Synthesis and bioevaluation of pyrazole-benzimidazolone hybrids as novel human 4-Hydroxyphenylpyruvate dioxygenase inhibitors

Structure-based discovery of pyrazole-benzothiadiazole hybrid as human HPPD inhibitors

4-Hydroxyphenylpyruvate dioxygenase (HPPD) has attracted increasing attention as a target for treating type I tyrosinemia and other diseases with defects in tyrosine catabolism. Only one commercial drug, 2-(2-nitro-4-trifluoromethylbenzoyl)-1, 3-cyclohexanedione (NTBC), clinically treat type I tyrosinemia, but show some severe side effects in clinical application. Here, we determined the structure of human HPPD-NTBC complex, and developed new pyrazole-benzothiadiazole 2,2-dioxide hybrids from the binding of NTBC. These compounds showed improved inhibition against human HPPD, among which compound a10 was the most active candidate. The Absorption Distribution Metabolism Excretion Toxicity (ADMET) predicted properties suggested that a10 had good druggability, and was with lower toxicity than NTBC. The structure comparison between inhibitor-bound and ligand-free form human HPPD showed a large conformational change of the C-terminal helix. Furthermore, the loop 1 and α7 helix were found adopting different conformations to assist the gating of the cavity, which explains the gating mechanism of human HPPD.

Benzimidazolone-piperazine/triazole/thiadiazole/furan/thiophene conjugates: Synthesis, in vitro urease inhibition, and in silico molecular docking studies

This study describes the synthesis, in vitro urease inhibition, and molecular docking studies of benzimidazolone derivatives incorporating the piperazine, triazole, thiadiazole, furan, thiophene, and thiosemicarbazide moieties. All newly synthesized compounds demonstrated varying degrees of urease inhibitory activity, with IC50 values ranging between 0.64 ± 0.099 and 0.11 ± 0.017 µM, when compared with the standard drug thiourea (IC50 value of 0.51 ± 0.028 µM). To confirm the experimental urease inhibition results and elucidate the mode of interaction of the synthesized compounds with the binding site of the urease enzyme, molecular docking studies were performed using the Schrödinger Suite package. Molecular docking studies showed that compounds with high in vitro urease inhibition interacted with key residues of the urease active site such as His221, Glu222, Asp223, His322, Arg338, and Ni2+ cations via hydrogen bonding, metal coordination, salt bridge, π-π stacking, and π-cation interactions.

Discovery of Subnanomolar Inhibitors of 4-Hydroxyphenylpyruvate Dioxygenase via Structure-Based Rational Design

High-potency 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitors are usually featured by time-dependent inhibition. However, the molecular mechanism underlying time-dependent inhibition by HPPD inhibitors has not been fully elucidated. Here, based on the determination of the HPPD binding mode of natural products, the π-π sandwich stacking interaction was found to be a critical element determining time-dependent inhibition. This result implied that, for the time-dependent inhibitors, strengthening the π-π sandwich stacking interaction might improve their inhibitory efficacy. Consequently, modification with one methyl group on the bicyclic ring of quinazolindione inhibitors was achieved, thereby strengthening the stacking interaction and significantly improving the inhibitory efficacy. Further introduction of bulkier hydrophobic substituents with higher flexibility resulted in a series of HPPD inhibitors with outstanding subnanomolar potency. Exploration of the time-dependent inhibition mechanism and molecular design based on the exploration results are very successful cases of structure-based rational design and provide a guiding reference for future development of HPPD inhibitors.

Structure-Activity Relationship Study of Xanthoxyline and Related Small Methyl Ketone Herbicides

Xanthoxyline (1), a small natural methyl ketone, was previously reported as a plant growth inhibitor. In this research, related methyl ketones bearing electron-donating and electron-withdrawing groups, together with heteroaromatics, were investigated against seed germination and seedling growth of Chinese amaranth (Amaranthus tricolor L.) and barnyard grass [Echinochloa crus-galli (L.) Beauv]. The structure-activity relationships (SARs) of methyl ketone herbicides were clarified, and which types and positions of substituents were crucially important for activity were also clarified. Indole derivatives, namely, 3-acetylindole (43) and 3-acetyl-7-azaindole (44) were found to be the most active methyl ketones that highly suppressed plant growth at low concentrations. The molecular docking on the 4-hydroxyphenylpyruvate dioxygenase (HPPD) enzyme indicated that carbonyl, aromatic, and azaindole were key interactions of HPPD inhibitors. This finding would be useful for the development of small ketone herbicides.

