Leveraging shape screening and molecular dynamics simulations to optimize PARP1-Specific chemo/radio-potentiators for antitumor drug design.

PARP1 plays a pivotal role in DNA repair within the base excision pathway, making it a promising therapeutic target for cancers involving BRCA mutations. Current study is focused on the discovery of PARP inhibitors with enhanced selectivity for PARP1. Concurrent inhibition of PARP1 with PARP2 and PARP3 affects cellular functions, potentially causing DNA damage accumulation and disrupting immune responses. In step 1, a virtual library of 593 million compounds has been screened using a shape-based screening approach to narrow down the promising scaffolds. In step 2, hierarchical docking approach embedded in Schrödinger suite was employed to select compounds with good dock score, drug-likeness and MMGBSA score. Analysis supplemented with decomposition energy, molecular dynamics (MD) simulations and hydrogen bond frequency analysis, pinpointed that active site residues; H862, G863, R878, M890, Y896 and F897 are crucial for specific binding of ZINC001258189808 and ZINC000092332196 with PARP1 as compared to PARP2 and PARP3. The binding of ZINC000656130962, ZINC000762230673, ZINC001332491123, and ZINC000579446675 also revealed interaction involving two additional active site residues of PARP1, namely N767 and E988. Weaker or no interaction was observed for these residues with PARP2 and PARP3. This approach advances our understanding of PARP-1 specific inhibitors and their mechanisms of action, facilitating the development of targeted therapeutics.

Morphological Transformation and Surface Engineering of Glycovesicles Driven by Bioinspired Hydrogen Bonds of Nucleobases.

Glycopolymer-based supramolecular glycoassemblies with signal-driven cascade morphological deformation and accessible surface engineering toward bioinspired functional glycomaterials have attracted much attention due to their diverse applications in fundamental and practical scenarios. Herein, we achieved the cascade morphological transformation and surface engineering of a nucleobase-containing polymeric glycovesicle through exploiting the bioinspired complementary multiple hydrogen bonds of complementary nucleobases. First, the synthesized thymine-containing glycopolymers (PGal30-b-PTAm249) are capable of self-assembling into well-defined glycovesicles. Several kinds of amphiphilic adenine-containing block copolymers with neutral, positive, and negative charges were synthesized to engineer the glycovesicles through the multiple hydrogen bonds between adenine and thymine. A cascade of morphological transformations from vesicles to ruptured vesicles with tails, to worm-like micelles, and finally to spherical micelles were observed via continuously adding the adenine-containing polymer into the thymine-containing glycovesicles. Furthermore, the surface charge properties of these glyconano-objects can be facilely regulated through incorporating various adenine-containing polymers. This work demonstrates the potential application of a unique bioinspired approach to precisely engineer the morphology and surface properties of glycovesicles for boosting their biological applications.

Role of the Solvent and Intramolecular Hydrogen Bonds in the Antioxidative Mechanism of Prenylisoflavone from Leaves of Vatairea guianensis.

This work discusses the electron structure, antioxidative properties, and solvent contribution of two new antioxidant molecules discovered, named S10 and S11, extracted from a medicinal plant called Vatairea guianensis, found in the Amazon rain-forest. To gain a better understanding, a study using density functional theory coupled with the polarizable-continuum model and the standard 6-311++G(d,p) basis set was conducted. The results indicate that S10 has a higher antioxidant potential than S11, confirming the experimental expectations. In the gas phase, the hydrogen atom transfer route dominates the hydrogen scavenging procedure. However, in the water solvents, the antioxidant mechanism prefers the sequential proton loss electron transfer mechanism. Furthermore, the solvent plays a fundamental role in the antioxidant mechanism. The formation of an intramolecular OH···OCH3 hydrogen bond is crucial for accurately describing the hydrogen scavenging phenomenon, better aligning with the experimental data. The results suggest that the two isoflavones investigated are promising for the pharmacologic and food industries.

A Novel Demulsifier with Strong Hydrogen Bonding for Effective Breaking of Water-in-Heavy Oil Emulsions.

