Biological Activity of Complexes Involving Nitro-Containing Ligands and Crystallographic-Theoretical Description of 3,5-DNB Complexes.

Drug resistance in infectious diseases developed by bacteria and fungi is an important issue since it is necessary to further develop novel compounds with biological activity that counteract this problem. In addition, new pharmaceutical compounds with lower secondary effects to treat cancer are needed. Coordination compounds appear to be accessible and promising alternatives aiming to overcome these problems. In this review, we summarize the recent literature on coordination compounds based on nitrobenzoic acid (NBA) as a ligand, its derivatives, and other nitro-containing ligands, which are widely employed owing to their versatility. Additionally, an analysis of crystallographic data is presented, unraveling the coordination preferences and the most effective crystallization methods to grow crystals of good quality. This underscores the significance of elucidating crystalline structures and utilizing computational calculations to deepen the comprehension of the electronic properties of coordination complexes.

Crystal structure, intermolecular interactions, charge-density distribution and ADME properties of the acridinium 4-nitrobenzoate and 2-amino-3-methylpyridinium 4-nitrobenzoate salts: a combined experimental and theoretical study.

Acridines are a class of bioactive agents which exhibit high biological stability and the ability to intercalate with DNA; they have a wide range of applications. Pyridine derivatives have a wide range of biological activities. To enhance the properties of acridine and 2-amino-3-methylpyridine as the active pharmaceutical ingredient (API), 4-nitrobenzoic acid was chosen as a coformer. In the present study, a mixture of acridine and 4-nitrobenzoic acid forms the salt acridinium 4-nitrobenzoate, C13H10N+·C7H4NO4- (I), whereas a mixture of 2-amino-3-methylpyridine and 4-nitrobenzoic acid forms the salt 2-amino-3-methylpyridinium 4-nitrobenzoate, C6H9N2+·C7H4NO4- (II). In both salts, protonation takes place at the ring N atom. The crystal structure of both salts is predominantly governed by hydrogen-bond interactions. In salt I, C-H...O and N-H...O interactions form an infinite chain in the crystal, whereas in salt II, intermolecular N-H...O interactions form an eight-membered R22(8) ring motif. A theoretical charge-density analysis reveals the charge-density distribution of the inter- and intramolecular interactions of both salts. An in-silico ADME analysis predicts the druglikeness properties of both salts and the results confirm that both salts are potential drug candidates with good bioavailability scores and there is no violation of the Lipinski rules, which supports the druglikeness properties of both salts. However, although both salts exhibit drug-like properties, salt I has higher gastrointestinal absorption than salt II and hence it may be considered a potential drug candidate.

Preparation of Acifluorfen-Based Ionic Liquids with Fluorescent Properties for Enhancing Biological Activities and Reducing the Risk to the Aquatic Environment.

In this work, 12 novel herbicidal ionic liquids (HILs) based on acifluorfen were prepared by pairing with the fluorescent hydrazides or different alkyl chains for increasing activities and reducing negative impacts on the aquatic environment. The results showed that the fluorescence of coumarin hydrazide in the HILs was applied as the internal and supplementary light source to meet the requirement of light wavelength range of acifluorfen, which improved the phytotoxicity of acifluorfen to weeds by enhancing singlet oxygen generation with increased sunlight utilization. The herbicidal activities of HILs were related positively with the length of chain of cation under high light intensity and depended mainly on the fluorescence characteristic of the cation under low light intensity, and the double salt IL forms of acifluorfen containing coumarin hydrazide and n-hexadecyltrimethylammonium had enhanced efficacies against broadleaf weeds in the field. Compared with acifluorfen sodium, HILs had lower water solubility, better surface activity, weaker mobility in soils, and higher decomposition temperature. These results demonstrated that HILs containing different cations provided a wider scope for fine-tuning of the physicochemical and biological properties of herbicides and established a promising way for the development of environmentally friendly herbicidal formulations.

