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Journal articles on the topic 'Molecuar dynamics and docking simulation'

Author: Grafiati

Published: 14 March 2023

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1

Naqvi, Ahmad Abu Turab, Taj Mohammad, Gulam Mustafa Hasan, and Md Imtaiyaz Hassan. "Advancements in Docking and Molecular Dynamics Simulations Towards Ligand-receptor Interactions and Structure-function Relationships." Current Topics in Medicinal Chemistry 18, no. 20 (2018): 1755–68. http://dx.doi.org/10.2174/1568026618666181025114157.

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Protein-ligand interaction is an imperative subject in structure-based drug design and protein function prediction process. Molecular docking is a computational method which predicts the binding of a ligand molecule to the particular receptor. It predicts the binding pose, strength and binding affinity of the molecules using various scoring functions. Molecular docking and molecular dynamics simulations are widely used in combination to predict the binding modes, binding affinities and stability of different protein-ligand systems. With advancements in algorithms and computational power, molec

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李, 博. "Progress in Molecular Docking and Molecular Dynamics Simulation." Journal of Comparative Chemistry 03, no. 01 (2019): 1–10. http://dx.doi.org/10.12677/cc.2019.31001.

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Miyagawa, Hiroh, and Kunihiro Kitamura. "1P565 Molecular dynamics simulations of association and docking between an inhibitor and an enzyme.(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S288. http://dx.doi.org/10.2142/biophys.46.s288_1.

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Meng, Fancui. "Molecular Dynamics Simulation of VEGFR2 with Sorafenib and Other Urea-Substituted Aryloxy Compounds." Journal of Theoretical Chemistry 2013 (December 4, 2013): 1–7. http://dx.doi.org/10.1155/2013/739574.

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The binding mode of sorafenib with VEGFR2 was studied using molecular docking and molecular dynamics method. The docking results show that sorafenib forms hydrogen bonds with Asp1046, Cys919, and Glu885 of VEGFR2 receptor. Molecular dynamics simulation suggests that the hydrogen bond involving Asp1046 is the most stable one, and it is almost preserved during all the MD simulation time. The hydrogen bond formed with Cys919 occurs frequently after 6 ns, while the bifurcated hydrogen bonds involving Glu885 occurs occasionally. Meantime, molecular dynamics simulations of VEGFR2 with 11 other urea-

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Bathelt, Christine, Rolf Schmid, and Jürgen Pleiss. "Regioselectivity of CYP2B6: homology modeling, molecular dynamics simulation, docking." Journal of Molecular Modeling 8, no. 11 (2002): 327–35. http://dx.doi.org/10.1007/s00894-002-0104-y.

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Kurniawan, Isman, Muhammad Salman Fareza, and Ponco Iswanto. "CoMFA, Molecular Docking and Molecular Dynamics Studies on Cycloguanil Analogues as Potent Antimalarial Agents." Indonesian Journal of Chemistry 21, no. 1 (2020): 66. http://dx.doi.org/10.22146/ijc.52388.

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Malaria is a disease that commonly infects humans in many tropical areas. This disease becomes a serious problem because of the high resistance of Plasmodium parasite against the well-established antimalarial agents, such as Artemisinin. Hence, new potent compounds are urgently needed to resolve this resistance problem. In the present study, we investigated cycloguanil analogues as a potent antimalarial agent by utilizing several studies, i.e., comparative of molecular field analysis (CoMFA), molecular docking and molecular dynamics (MD) simulation. A CoMFA model with five partial least square

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Khare, Noopur, Sanjiv Kumar Maheshwari, Syed Mohd Danish Rizvi, et al. "Homology Modelling, Molecular Docking and Molecular Dynamics Simulation Studies of CALMH1 against Secondary Metabolites of Bauhinia variegata to Treat Alzheimer’s Disease." Brain Sciences 12, no. 6 (2022): 770. http://dx.doi.org/10.3390/brainsci12060770.

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Calcium homeostasis modulator 1 (CALHM1) is a protein responsible for causing Alzheimer’s disease. In the absence of an experimentally designed protein molecule, homology modelling was performed. Through homology modelling, different CALHM1 models were generated and validated through Rampage. To carry out further in silico studies, through molecular docking and molecular dynamics simulation experiments, various flavonoids and alkaloids from Bauhinia variegata were utilised as inhibitors to target the protein (CALHM1). The sequence of CALHM1 was retrieved from UniProt and the secondary structur

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Zaki, Magdi E. A., Sami A. Al-Hussain, Vijay H. Masand, et al. "Identification of Anti-SARS-CoV-2 Compounds from Food Using QSAR-Based Virtual Screening, Molecular Docking, and Molecular Dynamics Simulation Analysis." Pharmaceuticals 14, no. 4 (2021): 357. http://dx.doi.org/10.3390/ph14040357.

