Life Sciences
All scientific publications in Area Science Park
Chirality Unlocks Sub-Terahertz Molecular Dynamics in Peptide Nanotubes
Abstract Low-frequency modes in the picosecond range play a key role in molecular recognition and biomolecular function. Here, we investigate how these dynamics at the interfaces of self-assembled peptide biomaterials relate to fine structural details of the supramolecular assembly. We resolve terahertz and mid-infrared modes in individual diphenylalanine nanotubes by nanoscale microspectroscopy, uncovering a direct correlation between supramolecular chirality, molecular arrangement, and picosecond dynamics at the nanotube-environment boundary. By combining THz and mid-IR nanoscopy with a multiscale strategy spanning single nanotubes and ensemble measurements, supported by density functional theory calculations, we access the intrinsic picosecond response of peptide assemblies beyond the limits of conventional microscopy and ensemble averaging. Heterochiral (D-L) nanotubes display sharp resonances, whereas homochiral (L-L) nanotubes exhibit a comparatively featureless sub-THz profile, revealing a clear chirality-dependent contrast. Mode assignments show that the heterochiral features are dominated by localized torsional and bending motions of phenyl rings relative to the peptide backbone. Overall, chirality-dependent THz fingerprints emerge as sensitive descriptors of peptide nanotube architecture, while low-frequency nanospectroscopy provides a route to interrogate biomaterial interfaces under biologically relevant conditions. Authors Rajat Kumar, Erica Scarel, Andrea Perucchi, Lisa Vaccari, Prasanta Kumar Datta, Francesco D’amico, Paola Di Pietro, Silvia Marchesan, Federica Piccirilli Journal ChemrXiv Publication date 11/03/2026 Consult the publication
Ultrafast Intermolecular Dynamics of Nanoconfined Water in Swollen Lipid Cubic Mesophases
Abstract Understanding the structure and dynamics of the hydrogen-bond network ofwater in topologically distinct swollen lipidic mesophases, is fundamental fortheir application in biomedical, pharmaceutical, and food science fields. Here,a positive and non-linear correlation between water hydrogen-bond dynamicsand interfacial water population is uncovered in inverse bicontinuous swollenmesophases across an extended temperature range (298–340 K). Particularly,small-angle X-ray scattering determines the mesophase’s structural features,uncovering a temperature-driven re-entrant phenomenon (reappearance) ofPn̄ 3m phase upon heating. This topologically rich environment, however, hasno detectable impact on the temperature dependence of the intermolecularmodes of water, as revealed by terahertz absorption spectroscopy. Specifically,these modes show distinct dynamics: the stretching mode exhibits longerlifetimes than the libration mode, yet with a higher temperature-dependence,with approximately two-fold lower Arrhenius activation energies. In contrast,both stretching and libration modes exhibit a monotonic decrease in lifetimewith increasing temperature, due to the increasing disruption of thehydrogen-bond network. Atomistic molecular dynamics simulations enablethe quantification of interfacial water population, which shows a positivecorrelation with intermolecular lifetimes in a nonlinear manner, revealing anon-additive coupling between interfacial water population and waterhydrogen-bond network dynamics within these systems. Authors Eva Zunzunegui-Bru, Serena Rosa Alfarano, Patrick Züblin, Laura Baraldi,Hendrik Vondracek, Federica Piccirilli, Lisa Vaccari, and Raffaele Mezzenga Journal Small Publication date 03/10/2025 Consult the publication
Rational optimization of D3R/GSK-3β dual target-directed ligands as potential treatment for bipolar disorder: Design, synthesis, X-ray crystallography, molecular dynamics simulations, in vitro ADME, and in vivo pharmacokinetic studies
