Articles

Editorial: The metabolic pathways of archaea
- Myllykallio Hannu
- Qin Wei
- Berg Ivan
Frontiers in Microbiology, Frontiers Media , 2025, 16 . (10.3389/fmicb.2025.1648560)
DOI : 10.3389/fmicb.2025.1648560
Time Delay Distribution and Laser Stability in Arbitrary Detuning Asynchronous Optical Sampling
- Antonucci Laura
- Bonvalet A.
- Solinas X.
- Joffre M.
Journal of Physical Chemistry A, American Chemical Society , 2025, 129 (27), pp.6121-6132 . Arbitrary Detuning ASynchronous OPtical Sampling (ADA-SOPS) is an emerging technique for extending standard pump−probe experiments performed with two femtosecond lasers to multitimescale experiments, which are of great interest for the study of complex systems. Although no specific requirements are needed for laser repetition rates, their ratio determines the achievable delay distribution and therefore is strongly related to the temporal resolution of the technique. We report a detailed theoretical analysis of measurement performances with respect to laser repetition rates, and we validate our model with experimental data. In the case of amplified laser systems, we demonstrate that achieved delays are inherently correlated to the time interval between amplified pulses, which affects the pulse energy and can generate artifacts. Nevertheless, a deep understanding of the origin of such artifacts allows to suggest several compensation strategies, either during data analysis or at the conception of the experimental setup. Finally we present a new algorithm integrated into the ADASOPS device: by selecting pairs of probe pulses having the same elapsed time with respect to the previous pulse, it automatically compensates any effect of energy fluctuation. (10.1021/acs.jpca.5c01853)
DOI : 10.1021/acs.jpca.5c01853
IgG detection in human serum employing non-functionalized chromium doped zinc gallate nanoparticles
- Ferjaoui Zied
- Zimmer Capucine
- Matuszewska Celina
- Chanéac Corinne
- Viana Bruno
- Bouzigues Cédric
- Scherman Daniel
- Mignet Nathalie
- Richard Cyrille
Next Nanotechnology, Elsevier , 2025, 8, pp.100199 . Chromium-doped zinc gallate (ZnGa2O4:Cr3 +) nanoparticles (ZGO) show promising potential for antigen immunodetection using persistent luminescence, thereby reducing autofluorescence interference. Recently, we have shown that ZGO prepared by hydrothermal treatment at 120°C for 24 h can be used for in vitro biodetection in simple media such as phosphate-buffered saline. In this study, we investigated the effect of the protocol used to synthesize these ZGO nanoparticles, using a hydrothermal treatment at 220°C for different durations (6 h, 12 h, and 24 h), followed by calcination at 500°C. The nanoparticle size determined by transmission electron microscopy after grinding and centrifugation was found to be around 15 nm. The persistent luminescence signal of the ZGO nanoparticles varied with the hydrothermal synthesis conditions. Moreover, in the presence of H2O2, these nanoparticles show a signal enhancement dependent on the hydrothermal duration, with a 12 h treatment showing the highest 8-fold luminescence increase in the presence of H2O2 produced by glucose oxidase mediated glucose degradation. Based on these results, these non-functionalized nanoparticles were successfully used to develop a persistent luminescence-based sandwich immunoassay for autofluorescence-free detection of antigens in undiluted human serum samples, using rabbit IgG as a model antigen. This study highlights the promising potential for biosensing applications of persistent ZGO nanophosphors for IgG detection in a complex medium (undiluted human serum), with a linear range from 1 ng mL−1 to 104 ng mL−1 and a limit of detection of 0.01 ng mL−1. The present optimization of ZGO nanophosphor synthesis offers promising prospects for medical diagnostics due to their increased sensitivity and ability to eliminate autofluorescence interference, as well as their ease of use, since no functionalization of the ZGO NPs is required before use. (10.1016/j.nxnano.2025.100199)
DOI : 10.1016/j.nxnano.2025.100199
Laser driven FLASH radiobiology using a high dose and ultra high dose rate single pulse proton source
- Flacco A
- Bayart E.
- Romagnani L
- Cavallone M.
- de Marzi L.
- Fouillade C
- Giaccaglia C.
- Heinrich S.
- Lamarre-Jouenne I.
- Monzac J.
- Parodi K.
