Docking and 3D QSAR studies of protoporphyrinogen oxidase inhibitor 3H-pyrazolo[3,4-d][1,2,3]triazin-4-one derivatives

Unsupervised machine learning, QSAR modelling and web tool development for streamlining the lead identification process of antimalarial flavonoids

Identification of lead compounds with the traditional laboratory approach is expensive and time-consuming. Nowadays, in silico techniques have emerged as a promising approach for lead identification. In this study, we aim to develop robust and predictive 2D-QSAR models to identify lead flavonoids by predicting the IC₅₀ against Plasmodium falciparum. We applied machine learning algorithms (Principal component analysis followed by K-means clustering) and Pearson correlation analysis to select 9 molecular descriptors (MDs) for model building. We selected and validated the three best QSAR models after execution of multiple linear regression (MLR) 100 times with different combinations of MDs. The developed models have fulfilled the five principles for QSAR models as specified by the Organization for Economic Co-operation and Development. The outcome of the study is a reliable and sustainable in silico method of IC₅₀ (Mean ± SD) prediction that will positively impact the antimalarial drug development process by reducing the money and time required to identify potential antimalarial lead compounds from the class of flavonoids. We also developed a web tool (JazQSAR, https://etflin.com/news/4) to offer an easily accessible platform for the developed QSAR models.

Synthesis of new pyrazolo[1,2,3]triazines by cyclative cleavage of pyrazolyltriazenes

We describe the synthesis of so far synthetically not accessible 3,6-substituted-4,6-dihydro-3H-pyrazolo[3,4-d][1,2,3]triazines as nitrogen-rich heterocycles. The target compounds were obtained in five steps, including an amidation and a cyclative cleavage reaction as key reaction steps. The introduction of two side chains allowed a variation of the pyrazolo[3,4-d][1,2,3]triazine core with commercially available building blocks, enabling the extension of the protocol to gain other derivatives straightforwardly. Attempts to synthesize 3,7-substituted-4,7-dihydro-3H-pyrazolo[3,4-d][1,2,3]triazines, the regioisomers of the successfully gained 3,6-substituted 4,6-dihydro-3H-pyrazolo[3,4-d][1,2,3]triazines, were not successful under similar conditions due to the higher stability of the triazene functionality in the regioisomeric precursors and thus, the failure of the removal of the protective group.

Pyrazolotriazines: Biological activities, synthetic strategies and recent developments

Heterocyclic compounds create an important class of molecules that demonstrates various chemical spaces for the definition of effective medicines. Many N-heterocycles display numerous biological activities. Among condensed heterocycles, pyrazolotriazine derivatives have received the attention of researchers owing to the extensive spectrum of biological activities. The reactivity of identified compounds was similar to the free azoles and triazines. The pyrazolotriazine scaffold exhibited antiasthma, antiinflammatory, anticancer, antithrombogenic activity and showed activity for major depression and pathological anxiety. Pyrazolotriazine derivatives also exhibited antibacterial, anticancer, antimetabolites, antidiabetic, antiamoebic, anticonvulsant, antiproliferative activity, human carbonic anhydrase inhibition, cyclin-dependent kinase 2 inhibition, tyrosinase and urease inhibition, MAO-B inhibition, TTK inhibition, thymidine phosphorylase inhibition, tubulin polymerization inhibition, protoporphyrinogen oxidase inhibition, GABA_A agonistic activity, hCRF1 receptor antagonistic activity, and CGRP receptor antagonistic activity. This paper structurally categorized various pyrazolotriazines to isomeric classes into six groups that containing pyrazolo [1,5-d] [1,2,4] triazine, pyrazolo [5,1-c] [1,2,4] triazine, pyrazolo [3,4-e] [1,2,4] triazine, pyrazolo [4,3-e] [1,2,4] triazines, pyrazolo [1,5-a] [1,3,5] triazine, and pyrazolo [3,4-d] [1,2,3] triazine and expressed biological activity, the synthetic procedures for each class of pyrazolotriazines, structure-activity relationship and their mechanism of action. Generally, this review summarily indicated the past and present studies about the discovery of new lead compounds with good biological activity.

