On the Single Wall Carbon Nanotube Surface Plasmon Stability

Acknowledgements We thank the Laboratory for Advanced Computing (LCA) of the University of Coimbra for the computer time allocated to this project.Peer reviewedPublisher PD

Modeling Soft Supramolecular Nanostructures by Molecular Simulations

The design and assembly of soft supramolecular structures based on small building blocks are governed by non-covalent interactions, selective host-guest interactions, or a combination of different interaction types. There is a surprising number of studies supporting the use of computational models for mimicking supramolecular nanosystems and studying the underlying patterns of molecular recognition and binding, in multi-dimensional approaches. Based on physical properties and mathematical concepts, these models are able to provide rationales for the conformation, solvation and thermodynamic characterization of this type of systems. Molecular dynamics (MD), including free-energy calculations, yield a direct coupling between experimental and computational investigation. This chapter provides an overview of the available MD-based methods, including path-based and alchemical free-energy calculations. The theoretical background is briefly reviewed and practical instructions are introduced on the selection of methods and post-treatment procedures. Relevant examples in which non-covalent interactions dominate are presented

Computational Repurposing of Mitoxantrone-Related Structures against Monkeypox Virus : A Molecular Docking and 3D Pharmacophore Study

Acknowledgments: A sincere thanks to P.S. Oberoi (I.C.A.R, N.D.R.I., India) and Rishi Vachaspathy Astakala (Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, UK) for their constructive suggestions. Additionally, thank Nidhan Singh Oberoi and Albrn Care, India. Funding: B.F.M. acknowledges national funds from the Portuguese FCT—Fundação para a Ciência e a Tecnologia, I.P., within the projects UIDB/04564/2020 and UIDP/04564/2020.Peer reviewedPublisher PD

Structure-Based Design, Synthesis and Bioactivity of a New Anti-TNFα Cyclopeptide

As opposed to small molecules, macrocyclic peptides possess a large surface area and are recognised as promising candidates to selectively treat diseases by disrupting specific protein–protein interactions (PPIs). Due to the difficulty in predicting cyclopeptide conformations in solution, the de novo design of bioactive cyclopeptides remains significantly challenging. In this study, we used the combination of conformational analyses and molecular docking studies to design a new cyclopeptide inhibitor of the interaction between the human tumour necrosis factor alpha (TNFα) and its receptor TNFR-1. This interaction is a key in mediating the inflammatory response to tissue injury and infection in humans, and it is also an important causative factor of rheumatoid arthritis, psoriasis and inflammatory bowel disease. The solution state NMR structure of the cyclopeptide was determined, which helped to deduce its mode of interaction with TNFα. TNFα sensor cells were used to evaluate the biological activity of the peptide

Discovery and structural assignment of (S)-sydosine from amphipod-derived Aspergillus sydowii MBC15-11F through HRMS, advanced Mosher, and molecular modelling analyses

AimsThis study aims to prioritize fungal strains recovered from under-explored habitats that produce new metabolites. HRMS dereplication is used to avoid structure redundancy, and molecular modelling is used to assign absolute configuration.Methods and resultsMBC15-11F was isolated from an amphipod and identified using ITS, 28S, and β-tubulin phylogeny as Aspergillus sydowii. Chemical profiling using taxonomic-based dereplication identified structurally diverse metabolites, including unreported ones. Large-scale fermentation led to the discovery of a new N-acyl adenosine derivative: (S)-sydosine (1) which was elucidated by NMR and HRESIMS analyses. Two known compounds were also identified as predicted by the initial dereplication process. Due to scarcity of 1, molecular modelling was used to assign its absolute configuration without hydrolysis, and is supported by advanced Mosher derivatization. When the isolated compounds were assessed against a panel of bacterial pathogens, only phenamide (3) showed anti-Staphylococcus aureus activity.ConclusionFermentation of A. sydowii yielded a new (S)-sydosine and known metabolites as predicted by HRESIMS-aided dereplication. Molecular modelling prediction of the absolute configuration of 1 agreed with advanced Mosher analysis

LC-HRMS-Database Screening Metrics for Rapid Prioritization of Samples to Accelerate the Discovery of Structurally New Natural Products

In order to accelerate the isolation and characterization of structurally new or novel secondary metabolites, it is crucial to develop efficient strategies that prioritize samples with greatest promise early in the workflow so that resources can be utilized in a more efficient and cost-effective manner. We have developed a metrics-based prioritization approach using exact LC-HRMS, which uses data for 24 618 marine natural products held in the PharmaSea database. Each sample was evaluated and allocated a metric score by a software algorithm based on the ratio of new masses over the total (sample novelty), ratio of known masses over the total (chemical novelty), number of peaks above a defined peak area threshold (sample complexity), and peak area (sample diversity). Samples were then ranked and prioritized based on these metric scores. To validate the approach, eight marine sponges and six tunicate samples collected from the Fiji Islands were analyzed, metric scores calculated, and samples targeted for isolation and characterization of new compounds. Structures of new compounds were elucidated by spectroscopic techniques, including 1D and 2D NMR, MS, and MS/MS. Structures were confirmed by computer-assisted structure elucidation methods (CASE) using the ACD/Structure Elucidator Suite

Different molecular conformations in the crystal structures of three 5-nitroimidazolyl derivatives

Acknowledgements We thank the EPSRC National Crystallography Service (University of Southampton) for the X-ray data collections.Peer reviewedPublisher PD

The Peculiar SN 2005hk: Do Some Type Ia Supernovae Explode as Deflagrations?

We present extensive u'g'r'i'BVRIYJHKs photometry and optical spectroscopy of SN 2005hk. These data reveal that SN 2005hk was nearly identical in its observed properties to SN 2002cx, which has been called ``the most peculiar known type Ia supernova.'' Both supernovae exhibited high ionization SN 1991T-like pre-maximum spectra, yet low peak luminosities like SN 1991bg. The spectra reveal that SN 2005hk, like SN 2002cx, exhibited expansion velocities that were roughly half those of typical type Ia supernovae. The R and I light curves of both supernovae were also peculiar in not displaying the secondary maximum observed for normal type Ia supernovae. Our YJH photometry of SN 2005hk reveals the same peculiarity in the near-infrared. By combining our optical and near-infrared photometry of SN 2005hk with published ultraviolet light curves obtained with the Swift satellite, we are able to construct a bolometric light curve from ~10 days before to ~60 days after B maximum. The shape and unusually low peak luminosity of this light curve, plus the low expansion velocities and absence of a secondary maximum at red and near-infrared wavelengths, are all in reasonable agreement with model calculations of a 3D deflagration which produces ~0.25 M_sun of 56Ni.Comment: Accepted by PASP, to appear in April 2007 issue, 63 pages, 16 figures, 11 table