Search Results (26)

The selective detection of small, highly hydrophilic metabolites differing only in stereochemistry represents a major challenge in biosensor development. Here, we present a computational investigation to elucidate the molecular basis of the experimentally observed selectivity of a protein-based electrochemical biosensor toward myo-inositol over D-chiro-inositol. Although the two stereoisomers differ only in the orientation of a single hydroxyl group, they induce distinct dynamic effects on the protein recognition element. Molecular docking revealed comparable binding regions and similar affinity scores, indicating that selectivity does not arise from differences in binding site or docking energy. To investigate dynamic contributions, all-atom molecular dynamics simulations were performed in triplicate (3 × 100 ns) using the AMBER99SB force field and explicit TIP3P water. Trajectory analyses showed that myo-inositol forms a more persistent hydrogen bond network, resulting in reduced residue-level flexibility, more stable ligand–protein interactions, and enhanced local structural stabilization. Overall, these findings support a dynamic model of stereoselective recognition in which ligand-induced modulation of protein conformational ensembles, rather than static affinity, governs biosensor performance. This work highlights the value of molecular dynamics simulations in the rational design of biosensors targeting structurally similar analytes. Full article

Triple-negative breast cancer (TNBC) is a clinically aggressive malignancy with extremely limited effective targeted therapies. Natural products are promising alternatives for anticancer drug discovery, whereas integrated computational approaches serve as efficient tools for novel lead identification. Herein, four novel spiro-polycyclic sesquiterpene [4+2] trimers (Inubritantrimers A–D) and eight synthetic derivatives from Inula britannica L. were investigated via DFT calculations at the ωB97xD/6-311++G(2d,p) level (for geometric, electronic, spectral, and reactivity parameters), network pharmacology, molecular docking against seven core breast cancer-related targets, 500 ns all-atom molecular dynamics (MD) simulation, and MM/PBSA analysis. The results showed that the endo-type cycloaddition products had superior structural stability, with all reactions thermodynamically spontaneous (ΔG < 0). Compound 11 exhibited the most potent and balanced binding activity, with a docking free energy of −13.45 kcal/mol to MTOR; MD and MM/PBSA confirmed stable complex formation (total binding free energy −21.13 kcal/mol), driven predominantly by hydrophobic interactions. This study first established a comprehensive stereochemistry–electronic structure–property–activity relationship for this rare sesquiterpene trimer class and identified compound 11 as a promising MTOR-targeted TNBC lead. It provided a theoretical basis for developing high-efficiency, low-toxicity natural anticancer agents. Full article

Water is fundamental to structural integrity, stability, and functional properties of food systems, biomaterials, and biobased industries. The dynamics of hydration, including hydrogen bonding, hydration shell formation, plasticization, and phase transitions, dictate molecular behavior and exert broad influence on energy consumption, shelf life, biodegradability, and resource efficiency. However, the nonlinear and multiscale characteristics of hydration have constrained the predictive capabilities of conventional empirical methods. This study introduces a comprehensive framework that integrates foundational hydration science with advanced computational intelligence to model, predict, and optimize hydration-driven phenomena across diverse biopolymer classes. Leveraging classical insights into carbohydrate stereochemistry, protein hydrophobic hydration, and phospholipid-bound water, we demonstrate how computational approaches can reduce resource use in bioprocessing by 30–50% and optimize drying curves to lower energy consumption by 25%. By establishing hydration as a strategic design parameter, this work charts a pathway toward a resilient and sustainable economy where predictive error rates for hydration dynamics are significantly minimized through data-driven calibration. Full article

Bufadienolides exert broad-spectrum pharmacological activities relevant to cardiology and novel cancer treatments. Their efficacy, toxicity, and pharmacokinetic profiles are significantly affected by modifications at carbon-3 (C3) of the steroid core. We have applied molecular dynamics simulations to characterize the consequences of (i) variations in size of the substituent at C3, (ii) the type of linker at C3 (ether vs. N-methoxy), and (iii) stereochemistry (C3β vs. C3α) for derivatives’ interactions with Na⁺,K⁺-ATPase. The model compounds included bufalin, bufalin-N-glucose, bufalin-O-glucose as well as digoxigenin, digoxigenin monodigitoxoside and digoxin. It was shown that the optimal size of the substituent is a trade-off between the ability to form stabilizing interactions and steric and entropic interferences. The former is strongly affected by the nature of the linker due to its impact on the spatial position of the ligand: N-methoxy linker imposes rotational restrictions and places the core into a less favorable position compared to an ether bond. Similarly, the change from β- to α-anomer delocalizes the substituent precluding contacts with amino acid residues of the binding site. The presented mechanistic model of bufadienolide interactions with Na⁺,K⁺-ATPase helps to anticipate the consequences of modifications while designing derivatives with high anticancer activity but reduced cardiotoxicity. Full article

