Muons penetrate much further than X-rays, they do essentially zero damage, and they are provided for free by the cosmos.
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Contributed by John E. Casida, December 12, 2007 (received for review November 14, 2007)
Abstract
The nicotinic acetylcholine (ACh) receptor (nAChR) plays a crucial role in excitatory neurotransmission and is an important target for drugs and insecticides. Diverse nAChR subtypes with various subunit combinations confer differential selectivity for nicotinic drugs. We investigated the subtype selectivity of nAChR agonists by comparing two ACh-binding proteins (AChBPs) as structural surrogates with distinct pharmacological profiles [i.e., Lymnaea stagnalis (Ls) AChBP of low neonicotinoid and high nicotinoid sensitivities and Aplysia californica (Ac) AChBP of high neonicotinoid sensitivity] mimicking vertebrate and insect nAChR subtypes, respectively. The structural basis of subtype selectivity was examined here by photoaffinity labeling. Two azidoneonicotinoid probes in the Ls-AChBP surprisingly modified two distinct and distant subunit interface sites: loop F Y164 of the complementary or (−)-face subunit and loop C Y192 of the principal or (+)-face subunit, whereas three azidonicotinoid probes derivatized only Y192. Both the neonicotinoid and nicotinoid probes labeled Ac-AChBP at only one position at the interface between loop C Y195 and loop E M116. These findings were used to establish structural models of the two AChBP subtypes. In the Ac-AChBP, the neonicotinoids and nicotinoids are nestled in similar bound conformations. Intriguingly, for the Ls-AChBP, the neonicotinoids have two bound conformations that are inverted relative to each other, whereas nicotinoids appear buried in only one conserved conformation as seen for the Ac-AChBP subtype. Accordingly, the subtype selectivity is based on two disparate bound conformations of nicotinic agonists, thereby establishing an atypical concept for neonicotinoid versus nicotinoid selectivity between insect and vertebrate nAChRs.
The nicotinic acetylcholine (ACh) receptor (nAChR) is critically important in synaptic neurotransmission and the target of potential therapeutic agents for neurological dysfunction and of major neonicotinoid insecticides for crop protection and animal health. The drug-binding sites are localized at subunit interfaces of the nAChR pentameric structure. Specific vertebrate and insect subunit combinations make up diverse nAChR subtypes that differ in pharmacological profiles (1, 2). Highly subtype-selective nicotinic agents are required for development of therapeutics and insecticides. A family of peptide antagonists, the α-conotoxins, serve as important probes for studying structural determinants of subtype selectivity (3–5). However, the molecular mechanism of selectivity for small agonist molecules is not resolved because most of the key amino acids in the nAChR-binding pocket are conserved in all of the receptor subtypes and species and the binding region for antagonists extends over a large interfacial surface. Understanding drug–nAChR interactions was greatly facilitated by the discovery and crystallization of mollusk homopentameric ACh-binding proteins (AChBPs) as structural surrogates for the extracellular ligand-binding domain of the nAChR (6–8). Photoaffinity labeling combined with mass spectrometry (MS) technology provides a direct and physiologically relevant chemical biology method for three-dimensional structural investigation of drug–receptor interactions (9, 10). In the present study, two chemotypes of nicotinic agonists (neonicotinoids and nicotinoids) with distinct pharmacophores are used as photoaffinity probes [supporting information (SI) Fig. 4] precisely capturing unique bound conformations (Fig. 1) at two AChBP subtypes that differ in pharmacological profiles, thereby defining an intriguing mechanistic basis for subtype-selective agonist action at insect and vertebrate nAChRs.
Fig. 1.
Structures of IMI and derivatives. R designates position of H in the insecticide IMI, azido (N3) in the photoaffinity probe, or nitrene (N) after photoactivation, capturing normal and inverted bound conformations. Asterisk designates the nitro tip oxygen. Other neonicotinoids and nicotinoids studied are shown in SI Fig. 4.
Results
Subtype Selectivity.