In the heavy petroleum industry, the development of efficient demulsifiers for the effective breaking of interfacially active asphaltenes (IAA)-stabilized water-in-heavy oil (W/HO) emulsions is a highly attractive but challenging goal. Herein, a novel nitrogen and oxygen containing demulsifier (JXGZ) with strong hydrogen bonding has been successfully synthesized through combining esterification, polymerization and amidation. Bottle tests indicated that JXGZ is effectual in quickly demulsifying the IAA-stabilized W/HO emulsions; complete dehydration (100%) to the emulsions could be achieved in 4 min at 55 °C using 400 ppm of JXGZ. In addition, the effects of demulsifier concentration, temperature and time on the demulsification performance of JXGZ are systematically analyzed. Demulsification mechanisms reveal that the excellent demulsification performance of JXGZ is attributed to the strong hydrogen bonding between JXGZ and water molecules (dual swords synergistic effect under hydrogen bond reconstruction). The interaction of the "dual swords synergistic effect" generated by two types of hydrogen bonds can quickly break the non-covalent interaction force (π-π stacking, Van der Waals force, hydrogen bonds) of IAA at the heavy oil-water interface, quickly promote the aggregation and coalescence of water molecules and finally achieve the demulsification of W/HO emulsions. These findings indicate that the JXGZ demulsifier shows engineering application prospects in the demulsification of heavy oil-water emulsions, and this work provides the key information for developing more efficient chemical demulsifiers suitable for large-scale industrial applications.

Design, synthesis and bioactivity evaluation of selenium-containing PI3Kδ inhibitors.

PI3Kδ inhibitors play an important role in the treatment of leukemia, lymphoma and autoimmune diseases. Herein, using our reported compounds as the lead compound, we designed and synthesized a series of selenium-containing PI3Kδ inhibitors based on quinazoline and pyrido[3,2-d]pyrimidine skeletons. Among them, compound Se15 showed sub-nanomolar inhibition against PI3Kδ and strong δ-selectivity. Moreover, Se15 showed potent anti-proliferative effect on SU-DHL-6 cells with an IC50 value of 0.16 µM. Molecular docking study showed that Se15 was able to form multiple hydrogen bonds with PI3Kδ and was close proximity and stacking with PI3Kδ selective region. In conclusion, the Se-containing compound Se15 bearing pyrido[3,2-d]pyrimidine scaffold is a novel potent and selective PI3Kδ inhibitor. The introduction of selenium can enrich the structure of PI3Kδ inhibitors and provide a new idea for design of novel PI3Kδ inhibitors.

Intramolecular hydrogen bonds interactions in the isomers of the bilirubin molecule: DFT and QTAIM analysis.

CONTEXT: Bilirubin is an important molecule, used as a marker of some liver diseases, and it can also be toxic and cause jaundice, especially in newborns. The main treatment for neonatal jaundice is phototherapy with blue light, which is still widely studied because the photophysical processes involved are not fully understood. METHODS: Calculations based on the density functional theory (DFT) at M062X/6-31G(d,p) level were performed in order to evaluate the structural, electronic, and topological properties of bilirubin isomers. It was found that the ZZ conformation can form a greater number of hydrogen bonds, which gives the isomer greater energy stabilization compared to the other ZE, EZ, and EE isomers, and that the EE isomer is the conformer with the lowest energy of stabilization. The hydrogen bonds were characterized by the quantum theory of atoms in molecules (QTAIM) and for the ZZ isomer four hydrogen bonds (HBs) were found classified as intermediate, ∇2ρ(r) > 0, H(r) > 0. The ZE, EZ, and EE isomers show weak HBs, ∇2ρ(r) > 0, H(r) > 0.

The effect of chemical bond and solvent solubility parameter on stability and absorption value of functionalized PU sponge.

