Somatic mutations in PI3Kα: Structural basis for enzyme activation and drug design

Gabelli, Sandra B.; Mandelker, Diana; Schmidt‐Kittler, Oleg; Vogelstein, Bert; Amzel, L. Mario

doi:10.1016/j.bbapap.2009.11.020

Cited by 19 publications

(16 citation statements)

References 53 publications

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“…In all crystal structures described thus far, the activation loop is disordered and not able to be seen, suggesting that the loop is flexible or disordered. Gabelli et al (2010), in their p110␣ structures comparing unliganded enzyme with enzyme bound to wortmannin, noted that the loop containing amino acids 772 to 776 (within region 2) changes conformation. Their modeling studies suggested that this loop was in the binding site for PIP 2 and that this mode of binding correctly positioned the lipid for phosphoryl transfer from ATP.…”

Section: Discussionmentioning

confidence: 99%

Isoform-Selective Inhibition of Phosphoinositide 3-Kinase: Identification of a New Region of Nonconserved Amino Acids Critical for p110α Inhibition

et al. 2011

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The combination of molecular modeling and X-ray crystallography has failed to yield a consensus model of the mechanism for selective binding of inhibitors to the phosphoinositide 3-kinase (PI3K) p110 ␣-isoform. Here we have used kinetic analysis to determine that the p110␣-selective inhibitor 2-methyl-5-nitro-2-[(6-bromoimidazo[1,2-␣]pyridin-3-yl)methylene]-1-methylhydrazide-benzenesulfonic acid (PIK-75) is a competitive inhibitor with respect to a substrate, phosphatidylinositol (PI) in contrast to most other PI3K inhibitors, which bind at or near the ATP site. Using sequence analysis and the existing crystal structures of inhibitor complexes with the p110␥ and -␦ isoforms, we have identified a new region of nonconserved amino acids (region 2) that was postulated to be involved in PIK-75 p110␣ selectivity. Analysis of region 2, using in vitro mutation of identified nonconserved amino acids to alanine, showed that Ser773 was a critical amino acid involved in PIK-75 binding, with an 8-fold-increase in the IC 50 compared with wild-type. Kinetic analysis showed that, with respect to PI, the PIK-75 K i for the isoform mutant S773D increased 64-fold compared with wild-type enzyme. In addition, a nonconserved amino acid, His855, from the previously identified region 1 of nonconserved amino acids, was found to be involved in PIK-75 binding. These results show that these two regions of nonconserved amino acids that are close to the substrate binding site could be targeted to produce p110␣ isoformselective inhibitors.

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Section: Discussionmentioning

confidence: 99%

Isoform-Selective Inhibition of Phosphoinositide 3-Kinase: Identification of a New Region of Nonconserved Amino Acids Critical for p110α Inhibition

et al. 2011

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“…Currently, several PI3K inhibitors are under development as possible cancer therapeutic agents . However, as different PI3K isoforms have different biological functions, an effective PI3K inhibitor has to be isoform‐selective to avoid side effects . Furthermore, depending on the activation mechanism of the associated oncogenic mutation, it may be necessary to design mutant‐specific inhibitors.…”

Section: Introductionmentioning

confidence: 99%

Oncogenic mutations weaken the interactions that stabilize the p110α‐p85α heterodimer in phosphatidylinositol 3‐kinase α

