Conformational Studies Research Articles

A Review of Online Social Conformity: Outcomes and Determinants

Social conformity occurs when individuals forego their personal judgements to agree with opposing judgements of a group majority. While conformity was initially observed and investigated in physical groups, recently there has been an increasing interest to understand dynamics of this phenomenon in online group settings. This survey summarises 36 years of social conformity literature (1988–2023) and reviews its occurrences, positive and negative outcomes, and contextual and personal determinants in online groups. By doing so, we identify gaps in the conformity literature that require further investigation, discuss common challenges and inform the design of future online conformity studies.

Inducible cell lines producing replication-defective human immunodeficiency virus particles containing envelope glycoproteins stabilized in a pretriggered conformation.

During the process by which human immunodeficiency virus (HIV-1) enters cells, the envelope glycoprotein (Env) trimer on the virion surface engages host cell receptors. Binding to the receptor CD4 induces Env to undergo transitions from a pretriggered, "closed" (State-1) conformation to more "open" (State 2/3) conformations. Most broadly neutralizing antibodies (bNAbs), which are difficult to elicit, recognize the pretriggered (State-1) conformation. More open Env conformations are recognized by poorly neutralizing antibodies (pNAbs), which are readily elicited during natural infection and vaccination with current Env immunogens. Env heterogeneity likely contributes to HIV-1 persistence by skewing antibody responses away from the pretriggered conformation. The conformationally flexible gp160 Env precursor on the infected cell or virion surface potentially presents multiple pNAb epitopes to the host immune system. Although proteolytic cleavage to produce the functional, mature Env trimer [(gp120/gp41)3] stabilizes State-1, many primary HIV-1 Envs spontaneously sample more open conformations. Here, we establish inducible cell lines that produce replication-defective HIV-1 particles with Env trimers stabilized in a pretriggered conformation. The mature Env is enriched on virus-like particles (VLPs). Using complementary approaches, we estimate an average of 25-50 Env trimers on each VLP. The stabilizing changes in Env limit the natural conformational heterogeneity of the VLP Env trimers, allowing recognition by bNAbs but not pNAbs. These defective VLPs provide a more homogeneous source of pretriggered Env trimers in a native membrane environment. Thus, these VLPs may facilitate the characterization of this functionally important Env conformation and its interaction with the immune system.IMPORTANCEA major impediment to the development of an effective HIV/AIDS vaccine is the inefficiency with which human immunodeficiency virus (HIV-1) envelope glycoproteins elicit antibodies that neutralize multiple virus strains. Neutralizing antibodies recognize a particular shape of the envelope glycoproteins that resides on the viral membrane before the virus engages the host cell. Here, we report the creation of stable cell lines that inducibly produce non-infectious HIV-like particles. The normally flexible envelope glycoprotein spikes on these virus-like particles have been stabilized in a conformation that is recognized by broadly neutralizing antibodies. These virus-like particles allow the study of the envelope glycoprotein conformation, its modification by sugars, and its ability to elicit desired neutralizing antibodies.

Quantitative Examination and Mechanistic Insights of Polymer Chain Conformation Confined in Nanopores by Time-Resolved Fluorescence Resonance Energy Transfer.

The conformational studies of polymers confined at the nanoscale remain challenging and controversial due to the limitations of characterization techniques. In this study, we utilized the high sensitivity of time-resolved fluorescence resonance energy transfer (trFRET) and a site-specific dye-labeling strategy to characterize the conformation of polymer chains confined in anodic aluminum oxide (AAO) nanopores. This strategy introduced a fluorescent donor (carbazole) and acceptor (anthracene) at the center of poly(butyl methacrylate) (PBMA) chains grown by atom transfer radical polymerization (ATRP). By quantitatively analyzing fluorescence decay through the Förster mechanism and the Drake-Klafter-Levitz (DKL) formalism, we can determine both the energy transfer efficiency and the spatial distribution of the dyes. This analysis revealed that the PBMA chains, with a molecular weight of 40 kDa, maintained their bulk-like conformation even when confined within nanopores as small as 10 nm in diameter. This study is the first to demonstrate the use of trFRET for investigating chain conformation in confined polymer systems, which can be generalized to other polymer types and polymer topologies in different confined geometries.

