Structure-Based Virtual Screening for Potential Inhibitors of Influenza A Virus RNA Polymerase PA Subunit Haixin Ai • Fangliang Zheng • Fangbo Deng • Chunyu Zhu • Ying Gu • Li Zhang • Xuejiao Li • Alan K. Chang • Jian Zhao • Junfeng Zhu • Hongsheng Liu Accepted: 10 November 2014 Ó Springer Science+Business Media New York 2014 Abstract The amino terminus of RNA polymerase A (PA-N) of influenza virus is an important target for the design of new antiviral agents. In this study, molecular docking was used to screen for compounds that specifically target the deep cleft at the endonuclease active site in N-terminus of the RNA polymerase. Four potential com- pounds (NCI100226, NCI122653, NCI625583, and NCI403587) with high binding affinity for the active site were identified. Structural analysis of the binding confor- mation of each of these compound-PA-N complexes revealed that hydrophobic interaction and manganese ion chelation comprised the main interaction between the compounds and enzyme. The binding configuration sta- bility and the number of hydrogen and ionic bonds were investigated by molecular dynamic simulations. The results indicated that NCI403587 could be a promising PA-N inhibitor, and may represent a potential new agent for the treatment of influenza. Keywords Influenza A virus Á RNA polymerase A Á Docking Á Molecular simulation Introduction Influenza A viruses are important human and animal respiratory pathogens responsible for both the seasonal ‘flu’ outbreaks and periodic worldwide pandemics. Anti- viral drugs are particularly beneficial for combating a fast- spreading pandemic. Several drugs have been used to treat infection caused by influenza virus. These drugs are mainly directed against the M2 ion-channel protein (adamantanes) and NA protein (zanamivir and oseltamivir) (Das et al. 2010). However, drug-resistant viruses have gradually emerged, and the development of new effective anti- influenza drugs targeting different proteins of the virus is urgently needed. The RNA polymerase of influenza virus is a heterotri- meric complex consisting of PB1, PB2 and PA subunits, and is responsible for carrying out the transcription and replication of the viral genome during infection (Kashiwagi et al. 2009). The primary roles of PB1, PB2 and PA in viral RNA synthesis have been delineated by various biochem- ical and genetic studies (Blaas et al. 1982; Biswas and Nayak 1994; Gonza ´lez and Ortı ´n 1999; Obayashi et al. 2008; Dias et al. 2009; Hara et al. 2006). PB1, the core of the RNA polymerase complex contains RNA-dependent RNA polymerase activity and it can recognize and bind to the specific conserved sequences of viral genomic RNA segments (vRNAs) and viral cRNAs (Blaas et al. 1982; Gonza ´lez and Ortı ´n 1999). The RNA polymerase tran- scribes viral RNA using short capped primers derived from host cell pre-mRNAs by a unique ‘cap snatching’ mecha- nism (Plotch et al. 1981). In this mechanism, the PB2 subunit binds the cap of host pre-mRNA and the PB1 subunit cleaves it at nucleotide 10-13 (Li et al. 2001; Gu- illigay et al. 2008). The PA subunit has endonuclease and protease activities, and has been implicated in a diverse Haixin Ai and Fangliang Zheng contributed equally to this work. H. Ai Á F. Zheng Á F. Deng Á C. Zhu Á Y. Gu Á L. Zhang Á X. Li Á A. K. Chang Á J. Zhao Á J. Zhu Á H. Liu (&) School of Life Science, Liaoning University, Shenyang 110036, China e-mail: liuhongsheng@lnu.edu.cn H. Ai Á L. Zhang Á H. Liu Research Center for Computer Simulating and Information Processing of Bio-macromolecules of Liaoning, Shenyang 110036, China 123 Int J Pept Res Ther DOI 10.1007/s10989-014-9442-8