Design, Synthesis, and Evaluation of Functionalized 5-(4-arylpiperazin-1-yl)-N-Quinolinyl-pentanamides as Selective Dopamine D3 Receptor Ligands

Dopamine (1) plays a key role in normal physiological pathways in both the central nervous system and the periphery. The physiological impact of this neurotransmitter is mediated through its interaction with family of G-protein-coupled receptors (GPCRs). These receptors are designated as D1, D2, D3, D4, and D5 and divided into two sub-families, the D1-like sub-family (D1 and D5) and D2-like sub-family (D2, D3 and D4) based on pharmacological properties, amino acid homology, and genetic organization. Aberrant D3 activity has been linked to multiple diseases and conditions such as depression, schizophrenia, substance use disorder, inflammatory diseases, and Parkinson’s disease (PD). As part of our on-going program focused on the identification of novel D3 ligands, we have identified a novel series of 5-(4-arylpiperazin-1-yl)-N-quinolinyl-pentanamides that are high affinity ligands for this receptor.

Fast and Versatile Chromatography Process Design and Operation Optimization with the Aid of Artificial Intelligence

Preparative and process chromatography is a versatile unit operation for the capture, purification, and polishing of a broad variety of molecules, especially very similar and complex compounds such as sugars, isomers, enantiomers, diastereomers, plant extracts, and metal ions such as rare earth elements. Another steadily growing field of application is biochromatography, with a diversity of complex compounds such as peptides, proteins, mAbs, fragments, VLPs, and even mRNA vaccines. Aside from molecular diversity, separation mechanisms range from selective affinity ligands, hydrophobic interaction, ion exchange, and mixed modes. Biochromatography is utilized on a scale of a few kilograms to 100,000 tons annually at about 20 to 250 cm in column diameter. Hence, a versatile and fast tool is needed for process design as well as operation optimization and process control. Existing process modeling approaches have the obstacle of sophisticated laboratory scale experimental setups for model parameter determination and model validation. For a broader application in daily project work, the approach has to be faster and require less effort for non-chromatography experts. Through the extensive advances in the field of artificial intelligence, new methods have emerged to address this need. This paper proposes an artificial neural network-based approach which enables the identification of competitive Langmuir-isotherm parameters of arbitrary three-component mixtures on a previously specified column. This is realized by training an ANN with simulated chromatograms varying in isotherm parameters. In contrast to traditional parameter estimation techniques, the estimation time is reduced to milliseconds, and the need for expert or prior knowledge to obtain feasible estimates is reduced.

DNA origami patterning of synthetic T cell receptors reveals spatial control of the sensitivity and kinetics of signal activation

Receptor clustering plays a key role in triggering cellular activation, but the relationship between the spatial configuration of clusters and the elicitation of downstream intracellular signals remains poorly understood. We developed a DNA-origami–based system that is easily adaptable to other cellular systems and enables rich interrogation of responses to a variety of spatially defined inputs. Using a chimeric antigen receptor (CAR) T cell model system with relevance to cancer therapy, we studied signaling dynamics at single-cell resolution. We found that the spatial arrangement of receptors determines the ligand density threshold for triggering and encodes the temporal kinetics of signaling activities. We also showed that signaling sensitivity of a small cluster of high-affinity ligands is enhanced when surrounded by nonstimulating low-affinity ligands. Our results suggest that cells measure spatial arrangements of ligands, translate that information into distinct signaling dynamics, and provide insights into engineering immunotherapies.

A conformational switch controlling the toxicity of the prion protein

SummaryPrion infections cause conformational changes of PrPC and lead to progressive neurological impairment. Here we show that toxic, prion-mimetic ligands induce an intramolecular R208-H140 hydrogen bond (“H-latch”) altering the flexibility of the α2-α3 and β2-α2 loops of PrPC. Expression of a PrP2Cys mutant mimicking the H-latch was constitutively toxic, whereas a PrPR207A mutant unable to form the H-latch conferred resistance to prion infection. High-affinity ligands that prevented H-latch induction repressed prion-related neurodegeneration in organotypic cerebellar cultures. We then selected phage-displayed ligands binding wild-type PrPC, but not PrP2Cys. These binders depopulated H-latched conformers and conferred protection against prion toxicity. Finally, brain-specific expression of an antibody rationally designed to prevent H-latch formation, prolonged the life of prion-infected mice despite unhampered prion propagation, confirming that the H-latch is causally linked to prion neurotoxicity.

