Biology subjects

MONARI, A.

Publications and source records attributed to MONARI, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Molecular dynamics insights into biomineralisation mediated by acidic intrinsically disordered proteins: a case study of molluscan Aspein from the pearl oyster Pinctada fucata

Biomineralisation is a ubiquitous phenomenon that still fascinates the scientific community. Mineralised structures are most notably encountered in marine lifeforms the shell or exoskeleton of which are formed by precipitating specific calcium carbonate (CaCO3) polymorphs, known as amorphous (ACC), vaterite, aragonite, and calcite. To control crystalline polymorphism in their shell layers, bivalves have evolved strategies involving ion-binding secretomes composed of shell matrix proteins (SMPs). Secreted in the prismatic layer of the pearl oyster Pinctada fucata, Aspein is an unusually acid-rich protein exclusively aspartic and famously recognised as the most acidic SMP known to date. Through in vitro crystallisation experiments, Aspein was shown to select calcite over aragonite in modern seawater conditions. However, how it exerts its selectivity with respect to its structural properties remains enigmatic. By combining sequence-based predictions with all-atom molecular dynamics simulations, we unveiled that Aspein is an intrinsically disordered organic matrix protein (IDOMP) undergoing ion-specific chain collapse and phase separation. Thanks to its unique Asp density and conformational fuzziness, Aspein first sequesters Ca2+ then attracts CO32- ions before stabilising ACC and calcite-like phases, while precluding the incorporation of Mg2+ to avoid aragonite formation. Indeed, via Asp-Ca2+ bridges, structure-less clusters coalescence into supersaturated protein-CaCO3 assemblies initiates calcite crystallisation. Therefore, Aspein plasticity, condensation susceptibility, and aspartic density critically modulate the pathway that defines CaCO3 polymorphism by inhibiting nucleation and controlling the growth of biogenic minerals. From a broader perspective, our study underpins some of the molecular and physico-chemical principles governing biomineralisation processes mediated by IDOMPs, the overlooked, yet prevalent, role of which was mechanistically unexplored.

biophysics↗

bioRxiv2026

The Conformation of the Complementary Strand and the Deformation of the DNA Groove upon DDB2 Binding Justifies the Different Repair Rates for Cyclobutane Pyrimidine Dimers.

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 {pi}-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. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=186 SRC="FIGDIR/small/724087v2_ufig1.gif" ALT="Figure 1"> View larger version (63K): org.highwire.dtl.DTLVardef@1c02e6forg.highwire.dtl.DTLVardef@28b3c1org.highwire.dtl.DTLVardef@3143fborg.highwire.dtl.DTLVardef@664d48_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2025

Rational Molecular Design of Two-Photon Activated Temoporfin: A Computational Study for Advanced Photodynamic Therapy

Photodynamic therapy (PDT) is a promising, non-invasive cancer treatment that relies on the activation of photosensitizers (PS) 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 infrared activable PS. Furthermore, PS 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 ({sigma}) 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 {beta}-cyclodextrins ({beta}-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.

biochemistry↗

bioRxiv2025

In Silico Study of Active Delivery of a Photodynamic Therapy Drug Targeting the Folate Receptor

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 -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 (FR-), 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.

biophysics↗

bioRxiv2025

Influencing Iron Homeostasis by Transition Metal Complexes Interacting with a messenger-RNA Stem Loop in the Iron Regulating Element

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.

biophysics↗

bioRxiv2024

AGAPE (computAtional G-quadruplex Affinitiy PrEdiction): The first AI In-silico workflow for G-quadruplex binding affinity prediction.

