Applicability and Limitations of Cell-Penetrating Peptides in Noncovalent Mucosal Drug or Carrier Delivery Systems

Research progress of colon-targeted oral hydrogel system based on natural polysaccharides

The quality of life is significantly impacted by colon-related diseases. There have been a lot of interest in the oral colon-specific drug delivery system (OCDDS) as a potential carrier to decrease systemic side effects and protect drugs from degradation in the upper gastrointestinal tract (GIT). Hydrogels are effective oral colon-targeted drug delivery carriers due to their high biodegradability, substantial drug loading, and great biocompatibility. Natural polysaccharides give the hydrogel system unique structure and function to effectively respond to the complex environment of the GIT and deliver drugs to the colon. In this paper, the physiological factors of colonic drug delivery and the pathological characteristics of common colonic diseases are summarized, and the latest advances in the design, preparation and characterization of natural polysaccharide hydrogels are reviewed, which are expected to provide new references for colon-targeted oral hydrogel systems using natural polysaccharides as raw materials.

SiameseCPP: a sequence-based Siamese network to predict cell-penetrating peptides by contrastive learning

BACKGROUND

Cell-penetrating peptides (CPPs) have received considerable attention as a means of transporting pharmacologically active molecules into living cells without damaging the cell membrane, and thus hold great promise as future therapeutics. Recently, several machine learning-based algorithms have been proposed for predicting CPPs. However, most existing predictive methods do not consider the agreement (disagreement) between similar (dissimilar) CPPs and depend heavily on expert knowledge-based handcrafted features.

RESULTS

In this study, we present SiameseCPP, a novel deep learning framework for automated CPPs prediction. SiameseCPP learns discriminative representations of CPPs based on a well-pretrained model and a Siamese neural network consisting of a transformer and gated recurrent units. Contrastive learning is used for the first time to build a CPP predictive model. Comprehensive experiments demonstrate that our proposed SiameseCPP is superior to existing baseline models for predicting CPPs. Moreover, SiameseCPP also achieves good performance on other functional peptide datasets, exhibiting satisfactory generalization ability.

DeepCPPred: A Deep Learning Framework for the Discrimination of Cell-Penetrating Peptides and Their Uptake Efficiencies

Cell-penetrating peptides (CPPs) are special peptides capable of carrying a variety of bioactive molecules, such as genetic materials, short interfering RNAs and nanoparticles, into cells. Recently, research on CPP has gained substantial interest from researchers, and the biological mechanisms of CPPS have been assessed in the context of safe drug delivery agents and therapeutic applications. Correct identification and synthesis of CPPs using traditional biochemical methods is an extremely slow, expensive and laborious task particularly due to the large volume of unannotated peptide sequences accumulating in the World Bank repository. Hence, a powerful bioinformatics predictor that rapidly identifies CPPs with a high recognition rate is urgently needed. To date, numerous computational methods have been developed for CPP prediction. However, the available machine-learning (ML) tools are unable to distinguish both the CPPs and their uptake efficiencies. This study aimed to develop a two-layer deep learning framework named DeepCPPred to identify both CPPs in the first phase and peptide uptake efficiency in the second phase. The DeepCPPred predictor first uses four types of descriptors that cover evolutionary, energy estimation, reduced sequence and amino-acid contact information. Then, the extracted features are optimized through the elastic net algorithm and fed into a cascade deep forest algorithm to build the final CPP model. The proposed method achieved 99.45 percent overall accuracy with the CPP924 benchmark dataset in the first layer and 95.43 percent accuracy in the second layer with the CPPSite3 dataset using a 5-fold cross-validation test. Thus, our proposed bioinformatics tool surpassed all the existing state-of-the-art sequence-based CPP approaches.

Genome editing via non-viral delivery platforms: current progress in personalized cancer therapy

Cancer is a severe disease that substantially jeopardizes global health. Although considerable efforts have been made to discover effective anti-cancer therapeutics, the cancer incidence and mortality are still growing. The personalized anti-cancer therapies present themselves as a promising solution for the dilemma because they could precisely destroy or fix the cancer targets based on the comprehensive genomic analyses. In addition, genome editing is an ideal way to implement personalized anti-cancer therapy because it allows the direct modification of pro-tumor genes as well as the generation of personalized anti-tumor immune cells. Furthermore, non-viral delivery system could effectively transport genome editing tools (GETs) into the cell nucleus with an appreciable safety profile. In this manuscript, the important attributes and recent progress of GETs will be discussed. Besides, the laboratory and clinical investigations that seek for the possibility of combining non-viral delivery systems with GETs for the treatment of cancer will be assessed in the scope of personalized therapy.

