Skip to main content
U.S. flag

An official website of the United States government

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.

Computational study of the inhibitory mechanism of the kinase CDK5 hyperactivity by peptide p5 and derivation of a pharmacophore



Antonio Cardone, Mary C. Brady, Ram D. Sriram, Harish C. Pant, Sergio Hassan


The hyperactivity of the cyclic dependent kinase 5 (CDK5) induced by the activator protein p25 has been linked to a number of pathologies of the brain. The CDK5–p25 complex has thus emerged as a major therapeutic target for Alzheimer’s disease (AD) and other neurodegenerative conditions. Experiments have shown that the peptide p5 reduces the CDK5–p25 activity without affecting the endogenous CDK5–p35 activity, whereas the peptide TFP5, obtained from p5, elicits similar inhibition, crosses the blood–brain barrier, and exhibits behavioral rescue of AD mice models with no toxic side effects. The molecular basis of the kinase inhibition is not currently known, and is here investigated by computer simulations. It is shown that p5 binds the kinase at the same CDK5/p25 and CDK5/p35 interfaces, and is thus a non-selective competitor of both activators, in agreement with available experimental data in vitro. Binding of p5 is enthalpically driven with an affinity estimated in the low micro molar range. A quantitative description of the binding site and pharmacophore is presented, and options are discussed to increase the binding affinity and selectivity in the design of druglike compounds against AD.
Journal of Computer-Aided Molecular Design


CDK5, p5, p25, p35, TFP5, Alzheimer’s disease, beta amyloid, hyperphosphorylation, protein-protein association, computer simulation, molecular dynamics.


Cardone, A. , Brady, M. , Sriram, R. , Pant, H. and Hassan, S. (2016), Computational study of the inhibitory mechanism of the kinase CDK5 hyperactivity by peptide p5 and derivation of a pharmacophore, Journal of Computer-Aided Molecular Design, [online], (Accessed May 20, 2024)


If you have any questions about this publication or are having problems accessing it, please contact

Created July 8, 2016, Updated November 10, 2018