Chelerythrine Chloride: a Potential Rumen Microbial Urease Inhibitor Screened by Targeting Ureg
Total Page：16
File Type：pdf, Size：1020Kb
International Journal of Molecular Sciences Article Chelerythrine Chloride: A Potential Rumen Microbial Urease Inhibitor Screened by Targeting UreG Xiaoyin Zhang, Yue He, Zhanbo Xiong, Min Li, Ming Li , Nan Zheng, Shengguo Zhao * and Jiaqi Wang * State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; [email protected] (X.Z.); [email protected] (Y.H.); [email protected] (Z.X.); [email protected] (M.L.); [email protected] (M.L.); [email protected] (N.Z.) * Correspondence: [email protected] (S.Z.); [email protected] (J.W.) Abstract: Inhibition of ruminal microbial urease is of particular interest due to its crucial role in regulating urea-N utilization efficiency and nitrogen pollution in the livestock industry. Acetohy- droxamic acid (AHA) is currently the only commercially available urease inhibitor, but it has adverse side effects. The urease accessory protein UreG, which facilitates the functional incorporation of the urease nickel metallocentre, has been proposed in developing urease inhibitor through disrupting urease maturation. The objective of this study was to screen natural compounds as potential urease inhibitors by targeting UreG in a predominant ruminal microbial urease. In silico screening and in vitro tests for potential inhibitors were performed using molecular docking and an assay for the GTPase activity of UreG. Chelerythrine chloride was selected as a potential urease inhibitor of UreG with an inhibition concentration IC50 value of 18.13 µM. It exhibited mixed inhibition, with the Ki value being 26.28 µM. We further explored its inhibition mechanism using isothermal titration Citation: Zhang, X.; He, Y.; Xiong, Z.; calorimetry (ITC) and circular dichroism (CD) spectroscopy, and we found that chelerythrine chloride Li, M.; Li, M.; Zheng, N.; Zhao, S.; Wang, J. Chelerythrine Chloride: A inhibited the binding of nickel to UreG and induced changes in the secondary structure, especially Potential Rumen Microbial Urease the α-helix and β-sheet of UreG. Chelerythrine chloride formed a pi-anion interaction with the Asp41 Inhibitor Screened by Targeting UreG. residue of UreG, which is an important residue in initiating the conformational changes of UreG. In Int. J. Mol. Sci. 2021, 22, 8212. conclusion, chelerythrine chloride exhibited a potential inhibitory effect on urease, which provided https://doi.org/10.3390/ new evidence for strategies to develop novel urease inhibitors targeting UreG to reduce nitrogen ijms22158212 excretion from ruminants. Academic Editors: Csaba Hetényi Keywords: urease inhibitor; UreG; chelerythrine chloride; ammonia production; rumen and Uko Maran Received: 15 July 2021 Accepted: 27 July 2021 1. Introduction Published: 30 July 2021 Urea is commonly used as a cost-efficient replacement of feed proteins to provide the Publisher’s Note: MDPI stays neutral sole nitrogen source for urease [1–3]. In rumens, urease catalyzes the hydrolysis of urea with regard to jurisdictional claims in into ammonia, which can be synthesized into microbial protein to support the requirements published maps and institutional affil- for animal growth, meat or milk production [4]. However, the high urease activity leads to iations. excessive ammonia production, which not only results in the explosion of toxic ammonia in the blood, but is also converted to volatile ammonia and escapes into the environment [5,6]. Emissions of nitrogen have been recognized as one of the major drivers in the production of greenhouse gases and wastewater and soil pollution. The livestock industry contributes approximately 65 Tg·N·yr−1, which is roughly one-third of the global human-induced Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. nitrogen emissions [7]. Ruminant nitrogen is the major source of livestock pollution, · · −1 This article is an open access article with approximately 46 Tg N yr , equivalent to 71% of the total nitrogen emissions from distributed under the terms and livestock [7]. For ruminants, the dietary nitrogen utilization efficiency is only about conditions of the Creative Commons 25% [8,9], with as much as 60–90% of the feed nitrogen being excreted [10]. Taken together, Attribution (CC BY) license (https:// regulation of urease activity is crucial to reduce ammonia emissions and improve the creativecommons.org/licenses/by/ efficiency of urea-N utilization in ruminants, and urease inhibitors have been recognized 4.0/). as one of the most effective strategies. Int. J. Mol. Sci. 2021, 22, 8212. https://doi.org/10.3390/ijms22158212 https://www.mdpi.com/journal/ijms Int. J. Mol. Sci. 2021, 22, 8212 2 of 13 There are many kinds of urease inhibitors (Table S1), including those