Flavoenzyme-mediated reduction reactions and antitumor activity of nitrogen-containing tetracyclic ortho-quinone compounds and their nitrated derivatives

Nitrogen-based tetracyclic ortho-quinones (naphtho[1'2':4.5]imidazo[1,2-a]pyridine-5,6-diones, NPDOs) and their nitro-substituted derivatives (nitro-(P)NPDOs) were obtained by condensation of substituted 2,3-dichloro- 1,4-naphthoquinones with 2-amino-pyridine and -pyrimidine and nitration at an elevated temperature. The structural features of the compounds as well as their global and regional electrophilic potency were characterized by means of DFT computation. The compounds were highly reactive substrates of single- and two-electron (hydride)- transferring P-450R (CPR; EC 1.6.2.4) and NQO-1 (DTD; EC 1.6.99.2), respectively, concomitantly producing reactive oxygen species. Their catalytic efficiency defined in terms of the apparent second-order rate constant (kcat/KM (Q)) values in P-450R- and NQO-1-mediated reactions varied in the range of 3-6 × 107 M-1 s-1 and 1.6-7.4 × 108 M-1 s-1, respectively. The cytotoxic activities of the compounds on tumor cell lines followed the concentration-dependent manner exhibiting relatively high cytotoxic potency against breast cancer MCF-7, with CL50 values of 0.08-2.02 µM L-1 and lower potency against lung cancer A-549 (CL50 = 0.28-7.66 µM L-1). 3-nitro-pyrimidino- NPDO quinone was the most active compound against MCF-7 with CL50 of 0.08 ± 0.01 µM L-1 (0.02 µg mL-1)) which was followed by 3-nitro-NPDO with CL50 of 0.12 ± 0.03 µM L-1 (0.035 µg mL-1)) and 0.28 ± 0.08 µM L-1 (0.08 µg mL-1) on A-549 and MCF-7 cells, respectively, while 1- and 4-nitro-quinoidals produced the least cyto- or cells quantified by AO/EB staining showed that the cell death induced by the compounds occurs primarily through apoptosis

Garbage in, garbage out: how reliable training data improved a virtual screening approach against SARS-CoV-2 MPro

Introduction: The identification of chemical compounds that interfere with SARS-CoV-2 replication continues to be a priority in several academic and pharmaceutical laboratories. Computational tools and approaches have the power to integrate, process and analyze multiple data in a short time. However, these initiatives may yield unrealistic results if the applied models are not inferred from reliable data and the resulting predictions are not confirmed by experimental evidence.Methods: We undertook a drug discovery campaign against the essential major protease (MPro) from SARS-CoV-2, which relied on an in silico search strategy –performed in a large and diverse chemolibrary– complemented by experimental validation. The computational method comprises a recently reported ligand-based approach developed upon refinement/learning cycles, and structure-based approximations. Search models were applied to both retrospective (in silico) and prospective (experimentally confirmed) screening.Results: The first generation of ligand-based models were fed by data, which to a great extent, had not been published in peer-reviewed articles. The first screening campaign performed with 188 compounds (46 in silico hits and 100 analogues, and 40 unrelated compounds: flavonols and pyrazoles) yielded three hits against MPro (IC50 ≤ 25 μM): two analogues of in silico hits (one glycoside and one benzo-thiazol) and one flavonol. A second generation of ligand-based models was developed based on this negative information and newly published peer-reviewed data for MPro inhibitors. This led to 43 new hit candidates belonging to different chemical families. From 45 compounds (28 in silico hits and 17 related analogues) tested in the second screening campaign, eight inhibited MPro with IC50 = 0.12–20 μM and five of them also impaired the proliferation of SARS-CoV-2 in Vero cells (EC50 7–45 μM).Discussion: Our study provides an example of a virtuous loop between computational and experimental approaches applied to target-focused drug discovery against a major and global pathogen, reaffirming the well-known “garbage in, garbage out” machine learning principle

