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Majhi B, Bora A, Palit S, Dev S, Majumdar P, Dutta S. Metal-free internal nucleophile-triggered domino route for synthesis of fused quinoxaline [1,4]-diazepine hybrids and the evaluation of their DNA binding properties. Bioorg Chem 2024; 151:107694. [PMID: 39151388 DOI: 10.1016/j.bioorg.2024.107694] [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: 05/24/2024] [Revised: 07/26/2024] [Accepted: 08/03/2024] [Indexed: 08/19/2024]
Abstract
An unprecedented metal-free synthesis of fused quinoxaline 1,5-disubstituted-[1,4]-diazepine hybrids have been reported under mild conditions through a domino intermolecular SNAr followed by an internal nucleophile-triggered intramolecular SNAr pathway. Our strategy offers the flexibility for the introduction of a broad variety of functionalities at the N-1 position of fused diazepine moiety by using suitable diamine tails to design structurally diverse scaffolds. The DNA binding properties of representative quinoxaline diazepine hybrids were studied using UV-vis absorbance and EtBr displacement assay and were found to be governed by the functionalities at the N-1 position. Interestingly, compound 11f containing the N-1 benzyl substitution demonstrated significant DNA binding (KBH ∼ 2.15 ± 0.25 × 104 M-1 and Ksv ∼ 12.6 ± 1.41 × 103 M-1) accompanied by a bathochromic shift (Δλ ∼ 5 nm). In silico studies indicated possible binding of diazepine hybrid 11f at the GC-rich major groove in the ct-DNA hexamer duplex and showed comparable binding energies to that of ethidium bromide. The antiproliferative activity of compounds was observed in the given order in different cell lines: (HeLa > HT29 > SKOV 3 > HCT116 > HEK293). Lead compound 11f demonstrated maximum cytotoxicity (IC50 value of 13.30 μM) in HeLa cell lines and also caused early apoptosis-mediated cell death in cancer cell lines. We envision that our work will offer newer methodologies for the construction of fused quinoxaline 1,5-disubstituted-[1,4]-diazepine class of molecules.
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Affiliation(s)
- Bhim Majhi
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, India
| | - Achyut Bora
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, India
| | - Subhadeep Palit
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, India
| | - Samrat Dev
- Mrinalini Dutta Mahavidyapith, Vidyapith Rd, Pratiraksha Nagar, Kolkata 700051, India
| | - Papiya Majumdar
- Department of Chemistry, Sister Nivedita University, DG 1/2, Newtown, Kolkata 700156, India
| | - Sanjay Dutta
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, India.
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Majhi B, Ganguly S, Palit S, Parwez A, Saha R, Basu G, Dutta S. Sequence-Specific Dual DNA Binding Modes and Cytotoxicities of N-6-Functionalized Norcryptotackieine Alkaloids. JOURNAL OF NATURAL PRODUCTS 2023; 86:1667-1676. [PMID: 37285507 DOI: 10.1021/acs.jnatprod.2c01045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Norcryptotackieine (1a) belongs to the indoloquinoline class of alkaloids isolated from Cryptolepis sanguinolenta, a plant species that has been traditionally used as an antimalarial agent. Additional structural modifications of 1a can potentially enhance its therapeutic potency. Indoloquinolines such as cryptolepine, neocryptolepine, isocryptolepine, and neoisocryptolepine show restricted clinical applications owing to their cytotoxicity deriving from interactions with DNA. Here, we examined the effect of substitutions at the N-6 position of norcryptotackieine on the cytotoxicity, as well as structure-activity relationship studies pertaining to sequence specific DNA-binding affinities. The representative compound 6d binds DNA in a nonintercalative/pseudointercalative fashion, in addition to nonspecific stacking on DNA, in a sequence selective manner. The DNA-binding studies clearly establish the mechanism of DNA binding by N-6-substituted norcryptotackieines and neocryptolepine. The synthesized norcryptotackieines 6c,d and known indoloquinolines were screened on different cell lines (HEK293, OVCAR3, SKOV3, B16F10, and HeLa) to assess their cytotoxicity. Norcryptotackieine 6d (IC50 value of 3.1 μM) showed 2-fold less potency when compared to the natural indoloquinoline cryptolepine 1c (IC50 value of 1.64 μM) in OVCAR3 (ovarian adenocarcinoma) cell lines.