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Due to the genetic similarity between SARS-CoV-2 and SARS-CoV, the present work endeavored to derive a balanced Quantitative Structure−Activity Relationship (QSAR) model, molecular docking, and molecular dynamics (MD) simulation studies to identify novel molecules having inhibitory potential against the main protease (Mpro) of SARS-CoV-2. The QSAR analysis developed on multivariate GA–MLR (Genetic Algorithm–Multilinear Regression) model with acceptable statistical performance (R2 = 0.898, Q2loo = 0.859, etc.). QSAR analysis attributed the good correlation with different types of atoms like non

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De Paris, Renata, Christian V. Quevedo, Duncan D. Ruiz, Osmar Norberto de Souza, and Rodrigo C. Barros. "Clustering Molecular Dynamics Trajectories for Optimizing Docking Experiments." Computational Intelligence and Neuroscience 2015 (2015): 1–9. http://dx.doi.org/10.1155/2015/916240.

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Molecular dynamics simulations of protein receptors have become an attractive tool for rational drug discovery. However, the high computational cost of employing molecular dynamics trajectories in virtual screening of large repositories threats the feasibility of this task. Computational intelligence techniques have been applied in this context, with the ultimate goal of reducing the overall computational cost so the task can become feasible. Particularly, clustering algorithms have been widely used as a means to reduce the dimensionality of molecular dynamics trajectories. In this paper, we d

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Luo, Lianxiang, Ai Zhong, Qu Wang, and Tongyu Zheng. "Structure-Based Pharmacophore Modeling, Virtual Screening, Molecular Docking, ADMET, and Molecular Dynamics (MD) Simulation of Potential Inhibitors of PD-L1 from the Library of Marine Natural Products." Marine Drugs 20, no. 1 (2021): 29. http://dx.doi.org/10.3390/md20010029.

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Background: In the past decade, several antibodies directed against the PD-1/PD-L1 interaction have been approved. However, therapeutic antibodies also exhibit some shortcomings. Using small molecules to regulate the PD-1/PD-L1 pathway may be another way to mobilize the immune system to fight cancer. Method: 52,765 marine natural products were screened against PD-L1(PDBID: 6R3K). To identify natural compounds, a structure-based pharmacophore model was generated, following by virtual screening and molecular docking. Then, the absorption, distribution, metabolism, and excretion (ADME) test was c

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Hung, Tzu-Chieh, Wen-Yuan Lee, Kuen-Bao Chen, Yueh-Chiu Chan, and Calvin Yu-Chian Chen. "Investigation of Estrogen Receptor (ESR1) for Breast Cancer from Traditional Chinese Medicine." BioMed Research International 2014 (2014): 1–12. http://dx.doi.org/10.1155/2014/321486.

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Recently, an important topic of breast cancer had been published in 2013. In this report, estrogen receptor (ESR1) had defined the relation of hormone-cause breast cancer. The screening of traditional Chinese medicine (TCM) database has found the molecular compounds by simulating molecular docking and molecular dynamics to regulate ESR1. S-Allylmercaptocysteine and 5-hydroxy-L-tryptophan are selected according to the highest docking score than that of other TCM compounds and Raloxifene (control). The simulation from molecular dynamics is helpful in analyzing and detecting the protein-ligand in

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Zhao, Yilan, Honghao Yang, Fengshou Wu, et al. "Exploration of N-Arylsulfonyl-indole-2-carboxamide Derivatives as Novel Fructose-1,6-bisphosphatase Inhibitors by Molecular Simulation." International Journal of Molecular Sciences 23, no. 18 (2022): 10259. http://dx.doi.org/10.3390/ijms231810259.

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A series of N-arylsulfonyl-indole-2-carboxamide derivatives have been identified as potent fructose-1,6-bisphosphatase (FBPase) inhibitors (FBPIs) with excellent selectivity for the potential therapy of type II diabetes mellitus. To explore the structure–activity relationships (SARs) and the mechanisms of action of these FBPIs, a systematic computational study was performed in the present study, including three-dimensional quantitative structure–activity relationship (3D-QSAR) modeling, pharmacophore modeling, molecular dynamics (MD), and virtual screening. The constructed 3D-QSAR models exhib

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Sahu, Satya Narayan, and Subrat Kumar Pattanayak. "Molecular docking and molecular dynamics simulation studies on PLCE1 encoded protein." Journal of Molecular Structure 1198 (December 2019): 126936. http://dx.doi.org/10.1016/j.molstruc.2019.126936.