Seawater pollution from various sources such as industrial effluents, ship washing at sea, and oil spills harm humans and the marine environment. Therefore, finding ways to eliminate this pollution is crucial. This study successfully modified a polyurethane sponge through a simple dip-coating method with functionalized graphene oxide incorporating octadecylamine and oleic acid, resulting in a hydrophobic sponge capable of absorbing crude oil and various organic solvents. Characterization analyses confirmed the synthesis. The absorption capacity of the modified sponges was examined, for example, the PU sponge has absorbed 4 g/g engine oil, while the modified GO-ODA-PU sponge has increased its absorption to 36 g/g. The GO-ODA-PU sponge demonstrated great reusability compared to the GO-OA-PU sponge owing to the strong covalent bond formed between GO and ODA, which is superior to the weak hydrogen bond formed between GO and OA. The absorption capacity of the GO-OA-PU sponge decreased by 30%. The contact angle test showed that GO-ODA-PU and GO-OA-PU sponges had contact angles of 131° and 115°, respectively. Additionally, the GO-ODA-PU sponge performed optimally for semi-polar solvents in the solubility parameter range of 18-19, with its absorption capacity reaching its maximum value. The amount of oil recycling is even possible up to 98%.

Thymine-Modified Silicones: A Bioinspired Approach to Cross-Linked, Recyclable Silicone Polymers.

In DNA, thymine typically forms hydrogen bonds with adenine to hold two complementary strands together and to preserve the genetic code. While thymine is typically absent in RNA, a thymine-thymine hydrogen bonding structure is reminiscent of the wobble region in tRNA recognition, where noncanonical base pairing can occur. This noncanonical base pairing can be applied to synthetic polymer systems, where thymine is free to hydrogen bond with itself. In this work, the natural hydrogen bonding capacity of thymine was used to produce silicone polymer systems designed to be cross-linked by hydrogen bonds. Backbone and end-group-modified silicones were synthesized with differing concentrations of thymine, which facilitated the cross-linking of the polymeric strands. Removing the hydrogen on N3─which is typically involved in hydrogen bonding─resulted in systems with similar viscosities to the starting material and that were devoid of any apparent cross-links. Differential scanning calorimetry (DSC) studies of the thymine-modified polymers displayed thermal absorptions and releases, indicative of bond breaking and reformation, around 100 and 60 °C, respectively. The cycle of bond breaking and formation could be repeated without any noticeable degradation of the chemical structure of the polymers. These polymeric materials could be readily recycled and remolded by heating them at 110 °C for 5 min, followed by cooling to room temperature, confirming their thermoplastic nature.

The anti-breast cancer potential of dihydroartemisinin-isatin hybrids with hydrogen bond donors at C-3 position of isatin moiety.

Hydrogen bond effect plays a pivotal role in protein-ligand interaction and represents one of the fundamental bases in pharmaceutical design. To evaluate the influence of hydrogen bond interaction on the anti-breast cancer activity, fifteen dihydroartemisinin-isatin hybrids 7a-o with hydrogen bond donors at C-3 position of isatin moiety were designed, synthesized and evaluated for their antiproliferative activity against MCF-7, MDA-MB-231, MCF-7/ADR and MDA-MB-231/ADR breast cancer cell lines. The preliminary results illustrated that introduction of hydrogen bond donors especially thiosemicarbazide into C-3 position of isatin moiety was beneficial for the activity, and substituents at C-5 position of isatin fragment as well as the length of the carbon spacers between dihydroartemisinin and isatin moieties also have significant influence on the activity. The enriched structure-activity relationships may provide useful information for further rational design of the candidates with higher activity.

Plant polysaccharide itself as hydrogen bond donor in a deep eutectic system-based mechanochemical extraction method.

A deep eutectic system (DESys) is formed when a hydrogen bond acceptor (HBA) is processed with polysaccharide (hydrogen bond donor, HBD) containing plant substance in water to dissolve, extract, and recover the polysaccharide directly, instead of using a traditional deep eutectic solvent (DES). The extraction efficiency is enhanced by the direct formation of the DESys, in a mechanochemical extraction (MCE) system. Key factors affecting the extraction efficiency were systematically studied and optimized. The effects of the DESys on the structure and physicochemical properties of polysaccharides were studied by several analytical techniques. The findings demonstrated that the direct DESys formation extraction efficiency was superior than that of traditional extraction methods while retaining physicochemical properties of polysaccharides. Moreover, the composition of polysaccharides extracted with this method is different from that obtained by conventional methods. The recovery and purification process of polysaccharides is simplified by eliminating the need for an additional HBD.