- Patriarca A
- Rösch T
- Schreiber J
- Tischendorf L
Scientific Reports, Nature Publishing Group , 2025, 15, pp.16511 . Laser-driven proton sources have long been developed with an eye on their potential for medical application to radiation therapy. These sources are compact, versatile, and show peculiar characteristics such as extreme instantaneous dose rates, short duration and broad energy spectrum. Typical temporal modality of laser-driven irradiation, the so-called fast-fractionation, results from the composition of multiple, temporally separated, ultra-short dose fractions. In this paper we present the use of a high-energy laser system for delivering the target dose in a single nanosecond pulse, for ultra-fast irradiation of biological samples. A transport line composed by two permanent-magnet quadrupoles and a scattering system is used to improve the dose profile and to control the delivered dose-per-pulse. A single-shot dosimetry protocol for the broad-spectrum proton source using Monte Carlo simulations was developed. Doses as high as 20 Gy could be delivered in a single shot, lasting less than 10 ns over a 1 cm diameter biological sample, at a dose-rate exceeding 10 9 Gy s -1 . Exploratory application of extreme laser-driven irradiation conditions, falling within the FLASH irradiation protocol, are presented for irradiation in vitro and in vivo. A reduction of radiation-induced oxidative stress in vitro and radiation-induced developmental damage compatible with the onset of FLASH effect were observed in vivo, whereas anti-tumoral efficacy was confirmed by cell survival assay. (10.1038/s41598-025-01105-z)
DOI : 10.1038/s41598-025-01105-z
Two-dimensional infrared spectroscopy using a fast-scanning interferometer and chirped pulse up-conversion at 100 kHz
- Jonušas Mindaugas
- Bournet Quentin
- Bonvalet Adeline
- Natile Michele
- Ersen Andrei-Ovidiu
- Guichard Florent
- Zaouter Yoann
- Georges Patrick
- Druon Frédéric
- Hanna Marc
- Joffre Manuel
The Journal of Chemical Physics, American Institute of Physics , 2025, 162 (17), pp.174201 . We report on a 100-kHz two-dimensional infrared (2DIR) spectrometer in the pump-probe geometry, which we apply to the measurement of the 2DIR spectrum of carboxy-hemoglobin. The probe pulses are spectrally resolved by chirped-pulse upconversion (CPU) using a fast 2048-pixel linescan CMOS camera. The two-pulse pump sequence is generated using a conventional interferometer with a fast-scanning mechanical delay line allowing to achieve a scanning frequency of 2 Hz. The resulting modulation frequency of 3.1 kHz is large enough to shift the relevant signal away from the low-frequency noise of the laser source. The combined use of an interferometer on the pump side and of CPU on the probe side opens the way to an improved spectral resolution in both pump and probe dimensions, as compared to currently-available 100-kHz 2DIR spectrometers based on pulse shapers and Mercury-Cadmium Telluride (MCT) detector arrays. (10.1063/5.0261494)
DOI : 10.1063/5.0261494
Genome wide analyses reveal the role of mutator phenotypes in Mycobacterium tuberculosis drug resistance emergence
- Zein-Eddine R.
- Le Meur Adrien
- Skouloubris S.
- Jelsbak L.
- Refrégier Guislaine
- Myllykallio Hannu Hannu
npj Antimicrobials and Resistance, Springer Nature , 2025, 3 (1), pp.35 . Antimicrobial combination therapy is widely used to combat Mycobacterium tuberculosis (Mtb), yet resistance rates continue to rise. Mutator strains, with defects in DNA repair genes, drive resistance in other bacterial infections, but their role in Mtb remains unclear. Here, we study the contribution of single nucleotide polymorphisms (SNPs) in DNA Repair, Replication, and Recombination (3 R) genes to Mtb resistance. Through large-scale bioinformatics analysis of 53,589 whole-genomes, we identified 18 novel SNPs in lineages 2 and 4 linked to genotypic drug resistance in 3 R genes, covering 12.5% of clinical isolates with available genome sequences. Notably, a number of the detected SNPs were positively selected during Mtb evolution. Experimental tests showed that mutM, fpgg2, xthA, and nucS mutants had increased the mutation frequency compared to the wild type. Our findings highlight the role of 3 R gene mutations in resistance, emphasizing the need for surveillance to improve early detection and control strategies. (10.1038/s44259-025-00107-1)
DOI : 10.1038/s44259-025-00107-1
In vivo autofluorescence lifetime imaging of the Drosophila brain captures metabolic shifts associated with memory formation
- Roussel Philémon
- Zhou Mingyi
- Stringari Chiara
- Preat Thomas
- Plaçais Pierre-Yves
- Genovesio Auguste
