AGAPE (computational G-quadruplex stabilization prediction) is a novel machine learning (ML)-based tool designed to predict the stabilizing potential of small molecules targeting G-quadruplexes (G4s). G4s, prevalent in telomeres and oncogene promoters, are promising therapeutic targets, but designing selective binders remains challenging. Building upon a curated data set of 1217 compounds labeled through Förster Resonance Energy Transfer (FRET) melting assay data, AGAPE integrates 5666 molecular descriptors, both classical and quantum chemical. It captures features relevant to G4 recognition, driving researchers to predict the potential G4 stabilization of small molecules, including both organic ligands and metal complexes. Among the trained ML models, XGBoost achieved the best performance with an accuracy of nearly 91%, using 489 selected features. SHAP analysis highlighted descriptors related to molecular topology, polarizability, and electrostatic potential as key contributors to the classification. AGAPE is deployed through a user-friendly web interface, http://agape.fondazionerimed.com/, supporting batch prediction and secure data handling, and provides a robust and interpretable tool to accelerate the discovery of G4-stabilizing compounds, integrating quantum chemical information within an ML-driven cheminformatics framework.

Cancer immunotherapy has transformed cancer treatment; however, durable responses remain limited by suppressive myeloid populations within the tumor microenvironment. Leukocyte immunoglobulin-like receptor B4 (LILRB4/ILT3) is an emerging myeloid immune checkpoint implicated in immune evasion and resistance to immunotherapy, yet small molecule targeting of ILT3 remains largely unexplored. Here, we report the discovery of small molecule ILT3 modulators identified using a Dianthus-based temperature-related intensity change (TRIC) screening platform. Screening of an 8961-member Enamine Protein Mimetic Library identified multiple direct ILT3 binders, with lead compound ICB-7 demonstrating high-affinity binding to recombinant human ILT3 by microscale thermophoresis (KD = 156 nM) and robust cellular target engagement in CETSA assays. Molecular docking and molecular dynamics simulations revealed a stable hydrophobic binding pocket within the D2 domain of ILT3. Functionally, ICB-7 disrupted the ILT3-SCG2 interaction and inhibited downstream SHP1, SHP2, and STAT3 signaling. In patient-derived colorectal cancer and acute myeloid leukemia co-culture models, ICB-7 restored IFN-γ and IL-2 secretion, enhanced cytotoxic T-cell activity, and reduced tumor-cell viability. The compound also demonstrated favorable pharmacokinetic and safety properties together with significant anti-tumor efficacy in the CT26 syngeneic colorectal carcinoma model. Collectively, these findings establish ILT3 as a tractable target for small-molecule immunomodulation and support pharmacological targeting of suppressive myeloid checkpoints as a promising cancer immunotherapy strategy.

Antibiotic resistance represents an emerging global health threat. In this contribution, we report all-atom molecular dynamics simulations of a bacterial protein in Acinetobacter baumanii. By using enhanced sampling we show the favorable internalization of the antibiotic via the CarO porin. This result correlates with the knockout or the mutation of the porin as a resistance mechanism.

The influence of the Mucin-1 (Muc-1) receptor in cancer progression and its bad prognosis makes it a potentially ideal target in pharmacology. However, the mechanism of action and its interaction with the cellular membrane are not fully characterized at a proper atomistic level. In this contribution, using long all-atom molecular dynamic simulation, largely exceeding the µs time-scale, we analyze the interaction of the membrane embedded Muc-1 b subunit with a peptide mimicking the MLuc-1 a interface. Despite showing the stability of the protein/peptide aggregate, which can be exploited for drug delivery, we also show and characterize the long-range structural modification of the transmembrane subunit upon peptide binding. This represents the first modeling of the initial Muc-1 signal transduction determined by the formation of the a/b hetordimer.

Hybrid organic-inorganic perovskites (HOIPs) are promising materials in optoelectronics, particularly for photovoltaic applications, due to their tunable properties and ease of fabrication. Among them, chiral HOIPs are gaining attention for their unique chiroptical properties, by the incorporation of chiral organic molecules into their structure. Despite their potential, the relationship between chiral HOIP structures and their chiroptical properties, such as circular dichroism (CD) spectra, remains challenging to decrypt. This study introduces a simulation workflow based on Density Functional Theory (DFT) and Time-Dependent DFT (TD-DFT) to model the CD spectrum of the chiral 2D perovskite encapsulating S-1-(3-bromophenyl)-ethylamine (S-(3Br-MBA)(2)PbI4). The approach combines ab-initio molecular dynamics (AIMD) with TD-DFT calculations evaluating the contributions on the whole chiral hybrid perovskite scaffold and those of the isolated ligands, allowing us to dissect the contributions to the CD spectrum of chiral ligands and of the metal-halide sublattice. Additionally, the absorption dissymmetry factor gabs has been also computed finding good agreement with the experimental value.This work provides valuable insights for the design of advanced chiroptoelectronic materials.

