Biological effects of Tat cell-penetrating peptide: a multifunctional Trojan horse?

Transduction of jellyfish superoxide dismutase mediated by TAT peptide ameliorates H2O2-induced oxidative stress in HaCaT cells

Superoxide dismutase (SOD) plays important roles in the balance of oxidation and antioxidation in body mostly by scavenging superoxide anion free radicals (O2.-). Previously, we reported a novel Cu/Zn SOD from jellyfish Cyanea capillata, named CcSOD1, which exhibited excellent SOD activity and high stability. TAT peptide is a common type of cell penetrating peptides (CPPs) that efficiently deliver extracellular biomacromolecules into cytoplasm. In this study, we constructed a recombinant expression vector that combined the coding sequences of TAT peptide and CcSOD1, and then obtained sufficient and high-purity TAT-CcSOD1 fusion protein. Compared with some reported SODs/CPP-SODs, TAT-CcSOD1 possessed stronger tolerance to heat and acid-base environment. TAT-CcSOD1 efficiently penetrated cell membrane and significantly enhanced the O2.- scavenging ability in cells, and attenuated H2O2-induced cytotoxicity and NO generation in HaCaT cells. This study serves as a critical step forward for the application of TAT-CcSOD1 as a potential protective/therapeutic agent against oxidative stress-related conditions in the future.

The role of liquid-liquid phase separation in the disease pathogenesis and drug development

Misfolding and aggregation of specific proteins are associated with liquid-liquid phase separation (LLPS), and these protein aggregates can interfere with normal cellular functions and even lead to cell death, possibly affecting gene expression regulation and cell proliferation. Therefore, understanding the role of LLPS in disease may help to identify new mechanisms or therapeutic targets and provide new strategies for disease treatment. There are several ways to disrupt LLPS, including screening small molecules or small molecule drugs to target the upstream signaling pathways that regulate the LLPS process, selectively dissolve and destroy RNA droplets or protein aggregates, regulate the conformation of mutant protein, activate the protein degradation pathway to remove harmful protein aggregates. Furthermore, harnessing the mechanism of LLPS can improve drug development, including preparing different kinds of drug delivery carriers (microneedles, nanodrugs, imprints), regulating drug internalization and penetration behaviors, screening more drugs to overcome drug resistance and enhance receptor signaling. This review initially explores the correlation between aberrant LLPS and disease, highlighting the pivotal role of LLPS in preparing drug development. Ultimately, a comprehensive investigation into drug-mediated regulation of LLPS processes holds significant scientific promise for disease management.

Conjugates of adenosine mimetics and arginine-rich peptides serve as inhibitors and fluorescent probes but not as long-lifetime photoluminescent probes for protein arginine methyltransferases

The conjugates of an adenosine mimetic and oligo-l-arginine or oligo-d-arginine (ARCs) were initially designed in our research group as inhibitors and photoluminescent probes targeting basophilic protein kinases. Here, we explored a panel of ARCs and their fluorescent derivatives in biochemical assays with members of the protein arginine methyltransferase (PRMT) family, focusing specifically on PRMT1. In the binding/displacement assay with detection of fluorescence anisotropy, we found that ARCs and arginine-rich peptides could serve as high-affinity ligands for PRMT1, whereas the equilibrium dissociation constant values depended dramatically on the number of arginine residues within the compounds. The fluorescently labeled probe ARC-1081 was displaced from its complex with PRMT1 by both S-adenosyl-l-methionine (SAM) and S-adenosyl-l-homocysteine (SAH), indicating binding of the adenosine mimetic of ARCs to the SAM/SAH-binding site within PRMT1. The ARCs that had previously shown microsecond-lifetime photoluminescence in complex with protein kinases did not feature such property in complex with PRMT1, demonstrating the selectivity of the time-resolved readout format. When tested against a panel of PRMT family members in single-dose inhibition experiments, a micromolar concentration of ARC-902 was required for the inhibition of PRMT1 and PRMT7. Overall, our results suggest that the compounds containing multiple arginine residues (including the well-known cell-penetrating peptides) are likely to inhibit PRMT and thus interfere with the epigenetic modification status in complex biological systems, which should be taken into consideration during interpretation of the experimental data.

