While chemicals could be used for many useful purposes, sometimes they get used for other harmful purposes such as wars, terrorist attacks, assassinations, self-harm, or mass suicide. Thus, the terms chemical weapons and chemical warfare agents (CWAs) arose from such harmful uses of chemical substances. Various classes of CWAs have been used throughout history, including organophosphorus (OP) compounds, blister agents, blood agents, pulmonary agents, incapacitating agents, and riot control agents (RCAs). While the first four classes are meant to cause severe health effects and death of the victims, incapacitating agents and RCAs are meant to cause moderate to mild health effects.
OP compounds are classified into chemical nerve agents and pesticides. OP nerve agents have been used intentionally in warfare, terrorist attacks, and assassinations, while OP pesticides are used in agriculture, often in developing countries; however, they also lead to thousands of poisoning cases annually due to overexposure, mishandling, or self-harm. The main targets of OP compounds are cholinesterases (ChEs), which are serine hydrolases that are responsible for the hydrolysis of esters. Acetylcholinesterase (AChE) is a specific ChE for the hydrolysis of the neurotransmitter, acetylcholine (ACh). Butyrylcholinesterase (BChE) is a non-specific ChE that hydrolyzes both ACh and other esters. The inhibition of AChE by OP compounds results in the accumulation of ACh at neurosynaptic junctions, causing persistent binding of ACh to its receptors and leading to a cholinergic crisis and other severe adverse effects.
OP inhibition of ChEs is often followed by a dealkylation event, termed aging of the enzyme. Countermeasures against OP poisoning involves pre-exposure, post-inhibition, and post-aging treatments. Pre-exposure treatments are prophylactic and mainly available for military people who expect to be exposed to OP compounds. Post-inhibition treatments target the OP-inhibited form of ChEs and are available for either military or civilian use. To date, there is still no approved post-aging treatments to target the OP-aged form of ChEs. In the Hadad group, the first compounds to show in vitro activity against the OP-aged form of AChE were designed, prepared and screened. This class of new drug-like molecules, quinone methide precursors (QMPs), is hypothesized to realkylate the OP-aged AChEs and then to reactivate the realkylated form back to the native AChE.
In this dissertation, different computer-aided drug design and medicinal chemistry approaches will be presented towards the discovery of novel therapeutics for OP poisoning. In chapter two, molecular docking and molecular dynamics (MD) simulations were carried out for different QMPs with the 3-hydroxypyridine framework in their neutral and some protonation states against the methylphosphonate-aged or isopropylphosphoryl-aged human AChE (hAChE). The results showed that the addition of methyl groups to QMPs improves their affinity to the OP-aged hAChE active site, while the addition of halogens relatively worsen it. Replacement of the pyridine ring by diazine rings or a quinoline ring did not show significant effects on binding affinity. The (R)-2-methylpyrrolidine derivative showed relatively better results against the isopropylphosphoryl-aged hAChE compared to its (S)-enantiomer or unmethylated analogue. Among the different protonation states under computational study, the net protonated and net neutral species showed better results than the deprotonated one, especially the aminium and zwitterionic aminium species, followed by the neutral and zwitterionic pyridinium species.
In chapter three, a virtual screening (VS) study was performed for a library of compounds from the ZINC15 database after a substructure search for compounds containing our basic QMP scaffold. The VS results were then analyzed based on both the binding energy to the isopropylphosphoryl-aged hAChE and the intermolecular distance (BnC–OP distance) between the QMPs benzylic position and phosphylated oxyanion. The top hits were then identified, purchased and tested against the aged and inhibited hAChE forms using various OPs; however, all of them were found to be inactive. Taking into account that all of the VS compounds possessed a 6-methyl group on the pyridine ring, a structural optimization of our in-house QMPs was achieved via the addition of a 6-methyl group, leading to significant improvement in activity. The VS results also suggest that linking QMPs at the aromatic ring maybe a much better option rather than linking at the amine.
In chapter four, quantum mechanical calculations were employed to compute the thermodynamics for quinone methide (QM) formation. Diverse structural modifications were also considered, and a structure-free energy relationship was established. The results demonstrated that rings with electron-donating groups lead to more favored QM formation than electron-poor rings. Amine group elongation, branching or aromatization also help in favoring QM formation. Cyclization of the benzylic position and the amino group into an imidazolidine favors QM formation more than into a pyrrolidine. Correlation of the results with the Topliss Aromatic Decision Tree resulted in more promising results after following both the methyl and methoxy branches. Protonation states of a group of QMPs at different pH ranges were also predicted. At physiological pH, the zwitterionic species were predicted to be more dominant than the other ones.
In chapter five, similar quantum mechanical calculations were implemented for the assessment of protonation state stability as well as QM formation for each protonation state. For the net neutral species, the zwitterionic aminium species was found to be the most stable, while for the net protonated species, the aminium or the doubly zwitterionic pyridinium–aminium species were found to be the most stable. Four species possessed lower energy of QM formation than their peers: the neutral, zwitterionic aminium, aminium, and the doubly zwitterionic pyridinium–aminium species.
In chapter six, diverse medicinal chemistry approaches are presented. First, substructure searches were carried out for drugs containing our QMP scaffolds in the ZINC15 and DrugBank databases towards drug repurposing. The search yielded several promising candidates, and four drugs were purchased and tested against the OP-aged hAChE – but they were found to be ineffective for in vitro studies with AChE. Second, similar searches were performed in the ZINC15 and Reaxys databases, but this time for compounds containing designed bis- or tris-QMP moieties to-wards designing new classes of compounds. Based on the results, several models of compounds were designed, including bis-QMPs, tris-QMPs, compounds with multiple QMP moieties, mono and bifunctional benzoxazines, and more substituted analogues. Third, molecular modeling was employed for a number of our in-house QMPs with the phenyl, pyridine, or pyridine-N-oxide frameworks as well as a few basic benzoxazines. The results emphasized the essential role of the additional aminium proton in attracting ligands towards the negatively charged phosphylated adduct. In addition, benzoxazines showed similar binding affinities to QMPs for the OP-aged hAChE active site. Fourth, a QSAR study was done for a library of QMPs and a QSAR model was generated; however, the model was not successful in estimating the relative activity beyond the test set. Fifth, the ADME (absorption, distribution, metabolism and elimination) related properties were calculated for some sets of QMPs in comparison to reference drugs. The results revealed that our most basic QMPs exhibit better properties than the other designed sets of compounds.