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Xie Z, Zhang S, Wu Y, Liang J, Yao W, Qu R, Tong X, Zhang G, Yang H. Interaction of isoquinoline alkaloids with pyrimidine motif triplex DNA by mass spectrometry and spectroscopies reveals diverse mechanisms. Heliyon 2023; 9:e14954. [PMID: 37082631 PMCID: PMC10112036 DOI: 10.1016/j.heliyon.2023.e14954] [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: 07/21/2022] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 04/22/2023] Open
Abstract
Isoquinoline alkaloids represent an important class of molecules due to their broad range of pharmacology and clinical utility. Prospective development and use of these alkaloids as effective anticancer agents have elicited great interest. In this study, in order to reveal structure-activity relationship, we present the characterization of bioactive isoquinoline alkaloid-DNA triplex interactions, with particular emphasis on the sequence selectivity and preference of binding to the two types of DNA triplexes, by electrospray ionization mass spectrometry (ESI-MS) and various spectroscopic techniques. The six alkaloids, including coptisine, columbamine, epiberberine, berberrubine, jateorhizine, and fangchinoline, were selected to explore their interactions with the TC and TTT triplex DNA structures. Berberrubine, fangchinoline, coptisine, columbamine, and epiberberine have preference for TC rich DNA sequences compared to TTT rich DNA triplex based on affinity values in MS. The experimental results from different fragmentation modes in tandem MS, subtractive and hyperchromic effects in UV absorption spectra, fluorescence quenching and enhancement in fluorescence spectra, and strong conformational changes in circular dichroism (CD) hinted that the interaction between isoquinoline alkaloid-TC/TTT DNA had diverse mechanisms including at least two different binding modes: the electrostatic binding and the intercalation binding. Interestingly, columbamine, berberrubine, and fangchinoline can stabilize TTT triplex as inferred from optical thermal melting profiles, while it was not the case in TC triplex. These results provide new insights into binding of isoquinoline alkaloids to pyrimidine motif triplex DNA.
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Affiliation(s)
- Zhaoyang Xie
- Northeast Asia Institute of Chinese Medicine, Changchun University of Chinese Medicine, Changchun, 130021, China
| | - Sunuo Zhang
- School of Materials Science and Engineering, Nankai University, Tianjin, 300350, China
| | - Yi Wu
- Northeast Asia Institute of Chinese Medicine, Changchun University of Chinese Medicine, Changchun, 130021, China
| | - Jinling Liang
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, 130117, China
| | - Wenbin Yao
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, 130117, China
| | - Ruoning Qu
- China-Japan Union Hospital of Jilin University, Changchun, 130033, China
| | - Xiaole Tong
- Jilin Jian Yisheng Pharmaceutical Co., Ltd., Jian, 134200, China
| | - Guang Zhang
- China-Japan Union Hospital of Jilin University, Changchun, 130033, China
- Corresponding author.
| | - Hongmei Yang
- Northeast Asia Institute of Chinese Medicine, Changchun University of Chinese Medicine, Changchun, 130021, China
- Corresponding author.
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Miranda de Souza Duarte-Filho LA, Ortega de Oliveira PC, Yanaguibashi Leal CE, de Moraes MC, Picot L. Ligand fishing as a tool to screen natural products with anticancer potential. J Sep Sci 2023:e2200964. [PMID: 36808885 DOI: 10.1002/jssc.202200964] [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: 11/24/2022] [Revised: 02/07/2023] [Accepted: 02/07/2023] [Indexed: 02/23/2023]
Abstract
Cancer is the second leading cause of death in the world and its incidence is expected to increase with the aging of the world's population and globalization of risk factors. Natural products and their derivatives have provided a significant number of approved anticancer drugs and the development of robust and selective screening assays for the identification of lead anticancer natural products are essential in the challenge of developing personalized targeted therapies tailored to the genetic and molecular characteristics of tumors. To this end, a ligand fishing assay is a remarkable tool to rapidly and rigorously screen complex matrices, such as plant extracts, for the isolation and identification of specific ligands that bind to relevant pharmacological targets. In this paper, we review the application of ligand fishing with cancer-related targets to screen natural product extracts for the isolation and identification of selective ligands. We provide critical analysis of the system configurations, targets, and key phytochemical classes related to the field of anticancer research. Based on the data collected, ligand fishing emerges as a robust and powerful screening system for the rapid discovery of new anticancer drugs from natural resources. It is currently an underexplored strategy according to its considerable potential.
