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Reflection on design and testing of pancreatic alpha-amylase inhibitors: an in silico comparison between rat and rabbit enzyme models.

Khalil-Moghaddam S, Ebrahim-Habibi A, Pasalar P, Yaghmaei P, Hayati-Roodbari N - Daru (2012)

Bottom Line: In order to find compounds that would be effective amylase inhibitors, in vitro and in vivo models are usually used.The overall result is that rabbit enzyme could probably be a better choice in this regard, but in the case of large ligands, which could make putative interactions with the -4 subsite of pancreatic alpha-amylase, interpretation of results should be made cautiously.In the case of alpha-amylase, three-dimensional structures of animal enzymes show differences with the human one which should be taken into account when testing potential new drugs.

View Article: PubMed Central - HTML - PubMed

Affiliation: Biology Department, Science and Research Branch, Islamic Azad University, Tehran, Iran. yaghmaei_p@srbiau.ac.ir.

ABSTRACT

Background: Inhibitors of pancreatic alpha-amylase are potential drugs to treat diabetes and obesity. In order to find compounds that would be effective amylase inhibitors, in vitro and in vivo models are usually used. The accuracy of models is limited, but these tools are nonetheless valuable. In vitro models could be used in large screenings involving thousands of chemicals that are tested to find potential lead compounds. In vivo models are still used as preliminary mean of testing compounds behavior in the whole organism. In the case of alpha-amylase inhibitors, both rats and rabbits could be chosen as in vivo models. The question was which animal could present more accuracy with regard to its pancreatic alpha-amylase.

Results: As there is no crystal structure of these enzymes, a molecular modeling study was done in order to compare the rabbit and rat enzymes with the human one. The overall result is that rabbit enzyme could probably be a better choice in this regard, but in the case of large ligands, which could make putative interactions with the -4 subsite of pancreatic alpha-amylase, interpretation of results should be made cautiously.

Conclusion: Molecular modeling tools could be used to choose the most suitable model enzyme that would help to identify new enzyme inhibitors. In the case of alpha-amylase, three-dimensional structures of animal enzymes show differences with the human one which should be taken into account when testing potential new drugs.

No MeSH data available.


Related in: MedlinePlus

Superimposed backbone structures of human (red ribbons), rabbit (green ribbons), and rat (blue ribbons) pancreatic alpha-amylases. Human structure is obtained from the 3OLI.pdb file, and rabbit and rat enzymes are modeled. The three main domains of the enzymes are indicated (A,B, and C). The two spheres are one calcium (in the left side of the picture, yellow) and one chloride atom (in the center, cyan), which are located in their conserved position among all three enzymes. The arrow indicated the shorter loop of the rat enzymes which lacks residues 143–145 of human and rabbit enzymes.
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Figure 2: Superimposed backbone structures of human (red ribbons), rabbit (green ribbons), and rat (blue ribbons) pancreatic alpha-amylases. Human structure is obtained from the 3OLI.pdb file, and rabbit and rat enzymes are modeled. The three main domains of the enzymes are indicated (A,B, and C). The two spheres are one calcium (in the left side of the picture, yellow) and one chloride atom (in the center, cyan), which are located in their conserved position among all three enzymes. The arrow indicated the shorter loop of the rat enzymes which lacks residues 143–145 of human and rabbit enzymes.

Mentions: The superimposed minimized backbone structures of the three enzymes are shown in Figure 2, where the three domains of the enzymes (A-C) are indicated. Positioning of the calcium and chloride ions are related to the human one, and could be assumed to be similar in RPA and RABPA. The nearby residues interacting with these ions are shown in Figure 3a and b for comparison means and indicate no major difference between the three enzymes, a fact that is a further indication of the biological plausibility of the models. The calcium ion of HPA makes its interactions with the residues of domain B, with the exception of His201 which belongs to Domain A [20]. This ion is considered to be “a central organizing structural feature of Domain B” [24], is needed for alpha-amylase catalytic activity, and its binding pocket is essential to maintain the fold stability [25]. The chloride ion was previously thought to be a feature of mammalian amylase, and shown to possess activating property [26]. In a thorough study to characterize the chloride binding pocket of alpha-amylases, the anion was found to be coordinated by one arginine, one arginine/lysine and an asparagine residue throughout chloride-dependent amylases, with R337 (PPA numbering) being a key feature for the anion binding [27].


