297 research outputs found
Computational Alanine Scanning and Structural Analysis of the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Complex
No full textThe recent emergence of the pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent for the coronavirus disease 2019 (COVID-19), is causing a global pandemic that poses enormous challenges to global public health and economies. SARS-CoV-2 host cell entry is mediated by the interaction of the viral transmembrane spike glycoprotein (S-protein) with the angiotensin-converting enzyme 2 gene (ACE2), an essential counter-regulatory carboxypeptidase of the renin-angiotensin hormone system that is a critical regulator of blood volume, systemic vascular resistance, and thus cardiovascular homeostasis. Accordingly, this work reports an atomistic-based, reliable in silico structural and energetic framework of the interactions between the receptor-binding domain of the SARS-CoV-2 S-protein and its host cellular receptor ACE2 that provides qualitative and quantitative insights into the main molecular determinants in virus/receptor recognition. In particular, residues D38, K31, E37, K353, and Y41 on ACE2 and Q498, T500, and R403 on the SARS-CoV-2 S-protein receptor-binding domain are determined as true hot spots, contributing to shaping and determining the stability of the relevant protein-protein interface. Overall, these results could be used to estimate the binding affinity of the viral protein to different allelic variants of ACE2 receptors discovered in COVID-19 patients and for the effective structure-based design and development of neutralizing antibodies, vaccines, and protein/protein inhibitors against this terrible new coronavirus
Structure of the σ1 Receptor and its Ligand Binding Site
No full textThe exact 3D structure of the enigmatic σ1 receptor is unknown, as the crystal structure of this protein has not been solved so far. Many efforts have been devoted to unveil the structure of the sigma1 receptor and, specifically, its binding site, which include photoaffinity labeling, site directed mutagenesis, and homology modeling. Aim of the present communication is to give a short overview of all results which contribute to the current knowledge of the σ1 receptor and its ligand binding site
Self-assembling Nanotechnology for Cancer Personalized Medicine
No full textTheranostics is a new field of medicine, which combines specific targeted therapies and diagnostic tests. With a key focus on patient centered care, theranostics provides a transition from conventional medicine to a contemporary personalized and precision medicine approach. The theranostic paradigm in cancer involves nanoscience to unite diagnostic and therapeutic applications to form nanosized agents for diagnosis, drug/gene delivery and treatment response monitoring. These nanocarriers can indeed be engineered to precisely control drug/gene/sensor-release rate and/or target specific organs/tissues within the body with a specific amount of therapeutic/diagnostic agent. In order to fulfill these expectations, any nanovector system must be designed to transport the optimum amount of therapeutic/diagnostic cargo to the desired target site where the active principle is to be released at an optimal rate during a specific time window. Keeping the promises of theranostics is a current formidable challenge in (bio)nanotechnology, and major efforts are devoted to the design of integrated multifunctional and multivalent nanovectors able to provide selective recognition combined with sustained release and/or diagnostic reporting. In this contribution, the pathway leading to two types of nanosystems obtained by exploiting the quintessence of nanotechnology, i.e., the self-assembling process of small, amphiphilic molecules, is reported. Depending on the specific chemistry adopted, these nanomicelles are able to perform specific and effective gene silencing via targeted small interfering RNA (siRNA) delivery, and provide PET images with significantly superior imaging quality relating
to sensitivity, specificity and accuracy when compared to the clinical standard [18F]FDG
Cationic Dendrimers for siRNA Delivery: Computational Approaches for Characterization
No full textNowadays, computer simulations have been established as a fundamental tool in the design and development of new dendrimer-based nanocarriers for drug and gene delivery. Moreover, the level of detail contained in the information that can be gathered by performing atomistic-scale simulations cannot be obtained with any other available experimental technique. In this chapter we describe the main computational toolbox that can be exploited in the different stages of novel dendritic nanocarrier production-from the initial conception to the stage of biological intermolecular interactions
PET/PEN blends of industrial interest as barrier materials. Part I. Many-scale molecular modeling of PET/PEN blends
No full textMesoscale molecular simulations, based on parameters obtained through atomistic molecular dynamics and Monte Carlo calculations, have
been used for modeling and predicting the behavior of PET/PEN blends. Different simulations have been performed in order to study and compare