Association Complexes of Calix[6]arenes with Amino Acids Explained by Energy-Partitioning Methods.

Intermolecular complexes with calixarenes are intriguing because of multiple possibilities of noncovalent binding for both polar and nonpolar molecules, including docking in the calixarene cavity. In this contribution calix[6]arenes interacting with amino acids are studied with an additional aim to show that tools such as symmetry-adapted perturbation theory (SAPT), functional-group SAPT (F-SAPT), and systematic molecular fragmentation (SMF) methods may provide explanations for different numbers of noncovalent bonds and of their varying strength for various calixarene conformers and guest molecules. The partitioning of the interaction energy provides an easy way to identify hydrogen bonds, including those with unconventional hydrogen acceptors, as well as other noncovalent bonds, and to find repulsive destabilizing interactions between functional groups. Various other features can be explained by energy partitioning, such as the red shift of an IR stretching frequency for some hydroxy groups, which arises from their attraction to the phenyl ring of calixarene. Pairs of hydrogen bonds and other noncovalent bonds of similar magnitude found by F-SAPT explain an increase in the stability of both inclusion and outer complexes.

Transparent, Robust, and Photochemical Antibacterial Surface Based on Hydrogen Bonding between a Si-Al and Cationic Dye.

Healthcare-associated infections can occur and spread through direct contact with contaminated fomites in a hospital, such as mobile phones, tablets, computer keyboards, doorknobs, and other surfaces. Herein, this study shows a transparent, robust, and visible light-activated antibacterial surface based on hydrogen bonds between a transparent silica-alumina (Si-Al) sol-gel and a visible light-activated photosensitizer, such as crystal violet (CV). The study of the bonding mechanisms revealed that hydrogen bonding predominantly occurs between the N of CV and Al-OH. Apart from CV, Si-Al can be combined with a variety of dyes, highlighting its potential for wide application. The Si-Al@CV film selectively generates singlet oxygen using ambient visible light, triggering potent photochemical antibacterial performance against Gram-positive and Gram-negative bacteria. Additionally, the Si-Al@CV film is stable even after mechanical stability tests such as tape adhesion, scratch, bending, and water immersion. In vitro cytotoxicity tests using C2C12 myoblast cells showed that the Si-Al@CV film is a biocompatible material. This work suggests a new approach for designing a transparent and robust touchscreen surface with photochemical antibacterial capability against healthcare-associated infections.

CaCO3 Crystals with Unique Morphologies Controlled by the Hydrogen-Bonded Supramolecular Assemblies of Ureido-Pyrimidinone-Amino Acid Derivatives.

Biomineral materials such as nacre of shells exhibit high mechanical strength and toughness on account of their unique "brick-mortar" multilayer structure. 2-Ureido-4[1H]-pyrimidinone (UPy) derivatives with different types of end groups, due to the self-complementary quadruple hydrogen bonds and abundant Ca2+ binding sites, can easily self-assemble into supramolecular aggregates and act as templates and skeleton in the process of inducing mineral crystallization. In this work, UPy derivatives were used as templates to induce the mineralization and growth of CaCO3 through a CO2 diffusion method. The morphology of CaCO3 crystals was modulated and analyzed by adjusting the synthesizing parameters including Ca2+ concentration, pH, and end groups. The results showed that, by the regulatory role of the mineralization template, it was easier to realize the multilayer crystal structure at a lower concentration of Ca2+ (less than 0.01 mol L-1). Under alkaline regulation, the quadruple hydrogen bonds would be destroyed, and the template's regulation effect on the morphology of CaCO3 crystals would be weakened. Moreover, by comparing different types of end groups, it was proven that the UPy derivatives with carboxylic acid groups (-COOH) played a crucial role in the process of CaCO3 crystallization with unique morphologies.

Two-Site O-H Addition to an Iridium Complex Featuring a Nonspectator Tricoordinate Phosphorus Ligand.

