Highly branched HK peptides are effective carriers of siRNA

Evolution of Lipo-Xenopeptide Carriers for siRNA Delivery: Interplay of Stabilizing Subunits

Although small interfering RNA (siRNA) holds immense promise for treating genetic diseases and cancers, its clinical application is constrained by instability, cellular uptake barriers, and inefficient cytosolic delivery, underscoring the need for effective delivery systems. Therefore, this study focuses on screening novel T-shaped lipo-xenopeptide (XP) nanocarriers for siRNA polyplex formulation, integrating two single succinoyl-tetraethylene pentamine (Stp) units for electrostatic interaction and tyrosine tripeptides (Y3) for aromatic stabilization, along with structural modifications such as the addition of histidine (H) with or without terminal cysteines (C), and the incorporation of various fatty acids (FAs). A systematic evaluation of siRNA binding, nanoparticle stability, and gene silencing efficiency in multiple cell lines illustrated that the novel Stp1-HC lipo-XPs carriers outperform their Stp2-HC analogs, despite having fewer cationizable Stp units. This advantage stems from increased fatty acid, Y3, and C density, which compensates for reduced electrostatic interactions. The presence of H in combination with unsaturated FAs significantly improved the functional siRNA delivery. Our findings highlight the complex interplay of electrostatic, hydrophobic, covalent, hydrogen-bonded, and aromatic interactions to achieve efficient siRNA delivery, which is best-balanced in the oleic acid-containing Stp1-HC/OleA lipo-XP, exceeding the previously best standard carrier Stp2-HC/OleA in efficiency.

Ionic Coating of siRNA Polyplexes with cRGD-PEG-Hyaluronic Acid To Modulate Serum Stability and In Vivo Performance

Efficient delivery of siRNA-based polyplexes to tumors remains a major challenge. Nonspecific interactions in the bloodstream, limited circulation time, and nontargeted biodistribution hamper sufficient tumor accumulation. To address these challenges, we developed an ionic hyaluronic acid (HA) coating to shield sequence-defined oligoaminoamide-based polyplexes. This coating should shield the positive polyplex surface charge, thus reducing nonspecific interactions and enhancing serum stability. Additionally, we modified the HA coating with the cyclic RGDfK (cRGD) peptide to specifically target tumor endothelial cells (TECs). Optionally, a polyethylene glycol (PEG) spacer was also introduced to improve ligand presentation on the polyplex surface. The HA-coated polyplexes exhibited favorable physicochemical properties, including a negative zeta potential and effective siRNA retention within the polyplex, which was not adversely affected by PEG or cRGD modification. In vitro analyses revealed that these polyplexes not only enhanced tumor cell association and preserved the high transfection efficiency of plain cationic polyplexes but also exhibited coating-dependent cellular internalization, as evidenced by a competitive inhibition experiment. Even in the presence of serum, the HA-coated polyplexes encapsulated siRNA effectively, exhibited suitable particle sizes, and maintained a high gene silencing efficiency. In vivo studies involving intravenous administration into Neuro2a tumor-bearing mice showed that the HA coating, particularly when modified with PEG and cRGD, significantly increased the tumor accumulation of polyplexes. HA-PEG-cRGD-shielded polyplexes exhibited significantly enhanced in vivo gene silencing in tumors compared with plain polyplexes. Collectively, our results indicate a superior performance of HA-coated polyplexes in terms of stability and cellular uptake, both in vitro and in vivo.

A Facile and Promising Delivery Platform for siRNA to Solid Tumors

Over 20 years have passed since siRNA was brought to the public's attention. Silencing genes with siRNA has been used for various purposes, from creating pest-resistant plants to treating human diseases. In the last six years, several siRNA therapies have been approved by the FDA, which solely target disease-inducing proteins in the liver. The extrahepatic utility of systemically delivered siRNA has been primarily limited to preclinical studies. While siRNA targeting the liver comprises relatively simple ligand-siRNA conjugates, siRNA treating extrahepatic diseases such as cancer often requires complex carriers. The complexity of these extrahepatic carriers of siRNA reduces the likelihood of their widespread clinical use. In the current report, we initially demonstrated that a linear histidine-lysine (HK) carrier of siRNA, injected intravenously, effectively silenced luciferase expressed by MDA-MB-435 tumors in a mouse model. This non-pegylated linear peptide carrier was easily synthesized compared to the complex cRGD-conjugated pegylated branched peptides our group used previously. Notably, the tumor-targeting component, KHHK, was embedded within the peptide, eliminating the need to conjugate the ligand to the carrier. Moreover, brief bath sonication significantly improved the in vitro and in vivo silencing of these HK siRNA polyplexes. Several other linear peptides containing the -KHHK- sequence were then screened with some carriers of siRNA, silencing 80% of the tumor luciferase marker. Additionally, silencing by these HK siRNA polyplexes was confirmed in a second tumor model. Not only was luciferase activity reduced, but these siRNA polyplexes also reduced the Raf-1 oncogene in the MDA-MB-231 xenografts. These simple-to-synthesize, effective, linear HK peptides are promising siRNA carriers for clinical use.

Dynamic carriers for therapeutic RNA delivery

Carriers for RNA delivery must be dynamic, first stabilizing and protecting therapeutic RNA during delivery to the target tissue and across cellular membrane barriers and then releasing the cargo in bioactive form. The chemical space of carriers ranges from small cationic lipids applied in lipoplexes and lipid nanoparticles, over medium-sized sequence-defined xenopeptides, to macromolecular polycations applied in polyplexes and polymer micelles. This perspective highlights the discovery of distinct virus-inspired dynamic processes that capitalize on mutual nanoparticle-host interactions to achieve potent RNA delivery. From the host side, subtle alterations of pH, ion concentration, redox potential, presence of specific proteins, receptors, or enzymes are cues, which must be recognized by the RNA nanocarrier via dynamic chemical designs including cleavable bonds, alterable physicochemical properties, and supramolecular assembly-disassembly processes to respond to changing biological microenvironment during delivery.

