keyword
https://read.qxmd.com/read/38533567/md-investigation-on-the-differences-in-the-dynamic-interactions-between-the-specific-ligand-azamulin-and-two-cyp3a-isoforms-3a4-and-3a5
#21
JOURNAL ARTICLE
Shuhui Liu, Tao Jing, Ran Jia, Ji-Long Zhang, Fu-Quan Bai
The unmarked potential drug molecule azamulin has been found to be a specific inhibitor of CYP3A4 and CYP3A5 in recent years, but this molecule also shows different binding ability and affinity to the two CYP3A isoforms. In order to explore the microscopic mechanism, conventional molecular dynamics (MD) simulation methods were performed to study the dynamic interactions between two isoforms and azamulin. The simulation results show that the binding of the ligand leads to different structural properties of two CYP3A proteins...
March 27, 2024: Journal of Biomolecular Structure & Dynamics
https://read.qxmd.com/read/38533537/network-pharmacology-approach-to-identify-the-calotropis-phytoconstituents-potential-epileptic-targets-and-evaluation-of-molecular-docking-md-simulation-and-mm-pbsa-performance
#22
JOURNAL ARTICLE
Punam Salaria, Amarendar Reddy M
Epilepsy originates from unusual electrical rhythm within brain cells, causes seizures. Calotropis species have been utilized to treat a wide spectrum of ailments since antiquity. Despite chemical and biological investigations, there have been minimal studies on their anticonvulsant activity, and the molecular targets of this plant constituents are unexplored. This study was aimed at investigating the plausible epileptic targets of Calotropis phytoconstituents through network pharmacology, and to evaluate their binding strength and stability with the identified targets...
March 27, 2024: Chemistry & Biodiversity
https://read.qxmd.com/read/38533298/computational-analysis-of-dimer-g6pd-structure-to-elucidate-pathogenicity-of-g6pd-variants
#23
JOURNAL ARTICLE
Shamini Chandran, Naveen Eugene Louis, Syazwani Itri Amran, Nurriza Ab Latif, Muaawia Ahmed Hamza, Mona Alonazi
An inherent genetic enzyme disorder in humans, known as glucose-6-phosphate dehydrogenase (G6PD) deficiency, arises due to specific mutations. While the prevailing approach for investigating G6PD variants involves biochemical analysis, the intricate structural details remain limited, impeding a comprehensive understanding of how different G6PD variants of varying classes impact their functionality. This study 22 examined the dynamic properties of G6PD wild types and six G6PD variants from 23 different classes using molecular dynamic simulation (MDS)...
2024: BioMedicine
https://read.qxmd.com/read/38533097/-in-silico-identification-of-multi-target-inhibitors-from-medicinal-fungal-metabolites-against-the-base-excision-repair-pathway-proteins-of-african-swine-fever-virus
#24
JOURNAL ARTICLE
Mark Andrian B Macalalad, Fredmoore L Orosco
African swine fever virus (ASFV) has emerged as a serious threat to the pork industry resulting in significant economic losses and heightened concerns about food security. With no known cure presently available, existing control measures center on animal quarantine and culling. Considering the severity and challenges posed by ASFV, it is imperative to discover new treatment strategies and implement additional measures to prevent its further spread. This study recognized the potential of 1830 fungal metabolites from medicinal fungi as antiviral compounds against base excision repair (BER) proteins of ASFV, specifically ASFV AP, ASFV PolX, and ASFV Lig...
March 20, 2024: RSC Advances
https://read.qxmd.com/read/38533069/molecular-investigation-of-antimicrobial-peptides-against-helicobacter-pylori-proteins-using-a-peptide-protein-docking-approach
#25
JOURNAL ARTICLE
Alfizah Hanafiah, Siti Nur Arifah Abd Aziz, Zarith Nameyrra Md Nesran, Xavier Chee Wezen, Mohd Fadzli Ahmad
The impact of H. pylori resistance on patient's treatment failure is a major concern. Therefore, the development of novel or alternative therapies for H. pylori is urgently needed. The purpose of this study was to investigate the molecular interactions of various antimicrobial peptides (AMPs) to H. pylori proteins. We performed the peptide-protein molecular docking using HADDOCK 2.4 webserver. Fourteen AMPs were tested for their binding efficacy against four H. pylori proteins. Simulation of the peptide-protein complex was performed using molecular dynamic software package AMBER20...
