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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

Results of the ClustalW [[13]] alignment for the pancreatic alpha-amylase amino acid sequences of human, rabbit (Oryctolagus cuniculus), and rat (Rattus norvegicus) enzymes. Conserved regions are shown with asterisk. Colour codes of amino acids are as follows: residues A,V,F,P,M,I,L, and W (small + hydrophobic (incl.aromatic -Y))in red, residues Dand E (acidic) in blue, residues R and K (basic) in magenta, residues S,T,Y,H,C,N,G, and Q (Hydroxyl + sulfhydryl + amine + G) in green.
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Figure 1: Results of the ClustalW [[13]] alignment for the pancreatic alpha-amylase amino acid sequences of human, rabbit (Oryctolagus cuniculus), and rat (Rattus norvegicus) enzymes. Conserved regions are shown with asterisk. Colour codes of amino acids are as follows: residues A,V,F,P,M,I,L, and W (small + hydrophobic (incl.aromatic -Y))in red, residues Dand E (acidic) in blue, residues R and K (basic) in magenta, residues S,T,Y,H,C,N,G, and Q (Hydroxyl + sulfhydryl + amine + G) in green.

Mentions: The first stage in the process of choosing the more suitable model between rat (RPA) and rabbit (RABPA) enzymes is the comparison of their amino acid sequences with the human one (HPA). Figure 1 shows the result of a multiple alignment between the three sequences. A pairwise alignment performed with BLAST reveals that the rat and human enzyme have 84% identities and 92% similarity. For the rabbit enzyme these figures become 87% and 92% respectively. However, beside the higher identities of the rabbit and human enzyme, it is interesting to notice the presence of a gap in the rat sequence, which is located at the position of amino acids 143–145 of HPA and RABPA. This gap makes the rat alpha-amylase 3 residues shorter than the human and rabbit one. The same gap is seen in the mouse sequence. This sequence is TGS in HPA and SGS in RABPA, which could be estimated to be conserved between human and rabbit enzymes. The TGS sequence is also detected in primates (e.g. Macaca mulatta, Gorilla gorilla), Equus caballus, Bos taurus, Canis familiaris, Taeniopygia guttata, monodelphis domestica, Danio rerio, Myxocyprinus asiaticus, and Xenopus tropicalis; as TAS in Sus scrofa, Meleagris gallopavo, and Gallus gallus, and as TYS in Anolis carolinensis.


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)

Results of the ClustalW [[13]] alignment for the pancreatic alpha-amylase amino acid sequences of human, rabbit (Oryctolagus cuniculus), and rat (Rattus norvegicus) enzymes. Conserved regions are shown with asterisk. Colour codes of amino acids are as follows: residues A,V,F,P,M,I,L, and W (small + hydrophobic (incl.aromatic -Y))in red, residues Dand E (acidic) in blue, residues R and K (basic) in magenta, residues S,T,Y,H,C,N,G, and Q (Hydroxyl + sulfhydryl + amine + G) in green.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Results of the ClustalW [[13]] alignment for the pancreatic alpha-amylase amino acid sequences of human, rabbit (Oryctolagus cuniculus), and rat (Rattus norvegicus) enzymes. Conserved regions are shown with asterisk. Colour codes of amino acids are as follows: residues A,V,F,P,M,I,L, and W (small + hydrophobic (incl.aromatic -Y))in red, residues Dand E (acidic) in blue, residues R and K (basic) in magenta, residues S,T,Y,H,C,N,G, and Q (Hydroxyl + sulfhydryl + amine + G) in green.
Mentions: The first stage in the process of choosing the more suitable model between rat (RPA) and rabbit (RABPA) enzymes is the comparison of their amino acid sequences with the human one (HPA). Figure 1 shows the result of a multiple alignment between the three sequences. A pairwise alignment performed with BLAST reveals that the rat and human enzyme have 84% identities and 92% similarity. For the rabbit enzyme these figures become 87% and 92% respectively. However, beside the higher identities of the rabbit and human enzyme, it is interesting to notice the presence of a gap in the rat sequence, which is located at the position of amino acids 143–145 of HPA and RABPA. This gap makes the rat alpha-amylase 3 residues shorter than the human and rabbit one. The same gap is seen in the mouse sequence. This sequence is TGS in HPA and SGS in RABPA, which could be estimated to be conserved between human and rabbit enzymes. The TGS sequence is also detected in primates (e.g. Macaca mulatta, Gorilla gorilla), Equus caballus, Bos taurus, Canis familiaris, Taeniopygia guttata, monodelphis domestica, Danio rerio, Myxocyprinus asiaticus, and Xenopus tropicalis; as TAS in Sus scrofa, Meleagris gallopavo, and Gallus gallus, and as TYS in Anolis carolinensis.

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