Nature and Hierarchy of Hydrogen-Bonding Interactions in Binary Complexes of Azoles with Water and Hydrogen Peroxide

Pyrano[2,3-c]pyrazole fused spirooxindole-linked 1,2,3-triazoles as antioxidant agents: Exploring their utility in the development of antidiabetic drugs via inhibition of α-amylase and DPP4 activity

Environment-benign, multicomponent synthetic methodologies are vital in modern pharmaceutical research and facilitates multi-targeted drug development via synergistic approach. Herein, we reported green and efficient synthesis of pyrano[2,3-c]pyrazole fused spirooxindole linked 1,2,3-triazoles using a tea waste supported copper catalyst (TWCu). The synthetic approach involves a one-pot, five-component reaction using N-propargylated isatin, hydrazine hydrate, ethyl acetoacetate, malononitrile/ethyl cyanoacetate and aryl azides as model substrates. Mechanistically, the reaction was found to proceed via in situ pyrazolone formation followed by Knoevenagel condensation, azide alkyne cycloaddition and Michael's addition reactions. The molecules were developed using structure-based drug design. The primary goal is to identifying anti-oxidant molecules with potential ability to modulate α-amylase and DPP4 (dipeptidyl-peptidase 4) activity. The anti-oxidant analysis, as determined via DPPH, suggested that the synthesized compounds, A6 and A10 possessed excellent anti-oxidant potential compared to butylated hydroxytoluene (BHT). In contrast, compounds A3, A5, A8, A9, A13, A15, and A18 were found to possess comparable anti-oxidant potential. Among these, A3 and A13 possessed potential α-amylase inhibitory activity compared to the acarbose, and A3 further emerged as dual inhibitors of both DPP4 and α-amylase with anti-oxidant potential. The relationship of functionalities on their anti-oxidant and enzymatic inhibition was explored in context to their SAR that was further corroborated using in silico techniques and enzyme kinetics.

Two metastable high hydrates of energetic material 3,3',5,5'-tetranitro-4,4'-bipyrazole

Poly-stoichiometry of hydrated phases is relatively uncommon for organic materials and extended libraries of such species adopting different aqua-to-substrate ratios are still rare. The kinetically controlled higher hydrates could be particularly interesting for their structural relationships, which presumably may imprint some features of the substrate/substrate and aqua/substrate bonding in solutions, and provide insights into the nucleation stage. Two metastable high hydrates are prepared by crash crystallization. The crystal structures of 3,3',5,5'-tetranitro-4,4'-bipyrazole tetrahydrate, C6H2N8O8·4H2O, (1), and 3,3',5,5'-tetranitro-4,4'-bipyrazole pentahydrate, C6H2N8O8·5H2O, (2), are intrinsically related to the previously reported anhydrate and monohydrate, while displaying natural evolution of the patterns upon progressive watering. The accumulation of the water molecules causes their clustering, with the generation of one-dimensional tapes and two-dimensional layers in the genuine channel hydrates (1) and (2), respectively, versus the pocket hydrate structure of C6H2N8O8·H2O. The hydration primarily affects the pyrazole sites. It conditions the emergence of N-H...O and O-H...N hydrogen bonds, which is a destructive factor for pyrazole/pyrazole N-H...N hydrogen bonding. At the same time, extensive noncovalent interactions of the organic molecules, namely, lone pair-π-hole O...N interactions of the NO2/NO2 and NO2/pyrazole types, are more competitive to the hydrogen bonding and the motifs of mutual organic/organic stacks remain intact with the increase in hydration. These trends agree with the results of Hirshfeld surface analysis. The contributions of the contacts involving H atoms are increased in line with the growing number of water molecules, while the fraction of O...N/N...O (NO2) contacts is nearly invariant. One may postulate the significance of the lone pair-π-hole interactions to the aggregation of nitro species in solutions and their relevance for the sebsequent development of the solid-state patterns through nucleation.