The impact of counterion structure, especially variations in constitutional and stereochemical isomers, on the properties and performance of AABSs remains under-explored. This study investigates how structural variations, particularly the stereochemistry of diammonium cyclohexane (DACH) counterions, influence the self-assembly behavior of AABSs. Four AABSs: undecanoyl-glycine, -L-alanine, -L-valine, and -L-leucine, were paired with six DACH counterions representing cis/trans isomers of 1,2-, 1,3-, and 1,4-DACH. Critical micelle concentrations (CMCs) were determined via conductimetry, and micellar sizes were measured using dynamic light scattering. The degree of counterion binding (β) was calculated to probe micelle stability, while geometry-optimized structures of the DACH isomers were obtained using density functional theory. Lastly, pH measurements were taken to probe the protonation of DACH counterions at their natural pH, where both the DACH counterion and AABS headgroups intrinsically behave as buffers. Results indicate that while surfactant hydrophobicity primarily dictates CMC in other AABS/DACH combinations, trans-1,3-DACH leads to consistently higher CMCs. This deviation likely arises from its structural conformation, which positions the amine groups an intermediate distance of ~4.4–4.5 Å apart, allowing a small fraction of divalently charged counterions to form strong electrostatic bridging pockets at the micelle interface. These interactions dominate over headgroup effects, leading to elevated and surfactant-independent CMC values. Regarding size and other unusual trends in the systems, cis- isomers formed slightly larger micelles, and trans-1,4-DACH induces abnormal aggregation in undecanoyl-glycine leading to temperature dependent gel formation. These findings highlight the significant influence of counterion structure on AABS behavior and support counterion design as a strategy for enhancing surfactant performance in sustainable applications. Full article

Accurate prediction of drug–drug interactions (DDIs) is essential for ensuring medication safety and optimizing combination-therapy strategies. However, existing DDI models face limitations in handling interactions related to stereochemistry and precisely locating drug interaction sites. These limitations reduce the prediction accuracy for conformation-dependent interactions and the interpretability of molecular mechanisms, potentially posing risks to clinical safety. To address these challenges, we introduce LSA-DDI, a Spatial-Contrastive-Attention-Based Drug–Drug Interaction framework. Our 3D feature extraction method captures the spatial structure of molecules through three features—coordinates, distances, and angles—and fuses them to enhance the model of molecular spatial structures. Concurrently, we design and implement a Dynamic Feature Exchange (DFE) mechanism that dynamically regulates the flow of information across modalities via an attention mechanism, achieving bidirectional enhancement and semantic alignment of 2D topological and 3D spatial structure features. Additionally, we incorporate a dynamic temperature-regulated multiscale contrastive learning framework that effectively aligns multiscale features and enhances the model’s generalizability. Experiments conducted on public drug databases under both warm-start and cold-start scenarios demonstrated that LSA-DDI achieved competitive performance, with consistent improvements over existing methods. Full article

We report the results of our computations of the spectral polynomials and spectra of a number of graphs possessing automorphism symmetries beyond cubic and icosahedral symmetries. The spectral (characteristic) polynomials are computed in fully expanded forms. The coefficients of these polynomials contain a wealth of combinatorial information that finds a number of applications in many areas including nanomaterials, genetic networks, dynamic stereochemistry, chirality, and so forth. This study focuses on a number of symmetric and semi-symmetric graphs with automorphism groups of high order. In particular, Heawood, Coxeter, Pappus, Möbius–Kantor, Tutte–Coxeter, Desargues, Meringer, Dyck, n-octahedra, n-cubes, icosahedral fullerenes such as C₈₀(I_h), golden supergiant C₂₄₀(I_h), Archimedean (I_h), and generalized Petersen graphs up to 720 vertices, among others, have been studied. The spectral polynomials are computed in fully expanded forms as opposed to factored forms. Several applications of these polynomials are briefly discussed. Full article

