Thermal titration molecular dynamics (TTMD): shedding light on the stability of RNA-small molecule complexes.

Ribonucleic acids are gradually becoming relevant players among putative drug targets, thanks to the increasing amount of structural data exploitable for the rational design of selective and potent binders that can modulate their activity. Mainly, this information allows employing different computational techniques for predicting how well would a ribonucleic-targeting agent fit within the active site of its target macromolecule. Due to some intrinsic peculiarities of complexes involving nucleic acids, such as structural plasticity, surface charge distribution, and solvent-mediated interactions, the application of routinely adopted methodologies like molecular docking is challenged by scoring inaccuracies, while more physically rigorous methods such as molecular dynamics require long simulation times which hamper their conformational sampling capabilities. In the present work, we present the first application of Thermal Titration Molecular Dynamics (TTMD), a recently developed method for the qualitative estimation of unbinding kinetics, to characterize RNA-ligand complexes. In this article, we explored its applicability as a post-docking refinement tool on RNA in complex with small molecules, highlighting the capability of this method to identify the native binding mode among a set of decoys across various pharmaceutically relevant test cases.

A comprehensive study of SARS-CoV-2 main protease (Mpro) inhibitor-resistant mutants selected in a VSV-based system.

Nirmatrelvir was the first protease inhibitor (PI) specifically developed against the SARS-CoV-2 main protease (3CLpro/Mpro) and licensed for clinical use. As SARS-CoV-2 continues to spread, variants resistant to nirmatrelvir and other currently available treatments are likely to arise. This study aimed to identify and characterize mutations that confer resistance to nirmatrelvir. To safely generate Mpro resistance mutations, we passaged a previously developed, chimeric vesicular stomatitis virus (VSV-Mpro) with increasing, yet suboptimal concentrations of nirmatrelvir. Using Wuhan-1 and Omicron Mpro variants, we selected a large set of mutants. Some mutations are frequently present in GISAID, suggesting their relevance in SARS-CoV-2. The resistance phenotype of a subset of mutations was characterized against clinically available PIs (nirmatrelvir and ensitrelvir) with cell-based and biochemical assays. Moreover, we showed the putative molecular mechanism of resistance based on in silico molecular modelling. These findings have implications on the development of future generation Mpro inhibitors, will help to understand SARS-CoV-2 protease-inhibitor-resistance mechanisms and show the relevance of specific mutations in the clinic, thereby informing treatment decisions.

Thermal Titration Molecular Dynamics (TTMD): Not Your Usual Post-Docking Refinement.

Molecular docking is one of the most widely used computational approaches in the field of rational drug design, thanks to its favorable balance between the rapidity of execution and the accuracy of provided results. Although very efficient in exploring the conformational degrees of freedom available to the ligand, docking programs can sometimes suffer from inaccurate scoring and ranking of generated poses. To address this issue, several post-docking filters and refinement protocols have been proposed throughout the years, including pharmacophore models and molecular dynamics simulations. In this work, we present the first application of Thermal Titration Molecular Dynamics (TTMD), a recently developed method for the qualitative estimation of protein-ligand unbinding kinetics, to the refinement of docking results. TTMD evaluates the conservation of the native binding mode throughout a series of molecular dynamics simulations performed at progressively increasing temperatures with a scoring function based on protein-ligand interaction fingerprints. The protocol was successfully applied to retrieve the native-like binding pose among a set of decoy poses of drug-like ligands generated on four different pharmaceutically relevant biological targets, including casein kinase 1δ, casein kinase 2, pyruvate dehydrogenase kinase 2, and SARS-CoV-2 main protease.

Qualitative Estimation of Protein-Ligand Complex Stability through Thermal Titration Molecular Dynamics Simulations.

The prediction of ligand efficacy has long been linked to thermodynamic properties such as the equilibrium dissociation constant, which considers both the association and the dissociation rates of a defined protein-ligand complex. In the last 15 years, there has been a paradigm shift, with an increased interest in the determination of kinetic properties such as the drug-target residence time since they better correlate with ligand efficacy compared to other parameters. In this article, we present thermal titration molecular dynamics (TTMD), an alternative computational method that combines a series of molecular dynamics simulations performed at progressively increasing temperatures with a scoring function based on protein-ligand interaction fingerprints for the qualitative estimation of protein-ligand-binding stability. The protocol has been applied to four different pharmaceutically relevant test cases, including protein kinase CK1δ, protein kinase CK2, pyruvate dehydrogenase kinase 2, and SARS-CoV-2 main protease, on a variety of ligands with different sizes, structures, and experimentally determined affinity values. In all four cases, TTMD was successfully able to distinguish between high-affinity compounds (low nanomolar range) and low-affinity ones (micromolar), proving to be a useful screening tool for the prioritization of compounds in a drug discovery campaign.