Challenge to overcome current limitations of cell-penetrating peptides

The penetration of biological membranes is a prime obstacle for the delivery of pharmaceutical drugs. Cell-penetrating peptide (CPP) is an efficient vehicle that can deliver various cargos across the biological membranes. Since the discovery, CPPs have been rigorously studied to unveil the underlying penetrating mechanism as well as to exploit CPPs for various biomedical applications. This review will focus on the various strategies to overcome current limitations regarding stability, selectivity, and efficacy of CPPs.

Oral mucus-penetrating PEGylated liposomes to improve drug absorption: Differences in the interaction mechanisms of a mucoadhesive liposome

We investigated the feasibility of densely polyethylene glycol (PEG2000)-modified liposomes as mucus-penetrating particles (MPPs) for oral delivery of systemically absorbed peptides. The oral absorption of MPPs and mucoadhesive liposomes modified with glycol chitosan (GCS) was compared. In an in vitro artificial mucus model, the densely PEGylated liposomes showed mucus permeability. Intracellular uptake of liposomes was evaluated in a Caco-2 and mucus-secreting Caco-2/HT29 co-culture. Intracellular uptake of MPPs was unaffected by mucus in the co-culture system, whereas the cellular uptake of GCS-liposomes was lower with a mucus layer than in Caco-2 alone. Rat in vivo oral absorption of liposomes was evaluated by using fluorescein isothiocyanate dextran (FD) as a model peptide drug. Oral absorption was higher for densely PEGylated than for unmodified liposomes and was PEG-concentration dependent, but excessive PEGylation decreased FD blood concentration. PEGylated liposomes incorporating spermine (SPM) as an absorption enhancer were then designed and showed the highest in vivo absorption of FD of all tested formulations. The pharmacological effects of the oral liposomes were evaluated by using elcatonin and did not correlate with FD oral absorption. The non-PEGylated SPM liposomes showed the highest pharmacological effect, suggesting the need for drug-specific optimization of liposomal components and surface modifiers.

StackCPPred: a stacking and pairwise energy content-based prediction of cell-penetrating peptides and their uptake efficiency

Motivation

Cell-penetrating peptides (CPPs) are a vehicle for transporting into living cells pharmacologically active molecules, such as short interfering RNAs, nanoparticles, plasmid DNAs and small peptides, thus offering great potential as future therapeutics. Existing experimental techniques for identifying CPPs are time-consuming and expensive. Thus, the prediction of CPPs from peptide sequences by using computational methods can be useful to annotate and guide the experimental process quickly. Many machine learning-based methods have recently emerged for identifying CPPs. Although considerable progress has been made, existing methods still have low feature representation capabilities, thereby limiting further performance improvements.

Results

We propose a method called StackCPPred, which proposes three feature methods on the basis of the pairwise energy content of the residue as follows: RECM-composition, PseRECM and RECM–DWT. These features are used to train stacking-based machine learning methods to effectively predict CPPs. On the basis of the CPP924 and CPPsite3 datasets with jackknife validation, StackDPPred achieved 94.5% and 78.3% accuracy, which was 2.9% and 5.8% higher than the state-of-the-art CPP predictors, respectively. StackCPPred can be a powerful tool for predicting CPPs and their uptake efficiency, facilitating hypothesis-driven experimental design and accelerating their applications in clinical therapy.

Availability and implementation

Source code and data can be downloaded from https://github.com/Excelsior511/StackCPPred.

Supplementary information

Supplementary data are available at Bioinformatics online.

α-Helical cell-penetrating peptide-mediated nasal delivery of resveratrol for inhibition of epithelial-to-mesenchymal transition

In the present study, we examined the potential of cell-penetrating peptide (CPP)-based intranasal drug delivery for the treatment of localized nasal diseases. Many charged or non-hydrophobic drugs have difficulty penetrating into the nasal epithelium due to intrinsic membrane impermeability and rapid mucociliary clearance in the nasal cavity. To treat chronic rhinosinusitis with nasal polyps (CRSwNP), one of the most common localized nasal diseases, we conjugated resveratrol (RSV) to an amphiphilic α-helical leucine (L)- and lysine (K)-rich CPP (LK) and intranasally delivered it to the interior of nasal epithelial cells for inhibiting epithelial-to-mesenchymal transition (EMT) caused by hypoxia-inducible factor 1α. The RSV-LK conjugate could penetrate into the nasal epithelium and efficiently inhibit EMT, nasal polyp formation, epithelial disruption, and related inflammation in an eosinophilic CRSwNP mouse model, at 10-fold lower doses and with 3-fold less frequent administration than free RSV. Due to the rapid penetration into the nasal epithelium and the therapeutic effect of the RSV-LK conjugate at much lower doses than free RSV, this CPP-based delivery system, with the ability to overcome the tight nasal epithelial barrier, may provide a new strategy for the treatment of localized nasal diseases without the systemic side effects of cargo drugs.

