Relevant bibliographies by topics / Molecuar dynamics and docking simulation

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Academic literature on the topic 'Molecuar dynamics and docking simulation'

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Published: 14 March 2023

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

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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 (December 31, 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, molecular dynamics simulation is now a fundamental tool to investigative bio-molecular assemblies at atomic level. These methods in association with experimental support have been of great value in modern drug discovery and development. Nowadays, it has become an increasingly significant method in drug discovery process. In this review, we focus on protein-ligand interactions using molecular docking, virtual screening and molecular dynamics simulations. Here, we cover an overview of the available methods for molecular docking and molecular dynamics simulations, and their advancement and applications in the area of modern drug discovery. The available docking software and their advancement including application examples of different approaches for drug discovery are also discussed. We have also introduced the physicochemical foundations of molecular docking and simulations, mainly from the perception of bio-molecular interactions.
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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-substituted aryloxy compounds have also been performed, and the results indicate that a potent VEGFR2 inhibitor should have lower interaction energy with VEGFR2 and create at least 2 hydrogen bonds with VEGFR2.
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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 (November 1, 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 (September 14, 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 regressions (PLSR) was developed to predict the pIC50 value of the compound by utilizing a data set of 42 cycloguanil analogues. From statistical analysis, we obtained the r2 values of the training and test sets that were 0.85 and 0.70, respectively, while q2 of the leave-one-out cross-validation was 0.77. The contour maps of the CoMFA model were also interpreted to analyze the structural requirement regarding electrostatic and steric factors. The most active compound (c33) and least active compound (c8) were picked for molecular docking and MD analysis. From the docking analysis, we found that the attached substituent on the backbone structure of cycloguanil gives a significant contribution to antimalarial activity. The results of the MD simulation confirm the stability of the binding pose obtained from the docking simulations.
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Khare, Noopur, Sanjiv Kumar Maheshwari, Syed Mohd Danish Rizvi, Hind Muteb Albadrani, Suliman A. Alsagaby, Wael Alturaiki, Danish Iqbal, 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 (June 12, 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 structure prediction of CALHM1 was done through CFSSP, GOR4, and SOPMA methods. The structure was identified through LOMETS, MUSTER, and MODELLER and finally, the structures were validated through Rampage. Bauhinia variegata plant was used to check the interaction of alkaloids and flavonoids against CALHM1. The protein and protein–ligand complex were also validated through molecular dynamics simulations studies. The model generated through MODELLER software with 6VAM A was used because this model predicted the best results in the Ramachandran plot. Further molecular docking was performed, quercetin was found to be the most appropriate candidate for the protein molecule with the minimum binding energy of −12.45 kcal/mol and their ADME properties were analysed through Molsoft and Molinspiration. Molecular dynamics simulations showed that CALHM1 and CALHM1–quercetin complex became stable at 2500 ps. It may be seen through the study that quercetin may act as a good inhibitor for treatment. With the help of an in silico study, it was easier to analyse the 3D structure of the protein, which may be scrutinized for the best-predicted model. Quercetin may work as a good inhibitor for treating Alzheimer’s disease, according to in silico research using molecular docking and molecular dynamics simulations, and future in vitro and in vivo analysis may confirm its effectiveness.
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Zaki, Magdi E. A., Sami A. Al-Hussain, Vijay H. Masand, Siddhartha Akasapu, Sumit O. Bajaj, Nahed N. E. El-Sayed, Arabinda Ghosh, and Israa Lewaa. "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 (April 13, 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-ring Carbons and Nitrogens, amide Nitrogen, sp2-hybridized Carbons, etc. Thus, the QSAR model has a good balance of qualitative and quantitative requirements (balanced QSAR model) and satisfies the Organisation for Economic Co-operation and Development (OECD) guidelines. After that, a QSAR-based virtual screening of 26,467 food compounds and 360 heterocyclic variants of molecule 1 (benzotriazole–indole hybrid molecule) helped to identify promising hits. Furthermore, the molecular docking and molecular dynamics (MD) simulations of Mpro with molecule 1 recognized the structural motifs with significant stability. Molecular docking and QSAR provided consensus and complementary results. The validated analyses are capable of optimizing a drug/lead candidate for better inhibitory activity against the main protease of SARS-CoV-2.
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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 develop a novel methodology for clustering entire trajectories using structural features from the substrate-binding cavity of the receptor in order to optimize docking experiments on a cloud-based environment. The resulting partition was selected based on three clustering validity criteria, and it was further validated by analyzing the interactions between 20 ligands and a fully flexible receptor (FFR) model containing a 20 ns molecular dynamics simulation trajectory. Our proposed methodology shows that taking into account features of the substrate-binding cavity as input for thek-means algorithm is a promising technique for accurately selecting ensembles of representative structures tailored to a specific ligand.
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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 (December 25, 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 carried out to select the most suitable compounds. Finally, molecular dynamics simulation was also performed to validate the binding property of the top compound. Results: Initially, 12 small marine molecules were screened based on the pharmacophore model. Then, two compounds were selected for further evaluation based on the molecular docking scores. After ADME and toxicity studies, molecule 51320 was selected for further verification. By molecular dynamics analysis, molecule 51320 maintains a stable conformation with the target protein, so it has the chance to become an inhibitor of PD-L1. Conclusions: Through structure-based pharmacophore modeling, virtual screening, molecular docking, ADMET approaches, and molecular dynamics (MD) simulation, the marine natural compound 51320 can be used as a small molecule inhibitor of PD-L1.
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Dissertations / Theses on the topic "Molecuar dynamics and docking simulation"

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Trezza, Alfonso. "A novel computational way to unlock drug targets deep and transient secretes." Doctoral thesis, Università di Siena, 2019. http://hdl.handle.net/11365/1072788.

