Dataset for article Morphology control in benzoic imine-linked polymer-drug conjugates for adaptive drug delivery and enhanced in vivo efficacy

---------------------------------------------------------------------------------------------------------------------------- Dataset for article Morphology control in benzoic imine-linked polymer-drug conjugates for adaptive drug delivery and enhanced in vivo efficacy ---------------------------------------------------------------------------------------------------------------------------- ReadMe version: 1.0 (2026-07-07) Dataset version: 1.0 (2026-07-07) Dataset DOI: 10.5281/zenodo.21233072 Related article: Martina Vragovic, Jan Pankrac, Peter Paral, Martin Bajecny, Alessandro Jager, Vladimir Sincari, Jan Kucka, Martin Hruby, Marcela Filipova, Rafal Konefal, Fernando Carlos Giacomelli, Ludek Sefc, Eliezer Jager, Morphology control in benzoic imine-linked polymer-drug conjugates for adaptive drug delivery and enhanced in vivo efficacy, European Polymer Journal 244 (2026) 114500, https://doi.org/10.1016/j.eurpolymj.2026.114500 -------------------------------------------------------------------- CONTACT -------------------------------------------------------------------- Eliezer Jager [e-mail] ORCID: 0000-0001-9939-2355 Institute of Macromolecular Chemistry, Czech Academy of Sciences (IMC CAS) Heyrovsky Sq. 2, 162 06 Prague 6, Czech Republic ______Creators______ Martina Vragovic (ORCiD 0000-0002-6128-4719; IMC CAS) Methodology, Investigation, Formal analysis, Data curation Jan Pankrac (ORCiD 0000-0002-9574-1391; Charles University, First Faculty of Medicine, CAPI) Methodology, Investigation, Data curation Peter Paral (Charles University, First Faculty of Medicine, CAPI) Methodology Martin Bajecny (ORCiD 0000-0002-3028-8055; Charles University, First Faculty of Medicine, CAPI) Methodology Alessandro Jager (ORCiD 0000-0001-6171-4718; IMC CAS) Methodology, Investigation Vladimir Sincari (ORCiD 0000-0002-7379-066X; IMC CAS) Methodology, Investigation Jan Kucka (ORCiD 0000-0003-2489-5315; IMC CAS) Methodology, Investigation Martin Hruby (ORCiD 0000-0002-5075-261X; IMC CAS) Methodology, Investigation Marcela Filipova (ORCiD 0000-0003-3503-7973; IMC CAS) Methodology, Investigation, Formal analysis, Data curation Rafal Konefal (ORCiD 0000-0003-4568-4891; IMC CAS & NanoBioMedical Centre, Adam Mickiewicz University) Methodology, Formal analysis Fernando Carlos Giacomelli (ORCiD 0000-0002-6872-9354; Centro de Ciencias Naturais e Humanas, Universidade Federal do ABC) Formal analysis Luděk Sefc (ORCiD 0000-0003-2846-220X; Charles University, First Faculty of Medicine, CAPI) Methodology, Investigation Eliezer Jager (ORCID 0000-0001-9939-2355; IMC CAS), Writing - review and editing; Writing - original draft; Supervision; Resources; Project administration; Methodology; Investigation; Funding acquisition; Conceptualization -------------------------------------------------------------------- DATA AVAILABILITY AND ACCESS INSTRUCTIONS -------------------------------------------------------------------- The dataset is openly accessible under the DOI listed above. The license and terms of reuse are shown in the following chapter below. -------------------------------------------------------------------- LICENSE -------------------------------------------------------------------- ______ReadMe file license______ ReadMe by Martin Hruby and co-authors is licensed under CC BY 4.0. License information: https://creativecommons.org/licenses/by/4.0/ ______Dataset license______ Dataset for article Morphology control in benzoic imine-linked polymer-drug conjugates for adaptive drug delivery and enhanced in vivo efficacy by Martina Vragovic, Jan Pankrac, Peter Paral, Martin Bajecny, Alessandro Jager, Vladimir Sincari, Jan Kucka, Martin Hruby, Marcela Filipova, Rafal Konefal, Fernando Carlos Giacomelli, Ludek Sefc, and Eliezer Jager is licensed under CC BY 4.0. License information: https://creativecommons.org/licenses/by/4.0/ -------------------------------------------------------------------- DESCRIPTION AND METHODOLOGY -------------------------------------------------------------------- ______About the dataset______ The related study developed pH-responsive polymer-drug nanoconjugates based on poly[N-(2-hydroxypropyl)methacrylamide] (PHPMAm) and benzoic imine linkages. The platform