New Biocatalyst Including a 4-Nitrobenzoic Acid Mediator Embedded by the Cross-Linking of Chitosan and Genipin and Its Use in an Energy Device.

A new anodic catalyst consisting of carbon nanotube, 4-nitrobenzoic acid, chitosan, genipin, and glucose oxidase (GOx) (CNT/4-NBA/[Chit/GOx/GP]) is suggested to promote the glucose oxidation reaction (GOR) and the performance of enzymatic biofuel cell (EBC). In this catalyst, through the cross-linked structure of chitosan and genipin and the proper distribution of amine groups within chitosan, many GOx molecules are maximally captured, their leaching out is suppressed, and the GOR is improved upon. In addition, 4-nitrobenzoic acid plays the role of mediator well. The effect induced by the cross-linked structure is evaluated by ultraviolet-visible (UV-vis) spectroscopy, pH measurements, and electrochemical characterizations. According to the characterizations, the new CNT/4-NBA/[Chit/GOx/GP] catalyst contains a large amount of GOx (17.8 mg/mL) and produces a high anodic current (331 µA/cm2 at 0.3 V vs Ag/AgCl) with a low onset potential (0.05 V vs Ag/AgCl) because its catalytic activity follows the desirable reaction pathway that minimizes creation of a protonated amine group that interferes with GOR. When the performance of EBC using this catalyst as an anodic electrode is measured, the EBC shows a high open-circuit voltage of 0.54 V and a maximum power density of 38 µW/cm2.

Multiple Hydrogen Loss from [M + H]+ and [a]+ ions of Peptides in MALDI In-Source Decay Using a Dinitro-Substituted Matrix.

The formation and radical-directed dissociation of multiple hydrogen-abstracted peptide cations [M + H - mH]·+ has been reported using MALDI-ISD with dinitro-substituted matrices. The MALDI-ISD of synthetic peptides using 3,5-dinitrosalicylic acid (3,5-DNSA) and 3,4-dinitrobenzoic acid (3,4-DNBA) as matrices resulted in multiple hydrogen abstraction from the analyte [M + H]+ and fragment [a]+ ions, i.e., [M + H - mH]+ and [a - mH]+ (m = 1-8). All of the ISD spectra showed unusually intense [a]+ ions originating from cleavage at the Cα-C bond of the Leu-Xxx residues when peptides without Phe/Tyr/His/Cys residues were used. The intensity of the [an]+ series ions generated using 3,5-DNSA and 3,4-DNBA rapidly decreased with increasing residue number n, suggesting cleavage at multiradical sites of [M + H - mH]•+. It was suggested that multiple hydrogen abstraction from protonated peptides [M + H]+ mainly takes place from the backbone amide nitrogen.

Asymmetric ligand binding in homodimeric Enterobacter cloacae nitroreductase yields the Michaelis complex for nitroaromatic substrates.

Nitroreductase enzymes are of interest as antibiotic targets and as activators in enzyme prodrug therapy, but the precise substrate binding orientation and reaction mechanism are poorly understood. In order to design more effective antibiotics and improve enzyme prodrug therapy, an atomistic description of nitroaromatic substrate binding in the active Michaelis complex is highly desirable. Here, using an iterative molecular dynamics (MD) simulation protocol, the binding of p-nitrobenzoic acid (p-NBA) in oxidized and reduced Enterobacter cloacae nitroreductase (NR) was investigated. For the oxidized NR, the MD simulations distinguished between the two possible binding orientations of p-NBA in NR from X-ray crystal structure data. For the reduced NR, a distinct active binding orientation of p-NBA was found when the second active site of the NR homodimer was occupied by a NADH analogue. This model of the active Michaelis complex of p-NBA with NR provides a rationale for the reduction of p-NBA by NR via a hydride transfer reaction mechanism suggested by experimental results, and brings the proposed reaction mechanism from experiment and computational models into agreement.

Molecular Interpretation of the Compaction Performance and Mechanical Properties of Caffeine Cocrystals: A Polymorphic Study.