The synthesis and reactivity of an ambiphilic iridium complex IrCl(PPh3)(L1) (1; L1 = P(N(o-N(2-pyridyl)C6H4)2)) featuring a chelating nontrigonal phosphorus triamide ligand is reported. The tandem Lewis basic Ir and Lewis acidic P of 1 achieve a two-site oxidative addition of phenol giving the iridaphenoxyphosphorane species IrHCl(PPh3)(L1OPh) (3'). In contrast, reactions of 1 with benzenethiol and benzeneselenol do not engage L1 and instead proceed via metal-centered oxidative addition of the chalcogen-hydrogen bond. These findings establish metal-ligand cooperation involving nonspectator reactivity of tricoordinate phosphorus ligands.

Endohedrally Functionalized Heteroleptic Coordination Cages for Phosphate Ester Binding.

Metallosupramolecular hosts of nanoscopic dimensions, which are able to serve as selective receptors and catalysts, are usually composed of only one type of organic ligand, restricting diversity in terms of cavity shape and functional group decoration. We report a series of heteroleptic [Pd2 A2 B2 ] coordination cages that self-assemble from a library of shape complementary bis-monodentate ligands in a non-statistical fashion. Ligands A feature an inward pointing NH function, able to engage in hydrogen bonding and amenable to being functionalized with amide and alkyl substituents. Ligands B comprise tricyclic aromatic backbones of different shape and electronic situation. The obtained heteroleptic coordination cages were investigated for their ability to bind phosphate diesters as guests. All-atom molecular dynamics (MD) simulations in explicit solvent were conducted to understand the mechanistic relationships behind the experimentally determined guest affinities.

Hydrogen Bond-Mediated Supramolecular Polymeric Nanomedicine with pH/Light-Responsive Methotrexate Release and Synergistic Chemo-/Photothermal Therapy.

Complete cancer cure and healing are still difficult, owing to its complexity and heterogeneity. Integration of supramolecular forces, for example, hydrogen bonds (H-bonds), to anti-cancer nanomedicine affords new scaffolds for biomedical material decoration, featuring the advantages of dynamic property and easier processability. Here, we target the construction of H-bond-mediated supramolecular polymer micelles, loaded with a chemotherapeutic drug along with a photothermal agent for synergistic chemo-/photothermal therapies (CT/PTT). To do so, we design and synthesize an amphiphilic ABA-type triblock copolymer, bearing H-bonding moiety (barbiturate, Ba) within the middle hydrophobic B block. The presence of pendant Ba moieties within the hydrophobic core promotes the loading capability of methotrexate (MTX) and transportation stability, benefitting from the formation of specific Ba/MTX H-bonding interactions. IR780, a photothermal agent, concomitantly encapsulated via hydrophobic interactions, facilitates the development of a synergistic CT/PTT modalities, where MTX can be released on demand owing to the dissociation of Ba/MTX H-bonding interactions induced by elevated temperature. Such H-bonding nanomedicine possesses enhanced drug loading capacity and transport performance and can also trigger stimuli-responsive drug release in the tumor zone. We believe that H-bonded nanomedicines provide a fine toolbox that is conducive to attaining biomedical requirements with remarkable values in theranostics that are highly promising in clinical applications.

Effects of ultrasonic on structure, chain conformation and morphology of pectin extracted from Premna microphylla Turcz.

In this study, ultrasonic effects on structure, chain conformation and morphology of pectin extracted from Premna microphylla Turcz (PEP) and its probable mechanism were investigated. In the process of ultrasonic treatments, the chains of PEP were fractured rapidly within the initial 10 min and then the degradation rate gradually slowed down. The primary structure of PEP nearly remained unchanged after ultrasonic degradation. The rigid semi-flexible chains of PEP were converted into flexible chains, flexible coils, even compact coils. Sonication at low intensity for short time made PEP molecular chains curly collapse and tighten up. Long duration sonication at high intensity generated excessive small rigidness segments that mutually aggregated because of hydrogen bonds and inhibited the self-coiling of PEP chains. Atomic force microscopy (AFM) analysis supported the conformation transition of PEP chains. The results provided a fundamental basis for orientation design and process control of PEP structure.