eLife, eLife Sciences Publication , 2025 . Abstract Neuronal energy regulation is increasingly recognized as a critical factor underlying brain functions and their pathological alterations, yet the metabolic dynamics that accompany cognitive processes remain poorly understood. As a label-free and minimally invasive technique, fluorescence lifetime imaging (FLIM) of coenzymes NADH and NADPH (collectively referred to as NAD(P)H) offers the possibility to resolve cellular metabolic profiles with high spatial precision. However, NAD(P)H FLIM’s capacity to detect subtle changes in neuronal metabolism associated with cognition has not been demonstrated. In this study, we applied NAD(P)H FLIM to map the metabolic profiles of Drosophila neurons in vivo across multiple scales, focusing on the primary centers for associative memory: the mushroom bodies (MBs). At a broad scale, we obtained an overview of the metabolic signatures of the main brain tissue and identified a marked difference between neuropil and cortex areas. At a finer scale, our findings revealed notable heterogeneity in the basal metabolic profiles of distinct MB neuron subtypes. Measurements performed after associative olfactory learning also uncovered a subtype-specific metabolic shift associated with memory formation, demonstrating the utility of NAD(P)H FLIM in detecting physiology-driven changes linked to brain function. These results establish a promising framework for studying cerebral energy dynamics in vivo. (10.7554/eLife.106040.1)
DOI : 10.7554/eLife.106040.1
Ultra-Specific G-Quadruplex–Colistin Interaction for Efficient Transcriptome-Wide G4 Mapping
- Wei Shijiong
- Zhang Xiaobo
- Feng Yilong
- Tao Shentong
- Qiu Dehui
- Yan Xinrong
- Li Guangming
- Guittat Lionel
- Zhang Wenli
- Monchaud David
- Mergny Jean-Louis
- Ju Huangxian
- Zhou Jun
Journal of the American Chemical Society, American Chemical Society , 2025, 147, pp.9962 - 9971 . G-quadruplexes (G4s) are challenging targets for chemical biology interventions, notably because of their dynamic topological polymorphism. We found that the antibiotic smallmolecule colistin (COL) interacts specifically with a single subtype of G4 structures, the so-called parallel G4s. This interaction triggers the aggregation of the G4/COL complexes in a structure-specific manner, which can thus be separated from the bulk solution by centrifugation. This unprecedented mode of affinity-precipitation was exploited here to design the COL-induced RNA G4 precipitation and sequencing (CoRP-seq) protocol, which allows for the assessment of the prevalence of RNA G4s in the transcriptome of human cells in a straightforward manner. CoRP-seq shines by its ultraspecificity, simplicity, and practical convenience, which thus advances G4 mapping further and addresses unmet needs in the field of G4omics. (10.1021/jacs.5c01172)
DOI : 10.1021/jacs.5c01172
Increasing the Accuracy and Robustness of the CHARMM General Force Field with an Expanded Training Set
- Croitoru Anastasia
- Kumar Anmol
- Lambry Jean-Christophe
- Lee Jihyeon
- Sharif Suliman
- Yu Wenbo
- Mackerell Alexander
- Aleksandrov Alexey
Journal of Chemical Theory and Computation, American Chemical Society , 2025, 21 (6), pp.3044-3065 . <div><p>Small molecule empirical force fields (FFs), including the CHARMM General Force Field (CGenFF), are designed to have wide coverage of organic molecules and to rapidly assign parameters to molecules not explicitly included in the FF. Assignment of parameters to new molecules in CGenFF is based on a trained bond-angledihedral charge increment linear interpolation scheme for the partial atomic charges along with bonded parameters assigned based on analogy using a rules-based penalty score scheme associated with atom types and chemical connectivity. Accordingly, the accuracy of CGenFF is related to the extent of the training set of available parameters. In the present study that training set is extended by 1,390 molecules selected to represent connectivities new to CGenFF training compounds. Quantum mechanical (QM) data for optimized geometries, bond, valence angle, and dihedral angle potential energy scans, interactions with water, molecular dipole moments, and electrostatic potentials were used as target data. The resultant bonded parameters and partial atomic charges were used to train a new version of the CGenFF program, v5.0, which was used to generate parameters for a validation set of molecules, including drug-like molecules approved by the FDA, which were then benchmarked against both experimental and QM data. CGenFF v5.0 shows overall improvements with respect to QM intramolecular geometries, vibrations, dihedral potential energy scans, dipole moments and interactions with water. Tests of pure solvent properties of 216 molecules show small improvements versus the previous release of CGenFF v2.5.1 reflecting the high quality of the Lennard-Jones parameters that were explicitly optimized during the initial optimization of both the CGenFF and the CHARMM36 force field. CGenFF v5.0 represents an improvement that is anticipated to more accurately model intramolecular geometries and strain energies as well as non-covalent interactions of drug-like and other organic molecules.</p></div> (10.1021/acs.jctc.5c00046)
DOI : 10.1021/acs.jctc.5c00046
Nance-Horan-Syndrome-like 1b controls mesodermal cell migration by regulating protrusion and actin dynamics during zebrafish gastrulation.
