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Assessing the structural conservation of protein pockets to study functional and allosteric sites: implications for drug discovery.

Panjkovich A, Daura X - BMC Struct. Biol. (2010)

Bottom Line: Although these different measures do not tend to correlate, their combination is useful in selecting functional and regulatory sites, as a detailed analysis of a handful of protein families shows.Our results show that structurally conserved pockets are a common feature of protein families.The structural conservation of protein pockets, combined with other characteristics, can be exploited in drug discovery procedures, in particular for the selection of the most appropriate target protein and pocket for the design of drugs against entire protein families or subfamilies (e.g. for the development of broad-spectrum antimicrobials) or against a specific protein (e.g. in attempting to reduce side effects).

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Biotechnology and Biomedicine (IBB), Universitat Autònoma de Barcelona (UAB), Bellaterra, E-08193, Spain.

ABSTRACT

Background: With the classical, active-site oriented drug-development approach reaching its limits, protein ligand-binding sites in general and allosteric sites in particular are increasingly attracting the interest of medicinal chemists in the search for new types of targets and strategies to drug development. Given that allostery represents one of the most common and powerful means to regulate protein function, the traditional drug discovery approach of targeting active sites can be extended by targeting allosteric or regulatory protein pockets that may allow the discovery of not only novel drug-like inhibitors, but activators as well. The wealth of available protein structural data can be exploited to further increase our understanding of allosterism, which in turn may have therapeutic applications. A first step in this direction is to identify and characterize putative effector sites that may be present in already available structural data.

Results: We performed a large-scale study of protein cavities as potential allosteric and functional sites, by integrating publicly available information on protein sequences, structures and active sites for more than a thousand protein families. By identifying common pockets across different structures of the same protein family we developed a method to measure the pocket's structural conservation. The method was first parameterized using known active sites. We characterized the predicted pockets in terms of sequence and structural conservation, backbone flexibility and electrostatic potential. Although these different measures do not tend to correlate, their combination is useful in selecting functional and regulatory sites, as a detailed analysis of a handful of protein families shows. We finally estimated the numbers of potential allosteric or regulatory pockets that may be present in the data set, finding that pockets with putative functional and effector characteristics are widespread across protein families.

Conclusions: Our results show that structurally conserved pockets are a common feature of protein families. The structural conservation of protein pockets, combined with other characteristics, can be exploited in drug discovery procedures, in particular for the selection of the most appropriate target protein and pocket for the design of drugs against entire protein families or subfamilies (e.g. for the development of broad-spectrum antimicrobials) or against a specific protein (e.g. in attempting to reduce side effects).

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Structural conservation. Histograms displaying protein family coverage of different pocket clusters, for a total of 1,128 protein families with five or more representatives in the data set.
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Figure 1: Structural conservation. Histograms displaying protein family coverage of different pocket clusters, for a total of 1,128 protein families with five or more representatives in the data set.

Mentions: After parameterizing the clustering method using active sites as reference, we applied it to all protein families having at least 5 representative structures in the data set (a total of 1,128 protein families satisfied this requisite). We then analyzed the resulting clusters of pockets in terms of the percentage of representative structures covered by each cluster. A very well conserved pocket would be expected to appear in all representative structures of the protein family, i.e. 100% coverage. Thus, this coverage can be taken (and will be taken throughout this study) as a measure of the pocket's structural conservation within the protein family. This analysis was performed, for each family, for the first three clusters and for the cluster containing the largest amount of active sites (active-site cluster). The results are illustrated in Figure 1. Note that cluster ranking is based on average pocket size and coverage as described in the Methods, and that the active site cluster overlaps with the 1st, 2nd and 3rd clusters in 117, 38 and 13 families, respectively.


Assessing the structural conservation of protein pockets to study functional and allosteric sites: implications for drug discovery.

Panjkovich A, Daura X - BMC Struct. Biol. (2010)

Structural conservation. Histograms displaying protein family coverage of different pocket clusters, for a total of 1,128 protein families with five or more representatives in the data set.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2864279&req=5

Figure 1: Structural conservation. Histograms displaying protein family coverage of different pocket clusters, for a total of 1,128 protein families with five or more representatives in the data set.
Mentions: After parameterizing the clustering method using active sites as reference, we applied it to all protein families having at least 5 representative structures in the data set (a total of 1,128 protein families satisfied this requisite). We then analyzed the resulting clusters of pockets in terms of the percentage of representative structures covered by each cluster. A very well conserved pocket would be expected to appear in all representative structures of the protein family, i.e. 100% coverage. Thus, this coverage can be taken (and will be taken throughout this study) as a measure of the pocket's structural conservation within the protein family. This analysis was performed, for each family, for the first three clusters and for the cluster containing the largest amount of active sites (active-site cluster). The results are illustrated in Figure 1. Note that cluster ranking is based on average pocket size and coverage as described in the Methods, and that the active site cluster overlaps with the 1st, 2nd and 3rd clusters in 117, 38 and 13 families, respectively.

Bottom Line: Although these different measures do not tend to correlate, their combination is useful in selecting functional and regulatory sites, as a detailed analysis of a handful of protein families shows.Our results show that structurally conserved pockets are a common feature of protein families.The structural conservation of protein pockets, combined with other characteristics, can be exploited in drug discovery procedures, in particular for the selection of the most appropriate target protein and pocket for the design of drugs against entire protein families or subfamilies (e.g. for the development of broad-spectrum antimicrobials) or against a specific protein (e.g. in attempting to reduce side effects).

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Biotechnology and Biomedicine (IBB), Universitat Autònoma de Barcelona (UAB), Bellaterra, E-08193, Spain.

ABSTRACT

Background: With the classical, active-site oriented drug-development approach reaching its limits, protein ligand-binding sites in general and allosteric sites in particular are increasingly attracting the interest of medicinal chemists in the search for new types of targets and strategies to drug development. Given that allostery represents one of the most common and powerful means to regulate protein function, the traditional drug discovery approach of targeting active sites can be extended by targeting allosteric or regulatory protein pockets that may allow the discovery of not only novel drug-like inhibitors, but activators as well. The wealth of available protein structural data can be exploited to further increase our understanding of allosterism, which in turn may have therapeutic applications. A first step in this direction is to identify and characterize putative effector sites that may be present in already available structural data.

Results: We performed a large-scale study of protein cavities as potential allosteric and functional sites, by integrating publicly available information on protein sequences, structures and active sites for more than a thousand protein families. By identifying common pockets across different structures of the same protein family we developed a method to measure the pocket's structural conservation. The method was first parameterized using known active sites. We characterized the predicted pockets in terms of sequence and structural conservation, backbone flexibility and electrostatic potential. Although these different measures do not tend to correlate, their combination is useful in selecting functional and regulatory sites, as a detailed analysis of a handful of protein families shows. We finally estimated the numbers of potential allosteric or regulatory pockets that may be present in the data set, finding that pockets with putative functional and effector characteristics are widespread across protein families.

Conclusions: Our results show that structurally conserved pockets are a common feature of protein families. The structural conservation of protein pockets, combined with other characteristics, can be exploited in drug discovery procedures, in particular for the selection of the most appropriate target protein and pocket for the design of drugs against entire protein families or subfamilies (e.g. for the development of broad-spectrum antimicrobials) or against a specific protein (e.g. in attempting to reduce side effects).

Show MeSH
Related in: MedlinePlus