Abstract
DNA replication is an exceptional point of therapeutic intervention for many cancer types and several small molecules targeting DNA have been developed into clinically used antitumor agents. Many of these molecules are naturally occurring metabolites from plants and microorganisms, such as the widely used chemotherapeutic doxorubicin. While natural product sources contain a vast number of DNA binding small molecules, isolating and identifying these molecules is challenging. Typical screening campaigns utilize time-consuming bioactivity-guided fractionation approaches, which use sequential rounds of cell-based assays to guide the isolation of active compounds. In this study, we explore the use of biolayer interferometry (BLI) as a tool for rapidly screening natural product sources for DNA targeting small molecules. We first verified that BLI robustly detected DNA binding using designed GC- and AT-rich DNA oligonucleotides with known DNA intercalating, groove binding, and covalent binding agents including actinomycin D (1), doxorubicin (2), ethidium bromide (3), propidium iodide (4), Hoechst 33342 (5), and netropsin (6). Although binding varied with the properties of the oligonucleotides, measured binding affinities agreed with previously reported values. We next utilized BLI to screen over 100 bacterial extracts from our microbial library for DNA binding activity and found three highly active extracts. Binding-guided isolation was used to isolate the active principle component from each extract, which were identified as echinomycin (8), actinomycin V (9), and chartreusin (10). This biosensor-based DNA binding screen is a novel, low-cost, easy to use, and sensitive approach for medium-throughput screening of complex chemical libraries.
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References
Zhu W, Wang Y, Li K, Gao J, Huang C-H, Chen C-C, et al. Antibacterial drug leads: DNA and enzyme multitargeting. J Med Chem. 2015;58(3):1215–27.
Bottini A, De SK, Wu B, Tang C, Varani G, Pellecchia M. Targeting influenza a virus RNA promoter. Chem Biol Drug Des. 2015;86(4):663–73.
Wang M, Yu Y, Liang C, Lu A, Zhang G. Recent advances in developing small molecules targeting nucleic acid. Int J Mol Sci. 2016;17(6):779–803.
Bhaduri S, Ranjan N, Arya DP. An overview of recent advances in duplex DNA recognition by small molecules. Beilstein J Org Chem. 2018;14:1051–86. https://doi.org/10.3762/bjoc.14.93.
Cheung-Ong K, Giaever G, Nislow C. DNA-damaging agents in cancer chemotherapy: serendipity and chemical biology. Chem Biol. 2013;20(5):648–59.
Müller S. DNA damage-inducing compounds: unraveling their pleiotropic effects using high throughput sequencing. Curr Med Chem. 2017;24(15):1558–85.
Brockmann H, Bauer K. Naturwissenschaften. 1950;37:492–493. http://link.springer.com/article/10.1007/BF00623151
Williamá Lown J. Discovery and development of anthracycline antitumour antibiotics. Chem Soc Rev. 1993;22(3):165–76.
Rescifina A, Zagni C, Varrica MG, Pistarà V, Corsaro A. Recent advances in small organic molecules as DNA intercalating agents: synthesis, activity, and modeling. Eur J Med Chem. 2014;74:95–115.
Lipshultz SE, Herman EH. Anthracycline cardiotoxicity: the importance of horizontally integrating pre-clinical and clinical research. Cardiovasc Res. 2018;114:205–9.
McGowan JV, Chung R, Maulik A, Piotrowska I, Walker JM, Yellon DM. Anthracycline chemotherapy and cardiotoxicity. Cardiovasc Drugs Ther. 2017;31(1):63–75.
Cancer Statistics. cancer.gov: National Cancer Institute 2018 Contract No.: December 2018.
Blum JL, Flynn PJ, Yothers G, Asmar L, Geyer CE Jr, Jacobs SA, et al. Anthracyclines in early breast cancer: the ABC trials—USOR 06-090, NSABP B-46-I/USOR 07132, and NSABP B-49 (NRG Oncology). J Clin Oncol. 2017;35(23):2647–55.
Bozko M, Bozko A, Scholta T, Malek NP, Bozko P. DNA damage as a strategy for anticancer chemotherapy. Curr Med Chem. 2017;24(15):1487.
Chaires JB. A thermodynamic signature for drug–DNA binding mode. Arch Biochem Biophys. 2006;453(1):26–31.
Rosu F, Gabelica V, Houssier C, De Pauw E. Determination of affinity, stoichiometry and sequence selectivity of minor groove binder complexes with double-stranded oligodeoxynucleotides by electrospray ionization mass spectrometry. Nucleic Acids Res. 2002;30(16):e82.
Cummins LL, Chen S, Blyn LB, Sannes-Lowery KA, Drader JJ, Griffey RH, et al. Multitarget affinity/specificity screening of natural products: finding and characterizing high-affinity ligands from complex mixtures by using high-performance mass spectrometry. J Nat Prod. 2003;66(9):1186–90.
