All Outputs (32)

Protein Oxidative Modifications in Neurodegenerative Diseases: From Advances in Detection and Modelling to Their Use as Disease Biomarkers (2024)
Journal Article

Oxidation–reduction post-translational modifications (redox-PTMs) are chemical alterations to amino acids of proteins. Redox-PTMs participate in the regulation of protein conformation, localization and function, acting as signalling effectors that im... Read More about Protein Oxidative Modifications in Neurodegenerative Diseases: From Advances in Detection and Modelling to Their Use as Disease Biomarkers.

Optimizing Excipient Properties to Prevent Aggregation in Biopharmaceutical Formulations (2023)
Journal Article

Excipients are included within protein biotherapeutic solution formulations to improve colloidal and conformational stability but are generally not designed for the specific purpose of preventing aggregation and improving cryoprotection in solution.... Read More about Optimizing Excipient Properties to Prevent Aggregation in Biopharmaceutical Formulations.

Design, Synthesis, and Application of Fluorescent Ligands Targeting the Intracellular Allosteric Binding Site of the CXC Chemokine Receptor 2 (2023)
Journal Article

The inhibition of CXC chemokine receptor 2 (CXCR2), a key inflammatory mediator, is a potential strategy in the treatment of several pulmonary diseases and cancers. The complexity of endogenous chemokine interaction with the orthosteric binding site... Read More about Design, Synthesis, and Application of Fluorescent Ligands Targeting the Intracellular Allosteric Binding Site of the CXC Chemokine Receptor 2.

Linear Binary Classifier to Predict Bacterial Biofilm Formation on Polyacrylates (2023)
Journal Article

Bacterial infections are increasingly problematic due to the rise of antimicrobial resistance. Consequently, the rational design of materials naturally resistant to biofilm formation is an important strategy for preventing medical device-associated i... Read More about Linear Binary Classifier to Predict Bacterial Biofilm Formation on Polyacrylates.

In Vitro Anticancer Properties of Novel Bis-Triazoles (2022)
Journal Article

Here, we describe the anticancer activity of our novel bis-triazoles MS47 and MS49, developed previously as G-quadruplex stabilizers, focusing specifically upon the human melanoma MDA-MB-435 cell line. At the National Cancer Institute (NCI), USA, bis... Read More about In Vitro Anticancer Properties of Novel Bis-Triazoles.

Development of fluorescent peptide G protein-coupled receptor activation biosensors for NanoBRET characterization of intracellular allosteric modulators (2022)
Journal Article

G protein-coupled receptors (GPCRs) are widely therapeutically targeted, and recent advances in allosteric modulator development at these receptors offer further potential for exploitation. Intracellular allosteric modulators (IAM) represent a class... Read More about Development of fluorescent peptide G protein-coupled receptor activation biosensors for NanoBRET characterization of intracellular allosteric modulators.

GLIMPS: A Machine Learning Approach to Resolution Transformation for Multiscale Modeling (2021)
Journal Article

We describe a general approach to transforming molecular models between different levels of resolution, based on machine learning methods. The approach uses a matched set of models at both levels of resolution for training, but requires only the coor... Read More about GLIMPS: A Machine Learning Approach to Resolution Transformation for Multiscale Modeling.

Nanoformulation-by-design: an experimental and molecular dynamics study for polymer coated drug nanoparticles (2020)
Journal Article

© The Royal Society of Chemistry 2020. The formulation of drug compounds into nanoparticles has many potential advantages in enhancing bioavailability and improving therapeutic efficacy. However, few drug molecules will assemble into stable, well-def... Read More about Nanoformulation-by-design: an experimental and molecular dynamics study for polymer coated drug nanoparticles.

Ligand-induced conformational selection predicts the selectivity of cysteine protease inhibitors (2019)
Journal Article

Cruzain, a cysteine protease of Trypanosoma cruzi, is a validated target for the treatment of Chagas disease. Due to its high similarity in three-dimensional structure with human cathepsins and their sequence identity above 70% in the active site reg... Read More about Ligand-induced conformational selection predicts the selectivity of cysteine protease inhibitors.

