Limits...
Structural analysis of inhibition of E. coli methionine aminopeptidase: implication of loop adaptability in selective inhibition of bacterial enzymes.

Ma ZQ, Xie SX, Huang QQ, Nan FJ, Hurley TD, Ye QZ - BMC Struct. Biol. (2007)

Bottom Line: When compared with the human isozymes, this loop either becomes buried in the human type I enzyme due to an N-terminal extension that covers its position or is replaced by a unique insert in the human type II enzyme.The adaptability of the YHGY loop in E. coli methionine aminopeptidase, and likely in other bacterial methionine aminopeptidases, enables the enzyme active pocket to accommodate inhibitors of differing size.The differences in this adaptable loop between the bacterial and human methionine aminopeptidases is a structural feature that can be exploited to design inhibitors of bacterial methionine aminopeptidases as therapeutic agents with minimal inhibition of the corresponding human enzymes.

View Article: PubMed Central - HTML - PubMed

Affiliation: High Throughput Screening Laboratory, University of Kansas, Lawrence, Kansas 66047, USA. zeqiang.ma@vanderbilt.edu

ABSTRACT

Background: Methionine aminopeptidase is a potential target of future antibacterial and anticancer drugs. Structural analysis of complexes of the enzyme with its inhibitors provides valuable information for structure-based drug design efforts.

Results: Five new X-ray structures of such enzyme-inhibitor complexes were obtained. Analysis of these and other three similar structures reveals the adaptability of a surface-exposed loop bearing Y62, H63, G64 and Y65 (the YHGY loop) that is an integral part of the substrate and inhibitor binding pocket. This adaptability is important for accommodating inhibitors with variations in size. When compared with the human isozymes, this loop either becomes buried in the human type I enzyme due to an N-terminal extension that covers its position or is replaced by a unique insert in the human type II enzyme.

Conclusion: The adaptability of the YHGY loop in E. coli methionine aminopeptidase, and likely in other bacterial methionine aminopeptidases, enables the enzyme active pocket to accommodate inhibitors of differing size. The differences in this adaptable loop between the bacterial and human methionine aminopeptidases is a structural feature that can be exploited to design inhibitors of bacterial methionine aminopeptidases as therapeutic agents with minimal inhibition of the corresponding human enzymes.

Show MeSH
Binding modes of the inhibitors at the active site of E. coli MetAP. In the stereo views, only five conserved residues that coordinate with Mn(II) ions (D97, D108, H171, E204, E235) and two conserved histdines (H79, H178) are shown. The bound inhibitors are 4 (A), 5 (B), 6 (C), 7 (D), and 8 (E), respectively. The colour scheme is as follows: gray, carbon (protein residues); yellow, carbon (inhibitor); blue, nitrogen; red, oxygen; green, chlorine; and cyan, fluorine. Mn(II) ions are shown as green spheres. SigmaA-weighted Fobs-Fcalc standard omit maps (inhibitor and metal ions were not included in the model for the structure-factor calculation) are shown superimposed on the refined structures as blue meshes contoured at 3.5 standard deviations of the resulting electron density map.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2238726&req=5

Figure 3: Binding modes of the inhibitors at the active site of E. coli MetAP. In the stereo views, only five conserved residues that coordinate with Mn(II) ions (D97, D108, H171, E204, E235) and two conserved histdines (H79, H178) are shown. The bound inhibitors are 4 (A), 5 (B), 6 (C), 7 (D), and 8 (E), respectively. The colour scheme is as follows: gray, carbon (protein residues); yellow, carbon (inhibitor); blue, nitrogen; red, oxygen; green, chlorine; and cyan, fluorine. Mn(II) ions are shown as green spheres. SigmaA-weighted Fobs-Fcalc standard omit maps (inhibitor and metal ions were not included in the model for the structure-factor calculation) are shown superimposed on the refined structures as blue meshes contoured at 3.5 standard deviations of the resulting electron density map.

Mentions: Common features of the Mn(II)-form selective inhibitors 4–8 bound to E. coli MetAP in the five new structures are that all use their carboxylate group to coordinate with the two Mn(II) ions at the dinuclear metal site and all take a non-coplanar or twisted conformation for the two aromatic rings (Fig. 3), consistent with our previously reported structures of E. coli MetAP complexed with 1–3 [17]. The twisted conformation found in all of the Mn(II)-form-selective inhibitors 1–8 is in agreement with the requirement of a hydrophobic ortho-substitution, such as chlorine, on the phenyl ring for inhibitory activity [17,18]. This twisting is usually explained in terms of repulsion between ortho hydrogens or substituents in a planar conformation. The twist angles observed in the MetAP complexes of 1–8 range from the smallest 23.3° for 6 to the largest 52.9° for 4, suggesting that in general, the phenylfuran-based inhibitors dock into the active site in a conformation that may correspond to a minimum-energy solution conformation. This in turn would enhance their binding by decreasing the fraction of binding energy that would be "wasted" to distort the molecule to a less-favorable conformation in the bound state.


