2,4-Diaminopyrimidine MK2 inhibitors. Part I: Observation of an unexpected inhibitor binding mode

ABSTRACTSelectivity remains a challenge for ATP-mimetic kinase inhibitors, an issue that may be overcome by targeting unique residues or binding pockets. However, to date only few strategies have been developed. Here we identify that bulky residues located N-terminal to the DFG motif (DFG-1) represent an opportunity for designing highly selective inhibitors with unexpected binding modes. We demonstrate that several diverse inhibitors exerted selective, non-canonical binding modes that exclusively target large hydrophobic DFG-1 residues present in many kinases including PIM, CK1, DAPK and CLK. Using the CLK family as a model, structural and biochemical data revealed that the DFG-1 valine controlled a non-canonical binding mode in CLK1, providing a rational for selectivity over the closely-related CLK3 which harbors a smaller DFG-1 alanine. Our data suggests that targeting the restricted back pocket in the small fraction of kinases that harbor bulky DFG-1 residues offers a versatile selectivity filter for inhibitor design.

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Tn5 transposase as a useful platform to simulate HIV-1 integrase inhibitor binding mode

Biochemical and Biophysical Research Communications ◽

10.1016/j.bbrc.2007.08.199 ◽

2007 ◽

Vol 363 (3) ◽

pp. 554-560 ◽

Cited By ~ 13

Author(s):

Maria Letizia Barreca ◽

Francesco Ortuso ◽

Nunzio Iraci ◽

Laura De Luca ◽

Stefano Alcaro ◽

...

Keyword(s):

Integrase Inhibitor ◽

Binding Mode ◽

Inhibitor Binding ◽

Tn5 Transposase ◽

Hiv 1

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Escherichia coliTopoisomerase IV E Subunit and an Inhibitor Binding Mode Revealed by NMR Spectroscopy

Journal of Biological Chemistry ◽

10.1074/jbc.m116.737429 ◽

2016 ◽

Vol 291 (34) ◽

pp. 17743-17753 ◽

Cited By ~ 9

Author(s):

Yan Li ◽

Ying Lei Wong ◽

Fui Mee Ng ◽

Boping Liu ◽

Yun Xuan Wong ◽

...

Keyword(s):

Nmr Spectroscopy ◽

Binding Mode ◽

Inhibitor Binding

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Structural basis of main proteases of coronavirus bound to drug candidate PF-07321332

10.1101/2021.11.05.467529 ◽

2021 ◽

Author(s):

Jian Li ◽

Cheng Lin ◽

Xuelan Zhou ◽

Fanglin Zhong ◽

Pei Zeng ◽

...

Keyword(s):

Binding Site ◽

Binding Sites ◽

Binding Mode ◽

Structural Basis ◽

Drug Candidate ◽

Structural Determinants ◽

Inhibitor Binding ◽

Mechanism Of Inhibition ◽

Main Protease ◽

Multiple Variants

The high mutation rate of COVID-19 and the prevalence of multiple variants strongly support the need for pharmacological options to complement vaccine strategies. One region that appears highly conserved among different genus of coronaviruses is the substrate binding site of the main protease (Mpro or 3CLpro), making it an attractive target for the development of broad-spectrum drugs for multiple coronaviruses. PF-07321332 developed by Pfizer is the first orally administered inhibitor targeting the main protease of SARS-CoV-2, which also has shown potency against other coronaviruses. Here we report three crystal structures of main protease of SARS-CoV-2, SARS-CoV and MERS-CoV bound to the inhibitor PF-07321332. The structures reveal a ligand-binding site that is conserved among SARS-CoV-2, SARS-CoV and MERS-CoV, providing insights into the mechanism of inhibition of viral replication. The long and narrow cavity in the cleft between domains I and II of main protease harbors multiple inhibitor binding sites, where PF-07321332 occupies subsites S1, S2 and S4 and appears more restricted compared with other inhibitors. A detailed analysis of these structures illuminated key structural determinants essential for inhibition and elucidated the binding mode of action of main proteases from different coronaviruses. Given the importance of main protease for the treatment of SARS-CoV-2 infection, insights derived from this study should accelerate the design of safer and more effective antivirals.

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Inhibitor Binding Mode Differences Within the AGC Subfamily

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s2053273314083594 ◽

2014 ◽

Vol 70 (a1) ◽

pp. C1640-C1640

Author(s):

Silvia Delker ◽

Dale Robinson ◽

Sami Bahmanyar ◽

Barbra Pagarigan ◽

Wei Fang ◽

...

Keyword(s):

Drug Targets ◽

Kinase Inhibitors ◽

Catalytic Domain ◽

Binding Mode ◽

Binding Modes ◽

Inhibitor Binding ◽

Specific Sequence ◽

Activity Spectrum ◽

Ribosomal S6 Kinase ◽

High Level

Designing potent selective kinase inhibitors is an ongoing challenge due to the high level of homology within the protein kinome. The AGC family comprises ~12% of the kinome and includes many important drug targets. We compared the binding mode of two inhibitors within the catalytic domain of a set of AGC kinase family members: PKC related kinase (PRK), p90 ribosomal s6 kinase N terminal domain (RSKn), and protein kinase A (PKA). We observed that even within the closely related AGC kinase subfamily, the two ligands can bind in alternate orientations. Alternative binding modes can be attributed to specific sequence variations and structural differences, however the observation of multiple inhibitor binding modes within a subfamily highlights the difficulties in predicting the activity spectrum of kinase inhibitors. The crystal structures described herein may help in the design of potent, selective kinase inhibitors to these or related kinases.

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