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.

Molecular photoswitches capable of controlling membrane properties under light stimulation represent promising tools for manipulating biomimetic and biological interfaces. We report the synthesis and photophysical characterization of amphiphilic P-type photoswitches exhibiting efficient and reversible E↔Z photoisomerization under both one-photon (1PA: 375/300 nm) and two-photon (2PA: 750/630 nm) excitation. Their incorporation into DPPC monolayers and bilayers enables light-driven modulation of membrane structure. Short-chain analogues (C4 derivatives) remain well-mixed with DPPC and promote curvature upon E↔Z photoisomerization, regardless of the polarity of their headgroup (hydroxyl, OH, or hexaethylenglycol, HEG). In contrast, long-chain derivatives (C12) behave either as light-activated compressants or expanders depending on the strength of their headgroup interactions. The HEG-terminated C12 photoswitch (Sw-HEG-C12) favors anchoring at the interface and induces lateral demixing (microsegregation) and domain stiffening, leading to a decrease in surface pressure in DPPC monolayers and an increase in vesicle size upon E→Z isomerization. Conversely, the hydroxylated analogue (Sw-OH-C12) mixes nearly ideally with DPPC but occupies different depths within the bilayer depending on isomerization state (E near the interface, Z internalized), resulting in an increase in surface pressure and a decrease in vesicle size upon E→Z isomerization. The two-photon-responsive photoswitches reported herein appear thus as versatile tools for the optical control of membrane architecture in biological environments where NIR light is required.

The repair of photo-induced DNA lesions through nucleotide excision repair machinery is still the source of important questions. It has been observed that the repair rate of the different cyclobutane pyrimidine dimers, i.e. the photoproducts induced by dimerization of two π-stacked pyrimidines (T < > T, T < > C, C < > T, C < > C), depends on the nucleobases involved in the lesion. TT derivatives (T < > T) are removed more slowly than those containing cytosine, especially in 5'. Using all-atom molecular dynamics simulations, we demonstrate that the variation of the repair rate observed in human skin and in cultured cutaneous cell may be associated to the recognition of the four lesions by the DDB2 protein moiety, and more specifically by the differential structural deformation induced on the complementary strand and the major groove. These effects may then hamper differentially the downstream recruitment of the repair complexes. The observed DNA deformation correlates with the experimental repair rate and suggests a structural rationale for the different repair rates of CPD by nucleotide excision repair machinery.

We have synthesized and characterized three Zn(II) Salphen complexes with different ligand modifications to evaluate their biological properties in terms of DNA binding, cellular uptake and anticancer activity. Particular attention was given to the synthesis of an asymmetric Salphen complex using mechanochemistry to prevent unwanted side products. The symmetric neutral complex bearing lateral chlorine substituents showed low aqueous solubility, no detectable binding to G-quadruplex (G4) DNA, yet good cytotoxicity. In contrast, the symmetric dicationic derivative exhibited effective G4 stabilization only at high concentrations but lacked cellular activity. Notably, the asymmetric monocationic complex, combining both substituents, achieved a more favorable balance of properties, displaying improved water solubility relative to the neutral analogue, enhanced membrane permeation, and retained cytotoxicity against pancreatic cancer cells. Cellular uptake studies confirmed its efficient internalization via passive transport, and fluorescence microscopy revealed cytoplasmic accumulation. Notably, the asymmetric complex significantly reduced cancer cell viability, inhibited proliferation, and induced apoptotic cell death, as evidenced by PARP cleavage. These findings underscore the potential of asymmetric Salphen complexes as promising anticancer agents and provide valuable insights for the rational design of metal-based therapeutics based on the Salphen scaffold.

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.

Despite its wide use in the past, the UVB filter p-aminobenzoic acid (PABA) is currently considered unsafe in the cosmetic industry. Among other reasons, there is the claimed formation of photoadducts with the nucleobases in DNA. We provide theoretical evidence showing the spontaneous intercalation of PABA in a (dAdT)6 · (dAdT) strand. The π − π stacking interactions between PABA and the nucleobases result in an effective coupling of the native excited states of both molecules, altering the optical properties of DNA. Transition density matrix analysis shows that although the absorption spectrum of the DNA-PABA complex is dominated by excitons, the dark charge-separated states, which have been associated with photodamaging radical reactions in the literature, are overall more numerous in the entire absorption energy range. We show that PABA→DNA charge transfer states are more abundant, more energetically accessible and potentially longer-lived than those across nucleobases, hence explaining the radicallic origin of the photoadducts between the filter and DNA.