was designed to combine a stealth PHPMAm corona with a hydrophobic, acid-labile benzoic-imine block able to conjugate doxorubicin (DOX) or the near-infrared dye Cyanine 7 (Cy7). By varying polymer architecture and hydrophilic block length, the study compared block copolymers BC1, BC2 and BC3, the random copolymer BCR, and a PEG113-based reference system. The raw-data package supports the main conclusions of the article: synthesis and structural assignment of PHPMAm macro-chain-transfer agents, acetal/aldehyde-containing block copolymers and DOX/Cy7 conjugates; self-assembly into morphology-dependent nanomedicines; pH-selective DOX release; in vitro uptake and cytotoxicity in EL4 and MCF-7 cells; and in vivo antitumor efficacy, blood circulation and biodistribution in mouse models. The files are a mixture of raw/primary instrument exports, scanned/photographed spectra, curated Excel workbooks and OriginPro project files used for figures and analysis. ______Ethics______ No personal, patient-identifiable or sensitive human data are included in the supplied dataset. The related article reports in vitro cell-culture experiments and in vivo mouse experiments. The animal experiments were conducted under the authority-approved protocol MSMT-34384/2019-2. Biodistribution and tumor-accumulation experiments were performed according to Czech legislation for experimental work with animals (Act No. 246/1992 and Decree No. 419/2012) and in agreement with European Union directives. The data files deposited here contain experimental outputs, numerical results and images/graphs, but no animal-identifiable personal information. ______Sample preparation______ The materials in the study were prepared from PHPMAm macro-chain-transfer agents (PHPMAm mCTA1, mCTA2 and mCTA3) synthesized by RAFT polymerization. An acetal-protected benzaldehyde methacrylate monomer, 4-(O-methacryloyloxymethyl)benzaldehyde dimethyl acetal, was polymerized from these macroCTAs to yield block copolymers BC1, BC2 and BC3 with different PHPMAm chain lengths. A random copolymer BCR was prepared from HPMAm and the acetal monomer under RAFT conditions. A PEG113-block copolymer analogue was also synthesized for comparison. The acetal-protected copolymers were deprotected in THF/MeOH with trifluoroacetic acid to expose aldehyde groups. Doxorubicin was coupled to these aldehyde-bearing polymers through benzoic imine formation in anhydrous DMSO with acetic acid and magnesium sulfate, giving BC1-DOX, BC2-DOX, BC3-DOX and BCR-DOX. Cyanine 7 amine was coupled in the same general manner to generate BC3-Cy7 and PEG113-Cy7 for in vivo fluorescence studies. For nanoparticle characterization, the copolymers or conjugates were dispersed in water for injection or buffer at the concentrations described in the article. For release experiments, DOX-loaded conjugates were placed in dialysis devices and dialyzed against PBS pH 7.4 or acidic buffers at pH 6.5 and/or pH 5.3 at 37 deg C. For in vitro experiments, EL4 and MCF-7 cells were cultured in the media described in the article and treated with free DOX or BC-DOX conjugates. For in vivo efficacy and biodistribution, C57BL/6N mice bearing EL4 lymphoma tumors or healthy control mice received intravenous injections of the formulations described in the article. ______Methods of data collection______ * 1H NMR spectroscopy Instruments reported in the article: Bruker Avance Neo 400 MHz NMR spectrometer and Bruker Avance III 600 MHz NMR spectrometer. Solvents: MeOD, CDCl3, DMF-d7 or DMSO-d6, depending on analyte. Temperature: 25 deg C. Chemical shifts: reported in ppm relative to TMS using hexamethyldisiloxane (HMDSO, 0.05 for 1H NMR) as internal standard. Archive content: nmr/IMG_3520.jpg to nmr/IMG_3524.jpg are JPEG photographs/scans of representative printed or annotated NMR spectra. The exact mapping of each JPEG to a given SI figure is not explicit from the filenames; based on the Supporting Information, these images are associated with polymerization conversion, purified PHPMAm mCTA/block copolymer spectra, deprotected copolymers, BC3-DOX and/or BC3-Cy7 spectra. * FTIR spectroscopy Instrument reported in the article: PerkinElmer Spectrum 2 spectrometer. Archive content: other/BC3_Martina.asc and other/BC3_DOXMartina.asc are PerkinElmer IR ASCII spectral exports for BC3 and BC3-DOX. The Supporting Information