pure homopolymer blends with blends characterized by the presence of PET/PEN block copolymers acting as compatibilizer. A many-scale
molecular modeling strategy was devised to evaluate PET/PEN blend characteristics, simulate phase segregation in pure PET/PEN blends, and
demonstrate the improvement of miscibility due to the presence of the transesterification reaction products. The behavior of distribution densities
and order parameters of the compatibilized blends demonstrates that mixing properties improve significantly, in agreement with experimental
evidences. Barrier properties such as oxygen diffusivity and permeability have also been evaluated by finite element simulations. Accordingly,
many-scale modeling seems to be a successful way to estimate PET/PEN blend properties and behavior upon different concentrations and
processing conditions
Direct Identification of α-Bisabolol Enantiomers in an Essential Oil Using a Combined Ion Mobility-Mass Spectrometry/Quantum Chemistry Approach
No full textEnantiomer-specific identification of chiral molecules in natural extracts is a challenging task, as many routine analytical techniques fail to provide selectivity in multicomponent mixtures. Here we describe an alternative approach, based on the combination of ion mobility-mass spectrometry (IM-MS) and quantum chemistry (QM), for the direct enantiomers differentiation in crude essential oils. The identification of α-bisabolol enantiomers contained in the raw essential oil (EO) from the Corsican Xanthium italicum fruits is reported as a proof-of-concept. Accordingly, IM-MS experiments performed in Ag+-doped methanol revealed the presence of both (+)- and (-)-α-bisabolol in the EO, while molecular simulations provided the structures of the two α-bisabolol enantiomer silver(I) adducts
Unchain my blood: Lessons learned from self-assembled dendrimers as nanoscale heparin binders
No full textThis review work reports a collection of coupled experimental/computational results taken from our own experience in the field of self-assembled dendrimers for heparin binding. These studies present and discuss both the potentiality played by this hybrid methodology to the design, synthesis, and development of possible protamine replacers for heparin anticoagulant activity reversal in biomedical applications, and the obstacles this field has still to overcome before these molecules can be translated into nanomedicines available in clinical settings
Cationic Dendrimers for siRNA Delivery: An Overview of Methods for In Vitro/In Vivo Characterization
No full textThis chapter reviews the different techniques for analyzing the chemical-physical properties, transfection efficiency, cytotoxicity, and stability of covalent cationic dendrimers (CCDs) and self-assembled cationic dendrons (ACDs) for siRNA delivery in the presence and absence of their nucleic cargos. On the basis of the reported examples, a standard essential set of techniques is described for each step of a siRNA/nanovector (NV) complex characterization process: (1) analysis of the basic chemical-physical properties of the NV per se; (2) characterization of the morphology, size, strength, and stability of the siRNA/NV ensemble; (3) characterization and quantification of the cellular uptake and release of the siRNA fragment; (4) in vitro and (5) in vivo experiments for the evaluation of the corresponding gene silencing activity; and (6) assessment of the intrinsic toxicity of the NV and the siRNA/NV complex
2(3)-aryl-thio(oxy)-methylquinoxaline derivatives: a new class of P-glycoprotein-mediated drug efflux inhibitor
No full textA series of quinoxalines variously substituted, namely 3-arylthiomethyl-1,6-dimethylquinoxalin-2-ones (6a-f), 3-arylthiomethyl-1-benzyl-7-trifluoromethylquinoxalin-2-ones (8a-g) and 2-arylthiomethyl-3-benzyloxy-6-trifluoro-methylquinoxalines (10a,b,e-h), were synthesized and compared with previous arylphenoxymethylquinoxalines (1a-f, 2a-f and 3a-b). The purpose was to verify whether the replacement of oxygen with sulphur atom and the insertion of different substituents on the phenyl side chain were able to improve the capability to inhibit the Pgp pump and restore the antiproliferative activity of clinically useful drugs, such as doxorubicin (Doxo), vincristine (VCR) and etoposide (VP16), in drug-resistant human nasopharyngeal carcinoma KB cells (KB(wt), KB(MDR), KB(7D) and KB(V20C)). Furthermore, 2,3-bis(aryloxy-methyl)-6-trifluoromethylquinoxalines (13a-c) were designed with the objective to evaluate the capability of the double side chain to potentiate the antiproliferative activity of the drugs tested. Biological assays showed that title compounds were, in general, endowed with good activity as Pgp inhibitors. In particular compound 3a, bearing 2-CONHPh substituent on phenoxymethyl side chain, resulted the most effective, while the double side chain (compound 13c) gives the ability to inhibit a different MRP pump (a membrane glycoprotein named mrp). Furthermore, we can conclude that replacement of oxygen with sulphur atom did not improve the biological activity
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