Abstract Bipolar disorder is a complex neuropsychiatric condition with a significant unmet medical need, as current treatments lack disease-modifying properties and multimodal therapeutic effects. To overcome the limitations of single-target drugs, we designed dual-target ligands that combine partial agonism at the dopamine D3 receptor (D3R) with inhibition of glycogen synthase kinase-3β (GSK-3β). We previously identified ARN24161 (1) as a promising prototype, demonstrating partial agonism at D3R (EC50 = 10.1 nM, % Eff. = 26.3) and GSK-3β inhibition (IC50 = 561 nM). However, its drug-like properties remained suboptimal. To optimize this compound, we initiated a multidisciplinary refinement campaign, leveraging computational modeling and crystallographic data to fine-tune the balance between D3R and GSK-3β activity, reduce P-glycoprotein (P-gp) affinity, and improve the pharmacokinetic profile. This effort led to the identification of ARN25297 (5), a moderately balanced dual-target ligand that exhibits partial agonism at D3R (EC50 = 13.1 nM, % Eff. = 17.1) and potent GSK-3β inhibition (IC50 = 47.0 nM). Notably, ARN25657 (16) emerged as the most well-balanced candidate, demonstrating enhanced D3R partial agonism (EC50 = 15.2 nM, % Eff. = 37.7) alongside strong GSK-3β inhibition (IC50 = 19.3 nM). Compound 16 also exhibited the lowest P-gp inhibition and significant improvements in in vitro ADME properties compared to prototype 1, while maintaining a balanced dual target profile. Although the PK profile of 16 remained comparable to that of prototype 1, these findings lay the groundwork for further lead optimization and structural refinement, driving future in vivo proof-of-concept toward innovative therapeutic strategies for bipolar disorder and related neuropsychiatric conditions. Authors RMC Di Martino, D Russo, I Penna, Andrea Dalle Vedove, R Spabnuolo, G Ottonello, M Summa, J Desantis, A Valeri, L Pruccoli, SK Tripathi, A Tarozzi, Paola Storici, S Girotto, R Bertorelli, A Armirotti, G Cruciani, T Bandiera, A Cavalli, G Bottegoni Journal European Journal of Medicinal Chemistry Publication date 25/06/2025 Consult the publication
FL30: an epidermal growth factor kinase inhibitor overcoming T790M and C797S mutations through unique conformational modulation mechanism
Abstract Tyrosine kinase inhibitors (TKIs) targeting the oncogene Epidermal Growth Factor Receptor (EGFR) are widely used in the treatment of non-small cell lung cancer (NSCLC). In this context, the introduction of fourth-generation TKIs has significantly advanced targeted therapy for T790M and C797S EGFR mutations. Current therapeutic strategies are increasingly focusing on the design of orthoallosteric TKIs, which have shown promise in stabilizing the inactive conformation of mutated EGFR. In this context, we report the discovery of FL30, a small molecule with a flavone core that exhibits nanomolar potency against the EGFR-L858R/T790M mutation, even in the presence of the C797S mutation. The IC50 comparable to the Osimertinib – one of the most renowned EGFR-TKIs – emphasizes the remarkable success of the design approach. In NSCLC models, FL30 effectively inhibits cancer growth and EGFR phosphorylation selectively in cells with the EGFR mutations. Kinetic studies, molecular modeling, and Plasmon Internal Reflection Surface-Enhanced Infrared Absorption (PIR-SEIRA) microscopy suggests that FL30 binds to the orthosteric site while inducing the transition of the mutant EGFR toward an inactive-like state. These findings highlight FL30’s potential for further optimization and propose a novel approach for developing targeted therapies that combine orthosteric binding with allosteric modulation. Authors Elena Romagnoli, Emiliano Laudadio, Giovanna Mobbili, Leonardo Sorci, Giovanni Birarda, Federica Piccirilli, Lisa Vaccari, Hendrik Vondracek, Brenad Romaldi, Massimo Marcaccio, Paola Storici, Marta Semrau, Roberta Galeazzi, Andrea Toma, Vincenzo Aglieri, Pierluigi Stipa, Tatiana Armeni, Cristina Minnelli Journal International Journal of Biological Macromolecules Publication date 21/06/2025 Consult the publication
A supported lipid bilayer to model solid-ordered membrane domains
Abstract Membrane models are widely used to mimic the behaviour of native plasma membranes and to simulate interactions occurring at their interface. Such models can be built up with different molecular compositions, ranging from single phospholipids to more complex, heterogeneous mixtures of phospho- and sphingo-lipids, possibly enriched with cholesterol and proteins. In particular, mixing different lipids and cholesterol is instrumental to promote the formation of phase-separated, ordered domains, which resemble the structure of lipid rafts, specialized functional domains of real membranes. According to the specific lipid composition, physical characteristics of the rafts can be tuned, such as fluidity, strongly related to membrane biological activity. Here, we introduce a novel three-component membrane model constituted by the