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Flavin-like ligands (L-1 and L-2) with extended π-conjugation were synthesized using microwave-assisted techniques. An N,N-chelating fragment was integrated into alloxazine units, providing binding sites for metal ions while retaining redox activity. The complexation capability of L-1 and L-2 with two prototypical Ru-scaffolds was examined to design Ru(II) complexes (M-1 and M-2), whose electronic properties were studied and compared with their corresponding ligands via absorption and emission spectroscopy, computational analysis (density functional theory (DFT) and time-dependent DFT (TD-DFT)), and cyclic voltammetry (CV). The ability of L-1 and M-1 to undergo alloxazine/isoalloxazine tautomerization was demonstrated to play a crucial role in the photocatalytic oxidation of NADH, including under green and red wavelengths. Moreover, the interaction of M-1 and M-2 with B-DNA and G-quadruplex structures was investigated. M-2 showed high stabilization of Kit1 and h-Telo oligonucleotides. Meanwhile, M-1 demonstrated switchable emissive properties with B-DNA and induced conformational changes in the h-Telo G-quadruplex structure.
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In this contribution we report the synthesis, characterization and in vitro anticancer activity of novel cyclometalated 4-phenylthiazole-derived ruthenium(II) (2a-e) and osmium(II) (3a-e) complexes. Formation and sufficient purity of the complexes were unambigiously confirmed by 1H-, 13C- and 2D-NMR techniques, X-ray diffractometry, HRMS and elemental analysis. The binding preferences of these cyclometalates to selected amino acids and to DNA models including G-quadruplex structures were analyzed. Additionally, their stability and behaviour in aqueous solutions was determined by UV-Vis spectroscopy. Their cellular accumulation, their ability of inducing apoptosis, as well as their interference in the cell cycle were studied in SW480 colon cancer cells. The anticancer potencies were investigated in three human cancer cell lines and revealed IC50 values in the low micromolar range, in contrast to the biologically inactive ligands.
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Antineoplásicos , Complejos de Coordinación , Rutenio , Humanos , Estructura Molecular , Modelos Moleculares , Línea Celular Tumoral , Antineoplásicos/química , Ciclo Celular , Rutenio/farmacología , Rutenio/química , Complejos de Coordinación/químicaRESUMEN
While platinum(II)-based drugs continue to be employed in cancer treatments, the escalating occurrence of severe side effects has spurred researchers to explore novel sources for potential therapeutic agents. Notably, cobalt(III) has emerged as a subject of considerable interest due to its ubiquitous role in human physiology. Several studies investigating the anticancer effects of Salphen complexes derived from cobalt(III) have unveiled intriguing antiproliferative properties. In a bid to enhance our understanding of this class of compounds, we synthesized and characterized two novel half Salphen cobalt(III) complexes. Both compounds exhibited notable stability, even in the presence of physiologically relevant concentrations of glutathione. The application of spectroscopic and computational methodologies unravelled their interactions with duplex and G4-DNAs, suggesting an external binding affinity for these structures, with preliminary indications of selectivity trends. Importantly, antiproliferative assays conducted on 3D cultured SW-1353 cancer cells unveiled a compelling anticancer activity at low micromolar concentrations, underscoring the potential therapeutic efficacy of this novel class of cobalt(III) complexes.