Neonicotinoids such as imidacloprid (IMI) and thiacloprid (THIA) with the distinctive electronegative nitro or cyano pharmacophore, respectively, are not protonated at physiological pH and are selective agonists for the insect receptor subtype, whereas four nicotinoids [epibatidine (EPI), descyanothiacloprid (DCTHIA), desnitroimidacloprid (DNIMI), and nicotine (NIC)] with a cationic functionality preferentially act on the vertebrate subtype (2). AChBP from the freshwater snail Lymnaea stagnalis (Ls) (6, 7) has higher affinity for nicotinoids than neonicotinoids (Table 1), pharmacology reminiscent of the vertebrate nAChR subtype. Another AChBP from the saltwater mollusk Aplysia californica (Ac) (8) has similar affinity for both neonicotinoids and nicotinoids and may therefore serve as a structural surrogate for interactions of both neonicotinoids with the insect receptor subtype and nicotinoids with the vertebrate subtype (9, 10). Thus, two AChBPs from mollusks have distinct pharmacology suggestive of the nAChRs from species as divergent as mammals and insects. Ac-AChBP has Y55 on loop D in contrast to tryptophan at the equivalent position (W53) with Ls-AChBP and all of the nAChR subtypes. Interestingly, the Y55W mutant of the Ac-AChBP gives a similar neonicotinoid affinity profile to that of the wild type (WT) (except for IMI with 5- to 14-fold enhanced potency), whereas Y55W has fundamentally higher affinity for nicotinoids than the WT (SI Table 3).
View this table:
Table 1.
Comparison of pharmacological profiles for [3H]EPI binding site in two AChBP subtypes
Photoaffinity Labeling.
Azidoneonicotinoid and azidonicotinoid photoaffinity probes (acting as photoactivated nitrenes) adequately and specifically modified Ls-AChBP with up to one agonist molecule for each subunit based on analysis of the intact derivatized protein (SI Fig. 5 and SI Table 4). MS/MS analysis for three nicotinoid probes precisely pinpointed one and only one derivatized site at Y192 on loop C of the (+)-face subunit (SI Table 5). Stunningly, the two neonicotinoid nitrene molecules captured two distinct sites: the expected Y192 and the distant Y164 on loop F of the (−)-face subunit established by unambiguous adduct fragments (Fig. 2, SI Fig. 6, and SI Table 5). In the Ac-AChBP, both neonicotinoid and nicotinoid probes photoaffinity labeled loop C Y195 and loop E M116, residues that presumably are spatial neighbors to the azido substituent of the probes (Table 2) (9, 10).
Fig. 2.
Collision-induced dissociation spectrum of m/z 946.38(3+) corresponding to triply charged IMI nitrene-labeled peptide (E149 to R170) from Ls-AChBP (given as representative data). The site of modification is indicated unambiguously as Y164 by the modified immonium ion and the appearance of the appropriately shifted C-terminal (y) and N-terminal (b) fragment ions. The immonium ion and the first modified ions in the y and b series are printed in red.
View this table:
Table 2.
Photoaffinity probes and modified site(s) in AChBPs
Multiple Bound Conformations on AChBP.
