scholarly journals DFT Studies and Molecular Dynamics of the Molecular and Electronic Structure of Cu (II) and Zn (II) Complexes with the Symmetric Ligand (Z)-2-((3,5-dimethyl-2H-pyrrol-2-yl) methylene)-3,5-dimethyl-2H-pyrrole

2021 ◽  
Vol 12 (5) ◽  
pp. 5953-5968
Keyword(s):  
Molecular Dynamics ◽  
Md Simulation ◽  
Nbo Analysis ◽  
Docking Studies ◽  
Binding Motifs ◽  
Ligand Coordination ◽  
Dependent Protein ◽  
The Stability ◽  
Symmetric Ligands ◽  
Molecular And Electronic Structure

The binding patterns of the metal cations Cu 2+ and Zn 2+ with the symmetric ligands (Z)-2-((3,5-dimethyl-2H-pyrrol-2-yl) methylene)-3,5-dimethyl-2H-pyrrole (L1) and (Z)-2-(1-(3,5-dimethyl-2H-pyrrol-2-yl)ethylidene)-3,5-dimethyl-2H-pyrrole (L2), have been investigated at B3LYP and MM2 level of theories in the gas phase and a solution respectively. Natural bond orbital (NBO) analysis has been applied to explore the character of metal-ligand coordination. The stability of the most favorable binding motifs of the metal ions has also been investigated by the molecular dynamics (MD) simulation. Finally, the inhibition activity of the complexes (L1Cu2+), (L2Cu2+), (L1Zn2+), and (L2Zn2+) against the DNA dependent protein kinase also have been investigated by molecular docking studies.

scholarly journals Optimized structure of monoubiquitinated FANCD2 (human) at Lys 561: a theoretical approach

2021 ◽  
Author(s):  
Sudipa Mondal ◽  
Subba Reddy ◽  
Sudit S. Mukhopadhyay
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Theoretical Approach ◽  
Md Simulation ◽  
Docking Studies ◽  
Fanconi Anaemia ◽  
Cross Linking ◽  
Structural Differences ◽  
The Stability ◽  
Dna Docking

AbstractFanconi anaemia pathway repairs inter-strand cross linking damage (ICL) of the DNA. Monoubiquitination of FANCD2 and FANCI is very crucial for ICL repairing. In this work we have tried to understand the monoubiquitinated FANCD2 structure, which facilitates the FANCD2 for binding the damage part of the chromatin. Crystal structure of the monoubiquitinated FANCD2 alone is not available, therefore we have developed the optimized structure of the human monoubiquitinated (Lys 561) FANCD2. As there is no suitable software or web server we have developed a method for building up monoubiquitinated product and validated on simplest monoubiquitinated protein, diubiquitin. We have predicted the structure of human monoubiquitinated FANCD2 by using our method and studied the interaction with DNA by docking studies. Molecular Dynamics (MD) simulation was used to understand the stability of the structure. Large structural differences have been observed between FANCD2 and monoubiquitinated FANCD2. DNA docking studies suggest that the binding site varies for the FANCD2 and monoubiquitinated FANCD2.

Design of potential IKK-β inhibitors using molecular docking and molecular dynamics techniques for their anti-cancer potential

2020 ◽  
Vol 16 ◽  
Author(s):  
Salam Pradeep Singh ◽  
Iftikar Hussain ◽  
Bolin Kumar Konwar ◽  
Ramesh Chandra Deka ◽  
Chingakham Brajakishor Singh
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Md Simulation ◽  
Inflammatory Diseases ◽  
Binding Free Energy ◽  
Anti Cancer ◽  
Dietary Phytochemicals ◽  
Toxicity Analysis ◽  
The Stability ◽  
Stable Trajectory