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Antineoplásicos , Complejos de Coordinación , Humanos , Complejos de Coordinación/química , Cobalto/farmacología , Cobalto/química , Fenilendiaminas/química , ADN/química , Antineoplásicos/químicaRESUMEN
Ruthenium(II) complexes containing diimine ligands have contributed to the development of agents for photoactivated chemotherapy. Several approaches have been used to obtain photolabile Ru(II) complexes. The two most explored have been the use of monodentate ligands and the incorporation of steric effects between the bidentate ligands and the Ru(II). However, the introduction of electronic effects in the ligands has been less explored. Herein, we report a systematic experimental, theoretical, and photocytotoxicity study of a novel series of Ru(II) complexes Ru1-Ru5 of general formula [Ru(phen)2(Nâ§N')]2+, where Nâ§N' are different minimal strained ligands based on the 1-aryl-4-benzothiazolyl-1,2,3-triazole (BTAT) scaffold, being CH3 (Ru1), F (Ru2), CF3 (Ru3), NO2 (Ru4), and N(CH3)2 (Ru5) substituents in the R4 of the phenyl ring. The complexes are stable in solution in the dark, but upon irradiation in water with blue light (λex = 465 nm, 4 mW/cm2) photoejection of the ligand BTAT was observed by HPLC-MS spectrometry and UV-vis spectroscopy, with t1/2 ranging from 4.5 to 14.15 min depending of the electronic properties of the corresponding BTAT, being Ru4 the less photolabile (the one containing the more electron withdrawing substituent, NO2). The properties of the ground state singlet and excited state triplet of Ru1-Ru5 have been explored using density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations. A mechanism for the photoejection of the BTAT ligand from the Ru complexes, in H2O, is proposed. Phototoxicity studies in A375 and HeLa human cancer cell lines showed that the new Ru BTAT complexes were strongly phototoxic. An enhancement of the emission intensity of HeLa cells treated with Ru5 was observed in response to increasing doses of light due to the photoejection of the BTAT ligand. These studies suggest that BTAT could serve as a photocleavable protecting group for the cytotoxic bis-aqua ruthenium warhead [Ru(phen)2(OH2)2]2+.
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Neoplasias , Rutenio , Humanos , Quelantes , Rutenio/farmacología , Rutenio/química , Ligandos , Células HeLa , Dióxido de NitrógenoRESUMEN
MAIN CONCLUSION: SMAX/SMXL family genes were successfully identified and characterized in the chickpea and lentil and gene expression data revealed several genes associated with the modulation of plant branching and powerful targets for use in transgenesis and genome editing. Strigolactones (SL) play essential roles in plant growth, rooting, development, and branching, and are associated with plant resilience to abiotic and biotic stress conditions. Likewise, karrikins (KAR) are "plant smoke-derived molecules" that act in a hormonal signaling pathway similar to SL playing an important role in seed germination and hairy root elongation. The SMAX/SMXL family genes are part of these two signaling pathways, in addition to some of these members acting in a still little known SL- and KAR-independent signaling pathway. To date, the identification and functional characterization of the SMAX/SMXL family genes has not been performed in the chickpea and lentil. In this study, nine SMAX/SMXL genes were systematically identified and characterized in the chickpea and lentil, and their expression profiles were explored under different unstressless or different stress conditions. After a comprehensive in silico characterization of the genes, promoters, proteins, and protein-protein interaction network, the expression profile for each gene was determined using a meta-analysis from the RNAseq datasets and complemented with real-time PCR analysis. The expression profiles of the SMAX/SMXL family genes were very dynamic in different chickpea and lentil organs, with some genes assuming a tissue-specific expression pattern. In addition, these genes were significantly modulated by different stress conditions, indicating that SMAX/SMXL genes, although working in three distinct signaling pathways, can act to modulate plant resilience. Most CaSMAX/SMXL and partner genes such as CaTiE1 and CaLAP1, have a positive correlation with the plant branching level, while most LcSMAX/SMXL genes were less correlated with the plant branching level. The SMXL6, SMXL7, SMXL8, TiE1, LAP1, BES1, and BRC1 genes were highlighted as powerful targets for use in transgenesis and genome editing aiming to develop chickpea and lentil cultivars with improved architecture. Therefore, this study presented a detailed characterization of the SMAX/SMXL genes in the chickpea and lentil, and provided new insights for further studies focused on each SMAX/SMXL gene.
