Molecular dynamics simulations of cRGD-conjugated PEGylated TiO2_2 nanoparticles for targeted photodynamic therapy

The conjugation of high-affinity cRGD-containing peptides is a promising approach in nanomedicine to efficiently reduce off-targeting effects and enhance the cellular uptake by integrin-overexpressing tumor cells. Herein we utilize atomistic molecular dynamics simulations to evaluate key structural-functional parameters of these targeting ligands for an effective binding activity towards $\alpha_V\beta_3$ integrins. An increasing number of cRGD ligands is conjugated to PEG chains grafted to highly curved TiO$_2$ nanoparticles to unveil the impact of cRGD density on the ligand's presentation, stability, and conformation in an explicit aqueous environment. We find that a low density leads to an optimal spatial presentation of cRGD ligands out of the "stealth" PEGylated layer around the nanosystem, favoring a straight upward orientation and spaced distribution of the targeting ligands in the bulk-water phase. On the contrary, high densities favor clustering and internalization of cRGD ligands in the inner region of the PEGylated layer, driven by a concerted mechanism of enhanced ligand-ligand interactions and reduced water accessibility over the ligand's molecular surface. These findings strongly suggest that the ligand density modulation is a key factor in the design of cRGD-targeting nanodevices to maximize their binding efficiency into over-expressed $\alpha_V\beta_3$ integrin receptors

Selective Anticancer Therapy Based on a HA-CD44 Interaction Inhibitor Loaded on Polymeric Nanoparticles

This research was funded by the Consejeria de Economia, Conocimiento, Empresas y Universidad of the Junta de Andalucia (grant number Excellence Research Project P18-RT-1679) and the Research Results Transfer Office (OTRI) of the University of Granada (grant number PR/17/006 project). This work was partially supported by grants from the Spanish Ministry of Economy and Competitiveness (MINECO), grant number PID2019.110987RB.I00; the Health Institute Carlos III (ISCIII), grant number DTS18/00121 the Junta de Andalucia-FEDER, Ministry of Economy, Knowledge, Companies, and University (FEDER 2018: ref. B-FQM-475-UGR18, PAIDI2020: ref. PT18-TP-4160); and the Andalusian Regional Government, grant number PAIDI-TC-PVT-PSETC-2.0. C.D. thanks HECBioSim, the UK High End Computing Consortium for Biomolecular Simulation (hecbiosim.ac.uk), which is supported by the EPSRC (EP/L000253/1) for awarding computing time in Jade, a UK Tier-2 resource. B.R.-R. gratefully acknowledges funding from the European Union's Horizon 2020 Research and Innovation Program under Marie Sklodowska-Curie Grant Agreement no. 754446 and UGR Research and Knowledge Transfer Fund-Athenea3i. J.M.E.-R. thanks the Spanish Ministry of Education for PhD funding (scholarship FPU 16/02061). V.C.-C. thanks the Andalusian Regional Government for her postdoctoral fellowship (POSTDOC_21_00118).Hyaluronic acid (HA), through its interactions with the cluster of differentiation 44 (CD44), acts as a potent modulator of the tumor microenvironment, creating a wide range of extracellular stimuli for tumor growth, angiogenesis, invasion, and metastasis. An innovative antitumor treatment strategy based on the development of a nanodevice for selective release of an inhibitor of the HACD44 interaction is presented. Computational analysis was performed to evaluate the interaction of the designed tetrahydroisoquinoline-ketone derivative (JE22) with CD44 binding site. Cell viability, efficiency, and selectivity of drug release under acidic conditions together with CD44 binding capacity, effect on cell migration, and apoptotic activity were successfully evaluated. Remarkably, the conjugation of this CD44 inhibitor to the nanodevice generated a reduction of the dosis required to achieve a significant therapeutic effect.Junta de Andalucia P18-RT-1679Research Results Transfer Office (OTRI) of the University of Granada PR/17/006Spanish Government PID2019.110987RB.I00Health Institute Carlos III (ISCIII) DTS18/00121Junta de Andalucia-FEDER, Ministry of Economy, Knowledge, Companies, and University (FEDER) B-FQM-475-UGR18 PT18-TP-4160Andalusian Regional Government POSTDOC_21_00118UK Research & Innovation (UKRI)Engineering & Physical Sciences Research Council (EPSRC) EP/L000253/1European Union's Horizon 2020 Research and Innovation Program under Marie Sklodowska-Curie Grant 754446UGR Research and Knowledge Transfer Fund-Athenea3iSpanish Government FPU 16/0206

The current structural glycome landscape and emerging technologies.

