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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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Electrostatic potential. Two-dimensional histograms comparing structural conservation and electrostatic potential for pocket clusters of the different families in the data set. The panels on the left display the values for pocket clusters 1 to 3 of 1,128 distinct protein families and the right panels show the distribution for clusters containing the majority of active sites for 229 protein families. These plots only include protein families with at least five representative structures.
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Figure 4: Electrostatic potential. Two-dimensional histograms comparing structural conservation and electrostatic potential for pocket clusters of the different families in the data set. The panels on the left display the values for pocket clusters 1 to 3 of 1,128 distinct protein families and the right panels show the distribution for clusters containing the majority of active sites for 229 protein families. These plots only include protein families with at least five representative structures.

Mentions: The electrostatic potential, as estimated by solving the Poisson-Boltzmann equation for protein structures with force-field-based charge distributions [35] has been previously used to characterize and predict enzymatic active sites [24]. For each pocket in the data set we estimated the electrostatic potential at the pocket's center of mass as described in the Methods section and computed the average value over the pockets for each of the first three pocket clusters in every protein family. The combined distribution of average electrostatic potential and structural conservation of pocket clusters is shown in Figure 4. Clearly, this property does not correlate either with structural conservation. Most values cluster between -5 and 2.5 kT/e, even for active site pockets. However, this measure is probably the least conserved across the different pockets of a given cluster. In fact, for 42.4% of the pocket clusters included in the left panel of Figure 4, the standard deviation is larger than the average absolute value. It appears that the pocket's electrostatic potential, as estimated here, is largely protein specific, and that this measure is hard to extrapolate across the different proteins in a family. Nevertheless, the values of electrostatic potential can still be used in refining the selection of pockets for drug-screening procedures, given that drug-like ligands may be easier to find for more neutral sites than for strongly charged or polarized pockets [2]. These values could also be used to distinguish putative active sites from allosteric sites in the lack of proper annotation (see PIG-L below).


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)

Electrostatic potential. Two-dimensional histograms comparing structural conservation and electrostatic potential for pocket clusters of the different families in the data set. The panels on the left display the values for pocket clusters 1 to 3 of 1,128 distinct protein families and the right panels show the distribution for clusters containing the majority of active sites for 229 protein families. These plots only include protein families with at least five representative structures.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Electrostatic potential. Two-dimensional histograms comparing structural conservation and electrostatic potential for pocket clusters of the different families in the data set. The panels on the left display the values for pocket clusters 1 to 3 of 1,128 distinct protein families and the right panels show the distribution for clusters containing the majority of active sites for 229 protein families. These plots only include protein families with at least five representative structures.
Mentions: The electrostatic potential, as estimated by solving the Poisson-Boltzmann equation for protein structures with force-field-based charge distributions [35] has been previously used to characterize and predict enzymatic active sites [24]. For each pocket in the data set we estimated the electrostatic potential at the pocket's center of mass as described in the Methods section and computed the average value over the pockets for each of the first three pocket clusters in every protein family. The combined distribution of average electrostatic potential and structural conservation of pocket clusters is shown in Figure 4. Clearly, this property does not correlate either with structural conservation. Most values cluster between -5 and 2.5 kT/e, even for active site pockets. However, this measure is probably the least conserved across the different pockets of a given cluster. In fact, for 42.4% of the pocket clusters included in the left panel of Figure 4, the standard deviation is larger than the average absolute value. It appears that the pocket's electrostatic potential, as estimated here, is largely protein specific, and that this measure is hard to extrapolate across the different proteins in a family. Nevertheless, the values of electrostatic potential can still be used in refining the selection of pockets for drug-screening procedures, given that drug-like ligands may be easier to find for more neutral sites than for strongly charged or polarized pockets [2]. These values could also be used to distinguish putative active sites from allosteric sites in the lack of proper annotation (see PIG-L below).

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