Novel Thiazole Phenoxypyridine Derivatives Protect Maize from Residual Pesticide Injury Caused by PPO-Inhibitor Fomesafen

The herbicide fomesafen has the advantages of low toxicity and high selectivity, and the target of this compound is protoporphyrinogen IX oxidase (PPO, EC 1.3.3.4). However, this herbicide has a long residual period and can have phytotoxic effects on succeeding crops. To protect maize from fomesafen, a series of thiazole phenoxypyridines were designed based on structure–activity relationships, active substructure combinations, and bioisosterism. Bioassays showed that thiazole phenoxypyridines could improve maize tolerance under fomesafen toxicity stress to varying degrees at a dose of 10 mg·kg⁻¹. Compound 4i exhibited the best effects. After being treated by compound 4i, average recovery rates of growth index exceeded 72%, glutathione content markedly increased by 167% and glutathione S-transferase activity was almost 163% of fomesafen-treated group. More importantly, after being treated by compound 4i, the activity of PPO, the main target enzyme of fomesafen, recovered to 93% of the control level. The molecular docking result exhibited that the compound 4i could compete with fomesafen to bind with the herbicide target enzyme, which consequently attained the herbicide detoxification. The present work suggests that compound 4i could be developed as a potential safener to protect maize from fomesafen.

Design, Herbicidal Activity, and QSAR Analysis of Cycloalka[d]quinazoline-2,4-dione-Benzoxazinones as Protoporphyrinogen IX Oxidase Inhibitors

In continuation of our search for potent protoporphyrinogen IX oxidase (PPO, EC 1.3.3.4) inhibitors, we designed and synthesized a series of novel herbicidal cycloalka[d]quinazoline-2,4-dione-benzoxazinones. The bioassay results of these synthesized compounds indicated that most of the compounds exhibited very strong Nicotiana tabacum PPO (NtPPO) inhibition activity. More than half of the 37 synthesized compounds displayed over 80% control of all three tested broadleaf weeds at 37.5-150 g ai/ha by postemergent application, and a majority of them showed no phytotoxicity toward at least one kind of crop at 150 g ai/ha. Promisingly, 17i (Ki = 6.7 nM) was 6 and 4 times more potent than flumioxazin (Ki = 46 nM) and trifludimoxazin (Ki = 31 nM), respectively. Moreover, 17i displayed excellent, broad-spectrum herbicidal activity, even at levels as low as 37.5 g ai/ha, and it was determined to be safe for wheat at 150 g ai/ha in postemergent application, indicating the great potential for 17i development as a herbicide for weed control in wheat fields.

Quantitative Structure Activity Relationship Studies and Molecular Dynamics Simulations of 2-(Aryloxyacetyl)cyclohexane-1,3-Diones Derivatives as 4-Hydroxyphenylpyruvate Dioxygenase Inhibitors

4-Hydroxyphenylpyruvate dioxygenase (HPPD) is a significant enzyme in the biosynthesis of plastoquinone and tocopherol. Moreover, it is also a potential target to develop new herbicide. The technology of computer-aided drug design (CADD) is a useful tool in the efficient discovery of new HPPD inhibitors. Forty-three compounds with known activities were used to generate comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) models based on common framework and molecular docking. The structural contribution to the activity was determined, which provided further information for the design of novel inhibitors. Molecular docking was used to explain the changes in activity caused by the binding mode between ligand and protein. The molecular dynamics (MD) results indicated that the electrostatic energy was the major driving force for ligand–protein interaction and the Phe403 made the greatest contribution to the binding. The present work has provided useful information for the rational design of novel HPPD inhibitors with improved activity.

Ghrelin therapy mitigates bone marrow injury and splenocytopenia by sustaining circulating G-CSF and KC increases after irradiation combined with wound

Background

Radiation injury combined wound (CI) enhances acute radiation syndrome and subsequently mortality as compared to radiation injury alone (RI). We previously reported that ghrelin (a 28-amino-acid-peptide secreted from the stomach) treatment significantly increased a 30-day survival, mitigated hematopoietic death, circulating white blood cell (WBC) depletion and splenocytopenia and accelerated skin-wound healing on day 30 after CI. Herein, we aimed to study the ghrelin efficacy at early time points after CI.

Methods

B6D2F1/J female mice were exposed to ⁶⁰Co-γ-photon radiation at 9.5 Gy (LD_50/30) followed by a 15% total-body-surface-area skin wound. Several endpoints were measured at 4-5 h, days 1, 3, 7 and 15.