Peptide-Based Nanoparticles for Systemic Extrahepatic Delivery of Therapeutic Nucleotides

Peptide-based nanoparticles (PBN) for nucleotide complexation and targeting of extrahepatic diseases are gaining recognition as potent pharmaceutical vehicles for fine-tuned control of protein production (up- and/or down-regulation) and for gene delivery. Herein, we review the principles and mechanisms underpinning self-assembled formation of PBN, cellular uptake, endosomal release, and delivery to extrahepatic disease sites after systemic administration. Selected examples of PBN that have demonstrated recent proof of concept in disease models in vivo are summarized to offer the reader a comparative view of the field and the possibilities for clinical application.

Stimuli-Responsive Polypeptide Nanoparticles for Enhanced DNA Delivery

The development of non-viral delivery systems for effective gene therapy is one of the current challenges in modern biomedicinal chemistry. In this paper, the synthesis of pH- and redox-responsive amphiphilic polypeptides for intracellular DNA delivery is reported and discussed. Two series of polypeptides consisting of L-lysine, L-phenylalanine, L-histidine, and L-cysteine as well as the same amino acids with L-glutamic acid were synthesized by a combination of copolymerization of N-carboxyanhydrides of α-amino acids and post-polymerization modification of the resulting copolymers. The presence of histidine provided pH-sensitive properties under weakly acidic conditions specific to endosomal pH. In turn, the presence of cysteine allowed for the formation of redox-responsive disulfide bonds, which stabilized the self-assembled nanoparticles in the extracellular environment but could degrade inside the cell. The formation of intraparticle disulfide bonds resulted in their compactization from 200-250 to 55-100 nm. Empty and pDNA-loaded cross-linked nanoparticles showed enhanced stability in various media compared to non-crosslinked nanoparticles. At the same time, the addition of glutathione promoted particle degradation and nucleic acid release. The delivery systems were able to retain their size and surface charge at polypeptide/pDNA ratios of 10 or higher. GFP expression in HEK 293 was induced by the delivery of pEGFP-N3 with the developed polypeptide nanoparticles. The maximal transfection efficacy (70%) was observed when the polypeptide/pDNA ratio was 100.

Approaches to Modulate the Chronic Wound Environment Using Localized Nucleic Acid Delivery

Significance: Nonhealing wounds have been the subject of decades of basic and clinical research. Despite new knowledge about the biology of impaired wound healing, little progress has been made in treating chronic wounds, leaving patients with few therapeutic options. Diabetic ulcers are a particularly common form of nonhealing wound. Recent Advances: Recently, investigation of therapeutic nucleic acids (TNAs), including plasmid DNA, small interfering RNA, microRNA mimics, anti-microRNA oligonucleotides, messenger RNA, and antisense oligonucleotides, has created a new treatment strategy for chronic wounds. TNAs can modulate the wound toward a prohealing environment by targeting gene pathways associated with inflammation, proteases, cell motility, angiogenesis, epithelialization, and oxidative stress. A variety of delivery systems have been investigated for TNAs, including dendrimers, lipid nanoparticles (NPs), polymeric micelles, polyplexes, metal NPs, and hydrogels. This review summarizes recent developments in TNA delivery for therapeutic targets associated with chronic wounds, with an emphasis on diabetic ulcers. Critical Issues: Translational potential of TNAs remains a key challenge; we highlight some drug delivery approaches for TNAs that may hold promise. We also describe current commercial efforts to locally deliver nucleic acids to modulate the wound environment. Future Directions: Localized nucleic acid delivery holds promise for the treatment of nonhealing chronic wounds. Future efforts to improve targeting of these nucleic acid therapies in the wound with both spatial and temporal control through drug delivery systems will be crucial to successful clinical translation.

Artificial peptides for antitumoral siRNA delivery

Intracellular delivery has been critical for the success of siRNA and related therapeutic nucleic acids. Improvement of delivery carriers will positively influence the efficacy of future nanomedicines. Our strategy for optimizing siRNA nanocarriers focuses on a bioinspired sequence-defined process including (i) identification of artificial amino acids active in specific delivery steps, (ii) assembly into defined sequences by solid phase-assisted synthesis (SPS), and (iii) screening for siRNA delivery, selection of top candidates and understanding structure-activity relations, followed by (iv) sequence variation for the next round of carrier selection. In the current review, our experience with this artificial peptide evolution in tumor-directed siRNA delivery is addressed. The medium-sized oligoaminoamides show better biological compatibility and can be functionalized to meet the requirements of siRNA delivery, such as formation of stable nanoparticles, shielding against proteins in the bloodstream, targeting into tumor tissue, and intracellular siRNA release in bioactive form.

A Global Review on Short Peptides: Frontiers and Perspectives

Peptides are fragments of proteins that carry out biological functions. They act as signaling entities via all domains of life and interfere with protein-protein interactions, which are indispensable in bio-processes. Short peptides include fundamental molecular information for a prelude to the symphony of life. They have aroused considerable interest due to their unique features and great promise in innovative bio-therapies. This work focusing on the current state-of-the-art short peptide-based therapeutical developments is the first global review written by researchers from all continents, as a celebration of 100 years of peptide therapeutics since the commencement of insulin therapy in the 1920s. Peptide "drugs" initially played only the role of hormone analogs to balance disorders. Nowadays, they achieve numerous biomedical tasks, can cross membranes, or reach intracellular targets. The role of peptides in bio-processes can hardly be mimicked by other chemical substances. The article is divided into independent sections, which are related to either the progress in short peptide-based theranostics or the problems posing challenge to bio-medicine. In particular, the SWOT analysis of short peptides, their relevance in therapies of diverse diseases, improvements in (bio)synthesis platforms, advanced nano-supramolecular technologies, aptamers, altered peptide ligands and in silico methodologies to overcome peptide limitations, modern smart bio-functional materials, vaccines, and drug/gene-targeted delivery systems are discussed.