Docking, conformational searches, and molecular dynamics (MD) simulations using the AChBP crystal structures gave models for binding site interactions consistent with the observed ligand potency and photolabeling. For neonicotinoids with a nitro or cyano substituent, the Ls-AChBP subtype binds the ligands in two distinct bound conformations with similar energy and yield (Fig. 3 and SI Fig. 7). One neonicotinoid-bound conformation is completely inverted compared with the common conformation. In this inverted form, loop F Y164 from the (−)-face subunit is spatially positioned to be modified by the photoreactive nitrene of the neonicotinoid [MD distance between putative nitrene position and OH oxygen of Y164 is ≈4 Å (nuclei to nuclei)]. The IMI nitro tip oxygen H bonds with the backbone M114 HN (2.1 Å) of loop E on the complementary subunit and/or possibly undergoes water-bridging to L102 and M114 (2–4 Å). The chlorine atom is proximal to the Y164 side chain (≈4 Å). Imidazolidine hydrogens on the C4 and C5 carbons are near the C187 and C188 sulfurs and the Y192 OH (2–4 Å) on loop C from the (+)-face subunit. Similar interactions are also observed for THIA with cyano nitrogen in place of nitro oxygen (SI Fig. 7). In the normal bound conformation with the Ls-AChBP subtype, chlorine faces the backbone carbonyl oxygens of loop E L102 and L112 for van der Waals contacts (3.0 and 4.6 Å, respectively) and the pyridine nitrogen is expected to H bond with the backbone carbonyl oxygens of M114 and W143 (3.1 and 3.8 Å, respectively) possibly by solvent bridge(s). The loop C Y192 OH oxygen from the (+)-face subunit is also suitably positioned for photoderivatization by the nitrene (≤4 Å). The nitro or cyano tip atom contacts loop C C187 HN and the backbone of S186 (not displayed) (2–4 Å) and the guanidine/amidine plane π-stacks with Y185 (3–4 Å). These interactions in the normal bound conformation are the same as those in Ac-AChBP (10). Each of three nicotinoids with a cationic functionality is nestled with one conserved conformation in the agonist-binding site of Ls-AChBP (SI Fig. 8): that is, the chloropyridine moiety interacts with loop E and a part of loop B for van der Waals contacts and H bondings, whereas the ammonium/iminium moiety primarily H bonds with the backbone carbonyl oxygen of loop B W143 and secondarily undergoes cation-π interaction with the side chain of W143. Aromatic residues Y89, Y185, Y192, and W53 surround this region.
Fig. 3.
Structural models for IMI-binding site interactions with AChBP and nAChR subtypes. (Upper) For AChBP subtypes, IMI is docked onto the Lymnaea stagnalis (Ls) AChBP 1UW6 (7) and Aplysia californica (Ac) AChBP 2BYQ (8) crystal structures. (Lower) IMI binds to the homology models for chick α4β2 and Myzus α2β1 nAChR subtypes established with 1UW6 and 2BYQ, respectively, as the scaffolds. The right and center four IMI-bound structures are in the normal position and the left two are inverted (see also Fig. 1). Amino acids in green are from the (+)-face or α-subunit, and in brown are from the (−)-face or β-subunit. THIA-docked AChBP and nAChR subtypes and the EPI-bound structure of Ls-AChBP based on the present photoaffinity-labeling results are shown in SI Figs. 7 and 8, respectively.
nAChR Structural Models.
Molecular models of Ls- and Ac-AChBPs described above serve as the basis to develop nAChR structural templates describing the interactions of subtype-selective nicotinic agonists. Two models for interfacial agonist-binding domains of nAChR subtypes of chick α4β2 (low neonicotinoid sensitivity) and an insect (Myzus) nAChR (high neonicotinoid sensitivity) are established based on crystal structures from Ls-AChBP (1UW6) and Ac-AChBP (2BYQ), respectively (Fig. 3 and SI Fig. 7). As with Ls-AChBP, the chick α4β2 receptor yields two bound conformations for IMI or THIA that are once again inverted relative to each other. In the inverted IMI/THIA-bound conformation, the nitro or cyano tip oxygen/nitrogen H bonds with loop E L139 HN (1.8 Å) and possibly makes water bridges involving L139 and N127. Chlorine forms van der Waals contacts with loop F D189 carboxyl oxygen (3.7 Å). The alternative normal conformation of IMI/THIA is also consistent with that in the Ls-AChBP. The aphid Myzus persicae nAChR subtype (11–13) was selected for modeling because it is highly neonicotinoid sensitive and, in contrast to many other insects of defined genomic sequence, it is a major target worldwide in neonicotinoid use. In the Myzus α2β1 interface, IMI and THIA occupy the binding site in the normal bound conformation defined by the Ac-AChBP subtype (10) and the normal one in Ls-AChBP. In addition, variable loop E residues among the AChBPs and nAChRs are spatially and functionally consistent in each case. Nicotinoids (EPI, DNIMI, and DCTHIA) yield one common bound conformation (images not shown) as with those in Ac-AChBP (8–10).