mixing of a saturated phospholipid, 1,2-dimyristoyl-sn–glycero-3-phosphocholine (DMPC), sphingomyelin and cholesterol to mimic the presence of solid ordered rafts and to study their behaviour. Differential scanning calorimetry, neutron reflectometry, and atomic force microscopy were synergistically applied to gain information on the membrane’s transverse and lateral organization, as well as on its thermotropic behaviour. The membrane model benefits from the use of DMPC, a lipid (i) characterized by an accessible transition temperature; (ii) saturated; (iii) fluid at physiological temperature and (iv) commercially available in both protiated and deuterated forms. The proposed model, along with the wide range of biophysical techniques employed, constitutes an ideal system to study the molecular mechanisms and the physical properties that govern membrane functions, such as molecular signalling and membrane trafficking. Authors Sally Helmy, Paola Brocca, Alexandros Koutsioubas, Stephen C.L. Hall, Luca Puricelli, Pietro Parisse, Loredana Casalis, Valeria Rondelli Journal Journal of Colloid and Interface Science Publication Date 14/03/2025 Consult the publication
Ultrasensitive detection and quantification of bovine Deltapapillomavirus in the semen of healthy horses.
Abstract BPV1, BPV2, BPV13, and BPV14 are all genotypes of bovine delta papillomaviruses (δPV), of which the first three cause infections in horses and are associated with equine sarcoids. However, BPV14 infection has never been reported in equine species. In this study, we examined 58 fresh and thawed commercial semen samples from healthy stallions. In 34 (58.6%), bovine δPV DNA was detected and quantified using droplet digital polymerase chain reaction (ddPCR). Real time quantitative PCR (qPCR) was able to identify bovine δPV DNA in 5 samples (8.6%). Of the BPV-infected semen samples, 15 were positive for BPV2 (~ 44.1%) on ddPCR and 4 (~ 11.7%) on qPCR; 12 (~ 35.3%) for BPV14 on ddPCR and 1 (~ 3%) by qPCR; 4 (~ 11.7%) for BPV1 on ddPCR, whereas qPCR failed to reveal this infection; 3 (~ 8.8%) for BPV13 on ddPCR; and BPV13 infection was not detected by qPCR. Our study showed for the first time that BPV14 is an additional infectious agent potentially responsible for infection in horses, as its transcripts were detected and quantified in some semen samples. Large-scale BPV14 screening is necessary to provide substantial data on the molecular epidemiology for a better understanding of the geographical divergence of BPV14 prevalence in different areas and how widespread BPV14 is among equids. Authors Anna Cutarelli, Francesca De Falco, Francesco Serpe, Simona Izzo, Giovanna Fusco, Cornel Catoi, Sante Roperto Journal Scientific Report Publication date 04/01/2025 Consult the publication
Limiting serine availability during tumor progression promotes muscle wasting in cancer cachexia
Abstract Cancer cachexia is a multifactorial syndrome characterized by a progressive loss of body weight occurring in about 80% of cancer patients, frequently representing the leading cause of death. Dietary intervention is emerging as a promising therapeutic strategy to counteract cancer-induced wasting. Serine is the second most-consumed amino acid (AA) by cancer cells and has emerged to be strictly necessary to preserve skeletal muscle structure and functionality. Here, we demonstrate that decreased serine availability during tumor progression promotes myotubes diameter reduction in vitro and induces muscle wasting in in vivo mice models. By investigating the metabolic crosstalk between colorectal cancer cells and muscle cells, we found that incubating myotubes with conditioned media from tumor cells relying on exogenous serine consumption triggers pronounced myotubes diameter reduction. Accordingly, culturing myotubes in a serine-free medium induces fibers width reduction and suppresses the activation of the AKT-mTORC1 pathway with consequent impairment in protein synthesis, increased protein degradation, and enhanced expression of the muscle atrophy-related genes Atrogin1 and MuRF1. In addition, serine-starved conditions affect myoblast differentiation and mitochondrial oxidative metabolism, finally inducing oxidative stress in myotubes. Consistently, serine dietary deprivation strongly strengthens cancer-associated weight loss and muscle atrophy in mice models. These findings uncover serine consumption by tumor cells as a previously undisclosed driver in cancer cachexia, opening new routes for possible therapeutic approaches. Authors Erica Pranzini, Livio Muccillo, Ilaria Nesi, Alice Santi, Caterina Mancini, Giulia Lori, Massimo Genovese, Tiziano Lottini, Giuseppina Comito, Anna Caselli, Annarosa Arcangeli, Lina Sabatino, Vittorio Colantuoni, Maria Letizia Taddei, Paolo Cirri, Paolo Paoli Journal Cell Death Discovery Publication date 21/12/2024 Consult the publication
