Predominant Conformation Research Articles

Synthesis and structural analysis of 1,4′-pyrazolo[3,4-e][1,4]thiazepin-7′(6H)ones: An example of conformational chirality in seven-membered heterocycles

A series of five new N-alkylspiro[1,4]thiazepin-2-ones was obtained in good yields using a two-step synthesis strategy involving the preparation of the spirothiazepinone core, followed by the N-alkylation using alkyl halides in alkaline conditions. The latter N-alkylation reaction gave rise to conformational chirality, evidenced in NMR spectra, polarimetry, chiral HPLC, and X-ray diffraction analysis. X-ray studies revealed the presence of enantiomorphic boat-type conformers in centrosymmetric unit cells interacting by van der Waals forces, in contrast to a predominant conformer in solution supported by the chiral properties of the N-alkylated derivatives. The present work makes an important contribution to the study of the structural properties of 1,4-thiazepinone systems and the phenomenon of conformational chirality in seven-membered N-heterocycles.

Conformations of α-cyclodextrin and its role on the stability of inclusion complexes in aqueous solution

α-Cyclodextrin (αCD), a cyclic carbohydrate polymer, presents a wealth of opportunities for drug delivery and various industrial applications. Its high affinity and selectivity in encapsulating target molecules have been well-documented. However, the influence of αCD's conformational variations on its encapsulation capacity remains a promising area for further exploration. This study explores the conformational dynamics of αCD and its relationship with the formation of inclusion complexes (ICs) in aqueous solutions, focusing on understanding the forces driving these dynamics and the formation of stable ICs. Classical molecular dynamics (CMD) demonstrate that αCD solvated in water can adopt two conformations: a truncated cone shape with a suitable cavity for encapsulation and a distorted cone shape with a collapsed cavity. The predominant conformation observed in the CMD trajectory of pristine αCD is the distorted cone. However, under complexation conditions with aliphatic molecules, the guest molecule's size dictates the ICs' stability, forcing αCD to maintain the truncated cone conformation. Quantum chemistry methods and electron density analyses (Quantum Theory of Atoms in Molecules and Non-Covalent Interactions index) support CMD observations by characterizing and quantifying non-covalent interactions. Findings indicate that the shift from the truncated to the distorted cone conformation in αCD is primarily driven by intramolecular non-covalent interactions and the reconfiguration of water molecules surrounding αCD. The ICs' analysis displays a significant correlation between the size of the aliphatic chain and the intensity of intermolecular interactions. The strength of these interactions can effectively disrupt the αCD intramolecular non-covalent interactions that lead to a conformational change and, consequently, the loss of the inclusion complex. In conclusion, although αCD's conformational change can affect encapsulation, guest molecules can manipulate the conformational preference. The systematic analysis of non-covalent interactions offers a way to characterize and quantify these forces, enhancing our ability to understand and predict the stability of inclusion complexes.

Applying Machine Learning and SERS for Precise Typing of DNA Secondary Structures.

Surface-enhanced Raman spectroscopy (SERS) has been demonstrated as an effective method for elucidating secondary structural characteristics of DNA. However, the inherent complexity of the DNA conformation and the lack of SERS samples pose challenges for identifying numerous secondary structures. To address these issues, a synergistic method integrating machine learning with SERS was proposed so as to analyze the SERS spectra of 54 well-defined conformational oligonucleotides, namely, G-quadruplex (G4), i-motif (iM), double-strand (DS), and single-strand (SS) configurations. Principal component analysis (PCA) effectively segregated the oligonucleotides into three distinct conformational groups (G4s, iMs, and others). Furthermore, linear discriminant analysis (LDA), K-nearest neighbor (KNN), and support vector machine (SVM) approaches were utilized to improve the typing accuracy of 54 trained sequences. This enabled the correct classification of the structures of five untrained sequences, as well as the identification of the predominant conformations including G4, iM, and DS formed by two complementary G-rich and C-rich sequences in acidic and neutral pH conditions. The results of this study demonstrated the potential of the proposed methodology for rapid screening and prediction of secondary DNA conformations.

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.