Carbohydrates represent one of the building blocks of life, along with nucleic acids, proteins and lipids. Although glycans are involved in a wide range of processes from embryogenesis to protein trafficking and pathogen infection, we are still a long way from deciphering the glycocode. In this review, we aim to present a few of the challenges that researchers working in the area of glycobiology can encounter and what strategies can be utilised to overcome them. Our goal is to paint a comprehensive picture of the current saccharide landscape available in the Protein Data Bank (PDB). We also review recently updated repositories relevant to the topic proposed, the impact of software development on strategies to structurally solve carbohydrate moieties, and state-of-the-art molecular and cellular biology methods that can shed some light on the function and structure of glycans

Novel multi-objective affinity approach allows to identify pH-specific μ-opioid receptor agonists

Opioids are essential pharmaceuticals due to their analgesic properties, however, lethal side effects, addiction, and opioid tolerance are extremely challenging. The development of novel molecules targeting the -opioid receptor (MOR) in inflamed, but not in healthy tissue, could significantly reduce these unwanted effects. Finding such novel molecules can be achieved by maximizing the binding affinity to the MOR at acidic pH while minimizing it at neutral pH, thus combining two conflicting objectives. Here, this multi-objective optimal affinity approach is presented, together with a virtual drug discovery pipeline for its practical implementation. When applied to finding pH-specific drug candidates, it combines protonation state-dependent structure and ligand preparation with high-throughput virtual screening. We employ this pipeline to characterize a set of MOR agonists identifying a morphine-like opioid derivative with higher predicted binding affinities to the MOR at low pH compared to neutral pH. Our results also confirm existing experimental evidence that NFEPP, a previously described fentanyl derivative with reduced side effects, and recently reported -fluorofentanyls and -morphines show an increased specificity for the MOR at acidic pH when compared to fentanyl and morphine. We further applied our approach to screen a >50K ligand library identifying novel molecules with pH-specific predicted binding affinities to the MOR. The presented differential docking pipeline can be applied to perform multi-objective affinity optimization to identify safer and more specific drug candidates at large scale

Investigating the Unbinding of Muscarinic Antagonists from the Muscarinic 3 Receptor

Patient symptom relief is often heavily influenced by the residence time of the inhibitor–target complex. For the human muscarinic receptor 3 (hMR3), tiotropium is a long-acting bronchodilator used in conditions such as asthma or chronic obstructive pulmonary disease (COPD). The mechanistic insights into this inhibitor remain unclear; specifically, the elucidation of the main factors determining the unbinding rates could help develop the next generation of antimuscarinic agents. Using our novel unbinding algorithm, we were able to investigate ligand dissociation from hMR3. The unbinding paths of tiotropium and two of its analogues, N-methylscopolamin and homatropine methylbromide, show a consistent qualitative mechanism and allow us to identify the structural bottleneck of the process. Furthermore, our machine learning-based analysis identified key roles of the ECL2/TM5 junction involved in the transition state. Additionally, our results point to relevant changes at the intracellular end of the TM6 helix leading to the ICL3 kinase domain, highlighting the closest residue L482. This residue is located right between two main protein binding sites involved in signal transduction for hMR3′s activation and regulation. We also highlight key pharmacophores of tiotropium that play determining roles in the unbinding kinetics and could aid toward drug design and lead optimization

Investigating the Unbinding of Muscarinic Antagonists from the Muscarinic 3 Receptor

Patient symptom relief is often heavily influenced by the residence time of the inhibitor-target complex. For the human muscarinic receptor 3 (hMR3), tiotropium is a long-acting bronchodilator used in conditions such as asthma or chronic obstructive pulmonary disease (COPD). The mechanistic insights into this inhibitor remain unclear; specifically, the elucidation of the main factors determining the unbinding rates could help develop the next generation of antimuscarinic agents. Using our novel unbinding algorithm, we were able to investigate ligand dissociation from hMR3. The unbinding paths of tiotropium and two of its analogues, N-methylscopolamin and homatropine methylbromide, show a consistent qualitative mechanism and allow us to identify the structural bottleneck of the process. Furthermore, our machine learning-based analysis identified key roles of the ECL2/TM5 junction involved in the transition state. Additionally, our results point to relevant changes at the intracellular end of the TM6 helix leading to the ICL3 kinase domain, highlighting the closest residue L482. This residue is located right between two main protein binding sites involved in signal transduction for hMR3's activation and regulation. We also highlight key pharmacophores of tiotropium that play determining roles in the unbinding kinetics and could aid toward drug design and lead optimization

BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based plartform for biomolecular simulations.