Results

Histological analysis of sternums on day 15 showed that CI induced more adipocytes and less megakaryocytes than RI. Bone marrow cell counts from femurs also indicated CI resulted in lower bone marrow cell counts on days 1, 7 and 15 than RI. Ghrelin treatment mitigated these CI-induced adverse effects. RI and CI decreased WBCs within 4-5 h and continued to decrease to day 15. Ghrelin treatment mitigated decreases in CI mice, mainly from all types of WBCs, but not RBCs, hemoglobin levels and hematocrit values. Ghrelin mitigated the CI-induced thrombocytopenia and splenocytopenia. CI increased granulocyte-colony stimulating factor (G-CSF) and keratinocyte chemoattractant (KC) in blood and bone marrow. Ghrelin therapy was able to enhance and sustain the increases in serum on day 15, probably contributed by spleen and ileum, suggesting the correlation between G-CSF and KC increases and the neutropenia mitigation. Activated caspase-3 levels in bone marrow cells were significantly mitigated by ghrelin therapy on days 3 and 15.

Conclusions

Our novel results are the first to suggest that ghrelin therapy effectively decreases hematopoietic death and splenocytopenia by sustaining circulating G-CSF and KC increases after CI. These results demonstrate efficacy of ghrelin as a radio-mitigator/therapy agent for CI.

Ghrelin accelerates wound healing in combined radiation and wound injury in mice

Impaired wound healing caused by radiation happens frequently in clinical practice, and the exact mechanisms remain partly unclear. Various countermeasures have been taken to tackle with this issue. Ghrelin was considered as a potent endogenous growth hormone-releasing peptide, and its role in enhancing wound repair and regeneration was firstly investigated in whole-body irradiated (γ-ray) mice in this study. Collagen deposition and neovascularization were mostly discussed. The results demonstrated that ghrelin administration promoted cutaneous wound healing in irradiated mice, followed with reduced average wound closure time, increased spleen index (SI) and improved haematopoiesis. After isolation and analysis of granulation tissues in combined radiation and wound injury (CRWI) mice treated with and without ghrelin, a phenomenon of increased DNA, hexosamine, nitrate and nitrite synthesis, elevated collagen content and enhanced neovascularization was observed after ghrelin treatment. Western blotting indicated that ghrelin also increased the expression of vascular endothelial growth factor (VEGF) and transforming growth factor-β (TGF-β), both responsible for wound healing. However, previous administration of growth hormone secretagogue receptor 1a (GHS-R1a) blocker blunted these therapeutic effects of ghrelin on CRWI mice. Our results identify ghrelin as a novel peptide that could be used for radiation-induced impaired wound healing.

Computer-aided drug design of capuramycin analogues as anti-tuberculosis antibiotics by 3D-QSAR and molecular docking

Capuramycin and a few semisynthetic derivatives have shown potential as anti-tuberculosis antibiotics.To understand their mechanism of action and structureactivity relationships a 3D-QSAR and molecular docking studies were performed. A set of 52 capuramycin derivatives for the training set and 13 for the validation set was used. A highly predictive MFA model was obtained with crossvalidated q2 of 0.398, and non-cross validated partial least-squares (PLS) analysis showed a conventional r2 of 0.976 and r2pred of 0.839. The model has an excellent predictive ability. Combining the 3D-QSAR and molecular docking studies, a number of new capuramycin analogs with predicted improved activities were designed. Biological activity tests of one analog showed useful antibiotic activity against Mycobacterium smegmatis MC2 155 and Mycobacterium tuberculosis H37Rv. Computer-aided molecular docking and 3D-QSAR can improve the design of new capuramycin antimycobacterial antibiotics.

Flumioxazin metabolism in pregnant animals and cell-based protoporphyrinogen IX oxidase (PPO) inhibition assay of fetal metabolites in various animal species to elucidate the mechanism of the rat-specific developmental toxicity