Mazzitelli CL, Chu Y, Reczek JJ, Iverson BL, Brodbelt JS. Screening of threading bis-intercalators binding to duplex DNA by electrospray ionization tandem mass spectrometry. J Am Soc Mass Spectrom. 2007;18(2):311–21.
Geierstanger BH, Jacobsen JP, Mrksich M, Dervan PB, Wemmer DE. Structural and dynamic characterization of the heterodimeric and homodimeric complexes of distamycin and 1-methylimidazole-2-carboxamide-netropsin bound to the minor groove of DNA. Biochemistry. 1994;33(10):3055–62.
Ren J, Jenkins TC, Chaires JB. Energetics of DNA intercalation reactions. Biochemistry. 2000;39(29):8439–47.
Sirajuddin M, Ali S, Badshah A. Drug–DNA interactions and their study by UV–visible, fluorescence spectroscopies and cyclic voltametry. J Photochem Photobiol B. 2013;124:1–19.
Pasternack RF, Bustamante C, Collings PJ, Giannetto A, Gibbs EJ. Porphyrin assemblies on DNA as studied by a resonance light-scattering technique. J Am Chem Soc. 1993;115(13):5393–9.
Boger DL, Fink BE, Brunette SR, Tse WC, Hedrick MP. A simple, high-resolution method for establishing DNA binding affinity and sequence selectivity. J Am Chem Soc. 2001;123(25):5878–91.
Nowicka AM, Zabost E, Donten M, Mazerska Z, Stojek Z. Electroanalytical and spectroscopic procedures for examination of interactions between double stranded DNA and intercalating drugs. Anal Bioanal Chem. 2007;389(6):1931–40.
Nguyen B, Tanious FA, Wilson WD. Biosensor-surface plasmon resonance: quantitative analysis of small molecule–nucleic acid interactions. Methods. 2007;42(2):150–61.
Chaires JB. Drug—DNA interactions. Curr Opin Struct Biol. 1998;8(3):314–20.
Sultana A, Lee JE. Measuring protein-protein and protein-nucleic acid interactions by Biolayer Interferometry. Curr Protoc Protein Sci. 2015;79(1):1–26.
Palchaudhuri R, Hergenrother PJ. DNA as a target for anticancer compounds: methods to determine the mode of binding and the mechanism of action. Curr Opin Biotechnol. 2007;18(6):497–503.
Cao Y, Li Y-h, Lv D-y, Chen X-f, Chen L-d, Zhu Z-y, et al. Identification of a ligand for tumor necrosis factor receptor from Chinese herbs by combination of surface plasmon resonance biosensor and UPLC-MS. Anal Bioanal Chem. 2016;408(19):5359–67.
Wartchow CA, Podlaski F, Li S, Rowan K, Zhang X, Mark D, et al. Biosensor-based small molecule fragment screening with biolayer interferometry. J Comput Aided Mol Des. 2011;25(7):669.
Shah NB, Duncan TM. Bio-layer interferometry for measuring kinetics of protein-protein interactions and allosteric ligand effects. J Vis Exp. 2014;84:e51383. https://doi.org/10.3791/51383
Kachko A, Loesgen S, Shahzad-Ul-Hussan S, Tan W, Zubkova I, Takeda K, et al. Inhibition of hepatitis C virus by the cyanobacterial protein Microcystis viridis lectin: mechanistic differences between the high-mannose specific lectins MVL, CV-N, and GNA. Mol Pharm. 2013;10(12):4590–602. https://doi.org/10.1021/mp400399b.
Sharma P, Tomar AK, Kundu B. Interplay between CedA, rpoB and double stranded DNA: a step towards understanding CedA mediated cell division in E. coli. Int J Biol Macromol. 2018;107:2026–33.
Müller-Esparza H, Osorio-Valeriano M, Steube N, Thanbichler M, Randau L. Bio-layer interferometry analysis of the target binding activity of CRISPR-Cas effector complexes. Front Mol Biosci. 2020;7:98.
Normand A, Rivière E, Renodon-Cornière A. Identification and characterization of human Rad51 inhibitors by screening of an existing drug library. Biochem Pharmacol. 2014;91(3):293–300.
McGrath TF, Campbell K, Fodey TL, O’Kennedy R, Elliott CT. An evaluation of the capability of a biolayer interferometry biosensor to detect low-molecular-weight food contaminants. Anal Bioanal Chem. 2013;405(8):2535–44.
Patiny L, Borel A. ChemCalc: a building block for tomorrow’s chemical infrastructure. J Chem Inf Model. 2013;53(5):1223–8.
Petersen RL. Strategies using bio-layer interferometry biosensor technology for vaccine research and development. Biosensors. 2017;7(4):49.
David B, Wolfender J-L, Dias DA. The pharmaceutical industry and natural products: historical status and new trends. Phytochem Rev. 2015;14(2):299–315.
Birmingham A, Selfors LM, Forster T, Wrobel D, Kennedy CJ, Shanks E, et al. Statistical methods for analysis of high-throughput RNA interference screens. Nat Methods. 2009;6(8):569–75.