March 30, 2024: Heliyon
https://read.qxmd.com/read/38533033/elucidating-the-anti-cancer-potential-of-cinnamomum-tamala-essential-oil-against-non-small-cell-lung-cancer-a-multifaceted-approach-involving-gc-ms-profiling-network-pharmacology-and-molecular-dynamics-simulations
#26
JOURNAL ARTICLE
Debajani Mohanty, Sucheesmita Padhee, Arpita Priyadarshini, Bibhuti Bhusan Champati, Prabhat Kumar Das, Sudipta Jena, Ambika Sahoo, Pratap Chandra Panda, Sanghamitra Nayak, Asit Ray
Cinnamomum tamala (Buch.-Ham.) T.Nees & Eberm., or Indian Bay Leaf, is a well-known traditional ayurvedic medicine used to treat various ailments. However, the molecular mechanism of action of Cinnamomum tamala essential oil (CTEO) against non-small cell lung cancer (NSCLC) remains elusive. The present study aims to decipher the molecular targets and mechanism of CTEO in treating NSCLC. GC-MS analysis detected 49 constituents; 44 successfully passed the drug-likeness screening and were identified as active compounds...
March 30, 2024: Heliyon
https://read.qxmd.com/read/38532924/high-energy-electron-diffraction-instrument-with-tunable-camera-length
#27
JOURNAL ARTICLE
P Denham, Y Yang, V Guo, A Fisher, X Shen, T Xu, R J England, R K Li, P Musumeci
Ultrafast electron diffraction (UED) stands as a powerful technique for real-time observation of structural dynamics at the atomic level. In recent years, the use of MeV electrons from radio frequency guns has been widely adopted to take advantage of the relativistic suppression of the space charge effects that otherwise limit the temporal resolution of the technique. Nevertheless, there is not a clear choice for the optimal energy for a UED instrument. Scaling to beam energies higher than a few MeV does pose significant technical challenges, mainly related to the inherent increase in diffraction camera length associated with the smaller Bragg angles...
March 2024: Structural Dynamics (Melville, N.Y.)
https://read.qxmd.com/read/38532877/corrigendum-state-of-the-art-and-novel-approaches-to-mild-solubilization-of-inclusion-bodies
#28
Robert Klausser, Julian Kopp, Eva Prada Brichtova, Florian Gisperg, Mohamed Elshazly, Oliver Spadiut
[This corrects the article DOI: 10.3389/fbioe.2023.1249196.].
2024: Frontiers in Bioengineering and Biotechnology
https://read.qxmd.com/read/38532839/enhanced-recovery-of-oil-mixtures-from-calcite-nanopores-facilitated-by-co-2-injection
#29
JOURNAL ARTICLE
Hongwei Zhang, Shihao Wang, Xin Wang, Rui Qiao
Slow production, preferential recovery of light hydrocarbons, and low recovery factors are common challenges in oil production from unconventional reservoirs dominated by nanopores. Gas injection-based techniques such as CO2 Huff-n-Puff have shown promise in addressing these challenges. However, a limited understanding of the recovery of oil mixtures on the nanopore scale hinders their effective optimization. Here, we use molecular dynamics simulations to study the recovery of an oil mixture (C10 + C19) from a single 4 nm-wide calcite dead-end pore, both with and without CO2 injection...
March 21, 2024: Energy & Fuels
https://read.qxmd.com/read/38532715/role-of-udp-n-acetylmuramic-acid-in-the-regulation-of-mura-activity-revealed-by-molecular-dynamics-simulations
#30
JOURNAL ARTICLE
Maycon Vinicius Damasceno de Oliveira, Kauê S da Costa, José Rogério A Silva, Jerônimo Lameira, Anderson H Lima
The peptidoglycan biosynthesis pathway plays a vital role in bacterial cells, and facilitates peptidoglycan layer formation, a fundamental structural component of the bacterial cell wall. The enzymes in this pathway are candidates for antibiotic development, as most do not have mammalian homologues. The UDP-N-acetylglucosamine (UNAG) enolpyruvyl transferase enzyme (MurA) in the peptidoglycan pathway cytoplasmic step is responsible for the phosphoenolpyruvate (PEP)-UNAG catalytic reaction, forming UNAG enolpyruvate and inorganic phosphate...