Unveiling the conformational landscape of tizanidine and its effects on selective nucleation: Enabling controlled manipulation of polymorphs and solvates

The intricate relationship between conformational diversity and polymorphic nucleation is evident, while the underlying mechanisms remain unclear. In this work, tizanidine (TZND) was selected as the model compound to investigate its selective nucleation behavior and the association between conformations and polymorphs. Crystallization experiments were conducted using TZND in seven solvents, resulting in two polymorphs and four solvates, five of which are reported for the first time. Quantum chemical calculations were employed to explore the conformational landscape of TZND. Furthermore, 2D nuclear Overhauser effect spectroscopy and molecular dynamics were utilized to analyze the predominant conformation and its evolution in different solvents with varying concentrations. The results revealed that the dominant conformation of TZND could nucleate directly in methanol and acetone, while a conformational transition occurred during nucleation in acetonitrile and dichloromethane. Additionally, proton transfer in DMSO, chloroform, and DMF resulted in the emergence of new conformational forms. Moreover, crystallographic analysis, spectroscopic studies and quantum chemical calculations were adopted to investigate the molecular mechanisms governing selective nucleation and the formation of polymorphs or solvates. The results indicated that the free energy and solute–solvent interaction energy at specific sites influence the dominant conformation and its evolution in the solution. Finally, the nucleation mechanisms of different polymorphs and solvates were proposed and discussed, illustrating an efficient and environmentally friendly regulation method through solvent switching.

Unlocking the potential of waxworm (Galleria mellonella) proteins: Extraction, fractionation, and protein quality assessment

Edible insects are increasingly recognized as an alternative and sustainable protein source to meet future protein demands. Owing to its significant protein content (33.43%), the edible insect Waxworm (Galleria mellonella) was characterized in this study for its protein extractability, structural properties, and protein quality. Protein extractability under various pH levels and ionic strengths was evaluated. Subsequently, Osborne fractionation was employed to characterize protein fractions based on their preferential solubilities. The extracted proteins and their respective fractions were visualized by SDS-PAGE, and the most intense bands were excised for proteomics data analysis. Secondary structure, pI, molecular mass, and denaturation temperature were also examined. The quality of waxworm protein was assessed by determining the IVPD, PDCAAS, and amino acid profile. Waxworm proteins exhibited greater stability in alkaline conditions compared to acidic environments. These might also be more sensitive to ionic strength than other alternative proteins, such as those derived from plants. The allergen tropomyosin was identified by SDS-PAGE with an approximate molecular weight of ∼32.5 kDa; however, it can be selectively removed by salt extraction. The secondary structures of waxworm proteins, extracted under various conditions, appeared stable, with α-helix and β-conformation being the predominant conformation. Among the protein fractions, prolamins displayed an α-helix conformation, while albumins, globulins, and glutelins predominantly adopted a β-sheet structure. It was observed that structural features could influence the overall quality of the protein. As for the protein quality, globulins are the protein fraction recommended as these showed the highest EAAI% (924.02), PDCAAS (0.84) and IVPD (76.33%) values.

Does Inter-Residue Hydrogen Bonding in β-(1→4)-Linked Disaccharides Influence Linkage Conformation in Aqueous Solution?

Two disaccharides, methyl β-d-galactopyranosyl-(1→4)-α-d-glucopyranoside (1) and methyl β-d-galactopyranosyl-(1→4)-3-deoxy-α-d-ribo-hexopyranoside (3), were prepared with selective 13C-enrichment to allow measurement of six trans-O-glycosidic J-couplings (2JCOC, 3JCOCH, and 3JCOCC) in each compound. Density functional theory (DFT) was used to parameterize Karplus-like equations that relate these J-couplings to either ϕ or ψ. MA'AT analysis was applied to both linkages to determine mean values of ϕ and ψ in each disaccharide and their associated circular standard deviations (CSDs). Results show that deoxygenation at C3 of 1 has little effect on both the mean values and librational motions of the linkage torsion angles. This finding implies that, if inter-residue hydrogen bonding between O3H and O5' of 1 is present in aqueous solution and persistent, it plays little if any role in dictating preferred linkage conformation. Hydrogen bonding may lower the energy of the preferred linkage geometry but does not determine it to any appreciable extent. Aqueous 1-μs MD simulation supports this conclusion and also indicates greater conformational flexibility in deoxydisaccharide 3 in terms of sampling several, conformationally distinct, higher-energy conformers in solution. The populations of these latter conformers are low (3-14%) and could not be validated by MA'AT analysis. If the MD model is correct, however, C3 deoxygenation does enable conformational sampling over a wider range of ϕ/ψ values, but linkage conformation in the predominant conformer is essentially identical in both 1 and 3.