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Ullmann, G. Matthias. "Simulation and analysis of docking and molecular dynamics of electron transfer protein complexes." [S.l. : s.n.], 1998. http://darwin.inf.fu-berlin.de/1998/23/index.html.

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Madhusudhan, M. S. "Computer Modeling and Molecular Dynamics Simulation Of Angiogenins And Its Ligand Bound Complexes." Thesis, Indian Institute of Science, 2000. http://hdl.handle.net/2005/211.

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Computational structural biology Even with rapid advances in structure determination methods, there is a long gap to be bridged between the number of proteins that have been sequenced and the number whose three-dimensional structures have been experimentally elucidated. Experimentally protein structures are determined by X-ray crystallography or by nuclear magnetic resonance spectroscopy (NMR). X-ray crystal structures give a time averaged picture but little information on conformational dynamics. Though NMR gives dynamical information, the technique cannot be applied to systems whose molecular weight is large. Only small proteins fall within the ken of NMR experiments. In most cases the three dimensional structure of the protein alone cannot give a complete picture of its mechanism. It is also essential to know the interactions of proteins with other proteins, with their ligands and substrates in order to have a better understanding of their functioning. Computer modeling and simulations are now indispensable supplements to experimental structural biology. The last word in protein structure prediction method is far from being said but the ever-improving homology and ab-initio modeling methods give rise to optimism that sometime in the near future these methods will become almost as reliable as experimental techniques. Ligand docking onto protein molecules is as challenging a problem as protein structure predicting itself. Computer modeling methods to dock ligands have to search a wide region of conformational space besides taking into consideration issues of charge and shape complementarities.
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Sousa, Rui. "Structural insights of Interleukin-15 through Molecular Dynamics simulations : Towards the rational design of specific inhibitors." Thesis, Nantes, 2019. http://www.theses.fr/2019NANT4081.

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L’Interleukine-15 (IL-15) est une cytokine impliquée dans un grand nombre de fonctions cellulaires. Elle participe ainsi notamment au développement et à l’activation de la réponse immunitaire. L’IL-15 est donc apparue comme une cible potentielle pour différentes applications thérapeutiques. La structure de cette cytokine est basée sur un complexe quaternaire entre IL-15 et ces récepteurs a (IL-15Ra), b (IL- 2Rb et y (yc). La modulation fonctionnelle d’IL-15 est liée à son interaction avec ces récepteurs, notamment avec IL-2Rβ L’interleukine-2 (IL-2) partageant deux de ses trois récepteurs ( IL-2Rβ et yc) avec l’IL-15, la recherche d’inhibiteurs spécifiques de l’IL-15 doit intégrer ces caractéristiques. Dans le cadre de ce travail, par des approches de Modélisation Moléculaire, en particulier de Dynamique Moléculaire (MD), nous avons: (i) déterminé l’influence de la forme complexée de l’IL-15 (dimère, trimère ou tétramère) sur les propriétés des interfaces (ii) mis en évidence les acides aminés « clés » des différentes interfaces (iii) étudié l’impact de mutations de certains de ces acides aminés (iv) utilisé ces informations pour mettre au point un pharmacophore ayant permis, dans un second temps, la découverte de nouveaux composés de faible poids moléculaire capables de cibler spécifiquement une des interfaces (IL-15/ IL-2Rβ). L’ensemble des données issues de ce travail a été confronté à des résultats biologiques obtenus dans le cadre du projet
Interleukin 15 (IL-15) is a cytokine involved in a plethora of different cellular functions. It participates, for instance, in the development and activation of immune responses. IL-15 has, therefore, clearly appeared as a potential target for several therapeutic applications. The structure of this cytokine is based on a quaternary complex between IL-15 and its a (IL-15Ra), b ( IL-2Rβ) and y (yc) receptors. The key to the functional modulation of IL-15 lies on its interaction with its receptors and, more particularly, with IL-2Rβ. Interleukin-2 sharing two out of the three receptors 2Rβ and yc), the search for specific IL-15 inhibitors has to take into account these features. In this work, through various Molecular Modeling approaches, specifically Molecular Dynamics (MD) simulations, we have (i) determined the influence of the complexed form of IL-15 (dimer, trimer or tetramer) on the interface properties (ii) highlighted the key amino acid (“hot spots”) of the various interfaces (iii) studied the impact of mutations of selected residues (iv) used this information to design a pharmacophore which has allowed, in a subsequent step, the discovery of new low-molecular weight compounds able to specifically target one of the IL-15 interfaces (IL- 15/ IL-2Rβ). The theoretical data have been compared to the results of biological experiments carried out in the framework of the project
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Madeleine, Noelly. "Recherche d'inhibiteurs de l'interaction Lutheran-Laminine par des techniques de modélisation et de simulation moléculaires." Thesis, La Réunion, 2017. http://www.theses.fr/2017LARE0054/document.

