Circular Dichroism Experiments Research Articles

New sesquiterpenoids with neuroprotective effects in vitro and in vivo from the Picrasma chinensis

Three undescribed sesquiterpenes, designed as pichinenoid A-C (1–3), along with nine known ones (4–12) were isolated from the stems and leaves of Picrasma chinensis. The new isolates including their absolute configurations were elucidated based on extensive spectroscopic methods, single crystal X-ray diffraction, and electronic circular dichroism (ECD) experiments, as well as comparison with literature data. Structurally, compounds 1 and 2 are descending sesquiterpenes, while pichinenoid C (3) is a rare sesquiterpene bearing a 2-methylenebut-3-enoic acid moiety at the C-6 side chain. All the isolated compounds were tested for their neuroprotective effects against the H2O2-induced damage on human neuroblastoma SH-SY5Y cells, and most of them showed moderate neuroprotective activity. Especially, compounds 1, 3–5, and 7 showed a potent neuroprotective effect at 25 or 50 μM. Moreover, the neuroprotective effects of compounds 1 and 4 were tested on a 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced Parkinson's disease (PD) mouse model. Results of western blot and immunofluorescence indicated that compound 4 significantly counteract the toxicity of MPTP, and reversed the expression of tyrosine hydroxylase (TH) in substantia nigra (SN) and striatum (ST) of the mouse brain. Interestingly, western blot data suggested compound 4 also enhanced B-cell lymphoma-2 (Bcl-2) and heme oxygenase 1 (HO-1) expressions in the brain tissues from MPTP damaged mouse.

Undescribed secondary metabolites derived from Cinnamomum migao H. W. Li, showcasing anti-inflammatory, antioxidant, and in silico properties

Inflammatory processes are renowned as the fundamental basis for numerous pathological conditions. The objective of this study was to assess the antioxidant, anti-inflammatory, molecular docking, and molecular dynamics simulation properties of 3 previously undescribed and 1 known guaiane-type sesquiterpenoids isolated from Cinnamomum migao. The structures of these compounds were confirmed using numerous chromatographic and spectroscopic methods, such as high-resolution electrospray ionization mass spectrometry (HRESIMS), one-dimensional nuclear magnetic resonance (1D NMR), two-dimensional nuclear magnetic resonance (2D NMR), and experimental circular dichroism (ECD). Additionally, in oxidatively stressed mouse hepatocytes, all tested compounds at a concentration of 50 µM increased the levels of natural antioxidant enzymes such as CAT, SOD, POD, and Nrf-2 compared to those in untreated cells. Compounds 1 and 2 strongly suppressed NO generation and proinflammatory cytokine production, with IC50 values of 8.76 and 5.45 µM, respectively, against TNF-α mRNA. Furthermore, the molecular docking and simulations explore the high affinity of the selected compounds and best fit in the TNF-α active site. Compounds 1 and 2 show prominent binding energies and bring significant confirmational changes in the TNF-α protein. The results of this study provide further validation for the traditional use of C. migao in the treatment of inflammation and pain, providing novel evidence regarding the therapeutic potential of the identified guaiane-type sesquiterpenoids.

Pathogenic Homocystinuria-Associated T236N Mutation Dramatically Alters the Biochemical Properties of Cystathionine Beta-Synthase Protein.

Cystathione beta-synthase (CBS) T236N is a novel mutation associated with pyridoxine non-responsiveness, which presents a significant difficulty in the medical treatment of homocystinuria. Reported severe phenotypes in homocystinuria patients highlight the urgent requirement to comprehend the molecular mechanisms underlying mutation pathogenicity for the advancement of the disease. In this study, we used a multidisciplinary approach to investigate the molecular properties of bacterially expressed and purified recombinant CBST236N protein, which we directly compared to those of the wild-type (CBSWT) protein. Our data revealed a profound impact of the p.T236N mutation on CBS enzymatic activity, with a dramatic reduction of ~96% compared to the CBSWT protein. Circular dichroism (CD) experiments indicated that the p.T236N mutation did not significantly alter the secondary structure of the protein. However, CD spectra unveiled distinct differences in the thermal stability of CBSWT and CBST236N mutant protein species. In addition, chemical denaturation experiments further highlighted that the CBSWT protein exhibited greater thermodynamic stability than the CBST236N mutant, suggesting a destabilizing effect of this mutation. Our findings provide an explanation of the pathogenicity of the p.T236N mutation, shedding light on its role in severe homocystinuria phenotypes. This study contributes to a deeper understanding of CBS deficiency and may improve the development of targeted therapeutic strategies for affected individuals.

