Olalla Vázquez

A substantial body of research implicates PRMTs in the pathogenesis of human diseases, primarily as oncoproteins or tumor suppressors in cancer. Starting from structure-based in silico screening of small-molecule databases, we predicted, synthesized, and assayed compounds aimed at specifically inhibiting selected PRMT family members. Unexpectedly, among several PRMT-inhibitory molecules we identified TR-07, a compound that selectively enhances the catalytic activity of PRMT1 in vitro. SAR analyses led to the design and synthesis of derivatives with increased potency in activating PRMT1 compared to TR-07 but at the cost of selectivity. TR-07 and its derivatives bind to the αY helix near the catalytic core of PRMT1. Treatment of pancreatic tumor cells with these PRMT1 activators enhanced global ADMA levels and augmented PRMT1’s apoptotic function in cell culture and mouse models. Our results establish TR-07 as the first selective, cell-active PRMT1 activator and underscore the therapeutic promise of this novel class of modulators.

Targeting RNA is a rich, yet largely untackled opportunity for controlling biological functions, with high potential for therapeutic intervention. However, it remains inherently challenging. Beyond RNA structural diversity, functional RNA motifs are frequently context‐dependent and transient, complicating the rational design of selective small‐molecule binders. We here develop novel photoswitchable ligands to target RNA. They offer highly desirable, precise intervention by enabling light‐controlled regulation of both direct RNA interactions and downstream events. Unfortunately, access to such photoswitchable RNA molecular tools is scarce, requiring complex and lengthy synthesis routes. We present a readily adaptable platform for the straightforward synthesis of photoswitchable RNA binders capable of targeting pre‐mRNA and restoring functional survival motor neuron (SMN) protein levels by rescuing exon inclusion. Evaluation of our compounds demonstrated that both fluorination and heteroaryl groups (e.g., benzo‐ and thioxozaole) enhance binding affinity to the targeted dsRNA with in‐cellulo activity. Importantly, molecular recognition and structure–activity relationships were rationalized through a combination of computational studies and NMR spectroscopy.

The Wood-Ljungdahl pathway is one of biology's most ancient routes for carbon fixation and energy metabolism, used by organisms such as methanogenic archaea. One of its central metabolic complexes is the acetyl-CoA decarbonylase/synthase (ACDS) complex, catalyzing acetyl-CoA synthesis and cleavage through the coordinated action of carbon monoxide dehydrogenase (CODH), acetyl-CoA synthase (ACS), and corrinoid iron-sulfur protein (CoFeSP). Unlike bacterial CODH/ACS, archaeal ACDS lacks a stable bifunctional CODH-ACS architecture, raising the question of how reactive CO and methyl intermediates are efficiently transferred between catalytic modules. Using cryo-electron microscopy, crosslinking mass spectrometry, small-angle X-ray scattering, and biophysical analyses, we resolved the organization and dynamics of the ~2 MDa archaeal ACDS supercomplex from Methanosarcina acetivorans. We identified CoFeSP as a central architectural scaffold that self-assembles into hexa- to octameric oligomers via a conserved N-terminal region of the CdhD subunit. This scaffold likely tethers CODH and ACS through conserved disordered terminal regions, positioning the catalytic modules in the complex's periphery. We propose a mechanism in which ACS transiently alternates between CODH and CoFeSP, enabling efficient CO and methyl-group transfer without stable binary complexes. This dynamic organization represents a fundamental difference to the stable bifunctional CODH/ACS in bacteria, highlighting how transient interactions enable efficient acetyl-CoA metabolism in archaea.

Methanogens are central to global carbon cycling and among the largest biological sources of methane, a potent greenhouse gas ¹ . At the heart of their energy metabolism lies the Hdr–Vhu–Fwd super-assembly, which couples H ₂ oxidation with CO ₂ reduction through flavin-based electron bifurcation. Here we present the cryogenic electron microscopy structure of the Hdr–Vhu–Fwd super-assembly from Methanococcus maripaludis , revealing an 8 MDa complex comprising 252 polypeptide chains and over 600 redox cofactors. Cryo-electron tomography further support that this super-assembly forms an intact structure within the cytoplasm of intact cells. This architecture comprises two hexameric HdrABC–Vhu rings linked by a tetrameric FwdF core, forming a continuous, circular electron chain. In this unique arrangement, 12 polyferredoxin subunits (VhuB) connect the Vhu–Hdr and Fwd complexes, thereby coupling electron bifurcation with CO ₂ reduction and directly linking the last and the first step of methanogenesis. Moreover, we identify a modular variant of the complex in which the [NiFe]-hydrogenase Vhu is substituted by tungsten-containing formate dehydrogenase (FdhAB), indicating flexible integration of electron-input modules facilitating metabolic adaptation under diverse environmental conditions ² . Analysis of the taxonomic distribution reveals that this architecture is specific to class I methanogens and is distinct from the smaller Hdr–Fmd complex of class II ³ . Together, our study reveals that the the Hdr–Vhu–Fwd super-assembly has a modular and adaptable bioenergetic assembly, suggesting a lineage-specific architecture to adapt to diverse anaerobic niches.