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Takemura, Kazuhiro, Chika Sato, and Akio Kitao. "ColDock: Concentrated Ligand Docking with All-Atom Molecular Dynamics Simulation." Journal of Physical Chemistry B 122, no. 29 (2018): 7191–200. http://dx.doi.org/10.1021/acs.jpcb.8b02756.

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Di Nola, Alfredo, Danilo Roccatano, and Herman J. C. Berendsen. "Molecular dynamics simulation of the docking of substrates to proteins." Proteins: Structure, Function, and Genetics 19, no. 3 (1994): 174–82. http://dx.doi.org/10.1002/prot.340190303.

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Luo, Lianxiang, Qu Wang, and Yinglin Liao. "The Inhibitors of CDK4/6 from a Library of Marine Compound Database: A Pharmacophore, ADMET, Molecular Docking and Molecular Dynamics Study." Marine Drugs 20, no. 5 (2022): 319. http://dx.doi.org/10.3390/md20050319.

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Background: CDK4/6 (Cyclin-dependent kinases 4/6) are the key promoters of cell cycle transition from G1 phase to S phase. Thus, selective inhibition of CDK4/6 is a promising cancer treatment. Methods: A total of 52,765 marine natural products were screened for CDK4/6. To screen out better natural compounds, pharmacophore models were first generated, then the absorption, distribution, metabolism, elimination, and toxicity (ADMET) were tested, followed by molecular docking. Finally, molecular dynamics simulation was carried out to verify the binding characteristics of the selected compounds. Re

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Kenneth Obiakor, Onyeka Chinwuba Obidiegwu, Keziah Uchechi Ajah, Christian Chidebe, Ajuzie Henry Ogechi, and Ikemefuna Chijioke Uzochukwu. "Discovery of antiadhesins of Helicobacter pylori from existing drugs and medicines for malaria ventures pathogen box compounds." GSC Biological and Pharmaceutical Sciences 20, no. 3 (2022): 198–212. http://dx.doi.org/10.30574/gscbps.2022.20.3.0356.

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Background: Helicobacter pylori infection is a worldwide problem with more than half of the world's population in both developed and developing countries are infected with this organism. The best-characterized H. pylori adhesins, Blood group antigen binding Adhesin (BabA) and Sialic acid binding Adhesin (SabA) are virulent factors which facilitate adhesion of the bacteria to the host cells. Methods: We determined the binding affinities of selected existing drugs and medicines for malaria venture pathogen box compounds to H. pylori adhesin receptors by molecular docking simulations. The 3D crys

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Ifaya, Mus, Ida Musfiroh, Sahidin та ін. "MOLECULAR DOCKING AND DYNAMICS SIMULATIONS OF FENOLIC CONTENTS ON HENNA PLANT (Lawsonia inermis L.) AS ANTIDIBETIC THROUGH INHIBITION OF DIGESTIVE ENZYME α-AMYLASE". RASAYAN Journal of Chemistry 15, № 02 (2022): 861–69. http://dx.doi.org/10.31788/rjc.2022.1526654.

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Diabetes mellitus is a disease caused by high blood glucose levels, and one way to overcome it is by inhibiting the digestive enzyme, α-amylase. The henna plant (Lawsonia inermis L.) has been shown to show potential as an antidiabetic through inhibition of the enzyme digestive, but its molecular mechanism has not been revealed. Therefore, the aim of this study was to reveal the α-amylase enzyme inhibitory activity of phenolic compounds in the henna plant by molecular docking and molecular dynamics. The protein used was a high-resolution α-amylase crystallographic protein with the code PDB: 1XD

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Kumar, Anish. "STRUCTURAL AND FUNCTIONAL IMPACT OF G2032R MUTATION IN ROS1 – A THEORETICAL PERSPECTIVE." Asian Journal of Pharmaceutical and Clinical Research 10, no. 5 (2017): 339. http://dx.doi.org/10.22159/ajpcr.2017.v10i5.17661.

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Objective: Drug resistance is an imperative issue in the treatment of patients with lung cancer. In this work, investigation of the drug resistance mechanism of G2032R mutation in ROS1 is carried out using computational simulation techniques.Methods: Molecular docking and molecular dynamics (MD) simulation approach have been utilized to uncover the mechanism behind crizotinib resistance in ROS1 at a molecular level. Normal mode analysis was carried out using ElNemo server which examines the movements and conformational changes in the protein structure. ArgusLab, PEARLS, and Autodock were emplo

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Seniya, Chandrabhan, Ghulam Jilani Khan, and Kuldeep Uchadia. "Identification of Potential Herbal Inhibitor of Acetylcholinesterase Associated Alzheimer’s Disorders Using Molecular Docking and Molecular Dynamics Simulation." Biochemistry Research International 2014 (2014): 1–7. http://dx.doi.org/10.1155/2014/705451.

