Spectroscopic and Theoretical Explorations on 6-Hydromethyl-4-Methoxy-4- Methoxytetrahydro-Pyran-2, 3, 5-Triol-A Biomolecule

The chemical compound 6-hydromethyl-4-methoxy-4- methoxytetrahydro-pyran-2, 3, 5-triol (C7H14O6), was derived from the ethanol extract of Senna auriculata flower via GC-MS. FT-IR and NMR characterization of the compound support covalent bonding information and degree of degeneracy, respectively. 3D molecular structure was optimized to enhance the accuracy of computations. MEP, NBO, HOMO-LUMO, and Mulliken charge distribution studies provide details like reactive sites, electron density dislocation, and molecular interactions, charge transfer within the molecule and frontier orbital energies, electron density on the individual atom, and these were computed using hybrid B3-LYP quantum level with 6-311++G(d, p) basis set. Thermodynamic properties such as heat capacity, entropy, enthalpy, and their relation with temperature changes for the title molecule were also analyzed using THERMO.PL software. Non-linear optical properties namely polarizability, first-order hyperpolarizability, and electronic dipole moment have also been computed at B3-LYP level with 6-311++G (d, p) basis set. Docking simulation was initiated on the title molecule using Autodock 4.2 software and found to be an excellent inhibitor of ALR2, an enzyme.

Relative configuration of micrograms of natural compounds using proton residual chemical shift anisotropy

3D molecular structure determination is a challenge for organic compounds or natural products available in minute amounts. Proton/proton and proton/carbon correlations yield the constitution. J couplings and NOEs oftentimes supported by one-bond 1H,13C residual dipolar couplings (RDCs) or by 13C residual chemical shift anisotropies (RCSAs) provide the relative configuration. However, these RDCs or carbon RCSAs rely on 1% natural abundance of 13C preventing their use for compounds available only in quantities of a few 10’s of µgs. By contrast, 1H RCSAs provide similar information on spatial orientation of structural moieties within a molecule, while using the abundant 1H spin. Herein, 1H RCSAs are accurately measured using constrained aligning gels or liquid crystals and applied to the 3D structural determination of molecules with varying complexities. Even more, deuterated alignment media allow the elucidation of the relative configuration of around 35 µg of a briarane compound isolated from Briareum asbestinum.

Computational Methods for Single-Particle Electron Cryomicroscopy

Single-particle electron cryomicroscopy (cryo-EM) is an increasingly popular technique for elucidating the three-dimensional (3D) structure of proteins and other biologically significant complexes at near-atomic resolution. It is an imaging method that does not require crystallization and can capture molecules in their native states. In single-particle cryo-EM, the 3D molecular structure needs to be determined from many noisy 2D tomographic projections of individual molecules, whose orientations and positions are unknown. The high level of noise and the unknown pose parameters are two key elements that make reconstruction a challenging computational problem. Even more challenging is the inference of structural variability and flexible motions when the individual molecules being imaged are in different conformational states. This review discusses computational methods for structure determination by single-particle cryo-EM and their guiding principles from statistical inference, machine learning, and signal processing, which also play a significant role in many other data science applications.

The Glycine Receptor Allosteric Ligands Library (GRALL)

Motivation Glycine receptors (GlyRs) mediate fast inhibitory neurotransmission in the brain and have been recognized as key pharmacological targets for pain. A large number of chemically diverse compounds that are able to modulate GlyR function both positively and negatively have been reported, which provides useful information for the development of pharmacological strategies and models for the allosteric modulation of these ion channels. Results Based on existing literature, we have collected 218 unique chemical entities with documented modulatory activities at homomeric GlyR-α1 and -α3 and built a database named GRALL. This collection includes agonists, antagonists, positive and negative allosteric modulators and a number of experimentally inactive compounds. Most importantly, for a large fraction of them a structural annotation based on their putative binding site on the receptor is provided. This type of annotation, which is currently missing in other drug banks, along with the availability of cooperativity factors from radioligand displacement experiments are expected to improve the predictivity of in silico methodologies for allosteric drug discovery and boost the development of conformation-based pharmacological approaches. Availability and implementation The GRALL library is distributed as a web-accessible database at the following link: https://ifm.chimie.unistra.fr/grall. For each molecular entry, it provides information on the chemical structure, the ligand-binding site, the direction of modulation, the potency, the 3D molecular structure and quantum-mechanical charges as determined by our in-house pipeline. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

Molecular docking of rutenum complex with epiisopyloturin and nitric oxide against nucleoside diphosphate kinase protein Leishmania

Leishmaniasis is an infectious disease that affects both animals and humans, caused by flagellated parasites belonging to the genus Leishmania may present in different clinical forms depending on the infecting strain and the immune reaction of the host. The disease is estimated to reach about 700,000 to 1 million people, causing the deaths of 20 to 30,000 individuals annually. Thus, the present study aims to perform a molecular coupling simulation of the ruthenium complex with epiisopiloturin and nitric oxide against the protein Nucleoside diphosphate kinase from Leishmania amazonensis. The NDK 3D molecule was extracted from the PDB nucleic proteins and acids database. The 3D molecular structure of the Epiruno2 complex was designed using gaussview 5.0 software. The NDK target and Epiruno2 complex were prepared for docking simulations, where NDK was considered rigid and Epiruno2 was considered flexible. The Epiruno2 complex presented a good molecular affinity rate with the target protein, making it attractive for experimental trials in laboratories for Leishmania's NDK protein and NDKs of other pathogens, however, the drug miltefosin presented low molecular affinity for the same target, corroborating studies presented in the literature on the reduced efficacy of current drugs against leishmaniosis.

Molecular Modeling and Docking of Aquaporin Inhibitors to Reveal New Insights Into Schistosomiasis Treatment

: Schistosomiasis (snail fever/bilharzia), a disease caused by parasitic flatworms (schistosomes), infects millions of people worldwide. Aquaporins from these organisms were found to be a potent drug target. We investigate the possible mechanism of inhibition of Aquaporin (AQP) from S.mansoni by 5 drug molecules (Praziquantel, Metrifonate, Artemisinin, Albendazole, and Amoscanate). 3D molecular structure of Aquaporin was obtained through homology modeling and further protein-ligand docking and MD simulation were performed. VAL-75, ASN-91, ALA-220, ASN-222, ARG-225 amino acids were found to play a crucial role in ligand binding. TRP-71 and other residues have hydrophobic interactions stabilizing protein-ligand complexes. This study (with the newly identified Aquaporin targets) supports the development of structure and pharmacophore-based novel S.mansoni drugs to control and curb Schistosomiasis.