Nanotechnology: aptamers for specific & better delivery systems of existing drugs
Larry H. Bernstein, MD, FCAP, Curator
LPBI
Oligonucleotide Aptamers: New Tools for Targeted Cancer Therapy
Hongguang Sun1, Xun Zhu2, Patrick Y Lu3, Roberto R Rosato1, Wen Tan4and Youli Zu1
Molecular Therapy Nucleic Acids (2014) 3, e182; http://dx.doi.org:/10.1038/mtna.2014.32
Aptamers are a class of small nucleic acid ligands that are composed of RNA or single-stranded DNA oligonucleotides and have high specificity and affinity for their targets. Similar to antibodies, aptamers interact with their targets by recognizing a specific three-dimensional structure and are thus termed “chemical antibodies.” In contrast to protein antibodies, aptamers offer unique chemical and biological characteristics based on their oligonucleotide properties. Hence, they are more suitable for the development of novel clinical applications. Aptamer technology has been widely investigated in various biomedical fields for biomarker discovery, in vitro diagnosis, in vivo imaging, and targeted therapy. This review will discuss the potential applications of aptamer technology as a new tool for targeted cancer therapy with emphasis on the development of aptamers that are able to specifically target cell surface biomarkers. Additionally, we will describe several approaches for the use of aptamers in targeted therapeutics, including aptamer-drug conjugation, aptamer-nanoparticle conjugation, aptamer-mediated targeted gene therapy, aptamer-mediated immunotherapy, and aptamer-mediated biotherapy.
Keywords: cell surface biomarker; nanomedicine; oligonucleotide aptamer; SELEX; targeted cancer therapy
The terms “aptamer” and “SELEX” were introduced by two independent groups in 1990.1,2 The term “aptamer” refers to small nucleic acid ligands that exhibit specific therapeutic functions and an unambiguous binding affinity for their targets. Conversely, Systematic Evolution of Ligands by EXponential enrichment (SELEX) technology is the method used for aptamer development. Although using small molecule nucleic acids as therapeutics has been explored for decades, development of SELEX and aptamer technology revolutionized this field.
The most important property of an aptamer, from the Latin aptus (to fit), is its high target selectivity. These short, chemically synthesized, single-stranded (ss) RNA or DNA oligonucleotides fold into specific three-dimensional (3D) structures with dissociation constants usually in the pico- to nano-molar range.3 Moreover, in contrast to other nucleic acid molecular probes, aptamers interact with and bind to their targets through structural recognition (Figure 1), a process similar to that of an antigen-antibody reaction. Thus, aptamers are also referred to as “chemical antibodies.”
Due to their small size and oligonucleotide properties, aptamers offer several advantages over protein antibodies in both their extensive clinical applicability and a less challenging industrial synthesis process. Specifically, (i) aptamers can penetrate tissues faster and more efficiently due to their significantly lower molecular weight (8–25 kDa aptamers versus ~150 kDa of antibodies). Therefore, aptamers penetrate tissues barriers and reach their target sites in vivo more efficiently than the larger-sized protein antibodies. (ii) Aptamers are virtually nonimmunogenic in vivo. In principal, as aptamers are oligonucleotides they should not be recognized by the immune system. In practice, a recent clinical study showed that aptamers did not stimulate an immune response in vivo,4,5 as compared to protein antibodies that are highly immunogenic, especially following repeat injections. (iii) Aptamers are thermally stable. Based on the intrinsic property of oligonucleotides, even after a 95 °C denaturation, aptamers can refold into their correct 3D conformations once cooled to room temperature. In comparison, protein-based antibodies permanently lose their activity at high temperatures. More importantly, a well-established synthesis protocol and chemical modification technology lead to (iv) rapid, large-scale aptamer synthesis and modification capacity that includes a variety of