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Cholinesterase inhibitors (ChE-Is) are the standard for the therapy of AD associated disorders and are the only class of approved drugs by the Food and Drug Administration (FDA). Additionally, acetylcholinesterase (AChE) is the target for many Alzheimer’s dementia drugs which block the function of AChE but have some side effects. Therefore, in this paper, an attempt was made to elucidate cholinesterase inhibition potential of secondary metabolite fromCannabisplant which has negligible or no side effect. Molecular docking of 500 herbal compounds, against AChE, was performed using Autodock 4.2 a

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Talarico, Carmine, Silvia Gervasoni, Candida Manelfi, Alessandro Pedretti, Giulio Vistoli, and Andrea R. Beccari. "Combining Molecular Dynamics and Docking Simulations to Develop Targeted Protocols for Performing Optimized Virtual Screening Campaigns on the hTRPM8 Channel." International Journal of Molecular Sciences 21, no. 7 (2020): 2265. http://dx.doi.org/10.3390/ijms21072265.

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Background: There is an increasing interest in TRPM8 ligands of medicinal interest, the rational design of which can be nowadays supported by structure-based in silico studies based on the recently resolved TRPM8 structures. Methods: The study involves the generation of a reliable hTRPM8 homology model, the reliability of which was assessed by a 1.0 μs MD simulation which was also used to generate multiple receptor conformations for the following structure-based virtual screening (VS) campaigns; docking simulations utilized different programs and involved all monomers of the selected frames; t

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Pitaloka, Dian Ayu Eka, Sophi Damayanti, Aluicia Anita Artarini, and Elin Yulinah Sukandar. "Molecular Docking, Dynamics Simulation, and Scanning Electron Microscopy (SEM) Examination of Clinically Isolated Mycobacterium tuberculosis by Ursolic Acid: A Pentacyclic Triterpenes." Indonesian Journal of Chemistry 19, no. 2 (2019): 328. http://dx.doi.org/10.22146/ijc.33731.

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The purpose of this study was to analyze the inhibitory action of ursolic acid (UA) as an antitubercular agent by computational docking studies and molecular dynamics simulations. The effect of UA on the cell wall of Mycobacterium tuberculosis (MTB) was evaluated by using Scanning Electron Microscopy (SEM). UA was used as a ligand for molecular interaction and investigate its binding activities to a group of proteins involved in the growth of MTB and the biosynthesis of the cell wall. Computational docking analysis was performed by using autodock 4.2.6 based on scoring functions. UA binding wa

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Milanović, Žiko, Dušan Dimić, Jasmina Dimitrić Marković, Marijana Stanojević-Pirković, Edina Avdović та Zoran Marković. "THE INTERACTION OF PROTONATED OCTOPAMINE AND NOREPINEPHRINE WITH Β1-ADRENERGIC RECEPTOR: MOLECULAR DOCKING AND DYNAMICAL SIMULATION". Journal of the Serbian Society for Computational Mechanics, Special (1 червня 2020): 13–25. http://dx.doi.org/10.24874/jsscm.2020.01.02.

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In the current study, the interaction mechanisms between protonated neurotransmitters: octopamine (4-(2-amino-1-hydroxyethyl)phenol) and norepinephrine (4-[(1R)-2-amino-1-hydroxyethyl]benzene-1,2-diol) with the β-1 adrenergic receptor (β1AR) were examined by molecular docking, molecular dynamics (MD) simulations and MM/PBSA free energy calculations. The investigated receptor belongs to the G-protein coupled receptor group. The investigation was carried out at physiological pH=7.4. It was estimated that both compounds exist in the protonated form in the water at physiological pH. It was found t

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Lu, Shao-Yong, Yong-Jun Jiang, Jing Lv, Tian-Xing Wu, Qing-Sen Yu, and Wei-Liang Zhu. "Molecular docking and molecular dynamics simulation studies of GPR40 receptor–agonist interactions." Journal of Molecular Graphics and Modelling 28, no. 8 (2010): 766–74. http://dx.doi.org/10.1016/j.jmgm.2010.02.001.

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Al-hussaniy, Hany Akeel. "The development of molecular docking and molecular dynamics and their application in the field of chemistry and computer simulation." Journal of medical pharmaceutical and allied sciences 12, no. 1 (2023): 5552–62. http://dx.doi.org/10.55522/jmpas.v12i1.4137.