Discussion
Neonicotinoid-Binding Site Interactions and Selectivity.
Neonicotinoids are selective agonists for the insect versus vertebrate nAChR subtypes. The distinct neonicotinoid nitro or cyano pharmacophore may be recognized by a specific site existing only in the insect subtype (14–16). Sequence alignments of the nAChR β-subunits from diverse species of insects and vertebrates suggest a purported site for interaction with the nitro/cyano electronegative tip, that is, a basic residue (arginine or lysine) adjacent to the loop D tryptophan in various insect β-subunits. Pentameric stoichiometries of the various insect nAChRs have not been resolved, because they can be examined functionally only as recombinant hybrids consisting of various insect α-subunits and a vertebrate β2-subunit (17–21). A mutant of Drosophila α2/chick β2 hybrid nAChR with a basic residue (T77R or K) on the β2-subunit attenuates IMI-elicited agonist responses, but the influence of the mutation is modest (21) compared with that in WT vertebrate β2-containing hybrid receptors (18, 20); therefore, this residue may play an alternative or supplemental role associated with conformational rearrangements of the binding pocket after ligand binding (10). Target-site resistance to some neonicotinoids in the brown planthopper results from a nAChR mutation in which a tyrosine on loop B of the Nlα1 or Nlα3 subunit is substituted by serine (T151S), presumably inducing an indirect conformational alteration of the neonicotinoid-binding pocket (19, 22). Hence, the Ac-AChBP, as a structural surrogate, provides a suitable template for delineating the determinants of neonicotinoid binding to the insect receptor (10). The neonicotinoid nitro or cyano pharmacophore interacts primarily with loop C C190 and S189. In contrast, the cationic functionality of three nicotinoids (EPI, DNIMI, and DCTHIA) faces in the opposite direction contacting loop B W147 for H bonding and cation-π interaction (8–10).
Atypical Concept for Subtype Selectivity.
The functional amino acids forming the binding pockets are fully conserved in all of the AChBPs and diverse nAChR subtypes, yet there is considerable neonicotinoid selectivity. This suggests a limitation for the pharmacological approach combined with site-directed mutagenesis. In the present investigation, we discovered for two AChBP subtypes that one has low affinity (Ls-AChBP) and the other high affinity (Ac-AChBP) for neonicotinoids. Thus, the present direct comparison of the two AChBPs in neonicotinoid-binding site interactions structurally defines the mechanism of subtype selectivity, consequently rationalizing the high and low affinities of the insect and vertebrate nAChR subtypes, respectively. Neonicotinoid photoaffinity labeling of Ls-AChBP in physiologically relevant media yields two distant modification sites at loop F Y164 and loop C Y192. However, only one site Y192 is assigned in nicotinoid photolabeling. In the Ac-AChBP, both chemotypes of probes bind at one interfacial position between Y195 and M116 on loops C and E, respectively (9, 10). Our results lead to three conclusions. First, a mixture of two very disparate bound ligand conformations at the Ls-AChBP subtype reveals the inferior affinity of neonicotinoids at the site. Second, only one substantial bound conformation at the Ac-AChBP leads to its high neonicotinoid sensitivity. This relationship between Ls- and Ac-AChBPs in neonicotinoid selectivity is clearly interpretable to that for vertebrate and insect nAChR subtypes. Finally, in nicotinoids, one fundamental bound conformation is conserved for all AChBP and nAChR subtypes (7–10, 23). The same agonist molecule can also adopt different binding orientations at other Cys-loop receptors, depending on the nature and position of aromatic amino acid side chains, that is, serotonin (5-HT) at 5-HT3 versus MOD-1 receptors and γ-aminobutyric acid (GABA) at GABAA versus GABAC receptors (24, 25).