Exploring replica-Potts CFTs in two dimensions

We initiate a numerical conformal bootstrap study of CFTs with Sn ⋉ (SQ)n global symmetry. These include CFTs that can be obtained as coupled replicas of two-dimensional critical Potts models. Particular attention is paid to the special case S3 ⋉ (S3)3, which governs the critical behaviour of three coupled critical 3-state Potts models, a multi-scalar realisation of a (potentially) non-integrable CFT in two dimensions. The model has been studied in earlier works using perturbation theory, transfer matrices, and Monte Carlo simulations. This work represents an independent non-perturbative analysis. Our results are in agreement with previous determinations: we obtain an allowed peninsula within parameter space for the scaling dimensions of the three lowest-lying operators in the theory, which contains the earlier predictions for these scaling dimensions. Additionally, we derive numerous bounds on admissible scaling dimensions in the theory, which are compatible with earlier results. Our work sets the necessary groundwork for a future precision study of these theories in the conformal bootstrap.

Identification and Characterization of a Novel Protein Drug Target WP_145928235.1 in Providencia Through Subtractive Proteomics and Molecular Dynamics Simulations

AbstractProvidencia stuartii, the most prevalent strain in its genus, is a significant cause of a range of potentially fatal diseases involving urinary tract infections, lung diseases, and endocarditis, often exhibiting resistance to multiple antibiotics, necessitating alternative therapeutic approaches. Unlike previous efforts focused on known virulence factors, this study delves into the physicochemical and functional characterization of 72 essential hypothetical proteins (EsHPs) from the P. stuartii BE246 genome. Subcellular localization identified 47 cytoplasmic EsHPs as potential drug targets, with the remainder 25 identified as vaccine targets. Subtractive analysis uncovered 68 virulent proteins, 4 of which were nonhomologous to both host and gut microbiota proteomes. Among these, WP_145928235.1 (147 amino acids), a cytoplasmic EsHP, emerged as a novel drug target due to its homologous broad‐spectrum hit. WP_145928235.1 displayed an instability index (II) of 33.14, an aliphatic index of 92.79, and the GRAVY score was ‐0.065 (hydrophilic). Molecular dynamics simulation‐aided conformational study and secondary structure analysis highlighted the protein's flexibility and propensity to interact with inhibitors. Key residues in the 60–90 region, including Asn62, Gly75, Glu81, and Asp85, were critical for interactions and stability, with low frustration indicating residual conservancy. WP_145928235.1 presents a promising target for therapeutic intervention against multidrug‐resistant P. stuartii infections.

Single Nucleotide Polymorphisms (SNPs) in the Shadows: Uncovering their Function in Non-Coding Region of Esophageal Cancer.

Esophageal cancer is a complex disease influenced by genetic and environmental factors. Single nucleotide polymorphisms (SNPs) in non-coding regions of the genome have emerged as crucial contributors to esophageal cancer susceptibility. This review provides a comprehensive overview of the role of SNPs in non-coding regions and their association with esophageal cancer. The accumulation of SNPs in the genome has been implicated in esophageal cancer risk. Various studies have identified specific locations in the genome where SNPs are more likely to occur, suggesting a location-specific response. Chromatin conformational studies have shed light on the localization of SNPs and their impact on gene transcription, posttranscriptional modifications, gene expression regulation, and histone modification. Furthermore, miRNA-related SNPs have been found to play a significant role in esophageal squamous cell carcinoma (ESCC). These SNPs can affect miRNA binding sites, thereby altering target gene regulation and contributing to ESCC development. Additionally, the risk of ESCC has been linked to base excision repair, suggesting that SNPs in this pathway may influence disease susceptibility. Somatic DNA segment alterations and modified expression quantitative trait loci (eQTL) have also been associated with ESCC. These alterations can lead to disrupted gene expression and cellular processes, ultimately contributing to cancer development and progression. Moreover, SNPs have been found to be associated with the long non-coding RNA HOTAIR, which plays a crucial role in ESCC pathogenesis. This review concludes with a discussion of the current and future perspectives in the field of SNPs in non-coding regions and their relevance to esophageal cancer. Understanding the functional implications of these SNPs may lead to the identification of novel therapeutic targets and the development of personalized approaches for esophageal cancer prevention and treatment.