The primary objective of this study is the computation of the matching polynomials of a number of symmetric, semisymmetric, double group graphs, and solids in third and higher dimensions. Such computations of matching polynomials are extremely challenging problems due to the computational and combinatorial complexity of the problem. We also consider a series of recursive graphs possessing symmetries such as D_2h-polyacenes, wheels, and fans. The double group graphs of the Möbius types, which find applications in chemically interesting topologies and stereochemistry, are considered for the matching polynomials. Hence, the present study features a number of vertex- or edge-transitive regular graphs, Archimedean solids, truncated polyhedra, prisms, and 4D and 5D polyhedra. Such polyhedral and Möbius graphs present stereochemically and topologically interesting applications, including in chirality, isomerization reactions, and dynamic stereochemistry. The matching polynomials of these systems are shown to contain interesting combinatorics, including Stirling numbers of both kinds, Lucas polynomials, toroidal tree-rooted map sequences, and Hermite, Laguerre, Chebychev, and other orthogonal polynomials. Full article

Ribitol (C₅H₁₂O₅) is an acyclic sugar alcohol that was recently identified in O-mannose glycan on mammalian $\mathsf{\alpha }$-dystroglycan. The conformation and dynamics of acyclic sugar alcohols such as ribitol are dependent on the stereochemistry of the hydroxyl groups; however, the dynamics are not fully understood. To gain insights into the conformation and dynamics of sugar alcohols, we carried out comparative analyses of ribitol, d-arabitol and xylitol by a crystal structure database search, solution NMR analysis and molecular dynamics (MD) simulations. The crystal structures of the sugar alcohols showed a limited number of conformations, suggesting that only certain stable conformations are prevalent among all possible conformations. The three-bond scholar coupling constants and exchange rates of hydroxyl protons were measured to obtain information on the backbone torsion angle and possible hydrogen bonding of each hydroxyl group. The 100 ns MD simulations indicate that the ribitol backbone has frequent conformational transitions with torsion angles between 180${}^{\circ }$ and ±60${}^{\circ }$, while d-arabitol and xylitol showed fewer conformational transitions. Taking our experimental and computational data together, it can be concluded that ribitol is more flexible than d-arabitol or xylitol, and the flexibility is at least in part defined by the configuration of the OH groups, which may form intramolecular hydrogen bonds. Full article

As small protein assemblies and even small proteins are becoming more amenable to cryo-Electron Microscopy (EM) structural studies, it is important to consider the complementary dynamic information present in the data. Current computational strategies are limited in their ability to resolve minute differences among low molecular weight entities. Here, we demonstrate a new combinatorial approach to delineate flexible conformations among small proteins using real-space refinement applications. We performed a meta-analysis of structural data for the SARS CoV-2 Nucleocapsid (N) protein using a combination of rigid-body refinement and simulated annealing methods. For the N protein monomer, we determined three new flexible conformers with good stereochemistry and quantitative comparisons provided new evidence of their dynamic properties. A similar analysis performed for the N protein dimer showed only minor structural differences among the flexible models. These results suggested a more stable view of the N protein dimer than the monomer structure. Taken together, the new computational strategies can delineate conformational changes in low molecular weight proteins that may go unnoticed by conventional assessments. The results also suggest that small proteins may be further stabilized for structural studies through the use of solution components that limit the movement of external flexible regions. Full article

Human lipoxygenase 12 (hALOX12) catalyzes the conversion of docosahexaenoic acid (DHA) into mainly 14S-hydroperoxy-4Z,7Z,10Z,12E,16Z,19Z-docosahexaenoic acid (14S-H(p)DHA). This hydroperoxidation reaction is followed by an epoxidation and hydrolysis process that finally leads to maresin 1 (MaR1), a potent bioactive specialized pro-resolving mediator (SPM) in chronic inflammation resolution. By combining docking, molecular dynamics simulations, and quantum mechanics/molecular mechanics calculations, we have computed the potential energy profile of DHA hydroperoxidation in the active site of hALOX12. Our results describe the structural evolution of the molecular system at each step of this catalytic reaction pathway. Noteworthy, the required stereospecificity of the reaction leading to MaR1 is explained by the configurations adopted by DHA bound to hALOX12, along with the stereochemistry of the pentadienyl radical formed after the first step of the mechanism. In pig lipoxygenase 15 (pigALOX15-mini-LOX), our calculations suggest that 14S-H(p)DHA can be formed, but with a stereochemistry that is inadequate for MaR1 biosynthesis. Full article

