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Journal of Integrative Agriculture  2020, Vol. 19 Issue (3): 735-747    DOI: 10.1016/S2095-3119(19)62813-3
Special Issue: 植物病理合辑Plant Protection—Plant Pathology 植物细菌真菌合辑Plant Bacteria/Fungus
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Functional analysis and screening small molecules to RpfF protein in Xanthomonas oryzae involved in rice bacterial blight disease
Mundla SRILATHA1, Naina PATYAL2, Madhu Sudhana SADDALA3
1 Department of Biotechnology, Sri Venkateswara University, Tirupati 517502, India
2 Department of Bioinformatics and Computational Biology, Central University of Himachal Pradesh, Kangra 176206, India
3 Mason Eye Institute, University of Missouri School of Medicine, Columbia 65202, USA
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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.  3D 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-3D.  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.
Keywords:  RpfF        virtual screening        molecular dynamics        docking        Zinc Database  
Received: 28 April 2019   Accepted:
Corresponding Authors:  Correspondence Madhu Sudhana SADDALA, E-mail:   
About author:  Mundla Srilatha, E-mail:;

Cite this article: 

Mundla SRILATHA, Naina PATYAL, Madhu Sudhana SADDALA. 2020. Functional analysis and screening small molecules to RpfF protein in Xanthomonas oryzae involved in rice bacterial blight disease. Journal of Integrative Agriculture, 19(3): 735-747.

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