Implementing a Scoring Function Based on Interaction Fingerprint for Autogrow4: Protein Kinase CK1δ as a Case Study.

In the last 20 years, fragment-based drug discovery (FBDD) has become a popular and consolidated approach within the drug discovery pipeline, due to its ability to bring several drug candidates to clinical trials, some of them even being approved and introduced to the market. A class of targets that have proven to be particularly suitable for this method is represented by kinases, as demonstrated by the approval of BRAF inhibitor vemurafenib. Within this wide and diverse set of proteins, protein kinase CK1δ is a particularly interesting target for the treatment of several widespread neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. Computational methodologies, such as molecular docking, are already routinely and successfully applied in FBDD campaigns alongside experimental techniques, both in the hit-discovery and in the hit-optimization stage. Concerning this, the open-source software Autogrow, developed by the Durrant lab, is a semi-automated computational protocol that exploits a combination between a genetic algorithm and a molecular docking software for de novo drug design and lead optimization. In the current work, we present and discuss a modified version of the Autogrow code that implements a custom scoring function based on the similarity between the interaction fingerprint of investigated compounds and a crystal reference. To validate its performance, we performed both a de novo and a lead-optimization run (as described in the original publication), evaluating the ability of our fingerprint-based protocol to generate compounds similar to known CK1δ inhibitors based on both the predicted binding mode and the electrostatic and shape similarity in comparison with the standard Autogrow protocol.

Efeito antiedematogênico de óleos contendo ácidos graxos ômega-3 e 6 em camundongos / Antiedematous effect of oils containing the fatty acids omega-3 and 6 in mice

O presente trabalho teve por objetivo avaliar o efeito antiedematogênico tópico de óleos de semente de girassol, de uva, de prímula e óleo de peixe marinho, os quais apresentam em sua composição os ácidos graxos insaturados das famílias ômega-6 e ômega-3. Os ensaios farmacológicos, conduzidos nas orelhas dos camundongos, foram realizados após a aplicação prévia de um agente edematogênico, o óleo de cróton, e posterior tratamento com os óleos vegetais e de peixe utilizando o controle positivo (aplicação de dexametasona) e o controle negativo (aplicação de solução acetona/água 70:30). Os resultados revelaram valores de redução do edema em 31,5%, 29,2%, 20,4% e 7,3% para os óleos de girassol, uva, prímula e peixe, respectivamente, quando comparado ao grupo-controle negativo. Os óleos de girassol, uva e prímula, quando associados ao veículo cáprico-caprílico, mostraram melhora significativa no efeito antiedematogênico, com valores de redução do edema em 38,2% 40,6% e 30,2%, respectivamente (P<0,05). Portanto, foi evidenciado que o ácido linoleico, o principal ácido graxo da família ômega-6 presente nas amostras, associado com os ácidos caprílico e cáprico possui potente ação antiedematogênica tópica. Este efeito não foi observado para os ácidos graxos de cadeia longa da família ômega-3 presentes no óleo marinho.

O perfume e o alquimista / The fragrance and the alchemist

Os autores apresentam revisäo da literatura sobre perfumes cotizando dados históricos, classificaçäo brasileira dos perfumes, composiçäo, controle de qualidade, estabilidade e aplicaçöes principais.

Estudo da estabilidade à temperatura ambiente de soluçöes de PVP-I tópica e degermante ( / Study of topic and soap PVP-I solutions at room temperature

A polivinilpirrolidona-iodo, também conhecida como PVP-I, é um dos anti-sépticos mais utilizados pelos profissionais da área da saúde, por possuir as mesmas propriedades germicidasdo iodo sem as desvantagens deste, ou seja, causar irritaçäo à pele e às mucosas, ser tóxico, apresentar baixa solubilidade em água. Esse produto é comercializado sob diversas formas farmacêuticas, sendo as mais conhecidas as soluçöes para uso tópico, degermante e tintura. Säo escassas as refências sobre a estabilidade dessas formas farmacêuticas. Neste trabalho, soluçöes de PVP-I aqüosas e degermante (existentes no mercado e por nós desenvolvidas), foram mantidas em prateleira à temperatura ambientepor um ano, analizando-se o teor de iodo e medindo-se o pH a cada 30 dias.