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Binding mode prediction of conformationally restricted anandamide analogs within the CB1 receptor.

Padgett LW, Howlett AC, Shim JY - J Mol Signal (2008)

Bottom Line: To better understand the molecular interactions associated with binding and steric trigger mechanisms of receptor activation, a series of conformationally-restricted anandamide analogs having a wide range of affinity and efficacy were evaluated.A ligand possessing both high affinity and cannabinoid agonist efficacy was able to interact with both polar and hydrophobic interaction sites utilized by the potent and efficacious non-classical cannabinoid CP55940.In contrast, other analogs characterized by reduced affinity or efficacy exhibited less favorable interactions with those key residues.

View Article: PubMed Central - HTML - PubMed

Affiliation: Neuroscience of Drug Abuse Research Program, Julius L, Chambers Biomedical/Biotechnology Research Institute, North Carolina Central University, Durham, NC 27707, USA. jyshim@nccu.edu.

ABSTRACT

Background: CB1 cannabinoid receptors are G-protein coupled receptors for endocannabinoids including anandamide and 2-arachidonoylglycerol. Because these arachidonic acid metabolites possess a 20-carbon polyene chain as the alkyl terminal moiety, they are highly flexible with the potential to adopt multiple biologically relevant conformations, particularly those in a bent form. To better understand the molecular interactions associated with binding and steric trigger mechanisms of receptor activation, a series of conformationally-restricted anandamide analogs having a wide range of affinity and efficacy were evaluated.

Results: A CB1 receptor model was constructed to include the extracellular loops, particularly extracellular loop 2 which possesses an internal disulfide linkage. Using both Glide (Schrödinger) and Affinity (Accelrys) docking programs, binding conformations of six anandamide analogs were identified that conform to rules applicable to the potent, efficacious and stereoselective non-classical cannabinoid CP55244. Calculated binding energies of the optimum structures from both procedures correlated well with the reported binding affinity values. The most potent and efficacious of the ligands adopted conformations characterized by interactions with both the helix-3 lysine and hydrophobic residues that interact with CP55244. The other five compounds formed fewer or less energetically favorable interactions with these critical residues. The flexibility of the tested anandamide analogs, measured by torsion angles around the benzene as well as the stretch between side chain moieties, could contribute to the differences in ability to interact with the CB1 receptor.

Conclusion: Analyses of multiple poses of conformationally-restricted anandamide analogs permitted identification of favored amino acid interactions within the CB1 receptor binding pocket. A ligand possessing both high affinity and cannabinoid agonist efficacy was able to interact with both polar and hydrophobic interaction sites utilized by the potent and efficacious non-classical cannabinoid CP55940. In contrast, other analogs characterized by reduced affinity or efficacy exhibited less favorable interactions with those key residues.

No MeSH data available.


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Glide/Prime models of CP55244 compound 1, 2 and 6. (A) Overlay of the Glide/Prime models of CP55244 and compound 1. (B) Key amino acid residues of the CB1 receptor for binding with the Glide/Prime model of compound 1. H-bonding between compound 1 and the binding pocket residues are represented with white dots. (C) Overlay of the Glide/Prime model of compound 2 with compound 1. (D) Overlay of the Glide/Prime model of compound 6 with compound 1.
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Figure 5: Glide/Prime models of CP55244 compound 1, 2 and 6. (A) Overlay of the Glide/Prime models of CP55244 and compound 1. (B) Key amino acid residues of the CB1 receptor for binding with the Glide/Prime model of compound 1. H-bonding between compound 1 and the binding pocket residues are represented with white dots. (C) Overlay of the Glide/Prime model of compound 2 with compound 1. (D) Overlay of the Glide/Prime model of compound 6 with compound 1.

