ArticleJournal of molecular modeling2010
Study of a structurally similar kappa opioid receptor agonist and antagonist pair by molecular dynamics simulations.
Article in Journal of molecular modeling, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
6 citing papers in PubMed, 28 citations in OpenAlex.
- Multiscale Modeling of Amyloid Fibrils Formed by Aggregating Peptides Derived from the Amyloidogenic Fragment of the A-Chain of Insulin.International journal of molecular sciences · 2021Article
- Fentanyl Family at the Mu-Opioid Receptor: Uniform Assessment of Binding and Computational Analysis.Molecules (Basel, Switzerland) · 2019Article
- Structure prediction of the second extracellular loop in G-protein-coupled receptors.Biophysical journal · 2014Article
- Action of molecular switches in GPCRs--theoretical and experimental studies.Current medicinal chemistry · 2012Review
- The role of water in activation mechanism of human N-formyl peptide receptor 1 (FPR1) based on molecular dynamics simulations.PloS one · 2012Article
- Modeling of ligand binding to G protein coupled receptors: cannabinoid CB1, CB2 and adrenergic β 2 AR.Journal of molecular modeling · 2011Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Among the structurally similar guanidinonaltrindole (GNTI) compounds, 5'-GNTI is an antagonist while 6'-GNTI is an agonist of the kappaOR opioid receptor. To explore how a subtle alteration of the ligand structure influences the receptor activity, we investigated two concurrent processes: the final steps of ligand binding at the receptor binding site and the initial steps of receptor activation. To trace these early activation steps, the membranous part of the receptor was built on an inactive receptor template while the extracellular loops were built using the ab initio CABS method. We used the simulated annealing procedure for ligand docking and all-atom molecular dynamics simulations to determine the immediate changes in the structure of the ligand-receptor complex. The binding of an agonist, in contrast to an antagonist, induced the breakage of the "3-7 lock" between helices TM3 and TM7. We also observed an action of the extended rotamer toggle switch which suggests that those two switches are interdependent.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.