et al. 2015

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Phosphatidylinositol 3-kinase α (PI3Kα) is a heterodimeric lipid kinase that catalyzes the conversion of phosphoinositide-4,5-bisphosphate (PIP2) to phosphoinositide-3,4,5-trisphosphate (PIP3). The PI3Kα signaling pathway plays an important role in cell growth, proliferation and survival. This pathway is activated in numerous cancers, where the PI3KCA gene, which encodes for the p110α PI3Kα subunit, is mutated. Its mutation often results in gain of enzymatic activity; however, the mechanism of activation by oncogenic mutations remains unknown. Here, using computational methods, we show that oncogenic mutations that are far from the catalytic site and increase the enzymatic affinity, destabilize the p110α/p85α dimer. By affecting the dynamics of the protein, these mutations favor the conformations that reduce the autoinhibitory effect of the p85α nSH2 domain. For example, we determined that in all the mutants, the nSH2 domain exhibits increased positional heterogeneity compared to the wild type (WT), as evidenced by changes in the fluctuation profiles computed by normal mode analysis (NMA) of coarse-grained elastic network models (ENM). Analysis of the inter-domain interactions of the WT and mutants at the p110α/p85α interface obtained using molecular dynamics (MD) simulations suggest that all the tumor-associated mutations effectively weaken the interactions between the p110α and the p85α subunits by disrupting key stabilizing interactions. These findings have important implications for understanding how oncogenic mutations change the conformational multiplicity of PI3Kα and lead to increased enzymatic activity. This mechanism may apply to other enzymes and/or macromolecular complexes that play a key role in cell signaling.

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“…Subclass IA kinases are heterodimers composed of two subunits, a catalytic p110 subunit and a regulatory p85 subunit. The three PI3K isoforms (PI3Kα, PI3Kβ, and PI3Kδ) contain different p110 sequences (p110α, p110β, and p110δ) (Gabelli et al 2010). …”

Section: Introductionmentioning

confidence: 99%

Activation of PI3Kα by physiological effectors and by oncogenic mutations: structural and dynamic effects

et al. 2014

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PI3Kα, a heterodimeric lipid kinase, catalyzes the conversion of phosphoinositide-4,5-bisphosphate (PIP2) to phosphoinositide-3,4,5-trisphosphate (PIP3), a lipid that recruits to the plasma membrane proteins that regulate signaling cascades that control key cellular processes such as cell proliferation, carbohydrate metabolism, cell motility, and apoptosis. PI3Kα is composed of two subunits, p110α and p85, that are activated by binding to phosphorylated receptor tyrosine kinases (RTKs) or their substrates. The gene coding for p110α, PIK3CA, has been found to be mutated in a large number of tumors; these mutations result in increased PI3Kα kinase activity. The structure of the complex of p110α with a fragment of p85 containing the nSH2 and the iSH2 domains has provided valuable information about the mechanisms underlying the physiological activation of PI3Kα and its pathological activation by oncogenic mutations. This review discusses information derived from x-ray diffraction and theoretical calculations regarding the structural and dynamic effects of mutations in four highly mutated regions of PI3K p110α, as well as the proposed mechanisms by which these mutations increase kinase activity. During the physiological activation of PI3Kα, the phosphorylated tyrosine of RTKs binds to the nSH2 domain of p85, dislodging an inhibitory interaction between the p85 nSH2 and a loop of the helical domain of p110α. Several of the oncogenic mutations in p110α activate the enzyme by weakening this autoinhibitory interaction. These effects involve structural changes as well as changes in the dynamics of the enzyme. One of the most common p110α mutations, H1047R, activates PI3Kα by a different mechanism: it increases the interaction of the enzyme with the membrane, maximizing the access of the PI3Kα to its substrate PIP2, a membrane lipid.

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Somatic mutations in PI3Kα: Structural basis for enzyme activation and drug design

Cited by 19 publications

References 53 publications

Isoform-Selective Inhibition of Phosphoinositide 3-Kinase: Identification of a New Region of Nonconserved Amino Acids Critical for p110α Inhibition

Isoform-Selective Inhibition of Phosphoinositide 3-Kinase: Identification of a New Region of Nonconserved Amino Acids Critical for p110α Inhibition

Oncogenic mutations weaken the interactions that stabilize the p110α‐p85α heterodimer in phosphatidylinositol 3‐kinase α

Activation of PI3Kα by physiological effectors and by oncogenic mutations: structural and dynamic effects

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