April 2024: Protein Science
https://read.qxmd.com/read/38532249/zwitterionic-polymer-ionogel-electrolytes-supported-by-coulombic-cross-links-impacts-of-alkali-metal-cation-identity
#31
JOURNAL ARTICLE
Mossab K Alsaedi, Meron Y Tadesse, Venkat Ganesan, Matthew J Panzer
Zwitterionic (ZI) polymers enable the formation of noncovalent cross-links within ionic liquid electrolytes (ILEs) to create nonflammable, mechanically robust, and highly conductive ionogel electrolytes. In this study, ZI homopolymer poly(2-methacryloyloxyethyl phosphorylcholine) [poly(MPC)] scaffolds are synthesized in situ within lithium and/or sodium salt-based ILEs to construct a series of ionogels that contain between 3 and 15 wt % poly(MPC). Room-temperature ionic conductivity values of these ionogels are found to vary between approximately 1...
March 26, 2024: Journal of Physical Chemistry. B
https://read.qxmd.com/read/38532068/a-comprehensive-computational-study-to-explore-promising-natural-bioactive-compounds-targeting-glycosyltransferase-murg-in-escherichia-coli-for-potential-drug-development
#32
JOURNAL ARTICLE
Amneh Shtaiwi, Shafi Ullah Khan, Meriem Khedraoui, Mohd Alaraj, Abdelouahid Samadi, Samir Chtita
Peptidoglycan is a carbohydrate with a cross-linked structure that protects the cytoplasmic membrane of bacterial cells from damage. The mechanism of peptidoglycan biosynthesis involves the main synthesizing enzyme glycosyltransferase MurG, which is known as a potential target for antibiotic therapy. Many MurG inhibitors have been recognized as MurG targets, but high toxicity and drug-resistant Escherichia coli strains remain the most important problems for further development. In addition, the discovery of selective MurG inhibitors has been limited to the synthesis of peptidoglycan-mimicking compounds...
March 26, 2024: Scientific Reports
https://read.qxmd.com/read/38531526/synthesis-in-vitro-and-in-silico-studies-of-morpholine-based-thiosemicarbazones-as-ectonucleotide-pyrophosphatase-phosphodiesterase-1-and-3-inhibitors
#33
JOURNAL ARTICLE
Mussarat Tasleem, Julie Pelletier, Jean Sévigny, Zahid Hussain, Muhammad Ajmal, Ahmed Al-Harrasi, Attalla F El-Kott, Parham Taslimi, Sally Negm, Zahid Shafiq, Jamshed Iqbal
An extensive range of new biologically active morpholine based thiosemicarbazones derivatives 3a-r were synthesized, characterized by spectral techniques and evaluated as inhibitors of ENPP isozymes. Most of the novel thiosemicarbazones exhibit potent inhibition towards NPP1 and NPP3 isozymes. Compound 3 h was potent inhibitor of NPP1 with IC50 value of 0.55 ± 0.02. However, the most powerful inhibitor of NPP3 was 3e with an IC50 value of 0.24 ± 0.02. Furthermore, Lineweaver-Burk plot for compound 3 h against NPP1 and for compound 3e against NPP3 was devised through enzymes kinetics studies...
March 24, 2024: International Journal of Biological Macromolecules
https://read.qxmd.com/read/38530933/simulating-attochemistry-which-dynamics-method-to-use
#34
JOURNAL ARTICLE
Thierry Tran, Anthony Ferté, Morgane Vacher
Attochemistry aims to exploit the properties of coherent electronic wavepackets excited via attosecond pulses to control the formation of photoproducts. Such molecular processes can, in principle, be simulated with various nonadiabatic dynamics methods, yet the impact of the approximations underlying the methods is rarely assessed. The performances of widely used mixed quantum-classical approaches, Tully surface hopping, and classical Ehrenfest methods are evaluated against the high-accuracy DD-vMCG quantum dynamics...
March 26, 2024: Journal of Physical Chemistry Letters
https://read.qxmd.com/read/38530903/sequence-dependence-in-nucleosome-dynamics
#35
JOURNAL ARTICLE
Prabir Khatua, Phu K Tang, Abhik Ghosh Moulick, Rutika Patel, Anjela Manandhar, Sharon M Loverde
The basic packaging unit of eukaryotic chromatin is the nucleosome that contains 145-147 base pair duplex DNA wrapped around an octameric histone protein. While the DNA sequence plays a crucial role in controlling the positioning of the nucleosome, the molecular details behind the interplay between DNA sequence and nucleosome dynamics remain relatively unexplored. This study analyzes this interplay in detail by performing all-atom molecular dynamics simulations of nucleosomes, comparing the human α-satellite palindromic (ASP) and the strong positioning "Widom-601" DNA sequence at time scales of 12 μs...