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Affiliation(s)
- Bhim Majhi
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sudakshina Ganguly
- Department of Biophysics, Centenary Campus Bose Institute, P-1/12 C.I.T. Scheme VII-M, Kolkata 700054, India
| | - Subhadeep Palit
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, India
| | - Aymen Parwez
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Rimita Saha
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Gautam Basu
- Department of Biophysics, Centenary Campus Bose Institute, P-1/12 C.I.T. Scheme VII-M, Kolkata 700054, India
| | - Sanjay Dutta
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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Anjomshoa M, Amirheidari B. Nuclease-like metalloscissors: Biomimetic candidates for cancer and bacterial and viral infections therapy. Coord Chem Rev 2022; 458:214417. [PMID: 35153301 PMCID: PMC8816526 DOI: 10.1016/j.ccr.2022.214417] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 01/09/2022] [Indexed: 12/25/2022]
Abstract
Despite the extensive and rapid discovery of modern drugs for treatment of cancer, microbial infections, and viral illnesses; these diseases are still among major global health concerns. To take inspiration from natural nucleases and also the therapeutic potential of metallopeptide antibiotics such as the bleomycin family, artificial metallonucleases with the ability of promoting DNA/RNA cleavage and eventually affecting cellular biological processes can be introduced as a new class of therapeutic candidates. Metal complexes can be considered as one of the main categories of artificial metalloscissors, which can prompt nucleic acid strand scission. Accordingly, biologists, inorganic chemists, and medicinal inorganic chemists worldwide have been designing, synthesizing and evaluating the biological properties of metal complexes as artificial metalloscissors. In this review, we try to highlight the recent studies conducted on the nuclease-like metalloscissors and their potential therapeutic applications. Under the light of the concurrent Covid-19 pandemic, the human need for new therapeutics was highlighted much more than ever before. The nuclease-like metalloscissors with the potential of RNA cleavage of invading viral pathogens hence deserve prime attention.
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Recent advancement in small molecules as HCV inhibitors. Bioorg Med Chem 2022; 60:116699. [PMID: 35278819 DOI: 10.1016/j.bmc.2022.116699] [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: 09/21/2021] [Revised: 02/18/2022] [Accepted: 03/02/2022] [Indexed: 11/24/2022]
Abstract
Hepatitis C virus (HCV) has caused a considerable threat to human health. To date, no treatments are without side effects. The proteins and RNA associated with HCV have specific functions during the viral life cycle. The vulnerabilities to virus are associated with those proteins or RNA. Thus, targeting these proteins and RNA is an efficient strategy to develop anti-HCV therapeutics. The treatment for HCV-infected patients has been greatly improved after the approval of direct-acting antivirals (DAAs). However, the cost of DAAs is unusually high, which adds to the economic burden on patients with chronic liver diseases. So far, many efforts have been devoted to the development of small molecules as novel HCV inhibitors. Investigations on the inhibitory activities of these small molecules have involved the target identification and the mechanism of action. In this mini-review, these small molecules divided into four kinds were elaborated, which focused on their targets and structural features. Furthermore, we raised the current challenges and promising prospects. This mini-review may facilitate the development of small molecules with improved activities targeting HCV based on the chemical scaffolds of HCV inhibitors.