Preparation and characterization of cationic energetic salts of 5-amino-3-[(2,4,6-trinitrophenyl)amino]-1H-1,2,4-triazole (APATO)

The synthesis and properties of some 5-amino-3-[(2,4,6-trinitrophenyl)amino]-1H-1,2,4-triazole (APATO) cationic salts are described. A detailed structure of one of the salts obtained, 5-amino-3-[(2,4,6-trinitrophenyl)amino]-1H-1,2,4-triazol-4-ium perchlorate (APATO·HClO4) was characterized using low temperature (173 K) single crystal X-ray diffraction: orthorhombic yellow block, space group ‘Pbc21’, crystal density at 173 K (calculated) and at 293 K (pycnom.) were 1.863 and 1.840 g/cm3, respectively. The APATO salts were characterized by spectroscopic methods and thermal analysis. Preliminary computer calculated energetic characteristics showed that the synthesized salts possess increased energetic characteristics, superior in comparison to the TNT. The APATO perchlorate salt may deserve special attention as a thermostable HEDM

Computational studies of energetic property peculiarities in trinitrophenyl-substituted nitramines

This research was performed using Becke’s three-parameter hybrid functional approach with non-local correlation provided by Lee, Yang, and Parr and the cc-pVTZ basis set. The geometry, total energy, and heat of formation of the most stable conformers of the nitramines under study were obtained to obtain the density, resistance to shock stimuli, detonation pressure, and velocity of the materials under study. The results obtained allow us to predict new multipurpose energetic materials with a good balance between energy and stability. Our findings show that N-(2- nitroethyl)-N-(2,4,6-trinitrophenyl)nitramine, N-(2,4,6-trinitrophenyl)-N-[(3,4,5-trinitro-1H-pyrazol1-yl)methyl]nitramine, N-(2,2-dinitroethyl)-N-(2,4,6-trinitrophenyl)nitramine, N-(2,2,2-trinitroethyl)- N-(2,4,6-trinitrophenyl)nitramine, and N-(trinitromethyl)-N-(2,4,6-trinitrophenyl)nitramine possess better explosive properties and a greater stability compared to tetryl, although they remain sensitive to shock stimuli. Referring to the results obtained, we recommend new tetryl analogs containing dinitroethyl, trinitroethyl, and trinitromethyl substituents for practical usage

An Efficient Synthesis and Preliminary Investigation of Novel 1,3-Dihydro-<i>2H</i>-benzimidazol-2-one Nitro and Nitramino Derivatives

The preparation and properties of a series of novel 1,3-dihydro-2H-benzimidazol-2-one nitro and nitramino derivatives are described. A detailed crystal structure of one of the obtained compounds, 4,5,6-trinitro-1,3-dihydro-2H-benzimidazol-2-one (TriNBO), was characterized using low temperature single crystal X-ray diffraction, namely an orthorhombic yellow prism, space group ‘P 2 21 21′, experimental crystal density 1.767 g/cm3 (at 173 K). Methyl analog, 5-Me-TriNBO-monoclinic red plates, space group, P 21/c, crystal density 1.82 g/cm3. TriNBO contains one activated nitro group at the fifth position, which was used for the nucleophilic substitution in the aminolysis reactions with three monoalkylamines (R=CH3, C2H5, (CH2)2CH3) and ethanolamine. The 5-R-aminoderivatives were further nitrated with N2O5/ HNO3 and resulted in a new group of appropriate nitramines: 1,3-dihydro-2H-5-R-N(NO2)-4,6-dinitrobenzimidazol-2-ones. Thermal analysis (TGA) of three selected representatives was performed. The new compounds possess a high melting point (200–315 °C) and thermal stability and can find a potential application as new thermostable energetic materials. Some calculated preliminary energetic characteristics show that TriNBO, 5-Me-TriNBO, 5-methylnitramino-1,3-dihydro-2H-4,6-dinitrobenzimidazol-2-one, and 5-nitratoethylnitramino-1,3-dihydro-2H-4,6-dinitrobenzimidazol-2-one possess increased energetic characteristics in comparison with TNT and tetryl. The proposed nitrocompounds may find potential applications as thermostable high-energy materials