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With the rapid development of modern life science, computational Molecular docking has gradually become one of the core disciplines and methods of modern life science research. Computational docking studies the relationship between the structure and pharmacodynamics of biological macromolecules and the interaction between biological macromolecules and ligands. It promotes the development of protein engineering, protein design, and computer-aided drug design with powerful and various docking software in predicting the three-dimensional structure and dynamic characteristics of proteins from prot

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Harathi, N., Madhusudana Pulaganti, C. M. Anuradha, and Suresh Kumar Chitta. "Inhibition of Mycobacterium-RmlA by Molecular Modeling, Dynamics Simulation, and Docking." Advances in Bioinformatics 2016 (February 14, 2016): 1–13. http://dx.doi.org/10.1155/2016/9841250.

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The increasing resistance to anti-tb drugs has enforced strategies for finding new drug targets against Mycobacterium tuberculosis (Mtb). In recent years enzymes associated with the rhamnose pathway in Mtb have attracted attention as drug targets. The present work is on α-D-glucose-1-phosphate thymidylyltransferase (RmlA), the first enzyme involved in the biosynthesis of L-rhamnose, of Mtb cell wall. This study aims to derive a 3D structure of RmlA by using a comparative modeling approach. Structural refinement and energy minimization of the built model have been done with molecular dynamics.

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de Molfetta, Fábio Alberto, Renato Ferreira de Freitas, Albérico Borges Ferreira da Silva, and Carlos Alberto Montanari. "Docking and molecular dynamics simulation of quinone compounds with trypanocidal activity." Journal of Molecular Modeling 15, no. 10 (2009): 1175–84. http://dx.doi.org/10.1007/s00894-009-0468-3.

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Kumaresan, J., T. Kothai, and B. S. Lakshmi. "In silicoapproaches towards understanding CALB using molecular dynamics simulation and docking." Molecular Simulation 37, no. 12 (2011): 1053–61. http://dx.doi.org/10.1080/08927022.2011.589050.

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Kumar, Rakesh, and Shweta Saran. "Structure, molecular dynamics simulation, and docking studies ofDictyostelium discoideumand human STRAPs." Journal of Cellular Biochemistry 119, no. 9 (2018): 7177–91. http://dx.doi.org/10.1002/jcb.26840.

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Mukerjee, Nobendu, Anubhab Das, Swastika Maitra, et al. "Dynamics of natural product Lupenone as a potential fusion inhibitor against the spike complex of novel Semliki Forest Virus." PLOS ONE 17, no. 2 (2022): e0263853. http://dx.doi.org/10.1371/journal.pone.0263853.

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The Semliki Forest Virus (SFV) is an RNA virus with a positive-strand that belongs to the Togaviridae family’s Alphavirus genus. An epidemic was observed among French troops stationed in the Central African Republic, most likely caused by the SFV virus. The two transmembrane proteins El and E2 and the peripheral protein E3 make up the viral spike protein. The virus binds to the host cell and is internalized via endocytosis; endosome acidification causes the E1/E2 heterodimer to dissociate and the E1 subunits to trimerize. Lupenone was evaluated against the E1 spike protein of SFV in this study

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Pandya, Medha D., Shweta D. Dabhi, Prafulla K. Jha, and Rakesh Rawal. "Targeting MLL-CXXC Domain with Synthetic CpG Dinucleotides: Docking and Molecular Dynamics Simulation Based Approach." Advanced Materials Research 1141 (August 2016): 115–20. http://dx.doi.org/10.4028/www.scientific.net/amr.1141.115.

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Mixed lineage leukemia (MLL) is an aggressive type of childhood leukemia characterized by the presence of MLL fusion proteins resultant of chromosomal translocations affecting the MLL gene. These resulting chimeric proteins act as transcriptional regulators that take control of MLL targets. MLL fuses with more than 60 different partner genes, these fusion proteins retain the CXXC domain which binds to nonmethylated CpG DNA. The Molecular docking of CXXC domain and CpG dinucleotides were performed, large scale and long time (10 ns each) molecular dynamics simulation on CXXC domain wild type and

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Vedhashree, Jangampally, Raynee Kirthi, Abbaraju krishna sailaja, M. Suma kanth, Mallepally Deepa Reddy, and M. Praveen Kumar. "Ayurvedic Formulations for the Treatment of Covid -19." Biomedical Research and Clinical Reviews 6, no. 4 (2022): 01–09. http://dx.doi.org/10.31579/2692-9406/108.

