Title: Structure-based design of allosteric calpain-1 inhibitors populating a novel bioactivity space


Citation
Kalash L, Cresser-Brown J, Habchi J, et al. (2018). Structure-based design of allosteric calpain-1 inhibitors populating a novel bioactivity space. Cardiff University. http://doi.org/10.17035/d.2018.0061359778



Access Rights: Data can be made freely available subject to attribution

Access Method: Click to email a request for this data to opendata@cardiff.ac.uk


Cardiff University Dataset Creators


Dataset Details

Publisher: Cardiff University

Date (year) of data becoming publicly available: 2018

Coverage start date: 04/09/2017

Coverage end date: 30/03/2018

Data format: .pdf, .docx, .xls

Estimated total storage size of dataset: Less than 1 gigabyte

Number of Files In Dataset: 30

DOI : 10.17035/d.2018.0061359778

DOI URL: http://doi.org/10.17035/d.2018.0061359778

Related URL: https://www.ncbi.nlm.nih.gov/pubmed/30195237


Description

Dimeric calpains constitute a promising therapeutic target for many diseases such as cardiovascular, neurodegenerative and ischaemic disease. The discovery of selective calpain inhibitors, however, has been extremely challenging. Previously, allosteric inhibitors of calpains, such as PD150606, which included a specific α-mercaptoacrylic acid sub-structure, were reported to bind to the penta-EF hand calcium binding domain, PEF(S) of calpain. Although these are selective to calpains over other cysteine proteases, their mode of action has remained elusive due to their ability to inhibit the active site domain with and without the presence of PEF(S), with similar potency. These findings have led to the question of whether the inhibitory response can be attributed to an allosteric mode of action or alternatively to inhibition at the active site. In order to address this problem, we studied a structure-based virtual screening protocol as a novel approach for the discovery of PEF(S) binders that populate a novel chemical space. We have identified compound 1, Vidupiprant, which is shown to bind to the PEF(S) domain by the TNS displacement method, and it exhibited specificity in its allosteric mode of inhibition. Compound 1 inhibited the full-length calpain-1 complex with a higher potency (IC50 = 7.5 μM) than the selective, cell-permeable non-peptide calpain inhibitor, PD150606 (IC50 = 19.3 μM), where the latter also inhibited the active site domain in the absence of PEF(S) (IC50 = 17.8 μM). Hence the method has identified known compounds with a novel allosteric mechanism for the inhibition of calpain-1. We show for the first time that the inhibition of enzyme activity can be attributed to an allosteric mode of action, which may offer improved selectivity and a reduced side-effects profile.

This dataset includes:

IC50 measurements for computationally designed compounds on calpain-1 using a fluorgenic substrate as an indicator of enzyme activity.

IC50 measurements for computationally designed compounds on the active site of calpain-1 using a fluorgenic substrate as an indicator of enzyme activity.

Fluorescence displacement assay results to indicate whether compounds bind to an allosteric site by displacement of a fluorescent probe from the protein to the aqueous environment.

Research results based upon these data are published at https://doi.org/10.1016/j.ejmech.2018.08.049


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Last updated on 2018-05-11 at 12:35