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Molecular dynamics simulations of HIV-1 protease complexed with saquinavir

Watson, S.J.; (2009) Molecular dynamics simulations of HIV-1 protease complexed with saquinavir. Doctoral thesis, UCL (University College London). Green open access

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Abstract

Inhibition of the Human Immunodeficiency virus type-1 (HIV-1) protease enzyme blocks HIV-1 replication. Protease inhibitor drugs have successfully been used as a therapy for HIV-infected individuals to reduce their viral loads and slow the progression to Acquired Immune Deficiency Syndrome (AIDS). However, mutations readily and rapidly accrue in the protease gene resulting in a reduced sensitivity of the protein to the inhibitor. In this thesis, molecular dynamics simulations (MDS) were run on HIV proteases complexed with the protease inhibitor saquinavir, and the strength of affinity calculated through MMPBSA and normal mode analysis. We show in this thesis that at least 13 residues can be computationally mutated in the proteases sequence without adversely affecting its structure or dynamics, and can still replicate the change in binding affinity to saquinavir caused by said mutations. Using 6 protease genotypes with an ordered decrease in saquinavir sensitivity we use MDS to calculate drug binding affinity. Our results show that single 10ns simulations of the systems resulted in good concurrence for the wild-type (WT) system, but an overall strong anti-correlation to biochemically derived results. Extension of the WT and multi-drug resistant (MDR) systems to 50ns yielded no improvement in the correlation to experimental. However, expansion of these systems to a 10-repetition ensemble MDS considerably improved the MDR binding affinity compared to the biochemical result. Principle components analysis on the simulations revealed that a much greater configurational sampling was achieved through ensemble MD than simulation extension. These data suggest a possible mechanism for saquinavir resistance in the MDR system, where a transitioning to a lower binding-affinity configuration than WT occurs. Furthermore, we show that ensembles of 1ns in length sample a significant proportion of the configurations adopted over 10ns, and generate sufficiently similar binding affinities.

Type:Thesis (Doctoral)
Title:Molecular dynamics simulations of HIV-1 protease complexed with saquinavir
Open access status:An open access version is available from UCL Discovery
Language:English

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