AN OVERVIEW OF EPIGENETIC DRUGS, AND THEIR VIRTUAL SCREENING STUDY RETRIEVED FROM ZINC DATABASE ALONG WITH AN AUTODOCK STUDY OF THE BEST INHIBITOR

Objective: Over the last 30 y cancer epigenetics research has grown extensively. It is note-worthy to recognize that epigenetic misregulation could substantiate the development of cancer and we need to continue to look for anti-neoplastic epi-drugs. Taking into consideration this phenomenon, our first aim is to search for an effective epi-drugs by virtual screening from ZINC database and to explore the validity of the virtual screening. The second aim is to explore a binding conformation of the top affinity ligands against macromolecules, by docking experiment. Methods: The virtual screening was conducted by our Virtual Screening by Docking (VSDK) algorithm and procedure. Small molecules were randomly downloaded by ZINC database. For docking experiment, AutoDock 4.2.6 and AutoDock Tool were used. Results: It took eight to ten hours for the successful virtual screening of the 2778 small compounds retrieved at random from ZINC database. Among histone H2B E76K mutant (HHEM) inhibitors and DNA methyltransferase (DNMT) inhibitors, the first ranked inhibitors were 1H-1,2,4-triazole-3,5-diamine and 2-ethyl-1,3,4-oxadiazole respectively. Conclusion: As for the molecular structures obtained from virtual screening, most of the top ten HHEM and DNMT inhibitors contained 5-member rings. More than two times in affinity difference between the top and bottom ten compounds would indicate a successful virtual screening experiment. The histogram chart of AutoDock4 runs appeared in the lowest affinity region with two or three hydrogen bonds indicating a reliable conformation docking.

TRIM21 chimeric protein as a new molecular tool for multispecies IgG detection

G-type immunoglobulins (IgGs) are extensively used in the pharmaceutical industry against various diseases, being also crucial in multiple immunoassays. The production of secondary monoclonal antibodies (Abs) for IgG detection is not cost-effective, while polyclonal antibody production still depends on laboratory animals, which raises concerns regarding animal welfare. As alternatives, bacterial proteins (A and G) have been widely exploited; however, several difficulties are encountered regarding their use for IgG detection and purification. The widespread use of IgGs in the pharmaceutical industry and the increasing number and variety of new Abs entering the market impose the need to develop new detection and purification strategies. The TRIM21 protein is a soluble intracellular IgG receptor that binds to the Fc region of many species with high affinity. We created a chimeric protein containing a mutated form of the C-terminal domain of mouse TRIM21 linked to a streptavidin moiety to detect IgGs from a wide range of species. The protein is promptly produced by heterologous expression and consists of an improved molecular tool, expanding the portfolio of Ab-affinity ligands for immunoassays.

Downstream processing of virus, virus-like particles and nanoparticulate inclusion bodies to be used as gene delivery vehicles for human gene therapy applications

Design and analyze future affinity ligands such as antibodies, aptamers, metal affinity, peptides, triazine dyes, and red blood cell carriers to increase monolithic chromatography selectivity and two-phase affinity-aqueous systems. Monolithic chromatography systems may be constructed and optimized by examining viruses, virus-like particles, and nanoparticulate inclusion bodies from difficult culture media. Different chromatographic characteristics such as monolithic supports, active monolith groups, binding and elution buffers, elution gradients, column equilibrium volumes, and regeneration should be investigated with the aim of optimizing monolithic chromatography separation and recovery. To develop and optimize aqueous two-phase systems, several different parameters need to be investigated and compared, such as polymer type and concentration, salt solution, surfactants and ions, polymer molecular weight, ion nature and ionic strength, present affinity ligands, volumetric ratio, temperature, pH, and sample load, to name a few.Several relevant biological models, such as Newcastle disease (NDV), herpes (HPr), or viral vectors bluetongue (BTV), can be employed to establish different patterns and predict the generalized mechanistic process of enhanced purification systems. Because optimal systems are intended to be deployed at the industrial level, a comparison of typical downstream processing and alternatives in terms of recovery, technological advantages, economic feasibility, and environmental sustainability is needed. Cell separation, viral concentration and viral purification may all be reduced to one step utilizing integrated chromatography platforms on monolith supports and aqueous two-phase systems. In addition, the efficiency of separation and purification yields achieved after these integrated systems are predicted to be substantially higher than those produced in conventional procedures. As a result, the benefits of these alternative and cutting-edge technologies are predicted to contribute to more efficient, long-term, and cost-effective downstream processing of virus-like particles.

Protein L—More Than Just an Affinity Ligand

In the past 30 years, highly specific drugs, known as antibodies, have conquered the biopharmaceutical market. In addition to monoclonal antibodies (mAbs), antibody fragments are successfully applied. However, recombinant production faces challenges. Process analytical tools for monitoring and controlling production processes are scarce and time-intensive. In the downstream process (DSP), affinity ligands are established as the primary and most important step, while the application of other methods is challenging. The use of these affinity ligands as monitoring tools would enable a platform technology to monitor process steps in the USP and DSP. In this review, we highlight the current applications of affinity ligands (proteins A, G, and L) and discuss further applications as process analytical tools.