Zhang J-H, Chung TD, Oldenburg KR. A simple statistical parameter for use in evaluation and validation of high throughput screening assays. J Biomol Screen. 1999;4(2):67–73.
Perspicace S, Banner D, Benz J, Müller F, Schlatter D, Huber W. Fragment-based screening using surface plasmon resonance technology. J Biomol Screen. 2009;14(4):337–49.
Piehler J, Brecht A, Gauglitz G, Zerlin M, Maul C, Thiericke R, et al. Label-free monitoring of DNA–ligand interactions. Anal Biochem. 1997;249(1):94–102.
Hollstein U. Actinomycin. Chemistry and mechanism of action. Chem Rev. 1974;74(6):625–52.
Nafisi S, Saboury AA, Keramat N, Neault J-F, Tajmir-Riahi H-A. Stability and structural features of DNA intercalation with ethidium bromide, acridine orange and methylene blue. J Mol Struct. 2007;827(1–3):35–43.
Chou WY, Marky LA, Zaunczkowski D, Breslauer KJ. The thermodynamics of drug-DNA interactions: ethidium bromide and propidium iodide. J Biomol Struct Dyn. 1987;5(2):345–59.
Winston CT, Boger DL. Sequence-selective DNA recognition: natural products and nature’s lessons. Chem Biol. 2004;11(12):1607–17.
Hirayama H, Tamaoka J, Horikoshi K. Improved immobilization of DNA to microwell plates for DNA-DNA hybridization. Nucleic Acids Res. 1996;24(20):4098–9.
Yang F, Teves SS, Kemp CJ, Henikoff S. Doxorubicin, DNA torsion, and chromatin dynamics. BBA-Rev Cancer. 2014;1845(1):84–9. https://doi.org/10.1016/j.bbcan.2013.12.002
Bailly C, Chessari G, Carrasco C, Joubert A, Mann J, Wilson WD, et al. Sequence-specific minor groove binding by bis-benzimidazoles: water molecules in ligand recognition. Nucleic Acids Res. 2003;31(5):1514–24.
Bailly C, Chaires JB. Sequence-specific DNA minor groove binders. Design and synthesis of netropsin and distamycin analogues. Bioconjug Chem. 1998;9(5):513–38.
Fornander LH, Wu L, Billeter M, Lincoln P, Nordén B. Minor-groove binding drugs: where is the second Hoechst 33258 molecule? J Phys Chem B. 2013;117(19):5820–30.
Marky LA, Breslauer KJ. Origins of netropsin binding affinity and specificity: correlations of thermodynamic and structural data. Proc Natl Acad Sci U S A. 1987;84(13):4359–63.
Lam KS. New aspects of natural products in drug discovery. Trends Microbiol. 2007;15(6):279–89.
Garcia DE, Baidoo EE, Benke PI, Pingitore F, Tang YJ, Villa S, et al. Separation and mass spectrometry in microbial metabolomics. Curr Opin Microbiol. 2008;11(3):233–9.
Concepcion J, Witte K, Wartchow C, Choo S, Yao D, Persson H, et al. Label-free detection of biomolecular interactions using BioLayer interferometry for kinetic characterization. Comb Chem High Throughput Screen. 2009;12(8):791–800.
Fox KR, Wakelin LP, Waring MJ. Kinetics of the interaction between echinomycin and deoxyribonucleic acid. Biochemistry. 1981;20(20):5768–79.
Van Dyke MM, Dervan PB. Echinomycin binding sites on DNA. Science. 1984;225(4667):1122–7.
Barceló F, Capó D, Portugal J. Thermodynamic characterization of the multivalent binding of chartreusin to DNA. Nucleic Acids Res. 2002;30(20):4567–73.
Li H, Jiang Z, Zhang R. Fluorescence quenching and the binding interaction of lumichrome with nucleic acids. Chin Sci Bull. 2010;55(25):2829–34.
Eldridge GR, Vervoort HC, Lee CM, Cremin PA, Williams CT, Hart SM, et al. High-throughput method for the production and analysis of large natural product libraries for drug discovery. Anal Chem. 2002;74(16):3963–71.
Acknowledgements
Thanks to Khaled Attia Mahmoud and Jon Thorson (Center for Pharmaceutical Research and Innovation, Lexington KY) for their kind donation of the bacterial strain RM1-1. Thanks to James A. Strother (UF) for fruitful discussions. We acknowledge the support of the Oregon State University’s NMR Facility funded in part by the National Institutes of Health, HEI grant 1S10OD018518, and by the M. J. Murdock Charitable Trust grant no. 2014162.
Funding
This work was supported by OSU start-up funds and by the National Science Foundation under grant CHE 1808717.
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Overacker, R.D., Plitzko, B. & Loesgen, S. Biolayer interferometry provides a robust method for detecting DNA binding small molecules in microbial extracts. Anal Bioanal Chem 413, 1159–1171 (2021). https://doi.org/10.1007/s00216-020-03079-5
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DOI: https://doi.org/10.1007/s00216-020-03079-5