Survey on the Recent Advances in 4-Hydroxyphenylpyruvate Dioxygenase (HPPD) Inhibition by Diketone and Triketone Derivatives and Congeneric Compounds: Structural Analysis of HPPD/Inhibitor Complexes and Structure-Activity Relationship Considerations

The serendipitous discovery of the HPPD inhibitors from allelopathic plants opened the way for searching new and effective herbicidal agents by application of classical hit-to-lead optimization approaches. A plethora of active and selective compounds were discovered that belong to three major classes of cyclohexane-based triketones, pyrazole-based diketones, and diketonitriles. In addition, to enhance inhibitory constant and herbicidal activity, many efforts were also made to gain broader weed control, crop safety, and eventual agricultural applicability. Moreover, HPPD inhibitors emerged as therapeutic agents for inherited and metabolic human diseases as well as vector-selective insecticides in the control of hematophagous arthropods. Given the large set of experimental data available, structure-activity relationship analysis could be used to derive suggestions for next generation optimized compounds.

Recent research progress and outlook in agricultural chemical discovery based on quinazoline scaffold

The discovery of new scaffolds and targets for pesticides is still a huge challenge facing the sustainable development of modern agriculture. In recent years, quinazoline derivatives have achieved great progress in drug discovery and have attracted great attention. Quinazoline is a unique bicyclic scaffold with a variety of biological activities, which increases the possibilities and flexibility of structural modification, showing enormous appeal in the discovery of new pesticides. Therefore, the agricultural biological activities, structure-activity relationships (SAR), and mechanism of action of quinazoline derivatives in the past decade were reviewed systematically, with emphasis on SAR and mechanism. Then, we prospected the application of the quinazoline scaffold as a special structure in agricultural chemical discovery, hoping to provide new ideas for the rational design and mechanism of novel quinazoline agricultural chemicals in the future.

Modulating catalytic activity of a modified flavin analogue via judicially positioned metal ion toward aerobic sulphoxidation

This manuscript describes the synthesis, spectroscopic and crystallographic characterization of a cadmium complex of 10-propoylisoalloxazine-7-carboxylic acid (Flc-Cd). Catalytic activity of Flc-Cd towards aerobic sulphoxidation reaction was investigated in the presence of l-ascorbic acid as the reducing agent. Notably the neutral un-metalated flavin analogue did not show any significant catalytic activity. The design strategy for Flc provides a close proximity of the metal centre to the flavin core without compromising the catalytic site thereby assisting the product formation when compared to unmetallated Flc. Minor enantioselectivity is also observed in cases where unsymmetrical sulphides were used; indicative of the possible involvement of chiral l-ascorbic acid in the intermediate formation.

Design and synthesis of a catalytically efficient metal-flavin complex toward aerobic sulphoxidation was achieved via judicially positioning the metal ion near the catalytic site thereby assisting the intermediate formation.

Critical Insight into Plausible Acquired Tocopherol Pathway in Neglected Human Trypanosomatids

Despite global therapeutic advancements, tropical parasitic infections like trypanosomiasis and leishmaniasis continue to be a major health concern in developing countries. These two tropical infectious diseases lead to enormous economic loss, significant disability, and morbidity, accounting for over one million deaths per year worldwide. The causative parasites, which shuttle between an insect vector and a mammalian host, thrive either in the bloodstream or in the intramacrophage environments. Essentially, the parasites live in an environment of oxidative stress and therefore require metabolic pathways to counterbalance the host immune response and survive the adverse conditions. Apart from the trypanothione pathway elucidated in the parasites, there exists a tocopherol pathway that functions to scavenge the reactive chemical species. This pathway, unique to photosynthetic organisms, is essential for the parasite's survival, though the enzymes involved remain largely uncharacterized. Consequently, an understanding of the origin of the pathway and where and how the interconnected tocopherol pathway functions may result in the identification of promising and potential therapeutic interventions to combat these deadly diseases. Recent works underline the presence of the tocopherol pathway in trypanosomatids and hypothesize that trypanosomatids may be tocopherol prototrophs. This review focuses on the biosynthesis of tocopherols in Trypanosoma and Leishmania in light of the current evidence.