The 1:1 caffeine (CAF) and 3-nitrobenzoic acid (NBA) cocrystal (CAF:NBA) displays polymorphism. Each polymorph shares the same docking synthon that connects individual CAF and NBA molecules within the asymmetric unit; however, the extended intermolecular interactions are significantly different between the two polymorphic modifications. These alternative interaction topologies translate to distinct structural motifs, mechanical properties, and compaction performance. To assist our molecular interpretation of the structure-mechanics-performance relationships for these cocrystal polymorphs, we combine powder Brillouin light scattering (p-BLS) to determine the mechanical properties with energy frameworks calculations to identify potentially available slip systems that may facilitate plastic deformation. The previously reported Form 1 for CAF:NBA adopts a 2D-layered crystal structure with a conventional 3.4 Å layer-to-layer separation distance. For Form 2, a columnar structure of 1D-tapes is displayed with CAF:NBA dimers running parallel to the (110) crystallographic direction. Consistent with the layered crystal structure, the shear modulus for Form 1 is significantly reduced relative to Form 2, and moreover, our p-BLS spectra for Form 1 clearly display the presence of low-velocity shear modes, which support the expectation of a low-energy slip system available for facile plastic deformation. Our energy frameworks calculations confirm that Form 1 displays a favorable slip system for plastic deformation. Combining our experimental and computational data indicates that the structural organization in Form 1 of CAF:NBA improves the compressibility and plasticity of the material, and from our tabletability studies, each of these contributions confers superior tableting performance to that of Form 1. Overall, mechanical and energy framework data permit a clear interpretation of the functional performance of polymorphic solids. This could serve as a robust screening approach for early pharmaceutical solid form selection and development.

Functional insights of a molecular complex pyrazolium 3,5-dinitrobenzoate:3,5-dinitrobenzoic acid on infectious agents and ctDNA - A comparative biological screening and complementary theoretical calculations.

Systematic identification and quantification of active radical sites in a small molecule, pyrazolium 3,5-dinitrobenzoate:3,5-dinitrobenzoic acid as well as in the stable free radical (DPPH•) were carried out by Fukui functions calculation using DFT functional with B3LYP/6-311++G(d,p) level of basis set. Bioactive Lewis acid-base compound, pyrazolium 3,5-dinitrobenzoate:3,5-dinitrobenzoic acid (PDNB:DNBA) has been synthesized and crystallized by slow evaporation - solution method at 30 °C. Various functional groups and the structural arrangements were ascertained from spectral and XRD analyses, respectively. UV-vis spectral analysis was used to find out the stability of the anticipated drug for about 60 min using methanol as a solvent. Stabilization of the compound was linked to the presence of enormous N-H…O, O-H…O and C-H…O hydrogen bonding interactions identified through Hirshfeld surface analysis. Chemical stability and reactivity of the drug were validated from theoretical optimization and HOMO-LUMO analysis. Active nucleophilic, electrophilic and radical sites of PDNB:DNBA were also identified from molecular electrostatic potential analysis. Inhibition of growth of pathogens in screening experiments by the proposed drug attests its suitability in biological applications. Antioxidant activity of the compound, PDNB:DNBA, endorses its aptness for scavenging reactive radicals. Fluorimetry experiments confirm hyperchromism in DNA binding analysis proving groove mode of binding. Molecular docking explored the various modes of intermolecular interactions of the drug with microbes as well as DNA.

Effect of 4-amino-3-nitrobenzoic acid on the expression level of the trans-sialidase gene in Trypanosoma cruzi epimastigotes.