March 26, 2024: Journal of Physical Chemistry. B
https://read.qxmd.com/read/38530754/lithium-grafted-si-doped-%C3%AE-graphyne-as-a-reversible-hydrogen-storage-host-material
#36
JOURNAL ARTICLE
Nidhi Duhan, T J Dhilip Kumar
In recent years, hydrogen (H2 ) has become the most sought-after sustainable energy carrier by virtue of its high energy content and carbon-free emission. The practical implementation of hydrogen as an alternative fuel calls for an efficient and secure storage medium. Within this framework, we have investigated Li-grafted Si-doped γ-graphyne for H2 storage applications by implementing the cutting-edge density functional theory (DFT). A dynamically and thermally stable Si-doped γ-graphyne (SiG) monolayer is functionalized with Li metal atoms that augmented the hydrogen binding strength of the nanolayer by almost three times, owing to the polarization effect of the Li atoms...
March 26, 2024: Physical Chemistry Chemical Physics: PCCP
https://read.qxmd.com/read/38530707/molecular-dynamics-simulation-of-thermal-nonequilibrium-and-chemical-reaction-processes-in-hydrogen-combustion
#37
JOURNAL ARTICLE
Yimiao Wu, Yongxin Hu, Zhiwei Li, Jianyi Ma
Using reactive force field (ReaxFF) and molecular dynamics simulation, we investigate the combustion process of hydrogen-oxygen systems in initial thermal nonequilibrium states with different translational and rovibrational temperatures for oxygen. The system studied in this work contains 300 oxygen molecules and 700 hydrogen molecules with a density of 7 times the air density. For this system, the characteristic relaxation times of oxygen and hydrogen vibrational energies are 0.173 and 0.249 ns, respectively...
March 26, 2024: Journal of Physical Chemistry. A
https://read.qxmd.com/read/38530420/selective-hydrolysis-of-ovalbumin-by-zr-based-lacunary-polyoxotungstate-in-surfactant-solutions
#38
JOURNAL ARTICLE
Malihe Babaei Zarch, Maryam Bazargan, Masoud Mirzaei
This study aims to design an artificial metalloprotease based on a Zr-containing polyoxometalate Na8 [Zr(W5 O18 )2 ] [Zr(W5 )2 ] for the hydrolysis of ovalbumin (OVA) in the presence of different surfactants, which can be used in many areas of the biological and medical sciences, particularly for targeted proteolytic drug design. For this reason, parameters, including the free energy of binding, the chemical nature of amino acid residues, secondary structures, and electrostatic potentials, of Zr(W5 )2 -OVA and Zr(W5 )2 -OVA-surfactant were analyzed by molecular docking simulations...
March 26, 2024: Inorganic Chemistry
https://read.qxmd.com/read/38530284/structure-and-internal-dynamics-of-short-rna-duplexes-determined-by-a-combination-of-pulsed-epr-methods-and-md-simulations
#39
JOURNAL ARTICLE
Maximilian Gauger, Marcel Heinz, Anna-Lena J Halbritter, Lukas S Stelzl, Nicole Erlenbach, Gerhard Hummer, Snorri Th Sigurdsson, Thomas Prisner
We used EPR spectroscopy to characterize the structure of RNA duplexes and their internal twist, stretch and bending motions. We prepared eight 20 base-pair long RNA duplexes containing the rigid spin-label Çm, a cytidine analogue, at two positions and acquired orientation-selective PELDOR/DEER data. By using different frequency bands (X-, Q-, G-band), detailed information about the distance and orientation of the labels was obtained and provided insights into the global conformational dynamics of the RNA duplex...
March 26, 2024: Angewandte Chemie
https://read.qxmd.com/read/38530008/using-machine-learning-with-atomistic-surface-and-local-water-features-to-predict-heterogeneous-ice-nucleation
#40
JOURNAL ARTICLE
Abhishek Soni, G N Patey
Heterogeneous ice nucleation (HIN) has applications in climate science, nanotechnology, and cryopreservation. Ice nucleation on the earth's surface or in the atmosphere usually occurs heterogeneously involving foreign substrates, known as ice nucleating particles (INPs). Experiments identify good INPs but lack sufficient microscopic resolution to answer the basic question: What makes a good INP? We employ molecular dynamics (MD) simulations in combination with machine learning (ML) to address this question...
March 28, 2024: Journal of Chemical Physics
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