Elucidating the conformational change of dengue envelope protein using the Markov state model

Abstract

ABSTRACT Dengue virus, an arbovirus of genus flavivirus, is one of the most prevalent infectious disease causing organisms in the tropical environment leading to numerous deaths every year. The envelope protein plays a crucial role in the viral genome entry into the host cell. This is achieved through structure and oligomeric status change in the dengue envelope protein. The pre-fusion and post-fusion states’ structures of the dengue envelope protein are known although the pathway and intermediate structures involved in this process have remained in the dark till date. In this study, we have used targeted molecular dynamics (MD) simulation followed by conventional MD simulation and the Markov state model analysis to elucidate this pathway of change in conformation from the pre-fusion state to the post-fusion state. Intermediate conformations which may in the future serve as therapeutic targets have also been deduced from the Markov state model. This pathway determination may pave the way for the design of transition state analog inhibitors which prevent the dengue virus envelope protein from changing its conformation and thus establishing infection. The results obtained could lead to development of novel drugs to combat the viral infection.