826 research outputs found

    A journey from molecule to physiology and in silico tools for drug discovery targeting the transient receptor potential vanilloid type 1 (TRPV1) channel

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    The heat and capsaicin receptor TRPV1 channel is widely expressed in nerve terminals of dorsal root ganglia (DRGs) and trigeminal ganglia innervating the body and face, respectively, as well as in other tissues and organs including central nervous system. The TRPV1 channel is a versatile receptor that detects harmful heat, pain, and various internal and external ligands. Hence, it operates as a polymodal sensory channel. Many pathological conditions including neuroinflammation, cancer, psychiatric disorders, and pathological pain, are linked to the abnormal functioning of the TRPV1 in peripheral tissues. Intense biomedical research is underway to discover compounds that can modulate the channel and provide pain relief. The molecular mechanisms underlying temperature sensing remain largely unknown, although they are closely linked to pain transduction. Prolonged exposure to capsaicin generates analgesia, hence numerous capsaicin analogs have been developed to discover efficient analgesics for pain relief. The emergence of in silico tools offered significant techniques for molecular modeling and machine learning algorithms to indentify druggable sites in the channel and for repositioning of current drugs aimed at TRPV1. Here we recapitulate the physiological and pathophysiological functions of the TRPV1 channel, including structural models obtained through cryo-EM, pharmacological compounds tested on TRPV1, and the in silico tools for drug discovery and repositioning

    Exploring transition metal catalysis in water for <i>in vivo </i>applications

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    Transition metal catalysis proves a powerful tool to achieve otherwise synthetically challenging, or even impossible, transformations with (high) selectivity and is therefore employed in various areas of chemistry. Recently, transition metal-catalysed reactions have been successfully performed in cells (in vitro) and living systems (in vivo). The achievements made thus far reveal the potential of transition metal catalysis and its applications in such biological settings. Interestingly, the scope is limited compared to the breadth of transition metal-catalysed reactions that have been unlocked for synthetic applications. Translating transition metal-catalysed reactions from flasks to cells is non-trivial as the conditions in cells are fairly different compared to the highly controlled and adaptable conditions achieved in a flask. The development of catalytic systems for future applications in vivo therefore proceeds through many steps, starting with evaluating their reactivity, selectivity, and stability in water and under biologically relevant and biomimetic conditions. By exploring transition metal-catalysed reactions in water for in vivo applications, this dissertation has contributed to the subfield of bioorthogonal chemistry devoted to complementing Nature’s repertoire of reactions. Our studies have revealed the challenges associated with the performance of transition metal catalysis in aqueous media and how a detailed understanding of a catalytic system can address them. Apart from these fundamental studies, we have performed explorative studies under biologically relevant and biomimetic conditions in the context of intracellular drug synthesis. Moreover, we have developed a new and compatible protocol that enables detailed kinetic studies in complex reaction media, comparable to the cellular environment, to facilitate the translation of transition metal catalysis from flasks to cells

    University of Arkansas, Chemistry and Biochemistry Department Research Publications, 2014- November 2023. 107p.

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    This report provides a compilation of the research publications by the Chemistry and Biochemistry faculty for the period: 2014 - November 2023. The information was gathered from major databases in science and technology including Web of Science, SciFinder, Reaxys, PubMed, IEEE Explore and Engineering Index. At least one author in each of the publications has the CHBC department as its affiliation. It includes a table summarizing the research. The listing is organized according to type of publications within specific years

    Multiscale QM/MM modelling of catalytic systems with ChemShell

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    Hybrid quantum mechanical/molecular mechanical (QM/MM) methods are a powerful computational tool for the investigation of all forms of catalysis, as they allow for an accurate description of reactions occurring at catalytic sites in the context of a complicated electrostatic environment. The scriptable computational chemistry environment ChemShell is a leading software package for QM/MM calculations, providing a flexible, high performance framework for modelling both biomolecular and materials catalysis. We present an overview of recent applications of ChemShell to problems in catalysis and review new functionality introduced into the redeveloped Python-based version of ChemShell to support catalytic modelling. These include a fully guided workflow for biomolecular QM/MM modelling, starting from an experimental structure, a periodic QM/MM embedding scheme to support modelling of metallic materials, and a comprehensive set of tutorials for biomolecular and materials modelling

    Molecular modeling of the monoamine transporters and their interactions with psychostimulants and other substances

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    The monoamines (i.e., dopamine, serotonin, and norepinephrine) are vital to the ontogeny, function, and plasticity of the nervous system. These neurotransmitters affect each other and regulate, amongst others, motor function, cognitive state, motivation, and stress reactions. The neurotransmission is mainly terminated by reuptake in monoamine transporters (MATs), i.e., the dopamine-, serotonin-, and norepinephrine transporter. These transporters are the focus of the current study. Imbalance in the monoamine systems in the central nervous system (CNS) is associated with neurological- and psychiatric disorders, where the MATs are targets for several therapeutic drugs. Most of these drugs bind the outward-facing conformation of the MATs, and their effects depend highly on the selectivity for a single MAT. On the other hand, the increased use of illicit stimulants, predominantly acting on DAT, has risen alarms due to their unpredictable effects and high abuse potential. Regarding this, some research standards (atypical inhibitors), suggested to bind the inward-facing conformation of the MATs, have been shown to exert anti-addictive properties – being valuable in future treatment of addiction and withdrawal symptoms. The main aim of this thesis was to construct outward-and inward facing human MAT-models, based on homology modeling, to identify determinants for selective binding to each MAT, by utilizing induced fit docking and molecular dynamics simulations. Therapeutic psychostimulants, illicit psychostimulants, antidepressants, non-stimulants, atypical inhibitors, and some research standards were studied. The results indicate that divergent residues in the S1-site play a key role in MAT-selectivity. These residues shape the polarity and steric environment in the orthosteric (S1) pocket, thus affecting the stabilization, interactions, and orientation of ligands in each MAT. Structural features in the ligands appeared to also play a role in the selectivity for a MAT, concerning the binding mode and formation of interactions