Exploring chemical space, scaffold diversity, and activity landscape of spleen tyrosine kinase active inhibitors

This study aims to comprehensively characterize 576 inhibitors targeting Spleen Tyrosine Kinase (SYK), a non-receptor tyrosine kinase primarily found in haematopoietic cells, with significant relevance to B-cell receptor function. The objective is to gain insights into the structural requirements essential for potent activity, with implications for various therapeutic applications. Through chemoinformatic analyses, we focus on exploring the chemical space, scaffold diversity, and structure-activity relationships (SAR). By leveraging ECFP4 and MACCS fingerprints, we elucidate the relationship between chemical compounds and visualize the network using RDKit and NetworkX platforms. Additionally, compound clustering and visualization of the associated chemical space aid in understanding overall diversity. The outcomes include identifying consensus diversity patterns to assess global chemical space diversity. Furthermore, incorporating pairwise activity differences enhances the activity landscape visualization, revealing heterogeneous SAR patterns. The dataset analysed in this work has three activity cliff generators, CHEMBL3415598, CHEMBL4780257, and CHEMBL3265037, compounds with high affinity to SYK are very similar to compounds analogues with reasonable potency differences. Overall, this study provides a critical analysis of SYK inhibitors, uncovering potential scaffolds and chemical moieties crucial for their activity, thereby advancing the understanding of their therapeutic potential.

Calcium l-Malate and d-Tartarate Frameworks as Adjuvants for the Sustainable Delivery of a Fungicide

Agrichemical adjuvants that combine a highly selective, efficient, and active mode of operation are critically needed to realize a more sustainable approach to their usage. Herein, we report the synthesis and full characterization of two new metal-organic frameworks (MOFs), termed UPMOF-1 and UPMOF-2, that were constructed from eco-friendly Ca2+ ions and naturally occurring, low-molecular weight plant acids, l-malic and d-tartaric acid, respectively. Upon structural elucidation of both MOFs, a widely used fungicide, hexaconazole (Hex), was loaded on the structures, reaching binding affinities of -5.0 and -3.5 kcal mol-1 and loading capacities of 63% and 62% for Hex@UPMOF-1 and Hex@UPMOF-2, respectively, as a result of the formation of stable host-guest interactions. Given the framework chemistry of the MOFs and their predisposition to disassembly under relevant agricultural conditions, the sustained release kinetics were determined to show nearly quantitative release (98% and 95% for Hex@UPMOF-1 and Hex@UPMOF-2, respectively) after >500 h, a release profile drastically different than the control (>80% release in 24 h), from which the high efficiency of these new systems was established. To confirm their high selectivity and activity, in vitro and in vivo studies were performed to illustrate the abilities of Hex@UPMOF-1 and Hex@UPMOF-2 to combat the known aggressive pathogen Ganoderma boninense that causes basal stem rot disease in oil palm. Accordingly, at an extremely low concentration of 0.05 μg mL-1, both Hex@UPMOF-1 and Hex@UPMOF-2 were demonstrated to completely inhibit (100%) G. boninense growth, and during a 26 week in vivo nursery trial, the progression of basal stem rot infection was completely halted upon treatment with Hex@UPMOF-1 and Hex@UPMOF-2 and seedling growth was accelerated given the additional nutrients supplied via the disassembly of the MOFs. This study represents a significant step forward in the design of adjuvants to support the environmentally responsible use of agrichemical crop protection.

The Importance of the Pyrazole Scaffold in the Design of Protein Kinases Inhibitors as Targeted Anticancer Therapies

The altered activation or overexpression of protein kinases (PKs) is a major subject of research in oncology and their inhibition using small molecules, protein kinases inhibitors (PKI) is the best available option for the cure of cancer. The pyrazole ring is extensively employed in the field of medicinal chemistry and drug development strategies, playing a vital role as a fundamental framework in the structure of various PKIs. This scaffold holds major importance and is considered a privileged structure based on its synthetic accessibility, drug-like properties, and its versatile bioisosteric replacement function. It has proven to play a key role in many PKI, such as the inhibitors of Akt, Aurora kinases, MAPK, B-raf, JAK, Bcr-Abl, c-Met, PDGFR, FGFRT, and RET. Of the 74 small molecule PKI approved by the US FDA, 8 contain a pyrazole ring: Avapritinib, Asciminib, Crizotinib, Encorafenib, Erdafitinib, Pralsetinib, Pirtobrutinib, and Ruxolitinib. The focus of this review is on the importance of the unfused pyrazole ring within the clinically tested PKI and on the additional required elements of their chemical structures. Related important pyrazole fused scaffolds like indazole, pyrrolo[1,2-b]pyrazole, pyrazolo[4,3-b]pyridine, pyrazolo[1,5-a]pyrimidine, or pyrazolo[3,4-d]pyrimidine are beyond the subject of this work.

