Measurement of electron transfer through cytochrome P450 protein on nanopillars and the effect of bound substrates

Affinity Chromatographic Method for Determining Drug-Protein Interaction with Enhanced Speed Than Typical Frontal Analysis

Revealing drug-protein interaction is highly important to select a drug candidate with improved drug-like properties in the early stages of drug discovery. This highlights the urgent need to develop assays that enable the analysis of drug-protein interaction with high speed. Herein, this purpose was realized by the development of an affinity chromatographic method with a two-fold higher speed than typical assays like frontal analysis and zonal elution. The method involved synthesis of a stationary phase by immobilizing poly(ADP-ribose) polymerase-1 (PARP1) onto macroporous silica gel through a one-step bioorthogonal reaction, characterization of mutual displacement interaction of two canonical drugs to the immobilized PARP1, determination of the interaction between three (iniparib, rucaparib, and olaparib) drugs and the protein, and validation of these parameters by typical frontal analysis. The numbers of binding sites on the column were (2.85 ± 0.05) × 10-7, (1.89 ± 0.71) × 10-6, and (1.49 ± 0.06) × 10-7 M for iniparib, rucaparib, and olaparib, respectively. On these sites, the association constants of the three drugs to the protein were (9.85 ± 0.56) × 104, (2.85 ± 0.34) × 104, and (1.07 ± 0.35) × 105 M-1. The determined parameters presented a good agreement with the calculation by typical frontal analyses, which indicated that the current continuous competitive frontal analysis method was reliable for determining drug-protein interaction. Application of the methods was achieved by screening tubeimosides I and II as the bioactive compounds against breast cancer in Bolbostemma paniculatum. Their mechanism may be the interference of DNA repair via down-regulating PARP1 and meiotic recombination 11 expressions, thus leading to oncogene mutations and death of cancer cells. The method was high speed since it allowed simultaneous determination of binding parameters between two drugs and a protein with a smaller number of experiments to be performed. Such a feature made the method an attractive alternative for high-speed analysis of drug-protein interaction or the other bindings in a binary system.

Advanced Understanding of the Electron Transfer Pathway of Cytochrome P450s

Cytochrome P450s are heme-thiolate enzymes that participate in carbon source assimilation, natural compound biosynthesis and xenobiotic metabolism in all kingdoms of life. P450s can catalyze various reactions by using a wide range of organic compounds, thus exhibiting great potential in biotechnological applications. The catalytic reactions of P450s are driven by electron equivalents that are sourced from pyridine nucleotides and delivered by cognate or matching redox partners (RPs). The electron transfer (ET) route from RPs to P450s involves one or more redox center-containing domains. As the rate of ET is one of the main determinants of P450 efficacy, an in-depth understanding of the P450 ET pathway should increase our knowledge of these important enzymes and benefit their further applications. Here, the various P450 RP systems along with current understanding of their ET routes will be reviewed. Notably, state-of-the-art structural studies of the two main types of self-sufficient P450 will also be summarized.

Analysis of the Molecular Interactions between Cytochromes P450 3A4 and 1A2 and Aflatoxins: A Docking Study

Mycotoxins known as aflatoxins (AF) are produced as a secondary metabolite by some species of Aspergillus fungi. They are considered carcinogenic, hepatotoxic, teratogenic, and mutagenic. In this study, the molecular structure, chemical reactivity, and charge transfer values of AFB1, B2, G1, and G2 were analyzed using density functional theory. Different methodologies—B3LYP/6-311G(d,p) and M06-2X/6-311G(d,p)—were applied for geometrical calculations. Chemical reactivity parameters were used in the calculation of charge transfer values during the interaction between protein and ligand. The binding energy, the electrostatic interactions, and the amino acids of the active site were determined by molecular docking analysis between AF and cytochromes P450 (3A4 and 1A2), employing different PDB files (CYP3A4:1TQN, 2V0M, 4NY4 and 1W0E, and CYP1A2:2HI4). Molecular docking analysis indicated that the central rings of the AF are involved in the interaction with the HEM group of the active site. The differences in the molecular structure of the AF affect their position regarding the HEM group. The resulting configurations presented considerable variation in the amino acids and the position of the coupling. The charge transfer values showed that there is oxidative damage inside the active site and that the HEM group is responsible for the main charge transferences.

Overcoming the Pitfalls of Cytochrome P450 Immobilization through the Use of Fusogenic Liposomes

This work describes a new nanotechnology-based immobilization strategy for cytochrome P450s (CYPs), the major class of drug metabolizing enzymes. Immobilization of CYPs on solid supports provides a significant leap forward compared with soluble enzyme assays by enabling the implementation of through-flow microreactors for, for example, determination of time-dependent inhibition. Immobilization of the complex CYP membrane-protein system is however particularly challenging as the preservation of the authentic enzyme kinetic parameters requires the full complexity of the lipid environment. The developed strategy is based on the spontaneous fusion of biotinylated fusogenic liposomes with lipid bilayers to facilitate the gentle biotinylation of human liver microsomes that incorporate all main natural CYP isoforms. The same process is also feasible for the biotinylation of recombinant CYPs expressed in insect cells, same as any membrane-bound enzymes in principle. As a result, CYPs could be immobilized on streptavidin-functionalized surfaces, both those of commercial magnetic beads and customized microfluidic arrays, so that the enzyme kinetic parameters remain unchanged, unlike in previously reported immobilization approaches that often suffer from restricted substrate diffusion to the enzyme's active site and steric hindrances. The specificity and robustness of the functionalization method of customized microfluidic CYP assays are also carefully examined.

