IN SILICO PERSPECTIVES OF ANTI-MALARIAL DRUG: ARTEMISININ, ITS MECHANISM AND DRUG RESISTANCE

Abstract

Abstract Malaria remains as a global public health problem and it is worsening with the grow- ing resistance of Plasmodium falciparum to Artemisinin-based Combination Therapies (ACTs), the latest and most effective antimalarial drugs. Despite the widespread use of ACTs, the mechanism of artemisinin activation remains elusive. The activation of artemisinin i.e., cleavage of the endoperoxide bond generates the radical species inside the food vacuole of the parasite and is responsible for the antimalarial activities. Emer- gence of resistance to artemisinin is another global concern for drug efficacy. Mutations in PfKelch13 (PfK13) protein is linked with drug resistance. Despite of knowing the crystal structure of the artemisinin, the active form of the drug is still unknown to the community. The identification of efficient drug is therefore important for the imple- mentation of mitigation strategies. In the following paragraphs, the various challenges related to the artemisinin activation and its resistance have been discussed. In the first part of the thesis, the molecular mechanism of artemisinin with the one electron reduction process as well as with the neutral mechanism has been investigated by adopting state-of-the-art computational techniques based on the spin-constraint den- sity functional theory (CDFT). We have investigated that the biradical activation of artemisinin, which is quite viable and could occur in parallel to the reductive cleavage. To understand the effect of mutations on the structural dynamics of protein on PfK13 protein, the classical molecular dynamics (MD) simulation is performed. The single site mutation, mainly in C580Y and Y493H leads to enhanced fluctuations in the BTB- domain that could affect the protein-protein binding interactions (PfK13-Cullin) in the ubiquitination process and eventually lead to anti-malarial drug resistance. In the third part, we have explored all the possible stereoisomers of artemisinin and unveiled few stereoisomers that have lowest energy of activation. Moreover, we have found reasons why the widely known x-ray crystallography structure cannot act as an efficient drug. Finally, the different micelles have been studied for the encapsulation of artemisinin for target site delivery. The molecular dynamics simulation studies reveal that artemisinin could be encapsulated in the micelles keeping the endoperoxide bonds intact. This ob- servation provides new insights into the nano-drug delivery system of endoperoxide based drugs. In summary, the outcome of this thesis work provides a comprehensive understand- ing of the activation of the drug as well the root caused for the drug resistance. Further- more, we were able to identify a number of stereoisomers that poised as much better efficient drug compared to known isomer (crystal structure) of artemisinin. Keywords: Malaria, Artemisinin, Drug-Resistance, Stereoisomers, Micelles, DFT, MD Simulation.