ABC block copolymer micelles driving the thermogelation: Scattering, imaging and spectroscopy

Thermoresponsive polymers have attracted much scientific attention due to their capacity for temperature-driven hydrogel formation. For biomedical applications, such as drug delivery, this transition should be tuned below body temperature to facilitate controlled and targeted drug release. We have recently developed a thermoresponsive polymer that forms gel at low concentrations (2 w/w%) in aqueous media and offers a cost-effective alternative to thermoresponsive systems currently being applied in clinics. This polymer is an ABC triblock terpolymer, where A, B, and C correspond to oligo(ethylene glycol) methyl ether methacrylate with average Mn 300 g mol−1 (OEGMA300), n-butyl methacrylate (BuMA), and di(ethylene glycol) methyl ether methacrylate (DEGMA). To investigate the self-assembly and the gelation mechanism in diluted solutions, we used small-angle neutron scattering (SANS) on 1 w/w% (below the gelation concentration) and 5 w/w% solutions (above the gelation concentration). As a comparison, we also investigated the solutions of the most studied thermoresponsive polymer, namely, Pluronic F127, an ABA triblock bipolymer made of ethylene glycol (A) and propylene glycol (B) blocks. SANS revealed that the in-house synthesised polymer forms elliptical cylinders, whose length increases significantly with temperature. In contrast, Pluronic F127 solutions form core-shell spherical micelles, which slightly elongate with temperature. Transmission electron microscopy images support the SANS findings, with tubular/worm structures being present. Variable-temperature circular dichroism (CD) and proton nuclear magnetic resonance (1H NMR) spectroscopy experiments reveal insights on the tacticity, structural changes, and molecular origin of the self-assembly.

Synthesis of substituted terpyridine nickel nitrate complexes and their inhibitory selectivity against cancer cell lines

Six terpyridine‑nickel complexes 1–6 were formed by the coordination of 4′-(4-R-phenyl)-2,2′:6′,2″-terpyridine (R = hydroxyl (L1), methoxyl (L2), methylsulfonyl (L3), fluoro (L4), bromo (L5), iodo (L6)) derivatives to nickel nitrate. The compositions and structures of these complexes were analyzed by Fourier Transform infrared spectroscopy (FT-IR), elemental analyses, electrospray ionization mass spectra (ESI-MS), solid-state ultraviolet-visible (UV–Vis) spectroscopy, and single crystal X-ray diffraction (1, 2 and 4) studies. In vitro anticancer cell proliferation experiments against SiHa (human cervical squamous cancer cell line) cells, Bel-7402 (human hepatoma cancer cell line), Eca-109 (human esophageal cancer cell line) and HL-7702 (human normal hepatocyte cell line) indicate that they have more excellent anti-proliferation effects than the cis-platin against Siha cells, Bel-7402 cells and Eca-109 cells. Especially, complex 5 showed a rather outstanding inhibitory effect against the SiHa cell line and was less toxic than the other compounds to the HL-7702 cell line, implying an obvious specific inhibitory effect. Therefore, complex 5 has the potential value to be developed as an anticancer cell-specific drug against human cervical squamous carcinoma. Molecular docking simulation, UV–vis absorption spectroscopy and circular dichroism experiments show that they prefer to bind to DNA part in an embedded binding manner.

Unraveling the Nano-Bio Interface Interactions of a Lipase Adsorbed on Gold Nanoparticles under Laser Excitation.

The complex nature and structure of biomolecules and nanoparticles and their interactions make it challenging to achieve a deeper understanding of the dynamics at the nano-bio interface of enzymes and plasmonic nanoparticles subjected to light excitation. In this study, circular dichroism (CD) and Raman spectroscopic experiments and molecular dynamics (MD) simulations were used to investigate the potential changes at the nano-bio interface upon plasmonic excitation. Our data showed that photothermal and thermal heating induced distinct changes in the secondary structure of a model nanobioconjugate composed of lipase fromCandida antarcticafraction B (CALB) and gold nanoparticles (AuNPs). The use of a green laser led to a substantial decrease in the α-helix content of the lipase from 66% to 13% and an increase in the β-sheet content from 5% to 31% compared to the initial conformation of the nanobioconjugate. In contrast, the differences under similar thermal heating conditions were only 55% and 11%, respectively. This study revealed important differences related to the enzyme secondary structure, enzyme-nanoparticle interactions, and the stability of the enzyme catalytic triad (Ser105-Asp187-His224), influenced by the instantaneous local temperature increase generated from photothermal heating compared to the slower rate of thermal heating of the bulk. These results provide valuable insights into the interactions between biomolecules and plasmonic nanoparticles induced by photothermal heating, advancing plasmonic biocatalysis and related fields.