functional moieties; (v) low structural variation during chemical synthesis; and (vi) have lower production costs. Moreover, aptamers specifically recognize a wide range of targets, such as ions, drugs, toxins, peptides, proteins, viruses, bacteria, cells, and even tissues.6,7,8,9,10,11,12 In the clinic, aptamer-based therapeutics are gaining momentum. For example, Macugen, a modified RNA aptamer, specifically targets vascular endothelial growth factor. It has been approved by the US Food and Drug Administration (FDA)13 for the treatment of wet age-related macular degeneration and is under evaluation for other conditions.14 In the cancer setting, AS1411 targets nucleolin, a protein over-expressed in a variety of tumors. It is currently being evaluated as a potential treatment option in solid tumors and acute myeloid leukemia.15 An updated list of therapeutic aptamers undergoing clinical trials is included in ref. 16 and Table 1. Taken together, these clinical studies highlight many possible uses that aptamers may have in a variety of biomedical fields, including therapeutics.17
A list of therapeutic aptamers undergoing clinical trials
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Since aptamer technology was first introduced, the RNA-based sequence library has been widely used for SELEX. Based on the existing evidence, it is believed that the presence of a 2′-OH group and non-Watson-Crick base pairing allows RNA aptamer oligonucleotides to fold into more diverse 3D structures than ssDNA molecules. Consequently, using the more flexible RNA sequences simplifies the development of high-affinity and -specificity aptamers. Despite their advantages, RNA sequences are very sensitive to nucleases present in biological environments and can be rapidly degraded.18 To increase nuclease resistance of RNA-based aptamers, several chemical modifications have been investigated. Evidence shows that 2′-OH group and phosphodiester linkages of RNA sequences are the sites of nuclease hydrolysis. Subsequently, substitutions of the 2′-OH functional group by 2′-fluoro, 2′-amino, or 2′-O-methoxy motifs, and/or changes to the phosphodiester backbone with boranophosphate or phosphorothioate are the most common modifications aimed at increasing nuclease resistance.19 More recently, Wu et al. developed a novel chemical modification method to increase siRNA stability, in which phosphorodithioate and 2′-O-Methyl were simultaneously substituted in the same nucleotide.20 This modification method significantly enhanced siRNA stability and represents a potential new direction for utilization of RNA-based therapies in complex biological systems. Other effective modifications recently reported utilize the locked nucleic acid technology16,21 or generate “mirror” RNA sequence structures, termed spiegelmers.22 These modifications result in structural changes to the RNA sequences, which cannot be digested by nucleases.
In addition to RNA aptamers, ssDNA-based aptamers have also been developed. Due to their lack of 2′-OH groups, DNA molecules are naturally resistant to 2′-endonucleases and are stable in biological environments. Recently, our group developed a biostable DNA-based aptamer specific for CD30, a protein biomarker that is over-expressed in Hodgkin and anaplastic large cell lymphomas. Functional analysis demonstrated that this ssDNA-based aptamer exhibited high CD30 binding affinity as low as 2 nmol/l and was stable in human serum for up to 8 hours. Conversely, an RNA-based CD30 aptamer was digested within 10 minutes under similar conditions.23
In summary, unique chemical features and biological functions have made aptamers a very attractive tool in biomedical research over the past two decades. Currently, there are over 4,000 published articles referenced in the PubMed database that include the term “aptamer.” Research areas that include aptamer technology cover bioassays, drug development, cell detection, tissue staining, in vitro and in vivoimaging, nanotechnology, and targeted therapy. As chemical antibodies, aptamers represent an excellent alternative to replace or supplement protein antibodies, which have been extensively used in the clinic.
