Yadav Kanchan, Patel Kavita, Mani Ashutosh, Yadav Sangeeta, Yadav Dinesh
Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, 273009, Uttar Pradesh, India.
Department of Biotechnology, Motilal Nehru National Institute of Technology, Prayagraj, 211004, Uttar Pradesh, India.
Biochem Biophys Res Commun. 2025 Jan;742:151111. doi: 10.1016/j.bbrc.2024.151111. Epub 2024 Dec 4.
Pectin lyase is an industrially important enzyme, predominately used in fruit juice clarification and retting of fibers. It also promotes pathogenesis via the degradation of the pectin. The phytopathogen, Fusarium infects various crops and causes several diseases. Trichoderma sp. is a promising biocontrol agent that is vital in maintaining plant health and disease prevention. In the current study, a computational approach utilizing structure prediction, molecular docking, molecular dynamics, and MM-PBSA analysis was used to analyze the potential role of bioactive compounds secreted by Trichoderma sp. in inhibiting the pectin lyase enzyme from Fusarium proliferatum, F. fujikuroi, F. graminearum, F. oxysporum and F. verticillioides. Molecular docking with secondary metabolites revealed that Viridiofungin A secreted by Trichoderma harzianum and Virone secreted by T. virens are bioactive compounds with immense potential to inhibit PNLs of Fusarium species. Further, the rigidity of the structure and stability of the docked complex were confirmed via Molecular dynamic simulations assessed through multiple parameters from the simulation trajectory data. Dual culture assay of T. harzianum and T. virens with F. proliferatum, F. fujikuroi, F. graminearum, F. oxysporum, and F. verticillioides showed variable mycelial inhibition. The research provides insight into the potential of the bioactive compounds secreted by Trichoderma species as an effective agent for the inhibition of pectin lyases produced by phytopathogens, especially Fusarium species. The proposed research can be used to develop bioformulations that function as biopesticides, offering a sustainable replacement for chemical products.
果胶裂解酶是一种具有重要工业价值的酶，主要用于果汁澄清和纤维脱胶。它还通过降解果胶促进发病机制。植物病原体镰刀菌感染各种作物并引发多种疾病。木霉菌是一种有前景的生物防治剂，对维持植物健康和预防疾病至关重要。在本研究中，采用了一种利用结构预测、分子对接、分子动力学和MM-PBSA分析的计算方法，来分析木霉菌分泌的生物活性化合物在抑制层出镰刀菌、藤仓镰刀菌、禾谷镰刀菌、尖孢镰刀菌和轮枝镰刀菌的果胶裂解酶方面的潜在作用。与次生代谢产物的分子对接表明，哈茨木霉分泌的绿菌素A和绿粘帚木霉分泌的绿菌素是具有巨大潜力抑制镰刀菌属PNLs的生物活性化合物。此外，通过对模拟轨迹数据的多个参数评估的分子动力学模拟，证实了对接复合物结构的刚性和稳定性。哈茨木霉和绿粘帚木霉与层出镰刀菌、藤仓镰刀菌、禾谷镰刀菌、尖孢镰刀菌和轮枝镰刀菌的双培养试验显示出不同程度的菌丝抑制。该研究深入了解了木霉菌种分泌的生物活性化合物作为抑制植物病原体特别是镰刀菌属产生的果胶裂解酶的有效剂的潜力。所提出的研究可用于开发作为生物农药的生物制剂，为化学产品提供可持续的替代品。