- Escot Sophie
- Hassanein Yara
- Elouin Amélie
- Torres-Paz Jorge
- Mellottee Lucille
- Ignace Amandine
- David Nicolas B
Communications Biology, Nature Publishing Group , 2025, 8 (1), pp.328 . Cell migrations are crucial for embryonic development, wound healing, the immune response, as well as for cancer progression. In most cells, the RAC1/Arp2/3/WAVE signalling pathway induces branched actin polymerisation, which protrudes the membrane and allows migration. Fine-tuning the activity of the RAC1/Arp2/3/WAVE complex modulates protrusion lifetime and migration persistence. Recently, NHSL1, a novel interactor in this complex has been identified as a negative regulator of cell migration in vitro. We here analysed its function in vivo, during zebrafish gastrulation, as nhsl1b is specifically expressed in migrating mesodermal cells. Loss and gain of function experiments revealed that nhsl1b is required for the proper migration of the mesoderm, controlling cell speed and migration persistence. Consistent with a role in regulating actin dynamics, Nhsl1b localises to the tip of actin-rich protrusions. However, in contrast to the in vitro situation, it appears to be a positive regulator of migration, with its loss of function reducing the length and lifetime of protrusions, whereas overexpression has the opposite effect. These results reveal that the effects of actin modulators depend on the cellular context, and highlight the importance of analysing their function in physiological contexts. (10.1101/2023.01.28.526006)
DOI : 10.1101/2023.01.28.526006
Fast and Efficient Red‐absorbing Photoswitching Proteins Based on Flavin–Ligand Charge Transfer Complexes
- Zhuang Bo
- Liebl Ursula
- Vos Marten
- Sliwa Michel
ChemPhotoChem, Wiley , 2025 . Recently a novel class of reversible protein photoswitches has been discovered that is based on a charge transfer (CT) complex composed of the flavin cofactor and a substrate‐analogue inhibitor molecule in the family of sarcosine oxidase flavoproteins. Here, excitation of the CT band results in barrierless dissociation of the CT complex on the femtosecond timescale followed by its thermally activated reformation, on the timescale of a few nanoseconds at ambient temperature. The photoreaction is thought to involve a well‐defined isomerization of the inhibitor without its dissociation from the protein. This reaction occurs with an unusually high quantum yield (~80%), is initiated by absorption in the red part of the visible absorption spectrum, and leads to a photoproduct absorbing in the blue spectral region (negative photochromism). Therefore, this class of photoswitches can be considered a promising template for developing a new class of fast negative photochromic compounds for Life Science applications provided the lifetime of the photoproducts (‘light state’) can be prolonged. Potential future developments will be discussed. (10.1002/cptc.202500012)
DOI : 10.1002/cptc.202500012
G-quadruplexes are promoter elements controlling nucleosome exclusion and RNA polymerase II pausing
- Esnault Cyril
- Zine El Aabidine Amal
- Robert Marie-Cécile
- Cucchiarini Anne
- Magat Talha
- Pigeot Alexia
- Bouchouika Soumya
- Garcia-Oliver Encar
- Gawron Kevin
- Basyuk Eugénia
- Karpinska Magdalena A
- Kozulic-Pirher Alja
- Luo Yu
- Verga Daniela
- Mourad Raphael
- Radulescu Ovidiu
- Mergny Jean-Louis
- Bertrand Edouard
- Andrau Jean-Christophe
Nature Genetics, Nature Publishing Group , 2025, 57 (8), pp.1981-1993 . Despite their central role in transcription, it has been difficult to define universal sequences associated to eukaryotic promoters. Within chromatin context, recruitment of the transcriptional machinery requires promoter opening but how DNA elements could contribute to this process is unclear. Here, we show that G-quadruplex (G4) secondary DNA structures are highly enriched at mammalian promoters. G4s are located at the deepest point of nucleosome exclusion at promoters and correlate with maximum promoter activity. We found that experimental G4s exclude nucleosomes in vivo and in vitro while favouring strong positioning. At model promoters, impairing G4s affected both transcriptional activity and chromatin opening. G4 destabilization also resulted in an inactive promoter state and affected transition to effective RNA production. Finally, G4 stabilization resulted in global reduction of proximal promoter pausing. Altogether, our data introduce G4s as bona fide promoter elements allowing nucleosome exclusion and facilitating pause release by the RNA Polymerase II. (10.1038/s41588-025-02263-6)
DOI : 10.1038/s41588-025-02263-6
Understanding the key challenges in tuberculosis drug discovery: what does the future hold?
- Zein-Eddine Rima
- Ramuz Masoud
- Refrégier Guislaine
- Lutzeyer Johannes F
- Aleksandrov Alexey
- Myllykallio Hannu