Bacterial resistance and nosocomial infections are serious threats compromising public health in numerous countries. Acinetobacter baumannii has been identified as one of the most serious pathogens, due to its potential virulence and the development of multiple resistance. In this contribution by using all-atom molecular dynamics simulation, we analyze the structure and the properties of the OmpA protein, which is present in the bacterial external membrane. We also analyze the structure of possible protein/protein complexes formed between OmpA and the human fibronectin, which may ultimately lead to the immune escape of the bacteria. We provide a plausible structure of the complex, also identifying suitable amino acids mediating the interaction, and thus, constituting suitable drug targets to disrupt the complex formation.

Hypochondroplasia is a rare genetic form of skeletal dysplasia, caused by gain-of-function pathogenic variants in the FGF receptor 3 (FGFR3). It is characterized by disproportionate short stature and has a wide spectrum of clinical features. Currently, there are no precision therapeutic options approved for hypochondroplasia. Infigratinib is an orally bioavailable FGFR1-3 selective tyrosine kinase inhibitor in development for achondroplasia and hypochondroplasia. Infigratinib acts directly at the source of the pathophysiological cause of both conditions by inhibiting the phosphorylation of FGFR3 and attenuating both main downstream signaling pathways that are involved in the conditions. Results from a phase 2 study support the concept that infigratinib has a potential to improve bone growth in achondroplasia. We report results of a step-wise evaluation of the therapeutic relevance of infigratinib for hypochondroplasia: in silico assessment of infigratinib with hypochondroplasia associated FGFR3 variants suggest strong interaction; in vitro, infigratinib showed potent inhibitory effect; in a mouse model of hypochondroplasia (Fgfr3N534K/+), infigratinib resulted in significant improvement in skeletal growth. These data in addition to the clinical results from the phase 2 study conducted in children with achondroplasia provide support for the development of infigratinib in the treatment of hypochondroplasia.

Injectable hydrogels are promising candidates as local drug delivery platforms for the treatment of infected wounds. Self‐assembled small peptide hydrogels are of interest due to their high biocompatibility, degradability, and ease of synthesis. This study describes the formation of an injectable hydrogel based on the self‐assembly of Fmoc‐FFpY (Fmoc: fluorenylmethoxycarbonyl, F: phenylalanine, pY: tyrosine phosphate) triggered by electrostatic interactions in the presence of Fe3+ ions. Stabilized by H bonding and π–π stacking, the hydrogels exhibit high mechanical stiffness with a G′ (storage modulus) of ≈8000 Pa and a self‐recovery up to G′ ≈100 Pa. Peptide self‐assembly yields β‐sheets twisted into fibrillar helices of 12 nm in diameter and pitch. Molecular dynamics simulations confirm 1) the aggregation of Fmoc‐FFpY in the presence of Fe3+ and the adopted secondary structure and show that 2) the aggregated Fmoc‐FFpY/Fe3+ disrupts the bacterial membrane of Staphylococcus aureus and Pseudomonas aeruginosa, favoring the passive entry of Fe3+ into the pathogen. In full agreement with the simulations, the hydrogels exhibit antibacterial activity against both bacteria, likely due to the increased Fe3+ entry into the cell, resulting in enhanced production of reactive oxygen species. This work paves the way for ferroptosis‐inducing treatment of bacterial infections using injectable ultrashort peptides.

Bacterial resistance and nosocomial infections are serious threats compromising public health in numerous countries. Acinetobacter baumannii has been identified as one of the most serious pathogens, due to its potential virulence and the development of multiple resistance. In this contribution by using all-atom molecular dynamics simulation, we analyze the structure and the properties of the OmpA protein, which is present in the bacterial external membrane. We also analyze the structure of possible protein/protein complexes formed between OmpA and the human fibronectin, which may ultimately lead to the immune escaping of the bacteria. For the first time, we provide for the first time plausible structure of the complex also identifying suitable amino acid mediating the interaction, and thus, constituting suitable drug targets to disrupt the complex formation. ### Competing Interest Statement The authors have declared no competing interest.

Guanine quadruplexes (G4s) are nucleic acid structures present in diverse regions of the genome, such as telomeres and transcription initiators. Recently, the different biological roles of G4s have been evidenced as well as their role as biomarkers for tumors or viral infections. However, the fast and efficient detection of G4s in complex matrices remains elusive. In this contribution, by using long-scale molecular dynamics simulations, we propose the design of a biosensor based on organic field-effect transistors recognizing G4s. In particular, we show that the interaction of the G4s with the biosensor is translated into a change in the charge density profile, which correlates with the electrical transduction of the signal, thus allowing the detection of the nucleic acid structure. We also provide rules of thumb for the optimization of the design of the device and more generally for the integration of computationally driven design approaches.

