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Department of Pharmacology

 

Our research groups have been hard at work over the last few months. We've collected all the latest publications for your reading enjoyment here.

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Can Current Molecular Docking Methods Accurately Predict RNA Inhibitors?

Thu, 18/07/2024 - 11:00

J Chem Inf Model. 2024 Jul 18. doi: 10.1021/acs.jcim.4c00235. Online ahead of print.

ABSTRACT

Ribonucleic acids (RNAs), particularly the noncoding RNAs, play key roles in cancer, making them attractive drug targets. While conventional methods such as high throughput screening are resource-intensive, computational methods such as RNA-ligand docking can be used as an alternative. However, currently available docking methods are fine-tuned to perform protein-ligand and protein-protein docking. In this work, we evaluated three commonly used docking methods─AutoDock Vina, HADDOCK, and HDOCK─alongside RLDOCK, which is specifically designed for RNA-ligand docking. Our evaluation was based on several criteria including cognate docking, blind docking, scoring potential, and ranking potential. In cognate docking, only RLDOCK showed a success rate of 70% for the top-scoring docked pose. Despite this, all four docking methods did not achieve an overall success rate exceeding 50% amidst our attempt to refine the top-scoring docked poses using molecular dynamics simulations. Meanwhile, all four docking methods showed poor performance in scoring potential evaluation. Although AutoDock Vina achieved an area under the receiver operating characteristic curve of 0.70, it showed poor performance in terms of Matthews' correlation coefficient, precision, enrichment factors, and normalized enrichment factors at 1, 2, and 5%. These results highlight the growing need for further optimization of docking methods to assess RNA-ligand interactions.


α-Synuclein Oligomers Displace Monomeric α-Synuclein from Lipid Membranes

Tue, 25/06/2024 - 11:00

ACS Nano. 2024 Jun 25. doi: 10.1021/acsnano.3c10889. Online ahead of print.

ABSTRACT

Parkinson's disease (PD) is an increasingly prevalent and currently incurable neurodegenerative disorder linked to the accumulation of α-synuclein (αS) protein aggregates in the nervous system. While αS binding to membranes in its monomeric state is correlated to its physiological role, αS oligomerization and subsequent aberrant interactions with lipid bilayers have emerged as key steps in PD-associated neurotoxicity. However, little is known of the mechanisms that govern the interactions of oligomeric αS (OαS) with lipid membranes and the factors that modulate such interactions. This is in large part due to experimental challenges underlying studies of OαS-membrane interactions due to their dynamic and transient nature. Here, we address this challenge by using a suite of microfluidics-based assays that enable in-solution quantification of OαS-membrane interactions. We find that OαS bind more strongly to highly curved, rather than flat, lipid membranes. By comparing the membrane-binding properties of OαS and monomeric αS (MαS), we further demonstrate that OαS bind to membranes with up to 150-fold higher affinity than their monomeric counterparts. Moreover, OαS compete with and displace bound MαS from the membrane surface, suggesting that disruption to the functional binding of MαS to membranes may provide an additional toxicity mechanism in PD. These findings present a binding mechanism of oligomers to model membranes, which can potentially be targeted to inhibit the progression of PD.


Intestinal barrier function in the naked mole-rat: an emergent model for gastrointestinal insights

Tue, 25/06/2024 - 11:00

Am J Physiol Gastrointest Liver Physiol. 2024 Jun 25. doi: 10.1152/ajpgi.00080.2024. Online ahead of print.

ABSTRACT

The intestinal barrier plays a crucial role in homeostasis, both by facilitating absorption of nutrients and fluids, and providing a tight shield to prevent the invasion by either pathogen or commensal microorganisms. Intestinal barrier malfunction is associated with systemic inflammation, oxidative stress, and decreased insulin sensitivity, which may lead to the dysregulation of other tissues. Therefore, a deeper understanding of physiological aspects related to an enhanced barrier function is of significant scientific and clinical relevance. The naked mole-rat has many unusual biological features, including attenuated colonic neuron sensitivity to acid and bradykinin, and resistance to chemical-induced intestinal damage. However, insight into their intestinal barrier physiology is scarce. Here, we observed notable macroscopic and microscopic differences in intestinal tissue structure between naked mole-rats and mice. Moreover, naked mole-rats showed increased number of larger goblet cells and elevated mucus content. In measuring gut permeability, naked mole-rats showed reduced permeability compared to mice, measured as transepithelial electrical resistance, especially in ileum. Furthermore, intestinal ion secretion induced by serotonin, bradykinin, histamine, and capsaicin was significantly reduced in naked mole-rats compared to mice, despite the expression of receptors for all these agonists. In addition, naked mole-rats exhibited reduced pro-secretory responses to the non-selective adenylate cyclase activator forskolin. Collectively, these findings indicate that naked mole-rats possess a robust and hard-to-penetrate gastrointestinal barrier, that is resistant to environmental and endogenous irritants. Naked mole-rats may therefore provide valuable insights into the physiology of the intestinal barrier and set the stage for the development of innovative and effective therapies.


Dissecting the roles of dynamin and clathrin in platelet pinocytosis

Thu, 13/06/2024 - 11:00

Biochem Biophys Res Commun. 2024 Jun 10;725:150250. doi: 10.1016/j.bbrc.2024.150250. Online ahead of print.

ABSTRACT

Platelets endocytose many molecules from their environment. However, this process of pinocytosis in platelets is poorly understood. Key endocytic regulators such as dynamin, clathrin, CDC42 and Arf6 are expressed in platelets but their roles in pinocytosis is not known. Stimulated platelets form two subpopulations of pro-aggregatory and procoagulant platelets. The effect of stimulation on pinocytosis is also poorly understood. In this study, washed human platelets were treated with a range of endocytosis inhibitors and stimulated using different activators. The rate of pinocytosis was assessed using pHrodo green, a pH-sensitive 10 kDa dextran. In unstimulated platelets, pHrodo fluorescence increased over time and accumulated as intracellular puncta indicating constituently active pinocytosis. Stimulated platelets (both pro-aggregatory and procoagulant) had an elevated pinocytosis rate compared to unstimulated platelets. Dynamin inhibition blocked pinocytosis in unstimulated, pro-aggregatory and procoagulant platelets indicating that most platelet pinocytosis is dynamin dependent. Although pinocytosis was clathrin-independent in unstimulated and procoagulant populations, clathrin partially contributed to pinocytosis in pro-aggregatory platelets.

PMID:38870846 | DOI:10.1016/j.bbrc.2024.150250