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Background and objective: To recognize natural phytochemicals from medicinal plants, in order to reutilize them against COVID-19 by the virtue of molecular dynamics (MD) simulation study and molecular docking study COVID-19 is a transmissible disease that is initiated and propagated through a new virus strain SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2). Since 31st December 2019 in Wuhan city of China and the infection has outspread globally infecting many countries. Methods: Molecular dynamics MD simulation interaction analysis, Salt bridge analysis, Flexibility analysis, Ace-

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Adedeji, Eunice O., Gbolahan O. Oduselu, Olubanke O. Ogunlana, Segun Fatumo, Rainer Koenig, and Ezekiel Adebiyi. "Anopheles gambiae Trehalase Inhibitors for Malaria Vector Control: A Molecular Docking and Molecular Dynamics Study." Insects 13, no. 11 (2022): 1070. http://dx.doi.org/10.3390/insects13111070.

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Trehalase inhibitors are considered safe alternatives for insecticides and fungicides. However, there are no studies testing these compounds on Anopheles gambiae, a major vector of human malaria. This study predicted the three-dimensional structure of Anopheles gambiae trehalase (AgTre) and identified potential inhibitors using molecular docking and molecular dynamics methods. Robetta server, C-I-TASSER, and I-TASSER were used to predict the protein structure, while the structural assessment was carried out using SWISS-MODEL, ERRAT, and VERIFY3D. Molecular docking and screening of 3022 compoun

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Mukherjee, Sunny, Sucharita Das, Navneeth Sriram, Sandipan Chakraborty, and Mahesh Kumar Sah. "In silico investigation of the role of vitamins in cancer therapy through inhibition of MCM7 oncoprotein." RSC Advances 12, no. 48 (2022): 31004–15. http://dx.doi.org/10.1039/d2ra03703c.

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Huang, Yechuan, Xicai Zhang та Huayi Suo. "Interaction between β-lactoglobulin and EGCG under high-pressure by molecular dynamics simulation". PLOS ONE 16, № 12 (2021): e0255866. http://dx.doi.org/10.1371/journal.pone.0255866.

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The binding between β-lactoglobulin and epigallocatechin gallate (EGCG) under the pressure of 600 MPa was explored using molecular docking and molecular dynamics (MD) simulation. EGCG bound mainly in two regions with site 1 in internal cavity of the β-barrel and site 2 on the surface of protein. 150 ns MD was performed starting from the structure with the optimal binding energy at the two sites in molecular docking, respectively. It was found that the protein fluctuated greatly when small molecule bound to site 2 at 0.1 MPa, and the protein fluctuation and solvent accessible surface area becam

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Yuan, Jiaying, Yiqing Zhu, Jiayi Zhao, et al. "Network Pharmacology, Molecular Docking and Molecular Dynamics Simulation Studies of the Molecular Targets and Mechanisms of ChuanKeZhi in the Treatment of COVID-19." Natural Product Communications 17, no. 8 (2022): 1934578X2211169. http://dx.doi.org/10.1177/1934578x221116977.

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Objectives: Coronavirus disease 2019 (COVID-19) has had a global impact and is spreading quickly. ChuanKeZhi injection (CKZI) is widely used in asthma patients. In this paper, we aimed to explore active compounds of CKZ and determine potential mechanisms against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) through network pharmacology, molecular docking and dynamic simulation studies. Materials and Methods: We used the Systematic Pharmacology Database and Analysis Platform of Traditional Chinese Medicine (TCMSP) to screen active compounds and potential target proteins of CKZ. C

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Evren, Asaf Evrim, Demokrat Nuha, and Leyla Yurttaş. "Focusing on the moderately active compound (MAC) in the design and development of strategies to optimize the apoptotic effect by molecular mechanics techniques." European Journal of Life Sciences 1, no. 3 (2023): 118–26. http://dx.doi.org/10.55971/ejls.1209591.

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Today, chemotherapeutic agents are mostly used to fight cancer in clinics. But even though they have selectivity for cancer cells, their mechanism of action could result in necrosis. Therefore, we aimed to suggest new design strategies using a moderately active compound (MAC) to get better activity and increase the apoptotic effect in this study. Although MAC, previously synthesized and evaluated for its anticancer properties, has been marked as a moderately active compound, it has let us develop new molecules using its molecular core supported by molecular docking and molecular dynamics simul

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Salehi, Farnaz, Leila Emami, Zahra Rezaei, Soghra Khabnadideh, Behnaz Tajik, and Razieh Sabet. "Fluconazole-Like Compounds as Potential Antifungal Agents: QSAR, Molecular Docking, and Molecular Dynamics Simulation." Journal of Chemistry 2022 (March 31, 2022): 1–16. http://dx.doi.org/10.1155/2022/5031577.

