Efficient prediction of drug-drug interaction using deep learning models

A drug-drug interaction or drug synergy is extensively utilised for cancer treatment. However, prediction of drug-drug interaction is defined as an ill-posed problem, because manual testing is only implementable on small group of drugs. Predicting the drug-drug interaction score has been a popular research topic recently. Recently many machine learning models have proposed in the literature to predict the drug-drug interaction score efficiently. However, these models suffer from the over-fitting issue. Therefore, these models are not so-effective for predicting the drug-drug interaction score. In this work, an integrated convolutional mixture density recurrent neural network is proposed and implemented. The proposed model integrates convolutional neural networks, recurrent neural networks and mixture density networks. Extensive comparative analysis reveals that the proposed model significantly outperforms the competitive models.

Involvement of a Rac1-Dependent Macropinocytosis Pathway in Plasmid DNA Delivery by Electrotransfection

Electrotransfection is a widely used method for delivering genes into cells with electric pulses. Although different hypotheses have been proposed, the mechanism of electrotransfection remains controversial. Previous studies have indicated that uptake and intracellular trafficking of plasmid DNA (pDNA) are mediated by endocytic pathways, but it is still unclear which pathways are directly involved in the delivery. To this end, the present study investigated the dependence of electrotransfection on macropinocytosis. Data from the study demonstrated that electric pulses induced cell membrane ruffling and actin cytoskeleton remodeling. Using fluorescently labeled pDNA and a macropinocytosis marker (i.e., dextran), the study showed that electrotransfected pDNA co-localized with dextran in intracellular vesicles. Furthermore, electrotransfection efficiency could be decreased significantly by reducing temperature or treatment of cells with a pharmacological inhibitor of Rac1 and could be altered by changing Rac1 activity. Taken together, the findings suggested that electrotransfection of pDNA involved Rac1-dependent macropinocytosis.

Endosomolytic Nano-Polyplex Platform Technology for Cytosolic Peptide Delivery To Inhibit Pathological Vasoconstriction

A platform technology has been developed and tested for delivery of intracellular-acting peptides through electrostatically complexed nanoparticles, or nano-polyplexes, formulated from an anionic endosomolytic polymer and cationic therapeutic peptides. This delivery platform has been initially tested and optimized for delivery of two unique vasoactive peptides, a phosphomimetic of heat shock protein 20 and an inhibitor of MAPKAP kinase II, to prevent pathological vasoconstriction (i.e., vasospasm) in human vascular tissue. These peptides inhibit vasoconstriction and promote vasorelaxation by modulating actin dynamics in vascular smooth muscle cells. Formulating these peptides into nano-polyplexes significantly enhances peptide uptake and retention, facilitates cytosolic delivery through a pH-dependent endosomal escape mechanism, and enhances peptide bioactivity in vitro as measured by inhibition of F-actin stress fiber formation. In comparison to treatment with the free peptides, which were endowed with cell-penetrating sequences, the nano-polyplexes significantly increased vasorelaxation, inhibited vasoconstriction, and decreased F-actin formation in the human saphenous vein ex vivo. These results suggest that these formulations have significant potential for treatment of conditions such as cerebral vasospasm following subarachnoid hemorrhage. Furthermore, because many therapeutic peptides include cationic cell-penetrating segments, this simple and modular platform technology may have broad applicability as a cost-effective approach for enhancing the efficacy of cytosolically active peptides.

Observing the translocation of a mitochondria-penetrating peptide with solid-state NMR

A new class of penetrating peptides that can target the mitochondria with high specificity was recently discovered. In this work, we developed a model inner mitochondrial membrane, equipped with a transmembrane gradient, suitable for solid-state NMR experiments. Using solid-state NMR, we observed a mitochondria-penetrating peptide interacting with the model inner mitochondrial membrane to gain insight into the mechanism of translocation. The paramagnetic relaxation effect due to Mn(2+) ions on (13)C magic angle spinning NMR was used to measure the insertion depth of the peptide and its distribution in each monolayer of the membrane. We found that at low peptide concentration the peptide binds to the outer leaflet and at high concentration, it crosses the hydrophobic bilayer core and is distributed in both leaflets. In both concentration regimes, the peptide binds at the C2 position on the lipid acyl chain. The mitochondria-penetrating peptide crossed to the inner leaflet of the model membranes without disrupting the lamellarity. These results provide evidence that supports the electroporation model of translocation. We estimated the energy associated with crossing the inner mitochondrial membrane. We found that the transmembrane potential provides sufficient energy for the peptide to cross the hydrophobic core, which is the most unfavorable step in translocation.