Predicting cell-penetrating peptides using machine learning algorithms and navigating in their chemical space

Cell-penetrating peptides (CPPs) are naturally able to cross the lipid bilayer membrane that protects cells. These peptides share common structural and physicochemical properties and show different pharmaceutical applications, among which drug delivery is the most important. Due to their ability to cross the membranes by pulling high-molecular-weight polar molecules, they are termed Trojan horses. In this study, we proposed a machine learning (ML)-based framework named BChemRF-CPPred (beyond chemical rules-based framework for CPP prediction) that uses an artificial neural network, a support vector machine, and a Gaussian process classifier to differentiate CPPs from non-CPPs, using structure- and sequence-based descriptors extracted from PDB and FASTA formats. The performance of our algorithm was evaluated by tenfold cross-validation and compared with those of previously reported prediction tools using an independent dataset. The BChemRF-CPPred satisfactorily identified CPP-like structures using natural and synthetic modified peptide libraries and also obtained better performance than those of previously reported ML-based algorithms, reaching the independent test accuracy of 90.66% (AUC = 0.9365) for PDB, and an accuracy of 86.5% (AUC = 0.9216) for FASTA input. Moreover, our analyses of the CPP chemical space demonstrated that these peptides break some molecular rules related to the prediction of permeability of therapeutic molecules in cell membranes. This is the first comprehensive analysis to predict synthetic and natural CPP structures and to evaluate their chemical space using an ML-based framework. Our algorithm is freely available for academic use at http://comptools.linc.ufpa.br/BChemRF-CPPred .

A high-affinity, bivalent PDZ domain inhibitor complexes PICK1 to alleviate neuropathic pain

Maladaptive plasticity involving increased expression of AMPA-type glutamate receptors is involved in several pathologies, including neuropathic pain, but direct inhibition of AMPARs is associated with side effects. As an alternative, we developed a cell-permeable, high-affinity (~2 nM) peptide inhibitor, Tat-P₄ -(C5)₂ , of the PDZ domain protein PICK1 to interfere with increased AMPAR expression. The affinity is obtained partly from the Tat peptide and partly from the bivalency of the PDZ motif, engaging PDZ domains from two separate PICK1 dimers to form a tetrameric complex. Bivalent Tat-P₄ -(C5)₂ disrupts PICK1 interaction with membrane proteins on supported cell membrane sheets and reduce the interaction of AMPARs with PICK1 and AMPA-receptor surface expression in vivo. Moreover, Tat-P₄ -(C5)₂ administration reduces spinal cord transmission and alleviates mechanical hyperalgesia in the spared nerve injury model of neuropathic pain. Taken together, our data reveal Tat-P₄ -(C5)₂ as a novel promising lead for neuropathic pain treatment and expand the therapeutic potential of bivalent inhibitors to non-tandem protein-protein interaction domains.

Fluorescent and Photosensitizing Conjugates of Cell-Penetrating Peptide TAT(47-57): Design, Microwave-Assisted Synthesis at 60 °C, and Properties