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Today, fungal infection has become more common disease especially in some cases, such as AIDS, cancer, and organ transplant which the immune system is suppressed. On the other hand, due to the increasing resistance to current antifungal drugs, more and more options for design of novel more efficient compounds with higher resistance are needed. In this study, a series of a fluconazole analogues were subjected to quantitative structure-activity relationship analysis to find the structure requirements for modeling adequate candidate. The best multiple linear regression equation was achieved from

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Abdjan, Muhammad Ikhlas, Nanik Siti Aminah, Alfinda Novi Kristanti та ін. "Structure-based approach: molecular insight of pyranocumarins against α-glucosidase through computational studies". RSC Advances 13, № 6 (2023): 3438–47. http://dx.doi.org/10.1039/d2ra07537g.

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We presented the structure-based approach (molecular docking and MD simulation) to understand the dynamics behavior and inhibitory efficiency of pyranocoumarin derivatives against α-glucosidase at the molecular level.

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Khade, Amol B., Sidhartha S. Kar, Cinu T. Alummoottil, et al. "Synthesis, Biological Evaluation and Molecular Dynamics Simulation Studies of Novel Diphenyl Ethers." Medicinal Chemistry 16, no. 2 (2020): 256–70. http://dx.doi.org/10.2174/1573406415666190306152907.

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Background: The well-known antibacterial agent Triclosan (TCL) that targets bacterial enoylacyl protein reductase has been described to inhibit human fatty acid synthase (FASN) via the enoylacyl reductase domain. A Literature survey indicates that TCL is selectively toxic to cancer cells and furthermore might indeed reduce cancer incidence in vivo. A recent study found that TCL inhibits FASN by acting as an allosteric protein-protein interface (PPI) inhibitor. It induces dimer orientation changes that effect in a downstream reorientation of catalytic residues in the NADPH binding site proposin

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Tripathi, Manish Kumar, Mohammad Yasir, Pushpendra Singh, and Rahul Shrivastava. "A Comparative Study to Explore the Effect of Different Compounds in Immune Proteins of Human Beings Against Tuberculosis: An In-silico Approach." Current Bioinformatics 15, no. 2 (2020): 155–64. http://dx.doi.org/10.2174/1574893614666190226153553.

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Background: The lungs are directly exposed to pollutants, pathogens, allergens, and chemicals, which might lead to physiological disorders. During the Bhopal gas disaster, the lungs of the victims were exposed to various chemicals. Here, using molecular modelling studies, we describe the effects of these chemicals (Dimethyl urea, Trimethyl urea, Trimethyl isocyanurate, Alphanaphthol, Butylated hydroxytoluene and Carbaryl) on pulmonary immune proteins. Objective: In the current study, we performed molecular modelling methods like molecular docking and molecular dynamics simulation studies to id

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Rizqillah, Raihan Kenji, Jaka Fajar Fatriansyah, Fadilah, et al. "In silico molecular docking and molecular dynamics examination of Andrographis paniculata compounds of Andrographolide, Neoandrographolide, and 5-hydroxy-7,8,2’,3’-tetramethoxyflavone inhibition activity to SARS-CoV-2 main protease." BIO Web of Conferences 41 (2021): 07002. http://dx.doi.org/10.1051/bioconf/20214107002.

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In this work, Andrographis paniculata compounds of Andrographolide, Neoandrographolide, and 5-hydroxy-7,8,2’,3’-tetramethoxyflavone inhibition activity to SARS CoV-2 main protease were examined through in silico molecular docking and molecular dynamics simulation, with Remdesivir as control ligand. Docking score and MMGBSA were examined as well as molecular dynamics parameters: RMSD, RMSF and Protein ligand contact fraction. Our study found that Andrographis paniculata compounds of Andrographolide, Neoandrographolide, and 5-hydroxy-7,8,2’,3’-tetramethoxyflavone have comparable inhibition activ

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Halder, Sajal Kumar, Maria Mulla Mim, Md Meharab Hassan Alif та ін. "Oxa-376 and Oxa-530 variants of β-lactamase: computational study uncovers potential therapeutic targets of Acinetobacter baumannii". RSC Advances 12, № 37 (2022): 24319–38. http://dx.doi.org/10.1039/d2ra02939a.

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Determining novel therapeutic targets of Acinetobacter baumannii. Deleterious variants, causing antibiotic resistance, were identified by molecular docking and molecular dynamics simulation suggesting new therapeutic targets Oxa-376 and Oxa-530.

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Kalva, Sukesh, Nikhil Agrawal, Adam A. Skelton, and Lilly M. Saleena. "Identification of novel selective MMP-9 inhibitors as potential anti-metastatic lead using structure-based hierarchical virtual screening and molecular dynamics simulation." Molecular BioSystems 12, no. 8 (2016): 2519–31. http://dx.doi.org/10.1039/c6mb00066e.