Trans-sialidase of Trypanosoma cruzi (TcTS) is a key enzyme in the infection process from parasite to host; therefore, it has been considered an important target for developing new anti-Chagas drugs. Different compounds with trypanocidal activity and/or inhibition of TcTS have been reported; however, some benzoic acid derivatives have shown high enzymatic inhibition but low trypanocidal activity and viceversa. These results show that each compound may possess a different mechanism of action. Based on the above, the compound 4-amino-3-nitrobenzoic acid (16), a potent TcTS inhibitor (77% inhibition in enzymatic assays) was selected to evaluate its effects on the expression level of the TS gene in T. cruzi epimastigotes and determine its involvement in the mechanism of action. Results showed an increase in the expression level of the TcTS gene, which confirmed that compound 16, has a direct effect on TcTS.

LC-MS/MS study of the degradation processes of nitisinone and its by-products.

Nitisinone (2-(2-nitro-4-trifluoromethylbenzoyl)-1,3-cyclohexanedione, NTBC) was the first synthetically produced triketone herbicide. However, its unsatisfactory herbicidal properties, negative impact on the natural environment and the high cost of synthesis have hindered its commercialization as a plant protection agent. Nevertheless, NTBC has become the medical treatment of choice for a rare hereditary metabolic disease -hepatorenal tyrosinemia. Literature review shows that most research on nitisinone focuses on its medical applications, while there are neither in-depth studies of its stability nor its degradation pathways. Therefore, the aim of our study was to employ liquid chromatography coupled with mass spectrometry (LC-MS/MS) to determine the stability of NTBC in different experimental conditions (pH of solution, temperature, time of incubation, ultraviolet radiation), identify its degradation products and determine the stability of the latter. Electrospray ionization (ESI) in the negative ion mode was used as an ionization method and the analytes were detected by multiple reaction monitoring. We show that nitisinone stability increases with increasing pH of the solution. At pH similar to that of gastric juice in the human stomach, two major products of NTBC degradation are formed: 2-amino-4-(trifluoromethyl)benzoic acid (ATFA) and 2-nitro-4-(trifluoromethyl)benzoic acid (NTFA), which show considerable stability under studied conditions. The results of these studies shed new light on the properties of NTBC, therefore contributing to better understanding of possible risks and benefits of its medical application.

Prevention of haemoglobin glycation by acetylsalicylic acid (ASA): A new view on old mechanism.

Diabetic hyperglycemia provokes glycation of haemoglobin (Hb), an abundant protein in red blood cells (RBCs), by increasing its exposure to carbohydrates. Acetylsalicylic acid (ASA; Aspirin) is one of the first agents, which its antiglycation effect was witnessed. Although the precise molecular mechanism of action of ASA on protein glycation is not indisputably perceived, acetylation as its main molecular mechanism has been proposed. This report aims to unravel the meticulous mechanism of action of ASA by using two ASA analogues; benzoic acid (BA) and para-nitrobenzoic acid (NBA), despite their lack of acetyl group. In this regard, the inhibitory effect of these two chemicals in comparison with ASA on Hb fructation is reported. UV-visible spectroscopy, intrinsic advanced glycation end products (AGE) fluorescence spectroscopy, extrinsic thioflavin T (ThT) binding fluorescence spectroscopy, 2,4,6-trinitrobenzenesulfonic acid (TNBSA) assay, and single cell gel electrophoresis (SCGE) were used to explore the effects of BA and NBA in comparison with aforementioned chemicals in the context of protein glycation. In spite of the lack of acetyl substitution, NBA is reported as a novel agent with prominent inhibitory efficacy than ASA on the protein glycation. This fact brings up a possible new mechanism of action of ASA and reconsiders acetylation as the sole mechanism of inhibition of protein glycation.

A resorufin-based fluorescent probe for imaging polysulfides in living cells.

As the oxidative metabolites of the endogenous gasotransmitter H2S, H2Sn have attracted ever-increasing attention in the field of biomedical research due to their vital functions in biological systems. Herein, we report a resorufin-based "turn-on" probe for H2Sn sensing. An SNAr substitution-intramolecular cyclization cascade reaction was used in this probe for detecting exogenous and endogenous H2Sn. The detection process could be monitored using UV-Vis and fluorescence spectroscopy and the naked eye. The emission response of the probe towards H2Sn presented a good linear relationship in the 0-50 µM concentration range, and the LOD of this probe was 24 nM. The probe was used successfully to visualize endogenous H2Sn generated in the RAW 246.7 cells under external stimulation.

