The emergence of drug resistant strains of HIV represents a major challenge in the treatment of
patients who contract the virus. We investigate the use of classical molecular dynamics to give
quantitative and qualitative molecular insight into the causes of resistance in the two main drug
targets in HIV, protease and reverse transcriptase.
We initially establish a simulation and free energy analysis protocol for the study of resistance
in protease. Focusing on the binding of the inhibitor lopinavir to a series of six mutants with
increasing resistance we demonstrate that ensemble simulations exhibit significantly enhanced
thermodynamic sampling over single long simulations. We achieve accurate and converged relative
binding free energies, reproducible to within 0.5 kcal mol^-1. The experimentally derived
ranking of the systems is reproduced with a correlation coefficient of 0.89 and a mean relative
deviation from experiment of 0.9 kcal mol^-1.
Our protocol is then applied to investigate a patient derived viral sequence for which contradictory
resistance assessments for lopinavir were obtained from existing clinical decision support
systems (CDSS). Mutations at only three locations (L10I, A71I/V and L90M) in
uenced the
ranking. Free energies were computed for HXB2 wildtype sequences incorporating each mutation
individually and all possible combinations, along with the full patient sequence. Only in the
case of the patient sequence was any resistance observed. This observation suggests an explanation
for the discordance found using the CDSS. The effects on drug binding of the mutations at
positions 10, 71 and 90 appear to be highly dependent on the background mutations present in
the remainder of the sequence.
In preparation for the extension of our simulation and free energy protocol to reverse transcriptase
the impact of binding both natural DNA substrates and two non nucleoside reverse
transcriptase inhibitor (NNRTI) class drugs on the dynamics of reverse transcriptase are investigated.
Free energies of both inhibitors (efavirenz and neviripine) are determined which are seen
to be independent of the subdomain motions of the protein observed during simulation. Preliminary
calculations of the free energies for a set of NNRTI resistant mutants bound to efavirenz
are also presented