Mentions: In its optimum conformation within the binding pocket, compound 1 occupies the same hydrophobic region of the receptor as that occupied by the C3 side chain of CP55244 (Fig. 5A). Compared to the model for CP55244, the aromatic ring of compound 1 occupies the same location as the A-ring of CP55244, but is oriented nearly perpendicular to it. The amide side chain occupies the same location as the C/D fused cyclic region of CP55244, but is oriented in such a way that the compound 1 terminal hydroxyl does not overlap with the D-ring hydroxyl of CP55244. There is potential for aromatic stacking between the compound 1 aromatic ring and F3.25(189), which are 6.8 Å apart in this pose. Compound 1 showed the presence of three hydrogen bonds: the amide NH with the backbone O of F7.35(379), the carbonyl oxygen of the amide with the side chain N of K3.28(192), and the terminal hydroxyl with the imidazole ring N of H2.65(178) (Fig. 5B). Compounds 1 and 2, which differ in the linker that separates the amide moiety from the aromatic ring, have the greatest affinity (Ki = 38 nM and 59 nM, respectively) for the receptor (see Table 1). In the best Glide/Prime pose for compound 2, the benzene ring was perpendicular to the position of the aromatic ring in compound 1 as a result of the considerable aromatic stacking with F2.61(174), F2.64(177) and F3.25(189) (Fig. 5C). Compared with compound 1, compound 2 partially occupied the hydrophobic pocket and formed H-bonds between the amide O and the side chain N of K7.32(376) and between the amide N and the side chain hydroxyl O of S7.39(383), but no H-bond with K3.28(192). Compound 3 which lacks the methyl group of compound 2, exhibited limited hydrophobic interaction with neighboring residues such as I1.35(119) and M7.40(383) (data not shown). Compound 4, which lacks the methyl group of compound 1, was raised up toward the extracellular surface compared with the position of the aromatic ring in compound 1, such that the alkyl tail of 4 could not extend as deeply into the pocket (data not shown). Comparisons of the docking of compounds 5 and 6 with 1 indicate that the ortho-substituted aromatic ring was severely displaced toward the extracellular surface and TM2 and TM3, and the heptenyl tail failed to occupy the hydrophobic pocket (Fig. 5D). The degrees of interaction with the hydrophobic pocket for compounds 1, 2, 5 and 6 were estimated by a root mean square deviation (RMSD) from the corresponding carbons of CP55244. The RMSD for the six tail carbons were 2.8 Å, 4.8 Å, 4.6 Å and 5.4 Å, respectively.


Binding mode prediction of conformationally restricted anandamide analogs within the CB1 receptor.

Padgett LW, Howlett AC, Shim JY - J Mol Signal (2008)

Glide/Prime models of CP55244 compound 1, 2 and 6. (A) Overlay of the Glide/Prime models of CP55244 and compound 1. (B) Key amino acid residues of the CB1 receptor for binding with the Glide/Prime model of compound 1. H-bonding between compound 1 and the binding pocket residues are represented with white dots. (C) Overlay of the Glide/Prime model of compound 2 with compound 1. (D) Overlay of the Glide/Prime model of compound 6 with compound 1.
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Figure 5: Glide/Prime models of CP55244 compound 1, 2 and 6. (A) Overlay of the Glide/Prime models of CP55244 and compound 1. (B) Key amino acid residues of the CB1 receptor for binding with the Glide/Prime model of compound 1. H-bonding between compound 1 and the binding pocket residues are represented with white dots. (C) Overlay of the Glide/Prime model of compound 2 with compound 1. (D) Overlay of the Glide/Prime model of compound 6 with compound 1.
Mentions: In its optimum conformation within the binding pocket, compound 1 occupies the same hydrophobic region of the receptor as that occupied by the C3 side chain of CP55244 (Fig. 5A). Compared to the model for CP55244, the aromatic ring of compound 1 occupies the same location as the A-ring of CP55244, but is oriented nearly perpendicular to it. The amide side chain occupies the same location as the C/D fused cyclic region of CP55244, but is oriented in such a way that the compound 1 terminal hydroxyl does not overlap with the D-ring hydroxyl of CP55244. There is potential for aromatic stacking between the compound 1 aromatic ring and F3.25(189), which are 6.8 Å apart in this pose. Compound 1 showed the presence of three hydrogen bonds: the amide NH with the backbone O of F7.35(379), the carbonyl oxygen of the amide with the side chain N of K3.28(192), and the terminal hydroxyl with the imidazole ring N of H2.65(178) (Fig. 5B). Compounds 1 and 2, which differ in the linker that separates the amide moiety from the aromatic ring, have the greatest affinity (Ki = 38 nM and 59 nM, respectively) for the receptor (see Table 1). In the best Glide/Prime pose for compound 2, the benzene ring was perpendicular to the position of the aromatic ring in compound 1 as a result of the considerable aromatic stacking with F2.61(174), F2.64(177) and F3.25(189) (Fig. 5C). Compared with compound 1, compound 2 partially occupied the hydrophobic pocket and formed H-bonds between the amide O and the side chain N of K7.32(376) and between the amide N and the side chain hydroxyl O of S7.39(383), but no H-bond with K3.28(192). Compound 3 which lacks the methyl group of compound 2, exhibited limited hydrophobic interaction with neighboring residues such as I1.35(119) and M7.40(383) (data not shown). Compound 4, which lacks the methyl group of compound 1, was raised up toward the extracellular surface compared with the position of the aromatic ring in compound 1, such that the alkyl tail of 4 could not extend as deeply into the pocket (data not shown). Comparisons of the docking of compounds 5 and 6 with 1 indicate that the ortho-substituted aromatic ring was severely displaced toward the extracellular surface and TM2 and TM3, and the heptenyl tail failed to occupy the hydrophobic pocket (Fig. 5D). The degrees of interaction with the hydrophobic pocket for compounds 1, 2, 5 and 6 were estimated by a root mean square deviation (RMSD) from the corresponding carbons of CP55244. The RMSD for the six tail carbons were 2.8 Å, 4.8 Å, 4.6 Å and 5.4 Å, respectively.