Hydrophobicity-oriented drug design (HODD) of new human 4-hydroxyphenylpyruvate dioxygenase inhibitors.

Involved in the tyrosine degradation pathway, 4-hydroxyphenylpyruvate dioxygenase (HPPD) is an important target for treating type I tyrosinemia. To discover novel HPPD inhibitors, we proposed a hydrophobicity-oriented drug design (HODD) strategy based on the interactions between HPPD and the commercial drug NTBC. Most of the new compounds showed improved activity, compound d23 being the most active candidate (IC50 = 0.047 µM) with about 2-fold more potent than NTBC (IC50 = 0.085 µM). Therefore, compound d23 is a potential drug candidate to treat type I tyrosinemia.

An alternative, single-point method for creatinine determination in urine samples with optoelectronic detector. Critical comparison to Jaffé method.

A rapid, single-point method for colorimetric creatinine determination has been developed as an alternative for a well-established Jaffé assay, which lacks analytical specificity. 3,5-dinitrobenzoic acid was employed in an alkaline environment as a chromophore instead of picric acid. Apart from the spectrophotometer, a simple optoelectronic detector was applied as an alternative detection method. The conditions of the reaction were optimized to provide satisfactory analytical parameters. The linear ranges of the proposed assays were 40-4000 and 10-300 µmol L-1 of creatinine for conventional spectrophotometry and a PEDD detector, respectively. A broad spectrum of potential interferents was examined. The presence of compounds such as glucose, urea or uric acid was the source of a significantly smaller bias in the examined method than in the case of the Jaffé method variants. The presented method was validated with the use of 10 human urine samples with the creatinine level determined by the recommended method. Two-tail paired Student's t-tests with 9 degrees of freedom at the 95% confidence level showed the agreement between the proposed and the reference methods.

Molecular insights into the mechanism of 4-hydroxyphenylpyruvate dioxygenase inhibition: enzyme kinetics, X-ray crystallography and computational simulations.

Slow-binding inhibitors with long residence time on the target often display superior efficacy in vivo. Rationally designing inhibitors with low off-target rates is restricted by a limited understanding of the structural basis of slow-binding inhibition kinetics in enzyme-drug interactions. 4-Hydroxyphenylpyruvate dioxygenase (HPPD) is an important target for drug and herbicide development. Although the time-dependent behavior of HPPD inhibitors has been studied for decades, its structural basis and mechanism remain unclear. Herein, we report a detailed experimental and computational study that explores structures for illustrating the slow-binding inhibition kinetics of HPPD. We observed the conformational change of Phe428 at the C-terminal α-helix in the inhibitor-bound structures and further identified that the inhibition kinetics of drugs are related to steric hindrance of Phe428. These detailed structural and mechanistic insights illustrate that steric hindrance is highly associated with the time-dependent behavior of HPPD inhibitors. These findings may enable rational design of new potent HPPD-targeted drugs or herbicides with longer target residence time and improved properties. DATABASE: Structure data are available in the PDB under the accession numbers 5CTO (released), 5DHW (released), and 5YWG (released).

A photo-controlled hyaluronan-based drug delivery nanosystem for cancer therapy.

In this paper, a novel photo-controlled drug-loaded nanomicelles were self-assembled by the amphiphile of hyaluronan-o-nitrobenzyl-stearyl chain (HA-NB-SC) with doxorubicin (DOX) encapsulated within the hydrophobic core. DOX-loaded HA-NB-SC nanomicelles are ∼139 nm in diameter. CD44-overexpressed HeLa cells can easily take up HA-NB-SC micelles through recognition of HA moiety. DOX-loaded HA-NB-SC nanomicelles could be disassembled upon UV light (365 nm) and consequently, release DOX at desired pathological sites. Furtherly, nitrosobenzaldehyde derivative, photo-induced products of HA-NB-SC and DOX could inhibit the proliferation of HeLa cells together. This strategy may shed some light on delivery of hydrophobic anti-cancer drugs in a controlled manner.

