Rational Design of Potent Inhibitors of a Metallohydrolase Using a Fragment-Based Approach

Metallohydrolases form a large group of enzymes that have fundamental importance in a broad range of biological functions. Among them, the purple acid phosphatases (PAPs) have gained attention due to their crucial role in the acquisition and use of phosphate by plants and also as a promising target for novel treatments of bone-related disorders and cancer. To date, no crystal structure of a mammalian PAP with drug-like molecules bound near the active site is available. Herein, we used a fragment-based design approach using structures of a mammalian PAP in complex with the Maybridge^TM fragment CC063346, the amino acid L-glutamine and the buffer molecule HEPES, as well as various solvent molecules to guide the design of highly potent and efficient mammalian PAP inhibitors. These inhibitors have improved aqueous solubility when compared to the clinically most promising PAP inhibitors available to date. Furthermore, drug-like fragments bound in newly discovered binding sites mapped out additional scaffolds for further inhibitor discovery, as well as scaffolds for the design of inhibitors with novel modes of action.     

Two Methods,One Goal: Structural Differences between Cocrystallization and Crystal Soaking to Discover Ligand Binding Poses

In lead optimization, protein crystallography is an indispensable tool to analyze drug binding. Binding modes and non-covalent interaction inventories are essential to design follow-up synthesis candidates. Two protocols are commonly applied to produce protein–ligand complexes: cocrystallization and soaking. Because of its time and cost effectiveness, soaking is the more popular method. Taking eight ligand hinge binders of protein kinase A, we demonstrate that cocrystallization is superior. Particularly for flexible proteins, such as kinases, and larger ligands cocrystallization captures more reliable the correct binding pose and induced protein adaptations. The geometrical discrepancies between soaking and cocrystallization appear smaller for fragment-sized ligands. For larger flexible ligands that trigger conformational changes of the protein, soaking can be misleading and underestimates the number of possible polar interactions due to inadequate, highly impaired positions of protein amino-acid side and main chain atoms. Thus, if applicable cocrystallization should be the gold standard to study protein–ligand complexes.     

Novel BQCA- and TBPB-Derived M1 Receptor Hybrid Ligands: Orthosteric Carbachol Differentially Regulates Partial Agonism

Recently, investigations of the complex mechanisms of allostery have led to a deeper understanding of G protein-coupled receptor (GPCR) activation and signaling processes. In this context, muscarinic acetylcholine receptors (mAChRs) are highly relevant due to their exemplary role in the study of allosteric modulation. In this work, we compare and discuss two sets of putatively dualsteric ligands, which were designed to connect carbachol to different types of allosteric ligands. We chose derivatives of TBPB [1-(1′-(2-tolyl)-1,4′-bipiperidin-4-yl)-1H-benzo[d]imidazol-2(3H)-one] as M₁-selective putative bitopic ligands, and derivatives of benzyl quinolone carboxylic acid (BQCA) as an M₁ positive allosteric modulator, varying the distance between the allosteric and orthosteric building blocks. Luciferase protein complementation assays demonstrated that linker length must be carefully chosen to yield either agonist or antagonist behavior. These findings may help to design biased signaling and/or different extents of efficacy.     

Effect of load reduction mechanisms on loads and blade bearing movements of wind turbines

The power control of wind turbines is usually realized via a change in the pitch angle of the rotor blades. Pitching facilitates the exact control of the turbines and the reliable deceleration of the rotor when required. Pitch movements can moreover be used for load control. One of these methods is called individual pitch control (IPC). IPC controls the blades individually and brings about a significant reduction in the fatigue loads and extreme loads placed on the structural components, while at the same time reducing the yield of the turbine only slightly. The lower loads reduce material costs, and thus, the cost of energy (CoE) is reduced, despite the slight reduction in yield. The method is nevertheless not used everywhere since the additional movement cycles put the rotor blade bearings in particular under stress. Special attention must be paid to small amplitude oscillating movements, which carry a high risk of inducing surface damage in the rolling contacts of the blade bearings. This paper uses a cycle analysis of the IWT7.5‐164 reference turbine to illustrate the differences in the movement patterns of wind turbine blade bearings with and without IPC. Moreover, model calculations with single contacts are used to show which of the movement patterns carries a risk of inducing surface damage. The use of IPC leads to the expected load reduction at the blade root. In current literature, IPC is usually assumed to have a negative influence on the life expectancy of blade bearings, but the findings of this study contradict this. The summed blade bearing movement is increased, although the number of very small pitch angles occurring is reduced. This reduction reduces the risk of wear in the blade bearings.     

