Synthesis and Structure-Activity Relationship Analysis of 2-Substituted-1,2,4-Triazolo[1,5-a]Pyrimidin-7-Ones and their 6-Carboxylate Derivatives as Xanthine Oxidase Inhibitors.

Hyperuricemia is characterised by high blood levels of uric acid, and it can degenerate into gout when monosodium urate crystals precipitate in joints and other tissues. Uric acid is produced during the catabolism of xanthine by the enzyme xanthine oxidase (XO), which is the primary therapeutic target in gout treatment. Current XO inhibitors approved to treat gout, such as allopurinol and febuxostat, suffer from serious adverse effects, creating the need for new drug molecules.

An atomistic characterization of high-density lipoproteins and the conserved "LN" region of apoA-I.

The physicochemical characteristics of the various subpopulations of high-density lipoproteins (HDLs) and, in particular, their surface properties determine their ability to scavenge lipids and interact with specific receptors and peptides. Five representative spheroidal HDL subpopulation models were mapped from a previously reported equilibrated coarse-grained (CG) description to an atomistic representation for subsequent molecular dynamics simulation. For each HDL model a range of finer-level analyses was undertaken, including the component-wise characterization of HDL surfaces, the average size and composition of hydrophobic surface patches, dynamic protein secondary structure monitoring, and the proclivity for solvent exposure of the proposed β-amyloid (Aβ) binding region of apolipoprotein A-I (apoA-I), "LN.

What determines sub-diffusive behavior in crowded protein solutions?

The aqueous environment inside cells is densely packed. A typical cell has a macromolecular concentration in the range 90-450 g/L, with 5%-40% of its volume being occupied by macromolecules, resulting in what is known as macromolecular crowding. The space available for the free diffusion of metabolites and other macromolecules is thus greatly reduced, leading to so-called excluded volume effects.

The Molecular Docking of MAX Fungal Effectors with Plant HMA Domain-Binding Proteins.

Fungal effector proteins are important in mediating disease infections in agriculturally important crops. These secreted small proteins are known to interact with their respective host receptor binding partners in the host, either inside the cells or in the apoplastic space, depending on the localisation of the effector proteins. Consequently, it is important to understand the interactions between fungal effector proteins and their target host receptor binding partners, particularly since this can be used for the selection of potential plant resistance or susceptibility-related proteins that can be applied to the breeding of new cultivars with disease resistance.

Unravelling the influence of surface lipids on the structure, dynamics and interactome of high-density lipoproteins.

Surface lipids influence the biological activities of high-density lipoproteins (HDLs) but their species-specific effects on HDL structure, dynamics, and surface interactome has remained unclear. Building upon the five-lipid species HDL models developed and characterised in previous work, representative models of the major HDL subpopulations found in human plasma containing apolipoprotein A-I (apoA-I) have been studied using molecular dynamics simulation to describe their varying degrees of surface lipidome complexity. Specifically, two additional sets of representative HDL subpopulation particles were developed, one with sphingomyelin (SM) and the other with SM, phosphatidylethanolamine, phosphatidylinositol, and ceramide in quantities reflecting average levels characterised for HDL subpopulations derived from normolipidemic patients.

Ab Initio Modelling of the Structure of ToxA-like and MAX Fungal Effector Proteins.

Pathogenic fungal diseases in crops are mediated by the release of effector proteins that facilitate infection. Characterising the structure of these fungal effectors is vital to understanding their virulence mechanisms and interactions with their hosts, which is crucial in the breeding of plant cultivars for disease resistance. Several effectors have been identified and validated experimentally; however, their lack of sequence conservation often impedes the identification and prediction of their structure using sequence similarity approaches.

Template-Based Modelling of the Structure of Fungal Effector Proteins.

The discovery of new fungal effector proteins is necessary to enable the screening of cultivars for disease resistance. Sequence-based bioinformatics methods have been used for this purpose, but only a limited number of functional effector proteins have been successfully predicted and subsequently validated experimentally. A significant obstacle is that many fungal effector proteins discovered so far lack sequence similarity or conserved sequence motifs.

A Simple but Effective Combination of pH Indicators for Plant Tissue Culture.