Expert Opinion on Drug Discovery, Informa Healthcare , 2025, 20 (9), pp.1115-1130 . Introduction: Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a major global health concern. It spreads through airborne droplets and has a high mortality rate, particularly without treatment. Drug resistance is rising, with treatments against multidrug-resistant TB (MDR-TB) showing poor treatment success rates. The thick, lipid-rich wall of Mtb and its slow growth reduce antibiotic effectiveness, requiring long treatment courses of 4-6 months. Current therapies often fail against drugresistant strains, highlighting the urgent need for new, short-course treatment, affordable, and combination-friendly drugs. Areas covered: Within this perspective, the authors review and comment on the following topics regarding Mtb resistance emergence and treatment strategies: i) Existing treatment ii) Resistance evolution in Mtb; iii) Key challenges in drug discovery targeting Mtb; iv) emerging strategies and recent advances in Mtb drug discovery, and v) Next-generation approaches. Literature was identified through a search of PubMed, google scholar, and web of science, from January 2010 to March 2025. Expert opinion: AI is accelerating the discovery of bioavailable and safe preclinical drug candidates for TB, though data limitations and biological complexity remain challenging. Future progress requires multi-modal models, open-access datasets, and interdisciplinary collaboration. (10.1080/17460441.2025.2531229)
DOI : 10.1080/17460441.2025.2531229
The Mappa mundi of Albi: Insight into the manufacturing, life and conservation state of an 8th century world map
- Robinet Laurianne
- Heu-Thao Sylvie
- Galante Giulia
- Latour Gaël
- Tournié Aurélie
- Daher Céline
- Dan Anca
- Schanne-Klein Marie-Claire
- Michelin Anne
- Deschaux Jocelyne
Journal of Cultural Heritage, Elsevier , 2025, 74, pp.341-352 . The Mappa mundi of Albi is one of the oldest examples of spatial representation of the Western world. The small map conserved on the verso of folio 57 in manuscript 29 of the Médiathèque Pierre Amalric in Albi (France) was drawn on parchment, probably made in the second half of the 8th century, somewhere between south-western France and northern Spain, maybe in Albi itself. Because of its exceptional importance for the history of space representation, the map, together with the Index of seas and winds facing it, on the recto of folio 58, was recorded in the UNESCO Memory of the World Register in 2015. The detailed study published here has examined the manuscript’s structure and characterised the different constitutive materials. Observations and physicochemical analyses were performed on the map and the index, from the micro to the macroscale, combining optical microscopy, XRF, FORS, FTIR, and micro-Raman spectroscopy, hyperspectral imaging, proteomic analysis, and non-linear optical microscopy. Three manuscripts conserved at the same library or suspected to have been produced in the scriptorium of Albi have also been examined for comparisons. This material investigation complements the historical studies of the map by shedding new light on the manufacturing, life, and conservation state of this exceptional document. (10.1016/j.culher.2025.05.013)
DOI : 10.1016/j.culher.2025.05.013
A Chimeric Photo-Controllable CRISPR/Cas12a System for Universal and Fast Diagnostics
- Yan Xinrong
- Liu Bin
- Zhou Shuguang
- Fan Yanjun
- Wei Shijiong
- Qiu Dehui
- Xiang Henglong
- Zhou Jiahang
- Mergny Jean-Louis
- Monchaud David
- Ju Huangxian
- Zhou Jun
Analytical Chemistry, American Chemical Society , 2025, 97 (44), pp.24634 - 24642 . The potential of clustered regularly interspaced short palindromic repeats (CRISPR) and corresponding CRISPR-associated (Cas) protein systems (CRISPR/Cas) systems for biomedical applications is tremendous; however, precise control of their activity is essential to better harness this potential and, beyond this, to develop reliable diagnostic reagents. Herein, we report on such a strategy by controlling the CRISPR/Cas12a activity using a photo-controllable CRISPR RNA (crRNA). To this end, the 3′ end of crRNA was conjugated to a G-quadruplex (G4) block through a photocleavable linker: upon photo irradiation, the G4 trigger is removed, thus allowing for the DNA target to access and hybridize with the crRNA, and thus be processed by the CRISPR/Cas12a system. The efficiency of this approach was demonstrated by the detection of human papillomavirus 16 DNA in 50 clinical samples: our one-pot strategy was found to be as efficient as the routinely implemented method (qPCR), with 95.7% sensitivity and 100% specificity, in addition to be faster (25 versus 60 min) and both simpler and less expensive (being implementable as lateral flow test strips). Collectively, this new and fully controllable CRISPR/Cas system holds great potential for next-generation clinical diagnostics. (10.1021/acs.analchem.5c04782)
DOI : 10.1021/acs.analchem.5c04782
Intrinsic variation of the polarization-resolved SHG from collagen: Multiscale analysis and application to parchments
- Galante Giulia
- Robinet Laurianne
- Heu-Thao Sylvie
- Caporal Clément
- Latour Gaël
- Schanne-Klein Marie-Claire
APL Photonics, AIP Publishing LLC , 2025, 10 (5), pp.056106 . Second harmonic generation (SHG) microscopy is nowadays the gold standard technique for collagen structural imaging in intact tissues with sub-micrometer resolution. This multiphoton modality can be combined with polarimetry to provide key information about the 3D hierarchical organization of collagen. Notably, the so-called anisotropy parameter processed from polarization-resolved SHG (P-SHG) has been shown to vary with the orientational disorder of the fibrils within the focal volume and with their out-of-plane orientation. However, analytical equations describing both effects within the same formalism are still lacking. In this work, we present a unified multiscale theoretical approach of the intrinsic variations of the anisotropy parameter. We then measure these variations in the very same collagen samples to ensure reliable comparisons. To that end, we use parchments, which are materials made from animal skins and which contain almost exclusively collagen. These parchments are manufactured in different ways to obtain different collagen distributions. Our series of measurements exhibit a good agreement with our theoretical approach, which shows the relevance of P-SHG measurements to probe collagen multiscale organization in tissues. (10.1063/5.0250484)