that attack the active center of urease, such as urea analogues [11], hydroxamic acids [12], phosphoramide and their derivatives [13], as well as other inhibitors that interact with the flap regions near active centers, such as 1, 4-benzoquinone [14], catechol [15], and some heavy metal ions [16]. However, only acetohydroxamic acid (AHA) is a commercially available urease inhibitor approved by the Food and Drug Administration for the treatment of humans and animals [17]. Unfortunately, significant adverse effects, including deep-vein phlebothrom- bosis, lower-extremity phlebitis, and malformation of embryos, have been reported [18]. In rumens, AHA was found to degrade rapidly, and inhibit the growth of rumen microor- ganisms other than urease-producing bacteria [19]. In recent years, plant-derived natural compounds (including that shown in Graphical Abstract [20–23]) have been preferred for their low toxicity, chemically stability, eco-friendliness and high efficiency at low con- centrations [24]. Gnetegha Ayemele et al. [25] screened giant milkweed as an alternative plant-derived feed additive, which could improve nitrogen utilization efficiency by inhibit- ing protozoa in ruminants without impairing fermentation. Limited studies have found that natural compounds such as terpenoids, phenolic compounds, alkaloids, and other substances were inhibitory towards the activities of plant and microbial ureases [26]. These findings suggest that natural compounds have great potential as urease inhibitors. The active center of urease is deeply buried in apo-urease, with an unobserved wide- open state [27]. Additionally, urease is a highly specific substrate of urea [28], which makes it challenging to design new urease inhibitors based on the active center. Accessory protein UreG, which is a GTPase involved in transferring nickel to the active center and activating urease upon GTP hydrolysis, plays an important role in urease maturation [29]. It has been reported [30,31] that UreG receives nickel from the accessory protein UreE through the formation of an UreE-UreG complex. Subsequently, nickel-charged UreG delivered nickel to the active center of apo-urease by forming an UreG-UreFH complex and apo- urease/UreGFH super-complex, in which GTP hydrolysis induced the conformational changes of UreG, and promoted the insertion of nickel into the active center. Moreover, UreG and urease maturation are relatively conserved among different urease-producing bacteria [32]. Disruption of the urease maturation process by abolishing UreG function has been proposed as a new strategy to develop urease inhibitors. We identified a predominant urease gene cluster from an uncultured ruminal bac- terium using metagenome, and revealed the characteristics of UreG interacting with UreE as well as transferring nickel previously [33]. This study aimed to select potential rumi- nal microbial urease inhibitors from natural compounds by using UreG as a regulatory target. A natural compound was identified by detecting GTPase activity of UreG and virtual screening using molecular docking. The inhibition mechanisms were evaluated by kinetic study. Whether this compound could affect nickel binding to UreG, as well as the influencing mechanism were further explored. This study provides a new strategy of screening ruminal microbial urease inhibitors, and a novel natural compound of regulating ruminal urease activity. 2. Results 2.1. Screening of Urease Inhibitor A set of 1130 natural compounds were collected for preliminary screening of UreG inhibition by detecting their inhibition rate. Given that 1130 natural compounds would consume a large amount of UreG, these screening tests were not repeated. Then, the top 48 compounds with a strong inhibitory rate were re-screened in triplicate. The top 20 natural compounds are shown in Figure1A. Isochlorogenic acid C, isochlorogenic acid B, and anemosapogenin had a higher inhibitory effect than others, and inhibited the GTPase activity of UreG by almost 100%. Considering the cost performance, application prospects, sources and categories of the compounds, isochlorogenic acid C and chelerythrine chloride were selected for further analysis. Int. J. Mol. Sci. 2021, 22, 8212 3 of 13 Figure 1. Effect of natural compounds on GTPase activity of UreG and ammonia emission. (A) Inhibition rates of the top 20 natural compounds on UreG GTPase activity. In this process, 100 µM natural compound was added to GTPase assay buffer (2 mM MgSO4, 300 µM GTP, 200 mM NaCl, 1 mM Tris(2-carboxyethyl)phosphine (TCEP), 10 mM KHCO3, 20 µM NiSO4, 20 mM HEPES, pH 7.5) containing 3 µM UreG. (B) Inhibition of GTPase activity of UreG by isochlorogenic acid C and chelerythrine chloride. Coptisine chloride is shown for comparison. The IC50 values against GTPase