The binding orientation of epibatidine at α7 nACh receptors

Thompson, Andrew; Metzger, Simon; Lochner, Martin; Ruepp, Marc-David

doi:10.1016/j.neuropharm.2017.01.008

Cited by 13 publications

(15 citation statements)

References 35 publications

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“…The marine mollusk Aplysia californica expresses a watersoluble protein called AChBP that functions to modulate AChmediated synaptic transmission in this organism (31). X-ray crystallography studies of the AChBP have been used to elucidate binding interactions between ligands and nAChRs (32)(33)(34)(35). Several high-resolution crystal structures have been reported for the AChBP complexed with ␣-Ctxs (36 -39) but not with PeIA.…”

Section: X-ray Crystallography Of Peia Complexed With Aplysia Califormentioning

confidence: 99%

Molecular determinants of α-conotoxin potency for inhibition of human and rat α6β4 nicotinic acetylcholine receptors

Hone¹,

Talley

Bobango

et al. 2018

Journal of Biological Chemistry

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Edited by Wolfgang PetiNicotinic acetylcholine receptors (nAChRs) containing ␣6 and ␤4 subunits are expressed by dorsal root ganglion neurons and have been implicated in neuropathic pain. Rodent models are often used to evaluate the efficacy of analgesic compounds, but species differences may affect the activity of some nAChR ligands. A previous candidate ␣-conotoxin-based therapeutic yielded promising results in rodent models, but failed in human clinical trials, emphasizing the importance of understanding species differences in ligand activity. Here, we show that human and rat ␣6/␣3␤4 nAChRs expressed in Xenopus laevis oocytes exhibit differential sensitivity to ␣-conotoxins. Sequence homology comparisons of human and rat ␣6␤4 nAChR subunits indicated that ␣6 residues forming the ligand-binding pocket are highly conserved between the two species, but several residues of ␤4 differed, including a Leu-Gln difference at position 119. X-ray crystallography of ␣-conotoxin PeIA complexed with the Aplysia californica acetylcholine-binding protein (AChBP) revealed that binding of PeIA orients Pro 13 in close proximity to residue 119 of the AChBP complementary subunit. Sitedirected mutagenesis studies revealed that Leu 119 of human ␤4 contributes to higher sensitivity of human ␣6/␣3␤4 nAChRs to ␣-conotoxins, and structure-activity studies indicated that PeIA Pro 13 is critical for high potency. Human and rat ␣6/␣3␤4 nAChRs displayed differential sensitivities to perturbations of the interaction between PeIA Pro 13 and residue 119 of the ␤4 subunit. These results highlight the potential significance of species differences in ␣6␤4 nAChR pharmacology that should be taken into consideration when evaluating the activity of candidate human therapeutics in rodent models.Nicotinic acetylcholine receptors (nAChRs) 5 are ligandgated ion channels formed by the pentameric assembly of individual subunits. There are 16 genes in mammals that encode these subunits and are represented by the Greek symbols ␣1-␣7, ␣9, ␣10, ␤1-␤4, ␦, ⑀, and ␥ (1). nAChRs are expressed by neurons in both the central and peripheral nervous systems and are involved in diverse physiological processes (2), including fast synaptic transmission (3), the modulation of neurotransmitter release (4 -10), and numerous immunological processes (11,12).Native nAChRs containing the ␣6 subunit are broadly classified into two subtype categories: those that contain the ␤2 subunit and those that contain the ␤4 subunit. The ␣6␤2* subtype (the asterisk denotes the potential presence of additional subunits in native receptors) has a limited distribution profile in the nervous system but is abundantly expressed in certain regions of the brain and spinal cord (13)(14)(15)(16)(17)(18)(19). The ␣6␤4* subtype probably has an even more restricted expression profile. Functional evidence for ␣6␤4* nAChR expression in sensory neurons of rat and mouse dorsal root ganglia (DRG) has been demonstrated (20, 21), although their functional role in these cells is mostly unknown.DRG contain neuron...

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Section: X-ray Crystallography Of Peia Complexed With Aplysia Califormentioning

confidence: 99%

Molecular determinants of α-conotoxin potency for inhibition of human and rat α6β4 nicotinic acetylcholine receptors

Hone¹,

Talley

Bobango

et al. 2018

Journal of Biological Chemistry

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“…The results show that their orientations differ, and question whether it is appropriate to use these receptor homologues for predicting ligand binding at different members of the Cys-loop family (Thompson et al., 2017). …”