    From recombinant proteins to cells: targeting TDP-43 in preclinical ALS and FTD therapeutic development

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    The transactive response DNA-binding protein 43 kDa (TDP-43) is a DNA and RNA binding protein involved in RNA transcription and translation. Accumulation of intracellular TDP-43 inclusions is a pathological hallmark in some patients with amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). To date, there are no disease-modifying treatments for these diseases. The pathological overlap of TDP-43 in both diseases makes it an attractive target for therapeutic intervention and PET ligand development. This thesis aimed to develop methods to inform lead development of small molecules that target TDP‑43 proteinopathy or bind to TDP-43. The use of cellular models is a common means to investigate potency of therapeutics in pre-clinical drug discovery. However, there is currently no consensus on which model most accurately replicates key aspects of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) pathology. By characterising two TDP-43 proteinopathy cellular models that were based on different aetiologies of disease, it was demonstrated that each cellular model captured different aspects of TDP-43, stress granule and ubiquitin pathology. When these two cellular models were exposed to small molecule chemical probes, different effects were observed across the two models. For example, a previously disclosed sulfonamide compound, 1, decreased cytoplasmic TDP-43 levels and increased soluble levels of stress granule marker TIA-1 in the cellular stress model without impacting these levels in a TDP-43 M337V mutant cell line. These evaluations highlight the challenges of using cellular models in lead development during drug discovery for ALS and FTD and reinforces the need to perform assessments of novel therapeutics across a variety of cell lines and aetiological models. To assist in development of therapeutic compounds and PET ligands, several previous studies have attempted to purify full-length TDP-43 with a reasonable yield, but limitations in reproducibility have been reported. We aimed to develop a method of full‑length TDP-43 production using two different plasmid constructs encoding full-length TDP‑43 expressed using E. coli bacterial expression systems. A novel purification protocol was successfully developed for one of the protein constructs consisting of full‑length TDP-43 with a hexahistidine and ubiquitin fusion tag (His-Ub-TDP-43). This novel protocol resulted in the preparation of pure, and soluble TDP-43 protein that was characterised using electrophoresis and mass spectrometry. Protein folding was revealed by far-UV circular dichroism which showed mostly random coil with some α‑helical and β-sheet structure. Self‑assembly was monitored with a turbidity assay and a thioflavin T fluorescence assay which revealed the formation of aggregates with an amyloid structure. In order to develop small molecule TDP-43 binders, the amplified luminescent proximity homogeneous assay (AlphaScreen™) was used to measure binding affinity against TDP-43. After assay optimisation, a library of twenty-one molecules were tested and three novel compounds were identified as TDP-43 binders. A novel chemotype 20 displayed partial inhibition of binding with low micromolar binding affinity. The compounds 24 and 25 exhibited novel two-site binding to TDP-43, with both compounds showing a high‑affinity site with nanomolar affinity and a low affinity site with micromolar binding affinity. The compounds 24 and 25 offer new opportunities as tools to further study the biological implications of compounds that occupy two TDP-43 binding sites. This work establishes a foundation for future iterative drug discovery, with the ultimate aim of producing therapeutics and PET ligands for use in ALS and FTD

    Micellar catalysis for eco-friendly hydroaminomethylation (HAM)

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    Hydroaminomethylation (HAM) is one of the most interesting atom economic metal catalysed process for the production of amines. Despite the large application of HAM in the synthesis of aliphatic amines, anilines, interesting intermediates in APIs synthesis, are still challenging substrates for this reaction. Herein it is reported the development of a protocol that combines micellar catalysis and microwave heating for the eco-friendly HAM of anilines by using water as the reaction medium. Secondary and tertiary anilines are obtained in good yields and regioselectivity with a full recovery of the catalyst in the water/micellar media that can be reused several times without drastic impacts on the reaction yields and regioselcetivity. The final amines are obtained as pure products by filtration on SCX columns. The characterization of the possible active catalytic species involved in the process is also reported. Mechanistic investigations suggest a different pathway compared to the commonly observed mechanism with homogeneous catalysts for the reported HAM reaction. Finally, LCA analysis of the protocol was performed, that demontrates the greeness and low environmental impact of the process. Beside this work, the synthesis of a small library of potential inhibitors of SIRT1, deacetylase involved in noumerous biological pathways and pathologies, included anxiety and depression, is reported. Finally, a third section is dedicated to design and early stage synthesis of a photolabeling probe precursor, by functionalization of quinoline compounds endowed with a good antibacterial activity, for the future further investigation of the interactions between these compounds and bacteria
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