Rational Redesign of Enzyme via the Combination of Quantum Mechanics/Molecular Mechanics, Molecular Dynamics, and Structural Biology Study

Increasing demands for efficient and versatile chemical reactions have prompted innovations in enzyme engineering. A major challenge in engineering α-ketoglutarate-dependent oxygenases is to develop a rational strategy which can be widely used for directly evolving the desired mutant to generate new products. Herein, we report a strategy for rational redesign of a model enzyme, 4-hydroxyphenylpyruvate dioxygenase (HPPD), based on quantum mechanics/molecular mechanics (QM/MM) calculation and molecular dynamic simulations. This strategy enriched our understanding of the HPPD catalytic reaction pathway and led to the discovery of a series of HPPD mutants producing hydroxyphenylacetate (HPA) as the alternative product other than the native product homogentisate. The predicted HPPD-Fe(IV)═O-HPA intermediate was further confirmed by the crystal structure of Arabidopsis thaliana HPPD/S267W complexed with HPA. These findings not only provide a good understanding of the structure-function relationship of HPPD but also demonstrate a generally applicable platform for the development of biocatalysts.

High-throughput quantification of ochronotic pigment formation in Escherichia coli to evaluate the potency of human 4-hydroxyphenylpyruvate dioxygenase inhibitors in multi-well format

4-hydroxyphenylpyruvate dioxygenase (HPD) is a key enzyme in the catabolism of tyrosine and therefore of great importance as a drug target to treat tyrosine-related inherited metabolic disorders (TIMD). Inhibition of this enzyme is therapeutically applied to prevent accumulation of toxic metabolites in TIMD patients. Nowadays an ex-herbicide, nitisinone, is used for this purpose and many more inhibitors are being explored and need to be tested. Here, we describe a colorimetric bacterial whole-cell screening system that allows quantifying the inhibitory effects of new human HPD inhibitors in a high-throughput and robust fashion. For this high-throughput screening (HTS) system we rely on the capability of recombinant E. coli that express human HPD, to generate a brown ochronotic pigment after the addition of tyrosine, whereafter this brown pigment can be quantified in a very specific and sensitive way by spectrophotometric analysis. Altogether, this robust and simple HTS screening system can be described as non-harmful, non-laborious and cost-effective with the aim to identify and evaluate novel therapeutic human HPD inhibitors for the treatment of TIMD.•

This robust high-throughput screening system enables rapid identification and evaluation of potential inhibitors of human 4-hydroxyphenylpyruvate dioxygenase.

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Simple and fast colorimetric quantification of the formation of ochronotic pigment.

Combined 3D-quantitative structure-activity relationships and topomer technology-based molecular design of human 4-hydroxyphenylpyruvate dioxygenase inhibitors

Aim: 4-Hydroxyphenylpyruvate dioxygenase (HPPD) has attracted increasing attention as an important target against tyrosinemia type I. This paper aimed to explore the structure-activity relationship of HPPD inhibitors with pyrazole scaffolds and to design novel HPPD inhibitors. Methodology & results: The best 3D-quantitative structure-activity relationships model was established by two different strategies based on 40 pyrazole scaffold-based analogs. Screening of molecular fragments by topomer technology, combined with molecular docking, 14 structures were identified for potential human HPPD inhibitory activity. Molecular dynamics results demonstrated that all the compounds obtained bound to the enzyme and possessed a satisfactory binding free energy. Conclusion: The quantitative structure-activity relationship of HPPD inhibitors of pyrazole scaffolds was clarified and 14 original structures with potential human HPPD inhibitory activity were obtained.