Bottom Line: To better understand the molecular interactions associated with binding and steric trigger mechanisms of receptor activation, a series of conformationally-restricted anandamide analogs having a wide range of affinity and efficacy were evaluated.A ligand possessing both high affinity and cannabinoid agonist efficacy was able to interact with both polar and hydrophobic interaction sites utilized by the potent and efficacious non-classical cannabinoid CP55940.In contrast, other analogs characterized by reduced affinity or efficacy exhibited less favorable interactions with those key residues.

View Article: PubMed Central - HTML - PubMed

Affiliation: Neuroscience of Drug Abuse Research Program, Julius L, Chambers Biomedical/Biotechnology Research Institute, North Carolina Central University, Durham, NC 27707, USA. jyshim@nccu.edu.

ABSTRACT

Background: CB1 cannabinoid receptors are G-protein coupled receptors for endocannabinoids including anandamide and 2-arachidonoylglycerol. Because these arachidonic acid metabolites possess a 20-carbon polyene chain as the alkyl terminal moiety, they are highly flexible with the potential to adopt multiple biologically relevant conformations, particularly those in a bent form. To better understand the molecular interactions associated with binding and steric trigger mechanisms of receptor activation, a series of conformationally-restricted anandamide analogs having a wide range of affinity and efficacy were evaluated.

Results: A CB1 receptor model was constructed to include the extracellular loops, particularly extracellular loop 2 which possesses an internal disulfide linkage. Using both Glide (Schrödinger) and Affinity (Accelrys) docking programs, binding conformations of six anandamide analogs were identified that conform to rules applicable to the potent, efficacious and stereoselective non-classical cannabinoid CP55244. Calculated binding energies of the optimum structures from both procedures correlated well with the reported binding affinity values. The most potent and efficacious of the ligands adopted conformations characterized by interactions with both the helix-3 lysine and hydrophobic residues that interact with CP55244. The other five compounds formed fewer or less energetically favorable interactions with these critical residues. The flexibility of the tested anandamide analogs, measured by torsion angles around the benzene as well as the stretch between side chain moieties, could contribute to the differences in ability to interact with the CB1 receptor.

Conclusion: Analyses of multiple poses of conformationally-restricted anandamide analogs permitted identification of favored amino acid interactions within the CB1 receptor binding pocket. A ligand possessing both high affinity and cannabinoid agonist efficacy was able to interact with both polar and hydrophobic interaction sites utilized by the potent and efficacious non-classical cannabinoid CP55940. In contrast, other analogs characterized by reduced affinity or efficacy exhibited less favorable interactions with those key residues.

No MeSH data available.


Related in: MedlinePlus