Ferritin adsorption onto chrysotile asbestos fibers influences the protein secondary structure
Abstract Asbestos fiber exposure triggers chronic inflammation and cancer. Asbestos fibers can adsorb different types of proteins. The mechanism of this adsorption, not yet completely understood, has been studied in detail mainly with serum albumin and was shown to induce structural changes in the bound protein. The findings of these works regarded mainly the changes of the protein structure, independently of any relation with asbestos-related diseases. For the first time, we have focused our attention to the consequences of the interaction between asbestos fibers and ferritin, a protein involved in iron metabolism, which is strongly modified in asbestos-related diseases. Even if it is known that ferritin can be adsorbed by asbestos fibers, the results of this interaction for the ferritin secondary structure has not previously been studied. One consequence of asbestos-ferritin interaction, is the formation of the so-called ferruginous/asbestos bodies (ABs). In the AB-coating material, the secondary structure of ferritin is modified, and at present, it is unclear whether or not this modification is a direct consequence of the asbestos interaction. In the present study, chrysotile asbestos, more than other asbestos fiber types tested, was found to rapidly bind holo-ferritin, and the presence of iron seemed to play a key role in this process, since iron-free apo-ferritin was adsorbed at a lower level, and iron-saturated chrysotile lost its ferritin-adsorbing capacity. To directly study the details of ferritin adsorption on asbestos fibers, High Resolution Transmission Electron Microscopy (HR-TEM) was employed together with FTIR microspectroscopy and Infrared nanoscopy, which to the best of our knowledge, have not previously been used for this purpose. Chrysotile-bound apo-ferritin underwent a significant change in secondary structure, showing a shift from a prevalent α-helix to a β-sheet conformation. Conversely, the adsorbed holo-ferritin structure appeared to be only weakly modified. These findings add a new potential mechanism to the toxic activities of asbestos: the fibers can modify the structure, and very likely, the function of adsorbed proteins. This, in relation to ferritin, could be a key mechanism in cell iron homeostasis alteration, typically reported in asbestos-related diseases. Authors Martina Zangari, Federica Piccirilli, Lisa Vaccari, Cristian Radu, Paola Zacchi, Annalisa Bernareggi, Sara Leone, Giuliano Zabucchi, Violetta Borelli Journal Helyon Publication date 30/10/2024 Consult the publication
Molecular simulations to investigate the impact of N6-methylation in RNA recognition: Improving accuracy and precision of binding free energy prediction
Abstract N6-Methyladenosine (m6A) is a prevalent RNA post-transcriptional modification that plays crucial roles in RNA stability, structural dynamics, and interactions with proteins. The YT521-B (YTH) family of proteins, which are notable m6A readers, functions through its highly conserved YTH domain. Recent structural investigations and molecular dynamics (MD) simulations have shed light on the mechanism of recognition of m6A by the YTHDC1 protein. Despite advancements, using MD to predict the stabilization induced by m6A on the free energy of binding between RNA and YTH proteins remains challenging due to inaccuracy of the employed force field and limited sampling. For instance, simulations often fail to sufficiently capture the hydration dynamics of the binding pocket. This study addresses these challenges through an innovative methodology that integrates metadynamics, alchemical simulations, and force-field refinement. Importantly, our research identifies hydration of the binding pocket as giving only a minor contribution to the binding free energy and emphasizes the critical importance of precisely tuning force-field parameters to experimental data. By employing a fitting strategy built on alchemical calculations, we refine the m6A partial charge parameters, thereby enabling the simultaneous reproduction of N6 methylation on both the protein binding free energy and the thermodynamic stability of nine RNA duplexes. Our findings underscore the sensitivity of binding free energies to partial charges, highlighting the necessity for thorough parametrization and validation against experimental observations across a range of structural contexts. Authors Valerio Piomponi, Miroslav Krepl, Jiri Sponer, Giovanni Bussi Journal The Journal of Physical Chemistry B, Vol 128, Issue 37 Publication Date 06/09/2024 Consult the paper
