Identification of 4-hydroxyphenylpyruvate dioxygenase inhibitors by virtual screening, molecular docking, molecular dynamic simulation.

BACKGROUND: 4-Hydroxyphenylpyruvate dioxygenase (HPPD) herbicides control broadleaf and gramineous weeds with better crop safety for corn, sorghum and wheat. Multiple screening models in silico have been established to obtain novel lead compounds as HPPD inhibition herbicides. RESULTS: Topomer comparative molecular field analysis (CoMFA) combined with topomer search technology and Bayesian, genetic approximation functions (GFA) and multiple linear regression (MLR) models generated by calculating different descriptors were constructed for the quinazolindione derivatives of HPPD inhibitors. The coefficient of determination (r2 ) of topomer CoMFA, MLR and GFA were 0.975, 0.970 and 0.968, respectively; all the models established displayed excellent accuracy and high predictive capacity. Five compounds with potential HPPD inhibition were obtained via screening fragment library combined with the validation of the above models and molecular docking studies. After molecular dynamics (MD) validation and absorption, distribution, metabolism, excretion and toxicity (ADMET) prediction, the compound 2-(2-amino-4-(4H-1,2,4-triazol-4-yl) benzoyl)-3-hydroxycyclohex-2-en-1-one not only exhibited stable interactions with the protein but also high solubility and low toxicity, and has potential as a novel HPPD inhibition herbicide. CONCLUSION: In this study, five compounds were obtained through multiple quantitative structure-activity relationship screening. Molecular docking and MD experiments showed that the constructed approach had good screening ability for HPPD inhibitors. This work provided molecular structural information for developing novel, highly efficient and low-toxicity HPPD inhibitors. © 2023 Society of Chemical Industry.

Virtual screening based on pharmacophore model for developing novel HPPD inhibitors.

4-Hydroxyphenylpyruvate dioxygenase (HPPD) is an important target for herbicide design. A multilayered virtual screening workflow was constructed by combining two pharmacophore models based on ligand and crystal complexes, molecular docking, molecular dynamics (MD), and biological activity determination to identify novel small-molecule inhibitors of HPPD. About 110, 000 compounds of Bailingwei and traditional Chinese medicine databases were screened. Of these, 333 were analyzed through docking experiments. Five compounds were selected by analyzing the binding pattern of inhibitors with amino acid residues in the active pocket. All five compounds could produce stable coordination with cobalt ion, and form favorable π-π interactions. MD simulation demonstrated that Phe381 and Phe424 made large contributions to the strength of binding. The enzyme activity experiment verified that compound-139 displayed excellent potency against AtHPPD (IC50 = 0.742 µM), however, compound-5222 had inhibitory effect on human HPPD (IC50 = 6 nM). Compound-139 exhibited herbicidal activity to some extent on different gramineous weeds. This work provided a strong insight into the design and development of novel HPPD inhibitor using in silico techniques.

Value of serum and follicular fluid sirtuin (SIRT)1 and SIRT2 protein levels in predicting the outcome of assisted reproduction.

BACKGROUND: To explore whether serum and follicular fluid (FF), sirtuin 1 (SIRT1), and SIRT2 could predict the outcome of assisted reproduction. METHODS: All patients underwent in vitro fertilization (IVF)/intracytoplasmic sperm injection (ICSI) for the first time in the Reproductive Medicine Center of the First Affiliated Hospital of Zhejiang University Medical College from March 2018 to December 2018. According to cumulative clinical pregnancy outcomes, the patients were divided into a pregnancy group and non-pregnancy group. We measured the serum levels of SIRT1, SIRT2, anti-Müllerian hormone (AMH), follicle-stimulating hormone (FSH), luteinizing hormone (LH), and estradiol (E2) from the second to the fifth day of menstruation, and the levels of SIRT1 and SIRT2 in serum and FF on the day of human chorionic gonadotropin (HCG) injection and oocyte retrieval. RESULTS: A total of 125 patients met the inclusion criteria. The pregnancy group comprised 56 cases and non-pregnancy group 69 cases. There were significant differences in basal level SIRT2 (bSIRT2), AMH, antral follicle count (AFC), number of oocytes obtained, number of mature eggs, number of fertilized eggs, number of excellent embryos, number of blastocyst formations, and number of transferred high-quality embryos between the two groups. The area under the curve (AUC) values of bSIRT2, AFC, AMH, and age were significantly different from those under the opportunity reference line (P<0.05). In the subsequent correlation analysis, FFSIRT2, and HCG day serum SIRT2 were negatively correlated with age (r=-0.35, r=-0.19), and positively correlated with AFC (r=0.2, r=0.02). Serum SIRT1 on HCG day was negatively correlated with the number of blastocysts and the number of frozen embryos (r=-0.18, r=-0.21). Levels of FF SIRT1 and FF SIRT2 were significantly lower than those in serum SIRT1 and SIRT2, and there was no significant difference in serum SIRT1 and SIRT2 before and after ovulation promotion. CONCLUSIONS: The results suggest that bSIRT2 has significant statistical significance in predicting the cumulative number of pregnancies. When combined with AMH, AFC, and age, bSIRT2 can predict the cumulative pregnancy outcome. In addition, the level of serum SIRT1 and SIRT2 were not affected by ovulation promotion.

Comparative study of assisted reproductive outcomes between young patients with occult premature ovarian insufficiency and advanced-age patients.