Yersinia pestis, the causative agent of plague, is capable of evading the human immune system response by recruiting the plasma circulating vitronectin proteins, which act as a shield and avoid its lysis. Vitronectin recruitment is mediated by its interaction with the bacterial transmembrane protein Ail, protruding from the Y. pestis outer membrane. By using all-atom long-scale molecular dynamic simulations of Ail embedded in a realistic model of the bacterial membrane, we have shown that vitronectin forms a stable complex, mediated by interactions between the disordered moieties of the two proteins. The main amino acids driving the complexation have also been evidenced, thus favoring the possible rational design of specific peptides which, by inhibiting vitronectin recruitment, could act as original antibacterial agents.

The first line of defense against invading pathogens usually relies on innate immune systems. In this context, the recognition of exogenous RNA structures is primordial to fight, notably, against RNA viruses. One of the most efficient immune response pathways is based on the sensing of RNA double helical motifs by the oligoadenylate synthase (OAS) proteins, which in turn triggers the activity of RNase L and, thus, cleaves cellular and viral RNA. In this contribution, by using long-range molecular dynamics simulations, complemented with enhanced sampling techniques, we elucidate the structural features leading to the activation of OAS by interaction with a model double-strand RNA oligomer mimicking a viral RNA. We characterize the allosteric regulation induced by the nucleic acid leading to the population of the active form of the protein. Furthermore, we also identify the free energy profile connected to the active vs. inactive conformational transitions in the presence and absence of RNA. Finally, the role of two RNA mutations, identified as able to downregulate OAS activation, in shaping the protein/nucleic acid interface and the conformational landscape of OAS is also analyzed.

The presence of a guanine quadruplex in the opening reading frame of the messenger RNA coding for the transmembrane serine protease 2 (TMPRSS2) may pave the way to original anticancer and host-oriented antiviral strategy. Indeed, TMPRSS2 in addition to being overexpressed in different cancer types, is also related to the infection of respiratory viruses, including SARS-CoV-2, by promoting the cellular and viral membrane fusion through its proteolytic activity. The design of selective ligands targeting TMPRSS2 messenger RNA requires a detailed knowledge, at atomic level, of its structure. Therefore, we have used an original experimental-computational protocol to predict the first resolved structure of the parallel guanine quadruplex secondary structure in the RNA of TMPRSS2, which shows a rigid core flanked by a flexible loop. This represents the first atomic scale structure of the guanine quadruplex structure present in TMPRSS2 messenger RNA.

The emergence of bacterial strains resistant to antibiotics is a major issue in the medical field. Antimicrobial peptides are widely studied as they do not generate as much resistant bacterial strains as conventional antibiotics and present a broad range of activity. Among them, the homopolypeptide poly(l-arginine) presents promising antibacterial properties, especially in the perspective of its use in biomaterials. Linear poly(l-arginine) has been extensively studied but the impact of its 3D structure remains unknown. In this study, the antibacterial properties of newly synthesized branched poly(l-arginine) peptides, belonging to the family of multiple antigenic peptides, are evaluated. First, in vitro activities of the peptides shows that branched poly(l-arginine) is more efficient than linear poly(l-arginine) containing the same number of arginine residues. Surprisingly, peptides with more arms and more residues are not the most effective. To better understand these unexpected results, interactions between these peptides and the membranes of Gram positive and Gram negative bacteria are simulated thanks to molecular dynamic. It is observed that the bacterial membrane is more distorted by the branched structure than by the linear one and by peptides containing smaller arms. This mechanism of action is in full agreement with in vitro results and suggest that our simulations form a robust model to evaluate peptide efficiency towards pathogenic bacteria.

The antitumoral activity of hydroxymethylene bisphosphonates (HMBP) such as alendronate or zoledronate is hampered by their exceptional bone-binding properties and their short plasmatic half-life which preclude their accumulation in non-skeletal tumors. In this context, the use of lipophilic prodrugs represents a simple and straightforward strategy to enhance the biodistribution of bisphosphonates in these tissues. We describe in this article the synthesis of light-responsive prodrugs of HMBP alendronate. These prodrugs include lipophilic photo-removable nitroveratryl groups which partially mask the highly polar alendronate HMBP scaffold. Photo-responsive prodrugs of alendronate are stable in physiological conditions and display reduced toxicity compared to alendronate against MDA-MB-231 cancer cells. However, the antiproliferative effect of these prodrugs is efficiently restored after cleavage of their nitroveratryl groups upon exposure to UV light. In addition, substitution of alendronate with such photo-responsive substituents drastically reduces its bone-binding properties, thereby potentially improving its biodistribution in soft tissues after i.v. administration. The development of such lipophilic photo-responsive prodrugs is a promising approach to fully exploit the anticancer effect of HMBPs on non-skeletal tumors.