Probing conformational dynamics of EGFR mutants via SEIRA spectroscopy: potential implications for tyrosine kinase inhibitor design
Abstract Missense mutations in EGFR’s catalytic domain alter its function, promoting cancer. SEIRA spectroscopy, supported by MD simulations, reveals structural differences in the compactness and hydration of helical motifs between active and inactive EGFR conformations models. These findings provide novel insights into the biophysical mechanisms driving EGFR activation and drug resistance, offering a robust method for studying emerging EGFR mutations and their structural impacts on TKIs efficacy. Authors Emiliano Laudadio, Federica Piccirilli, Henrick Vondracek, Giovanna Mobbili, Marta Stefania Semrau, Paola Storici, Roberta Galeazzi, Elena Romagnoli, Leonardo Sorci, Andrea Toma, Vincenzo Aglieri, Giovanni Birarda, Cristina Minnelli Journal Physical Chemistry Chemical Physics (PCCP) Publication Date 19/08/2024 Consult the publication
Molecular findings and virological assessment of bladder papillomavirus infection in cattle.
Abstract Bovine and ovine papillomaviruses (BPVs – OaPVs) are infectious agents that have an important role in bladder carcinogenesis of cattle. In an attempt to better understand territorial prevalence of papillomavirus genotypes and gain insights into their molecular pathway(s), a virological assessment of papillomavirus infection was performed on 52 bladder tumors in cattle using droplet digital polymerase chain reaction (ddPCR), an improved version of conventional PCR. ddPCR detected and quantified BPV DNA and mRNAs in all tumor samples, showing that these viruses play a determinant role in bovine bladder carcinogenesis. OaPV DNA and mRNA were detected and quantified in 45 bladder tumors. BPV14, BPV13, BPV2, OaPV2, OaPV1, and OaPV3 were the genotypes most closely related to bladder tumors. ddPCR quantified BPV1 and OaPV4 DNA and their transcripts less frequently. Western blot analysis revealed a significant overexpression of the phosphorylated platelet derived growth factor β receptor (PDGFβR) as well as the transcription factor E2F3, which modulate cell cycle progression in urothelial neoplasia. Furthermore, significant overexpression of calpain1, a Cys protease, was observed in bladder tumors related to BPVs alone and in BPV and OaPV coinfection. Calpain1 has been shown to play a role in producing free transcription factors of the E2F family, and molecular findings suggest that calpain family members work cooperatively to mutually regulate their protease activities in cattle bladder tumors. Altogether, these results showed territorial prevalence of BPV and OaPV genotypes and suggested that PDGFβR and the calpain system appeared to be molecular partners of both BPVs and OaPVs. Authors Francesca De Falco, Anna Cutarelli, Francesca Luisa Fedele, Cornel Catoi, Sante Roperto Journal Veterinary Quarterly Publication date 04/08/2024 Consult the publication
Enhancing predictions of protein stability changes induced by single mutations using MSA-based language models
Abstract Protein language models offer a new perspective for addressing challenges in structural biology, while relying solely on sequence information. Recent studies have investigated their effectiveness in forecasting shifts in thermodynamic stability caused by single amino acid mutations, a task known for its complexity due to the sparse availability of data, constrained by experimental limitations. To tackle this problem, we introduce two key novelties: leveraging a protein language model that incorporates Multiple Sequence Alignments to capture evolutionary information, and using a recently released mega-scale dataset with rigorous data preprocessing to mitigate overfitting. Authors Francesca Cuturello, Marco Celoria, Alessio Ansuini, Alberto Cazzaniga Journal Bioinformatics, 2024, 40 (7) Consult the paper