Quantum chemical investigation of predominant conformation of the antibiotic azithromycin in water and DMSO solutions: thermodynamic and NMR analysis.

Azithromycin (AZM) is a macrolide-type antibiotic used to prevent and treat serious infections (mycobacteria or MAC) that significantly inhibit bacterial growth. Knowledge of the predominant conformation in solution is of fundamental importance for advancing our understanding of the intermolecular interactions of AZM with biological targets. We report an extensive density functional theory (DFT) study of plausible AZM structures in solution considering implicit and explicit solvent effects. The best match between the experimental and theoretical nuclear magnetic resonance (NMR) profiles was used to assign the preferred conformer in solution, which was supported by the thermodynamic analysis. Among the 15 distinct AZM structures, conformer M14, having a short intramolecular C6-OH … N H-bond, is predicted to be dominant in water and dimethyl sulfoxide (DMSO) solutions. The results indicated that the X-ray structure backbone is mostly conserved in solution, showing that large flexible molecules with several possible conformations may assume a preferential spatial orientation in solution, which is the molecular structure that ultimately interacts with biological targets.

NMR Studies on the Structure and Functions of Small Biomolecules with Highly Flexible Conformation

Abstract In this review, we deal with the flexible structures of small biomolecules and discuss how spontaneous conformational changes are related to their biological functions, mainly focusing on our recent research results. In particular, we applied nuclear magnetic resonance (NMR)-based methods to biomolecules that largely comprise methylene-dominant chain(s) by observing spin-spin coupling constants in solution NMR and quadrupolar interactions and chemical shift anisotropy in solid-state NMR. In the study of spermidine and spermine, we investigated how the shape of a molecule changes when the ammonium groups interact with polyanions such as ATP. In membrane lipid studies, we examined the orientation and conformation of the choline phosphate moiety in the hydrophilic head group of membrane lipid molecules, and the average structure and fluctuations of the fatty acids, which were mainly alkane chains in the hydrophobic part. In these structural studies, the goal was not to determine the predominant conformation of biomolecules, but to elucidate the average conformation of multiple conformers that were interchanging at high speed. We used physicochemical parameters to describe the changes in the average structure of lipid in membranes. Computational methods were adopted to estimate the structural changes in molecules, but experimental results are still important to judge the reliability of the calculation results. Through these studies, we discuss how the flexibility of biomolecules is involved in the expression of biological function.

Revealing KRas4b topology on the membrane surface

KRas4b is a membrane-bound regulatory protein belonging to the family of small GTPases that function as a molecular switch, facilitating signal transduction from activated membrane receptors to intracellular pathways controlling cell growth and proliferation. Oncogenic mutations locking KRas4b in the active GTP state are responsible for nearly 85% of all Ras-driven cancers. Understanding the membrane-bound state of KRas4b is crucial for designing new therapeutic approaches targeting oncogenic KRas-driven signaling pathways. Extensive research demonstrates the significant involvement of the membrane bilayer in Ras-effector interactions, with anionic lipids playing a critical role in determining protein conformations The preferred topology of KRas4b for interacting with signaling partners has been a long-time question. Computational studies suggest a membrane-proximal conformation, while other biophysical methods like neutron reflectivity propose a membrane-distal conformation. To address these gaps, we employed FRET measurements to investigate the conformation of KRas4b. Using fully post-translationally modified KRas4b, we designed a Nanodisc based FRET assay to study KRas4b-membrane interactions. We suggest an extended conformation of KRas4b relative to the membrane surface. Measurement of FRET donor - acceptor distances reveal that a negatively charged membrane surface weakly favors closer association with the membrane surface. Our findings provide insights into the role of anionic lipids in determining the dynamic conformations of KRas4b and shed light on the predominant conformation of its topology on lipid headgroups.