Aim and Objective: To evaluate a set of seventy phytochemicals for their potential ability to bind the inhibitor of nuclear factor kappaB kinase beta (IKK-β) which is a prime target for cancer and inflammatory diseases. Materials and Methods: Seventy phytochemicals were screened against IKK-β enzyme using DFT-based molecular docking technique and the top docking hits were carried forward for molecular dynamics (MD) simulation protocols. The adme-toxicity analysis was also carried out for the top docking hits. Results: Sesamin, matairesinol and resveratrol were found to be the top docking hits with a total score of -413 kJ/mol, -398.11 kJ/mol and 266.73 kJ/mol respectively. Glu100 and Gly102 were found to be the most common interacting residues. The result from MD simulation observed a stable trajectory with a binding free energy of -107.62 kJ/mol for matairesinol, -120.37 kJ/mol for sesamin and -40.56 kJ/mol for resveratrol. The DFT calculation revealed the stability of the compounds. The ADME-Toxicity prediction observed that these compounds fall within the permissible area of Boiled-Egg and it does not violate any rule for pharmacological criteria, drug-likeness etc. Conclusion: The study interprets that dietary phytochemicals are potent inhibitors of IKK-β enzyme with favourable binding affinity and less toxic effects. In fact, there is a gradual rise in the use of plant-derived molecules because of its lesser side effects compared to chemotherapy. The study has also provided an insight by which the phytochemicals inhibited the IKK-β enzyme. The investigation would also provide in understanding the inhibitory mode of certain dietary phytochemicals in treating cancer.

COMPUTER SIMULATIONS TO INVESTIGATE STABILITY AND STRUCTURAL PROPERTIES OF PEPTIDE AMPHIPHILE NANOFIBERS

2007 ◽  
Vol 06 (03) ◽  
pp. 621-630
Author(s):  
RUO-YU CHEN ◽  
LING-YING WU ◽  
JUN-MIN LIAO ◽  
CHENG-LUNG CHEN
Keyword(s):  
Molecular Dynamics ◽  
Disulfide Bonds ◽  
Md Simulation ◽  
Intermolecular Hydrogen Bond ◽  
Intermolecular Distance ◽  
Peptide Amphiphile ◽  
Hydrogen Bond Interactions ◽  
Self Assembling ◽  
Polar Groups ◽  
The Stability

Molecular mechanics (MM) method followed by molecular dynamics (MD) simulation was carried out to investigate the stability of an aggregate formed by self-assembling of peptide amphiphile (PA) molecules. The MM + MD simulation confirms that the cylindrical shaped aggregate is very stable. The analysis showed that the remarkable stability of the aggregate was partly due to various intermolecular hydrogen-bond interactions between polar groups of PA molecules. The hydrophobic alkyl tails of PA molecules are packed loosely inside the interior of the aggregates. The packing of alkyl tails contribute further stability of the PA aggregate. Our simulations reproduce qualitatively experimental observations and support the fact that PA molecules are self-assembled within closed intermolecular distance to favor the forming of disulfide bonds.

Docking and Molecular Dynamic Simulation of Temozolomide with Carbonic Anhydrase XIII

2020 ◽  
Vol 5 (4) ◽  
pp. 332-339
Author(s):  
R. Meenashi ◽  
K. Selvaraju ◽  
P. Jayalakshmi ◽  
P.V. Nidhin ◽  
A. David Stephen
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Carbonic Anhydrase ◽  
Dynamic Simulation ◽  
Alkylating Agent ◽  
Docking Studies ◽  
Dynamics Simulation ◽  
Cancer Treatments ◽  
The Stability ◽  
Protein Environment

The effect of inhibition of temozolomide, an alkylating agent widely used in cancer treatments, with carbonic anhydrase XIII protein was investigated using docking studies. The stability of temozolomide in the protein environment was assessed and analyzed by molecular dynamics simulation. The topological and charge density variations of temozolomide were studied in detail to perceive the primary insight of the pharmaceutical actions.

scholarly journals Molecular Modeling of Some Benzodiazole Derivatives with EGFR Protein 1M17

2020 ◽  
pp. 84-95
Author(s):  
A. S. Sony ◽  
Xavier Suresh
Keyword(s):  
Molecular Dynamics ◽  
Molecular Modeling ◽  
Molecular Dynamics Simulation ◽  
Binding Affinity ◽  
Simulation Study ◽  
Docking Studies ◽  
Dynamics Simulation ◽  
Ligand Complex ◽  
Drug Candidates ◽  
The Stability