uses these spectra to show aldehyde C=O around 1730 cm^-1 and imine C=N around 1650 cm^-1. Data format: text header followed by two columns. In the supplied files the first column is wavenumber in cm^-1 and the second column is transmittance in percent (%T). * Dynamic light scattering (DLS) and electrophoretic light scattering (ELS) Instrument reported in the article: Zetasizer NanoZS ZEN3600 (Malvern Instruments, UK), 633 nm He-Ne laser, scattering angle 173 deg. Software reported in the article: Dispersion Technology Software version 6.01 from Malvern. Conditions reported in the article: samples diluted in water for injection, measured in single-use polystyrene half-micro cuvettes at 25 deg C; one 45 s run with five repetitions. Size and dispersity were obtained from averaged autocorrelation functions using the cumulant method. Zeta potentials were determined in folded capillary cells using the Smoluchowski approximation in the DTS program. Archive content: other/DLS.opju contains OriginPro graph/workbook data for hydrodynamic-size distributions of BC1, BC2, BC3 and BCR nanomedicines. other/DLS_BC3_PEG.opju contains the comparison of BC3-Cy7 and PEG113-Cy7 diameter distributions. Native Zetasizer .dts files are not included in the supplied archive. * Small-angle X-ray scattering (SAXS) Instrument reported in the article: pinhole camera (MolMet, Rigaku, Japan, modified by SAXSLAB/Xenocs) coupled to a Rigaku MicroMax 003 microfocused X-ray source (50 kV, 0.6 mA, 30 W) and a Pilatus 300 K detector. Conditions reported in the article: samples sealed in borosilicate capillaries; 8 h exposure; solvent background subtraction; fitting with form factors implemented in SASfit. Archive content: other/SAXS.opju contains OriginPro project data for SAXS scattering curves and model fits, including BC1, BC3 and BCR nanomedicines and shape/form-factor assignments. * UV-Vis and fluorescence spectroscopy UV-Vis instrument reported in the article: Helios Alpha spectrophotometer (Thermospectronic, UK). DOX was quantified from calibration curves in the linear range reported in the article. Fluorescence instrument reported in the article: Jasco FP 6200 spectrofluorometer (Tokyo, Japan), used for Cy7 quantification at 750/780 nm (Ex/Em). Archive content: other/Release.opju contains OriginPro project data for pH-dependent DOX-release curves, including pH 7.4 and acidic pH conditions. other/circulation_of_HPMA_based_Cy7.xlsx contains in vivo fluorescence measurements and derived organ/blood circulation tables for HPMA-based BC3-Cy7 and PEG113-Cy7 systems. * In vitro cytotoxicity and cell uptake Cell lines reported in the article: EL4 T lymphoma cells and MCF-7 breast cancer cells. Cell viability assay: Alamar Blue reagent; cells seeded in 96-well plates, treated with serial dilutions of BC-DOX conjugates or free DOX, incubated for 24 h, then incubated with Alamar Blue for 4 h. Fluorescence was measured on a Synergy Neo plate reader (Bio-Tek) at 570/600 nm (Ex/Em). Untreated cells and cells incubated with free DOX were used as controls. Samples were measured in triplicate in three independent experiments. Uptake/flow cytometry: the study monitored DOX fluorescence after incubation of cells with free DOX and DOX-conjugated BCs at equivalent concentration, with output reported as mean fluorescence intensity (MFI). The exact raw cytometer files are not present in the archive; the Excel workbook provides the curated values used for graphing. Archive content: other/data_grafs_cytotoxicity_and_flow_cytometry.xlsx contains sheets EL-4_cytotoxicity, MCF-7_cytotoxicity and flow_cytometry. The cytotoxicity sheets provide viability percentages versus concentration labels; the flow-cytometry sheet provides MFI values and SEM values for EL4 and MCF-7 cells. * In vivo antitumor activity, biodistribution and blood circulation Animal model reported in the article: healthy or EL4 tumor-bearing inbred C57BL/6N mice, females 8-10 weeks old. Antitumor efficacy: EL4 lymphoma cells were injected subcutaneously into the right flank. When tumors reached approximately 5.8-6.5 mm in diameter, mice were assigned to treatment groups receiving saline, free DOX or BC-DOX conjugates. Tumor volume was measured twice weekly, and survival was followed for 40 days. Biodistribution/circulation: BC3-Cy7 and PEG113-Cy7 were injected intravenously at