Modeling of hydrophobic tetrapeptides as a competitive inhibitor for HMG-CoA reductase

This study presents a modeling of hydrophobic tetrapeptides acting in a competitive manner against 3‑hydroxy-3-methylglutaryl coenzyme A reductase. This enzyme catalyzes the reductive deacylation of 3‑hydroxy-3-methylglutaryl coenzyme A to mevalonate, using two molecules of nicotinamide adenine dinucleotide phosphate as cofactors, and this reaction represents the rate-limiting step in cholesterol biosynthesis. Thus, it is a target of many investigations in order to control a cholesterol level because the elevated cholesterol level is known as a risk factor of hypercholesterolemia. In previous studies, the two hypocholesterolemic peptides were isolated from soy glicinin. Based on these sequences, a number of the tri-, tetra-, hexa- and heptapeptides were designed in order to improve their inhibitory activities. The peptide fragmentation was applied as a main tool in design. Using the developed design method, a new recognized motif in the designed tetrapeptides was identified. According to the design parameter, the IIIP peptide possessed the most rigid structure among the new designed tetrapeptides. The circular dichroism study confirmed that the observed predominant conformation of the IIIP peptide was close to the type I of a β-turn. The IIIP peptide was determined as the strongest inhibitor among the new designed tetrapeptides. The kinetic study revealed the competitive HMGR inhibition by the peptide, which acted as a bisubstrate blocking an access of HMG-CoA and NADPH to their binding sites. The correlation coefficient (r2) between the predicted and observed peptide activities of 0.91 suggests wide possibilities of the proposed approach to design new peptides that may differ from the previously designed peptides in the recognized motif, sequences, lengths and structural preferences.

Determining the Predominant Conformations of Mortiamides A-D in Solution Using NMR Data and Molecular Modeling Tools.

Macrocyclic peptidomimetics have been seriously contributing to our arsenal of drugs to combat diseases. The search for nature's discoveries led us to mortiamides A-D (found in a novel fungus from Northern Canada), which is a family of cyclic peptides that clearly have demonstrated impressive pharmaceutical potential. This prompted us to learn more about their solution-state properties as these are central for binding to target molecules. Here, we secured and isolated mortiamide D, and then acquired high-resolution nuclear magnetic resonance (NMR) data to learn more about its structure and dynamics attributes. Sets of two-dimensional NMR experiments provided atomic-level (through-bond and through-space) data to confirm the primary structure, and NMR-driven molecular dynamics (MD) simulations suggested that more than one predominant three-dimensional (3D) structure exist in solution. Further steps of MD simulations are consistent with the finding that the backbones of mortiamides A-C also have at least two prominent macrocyclic shapes, but the side-chain structures and dynamics differed significantly. Knowledge of these solution properties can be exploited for drug design and discovery.

DNA Aptamer Beacon Probe (ABP) for Monitoring of Adenosine Triphosphate Level in SW480 Cancer Cells Treated with Glycolysis Inhibitor 2-Deoxyglucose.

Early cancer screening enables timely detection of carcinogenesis, and aids in prompt clinical intervention. Herein, we report on the development of a simple, sensitive, and rapid fluorometric assay based on the aptamer probe (aptamer beacon probe, ABP) for monitoring the energy-demand biomarker adenosine triphosphate (ATP), an essential energy source that is released into the tumor microenvironment. Its level plays a significant role in risk assessment of malignancies. The operation of the ABP for ATP was examined using solutions of ATP and other nucleotides (UTP, GTP, CTP), followed by monitoring of ATP production in SW480 cancer cells. Then, the effect of a glycolysis inhibitor, 2-deoxyglucose (2-DG), on SW480 cells was investigated. The stability of predominant ABP conformations in the temperature range of 23-91 °C and the effects of temperature on ABP interactions with ATP, UTP, GTP, and CTP were evaluated based on quenching efficiencies (QE) and Stern-Volmer constants (KSV). The optimized temperature for best selectivity of ABP toward ATP was 40 °C (KSV = 1093 M-1, QE = 42%). We have found that the inhibition of glycolysis in SW480 cancer cells by 2-deoxyglucose resulted in lowering of ATP production by 31.7%. Therefore, monitoring and modulation of ATP concentration may aid in future cancer treatment.