Rapid Discovery of Aspartyl Protease Inhibitors Using an Anchoring Approach

Pharmacophore searches that include anchors, fragments contributing above average to receptor binding, combined with one-step syntheses are a powerful approach for the fast discovery of novel bioactive molecules. Here, we are presenting a pipeline for the rapid and efficient discovery of aspartyl protease inhibitors. First, we hypothesized that hydrazine could be a multi-valent warhead to interact with the active site Asp carboxylic acids. We incorporated the hydrazine anchor in a multicomponent reaction and created a large virtual library of hydrazine derivatives synthetically accessible in one-step. Next, we performed anchor-based pharmacophore screening of the libraries and resynthesized top-ranked compounds. The inhibitory potency of the molecules was finally assessed by an enzyme activity assay and the binding mode confirmed by several soaked crystal structures supporting the validity of the hypothesis and approach. The herein reported pipeline of tools will be of general value for the rapid generation of receptor binders beyond Asp proteases.     

Exploring design trade-offs for achieving social inclusion in multi-tiered design problems

ABSTRACT

The digital age of the future is ‘not out there to be discovered’, but it needs to be ‘designed’. The design challenge has to address questions about how we want to live, work, and learn (as individuals and as communities) and what we value and appreciate, e.g.: reflecting on quality of life and creating inclusive societies. An overriding design trade-off for the digital age is whether new developments will increase the digital divide or will create more inclusive societies. Sustaining inclusive societies means allowing people of all ages and all abilities to exploit information technologies for personally meaningful activities. Meta-design fosters the design of socio-technical environments that end-user developers can modify and evolve at use time to improve their quality of life and favour their inclusion in the society. This paper describes three case studies in the domain of assistive technologies in which end users themselves cannot act as end-user developers, but someone else (e.g.: a caregiver or a clinician) must accept this role requiring multi-tiered architectures. The design trade-offs and requirements for meta-design identified in the context of the case studies and other researchers’ projects are described to inform the development of future socio-technical environments focused on social inclusion.     

Knowledge‐Based Conceptual Synthesis of Industrial‐Scale Downstream Processes for Biochemical Products

A generic, knowledge‐based guideline assisting downstream process synthesis for biochemical products is presented. It offers process designers a structured process design methodology supporting them in capturing potentially relevant information, which might be beyond their expertise. The guideline is based on heuristic knowledge which was collected, structured in a generic way, and clearly represented. The generation of alternative downstream routes as starting points for experiments, simulation, and cost calculation is hereby accelerated. The application of the guideline is demonstrated on the example of penicillin V downstream processing from fermentation broth.     

Rheology of natural fibers thermoplastic compounds: Flow length and fiber distribution

The presented study investigates the flow length and the corresponding fiber content distribution in the injection‐moulded natural fiber reinforced thermoplastics and its relation to fiber type and processing parameters such as injection pressure, temperature, injection rate and mould tempering by increasing die temperature. In this research, polypropylene compounds with nominally 30 wt % hemp and sisal fibers are investigated. The influence of the injection pressure (500 and 1000 bar), melt temperature (180°C, 200°C, and 220°C), and die temperature (23°C and 80°C) on the fiber content distribution all over the sample is investigated. An increasing linear trend of fiber content along the spiral length is observed as an evidence of a fiber/polymer multiflow system. A pattern for fiber content distribution with respect to the fiber length along the injected spiral can be distinguished, where the longer fibers are usually found at the end of the injected part and the shorter fibers remain near mould entrance point. © 2013 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014 , 131, 39861.     

Aerosol Process for the In Situ Coating of Nanoparticles with a Polymer Shell

This article presents a novel method to encapsulate gas-borne nanoparticles with a polymeric shell. This method implies heterogeneous condensation of monomer vapor around the surface of nanoparticles as nuclei and polymerization is then subsequently started by addition of NH₃ as aerosol initiator. Ag and SiO₂ nanoparticles were generated as inorganic core by spark discharge and nebulization, respectively, and glycidyl methacrylate (GMA) was used as organic monomer. The effect of several parameters, including vapor pressure of monomer and properties of inorganic core such as morphology, material, particle size, and production method on the thickness of polymeric shell and morphology of resulting nanocomposites has been investigated. The particle size distribution and morphology of the resulting core-shell nanoparticles have been studied via scanning mobility particle sizer (SMPS) and transmission electron microscope (TEM). Finally, the coating efficiency was determined by aerosol photoemission (APE) and the results show that monomer and polymer coating efficiency are 99% and 60%, respectively.

Copyright 2014 American Association for Aerosol Research