Supervisors info:
Αντώνιος Κολοκούρης Αναπληρωτής Καθηγητής (Επιβλέπων), Εμμανουήλ Μικρός Καθηγητής, Ανδρέας Τσοτίνης Καθηγητής
Summary:
Adamantane derivatives, such as amantadine and rimantadine, have been reported
to block the M2
membrane protein of influenza A virus (A/M2TM), but their use has been
discontinued due to
reported resistance in humans. Understanding the mechanism of action of
amantadine derivatives
could assist in the development of novel potent inhibitors that overcome A/M2TM
resistance.
In this dissertation we validate that free energy calculations using the FEP
scheme and the Bennett
acceptance ratio method is valuable for determining the relative binding
potency of M2 inhibitors of the aminoadamantane type, in accordance to previous
studies. Furthermore, we prove that using DMPC to mimic membrane environment
yields a computational model with a better correlation between theoretical and
experimental values, compared to DPPC -tested in a previous reference study.
The further integration and optimization of the computational model (R2 = 0.66,
PI = 0.97),
encouraged its use for computer aided drug design. We applied FEP/MD
calculations to design and
synthesize three bulkier rimantadine analogues. Their binding affinities were
measured using ITC
against the M2TM tetramer at its closed form at pH 8, while their potency was
studied with antiviral
assays. One of the compounds proved to be a nanomolar inhibitor stronger than
rimantadine against S31 WSN/33 influenza A, a sensitive strain against the pore
blocking effect of aminoadamantanes, and also a micromolar inhibitor against
the mutated viral strain A/PR/8/34.
The computational model retains its reliability after the calculations of the
new compounds (R2 =
0.61, PI = 0.83). We also proceeded in an evaluation and commentary of the
thermodynamic profile of all the aminoadamantane ligands included in the model
according to their experimental values, which were derived from ITC
measurements.
In addition, in the present dissertation an adamantane compound was studied
using low-temperature Dynamic NMR Spectroscopy. Also, one-flask approaches were
applied for the synthesis of α,α,α-trisubstituted primary amines using as a
substrate a tertiary nitrile (1-adamantanecarbonitrile), mediated through Ti
complexes; a case which –to our knowledge- has not been reported in literature
so far.
Keywords:
Influenza A, M2 inhibitors, Free Energy Perturbation, Adamantanamines, Aminoadamantanes, In silico Drug Design, Dynamic NMR
