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Dalal RJ, Oviedo F, Leyden MC, Reineke TM. Polymer design via SHAP and Bayesian machine learning optimizes pDNA and CRISPR ribonucleoprotein delivery. Chem Sci 2024; 15:7219-7228. [PMID: 38756796 PMCID: PMC11095369 DOI: 10.1039/d3sc06920f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 03/25/2024] [Indexed: 05/18/2024] Open
Abstract
We present the facile synthesis of a clickable polymer library with systematic variations in length, binary composition, pKa, and hydrophobicity (clog P) to optimize intracellular pDNA and CRISPR-Cas9 ribonucleoprotein (RNP) performance. We couple physicochemical characterization and machine learning to interpret quantitative structure-property relationships within the combinatorial design space. For the first time, we reveal unexpected disparate design parameters for nucleic acid carriers; via explainable machine learning on 432 formulations, we discover that lower polymer pKa and higher percentages of benzimidazole ethanethiol enhance pDNA delivery, yet polymer length and captamine cation identity improve RNP delivery. Closed-loop Bayesian optimization of 552 formulation ratios further enhances in vitro performance. The top three polymers yield a higher signal and stable transgene expression over 20 days in vivo, and a 1.7-fold enhancement over controls. Our facile coupling of synthesis, characterization, and machine analysis provides powerful tools to quantitate performance parameters accelerating next-generation vehicles for nucleic acid medicines.
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Affiliation(s)
- Rishad J Dalal
- Department of Chemistry, University of Minnesota Minneapolis Minnesota 55455 USA
| | | | - Michael C Leyden
- Department of Chemical Engineering and Materials Science, University of Minnesota Minneapolis Minnesota 55455 USA
| | - Theresa M Reineke
- Department of Chemistry, University of Minnesota Minneapolis Minnesota 55455 USA
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2
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Schaefer S, Melodia D, Pracey C, Corrigan N, Lenardon MD, Boyer C. Mimicking Charged Host-Defense Peptides to Tune the Antifungal Activity and Biocompatibility of Amphiphilic Polymers. Biomacromolecules 2024; 25:871-889. [PMID: 38165721 DOI: 10.1021/acs.biomac.3c01038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
Invasive fungal infections impose a substantial global health burden. They cause more than 1.5 million deaths annually and are insufficiently met by the currently approved antifungal drugs. Antifungal peptides are a promising alternative to existing antifungal drugs; however, they can be challenging to synthesize, and are often susceptible to proteases in vivo. Synthetic polymers which mimic the properties of natural antifungal peptides can circumvent these limitations. In this study, we developed a library of 29 amphiphilic polyacrylamides with different charged units, namely, amines, guanidinium, imidazole, and carboxylic acid groups, representative of the natural amino acids lysine, arginine, histidine, and glutamic acid. Ternary polymers incorporating primary ammonium (lysine-like) or imidazole (histidine-like) groups demonstrated superior activity against Candida albicans and biocompatibility with mammalian cells compared to the polymers containing the other charged groups. Furthermore, a combination of primary ammonium, imidazole, and guanidinium (arginine-like) within the same polymer outperformed the antifungal drug amphotericin B in terms of therapeutic index and exhibited fast C. albicans-killing activity. The most promising polymer compositions showed synergistic effects in combination with caspofungin and fluconazole against C. albicans and additionally demonstrated activity against other clinically relevant fungi. Collectively, these results indicate the strong potential of these easily producible polymers to be used as antifungals.