Aims: To study the anticancer potential of benzodiazole derivatives using molecular modeling studies. Study Design: Molecular Dynamics simulation study. Place and Duration of Study: Sathyabama Institute of Science and Technology (SIST), Chennai, between June 2020 and August 2020. Methodology: We studied the anticancer potential of benzodiazole derivatives using molecular modeling. Docking studies of the ligands with EGFR protein 1M17 was carried out using AutoDock.Molecular Dynamics simulation study was carried out using Playmolecule was used to verify the stability of the protein-ligand complex. Results: Molecular docking studies showed a good binding affinity of the ligands with the protein 1m17. Benzodiazole derivative 4,6-dichloro-2-(trifluoromethyl)-1H-1,3-benzodiazole exhibited the lowest binding energy of (-6.42 kcal/mol) at the active site of EGFR (PDB code:1M17) consistent with its least inhibition coefficient (Ki =32.54 uM). Molecular dynamics simulation showed better stability of the ligand and protein complex. Conclusion: Molecular modeling study of selected benzodiazole derivatives showed a very good binding affinity to EGFR protein 1m17. MD simulation of the best-docked ligand showed that the complex was stable. Our study demonstrated that benzodiazole derivatives can be potential anticancer drug candidates

scholarly journals Conjugated β-Cyclodextrin Enhances the Affinity of Folic Acid towards FRα: Molecular Dynamics Study

Molecules ◽  
2021 ◽  
Vol 26 (17) ◽  
pp. 5304
Author(s):  
Mohammad G. Al-Thiabat ◽  
Amirah Mohd Gazzali ◽  
Noratiqah Mohtar ◽  
Vikneswaran Murugaiyah ◽  
Ezatul Ezleen Kamarulzaman ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Folic Acid ◽  
Root Mean Square ◽  
Active Site ◽  
Md Simulation ◽  
Binding Free Energy ◽  
Cancer Drug ◽  
Radius Of Gyration ◽  
Mean Square ◽  
The Stability

Drug targeting is a progressive area of research with folate receptor alpha (FRα) receiving significant attention as a biological marker in cancer drug delivery. The binding affinity of folic acid (FA) to the FRα active site provides a basis for recognition of FRα. In this study, FA was conjugated to beta-cyclodextrin (βCD) and subjected to in silico analysis (molecular docking and molecular dynamics (MD) simulation (100 ns)) to investigate the affinity and stability for the conjugated system compared to unconjugated and apo systems (ligand free). Docking studies revealed that the conjugated FA bound into the active site of FRα with a docking score (free binding energy < −15 kcal/mol), with a similar binding pose to that of unconjugated FA. Subsequent analyses from molecular dynamics (MD) simulations, root mean square deviation (RMSD), root mean square fluctuation (RMSF), and radius of gyration (Rg) demonstrated that FA and FA–βCDs created more dynamically stable systems with FRα than the apo-FRα system. All systems reached equilibrium with stable RMSD values ranging from 1.9–2.4 Å and the average residual fluctuation values of the FRα backbone atoms for all residues (except for terminal residues ARG8, THR9, THR214, and LEU215) were less than 2.1 Å with a consistent Rg value of around 16.8 Å throughout the MD simulation time (0–100 ns). The conjugation with βCD improved the stability and decreased the mobility of all the residues (except residues 149–151) compared to FA–FRα and apo-FRα systems. Further analysis of H-bonds, binding free energy (MM-PBSA), and per residue decomposition energy revealed that besides APS81, residues HIS20, TRP102, HIS135, TRP138, TRP140, and TRP171 were shown to have more favourable energy contributions in the holo systems than in the apo-FRα system, and these residues might have a direct role in increasing the stability of holo systems.