Optimizing synthetic nucleic acid and protein nanocarriers: The chemical evolution approach

Optimizing synthetic nanocarriers is like searching for a needle in a haystack. How to find the most suitable carrier for intracellular delivery of a specified macromolecular nanoagent for a given disease target location? Here, we review different synthetic 'chemical evolution' strategies that have been pursued. Libraries of nanocarriers have been generated either by unbiased combinatorial chemistry or by variation and novel combination of known functional delivery elements. As in natural evolution, definition of nanocarriers as sequences, as barcode or design principle, may fuel chemical evolution. Screening in appropriate test system may not only provide delivery candidates, but also a refined understanding of cellular delivery including novel, unpredictable mechanisms. Combined with rational design and computational algorithms, candidates can be further optimized in subsequent evolution cycles into nanocarriers with improved safety and efficacy. Optimization of nanocarriers differs for various cargos, as illustrated for plasmid DNA, siRNA, mRNA, proteins, or genome-editing nucleases.

Location of a single histidine within peptide carriers increases mRNA delivery

BACKGROUND

Previously, we determined that four-branched histidine-lysine (HK) peptides were effective carriers of plasmids and small interfering RNA. In the present study, we compared several branched HK carriers and, in particular, two closely-related H3K4b and H3K(+H)4b peptides for their ability as carriers of mRNA. The H3K(+H)4b peptide differed from its parent analogue, H3K4b, by only a single histidine in each branch.

METHODS

A series of four-branched HK peptides with varied sequences was synthesized on a solid-phase peptide synthesizer. The ability of these peptides to carry mRNA expressing luciferase to MDA-MB-231 cells was investigated. With gel retardation and heparin displacement assays, the stability of HK polyplexes was examined. We determined the intracellular uptake of HK polyplexes by flow cytometry and fluorescence microscopy. The size and polydispersity index of the polyplexes in several media were measured by dynamic light scattering.

RESULTS

MDA-MB-231 cells transfected by H3K(+H)4b-mRNA polyplexes expressed 10-fold greater levels of luciferase than H3K4b polyplexes. With gel retardation and heparin displacement assays, the H3K(+H)4b polyplexes showed greater stability than H3K4b. Intracellular uptake and co-localization of H3K(+H)4b polyplexes within acidic endosomes were also significantly increased compared to H3K4b. Similar to H3K(+H)4b, several HK analogues with an additional histidine in the second domain of their branches were effective carriers of mRNA. When combined with DOTAP liposomes, H3K(+H)4b was synergistic in delivery of mRNA.

CONCLUSIONS

H3K(+H)4b was a more effective carrier of mRNA than H3K4b. Mechanistic studies suggest that H3K(+H)4b polyplexes were more stable than H3K4b polyplexes. Lipopolyplexes formed with H3K(+H)4b markedly increased mRNA transfection.

Hyaluronate siRNA nanoparticles with positive charge display rapid attachment to tumor endothelium and penetration into tumors

A cationizable sequence-defined lipo-oligoaminoamide (lipo-OAA) conferring stable assembly of siRNA into ~200 nm sized complexes contains an N-terminal azidolysine for covalent coating of formed nanoparticles with dibenzocyclooctyne-amine (DBCO)-modified hyaluronic acid (HA). Depending on the applied equivalents of DBCO-HA, stable nanoparticles with either cationic or anionic surface charge can be formed. The unmodified and two types of covalent HA-modified siRNA nanoparticles differ in their biological characteristics. Both types of HA coated siRNA complexes show an enhanced cellular uptake over uncoated complexes and facilitate efficient gene silencing, but differ in intracellular uptake pathways and distribution. Upon intravenous administration in mice, beyond our expectation and in contrast to the in vitro findings, only the cationic HA nanoparticles but neither the non-coated cationic nor the anionic HA complexes were able to target subcutaneous Huh 7 tumors and exert potent (78%) gene silencing. The favorable and very fast accumulation of cationic HA nanoparticles was confirmed in another subcutaneous tumor model. As evidenced by 3D nanoparticle distribution within Huh 7 tumors evaluated at early time points of 5 min and 45 min, only the cationic HA-based nanoparticles rapidly attach to the tumor endothelium and subsequently penetrate into tumor, in contrast to the analogous anionic HA coated or the cationic non-coated formulation.

Non-Viral Targeted Nucleic Acid Delivery: Apply Sequences for Optimization

In nature, genomes have been optimized by the evolution of their nucleic acid sequences. The design of peptide-like carriers as synthetic sequences provides a strategy for optimizing multifunctional targeted nucleic acid delivery in an iterative process. The optimization of sequence-defined nanocarriers differs for different nucleic acid cargos as well as their specific applications. Supramolecular self-assembly enriched the development of a virus-inspired non-viral nucleic acid delivery system. Incorporation of DNA barcodes presents a complementary approach of applying sequences for nanocarrier optimization. This strategy may greatly help to identify nucleic acid carriers that can overcome pharmacological barriers and facilitate targeted delivery in vivo. Barcode sequences enable simultaneous evaluation of multiple nucleic acid nanocarriers in a single test organism for in vivo biodistribution as well as in vivo bioactivity.