OBJECTIVE: The purpose of this study was to compare the pregnancy outcomes among young patients with occult premature ovarian insufficiency (OPOI), advanced-age patients with diminished ovarian reserve (DOR), and advanced-age patients with normal ovarian reserve. METHODS: We retrospectively reviewed 324 women who underwent their first cycles of in vitro fertilization/intracytoplasmic sperm injection. The women were divided into the following groups: young women with OPOI, advanced-age women with DOR, and advanced-age women with normal ovarian reserve. The outcomes were compared among the different groups. RESULTS: The rates of live birth and embryo implantation in the young OPOI group were significantly higher than in the advanced-age DOR group, but comparable to those in the advanced-age normal ovarian reserve group. Moreover, the abortion rate was significantly lower in young OPOI patients compared with advanced-age patients with or without DOR. CONCLUSION: Higher embryo implantation and live birth rates and a lower abortion rate can be achieved in young patients with OPOI compared with older patients. The better outcomes in advanced-age patients with normal ovarian reserve compared with DOR may be related to egg quantity rather than quality.

Gentianella macrosperma, a new species of Gentianella (Gentianaceae) from Xinjiang, China.

Gentianella macrosperma Ma ex H.F. Cao, J.D. Ya & Q.R. Zhang, a new species of Gentianaceae from Xinjiang, Northwest China is described and illustrated. This new species is unique in having equal length of corolla lobe and corolla tube, nectaries located at the throat of the corolla tube and large seeds up to 1.6 mm in diameter. In addition, an updated identification key to the Chinese species of Gentianella is provided.

Combination of Virtual Screening Protocol by in Silico toward the Discovery of Novel 4-Hydroxyphenylpyruvate Dioxygenase Inhibitors.

4-Hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27, HPPD) is a potent new bleaching herbicide target. Therefore, in silico structure-based virtual screening was performed in order to speed up the identification of promising HPPD inhibitors. In this study, an integrated virtual screening protocol by combining 3D-pharmacophore model, molecular docking and molecular dynamics (MD) simulation was established to find novel HPPD inhibitors from four commercial databases. 3D-pharmacophore Hypo1 model was applied to efficiently narrow potential hits. The hit compounds were subsequently submitted to molecular docking studies, showing four compounds as potent inhibitor with the mechanism of the Fe(II) coordination and interaction with Phe360, Phe403, and Phe398. MD result demonstrated that nonpolar term of compound 3881 made great contributions to binding affinities. It showed an IC50 being 2.49 µM against AtHPPD in vitro. The results provided useful information for developing novel HPPD inhibitors, leading to further understanding of the interaction mechanism of HPPD inhibitors.

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.

New Research for Quinazoline-2,4-diones as HPPD Inhibitors Based on 2D-MLR and 3D-QSAR Models.

AIM AND OBJECTIVE: 4-Hydroxyphenylpyruvate dioxygenase (HPPD), converting phydroxyphenylpyruvate (HPPA) to homogentisate (HGA), is an important target for treating type I tyrosinemia and synthesizing novel herbicides due to its significant role in tyrosine catabolism. Hence, it is imperative to design novel HPPD inhibitors that can block HPPA-HGA conversion, which leads to the deficiency in isoprenoid redox cofactors such as plastoquinone and tocopherol, and finally caused growth inhibition. This study was undertaken to investigate structural requirements for their HPPD inhibition with better biological activity. MATERIALS AND METHODS: Based on the structure-activity relationships, a series of quinolinone-2,4- diones derivatives were studied using combined of 2D multiple linear regression (2D-MLR) and 3D quantitative structure-activity relationship (3D-QSAR). Firstly, genetic algorithm (GA) was applied and descriptors generated in DRAGON 5.5 software were used for building 2D-MLR models in the QSARINGS. Then CoMFA and CoMSIA models were performed by using alignment of the common framework and the pharmacophore model. The obtained models were validated through internal and external validation to verify predictive abilities. Especially, the CoMFA and CoMSIA contour maps were used to show vital structural characteristics related to HPPD inhibitors activities. RESULTS: The 2D-MLR liner equation and corresponding parameters were listed as follows: pKi = -38.2034Me+22.4078GATS2m-1.4265EEig15r-2.1849Hy+32.9158 ntr=28, npred=6, R2=0.863, Q2LOO=0.787, Q2LMO=0.607, Q2F1=0.780, Q2F2=0.780, Q2F3=0.860, CCCpred=0.920. RMSEtr=0.253, RMSEpred=0.555, F=36.289 The steric contours graph indicated that small and negative electrostatic substitutions at R1 and R2 regions were favorable for the better activity, and hydrogen-bond donors at this region would also increase the activity. Positive electrostatic and bulky substitutions in the R3 position would enhance the activity. The analysis of these models suggested that the steric factor of R4 position was crucial for activity of quinazoline-2,4-diones HPPD inhibitors, bulky substitutions might improve the bioactivity of these inhibitors greatly, meanwhile, hydrogen-bond acceptor groups in this position were required for higher activity. CONCLUSION: In this study, a combined 2D-MLR, CoMFA and CoMSIA models demonstrated satisfying results through internal and external validation, especially good predictive abilities and the CoMFA and CoMSIA contour maps showed vital structural characteristics related to HPPD inhibitors activities.