Comparison of metabolic soft spot predictions of CYP3A4, CYP2C9 and CYP2D6 substrates using MetaSite and StarDrop

Metabolite identification study plays an important role in determining the sites of metabolic liability of new chemical entities (NCEs) in drug discovery for lead optimization. Here we compare the two predictive software, MetaSite and StarDrop, available for this purpose. They work very differently but are used to predict the site of oxidation by major human cytochrome P450 (CYP) isoforms. Neither software can predict non-CYP catalyzed metabolism nor the rates of metabolism. For the purpose of comparing the two software packages, we tested known probe substrate for these enzymes, which included 12 substrates of CYP3A4 and 18 substrates of CYP2C9 and CYP2D6 were analyzed by each software and the results were compared. It is possible that these known substrates were part of the training set but we are not aware of it. To assess the performance of each software we assigned a point system for each correct prediction. The total points assigned for each CYP isoform experimentally were compared as a percentage of the total points assigned theoretically for the first choice prediction for all substrates for each isoform. Our results show that MetaSite and StarDrop are similar in predicting the correct site of metabolism by CYP3A4 (78% vs 83%, respectively). StarDrop appears to do slightly better in predicting the correct site of metabolism by CYP2C9 and CYP2D6 metabolism (89% and 93%, respectively) compared to MetaSite (63% and 70%, respectively). The sites of metabolism (SOM) from 34 in-house NCEs incubated in human liver microsomes or human hepatocytes were also evaluated using two prediction software packages and the results showed comparable SOM predictions. What makes this comparison challenging is that the contribution of each isoform to the intrinsic clearance (Clint) is not known. Overall the software were comparable except for MetaSite performing better for CYP2D6 and that MetaSite has a liver model that is absent in StarDrop that predicted with 82% accuracy.     

Striking patterns in natural magic squares’ associated electrostatic potentials: Matrices of the 4th and 5th order

A magic square is a square matrix whereby the sum of any row, column, or any one of the two principal diagonals is equal. A surrogate of this abstract mathematical construct, introduced in 2012 by Fahimi and Jaleh, is the “electrostatic potential (ESP)” that results from treating the matrix elements of the magic square as electric charges. The overarching idea is to characterize patterns associated with these matrices that can possibly be used, in the future, in reverse to generate these squares. This study focuses on squares of order 4 and 5 with 880 and 275,305,224 distinct (irreducible/unique) realizations, respectively. It is shown that characteristic patterns emerge from plots of the ESPs of the matrices representing the studied squares. The electrostatic potentials for natural magic squares exhibit a striking pattern of maxima and minima in all distinct 880 of the 4th order and all distinct 275,305,224 of the 5th order matrices. The minimum values of ESP of Dudeney groups are discussed. Equipotential points and certain constants are found among the ESP sums along horizontal and vertical lines on the square lattice. These findings may help to open a new perspective regarding magic squares unsolved problems. While mathematics often leads discovery in physics, the latter (physics) is used here to detect otherwise invisible patterns in a mathematical object such as magic squares.     

Near-Infrared Study of the Hydrogen Bonding in Acetone-Methanol and Acetone-Ethanol Mixtures: Roles of Mechanical and Electrical Anharmonicities of Hydroxyl Oscillator

Near-infrared spectra of methanol-acetone and ethanol-acetone mixtures in the entire mole fraction range in increments of 0.1 were recorded in the region of 7500–6000 cm^?1. The first overtone bands of the hydroxyl (OH) groups were assigned to the polymeric and oligomeric OH associations. In both solutions, the frequency of the polymeric OH band decreased with the increase in the mole fraction of alcohol, which indicated the increase in the hydrogen bonding strength. The integrated area of the polymeric OH band followed the opposite trend to the frequency with the mole fraction. The nonlinearity of the plot of the integrated band area of the polymeric OH band of methanol versus the mole fraction of acetone revealed the nonideal character of the methanol-acetone mixtures, whereas the opposite was observed for the ethanol-acetone mixtures. These observations have been explained in terms of mechanical and electrical anharmonicities of the OH oscillator.     

Lamellar phase of stacked two-dimensional rafts of actin filaments

We examined liquid crystalline phases of the cytoskeletal polyelectrolyte filamentous (F-)actin in the presence of multivalent counterions. As a function of increasing ion concentration, the F-actin rods in either an isotropic or a nematic phase will transform into a new and unexpected lamellar phase of cross-linked rafts (L(XR) phase), before condensing into a bundled phase of parallel, close-packed rods. This behavior is generic for alkali earth divalent ions Mg2+, Ca2+, Sr2+, and Ba2+, and the structural transitions are achieved without any architecture-specific actin-binding linker proteins.     

Hierarchical self-assembly of actin bundle networks: gels with surface protein skin layers

The networklike structure of actin bundles formed with the cross-linking protein alpha-actinin has been investigated via x-ray scattering and confocal fluorescence microscopy over a wide range of alpha-actinin/F-actin ratios. We describe the hierarchical structure of bundle gels formed at high ratios. Isotropic actin bundle gels form via cluster-cluster aggregation in the diffusion-limited aggregation regime at high alpha-actinin/actin ratios. This process is clearly observed by confocal fluorescence microscopy. Polylysine is investigated as an alternative bundling agent in the high-ratio regime and the effects of F-actin length are also discussed. One particularly fascinating aspect of this system is the presence of a structured skin layer at the gel/water interface. Confocal microscopy has elucidated the full three-dimensional structure of this layer and revealed several interesting morphologies. The protein skin layer is a micron-scale structure composed of a directed network of bundles and exhibits flat, crumpled, and tubelike shapes. We show that crumpling of the skin layer results from stresses due to the underlying gel. These biologically based geometric structures may detach from the gel, demonstrating potential for the generation of biological scaffolds with defined shapes for applications in cell encapsulation and tissue engineering. We demonstrate manipulation of the skin layer, producing hemispherical structures in solution.     