The Multifaceted Histidine-Based Carriers for Nucleic Acid Delivery: Advances and Challenges

Histidines incorporated into carriers of nucleic acids may enhance the extracellular stability of the nanoparticle, yet aid in the intracellular disruption of the nanoparticle, enabling the release of the nucleic acid. Moreover, protonation of histidines in the endosomes may result in endosomal swelling with subsequent lysis. These properties of histidine are based on its five-member imidazole ring in which the two nitrogen atoms may form hydrogen bonds or act as a base in acidic environments. A wide variety of carriers have integrated histidines or histidine-rich domains, which include peptides, polyethylenimine, polysaccharides, platform delivery systems, viral phages, mesoporous silica particles, and liposomes. Histidine-rich carriers have played key roles in our understanding of the stability of nanocarriers and the escape of the nucleic acids from endosomes. These carriers show great promise and offer marked potential in delivering plasmids, siRNA, and mRNA to their intracellular targets.

Promising approaches of small interfering RNAs (siRNAs) mediated cancer gene therapy

RNA interference (RNAi) has extensive potential to revolutionize every aspect of clinical application in biomedical research. One of the promising tools is the Small interfering RNA (siRNA) molecules within a cellular component. Principally, siRNA mediated innovative advances are increasing rapidly in support of cancer diagnosis and therapeutic purposes. Conversely, it has some delivery challenges to the site of action within the cells of a target organ, due to the progress of nucleic acids engineering and advance material science research contributing to the exceptional organ-specific targeted therapy. This siRNA based therapeutic technique definitely favors a unique and effective prospect to cancer patients. Herein, the significant drive also takes to review and summarize the major organ specific targets of diverse siRNAs based gene silencing mechanism. This machinery promisingly served as the inhibitor components for cancer development in the human model. Furthermore, the focus is also given to current applications on siRNA based quantifiable therapy leading to the silencing of cancer related gene expression in a sequence dependent and selective manner for cancer treatment. That might be a potent tool against the traditional chemotherapy techniques. Therefore, the siRNA mediated cancer gene therapy definitely require sharp attention like future weapons in opposition to cancer by the method of non-invasive siRNA delivery and effective gene silencing approaches.

Multifunctional Cationic PeptoStars as siRNA Carrier: Influence of Architecture and Histidine Modification on Knockdown Potential

RNA interference provides enormous potential for the treatment of several diseases, including cancer. Nevertheless, successful therapies based on siRNA require overcoming various challenges, such as poor pharmacokinetic characteristics of the small RNA molecule and inefficient cytosolic accumulation. In this respect, the development of functional siRNA carrier systems is a major task in biomedical research. To provide such a desired system, the synthesis of 3-arm and 6-arm PeptoStars is aimed for. The different branched polypept(o)idic architectures share a stealth-like polysarcosine corona for efficient shielding and a multifunctional polylysine core, which can be independently varied in size and functionality for siRNA complexation-, transport and intra cellular release. The special feature of star-like polypept(o)ides is in their uniform small size (<20 nm) and a core-shell structure, which implies a high stability and stealth-like properties and thus, they may combine long circulation times and a deep penetration of cancerous tissue. Initial toxicity and complement studies demonstrate well tolerated cationic PeptoStars with high complexation capability toward siRNA (N/P ratio up to 3:1), which can lead to potent RNAi for optimized systems. Here, the synthetic development of 3-arm and 6-arm polypept(o)idic star polymers, their modification with endosomolytic moieties, and first in vitro insights on RNA interference are reported on.

Enhancement of siRNA transfection by the optimization of fatty acid length and histidine content in the CPP

Depending on the pH, polyhistidines in the CPP influence interactions in CPP/siRNA nanoparticles by switching from hydrophobic to charged.

Efficient Shielding of Polyplexes Using Heterotelechelic Polysarcosines

Shielding agents are commonly used to shield polyelectrolyte complexes, e.g., polyplexes, from agglomeration and precipitation in complex media like blood, and thus enhance their in vivo circulation times. Since up to now primarily poly(ethylene glycol) (PEG) has been investigated to shield non-viral carriers for systemic delivery, we report on the use of polysarcosine (pSar) as a potential alternative for steric stabilization. A redox-sensitive, cationizable lipo-oligomer structure (containing two cholanic acids attached via a bioreducible disulfide linker to an oligoaminoamide backbone in T-shape configuration) was equipped with azide-functionality by solid phase supported synthesis. After mixing with small interfering RNA (siRNA), lipopolyplexes formed spontaneously and were further surface-functionalized with polysarcosines. Polysarcosine was synthesized by living controlled ring-opening polymerization using an azide-reactive dibenzo-aza-cyclooctyne-amine as an initiator. The shielding ability of the resulting formulations was investigated with biophysical assays and by near-infrared fluorescence bioimaging in mice. The modification of ~100 nm lipopolyplexes was only slightly increased upon functionalization. Cellular uptake into cells was strongly reduced by the pSar shielding. Moreover, polysarcosine-shielded polyplexes showed enhanced blood circulation times in bioimaging studies compared to unshielded polyplexes and similar to PEG-shielded polyplexes. Therefore, polysarcosine is a promising alternative for the shielding of non-viral, lipo-cationic polyplexes.

Cell-Penetrating Peptides to Enhance Delivery of Oligonucleotide-Based Therapeutics

The promise of nucleic acid based oligonucleotides as effective genetic therapies has been held back by their low bioavailability and poor cellular uptake to target tissues upon systemic administration. One such strategy to improve upon delivery is the use of short cell-penetrating peptides (CPPs) that can be either directly attached to their cargo through covalent linkages or through the formation of noncovalent nanoparticle complexes that can facilitate cellular uptake. In this review, we will highlight recent proof-of-principle studies that have utilized both of these strategies to improve nucleic acid delivery and discuss the prospects for translation of this approach for clinical application.