Exploiting conformational dynamics to modulate the function of designed proteins

With the recent success in calculating protein structures from amino acid sequences using artificial intelligence-based algorithms, an important next step is to decipher how dynamics is encoded by the primary protein sequence so as to better predict function. Such dynamics information is critical for protein design, where strategies could then focus not only on sequences that fold into particular structures that perform a given task, but would also include low-lying excited protein states that could influence the function of the designed protein. Herein, we illustrate the importance of dynamics in modulating the function of C34, a designed α/β protein that captures β-strands of target ligands and is a member of a family of proteins designed to sequester β-strands and β hairpins of aggregation-prone molecules that lead to a variety of pathologies. Using a strategy to "see" regions of apo C34 that are invisible to NMR spectroscopy as a result of pervasive conformational exchange, as well as a mutagenesis approach whereby C34 molecules are stabilized into a single conformer, we determine the structures of the predominant conformations that are sampled by C34 and show that these attenuate the affinity for cognate peptide. Subsequently, the observed motion is exploited to develop an allosterically regulated peptide binder whose binding affinity can be controlled through the addition of a second molecule. Our study emphasizes the unique role that NMR can play in directing the design process and in the construction of new molecules with more complex functionality.

The primary gas phase hydration shell of hydroxide.

The number of water molecules in hydroxide's primary hydration shell has been long debated to be three from the interpretation of experimental data and four from theoretical studies. Here, we provide direct evidence for the presence of a fourth water molecule in hydroxide's primary hydration shell from a combined study based on high-resolution cryogenic experimental photoelectron spectroscopy and high-level quantum chemical computations. Well-defined spectra of OH-(H2O)n clusters (n=2 to 5) yield accurate electron binding energies, which are, in turn, used as key signatures of the underlying molecular conformations. Although the smaller OH-(H2O)3 and OH-(H2O)4 clusters adopt close-lying conformations with similar electron binding energies that are hard to distinguish, the OH-(H2O)5 cluster clearly has a predominant conformation with a four-coordinated hydroxide binding motif, a finding that unambiguously determines the gas phase coordination number of hydroxide to be four.

Mitochondrial Genome Sequence of Salvia officinalis (Lamiales: Lamiaceae) Suggests Diverse Genome Structures in Cogeneric Species and Finds the Stop Gain of Genes through RNA Editing Events.

Our previous study was the first to confirm that the predominant conformation of mitochondrial genome (mitogenome) sequence of Salvia species contains two circular chromosomes. To further understand the organization, variation, and evolution of Salvia mitogenomes, we characterized the mitogenome of Salvia officinalis. The mitogenome of S. officinalis was sequenced using Illumina short reads and Nanopore long reads and assembled using a hybrid assembly strategy. We found that the predominant conformation of the S. officinalis mitogenome also had two circular chromosomes that were 268,341 bp (MC1) and 39,827 bp (MC2) in length. The S. officinalis mitogenome encoded an angiosperm-typical set of 24 core genes, 9 variable genes, 3 rRNA genes, and 16 tRNA genes. We found many rearrangements of the Salvia mitogenome through inter- and intra-specific comparisons. A phylogenetic analysis of the coding sequences (CDs) of 26 common protein-coding genes (PCGs) of 11 Lamiales species and 2 outgroup taxa strongly indicated that the S. officinalis was a sister taxon to S. miltiorrhiza, consistent with the results obtained using concatenated CDs of common plastid genes. The mapping of RNA-seq data to the CDs of PCGs led to the identification of 451 C-to-U RNA editing sites from 31 PCGs of the S. officinalis mitogenome. Using PCR amplification and Sanger sequencing methods, we successfully validated 113 of the 126 RNA editing sites from 11 PCGs. The results of this study suggest that the predominant conformation of the S. officinalis mitogenome are two circular chromosomes, and the stop gain of rpl5 was found through RNA editing events of the Salvia mitogenome.