DOI : 10.1063/5.0250484
Spatial distribution and stability of Gd<sub>0.6</sub>Eu<sub>0.4</sub>VO<sub>4</sub> nanoparticles injected in mouse ear pinnae
- Proiou Eleni
- Pinakidou Fani
- Paloura Eleni C
- Pétri Nicolas
- Gacoin Thierry
- Laplace-Builhé Corinne
- Schuck Götz
- Alexandrou Antigoni
- Katsikini Maria
Trends in Analytical Chemistry, Elsevier , 2025, 182, pp.118049 . X-Ray Fluorescence (XRF) mapping is employed for the study of the spatial distribution of GdVO<sub>4</sub>:Eu nanoparticles (NPs) after their injection into mouse ear pinnae. The injected NP colloids were detectable in a concentration range from 5 to 30 mM in vanadate ions (90-530 nM in NP concentrations). The distribution maps were recorded separately for Gd, Eu, and V and reveal that the three elements are collocalized, indicating the NP stability after the injection. The distribution pattern of the NPs is not homogeneous; they follow bifurcated paths of easy flow demonstrating the complexity of the tissue-colloid interactions. The V-K, Gd-L 3 and Eu-L 3 -edge Xray Absorption Fine Structure (XAFS) spectra of the NPs recorded prior to and after their injection confirm that the integrity of the nanoparticles is preserved after injection. This combined XRF/XAFS analysis paves the way for studies on the long-term fate of injected Gd-containing NPs in tissues. (10.1016/j.trac.2024.118049)
DOI : 10.1016/j.trac.2024.118049
Synthesis of new 1,3-bis[(4-(substituted-aminomethyl)phenyl)methyl]benzene and 1,3-bis[(4-(substituted-aminomethyl)phenoxy)methyl]benzene derivatives, designed as novel potential G-quadruplex antimalarial ligands
- Albenque-Rubio Sandra
- Guillon Jean
- Agnamey Patrice
- Damiani Céline
- Savrimoutou Solène
- Ronga Luisa
- Hanot Marie
- Zangmo Tshering
- Pinaud Noël
- Moreau Stéphane
- Mergny Jean-Louis
- Marchivie Mathieu
- Moukha Serge
- Estela Fabienne
- Dozolme Pascale
- Cohen Anita
- Sonnet Pascal
Drugs and Drug Candidates, MDPI , 2025, 4 (3), pp.39 . Background: Based on our previously reported series of novel 1,3,5-tris[(4-(substituted-aminomethyl)phenyl)methyl]benzene and 1,3,5-tris[(4-(substituted-aminomethyl)phenoxy)methyl]benzene derivatives, we have now designed, synthesized, and tested a new series of novel restricted and simplified structural analogues of these compounds against Plasmodium falciparum in vitro; i.e., the 1,3-bis[(4-(substituted-aminomethyl)phenyl)methyl]benzene and 1,3-bis[(4-(substituted-aminomethyl)phenoxy)methyl]benzene compounds. Methods & results: The pharmacological results revealed significant antimalarial activity, with IC50 values in the submicromolar to micromolar range. Additionally, the in vitro cytotoxicity of these new nitrogen-containing polyphenyl- or -phenoxymethylbenzene compounds was evaluated on human HepG2 cells. The compound 1f, the 1,3-bis[(4-(3-(morpholin-1-yl)propyl)aminomethyl)phenoxy)methyl]benzene derivative, emerged as one of the most potent and promising antimalarial candidates, demonstrating a cytotoxicity/antiprotozoal activity ratio of 594 against the chloroquine-sensitive Plasmodium falciparum 3D7 strain. Additionally, the 1,3-bis[((substituted aminomethyl)phenyl)methyl]benzene compound 1j and the 1,3-bis[((substituted aminomethyl)phenoxy)methyl]benzenes 2p and 2q also showed strong antimalarial potential, with selectivity indexes (SI) of over 303, 280, and 217, respectively, against the 3D7 strain, which has mefloquine-reduced sensitivity. Furthermore, the 1,3-bis[(4-(pyridin-2-ylethylaminomethyl)phenyl)methyl]benzene 2k was identified as the most noteworthy antimalarial compound, exhibiting a selectivity index (SI) that was superior to 178 against the chloroquine-resistant Plasmodium falciparum W2 strain. It has previously been suggested that the telomeres of P. falciparum may serve as potential targets for these polyaromatic compounds; thus, we assessed the ability of our novel derivatives to stabilize parasitic telomeric G-quadruplexes using a FRET melting assay. Conclusions: However, regarding the stabilization of the protozoan G-quadruplex, it was noted that the few substituted derivatives, which showed interesting stabilization profiles, were not necessarily the most effective antimalarial compounds against both Plasmodium strains. Moreover, these new compounds did not show promising stabilizing effects on the different G4 sequences. Therefore, no correlation arises between their antimalarial activity and the selectivity of their binding to G-quadruplexes. (10.3390/ddc4030039)
DOI : 10.3390/ddc4030039
I-motif formation in the promoter region of the B-MYB proto-oncogene
- Alves André
- Miranda André
- Zanin Irene
- Richter Sara N
- Mergny Jean-Louis
- Cruz Carla
International Journal of Biological Macromolecules, Elsevier , 2025, 296, pp.139582 . Understanding the mechanisms of carcinogenesis is essential to combat cancer. The search for alternative targets for anticancer therapy has gained interest, particularly when focused on upstream pathways. This strategy is particularly relevant when the encoded target proteins are knownor believed -to be "undruggable", as has been reported for the B-MYB oncogene. This gene, which regulates survival and cell cycle regulation, is overexpressed in cancer and correlates with an unfavorable prognosis. In this study, we focused on the identification of the i-motif (iM) structures in the promoter region of B-MYB as a possible anticancer target, with a complete biophysical characterization and in cell formation assessment using iM-CUT&Tag. Additionally, the interaction of the iM structures with a library of small molecules was investigated.</p></div> (10.1016/j.ijbiomac.2025.139582)