Design, synthesis, in vitro and in vivo evaluation of benzylpiperidine-linked 1,3-dimethylbenzimidazolinones as cholinesterase inhibitors against Alzheimer's disease

Cholinesterase inhibitor plays an important role in the treatment of patients with Alzheimer's disease (AD). Herein, we report the medicinal chemistry efforts leading to a new series of 1,3-dimethylbenzimidazolinone derivatives. Among the synthesised compounds, 15b and 15j showed submicromolar IC₅₀ values (15b, eeAChE IC₅₀ = 0.39 ± 0.11 µM; 15j, eqBChE IC₅₀ = 0.16 ± 0.04 µM) towards acetylcholinesterase (AChE) and butyrylcholinesterase (BChE). Kinetic and molecular modelling studies revealed that 15b and 15j act in a competitive manner. 15b and 15j showed neuroprotective effect against H₂O₂-induced oxidative damage on PC12 cells. This effect was further supported by their antioxidant activity determined in a DPPH assay in vitro. Morris water maze test confirmed the memory amelioration effect of the two compounds in a scopolamine-induced mouse model. Moreover, the hepatotoxicity of 15b and 15j was lower than tacrine. In summary, these data suggest 15b and 15j are promising multifunctional agents against AD.

Pyrazole-Isoindoline-1,3-dione Hybrid: A Promising Scaffold for 4-Hydroxyphenylpyruvate Dioxygenase Inhibitors

The discovery of 4-hydroxyphenylpyruvate dioxygenase (HPPD, EC 1.13.11.27) inhibitors has been an active area of research due to their great potential as herbicides for weed control. Starting from the binding mode of known inhibitors of HPPD, a series of HPPD inhibitors with new molecular scaffolds were designed and synthesized by hybridizing 2-benzoylethen-1-ol and isoindoline-1,3-dione fragments. The results of the in vitro tests indicated that the newly synthesized compounds showed good HPPD inhibitory activity with IC₅₀ values against the recombinant Arabidopsis thaliana HPPD (AtHPPD) ranging from 0.0039 μM to over 1 μM. Most promisingly, compound 4ae, 2-benzyl-5-(5-hydroxy-1,3-dimethyl-1H-pyrazole-4- carbonyl)isoindoline-1,3-dione, showed the highest AtHPPD inhibitory activity with a K_i value of 3.92 nM, making it approximately 10 times more potent than pyrasulfotole (K_i = 44 nM) and slightly more potent than mesotrione (K_i = 4.56 nM). In addition, the cocrystal structure of the AtHPPD-4ae complex was successfully resolved at a resolution of 1.8 Å. The X-ray diffraction analysis indicated that the two carbonyl groups of 2-benzoylethen-1-ol formed a bidentate chelating interaction with the metal ion, while the isoindoline-1,3-dione moiety formed pronounced π-π stacking interactions with Phe381 and Phe424. Moreover, water-mediated hydrogen bonding interactions were observed between Asn282 and the nitrogen atoms of the pyrazole ring of 4ae. The above results showed that the pyrazole-isoindoline-1,3-dione hybrid is a promising scaffold for developing HPPD inhibitors.

A robust bacterial assay for high-throughput screening of human 4-hydroxyphenylpyruvate dioxygenase inhibitors

Hereditary tyrosinemia type 1 (HT1) and alkaptonuria (AKU) are inherited metabolic disorders caused by defective enzymes involved in tyrosine catabolism. Nitisinone, an ex-herbicide and member of the β-triketone family, is therapeutically applied to prevent accumulation of toxic metabolites in patients by inhibiting the enzyme 4-hydroxyphenylpyruvate dioxygenase (HPD). Here, we developed a colorimetric bacterial whole-cell screening system that allows quantifying the inhibitory effects of human HPD inhibitors in a high-throughput and a robust fashion. The principle of our screening system is based on the degradation of tyrosine through 4-hydroxyphenylpyruvate into homogentisate by human HPD expressed in E. coli and subsequent production of a soluble melanin-like pigment. With the aim to optimise the assay, we tested different E. coli strains, expression and reaction temperatures, and time-points for supplementing the substrate. We found that in our assay the addition of prototypical β-triketone HPD inhibitors decreases pigment production in a dose-dependent manner with increasing inhibitor concentrations. In addition, plate uniformity, signal variability and spatial uniformity assessment showed that we have developed a robust high-throughput screening assay that is simple to use, cost-effective and enables identification and evaluation of novel therapeutic human HPD inhibitors for the treatment of tyrosine-related metabolic disorders.