Aptamers Specifically Targeting Cell Surface Biomarkers
Using SELEX technology to develop aptamers for cell surface biomarkers
Similar to protein antibody development, purified recombinant proteins or peptides expressed in prokaryotic or eukaryotic systems can be used as targets for aptamers selected by the SELEX method. However, because of the posttranslational modifications, especially in the case of highly glycosylated proteins, purified proteins or peptides often cannot fold into the correct 3D structure that is formed under physiologic conditions.32 Consequently, the newly synthesized aptamers may not be able to selectively recognize and interact with their corresponding targets, which would result in failure of the biomedical application. As this is a common problem, it is very important to choose biomarkers in their native conformation for aptamers selection. Taking this issue into an account, a modified SELEX technology that uses whole living cells, Cell-based SELEX (or Cell-SELEX), was recently established.33 To develop cell-specific aptamers, the Cell-SELEX method uses whole living cells that express surface biomarkers of interest. However, the presence of many different cell surface molecules in addition to the target biomarker(s) results in the synthesis of many unrelated/unwanted aptamers. Therefore, in addition to all the SELEX steps described above, Cell-SELEX technology also utilizes control cells that do not express the target biomarker(s) during the counter-selection step.33
Well-characterized biomarkers that are endogenously expressed at high levels, such as the ErbB superfamily, MUC1, EpCAM, and CD30, offer the best potential for cell-based aptamer development. Subsequently, cell lines that have high endogenous expression of cell-specific or cancer type-specific biomarker(s) are commonly used for Cell-SELEX. However, if such cell lines are unavailable, a biomarker of interest could be over-expressed in a particular cell line via gene transfection and the parental cells used for counter-selection. Using this approach, aptamers targeting the cancer stem cell (CSC) biomarker CD133 have been recently developed.34 In this study, CD133 cDNA was transfected into HEK293T cells that were then used for aptamer enrichment, with the parental HEK293T cells serving as a negative control. Similarly, an aptamer specific for the human receptor tyrosine kinase was recently developed.35
Despite the advantages offered by the Cell-SELEX system, this method provides low aptamer enrichment efficiency because many off-target surface biomarkers/molecules are coexpressed on the cells of interest. To overcome this obstacle, our lab introduced a modified SELEX method that combines the cell-based SELEX with purified protein-based SELEX techniques. This hybrid (or cross-over) SELEX had been used to develop Tenascin-C-specific RNA aptamers.36 In our lab, by employing the hybrid-SELEX approach, we developed a DNA aptamer specific for CD30-positive lymphoma tumor cells.23 As shown in Figure 2, the synthesized ssDNA sequence library was initially selected through the cell-based SELEX with CD30-expressing cells, followed by further enrichment with the purified CD30 protein-based SELEX. The current thought is that aptamers developed through this hybrid-SELEX process will be more selective in recognizing and binding to their target biomarker(s). In addition to our hybrid-SELEX approach, other modified Cell-SELEX technologies have been developed, such as internalized Cell-SELEX, designed to select functional aptamers that could be internalized by human cells,37,38,39,40,41,42,43 and FACS-SELEX, that is used to eliminate dead cells that nonspecifically bind nucleic acids and affect subsequent aptamer selection results.44,45
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Schematic diagram of our hybrid-SELEX method for selection of CD30-specific ssDNA aptamer. In our experiment, the hybrid-SELEX process is divided into (a) the cell-based SELEX selection and (b) CD30 protein-based SELEX enrichment. First, CD30-expressing lymphoma cells are used for positive selection and CD30-negative Jurkat cells are used in negative counter-selection. After 20 rounds of selection, the enriched aptamer pool is incubated with CD30 protein immobilized on magnetic beads for five additional rounds of enrichment. SELEX, Systematic Evolution of Ligands by EXponential enrichment.
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Aptamer-based biotherapy. (a) Schema showing receptor oligomerization-inducing downstream signaling. CD30-associated signaling is activated by its ligand through trimerization of the receptor, leading to varied outcomes that range from apoptosis to proliferation. (b) CD30-positive and -negative cells were incubated without any treatment or in the presence of control streptavidin, monomeric aptamer, and multimeric aptamer. Following 72-hour incubation, the multivalent CD30 aptamer induced cell death in the CD30-positive lymphoma cells, but had no effect on the CD30-negative control cells. Ratio of the dead/live cells was calculated by costaining the cells with Hoechst 33342 (live cells) and propidium iodide (dead cells).
Antibody-based targeted therapeutics provide high target specificity and affinity. However, their potential for immunogenicity is of a great concern, as is their high production cost, both of which have limited their clinical applicability. As discussed in this review, when compared to protein antibodies, oligonucleotide aptamers offer many advantages, including simple chemical synthesis, virtual nonimmunogenicity, smaller size, faster tissue penetration, ease of modification with different functional moieties, low cost of production, and high biological stability. Therefore, aptamers have become a promising new class of molecular ligands that could replace or supplement protein antibodies. In summary, aptamer technology has a strong market value and may be applied in various biomedical fields, including in vitro cancer cell detection, in vivo tumor imaging, and targeted cancer therapy (Figure 7).
Figure 7.