Differences in the molecular structure of curcumin and its breakdown products affect their inhibitory effect on pepsin: Kinetic and protein spatial conformation study

Curcumin, a natural phenolic compound with various bioactivities, is easily decomposed into stability ferulic acid and vanillin molecules. Whether the functional equivalence of decomposition products can match that of curcumin is a matter worth attention. In this work, the inhibition and interaction of curcumin and its decomposition products on pepsin were studied. The inhibition by curcumin and ferulic acid belonged to competitive inhibition, the quenching types were static quenching with spontaneous process. Binding energies of curcumin, ferulic acid and vanillin were -8.33±0.14, -7.88±0.09 and -6.12±0.08 kcal/mol, respectively, through H-bonds and hydrophobic interactions. All molecules significantly changed the secondary structure of pepsin and reduced the deformation temperature about 15 °C. The results show that better inhibition on pepsin from curcumin than ferulic acid, whereas vanillin did not show inhibition. The results provided the experimental basis for curcumin as potential inhibitors of pepsin in special diets.

4hJCHOCH Spin Coupling in a Lewisx Trisaccharide as Evidence of Inter-Residue C-H···O Hydrogen Bonding in Aqueous Solution.

Prior studies of the solution conformation of the Lewisx (Lex) trisaccharide, αFuc-(1→3)[βGal-(1→4)]-βGlcNAc, suggest that nonclassical inter-residue C-H···O hydrogen bonding in aqueous solution contributes to the stabilization of its 3D structure and affects its biological properties. Experimental evidence for this hydrogen bond in aqueous solution has been reported in the form of a 4hJCHOCH NMR spin-coupling constant between C5'Fuc and H1″Gal measured by 2D NMR methods in unlabeled samples. A methyl glycoside of Lex (MeβLex) was prepared containing selective 13C-labeling at C5'Fuc, and the H1″Gal signal was examined in high-field 1H NMR spectra for evidence of splitting or line-broadening caused by the 13C at C5'Fuc. High-resolution 1H NMR spectra obtained at high field and at different temperatures using different FID processing parameters showed no resolved splitting of the H1″Gal signal or evidence of line-broadening. Spectral simulation showed that this splitting and/or line-broadening would be observable if the reported J-value (∼1.1 Hz) is correct. DFT calculations on MeβLex and a carbon analog (O5″Gal replaced by a CH2 group) gave very small and nearly identical calculated 4hJC5',H1″ values, suggesting that the coupling is essentially zero. DFT calculations also showed that an alternate inter-residue 3hJH5',H1″ is small. Based on NMR analyses and DFT calculations, we found that 4hJC5',H1″ in MeβLex has an upper limit of ∼0.4 Hz and that the value could be lower, possibly zero, calling into question its value as experimental proof of persistent nonclassical hydrogen bonding in aqueous solutions of MeβLex and related structures.

Design, Synthesis and Computational Insight of Isolated and Thiophene fused 2H‐Pyran‐2‐ones as PPAR‐γ Agonist

AbstractPeroxisome proliferator‐activated receptor gamma (PPAR‐γ) is a well‐known member of the PPAR family and a potential target for the treatment of various disorders. Herein, we present the design and synthesis of various 6‐aryl‐4‐sec.amino‐2‐oxo‐2H‐pyran‐3‐carbonitrile derivatives and functionalized thieno[3,2‐c]pyran‐2‐ones, derived from ketene dithioacetal. Then all the synthesized compounds were docked for their activity as PPAR‐γ to predict the binding mechanism and affinities regarding rosiglitazone and muraglitazar. Our studies revealed that three compounds 10 e, 10 f, and 10 h showed significant binding affinities, with energy ranges comparable to standard drugs rosiglitazone and muraglitazar. The docking conformation studies revealed that the selected compounds nicely interact with PPAR‐γ in the ligand binding domain with positive predictive values. We also performed molecular dynamics of the most potent compounds to validate the result. Our results indicate that these novel compounds are potential PPAR‐γ ligands, offering new possibilities for therapeutic applications. This study underscores the potential of these synthesized compounds in the development of novel PPAR‐γ agonists.

Covalent modification of protein by chemical probe in living cells for structural and interaction studies.