Delving into the mechanism behind the molecular interactions at the atomic level of short-sequence peptides plays a key role in the development of nanomaterials with specific structure–property–function relationships from a bottom-up perspective.

The elucidation of structural interfaces between proteins and inorganic surfaces is a crucial aspect of bionanotechnology development. Despite its significance, the interfacial structures between proteins and metallic surfaces are yet to be fully understood, and the lack of experimental investigation has impeded the development of many devices. To overcome this limitation, we suggest considering the generation of protein/surface structures as a molecular docking problem with a homogenous plan as the target. To this extent, we propose a new software, DockSurf, which aims to quickly propose reliable protein/surface structures. Our approach considers the conformational exploration with Euler's angles, which provide a cartography instead of a unique structure. Interaction energies were derived from quantum mechanics computations for a set of small molecules that describe protein atom types and implemented in a Derjaguin, Landau, Verwey, and Overbeek potential for the consideration of large systems such as proteins. The validation of DockSurf software was conducted with molecular dynamics for corona proteins with gold surfaces and provided enthusiastic results. This software is implemented in the RPBS platform to facilitate widespread access to the scientific community.

The Transmembrane Protease Serine 2 (TMPRSS2) is a humanenzymewhich is involved in the maturation and post-translation of differentproteins. In addition to being overexpressed in cancer cells, TMPRSS2plays a further fundamental role in favoring viral infections by allowingthe fusion of the virus envelope with the cellular membrane, notablyin SARS-CoV-2. In this contribution, we resort to multiscale molecularmodeling to unravel the structural and dynamical features of TMPRSS2and its interaction with a model lipid bilayer. Furthermore, we shedlight on the mechanism of action of a potential inhibitor (nafamostat),determining the free-energy profile associated with the inhibitionreaction and showing the facile poisoning of the enzyme. Our study,while providing the first atomistically resolved mechanism of TMPRSS2inhibition, is also fundamental in furnishing a solid framework forfurther rational design targeting transmembrane proteases in a host-directedantiviral strategy.

The efficient immobilization of enzymes on surfaces remains a complex but central issue in the biomaterials field, which requires us to understand this process at the atomic level. Using a multiscale approach combining all-atom molecular dynamics and coarse-grain Brownian dynamics simulations, we investigated the adsorption behavior of β-glucosidase A (βGA) on bare and self-assembled monolayer (SAM)-functionalized gold surfaces. We monitored the enzyme position and orientation during the molecular dynamics (MD) trajectories and measured the contacts it forms with both surfaces. While the adsorption process has little impact on the protein conformation, it can nonetheless perturb its mechanical properties and catalytic activity. Our results show that compared to the SAM-functionalized surface, the adsorption of βGA on bare gold is more stable, but less specific, and more likely to disrupt the enzyme's function. This observation emphasizes the fact that the structural organization of proteins at the solid interface is a key point when designing devices based on enzyme immobilization, as one must find an acceptable stability-activity trade-off.

A gain-of-function mutation in the fibroblast growth factor receptor 3 gene (FGFR3) results in achondroplasia (ACH), the most frequent form of dwarfism. Constitutive activation of FGFR3 impairs bone formation and elongation and many signal transduction pathways. Identification of new and relevant compounds targeting the FGFR3 signaling pathway is of broad importance for the treatment of ACH, and natural plant compounds are prime drug candidate sources. Here, we found that the phenolic compound (-)-epicatechin, isolated from Theobroma cacao, effectively inhibited FGFR3's downstream signaling pathways. Transcriptomic analysis in an Fgfr3 mouse model showed that ciliary mRNA expression was modified and influenced significantly by the Indian hedgehog and PKA pathways. (-)-Epicatechin is able to rescue mRNA expression impairments that control both the structural organization of the primary cilium and ciliogenesis-related genes. In femurs isolated from a mouse model (Fgfr3Y367C/+) of ACH, we showed that (-)-epicatechin eliminated bone growth impairment during 6 days of ex vivo culture. In vivo, we confirmed that daily subcutaneous injections of (-)-epicatechin to Fgfr3Y367C/+ mice increased bone elongation and rescued the primary cilium defects observed in chondrocytes. This modification to the primary cilia promoted the typical columnar arrangement of flat proliferative chondrocytes and thus enhanced bone elongation. The results of the present proof-of-principle study support (-)-epicatechin as a potential drug for the treatment of ACH.