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Cicer , Lens (Planta) , Lens (Planta)/genética , Cicer/genética , Biotecnología , Edición Génica , Desarrollo de la PlantaRESUMEN
The genome of SARS-CoV-2 coronavirus is made up of a single-stranded RNA fragment that can assume a specific secondary structure, whose stability can influence the virus's ability to reproduce. Recent studies have identified putative guanine quadruplex sequences in SARS-CoV-2 genome fragments that are involved in coding for both structural and non-structural proteins. In this contribution, we focus on a specific G-rich sequence referred to as RG-2, which codes for the non-structural protein 10 (Nsp10) and assumes a guanine-quadruplex (G4) arrangement. We provide the secondary structure of RG-2 G4 at atomistic resolution by molecular modeling and simulation, validated by the superposition of experimental and calculated electronic circular dichroism spectra. Through both experimental and simulation approaches, we have demonstrated that pyridostatin (PDS), a widely recognized G4 binder, can bind to and stabilize RG-2 G4 more strongly than RG-1, another G4 forming sequence that was previously proposed as a potential target for antiviral drug candidates. Overall, this study highlights RG-2 as a valuable target to inhibit the translation and replication of SARS-CoV-2, paving the way towards original therapeutic approaches against emerging RNA viruses.
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The chemical shift (CS) values obtained by 1H NMR spectroscopy for the hydrogen atoms of a tetradentate N2O2-substituted Salphen ligand (H2L1) are differently shifted in its complexes of nickel(II), palladium(II), platinum(II), and zinc(II), all bearing the same charge on the metal ions. To rationalize the observed trends, DFT calculations have been performed in the implicit d6-DMSO solvent in terms of the electronic effects induced by the metal ion and of the nature and strength of the metal-N and metal-O bonds. Overall, the results obtained point out that, in the complexes involving group 10 elements, the CS values show the greater shift when considering the two hydrogen atoms at a shorter distance from the coordinated metal center and follow the decreasing metal charge in the order Ni > Pd > Pt. This trend suggests a more covalent character of the ligand-metal bonds with the increase of the metal atomic number. Furthermore, a slightly poorer agreement between experimental and calculated data is observed in the presence of the nickel(II) ion. Such discrepancy is explained by the formation of stacked oligomers, aimed at minimizing the repulsive interactions with the polar DMSO solvent.
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The present work analyzes the complex formation ability towards Pb2+ and Cd2+ of a series of kojic acid derivatives that join the chelating properties of the pyrone molecules and those of polyamines, with the aim of evaluating how the different effects of oxygen and nitrogen coordinating groups act on the stability of metal complexes. Experimental research is carried out using potentiometric and spectrophotometric techniques supported by 1H and 13C NMR spectroscopy and DFT calculations. Actually, a different coordination mechanism toward Pb2+ and Cd2+ was proved: in the case of Pb2+, coordination takes place exclusively via the oxygen atoms, while the contribute of the nitrogen atoms appears relevant in the case of Cd2+. Lead complexes of all the studied ligands are characterized by significantly stronger stability than those of cadmium. Finally, on the basis of the measured complex formation stabilities, some of the proposed molecules seems promising effective ligands for lead and cadmium ion decorporation from polluted soils or waste waters.
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Cadmio , Plomo , Ligandos , Pironas , Nitrógeno , OxígenoRESUMEN
Carotenoid cleavage dioxygenase (CCD) gene family is organized in two subfamilies: (i) 9-cis epoxycarotenoid dioxygenase (NCED) genes and (ii) CCD genes. NCED genes are essential for catalyzing the first step of the abscisic-acid (ABA) biosynthesis, while CCD genes produce precursors of the strigolactones hormone. The functional characterization of these gene subfamilies has not been yet performed in chickpea and lentil. Herein, were identified and systematically characterized two NCED and five CCD genes in the chickpea and two NCED and six CCD genes in lentil. After in silico sequence analysis and phylogeny, the expression profile of the NCED/CCD genes was determined by meta-analysis and real-time PCR in plants under different stress conditions. Sequence data revealed that NCED/CCD genes are highly conserved between chickpea and lentil. This conservation was observed both at gene and protein sequence levels and phylogenetic relationships. Analysis of the promoter sequences revealed that all NCED/CCD genes have a considerable number of cis-regulatory elements responsive to biotic and abiotic stress. Protein sequence analysis evidenced that NCED/CCD genes share several conserved motifs and that they have a highly interconnected interaction network. Furthermore, the three-dimensional structure of these proteins was determined and indicated that some proteins have structures with considerable similarity. The meta-analysis revealed that NCED/CCD genes are dynamically modulated in different organs and under different stress conditions, but they have a positive correlation with plant tolerance. In accordance, real-time PCR data showed that both NCED and CCD genes are differentially modulated in plants under drought stress. In particular, CaNCED2, CaCCD5, LcNCED2, LcCCD1, and LcCCD2 genes have a positive correlation with improved plant tolerance to drought stress. Therefore, this study presented a detailed characterization of the chickpea and lentil NCED/CCD genes and provided new insights to improve abiotic stress tolerance in these two important crops.