Although aptamer technology has a great potential in the biomedical field, several technical challenges remain and must be addressed. These include: (i) how can aptamers be rapidly adapted for specific targets by decreasing false-positive/-negative selection? Primarily dependent on the natural properties of targets of interest, such as proteins versus cells or tissues, the process of aptamer selection is usually time-consuming, and the success rate is sometimes low. To improve the speed and success rate, novel methods for aptamer selection have been recently described. They include bead-based selection, that can select aptamers as rapidly as a single round of selection,27,28 and the SOMAmer, which improves the aptamer production success rate from less than 30% to over 50%.29,30 More recently, a study by Cho et al.devised a Quantitative Parallel Aptamer Selection System (QPASS) method, which integrates microfluidic selection, NGS, and in situ-synthesized aptamer arrays. This approach allows for the simultaneous measurement of affinity and specificity for thousands of candidate aptamers in parallel.116 In addition to QPASS, evolving modifications to the Cell-SELEX approach are beginning to address difficulties with successful removal of the influence stemming from the presence of dead cells, slow enrichment aptamers recognizing targets of interest, and contamination with unwanted aptamer sequences. As described above, utilization of the above-mentioned FACS-mediated SELEX44,45and hybrid-SELEX23 offers novel approaches that address these technical challenges.
(ii) How can we select cancer-relevant targets for aptamer development and clinical applications? Tumorigenesis is a dynamic process that includes multiple constantly changing factors. Therefore, a one-size-fits-all cancer-specific biomarker is unlikely to ever be identified. Yet, it has been established that certain biomarkers present in healthy tissues are highly expressed in cancer cells. Moreover, certain biomarkers are associated with particular cancer cell types making them to be considered as useful targets for development of targeted cancer therapy. However, while use of cancer cells to identify biomarkers and to develop therapeutic agents is a reasonable approach, cultured cells, especially immortalized cell lines, greatly differ from tumor tissues in vivo. To overcome these limitations and to select more reliable cancer-relevant biomarkers for aptamer development, several innovative SELEX methods have been recently described. Of particular interest are the tissue-based SELEX117 and the in vivo-SELEX,118 which offer target selection under more relevant pathologic conditions. This cell/tissue-specific biomarker selection can also be utilized for development of noncancer related therapies, as shown for aptamers targeting the adipose tissue in obesity119 and for aptamers designed to penetrate the blood-brain barrier in order to combat brain diseases.120 Hence, we believe that the careful selection of cancer-associated biomarkers and cell/tissue type-specific biomarkers will expand the scopes of aptamer applicability and improve the feasibility of clinical applications.
(iii) What methods could improve aptamer biostability in vivo? Unmodified RNA-based aptamers are very susceptible to the nuclease-mediated degradation in vivo. Although many chemical modifications aimed at increasing biostability of the RNA aptamers have been developed, including 2′-modifications, 3′-modifications, phosphodiester backbone modifications,19,20 and utilizations of novel nucleic acids (locked nucleic acid and Spiegelmers),16,21,22 their effectiveness is still limited. When it was first described, PEGylation was a very attractive strategy for prolonging aptamer circulation half-life and enhancing their biostability. However, a recent report showed that the in vivo use of PEGylated aptamers induced production of anti-PEG antibodies,121emphasizing the need for the development of alternative approaches.
(iv) How can aptamer technology be modified to achieve a more effective drug delivery? Many drug delivery systems described in this review are tested in vitro or in animal models. Yet, as with any compound that is translated from the bench to the bedside, aptamer-drug conjugates may behave differently in a human patient than they do in laboratory animals. Therefore, aptamer-drug conjugation remains an important challenge that must be considered. Specifically, various coupling approaches lead to different pharmacokinetics, biodistribution, and tolerability in vivo, which in turn greatly affect treatment effectiveness. In the same vein, we must consider the effectiveness of aptamer-mediated target gene therapy. Gene therapy, including siRNA and miRNA aimed at silencing specific genes, is considered the next generation therapeutic approach. However, silencing a single pathogenic gene may not be a viable therapeutic option because tumorigenesis is a process regulated by multiple genes and signaling pathways. Therefore, combining targeted therapeutics with gene therapy may represent the most effective strategy. Such combinational therapy approaches can greatly improve the therapeutic efficacy while reducing the required dosages of both drugs and small molecule RNAs,122 and, more importantly, may offer new alternatives to combat chemotherapy-resistant cancers.110
(v) The last important point to consider is whether aptamer-mediated biotherapies can become effective, FDA-approved medications. Following Macugen approval by the FDA, many aptamer-mediated biotherapies have been evaluated in clinical trials. Of particular interest is AS1411, an antitumor aptamer that has completed several Phase I clinical trials.15 Trial results are promising and offer useful insights into further modifications that could be applied to therapeutic aptamer development.