Two new steroids with cytotoxicities from fungus Acrocalymma cycadis

Thirteen steroids (1–13), including two undescribed steroids, acrocalysterol C (1) and acrocalysterol D (2), were isolated from cultures of the fungus Acrocalymma cycadis using the OSMAC approach. Compounds 1 and 2 represent highly oxygenated steroids that contain an epoxy fragment. Through NMR and HRESIMS analyses, quantum chemical calculations, and electronic circular dichroism (ECD) experiments, their structures and absolute configurations were characterized. Then, the in vitro cytotoxicity of each compound was evaluated. Compounds 4 and 8-10 exhibited remarkable cytotoxicities against HeLa cells. Obviously, compound 10 exhibited twofold greater activity against HeLa than positive control, with IC50 values of 13.2 ± 1.23 μM. Additionally, compound 2 presented moderate potent cytotoxicity activities against three human cancer cells, comparable to the positive control. Thus, the bioactive metabolites of the strain A. cycadis may serve as a novel resource for development.

Influence of different pH milieu on the structure and function of human Aurora kinase B protein (AURK-B): Amalgamation of both spectroscopic and computational approach

Aurora kinase B (AURK-B) is a serine/threonine kinase protein that plays an essential role in chromosomal separation during the cell cycle event. AURK-B is highly expressed in various types of cancer such as human seminoma, thyroid carcinoma, non-small cell lung carcinoma (NSCLC), oral carcinoma, and gastric cancer. Hence, it is a potential therapeutic target in the treatment of various cancers. The structure of AURK-B in complex with one of its substrate inner centromeric protein (INCENP) is present, but the structural and functional characterization of native AURK-B at different pH environment is still unexplored.This study determines the effect of different pH milieu on the structure and function of AURK-B protein wherein the influence of pH on the protein conformation was probed using Circular dichroism (CD) and fluorescence spectroscopy. The structural studies were further combined with functional activity assay to observe the change in kinase activity at various pH milieu (2.0–11.0). CD and fluorescence spectroscopy experiments dictate that at high acidic conditions (pH 2.0 – 5.0), the secondary and tertiary structures of AURK-B become distorted, leading to diminished activity. The protein, however, was observed to stabilize towards pH 7.0 – 8.0 with minimal structure alteration over the basic pH range (pH 9.0 –11.0). The measured spectroscopic structural features were found to be in-line with obtained experimental kinase activity assays.Further, in-vitro experiments indicate that the enzyme is maximally active at pH 8.0. More ordered conformation and compact structure was observed at this pH (pH 8.0) as compared to other pH values through molecular dynamics simulation studies (MDS). As AURK-B localizes itself in the intracellular compartment, this study may provide a clue about the role of different pH environments in enhancing cancer growth, proliferation, and invasion.

Designing surface exposed sites on Bacillus subtilis lipase A for spin-labeling and hydration studies

Spin-labeling with electron paramagnetic resonance spectroscopy (EPR) is a facile method for interrogating macromolecular flexibility, conformational changes, accessibility, and hydration. Within we present a computationally based approach for the rational selection of reporter sites in Bacillus subtilis lipase A (BSLA) for substitution to cysteine residues with subsequent modification with a spin-label that are expected to not significantly perturb the wild-type structure, dynamics, or enzymatic function. Experimental circular dichroism spectroscopy, Michaelis-Menten kinetic parameters and EPR spectroscopy data validate the success of this approach to computationally select reporter sites for future magnetic resonance investigations of hydration and hydration changes induced by polymer conjugation, tethering, immobilization, or amino acid substitution in BSLA. Analysis of molecular dynamic simulations of the impact of substitutions on the secondary structure agree well with experimental findings. We propose that this computationally guided approach for choosing spin-labeled EPR reporter sites, which evaluates relative surface accessibility coupled with hydrogen bonding occupancy of amino acids to the catalytic pocket via atomistic simulations, should be readily transferable to other macromolecular systems of interest including selecting sites for paramagnetic relaxation enhancement NMR studies, other spin-labeling EPR studies or any method requiring a tagging method where it is desirable to not alter enzyme stability or activity.