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La drépanocytose est une maladie génétique qui se caractérise par des globules rouges en forme de faucille. Chez les personnes atteintes de drépanocytose, ces globules rouges (GR) adhèrent à l’endothélium vasculaire et provoquent ainsi une vaso-occlusion. Ce phénomène s’explique par la surexpression de la protéine Lutheran (Lu) à la surface des globules rouges falciformes qui se lie fortement à la Laminine (Ln) 511/521 exprimée par l’endothélium vasculaire enflammé. Le but de cette étude est d’identifier un inhibiteur d’interaction protéine-protéine (PPI) qui possède une forte probabilité de liaison à Lu afin d’inhiber l’interaction Lu-Ln 511/521. Un criblage virtuel de 1 295 678 composés ciblant la protéine Lu a été réalisé. La validation préalable d’un protocole de scoring a été envisagée sur la protéine CD80 qui présente un site de liaison avec des caractéristiquestopologiques et physico-chimiques similaires au site de liaison prédit sur Lu ainsi que plusieurs ligands avec des constantes d’affinité connues. Ce protocole contient différentes étapes de sélection basées sur les affinités calculées (scores), des simulations de dynamique moléculaire et les propriétés moléculaires. Un protocole de scoring fiable a été validé sur CD80 avec le programme de docking DOCK6 et les fonctions de scoring XSCORE et MM-PBSA ainsi qu’avec la méthode decalcul FMO. L’application de ce protocole sur Lu a permis d’obtenir deux ligands validés par des tests in vitro qui font l’objet d’un dépôt de brevet. La fonction de scoring XSCORE a permis d’identifier neuf autres ligands qui semblent aussi être des candidats prometteurs pour inhiber l’interaction Lu-Ln 511/521
Drepanocytosis is a genetic blood disorder characterized by red blood cells that assume an abnormal sickle shape. In the pathogenesis of vaso-occlusive crises of sickle cell disease, red blood cells bind to the vascular endothelium and promote vaso-occlusion. At the surface of these sickle red blood cells, the overexpressed protein Lutheran (Lu) strongly interacts with the Laminin (Ln) 511/521.The aim of this study was to identify a protein-protein interaction (PPI) inhibitor with a highprobability of binding to Lu for the inhibition of the Lu-Ln 511/521 interaction. A virtual screening was performed with 1 295 678 compounds that target Lu. Prior validation of a robust scoring protocol was considered on the protein CD80 because this protein has a binding site with similar topological and physico-chemical characteristics and it also has a series of ligands with known affinity constants. This protocol consisted of multiple filtering steps based on calculated affinities (scores), molecular dynamics simulations and molecular properties. A robust scoring protocol was validated on the protein CD80 with the docking program DOCK6 and the scoring functions XSCORE and MM-PBSA and also with the FMO method. This protocol was applied to the protein Lu and we found two compounds that were validated by in vitro studies. The protection of these ligands by a patent is under process. Nine other compounds were identified by the scoring functionXSCORE and seem to be promising candidates for inhibiting the Lu-Ln 511/521 interaction
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Haslak, Zeynep Pinar. "Approches numériques pour évaluer les propriétés de liaison de ligands : le cas du récepteur NMDA." Electronic Thesis or Diss., Université de Lorraine, 2019. http://www.theses.fr/2019LORR0240.