Molecular Dynamics Simulation of Nanobubbles

2003 ◽  
Author(s):  
Shu Takagi ◽  
Gota Kikugawa ◽  
Yoichiro Matsumoto
Keyword(s):  
Molecular Dynamics ◽  
Md Simulation ◽  
Pure Water ◽  
Simulation Method ◽  
Bubble Nucleation ◽  
Liquid Interface ◽  
Dynamics Simulation ◽  
Hydroxyl Groups ◽  
Surfactant System ◽  
The Stability

Some results have been reported recently related to the bubble formation with Molecular Dynamics (MD) simulation method. Some of them conduct the MD simulations of the bubble nucleation including impurity molecules with L-J potential [1,2]. In the present study, we investigate the stability of the nanometer size bubble in water, using molecular dynamics (MD) simulation method. MD simulation of an aqueous surfactant system: water liquid and alcohols below the liquid saturation density is carried out to investigate the stability of “nanobubbles” and the structure of the gas-liquid interface. To analyze the effect of surfactant structure, volume, and polarization on the stability of bubble nuclei, we use water by SPC/E model as the solvent molecules and 1-propanol, 1-pentanol, 1-heptanol as the surfactant molecules. Fig.1 shows the numerical result of instantaneous behavior of nanobubbles under the presence of surfactant in water. The calculation system is the cubic cell which has a side length of 25.057[Å], and a three-dimensional periodic boundary condition is applied. To include the intramolecular motion, AMBER force field [3] is adopted as a potential function. The momentum equations are integrated by velocity-Verlet argorithm [4]. Further, the time integration is extended to the Multi Time Scale algorithm by r-RESPA method [5]. As the surfactant molecules, to evaluate the influence of the hydrophobic effect of surfactants on the stability of bubble nuclei, we adopt 1-propanol (C3H7OH), 1-pentanol (C5H11OH), and 1-heptanol (C7H15OH), and to investigate the influence of the polarization of hydrophilic groups (-OH), “pseudo” 1-pentanol of which charge is cancelled away is also calculated. As a result, it was found that from the MD simulation at the condition that the bubble nuclei could not exist stably in pure water, a stable bubble is formed in aqueous surfactant system and hydroxyl groups of surfactants tend to point to the liquid phase at the gas-liquid interface. It is also shown that the longer hydrophobic chains the surfactants have, the more stably the bubble nuclei can exist.

scholarly journals In silico evaluation of the inhibitory effect of antiretrovirals Atazanavir and Darunavir on the main protease of SARS-CoV-2: docking studies and molecular dynamics

2020 ◽  
Vol 9 (8) ◽  
pp. e826986562
Author(s):  
José Danilo de Sousa Silva ◽  
Samuel da Costa Leite ◽  
Maria Thalita Sobral da Silva ◽  
Lyghia Maria Araújo Meirelles ◽  
Anderson Wilbur Lopes Andrade
Keyword(s):  
Molecular Dynamics ◽  
Electrostatic Interactions ◽  
Rna Virus ◽  
Inhibitory Effect ◽  
Docking Studies ◽  
Hiv Protease ◽  
Virus Family ◽  
Discovery Studio ◽  
The Stability ◽  
The One

SARS-CoV-2 is part of an RNA virus family described again in 2019, causing the Covid-19 disease. The integration of computational strategies is of great importance in the identification and development of promising new compounds. Atazanavir and Darunavir, were designed to combat resistance to mutant drugs mainly by increasing the number of polar interactions with the main atoms in the HIV protease chain. This study aims to assess the molecular interaction of the drugs Atazanavir and Darunavir with the main SARS-CoV-2 protease through docking and molecular dynamics studies. This is a descriptive, experimental study with a qualitative and quantitative approach on the subject. For that, using the programs BIOVIA Discovery Studio, PyMol, AutoDock Tools 1.5.6, AutoDock Vina, the modeling and simulation of the anchoring of the drug at the action site were carried out. Lower scores were demonstrated, with -7.0 (Darunavir) the closest to the UAW 247 Inhibitor. It is possible to notice that the drugs showed similar residual bonds, also, in relation to the protease structure, the closest tested molecule was Atazanavir. Taking into account the stability of the RMSD values, it is valid to infer that in relation to the UAW 247 inhibitor, the drug Atazanavir is the one that best resembles, unlike Darunavir, which presents greater variations. The two drugs fit into the binding site mainly due to electrostatic interactions and hydrogen bonds. Atazanavir is the most similar to molecular activity, and Darunavir is the one with the best anchoring score.