The role of cryptic ancestral symmetry in histone folding mechanisms across Eukarya and Archaea.

Histones compact and store DNA in both Eukarya and Archaea, forming heterodimers in Eukarya and homodimers in Archaea. Despite this, the folding mechanism of histones across species remains unclear. Our study addresses this gap by investigating 11 types of histone and histone-like proteins across humans, Drosophila, and Archaea through multiscale molecular dynamics (MD) simulations, complemented by NMR and circular dichroism experiments. We confirm and elaborate on the widely applied "folding upon binding" mechanism of histone dimeric proteins and report a new alternative conformation, namely, the inverted non-native dimer, which may be a thermodynamically metastable configuration. Protein sequence analysis indicated that the inverted conformation arises from the hidden ancestral head-tail sequence symmetry underlying all histone proteins, which is congruent with the previously proposed histone evolution hypotheses. Finally, to explore the potential formations of homodimers in Eukarya, we utilized MD-based AWSEM and AI-based AlphaFold-Multimer models to predict their structures and conducted extensive all-atom MD simulations to examine their respective structural stabilities. Our results suggest that eukaryotic histones may also form stable homodimers, whereas their disordered tails bring significant structural asymmetry and tip the balance towards the formation of commonly observed heterotypic dimers.

A trimeric glycosylated GH45 cellulase from the red abalone (Haliotis rufescens) exhibits endo and exoactivity.

The red abalone (Haliotis rufescens) represents North America's most important aquaculture species. Its hepatopancreas is rich in cellulases and other polysaccharide-degrading enzymes, which provide it the remarkable ability to digest cellulose-rich macroalgae; nevertheless, its cellulolytic systems are poorly explored. This manuscript describes some functional and structural properties of an endogenous trimeric glycosylated endoglucanase from H. rufescens. The purified enzyme showed a molecular mass of 23.4 kDa determined by MALDI-TOF mass spectrometry, which behaved as a homotrimer in gel filtration chromatography and zymograms. According to the periodic acid-Schiff reagent staining, detecting sugar moieties in SDS-PAGE gel confirmed that abalone cellulase is a glycoprotein. Hydrolysis of cello-oligosaccharides and p-nitrophenyl-β-D-glucopyranosides confirmed its endo/exoactivity. A maximum enzyme activity toward 0.5% (w/v) carboxymethylcellulose of 53.9 ± 1.0 U/mg was achieved at 45°C and pH 6.0. We elucidated the abalone cellulase primary structure using proteases and mass spectrometry methods. Based on these results and using a bioinformatic approach, we identified the gene encoding this enzyme and deduced its full-length amino acid sequence; the mature protein comprised 177 residues with a calculated molecular mass of 19.1 kDa and, according to sequence similarity, it was classified into the glycosyl-hydrolase family 45 subfamily B. An AlphaFold theoretical model and docking simulations with cellopentaose confirmed that abalone cellulase is a β-sheet rich protein, as also observed by circular dichroism experiments, with conserved catalytic residues: Asp26, Asn109, and Asp134. Interestingly, the AlphaFold-Multimer analysis indicated a trimeric assembly for abalone cellulase, which supported our experimental findings. The discovery and characterization of these enzymes may contribute to developing efficient cellulose bioconversion processes for biofuels and sustainable bioproducts.

Lignans and [11]-chaetoglobosins from Pseudeurotium bakeri and their immunosuppressive activity.

Two previously unreported lignans (1-2) and four undescribed [11]-chaetoglobosins (3-6) were obtained from the culture extract of an endophytic fungus Pseudeurotium bakeri P1-1-1. Their structures with absolute configurations were determined by spectroscopic data analysis, single-crystal X-ray diffraction, electronic circular dichroism (ECD) calculations, the modified Mosher's method, and Mo2(OAc)4-induced electronic circular dichroism (ICD) experiments. Compounds 5 and 6 showed moderate cytotoxic effects against seven human cancer cell lines. Compounds 2-4 exhibited immunosuppressive activities on concanavalin A-induced T cell proliferation with IC50 values of 3.7, 3.4, and 14.5 μM, and on lipopolysaccharide-induced B cell proliferation with IC50 values of 4.1, 3.9, and 14.2 μM, respectively. Further investigation revealed that 2 and 3 induced apoptosis in activated T cells in a dose-dependent manner.