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Affiliation(s)
- Sebastian Schaefer
- School of Chemical Engineering, University of New South Wales (UNSW), Sydney, New South Wales 2052, Australia
- Australian Centre for NanoMedicine, UNSW, Sydney, New South Wales 2052, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, New South Wales 2052, Australia
| | - Daniele Melodia
- School of Chemical Engineering, University of New South Wales (UNSW), Sydney, New South Wales 2052, Australia
- Australian Centre for NanoMedicine, UNSW, Sydney, New South Wales 2052, Australia
| | - Christopher Pracey
- Nuclear Magnetic Resonance Facility, Mark Wainwright Analytical Centre, UNSW, Sydney, New South Wales 2052, Australia
| | - Nathaniel Corrigan
- School of Chemical Engineering, University of New South Wales (UNSW), Sydney, New South Wales 2052, Australia
- Australian Centre for NanoMedicine, UNSW, Sydney, New South Wales 2052, Australia
| | - Megan D Lenardon
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, New South Wales 2052, Australia
| | - Cyrille Boyer
- School of Chemical Engineering, University of New South Wales (UNSW), Sydney, New South Wales 2052, Australia
- Australian Centre for NanoMedicine, UNSW, Sydney, New South Wales 2052, Australia
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3
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Wang Z, Liu Q, Liu Q, Qi H, Li Y, Song DP. Self-Assembly and In Situ Quaternization of Triblock Bottlebrush Block Copolymers via Organized Spontaneous Emulsification for Effective Loading of DNA. Macromol Rapid Commun 2023; 44:e2300192. [PMID: 37194368 DOI: 10.1002/marc.202300192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 04/23/2023] [Indexed: 05/18/2023]
Abstract
Microspheres bearing large pores are useful in the capture and separation of biomolecules. However, pore size is typically poorly controlled, leading to disordered porous structures with limited performances. Herein, ordered porous spheres with a layer of cations on the internal surface of the nanopores are facilely fabricated in a single step for effective loading of DNA bearing negative charges. Triblock bottlebrush copolymers (BBCPs), (polynorbornene-g-polystyrene)-b-(polynorbornene-g-polyethylene oxide)-b-(polynorbornene-g-bromoethane) (PNPS-b-PNPEO-b-PNBr), are designed and synthesized for fabrication of the positively charged porous spheres through self-assembly and in situ quaternization during an organized spontaneous emulsification (OSE) process. Pore diameter as well as charge density increase with the increase of PNBr content, resulting in a significant increase of loading density from 4.79 to 22.5 ng µg-1 within the spheres. This work provides a general strategy for efficient loading and encapsulation of DNA, which may be extended to a variety of different areas for different real applications.
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Affiliation(s)
- Zhaoxu Wang
- Tianjin Key Laboratory of Composite and Functional Materials, School of Materials Science and Engineering, Tianjin University, Tianjin, 300350, P. R. China
| | - Qiujun Liu
- Tianjin Key Laboratory of Composite and Functional Materials, School of Materials Science and Engineering, Tianjin University, Tianjin, 300350, P. R. China
| | - Qian Liu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Hao Qi
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Yuesheng Li
- Tianjin Key Laboratory of Composite and Functional Materials, School of Materials Science and Engineering, Tianjin University, Tianjin, 300350, P. R. China
| | - Dong-Po Song
- Tianjin Key Laboratory of Composite and Functional Materials, School of Materials Science and Engineering, Tianjin University, Tianjin, 300350, P. R. China
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Huang Y, Li S, Zettle LWC, Ma Y, Naguib HE, Kumacheva E. Nanogels designed for cell-free nucleic acid sequestration. NANOSCALE 2023; 15:14531-14542. [PMID: 37609883 DOI: 10.1039/d3nr03231k] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Chronic wounds exhibit over-expression of cell-free deoxyribonucleic acid (cfDNA), leading to a prolonged inflammation and non-healing wounds. Scavenging excessive cfDNA molecules is a promising strategy for chronic wound treatment. Nanoscopic particles act as efficient cfDNA scavengers due to their large surface area, however their efficiency in cfDNA uptake was limited by adsorption solely on the nanoparticle surface. In contrast, nanogels may provide multiple cfDNA binding sites in the nanoparticle interior, however their use for cfDNA scavenging is yet to be explored. Herein, we report cationic nanogels derived from a copolymer of chitosan and poly{2-[(acryloyloxy)ethyl]trimethylammonium chloride} end-grafted to the chitosan backbone as side chains. The nanogels retain their positive charge at the pH and ionic strength of chronic wound exudate, enabling electrostatically driven cfDNA scavenging. The network structure of the nanogels leads to the cfDNA sequestration in the nanogel interior, in addition to surface attachment. A key factor in cfDNA sequestration is the ratio of the pore size of the nanogel-to-cfDNA molecular dimensions. The enhanced cfDNA scavenging efficiency, along with biocompatibility of the nanogels, makes them a promising component of dressings for chronic wound treatment.
