Albany 2013: Book of Abstracts
June 11-15 2013
©Adenine Press (2012)
Network Analysis of Inhibition and Resistance Mechanisms in Viral Polymerases
Replication of viral genomes is one of the most important steps in the infection process, as viruses need to replicate inside the host cell in order to make many copies. Therefore, traditionally, this has been an important stage for drug targeting in anti-viral therapies. For the replication, viral genes can encode polymerase enzymes like Reverse Transcriptase (RT) in retroviruses, and RNA dependent RNA polymerase in RNA viruses. These polymerases have been important drug targets against several viruses (Walker & Hong, 2002), Sarafianos et. al (2009)). However, a major challenge has been the emergence of resistance owing to mutations in the genes coding for these enzymes, thereby rendering these drugs useless. Unravelling the mechanisms of inhibition and resistance is an important area of research that contributes to both basic understanding of the processes and clinical applications. In this work we have attempted to study the structural basis of the mechanisms of inhibition and resistance in Reverse Transcriptase in Human Immunodeficiency Virus (HIV-1), and compared that to the RNA dependent RNA polymerase in Hepatitis C Virus (HCV), using a network based approach. Though structure-based protein contact networks (PCN) have been used to understand the structure-function relationship in different proteins (Bagler & Sinha, 2007), del Sol & O’Meara, 2005)), using this approach to study such interactions has not been done before.
The PCNs of HIV-1 RT and HCV NS5B in inhibitor-bound and unbound states were developed in both coarse grained scale (Figure (a)), and by considering the side chains of the constituent amino acids. The contact patterns for all cases were analysed along with their network parameters. Though inhibitor binding and resistance mutations in RT cause significant functional changes, they are known to cause only subtle changes in the protein structures. Our results show that they can be easily identified by changes in the contact patterns of the active site and inhibitor binding site residues. Analysis of different network parameters (e.g., shortest paths, cliques and communities) provide an insight into the communication pathways between the inhibitor binding region and the active site. Study of the allosteric communication pathways, considering the dynamics of the proteins (Figure (b)), shows that small conformational fluctuations cause important changes in the communication pathways (Figure (c)), thus contributing to the overall effect of inhibition and resistance. These analyses can help in understanding the crucial residues involved in resistance mutation directly or indirectly in the mechanism of inhibition and evolution of resistance to drugs.
Sarafianos S G; Marchand B et. al. (2009), Structure and Function of HIV-1 Reverse Transcriptase: Molecular Mechanisms of Polymerization and Inhibition, J. Mol. Biol. 385, 693–713
Bagler, G. & Sinha, S. (2007). Assortative mixing in Protein Contact Networks and protein folding kinetics. Bioinformatics (Oxford, England) 23, 1760–7
del Sol, A. & O’Meara, P. (2005). Small-world network approach to identify key residues in protein-protein interaction. Proteins 58, 672–82