Opposing roles of organic salts on mini-protein structure.

We investigated the effects of 1-ethyl-3-methylimidazolium chloride ([EMIM][Cl]) and choline chloride ([Chol][Cl]) on the local environment and conformational landscapes of Trp-cage and Trpzip4 mini-proteins using experimental and computational approaches. Fluorescence experiments and computational simulations revealed distinct behaviors of the mini-proteins in the presence of these organic salts. [EMIM][Cl] showed a strong interaction with Trp-cage, leading to fluorescence quenching and destabilization of its native structural interactions. Conversely, [Chol][Cl] had a negligible impact on Trp-cage fluorescence at low concentrations but increased it at high concentrations, indicating a stabilizing role. Computational simulations elucidated that [EMIM][Cl] disrupted the hydrophobic core packing and decreased proline-aromatic residue contacts in Trp-cage, resulting in a more exposed environment for Trp residues. In contrast, [Chol][Cl] subtly influenced the hydrophobic core packing, creating a hydrophobic environment near the tryptophan residues. Circular dichroism experiments revealed that [Chol][Cl] stabilized the secondary structure of both mini-proteins, although computational simulations did not show significant changes in secondary content at the explored concentrations. The simulations also demonstrated a more rugged free energy landscape for Trp-cage and Trpzip4 in [EMIM][Cl], suggesting destabilization of the tertiary structure for Trp-cage and secondary structure for Trpzip4. Similar fluorescence trends were observed for Trpzip4, with [EMIM][Cl] quenching fluorescence and exhibiting stronger interaction, while [Chol][Cl] increased the fluorescence at high concentrations. These findings highlight the interplay between [EMIM][Cl] and [Chol][Cl] with the mini-proteins and provide a detailed molecular-level understanding of how these organic salts impact the nearby surroundings and structural variations. Understanding such interactions is valuable for diverse applications, from biochemistry to materials science.

New isoindolinone derivatives isolated from the fruiting bodies of the basidiomycete Hericium coralloides

Preparative high-performance liquid chromatography (HPLC) purification of the ethyl acetate extract derived from dried basidiomes of the European mushroom Hericium coralloides led to the identification of two previously undescribed isoindolinone derivatives named corallocins D and E (1-2). The structures of the compounds were elucidated based on HR-ESI-MS (high-resolution electron spray ionization mass spectrometry), interpretation of 1D and 2D NMR spectra, electronic circular dichroism (ECD) experiments, and comparisons with published and theoretical data. The metabolites were tested for their cytotoxic and antimicrobial effects in vitro where weak to moderate biological effects were observed against HeLa cells (KB 3.1), Mucor hiemalis and Bacillus subtilis.

BthTX-I, a phospholipase A2-like toxin, is inhibited by the plant cinnamic acid derivative: chlorogenic acid

Snakebite is a significant health concern in tropical and subtropical regions, particularly in Africa, Asia, and Latin America, resulting in more than 2.7 million envenomations and an estimated one hundred thousand fatalities annually. The Bothrops genus is responsible for the majority of snakebite envenomings in Latin America and Caribbean countries. Accidents involving snakes from this genus are characterized by local symptoms that often lead to permanent sequelae and death. However, specific antivenoms exhibit limited effectiveness in inhibiting local tissue damage. Phospholipase A2-like (PLA2-like) toxins emerge as significant contributors to local myotoxicity in accidents involving Bothrops species. As a result, they represent a crucial target for prospective treatments. Some natural and synthetic compounds have shown the ability to reduce or abolish the myotoxic effects of PLA2-like proteins. In this study, we employed a combination approach involving myographic, morphological, biophysical and bioinformatic techniques to investigate the interaction between chlorogenic acid (CGA) and BthTX-I, a PLA2-like toxin. CGA provided a protection of 71.8% on muscle damage in a pre-incubation treatment. Microscale thermophoresis and circular dichroism experiments revealed that CGA interacted with the BthTX-I while preserving its secondary structure. CGA exhibited an affinity to the toxin that ranks among the highest observed for a natural compound. Bioinformatics simulations indicated that CGA inhibitor binds to the toxin's hydrophobic channel in a manner similar to other phenolic compounds previously investigated. These findings suggest that CGA interferes with the allosteric transition of the non-activated toxin, and the stability of the dimeric assembly of its activated state.