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L'un des problèmes importants dans la conception de médicaments est l'identification de l'activité biologique des ligands en regard de leurs récepteurs. Le développement, la synthèse et les mesures d'activité des ligands revêtent une importance majeure dans la conception de médicaments. Cependant, les études expérimentales ne peuvent qu'être limitées: la synthèse de toutes les molécules potentiellement actives est par exemple irréaliste. Les études numériques pourraient donc apporter une aide précieuse aux études expérimentales, notamment dans le cas de la conception de ligands pour les récepteurs au glutamate comme le récepteur NMDA. En combinant les points forts des approches par dynamique moléculaire et par chimie quantique, il est possible d’établir une inspection, une caractérisation et une rationalisation plus ciblées des études de conception de médicaments. Dans cette thèse, des méthodes numériques ont été utilisées pour étudier les propriétés intrinsèques des molécules biologiquement actives responsables de la sélectivité. Les résultats de cette étude sont présentés en 4 chapitres. Dans les deux premiers chapitres, nous avons cherché à différencier les agonistes, les antagonistes et les agonistes partiels au récepteur NMDA en fonction de descripteurs tirés de la chimie quantique et d'énergies libres de liaison de Gibbs. Plusieurs propriétés moléculaires qui pourraient jouer un rôle dans la liaison du ligand à la sous-unité glycine GluN1 du récepteur NMDA ainsi que les énergies libres de liaison ont été utilisées pour établir un lien entre les efficacités et les affinités de liaison des ligands. La prédiction des constantes de dissociation acide d'acides aminés dans les protéines et les ligands nous permet d'avoir des informations sur l'affinité de liaison et l'efficacité des ligands envers leurs protéines cibles. Considérant l'importance des \pka, nous avons exploré dans le chapitre suivant comment les charges atomiques des acides carboxyliques peuvent être liées à la prédiction de \pka de ligands. Afin de mettre en lumière les origines de la stéréosélectivité de ligands biologiquement actifs, plusieurs voies mécanistiques ont été évalués dans le dernier chapitre pour les 2-thiohydantoïnes, qui sont de puissants antagonistes des récepteurs aux androgènes
One of the important issues in drug design is the identification of the biological activity of receptor ligands. Development, synthesis and activity measurements of ligands have a major importance in drug design. However, there are certain limits in experimental studies; synthesis of a large number of compounds to cover all the potentially active molecules is unrealistic. Computational studies could therefore provide a valuable aid to experimental studies on ligand design for glutamate receptors. By combining the strengths of Molecular Dynamics and Quantum Chemical approaches, a more focused inspection, characterisation and rationalization of the drug design studies is allowed to be established. In this dissertation, computational methods have been used to investigate the intrinsic properties of the biologically active molecules that cause the selectivity. The results of this study will be introduced in 4 chapters. In Chapters 4 and 5, we aimed to differentiate between agonists, antagonists and partial agonists based on Quantum Chemical descriptors and binding Gibbs free energies. Several molecular properties that could play a role in ligand binding to the glycine GluN1 subunit of NMDA and calculated binding Gibbs free energies were further used to provide a link between the efficacies and binding affinities of the ligands. Prediction of the acid dissociation constants of amino acids in proteins and ligands allows us to have information about the binding affinity and efficacy of the ligand to its target protein. Considering the significance of p\textit{K_a}'s, how atomic charges of carboxylic acids can be related to the prediction of p\textit{K_a} of the ligands have been explored in Chapter 6. In order to shed light on the origins of the stereoselectivity of biologically active ligands, several mechanistic pathways have been evaluated for 2-thiohydantoins which are potent androgen receptor antagonists and the results are given in Chapter 7
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Touzeau, Jérémy. "Modélisation multi-échelle de biomatériaux pour des problématiques expérimentales." Thesis, Sorbonne Paris Cité, 2018. https://theses.md.univ-paris-diderot.fr/Touzeau_jeremy_2_complete_20181203.pdf.

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La confection de dispositifs impliquant des biomolécules, notamment dans le cadre de la détection (biocapteurs) ou de la protection contre des pathogènes (revêtements antimicrobiens), compte toujours un grand nombre d’interrogations notamment à l’échelle atomique. Dans ce contexte, nous avons utilisé les outils de la modélisation moléculaire afin de réaliser des études multi-échelles (à la fois en quantique et en mécanique moléculaire) pour étudier des systèmes (expérimentaux) impliquant des biomolécules et solutionner des problématiques. L’étude a été menée au sein de deux projets. Dans le cadre du premier d’entre eux, nous nous sommes tout d’abord intéressé à l’optimisation d’un biocapteur impliquant un transistor à effet de champ de type EGOFET, en nous concentrant plus particulièrement sur le canal semi-conducteur du transistor. Dans un second temps, nous avons réalisé une étude autour de l’interaction biologique et spécifique du biocapteur. Dans le cadre du second projet, nous nous sommes intéressés à un revêtement antimicrobien. Celui-ci s’appuie sur le greffage d’un peptide comportant une séquence d’accroche, une séquence antimicrobienne ainsi qu’un site clivable par une enzyme spécifique au pathogène que l’on souhaite traiter. En présence de ce dernier uniquement, le peptide antimicrobien est ainsi libéré dans le milieu. Bien que ce système fonctionne parfaitement en solution, ses propriétés bactéricides sont perdues lorsqu’il est greffé sur une surface, une étape indispensable pour une utilisation dans le domaine biomédicale. Nous avons ainsi étudié ce système grâce à la modélisation moléculaire afin de comprendre la perte de ces propriétés
The tailoring of devices involving biomolecules, for applications such as the detection (biosensors) or protection against pathogens (antimicrobial coats), still introduce several interrogations at an atomic point of view. In this context, we used molecular modelling tools in order to realize multi-scale studies (quantic level and molecular mechanics level) about experimental systems and solve issues. We interested in two projects. In the first one, we firstly focused on biosensor involving filed effect transistor (EGOFET type), by studying the optimization of the semi-conductor channel. Then we interested in the specific biological interaction of the biosensor. In the second one, we interested in an antimicrobial coat. This device is composed by a peptide containing three parts: an anchoring one, a cleavable one which can be cut specifically by a surface protease of the target and so, release the last peptide in the area which involves antimicrobial properties. The system is very efficient in solution but when it’s grafted on a surface, antimicrobial properties disappear. Consequently, we used molecular modelling tools in order to prospect those antimicrobial properties loss
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Krebs, Fanny. "Etudes in silico et expérimentale de la DXR & synthèse de D- et L-GAP énantiomériquement purs." Thesis, Strasbourg, 2016. http://www.theses.fr/2016STRAF059/document.