Interactions between Paracetamol and Formaldehyde: Theoretical Investigation and Topological Analysis

In this work, noncovalent interactions including hydrogen bonds, C···C, N···O, and van der Waals forces between paracetamol and formaldehyde were investigated using the second-order perturbation theory MP2 in conjunction with the correlation consistent basis sets (aug-cc-pVDZ and aug-cc-pVTZ). Two molecular conformations of paracetamol were considered. Seven equilibrium geometries of dimers were found from the result of the interactions with formaldehyde for each conformation of paracetamol. Interaction energies of complexes with both ZPE and BSSE corrections range from -7.0 to -21.7 kJ mol^-1. Topological parameters (such as electron density, its Laplacian, and local electron energy density at the bond critical points) of the bonds from atoms in molecules theory were analyzed in detail. The natural bond orbital analysis showed that the stability of complexes was controlled by noncovalent interactions including O-H···O, N-H···O, C-H···O, C-H···N, C-H···H-C, C···C, and N···O. The red- and blue-shifted hydrogen bonds could both be observed in these complexes. The properties of these interactions were also further examined in water using a polarized continuum model. In water, the stability of the complex was slightly reduced as compared to that in the gas phase.

The influence of a single water molecule on the reaction of BrO + HONO

Quantum chemical computations and transition state theory are employed to systematically research the influence of a single molecule water on the BrO + HONO reaction. Two distinct reactions, namely BrO + trans-HONO and BrO + cis-HONO are explored for the reaction in the absence of water, which is mainly decided by the configuration of HONO. With introduction a single water molecule to the reaction, the rate coefficient of the channel starting from BrO + cis-HONO and BrO + trans-HONO are 2.43 × 10^-19 and 5.22 × 10^-22 cm³ molecule^-1 s^-1, which is larger than the reaction in the absence of water. For further comprehend the impact of water on the BrO + HONO reaction, it is necessary to compute the effective rate coefficient by taking into account the concentration of water. The water-assisted effective rate coefficients for the BrO + HONO reaction are smaller than that the reaction in the absence of water. The reaction of BrO with cis-HONO is feasible both in absence and existence of water.

Design of a Potent, Selective, and Brain-Penetrant Inhibitor of Wnt-Deactivating Enzyme Notum by Optimization of a Crystallographic Fragment Hit

Notum is a carboxylesterase that suppresses Wnt signaling through deacylation of an essential palmitoleate group on Wnt proteins. There is a growing understanding of the role Notum plays in human diseases such as colorectal cancer and Alzheimer's disease, supporting the need to discover improved inhibitors, especially for use in models of neurodegeneration. Here, we have described the discovery and profile of 8l (ARUK3001185) as a potent, selective, and brain-penetrant inhibitor of Notum activity suitable for oral dosing in rodent models of disease. Crystallographic fragment screening of the Diamond-SGC Poised Library for binding to Notum, supported by a biochemical enzyme assay to rank inhibition activity, identified 6a and 6b as a pair of outstanding hits. Fragment development of 6 delivered 8l that restored Wnt signaling in the presence of Notum in a cell-based reporter assay. Assessment in pharmacology screens showed 8l to be selective against serine hydrolases, kinases, and drug targets.

Synthesis, docking study, and structure activity relationship of novel anti-tumor 1, 2, 4 triazole derivatives incorporating 2-(2, 3- dimethyl aminobenzoic acid) moiety

A series of 1,2,4 triazole derivatives (H7-12) have been synthesized by reacting an excess of hydrazine hydrate with carbothioamide derivatives (H1-6). The final compounds (HB1-HB6) were synthesized by reacting the triazole derivatives with mefenamic acid using DCC as a coupling agent. The chemical structures were confirmed by FT-IR, 1H, and 13C-NMR spectra, and some physicochemical properties were determined. The cytotoxicity of the different compounds (HB1-HB6) was evaluated by the MTT assay against two human epithelial cancer cell lines, A549 lung carcinoma and Hep G2 hepatocyte carcinoma, and one normal human cell line WI-38 lung fibroblasts. The mode of cell killing (apoptosis versus necrosis), as well as the effect on cell cycle phases were evaluated via flow cytometry. Additionally, EGFR tyrosine kinase inhibition assay was performed. The results presented in the current study indicate that the six tested compounds exhibited cytotoxicity against both cancer cell lines, and the lowest IC50 was achieved with compound HB5 against Hep G2 cancer cells which was found to be highly selective against cancer cells. HB5-treated Hep G2 cells were arrested at the S and G2/M cell cycle phases. Compound HB5 caused cell killing via apoptosis rather than necrosis, and this was achieved by inhibiting EGFR tyrosine kinase activity needed for cell proliferation, and cell cycle progression. In silico pre-ADMET studies confirmed all final compounds don’t cause CNS side effects, with little liver dysfunction effect.