Reflection on design and testing of pancreatic alpha-amylase inhibitors: an in silico comparison between rat and rabbit enzyme models.

Khalil-Moghaddam S, Ebrahim-Habibi A, Pasalar P, Yaghmaei P, Hayati-Roodbari N - Daru (2012)

Superimposed backbone structures of human (red ribbons), rabbit (green ribbons), and rat (blue ribbons) pancreatic alpha-amylases. Human structure is obtained from the 3OLI.pdb file, and rabbit and rat enzymes are modeled. The three main domains of the enzymes are indicated (A,B, and C). The two spheres are one calcium (in the left side of the picture, yellow) and one chloride atom (in the center, cyan), which are located in their conserved position among all three enzymes. The arrow indicated the shorter loop of the rat enzymes which lacks residues 143–145 of human and rabbit enzymes.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3584935&req=5

Figure 2: Superimposed backbone structures of human (red ribbons), rabbit (green ribbons), and rat (blue ribbons) pancreatic alpha-amylases. Human structure is obtained from the 3OLI.pdb file, and rabbit and rat enzymes are modeled. The three main domains of the enzymes are indicated (A,B, and C). The two spheres are one calcium (in the left side of the picture, yellow) and one chloride atom (in the center, cyan), which are located in their conserved position among all three enzymes. The arrow indicated the shorter loop of the rat enzymes which lacks residues 143–145 of human and rabbit enzymes.
Mentions: The superimposed minimized backbone structures of the three enzymes are shown in Figure 2, where the three domains of the enzymes (A-C) are indicated. Positioning of the calcium and chloride ions are related to the human one, and could be assumed to be similar in RPA and RABPA. The nearby residues interacting with these ions are shown in Figure 3a and b for comparison means and indicate no major difference between the three enzymes, a fact that is a further indication of the biological plausibility of the models. The calcium ion of HPA makes its interactions with the residues of domain B, with the exception of His201 which belongs to Domain A [20]. This ion is considered to be “a central organizing structural feature of Domain B” [24], is needed for alpha-amylase catalytic activity, and its binding pocket is essential to maintain the fold stability [25]. The chloride ion was previously thought to be a feature of mammalian amylase, and shown to possess activating property [26]. In a thorough study to characterize the chloride binding pocket of alpha-amylases, the anion was found to be coordinated by one arginine, one arginine/lysine and an asparagine residue throughout chloride-dependent amylases, with R337 (PPA numbering) being a key feature for the anion binding [27].

Bottom Line: In order to find compounds that would be effective amylase inhibitors, in vitro and in vivo models are usually used.The overall result is that rabbit enzyme could probably be a better choice in this regard, but in the case of large ligands, which could make putative interactions with the -4 subsite of pancreatic alpha-amylase, interpretation of results should be made cautiously.In the case of alpha-amylase, three-dimensional structures of animal enzymes show differences with the human one which should be taken into account when testing potential new drugs.

View Article: PubMed Central - HTML - PubMed

Affiliation: Biology Department, Science and Research Branch, Islamic Azad University, Tehran, Iran. yaghmaei_p@srbiau.ac.ir.

ABSTRACT

Background: Inhibitors of pancreatic alpha-amylase are potential drugs to treat diabetes and obesity. In order to find compounds that would be effective amylase inhibitors, in vitro and in vivo models are usually used. The accuracy of models is limited, but these tools are nonetheless valuable. In vitro models could be used in large screenings involving thousands of chemicals that are tested to find potential lead compounds. In vivo models are still used as preliminary mean of testing compounds behavior in the whole organism. In the case of alpha-amylase inhibitors, both rats and rabbits could be chosen as in vivo models. The question was which animal could present more accuracy with regard to its pancreatic alpha-amylase.

Results: As there is no crystal structure of these enzymes, a molecular modeling study was done in order to compare the rabbit and rat enzymes with the human one. The overall result is that rabbit enzyme could probably be a better choice in this regard, but in the case of large ligands, which could make putative interactions with the -4 subsite of pancreatic alpha-amylase, interpretation of results should be made cautiously.

Conclusion: Molecular modeling tools could be used to choose the most suitable model enzyme that would help to identify new enzyme inhibitors. In the case of alpha-amylase, three-dimensional structures of animal enzymes show differences with the human one which should be taken into account when testing potential new drugs.

No MeSH data available.


Related in: MedlinePlus