Elucidating the Infrared Spectral Properties of Succinic Molecular Acid Crystals: Illustration of the Structure and the Hydrogen Bond Energies of the Crystal and Its Deuterated Analogs.

Herein, the infrared spectroscopic properties of molecular succinic acid crystals (SA) and their four isotopic analogs [C2H4(COOH)2, h6-SA; C2H4(COOD)2, d2-SA; C2D4(COOH)2, d4-SA; C2D4(COOD)2, d6-SA] are reported. The correlation between the structure of succinic acid molecules and their corresponding hydrogen bond energies is elucidated. The effects related to the isotopic dilution as well as the changes in the spectrum recording temperature on the fine structures of the vO-H and vO-D bands are interpreted. The infrared spectral anomalies detected in the spectra of isotopically neat succinic nanocrystal acids are confirmed by theoretical calculations using density functional theory (DFT). According to previous spectroscopic studies of succinic acid and those carried out for α,ω-dicarboxylic acids, a decent agreement between the experimental results and the theoretical DFT simulations is obtained. Moreover, the spectra of single crystals of the h6 and d4 succinic acid variants prove that the vibrational coupling mechanism between the (COOH)2 cycles is rigorously convergent to that detected in the spectra of aromatic carboxylic acids, suggesting thereby that the promotion of symmetry-forbidden high stretching IR transitions plays a crucial role. Furthermore, the obtained experimental results reveal that the succinic acid shows a spectral behavior significantly different from that characteristic of hydrogen associations of other acids of homologous series, such as the glutaric, adipic, malonic, and pimelic acid crystals. The results obtained herein shed light on the way to explore the revealed structure of isotopic derivatives of succinic acid crystals and may prove to be useful results for understanding the nature of unconventional interactions as well as the macroscopic energy effects directing the development of hydrogen associations.

Hydrogen Bonding Directed Reversal of 13 C NMR Chemical Shielding.

The deshielding or downfield 13 C NMR chemical shift of amide carbonyl carbon upon H-bonding is a widely observed phenomenon. This downfield shift is commonly used as a spectroscopic ruler for H-bonding. However, the very first observation of an upfield 13 C NMR of thiocarbonyl carbon in thioamides upon H-bonding encouraged us to explore the physical origin of the reversal of 13 C NMR chemical shielding. Careful NMR analysis shows that sulfur and selenium-centered H-bonds (S/SeCHBs) induce a shielding effect on the 13 CC=S(Se) while changing from amides to thioamides or selenoamides. In addition, natural chemical shielding (NCS) analysis shows that the σ11 and σ22 components of the isotropic shielding tensor (σ) have a crucial role in this unusual shielding.

Superhydrophilicity of α-alumina surfaces results from tight binding of interfacial waters to specific aluminols.

HYPOTHESIS: Understanding the microscopic driving force of water wetting is challenging and important for design of materials. The relations between structure, dynamics and hydrogen bonds of interfacial water can be investigated using molecular dynamics simulations. EXPERIMENTS AND SIMULATIONS: Contact angles at the alumina (0001) and (112‾0) surfaces are studied using both classical molecular dynamics simulations and experiments. To test the superhydrophilicity, the free energy cost of removing waters near the interfaces are calculated using the density fluctuations method. The strength of hydrogen bonds is determined by their lifetime and geometry. FINDINGS: Both surfaces are superhydrophilic and the (0001) surface is more hydrophilic. Interactions between surfaces and interfacial waters promote a templating effect whereby the latter are aligned in a pattern that follows the underlying lattice of the surfaces. Translational and rotational dynamics of interfacial water molecules are slower than in bulk water. Hydrogen bonds between water and both surfaces are asymmetric, water-to-aluminol ones are stronger than aluminol-to-water ones. Molecular dynamics simulations eliminate the impacts of surface contamination when measuring contact angles and the results reveal the microscopic origin of the macroscopic superhydrophilicity of alumina surfaces: strong water-to-aluminol hydrogen bonds.