid": "0000-0002-7268-9519", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ba57d44c650444aa51a030541d3bba7.json"}}, {"family": "Br\u00e4nnstr\u00f6m", "given": "Kristoffer", "initials": "K"}, {"family": "Hedenstr\u00f6m", "given": "Mattias", "initials": "M"}, {"family": "Nath Das", "given": "Rabindra", "initials": "R", "orcid": "0000-0001-6347-2169", "researcher": {"href": "https://publications.scilifelab.se/researcher/fec8d8bcbe8648258cfbab86693c77c6.json"}}, {"family": "Akhunzianov", "given": "Almaz", "initials": "A"}, {"family": "Deiana", "given": "Marco", "initials": "M", "orcid": "0000-0002-7815-4494", "researcher": {"href": "https://publications.scilifelab.se/researcher/f9efbe74ca3940029d782d3ba645fa34.json"}}, {"family": "Kasho", "given": "Kazutoshi", "initials": "K"}, {"family": "Sulis Sato", "given": "Sebastian", "initials": "S"}, {"family": "Pourbozorgi", "given": "Parham L", "initials": "PL"}, {"family": "Mason", "given": "James E", "initials": "JE"}, {"family": "Medini", "given": "Paolo", "initials": "P"}, {"family": "\u00d6hlund", "given": "Daniel", "initials": "D"}, {"family": "Wanrooij", "given": "Sjoerd", "initials": "S"}, {"family": "Chorell", "given": "Erik", "initials": "E", "orcid": "0000-0003-2523-1940", "researcher": {"href": "https://publications.scilifelab.se/researcher/ada783ae0a824621a3b8e1024aae13a4.json"}}, {"family": "Sabouri", "given": "Nasim", "initials": "N", "orcid": "0000-0002-4541-7702", "researcher": {"href": "https://publications.scilifelab.se/researcher/4bdc688dc85a4932acfdfffad8bfc443.json"}}], "type": "journal article", "published": "2020-02-12", "journal": {"volume": "142", "issn": "1520-5126", "issue": "6", "pages": "2876-2888", "title": "J. Am. Chem. Soc.", "issn-l": "0002-7863"}, "abstract": "The signal transducer and activator of transcription 3 (STAT3) protein is a master regulator of most key hallmarks and enablers of cancer, including cell proliferation and the response to DNA damage. G-Quadruplex (G4) structures are four-stranded noncanonical DNA structures enriched at telomeres and oncogenes' promoters. In cancer cells, stabilization of G4 DNAs leads to replication stress and DNA damage accumulation and is therefore considered a promising target for oncotherapy. Here, we designed and synthesized novel quinazoline-based compounds that simultaneously and selectively affect these two well-recognized cancer targets, G4 DNA structures and the STAT3 protein. Using a combination of in vitro assays, NMR, and molecular dynamics simulations, we show that these small, uncharged compounds not only bind to the STAT3 protein but also stabilize G4 structures. In human cultured cells, the compounds inhibit phosphorylation-dependent activation of STAT3 without affecting the antiapoptotic factor STAT1 and cause increased formation of G4 structures, as revealed by the use of a G4 DNA-specific antibody. As a result, treated cells show slower DNA replication, DNA damage checkpoint activation, and an increased apoptotic rate. Importantly, cancer cells are more sensitive to these molecules compared to noncancerous cell lines. This is the first report of a promising class of compounds that not only targets the DNA damage cancer response machinery but also simultaneously inhibits the STAT3-induced cancer cell proliferation, demonstrating a novel approach in cancer therapy.", "doi": "10.1021/jacs.9b11232", "pmid": "31990532", "labels": {"Swedish NMR Centre": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC7307907"}], "notes": [], "created": "2020-01-31T14:38:39.014Z", "modified": "2025-10-17T13:03:57.141Z"}]}