In summary, this investigation examining nicotinic agonist labeling of AChBP subtypes establishes that multiple bound ligand conformations may contribute to the binding constant, which therefore reflects a weighted average of a multiplicity of binding orientations, rather than the ligand residing in a single bound state or conformation.
Materials and Methods
Chemicals.
The neonicotinoids and nicotinoids including five photoaffinity probes were available from our previous studies (9, 10) except for [3H]EPI (±)-EPI, and (−)-NIC obtained from Amersham Biosciences, TOCRIS, and Sigma, respectively.
Biology.
Ls- and Ac-AChBP subtypes were expressed in HEK-293 cells by using cDNAs chemically synthesized from oligonucleotides engineered for mammalian codon usage and were purified as described in refs. 4, 8, and 26. Potencies of neonicotinoids and nicotinoids as displacers of specific radioligand binding to the AChBP were determined by a scintillation proximity assay (9, 10). Photoaffinity-labeling experiments and MS measurements of derivatized intact AChBP subunit and MS/MS analyses of tryptic fragments pinpointing the sites of modifications were performed according to our earlier methodology (9, 10).
Calculations.
Docking calculations were performed by using the AutoDock 4 suite (27, 28). The receptor was treated as rigid whereas flexible ligands were docked in a 15-Å cubic grid centered on the active site. In each case, 200 Lamarkian Genetic Algorithm searches were carried out. Good-quality hits were those with binding energies below −7 kcal/mol. A 1,000-step low mode Monte Carlo (MC) conformational search was performed on IMI and THIA in the Ls-AChBP 1UW6 (7) active site. THIA was then minimized in 1UW6 along with all side chains within 15 Å. Ligand docking was done with this minimized 1UW6. MD simulations involved NIC and IMI in the 1UW6 active site with varying numbers of explicit waters. These were equilibrated for 100 ps and simulated for 1 ns at 300 K with a 1-fs time step and SHAKE applied to all bonds to hydrogen. The MD and MC conformational search calculations were run by using Macromodel 9.1 in Maestro 7.5 (Schrödinger) (29) with the OPLS2005 forcefield and a water continuum model (30). Unless otherwise specified, all minimizations also used Macromodel with these parameters.
The Myzus α2β1 interface homology model was built by the Swiss-Model server (31) by using Ac-AChBP 2BYQ (chain A) (8) as a template based on sequence alignments made by using the CLUSTAL W web server at the European Bioinformatics Institute. 2BYQ chain A and chain E backbone atoms were then used as a scaffold to assemble the individual chains Myzus α2 and β1, respectively. The model side chains were optimized by using the Swiss PDB viewer. The model was further refined with Macromodel including minimization of all side chains within 15 Å of the binding pocket with the remainder of the structure fixed. The chick α4β2 interface homology model was established with 1UW6 as a scaffold according to our earlier procedure (9).
Acknowledgments
We thank Dennis Dougherty, Bruce Hammock, and Jeffrey Scott for important suggestions. This work was supported by the William Muriece Hoskins Chair in Chemical and Molecular Entomology (J.E.C.), National Institute of Environmental Health Sciences Grant R01 ES08424 (to M.T. and J.E.C.), National Center for Research Resources Grants RR015084, RR001614, and RR019934 (to D.M., K.F.M., and A.L.B.), National Institutes of Health Grants R37-GM18360 and UO1-NS05846 (to T.T.T. and P.T.), and National Science Foundation Grant CHE-0233882 (to K.A.D.).
Footnotes
- ¶To whom correspondence should be addressed. E-mail: ectl{at}nature.berkeley.edu
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Author contributions: M.T. and J.E.C. designed research; M.T., D.M., and T.T.T. performed research; M.T., D.M., T.T.T., K.A.D., K.F.M., A.L.B., P.T., and J.E.C. analyzed data; and M.T. and J.E.C. wrote the paper.
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The authors declare no conflict of interest.
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This article contains supporting information online at www.pnas.org/cgi/content/full/0711724105/DC1.
- © 2008 by The National Academy of Sciences of the USA
References
Atypical nicotinic agonist bound conformations conferring subtype selectivity
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