Flumioxazin, an N-phenylimide herbicide, inhibits protoporphyrinogen oxidase (PPO), a key enzyme in heme biosynthesis in mammals, and causes rat-specific developmental toxicity. The mechanism has mainly been clarified, but no research has yet focused on the contribution of its metabolites. We therefore conducted in vivo metabolism studies in pregnant rats and rabbits, and found 6 major known metabolites in excreta. There was no major rat-specific metabolite. The most abundant component in rat fetuses was APF, followed by flumioxazin and 5 identified metabolites. The concentrations of flumioxazin and these metabolites in fetuses were lower in rabbits than in rats. In vitro PPO inhibition assays with rat and human liver mitochondria showed that flumioxazin is a more potent PPO inhibitor than the metabolites. There were no species differences in relative intensity of PPO inhibition among flumioxazin and these metabolites. Based on the results of these in vivo and in vitro experiments, we concluded that flumioxazin is the causal substance of the rat-specific developmental toxicity. As a more reliable test system for research on in vitro PPO inhibition, cell-based assays with rat, rabbit, monkey, and human hepatocytes were performed. The results were consistent with those of the mitochondrial assays, and rats were more sensitive to PPO inhibition by flumioxazin than humans, while rabbits and monkeys were almost insensitive. From these results, the species difference in the developmental toxicity was concluded to be due to the difference in sensitivity of PPO to flumioxazin, and rats were confirmed to be the most sensitive of these species.

Medical countermeasures for unwanted CBRN exposures: part II radiological and nuclear threats with review of recent countermeasure patents

Introduction: The global threat of a chemical, biological, radiological, or nuclear (CBRN) disaster is an important priority for all government agencies involved in domestic security and public health preparedness. Radiological/nuclear (RN) attacks or accidents have become a larger focus of the United States Food and Drug administration (US FDA) over time because of their increased likeliness. Clinical signs and symptoms of a developing acute radiation syndrome (ARS) are grouped into three sub-syndromes named for the dominant organ system affected, namely the hematopoietic (H-ARS), gastrointestinal (GI-ARS), and neurovascular systems. The availability of safe and effective countermeasures against radiological/nuclear threats currently represents a significant unmet medical need.

Areas covered: This article reviews the development of RN threat medical countermeasures and highlights those specific countermeasures that have been recently patented and approved following the FDA Animal Rule. Patents for such agents from 2015 have been presented.

Expert opinion: Two granulocyte colony-stimulating factor (G-CSF)-based radiation countermeasures (Neupogen® (Amgen, Thousand Oaks, CA) and Neulasta® (Amgen, Thousand Oaks, CA)) have recently been approved by the FDA for treatment of H-ARS and both these agents are radiomitigators, used after radiation exposure. To date, there are no FDA-approved radioprotectors for ARS.

Molecular mechanism and therapeutic modulation of high mobility group box 1 release and action: an updated review

High mobility group box 1 (HMGB1) is an evolutionarily conserved protein, and is constitutively expressed in virtually all types of cells. Infection and injury converge on common inflammatory responses that are mediated by HMGB1 secreted from immunologically activated immune cells or passively released from pathologically damaged cells. Herein we review the emerging molecular mechanisms underlying the regulation of pathogen-associated molecular patterns (PAMPs)-induced HMGB1 secretion, and summarize many HMGB1-targeting therapeutic strategies for the treatment of infection- and injury-elicited inflammatory diseases. It may well be possible to develop strategies that specifically attenuate damage-associated molecular patterns (DAMPs)-mediated inflammatory responses without compromising the PAMPs-mediated innate immunity for the clinical management of infection- and injury-elicited inflammatory diseases.

A perspective on the role of quantitative structure-activity and structure-property relationships in herbicide discovery

BACKGROUND

For the last 15 years the agrochemical industry has focused on using genetic modification to put genes that confer resistance to existing commercial herbicides into crop plants rather than on discovering new herbicides with novel modes of action. The widespread appearance of weeds resistant to those herbicides is now causing the industry to revive their herbicide discovery programs.

RESULTS

Elucidation of quantitative structure-activity relationships (QSARs) played a major role in the discovery and development of existing commercial herbicides, but the advent of genetically modified crops has caused published work (at least) in the area to drift from the industrial arena into academic studies. The focus has also turned inward, to refining models for established herbicide targets instead of elucidating new ones.

CONCLUSION

This perspective highlights the importance of QSARs and quantitative structure-property relationships (QSPRs) to herbicide discovery in an historical context and provides some guidance as to how they might profitably be applied going forward.

The Interweaving of Cheminformatics and HTS

The aim of this chapter is to describe the stages of early drug discovery that can be assisted by techniques commonly used in the field of cheminformatics. In fact, cheminformatics tools can be applied all the way from the design of compound libraries and the analysis of HTS results, to the discovery of functional relationships between compounds and their targets.