Measuring interference of drug-like molecules with the respiratory chain: toward the early identification of mitochondrial uncouplers in lead finding

Comparative physiological, biochemical and transcriptomic analyses to reveal potential regulatory mechanisms in response to starvation stress in Cipangopaludina chinensis

Cipangopaludina chinensis, as a financially significant species in China, represents a gastropod in nature which frequently encounters starvation stress owing to its limited prey options. However, the underlying response mechanisms to combat starvation have not been investigated in depth. We collected C. chinensis under several times of starvation stress (0, 7, 30, and 60 days) for nutrient, biochemical characteristics and transcriptome analyses. The results showed that prolonged starvation stress (> 30 days) caused obvious fluctuations in the nutrient composition of snails, with dramatic reductions in body weight, survival and digestive enzyme activity (amylase, protease, and lipase), and markedly enhanced the antioxidant enzyme activities of the snails. Comparative transcriptome analyses revealed 3538 differentially expressed genes (DEGs), which were significantly associated with specific starvation stress-responsive pathways, including oxidative phosphorylation and alanine, aspartate, and glutamate metabolism. Then, we identified 40 candidate genes (e.g., HACD2, Cp1, CYP1A2, and GPX1) response to starvation stress through STEM and WGCNA analyses. RT-qPCR verified the accuracy and reliability of the high-throughput sequencing results. This study provides insights into snail overwintering survival and the potential regulatory mechanisms of snail adaptation to starvation stress.

Transcriptomic and proteomic analyses reveal the common and unique pathway(s) underlying different skin colors of leopard coral grouper (Plectropomus leopardus)

To gain a comprehensive and unbiased molecular understanding of the different skin colors of P. leopardus, we used Illumina HiSeq 2500 and TMT (Tandem Mass Tag) to compare transcription and protein levels between red and black skin of P. leopardus. We identified 797 upregulated and 314 downregulated genes (differentially expressed genes; DEGs) in red (RG) compared with black (BG) skin of P. leopardus. We also identified 377 differentially abundant proteins (DAPs), including 314 upregulated and 63 downregulated proteins. These DEGs and DAPs were significantly enriched in melanin synthesis (e.g., pyrimidine metabolism, Phenylalanine, tyrosine, and tryptophan biosynthesis, melanogenesis, phenylalanine metabolism, and tyrosine metabolism), oxidative phosphorylation (e.g., phosphonate and phosphinate metabolism, and oxidative phosphorylation), energy metabolism (e.g., HIF-1, glycolysis/gluconeogenesis, fatty acid biosynthesis, and fatty acid degradation), and signal transduction (e.g., Wnt, calcium, MAPK, and cGMP-PKG signaling pathways), etc. Further analysis of MAPKs showed that the activation levels of its main members JNK1 and ERK1/2 differed significantly between red and black skin colors. After RNAi was used to interfere with ERK1/2, it was found that the local skin of the tail of P. leopardus would turn black. Combined transcriptome and proteome analysis showed that most DEGs-DAPs in red skin were higher than in black skin (58 were upregulated, 1 was downregulated, and 4 were opposite). These DEGs-DAPs showed that the differences between red and black skin tissues of P. leopardus were related primarily to energy metabolism, signal transduction and cytoskeleton. These findings are not only conducive to understand the skin color regulation mechanism of P. leopardus and other coral reef fish, but also provide an important descriptive to the breeding of color strains. SIGNIFICANCE OF THE STUDY: The skin color of P. leopardus gradually darkens or blackens due to environmental factors such as changes in light intensity and human activities, and this directly affects its ornamental and economic value. In this study, RNAseq and TMT were used to conduct comparative quantitative transcriptomics and proteomics and analyze differences between red and black P. leopardus skin. The results showed that energy metabolism, signal transduction and cytoskeleton were the main metabolic pathways causing their skin color differences. These findings contribute to existing data describing fish skin color, and provide information about protein levels, which are of great significance to a deeper understanding of the skin color regulation mechanism in P. leopardus and other coral reef fishes.

A Solid Supported Membrane-Based Technology for Electrophysical Screening of B0AT1-Modulating Compounds