Conjugates based on cell-penetrating peptides (CPPs) are scientifically relevant owing to their structural complexity; their ability to enter cells and deliver drugs, labels, antioxidants, bioactive compounds, or DNA fragments; and, consequently, their potential for application in research and biomedicine. In this study, carboxyamidated fluorescently labeled conjugates FAM-GG-TAT(47-57)-NH2 and FAM-PEG6-TAT(47-57)-NH2 and photosensitizer-labeled conjugate Chk-PEG6-TAT(47-57)-NH2 [where TAT(47-57) is the CPP, 5(6)-carboxyfluorescein is the (FAM) fluorophore, chlorin k (Chk) is the photosensitizer, and the dipeptide glycyl-glycine (GG) or hexaethylene glycol (PEG6) is the spacer] were originally designed, prepared, and fully characterized. Practically, all chemical reactions of the synthetic steps (peptide synthesis, spacer incorporation, and conjugation) were microwave-assisted at 60 °C using optimized protocols to give satisfying yields and high-quality products. Detailed analyses of the conjugates using spectrofluorimetry and singlet oxygen detection showed that they display photophysical properties typical of FAM or Chk. Anticandidal activity assays showed that not only this basic property of TAT(47-57) was preserved in the conjugates but also that the minimal inhibitory concentration was slightly reduced for cells incubated with PS-bearing conjugate Chk-PEG6-TAT(47-57)-NH2. Overall, these results indicated that the synthetic approach on-resin assisted by microwaves at 60 °C is simple, straightforward, selective, metal-free, sufficiently fast, cleaner, and more cost-effective than those previously used for preparing this type of macromolecule. Furthermore, such new data show that microwaves at 60 °C and/or conjugation did not harm the integrity of the conjugates' constituents. Therefore, FAM-GG-TAT(47-57)-NH2, FAM-PEG6-TAT(47-57)-NH2, and Chk-PEG6-TAT(47-57)-NH2 have high potential for practical applications in biochemistry, biophysics, and therapeutics.

Nanosized, peptide-based multicomponent DNA delivery systems: optimization of endosome escape activity

Aim: Endosome escape is essential for developing effective nonviral gene delivery systems. Herein, three endosome-disrupting peptides (HA2(1–20), GALA and KALA) were incorporated into a multicomponent oligonucleotide delivery system to identify which peptide imparted the most favorable endosome escape and toxicity profile. Materials & methods: Copper (I)-catalyzed azide-alkyne cycloaddition was used to construct multicomponent delivery vectors. The systems were evaluated for size, toxicity, cellular uptake and endosome escape activity. Results: Each system condensed plasmid DNA to form nanosized particles. The highest cellular uptake and endosome escape were associated with GALA and KALA containing systems, with KALA incorporation correlating with greater toxicity. Conclusion: GALA was selected as the most promising endosome-disrupting peptide for incorporation into the nanosized oligonucleotide delivery system.

δV1-1 Reduces Pulmonary Ischemia Reperfusion-Induced Lung Injury by Inhibiting Necrosis and Mitochondrial Localization of PKCδ and p53

Ischemia-reperfusion (IR)-induced lung injury is one of the major contributing factors of morbidity and mortality after lung transplantation. To determine the IR-induced molecular changes in lung epithelial cells, we developed a cell-culture model that simulates lung preservation and transplantation. Six hours of cold ischemic time (CIT) and reperfusion elicited production of multiple inflammatory cytokines and chemokines and increased expression of endoplasmic reticulum (ER) proteins. Prolonged hypothermic condition (18 h CIT) reduced ER stress protein levels, and induced apoptosis and necrosis (via mechanisms related to mitochondrial permeability transition pore opening). Protein kinase C (PKCδ) was activated during CIT, and its downregulation via small interference (si) (in siRNA) RNA reduced IR-induced cytokine production and apoptotic cell death. δV1-1, a PKCδ peptide inhibitor, reduced translocation of PKCδ and p53 to the mitochondria after 18 h CIT, rescued ER stress protein expression, and converted the major mode of cell death from necrosis to apoptosis. Administration of δV1-1 effectively reduced lung transplantation and IR-induced pulmonary injury in rats. Therefore, inhibition of PKCδ by δV1-1 could be an effective strategy to ameliorate IR-induced lung injury by inhibiting the signaling pathways leading to necrosis.

Effective delivery of a rationally designed intracellular peptide drug with gold nanoparticle-peptide hybrids

A novel gold nanoparticle-peptide hybrid strategy was developed to intracellularly deliver a potent PKCδ inhibitor peptide for the treatment of acute lung injury. The gold nanoparticle-peptide hybrids showed good stability with high uptake, and demonstrated in vitro and in vivo efficacy. Our formulation strategy shows great promise in intracellular delivery of peptides.