RGD peptide-based non-viral gene delivery vectors targeting integrin αvβ3 for cancer therapy

Integrin α_vβ₃ is restrictedly expressed on angiogenic blood vessels and tumour cells. It plays a key role in angiogenesis for tumour growth and metastasis. RGD peptide can specifically recognise the integrin α_vβ₃, which serves as targeted molecular for anti-angiogenesis strategies. Therefore, the targeted delivery of therapeutics by RGD peptide-based non-viral vectors to tumour vasculature and tumour cells is recognised as a promising approach for treating cancer. In this review, we illustrate the interaction between RGD peptide and integrin α_vβ₃ from different perspectives. Meanwhile, four types of RGD peptide-based non-viral gene delivery vectors for cancer therapy, including RGD-based cationic polymers, lipids, peptides and hybrid systems, are summarised. The aim is to particularly highlight the enhanced therapeutic effects and specific targeting ability exhibited by these vectors for cancer gene therapy both in vitro and in vivo.

The neuropilin-1 receptor mediates enhanced tumor delivery of H2K polyplexes

BACKGROUND

Promising plasmid-based treatments have limited value without an effective delivery system. Recently, the linear H2K with a repeating -KHHK- pattern was determined to be an effective plasmid carrier to tumor xenografts in vivo. Although unpacking of the H2K polyplex within the tumor may have a role, the mechanism for the enhanced efficacy remains unclear.

METHODS

After solid-phase synthesis of linear and branched histidine-lysine (HK) peptide carriers of plasmids, the peptides were compared for their ability to lyse endosomes with a red blood cell model and to transfect MDA-MB-435 xenografts in the presence or absence of neuropilin-1 receptor (NRP-1) antibodies. To examine stability, polyplexes were incubated with trypsin or NaCl and then analyzed by electrophoresis.

RESULTS

After screening peptides with a model for endosomal lysis at two pHs, the 33-mer H3K peptide lysed red blood cells effectively at the lower pH. Combining H3K and H2K peptides as carriers of plasmids expressing luciferase were more effective than H2K alone. Based on the repeating -KHHK- sequences of H2K, we studied whether the widespread gene expression in the tumor may be mediated by NRP-1. By blocking NRP-1 in tumor-bearing mice, luciferase activity in tumors delivered by HK polyplexes was reduced by 96%, whereas activity in normal tissues was minimally reduced.

CONCLUSIONS

Combining an endosomolytic peptide, H3K, with H2K polyplexes as a carrier further enhanced transfection in vivo. Moreover, the widespread distribution of H2K polyplexes is mediated by NRP-1, suggesting that transcytosis of these polyplexes through the tumor endothelium may lead to efficient transfection. Copyright © 2016 John Wiley & Sons, Ltd.

Solid-phase supported design of carriers for therapeutic nucleic acid delivery

Nucleic acid molecules are important therapeutic agents in the field of antisense oligonucleotide, RNA interference, and gene therapies. Since nucleic acids are not able to cross cell membranes and enter efficiently into cells on their own, the development of efficient, safe, and precise delivery systems is the crucial challenge for development of nucleic acid therapeutics. For the delivery of nucleic acids to their intracellular site of action, either the cytosol or the nucleus, several extracellular and intracellular barriers have to be overcome. Multifunctional carriers may handle the different special requirements of each barrier. The complexity of such macromolecules however poses a new hurdle in medical translation, which is the chemical production in reproducible and well-defined form. Solid-phase assisted synthesis (SPS) presents a solution for this challenge. The current review provides an overview on the design and SPS of precise sequence-defined synthetic carriers for nucleic acid cargos.

Design of Poly-l-Glutamate-Based Complexes for pDNA Delivery

Due to the polyanionic nature of DNA, typically cationic or neutral delivery vehicles have been used for gene delivery. As a new approach, this study focuses on the design, development, and validation of nonviral polypeptide-based carriers for oligonucleotide delivery based on a negatively charged poly-l-glutamic acid (PGA) backbone partly derivatized with oligoaminoamide residues. To this end, PGA-derivatives modified with different pentameric succinyl tetraethylene pentamines (Stp₅ ) are designed. Optionally, histidines for modulation of endosomal buffer capacity and cysteines for pDNA complex stabilization are included, followed by characterization of biophysical properties and gene transfer efficiency in N2a neuroblastoma or 4T1 breast cancer cells.

History of Polymeric Gene Delivery Systems

As an option for genetic disease treatment and an alternative for traditional cancer chemotherapy, gene therapy achieves significant attention. Nucleic acid delivery, however, remains a main challenge in human gene therapy. Polymer-based delivery systems offer a safer and promising route for therapeutic gene delivery. Over the past five decades, various cationic polymers have been optimized for increasingly effective nucleic acid transfer. This resulted in a chemical evolution of cationic polymers from the first-generation polycations towards bioinspired multifunctional sequence-defined polymers and nanocomposites. With the increasing of knowledge in molecular biological processes and rapid progress of macromolecular chemistry, further improvement of polymeric nucleic acid delivery systems will provide effective tool for gene-based therapy in the near future.

Functional peptides for siRNA delivery

siRNA is considered as a potent therapeutic agent because of its high specificity and efficiency in suppressing genes that are overexpressed during disease development. For nearly two decades, a significant amount of efforts has been dedicated to bringing the siRNA technology into clinical uses. However, only limited success has been achieved to date, largely due to the lack of a cell type-specific, safe, and efficient delivery technology to carry siRNA into the target cells' cytosol where RNA interference takes place. Among the emerging candidate nanocarriers for siRNA delivery, peptides have gained popularity because of their structural and functional diversity. A variety of peptides have been discovered for their ability to translocate siRNA into living cells via different mechanisms such as direct penetration through the cellular membrane, endocytosis-mediated cell entry followed by endosomolysis, and receptor-mediated uptake. This review is focused on the multiple roles played by peptides in siRNA delivery, such as membrane penetration, endosome disruption, targeting, as well as the combination of these functionalities.