Exothermic binding and structural alteration of the carrier protein lysozyme induced by Yohimbine: A spectroscopic, calorimetric and cheminformatic insight

The crucial function of bioactive ligands in the interaction with diverse proteins has garnered significant attention in the fields of pharmacokinetics and pharmacodynamics, hence generating considerable interest in the discipline of medicinal chemistry. To better comprehend its molecular mechanism, we implored a detailed biophysical analyses (using multi-spectroscopic, calorimetric, and computational tools) of the carrier protein Lysozyme, Lyz (also known as “Muramidase”) with Yohimbine (Yoh). The binding constant (K) of the Lyz-Yoh complex was estimated to be 105 M−1, exhibiting a progressive decline as temperature increased. The thermodynamic-profiling indicated the binding to be associated with an exothermic interaction driven by entropy. The confirmation of spontaneous binding is evidenced by the observed decrease in free energy. The variation in ionic strength indicated that non-polyelectrolytic forces were involved in the association. In addition, it was investigated how different metal ions affected the Lyz-Yoh binding. Calorimetric studies revealed the binding to be exothermic in nature, which also aligns with spectroscopic data. Results from circular dichroism (CD) experiments, demonstrated the structural alterations brought about in Lyz by Yoh. The likely binding sites and protein residuals to the ligand (Yoh) were illustrated using theoretical techniques, viz., molecular docking and molecular dynamic (MD) simulation. In clinical and pharmaceutical assessments, these metrics are especially relevant for rational drug development.

IDPpred: a new sequence-based predictor for identification of intrinsically disordered protein with enhanced accuracy

Discovery of intrinsically disordered proteins (IDPs) and protein hybrids that contain both intrinsically disordered protein regions (IDPRs) along with ordered regions has changed the sequence–structure–function paradigm of protein. These proteins with lack of persistently fixed structure are often found in all organisms and play vital roles in various biological processes. Some of them are considered as potential drug targets due to their overrepresentation in pathophysiological processes. The major bottlenecks for characterizing such proteins are their occasional overexpression, difficulty in getting purified homogeneous form and the challenge of investigating them experimentally. Sequence-based prediction of intrinsic disorder remains a useful strategy especially for many large-scale proteomic investigations. However, worst accuracy still occurs for short disordered regions with less than ten residues, for the residues close to order–disorder boundaries, for regions that undergo coupled folding and binding in presence of partner, and for prediction of fully disordered proteins. Annotation of fully disordered proteins mostly relies on the far-UV circular dichroism experiment which gives overall secondary structure composition without residue-level resolution. Current methods including that using secondary structure information failed to predict half of target IDPs correctly in the recent Critical Assessment of protein Intrinsic Disorder prediction (CAID) experiment. This study utilized profiles of random sequential appearance of physicochemical properties of amino acids and random sequential appearance of order and disorder promoting amino acids in protein together with the existing CIDER feature for the prediction of IDP from sequence input. Our method was found to significantly outperform the existing predictors across different datasets.Communicated by Ramaswamy H. Sarma

Synthetic dimethoxyxanthones bind similarly to human serum albumin compared with highly oxygenated xanthones

Spectroscopic studies were carried out for the interaction of the bioactive compounds 2,3-dimethoxyxanthone (1) and 3,4-dimethoxyxanthone (2) with human serum albumin (HSA). The UV absorption, steady-state, and time-resolved fluorescence spectroscopy studies showed that 1 and 2 interact with HSA through a ground-state association. The decrease in the Stern-Volmer constant (KSV) values with increasing temperature, and the bimolecular quenching rate constant (kq) values in the order of 1012 M−1s−1 indicated a static fluorescence quenching mechanism, corroborating with time-resolved fluorescence decays. The association constant (Ka) values in the order of 104 M−1 indicated a moderate interaction between these xanthones and HSA. Circular dichroism experiments showed weak perturbation on the secondary structure of albumin after the interaction with 1 and 2. Thermodynamic parameters suggested that the binding is entropically (for HSA:1, ΔS° 0.012 ± 0.003 and for HSA:2 0.008 ± 0.002 J/molK) and enthalpically (for HSA:1, ΔH° -24.0 ± 0.99 and for HSA:2 -25.6 ± 0.67 kJ/mol) controlled, with a Gibbs free energy change (ΔG°) close to -28.0 kJ/mol in both cases. Competitive drug-displacement and molecular docking results showed that 1 and 2 could interact not only with subdomain IIA, where Trp-214 residue can be found, but also with subdomains IIIA and IB. Hydrogen bonding, electrostatic, and hydrophobic interactions were detected as the main binding forces to stabilize the association HSA:1 and HSA:2. Overall, the dimethoxyxanthones have similar binding affinity compared with highly oxygenated xanthones, e.g., mangiferin, gentiacaulein, and norswertianin.

