Research Article Identification of Novel Inhibitors for Tobacco Mosaic Virus Infection in Solanaceae Plants Archana Prabahar, 1,2 Subashini Swaminathan, 2 Arul Loganathan, 2 and Ramalingam Jegadeesan 2 1 Data Mining & Text Mining Laboratory, Department of Bioinformatics, School of Life Sciences, Bharathiar University, Coimbatore, Tamilnadu 641046, India 2 Department of Plant Molecular Biology & Bioinformatics, Centre for Plant Molecular Biology & Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamilnadu 641003, India Correspondence should be addressed to Ramalingam Jegadeesan; jrjagadish@yahoo.com Received 31 July 2015; Revised 27 September 2015; Accepted 28 September 2015 Academic Editor: Huixiao Hong Copyright © 2015 Archana Prabahar et al. Tis is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Tobacco mosaic virus (TMV) infects several crops of economic importance (e.g., tomato) and remains as one of the major concerns to the farmers. TMV enters the host cell and produces the capping enzyme RNA polymerase. Te viral genome replicates further to produce multiple mRNAs which encodes several proteins, including the coat protein and an RNA-dependent RNA polymerase (RdRp), as well as the movement protein. TMV replicase domain was chosen for the virtual screening studies against small molecules derived from ligand databases such as PubChem and ChemBank. Catalytic sites of the RdRp domain were identifed and subjected to docking analysis with screened ligands derived from virtual screening LigandFit. Small molecules that interact with the target molecule at the catalytic domain region amino acids, GDD, were chosen as the best inhibitors for controlling the TMV replicase activity. 1. Introduction TMV infects tobacco and other members in the Solanaceae family which includes economically important plants like tobacco, tomato, potato, and pepper [1]. Tobacco mosaic virus has a rod-like appearance [2]. TMV is the type member of the genus Tobamovirus and has been studied extensively for its ability to replicate and induce host disease or resistance responses [3, 4]. Plants infected with TMV may have many symptoms including patches of light and normal green pigment on the leaves, chlorosis, dwarfng, blistering of the leaves, and damage to the fruit [5]. Even though TMV is able to infect many species and spread quickly but, the virus rarely kills the host. Virus-infected plants ofen display developmental abnormalities that include stunting, leaf curling, and the loss of apical dominance [6]. TMV is a positive-stranded RNA virus that encodes at least four proteins [3]. Te two open reading frames (ORF) encode 126- and 183-kDa replicase proteins, where larger codon is produced through an amber stop codon [7]. Homology studies shows that the 126-kDa ORF protein encodes a methyl transferase domain (MT) involved in viral RNA capping and a helicase domain (HEL) involved in double-stranded RNA unwinding [8]. Te read-through portion of the 183-kDa ORF encodes the RNA-dependent RNA polymerase domain (POL), a 30-kDa protein required for cell-to-cell movement and the 17.5-kDa capsid proteins are produced from mRNAs in the subgenomic region [9, 10]. Te 183-kDa protein has amino acids motifs that are characteristic of RNA-dependent RNA polymerases (RdRp) and provides the catalytic activity for the synthesis of TMV RNA. While there has been no evidence for polymerase activity in vitro, TMV replicase complexes isolated from infected tissue have been shown to possess RdRp dependent polymerase activity [11]. Te RdRp (replicase) mediates the replication of tobacco mosaic virus (TMV) [12]. Hindawi Publishing Corporation Advances in Bioinformatics Volume 2015, Article ID 198214, 9 pages http://dx.doi.org/10.1155/2015/198214