Classical and recent free-volume models for polymer solutions: A comparative evaluation

In this work, two “classical” (UNIFAC-FV, Entropic-FV) and two “recent” free-volume (FV) models (Kannan-FV, Freed-FV) are comparatively evaluated for polymer–solvent vapor–liquid equilibria including both aqueous and non-aqueous solutions. Moreover, some further developments are presented here to improve the performance of a recent model, the so-called Freed-FV. First, we propose a modification of the Freed-FV model accounting for the anomalous free-volume behavior of aqueous systems (unlike the other solvents, water has a lower free-volume percentage than polymers). The results predicted by the modified Freed-FV model for athermal and non-athermal polymer systems are compared to other “recent” and “classical” FV models, indicating an improvement for the modified Freed-FV model for aqueous polymer solutions. Second, for the original Freed-FV model, new UNIFAC group energy parameters are regressed for aqueous and alcohol solutions, based on the physical values of the van der Waals volume and surface areas for both FV-combinatorial and residual contributions. The prediction results of both “recent” and “classical” FV models using the new regressed energy parameters are significantly better, compared to using the classical UNIFAC parameters, for VLE of aqueous and alcohol polymer systems.     

Controlled‐Potential Electromechanical Reshaping of Cartilage

An alternative to conventional “cut‐and‐sew” cartilage surgery, electromechanical reshaping (EMR) is a molecular‐based modality in which an array of needle electrodes is inserted into cartilage held under mechanical deformation by a jig. Brief (ca. 2 min) application of an electrochemical potential at the water‐oxidation limit results in permanent reshaping of the specimen. Highly sulfated glycosaminoglycans within the cartilage matrix provide structural rigidity to the tissue through extensive ionic‐bonding networks; this matrix is highly permselective for cations. Our studies indicate that EMR results from electrochemical generation of localized, low‐pH gradients within the tissue: fixed negative charges in the proteoglycan matrix are protonated, resulting in chemically induced stress relaxation of the tissue. Re‐equilibration to physiological pH restores the fixed negative charges, and yields remodeled cartilage that retains a new shape approximated by the geometry of the reshaping jig.     

Toward a comprehensive microextraction/determination unit: A chip silicon rubber polyaniline‐based system and its direct coupling with gas chromatography and mass spectrometry

An inexpensive silicon rubber‐based chip was constructed by fabricating a triangle‐shaped microcanal with a 135 μm width and 234 μm depth by laser ablation technique. The fabricated groove was sealed by a thin glass cover while two pieces of stainless‐steel tubing were connected to each side of the canal. Then, a thin polyaniline film was synthesized on the walls of the canal by chemical oxidation using a syringe pump to deliver the relevant reagents. The microfluidic system was eventually connected to a gas chromatography‐mass spectrometry. To evaluate the capability of the constructed microfluidic system, it was implemented to the analysis of submilliliter volumes of environmental samples spiked with the trace amounts of some pesticide residues. To show the applicability of the hyphenated system, the extraction/determination of triazines was implemented while only 500 μL sample with the limits of detection ranged from 0.2 to 0.5 ng/mL could be easily achieved. In addition, the influential extraction parameters such as sample volume, flow rate, and sample pH were optimized. Under the optimized conditions, the relative standard deviation values for double‐distillated water sample spiked with the selected triazines at 250 ng/mL were 6.5–12.5% (n = 3).     

Biosynthetic Strategies for Macrocyclic Peptides

Macrocyclic peptides are predominantly peptide structures bearing one or more rings and spanning multiple amino acid residues. Macrocyclization has become a common approach for improving the pharmacological properties and bioactivity of peptides. A variety of ribosomal-derived and non-ribosomal synthesized cyclization approaches have been established. The biosynthesis of backbone macrocyclic peptides using seven new emerging methodologies will be discussed with regard to the features and strengths of each platform rather than medicinal chemistry tools. The mRNA display variant, known as the random nonstandard peptide integrated discovery (RaPID) platform, utilizes flexible in vitro translation (FIT) to access macrocyclic peptides containing nonproteinogenic amino acids (NAAs). As a new discovery approach, the ribosomally synthesized and post-translationally modified peptides (RiPPs) method involves the combination of ribosomal synthesis and the phage screening platform together with macrocyclization chemistries to generate libraries of macrocyclic peptides. Meanwhile, the split-intein circular ligation of peptides and proteins (SICLOPPS) approach relies on the in vivo production of macrocyclic peptides. In vitro and in vivo peptide library screening is discussed as an advanced strategy for cyclic peptide selection. Specifically, biosynthetic bicyclic peptides are highlighted as versatile and attractive modalities. Bicyclic peptides represent another type of promising therapeutics that allow for building blocks with a heterotrimeric conjugate to address intractable challenges and enable multimer complexes via linkers. Additionally, we discuss the cell-free chemoenzymatic synthesis of macrocyclic peptides with a non-ribosomal catalase known as the non-ribosomal synthetase (NRPS) and chemo-enzymatic approach, with recombinant thioesterase (TE) domains. Novel insights into the use of peptide library tools, activity-based two-hybrid screening, structure diversification, inclusion of NAAs, combinatorial libraries, expanding the toolbox for macrocyclic peptides, bicyclic peptides, chemoenzymatic strategies, and future perspectives are presented. This review highlights the broad spectrum of strategy classes, novel platforms, structure diversity, chemical space, and functionalities of macrocyclic peptides enabled by emerging biosynthetic platforms to achieve bioactivity and for therapeutic purposes.