Limits...
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.


Related in: MedlinePlus

Affinity/SA models of CP55244 and compound 1, 2 and 6. (A) Overlay of the Affinity/SA models of CP55244 and compound 1. (B) Key amino acid residues of the CB1 receptor for binding with the Affinity/SA model of compound 1. H-bonding between compound 1 and the binding pocket residues is represented with white dots. (C) Overlay of the Affinity/SA model of compound 2 with compound 1. (D) Overlay of the Affinity/SA model of compound 6 with compound 1.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2289822&req=5

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

Mentions: As shown in Fig. 6A, the optimum fit of compound 1 is comparable to that occupied by CP55244, including the co-localization of the hydrophobic side chains of both molecules, and the aromatic ring of compound 1 with the A-ring of CP55244. Compound 1 (Fig. 6B) exhibits a H-bond between K3.28(192) and the carbonyl of the amide. The compound 1 terminal hydroxyl occupies the same location as the D-ring hydroxyl of CP55244. The superposition model of CP55244 and compound 1 suggests that the weaker binding affinity of compound 1 compared with CP55244 could be due to the missing moiety in compound 1 that could correspond to the C/D-ring moiety of CP55244. There is potential for aromatic stacking between the compound 1 aromatic ring and F3.25(189) as well as F7.35(379) as can be seen in the Compound 1 movie (Additional File 1). Compound 2 exhibited a greater variety of binding modes compared with compound 1. The pose shown in Fig. 6C lacked the H-bonding interaction with K3.28(192), although the C3 side chain occupied the same hydrophobic pocket as compound 1 and exhibited energetically favorable aromatic stacking with F5.42(278), which are 6.7 Å apart. Poses in which compound 2 exhibited H-bonding with K3.28(192) showed that the aromatic ring of compound 2 was displaced from the position of the aromatic ring in compound 1 (see Compound 2 movie (Additional File 2)). Compound 5 occupied an almost identical region as compound 1; in particular, its alkyl tail occupied the same region. It also exhibited a set of H-bonding interactions between the aromatic ring OH and K3.28(192), and between the terminal OH and S7.39(383). The aromatic ring of compound 5, which is 5.5 Å apart from F7.35(379), was skewed compared with compound 1 due to the presence of two carbon linker atoms between the aromatic ring and the amide moiety (not shown). Compound 6 showed H-bonding interactions for the amide and OH terminal with K3.28(192) and S7.39(383), as did compound 5 (data not shown). However, as a result of the reduced flexibility imposed by the ortho arrangement of the moieties on the ring (see below), the heptenyl tail moiety was severely restricted, thereby limiting interaction with the hydrophobic residues (Fig. 6D) (see Compound 6 movie (Additional File 3)). The RMSD, an estimate of the degree of interaction with the hydrophobic pocket, for the six tail carbons of compounds 1, 2, 5 and 6, when compared with CP55244, as were 2.2 Å, 2.7 Å, 0.9 Å and 7.2 Å, respectively.


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

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

Affinity/SA models of CP55244 and compound 1, 2 and 6. (A) Overlay of the Affinity/SA models of CP55244 and compound 1. (B) Key amino acid residues of the CB1 receptor for binding with the Affinity/SA model of compound 1. H-bonding between compound 1 and the binding pocket residues is represented with white dots. (C) Overlay of the Affinity/SA model of compound 2 with compound 1. (D) Overlay of the Affinity/SA model of compound 6 with compound 1.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2289822&req=5

Figure 6: Affinity/SA models of CP55244 and compound 1, 2 and 6. (A) Overlay of the Affinity/SA models of CP55244 and compound 1. (B) Key amino acid residues of the CB1 receptor for binding with the Affinity/SA model of compound 1. H-bonding between compound 1 and the binding pocket residues is represented with white dots. (C) Overlay of the Affinity/SA model of compound 2 with compound 1. (D) Overlay of the Affinity/SA model of compound 6 with compound 1.
Mentions: As shown in Fig. 6A, the optimum fit of compound 1 is comparable to that occupied by CP55244, including the co-localization of the hydrophobic side chains of both molecules, and the aromatic ring of compound 1 with the A-ring of CP55244. Compound 1 (Fig. 6B) exhibits a H-bond between K3.28(192) and the carbonyl of the amide. The compound 1 terminal hydroxyl occupies the same location as the D-ring hydroxyl of CP55244. The superposition model of CP55244 and compound 1 suggests that the weaker binding affinity of compound 1 compared with CP55244 could be due to the missing moiety in compound 1 that could correspond to the C/D-ring moiety of CP55244. There is potential for aromatic stacking between the compound 1 aromatic ring and F3.25(189) as well as F7.35(379) as can be seen in the Compound 1 movie (Additional File 1). Compound 2 exhibited a greater variety of binding modes compared with compound 1. The pose shown in Fig. 6C lacked the H-bonding interaction with K3.28(192), although the C3 side chain occupied the same hydrophobic pocket as compound 1 and exhibited energetically favorable aromatic stacking with F5.42(278), which are 6.7 Å apart. Poses in which compound 2 exhibited H-bonding with K3.28(192) showed that the aromatic ring of compound 2 was displaced from the position of the aromatic ring in compound 1 (see Compound 2 movie (Additional File 2)). Compound 5 occupied an almost identical region as compound 1; in particular, its alkyl tail occupied the same region. It also exhibited a set of H-bonding interactions between the aromatic ring OH and K3.28(192), and between the terminal OH and S7.39(383). The aromatic ring of compound 5, which is 5.5 Å apart from F7.35(379), was skewed compared with compound 1 due to the presence of two carbon linker atoms between the aromatic ring and the amide moiety (not shown). Compound 6 showed H-bonding interactions for the amide and OH terminal with K3.28(192) and S7.39(383), as did compound 5 (data not shown). However, as a result of the reduced flexibility imposed by the ortho arrangement of the moieties on the ring (see below), the heptenyl tail moiety was severely restricted, thereby limiting interaction with the hydrophobic residues (Fig. 6D) (see Compound 6 movie (Additional File 3)). The RMSD, an estimate of the degree of interaction with the hydrophobic pocket, for the six tail carbons of compounds 1, 2, 5 and 6, when compared with CP55244, as were 2.2 Å, 2.7 Å, 0.9 Å and 7.2 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