Crystal Structure of 4-Hydroxyphenylpyruvate Dioxygenase in Complex with Substrate Reveals a New Starting Point for Herbicide Discovery

4-Hydroxyphenylpyruvate dioxygenase (HPPD) is a promising target for drug and pesticide discovery. The unknown binding mode of substrate is still a big challenge for the understanding of enzymatic reaction mechanism and novel HPPD inhibitor design. Herein, we determined the first crystal structure of Arabidopsis thaliana HPPD (AtHPPD) in complex with its natural substrate (HPPA) at a resolution of 2.80 Å. Then, combination of hybrid quantum mechanics/molecular mechanics (QM/MM) calculations confirmed that HPPA takes keto rather than enol form inside the HPPD active pocket. Subsequent site-directed mutagenesis and kinetic analysis further showed that residues (Phe424, Asn423, Glu394, Gln307, Asn282, and Ser267) played important roles in substrate binding and catalytic cycle. Structural comparison between HPPA-AtHPPD and holo-AtHPPD revealed that Gln293 underwent a remarkable rotation upon the HPPA binding and formed H-bond network of Ser267-Asn282-Gln307-Gln293, resulting in the transformation of HPPD from an inactive state to active state. Finally, taking the conformation change of Gln293 as a target, we proposed a new strategy of blocking the transformation of HPPD from inactive state to active state to design a novel inhibitor with K_i value of 24.10 nM towards AtHPPD. The inhibitor has entered into industry development as the first selective herbicide used for the weed control in sorghum field. The crystal structure of AtHPPD in complex with the inhibitor (2.40 Å) confirmed the rationality of the design strategy. We believe that the present work provides a new starting point for the understanding of enzymatic reaction mechanism and the design of next generation HPPD inhibitors.

Synthesis and fabrication of novel quinone-based chromenopyrazole antioxidant-laden silk fibroin nanofibers scaffold for tissue engineering applications

Oxidative stress is critically attributed for impeding tissue repair and regeneration process. Elimination of over-accumulated, deleterious reactive oxygen species (ROS) could be elicited to accelerate healing in tissue engineering applications. Antioxidant biomolecules play a pivotal role in attenuating oxidative stress by neutralizing the free radical effects. Herein, we describe the synthesis and fabrication of novel quinone-based chromenopyrazole (QCP) antioxidant-laden silk fibroin (SF) electrospun nanofiber scaffold (QCP-SF) for tissue engineering applications. The spectral characterization of the synthesized compounds (6a-6h) were analysed by using NMR, FTIR and mass spectra and cell viability study of all the synthesized compounds were evaluated by MTT assay in primary rat bone marrow stem cells (rBMSCs). Among the prepared molecules, compound 6h showed an excellent cell viability, and antioxidant efficacy of compound 6h (QCP) was investigated through 1,1‑diphenyl‑2‑picrylhydiazyl (DPPH) scavenging assay. QCP expressed high antioxidant activity with IC50% of DPPH scavenging was observed about 5.506 ± 0.2786 μg. Novel QCP laden SF fiber scaffolds (QCP-SF) were characterized and incorporation of QCP did not affect the nanofiber architecture of QCP-SF scaffold. QCP-SF scaffold exhibited an enhanced thermal and mechanical stability when compared to native SF fiber mat. In vitro biocompatibility studies were evaluated using NIH 3T3 fibroblasts and rBMSCs. The QCP-SF scaffold displayed an increased cell attachment and proliferation in both cell types. In vitro wound healing study (scratch assay) of QCP-SF scaffold showed an excellent cell migration with NIH 3T3 cells into scratch area and complete cell migration occurred within 24 h. Based on results, we propose that QCP-loaded SF (QCP-SF) nanofibrous scaffolds can serve as a promising potential antioxidant fibrous scaffold for skin tissue engineering applications.