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Mandi C, Mahata T, Patra D, Chakraborty J, Bora A, Pal R, Dutta S. Cleavage of Abasic Sites in DNA by an Aminoquinoxaline Compound: Augmented Cytotoxicity and DNA Damage in Combination with an Anticancer Drug Chlorambucil in Human Colorectal Carcinoma Cells. ACS OMEGA 2022; 7:6488-6501. [PMID: 35252645 PMCID: PMC8892855 DOI: 10.1021/acsomega.1c04962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/07/2021] [Indexed: 06/14/2023]
Abstract
The elevated level of endogenous oxidative DNA damage and spontaneous deamination of DNA bases in cancer cells substantially increase the abasic sites in DNA via base excision repairs (BERs). Thus, the predominant BER pathway is a favorable target for cancer therapy. Interestingly, elevated levels of glutathione (GSH) in certain cancer cells, such as colon cancer, are associated with acquired resistance to several chemotherapeutic agents, which increase the difficulty for the treatment of cancer. Here, we have reported an ideal nitro group-containing monoquinoxaline DNA intercalator (1d), which is reduced into a fluorescent quinoxaline amine (1e) in the presence of GSH; concurrently, 1e (∼100 nM concentration) selectively causes the in vitro cleavage of abasic sites in DNA. 1e also binds to the tetrahydrofuran analogue of the abasic site in the nanomolar to low micromolar range depending on the nucleotide sequence opposite to the abasic site and also induces a structural change in abasic DNA. Furthermore, the amine compound (1e) augments the response of the specific bifunctional alkylating drug chlorambucil at a much lower concentration in the human colorectal carcinoma cell (HCT-116), and their combination shows a potential strategy for targeted therapy. Alone or in combination, 1d and 1e lead to a cascade of cellular events such as induction of DNA double-stranded breaks and cell arrest at G0/G1 and G2/M phases, eventually leading to apoptotic cell death in HCT-116 cells. Hence, the outcome of this study provides a definitive approach that will help optimize the therapeutic applications for targeting the abasic site in cancer cells.
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Affiliation(s)
- Chandra
Sova Mandi
- Organic
and Medicinal Chemistry Division, CSIR-Indian
Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, West
Bengal, India
| | - Tridib Mahata
- Organic
and Medicinal Chemistry Division, CSIR-Indian
Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, West
Bengal, India
| | - Dipendu Patra
- Organic
and Medicinal Chemistry Division, CSIR-Indian
Institute of Chemical Biology, 4, Raja S. C. Mullick Road, 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, Kolkata 700032, West
Bengal, India
| | - Achyut Bora
- Organic
and Medicinal Chemistry Division, CSIR-Indian
Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, West
Bengal, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ritesh Pal
- Organic
and Medicinal Chemistry Division, CSIR-Indian
Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, West
Bengal, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sanjay Dutta
- Organic
and Medicinal Chemistry Division, CSIR-Indian
Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, West
Bengal, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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Synthesis of Quinoxaline Derivatives as Intermediates to Obtain Erdafitinib. Pharm Chem J 2021. [DOI: 10.1007/s11094-021-02521-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Xu M, Hu S, Wang Y, Wang T, Dziugan P, Zhang B, Zhao H. Integrated Transcriptome and Proteome Analyses Reveal Protein Metabolism in Lactobacillus helveticus CICC22171. Front Microbiol 2021; 12:635685. [PMID: 34149633 PMCID: PMC8206810 DOI: 10.3389/fmicb.2021.635685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 04/29/2021] [Indexed: 11/13/2022] Open
Abstract
Lactobacillus helveticus is a homofermentative lactic acid bacterium. It is widely used in the fabrication of Swiss cheese and other dairy products. The aim of this study was to elucidate the mechanism by which L. helveticus utilizes protein. Lactobacillus helveticus CICC22171 were cultured in two different media with various nitrogen sources. The control contained 20 basic amino acids, while the experimental medium contained casein. De novo transcriptome and isobaric tags for relative and absolute quantification (iTRAQ) proteome analyses were applied to determine how L. helveticus utilizes protein. The casein underwent extracellular hydrolysis via ATP-binding cassette (ABC) transporter upregulation and Mn2+-associated cell envelope proteinase (CEP) downregulation. Sigma factors and EF-Tu were upregulated and Mg2+ was reduced in bacteria to accommodate DNA transcription and protein translation in preparation for proteolysis. Hydrolase activity was upregulated to digest intracellular polypeptides and control endopeptidase genes. In these bacteria, casein utilization affected glycolysis, trehalose phosphotransferase system (PTS), and key factors associated with aerobic respiration and reduced glucose consumption.
