Biology subjects

Maria Solano, M. A.

Publications and source records attributed to Maria Solano, M. A..

3 recordsLinked to original sources

bioRxiv2024

IN SILICO DESIGN AND BINDING MECHANISM OF E3 LIGASE UBR1 RECRUITERS

Proteolysis Targeting Chimeric Molecules (PROTACs) represent a promising avenue in drug discovery, as they can induce the targeted degradation of disease-relevant proteins within the cellular machinery. These compounds comprise a ligand tailored to bind the specific targeted protein connected to a recruiter molecule that engages with the E3 ligase. Despite their promise as therapeutic agents, their clinical advancement has encountered substantial challenges, primarily due to the limited availability of suitable E3 ligases. Additionally, cell permeability and proteolytic stability due to their peptide nature often hamper their application. In this study, we focus on the development of recruiters for the E3 ligase UBR1. This widely expressed protein has recently been demonstrated to be efficient in driving the degradation of oncogenic proteins. Our computational approach leverages a fragment-based peptidomimetics strategy, integrating pharmacophore filtering, docking, and fragment-linking optimization. Finally, we subject the wild-type peptide and the most promising combined fragments to advanced binding free energy calculations, unveiling insights into their dynamic water-mediated binding mechanisms and their potential as robust E3 ligase UBR1 recruiters, ultimately leading to the identification of promising compounds. This computational workflow is readily applicable to the development of related PROTACs and also to model protein-protein interactions with similar characteristics.

biophysics↗

bioRxiv2023

Structural insights into ion conduction by novel cation channel, TMEM87A, in Golgi apparatus

TMEM87 family is evolutionarily conserved eukaryotic transmembrane proteins residing in the Golgi1. TMEM87 members play a role in retrograde transport in Golgi and are also proposed mechanosensitive ion channel implicated in cancer and heart disease2-7. In an accompanying study, TMEM87A is described as a voltage-gated, pH-sensitive, non-selective cation channel whose genetic ablation in mice disrupts Golgi morphology, alters glycosylation and protein trafficking, and impairs hippocampal memory. Despite the pivotal functions of TMEM87s in Golgi, underlying molecular mechanisms of channel gating and ion conduction have remained unknown. Here, we present a high-resolution cryo-electron microscopy structure of human TMEM87A (hTMEM87A). Compared with typical ion channels, the architecture of hTMEM87A is unique: a monomeric cation channel consisting of a globular extracellular/luminal domain and a seven-transmembrane domain (TMD) with close structural homology to channelrhodopsin. The central cavity within TMD is occupied by endogenous phosphatidylethanolamine, which seals a lateral gap between two TMs exposed to the lipid bilayer. By combining electrophysiology and molecular dynamics analysis, we identify a funnel-shaped electro-negative luminal vestibule that effectively attracts cations, and phosphatidylethanolamine occludes ion conduction. Our findings suggest that a conformational switch of highly conserved positively-charged residues on TM3 and displacement of phosphatidylethanolamine are opening mechanisms for hTMEM87A, providing an unprecedented insight into the molecular basis for voltage-gated ion conduction in Golgi.

biophysics↗

bioRxiv2022

Dynamic allosteric networks drive adenosine A1 receptor activation and G-protein coupling

G-protein coupled receptors (GPCRs) present specific activation pathways and signaling among receptor subtypes. Hence, an extensive knowledge of the structural dynamics of the receptor is critical for the development of therapeutics. Here, we target the adenosine A1 receptor (A1R), for which a negligible number of drugs have been approved. We combine molecular dynamics simulations, enhanced sampling techniques, network theory and pocket detection to decipher the activation pathway of A1R, decode the allosteric networks and identify transient pockets. The A1R activation pathway reveal hidden intermediate and pre-active states together with the inactive and fully-active states observed experimentally. The protein energy networks computed throughout these conformational states successfully unravel the extra and intracellular allosteric centers and the communication pathways that couples them. We observe that the allosteric networks are dynamic, being increased along activation and fine-tuned in presence of the trimeric G-proteins. Overlap of transient pockets and energy networks uncover how the allosteric coupling between pockets and distinct functional regions of the receptor is altered along activation. By an in-depth analysis of the bridge between activation pathway, energy networks and transient pockets, we provide a further understanding of A1R. This information can be useful to ease the design of allosteric modulators for A1R.

biophysics↗