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Cicer , Dioxigenasas , Lens (Planta) , Cicer/genética , Lens (Planta)/genética , Lens (Planta)/metabolismo , Filogenia , Dioxigenasas/genética , Dioxigenasas/metabolismo , Plantas/metabolismo , Proteínas de Plantas/metabolismo , Carotenoides/metabolismo , Estrés Fisiológico/genética , Regulación de la Expresión Génica de las Plantas , Ácido Abscísico/metabolismoRESUMEN
The Transmembrane Protease Serine 2 (TMPRSS2) is a human enzyme which is involved in the maturation and post-translation of different proteins. In addition to being overexpressed in cancer cells, TMPRSS2 plays a further fundamental role in favoring viral infections by allowing the fusion of the virus envelope with 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 on 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.
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Antivirales , COVID-19 , Humanos , Antivirales/farmacología , Antivirales/química , SARS-CoV-2 , Membrana Celular , SerinaRESUMEN
Guanine quadruplexes (G4s) play essential protective and regulatory roles within cells, influencing gene expression. In several gene-promoter regions, multiple G4-forming sequences are in close proximity and may form three-dimensional arrangements. We analyze the interplay among the three neighboring G4s in the c-KIT proto-oncogene promoter (WK1, WSP, and WK2). We highlight that the three G4s are structurally linked and their cross-talk favors the formation of a parallel structure for WSP. Relying on all-atom molecular dynamic simulations exceeding the µs 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 can ultimately be used as a starting point for drug discovery.
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G-Cuádruplex , Regiones Promotoras Genéticas/genética , ADN/química , Proto-OncogenesRESUMEN
Sub-nanometer metal clusters have special physical and chemical properties, significantly different from those of nanoparticles. However, there is a major concern about their thermal stability and susceptibility to oxidation. In situ X-ray Absorption spectroscopy and Near Ambient Pressure X-ray Photoelectron spectroscopy results reveal that supported Cu5 clusters are resistant to irreversible oxidation at least up to 773â K, even in the presence of 0.15â mbar of oxygen. These experimental findings can be formally described by a theoretical model which combines dispersion-corrected DFT and first principles thermochemistry revealing that most of the adsorbed O2 molecules are transformed into superoxo and peroxo species by an interplay of collective charge transfer within the network of Cu atoms and large amplitude "breathing" motions. A chemical phase diagram for Cu oxidation states of the Cu5 -oxygen system is presented, clearly different from the already known bulk and nano-structured chemistry of Cu.
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Macrocyclic ligand L, in which a 2,6-bis(2-benzoxazolyl)phenol (bis-HBO) group is incorporated in triethylenetetramine, was designed and synthesized with the aim of creating a chemosensor with high selectivity and specificity for metal cations in an aqueous environment. The availability of several proton acceptors and donors, and amine and phenol hydroxy groups, respectively, affects the keto-enol equilibrium in both the ground and excited states, and the ligand properties show dependence on the pH of the solution. L is fluorescent in the visible range, through an excited-state intramolecular proton transfer (ESIPT) mechanism. The results of an exhaustive characterization of L by spectroscopic techniques and DFT calculations, as well as of its Zn(II), Cd(II) and Pb(II) complexes, show promising properties of L as a ratiometric metal cation chemosensor, since metal coordination prevents the ESIPT and gives rise to a peculiar displacement of the fluorescence emission from green to blue with Zn(II) and Cd(II), while with Pb(II) the fluorescence is quenched.