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Affiliation(s)
- Mengfan Xu
- College of Biological Science and Biotechnology, Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, China
| | - Shanhu Hu
- College of Biological Science and Biotechnology, Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, China
| | - Yiwen Wang
- College of Biological Science and Biotechnology, Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, China
| | - Tao Wang
- College of Biological Science and Biotechnology, Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, China
| | - Piotr Dziugan
- Institute of Fermentation Technology and Microbiology, Lodz University of Technology, Łódź, Poland
| | - Bolin Zhang
- College of Biological Science and Biotechnology, Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, China
| | - Hongfei Zhao
- College of Biological Science and Biotechnology, Beijing Key Laboratory of Forest Food Processing and Safety, Beijing Forestry University, Beijing, China
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Abstract
The structural and regulatory elements in therapeutically relevant RNAs offer many opportunities for targeting by small molecules, yet fundamental understanding of what drives selectivity in small molecule:RNA recognition has been a recurrent challenge. In particular, RNAs tend to be more dynamic and offer less chemical functionality than proteins, and biologically active ligands must compete with the highly abundant and highly structured RNA of the ribosome. Indeed, the only small molecule drug targeting RNA other than the ribosome was just approved in August 2020, and our recent survey of the literature revealed fewer than 150 reported chemical probes that target non-ribosomal RNA in biological systems. This Feature outlines our efforts to improve small molecule targeting strategies and gain fundamental insights into small molecule:RNA recognition by analyzing patterns in both RNA-biased small molecule chemical space and RNA topological space privileged for differentiation. First, we synthesized libraries based on RNA binding scaffolds that allowed us to reveal general principles in small molecule:recognition and to ask precise chemical questions about drivers of affinity and selectivity. Elaboration of these scaffolds has led to recognition of medicinally relevant RNA targets, including viral and long noncoding RNA structures. More globally, we identified physicochemical, structural, and spatial properties of biologically active RNA ligands that are distinct from those of protein-targeted ligands, and we have provided the dataset and associated analytical tools as part of a publicly available online platform to facilitate RNA ligand discovery. At the same time, we used pattern recognition protocols to identify RNA topologies that can be differentially recognized by small molecules and have elaborated this technique to visualize conformational changes in RNA secondary structure. These fundamental insights into the drivers of RNA recognition in vitro have led to functional targeting of RNA structures in biological systems. We hope that these initial guiding principles, as well as the approaches and assays developed in their pursuit, will enable rapid progress toward the development of RNA-targeted chemical probes and ultimately new therapeutic approaches to a wide range of deadly human diseases.
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Affiliation(s)
- Amanda E Hargrove
- Department of Chemistry, Duke University, 124 Science Drive, Box 90346, Durham, NC 27708, USA.
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Schmit D, Milewicz U, Boerneke MA, Burley S, Walsworth K, Um J, Hecht D, Hermann T, Bergdahl BM. Syntheses and Binding Testing of N1-Alkylamino-Substituted 2-Aminobenzimidazole Analogues Targeting the Hepatitis C Virus Internal Ribosome Entry Site. Aust J Chem 2020. [DOI: 10.1071/ch19526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A series of 2-aminobenzimidazole analogues have been synthesised and tested for binding to a previously established RNA target for viral translation inhibitors in the internal ribosome entry site (IRES) of the hepatitis C virus (HCV). Synthesis of new inhibitor compounds followed a highly convergent strategy which allowed for incorporation of diverse tertiary amino substituents in high overall yields (eight-steps, 4–22%). Structure–activity relationship (SAR) studies focussed on the tertiary amine substituent involved in hydrogen bonding with the RNA backbone at the inhibitor binding site. The SAR study was further correlated with in silico docking experiments. Analogous compounds showed promising activities (half maximal effective concentration, EC50: 21–89µM). Structures of the synthesised analogues and a correlation to their mode of binding, provided the opportunity to explore parameters required for selective targeting of the HCV IRES at the subdomain IIa which acts as an RNA conformational switch in HCV translation.
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