Mitochondrial Specific H2S n Fluorogenic Probe for Live Cell Imaging by Rational Utilization of a Dual-Functional-Photocage Group.

Reactive sulfur species play a very important role in modulating neural signal transmission. Hydrogen polysulfides (H2S n, n > 1) are recently suggested to be the actual signaling molecules. There are still few spatiotemporal controllable-based probes to detect H2S n. In this work, for the first time, we proposed the photocleavage product of the common photoremovable protecting group (2-nitrophenyl moiety) capable of trapping H2S n. Taking advantage of this, we constructed the probe H1 containing a photocontrollable group, a mitochondrial directing unit and a signal reporter fluorescein dye. H1 exhibited excellent fluorescence enhancement (50-fold) in response to H2S n under the aqueous buffer only after UV irradiation. H1 also showed high selectivity and sensitivity for H2S n over other reactive sulfur species, reactive oxygen species, and other analytes, especially biothoils including hydrogen sulfide, cysteine, homocysteine, and glutathione. We showed the utility of H1 to image H2S n in living cells with high spatiotemporal resolution.

Photocontrolled Multidirectional Differentiation of Mesenchymal Stem Cells on an Upconversion Substrate.

The effective guidance of mesenchymal stem cell (MSC) differentiation on a substrate by near-infrared (NIR) light is particularly attractive for tissue engineering and regenerative medicine. However, most of current substrates cannot control multidirectional differentiation of MSCs like natural tissues. Herein, a photocontrolled upconversion-based substrate was designed and constructed for guiding multidirectional differentiation of MSCs. The substrate enables MSCs to maintain their stem-cell characteristics due to the anti-adhesive effect of 4-(hydroxymethyl)-3-nitrobenzoic acid modified poly(ethylene glycol) (P1) attached on the upconversion substrate. Upon NIR irradiation, the P1 is released from the substrate by photocleavage. The detachment of P1 can change cell-matrix interactions dynamically. Moreover, MSCs cultured on the upconversion substrate can be specifically induced to differentiate to adipocytes or osteoblasts by adjusting the NIR laser. Our work provides a new way of using NIR-based upconversion substrate to modulate the multidirectional differentiation of MSCs.

Mapping the Relationship between Glycosyl Acceptor Reactivity and Glycosylation Stereoselectivity.

The reactivity of both coupling partners-the glycosyl donor and acceptor-is decisive for the outcome of a glycosylation reaction, in terms of both yield and stereoselectivity. Where the reactivity of glycosyl donors is well understood and can be controlled through manipulation of the functional/protecting-group pattern, the reactivity of glycosyl acceptor alcohols is poorly understood. We here present an operationally simple system to gauge glycosyl acceptor reactivity, which employs two conformationally locked donors with stereoselectivity that critically depends on the reactivity of the nucleophile. A wide array of acceptors was screened and their structure-reactivity/stereoselectivity relationships established. By systematically varying the protecting groups, the reactivity of glycosyl acceptors can be adjusted to attain stereoselective cis-glucosylations.

Development and Synthesis of DNA-Encoded Benzimidazole Library.

Encoded library technology (ELT) is an effective approach to the discovery of novel small-molecule ligands for biological targets. A key factor for the success of the technology is the chemical diversity of the libraries. Here we report the development of DNA-conjugated benzimidazoles. Using 4-fluoro-3-nitrobenzoic acid as a key synthon, we synthesized a 320 million-member DNA-encoded benzimidazole library using Fmoc-protected amino acids, amines and aldehydes as diversity elements. Affinity selection of the library led to the discovery of a novel, potent and specific antagonist of the NK3 receptor.