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La thèse porte sur l’étude des 2 premières enzymes de la voie du MEP: la DXS et DXR. La voie du MEP conduit à la biosynthèse des isoprénoïdes chez la plupart des bactéries, dont des pathogènes. Etant absente chez l’homme, les enzymes de cette voie cible idéale pour la recherche de nouveaux antimicrobiens. L’objectif principal était d’améliorer le développement de nouveaux antimicrobiens. Nous avons utilisé des outils computationnels : méthodes de docking et de mécanique moléculaire couplée à la méthode MM/PBSA. Nous avons identifié les résidus contribuant significativement à la fixation d’un ligand dans le site actif de la DXR. Ces résultats ont été utilisés lors de la conception de nouveaux candidats inhibiteurs de type bisubstrat, biligand et difluoro phosphonate, dont 2 ont pu être synthétisés. Nous avons également développé une méthode de synthèse donnant accès au L- et D-GAP énantiomeriquement purs, dans le but d’étudier l’énantiospécificité de la DXS face à son substrat D-GAP
This thesis concerns the study of the 2 first enzymes of the MEP pathway: DXS and DXR. The MEP pathway permits the biosynthesis of isoprénoïdes in most bacteria, including pathogenic one. As it is not present in human, enzymes of MEP pathway are effective targets in the research of new antimicrobial drugs. The objective was to advance the development of new antimicrobiotic compounds. We used computational tools: molecular docking and molecular dynamics simulations coupled with an MM/PBSA approach. We were able to identify residues that contribute significantly to the ligand binding in the DXR active site. These results were used to guide the conception of new inhibitor models, such as bisubstrates, biligands and α,α-difluoro phosphonates, two of which were synthetized. We also developed a synthesis method to obtain L- and D-GAP as enantiomerically pure molecules. The goal was to study the enantiospecificity of DXS to its substrate, D-GAP
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Abdulganiyyu, Ibrahim A. "A single AKH neuropeptide activating three different fly AKH-receptors: an insecticide study via computational methods." Doctoral thesis, Faculty of Science, 2021. http://hdl.handle.net/11427/33621.

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Flies are a widely distributed pest insect that poses a significant threat to food security. Flight is essential for the dispersal of the adult flies to find new food sources and ideal breeding spots. The supply of metabolic fuel to power the flight muscles of insects is regulated by adipokinetic hormones (AKHs). The fruit fly, Drosophila melanogaster, the flesh fly, Sarcophaga crassipalpis, and the oriental fruit fly, Bactrocera dorsalis all have the same AKH that is present in the blowfly, Phormia terraenovae; this AKH has the code-name Phote-HrTH. Binding of the AKH to the extracellular binding site of a G protein-coupled receptor causes its activation. In this thesis, the structure of Phote-HrTH in SDS micelle solution was determined using NMR restrained molecular dynamics. The peptide was found to bind to the micelle and be reasonably rigid, with an S 2 order parameter of 0.96. The translated protein sequence of the AKH receptor from the fruit fly, Drosophila melanogaster, the flesh fly, Sarcophaga crassipalpis, and the oriental fruit fly, Bactrocera dorsalis were used to construct two models for each receptor: Drome-AKHR, Sarcr-AKHR, and Bacdo-AKHR. It is proposed that these two models represent the active and inactive state of the receptor. The models based on the crystal structure of the β-2 adrenergic receptor were found to bind Phote-HrTH with a predicted binding free energy of –107 kJ mol–1 for Drome-AKHR, –102 kJ mol–1 for Sarcr-AKHR and –102 kJ mol–1 for Bacdo-AKHR. Under molecular dynamics simulation, in a POPC membrane, the β-2AR receptor-like complexes transformed to rhodopsin-like. The identification and characterisation of the ligand-binding site of each receptor provide novel information on ligand-receptor interactions, which could lead to the development of species-specific control substances to use discriminately against these pest flies.
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Lundborg, Magnus. "Computer-Assisted Carbohydrate Structural Studies and Drug Discovery." Doctoral thesis, Stockholms universitet, Institutionen för organisk kemi, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-56411.

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Carbohydrates are abundant in nature and have functions ranging from energy storage to acting as structural components. Analysis of carbohydrate structures is important and can be used for, for instance, clinical diagnosis of diseases as well as in bacterial studies. The complexity of glycans makes it difficult to determine their structures. NMR spectroscopy is an advanced method that can be used to examine carbohydrates at the atomic level, but full assignments of the signals require much work. Reliable automation of this process would be of great help. Herein studies of Escherichia coli O-antigen polysaccharides are presented, both a structure determination by NMR and also research on glycosyltransferases which assemble the polysaccharides. The computer program CASPER has been improved to assist in carbohydrate studies and in the long run make it possible to automatically determine structures based only on NMR data. Detailed computer studies of glycans can shed light on their interactions with proteins and help find inhibitors to prevent unwanted binding. The WaaG glycosyltransferase is important for the formation of E. coli lipopolysaccharides. Molecular docking analyses of structures confirmed to bind this enzyme have provided information on how inhibitors could be composed. Noroviruses cause gastroenteritis, such as the winter vomiting disease, after binding human histo-blood group antigens. In one of the projects, fragment-based docking, followed by molecular dynamics simulations and binding free energy calculations, was used to find competitive binders to the P domain of the capsid of the norovirus VA387. These novel structures have high affinity and are a very good starting point for developing drugs against noroviruses. The protein targets in these two projects are carbohydrate binding, but the techniques are general and can be applied to other research projects.
At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 4: Submitted. Paper 5: Manuscript. Paper 6. Manuscript.
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Books on the topic "Molecuar dynamics and docking simulation"

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Zaheer Ul-Haq and Angela K. Wilson, eds. Frontiers in Computational Chemistry: Volume 6. BENTHAM SCIENCE PUBLISHERS, 2022. http://dx.doi.org/10.2174/97898150368481220601.