Taken together, although some technical challenges remain to be addressed, oligonucleotide aptamers have become an attractive and promising tool for targeted cancer therapy. As more clinical data are accumulated, we and others will be better equipped to optimize aptamer formulations, leading to the expansion of aptamer use in the clinic.
- Ellington, AD and Szostak, JW (1990). In vitro selection of RNA molecules that bind specific ligands. Nature 346: 818–822. | Article | PubMed | ISI | CAS |
- Tuerk, C and Gold, L (1990). Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249: 505–510. | Article | PubMed | ISI | CAS |
- Nimjee, SM, Rusconi, CP and Sullenger, BA (2005). Aptamers: an emerging class of therapeutics. Annu Rev Med 56: 555–583. | Article | PubMed | ISI | CAS |
- Eyetech Study Group (2002). Preclinical and phase 1A clinical evaluation of an anti-VEGF pegylated aptamer (EYE001) for the treatment of exudative age-related macular degeneration. Retina22: 143–152. | PubMed | ISI |
- Eyetech Study Group (2003). Anti-vascular endothelial growth factor therapy for subfoveal choroidal neovascularization secondary to age-related macular degeneration: phase II study results. Ophthalmology 110: 979–986. | Article | PubMed |
- Parekh, P, Tang, Z, Turner, PC, Moyer, RW and Tan, W (2010). Aptamers recognizing glycosylated hemagglutinin expressed on the surface of vaccinia virus-infected cells. Anal Chem 82: 8642–8649. | Article | PubMed |
- Sefah, K, Tang, ZW, Shangguan, DH, Chen, H, Lopez-Colon, D, Li, Y et al. (2009). Molecular recognition of acute myeloid leukemia using aptamers. Leukemia 23: 235–244. | Article | PubMed | CAS |
- Bayrac, AT, Sefah, K, Parekh, P, Bayrac, C, Gulbakan, B, Oktem, HA et al. (2011). In vitro Selection of DNA Aptamers to Glioblastoma Multiforme. ACS Chem Neurosci 2: 175–181. | Article | PubMed | ISI |
- Bruno, JG and Kiel, JL (1999). In vitro selection of DNA aptamers to anthrax spores with electrochemiluminescence detection.Biosens Bioelectron 14: 457–464. | Article | PubMed | CAS |
- Kirby, R, Cho, EJ, Gehrke, B, Bayer, T, Park, YS, Neikirk, DP et al. (2004). Aptamer-based sensor arrays for the detection and quantitation of proteins. Anal Chem 76: 4066–4075. | Article | PubMed | CAS |
- Shangguan, D, Li, Y, Tang, Z, Cao, ZC, Chen, HW, Mallikaratchy, Pet al. (2006). Aptamers evolved from live cells as effective molecular probes for cancer study. Proc Natl Acad Sci USA 103: 11838–11843. | Article | PubMed | CAS |
- Tang, Z, Parekh, P, Turner, P, Moyer, RW and Tan, W (2009). Generating aptamers for recognition of virus-infected cells. Clin Chem 55: 813–822. | Article | PubMed | CAS |
- Que-Gewirth, NS and Sullenger, BA (2007). Gene therapy progress and prospects: RNA aptamers. Gene Ther 14: 283–291. | Article | PubMed | CAS |
- Sundaram, P, Kurniawan, H, Byrne, ME and Wower, J (2013). Therapeutic RNA aptamers in clinical trials. Eur J Pharm Sci 48: 259–271. | Article | PubMed |
- Ireson, CR and Kelland, LR (2006). Discovery and development of anticancer aptamers. Mol Cancer Ther 5: 2957–2962. | Article | PubMed | CAS |
Nanomedicine
From bioimaging to drug delivery and therapeutics, nanotechnology is poised to change the way doctors practice medicine.