The use of pH indicators provides a simple, semi-quantitative visual method for quickly assessing pH changes in tissue culture media; however, pH indicators are rarely used in routine plant tissue culture media. In this study, chlorophenol red, bromocresol purple, and bromocresol green were tested to assess their functionality in the growth medium for plant shoot cultures. In addition, a combination of bromocresol green and bromocresol purple was tested to determine if they would widen the observable colour change to better assess pH changes in the medium.

Characterisation of the Molecular Mechanism of Permeation of the Prodrug Me-5ALA across the Human Using Molecular Dynamics Simulations.

The barrier imposed by the outer layer of the skin, the , creates an almost impermeable environment for exogenous substances. Few lipophilic drugs with low molecular mass can passively diffuse through this layer, highlighting the need to develop methods to enable the delivery of more drugs via the transdermal route. The prodrug approach involves modifying the structure of a drug molecule to enhance its permeability across the skin, but it is often difficult to predict how exactly changes in chemical structure affect permeation.

How does metabolic rate in plant shoot tips change after cryopreservation?

Cryopreservation allows the long-term storage of plant germplasm, but can cause damage to plant tissues, which must be repaired for survival to occur. This repair process is fuelled by the metabolic function of mitochondria; however, little is known about how metabolic function is affected by the cryopreservation process in plants. We compared metabolic rates of shoot tips of two Australian native species, Androcalva perlaria and Anigozanthos viridis.

Characterization of the Conformations of Amyloid Beta 42 in Solution That May Mediate Its Initial Hydrophobic Aggregation.

Intrinsically disordered peptides, such as amyloid β42 (Aβ42), lack a well-defined structure in solution. Aβ42 can undergo abnormal aggregation and amyloidogenesis in the brain, forming fibrillar plaques, a hallmark of Alzheimer's disease. The insoluble fibrillar forms of Aβ42 exhibit well-defined, cross β-sheet structures at the molecular level and are less toxic than the soluble, intermediate disordered oligomeric forms.

Influence of force field choice on the conformational landscape of rat and human islet amyloid polypeptide.

Human islet amyloid polypeptide (hIAPP) is a naturally occurring, intrinsically disordered protein (IDP) whose abnormal aggregation into toxic soluble oligomers and insoluble amyloid fibrils is a pathological feature in type-2 diabetes. Rat IAPP (rIAPP) differs from hIAPP by only six amino acids yet has a reduced tendency to aggregate or form fibrils. The structures of the monomeric forms of IAPP are difficult to characterize due to their intrinsically disordered nature.

Review: Investigating the aggregation of amyloid beta with surface plasmon resonance: Do different approaches yield different results?

Aggregation of amyloid beta into amyloid plaques in the brain is a hallmark characteristic of Alzheimer's disease. Therapeutics aimed at preventing or retarding amyloid formation often rely on detailed characterization of the underlying mechanism and kinetics of protein aggregation. Surface plasmon resonance (SPR) spectroscopy is a robust technique used to determine binding affinity and kinetics of biomolecular interactions.

Myrtaceae in Australia: Use of Cryobiotechnologies for the Conservation of a Significant Plant Family under Threat.

The Myrtaceae is a very large and diverse family containing a number of economically and ecologically valuable species. In Australia, the family contains approximately 1700 species from 70 genera and is structurally and floristically dominant in many diverse ecosystems. In addition to threats from habitat fragmentation and increasing rates of natural disasters, infection by myrtle rust caused by is of significant concern to Australian Myrtaceae species.

Redefining the Molecular Interplay between Dimethyl Sulfoxide, Lipid Bilayers, and Dehydration.

The potentially damaging action of dimethyl sulfoxide (DMSO) on phospholipid bilayers remains a matter of controversy. We have conducted a series of long-scale molecular dynamics simulations of 1,2-dioleoyl--glycero-3-phosphocholine (DOPC) bilayers at various levels of hydration in the presence of variable quantities of DMSO. These simulations provide evidence for a non-destructive dehydrating mechanism of action for DMSO on DOPC bilayers across a wide concentration range and levels of hydration.

Novel Amylin Analogues Reduce Amyloid-β Cross-Seeding Aggregation and Neurotoxicity.