Classical high-throughput screening (HTS) technologies for the analysis of ionic currents across biological membranes can be performed using fluorescence-based, radioactive, and mass spectrometry (MS)-based uptake assays. These assays provide rapid results for pharmacological HTS, but the underlying, indirect analytical character of these assays can be linked to high false-positive hit rates. Thus, orthogonal and secondary assays using more biological target-based technologies are indispensable for further compound validation and optimization. Direct assay technologies for transporter proteins are electrophysiology-based, but are also complex, time-consuming, and not well applicable for automated profiling purposes. In contrast to conventional patch clamp systems, solid supported membrane (SSM)-based electrophysiology is a sensitive, membrane-based method for transporter analysis, and current technical developments target the demand for automated, accelerated, and sensitive assays for transporter-directed compound screening. In this study, the suitability of the SSM-based technique for pharmacological compound identification and optimization was evaluated performing cell-free SSM-based measurements with the electrogenic amino acid transporter B⁰AT1 (SLC6A19). Electrophysiological characterization of leucine-induced currents demonstrated that the observed signals were specific to B⁰AT1. Moreover, B⁰AT1-dependent responses were successfully inhibited using an established in-house tool compound. Evaluation of current stability and data reproducibility verified the robustness and reliability of the applied assay. Active compounds from primary screens of large compound libraries were validated, and false-positive hits were identified. These results clearly demonstrate the suitability of the SSM-based technique as a direct electrophysiological method for rapid and automated identification of small molecules that can inhibit B⁰AT1 activity.

Development and characterization of mitochondrial membrane affinity chromatography columns derived from skeletal muscle and platelets for the study of mitochondrial transmembrane proteins

Mitochondrial membrane fragments from human platelets and monkey skeletal muscles were successfully immobilized onto immobilized artificial membrane chromatographic support for the first time, resulting in mitochondrial membrane affinity chromatography (MMAC) columns. These columns were validated by characterization of translocator protein (TSPO), where multiple concentrations of dipyridamole were run and the binding affinities (K_d) determined. Further, the relative ranking data of TSPO ligands was consistent with previously reported rankings for both, the platelet (MMAC-Platelet) and the skeletal muscle (MMAC-Muscle) column (dipyridamole>PK11195>protoporphyrin IX>rotenone). The functional immobilization of the F-ATPase/ATP synthase was demonstrated on MMAC-Muscle column. Online hydrolysis of ATP to ADP and synthesis of ATP from ADP were both demonstrated on the MMAC-Muscle column. Hydrolysis of ATP to ADP was inhibited by oligomycin A with an IC₅₀ of 40.2±13.5nM (∼60% reduction in ATP hydrolysis, p<0.001), similar to previously reported values. Additionally, the Michaelis-Menten constant (Km) for ADP was found to be 1525±461μM based on the on column dose-dependent increase in ATP production.

Charge translocation by mitochondrial NADH:ubiquinone oxidoreductase (complex I) from Yarrowia lipolytica measured on solid-supported membranes

The charge translocation by purified reconstituted mitochondrial complex I from the obligate aerobic yeast Yarrowia lipolytica was investigated after adsorption of proteoliposomes to solid-supported membranes. In presence of n-decylubiquinone (DBQ), pulses of NADH provided by rapid solution exchange induced charge transfer reflecting steady-state pumping activity of the reconstituted enzyme. The signal amplitude increased with time, indicating 'deactive→active' transition of the Yarrowia complex I. Furthermore, an increase of the membrane-conductivity after addition of 5-(N-ethyl-N-isopropyl)amiloride (EIPA) was detected which questiones the use of EIPA as an inhibitor of the Na⁺/H⁺-antiporter-like subunits of complex I. This investigation shows that electrical measurements on solid-supported membranes are a suitable method to analyze transport events and 'active/deactive' transition of mitochondrial complex I.

Antiinfectives targeting enzymes and the proton motive force

There is a growing need for new antibiotics. Compounds that target the proton motive force (PMF), uncouplers, represent one possible class of compounds that might be developed because they are already used to treat parasitic infections, and there is interest in their use for the treatment of other diseases, such as diabetes. Here, we tested a series of compounds, most with known antiinfective activity, for uncoupler activity. Many cationic amphiphiles tested positive, and some targeted isoprenoid biosynthesis or affected lipid bilayer structure. As an example, we found that clomiphene, a recently discovered undecaprenyl diphosphate synthase inhibitor active against Staphylococcus aureus, is an uncoupler. Using in silico screening, we then found that the anti-glioblastoma multiforme drug lead vacquinol is an inhibitor of Mycobacterium tuberculosis tuberculosinyl adenosine synthase, as well as being an uncoupler. Because vacquinol is also an inhibitor of M. tuberculosis cell growth, we used similarity searches based on the vacquinol structure, finding analogs with potent (∼0.5-2 μg/mL) activity against M. tuberculosis and S. aureus. Our results give a logical explanation of the observation that most new tuberculosis drug leads discovered by phenotypic screens and genome sequencing are highly lipophilic (logP ∼5.7) bases with membrane targets because such species are expected to partition into hydrophobic membranes, inhibiting membrane proteins, in addition to collapsing the PMF. This multiple targeting is expected to be of importance in overcoming the development of drug resistance because targeting membrane physical properties is expected to be less susceptible to the development of resistance.