Focused Library Approach to Discover Discrete Dipeptide Bolaamphiphiles for siRNA Delivery

In this study, we report a new dipeptide functionalization strategy for developing new dendritic bolaamphiphile vectors for efficient siRNA transfection. A focused library of dipeptides was constructed using four amino acids: l-arginine, l-histidine, l-lysine, and l-tryptophan. The dipeptides were coupled to two dendritic bolaamphiphile scaffolds that we developed previously, allowing us to quickly access a focused library of discrete vectors with multivalent dendritic dipeptide functionalities. The resulting discrete bolaamphiphiles were screened for siRNA delivery in vitro in HEK-293 and HeLa cells. Bolaamphiphiles functionalized with dipeptides containing Lys or Arg and either His or Trp were the most effective for in vitro siRNA delivery. Necessary cationic charge to ensure efficient siRNA binding are provided by Arg and Lys residues, whereas endosomal escape is provided through pH responsive buffering of His or membrane interactions of Trp. The most effective vectors (F10 HR/RH) exhibited greater than 75% gene silencing in multiple cell lines and exhibited serum stability.

How to Tackle the Challenge of siRNA Delivery with Sequence-Defined Oligoamino Amides

RNA interference (RNAi) as a mechanism of gene regulation provides exciting opportunities for medical applications. Synthetic small interfering RNA (siRNA) triggers the knockdown of complementary mRNA sequences in a catalytic fashion and has to be delivered into the cytosol of the targeted cells. The design of adequate carrier systems to overcome multiple extracellular and intracellular roadblocks within the delivery process has utmost importance. Cationic polymers form polyplexes through electrostatic interaction with negatively charged nucleic acids and present a promising class of carriers. Issues of polycations regarding toxicity, heterogeneity, and polydispersity can be overcome by solid-phase-assisted synthesis of sequence-defined cationic oligomers. These medium-sized highly versatile nucleic acid carriers display low cytotoxicity and can be modified and tailored in multiple ways to meet specific requirements of nucleic acid binding, polyplex size, shielding, targeting, and intracellular release of the cargo. In this way, sequence-defined cationic oligomers can mimic the dynamic and bioresponsive behavior of viruses.

Sequence-defined shuttles for targeted nucleic acid and protein delivery

Molecular medicine opens into a space of novel specific therapeutic agents: intracellularly active drugs such as peptides, proteins or nucleic acids, which are not able to cross cell membranes and enter the intracellular space on their own. Through the development of cell-targeted shuttles for specific delivery, this restriction in delivery has the potential to be converted into an advantage. On the one hand, due to the multiple extra- and intracellular barriers, such carrier systems need to be multifunctional. On the other hand, they must be precise and reproducibly manufactured due to pharmaceutical reasons. Here we review the design of precise sequence-defined delivery carriers, including solid-phase synthesized peptides and nonpeptidic oligomers, or nucleotide-based carriers such as aptamers and origami nanoboxes.

Systematic Comparisons of Formulations of Linear Oligolysine Peptides with siRNA and Plasmid DNA

The effects of lysine peptide lengths on DNA and siRNA packaging and delivery were studied using four linear oligolysine peptides with 8 (K8), 16 (K16), 24 (K24) and 32 (K32) lysines. Oligolysine peptides with 16 lysines or longer were effective for stable monodisperse particle formation and optimal transfection efficiency with plasmid DNA (pDNA), but K8 formulations were less stable under anionic heparin challenge and consequently displayed poor transfection efficiency. However, here we show that the oligolysines were not able to package siRNA to form stable complexes, and consequently, siRNA transfection was unsuccessful. These results indicate that the physical structure and length of cationic peptides and their charge ratios are critical parameters for stable particle formation with pDNA and siRNA and that without packaging, delivery and transfection cannot be achieved.

Conjugates of small targeting molecules to non-viral vectors for the mediation of siRNA

To use siRNA (small interfering RNA) for gene therapy, a gene delivery system is often necessary to overcome several challenging requirements including rapid excretion, low stability in blood serum, non-specific accumulation in tissues, poor cellular uptake and inefficient intracellular release. Active and/or passive targeting should help the delivery system to reach the desired tissue or cell, to be internalized, and to deliver siRNA to the cytoplasm so that siRNA can inhibit protein synthesis. This review covers conjugates of small targeting molecules and non-viral delivery systems for the mediation of siRNA, with a focus on their transfection properties in order to help the development of new and efficient siRNA delivery systems, as the therapeutic solutions of tomorrow.

STATEMENT OF SIGNIFICANCE

The delivery of siRNA into cells or tissues remains to be a challenge for its applications, an alternative strategy for siRNA delivery systems is direct conjugation of non-viral vectors with targeting moieties for cellular delivery. In comparison to macromolecules, small targeting molecules have attracted great attention due to their many potential advantages including significant simplicity and ease of production, good repeatability and biodegradability. This review will focus on the most recent advances in the delivery of siRNA using conjugates of small targeting molecules and non-viral delivery systems. Based the editor's suggestions, we hope the revised manuscript could provide more profound understanding to the conjugates of targeting molecules to vectors for mediation of siRNA.

