Functional analysis and screening small molecules to RpfF protein in Xanthomonas oryzae involved in rice bacterial blight disease

Xanthomonas oryzae pv.oryzae(Xoo) is an important rice pathogen.This is a vascular pathogen entering the plant via the hydathodes causing rice bacterial blight.It has been known that most regulation of pathogenicity factor F(RpfF) genes in Xanthomonas regulates virulence in response to the diffusible signal factor(DSF).The RpfF recognized as an attractive drug target in bacterial rice blight disease.In this study,we performed the gene-gene interaction of RpfF and pathway functional analysis.3 D structure of RpfF protein was predicted using a homology modelling tool Swiss-Model and refined by molecular dynamics(MD) simulation.The refined model protein was predicted structural assessment using various tools such as PROCHECK,ERRAT,and VERIFY-3 D.We have collected 2 500 rifampicin analogues from Zinc Database by virtual screening.The screened compounds were docked into the active site of the RpfF protein using AutoDock Vina in PyRx Virtual Screening Tool.Furthermore,docking result and in silico ADMET analysis described that the compounds ZINC03056414,ZINC03205310,ZINC08673779,ZINC09100848,ZINC09729566,ZINC11415953,ZINC12810788,ZINC24989313,ZINC27441787 and ZINC32739565 have best binding energies and less toxicity than reference compound.This study revealed that the active site residues such as HIS-118,HIS-147,THR-148,ARG-179,ASP-207,ARG-240 and THR-244 are key roles in the pathogenicity.It could be beneficial in the design of small molecule therapeutics or the treatment of rice bacterial blight disease.

Potential treatment with Chinese and Western medicine targeting NSP14 of SARS-CoV-2

The outbreak of coronavirus disease 2019(COVID-19)caused by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)is a serious global health threat.This raises an urgent need for the development of effective drugs against the deadly disease.SARS-CoV-2 non-structural protein 14(NSP14)carrying RNA cap guanine N7-methyltransferase and 30-50 exoribonuclease activities could be a potential drug target for intervention.NSP14 of SARS-CoV-2 shares 98.7%of similarity with the one(PDB 5NFY)of acute respiratory syndrome(SARS)by ClustalW.Then,the SARS-CoV-2 NSP14 structures were modelled by Modeller 9.18 using SARS NSP14(PDB 5NFY)as template for virtual screening.Based on the docking score from AutoDock Vina1.1.2,18 small molecule drugs were selected for further evaluation.Based on the 5 ns MD simulation trajectory,binding free energy(DG)was calculated by MM/GBSA method.The calculated binding free energies of Saquinavir,Hypericin,Baicalein and Bromocriptine for the N-terminus of the homology model wereà37.2711±3.2160,à30.1746±3.1914,à23.8953±4.4800,andà34.1350±4.3683 kcal/mol,respectively,while the calculated binding free energies wereà60.2757±4.7708,à30.9955±2.9975,à46.3099±3.5689,andà59.8104±3.5389 kcal/mol,respectively,when binding to the C-terminus.Thus,the compounds including Saquinavir,Hypericin,Baicalein and Bromocriptine could bind to the N-terminus and C-terminus of the homology model of the SARS-CoV-2 NSP14,providing a candidate drug against SARS-CoV-2 for further study.