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Insilico design of an allosteric modulator targeting the protein–protein interaction site of 3 Phosphoinositide dependent Kinase-1: design, synthesis and biological activity

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Abstract

The signalling pathways in human cells mostly rely on protein–protein interactions (PPI) for their function. Such a PPI site in 3 Phosphoinositide dependent Kinase-1 (PDK1) is targeted to design the small molecule modulators. Based on the hotspot residues in its PPI site, a pharmacophore with seven different features was developed and screened against 2.9 million lead like compounds in Zinc database. A phthalazine derivative was identified as a potent allosteric inhibitor through virtual screening, molecular docking and 100 ns dynamics simulations. The modified hit possessed hydrogen bonds with Lys115, Arg131, Thr148, Glu150 as well as pi–pi stacking interactions with Phe157 which are the key residues in the PIF pocket of PDK1. Comparison between the free energy profiles by metadynamics simulation with the presence and absence of the modified ligand (MH) in the binding pocket indicates that the binding of MH enhances the hinge motion making PDK1 to adopt open conformation also and stabilizes the fluctuation of the end-to-end distance in αB helix of PDK1. The modified hit compound was synthesized, characterized and found to be cytotoxic to cancerous cells that are rich in PDK1 expression. These results propose that MH can serve as a new scaffold template for the design of novel drugs targeting PDK1 as well as promising allosteric regulator of PDK1 targeting its protein–protein interface.

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Acknowledgements

The Senior Research Associateship from CSIR, Govt. of India by Scientists’ pool scheme is greatly acknowledged by KNV. The cell cytotoxicity assays from ACTREC, Mumbai, India is also acknowledged by the authors.

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Authors and Affiliations

  1. The Gandhigram Rural Institute-Deemed to be University, Dindigul, Tamilnadu, 624302, India

    Vennila Kailasam Natesan & Elango KuppannaGounder Pitchaimuthu

  2. Teadus Pharma Private Limited, Hyderabad, Telangana, 500072, India

    Selvakumar Balaraman

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  1. Vennila Kailasam Natesan
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  2. Selvakumar Balaraman
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  3. Elango KuppannaGounder Pitchaimuthu
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VKN: idea, analysis, manuscript writing SB: synthesis of the compound and characterization, EKP: idea, results and Manuscript evaluation.

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Correspondence to Vennila Kailasam Natesan.

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Kailasam Natesan, V., Balaraman, S. & KuppannaGounder Pitchaimuthu, E. Insilico design of an allosteric modulator targeting the protein–protein interaction site of 3 Phosphoinositide dependent Kinase-1: design, synthesis and biological activity. In Silico Pharmacol. 11, 26 (2023). https://doi.org/10.1007/s40203-023-00160-6

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