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Frontiers in Computational Chemistry presents contemporary research on molecular modeling techniques used in drug discovery and the drug development process: computer aided molecular design, drug discovery and development, lead generation, lead optimization, database management, computer and molecular graphics, and the development of new computational methods or efficient algorithms for the simulation of chemical phenomena including analyses of biological activity. The sixth volume of this series features these six different perspectives on the application of computational chemistry in rational drug design: 1. Computer-aided molecular design in computational chemistry 2. The role of ensemble conformational sampling using molecular docking & dynamics in drug discovery 3. Molecular dynamics applied to discover antiviral agents 4. Pharmacophore modeling approach in drug discovery against the tropical infectious disease malaria 5. Advances in computational network pharmacology for Traditional Chinese Medicine (TCM) research 6. Progress in electronic-structure based computational methods: from small molecules to large molecular systems of biological significance
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Book chapters on the topic "Molecuar dynamics and docking simulation"

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Sapay, Nicolas, Alessandra Nurisso, and Anne Imberty. "Simulation of Carbohydrates, from Molecular Docking to Dynamics in Water." In Methods in Molecular Biology, 469–83. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-017-5_18.

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Ranimol, G., C. B. Devipriya, and Swetha Sunkar. "Docking and Molecular Dynamics Simulation Studies for the Evaluation of Laccase Mediated Biodegradation of Triclosan." In Proceedings of the Conference BioSangam 2022: Emerging Trends in Biotechnology (BIOSANGAM 2022), 205–13. Dordrecht: Atlantis Press International BV, 2022. http://dx.doi.org/10.2991/978-94-6463-020-6_20.

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AbstractTriclosan (TCA) is an antibacterial and antimicrobial compound that is incorporated into toothpaste, soap, and liquid dishwasher. Continuous TCA exposure may contribute to the emergence of antibiotic-resistant bacteria in the microbiome. Triclosan also reacts to form dioxins, which bioaccumulate and are toxic to aquatic organisms, impedes the thyroid hormone metabolism of the human body. Laccases are multi copper-containing enzymes that can degrade the aromatic compounds and thus reduce their toxicity. To effectively degrade the compound, it is essential to understand the molecular function of the enzyme. Hence, a molecular docking study of laccase enzymes with Triclosan was done. The Tramates versicolor laccase structure was retrieved from PDB and ligand structure was taken from Pubchem. The binding mode and interaction of TCA and laccase were studied using Auto dock Vina software and the stability of the docked complex had been explored via Molecular Dynamics (MD) simulation study using Schrodinger Desmonde. The binding affinity score was found to be −6.5kcal/mol. The majority of the residues in RMSF were within the 2.5Å limit. The radius of gyration remained within the range from 21.7 to 22.1Å for Laccase – TCA complex throughout the 50 ns simulation. MD simulation results show that the enzyme complex remains stable all through the catalytic action.
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Rodríguez, Maricarmen Hernández, Leticia Guadalupe Fragoso Morales, José Correa Basurto, and Martha Cecilia Rosales Hernández. "Molecular Docking and Molecular Dynamics Simulation to Evaluate Compounds That Avoid the Amyloid Beta 1-42 Aggregation." In Neuromethods, 229–48. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7404-7_9.

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Santos, Lucianna H. S., Rafaela S. Ferreira, and Ernesto R. Caffarena. "Integrating Molecular Docking and Molecular Dynamics Simulations." In Methods in Molecular Biology, 13–34. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9752-7_2.

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Kumar, A., E. Rathi, and S. G. Kini. "Fragment-based Design of Novel Inhibitors of HPV 16 E6 Oncoprotein: Molecular Docking, Molecular Dynamics Simulation and In Silico ADME Analysis." In Special Publications, 25–30. Cambridge: Royal Society of Chemistry, 2019. http://dx.doi.org/10.1039/9781839160783-00025.

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Bekker, Gert-Jan, and Narutoshi Kamiya. "Dynamic Docking Using Multicanonical Molecular Dynamics: Simulating Complex Formation at the Atomistic Level." In Methods in Molecular Biology, 187–202. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1209-5_11.

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Singh, Sakshi, Qanita Bani Baker, and Dev Bukhsh Singh. "Molecular docking and molecular dynamics simulation." In Bioinformatics, 291–304. Elsevier, 2022. http://dx.doi.org/10.1016/b978-0-323-89775-4.00014-6.

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Priya, Prerna, Minu Kesheri, Rajeshwar P. Sinha, and Swarna Kanchan. "Molecular Dynamics Simulations for Biological Systems." In Pharmaceutical Sciences, 1044–71. IGI Global, 2017. http://dx.doi.org/10.4018/978-1-5225-1762-7.ch040.