Background: Type 2 diabetes related human islet amyloid polypeptide (hIAPP) plays a dual role in Alzheimer's disease (AD). hIAPP has neuroprotective effects in AD mouse models whereas, high hIAPP concentrations can promote co-aggregation with amyloid-β (Aβ) to promote neurodegeneration. In fact, both low and high plasma hIAPP concentration has been associated with AD.

Review: The case for studying mitochondrial function during plant cryopreservation.

Cryopreservation has several advantages over other ex situ conservation methods, and indeed is the only viable storage method for the long term conservation of most plant species. However, despite many advances in this field, it is increasingly clear that some species are ill-equipped to overcome the intense stress imposed by the cryopreservation process, making protocol development incredibly difficult using traditional trial and error methods. Cryobiotechnology approaches have been recently recognised as a strategic way forward, utilising intimate understanding of biological systems to inform development of more effective cryopreservation protocols.

Mechanisms of Interaction of Small Hydroxylated Cryosolvents with Dehydrated Model Cell Membranes: Stabilization vs Destruction.

The mechanism by which cryosolvents such as alcohols modify and penetrate cell membranes as a function of their concentration and hydration state remains poorly understood. We conducted molecular dynamics simulations of 1,2-dioleoyl--glycero-3-phosphocholine bilayers in the presence of aqueous solutions of four common penetrating hydroxylated cryosolvents (methanol, ethylene glycol, propylene glycol, and glycerol) at varying concentration ranges and across three different hydration states. All cryosolvents were found to preferentially replace water at the bilayer interface, and a reduction in hydration state correlates with a higher proportion of cryosolvent at the interface for relative concentrations.

An automated and combinative method for the predictive ranking of candidate effector proteins of fungal plant pathogens.

Fungal plant-pathogens promote infection of their hosts through the release of 'effectors'-a broad class of cytotoxic or virulence-promoting molecules. Effectors may be recognised by resistance or sensitivity receptors in the host, which can determine disease outcomes. Accurate prediction of effectors remains a major challenge in plant pathology, but if achieved will facilitate rapid improvements to host disease resistance.

Design and Characterization of a Cell-Penetrating Peptide Derived from the SOX2 Transcription Factor.

SOX2 is an oncogenic transcription factor overexpressed in nearly half of the basal-like triple-negative breast cancers associated with very poor outcomes. Targeting and inhibiting SOX2 is clinically relevant as high SOX2 mRNA levels are positively correlated with decreased overall survival and progression-free survival in patients affected with breast cancer. Given its key role as a master regulator of cell proliferation, SOX2 represents an important scaffold for the engineering of dominant-negative synthetic DNA-binding domains (DBDs) that act by blocking or interfering with the oncogenic activity of the endogenous transcription factor in cancer cells.

Pharmacological and structure-activity relationship studies of oleoyl-lysophosphatidylinositol synthetic mimetics.

Metabolic diseases, such as obesity and type 2 diabetes, are relentlessly spreading worldwide. The beginning of the 21st century has seen the introduction of mechanistically novel types of drugs, aimed primarily at keeping these pathologies under control. In particular, an important family of therapeutics exploits the beneficial physiology of the gut-derived glucagon-like peptide-1 (GLP-1), with important clinical benefits, from glycaemic control to cardioprotection.

Does the SARS-CoV-2 Spike Protein Receptor Binding Domain Interact Effectively with the DPP4 (CD26) Receptor? A Molecular Docking Study.

ACE2 has been established as the main receptor for SARS-CoV-2. Since other human coronaviruses are known to use co-receptors for viral cell entry, it has been suggested that DPP4 (CD26) could be a potential additional binding target or co-receptor, supported by early molecular docking simulation studies. However, recent biophysical studies have shown this interaction to be very weak.

BZD9L1 sirtuin inhibitor: Identification of key molecular targets and their biological functions in HCT 116 colorectal cancer cells.

BZD9L1 was previously described as a SIRT1/2 inhibitor with anti-cancer activities in colorectal cancer (CRC), either as a standalone chemotherapy or in combination with 5-fluorouracil. BZD9L1 was reported to induce apoptosis in CRC cells; however, the network of intracellular pathways and crosstalk between molecular players mediated by BZD9L1 is not fully understood. This study aimed to uncover the mechanisms involved in BZD9L1-mediated cytotoxicity based on previous and new findings for the prediction and identification of related pathways and key molecular players.