Sequence-defined oligoaminoamides for the delivery of siRNAs

An iteration model for identifying essential proteins by combining comprehensive PPI network with biological information

Background

Essential proteins have great impacts on cell survival and development, and played important roles in disease analysis and new drug design. However, since it is inefficient and costly to identify essential proteins by using biological experiments, then there is an urgent need for automated and accurate detection methods. In recent years, the recognition of essential proteins in protein interaction networks (PPI) has become a research hotspot, and many computational models for predicting essential proteins have been proposed successively.

Results

In order to achieve higher prediction performance, in this paper, a new prediction model called TGSO is proposed. In TGSO, a protein aggregation degree network is constructed first by adopting the node density measurement method for complex networks. And simultaneously, a protein co-expression interactive network is constructed by combining the gene expression information with the network connectivity, and a protein co-localization interaction network is constructed based on the subcellular localization data. And then, through integrating these three kinds of newly constructed networks, a comprehensive protein–protein interaction network will be obtained. Finally, based on the homology information, scores can be calculated out iteratively for different proteins, which can be utilized to estimate the importance of proteins effectively. Moreover, in order to evaluate the identification performance of TGSO, we have compared TGSO with 13 different latest competitive methods based on three kinds of yeast databases. And experimental results show that TGSO can achieve identification accuracies of 94%, 82% and 72% out of the top 1%, 5% and 10% candidate proteins respectively, which are to some degree superior to these state-of-the-art competitive models.

Conclusions

We constructed a comprehensive interactive network based on multi-source data to reduce the noise and errors in the initial PPI, and combined with iterative methods to improve the accuracy of necessary protein prediction, and means that TGSO may be conducive to the future development of essential protein recognition as well.

Development of pH-responsive organic-inorganic hybrid nanocomposites as an effective oral delivery system of protein drugs

This research aimed to develop a pH-responsive organic-inorganic hybrid nanocomposite as an effective oral delivery system for protein drugs. Three different nanocomposites were prepared by using bovine serum albumin (BSA) as a model protein. A nanocomplex of BSA with 3-aminopropyl functionalized magnesium phyllosilicate (AC-BSA) was obtained via the spontaneous co-assembly and then sequentially coated with glycol-chitosan (GAC-BSA) and the pH sensitive polymer, Eudragit®L100-55 (EGAC-BSA). These organic-inorganic hybrid nanocomposites exhibited high entrapment efficiency (86-99%) and their structural characteristics were confirmed by using energy dispersive X-ray spectroscopy, Fourier transform infrared spectroscopy, and circular dichroism analysis, indicating that the secondary structure of BSA was well retained in the nanocomposites. At pH 1.2, AC-BSA achieved rapid drug release of about 80% within 2 h, while GAC-BSA and EGAC-BSA exhibited slow drug release of 30% and 15%, respectively, indicating that the surface-coated nanocomposites were more stable in the gastric condition. Furthermore, the conformational stability of BSA entrapped in EGAC-BSA was well retained in the presence of proteolytic enzymes, suggesting that EGAC-BSA should be effective in protecting the protein against gastrointestinal harsh environment. Compared to free BSA, all of tested nanocomposites demonstrated 2.1-3.8-fold higher cellular uptake in Caco-2 cells. Furthermore, energy-dependent endocytosis and paracellular pathway contributed to the cellular transport of nanoparticles. After oral administration in rats, EGAC-BSA significantly enhanced the intestinal permeation of BSA compared to free BSA. In conclusion, EGAC-BSA appears to be promising as an effective oral delivery system for proteins with enhanced intestinal absorption.

Virus-inspired and mimetic designs in non-viral gene delivery

Virus-inspired mimics for nucleic acid transportation have attracted much attention in the past decade, especially the derivative microenvironment stimuli-responsive designs. In the present mini-review, the smart designs of gene carriers that overcome biological barriers and realize an efficient delivery are categorized with respect to the different "triggers" provided by tumor cells, including pH, redox potentials, ATP, enzymes and reactive oxygen species. Some dual/multi-responsive gene vectors have also been introduced that show a more precise and efficient delivery in the complicated environment of human body. In addition, inspired by the special recognition mechanisms and components of viruses, improvements in the design of carriers relating to targeting/penetration properties, as well as chemical component evolution, are also addressed.