The accurate modeling of the excited state landscapes in chiral materials requires an optimal balance between the description of their electronic structure and the influence of environmental effects. In this work, using a prototypical lead halide chiral perovskite, we show that embedding a chromophore in point charges has a beneficial effect in correcting the spurious representation of charge-transfer states arising from hybrid or semilocal approximations within density functional theory (DFT). Notably, the effect of the embedding also outperforms the benefits induced by the range-separated functionals. While the nature of the state remains similar, we demonstrate that the addition of point charges significantly decreases the electron-hole distance. The combination of hybrid functionals with embedding provides the best description of the experimental absorption spectrum, with the only exception being excitonic states that cannot be reproduced when considering a model constituted by a single cell.

In this work, we present a comprehensive computational investigation of a series of meso-aminated chlorin derivatives to evaluate their suitability as next-generation photodynamic therapy photosensitizers. Ground- and excited-state properties were analyzed using density functional theory (DFT) and time-dependent DFT calculations, indicating that all derivatives preserve the characteristic chlorin electronic structure, while meso-substitution modulates Q-band intensities. Their excited-state energy landscapes reveal favorable intersystem crossing pathways, supporting the favorable production of singlet oxygen(1O2). To evaluate their behavior in biologically relevant environments, classical molecular dynamics simulations were performed for water solution, β-cyclodextrin encapsulated complex, and in proximity of lipid bilayers. These results show that stable 1:2 host-guest complexes with β-cyclodextrin can be formed, supporting the suitability of a passive drug-delivery strategy, which should increase bioavailability. Besides, the photosensitizers preferentially localize at the membrane interface stabilized by favorable interactions with lipid headgroups. QM/MM calculations further confirm that their photophysical properties are largely preserved in these environments. Overall, our results highlight meso-aminated chlorins as promising candidates for PDT and demonstrate the effectiveness of a multiscale computational screening strategy for guiding the design of improved photosensitizers.

In the past few years, the double PHD fingers 3 (DPF3) protein isoforms (DPF3b and DPF3a) have been identified as new amyloidogenic intrinsically disordered proteins (IDPs). Although such discovery is coherent and promising in light of their involvement in proteinopathies, their amyloidogenic pathway remains largely unexplored. As environmental variations in pH and ionic strength are relevant to DPF3 pathophysiological landscape, we therefore enquired the effect of these physicochemical parameters on the protein structural and prone-to-aggregation properties, by focusing on the more disordered DPF3a isoform. In the present study, we exploited in vitro and in silico strategies by combining spectroscopy, microscopy, and all-atom molecular dynamics methods. Very good consistency and complementary information were found between the experiments and the simulations. Acidification unequivocally abrogated DPF3a fibrillation upon maintaining the protein in highly hydrated and expanded conformers due to extensive repulsion between positively charged regions. In contrast, alkaline pH delayed the aggregation process due to loss in intramolecular contacts and chain decompaction, the extent of which was partly reduced thanks to the compensation of negative charge by arginine side chains. Through screening attractive electrostatic interactions, high ionic strength conditions (300 and 500 mM NaCl) shifted the conformational ensemble towards more swollen, heterogeneous, and less H-bonded structures, which were responsible for slowing down the conversion into β-sheeted species and restricting the fibril elongation. For defining the self-assembly pathway of DPF3a, we unveiled that the protein amyloidogenicity intimately communicates with its conformational landscape, which is particularly sensitive to modification of its physicochemical environment. As such, understanding how to modulate DPF3a conformational ensemble will help designing novel protein-specific strategies for targeting neurodegeneration.

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.

Based on the JOYCE quantum-derived force field for specific electronic states, we propose a non-adiabatic dynamic procedure named Nora, to study the photochemical evolution of different chromophores at the cost of classical molecular dynamics simulations. Notably, we present its application to the E/Z photoisomerization of a biomimetic cyclocurcumin-based photoswhitch, which may have applications in oxygen-independent photodynamic therapy or photo-immunotherapy. This new methodology opens an expansive timescale in the study of photochemical processes in biological environments.