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Molecular dynamics simulation is an important tool to capture the dynamicity of biological molecule and the atomistic insights. These insights are helpful to explore biological functions. Molecular dynamics simulation from femto seconds to milli seconds scale give a large ensemble of conformations that can reveal many biological mysteries. The main focus of the chapter is to throw light on theories, requirement of molecular dynamics for biological studies and application of molecular dynamics simulations. Molecular dynamics simulations are widely used to study protein-protein interaction, protein-ligand docking, effects of mutation on interactions, protein folding and flexibility of the biological molecules. This chapter also deals with various methods/algorithms of protein tertiary structure prediction, their strengths and weaknesses.
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Priya, Prerna, Minu Kesheri, Rajeshwar P. Sinha, and Swarna Kanchan. "Molecular Dynamics Simulations for Biological Systems." In Advances in Bioinformatics and Biomedical Engineering, 286–313. IGI Global, 2016. http://dx.doi.org/10.4018/978-1-4666-8811-7.ch014.

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Molecular dynamics simulation is an important tool to capture the dynamicity of biological molecule and the atomistic insights. These insights are helpful to explore biological functions. Molecular dynamics simulation from femto seconds to milli seconds scale give a large ensemble of conformations that can reveal many biological mysteries. The main focus of the chapter is to throw light on theories, requirement of molecular dynamics for biological studies and application of molecular dynamics simulations. Molecular dynamics simulations are widely used to study protein-protein interaction, protein-ligand docking, effects of mutation on interactions, protein folding and flexibility of the biological molecules. This chapter also deals with various methods/algorithms of protein tertiary structure prediction, their strengths and weaknesses.
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Anthony, Josephine, Vijaya Raghavan Rangamaran, Kumar T. Shivasankarasubbiah, Dharani Gopal, and Kirubagaran Ramalingam. "Applications of Molecular Docking." In Advances in Medical Technologies and Clinical Practice, 278–306. IGI Global, 2016. http://dx.doi.org/10.4018/978-1-5225-0362-0.ch011.

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Computational tools have extended their reach into different realms of scientific research. Often coupled with molecular dynamics simulation, docking provides comprehensive insight into molecular mechanisms of biological processes. Influence of molecular docking is highly experienced in the field of structure based drug discovery, wherein docking is vital in validating novel lead compounds. The significance of molecular docking is also understood in several environmental and industrial research, in order to untangle the interactions among macromolecules of non-medical interest. Various processes such as bioremediation (REMEDIDOCK), nanomaterial interactions (NANODOCK), nutraceutical interactions (NUTRADOCK), fatty acid biosynthesis (FADOCK), and antifoulers interactions (FOULDOCK) find the application of molecular docking. This chapter emphasizes the involvement of computational techniques in the aforementioned fields to expand our knowledge on macromolecular interacting mechanisms.
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Conference papers on the topic "Molecuar dynamics and docking simulation"

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Arba, Muhammad, Rahmana Emran Kartasasmita, and Daryono H. Tjahjono. "Molecular Docking and Molecular Dynamics Simulation of the Interaction of Cationic Imidazolium Porphyrin-Anthraquinone and Hsp90." In 3rd International Conference on Computation for Science and Technology (ICCST-3). Paris, France: Atlantis Press, 2015. http://dx.doi.org/10.2991/iccst-15.2015.1.

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Rahmatia, Fahmi, Tony Sumaryada, Setyanto Tri Wahyudi, and Hendradi Hardhienata. "Docking effects of curcuminoid ligands on protein L stability using molecular dynamics simulation with temperature variations." In INTERNATIONAL CONFERENCE ON SCIENCE AND APPLIED SCIENCE (ICSAS) 2021. AIP Publishing, 2022. http://dx.doi.org/10.1063/5.0073790.

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Kandt, Christian, Eliud O. Oloo, and D. Peter Tieleman. "Domain coupling in the ABC transporter system BtuCD/BtuF: molecular dynamics simulation, normal mode analysis and protein-protein docking." In 21st International Symposium on High Performance Computing Systems and Applications (HPCS'07). IEEE, 2007. http://dx.doi.org/10.1109/hpcs.2007.15.

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Jovanović-Šanta, Suzana S., Esma Isenović, Julijana A. Petrović, and Yaraslau U. Dzichenka. "BINDING OF 17-SUBSTITUTED 16-NITRILE 16,17-SECOESTRANE COMPOUNDS TO ESTROGEN RECEPTORS – „IN VITRO“ AND „IN SILICO“ STUDY." In 1st INTERNATIONAL Conference on Chemo and BioInformatics. Institute for Information Technologies, University of Kragujevac, 2021. http://dx.doi.org/10.46793/iccbi21.403js.

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About 75% of breast cancers express estrogen receptors (ERs), which is a good base for an efficient endocrine therapy. This gives the opportunity for the treatment of patients with antiestrogens, compounds that bind to the ERs and thus compete to estradiol (E2), preventing its action in progression of estrogen-depending cancers. Here we present results of testing the effect of the modified steroids, namely 17-substituted 16-nitrile 16,17-secoestrane compounds on the E2-ER complex forming, its stability, nuclear translocation and binding to DNA. Almost all compounds in moderate to high rate induced lower forming of this complex, destabilizing it – they increased Kd of this complex and decreased number of binding sites. Complex formed in the presence of some test secosteroids could pass to the nucleus, while other compounds inhibited translocation. In the presence of some compounds binding of the formed complex E2-ER to DNA was noticed. Docking followed molecular dynamics simulation was performed to reveal binding mode of E2 to ER in the presence of test secosteroids. Amino acids important for binding process and complex stabilization were detected. Analysis of the simulation data allowed identifying key amino acids and type of binding of the secoestrane compounds, important for high affinity binding of the steroidal compounds.
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Alvarado-Huayhuaz, Jesus Antonio, Wilmar Puma-Zamora, and Ana Cecilia Valderrama-Negrón. "In-silico study of antituberculous activity of Zn-pyrazinamide in pyrazinamidase." In VIII Simpósio de Estrutura Eletrônica e Dinâmica Molecular. Universidade de Brasília, 2020. http://dx.doi.org/10.21826/viiiseedmol2020-89.