Syndiotactic peptides for targeted delivery

Lack of cell-type specificity and proteolytic susceptibility have long been the major bottlenecks for the development of peptide-based biomaterials for targeted drug delivery. Though a poly-l backbone provides the adaptability to re-conform the peptide structure to bind to a receptor, it also makes the peptide more susceptible to proteolytic cleavage. We have attempted to address this issue by designing a set of syndiotactic peptides de novo, with alternating l- and d-amino acids in succession. The designed peptides have higher rates of cellular uptake than the Tat (48-60) peptide in breast and cervical cancer cells. The uptake is independent of concentration, temperature and endocytosis (clathrin mediated). Importantly, the peptides are stable in both human plasma and bovine serum. The peptide-drug conjugates are much less toxic to the non-cancerous cells than cancer cells. The designed peptides are a step forward towards the development of targeted drug delivery vectors on peptide templates. STATEMENT OF SIGNIFICANCE: Present options in chemotherapy have multiple side effects arising from the lack of cell-type specificity, which makes them synonymous with "a Pyrrhic victory". Proteolytic susceptibility and non-specificity towards cancer cells has stunted the development of peptide-based biomaterials for targeted drug delivery. We have designed a set of peptides, addressing the above-mentioned roadblocks at an in vitro level. The peptides were designed on the template of a naturally existing peptide antibiotic from Bacillus brevis. The designed peptides have higher rates of cellular transduction than the model peptide (Tat), and is majorly membrane based. The peptides are stable in serum and selective towards cancer cells. Observations presented in this work can potentially take the discipline of de novo design of biomaterial conjugates forward.

Improvements in chemical carriers of proteins and peptides

The successful intracellular delivery of biologically active proteins and peptides plays an important role for therapeutic applications. Indeed, protein/peptide delivery could overcome some problems of gene therapy, for example, controlling the expression levels and the integration of transgene into the host cell genome. Thus, protein/peptide drug delivery showed a promising and safe approach for treatment of cancer and infectious diseases. Due to the unique physical and chemical properties of proteins, their production (e.g., isolation, purification & formulation) and delivery represented significant challenges in pharmaceutical studies. Modification in the structural moieties of these protein/peptide drugs could improve their solubility, stability, crystallinity, lipophilicity, enzymatic susceptibility and targetability, and subsequently, therapies and cures against various diseases. Using the structural modification of protein/peptide, their delivery provided overall higher success rates including high specificity, high activity, bioreactivity and safety. Recently, biotechnological and pharmaceutical companies have tried to find novel techniques for the modifications and improve delivery systems/carriers. However, each carrier has its own benefits and drawbacks, and an appropriate carrier is often established by the physicochemical properties of protein or peptide, the ideal route of injection, and clinical characteristics of therapy. In this review, an attempt was made to give an overview on the chemical carriers for proteins and peptides as well as the recent advances in this field.

Preparation and Characterization of Functionalized Graphene Oxide Carrier for siRNA Delivery

A successful siRNA delivery system is dependent on the development of a good siRNA carrier. Graphene oxide (GO) has gained great attention as a promising nanocarrier in recent years. It has been reported that GO could be used to deliver a series of drugs including synthetic compounds, proteins, antibodies, and genes. Our previous research indicated that functionalized GO could deliver siRNA into tumor cells and induce a gene silencing effect, to follow up the research, in this research, GO-R8/cRGDfV(GRcR) was designed and prepared for VEGF-siRNA delivery as a novel carrier. The Zeta potential and particle size of the new designed GRcR carrier was measured at (29.46 ± 5.32) mV and (135.7 ± 3.3) nm respectively, and after transfection, the VEGF mRNA level and protein expression level were down-regulated by 48.22% (p < 0.01) and 38.3% (p < 0.01) in HeLa cells, respectively. The fluorescent images of the treated BALB/c nude mice revealed that GRcR/VEGF-siRNA could conduct targeted delivery of VEGF-siRNA into tumor tissues and showed a gene silencing effect as well as a tumor growth inhibitory effect (p < 0.01) in vivo. Further studies showed that GRcR/VEGF-siRNA could effectively inhibit angiogenesis by suppressing VEGF expression. Histology and immunohistochemistry studies demonstrated that GRcR/VEGF-siRNA could inhibit tumor tissue growth effectively and have anti-angiogenesis activity, which was the result of VEGF protein downregulation. Both in vitro and in vivo results demonstrated that GRcR/VEGF-siRNA could be used as an ideal nonviral tumor-targeting vector for VEGF-siRNA delivery in gene therapy.