Structural analysis of inhibition of E. coli methionine aminopeptidase: implication of loop adaptability in selective inhibition of bacterial enzymes.

Ma ZQ, Xie SX, Huang QQ, Nan FJ, Hurley TD, Ye QZ - BMC Struct. Biol. (2007)

Binding modes of the inhibitors at the active site of E. coli MetAP. In the stereo views, only five conserved residues that coordinate with Mn(II) ions (D97, D108, H171, E204, E235) and two conserved histdines (H79, H178) are shown. The bound inhibitors are 4 (A), 5 (B), 6 (C), 7 (D), and 8 (E), respectively. The colour scheme is as follows: gray, carbon (protein residues); yellow, carbon (inhibitor); blue, nitrogen; red, oxygen; green, chlorine; and cyan, fluorine. Mn(II) ions are shown as green spheres. SigmaA-weighted Fobs-Fcalc standard omit maps (inhibitor and metal ions were not included in the model for the structure-factor calculation) are shown superimposed on the refined structures as blue meshes contoured at 3.5 standard deviations of the resulting electron density map.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238726&req=5

Figure 3: Binding modes of the inhibitors at the active site of E. coli MetAP. In the stereo views, only five conserved residues that coordinate with Mn(II) ions (D97, D108, H171, E204, E235) and two conserved histdines (H79, H178) are shown. The bound inhibitors are 4 (A), 5 (B), 6 (C), 7 (D), and 8 (E), respectively. The colour scheme is as follows: gray, carbon (protein residues); yellow, carbon (inhibitor); blue, nitrogen; red, oxygen; green, chlorine; and cyan, fluorine. Mn(II) ions are shown as green spheres. SigmaA-weighted Fobs-Fcalc standard omit maps (inhibitor and metal ions were not included in the model for the structure-factor calculation) are shown superimposed on the refined structures as blue meshes contoured at 3.5 standard deviations of the resulting electron density map.
Mentions: Common features of the Mn(II)-form selective inhibitors 4–8 bound to E. coli MetAP in the five new structures are that all use their carboxylate group to coordinate with the two Mn(II) ions at the dinuclear metal site and all take a non-coplanar or twisted conformation for the two aromatic rings (Fig. 3), consistent with our previously reported structures of E. coli MetAP complexed with 1–3 [17]. The twisted conformation found in all of the Mn(II)-form-selective inhibitors 1–8 is in agreement with the requirement of a hydrophobic ortho-substitution, such as chlorine, on the phenyl ring for inhibitory activity [17,18]. This twisting is usually explained in terms of repulsion between ortho hydrogens or substituents in a planar conformation. The twist angles observed in the MetAP complexes of 1–8 range from the smallest 23.3° for 6 to the largest 52.9° for 4, suggesting that in general, the phenylfuran-based inhibitors dock into the active site in a conformation that may correspond to a minimum-energy solution conformation. This in turn would enhance their binding by decreasing the fraction of binding energy that would be "wasted" to distort the molecule to a less-favorable conformation in the bound state.

Bottom Line: When compared with the human isozymes, this loop either becomes buried in the human type I enzyme due to an N-terminal extension that covers its position or is replaced by a unique insert in the human type II enzyme.The adaptability of the YHGY loop in E. coli methionine aminopeptidase, and likely in other bacterial methionine aminopeptidases, enables the enzyme active pocket to accommodate inhibitors of differing size.The differences in this adaptable loop between the bacterial and human methionine aminopeptidases is a structural feature that can be exploited to design inhibitors of bacterial methionine aminopeptidases as therapeutic agents with minimal inhibition of the corresponding human enzymes.

View Article: PubMed Central - HTML - PubMed

Affiliation: High Throughput Screening Laboratory, University of Kansas, Lawrence, Kansas 66047, USA. zeqiang.ma@vanderbilt.edu

ABSTRACT

Background: Methionine aminopeptidase is a potential target of future antibacterial and anticancer drugs. Structural analysis of complexes of the enzyme with its inhibitors provides valuable information for structure-based drug design efforts.

Results: Five new X-ray structures of such enzyme-inhibitor complexes were obtained. Analysis of these and other three similar structures reveals the adaptability of a surface-exposed loop bearing Y62, H63, G64 and Y65 (the YHGY loop) that is an integral part of the substrate and inhibitor binding pocket. This adaptability is important for accommodating inhibitors with variations in size. When compared with the human isozymes, this loop either becomes buried in the human type I enzyme due to an N-terminal extension that covers its position or is replaced by a unique insert in the human type II enzyme.

Conclusion: The adaptability of the YHGY loop in E. coli methionine aminopeptidase, and likely in other bacterial methionine aminopeptidases, enables the enzyme active pocket to accommodate inhibitors of differing size. The differences in this adaptable loop between the bacterial and human methionine aminopeptidases is a structural feature that can be exploited to design inhibitors of bacterial methionine aminopeptidases as therapeutic agents with minimal inhibition of the corresponding human enzymes.

Show MeSH