Cellular activities are predominantly carried out by proteins that can dynamically adopt different structural conformations and differentially interact with other biomolecules according to cellular needs. Chemical probes are small molecules used to selectively interact and modulate the activities of specific proteins to study their functions such as the validation of potential drug targets. The remarkable performance of AlphaFold algorithms in the prediction of protein structures has pivoted interest toward elucidating the intracellular dynamics of protein structural conformation where covalent modification of proteins by chemical probes could be used to shed light upon. However, due to the barrier to entry by cell membrane and the general unfavorable reactive conditions of the intracellular environment, most studies using reactive chemical probes are still conducted on purified proteins and cell lysates. Nevertheless, recent progresses have been made in designing chemical probes with improved membrane permeability, stability and reactivity. This paper surveys the literature on recent advancements in membrane-permeable chemical probes and their applications with protein mass spectrometry for the intracellular studies of protein structural conformations and biomolecular interactions.

Potential Bioactivities, Chemical Composition, and Conformation Studies of Exopolysaccharide-Derived Aspergillus sp. Strain GAD7.

This research identified a marine fungal isolate, Aspergillus sp. strain GAD7, which produces an acidic and sulfated extracellular polysaccharide (EPS) with notable anticoagulant and antioxidant properties. Six fungal strains from the Egyptian Mediterranean Sea were screened for EPS production, with Aspergillus sp. strain GAD7 (EPS-AG7) being the most potent, yielding ~5.19 ± 0.017 g/L. EPS-AG7 was characterized using UV-Vis and FTIR analyses, revealing high carbohydrate (87.5%) and sulfate (24%) contents. HPLC and GC-MS analyses determined that EPS-AG7 is a heterogeneous acidic polysaccharide with an average molecular weight (Mw¯) of ~7.34 × 103 Da, composed of mannose, glucose, arabinose, galacturonic acid, galactose, and lyxose in a molar ratio of 6.6:3.9:1.8:1.3:1.1:1.0, linked through α- and β-glycosidic linkages as confirmed by NMR analysis. EPS-AG7 adopted a triple helix-like conformation, as evidenced by UV-Vis (Congo Red experiment) and circular dichroism (CD) studies. This helical arrangement demonstrated stability under various experimental conditions, including concentration, ionic strength, temperature, and lipid interactions. EPS-AG7 exhibited significant anticoagulant activity, doubling blood coagulation time at a concentration of 3.0 mg/mL, and showed significant antioxidant activity, with scavenging activities reaching up to 85.90% and 58.64% in DPPH and ABTS+ assays at 5.0 mg/mL, and EC50 values of 1.40 mg/mL and 3.80 mg/mL, respectively. These findings highlight the potential of EPS-AG7 for therapeutic applications due to its potent biological activities.

Computational Exploration of Isatin Derivatives for InhA Inhibition in Tuberculosis: Molecular Docking, MD Simulations and ADMET Insights.

Anti-tubercular drug discovery is a critical research area aimed at addressing the global health burden imposed by Mycobacterium tuberculosis. Nowadays, computational techniques have increased the likelihood of drug development compared to traditional, labor-intensive, and time-consuming drug design approaches. The pivotal goal of drug design is to identify compounds capable of selectively targeting protein, thereby disrupting its enzymatic activity. InhA, or NADH-dependent enoyl-acyl carrier protein reductase, stands at the forefront of targeted approaches in the battle against TB. Isatin derivatives have garnered interest for their diverse pharmacological activities. To identify novel isatin derivatives that could serve as potential chemical templates for anti-TB drug discovery by targeting InhA. The present work utilized various computational approaches, including molecular docking, binding free energy calculations, and conformational alignment studies to investigate the binding mode and interactions of carefully selected dataset of 88 isatin derivatives within InhA active site. Study also employed MD simulations of the most promising molecule to check the stability of the protein-ligand complex and in-silico ADMET profiling of the top compounds to predict their pharmacokinetic and toxicity properties. Results provided insights into the structural features contributing to InhA inhibition, assessing overall drug-like characteristics of isatin derivatives and identified compound 48 (BA= -10.4 kcal mol-1 ) with potential for further optimization. MD simulation analysis revealed that compound 48 binds firmly within the InhA protein, exhibiting minimal conformational fluctuations and enhanced stability. Considering the aforementioned, isatin derivatives represents a novel framework for creating targeted InhA inhibitors during anti-TB therapy. However, experimental validations and in-depth analyses are crucial to confirm efficacy and safety of these derivatives as potential InhA inhibitors for TB treatment.

Conformation Regulation of Trisresorcinarene Directed by Cavity Solvation.