DOI : 10.1016/j.ijbiomac.2025.139582
Mechanism of Ultrafast Flavin Photoreduction in the Active Site of Flavoenzyme LSD1 Histone Demethylase
- Zhuang Bo
- Ramodiharilafy Rivo
- Aleksandrov Alexey
- Liebl Ursula
- Vos Marten H
Chemical Science, The Royal Society of Chemistry , 2025, 16, pp.338 - 344 . Photoreduction of oxidized flavins has a functional role in photocatalytic and photoreceptor flavoproteins. In flavoproteins without light-dependent physiological functions, ultrafast, reversible flavin photoreduction is supposedly photoprotective by nature, and holds potential for nonnatural photocatalytic applications. In this work, we combine protein mutagenesis, ultrafast spectroscopy, molecular dynamics simulations and quantum mechanics calculations to investigate the nonfunctional flavin photoreduction in a flavoenzyme, lysine-specific demethylase 1 (LSD1) which is pivotal in DNA transcription. LSD1 harbors an oxidized flavin adenine dinucleotide (FAD) cofactor and multiple electron-donating residues in the active site. Upon photoexcitation, the FAD cofactor is photoreduced in < 200 fs by electron transfer (ET) from nearby residue(s), and the charge pairs recombine in ca. 2 ps. Site-directed mutagenesis pinpoints a specific tryptophan residue, W751, as the primary electron donor, whereas a tyrosine residue, Y761, despite being located closer to the flavin ring, does not effectively contribute to the process. Based on a hybrid quantum–classical computational approach, we characterize the W751–FAD and Y761–FAD charge-transfer states (CTW751 and CTY761, respectively), as well as the FAD locally excited state (LEFAD), and demonstrate that the coupling between LEFAD and CTW751 is larger than those involving CTY761 by an order of magnitude, rationalizing the experimental observations. More generally, this work highlights the role of the intrinsic protein environment and details of donor–acceptor molecular configurations on the dynamics of short-range ET involving a flavin cofactor and amino acid residue(s). (10.1039/D4SC06857B)
DOI : 10.1039/D4SC06857B
Ultrafast dynamics of the UV-induced electronic relaxation in DNA guanine-thymine dinucleotides: from the Franck-Condon states to the minima of the potential energy surfaces
- Petropoulos Vasilis
- Martinez-Fernandez Lara
- Uboldi Lorenzo
- Maiuri Margherita
- Cerullo Giulio
- Balanikas Evangelos
- Markovitsi Dimitra
Physical Chemistry Chemical Physics, Royal Society of Chemistry , 2025 . We study the DNA dinucleotide 5’-dGpdT-3’ (abbreviated as GT) as a model system for the relaxation of the electronic excited states in stacked nucleobases. Quantum chemistry calculations determine the Franck-Condon... (10.1039/D5CP00788G)
DOI : 10.1039/D5CP00788G
Factors Affecting the Population of Excited Charge Transfer States in Adenine/Guanine Dinucleotides: A Joint Computational and Transient Absorption Study
- Petropoulos Vasilis
- Martinez-Fernandez Lara
- Uboldi Lorenzo
- Maiuri Margherita
- Cerullo Giulio
- Balanikas Evangelos
- Markovitsi Dimitra
Biomolecules, MDPI , 2024, 14 (12), pp.1548 . There is compelling evidence that the absorption of low-energy UV radiation directly by DNA in solution generates guanine radicals with quantum yields that are strongly dependent on the secondary structure. Key players in this unexpected phenomenon are the photo-induced charge transfer (CT) states, in which an electric charge has been transferred from one nucleobase to another. The present work examines the factors affecting the population of these states during electronic relaxation. It focuses on two dinucleotides with opposite orientation: 5′-dApdG-3′ (AG) and 5′-dGpdA-3′ (GA). Quantum chemistry calculations determine their ground state geometry and the associated Franck–Condon states, map their relaxation pathways leading to excited state minima, and compute their absorption spectra. It has been shown that the most stable conformer is anti-syn for AG and anti-anti for GA. The ground state geometry governs both the excited states populated upon UV photon absorption and the type of excited state minima reached during their relaxation. Their fingerprints are detected in the transient absorption spectra recorded with excitation at 266 nm and a time resolution of 30 fs. Our measurements reveal that in the large majority of dinucleotides, chromophore coupling is already operative in the ground state and that the charge transfer process occurs within ~120 fs. The competition among various relaxation pathways affects the quantum yields of the CT state formation in each dinucleotide, which are estimated to be 0.18 and 0.32 for AG and GA, respectively. (10.3390/biom14121548)
DOI : 10.3390/biom14121548
Archaerhodopsin 3 is an ideal template for the engineering of highly fluorescent optogenetic reporters
- Herasymenko Krystyna
- Walisinghe Danushka
- Konno Masae
- Barneschi Leonardo
- de Waele Isabelle
- Sliwa Michel
- Inoue Keiichi
- Olivucci Massimo
- Haacke Stefan