AGAPE (computational G-quadruplex Affinity Prediction) is a novel machine learning (ML)-based tool designed to predict the binding and 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 dataset of 1217 compounds labelled through Forster Resonance Energy Transfer (FRET) melting assays, AGAPE integrates 5666 molecular descriptors, both classical and quantum chemical. It captures features relevant to G4 recognition, driving researcher 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 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.

bioinformatics↗

bioRxiv2024

The predominant binding mode of Palmatine to DNA

Palmatine is a protoberberine alkaloid, which may produce singlet oxygen under visible light irradiation and binds to DNA. The fact that singlet oxygen activation in palmatine may be triggered by environmental conditions, and in particular its interaction with nucleic acids, makes it a most suitable candidate for photodynamic therapy and DNA-targeted non-invasive anticancer strategies. Despite these remarkable properties the actual binding mode between palmatine and DNA has not been resolved, yet. Its elucidation has, indeed, led to contrasting hypothesis. In this contribution by using long-range molecular dynamic simulations and enhanced sampling approaches, we unequivocally identify that intercalation is the dominant binding mode of palmatine with DNA, from either a thermodynamic and kinetic point of view. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/613446v1_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@1f30e43org.highwire.dtl.DTLVardef@2d5e04org.highwire.dtl.DTLVardef@776b2aorg.highwire.dtl.DTLVardef@1ca206_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2024

Unraveling the Role of Azobenzene-Based Photoswitchable Lipids in Controlling Innate Immune Response

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 which the innate immune system TIM-3 sensors. We show, resorting to long-range molecular dynamic simulations including enhanced sampling, that the Z isomer lead 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. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=167 SRC="FIGDIR/small/605494v2_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@89c52eorg.highwire.dtl.DTLVardef@f08fe9org.highwire.dtl.DTLVardef@1780d8eorg.highwire.dtl.DTLVardef@c1f3b8_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOTOC GRAPHICC_FLOATNO C_FIG

biophysics↗

bioRxiv2024

Molecular bases and specificity behind the activation of the immune system OAS/RNAse L pathway by viral RNA.

The first line of defense against invading pathogens usually relies on the innate immune systems. In this context the recognition of exogenous RNA structure 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 turns triggers the activity of RNase L and, thus, cleaving cellular and viral RNA. In this contribution by using long range molecular dynamics simulation, complemented with enhanced sampling techniques, we elu-cidate 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 presence and absence of RNA. Finally, the role of two RNA mutations, identified as able to down-regulate OAS activation, in shaping the protein/nucleic acid interface and the conformational land-scape of OAS are also analyzed.

biophysics↗

bioRxiv2024

Intrinsic Disorder and Salt-dependent Conformational Changes of the N-terminal TFIP11 Splicing Factor

Tuftelin Interacting Protein 11 (TFIP11) was recently identified as a critical human spliceosome assembly regulator, interacting with multiple spliceosome proteins and localises in several membrane-less organelles. However, there is a lack of structural information on TFIP11, limiting the rationalisation of its biological role. TFIP11 has been predicted as a highly disordered protein, and more specifically concerning its N-terminal (N-TER) region. Intrinsically disordered proteins (IDPs) lack a defined tertiary structure, existing as a dynamic conformational ensemble, favouring their role as hubs in protein-protein and protein-RNA interaction networks. Furthermore, IDPs are involved in liquid-liquid phase separation (LLPS), driving the formation of subnuclear compartments. Combining disorder prediction, molecular dynamics, and spectroscopy methods, this contribution shows the first evidence TFIP11 N-TER may be described as a polyampholytic IDP, exhibiting a structural duality with the coexistence of ordered and disordered assemblies, depending on the ionic strength of the protein environment. Increasing the salt concentration enhances the protein conformational flexibility, presenting a fuzzier conformational landscape, a more globule-like shape, and an unstructured arrangement that could favour LLPS segregation and protein-RNA interaction. The regions mostly composed of charged and hydrophilic residues are the most impacted, including the G-Patch domain which is of crucial importance to TFIP11 function.

bioinformatics↗

bioRxiv2024

Interaction Between Yersinia pestis Ail Outer Membrane Protein and the C-Terminal Domain of Human Vitronectin