A cell penetrating peptide-integrated and enediyne-energized fusion protein shows potent antitumor activity

Arginine-rich peptides belong to a subclass of cell penetrating peptides that are taken up by living cells and can be detected freely diffusing inside the cytoplasm and nucleoplasm. This phenomenon has been attributed to either an endocytotic mode of uptake and a subsequent release from vesicles or a direct membrane penetration. Lidamycin is an antitumor antibiotic, which consists of an active enediyne chromophore (AE) and a noncovalently bound apoprotein (LDP). In the present study, a fusion protein (Arg)(9)-LDP composed of cell penetrating peptide (Arg)(9) and LDP was prepared by DNA recombination, and the enediyne-energized fusion protein (Arg)(9)-LDP-AE was prepared by molecular reconstitution. The data in fixed cells demonstrated that (Arg)(9)-LDP could rapidly enter cells, and the results based on fluorescence activated cell sorting indicated that the major route for (Arg)(9)-mediated cellular uptake of protein molecules was endocytosis. (Arg)(9)-LDP-AE demonstrated more potent cytotoxicity against different carcinoma cell lines than lidamycin in vitro. In the mouse hepatoma 22 model, (Arg)(9)-LDP-AE (0.3mg/kg) suppressed the tumor growth by 89.2%, whereas lidamycin (0.05 mg/kg) by 74.6%. Furthermore, in the glioma U87 xenograft model in nude mice, (Arg)(9)-LDP-AE at 0.2mg/kg suppressed tumor growth by 88.8%, compared with that of lidamycin by 62.9% at 0.05 mg/kg. No obvious toxic effects were observed in all groups during treatments. The results showed that energized fusion protein (Arg)(9)-LDP-AE was more effective than lidamycin and would be a promising candidate for glioma therapy. In addition, this approach to manufacturing fusion proteins might serve as a technology platform for the development of new cell penetrating peptides-based drugs.

Models of membrane electrostatics

Formulas are derived for the electrostatic potential of a charge in or near a membrane modeled as one or more dielectric slabs lying between two semi-infinite dielectrics. One can use these formulas in Monte Carlo codes to compute the distribution of ions near cell membranes more accurately than by using Poisson-Boltzmann theory or its linearized version. Here I use them to discuss the electric field of a uniformly charged membrane, the image charges of an ion, the distribution of salt ions near a charged membrane, the energy of a zwitterion near a lipid slab, and the effect of including the phosphate head groups as thin layers of high electric permittivity.

Delivery of intracellular-acting biologics in pro-apoptotic therapies

The recent elucidation of molecular regulators of apoptosis and their roles in cellular oncogenesis has motivated the development of biomacromolecular anticancer therapeutics that can activate intracellular apoptotic signaling pathways. Pharmaceutical scientists have employed a variety of classes of biologics toward this goal, including antisense oligodeoxynucleotides, small interfering RNA, proteins, antibodies, and peptides. However, stability in the in vivo environment, tumor-specific biodistribution, cell internalization, and localization to the intracellular microenvironment where the targeted molecule is localized pose significant challenges that limit the ability to directly apply intracellular-acting, pro-apoptotic biologics for therapeutic use. Thus, approaches to improve the pharmaceutical properties of therapeutic biomacromolecules are of great significance and have included chemically modifying the bioactive molecule itself or formulation with auxiliary compounds. Recently, promising advances in delivery of pro-apoptotic biomacromolecular agents have been made using tools such as peptide "stapling", cell penetrating peptides, fusogenic peptides, liposomes, nanoparticles, smart polymers, and synergistic combinations of these components. This review will discuss the molecular mediators of cellular apoptosis, the respective mechanisms by which these mediators are dysregulated in cellular oncogenesis, the history and development of both nucleic-acid and amino-acid based drugs, and techniques to achieve intracellular delivery of these biologics. Finally, recent applications where pro-apoptotic functionality has been achieved through delivery of intracellular-acting biomacromolecular drugs will be highlighted.