Influence of Side Chain Conformation on the Activity of Glycosidase Inhibitors.

Substrate side chain conformation impacts reactivity during glycosylation and glycoside hydrolysis and is restricted by many glycosidases and glycosyltransferases during catalysis. We show that the side chains of gluco and manno iminosugars can be restricted to predominant conformations by strategic installation of a methyl group. Glycosidase inhibition studies reveal that iminosugars with the gauche,gauche side chain conformations are 6- to 10-fold more potent than isosteric compounds with the gauche,trans conformation; a manno-configured iminosugar with the gauche,gauche conformation is a 27-fold better inhibitor than 1-deoxymannojirimycin. The results are discussed in terms of the energetic benefits of preorganization, particularly when in synergy with favorable hydrophobic interactions. The demonstration that inhibitor side chain preorganization can favorably impact glycosidase inhibition paves the way for improved inhibitor design through conformational preorganization.

Influence of Side Chain Conformation on the Activity of Glycosidase Inhibitors

AbstractSubstrate side chain conformation impacts reactivity during glycosylation and glycoside hydrolysis and is restricted by many glycosidases and glycosyltransferases during catalysis. We show that the side chains of gluco and manno iminosugars can be restricted to predominant conformations by strategic installation of a methyl group. Glycosidase inhibition studies reveal that iminosugars with the gauche,gauche side chain conformations are 6‐ to 10‐fold more potent than isosteric compounds with the gauche,trans conformation; a manno‐configured iminosugar with the gauche,gauche conformation is a 27‐fold better inhibitor than 1‐deoxymannojirimycin. The results are discussed in terms of the energetic benefits of preorganization, particularly when in synergy with favorable hydrophobic interactions. The demonstration that inhibitor side chain preorganization can favorably impact glycosidase inhibition paves the way for improved inhibitor design through conformational preorganization.

Effect of sterilization processes on alginate/gelatin inks for three-dimensional printing.

309Sterilization is a crucial step in the process of developing bioinks for tissue engineering applications. In this work, alginate/gelatin inks were subjected to three sterilization methods: ultraviolet (UV) radiation, filtration (FILT), and autoclaving (AUTO). In addition, to simulate the sterilization effect in a real environment, inks were formulated in two different media, specifically, Dulbecco's Modified Eagle's Medium (DMEM) and phosphate-buffered saline (PBS). First, rheological tests were performed to evaluate the flow properties of the inks, and we observed that UV samples showed shear thinning behavior, which was favorable for three-dimensional (3D) printing. Furthermore, the 3D-printed constructs developed with UV inks showed better shape and size fidelity than those obtained with FILT and AUTO. In order to relate this behavior to the material structure, Fourier transform infrared (FTIR) analysis was carried out and the predominant conformation in protein was determined by deconvolution of the amide I band, which confirmed that the prevalence of a-helix structure was greater for UV samples. This work highlights the relevance of sterilization processes, which are essential for biomedical applications, in the research field of bioinks.

Ultra‐Fast Continuous‐Flow Photo‐Thiol‐Ene Functionalization of Conformation‐Controlled Cinchona Alkaloids

AbstractIn this work, we describe ultra‐fast continuous flow photo‐thiol‐ene reactions on cinchona alkaloids derivatives through a control of the reactive conformation in solution. Flow thiol‐ene reactions proceed at 32 °C under light irradiation at 365 nm and require only 2.5 minutes of residence time to reach completion. The short path length of the tubular flow photochemical reactor, which maximizes and homogenizes the photon flux, associated to the fine tuning of the reactive conformation of cinchona alkaloids in solution are the main reasons for the high rates observed. The predominant conformation in solution of cinchona alkaloids was adjusted through the substitution of the hydroxyl group at C9 by a phenyl carbamate function.