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Abdjan, Muhammad Ikhlas, Nanik Siti Aminah, Imam Siswanto, Alfinda Novi Kristanti, Yoshiaki Takaya, and Muhammad Iqbal Choudhary. "Exploration of stilbenoid trimers as potential inhibitors of sirtuin1 enzyme using a molecular docking and molecular dynamics simulation approach." RSC Advances 11, no. 31 (2021): 19323–32. http://dx.doi.org/10.1039/d1ra02233d.

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Shi, Mingsong, Min Zhao, Lun Wang, et al. "Exploring the stability of inhibitor binding to SIK2 using molecular dynamics simulation and binding free energy calculation." Physical Chemistry Chemical Physics 23, no. 23 (2021): 13216–27. http://dx.doi.org/10.1039/d1cp00717c.

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The detailed interactions between SIK2 and four inhibitors, HG-9-91-01, KIN112, MRT67307, and MRT199665, were studied using molecular docking, molecular dynamics simulation, binding free energy calculation, and interaction fingerprint analysis.

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Sama-ae, Imran, Suthinee Sangkanu, Abolghasem Siyadatpanah, et al. "Targeting Acanthamoeba proteins interaction with flavonoids of Propolis extract by in vitro and in silico studies for promising therapeutic effects." F1000Research 11 (February 7, 2023): 1274. http://dx.doi.org/10.12688/f1000research.126227.2.

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Background: Propolis is a natural resinous mixture produced by bees. It provides beneficial effects on human health in the treatment/management of many diseases. The present study was performed to demonstrate the anti-Acanthamoeba activity of ethanolic extracts of Propolis samples from Iran. The interactions of the compounds and essential proteins of Acanthamoeba were also visualized through docking simulation. Methods: The minimal inhibitory concentrations (MICs) of Propolis extract against Acanthamoeba trophozoites and cysts was determined in vitro. In addition, two-fold dilutions of each of

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Sama-ae, Imran, Suthinee Sangkanu, Abolghasem Siyadatpanah, et al. "Targeting Acanthamoeba proteins interaction with flavonoids of Propolis extract by in vitro and in silico studies for promising therapeutic effects." F1000Research 11 (November 8, 2022): 1274. http://dx.doi.org/10.12688/f1000research.126227.1.

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Background: Propolis is a natural resinous mixture produced by bees. It provides beneficial effects on human health in the treatment/management of many diseases. The present study was performed to demonstrate the anti-Acanthamoeba activity of ethanolic extracts of Propolis samples from Iran. The interactions of the compounds and essential proteins of Acanthamoeba were also visualized through docking simulation. Methods: The minimal inhibitory concentrations (MICs) of Propolis extract against Acanthamoeba trophozoites and cysts was determined in vitro. In addition, two-fold dilutions of each of

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Xiong, Weixue, Jiahui Cai, Ruijia Li, Canhong Wen, and Haizhu Tan. "Rare Variant Analysis and Molecular Dynamics Simulation in Alzheimer’s Disease Identifies Exonic Variants in FLG." Genes 13, no. 5 (2022): 838. http://dx.doi.org/10.3390/genes13050838.

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Background: Although an increasing number of common variants contributing to Alzheimer’s disease (AD) are uncovered by genome-wide association studies, they can only explain less than half of the heritability of AD. Rare variant association studies (RVAS) has become an increasingly important area to explain the risk or trait variability of AD. Method: To investigate the potential rare variants that cause AD, we screened 70,209 rare variants from two cohorts of a 175 AD cohort and a 214 cognitively normal cohort from the Alzheimer’s Disease Neuroimaging Initiative database. MIRARE, a novel RVAS

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Gervasoni, Silvia, Carmine Talarico, Candida Manelfi, Alessandro Pedretti, Giulio Vistoli, and Andrea R. Beccari. "Extensive Sampling of Molecular Dynamics Simulations to Identify Reliable Protein Structures for Optimized Virtual Screening Studies: The Case of the hTRPM8 Channel." International Journal of Molecular Sciences 23, no. 14 (2022): 7558. http://dx.doi.org/10.3390/ijms23147558.

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(1) Background: Virtual screening campaigns require target structures in which the pockets are properly arranged for binding. Without these, MD simulations can be used to relax the available target structures, optimizing the fine architecture of their binding sites. Among the generated frames, the best structures can be selected based on available experimental data. Without experimental templates, the MD trajectories can be filtered by energy-based criteria or sampled by systematic analyses. (2) Methods: A blind and methodical analysis was performed on the already reported MD run of the hTRPM8

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