Yersinia pestis, the causative agent of plague, is capable to evade human immune system response by recruiting the plasma circulating vitronectin proteins, which acts as a shield and avoids its lysis. Vitronectin recruitment is mediated by its interaction with the bacterial transmembrane protein Ail, protruding from 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. TOC ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=186 SRC="FIGDIR/small/574511v1_ufig1.gif" ALT="Figure 1"> View larger version (140K): org.highwire.dtl.DTLVardef@1f43519org.highwire.dtl.DTLVardef@1ca1b0forg.highwire.dtl.DTLVardef@1b68510org.highwire.dtl.DTLVardef@1d9fe1d_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2023

Efficient Drug Delivering of a Photodynamic Therapy Agent into Cellular Membranes Rationalized by Molecular Dynamics

Photodynamic Therapy (PDT) represents a most attractive therapeutic strategy to reduce side effects of chemotherapy and improve the global quality of life of patients. Yet, many PDT drugs suffer from a poor bioavailability and cellular intake, and thus, drug delivery strategy are mandatory. In this article we rationalize the behavior of a temoporfin-based PDT drug, commercialized under the name of Foscan, complexed by two {beta}-cyclodextrin units, acting as drug carriers, in presence of a lipid bilayer. Our all atom simulations have unequivocally shown the internalization of the drug-deliovering complex and suggest its possible spontaneous dissociation in the lipid bilayer core. The factors favoring penetration and dissociation have also been analyzed, together with the membrane perturbation due to the interaction with the drug carrier complex. Our results confirm the suitability of this encapsulation strategy for PDT, and rationalize the experimental results concerning its efficacy.

biophysics↗

bioRxiv2023

Molecular Photoswitches Regulating the Activity of the Human Serotonin Transporter

Serotonin is an essential mediator regulating diverse neural processes, and its deregulation is related to debilitating neurological diseases. In particular, the human serotonin transporter (hSERT) is fundamental in completing the synaptic neural cycle by allowing the reuptake of serotonin. Its inhibition is particularly attractive, especially as a pharmacological target against depressive syndrome. Here, we analyze, by using long-range molecular dynamic simulations, the behavior of a molecular photoswitch whose cis- and trans-isomers inhibit the hSERT differently. In particular, we evidence the structural and molecular basis behind the higher inhibiting capacity of the cis-isomer, which blocks more efficiently the hSERT conformational cycle leading to serotonin uptake. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/558680v1_ufig1.gif" ALT="Figure 1"> View larger version (98K): org.highwire.dtl.DTLVardef@75d82dorg.highwire.dtl.DTLVardef@c38d43org.highwire.dtl.DTLVardef@6f3c90org.highwire.dtl.DTLVardef@f12399_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2023

Mechanism of the Covalent Inhibition of Human Transmembrane Protease Serine 2 as an Original Antiviral Strategy

The Transmembrane Protease Serine 2 (TMPRSS2) is a human enzyme which is involved in the maturation and post-translation of different proteins. In addition of being overexpressed in cancer cells, TMPRSS2 plays a further fundamental role in favoring viral infections by allowing the fusion of the virus envelope and the cellular membrane, notably in SARS-CoV-2. In this contribution we resort to multiscale molecular modeling to unravel the structural and dynamical features of TMPRSS2 and its interaction with a model lipid bilayer. Furthermore, we shed light into the mechanism of action of a potential inhibitor (Nafamostat), determining the free-energy profile associated with the inhibition reaction, and showing the facile poisoning of the enzyme. Our study, while providing the first atomistically resolved mechanism of TMPRSS2 inhibition, is also fundamental in furnishing a solid framework for further rational design targeting transmembrane proteases in a host-directed antiviral strategy. TOC GRAPHICS O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=193 SRC="FIGDIR/small/537985v1_ufig1.gif" ALT="Figure 1"> View larger version (108K): org.highwire.dtl.DTLVardef@19dd8c9org.highwire.dtl.DTLVardef@394c0org.highwire.dtl.DTLVardef@11ad383org.highwire.dtl.DTLVardef@347a8c_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2023