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Affiliation(s)
- Yuhang Huang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada.
| | - Shangyu Li
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Logan W C Zettle
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Yingshan Ma
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Hani E Naguib
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada.
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario M5S 3G8, Canada
- Department of Materials Science and Engineering, University of Toronto, Toronto, Ontario M5S 3E4, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3E4, Canada
| | - Eugenia Kumacheva
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada.
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3E4, Canada
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Hanson MG, Grimme CJ, Kreofsky NW, Panda S, Reineke TM. Blended Block Polycation Micelles Enhance Antisense Oligonucleotide Delivery. Bioconjug Chem 2023; 34:1418-1428. [PMID: 37437196 DOI: 10.1021/acs.bioconjchem.3c00186] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Nucleic acid-based medicines and vaccines are becoming an important part of our therapeutic toolbox. One key genetic medicine is antisense oligonucleotides (ASOs), which are short single-stranded nucleic acids that downregulate protein production by binding to mRNA. However, ASOs cannot enter the cell without a delivery vehicle. Diblock polymers containing cationic and hydrophobic blocks self-assemble into micelles that have shown improved delivery compared to linear nonmicelle variants. Yet synthetic and characterization bottlenecks have hindered rapid screening and optimization. In this study, we aim to develop a method to increase throughput and discovery of new micelle systems by mixing diblock polymers together to rapidly form new micelle formulations. We synthesized diblocks containing an n-butyl acrylate block chain extended with cationic moieties amino ethyl acrylamide (A), dimethyl amino ethyl acrylamide (D), or morpholino ethyl acrylamide (M). These diblocks were then self-assembled into homomicelles (A100, D100, and M100)), mixed micelles comprising 2 homomicelles (MixR%+R'%), and blended diblock micelles comprising 2 diblocks blended into one micelle (BldR%R'%) and tested for ASO delivery. Interestingly, we observed that mixing or blending M with A (BldA50M50 and MixA50+M50) did not improve transfection efficiency compared to A100; however, when M was mixed with D, there was a significant increase in transfection efficacy for the mixed micelle MixD50+M50 compared to D100. We further examined mixed and blended D systems at different ratios. We observed a large increase in transfection and minimal change in toxicity when M was mixed with D at a low percentage of D incorporation in mixed diblock micelles (i.e., BldD20M80) compared to D100 and MixD20+M80. To understand the cellular mechanisms that may result in these differences, we added proton pump inhibitor Bafilomycin-A1 (Baf-A1) to the transfection experiments. Formulations that contain D decreased in performance in the presence of Baf-A1, indicating that micelles with D rely on the proton sponge effect for endosomal escape more than micelles with A. This result supports our conclusion that M is able to modulate transfection of D, but not with A. This research shows that polymer blending in a manner similar to that of lipids can significantly boost transfection efficiency and is a facile way to increase throughput of testing, optimization, and successful formulation identification for polymeric nucleic acid delivery systems.
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Affiliation(s)
- Mckenna G Hanson
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Christian J Grimme
- Department of Chemical Engineering & Materials Science, University of Minnesota, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, United States
| | - Nicholas W Kreofsky
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Sidharth Panda
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Theresa M Reineke
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
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Wu X, Yang Y. Research progress on drug delivery systems for curcumin in the treatment of gastrointestinal tumors. World J Gastrointest Oncol 2023; 15:1342-1348. [PMID: 37663948 PMCID: PMC10473931 DOI: 10.4251/wjgo.v15.i8.1342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/11/2023] [Accepted: 07/11/2023] [Indexed: 08/10/2023] Open
Abstract
Curcumin is a natural compound with a diketone structure, which can control the growth, metastasis, recurrence, neovascularization, invasion, and drug resistance of gastrointestinal tumors by inhibiting nuclear factor κB, overexpression of tumor cells, vascular endothelial growth factor, etc. However, due to the low bioavailability of curcumin formulation, it did not fully exert its pharmacological effects, and its application and development in the treatment of various malignant tumors are still limited. This review summarizes the research on drug delivery systems of curcumin combating digestive tract tumors in order to further reduce the toxic side effects of curcumin-containing drugs and fully exert their pharmacological activities, and improve their bioavailability and clinical value.