Controlling molecular transport across membranes is a defining feature of living cells, yet replicating this functionality in synthetic systems remains a major challenge. Self-inserting protein nanopores, such as α-hemolysin (αHL), offer a promising route towards programmable membrane permeability due to their robust assembly, compatibility with diverse membrane systems, and intrinsic permeability for diverse biomolecules. Here, we explored the use of chemically functionalized αHL nanopores as tunable transport modules. To quantify translocation of peptide substrates across αHL-containing membranes, we developed a high-throughput luminescence-based breakage-controlled assay using large unilamellar vesicles. With this assay we introduce a one-pot nanopore modification and strategy, compatible with scalable workflows. Electrophysiology and molecular simulations demonstrate that the introduction of cysteine residues at defined pore locations, combined with targeted chemical modification, enables controlled tuning of αHL-nanopore selectivity based on peptide structure and charge. Together, these findings position engineered protein nanopores as versatile and responsive components for controlling membrane transport in synthetic biology.

Herein, we describe a novel azo-Povarov click reaction between N-carbonyl aryldiazenes and cis,trans-cycloocta-1,5-diene. This uncatalyzed [4 + 2] cycloaddition reaction enables the synthesis of a broad series of cinnoline derivatives at room temperature, in short reaction times and excellent yields (up to 98%). The functionality of the reaction has been also evidenced through the report of a high-yielding gram-scale synthesis as well as diverse transformations of the final cinnoline substrates. Furthermore, an activatable fluorogenic version of the reaction has been developed using quenched azo-fluorophores as starting materials.

Targeting RNA is a rich, yet largely untackled opportunity for controlling biological functions, with high potential for therapeutic intervention. However, it remains inherently challenging. Beyond RNA structural diversity, functional RNA motifs are frequently context-dependent and transient, complicating the rational design of selective small-molecule binders. We here develop novel photoswitchable ligands to target RNA. They offer highly desirable, precise intervention by enabling light-controlled regulation of both direct RNA interactions and downstream events. Unfortunately, access to such photoswitchable RNA molecular tools is scarce, requiring complex and lengthy synthesis routes. We present a readily adaptable platform for the straightforward synthesis of photoswitchable RNA binders capable of targeting pre-mRNA and restoring functional survival motor neuron (SMN) protein levels by rescuing exon inclusion. Evaluation of our compounds demonstrated that both fluorination and heteroaryl groups (e.g., benzo- and thioxozaole) enhance binding affinity to the targeted dsRNA with in-cellulo activity. Importantly, molecular recognition and structure–activity relationships were rationalised through a combination of computational studies and NMR spectroscopy

The azobenzene-containing agonist of the vitamin D receptor, PhotoVDRM, enables spatiotemporal psoriasis treatment in mice; its cisoid form induces potent anti-inflammation without hypercalcemia.

A substantial and growing body of research implicates protein‑arginine methyltransferases (PRMTs) in the pathogenesis of a range of human diseases, most prominently cancer. Their role – as oncoproteins or tumor suppressors – depends on both the cellular context and the specific type of malignancy. Starting from structure-based in silico screening of small-molecule databases, we predicted, synthesized, and assayed compounds aimed at specifically inhibiting selected PRMT family members. Unexpectedly, among several PRMT-inhibitory molecules we identified TR-07, a compound that selectively enhances the catalytic activity of PRMT1 in vitro. The following structure-activity-relationship analyses led to the design and synthesis of derivatives that were more potent in activating PRMT1 than TR-07, but at the cost of selectivity relative to other PRMTs. Hydrogen/Deuterium Exchange mass spectrometry and protein-protein interaction assays revealed that TR-07 and its derivatives bind to the αY helix near the catalytic core of PRMT1. Treatment of pancreatic tumor cells with these PRMT1 activators enhanced global ADMA levels and augmented PRMT1’s apoptotic function in cell culture and mouse experiments. Our results establish TR-07 as the first selective, cell-active PRMT1 activator and underscore the therapeutic promise of this novel class of modulators, particularly in disease conditions where PRMT1 is linked to a more favorable outcome.

Oxygen levels and its distribution are tightly regulated due to their critical impact on health. Hypoxia‐inducible factors (HIFs) are traditionally recognized as key regulators of the transcriptional response to low oxygen (hypoxia). Recent research expanded their functions, highlighting their potential as therapeutic targets. Despite these advances, there is still a need for chemical biology tools that offer precise spatiotemporal control within the HIF network and output. Here, we introduce an optochemical approach that enables significant differences in expression of HIF1α‐target genes depending on the photostationary state (PSS). Our photoswitchable stapled peptide PS _B ‐BCB‐04 stabilized HIF1α under normoxic conditions by targeting EloBC ( k _i = 7.9 ± 1.3 nM) and preventing VHL‐mediated degradation. Visible light allowed reversible regulation of peptide conformation, which entailed a sevenfold difference in its EloBC‐binding capacity. In a proof‐of‐concept study, we demonstrated that inhibition of HIF1α degradation enabled isomer‐specific expression of the vascular endothelial growth factor (VEGFA) in prostate cancer cells. Our results validated the potential of photopharmacological stabilization of HIF1α and provided a new toolbox for on‐demand photocontrol over the HIF‐signaling pathway as well as VHL‐mediated degradation.