A single water molecule accelerating the atmospheric reaction of HONO with ClO

The role of a single water molecule on the atmospheric reaction of HONO + ClO is systematically investigated employing quantum chemical calculation combined with harmonic transition state theory. Two reaction pathways, cis-HONO + ClO and trans-HONO + ClO, are identified for the naked reaction, which depends on the configurations of HONO. When adding a single water molecule to this reaction, the rate constants of cis-HONO + ClO and trans-HONO + ClO pathways are 7.97 × 10^-21 and 2.29 × 10^-17 cm³ molecule^-1 s^-1, respectively, larger than the corresponding naked reaction. To further understand the role of water on the HONO + ClO reaction, it is necessary to calculate the effective rate constant by considering the concentration of water. It shows that the effective rate constants of water-assisted cis-HONO + ClO pathway are much smaller than those of the naked reaction, whereas the presence of water accelerates the trans-HONO + ClO at room temperature. This study demonstrates that water has a positive role in the pathway of trans-HONO + ClO by modifying the stabilities of reactant complexes and transition states through the hydrogen bond formation, which contributes to the sink of atmospheric HONO. In addition, the kinetic branching ratio indicates that the favorable reaction is the trans-HONO + ClO instead of the cis-HONO + ClO pathway, in contrast to the naked reaction. These results reveal the importance of water in the evaluation of the fate of active species in the atmosphere. Graphical Abstract.

Effects of methylation in acceptors on the hydrogen bond complexes between 2,2,2-trifluoroethanol and cyclic ethers

In order to explore the effect of methylation on the stability and spectral shift of hydrogen bond complexes, the complexes of 2,2,2-trifluoroethanol (TFE) with propylene oxide (PO) and isobutylene oxide (IBO) were investigated by Fourier transform infrared (FTIR) spectroscopy and ab initio computations. The comparable OH-stretching red shifts were observed upon complexation, and an enhancement of the OH-stretching band is shown with the partial pressure of monomers increasing. The OH-stretching frequency of TFE is red shifted by 180 and 201 cm^-1 with PO and IBO, respectively. By using quantum chemical calculations, we predicted the geometric parameters, binding energies, and spectral shifts of TFEPO/IBO hydrogen bond complexes. The calculated and observed spectral shifts follow the same trends. Compared with the TFEethylene oxide (EO) complex, the strength of the hydrogen bond in complex increases with the addition of methyl group, which likely results from the increase in basicity of the hydrogen bond acceptor. By combining the experimental integrated absorbance and the calculated IR intensity of the OH-stretching vibrational transition, the equilibrium constant for the complex formation was determined. In addition, atoms-in-molecules (AIM) and natural bond orbital (NBO) analyses were carried out to explain the red shift and the nature of the interaction in these complexes.

Exploring the Role of Consecutive Addition of Nitrogen Atoms on Stability and Reactivity of Hydrogen-Bonded Azine-Water Complexes

The second-order Møller-Plesset perturbation theory (MP2) and density functional theory with dispersion function calculations have been applied to investigate the hydrogen-bonding interaction between azines and water. The study suggests that the ability of nitrogen present in azine to act as a hydrogen-bond acceptor decreases in the order of pyridine (PY) > diazine (DZ) > triazine (TZ) > tetrazine (TTZ) > pentazine (PZ) > hexazine (HZ). Natural bond orbital (NBO) analysis, atoms in molecules, symmetry-adapted perturbation theory (SAPT), and molecular electrostatic potential studies reflect the factors important for hydrogen-bond strength as well as for the structural, electronic, and vibrational changes occurring during complexation. NBO analysis reflects that upon gradual addition of nitrogen atoms, hyperconjugation leads to an increase in the population of antibonding O-H bond, thus causing elongation and weakening of O-H bond in complexes incorporating N···H-O_W interaction, whereas rehybridization leads to an increase in the s character of the carbon hybrid orbital in C-H bond, thus causing contraction and shortening of C-H bond in complexes having C-H···O_W interactions. From the topological analysis, an excellent linear correlation is found to exist between stabilization energy (ΔE _BSSE), electron density (ρ_c), and its Laplacian (∇²ρ_c) at the bond critical points.