the Cy7 dose reported in the article. Fluorescence imaging was performed on an Xtreme In Vivo Imaging System (Bruker, Germany) with excitation 750 nm and emission 830 nm. Mice were anesthetized with isoflurane. Image intensity was quantified in Fiji by region-of-interest analysis; blood was collected from the retro-orbital sinus, and samples were analyzed by fluorescence, veterinary hematology and flow cytometry as described in the article. Archive content: other/Atualizado_Kaplan_Meyer.opju contains OriginPro project data/graphs for survival and/or antitumor-efficacy analyses. other/circulation_of_HPMA_based_Cy7.xlsx contains raw ROI data, curated in vivo fluorescence tables and blood-circulation measurements. * Statistical analysis The article reports two-way ANOVA for group comparisons and Kaplan-Meier survival curves, with analyses performed in GraphPad Prism 6 and P < 0.05 considered significant. The supplied archive includes the OriginPro project Atualizado_Kaplan_Meyer.opju, which likely contains the graphing/curated data for the survival plots. ______Methods of data processing______ The dataset contains a mixture of primary files, instrument-export files and processed/curated analysis projects. For NMR, Bruker raw data. Original acquisition parameters and assignments are described in the article and Supporting Information as well as part of the folders creted by the MNova SW. For FTIR, .asc files are PerkinElmer ASCII exports and may be imported as two-column text data into OriginPro, Excel, R, Python, LibreOffice Calc or similar software. For DLS/ELS, SAXS, DOX release, Kaplan-Meier/survival and selected graph data, .opju files are OriginPro project files containing curated numerical tables, plots and/or fitted curves. They are not the native raw output of the instruments. Where further numerical export is needed, open these files in OriginPro and export the worksheets as CSV. For Excel workbooks, formulas and curated tables are preserved where present. In circulation_of_HPMA_based_Cy7.xlsx, the raw sheet contains image-analysis labels, ROI area, integrated density and derived mean intensity. The in_vivo sheet organizes organ, sample, mouse, time_h and mean_fl_int values. The blood sheet contains time-course blood-circulation values. In data_grafs_cytotoxicity_and_flow_cytometry.xlsx, the EL-4_cytotoxicity and MCF-7_cytotoxicity sheets contain cell-viability values, while the flow_cytometry sheet contains MFI and SEM values. Concentration units embedded in some workbook column headers are not explicit; when not stated in the file itself, they should be interpreted using the related article, where viability and uptake are expressed relative to DOX-equivalent dosing or the concentration ranges given in the methods. -------------------------------------------------------------------- DATASET STRUCTURE -------------------------------------------------------------------- ├── 000_ReadMe.txt├── 001_Data.zip│ ├── DLS│ │ ├── DLS_BC3_PEG.opju│ │ └── DLS.opju│ ├── FTIR│ │ ├── FTIR_BC3-DOX.asc│ │ └── FTIR_BC3.asc│ ├── NMR│ │ ├── 90│ │ ├── 91│ │ ├── 92│ │ └── 93│ └── other│ ├── CirculationOfHPMAbased_Cy7.xlsx (in vivo imaging ROI & blood circulation for Cy7-labeled syst.)│ ├── CytotoxicityAndFlowCytometry.xlsx (EL4/MCF-7 cytotoxicity and flow-cytometry uptake data)│ ├── Kaplan_Meyer_SurvivalAndAntiTumorEfficacy.opju│ ├── Release.opju (OriginPro project for pH-dependent DOX-release data and graphs)└───────└── SAXS.opju (OriginPro project for SAXS curves and model fitting) -------------------------------------------------------------------- FILENAME STRUCTURE -------------------------------------------------------------------- The raw-data package does not follow the dummy project/WP naming convention from the original template. It retains original laboratory, analysis and figure-oriented filenames. Use the following interpretation: * Article/sample names: BC1, BC2 and BC3 = PHPMAm-based block copolymers with different PHPMAm hydrophilic block lengths and a benzoic-imine-forming hydrophobic block. BCR = random copolymer analogue. BC-DOX = doxorubicin conjugate of the corresponding copolymer (BC1-DOX, BC2-DOX, BC3-DOX, BCR-DOX). BC3-Cy7 = Cy7-labeled PHPMAm-based BC3 conjugate. PEG113-Cy7 = PEG113-based Cy7-labeled reference conjugate. DOX = free doxorubicin control. Saline/PBS = negative or