August 1, 2014
|http://www.the-scientist.com/?articles.view/articleNo/40598/title/Nanomedicine/
Nanotechnology in Therapeutics
A Focus on Nanoparticles as a Drug Delivery System
Nanomedicine. 2012;7(8):1253-1271. http://www.medscape.com/viewarticle/770397_1
Continuing improvement in the pharmacological and therapeutic properties of drugs is driving the revolution in novel drug delivery systems. In fact, a wide spectrum of therapeutic nanocarriers has been extensively investigated to address this emerging need. Accordingly, this article will review recent developments in the use of nanoparticles as drug delivery systems to treat a wide variety of diseases. Finally, we will introduce challenges and future nanotechnology strategies to overcome limitations in this field.
- Nanocarriers & Their Applications
- Targeting Strategies
- Key Factors Impacting Drug Delivery
- Challenges of Nanotechnology for Drug Delivery
- Future Perspective
- Summary
Nanotechnology involves the engineering of functional systems at the molecular scale. Such systems are characterized by unique physical, optical and electronic features that are attractive for disciplines ranging from materials science to biomedicine. One of the most active research areas of nanotechnology is nanomedicine, which applies nanotechnology to highly specific medical interventions for the prevention, diagnosis and treatment of diseases.[1,2,401] The surge in nanomedicine research during the past few decades is now translating into considerable commercialization efforts around the globe, with many products on the market and a growing number in the pipeline. Currently, nanomedicine is dominated by drug delivery systems, accounting for more than 75% of total sales.[3]
Nanomaterials fall into a size range similar to proteins and other macromolecular structures found inside living cells. As such, nanomaterials are poised to take advantage of existing cellular machinery to facilitate the delivery of drugs. Nanoparticles (NPs) containing encapsulated, dispersed, absorbed or conjugated drugs have unique characteristics that can lead to enhanced performance in a variety of dosage forms. When formulated correctly, drug particles are resistant to settling and can have higher saturation solubility, rapid dissolution and enhanced adhesion to biological surfaces, thereby providing rapid onset of therapeutic action and improved bioavailability. In addition, the vast majority of molecules in a nanostructure reside at the particle surface,[4] which maximizes the loading and delivery of cargos, such as therapeutic drugs, proteins and polynucleotides, to targeted cells and tissues. Highly efficient drug delivery, based on nanomaterials, could potentially reduce the drug dose needed to achieve therapeutic benefit, which, in turn, would lower the cost and/or reduce the side effects associated with particular drugs. Furthermore, NP size and surface characteristics can be easily manipulated to achieve both passive and active drug targeting. Site-specific targeting can be achieved by attaching targeting ligands, such as antibodies or aptamers, to the surface of particles, or by using guidance in the form of magnetic NPs. NPs can also control and sustain release of a drug during transport to, or at, the site of localization, altering drug distribution and subsequent clearance of the drug in order to improve therapeutic efficacy and reduce side effects.
Nanotechnology could be strategically implemented in new developing drug delivery systems that can expand drug markets. Such a plan would be applied to drugs selected for full-scale development based on their safety and efficacy data, but which fail to reach clinical development because of poor biopharmacological properties, for example, poor solubility or poor permeability across the intestinal epithelium, situations that translate into poor bioavailability and undesirable pharmacokinetic properties.[5] The new drug delivery methods are expected to enable pharmaceutical companies to reformulate existing drugs on the market, thereby extending the lifetime of products and enhancing the performance of drugs by increasing effectiveness, safety and patient adherence, and ultimately reducing healthcare costs.[6–8]
Commercialization of nanotechnology in pharmaceutical and medical science has made great progress. Taking the USA alone as an example, at least 15 new pharmaceuticals approved since 1990 have utilized nanotechnology in their design and drug delivery systems. In each case, both product development and safety data reviews were conducted on a case-by-case basis, using the best available methods and procedures, with an understanding that postmarketing vigilance for safety issues would be ongoing. Some representative examples of therapeutic nanocarriers on the market are briefly described in Table 1.
In this review, we focus mainly on the application of nanotechnology to drug delivery and highlight several areas of opportunity where current and emerging nanotechnologies could enable novel classes of therapeutics. We look at challenges and general trends in pharmaceutical nanotechnology, and we also explore nanotechnology strategies to overcome limitations in drug delivery. However, this article can only serve to provide a glimpse into this rapidly evolving field, both now and what may be expected in the future.
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