Novel HPPD inhibitors: triketone 2H-benzo[b][1,4]oxazin-3(4H)-one analogs

BACKGROUND

Herbicides that inhibit 4-hydroxyphenylpyruvate dioxygenase (HPPD, EC 1.13.11.27) are very important for grass weed control. In order to discover novel HPPD herbicides, a series of triketone 2H-benzo[b] oxazin-3(4H)-one analogs was designed and synthesized.

RESULTS

In comparison with the commercial triketone HPPD herbicide mesotrione (IC₅₀ = 0.252 μM), some of these new triketone analogs displayed excellent HPPD inhibitory potency in vitro, for example B39 (IC₅₀ = 0.172 μM) and B41 (IC₅₀ = 0.156 μM). In addition, some of these compounds exhibited pre- and post-emergence herbicidal activity similar to mesotrione when applied at 375 g/ha.

CONCLUSION

Many of the title compounds described in this paper could be important lead structures for the further development of novel HPPD herbicides. © 2017 Society of Chemical Industry.

4-Hydroxyphenylpyruvate Dioxygenase Inhibitors: From Chemical Biology to Agrochemicals

The development of new herbicides is receiving considerable attention to control weed biotypes resistant to current herbicides. Consequently, new enzymes are always desired as targets for herbicide discovery. 4-Hydroxyphenylpyruvate dioxygenase (HPPD, EC 1.13.11.27) is an enzyme engaged in photosynthetic activity and catalyzes the transformation of 4-hydroxyphenylpyruvic acid (HPPA) into homogentisic acid (HGA). HPPD inhibitors constitute a promising area of discovery and development of innovative herbicides with some advantages, including excellent crop selectivity, low application rates, and broad-spectrum weed control. HPPD inhibitors have been investigated for agrochemical interests, and some of them have already been commercialized as herbicides. In this review, we mainly focus on the chemical biology of HPPD, discovery of new potential inhibitors, and strategies for engineering transgenic crops resistant to current HPPD-inhibiting herbicides. The conclusion raises some relevant gaps for future research directions.

3D Pharmacophore-Based Virtual Screening and Docking Approaches toward the Discovery of Novel HPPD Inhibitors

p-Hydroxyphenylpyruvate dioxygenase (HPPD) is not only the useful molecular target in treating life-threatening tyrosinemia type I, but also an important target for chemical herbicides. A combined in silico structure-based pharmacophore and molecular docking-based virtual screening were performed to identify novel potential HPPD inhibitors. The complex-based pharmacophore model (CBP) with 0.721 of ROC used for screening compounds showed remarkable ability to retrieve known active ligands from among decoy molecules. The ChemDiv database was screened using CBP-Hypo2 as a 3D query, and the best-fit hits subjected to molecular docking with two methods of LibDock and CDOCKER in Accelrys Discovery Studio 2.5 (DS 2.5) to discern interactions with key residues at the active site of HPPD. Four compounds with top rankings in the HipHop model and well-known binding model were finally chosen as lead compounds with potential inhibitory effects on the active site of target. The results provided powerful insight into the development of novel HPPD inhibitors herbicides using computational techniques.

4-Hydroxyphenylpyruvate Dioxygenase and Its Inhibition in Plants and Animals: Small Molecules as Herbicides and Agents for the Treatment of Human Inherited Diseases

This review mainly focuses on the physiological function of 4-hydroxyphenylpyruvate dioxygenase (HPPD), as well as on the development and application of HPPD inhibitors of several structural classes. Among them, one illustrative example is represented by compounds belonging to the class of triketone compounds. They were discovered by serendipitous observations on weed growth and were developed as bleaching herbicides. Informed reasoning on nitisinone (NTBC, 14), a triketone that failed to reach the final steps of the herbicidal design and development process, allowed it to become a curative agent for type I tyrosinemia (T1T) and to enter clinical trials for alkaptonuria. These results boosted the research of new compounds able to interfere with HPPD activity to be used for the treatment of the tyrosine metabolism-related diseases.

Design, synthesis, and herbicidal activity of pyrazole benzophenone derivatives

Design of pyrazole benzophenones as potent HPPD inhibitors with excellent herbicidal activities.