This compound is a synthetic macrocycle comprising three pivaloyl-protected resorcinarene units connected by six pentylene chains. We conducted a conformational study using 1H-NMR, X-ray diffraction (XRD), and computational analyses. The macrocycle adopts two conformers, one open, the other closed. The ratio of the open to closed forms depended on the solvent used. Only the open form existed in [D8]toluene, both forms coexisted in [D6]benzene, and the closed form was the major conformer in [D1]chloroform. The benzene-solvated open form observed in the solid state suggests that cavity solvation by solvent molecules directs the open form. The open form was the major or only conformer in [D10]o- and [D10]m-xylene and [D12]mesitylene, whereas the closed form was the major conformer in [D6]acetone. The open and closed forms were equally populated in [D10]p-xylene, suggesting that the size, shape, and dimensions of the solvent molecules most likely influenced the conformation of the protected trisresocinarene.

Interglycosidic C5–C6 rotamer distributions of alkyl O-rutinosides

The conformational study of carbohydrates is critical to understand the molecular recognition mechanisms underlying their biological functions. Moreover, the systematic study of their conformational patterns can unlock useful tools to design optimized glycomimetics and drug candidates. Using nuclear magnetic resonance, we studied the interglycosidic rotamer equilibria of ester-protected and deprotected alkyl O-rutinosides (α-L-Rha(1,6)β-D-GlcOR). In the protected series, the equilibrium about the C5–C6 bond distributes among the three possible rotamers gg, gt, and tg, being gt the predominant conformer. In these series, the flexibility about C5–C6 shows a marked dependency on the aglycone's structure, where the increase on the aglycone's volume leads to a progressive increment on the tg contributions at the expense of gt, with gg remaining practically constant along the series. The removal of the protective groups results in rutinosides displaying an equilibrium equally distributed between gg and gt with no tg contributions regardless of the aglycone's structure.

New ATP-competitive inhibitors of E. coli GyrB obtained from the mapping of the hydrophobic floor at the binding site: synthesis and biological evaluation.

We mapped the hydrophobic floor, an interesting subsite at the active site of DNA gyrase B (GyrB) from E. coli. We synthesized three new compounds with pendant groups targeting the hydrophobic floor and evaluated their inhibitory activities on DNA gyrase. A new benzothiazole derivative with a benzyl substituent at position 3 of the benzothiazole ring exhibited strong inhibitory activity against E. coli DNA gyrase (IC50 = 19 ± 3 nM). An exhaustive conformational study using potential energy surfaces (PESs) allowed us to map the new subsite evaluating all critical points on the surface and conformational interconversion pathways. We analyzed the molecular interactions using QTAIM calculations. Our data provide insights into the mechanism of action of these new ligands at the molecular level. Theoretical and experimental data suggest that new ligand optimization strategies should focus on strengthening interactions at the hydrophobic floor while preserving the binding mode of the main scaffold.

Use of DFT to Evaluate Properties of Viologen Derivatives for Redox Flow Batteries

