A review on description dynamics and conformational changes of proteins using combination of principal component analysis and molecular dynamics simulation.

Understanding how proteins behave dynamically and undergo conformational changes is essential to comprehending their biological roles. This review article examines the potent tool of using Molecular Dynamics simulations in conjunction with Principal Component Analysis (PCA) to explore protein dynamics. Molecular dynamics data can be made easier to read by removing prominent patterns through the use of PCA, a sophisticated dimensionality reduction approach.

Exploration of lipid bilayer mechanical properties using molecular dynamics simulation.

Important biological structures known for their exceptional mechanical qualities, lipid bilayers are essential to many cellular functions. Fluidity, elasticity, permeability, stiffness, tensile strength, compressibility, shear viscosity, line tension, and curvature elasticity are some of the fundamental characteristics affecting their behavior. The purpose of this review is to examine these characteristics in more detail by molecular dynamics simulation, elucidating their importance and the elements that lead to their appearance in lipid bilayers.

Proposing of fungal endophyte secondary metabolites as a potential inhibitors of 2019-novel coronavirus main protease using docking and molecular dynamics.

In this study, the inhibitory potential of 99 fungal derived secondary metabolites was predicted against SARS-CoV-2 main protease by using of computational approaches. This protein plays an important role in replication and is one of the important targets to inhibit viral reproduction. Among the 99 reported compounds, the 9 of them with the highest binding energy to Mpro obtained from the molecular docking method were selected for the molecular dynamic simulations.

Simultaneous Determination of Multicomponent Dosage Forms Using Benchtop NMR Spectroscopy: Application to Phenytoin-Phenobarbital Combination.

The use of nuclear magnetic resonance (NMR) spectroscopy as a tool for determining pharmaceutical molecules in bulk drugs and their dosage forms is growing. New advancements in benchtop NMR spectrometers with cryogen-free magnets have made this technique more appealing and accessible. Herein, we developed a method using a benchtop NMR spectrometer to quantify phenytoin (PhT) and phenobarbital (PhB) in bulk and combined dosage forms.

Determining the stoichiometry and binding constant of Lamotrigine with human serum albumin using voltammetry analysis and molecular modeling.

In this study, the interaction of an anticonvulsant drug that used in the treatment of epilepsy, Lamotrigine (LTG) with the most important transport protein of the blood, human serum albumin (HSA) has been studied by using the electrochemical methods and molecular modeling techniques. For this purpose, a simple carbon paste electrode (CPE) was applied for electrocatalytic oxidation and investigation of LTG interaction with HSA. The stoichiometry of the complex between LTG and HSA and the binding constant (K) of the reaction were calculated from the calibration curves.

Correction: Shedding light on the structural properties of lipid bilayers using molecular dynamics simulation: a review study.

[This corrects the article DOI: 10.1039/C8RA08441F.].

Shedding light on the structural properties of lipid bilayers using molecular dynamics simulation: a review study.

In recent years, a massive increase has been observed in the number of published articles describing accurate and reliable molecular dynamics simulations of lipid bilayers. This is due to several reasons, including the development of fast and efficient methods for treating long-range electrostatic interactions, significant progress in computer hardware, progress in atomistic simulation algorithms and the development of well-validated empirical molecular mechanical force fields. Although molecular dynamics is an effective approach for investigating different aspects of lipid bilayers, to the best of our knowledge, there is no review in the literature that explains the different analyses that can be carried out with membrane simulation.

Discovery of Novel Glucagon Receptor Antagonists Using Combined Pharmacophore Modeling and Docking.

Glucagon and the glucagon receptor are most important molecules control over blood glucose concentrations. These two molecules are very important to studies of type 2 diabetic patients. In literature, several classes of small molecule antagonists of the human glucagon receptor have been reported.

Insights from a combination of theoretical and experimental methods for probing the biomolecular interactions between human serum albumin and clomiphene.

In this study, the interaction of clomiphene (CLO), a non-steroidal and ovulatory stimulant drug employed in the treatment of infertility, with human serum albumin (HSA), the most abundant plasma transport protein, was investigated using spectrofluorometric, FT-IR, UV-Vis, and molecular modeling methods. The obtained results indicated that the binding of CLO to HSA led to intense fluorescence quenching of HSA a static quenching mechanism, and that the process of CLO binding to HSA was enthalpy driven. By using experimental and theoretical methods, it was confirmed that as a result of binding CLO, slight conformational changes in HSA occurred.