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Guanine quadruplexes (G4s) are nucleic acid structures exhibiting a complex structural behavior and exerting crucial biological functions in both cells and viruses. The specific interactions of peptides with G4s, as well as an understanding of the factors driving the specific recognition are important for the rational design of both therapeutic and diagnostic agents. In this review, we examine the most important studies dealing with the interactions between G4s and peptides, highlighting the strengths and limitations of current analytic approaches. We also show how the combined use of high-level molecular simulation techniques and experimental spectroscopy is the best avenue to design specifically tuned and selective peptides, thus leading to the control of important biological functions.
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G-Cuádruplex , PéptidosRESUMEN
DNA G-rich sequences can organize in four-stranded structures called G-quadruplexes (G4s). These motifs are enriched in significant sites within the human genomes, including telomeres and promoters of cancer related genes. For instance, KIT proto-oncogene promoter, associated with diverse cancers, contains three adjacent G4 units, namely Kit2, SP, and Kit1. Aiming at finding new and selective G-quadruplex binders, we have synthesized and characterized five non-charged metal complexes of Pt(II), Pd(II), Ni(II), Cu(II) and Zn(II) of a chlorine substituted Salphen ligand. The crystal structure of the Pt(II) and Pd(II) complexes was determined by XRPD. FRET measurements indicated that Pt(II) and Pd(II) compounds stabilize Kit1 and Kit2 G4s but not SP, telomeric and double stranded DNA. Spectroscopic investigations (UV-Vis, circular dichroism and fluorescence) suggested the Cu(II) complex as the most G4-selective compound. Interestingly, docking simulations indicate that the synthesized compounds fit groove binding pockets of both Kit1 and Kit2 G4s. Moreover, they exhibited dose-dependent cytotoxic activity in MCF-7, HepG2 and HeLa cancer cells.
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Antineoplásicos , Complejos de Coordinación , G-Cuádruplex , Humanos , Complejos de Coordinación/farmacología , Complejos de Coordinación/química , Antineoplásicos/farmacología , Fenilendiaminas/química , Dicroismo Circular , TelómeroRESUMEN
The defense system of freshwater crayfish Procambarus clarkii as a diversified source of bioactive molecules with antimicrobial properties was studied. Antimicrobial activity of two polypeptide-enriched extracts obtained from hemocytes and hemolymph of P. clarkii were assessed against Gram positive (Staphylococcus aureus, Enterococcus faecalis) and Gram negative (Pseudomonas aeruginosa, Escherichia coli) bacteria and toward the yeast Candida albicans. The two peptide fractions showed interesting MIC values (ranging from 11 to 700 µg/mL) against all tested pathogens. Polypeptide-enriched extracts were further investigated using a high-resolution mass spectrometry and database search and 14 novel peptides were identified. Some peptides and their derivatives were chemically synthesized and tested in vitro against the bacterial and yeast pathogens. The analysis identified a synthetic derivative peptide, which showed an interesting antifungal (MIC and MFC equal to 31.2 µg/mL and 62.5 µg/mL, respectively) and antibiofilm (BIC50 equal to 23.2 µg/mL) activities against Candida albicans and a low toxicity in human cells.