Renewable energy technologies, such as wind or solar energy, depend upon intermittent sources, which make long-term storage an important issue for a large-scale application. A way to efficiently store this energy is to use redox flow batteries, where electricity is stored in a liquid electrolyte circulating through an electrochemical cell. The main advantage of this system is the decoupling of power and energy, allowing to increase the storage more efficiently than other technologies, which is advantageous for large-scale stationary systems.1 Most commercial redox flow batteries currently use vanadium as the active material. Although it is a stable metal, its price is high and volatile, and vanadium extraction is responsible for more than 80% of the environmental cost of a vanadium-based redox flow battery. 2 A cheaper, more environment friendly and safer alternative to vanadium is to use organic molecules as active material in an aqueous solvent.3 Organic molecules also offer opportunities to easily tune properties by modifying their structure. This tunability of organic molecules is a great advantage to maximize desired properties: high solubility in water, low viscosity and optimal redox potential (high for positive electrolyte and low for the negative one). The possibilities of modification are however almost infinite and it would be unrealistic to evaluate experimentally all the possible derivatives of even only one family of redox centers. Therefore, computational chemistry, which permits to study molecules properties and draw tendencies within a shorter time frame, is an especially useful tool to assist the design of better performing molecules.4 In this work, we use DFT to study the effect of some structural modifications on the properties of viologen core molecules, with the aim of using them in aqueous organic redox flow batteries (AORFB). In the first part of this presentation, we show the study of PEG chain conformation of PEGylated viologen derivatives in order to explain experimental trends in solubility for different PEG chain lengths. We show that the experimental measure of solubility correlates with the folding of the PEG chain, which is more favored for longer chains. We also see a correlation between asymmetry, dipolar moment and solubility for these molecules, meaning that calculation of the dipole can give an approximate idea of solubility. However, no significant change in redox potential is measured with this type of structural modification.Therefore, in the second part of this study, we present a study of the effect of adding small functional groups directly on the viologen bipyridine core to tune their redox potential. We developed a computational method to calculate the theoretical redox potentials of these derivatives, and we correlate the values to experimental results, and obtained a R factor correlation of 0,9, supporting the validity of the method, which could be used to accurately predict redox potential of other viologen derivatives.These results show the insight computational chemistry can provide for interpretation of experimental data, and the potential of this method to predict and design new optimized molecules for aqueous organic redox flow batteries.References(1) Bai, H. Y.; Song, Z. Y. Lithium-ion battery, sodium-ion battery, or redox-flow battery: A comprehensive comparison in renewable energy systems. J Power Sources 2023, 580.(2) Weber, S.; Peters, J. F.; Baumann, M.; Weil, M. Life Cycle Assessment of a Vanadium Redox Flow Battery. Environ Sci Technol 2018, 52 (18), 10864-10873.(3) DeBruler, C.; Hu, B.; Moss, J.; Liu, X. A.; Luo, J. A.; Sun, Y. J.; Liu, T. L. Designer Two-Electron Storage Viologen Anolyte Materials for Neutral Aqueous Organic Redox Flow Batteries. Chem-Us 2017, 3 (6), 961-978.(4) Asenjo-Pascual, J.; Salmeron-Sanchez, I.; Mauleón, P.; Agirre, M.; Lopes, A. C.; Zugazua, O.; Sánchez-Díez, E.; Avilés-Moreno, J. R.; Ocón, P. DFT calculation, a practical tool to predict the electrochemical behaviour of organic electrolytes in aqueous redox flow batteries. J Power Sources 2023, 564. Figure 1

HP35 Protein in the Mesopore of MIL-101(Cr) MOF: A Model to Study Cotranslocational Unfolding.

The immobilization of enzymes in metal-organic framework (MOF) cages is important in biotechnology. In this context, the mechanism of translocation of proteins through the cavities of the MOF and the roles played by confinement and MOF chemistry in giving rise to stable protein intermediates that are otherwise transiently populated in the physiological environment are important questions to be addressed. These unexplored aspects are examined with villin headpiece (HP35) as a model protein confined within a mesopore of MIL-101(Cr) using molecular dynamics simulations. At equilibrium, the protein is located farther from the center of the cavity and closer to the MOF surface. Molecular interactions with the MOF partially unfold helix-1 at its N-terminus. Umbrella sampling simulations inform the range of conformations that HP35 undertakes during translocation from one cavity to another and associated changes in free energy. Relative to its equilibrium state within the cavity, the free energy barrier for the unfolded protein at the cage window is estimated to be 16 kcal/mol. This study of MOF-based protein conformation can also be a general approach to observing intermediates in folding-unfolding pathways.

High resolution far-infrared synchrotron spectroscopy of 2-furfural conformers: Fundamental and hot bands.

In the continuity of a previous jet-cooled rovibrational study of trans and cis conformers of 2-furfural in the mid-infrared region (700-1750cm-1) [Chawananon et al., Molecules 28 (10), 4165 (2023)], the present work investigates the far-infrared spectroscopy of 2-furfural using a long path absorption cell coupled to a high-resolution Fourier transform spectrometer and synchrotron radiation at the AILES beamline of the SOLEIL synchrotron. Guided by anharmonic calculations, vibrational energy levels and excited-state rotational constants are sufficiently predictive for a complete assignment of all fundamental and combination bands up to 700cm-1, as well as the rovibrational analysis of 4 (1) low-frequency modes of trans-(cis-)2-furfural. A global rovibrational simulation, including far-infrared rovibrational lines and microwave and millimeter-wave rotational lines assigned in a previous study [Motiyenko et al., J. Mol. Spectrosc., 244, 9 (2007)] provides a reliable set of ground- and excited-state rotational parameters involving ring torsion, bending, and ring puckering modes of 2-furfural. In a second step, a rovibrational analysis of several hot band sequences, mainly involving the lowest frequency ring CHO torsion mode, is carried out. Reliable values of some anharmonic coefficients are obtained experimentally and could serve as a benchmark for validating advanced anharmonic calculations related to these large amplitude motions of flexible molecules.