The electrochemical and photophysical properties of two series of ruthenium bis(bipyridine) complexes featuring either a pyridine-phosphonium ylide (PC) or a pyridine-iminophosphorane (PN) ligand were synthesized. Three different bipyridines were employed allowing the synthesis of six P-ylide RuII complexes. All the complexes were fully characterized by multinuclear NMR spectroscopy, HR-mass spectrometry, as well as X-ray crystallography, and no major difference was observed between them. In cyclic voltammetry, the measured potentials agree with the electronic properties of the bipyridine ligands and underline the strong electron donation of the phosphonium ylide. Indeed, the oxidation is facilitated and the reductions become more difficult compared to the corresponding [Ru(Rbpy)3] complexes. The absorption spectra of the PC and PN RuII complexes are similar, with a bathochromic shift compared to polypyridine RuII complexes, which is amplified in the presence of electron-withdrawing substituents on the bipyridine. Regarding luminescence, the PC complexes emit at a lower energy than the PN analogues. In addition, the associated lifetime depends on both the nature of the P-ylide and the substituents on the bipyridine ligand. This was related to the different adiabatic 3MC/3MLCT gap calculated at the DFT level, which is larger for two iminophosphorane complexes exhibiting a lifetime of the order of a few hundred nanoseconds.

The maintaining of the precise regulation of iron homeostasis is fundamental to assure cells viability. In this context the interplay between the messenger RNA iron response element (IRE) and the iron response protein 1 (IRP1) is crucial to regulate the expression of ferritin and hence the level of labile free iron pool. We have shown, using a combination of molecular modeling and experimental techniques, that tris bipyridine iron complexes (AIM3) interact specifically with the IRE RNA stem-loop in solution, without inducing noticeable structural deformations. Furthermore, we have also shown that, at a cellular level, this interaction may be traced back to the downregulation of ferritin translation, probably due to the stabilization of the IRE stem-loops thus favoring its binding to IRP1 or by inhibiting the downstream recruitment of ribosomal subunits.

Photodynamic therapy (PDT) is a promising, non-invasive cancer treatment that relies on the activation of photosensitizers (PSs) by suitable light to produce cytotoxic reactive oxygen species. However, the efficiency of PDT is often hindered by the limited penetration of visible light into tissues, requiring the use of an infrared activable PS. Furthermore, PSs are usually prone to aggregation and present solubility issues limiting their bioavailability. In this study, we explore the functionalization of temoporfin (mTHPC), a clinically approved second-generation PS, with two-photon absorption (TPA) chromophores to enhance its efficiency in deep tissues. Three TPA-temoporfin conjugates (DTP1-mTHPC, DTP2-mTHPC, and DPP-mTHPC) have been designed and their properties have been investigated using a combination of quantum mechanics (QM), molecular dynamics (MD), and hybrid QM/MM simulations. Computational analysis revealed that the TPA cross section (σ) of the parent DTP moieties significantly increase when anchored to mTHPC, thus allowing efficient absorption in the near-infrared (NIR) region. Additionally, we have shown that their encapsulation with β-cyclodextrins (β-CDs) improved solubility and prevented aggregation without altering the optical properties of the PS. Simulations in a biological membrane model confirmed favorable interactions and localization of the candidate PDT agents within lipid bilayers, supporting their potential for enhanced clinical applications. This study demonstrates that rational molecular design can improve both the optical properties and the drug-delivery proficiency of temoporfin, paving the way for more effective deep-tissue PDT treatments.

The control of the activation of the innate immune response, notably by using suitable visible light sources, may lead the way to the development of phototimmunotherapeutic strategies. In this contribution we analyze the effects of the E/Z interconversion on a phosphatidyl serine lipid containing an isomerizable azobenzene moiety, which has recently been shown to regulate the activation of natural killer cells and the production of cytokines [J. Am. Chem. Soc. 2022, 144, 3863 - 3874]. In particular, we analyze the differential interactions of the innate immune system TIM-3 sensors. We show, resorting to long-range molecular dynamic simulations including enhanced sampling, that the Z isomer leads to a slight decrease of the binding free energy coupled with a less pronounced rigidification of the protein compared to the E isomer and the native lipid, justifying its less pronounced activation of the immune response.

Photodynamic Therapy (PDT), which involves the combined action of a drug and its activation by suitable light, is a particularly attractive novel cancer therapy method due to less systemic side effects. However, the delivery and accumulation of the PDT drug into cancer cells is still problematic. Here, by using μ-scale molecular dynamic simulations combined with quantum mechanics/molecular mechanics approaches, we examine the behavior of a PDT drug functionalized with a folic acid unit targeting the folate receptor α (FR-α), which is overexpressed in ovarian cancer cells. We show that the PDT drug forms a stable complex with the folate receptor, albeit slightly disrupting the main interaction patterns as compared to the parent folate ligand. Furthermore, we also show that the optical properties of the PDT drug are not altered by its interaction with the protein. Our results confirm that coupling with folate is an attractive strategy for selective active delivery of PDT agents.