Principal nested shape space analysis of molecular dynamics data (2019)
Journal Article

Molecular dynamics simulations produce huge datasets of temporal sequences of molecules. It is of interest to summarize the shape evolution of the molecules in a succinct, low-dimensional representation. However, Euclidean techniques such as principa... Read More about Principal nested shape space analysis of molecular dynamics data.

BioSimSpace: An interoperable Python framework for biomolecular simulation (2019)
Journal Article

Poly(triazolyl methacrylate) glycopolymers as potential targeted unimolecular nanocarriers (2019)
Journal Article

Synthetic glycopolymers are increasingly investigated as multivalent ligands for a range of biological and biomedical applications. This study indicates that glycopolymers with fine-tuned balance between hydrophilic sugar pendant units and relatively... Read More about Poly(triazolyl methacrylate) glycopolymers as potential targeted unimolecular nanocarriers.

Tios: The Internet of Simulations. Turning Molecular Dynamics into a Data Streaming Web Application (2019)
Journal Article

The configuration of most current academic high-performance computing (HPC) resources tends to enforce ways of working with, and thinking about, molecular dynamics (MD) simulations that are not always optimal. For example, when the aim of the simulat... Read More about Tios: The Internet of Simulations. Turning Molecular Dynamics into a Data Streaming Web Application.

CoCo-MD: A Simple and Effective Method for the Enhanced Sampling of Conformational Space (2019)
Journal Article

© 2019 American Chemical Society. CoCo ("complementary coordinates") is a method for ensemble enrichment based on principal component analysis (PCA) that was developed originally for the investigation of NMR data. Here we investigate the potential of... Read More about CoCo-MD: A Simple and Effective Method for the Enhanced Sampling of Conformational Space.

Experimental study and computational modelling of cruzain cysteine protease inhibition by dipeptidyl nitriles (2018)
Journal Article

Chagas disease affects millions of people in Latin America. This disease is caused by the protozoan parasite Trypanossoma cruzi. The cysteine protease cruzain is a key enzyme for the survival and propagation of this parasite lifecycle. Nitrile-based... Read More about Experimental study and computational modelling of cruzain cysteine protease inhibition by dipeptidyl nitriles.

In Silico Screening for Solid Dispersions: The Trouble with Solubility Parameters and χFH (2018)
Journal Article

© Copyright 2018 American Chemical Society. The problem of predicting small molecule-polymer compatibility is relevant to many areas of chemistry and pharmaceutical science but particularly drug delivery. Computational methods based on Hildebrand and... Read More about In Silico Screening for Solid Dispersions: The Trouble with Solubility Parameters and χFH.

Development of a series of bis-triazoles as G-quadruplex ligands (2017)
Journal Article

Maintenance of telomeres – specialized complexes that protect the ends of chromosomes – is provided by the enzyme complex telomerase, which is a key factor that is activated in more than 80% of cancer cells, but absent in most normal cells. Targeting... Read More about Development of a series of bis-triazoles as G-quadruplex ligands.

Covariance analysis for temporal data, with applications to DNA modelling (2017)
Journal Article

We introduce methodology for analysing the mean size-and-shape and covariance matrix of landmark data that are collected over time. Motivated by a study of DNA damage, we study some permutation based tests for investigating significant differences in... Read More about Covariance analysis for temporal data, with applications to DNA modelling.

Unveiling a novel transient druggable pocket in BACE-1 through molecular simulations: conformational analysis and binding mode of multisite inhibitors (2017)
Journal Article

The critical role of BACE-1 in the formation of neurotoxic ß-amyloid peptides in the brain makes it an attractive target for an efficacious treatment of Alzheimer’s disease. However, the development of clinically useful BACE-1 inhibitors has proven t... Read More about Unveiling a novel transient druggable pocket in BACE-1 through molecular simulations: conformational analysis and binding mode of multisite inhibitors.

Rapid nano-gram scale screening method of micro-arrays to evaluate drug-polymer blends using high-throughput printing technology (2017)
Journal Article

A miniaturized, high-throughput assay was optimized to screen polymer-drug solid dispersions using a 2-D Ink-jet printer. By simply printing nanoliter amounts of polymer and drug solutions onto an inert surface, drug:polymer micro-dots of tunable com... Read More about Rapid nano-gram scale screening method of micro-arrays to evaluate drug-polymer blends using high-throughput printing technology.