Delivery of siRNA using ternary complexes containing branched cationic peptides: the role of peptide sequence, branching and targeting

Ternary nanocomplexes, composed of bifunctional cationic peptides, lipids and siRNA, as delivery vehicles for siRNA have been investigated. The study is the first to determine the optimal sequence and architecture of the bifunctional cationic peptide used for siRNA packaging and delivery using lipopolyplexes. Specifically three series of cationic peptides of differing sequence, degrees of branching and cell-targeting sequences were co-formulated with siRNA and vesicles prepared from a 1 : 1 molar ratio of the cationic lipid DOTMA and the helper lipid, DOPE. The level of siRNA knockdown achieved in the human alveolar cell line, A549-luc cells, in both reduced serum and in serum supplemented media was evaluated, and the results correlated to the nanocomplex structure (established using a range of physico-chemical tools, namely small angle neutron scattering, transmission electron microscopy, dynamic light scattering and zeta potential measurement); the conformational properties of each component (circular dichroism); the degree of protection of the siRNA in the lipopolyplex (using gel shift assays) and to the cellular uptake, localisation and toxicity of the nanocomplexes (confocal microscopy). Although the size, charge, structure and stability of the various lipopolyplexes were broadly similar, it was clear that lipopolyplexes formulated from branched peptides containing His-Lys sequences perform best as siRNA delivery agents in serum, with protection of the siRNA in serum balanced against efficient release of the siRNA into the cytoplasm of the cell.

Sequence-defined polymers for the delivery of oligonucleotides

Short synthetic oligonucleotides (ONs) are a group of therapeutic molecules with enormous clinical potential owing to their high specificity and ability to target the expression of virtually any single or group of genes. Clinical translation of ONs is hampered by the inadequate bioavailability in the target cells due to the substantial extracellular and intracellular barriers exposed to these molecules. Different cationic polymers have been successfully deployed for the delivery of ONs. However, heterogeneous nature of these classical polymers is not suitable for clinical applications and hence vectors with completely defined structure are required. In this review, we discuss recent advances with sequence-defined polymers and their application for the delivery of short ONs.

Increased tumor distribution and expression of histidine-rich plasmid polyplexes

Background

Selecting nonviral carriers for in vivo gene delivery is often dependent on determining the optimal carriers from transfection assays in vitro. The rationale behind this in vitro strategy is to cast a net sufficiently wide to identify the few effective carriers of plasmids for in vivo studies. Nevertheless, many effective in vivo carriers may be overlooked by this strategy because of the marked differences between in vitro and in vivo assays.

Methods

After solid-phase synthesis of linear and branched histidine/lysine (HK) peptides, the two peptide carriers were compared for their ability to transfect MDA-MB-435 tumor cells in vitro and then in vivo.

Results

By contrast to their transfection activity in vitro, the linear H2K carrier of plasmids was far more effective in vivo compared to the branch H2K4b. Surprisingly, negatively-charged polyplexes formed by the linear H2K peptide gave higher transfection in vivo than did those with a positive surface charge. To examine the distribution of plasmid expression within the tumor from H2K polyplexes, we found widespread expression by immunohistochemical staining. With a fluorescent tdTomato expressing-plasmid, we confirmed a pervasive distribution and gene expression within the tumor mediated by the H2K polyplex.

Conclusions

Although mechanisms underlying the efficiency of gene expression are probably multifactorial, unpacking of the H2K polyplex within the tumor appears to have a significant role. Further development of these H2K polyplexes represents an attractive approach for plasmid-based therapies of cancer. © 2014 The Authors. The Journal of Gene Medicine published by John Wiley & Sons, Ltd.

HIV-1 drug discovery: targeting folded RNA structures with branched peptides

Human immunodeficiency virus type 1 (HIV-1) is an RNA virus that is prone to high rates of mutation. While the disease is managed with current antiretroviral therapies, drugs with a new mode of action are needed. A strategy towards this goal is aimed at targeting the native three-dimensional fold of conserved RNA structures. This perspective highlights medium-sized peptides and peptidomimetics used to target two conserved RNA structures of HIV-1. In particular, branched peptides have the capacity to bind in a multivalent fashion, utilizing a large surface area to achieve the necessary affinity and selectivity toward the target RNA.

Peptides used in the delivery of small noncoding RNA

RNA interference (RNAi) is an endogenous process in which small noncoding RNAs, including small interfering RNAs (siRNAs) and microRNAs (miRNAs), post-transcriptionally regulate gene expressions. In general, siRNA and miRNA/miRNA mimics are similar in nature and activity except their origin and specificity. Although both siRNAs and miRNAs have been extensively studied as novel therapeutics for a wide range of diseases, the large molecular weight, anionic surface charges, instability in blood circulation, and intracellular trafficking to the RISC after cellular uptake have hindered the translation of these RNAs from bench to clinic. As a result, a great variety of delivery systems have been investigated for safe and effective delivery of small noncoding RNAs. Among these systems, peptides, especially cationic peptides, have emerged as a promising type of carrier due to their inherent ability to condense negatively charged RNAs, ease of synthesis, controllable size, and tunable structure. In this review, we will focus on three major types of cationic peptides, including poly(l-lysine) (PLL), protamine, and cell penetrating peptides (CPP), as well as peptide targeting ligands that have been extensively used in RNA delivery. The delivery strategies, applications, and limitations of these cationic peptides in siRNA/miRNA delivery will be discussed.

In vitro and in vivo therapeutic siRNA delivery induced by a tryptophan-rich endosomolytic peptide

At the forefront of medicine, gene therapy provides an effective way to treat a range of diseases by regulating defective genes at the root of the disease. Short interfering RNAs (siRNAs) hold great promise as therapeutic agents in this domain; however, intracellular delivery remains a major obstacle to clinical applications of therapeutic siRNAs. Here we report a peptide designed to mediate siRNA delivery. This peptide, C6M1, is rationally designed to promote the endosomal escape ability of an existing peptide sequence. Formed C6M1-siRNA nanoscale complexes are able to deliver siRNA into cells and induce specific gene knockdown with low toxicity. The increased membrane disruption ability under acidic conditions of the peptide with tryptophan residue substitution may contribute to the enhanced gene silence efficacy. Intratumoral injection of the complexes results in a marked reduction of tumor growth through downregulation of antiapoptotic Bcl-2 protein in mice. In addition, the C6M1-siRNA complex was proven safe at transfection concentration by cytotoxicity assay. These results demonstrate that the C6M1-siRNA complex is a potent system for efficient gene delivery in vitro and in vivo.

