In silico analysis of interaction of human positive transcription elongation factor B (P-TEFB) with viral proteins

Abstract

Due to the small genome size, viruses do not have the ability to reproduce on their own, but rely on host cellular proteins to facilitate its replication and complete the life cycle. As a result, many host proteins complexes are manipulated during viral infections, and these proteins that interact with viral proteins are deemed as potential drug target. One of the host protein complexes is the positive transcription elongation factor b (P-TEFb), which comprises cyclin-dependent kinase 9 (CDK9) and cyclin T1 that has been of great interest due to its interaction with human immunodeficiency virus-1 (HIV-1) Tat protein. Due to the critical role of host P-TEFb in viral replication, it is suspected that P-TEFb may act as central role for interaction with a number of viral proteins other than HIV-1 Tat. This dissertation aims to uncover the interaction mode of P-TEFb and viral protein complexes, specifically the HIV and human Herpes Simplex Virus (HSV), in hopes of identifying responsible binding site using computational approaches. To achieve the first aim, an integrated protein-protein interaction networks of selected HIV and HSV viral proteins and P-TEFb was constructed to understand how the human viruses control the host’s biological function. The second aim was to analyze the potential binding interfaces on viral proteins with P-TEFb, particularly between wild and mutant types of viral proteins by using molecular docking. The protein-protein docking revealed that HIV-1 Vpr protein has higher binding affinity for P-TEFb compared to HIV-1 Tat protein thus formed the best interaction. It was predicted that both HIV-1 Tat and Vpr bind to similar region of cyclin T1, suggesting that both viral proteins are unable to bind the host protein at the same time. Finally, the investigation of the key amino acids of viral proteins and their mutants by coarse-grained molecular dynamic (CGMD) revealed that mutation of both acidic/cysteine region of HIV-1 Tat as well as helix 3 of HIV-1 Vpr leads to the different orientation of protein-protein complexes when compared with the wild type, thus these regions may be responsible for the interaction with cyclin T1 domain. It is worth to note that both HIV-1 Tat and Vpr viral proteins are cooperatively in control of viral gene transcription and replication, as shown in the interaction network and in the in silico analyses. An additional analysis of HSV-1 viral proteins VP16 and ICP22 showed that both binding sites of the viral proteins have been identified as the transactivation domain and were predicted to bind at the same region of CDK9. It can be concluded that cyclin T1 (residue 162-259) and CDK9 subunit of P-TEFb (residue 46-260) could be potential target site for the drug design specifically to treat the human viral infections.