CPP-Ts: a new intracellular calcium channel modulator and a promising tool for drug delivery in cancer cells

Scorpion sting envenoming impacts millions of people worldwide, with cardiac effects being one of the main causes of death on victims. Here we describe the first Ca²⁺ channel toxin present in Tityus serrulatus (Ts) venom, a cell penetrating peptide (CPP) named CPP-Ts. We show that CPP-Ts increases intracellular Ca²⁺ release through the activation of nuclear InsP3R of cardiomyocytes, thereby causing an increase in the contraction frequency of these cells. Besides proposing a novel subfamily of Ca²⁺ active toxins, we investigated its potential use as a drug delivery system targeting cancer cell nucleus using CPP-Ts’s nuclear-targeting property. To this end, we prepared a synthetic CPP-Ts sub peptide^14–39 lacking pharmacological activity which was directed to the nucleus of specific cancer cell lines. This research identifies a novel subfamily of Ca²⁺ active toxins and provides new insights into biotechnological applications of animal venoms.

Glioma targeting peptide in combination with the P53 C terminus inhibits glioma cell proliferation in vitro

Glioma is a prevalent malignant primary brain tumor in adults, the treatment for which remains a challenge due to its high infiltration and recurrence. Hence, treatments that lead to the suppression of glioma cell migration and invasion may be used in addition to surgery to increase the therapeutic outcome. In this study, we aimed to construct a multifunctional protein that would exert an effect on glioma cell proliferation and migration. The protein is named GL1-P53C-11R and it consists of the glioma-targeting peptide GL1 (G), the P53 C terminus (Pc) and the cell-penetrating peptide arginine (R). GL1-P53C-R was expressed with the fusion protein ZZ and immunofluorescence analysis showed effective delivery of the fused ZZ-GL1-P53C-R protein represented as ZZ-GPcR. The ZZ-GPcR exhibited an inhibitory effect on the proliferation, migration and invasion of U87ΔEGFR cells. Western blotting results indicated that it caused significant changes in the expression levels of cell cycle and apoptotic proteins. Flow cytometric analysis showed increase apoptosis. Our findings suggest that the P53C in the fusion protein ZZ-GPcR can enter into glioma cells to exert its inhibitory effect.

A novel nanoemulsion-based method to produce ultrasmall, water-dispersible nanoparticles from chitosan, surface modified with cell-penetrating peptide for oral delivery of proteins and peptides

A simple and reproducible water-in-oil (W/O) nanoemulsion technique for making ultrasmall (<15 nm), monodispersed and water-dispersible nanoparticles (NPs) from chitosan (CS) is reported. The nano-sized (50 nm) water pools of the W/O nanoemulsion serve as “nano-containers and nano-reactors”. The entrapped polymer chains of CS inside these “nano-reactors” are covalently cross-linked with the chains of polyethylene glycol (PEG), leading to rigidification and formation of NPs. These NPs possess excessive swelling properties in aqueous medium and preserve integrity in all pH ranges due to chemical cross-linking with PEG. A potent and newly developed cell-penetrating peptide (CPP) is further chemically conjugated to the surface of the NPs, leading to development of a novel peptide-conjugated derivative of CS with profound tight-junction opening properties. The CPP-conjugated NPs can easily be loaded with almost all kinds of proteins, peptides and nucleotides for oral delivery applications. Feasibility of this nanoparticulate system for oral delivery of a model peptide (insulin) is investigated in Caco-2 cell line. The cell culture results for translocation of insulin across the cell monolayer are very promising (15%–19% increase), and animal studies are actively under progress and will be published separately.

Use of a non-covalent cell-penetrating peptide strategy to enhance the nasal delivery of interferon beta and its PEGylated form

The conjugation of therapeutic proteins to polyethylene glycol (PEG) is known as PEGylation. It improves their retention in the body and reduces the frequency of injections. Development of noninvasive delivery systems for biopharmaceuticals can improve the patients' quality of life. The present study aimed to evaluate the cell-penetrating peptides (CPPs), which act as bioenhancers, for the nasal delivery of protein drug interferon beta (IFN-β) and its PEGylated form (PEG-IFN-β). The ability of CPPs to enhance the nasal mucosal absorption of unmodified IFN-β was assessed in rats. It was shown that only d-amino acid forms of amphipathic CPPs, penetratin and PenetraMax significantly enhanced the nasal absorption of IFN-β. Especially, D-penetratin (up to 2mM) enhanced the absorption of INF-β in a dose-dependent manner. The maximum absolute bioavailability reached 8.26% following in situ nasal coadministration of IFN-β with d-penetratin (2mM). Furthermore, it was found that the coadministration of d-penetratin also facilitated the nasal absorption of PEG-IFN-β, which remained in the circulation for more than 6h. Moreover, the toxicity assessments showed no damage to the epithelial membranes after nasal administration of CPPs including penetratin and PenetraMax. Altogether, this study provides the first evidence that the noncovalent coadministration of PEGylated proteins with CPPs could be a potent strategy for the noninvasive and sustained nasal delivery of therapeutic proteins.