Predicting the Three-dimensional Structure of the c-KIT Oncogene Promoter and the Dynamics of Strongly Coupled Guanine-Quadruplexes

Guanine-quadruplexes (G4s) are non-canonical DNA structures that play important protective and regulatory roles within cells, influencing, for instance, gene expression. Although the secondary structure of many human G4s is well characterized, in several gene-promoter regions multiple G4s are located in close proximity and may form three-dimensional structures which could ultimately influence their biological roles. In this contribution, we analyze the interplay between the three neighboring G4s present in the c-KIT proto-oncogene promoter, namely WK1, WSP and WK2. In particular, we highlight how these three G4s are structurally linked and how their crosstalk favors the formation of a parallel structure for WSP, differently from what observed for this isolated G4 in solution. Relying on all-atom molecular dynamic simulations exceeding the s time-scale and using enhanced sampling methods, we provide the first computationally-resolved structure of a well-organized G4 cluster in the promoter of a crucial gene involved in cancer development. Our results indicate that neighboring G4s influence their mutual three-dimensional arrangement and provide a powerful tool to predict and interpret complex DNA structures that ultimately can be used as starting point for drug discovery purposes.

biophysics↗

bioRxiv2022

Molecular basis of the pH-controlled maturation of the tick-borne encephalitis flavivirus

Flaviviruses are enveloped viruses causing high public concerns. Their maturation spans several cellular compartments having different pH. Thus, complex control mechanisms are in place to avoid premature maturation. Here we report the dynamical behavior at neutral and acidic pH of the precursor of the membrane fusion protein E of tick-borne encephalitis, showing the different stabilization of the E dimer and the role played by the small fusion-assisting protomer (pr). The comprehension, at atomic resolution, of the fine regulation of viral maturation will be fundamental to the development of efficient strategies against emerging viral threats.

biophysics↗

bioRxiv2022

G-quadruplex recognition by DARPIns through epitope/paratope analogy

We investigated the mechanisms leading to the specific recognition of Guanine Guadruplex (G4) by DARPins peptides, which can lead to the design of G4s specific sensors. To this end we carried out all-atom molecular dynamic simulations to unravel the interactions between specific nucleic acids, including human-telomeric (h-telo), Bcl-2, and c-Myc, with different peptides, forming a DARPin/G4 complex. By comparing the sequences of DARPin with that of a peptide known for its high affinity for c-Myc, we show that the recognition cannot be ascribed to sequence similarity but, instead, depends on the complementarity between the three-dimensional arrangement of the molecular fragments involved: the -helix/loops domain of DARPin and the G4 backbone. Our results reveal that DARPins tertiary structure presents a charged hollow region in which G4 can be hosted, thus the more complementary the structural shapes, the more stable the interaction.

biophysics↗

bioRxiv2021

Never cared for what they do. High structural stability of Guanine-quadruplexes in presence of strand-break damages

DNA integrity is an important factor to assure genome stability and, more generally, cells and organisms viability. In presence of DNA damage, the normal cell cycle is perturbed while cells activate their repair processes. Although efficient, the repair system is not always able to ensure the complete restoration of gene integrity. In these cases, not only mutations may occur, but the accumulation of lesions can either lead to carcinogenesis or reach a threshold which induces apoptosis and the programmed cell death. Among the different types of DNA lesions, strand breaks produced by ionizing radiations are the most toxic, due to their inherently difficult repair, which may lead to genomic instability. In this article we show, by using classical molecular simulations techniques, that differently from the canonical double-helical B-DNA, guanine-quadruplex (G4) arrangements show a remarkable structural stability, even in presence of two strand breaks. Since G4-DNA are recognized for their regulatory roles in cell senescence and gene expression, also involving oncogene, their stability can be related to an evolutionary cellular response aimed at minimizing the effects of ionizing radiation.

biophysics↗