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Tuberculosis is caused by Mycobacterium tuberculosis and is one of the leading causes of death. Treatment with pyrazinamide depends on the formation of the bioactive species, pyrazinoic acid (POA), catalyzed by the enzyme pyrazinamidase (PZAse). New mutant strains show resistance to PZA, therefore, it is necessary to search for new drugs. Metallodrugs can offer a synergistic effect on the biological activity of the metal and the drug. Recent studies by our group show anti-tuberculosis activity of pyrazinamide coordinated with Zn, however, the mechanism of action is unknown. In this work, an in-silico study was carried out in three stages: Quantum mechanical, molecular docking and molecular dynamics simulations. ZnPZA (Egap = 4.12 eV) presented greater chemical reactivity than PZA (Egap = 4.97 eV). Greater binding energy was found in ZnPZA-PZAse (-6.98 kcal/mol) than in PZA-PZAse (-6.48 kcal/mol). RMSD and RMSF show stability in PZA-PZAse and ZnPZA-PZAse dockings. Hydrogen bonds interaction of ZnPZA with the catalytic amino acids Asp8 and Lys96 occurs for 83 and 40 ns, respectively. It is concluded that ZnPZA could serve as a transporter of PZA to the active site of PZAse, to promote the production of POA and the antituberculous effect; however, further experimental studies are needed.
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Ghofranian, Siamak, Matthew Schmidt, John Schliesing, Tim Briscoe, and John McManamen. "Simulation of Shuttle/Mir docking." In 36th Structures, Structural Dynamics and Materials Conference. Reston, Virigina: American Institute of Aeronautics and Astronautics, 1995. http://dx.doi.org/10.2514/6.1995-1197.

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Dimić, Dušan, Dejan Milenković, Edina Avdović, Goran Kaluđerović, and Jasmina Dimitrić Marković. "MOLECULAR DOCKING AND MOLECULAR DYNAMICS STUDIES OF THE INTERACTION BETWEEN COUMARIN-NEUROTRANSMITTER DERIVATIVES AND CARBONIC ANHYDRASE IX." In 1st INTERNATIONAL Conference on Chemo and BioInformatics. Institute for Information Technologies, University of Kragujevac,, 2021. http://dx.doi.org/10.46793/iccbi21.056d.

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Novel biologically active compounds can be obtained by the structural modification of coumarins. In this contribution, five new derivatives of 4-hydroxycoumarin with tyramine, octopamine, norepinephrine, 3-methoxytyramine, and dopamine were obtained. Their structures were optimized based on the previously obtained crystal structure of the 4-hydroxycoumarin-dopamine derivative. The special emphasis was put on the effect of various substituents on the structure of obtained compounds and intramolecular interactions governing the stability. To investigate their possible antitumor activity, molecular docking and molecular dynamics simulations were performed with Carbonic anhydrase, a prognostic factor in several cancers, and compared to the native ligand, 5-acetamido-1,3,4-thiadiazole- 2-sulfonamide. The results have shown that all of the coumarin-neurotransmitter derivatives bind to the active pocket of protein with the binding energies higher than for the native ligand. The main contributions to the binding energies were discussed. The Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), and Radius of gyration (Rg), as results of MD simulations, were used to predict the activity of compounds towards chosen protein. The highest MD binding energies were obtained for the derivatives with dopamine and 3-methoxytyramine, with the van der Waals interaction and hydrogen bonds being the most important contributors.
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Probe, Austin, and John L. Junkins. "Robotic Simulation Experiments Demonstrating Docking Proximity Operations and Contact Dynamics." In AIAA Modeling and Simulation Technologies Conference. Reston, Virginia: American Institute of Aeronautics and Astronautics, 2014. http://dx.doi.org/10.2514/6.2014-1493.

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Krenek, Ales, Martin Petrek, Jan Kmunicek, Jiri Filipovic, Zdenek Sustr, Frantisek Dvorak, Jiri Sitera, Jiri Wiesner, and Ludek Matyska. "Multiple Ligand Trajectory Docking Study - Semiautomatic Analysis of Molecular Dynamics Simulations using EGEE gLite Services." In 16th Euromicro Conference on Parallel, Distributed and Network-Based Processing (PDP 2008). IEEE, 2008. http://dx.doi.org/10.1109/pdp.2008.71.

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Shi, Keke, Zhaowei Sun, Chuang Liu, and Dong Ye. "Dynamics modeling and simulation of space electromagnetic docking for CubeSat." In 2017 8th International Conference on Mechanical and Aerospace Engineering (ICMAE). IEEE, 2017. http://dx.doi.org/10.1109/icmae.2017.8038716.

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