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Silver nanoclusters of five atoms (Ag5) display outstanding catalytic activities for the deactivation of radicals. Using 2,2-diphenyl-1picrylhydrazyl (DPPH) radical as a model system, we observed a fast radical reduction to DPPH anions using only [Ag5] 3 to 4 orders of magnitude less than [DPPH]. Moreover, nanoclusters remain stable at the end of the reaction, and can deactivate again DPPH radicals at the same rate, indicating that they act as anti-radical catalysts. The radical scavenger catalytic activity of Ag5 proceeds selectively through the oxidation of methanol (used to dissolve the radical) to formaldehyde, which is supported by DFT calculations. The obtained catalytic rate constants are almost 2 orders of magnitude higher than oxidases, and more than 4 orders of magnitude larger than graphene quantum dots. We also show that Ag5 not only catalyze the reduction of radicals but also their oxidation, promoting the inhibition of the autoxidation mechanisms of hydrocarbon polymers, which are very sensitive to the presence of radicals. For this purpose, thin films of two industrially relevant polymers (polyisoprene and acrylonitrile-butadienestyrene copolymer), were exposed to standard simulated photo-ageing conditions in the presence of Ag5. Using Attenuated Total Reflection-FTIR and DFT modeling we observed that, although Ag5 nanoclusters, with ≈ 15% surface coverage, do not totally inhibit the oxidation, they favour a decomposition that yields inactive products, in contrast with the more detrimental ketone formation pathway. These results not only open new possibilities for developing a post-process inhibition of polymer degradation, for which nowadays there are no efficient procedures, but also, they could be used as very efficient dual-redox catalytic radical scavengers for different industrial or biomedical purposes.
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Acrilonitrilo , Grafito , Aniones , Compuestos de Bifenilo , Formaldehído , Cetonas , Metanol , Oxidación-Reducción , Oxidorreductasas , Polímeros , PlataRESUMEN
Lung cancer is one of the most common cancers worldwide, causing nearly one million deaths each year. Herein, we present the effect of 2-methoxyestradiol (2-ME), the endogenous metabolite of 17ß-estradiol (E2), on non-small cell lung cancer (NSCLC) cells. We observed that 2-ME reduced the viability of lung adenocarcinoma in two-dimensional (2D) and three-dimensional (3D) spheroidal A549 cell culture models. Molecular modeling was carried out aiming to visualize amino acid residues within binding pockets of the acyl-protein thioesterases, namely 1 (APT1) and 2 (APT2), and thus to identify which ones were more likely involved in the interaction with 2-ME. Our findings suggest that 2-ME acts as an APT1 inhibitor enhancing protein palmitoylation and oxidative stress phenomena in the lung cancer cell. In order to support our data, metabolomics of blood serum from NSCLC patients was also performed. Moreover, computational analysis suggests that 2-ME as compared to other estrogen metabolism intermediates is relatively safe in terms of its possible non-receptor bioactivity within healthy human cells due to a very low electrophilic potential and hence no substantial risk of spontaneous covalent modification of biologically protective nucleophiles. We propose that 2-ME can be used as a selective tumor biomarker in the course of certain types of lung cancers and possibly as a therapeutic adjuvant or neoadjuvant.
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We investigated the mechanisms leading to the specific recognition of Guanine Guadruplex (G4) by DARPins peptides, which can lead to the design of G4â s 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 α-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.
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G-Cuádruplex , Ácidos Nucleicos , Sitios de Unión de Anticuerpos , Proteínas de Repetición de Anquirina Diseñadas , Epítopos , Guanina/química , Humanos , Péptidos/química , Proteínas Proto-Oncogénicas c-bcl-2RESUMEN
The stimulator of interferon genes (STING) protein is a cornerstone of the human immune response. Its activation by cGAMP in the presence of cytosolic DNA stimulates the production of type I interferons and inflammatory cytokines. In the human population, several STING variants exist and exhibit dramatic differences in their activity, impacting the efficiency of the host defense against infections. Understanding the molecular mechanisms of these variants opens perspectives for personalized medicine treatments against diseases such as viral infections, cancers, or autoinflammatory diseases. Through microsecond-scale molecular modeling simulations, contact analyses, and machine learning techniques, we reveal the dynamic behavior of four STING variants (wild type, G230A, R293Q, and G230A/R293Q) and rationalize the variability of efficiency observed experimentally. Our results show that the decrease in STING activity is linked to a stiffening of key structural elements of the binding cavity together with changes in the interaction patterns within the protein.