Light exacerbates local and global effects induced by pH unfolding of Ipilimumab

Monoclonal antibodies (mAbs) are an essential class of therapeutic proteins for the treatment of cancer, autoimmune and rare diseases. During their production, storage, and administration processes, these proteins encounter various stressors such as temperature fluctuations, vibrations, and light exposure, able to induce chemico-physical modifications to their structure. Viral inactivation is a key step in downstream processes, and it is achieved by titration of the mAb at low pH, followed by neutralization. The changes of the pH pose a significant risk of unfolding and subsequent aggregation to proteins, thereby affecting their manufacturing.This study aims to investigate whether a combined exposure to light during the viral inactivation process can further affect the structural integrity of Ipilimumab, a mAb primarily used in the treatment of metastatic melanoma. The biophysical and biochemical characterization of Ipilimumab revealed that pH variation is a considerable risk for its stability with irreversible unfolding at pH 2. The threshold for Ipilimumab denaturation lies between pH 2 and 3 and is correlated with the loss of the protein structural cooperativity, which is the most critical factor determining the protein refolding. Light has demonstrated to exacerbate some local and global effects making pH-induced exposed regions more vulnerable to structural and chemical changes.Therefore, specific precautions to real-life exposure to ambient light during the sterilization process of mAbs should be considered to avoid loss of the therapeutic activity and to increase the yield of production. Our findings underscore the critical role of pH optimization in preserving the structural integrity and therapeutic efficacy of mAbs. Moreover, a detailed conformational study on the structural modifications of Ipilimumab may improve the chemico-physical knowledge of this effective drug and suggest new production strategies for more stable products under some kind of stress conditions.

Synthesis of isomeric β-cycloalkoxyphosphonated hydrazones containing a dioxaphosphorinane ring: Configurational and conformational investigation and molecular docking analysis

A series of Z/E isomeric β-cycloalkoxyphosphonated hydrazones [R1R2C(CH2O)2P(=O)CH2-C{=NN(H)R5}C(H)R3R4] 3 bearing a six-membered dioxaphosphorinane ring was prepared, structurally analysed, and subjected to in silico studies to assess their Acetylcholinesterase (AChE) and Butyrylcholinesterase (BuChE) inhibition activity. Furthermore, their ADMET (Absorption, Distribution, Metabolism, Excretion, Toxicity) properties were determined. Hydrazones 3 were prepared from their corresponding allenylphosphonates [R1R2C(CH2O)2P(=O)C(H)=C=CR3R4] 2 by addition of various hydrazines NH2NHR5. Since NMR studies indicated the occurrence of several isomeric species in solution, conformational and configurational studies, based on mechanistic elucidation and energy stability using Density functional theory (DFT) calculation at the B3LYP/6-311 G++ (d,p) level of theory, were performed to determine their relative predominance. The hydrazone 1-(2-oxo-1,3,2-dioxaphosphoranyl)-3-phenylpropanone 3c was crystallographically analysed by single-crystal X-ray diffraction (SCXRD), revealing the occurrence of strong intra- and intermolecular NH···O hydrogen bonding. These secondary interactions were further examined by a Hirshfeld surface analysis. The experimental SCXRD parameters are compared with the theoretical calculated ones and the preferred configuration of product 3c was determined. Furthermore, the crystal structure of the symmetric azine 2,2′-((2E,2′E)-hydrazine-1,2-diylidenebis(3-phenylpropan-1-yl-2-ylidene))bis(5-methyl-5-propyl-1,3,2-dioxaphosphinane 2-oxide) 4, resulting from the reaction between hydrazone 3a and allene 2a, has been determined. To predict whether hydrazones 3 are appropriate as anticholinesterase agents exhibiting a potential activity for treatment of the Alzheimer disease, in silico molecular docking simulations were employed to investigate the interaction modes between hydrazones 3 and the active sites of the BuChE and AChE enzymes. Additionally, an ADMET-properties prediction was carried out for selected hydrazones to determine their pharmacokinetics and drug-likeness properties.