Direct evidences for the groove binding of the Clomifene to double stranded DNA.

It has been reported that the antiestrogen Tamoxifen induces liver tumors in rats and genotoxic effects in vitro through DNA interaction. So, it can be proposed that its structural analogue, Clomifene, also can bind to DNA. To test this hypothesis, the DNA binding properties of Clomifene have been studied by absorption spectroscopy, fluorescence spectroscopy, cellular uptake, cell viability, cell proliferation and molecular modeling techniques.

Experimental and computational studies on the binding of diazinon to human serum albumin.

In the present research, the binding properties of diazinon (DZN), as an organophosphorus herbicide, to human serum albumin (HSA) were investigated using combination of spectroscopic, electrochemistry, and molecular modeling techniques. Changes in the UV-Vis and FT-IR spectra were observed upon ligand binding along with a significant degree of tryptophan fluorescence quenching on complex formation. The obtained results from spectroscopic and electrochemistry experiments along with the computational studies suggest that DZN binds to residues located in subdomains IIA of HSA with binding constant about 1410.

Molecular insight into the Grandivitin- matrix metalloproteinase 9 interactions.

Grandivitin (GRA), a natural coumarin, can inhibit Matrix metalloproteinase 9 (MMP9). Binding characteristics are therefore of interest for pharmacodynamics of GRA and coumarin derivatives. A combination of spectroscopic methods and molecular modeling techniques was used to characterize interaction of GRA with MMP9.

A coupling of homology modeling with multiple molecular dynamics simulation for identifying representative conformation of GPCR structures: a case study on human bombesin receptor subtype-3.

In this study, a computational pipeline was therefore devised to overcome homology modeling (HM) bottlenecks. The coupling of HM with molecular dynamics (MD) simulation is useful in that it tackles the sampling deficiency of dynamics simulations by providing good-quality initial guesses for the native structure. Indeed, HM also relaxes the severe requirement of force fields to explore the huge conformational space of protein structures.

Exploring binding properties of sertraline with human serum albumin: Combination of spectroscopic and molecular modeling studies.

Human serum albumin (HSA)-drug binding is an important factor to determine half life and bioavailability of drugs. In the present research, the interaction of sertraline (SER) to HSA was investigated using combination of spectroscopic and molecular modeling techniques. Changes in the UV-Vis, CD and FT-IR spectra as well as a significant degree of tryptophan fluorescence quenching were observed upon SER-HSA interaction.

Multi-spectroscopic and molecular modeling investigation of the interactions between prantschimgin and matrix metalloproteinase 9 (MMP9).

The binding of prantschimgin (PRAN) to matrix metalloproteinase 9 (MMP9) was investigated using multiple techniques. Fluorescence spectroscopy showed that PRAN could quench the MMP9 fluorescence spectra. Changes in the UV/vis and Fourier transform infrared (FTIR) spectra were observed upon ligand binding, along with a significant degree of tryptophan fluorescence quenching on complex formation.

Constructing an atomic-resolution model of human P2X7 receptor followed by pharmacophore modeling to identify potential inhibitors.

The P2X purinoceptor 7 (P2X7R) is a trimeric ATP-activated ion channel gated by extracellular ATP. P2X7R has important role in numerous diseases including pain, neurodegeneration, and inflammatory diseases such as rheumatoid arthritis and osteoarthritis. In this prospective, the discovery of small-molecule inhibitors for P2X7R as a novel therapeutic target has received considerable attention in recent years.

Combined spectroscopy and molecular modeling studies on the binding of galbanic acid and MMP9.

The molecular mechanism of galbanic acid (GBA) binding to matrix metalloproteinase 9 (MMP9) was investigated by fluorescence quenching, absorption spectroscopy, FT-IR, molecular docking and molecular dynamics (MD) simulation procedures. The fluorescence emission of MMP9 was quenched by GBA. The titration of MMP9 by various amount of GBA was also followed by UV-Vis absorption spectroscopy.