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Affiliation(s)
| | | | - Cíntia Emi Yanaguibashi Leal
- Departamento de Ciências Farmacêuticas, Pós-Graduação em Biociências (PGB) Universidade Federal do Vale do São Francisco, Petrolina, Brazil
| | - Marcela Cristina de Moraes
- Departamento de Química Orgânica, Laboratório BIOCROM, Instituto de Química, Universidade Federal Fluminense, Niterói, Brazil
| | - Laurent Picot
- UMR CNRS 7266 LIENSs, Département de Biotechnologie, La Rochelle Université, La Rochelle, France
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Fu Y, Si H, Chen J, Zhang W, Feng S, Xiao Z. A Novel “Turn‐On” Fluorescent Sensor for Screening Triplex DNA Binder Based upon Molecular Beacon. ChemistrySelect 2022. [DOI: 10.1002/slct.202203178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yuanxiang Fu
- School of Chemical Engineering Guizhou Institute of Technology 1st, Caiguan Road Guiyang 550003 P. R. China
| | - Hengdan Si
- School of Chemical Engineering Guizhou Institute of Technology 1st, Caiguan Road Guiyang 550003 P. R. China
| | - Juan Chen
- School of Chemical Engineering Guizhou Institute of Technology 1st, Caiguan Road Guiyang 550003 P. R. China
| | - Wenjuan Zhang
- School of Chemical Engineering Guizhou Institute of Technology 1st, Caiguan Road Guiyang 550003 P. R. China
| | - Shuang Feng
- School of Chemical Engineering Guizhou Institute of Technology 1st, Caiguan Road Guiyang 550003 P. R. China
| | - Zhiyou Xiao
- School of Chemical Engineering Guizhou Institute of Technology 1st, Caiguan Road Guiyang 550003 P. R. China
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Ma H, Liang H, Cai S, O'Keefe BR, Mooberry SL, Cichewicz RH. An Integrated Strategy for the Detection, Dereplication, and Identification of DNA-Binding Biomolecules from Complex Natural Product Mixtures. JOURNAL OF NATURAL PRODUCTS 2021; 84:750-761. [PMID: 33226219 PMCID: PMC9229839 DOI: 10.1021/acs.jnatprod.0c00946] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A fundamental factor in natural product drug discovery programs is the necessity to identify the active component(s) from complex chemical mixtures. Whereas this has traditionally been accomplished using bioassay-guided fractionation, we questioned whether alternative techniques could supplement and, in some cases, even supplant this approach. We speculated that a combination of ligand-fishing methods and modern analytical tools (e.g., LC-MS and online natural product databases) offered a route to enhance natural product drug discovery. Herein, a candidate solution referred to as the lickety-split ligand-affinity-based molecular angling system (LLAMAS) is described. This approach utilizes an ultrafiltration-based LC-PDA-MS/MS-guided DNA-binding assay in combination with the (i) Global Natural Products Social Molecular Networking, (ii) Dictionary of Natural Products, and (iii) SciFinder platforms to identify DNA binders in complex chemical mixtures. LLAMAS was initially vetted in tests using known small-molecule DNA binders and then optimized to a 96-well plate-based format. A set of 332 plant samples used in traditional Chinese medicine was screened for DNA-binding activity with LLAMAS, resulting in the identification of seven DNA-binding molecules, including berberine (12), palmatine (13), coptisine (14), fangchinoline (15), tetrandrine (16), daurisoline (17), and dauricine (18). These results demonstrate that LLAMAS is an effective natural product discovery platform for the efficient identification and dereplication of DNA-binding molecules from complex mixtures.
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Affiliation(s)
- Hongyan Ma
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, and Natural Products Discovery Group and Institute for Natural Products Applications and Research Technologies, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Huiyun Liang
- Department of Pharmacology, University of Texas Health Science Center, San Antonio, Texas 78229, United States
| | - Shengxin Cai
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, and Natural Products Discovery Group and Institute for Natural Products Applications and Research Technologies, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Barry R O'Keefe
- Natural Products Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, and Molecular Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Susan L Mooberry
- Department of Pharmacology, University of Texas Health Science Center, San Antonio, Texas 78229, United States
| | - Robert H Cichewicz
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, and Natural Products Discovery Group and Institute for Natural Products Applications and Research Technologies, University of Oklahoma, Norman, Oklahoma 73019, United States
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Del Mundo IMA, Vasquez KM, Wang G. Modulation of DNA structure formation using small molecules. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2019; 1866:118539. [PMID: 31491448 PMCID: PMC6851491 DOI: 10.1016/j.bbamcr.2019.118539] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 08/20/2019] [Accepted: 08/24/2019] [Indexed: 02/06/2023]
Abstract
Genome integrity is essential for proper cell function such that genetic instability can result in cellular dysfunction and disease. Mutations in the human genome are not random, and occur more frequently at "hotspot" regions that often co-localize with sequences that have the capacity to adopt alternative (i.e. non-B) DNA structures. Non-B DNA-forming sequences are mutagenic, can stimulate the formation of DNA double-strand breaks, and are highly enriched at mutation hotspots in human cancer genomes. Thus, small molecules that can modulate the conformations of these structure-forming sequences may prove beneficial in the prevention and/or treatment of genetic diseases. Further, the development of molecular probes to interrogate the roles of non-B DNA structures in modulating DNA function, such as genetic instability in cancer etiology are warranted. Here, we discuss reported non-B DNA stabilizers, destabilizers, and probes, recent assays to identify ligands, and the potential biological applications of these DNA structure-modulating molecules.
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Affiliation(s)
- Imee M A Del Mundo
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA.
| | - Guliang Wang
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA
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