Structural insights into the interaction of three Y-shaped ligands with PI3Kα

gmx_RRCS: A Precision Tool for Detecting Subtle Conformational Dynamics in Molecular Simulations

Understanding conformational changes in biomolecules is crucial for insights into their biological functions and drug design, often studied by molecular dynamics (MD) simulations. However, current measurements such as root mean square deviation (RMSD), root mean square fluctuation (RMSF), interface area, and minimum distances fail to capture subtle conformational changes, including hydrophobic packing. Our study introduces gmx_RRCS, a precision tool developed to detect subtle conformational dynamics in MD simulations by analyzing residue-residue contact score (RRCS). This tool quantifies interaction strengths between residues, enabling systematic analysis of both major and subtle conformational changes. Its application in investigating the molecular recognition of peptide 20 by glucagon-like peptide-1 receptor (GLP-1R) quantified the interactions of specific peptide moieties with the receptor, identified crucial positions for receptor binding, and highlighted key receptor residues involved in peptide recognition throughout the MD simulation. In phosphoinositide 3-kinase alpha (PI3Kα), gmx_RRCS revealed distinct conformational states of oncogenic hotspot residues by quantifying subtle sidechain reorientations and salt bridge dynamics. Similarly, in nucleic acid systems, the tool distinguished differential binding mechanisms between ochratoxin A and norfloxacin by revealing unique interaction patterns at critical nucleobases correlating with binding affinities. The tool has been validated through the analysis of over 150 simulation trajectories, covering 40,000 ns of total simulation time and 20 systems. gmx_RRCS significantly advances structural/molecular biology studies by enhancing our understanding of protein conformational dynamics, thereby facilitating rational drug design. gmx_RRCS is freely available on GitHub (https://github.com/RuijinHospitalRCMSB/gmx_RRCS) and PyPI (https://pypi.org/project/gmx-RRCS).

Understanding the conformational dynamics of PI3Kα due to helical domain mutations: insights from Markov state model analysis

Phosphoinositide 3-kinases (PI3Ks) phosphorylate phosphoinositides on the membrane, which act as secondary signals for various cellular processes. PI3Kα, a heterodimer of the p110α catalytic subunit and the p85α regulatory subunit, is activated by growth factor receptors or mutations. Among these mutations, E545K present in the helical domain is strongly associated with cancer, and is known to disrupt interactions between the regulatory and catalytic subunits, leading to its constitutive activation. However, while the mutation's role in disrupting autoinhibition is well documented, the molecular mechanisms linking this mutation in the helical domain to the structural changes in the kinase domain remain poorly understood. This study aims to understand the conformational events triggered by the E545K mutation, elucidate how these changes propagate from the helical domain to the kinase domain, and identify crucial residues involved in the activation process. Molecular dynamics (MD) simulations combined with Markov state modeling (MSM) were employed to explore the conformational landscapes of both the wild-type and mutant systems. Structural and energetic analyses, including Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) calculations, revealed that the E545K mutation significantly reduces the binding affinity between the regulatory and catalytic subunits. The mutation was found to induce a sliding motion of the regulatory subunit along the catalytic subunit, leading to the disruption of key salt-bridges between these domains. This disruption releases the inhibitory effect of the regulatory subunit, resulting in increased domain motion, particularly in the adaptor-binding domain (ABD). Enhanced flexibility in the ABD, helical, and C2 domains facilitates the rearrangement of the two lobes of kinase domain, thereby promoting activation. Additionally, the mutation appears to enhance PI3Kα's membrane affinity via the Ras-binding domain (RBD). Network analysis helped to identify key residues that may involve in allosteric signaling pathways, providing insights into the communication between domains. Druggable pockets in the metastable states were predicted followed by its docking with a PI3K inhibitor library. Docking studies revealed the crucial residues that may be participating in inhibitor binding. The identification of residues and regions involved in activation mechanisms using MSM helped to reveal the conformational events and the knowledge on probable allosteric pockets, which may be helpful in designing better therapeutics.

Molecular Basis of Oncogenic PI3K Proteins

The dysregulation of phosphatidylinositol 3-kinase (PI3K) signaling plays a pivotal role in driving neoplastic transformation by promoting uncontrolled cell survival and proliferation. This oncogenic activity is primarily caused by mutations that are frequently found in PI3K genes and constitutively activate the PI3K signaling pathway. However, tumorigenesis can also arise from nonmutated PI3K proteins adopting unique active conformations, further complicating the understanding of PI3K-driven cancers. Recent structural studies have illuminated the functional divergence among highly homologous PI3K proteins, revealing how subtle structural alterations significantly impact their activity and contribute to tumorigenesis. In this review, we summarize current knowledge of Class I PI3K proteins and aim to unravel the complex mechanism underlying their oncogenic traits. These insights will not only enhance our understanding of PI3K-mediated oncogenesis but also pave the way for the design of novel PI3K-based therapies to combat cancers driven by this signaling pathway.