A novel nonviral gene delivery system: multifunctional envelope-type nano device

In this review we introduce a new concept for developing a nonviral gene delivery system which we call "Programmed Packaging." Based on this concept, we succeeded in developing a multifunctional envelope-type nano device (MEND), which exerts high transfection activities equivalent to those of an adenovirus in a dividing cell. The use of MEND has been extended to in vivo applications. PEG/peptide/DOPE ternary conjugate (PPD)-MEND, a new in vivo gene delivery system for the targeting of tumor cells that dissociates surface-modified PEG in tumor tissue by matrix metalloproteinase (MMP) and exerts significant transfection activities, was developed. In parallel with the development of MEND, a quantitative gene delivery system, Confocal Image-assisted 3-dimensionally integrated quantification (CIDIQ), also was developed. This method identified the rate-limiting step of the nonviral gene delivery system by comparing it with adenoviral-mediated gene delivery. The results of this analysis provide a new direction for the development of rational nonviral gene delivery systems.

Peptide-Based Star Polymers as Potential siRNA Carriers

16- and 32-arm star polymers were synthesised using poly(amido amine) (PAMAM) dendrimers as multifunctional initiators for the ring-opening polymerisation (ROP) of ϵ-Z-l-lysine N-carboxyanhydride (Lys NCA) via the core-first approach. The resulting star polymers were subsequently post-functionalised with poly(ethylene glycol) (PEG) via carbodiimide coupling, potentially improving the biodistribution of the stars in vivo. De-protection of the carboxybenzyl (Cbz)-protected star arms yielded water-soluble cationic poly(l-lysine) (PLL) star polymers with hydrodynamic radii ranging from 2.0 to 3.3 nm. Successful complexation of the PLL star polymers with double-stranded oligodeoxynucleotides (ODNs)—a mimic for small interfering RNA (siRNA)—was achieved at a nitrogen-to-phosphate (N/P) ratio of 5. Cell viability studies using HEK293T cells indicated the ‘safe’ concentration for these polymers is within a suitable window for the delivery of siRNA therapeutics.

Polymers for nucleic acid transfer-an overview

For the last five decades cationic polymers have been used for nucleic acids transfection. Our understanding of polymer-nucleic acid interactions and their rational use in delivery has continuously increased. The great improvements in macromolecular chemistry and the recognition of distinct biological extra- and intracellular delivery hurdles triggered several breakthrough developments, including the discovery of natural and synthetic polycations for compaction of nucleic acids into stable nanoparticles termed polyplexes; the incorporation of targeting ligands and surface-shielding of polyplexes to enable receptor-mediated gene delivery into defined target tissues; and strongly improved intracellular transfer efficacy by better endosomal escape of vesicle-trapped polyplexes into the cytosol. These experiences triggered the development of second-generation polymers with more dynamic properties, such as endosomal pH-responsive release mechanisms, or biodegradable units for improved biocompatibility and intracellular release of the nucleic acid pay load. Despite a better biological understanding, significant challenges such as efficient nuclear delivery and persistence of gene expression persist. The therapeutic perspectives widened from pDNA-based gene therapy to application of novel therapeutic nucleic acids including mRNA, siRNA, and microRNA. The finding that different therapeutic pay loads require different tailor-made carriers complicates preclinical developments. Convincing evidence of medical efficacy still remains to be demonstrated. Bioinspired multifunctional polyplexes resembling "synthetic viruses" appear as attractive opportunity, but provide additional challenges: how to identify optimum combinations of functional delivery units, and how to prepare such polyplexes reproducibly in precise form? Design of sequence-defined polymers, screening of combinatorial polymer and polyplex libraries are tools for further chemical evolution of polyplexes.

Nanoparticle-Based Delivery of RNAi Therapeutics: Progress and Challenges

RNA interference (RNAi) is an evolutionarily conserved, endogenous process for post-transcriptional regulation of gene expression. Although RNAi therapeutics have recently progressed through the pipeline toward clinical trials, the application of these as ideal, clinical therapeutics requires the development of safe and effective delivery systems. Inspired by the immense progress with nanotechnology in drug delivery, efforts have been dedicated to the development of nanoparticle-based RNAi delivery systems. For example, a precisely engineered, multifunctional nanocarrier with combined passive and active targeting capabilities may address the delivery challenges for the widespread use of RNAi as a therapy. Therefore, in this review, we introduce the major hurdles in achieving efficient RNAi delivery and discuss the current advances in applying nanotechnology-based delivery systems to overcome the delivery hurdles of RNAi therapeutics. In particular, some representative examples of nanoparticle-based delivery formulations for targeted RNAi therapeutics are highlighted.

A review of polypeptide-based polymersomes

Self-assembled systems from biodegradable amphiphilic polymers at the nanometer scale, such as nanotubes, nanoparticles, polymer micelles, nanogels, and polymersomes, have attracted much attention especially in biomedical fields. Among these nano-aggregates, polymersomes have attracted tremendous interests as versatile carriers due to their colloidal stability, tunable membrane properties and ability of encapsulating or integrating a broad range of drugs and molecules. Biodegradable block polymers, especially aliphatic polyesters such as polylactide, polyglycolide and poly (ε-caprolactone) have been widely used as biomedical materials for a long time to well fit the requirement of biomedical drug carriers. To have a precise control of the aggregation behavior of nano-aggregates, the more ordered polypeptide has been used to self-assemble into the drug carriers. In this review we focus on the study of polymersomes which also named pepsomes formed by polypeptide-based copolymers and attempt to clarify the polypeptide-based polymersomes from following aspects: synthesis and characterization of the polypeptide-based copolymers, preparation, multifunction and application of polypeptide-based polymersomes.