Threatening cancer with nanoparticle aided combination oncotherapy

Employing combination therapy has become obligatory in cancer cases exhibiting high tumor load, chemoresistant tumor population, and advanced disease stages. Realization of this fact has now led many of the combination oncotherapies to become an integral part of anticancer regimens. Combination oncotherapy may encompass a combination of anticancer agents belonging to a similar therapeutic category or that of different therapeutic categories (e.g. chemotherapy + gene therapy). Differences in the physicochemical properties, pharmacokinetics and biodistribution pattern of different payloads are the major constraints that are faced by combination chemotherapy. Concordant efforts in the field of nanotechnology and oncology have emerged with several approaches to solve the major issues encountered by combination therapy. Unique colloidal behaviors of various types of nanoparticles and differential targeting strategies have accorded an unprecedented ability to optimize combination oncotherapeutic delivery. Nanocarrier based delivery of the various types of payloads such as chemotherapeutic agents and other anticancer therapeutics such as small interfering ribonucleic acid (siRNA), chemosensitizers, radiosensitizers, and antiangiogenic agents have been addressed in the present review. Various nano-delivery systems like liposomes, polymeric nanoparticles, polymerosomes, dendrimers, micelles, lipid based nanoparticles, prodrug based nanocarriers, polymer-drug conjugates, polymer-lipid hybrid nanoparticles, carbon nanotubes, nanosponges, supramolecular nanocarriers and inorganic nanoparticles (gold nanoparticles, silver nanoparticles, magnetic nanoparticles and mesoporous silica based nanoparticles) that have been extensively explored for the formulation of multidrug delivery is an imperative part of discussion in the review. The present review features the outweighing benefits of combination therapy over mono-oncotherapy and discusses several existent nanoformulation strategies that facilitate a successful combination oncotherapy. Several obstacles that may impede in transforming nanotechnology-based combination oncotherapy from bench to bedside, and challenges associated therein have also been discussed in the present review.

Combinatorial siRNA Polyplexes for Receptor Targeting

As synthetic small interfering RNA (siRNA) against antitumoral gene targets show promise for cancer treatment, different siRNA delivery systems have sparkled intense investigations. To develop tumor-specific carriers for cytosolic and systemic siRNA delivery, our laboratory has recently generated folate-conjugated targeted combinatorial siRNA polyplexes based on sequence-defined oligomer platform compatible with solid-phase-supported synthesis. These polyplexes presented efficient siRNA-mediated gene silencing in folate receptor-expressing tumors in vitro and in vivo. In this chapter, we provide a brief background on the formulation design and detailed protocols to evaluate polyplex formation, gene silencing efficiency, and receptor-directed cell killing in cancer cells using targeted combinatorial siRNA polyplexes.

Click-Shielded and Targeted Lipopolyplexes

Lipopolyplexes present well-established nucleic acid carriers assembled from sequence-defined cationic lipo-oligomers and DNA or RNA. They can be equipped with additional surface functionality, like shielding and targeting, in a stepwise assembly method using click chemistry. Here, we describe the synthesis of the required compounds, an azide-bearing lipo-oligomer structure and dibenzocyclooctyne (DBCO) click agents as well as the assembly of the compounds with siRNA into a surface-functionalized formulation. Both the lipo-oligomer and the DBCO-equipped shielding and targeting agents are produced by solid-phase synthesis (SPS). This enables for precise variation of all functional units, like variation in the amount of DBCO attachment sites or polyethylene glycol (PEG) length. Special cleavage conditions with only 5% trifluoroacetic acid (TFA) must be applied for the synthesis of the shielding and targeting agents due to acid lability of the DBCO unit. The two-step lipopolyplex assembly technique allows for separate optimization of the core and the shell of the formulation.

Sequence-Defined Cationic Lipo-Oligomers Containing Unsaturated Fatty Acids for Transfection

Sequence-defined cationic lipo-oligomers containing unsaturated fatty acids are potent nucleic acid carriers that are produced by solid-phase supported synthesis. However, the trifluoroacetic acid (TFA)-mediated removal of acid-labile protecting groups and cleavage from the resin can be accompanied by side products caused by an addition of TFA to the double bonds of unsaturated fatty acids. These TFA adducts are converted into hydroxylated derivatives under aqueous conditions. Here we describe an optimized cleavage protocol (precooling cleavage solution to 4 °C, 20 min cleavage at 22 °C), which minimizes TFA adduct formation, retains the unsaturated hydrocarbon chain character, and ensures high yields of the synthesis.