Imidazolidin-4-ones were investigated as hydrolytically cleavable profragrances to increase the long-lastingness of perfume perception in a fabric softener application. The reaction of different amino acid amides with 2-alkyl- or 2-alkenylcyclopentanones as the model fragrances to be released afforded the corresponding bi- or tricyclic imidazolidin-4-ones as mixtures of diastereoisomers, which were separated by column chromatography. In polar solution, the different stereoisomers equilibrated under thermodynamic conditions to form mixtures with constant isomeric distributions, as shown by NMR spectroscopy. Dynamic headspace analysis on dry cotton demonstrated the controlled fragrance release from the precursors in practical application. Under non-equilibrium conditions (continuous evaporation of the fragrance) and depending on the structure and stereochemistry of the profragrances, the recorded headspace concentrations of the fragrance released from the precursors increased by a factor of 2 up to 100 with respect to the unmodified reference. Prolinamide-based precursors released the highest amount of fragrance and were thus found to be particularly suitable for prolonging the evaporation of cyclopentanone-derived fragrances on a dry cotton surface. Full article

In this work, the solution conformations of seventeen 3,7-diacyl bispidines were studied by means of NMR spectroscopy including VT NMR experiments. The acyl groups included alkyl, alkenyl, aryl, hetaryl, and ferrocene moieties. The presence of syn/anti-isomers and their ratios were estimated, and some reasons explaining experimental facts were formulated. In particular, all aliphatic and heterocyclic units in the acylic R(CO) fragments led to an increased content of the syn-form in DMSO-d₆ solutions. In contrast, only the anti-form was detected in DMSO-d₆ and CDCl₃ in the case when R = Ph, ferrocenyl, (R)-myrtenyl. In the case of a chiral compound derived from the natural terpene myrtene, a new dynamic process was found in addition to the expected inversion around the amide N-C(O) bond. Here, rotation around the CO-C=C bond in the acylic R fragment was detected, and its energy was estimated. For this compound, ΔG for amide N-C(O) inversion was found to be equal to 15.0 ± 0.2 kcal/mol, and for the rotation around the N(CO)–C^2′ bond, it was equal to 15.6 ± 0.3 kcal/mol. NMR analysis of the chiral bispidine-based bis-amide was conducted for the first time. Two X-ray structures are reported. For the first time, the unique syn-form was found in the crystal of an acyclic bispidine-based bis-amide. Quantum chemical calculations revealed the unexpected mechanism for amide bond inversion. It was found that the reaction does not proceed as direct N-C(O) bond inversion in the double-chair (CC) conformation but rather requires the conformational transformation into the chair–boat (CB) form first. The amide bond inversion in the latter requires less energy than in the CC form. Full article

Being a methyl ester of partricin, the mepartricin complex is the active substance of a drug called Ipertrofan (Tricandil), which was proven to be useful in treatment of benign prostatic hyperplasia and chronic nonbacterial prostatitis/chronic pelvic pain syndrome. Nevertheless, no direct structural evidence on the stereochemistry of its components has been presented to date. In this contribution, we have conducted detailed, NMR-driven stereochemical studies on mepartricins A and B, aided by molecular dynamics simulations. The absolute configuration of all the stereogenic centers of mepartricin A and B was defined as 3R, 7R, 9R, 11S, 13S, 15R, 17S, 18R, 19S, 21R, 36S, 37R, and 38S, and proposed as 41R. The geometry of the heptaenic chromophore of both compounds has been established as 22E, 24E, 26E, 28Z, 30Z, 32E, and 34E. Our studies on mepartricin ultimately proved that partricins A and B are structurally identical to the previously described main components of the aureofacin complex: gedamycin and vacidin, respectively. The knowledge of the stereochemistry of this drug is a fundamental matter not only in terms of studies on its molecular mode of action, but also for potential derivatization, aiming at improvement of its pharmacological properties. Full article

The halogen elimination of 1,2-diiodoethane (C₂H₄I₂) and 1,2-diiodotetrafluoroethane (C₂F₄I₂) serves as a model reaction for investigating the influence of fluorination on reaction dynamics and solute–solvent interactions in solution-phase reactions. While the kinetics and reaction pathways of the halogen elimination reaction of C₂H₄I₂ were reported to vary substantially depending on the solvent, the solvent effects on the photodissociation of C₂F₄I₂ remain to be explored, as its reaction dynamics have only been studied in methanol. Here, to investigate the solvent dependence, we conducted a time-resolved X-ray liquidography (TRXL) experiment on C₂F₄I₂ in cyclohexane. The data revealed that (ⅰ) the solvent dependence of the photoreaction of C₂F₄I₂ is not as strong as that observed for C₂H₄I₂, and (ⅱ) the nongeminate recombination leading to the formation of I₂ is slower in cyclohexane than in methanol. We also show that the molecular structures of the relevant species determined from the structural analysis of TRXL data provide an excellent benchmark for DFT calculations, especially for investigating the relevance of exchange-correlation functionals used for the structural optimization of haloalkanes. This study demonstrates that TRXL is a powerful technique to study solvent dependence in the solution phase. Full article