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Affiliation(s)
- Xin Wu
- Department of Pharmacy, Harbin Medical University Cancer Hospital, Harbin 150081, Heilongjiang Province, China
| | - Yang Yang
- Department of Respiratory Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, Heilongjiang Province, China
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Hanson MG, Grimme CJ, Santa Chalarca CF, Reineke TM. Cationic Micelles Outperform Linear Polymers for Delivery of Antisense Oligonucleotides in Serum: An Exploration of Polymer Architecture, Cationic Moieties, and Cell Addition Order. Bioconjug Chem 2022; 33:2121-2131. [PMID: 36265078 DOI: 10.1021/acs.bioconjchem.2c00379] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Antisense oligonucleotides (ASOs) are an important emerging therapeutic; however, they struggle to enter cells without a delivery vehicle, such as a cationic polymer. To understand the role of polymer architecture for ASO delivery, five linear polymers and five diblock polymers (capable of self-assembly into micelles) were synthesized with varying cationic groups. After complexation of each polymer/micelle with ASO, it was found that less bulky cationic moieties transfected the ASO more effectively. Interestingly, however the ASO internalization trend was the opposite of the transfection trend for cationic moiety, indicating internalization is not the major factor in determining transfection efficiency for this series. Micelleplexes (micelle-ASO complexes) generally enable higher transfection efficacy as compared to polyplexes (linear polymer-ASO complexes). Additionally, the order of addition of cells and complexes was explored. Linear polyplexes showed better transfection efficiency in adhered cells, whereas micelleplexes delivered the ASO more efficiently when the cells and micelleplexes were added simultaneously. This phenomenon may be due to increased cell-complex interactions as micelleplexes have increased colloidal stability compared to polyplexes. These findings emphasize the importance of polymer composition and architecture in governing the cellular interactions necessary for transfection, thus allowing advancement in the design principles for nonviral nucleic acid delivery formulations.
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Affiliation(s)
- Mckenna G Hanson
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Christian J Grimme
- Department of Chemical Engineering & Materials Science, University of Minnesota, 421Washington Avenue SE, Minneapolis, Minnesota 55455, United States
| | - Cristiam F Santa Chalarca
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Theresa M Reineke
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
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Grimme CJ, Hanson MG, Corcoran LG, Reineke TM. Polycation Architecture Affects Complexation and Delivery of Short Antisense Oligonucleotides: Micelleplexes Outperform Polyplexes. Biomacromolecules 2022; 23:3257-3271. [PMID: 35862267 DOI: 10.1021/acs.biomac.2c00338] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Herein, we examine the complexation and biological delivery of a short single-stranded antisense oligonucleotide (ASO) payload with four polymer derivatives that form two architectural variants (polyplexes and micelleplexes): a homopolymer poly(2-dimethylaminoethyl methacrylate) (D), a diblock polymer poly(ethylene glycol)methylether methacrylate-block-poly(2-dimethylaminoethyl methacrylate) (ObD), and two micelle-forming variants, poly(2-dimethylaminoethyl methacrylate)-block-poly(n-butyl methacrylate) (DB) and poly(ethylene glycol)methylether methacrylate-block-poly(2-dimethylaminoethyl methacrylate)-block-poly(n-butyl methacrylate) (ObDB). Both polyplexes and micelleplexes complexed ASOs, and the incorporation of an Ob brush enhances colloidal stability. Micellplexes are templated by the size and shape of the unloaded micelle and that micelle-ASO complexation is not sensitive to formulation/mixing order, allowing ease, versatility, and reproducibility in packaging short oligonucleotides. The DB micelleplexes promoted the largest gene silencing, internalization, and tolerable toxicity while the ObDB micelleplexes displayed enhanced colloidal stability and highly efficient payload trafficking despite having lower cellular uptake. Overall, this work demonstrates that cationic micelles are superior delivery vehicles for ASOs denoting the importance of vehicle architecture in biological performance.
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Affiliation(s)
- Christian J Grimme
- Department of Chemical Engineering & Materials Science, University of Minnesota, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, United States
| | - Mckenna G Hanson
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Louis G Corcoran
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Theresa M Reineke
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
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