We present BioExcel Building Blocks Workflows, a web-based graphical user interface (GUI) offering access to a collection of transversal pre-configured biomolecular simulation workflows assembled with the BioExcel Building Blocks library. Available workflows include Molecular Dynamics setup, protein-ligand docking, trajectory analyses and small molecule parameterization. Workflows can be launched in the platform or downloaded to be run in the users' own premises. Remote launching of long executions to user's available High-Performance computers is possible, only requiring configuration of the appropriate access credentials. The web-based graphical user interface offers a high level of interactivity, with integration with the NGL viewer to visualize and check 3D structures, MDsrv to visualize trajectories, and Plotly to explore 2D plots. The server requires no login but is recommended to store the users' projects and manage sensitive information such as remote credentials. Private projects can be made public and shared with colleagues with a simple URL. The tool will help biomolecular simulation users with the most common and repetitive processes by means of a very intuitive and interactive graphical user interface. The server is accessible at https://mmb.irbbarcelona.org/biobb-wfs

Inhibition of mutant RAS-RAF interaction by mimicking structural and dynamic properties of phosphorylated RAS

Undruggability of RAS proteins has necessitated alternative strategies for the development of effective inhibitors. In this respect, phosphorylation has recently come into prominence as this reversible post-translational modification attenuates sensitivity of RAS towards RAF. As such, in this study, we set out to unveil the impact of phosphorylation on dynamics of HRASWT and aim to invoke similar behavior in HRASG12D mutant by means of small therapeutic molecules. To this end, we performed molecular dynamics (MD) simulations using phosphorylated HRAS and showed that phosphorylation of Y32 distorted Switch I, hence the RAS/RAF interface. Consequently, we targeted Switch I in HRASG12D by means of approved therapeutic molecules and showed that the ligands enabled detachment of Switch I from the nucleotide-binding pocket. Moreover, we demonstrated that displacement of Switch I from the nucleotide-binding pocket was energetically more favorable in the presence of the ligand. Importantly, we verified computational findings in vitro where HRASG12D/RAF interaction was prevented by the ligand in HEK293T cells that expressed HRASG12D mutant protein. Therefore, these findings suggest that targeting Switch I, hence making Y32 accessible might open up new avenues in future drug discovery strategies that target mutant RAS proteins

Uptake mechanism of iron-phytosiderophore from the soil based on the structure of yellow stripe transporter

植物が根から鉄を吸収する機構の解明 --不良土壌を改善する次世代肥料の開発に期待--. 京都大学プレスリリース. 2022-12-08.Calcareous soils cover one-third of all land and cause severe growth defects in plants due to the poor water solubility of iron at high pH. Poaceae species use a unique chelation strategy, whereby plants secrete a high-affinity metal chelator, known as phytosiderophores (mugineic acids), and reabsorb the iron-phytosiderophore complex by the yellow stripe 1/yellow stripe 1-like (YS1/YSL) transporter for efficient uptake of iron from the soil. Here, we present three cryo-electron microscopy structures of barley YS1 (HvYS1) in the apo state, in complex with an iron-phytosiderophore complex, Fe(III)-deoxymugineic acid (Fe(III)–DMA), and in complex with the iron-bound synthetic DMA analog (Fe(III)–PDMA). The structures reveal a homodimeric assembly mediated through an anti-parallel β-sheet interaction with cholesterol hemisuccinate. Each protomer adopts an outward open conformation, and Fe(III)–DMA is bound near the extracellular space in the central cavity. Fe(III)–PDMA occupies the same binding site as Fe(III)–DMA, demonstrating that PDMA can function as a potent fertilizer in an essentially identical manner to DMA. Our results provide a structural framework for iron-phytosiderophore recognition and transport by YS1/YSL transporters, which will enable the rational design of new, high-potency fertilizers

Cryo-EM structure of the photosynthetic RC-LH1-PufX supercomplex at 2.8-angstrom resolution

The reaction center (RC)−light-harvesting complex 1 (LH1) supercomplex plays a pivotal role in bacterial photosynthesis. Many RC-LH1 complexes integrate an additional protein PufX that is key for bacterial growth and photosynthetic competence. Here, we present a cryo–electron microscopy structure of the RC-LH1-PufX supercomplex from Rhodobacter veldkampii at 2.8-Å resolution. The RC-LH1-PufX monomer contains an LH ring of 15 αβ-polypeptides with a 30-Å gap formed by PufX. PufX acts as a molecular “cross brace” to reinforce the RC-LH1 structure. The unusual PufX-mediated large opening in the LH1 ring and defined arrangement of proteins and cofactors provide the molecular basis for the assembly of a robust RC-LH1-PufX supercomplex and efficient quinone transport and electron transfer. These architectural features represent the natural strategies for anoxygenic photosynthesis and environmental adaptation