Reduction of nitroaromatic compounds by NAD(P)H:quinone oxidoreductase (NQO1): the role of electron-accepting potency and structural parameters in the substrate specificity

We aimed to elucidate the role of electronic and structural parameters of nitroaromatic compounds in their two-electron reduction by NAD(P)H:quinone oxidoreductase (NQO1, DT-diaphorase, EC 1.6.99.2). The multiparameter regression analysis shows that the reactivity of nitroaromatic compounds (n = 38) increases with an increase in their single-electron reduction potential and the torsion angle between nitrogroup(s) and the aromatic ring. The binding efficiency of nitroaromatics in the active center of NQO1 exerted a less evident role in their reactivity. The reduction of nitroaromatics is characterized by more positive entropies of activation than the reduction of quinones. This points to a less efficient electronic coupling of nitroaromatics with the reduced isoalloxazine ring of FAD, and may explain their lower reactivity as compared to quinones. Another important but poorly understood factor enhancing the reactivity of nitroaromatics is their ability to bind at the dicumarol/quinone binding site in the active center of NQO1

Influence of nitro group substitutes to the stability and energetic properties of N-(2,4,6-trinitrophenyl)-1H- 1,2,4-triazol-3-amine

In the paper, we aim to show N-(2,4,6-trinitrophenyl)-1 H -1,2,4-triazol-3-amine (HM-I) as explosive material that satisfies requirements of sensitivity and hy- drolytically stability. The influence of nitro group substitutions on the thermal and chemical stability as well as the explosive performance of HM-I is also investigated. We found that nitro group substitution to the triazole ring of HM-I can significantly improve the properties of this new material. Only -NH 2 substitution position (but not their number) in the core molecule is ap- propriate to increase the stability and improve explosive performances of HM-I

Benzimidazole derivatives as energetic materials: a theoretical study

The explosive properties and stability of benzimidazole compounds are studied to deter- mine the influence of substituents and their position. The results obtained reveal the conjugation of substituents as one of the crucial factors for the thermal stability of these compounds. We also found that two -CH 3 substituents increase the thermal stability of the parent compound, while nitro groups decrease it. Moreover, the study clearly exhibits that the combination of an -NO 2 substituent with -CH 3 does not change the stability of the benzimidazole. On the other hand, nitro groups increase the chemical stability and explosive properties of the compounds under investigation, but their sensitivity could not fully satisfy the requirements of their safety and increase their toxicity. The main results of the study indicate that high thermal and chemical stability, low toxicity and sensitivity, and good explosive properties could be achieved by the precise combination of nitro, -CH 3 , and triazole ring substituents. These findings are very important for the design of new, effective, and non-sensitive explosives

Role of NAD(P)H:quinone oxidoreductase (NQO1) in apoptosis induction by aziridinylbenzoquinones RH1 and MeDZQ

We aimed to characterize the role of NAD(P)H:quinone oxidoreductase (NQO1) in apoptosis induction by antitumour quinones RH1 (2,5-diaziridinyl-3-hydroxymethyl-6-methyl-1,4-benzoquinone) and MeDZQ (2,5-dimethyl-3,6-diaziridinyl-1,4-benzoquinone). Digitonin-permeabilized FLK cells catalyzed NADPH-dependent single- and two-electron reduction of RH1 and MeDZQ. At equitoxic concentrations, RH1 and MeDZQ induced apoptosis more efficiently than the nonalkylating duroquinone or H2O2. The antioxidant N,N'-diphenyl-p-phenylene diamine, desferrioxamine, and the inhibitor of NQO1 dicumarol, protected against apoptosis induction by all compounds investigated, but to a different extent. The results of multiparameter regression analysis indicate that RH1 and MeDZQ most likely induce apoptosis via NQO1-linked formation of alkylating species but not via NQO1-linked redox cycling