Molecular docking, molecular dynamics simulation, and ADMET analysis of levamisole derivatives against the SARS-CoV-2 main protease (MPro)

Bioimpacts ◽  
2021 ◽  
Author(s):  
Khalil EL Khatabi ◽  
Ilham Aanouz ◽  
Marwa Alaqarbeh ◽  
Mohammed Aziz Ajana ◽  
Tahar Lakhlifi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Md Simulation ◽  
Antiviral Agents ◽  
Dynamics Simulation ◽  
Main Protease ◽  
In Silico Admet ◽  
Wet Lab ◽  
The Stability ◽  
Drug Leads

Introduction: The new species of coronaviruses (CoVs), SARS-CoV-2, was reported as responsible for an outbreak of respiratory disease. Scientists and researchers are endeavoring to develop new approaches for the effective treatment against of the COVID-19 disease. There are no finally targeted antiviral agents able to inhibit the SARS-CoV-2 at present. Therefore, it is of interest to investigate the potential uses of levamisole derivatives, which are reported to be antiviral agents targeting the influenza virus. Methods: In the present study, 12 selected levamisole derivatives containing imidazo[2,1-b]thiazole were subjected to molecular docking in order to explore the binding mechanisms between these derivatives and the SARS-CoV-2 Mpro (PDB: 7BQY). The levamisole derivatives were evaluated for in silico ADMET properties for wet-lab applicability. Further, the stability of the best-docked complex was checked using molecular dynamics (MD) simulation at 20 ns. Results: Levamisole derivatives and especially molecule N°6 showed more promising docking results, presenting favorable binding interactions as well as better docking energy compared to chloroquine and mefloquine. The results of ADMET prediction and MD simulation support the potential of the molecule N°6 to be further developed as a novel inhibitor able to stop the newly emerged SARS-CoV-2. Conclusion: This research provided an effective first line in the rapid discovery of drug leads against the novel CoV (SARS-CoV-2).

scholarly journals Choline-Based Ionic Liquids-Incorporated IRMOF-1 for H2S/CH4 Capture: Insight from Molecular Dynamics Simulation

Processes ◽  
2020 ◽  
Vol 8 (4) ◽  
pp. 412
Author(s):  
Mohamad Adil Iman Ishak ◽  
Mohd Faisal Taha ◽  
Mohd Dzul Hakim Wirzal ◽  
Muhammad Najib Nordin ◽  
Muslim Abdurrahman ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Ionic Liquids ◽  
Md Simulation ◽  
Metal Organic Framework ◽  
Dynamics Simulation ◽  
Crowding Effect ◽  
Metal Organic ◽  
The Stability ◽  
Stable Incorporation

The removal of H2S and CH4 from natural gas is crucial as H2S causes environmental contamination, corrodes the gas stream pipelines, and decreases the feedstock for industrial productions. Many scientific researches have shown that the metal-organic framework (MOF)/ionic liquids (ILs) have great potential as alternative adsorbents to capture H2S. In this work, molecular dynamics (MD) simulation was carried out to determine the stability of ILs/IRMOF-1 as well as to study the solubility of H2S and CH4 gases in this ILs/IRMOF-1 hybrid material. Three choline-based ILs were incorporated into IRMOF-1 with different ratios of 0.4, 0.8, and 1.2% w/w, respectively, in which the most stable choline-based ILs/IRMOF-1 composite was analysed for H2S/CH4 solubility selectivity. Among the three choline-based ILs/IRMOF-1, [Chl] [SCN]/IRMOF-1 shows the most stable incorporation. However, the increment of ILs loaded in the IRMOF-1 significantly reduced the stability of the hybrid due to the crowding effect. Solvation free energy was then computed to determine the solubility of H2S and CH4 in the [Chl] [SCN]/IRMOF-1. H2S showed higher solubility compared to CH4, where its solubility declined with the increase of choline-based IL loading.

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