Abstract A026: Synthesis and structure-activity studies of DNA- and RNA-binding nucleopeptides with a cell penetrating potential

Abstract In the field of modern biomedicine, significant progress has been made in countering or restoring faulty genes using exogenous nucleic acids or their mimetics (NAMs). This approach enables targeted and long-lasting therapeutic effects by circumventing the need of interventions at a protein level. Despite the boom of clinical approvals, the development of NAMs still faces crucial challenges, including susceptibility to metabolic breakdown, limited uptake by cells, self-aggregation, and the potential for immune reactions. In addition to employing advanced delivery strategies, alternative methods to address these issues involve modifying NAMs chemically or combining oligonucleotides (ONs) with cellular carriers, including cell-penetrating peptides. Against this background, herein we present the nucleopeptides (NPs) as a family of unexplored NAMs that bridge the gap between ONs and peptide structures. By incorporating two consecutive amino acids—one bearing a nucleobase on the side chain and the other remaining unaltered—we created a monomer that spans the length of a single nucleotide. This functional module possesses nucleobase recognition elements along with additional functional groups eligible to modulate physio-chemical properties. We investigated this class of macromolecules by preliminarily devising an efficient solid-phase peptide synthesis technique profitable for homo- and hetero-sequences and sparing the monomer assembly in solution. [1] The influence of the amino acid composition on target binding properties, metabolic stability, and cellular penetration, were assessed through the synthesis of a series of homothymine hexameric derivatives. This simplified model was also used to investigate the distance between the nucleobase and the backbone, the absolute configuration of the nucleobase- bearing element, and the polycationic/anionic nature of the unmodified amino acid. [2-4] We evaluated the recognition and the thermodynamic stability of NPs/DNA and NPs/RNA hetero-duplexes through circular dichroism and UV spectroscopy experiments, while we employed confocal microscopy with suitable FITC- labeled derivatives to determine the intracellular localization in target cells. [1,3] Our results suggested that NPs exhibit distinct binding properties towards complementary RNA and DNA sequences according to their aminoacidic composition, and are characterized by a higher affinity compared to ONs and PNAs, thus arising as promising cell penetrating NAMs. [1] Mercurio ME, Tomassi S, et al. J Org Chem. 2016, 81(23), 11612- 11625. [2] Tomassi S, Ieranò C, et al. Bioorg Med Chem. 2018, 26(9), 2539-2550. [3] Tomassi S, Montalban FF, et al. Symmetry 2019, 11(4), 567-582. [4] Tomassi S, Ieranò C, et al. Int J Mol Sci. 2022, 23(15), 8504-8518. Citation Format: Stefano Tomassi, Caterina Ieranò, Stefania Scala, Anna Messere, Salvatore Di Maro. Synthesis and structure-activity studies of DNA- and RNA-binding nucleopeptides with a cell penetrating potential [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr A026.

Inhibition of Aurora-A/N-Myc Protein-Protein Interaction Using Peptidomimetics: Understanding the Role of Peptide Cyclization.

Using N-Myc61-89 as a starting template we showcase the systematic use of truncation and maleimide constraining to develop peptidomimetic inhibitors of the N-Myc/Aurora-A protein-protein interaction (PPI); a potential anticancer drug discovery target. The most promising of these - N-Myc73-94-N85C/G89C-mal - is shown to favour a more Aurora-A compliant binding ensemble in comparison to the linear wild-type sequence as observed through fluorescence anisotropy competition assays, circular dichroism (CD) and nuclear magnetic resonance (NMR) experiments. Further in silico investigation of this peptide in its Aurora-A bound state, by molecular dynamics (MD) simulations, imply (i) the bound conformation is more stable as a consequence of the constraint, which likely suppresses dissociation and (ii) the constraint may make further stabilizing interactions with the Aurora-A surface. Taken together this work unveils the first orthosteric N-Myc/Aurora-A inhibitor and provides useful insights on the biophysical properties and thus design of constrained peptides, an attractive therapeutic modality.