vehicle control in biological experiments. * other/BC3_Martina.asc and other/BC3_DOXMartina.asc: FTIR files named by sample and analyst/laboratory identifier. BC3_Martina.asc corresponds to BC3; BC3_DOXMartina.asc corresponds to BC3-DOX. * .opju files: OriginPro projects named by analysis type: DLS, DLS_BC3_PEG, SAXS, Release and Atualizado_Kaplan_Meyer. These filenames describe the plotted/processed experiment rather than a single instrument acquisition. * .xlsx files: Excel workbooks named by analysis type. circulation_of_HPMA_based_Cy7.xlsx contains in vivo Cy7 imaging/circulation data. data_grafs_cytotoxicity_and_flow_cytometry.xlsx contains cytotoxicity and uptake/flow-cytometry graph data. -------------------------------------------------------------------- FILE TYPES & FORMATS, SOFTWARE TO OPEN AND DIMENSIONS & UNITS -------------------------------------------------------------------- * .pdf Content: article and Supporting Information. Software: any PDF reader. Units/dimensions: documentation only; not treated as raw numerical data. * NMR spectra Original Format: Raw acquisition directories containing parameter files (.ased, .temp, .info, .par and binary files like acqu, acqus) and data tracks (binary, e.g. fid or ser). These folders can be directly opened by the SW described below. SW to open: TopSpin (Bruker), Delta (JEOL), or MestReNova. * .asc Content: PerkinElmer FTIR ASCII spectral exports. Software: text editor, OriginPro, Excel/LibreOffice Calc, R, Python, MATLAB. Horizontal axis/first numerical column: wavenumber (cm^-1). Vertical axis/second numerical column: transmittance (%T). Approximate range in supplied files: 3996 to 650 cm^-1. * .opju Content: OriginPro project files containing numerical worksheets, plots and/or fitting results for DLS, SAXS, DOX release and survival/efficacy data. Software: OriginPro/OriginLab; .opju is a modern Origin project format and should be opened with Origin 2018 or newer. If necessary, export worksheets from OriginPro to .csv for use in R, Python or other platforms. Units: experiment-specific. DLS diameter values are in nm; SAXS q is in nm^-1 where shown; DOX release is plotted as time in hours versus cumulative release or drug remaining in percent; survival/Kaplan-Meier data are in days or experiment time versus survival fraction/percent. * .xlsx Content: curated numerical data for in vivo Cy7 fluorescence/circulation, cytotoxicity and flow cytometry. Software: Microsoft Excel, LibreOffice Calc, Google Sheets, R/openxlsx, Python/openpyxl or pandas. Units: as indicated by sheet headers and article methods. Examples include ROI area in pixels, integrated density in arbitrary fluorescence units, mean fluorescence intensity (MFI), time_h in hours, cell viability in percent of untreated control and SEM for flow-cytometry values. -------------------------------------------------------------------- FUNDING -------------------------------------------------------------------- * Ministry of Education, Youth and Sports of the Czech Republic: Advanced stimuli-responsive giant vesicles - towards the mimicking of essential cell functions (LUAUS24137). * Ministry of Education, Youth and Sports of the Czech Republic: Czech National Node to the European Infrastructure for Translational Medicine (LM2023053 / EATRIS-CZ ERIC). * Ministry of Education, Youth and Sports of the Czech Republic: National Infrastructure for Biological and Medical Imaging (LM2023050 / Czech-BioImaging). * Ministry of Education, Youth and Sports of the Czech Republic / European Regional Development Fund: Modernization and support of research activities of the national infrastructure for biological and medical imaging Czech-BioImaging (CZ.02.1.01/0.0/0.0/16_013/0001775). * Ministry of Education, Youth and Sports of the Czech Republic: New Technologies for Translational Research in Pharmaceutical Sciences/NETPHARM (CZ.02.01.01/00/22_008/0004607), co-funded by the European Union. * Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP): Arquitetando coloides via interacoes supramoleculares: de fundamentos a aplicacoes (2021/12071-6). * Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP): Regulando a comunicacao em vesiculas sinteticas utilizando polimeros sensiveis ao ambiente como ferramenta para a proxima geracao de nano e microrreatores cataliticos e modelos celulares (2024/10593-3).