Protein bioelectronics: a review of what we do and do not know

We review the status of protein-based molecular electronics. First, we define and discuss fundamental concepts of electron transfer and transport in and across proteins and proposed mechanisms for these processes. We then describe the immobilization of proteins to solid-state surfaces in both nanoscale and macroscopic approaches, and highlight how different methodologies can alter protein electronic properties. Because immobilizing proteins while retaining biological activity is crucial to the successful development of bioelectronic devices, we discuss this process at length. We briefly discuss computational predictions and their connection to experimental results. We then summarize how the biological activity of immobilized proteins is beneficial for bioelectronic devices, and how conductance measurements can shed light on protein properties. Finally, we consider how the research to date could influence the development of future bioelectronic devices.

Solid-state electrical applications of protein and peptide based nanomaterials

This review summarizes recent advancements in electrical properties and applications of natural proteins and mutated variants, synthetic oligopeptides and peptide–π conjugates.

A 17 GHz molecular rectifier

Molecular electronics originally proposed that small molecules sandwiched between electrodes would accomplish electronic functions and enable ultimate scaling to be reached. However, so far, functional molecular devices have only been demonstrated at low frequency. Here, we demonstrate molecular diodes operating up to 17.8 GHz. Direct current and radio frequency (RF) properties were simultaneously measured on a large array of molecular junctions composed of gold nanocrystal electrodes, ferrocenyl undecanethiol molecules and the tip of an interferometric scanning microwave microscope. The present nanometre-scale molecular diodes offer a current density increase by several orders of magnitude compared with that of micrometre-scale molecular diodes, allowing RF operation. The measured S₁₁ parameters show a diode rectification ratio of 12 dB which is linked to the rectification behaviour of the direct current conductance. From the RF measurements, we extrapolate a cut-off frequency of 520 GHz. A comparison with the silicon RF-Schottky diodes, architecture suggests that the RF-molecular diodes are extremely attractive for scaling and high-frequency operation.

Molecular electronics holds promise to overcome scaling limits of conventional technologies, but is currently limited to low frequency operation. Here, Trasobares et al. show radio frequencies of up to 17.8 GHz in a molecular diode based on ferrocenyl undecanethiol self-assembled monolayers on gold nanodots.

Long-Range Tunneling Processes across Ferritin-Based Junctions

The mechanism of long-range charge transport across tunneling junctions with monolayers of ferritin is investigated. It is shown that the mechanism can be switched between coherent tunneling, sequential tunneling, and hopping by changing the iron content inside the ferritin. This study shows that ferritins are an interesting class of biomolecules to control charge transport.

Nanoscale electron transport measurements of immobilized cytochrome P450 proteins

Gold nanopillars, functionalized with an organic self-assembled monolayer, can be used to measure the electrical conductance properties of immobilized proteins without aggregation. Measurements of the conductance of nanopillars with cytochrome P450 2C9 (CYP2C9) proteins using conducting probe atomic force microscopy demonstrate that a correlation exists between the energy barrier height between hopping sites and CYP2C9 metabolic activity. Measurements performed as a function of tip force indicate that, when subjected to a large force, the protein is more stable in the presence of a substrate. This agrees with the hypothesis that substrate entry into the active site helps to stabilize the enzyme. The relative distance between hopping sites also increases with increasing force, possibly because protein functional groups responsible for electron transport (ETp) depend on the structure of the protein. The inhibitor sulfaphenazole, in addition to the previously studied aniline, increased the barrier height for electron transfer and thereby makes CYP2C9 reduction more difficult and inhibits metabolism. This suggests that P450 Type II binders may decrease the ease of ETp processes in the enzyme, in addition to occupying the active site.

High speed e-beam lithography for gold nanoarray fabrication and use in nanotechnology

E-beam lithography has been used for reliable and versatile fabrication of sub-15 nm single-crystal gold nanoarrays and led to convincing applications in nanotechnology. However, so far this technique was either too slow for centimeter to wafer-scale writing or fast enough with the so-called dot on the fly (DOTF) technique but not optimized for sub-15 nm dots dimension. This prevents use of this technology for some applications and characterization techniques. Here, we show that the DOTF technique can be used without degradation in dots dimension. In addition, we propose two other techniques. The first one is an advanced conventional technique that goes five times faster than the conventional one. The second one relies on sequences defined before writing which enable versatility in e-beam patterns compared to the DOTF technique with same writing speed. By comparing the four different techniques, we evidence the limiting parameters for the writing speed. Wafer-scale fabrication of such arrays with 50 nm pitch allowed XPS analysis of a ferrocenylalkyl thiol self-assembled monolayer coated gold nanoarray.

Porphyrin assemblies and their scaffolds

The chlorophyll and heme molecules of chloroplasts and mitochondria are brought to life by "the global fold of the protein scaffolds". Proteins in hydrophobic cell regions touch the dye platelets from both sides, pushing and orienting them according to their life-spending activities in light and electron transfers. The conjugated π-electron systems or planarity of the porphyrin macrocycles are never disturbed. Most artificial porphyrin assemblies contain meso-tetraphenylporphyrins (TPPs), because the four phenyl groups rotate freely and carry their substituents above or below the macrocycle. A single porphyrin molecule can, for example, be attached to an anionic surface with ammonium groups on its 2,3-carbons, be located within a hydrophobic membrane with its alkyl chains on the 4-position, and then fixate a cationic polymer with 4,5-sulphonates. Charged TPPs also show unique spectroscopic changes at different pH values and a reversible loss of the macrocycle's planarity. On smooth silicate, graphite, or gold scaffolds TPPs have been attached irreversibly as single molecules, as extended non-covalent H or J aggregates as well as acetylene or thiophene-linked polymers. Soft, mobile porphyrin ladders conduct excited electrons ("excitons") better than rigid porphyrin wires ("polarons").