Chemical Science, The Royal Society of Chemistry , 2024, 16 (2), pp.761-774 . Archaerhodopsin-3 (AR-3) variants stand out among other rhodopsins in that they display a weak, but voltage-sensitive, near-infrared fluorescence emission. This has led to their application in optogenetics both in cell cultures and small animals. However, in the context of improving the fluorescence characteristics of the next generation of AR-3 reporters, an understanding of their ultrafast light-response in light-adapted conditions, is mandatory. To this end, we present a combined experimental and computational investigation of the excited state dynamics and quantum yields of AR-3 and its DETC and Arch-5 variants. The latter always display a mixture of all-trans/15-anti and 13-cis/15-syn isomers, which leads to a bi-exponential excited state decay. The isomerisation quantum yield is reduced more than 20 times as compared to WT AR-3 and proves that the steady-state fluorescence is induced by a single absorption photon event. In wild-type AR-3, we show that a 300 fs, barrier-less and vibrationally coherent isomerization is driven by an unusual covalent electronic character of its all-trans retinal chromophore leading to a metastable twisted diradical (TIDIR), in clear contrast to the standard charge-transfer scenario established for other microbial rhodopsins. We discuss how the presence of TIDIR makes AR-3 an ideal candidate for the design of variants with a one-photon induced fluorescence possibly reaching the emission quantum yield of the top natural emitter neorhodopsin (NeoR). (10.1039/d4sc05120c)
DOI : 10.1039/d4sc05120c
Design, Synthesis, and In Vitro Antimalarial Evaluation of New 1,3,5-Tris[(4-(Substituted-Aminomethyl)Phenoxy)Methyl]Benzenes
- Albenque-Rubio Sandra
- Guillon Jean
- Agnamey Patrice
- Damiani Céline
- Savrimoutou Solène
- Mustière Romain
- Pinaud Noël
- Moreau Stéphane
- Mergny Jean-Louis
- Ronga Luisa
- Kanavos Ioannis
- Marchivie Mathieu
- Moukha Serge
- Dozolme Pascale
- Sonnet Pascal
- Cohen Anita
Drugs and Drug Candidates, MDPI , 2024, 3 (3), pp.615-637 . By taking into account our previously described series of 1,3,5-tris[(4-(substituted-aminomethyl)phenyl)methyl]benzene compounds, we have now designed, prepared, and evaluated in vitro against Plasmodium falciparum a novel series of structural analogues of these molecules, i.e., the 1,3,5-tris[(4-(substituted-aminomethyl)phenoxy)methyl]benzene derivatives. The pharmacological data showed antimalarial activity with IC50 values in the sub and μM range. The in vitro cytotoxicity of these new nitrogen polyphenoxymethylbenzene compounds was also evaluated on human HepG2 cells. The 1,3,5-tris[(4-(substituted-aminomethyl)phenoxy)methyl]benzene derivative 1m was found as one of the most potent and promising antimalarial candidates with favorable cytotoxic to antiprotozoal properties in the P. falciparum strains W2 and 3D7. In conclusion, this 1,3,5-tris[(4-(pyridin-3-ylmethylaminomethyl)phenoxyl)methyl]benzene 1m (IC50 = 0.07 μM on W2, 0.06 μM on 3D7, and 62.11 μM on HepG2) was identified as the most promising antimalarial derivative with selectivity indexes (SI) of 887.29 on the W2 P. falciparum chloroquine-resistant strain, and of 1035.17 on the chloroquine-sensitive and mefloquine decreased sensitivity strain 3D7. It has been previously described that the telomeres of P. falciparum could represent potential targets for these types of polyaromatic compounds; therefore, the capacity of our novel derivatives to stabilize the parasitic telomeric G-quadruplexes was assessed using a FRET melting assay. However, with regard to the stabilization of the protozoal G-quadruplex, we observed that the best substituted derivatives 1, which exhibited some interesting stabilization profiles, were not the most active antimalarial compounds against the two Plasmodium strains. Thus, there were no correlations between their antimalarial activities and selectivities of their respective binding to G-quadruplexes. (10.3390/ddc3030035)
DOI : 10.3390/ddc3030035
The Balance Between Shear Flow and Extracellular Matrix in Ovarian Cancer‐on‐Chip
- Chen Changchong
- Boché Alphonse
- Wang Zixu
- Lopez Elliot
- Peng Juan
- Carreiras Franck
- Schanne-Klein Marie‐claire
- Chen Yong
- Lambert Ambroise
- Aimé Carole
Advanced Healthcare Materials, Wiley , 2024, 13 (23), pp.2400938 . Ovarian cancer is the most lethal gynecologic cancer in developed countries. In the tumor microenvironment, the extracellular matrix (ECM) and flow shear stress are key players in directing ovarian cancer cells invasion. Artificial ECM models based only on ECM proteins are used to build an ovarian tumor‐on‐chip to decipher the crosstalk between ECM and shear stress on the migratory behavior and cellular heterogeneity of ovarian tumor cells. This work shows that in the shear stress regime of the peritoneal cavity, the ECM plays a major role in driving individual or collective ovarian tumor cells migration. In the presence of basement membrane proteins, migration is more collective than on type I collagen regardless of shear stress. With increasing shear stress, individual cell migration is enhanced; while, no significant impact on collective migration is measured. This highlights the central position that ECM and flow shear stress should hold in in vitro ovarian cancer models to deepen understanding of cellular responses and improve development of ovarian cancer therapeutic platforms. In this frame, adding flow provides significant improvement in biological relevance over the authors’ previous work. Further steps for enhanced clinical relevance require not only multiple cell lines but also patient‐derived cells and sera. (10.1002/adhm.202400938)
DOI : 10.1002/adhm.202400938