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The Application of Fragment-based Approaches to the Discovery of Drugs for Neglected Tropical Diseases
Published in Venkatesan Jayaprakash, Daniele Castagnolo, Yusuf Özkay, Medicinal Chemistry of Neglected and Tropical Diseases, 2019
Christina Spry, Anthony G. Coyne
The MSGPP Consortium performed a number of X-ray crystallographic fragment screens to identify chemical starting points for inhibitors of leishmanial proteins crystallized by the consortium (Verlinde et al. 2009). A collection of fragment cocktails created in-house (the Biomolecular Structure Center (BMSC) collection), which was also used in the X-ray crystallographic fragment screens performed against TbNDRT and TcHisRS described in the previous section, was utilized for the screens.
FT-IR Studies of Molecular Conformation in Biological Membranes
Published in R. Michael Gendreau, Spectroscopy in the Biomedical Sciences, 1986
David G. Cameron, Richard A. Dluhy
There has been considerable success with the use of spectroscopic methods to determine the conformation of biomolecules. Techniques such as X-ray diffraction, nuclear magnetic resonance (NMR), electron spin resonance (ESR), fluorescence, infrared, and Raman have been used to obtain detailed information about biomolecular structure.1
Exploring Klebsiella pneumoniae capsule polysaccharide proteins to design multiepitope subunit vaccine to fight against pneumonia
Published in Expert Review of Vaccines, 2022
Jyotirmayee Dey, Soumya Ranjan Mahapatra, S Lata, Shubhransu Patro, Namrata Misra, Mrutyunjay Suar
Molecular dynamics analysis is pivotal to demonstrate the stability of the modeled biomolecular structure. The stability of the complex (TLR-2 and Vaccine construct) was studied by Molecular dynamics simulations using Gromacs2019 [42] using Charmm36-mar2019 force field for the protein parameters [43]. The complex was solvated explicitly using the TIP3P water model inside the cubic box, and its size extends 0.1 nm away from the protein on the edges of the box in each direction. The system’s overall charge was neutralized by adding a 0.1 M salt concentration (Na+Cl−). All the simulations were carried out in the GPU enabled Linux clusters. The entire system was minimized till the maximum force was less than 10 kj/mol with the maximum steps of 50,000. The system was then equilibrated for 5ns under NVT conditions with temperature coupling for two separate groups and water-ions, at 300 K. Lincs algorithm is used to constrain the bonds of the hydrogen atoms [44]. Berendsen thermostat and V-rescale were used to keep the temperature and pressure constant, respectively. The cutoff distances for Coulomb and van der Waals interactions were set as 1.2 nm. Particle mesh Ewald method (PME) was used to calculate the long-range electrostatic interactions. The final production run was carried out for 100ns at a temperature of 300 K and a pressure of 1 bar. The results were analyzed using the gromacs modules and VMD [45], the graphs were generated using xmgrace.
Electron microscopy overview of SARS-COV2 and its clinical impact
Published in Ultrastructural Pathology, 2022
Soheir Saiid Mansy, Mona Mahmoud AbouSamra
Many techniques, including NMR spectroscopy, X-ray solution scattering, neutron diffraction, various spectroscopic techniques, and X-ray crystallography, have been used to determine the shape and structure of biological molecules. Recently, cryo-electron microscopy has become the most effective tool in structural biology after the technical development of its resolutions, which permits the identification of the biomolecular structure in its natural state.59 Cryo-EM has an advantage over X-ray crystallography, and is the most effective tool in analyzing macromolecules during the last few years. Cryo-EM reveals structures in fast-frozen non-crystalline biological samples that are closer to their natural state at an atomic level. In addition, it requires much smaller macromolecule samples to work with, unlike X-ray crystallography, which needs large pieces of materials to optimize the crystallization conditions.59 Hence, cryo-EM has become the tool of choice for determining the structure of macromolecular complexes, especially supra-assemblies that are difficult to prepare in large quantities or virtually inaccessible to crystallize.59,61,62 Identifying the structural biology of viral protein complexes at molecular resolution is important for designing small drug molecules to bind and impair their function.32
Evaluation of the published kinase inhibitor set to identify multiple inhibitors of bacterial ATP-dependent mur ligases
Published in Journal of Enzyme Inhibition and Medicinal Chemistry, 2019
Martina Hrast, Kaja Rožman, Iza Ogris, Veronika Škedelj, Delphine Patin, Matej Sova, Hélène Barreteau, Stanislav Gobec, Simona Golič Grdadolnik, Anamarija Zega
The heteronuclear single quantum coherence (HSQC) spectra for 1H/13C were acquired with 1024 data points in t2, 32 scans, 64 complex points in t1, and relaxation delay of 1 s. The 1H and 13C sweep widths were 9470 and 3338 Hz, respectively. The spectra were processed and analysed with the Felix 2007 software package (Felix NMR Inc., Laboratory of Biomolecular Structure at National Institute of Chemistry). The spectra were zero-filled twice and apodised with a squared sine bell function shifted by π/2 in both dimensions using a linear prediction of the data in the incremented dimension. The combined 1H/13C chemical shift perturbations (Δδ) were calculated from the 1H and 13C chemical shift perturbations using Equation (1)32: