Relevant bibliographies by topics / Docking of ATP analogs

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Academic literature on the topic 'Docking of ATP analogs'

Author: Grafiati
Published: 29 March 2025

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Journal articles on the topic "Docking of ATP analogs"

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Choi, Kyudam, Yurim Lee, and Cheongwon Kim. "An In Silico Study for Expanding the Utility of Cannabidiol in Alzheimer’s Disease Therapeutic Development." International Journal of Molecular Sciences 24, no. 21 (November 6, 2023): 16013. http://dx.doi.org/10.3390/ijms242116013.

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Cannabidiol (CBD), a major non-psychoactive component of the cannabis plant, has shown therapeutic potential in Alzheimer’s disease (AD). In this study, we identified potential CBD targets associated with AD using a drug-target binding affinity prediction model and generated CBD analogs using a genetic algorithm combined with a molecular docking system. As a result, we identified six targets associated with AD: Endothelial NOS (ENOS), Myeloperoxidase (MPO), Apolipoprotein E (APOE), Amyloid-beta precursor protein (APP), Disintegrin and metalloproteinase domain-containing protein 10 (ADAM10), and Presenilin-1 (PSEN1). Furthermore, we generated CBD analogs for each target that optimize for all desired drug-likeness properties and physicochemical property filters, resulting in improved pIC50 values and docking scores compared to CBD. Molecular dynamics (MD) simulations were applied to analyze each target’s CBD and highest-scoring CBD analogs. The MD simulations revealed that the complexes of ENOS, MPO, and ADAM10 with CBD exhibited high conformational stability, and the APP and PSEN1 complexes with CBD analogs demonstrated even higher conformational stability and lower interaction energy compared to APP and PSEN1 complexes with CBD. These findings demonstrated the capable binding of the six identified targets with CBD and the enhanced binding stability achieved with the developed CBD analogs for each target.
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Elsawi, Ahmed E., Mai I. Shahin, Hager A. Elbendary, Tarfah Al-Warhi, Fatma E. Hassan, and Wagdy M. Eldehna. "1,2,4-Triazole-Tethered Indolinones as New Cancer-Fighting Small Molecules Targeting VEGFR-2: Synthesis, Biological Evaluations and Molecular Docking." Pharmaceuticals 17, no. 1 (January 8, 2024): 81. http://dx.doi.org/10.3390/ph17010081.

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Targeting the VEGFR-2 signaling pathway is an inveterate approach toward combating pancreatic and hepatocellular cancers. Based on Sunitinib, the FDA-approved VEGFR-2 inhibitor, novel indolin-2-one-triazole hybrids were designed and synthesized as anti-hepatocellular and anti-pancreatic cancer agents with VEGFR-2 inhibitory activity. All the targeted compounds were assessed for their anti-cancer activity, revealing IC50 values extending from 0.17 to 4.29 µM for PANC1 and 0.58 to 4.49 µM for HepG2 cell lines. An extensive SAR study was conducted to explore the effect of different substituents along with N-alkylation. The potent anti-cancer analogs 11d, 11e, 11g, 11k and 14c were evaluated for their VEGFR-2 inhibitory actions, where their IC50 values ranged from 16.3 to 119.6 nM compared to Sorafenib, which revealed an IC50 of 29.7 nM, having compound 11d as the most active analog. An in silico ADME study was performed to confirm the drug-likeness of the synthesized compounds. Finally, molecular docking simulation was conducted for the most potent VEGFR-2 inhibitor (11d), demonstrating the strong binding with the vital amino acid residues of the VEGFR-2 ATP binding site.
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Wu, Yifei, Tze-chen Hsieh, Joseph M. Wu, Xiaoxiao Wang, Joshua S. Christopher, Amanda H. Pham, Justin David-Li Swaby, Lei Lou, and Zhong-Ru Xie. "Elucidating the Inhibitory Effect of Resveratrol and Its Structural Analogs on Selected Nucleotide-Related Enzymes." Biomolecules 10, no. 9 (August 22, 2020): 1223. http://dx.doi.org/10.3390/biom10091223.

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Resveratrol, the most widely studied natural phytochemical, has been shown to interact with different target proteins. Previous studies show that resveratrol binds and inhibits DNA polymerases and some other enzymes; however, the binding and functioning mechanisms remain unknown. The elucidated knowledge of inhibitory mechanisms of resveratrol will assist us in new drug discovery. We utilized molecular docking and molecular dynamics (MD) simulation to reveal how resveratrol and structurally similar compounds bind to various nucleotide-dependent enzymes, specifically, DNA polymerases, HIV-1 reverse transcriptase, and ribonucleotide reductase. The results show that resveratrol and its analogs exert their inhibitory effects by competing with the substrate dNTPs in these enzymes and blocking elongation of chain polymerization. In addition, the results imply that resveratrol binds to a variety of other ATP-/NTP-binding proteins.
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Jayaraj, Premkumar, Chandrakala A. Narasimhulu, Andrei Maiseyeu, Rekha Durairaj, Shashidhar Rao, Sanjay Rajagopalan, Sampath Parthasarathy, and Rajagopal Desikan. "Methoxyphenol derivatives as reversible inhibitors of myeloperoxidase as potential antiatherosclerotic agents." Future Medicinal Chemistry 12, no. 2 (January 2020): 95–110. http://dx.doi.org/10.4155/fmc-2019-0080.

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Aim: To evaluate new chemical entities, based on ferulic acid scaffolds, as reversible myeloperoxidase inhibitors (MPOI). Methodology & results: In silico docking studies are performed with MPO protein as a target for several ferulic acid analogs followed by multiple in vitro assays to validate this approach. Two lead compounds 2a and 3 are identified with optimum docking and IC50 values: -7.95 kcal/mol, 0.9 μM and -8.35 kcal/mol, 8.5 μM, respectively. These MPOIs are able to inhibit oxidation of high-density lipoprotein and further promoted functionality of high-density lipoprotein. Conclusion: Lead analogs are potent MPOIs that exert specific effects on MPO-mediated oxidation as well as inflammatory pathways. It also acts as promoters of cholesterol efflux that sheds light on pharmacological approach in atherosclerosis treatment.
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Lande, Duc Hoàng, Abed Nasereddin, Arne Alder, Tim W. Gilberger, Ron Dzikowski, Johann Grünefeld, and Conrad Kunick. "Synthesis and Antiplasmodial Activity of Bisindolylcyclobutenediones." Molecules 26, no. 16 (August 5, 2021): 4739. http://dx.doi.org/10.3390/molecules26164739.

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Malaria is one of the most dangerous infectious diseases. Because the causative Plasmodium parasites have developed resistances against virtually all established antimalarial drugs, novel antiplasmodial agents are required. In order to target plasmodial kinases, novel N-unsubstituted bisindolylcyclobutenediones were designed as analogs to the kinase inhibitory bisindolylmaleimides. Molecular docking experiments produced favorable poses of the unsubstituted bisindolylcyclobutenedione in the ATP binding pocket of various plasmodial protein kinases. The synthesis of the title compounds was accomplished by sequential Friedel-Crafts acylation procedures. In vitro screening of the new compounds against transgenic NF54-luc P. falciparum parasites revealed a set of derivatives with submicromolar activity, of which some displayed a reasonable selectivity profile against a human cell line. Although the molecular docking studies suggested the plasmodial protein kinase PfGSK-3 as the putative biological target, the title compounds failed to inhibit the isolated enzyme in vitro. As selective submicromolar antiplasmodial agents, the N-unsubstituted bisindolylcyclobutenediones are promising starting structures in the search for antimalarial drugs, albeit for a rational development, the biological target addressed by these compounds has yet to be identified.
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Pislyagin, Evgeny A., Ekaterina S. Menchinskaya, Irina N. Gladkikh, Aleksandra N. Kvetkina, Oksana V. Sintsova, Darya V. Popkova, Sergei A. Kozlovskiy, et al. "Recombinant Analogs of Sea Anemone Kunitz-Type Peptides Influence P2X7 Receptor Activity in Neuro-2a Cells." Marine Drugs 21, no. 3 (March 20, 2023): 192. http://dx.doi.org/10.3390/md21030192.

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Purinergic P2X7 receptors (P2X7) have now been proven to play an important role and represent an important therapeutic target in many pathological conditions including neurodegeneration. Here, we investigated the impact of peptides on purinergic signaling in Neuro-2a cells through the P2X7 subtype in in vitro models. We have found that a number of recombinant peptides, analogs of sea anemone Kunitz-type peptides, are able to influence the action of high concentrations of ATP and thereby reduce the toxic effects of ATP. The influx of calcium, as well as the fluorescent dye YO-PRO-1, was significantly suppressed by the studied peptides. Immunofluorescence experiments confirmed that the peptides reduce the P2X7 expression level in neuronal Neuro-2a cells. Two selected active peptides, HCRG1 and HCGS1.10, were found to specifically interact with the extracellular domain of P2X7 and formed stable complexes with the receptor in surface plasmon resonance experiments. The molecular docking approach allowed us to establish the putative binding sites of the most active HCRG1 peptide on the extracellular domain of the P2X7 homotrimer and propose a mechanism for regulating its function. Thus, our work demonstrates the ability of the Kunitz-type peptides to prevent neuronal death by affecting signaling through the P2X7 receptor.
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Zhang, Xiaozhe, Shaodong Shi, Yang Su, Xiaoli Yang, Sining He, Xiuyan Yang, Jing Wu, Jian Zhang, and Feng Rao. "Suramin and NF449 are IP5K inhibitors that disrupt inositol hexakisphosphate–mediated regulation of cullin–RING ligase and sensitize cancer cells to MLN4924/pevonedistat." Journal of Biological Chemistry 295, no. 30 (June 3, 2020): 10281–92. http://dx.doi.org/10.1074/jbc.ra120.014375.

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Inositol hexakisphosphate (IP6) is an abundant metabolite synthesized from inositol 1,3,4,5,6-pentakisphosphate (IP5) by the single IP5 2-kinase (IP5K). Genetic and biochemical studies have shown that IP6 usually functions as a structural cofactor in protein(s) mediating mRNA export, DNA repair, necroptosis, 3D genome organization, HIV infection, and cullin–RING ligase (CRL) deneddylation. However, it remains unknown whether pharmacological perturbation of cellular IP6 levels affects any of these processes. Here, we performed screening for small molecules that regulate human IP5K activity, revealing that the antiparasitic drug and polysulfonic compound suramin efficiently inhibits IP5K in vitro and in vivo. The results from docking experiments and biochemical validations suggested that the suramin targets IP5K in a distinct bidentate manner by concurrently binding to the ATP- and IP5-binding pockets, thereby inhibiting both IP5 phosphorylation and ATP hydrolysis. NF449, a suramin analog with additional sulfonate moieties, more potently inhibited IP5K. Both suramin and NF449 disrupted IP6-dependent sequestration of CRL by the deneddylase COP9 signalosome, thereby affecting CRL activity cycle and component dynamics in an IP5K-dependent manner. Finally, nontoxic doses of suramin, NF449, or NF110 exacerbate the loss of cell viability elicited by the neddylation inhibitor and clinical trial drug MLN4924/pevonedistat, suggesting synergistic ef-fects. Suramin and its analogs provide structural templates for designing potent and specific IP5K inhibitors, which could be used in combination therapy along with MLN4924/pevonedistat. IP5K is a potential mechanistic target of suramin, accounting for suramin's therapeutic effects.
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Reddy, K. Kumar, R. S. Rathore, P. Srujana, R. R. Burri, C. Ravikumar Reddy, M. Sumakanth, Pallu Reddanna, and M. Rami Reddy. "Performance Evaluation of Docking Programs- Glide, GOLD, AutoDock & SurflexDock, Using Free Energy Perturbation Reference Data: A Case Study of Fructose-1, 6-bisphosphatase-AMP Analogs." Mini-Reviews in Medicinal Chemistry 20, no. 12 (July 23, 2020): 1179–87. http://dx.doi.org/10.2174/1389557520666200526183353.

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Background: The accurate ranking of analogs of lead molecules with respect to their estimated binding free energies to drug targets remains highly challenging in molecular docking due to small relative differences in their free energy values. Methods: Free energy perturbation (FEP) method, which provides the most accurate relative binding free energy values were earlier used to calculate free energies of many ligands for several important drug targets including Fructose-1,6-BisphosPhatase (FBPase). The availability of abundant structural and experimental binding affinity data for FBPase inhibitors provided an ideal system to evaluate four widely used docking programs, AutoDock, Glide, GOLD and SurflexDock, distinct from earlier comparative evaluation studies. Results: The analyses suggested that, considering various parameters such as docking pose, scoring and ranking accuracy, sensitivity analysis and newly introduced relative ranking score, Glide provided reasonably consistent results in all respects for the system studied in the present work. Whereas GOLD and AutoDock also demonstrated better performance, AutoDock results were found to be significantly superior in terms of scoring accuracy compared to the rest. Conclusion: Present analysis serves as a useful guide for researchers working in the field of lead optimization and for developers in upgradation of the docking programs.
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Tanneeru, Karunakar, Bandi Madhusudhan Reddy, and Lalitha Guruprasad. "Three-dimensional quantitative structure–activity relationship (3D-QSAR) analysis and molecular docking of ATP-competitive triazine analogs of human mTOR inhibitors." Medicinal Chemistry Research 21, no. 7 (April 6, 2011): 1207–17. http://dx.doi.org/10.1007/s00044-011-9629-x.

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Amin, Md Ruhul, Farhana Yasmin, Mohammed Anowar Hosen, Sujan Dey, Shafi Mahmud, Md Abu Saleh, Talha Bin Emran, et al. "Synthesis, Antimicrobial, Anticancer, PASS, Molecular Docking, Molecular Dynamic Simulations & Pharmacokinetic Predictions of Some Methyl β-D-Galactopyranoside Analogs." Molecules 26, no. 22 (November 20, 2021): 7016. http://dx.doi.org/10.3390/molecules26227016.

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A series of methyl β-D-galactopyranoside (MGP, 1) analogs were selectively acylated with cinnamoyl chloride in anhydrous N,N-dimethylformamide/triethylamine to yield 6-O-substitution products, which was subsequently converted into 2,3,4-tri-O-acyl analogs with different acyl halides. Analysis of the physicochemical, elemental, and spectroscopic data of these analogs revealed their chemical structures. In vitro antimicrobial testing against five bacteria and two fungi and the prediction of activity spectra for substances (PASS) showed promising antifungal functionality comparing to their antibacterial activities. Minimum inhibition concentration (MIC) and minimum bactericidal concentration (MBC) tests were conducted for four compounds (4, 5, 6, and 9) based on their activity. MTT assay showed low antiproliferative activity of compound 9 against Ehrlich’s ascites carcinoma (EAC) cells with an IC50 value of 2961.06 µg/mL. Density functional theory (DFT) was used to calculate the thermodynamic and physicochemical properties whereas molecular docking identified potential inhibitors of the SARS-CoV-2 main protease (6Y84). A 150-ns molecular dynamics simulation study revealed the stable conformation and binding patterns in a stimulating environment. In-silico ADMET study suggested all the designed molecules to be non-carcinogenic, with low aquatic and non-aquatic toxicity. In summary, all these antimicrobial, anticancer and in silico studies revealed that newly synthesized MGP analogs possess promising antiviral activity, to serve as a therapeutic target for COVID-19.
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Dissertations / Theses on the topic "Docking of ATP analogs"

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Samson, Samantha. "Profilage in silico de la protéine multifonctionnelle Mfd, une cible thérapeutique innovante dans la lutte contre l'antibiorésistance bactérienne." Electronic Thesis or Diss., université Paris-Saclay, 2024. http://www.theses.fr/2024UPASL125.

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Face à la montée préoccupante de la résistance aux antibiotiques, la recherche de nouveaux antimicrobiens constitue un enjeu de santé urgent. Nous avons identifié la protéine bactérienne Mutation Frequency Decline (Mfd) comme étant une cible thérapeutique innovante pour le développement de nouveaux médicaments. Un criblage in silico à haut débit a été réalisé, dans un premier temps, afin de sélectionner des molécules pouvant se lier spécifiquement au site actif de la protéine et inhiber son activité, empêchant donc la résistance bactérienne face au stress immunitaire de l'hôte. Les molécules identifiées se sont révélées efficaces in vitro et efficaces et non toxiques in vivo, dans un modèle d'infection chez l'insecte, sur au moins deux pathogènes bactériens. Ces données préliminaires ont constitué une preuve de concept du potentiel innovant de ces molécules et ont également servi de base aux travaux présentés dans cette thèse.L'objectif principal de ce travail était l'identification des interactions moléculaires critiques entre ces molécules inhibitrices et le site actif de Mfd chez E. coli, ainsi que l'élargissement de cette analyse aux pathogènes prioritaires du groupe ESKAPE. En conséquence de quoi, un modèle optimal d'inhibiteur a été déterminé et ses dérivés sont actuellement testés in vitro et in vivo en tant que potentiels agents antimicrobiens. En parallèle, l'analyse de la séquence et de la structure de Mfd, provenant de souches environnementales et cliniques, met en évidence les caractéristiques d'une corrélation moléculaire entre la séquence de Mfd et le phénotype de virulence du pathogène. La confirmation in vitro est actuellement en cours d'évaluation. Enfin, mon objectif final est de repositionner la fonction motrice de Mfd dans un cadre plus large de remodelage conformationnel et fonctionnel afin de mieux comprendre cette cible et son rôle dans la réparation par excision de nucléotides. En produisant plusieurs simulations de dynamique moléculaire sur des « linkers » clés qui relient les principaux modules fonctionnels de Mfd, l'investigation de leur flexibilité intrinsèque et de leur conservation vise à récapituler le remodelage extensif des conformations de Mfd au cours de son cycle fonctionnel, tel qu'il a été décrit précédemment par cryo-EM. Cela a pour but de documenter dans quelle mesure ces linkers, qui relient cette protéine multi-modulaire, sont plus que de simples "connecteurs" et portent, dans leur séquence et leur longueur, des propriétés internes leur permettant d'adopter des états discrets garantissant la transition boucle-hélice nécessaire au bon fonctionnement de Mfd
In an alarming context of antibiotic resistance, the search for new antimicrobials is an urgent health issue. We had identified the bacterial protein Mutation Frequency Decline (Mfd) as an innovative target for the development of new drugs. A high throughput in silico screening was initially performed in order to select molecules specifically binding to the active site of the target and inhibiting its activity, thereby preventing bacterial resistance to host immune stress. The identified hits were shown to be efficient in vitro and efficient and non-toxic in vivo, in an insect model of infection on at least two bacterial pathogens. These preliminary data have constituted a proof of concept of the innovative potential of these hits and were also the basis of this thesis.The main objective of this work was the identification of the critical molecular interaction found between those hits and the active site of Mfd in E. coli and also enlarged to the priority pathogens of the ESKAPE group. As a result, an optimal inhibitor scaffold was determined and its derivatives are currently tested in vitro and in vivo as potential antimicrobial agents. In parallel, the sequence and structure analysis of Mfd, from environmental and clinical strains, showcase the basic features of a molecular correlation between Mfd sequence and virulence phenotype. The in vitro confirmation is currently being evaluated. Finally, my goal reposition this motor function of Mfd into a larger conformational and functional remodeling of Mfd in order to get a better understanding of this target and its role in the Nucleotide Excision Repair. Using molecular dynamics simulation on distinguished linkers that connect the main functional modules of Mfd, the investigation of their intrinsic flexibility and resilience to recapitulate the extensive remodeling of Mfd conformations within its functional cycle that has been previously described by cryo-EM. This aims to document to which extent the linkers that connect this multi-module protein are more than "linkers" and harbor, in their sequence and length, internal properties to adopt discrete states that guarantee disorder-to-coil transition to assure the functional machinery of Mfd
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Dayl, Sudad Amer. "Molecular modelling of ATP-gated P2X receptor ion channels." Thesis, University of Leicester, 2018. http://hdl.handle.net/2381/42761.

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P2X receptors (P2XRs) are trimeric cation channels activated by extracellular ATP. Human P2XRs (P2X1-7) are expressed in nearly all mammalian tissues, and they are an important drug target because of their involvement in inflammation and neuropathic pain. The aim of this thesis is to address the following questions. P2XR crystal structures have revealed an unusual U-shape conformation for bound ATP; how does the U-shape conformation of ATP and its derivatives affect channel activation? Where and how do the selective, non-competitive inhibitors AZ10606120 and A438079 bind to P2X7R? What is the structure of the hP2X1R intracellular domain in the closed state? Molecular modelling and bioinformatics were used to answer these questions, hypotheses resulting from this work were tested in collaboration with Prof. Evans. Investigating the binding modes of ATP and its deoxy forms in hP2X1R showed that the ribose 2′-hydroxyl group is stabilising the U-shape conformation by a hydrogen bond to the γ-phosphate. The reduced ability of 2′-deoxy ATP to adopt the U-shape conformation could explain its weak agonist action in contrast to full agonists ATP and 3′-deoxy ATP. Ligand docking of AZ10606120 and A438079 into the hP2X7R predicted an allosteric binding site, this site has meanwhile been confirmed by P2X7R/antagonist X-ray structures. MD simulations suggested that unique P2X7R regions (residues 73-79 and T90/T94) contribute to an increase of the allosteric pocket volume compared to the hP2X1R. This difference in size might be the key for selectivity. The hP2X1R intracellular domain in the closed state was modelled ab initio, and interpreted in context of chemical cross-links (collaboration with Prof. Evans). This suggests a symmetrical arrangement of two short b-antiparallel strands within the Nterminal region and short a-helix in the C-terminal region and additional asymmetrical states.
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Panwar, Pankaj. "Relations structure-fonction des transporteurs nucléotides." Phd thesis, Université de Grenoble, 2012. http://tel.archives-ouvertes.fr/tel-00684264.

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Le transporteur NTT1 est responsable pour l'import d'ATP dans les chloroplastes afin de maintenir le métabolisme en période d'activité réduite ou nulle de la photosynthèse. Cependant, le mécanisme moléculaire de ce transporteur est encore méconnu, essentiellement du à la difficulté de manipulation des protéines membranaires. Nous avons réussi à développer un protocole pour la production de ce transporteur, permettant une bon rendement de solubilisation et obtention de protéines purifiées pour des études structurales. Combinant des caractérisations biochimiques et biophysiques, nous avons pu identifier des conditions de préparation d'échantillons qui ont mené aux premiers cristaux. Afin d'étendre notre connaissance sur les transporteurs de nucléotides, nous avons également entrepris des études structurales et fonctionnelles sur AAC, le transporteur ADP/ATP des mitochondries. AAC et NTT1 appartiennent à des familles de protéines différentes mais ont des fonctions voisines. À partir de la première structure d'AAC déjà connue, nous avons recherché par des criblages in silico de nouvelles molécules se liant au transporteur de façon compétitive avec le nucléotide et pouvant ainsi inhiber le transport. Les outils de docking ont été mis en place et ont permis à partir d'une librairie de 75000 composés d'identifier 17 molécules. Ensuite, nous avons testés ces molécules expérimentalement et montré qu'une d'entre elles inhibent le transport. De plus, trois nouveaux analogues d'ADP ont également été identifiés comme inhibiteurs.
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DI, MARINO DANIELE. "Molecular dynamics and docking simulations of the ADP/ATP mitochondrial carrier: structural-dynamical insights for the inactivation of pathological mutants and detection of potential ATP binding sites." Doctoral thesis, Università degli Studi di Roma "Tor Vergata", 2010. http://hdl.handle.net/2108/1174.

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Il carrier mitocondriale ADP/ATP (AAC) è stato cristallizato in complesso con il suo inibitore carboxyatractyloside (CATR). La proteina è composta da un fascio di sei eliche trans membrana che forma un canale all'interno della membrane mitocondriale interna che si presenta chiuso verso il lato matriciale ed aperto verso lo spazio intermembrana, conformazione dovuta alla presenza di una prolina sulle eliche dispari che forma una piegatura dell' elica. Il ruolo di questa proteina è di importare ADP nella matrice mitocondriale ed esportare ATP nel citosol. L' insorgenza di alcune patologie è stata associata ad un malfunzionamento di questa proteina. Al fine di capire meglio le proprietà dinamico/strutturali del trasportatore sono stati eseguiti due diversi esperimenti computazionali, per analizzare sia il meccanismo di trasporto che il ruolo di determinate mutazioni patologiche. In un primo esperimento sono state condotte tre simulazioni di Dinamica Molecolare di 20 ns della protein wild type, del mutante patologico Ala113Pro e del doppio mutante Ala113Pro/Val180Met immerse in un doppio strato lipidico, al fine di capire il ruolo della seconda mutazione Val180Met capace di restaurare il corretto funzionamento del mutante Ala113Pro . L' analisi delle componenti principali ha evidenziato per i tre sistemi che il moto della proteina è caratterizzato dal movimento dei loops matriciali e delle eliche dispari che presentano una proline conservata nella regione centrale dell 'elica. L' analisi del moto mostra un comportamento diverso del singolo mutante rispetto a wild type e doppio mutante. La singola mutazione induce una regolarizzazione dellâ elica H3, che viene persa in seguito allâ introduzione della seconda mutazione. Questo è direttamente correlato alla distribuzione della rete di ponti salini che coinvolge i residui Arg79, Asp134, Arg234 coinvolti nellâ 'interazione con il substrato. Infatti, nella simulazione del wild type sono visibili due ponti salini stabili lungo tutta la dinamica e cruciali per il legame con il substrato, Arg79:Asp134 e Arg234:Asp134. Uno di questi ponti salini è perso nella dinamica del singolo mutante e viene ristabilito nella dinamica del doppio mutante, che si comporta come il wild type. Questo causa nel singolo mutante un errato assetto del sito di legame dellâ 'ADP, spiegando il malfunzionamento del carrier. Inoltre, abbiamo descritto le interazioni tra il lato matriciale del trasportatore e il substrato ATP attraverso l' utilizzo di simulazioni di dinamica molecolare classica e docking proteina-ligando. Dalla dinamica molecolare di 20 ns del wild type sono state estratte 15 strutture rappresentative della proteina attraverso il clustering, e per ognuna di queste strutture sono state effettuate 50 runs di docking, per un totale di 750 (MD-docking) i risultati sono stati analizzati in comparazione con quelli ottenuti dalle 750 runs di docking effettuate sulla struttura X-Ray (X-docking). L' analisi mostra la presenza di un unico sito di interazione sulla struttura X-Ray, mantenuto anche nelle strutture estratte dalla dinamica. L' MD-docking mostra la presenza di un secondo sito di legame, non presente nell' X-docking. Il meccanismo di interazione tra la proteina e il substrato ATP è stato studiato analizzando la composizione e l' arrangiamento 3D delle 2 tasche di interazione individuate, e l' orientazione del substrato allâ interno di esse. E' stata quindi proposta una relazione diretta tra la struttura tripartite del carrier e la presenza di più siti di legame per l' ATP.
The mitochondrial adenosine diphosphate/adenosine triphosphate, ADP/ATP carrier (AAC) has been crystallized in complex with its specific inhibitor carboxyatractyloside (CATR). The protein is composed by a six trans-membrane helix bundle, defining the nucleotide translocation pathway, that is closed towards the matrix side due to sharp kinks in the odd-numbered helices. The role of the protein is to import ADP in the mitochondrial matrix and export ATP in the cytosol. Several disease have been associated to a malfunctioning of the protein. To better understand the structural/dynamical properties of the carrier, two different computational experiments have been performed, in order to understand both the translocation mechanism and the role of known pathological mutations. In a first experiment Molecular Dynamics simulations of the wild type bovine ADP/ATP mitochondrial carrier, and of the single Ala113Pro and double Ala113Pro/Val180Met mutants, embedded in a lipid bilayer, have been carried out for 20 ns to shed a light on the structural-dynamical changes induced by the Val180Met mutation restoring the carrier function in the Ala113Pro pathologic mutant. Principal component analysis indicates that, for the three systems, the protein dynamics is mainly characterized by the motion of the matrix loops and of the odd-numbered helices having a conserved proline in their central region. Analysis of the motions shows a different behaviour of single pathological mutant with respect of the other two systems. The single mutation induces a regularization and rigidity of the H3 helix, lost upon the introduction of the second mutation. This is directly correlated to the salt bridge distribution involving residues: Arg79, Asp134, Arg234; hypothesized to interact with the substrate. In fact, in the wild type simulation two stable inter-helices salt bridges, crucial for substrate binding, are present almost over all the simulation time. In line with the impaired ADP transport, one salt interaction is completely lost in the single mutant trajectory but reappears in the double mutant simulation, where a salt bridge network, as observed in the wild type, is restored. This causes a wrong assembly of the geometry of the binding site, explaining the impaired transport of the single mutant. Further, we describe the interaction between the matrix side of the AAC transporter and the ATP molecule using classical molecular dynamics simulation (MD) and protein-ligand docking procedure. From the 20 ns MD trajectory of the wild type protein, 15 structures have been extracted through clustering analysis and for each carrier conformation 50 docking runs have been carried out for a total of 750 (MD-docking). The results have been compared with 750 docking runs performed on the X-ray structure (X-docking). The docking procedure shows the presence of a single interaction site in the X-ray structure that is conserved in the structures extracted from the MD trajectory. MD-docking shows the presence of a second binding site, not found in the X-docking. The interaction strategy between the AAC transporter and the ATP molecule has been analyzed investigating the composition and 3D arrangement of the interaction pockets, together with the orientations of the substrate into them. A relationship between sequence repeats and the ATP binding sites in the AAC carrier structure is proposed.
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Tangella, Lokeswari Prathyusha. "An investigation on role of the ATP-binding cassette B5 (ABCB5) transporter as potential mediator of melanoma resistance to BRAF inhibition." Thesis, Edith Cowan University, Research Online, Perth, Western Australia, 2020. https://ro.ecu.edu.au/theses/2369.

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Cutaneous melanoma is a highly metastatic and drug-resistant skin cancer type, responsible for a disproportionate number of skin cancer deaths. Targeted therapies, in the form of BRAF inhibitors (BRAFis), have been effective at treating BRAFV600 mutant melanomas. However, majority of the melanoma patients fail to respond to BRAFis due to intrinsic or acquired resistance within one year of treatment commencement. Multiple mechanisms that contribute to BRAFi resistance in melanoma cells have been identified, as discussed in the review in Chapter 1. Overexpression of ATP-binding cassette (ABC) transporters has been linked to multidrug resistance in numerous cancer types. These transporters expel the anti-cancer drugs out of the cell, thereby decreasing the intracellular concentration of the drug. In melanoma, the ATP-binding cassette B5 transporter (a member of ABC superfamily) has been linked to chemoresistance by drug extrusion. Moreover, overexpression of ABCB5 has been observed in BRAFV600 melanoma cells after short-term BRAFi treatment. In this study we investigated the role of the ABCB5 transporter as potential mediators of resistance to BRAFis by drug expulsion. In Chapter 2, we showed increased ABCB5 expression in melanoma cell lines after short-term treatment with the BRAFis accompanied by an increased expression of melanocytic signature. Gene expression of fluorescent activated cell sorted melanoma cells into ABCB5high and ABCB5low populations, revealed an increased melanocytic signature in the ABCB5high population. Moreover, analysis of single-cell RNA sequencing (scRNAseq) data of two BRAFV600 melanoma cell lines, A2058 and 451Lu, revealed a strong association between ABCB5 expression and melanocytic signature. Based on these initial observations, the capacity of the ABCB5 transporter to efflux BRAFis was evaluated indirectly through an in-silico approach using molecular docking simulations (Chapter 3 and 4), and directly through in vitro experiments using an ABCB5 overexpressing melanoma BRAFV600 cell line (Chapter 5). In Chapter 3, a full-length ABCB5 model was generated, based on mouse ATP-binding cassette B1 transporter (ABCB1; Pgp1), a close homologue of ABCB5. Molecular dynamics simulations were performed in 2 model cell membranes and the dominant conformation was identified. Docking simulations of known ABCB5 substrates such as taxanes, anthracyclines, camptothecin and etoposide enabled the identification of at least three putative substrate binding sites in ABCB5. The overlap of these three binding sites with validated binding sites for these chemotherapeutic drugs in Pgp1 corroborate our findings. In Chapter 4, docking simulations revealed at least one overlapping binding site for BRAFis and chemotherapeutic drugs on ABCB5, suggesting that BRAFis could potentially act as a substrate for ABCB5. In Chapter 5, we generated an ABCB5 overexpressing BRAFV600E melanoma cell line. However, no differences in sensitivity to BRAF inhibition was observed as a result of ABCB5 overexpression. Intracellular drug accumulation analyses revealed no reduction in vemurafenib or dabrafenib concentrations, indicating that BRAFis do not act as substrates for ABCB5. Altogether, our studies suggest that ABCB5 expression is linked to the melanocytic program. However, despite the molecular docking evidence that BRAFis may be substrates of ABCB5, in vitro studies failed to demonstrate direct efflux of BRAFis by ABCB5.
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Liu, Man [Verfasser]. "Mapping the interactions between ATP and the sarcoplasmic reticulum Ca2+-ATPase with ATP and ATP analogs studied by Fourier transform infrared spectroscopy / vorgelegt von Man Liu." 2004. http://d-nb.info/970060815/34.

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Books on the topic "Docking of ATP analogs"

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Wang, Donald. Interaction of ATP analogs with myosin. 1994.

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Book chapters on the topic "Docking of ATP analogs"

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Yount, Ralpa G. "ATP Analogs." In Advances in Enzymology - and Related Areas of Molecular Biology, 1–56. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2006. http://dx.doi.org/10.1002/9780470122884.ch1.

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Anthony, Thilani M., Pavithra M. Dedigama-Arachchige, D. Maheeka Embogama, Todd R. Faner, Ahmed E. Fouda, and Mary Kay H. Pflum. "ATP Analogs in Protein Kinase Research." In Kinomics, 137–68. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2015. http://dx.doi.org/10.1002/9783527683031.ch6.

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Mathew, Alex J., Nixon N. Raj, M. Sugappriya, and Sangeetha M. Priyadarshini. "Modeling of ATP-Sensitive Inward Rectifier Potassium Channel 11 and Inhibition Mechanism of the Natural Ligand, Ellagic Acid, Using Molecular Docking." In Advances in Experimental Medicine and Biology, 489–95. New York, NY: Springer New York, 2010. http://dx.doi.org/10.1007/978-1-4419-5913-3_55.

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Zheng, Hui, Adnan Al-Ayoubi, and Scott T. Eblen. "Identification of Novel Substrates of MAP Kinase Cascades Using Bioengineered Kinases that Uniquely Utilize Analogs of ATP to Phosphorylate Substrates." In MAP Kinase Signaling Protocols, 167–83. Totowa, NJ: Humana Press, 2010. http://dx.doi.org/10.1007/978-1-60761-795-2_10.

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Mahant, Hemlata, Gitanjali Kashyap, Vinay Sagar Verma, and Achal Mishra. "MOLECULAR DOCKING OF VARIOUS CHALCONE ANALOGUES FOR THEIR ANTIHYPERLIPIDEMIC ACTIVITY USING MOLEGRO VIRTUAL DOCKER." In Futuristic Trends in Chemical Material Sciences & Nano Technology Volume 3 Book 12, 279–93. Iterative International Publishers, Selfypage Developers Pvt Ltd, 2024. http://dx.doi.org/10.58532/v3becs12p2ch12.

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A high quantity of fat particles (lipids) in the blood is a disorder known as hyperlipidemia. Antihyperlipidemic drugs work to enhance HDL cholesterol, while others work to lower triglyceride levels and low-density lipoprotein cholesterol levels. In this paper, we investigate many substituted chalcone analogs. Using the Molegro virtual Docker program, we analyze the docking experiments of the substituted chalcone analogus as the anti-hyperlipidemic drug in this study. Out of 650 compounds, our research found that over 10 compounds had substantial binding affinities with five different types of proteins. The five different protein receptor types 1EZF, 1OSH, 2ZNN, 2ZNQ, and 3LD6 each demonstrated strong binding affinity for the substances 444, 419, 380, 366, and 234. Researchers can create another powerful chemical that acts as an anti-hyperlipidemic drug using docking ex-periments.
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Kumar Gupta, Ajay, and Sanmati Kumar Jain. "DESIGNING AND DOCKING STUDIES OF ARYL BIOISOSTERES OF ENZALUTAMIDE FOR PROSTATE CANCER THERAPY." In Futuristic Trends in Chemical Material Sciences & Nano Technology Volume 3 Book 12, 167–79. Iterative International Publishers, Selfypage Developers Pvt Ltd, 2024. http://dx.doi.org/10.58532/v3becs12p2ch5.

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Cancer is a major health problem throughout the world. Androgens like testosterone and dihydrotestosterone are essential for the growth and development of the prostate gland. Androgenic receptors are overexpressed, which promotes the progression of prostate cancer (PC) therefore, androgenic receptors are a key target in the therapy of PC. A non-steroidal antiandrogen drug called enzalutamide (ENZ) is used to treat PC; however, it also causes toxicities such as cardiovascular toxicity, acute myocarditis, hypertension, and seizures. The study's goal is to use a bioisosteric approach to replace the aryl group in the ENZ molecule in order to generate a less toxic analogues with improve pharmacokinetic properties and reduce toxicity. The physicochemical, medicinal, pharmacokinetic, and toxicological characteristics of the designed analogues were calculated using ADMETlab 2.0. Drug likeness (DL) and drug score (DS) of analogues were calculated using OSIRIS property explorer (PEO). The docking analysis of designed ENZ analogues was carried out with the help of AutoDock Vina (ADV). Designed analogues met the requirements for acceptability and followed the Lipinski rule of five. The ADMET profile of designed analogues was found to be optimal to good. However, no hydrogen bond was found in docking interactions between ligands and protein. Based on their QED score, ADMET properties, toxicity score, DL, DS and docking interactions, ligands E6 and E20 may be used for further screening as androgen receptor (AR) antagonists in management of PC.
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Schoner, Wilhelm, and Georgios Scheiner-Bobis. "[29] Photoaffinity labeling with ATP analogs." In Methods in Enzymology, 312–22. Elsevier, 1988. http://dx.doi.org/10.1016/0076-6879(88)56032-9.

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Shimizu, Takashi, Yoko Y. Toyoshima, and Ronald D. Vale. "Chapter 12 Use of ATP Analogs in Motor Assays." In Methods in Cell Biology, 167–77. Elsevier, 1993. http://dx.doi.org/10.1016/s0091-679x(08)60169-7.

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Ahmed, Jessica. "Development of Specific Gamma Secretase Inhibitors." In Handbook of Research on Systems Biology Applications in Medicine, 423–37. IGI Global, 2009. http://dx.doi.org/10.4018/978-1-60566-076-9.ch025.

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Secretases are aspartic proteases, which specifically trim important, medically relevant targets such as the amyloid-precursor protein (APP) or the Notch-receptor. Therefore, changes in their activity can lead to dramatic diseases like M. Alzheimer caused by aggregation of peptidic fragments. On the other hand, the secretases are interesting targets for molecular therapy of the multiple myeloma, because the over-expressed Notch-receptor does not emerge into the native conformation until the cleavage by the presenilin, the active and catalytic subunit of the gamma secretase, occurs. Here, we focus on a novel methodology of structure-based drug development, feasible without prior knowledge of the target structure— analogy modeling. This combination of similarity screening, fold recognition, ligand-supported modeling, and docking is exemplarily illustrated for the structure of presenilin and specific inhibitors thereof.
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Kecel Gunduz, Serda, Bilge Bicak, and Aysen E. Ozel. "Advancements in Cancer Therapeutics." In Handbook of Research on Advancements in Cancer Therapeutics, 89–115. IGI Global, 2021. http://dx.doi.org/10.4018/978-1-7998-6530-8.ch003.

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In this chapter, computational approaches for the discovery of new drugs that are useful for diagnosis and treatment of disease will be described in three parts. MD technique uniquely supports protein design attempts by giving information about protein dynamics associated with atomic-level descriptions of the relationship between dynamics and function. The purpose of molecular docking is to provide an estimate of the ligand-receptor complex structure using computational methods. By this estimation, the mechanism of drug binding and action are described by determining the three-dimensional simulation of drug and drug-induced macrostructure. ADME characteristics are physicochemically significant descriptors and pharmacokinetically relevant properties used to design more effective drugs and new analogs. As a result, in-silico calculations can provide robust preliminary information as to drug activity and mechanism in the drug production process, as well as in vitro and in vivo studies.
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Conference papers on the topic "Docking of ATP analogs"

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Bosch Bruguera, Miquel, Santiago Lopez Bermudez, Gisela Detrell, and Reinhold Ewald. "Development of a Virtual Reality Space Docking Simulator for Research and Training - A Case Application in the Space Analogue SIRIUS-21." In IAF/IAA Space Life Sciences Symposium, Held at the 75th International Astronautical Congress (IAC 2024), 39–49. Paris, France: International Astronautical Federation (IAF), 2024. https://doi.org/10.52202/078355-0006.

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Kini, Suvarna, Jayant Chaudhary, and Sanjeev Arora. "In-vitro screening and docking study of fosinopril and its analogs." In 2009 International Conference on Biomedical and Pharmaceutical Engineering (ICBPE). IEEE, 2009. http://dx.doi.org/10.1109/icbpe.2009.5384099.

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Rakic, Aleksandra, Dusan Dimic, Jasmina Dimitric Markovic, Dejan Milenkovic, and Zoran Markovic. "Toxicity, structural analysis, and molecular docking studies of selected isonicotinohydrazide analogs." In 2021 IEEE 21st International Conference on Bioinformatics and Bioengineering (BIBE). IEEE, 2021. http://dx.doi.org/10.1109/bibe52308.2021.9635280.

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Monteiro, Alex, Marcus Scotti, and Luciana Scotti. "MOLECULAR DOCKING OF FRUCTOSE-DERIVED NUCLEOSIDE ANALOGS AGAINST REVERSE TRANSCRIPTASE OF HIV-1." In MOL2NET 2019, International Conference on Multidisciplinary Sciences, 5th edition. Basel, Switzerland: MDPI, 2019. http://dx.doi.org/10.3390/mol2net-05-06178.

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Jacob K, Sony, and Swastika Ganguly. "Molecular Docking Studies of Novel Pyrazole Analogs as Possible HIV-1-RT Inhibitors." In The 18th International Electronic Conference on Synthetic Organic Chemistry. Basel, Switzerland: MDPI, 2014. http://dx.doi.org/10.3390/ecsoc-18-b033.

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Gordon, J. L. "ADENINE NUCLEOTIDES AND THEREGULATION OF VASCULAR TONE." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643719.

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ATP, although known mainly as an intracellular energy source, is also capable of acting extracellularly as a vasoactive agent of great potency, at concentrations around lμM or less. ADP is approximately equipotent with ATP in its actions on extracellular receptors in the vasculature.ATP and ADP can arise extracellularly through release from the cytoplasm of cellsexposed to damaging stimuli or by degranulation of platelets. The concentration of the nucleotides in the cytoplasm of most cells (including vascular endothelial and smooth muscle cells) is more than ImM, and the concentration in the dense storage granules of platelets approaches 1M. Thus, there is potential for very high localised concentrations of ATP and ADP in the plasma following platelet degranulation or damageto cells of the vessel well. Release from vascular endothelial and smooth muscle cells can occur with no loss of cell viability or leakage of cytoplasmic proteins.The vasoactivity of ATP and ADP is mediated via P2 purinoceptors. Vasodilation can be induced through the release of EDRF from endothelial cells or through stimulation of PGI2 production (PGI2 is a vasodilator in many, althoughnot all, arterial beds). Purinoceptor-mediated prostacyclin production can be stimulated from perfused vascular beds (e.g. theheart andthe lung), from isolated blood vessels or from cultured endothelial cells.In some blood vessels, purinoceptor-mediated vasoconstriction can be induced by direct actionon the vascular smooth muscle cells. The receptors responsible are sub-classified as P2X (which induce vasoconstriction) and P2Y (whichinduce vasodilation). The P2Y purinoceptor that mediates EDRF production is very similar to that which is responsible for PGI2 production, although there are some intriguing differences inthe potency of ATP analogs at stimulating these two responses, even on the same cells. The intracellular mechanisms responsible have not yet been fully elucidated, but it appears that elevation of intracellular calcium is likely to play a causal role.Adenosine, which is the product of ATP and ADP metabolism by nucleotidases, can also induce vasodilation in many blood vessels, acting via P1] purinoceptors on the smooth muscle cells, but its potency is often less than that of ATP and ADP.The fate of adenine nucleotides released into the plasma is determined by ectonucleotidases on the luminal surface of the endothelial cells, not by enzymes in the blood itself (the half-life of ATP in samples of blood or plasma is many minutes, while in the microcirculation the half-life isless than one second). Endothelial ectonucleotidases have been detected in several vascular beds, and many of their characteristics are now known. These enzymes are distinct entities from the P2 purinoceptors on endothelium, as shown by the marked differences in potency of several ATP analogs as P2 receptor stimulants and as substrates for the nucleotidases.In summary, vascular endothelial and smooth muscle cells respond to extracellularATP and ADP, and can also metabolise thesenucleotides extracellularly by ectonucleotidases. In addition, ATP and ADP can be selectively released from the cells of the vessel wall and from activated platelets. Thus, the endothelial pericellular environment can be the site of complex interactions by which vascular tone is regulated through the release, actions and metabolism ofextracellular nucleotides.
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Nicolescu, Adrian C., Taranjit S. Gujral, Jordan DS Zelt, and Lois M. Mulligan. "Abstract 5139: Molecular docking exploration of potential RET tyrosine kinase inhibitors at non ATP-binding sites." In Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1538-7445.am2013-5139.

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Branković, Jovica, Zorica D. Petrović, and Vladimir P. Petrović. "In silico antibiofilm potency of phenolic N-acyl hydrazones against selected bacterial strains." In 2nd International Conference on Chemo and Bioinformatics. Institute for Information Technologies, University of Kragujevac, 2023. http://dx.doi.org/10.46793/iccbi23.495b.

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In the present work, fourteen phenolic hydrazone derivatives were evaluated for their in silico inhibitory activity against selected P. aeruginosa and S. maltophilia proteins involved in drug resistance and biofilm formation. Molecular docking analysis revealed the highest binding affinity of analogs n (-8.4 kcal/mol) and h (-7.3 kcal/mol) towards P. aeruginosa 7m1m and 7m1l proteins, respectively. In the case of S. maltophilia, analog k (-8.4 kcal/mol) expressed the highest binding affinity to 6qw7, whereas for 6uaf, the lowest binding energy was calculated for derivative d (-8.1 kcal/mol). The obtained in silico results highlight the potential inhibition potency of the selected hydrazone analogs against investigated proteins and represent a good basis for future in vitro antibiofilm investigations.
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Veeraragavan, Vijayakumar, Radhakrishnan Narayanaswamy, and Rameshkumar Chidambaram. "Molecular docking analysis of imidazole derivatives and polybenzimidazole analogs as inhibitors of superoxide dismutase (SOD) and xanthine oxidase (XO)." In 2017 IEEE International Conference on Smart Technologies and Management for Computing, Communication, Controls, Energy and Materials (ICSTM). IEEE, 2017. http://dx.doi.org/10.1109/icstm.2017.8089213.

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Gaikwad, Sunil. "Synthesis, ADME, and In Silico Molecular Docking Study of Novel N-Substituted β-Carboline Analogs as a Potential Anticancer Agent." In ECSOC 2024, 76. Basel Switzerland: MDPI, 2024. https://doi.org/10.3390/ecsoc-28-20166.

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Reports on the topic "Docking of ATP analogs"

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Sessa, Guido, and Gregory Martin. MAP kinase cascades activated by SlMAPKKKε and their involvement in tomato resistance to bacterial pathogens. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7699834.bard.

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The research problem: Pseudomonas syringae pv. tomato (Pst) and Xanthomonas campestrispv. vesicatoria (Xcv) are the causal agents of tomato bacterial speck and spot diseases, respectively. These pathogens colonize the aerial parts of the plant and cause economically important losses to tomato yield worldwide. Control of speck and spot diseases by cultural practices or chemicals is not effective and genetic sources of resistance are very limited. In previous research supported by BARD, by gene expression profiling we identified signaling components involved in resistance to Xcvstrains. Follow up experiments revealed that a tomato gene encoding a MAP kinase kinase kinase (MAPKKKe) is required for resistance to Xcvand Pststrains. Goals: Central goal of this research was to investigate the molecular mechanisms by which MAPKKKεand associated MAP kinase cascades regulate host resistance. Specific objectives were to: 1. Determine whether MAPKKKεplays a broad role in defense signaling in plants; 2. Identify components of MAP kinase cascades acting downstream of MAPKKKε; 3. Determine the role of phosphorylation-related events in the function of MAPKKKε; 4. Isolate proteins directly activated by MAPKKKε-associatedMAPK modules. Our main achievements during this research program are in the following major areas: 1. Characterization of MAPKKKεas a positive regulator of cell death and dissection of downstream MAP kinase cascades (Melech-Bonfil et al., 2010; Melech-Bonfil and Sessa, 2011). The MAPKKKεgene was found to be required for tomato resistance to Xcvand Pstbacterial strains and for hypersensitive response cell death triggered by different R gene/effector gene pairs. In addition, overexpression analysis demonstrated that MAPKKKεis a positive regulator of cell death, whose activity depends on an intact kinase catalytic domain. Epistatic experiments delineated a signaling cascade downstream of MAPKKKεand identified SIPKK as a negative regulator of MAPKKKε-mediated cell death. Finally, genes encoding MAP kinase components downstream of MAPKKKεwere shown to contribute to tomato resistance to Xcv. 2. Identification of tomato proteins that interact with MAPKKKεand play a role in plant immunity (Oh et al., 2011). We identified proteins that interact with MAPKKKε. Among them, the 14-3-3 protein TFT7 was required for cell death mediated by several R proteins. In addition, TFT7 interacted with the MAPKK SlMKK2 and formed homodimersin vivo. Thus, TFT7 is proposed to recruit SlMKK2 and MAPKKK client proteins for efficient signal transfer. 3. Development of a chemical genetic approach to identify substrates of MAPKKKε-activated MAP kinase cascades (Salomon et al., 2009, 2011). This approach is based on engineering the kinase of interest to accept unnatural ATP analogs. For its implementation to identify substrates of MAPKKKε-activated MAP kinase modules, we sensitized the tomato MAP kinase SlMPK3 to ATP analogs and verified its ability to use them as phosphodonors. By using the sensitized SlMPK3 and radiolabeled N6(benzyl)ATP it should be possible to tag direct substrates of this kinase. 4. Development of methods to study immunity triggered by pathogen-associated molecular patterns (PAMPs) in tomato and N. benthamiana plants (Kim et al., 2009; Nguyen et al. 2010). We developed protocols for measuring various PTI-associatedphenotypes, including bacterial populations after pretreatment of leaves with PAMPs, induction of reporter genes, callose deposition at the cell wall, activation of MAP kinases, and a luciferase-based reporter system for use in protoplasts. Scientific and agricultural significance: Our research activities discovered and characterized a signal transduction pathway mediating plant immunity to bacterial pathogens. Increased understanding of molecular mechanisms of immunity will allow them to be manipulated by both molecular breeding and genetic engineering to produce plants with enhanced natural defense against disease. In addition, we successfully developed new biochemical and molecular methods that can be implemented in the study of plant immunity and other aspects of plant biology.
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