Section: Introductionmentioning

confidence: 99%

The binding orientations of structurally-related ligands can differ; A cautionary note

et al. 2017

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Crystal structures can identify ligand-receptor interactions and assist the development of novel therapeutics, but experimental challenges sometimes necessitate the use of homologous proteins. Tropisetron is an orthosteric ligand at both 5-HT3 and α7 nACh receptors and its binding orientation has been determined in the structural homologue AChBP (pdbid: 2WNC). Co-crystallisation with a structurally-related ligand, granisetron, reveals an almost identical orientation (pdbid; 2YME). However, there is a >1000-fold difference in the affinity of tropisetron at 5-HT3 versus α7 nACh receptors, and α7 nACh receptors do not bind granisetron. These striking pharmacological differences prompt questions about which receptor the crystal structures most closely represent and whether the ligand orientations are correct. Here we probe the binding orientation of tropisetron and granisetron at 5-HT3 receptors by in silico modelling and docking, radioligand binding on cysteine-substituted 5-HT3 receptor mutants transiently expressed in HEK 293 cells, and synthetic modification of the ligands. For 15 of the 23 cysteine substitutions, the effects on tropisetron and granisetron were different. Structure-activity relationships on synthesised derivatives of both ligands were also consistent with different orientations, revealing that contrary to the crystallographic evidence from AChBP, the two ligands adopt different orientations in the 5-HT3 receptor binding site. Our results show that even quite structurally similar molecules can adopt different orientations in the same binding site, and that caution may be needed when using homologous proteins to predict ligand binding.

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“…However, little assessment has been done about some critical aspects of their conformational variability (15, 59). Recently, the crystallographic structure of the extracellular domain of the nicotinic receptor α7 in complex with epibatidine was reported (60). Although the interactions described for this complex agree with our results, it was found that the residues THR146, CYS187, and CYS186 could also be involved in the protein complex due to their molecular proximity (Fig 2).…”

Section: Discussionmentioning

confidence: 99%

Novel computational deep learning strategy for neuroprotection identification reveals unique set of nicotine analogs as potential therapeutic compounds against Parkinson’s disease

Rojas-Rodríguez

Morantes

Pinzón

et al. 2019

Preprint

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Dopaminergic replacement has been used for Parkinson’s Disease (PD) treatment with positive effects on motor symptomatology but with low effects over disease progression and prevention. Different epidemiological studies have shown that nicotine consumption decreases PD prevalence through the activation of neuroprotective mechanisms. Nicotine-induced neuroprotection has been associated with the overstimulation of intracellular signaling pathways (SP) such as Phosphatidyl Inositol 3-kinase/Protein kinase-B (PI3K/AKT) through nicotinic acetylcholine receptors (e.g α7 nAChRs) and the over-expression of the anti-apoptotic gene Bcl-2. Considering its harmful effects (toxicity and dependency), the search for nicotine analogs with decreased secondary effects, but similar neuroprotective activity, remains a promissory field of study. In this work, a computational strategy integrating structural bioinformatics, signaling pathway (SP) manual reconstruction, and deep learning was performed to predict the potential neuroprotective activity of a series of 8 novel nicotine analogs over the behavior of PI3K/AKT. We performed a protein-ligand analysis between nicotine analogs and α7 nAChRs receptor using geometrical conformers, physicochemical characterization of the analogs and developed a manually curated neuroprotective dataset to analyze their potential activity. Additionally, we developed a predictive machine-learning model for neuroprotection in PD through the integration of Markov Chain Monte-Carlo transition matrix for the SP with synthetic training datasets of the physicochemical properties and structural dataset. Our model was able to predict the potential neuroprotective activity of seven new nicotine analogs based on the binomial Bcl-2 response regulated by the activation of PI3K/AKT. We present a new computational strategy to predict the pharmacological neuroprotective potential of nicotine analogs based on SP architecture, using deep learning and structural data. Our theoretical strategy can be further applied to the study new treatments related with SP deregulation and may ultimately offer new opportunities for therapeutic interventions in neurodegenerative diseases.Author SummaryParkinson’s disease is one of the most prevalent neurodegenerative diseases across population over age 50. Affecting controlled movements and non-motor symptoms, treatments for Parkinson prevention are indispensable to reduce patient’s population in the future. Epidemiological data provide evidence that nicotine have a neuroprotective effect decreasing Parkinson prevalence. By interacting with nicotine receptors in neurons and modulating signaling pathways expressing anti-apoptotic genes nicotine arise as a putative neuroprotective therapy. Nevertheless, toxicity and dependency prevent the use of nicotine as a suitable drug. Nicotine analogs, structurally similar compounds emerge as an alternative for Parkinson preventive treatment. In this sense we developed a quantitative strategy to predict the potential neuroprotective activity of nicotine analogs. Our model is the first approach to predict neuroprotection in the context of Parkinson and signaling pathways using machine learning and computational chemistry.

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The binding orientation of epibatidine at α7 nACh receptors

Cited by 13 publications

References 35 publications

Molecular determinants of α-conotoxin potency for inhibition of human and rat α6β4 nicotinic acetylcholine receptors

Molecular determinants of α-conotoxin potency for inhibition of human and rat α6β4 nicotinic acetylcholine receptors

The binding orientations of structurally-related ligands can differ; A cautionary note

Novel computational deep learning strategy for neuroprotection identification reveals unique set of nicotine analogs as potential therapeutic compounds against Parkinson’s disease

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