Exploring combined verses single mode of inhibition of Mycobacterium Tuberculosis RNA polymerase as a therapeutic intervention to overcome drug resistance challenges: atomistic perspectives.
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Date
2017
Authors
Agoni, Clement.
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Abstract
The impact of Rifampin resistance on the overall global epidemic of antimicrobial resistance has
become very prominent in recent years and is eventually stifling current efforts being made to control
tuberculosis drug resistance. Rifampin resistance has significantly contributed to making TB the
leading cause of morbidity from an infectious disease globally. The RNA polymerase of
Mycobacterium tuberculosis has been extensively explored as a therapeutic target for Rifampin
resistance with recent studies exploring synergistic inhibition as an effective approach, by combining
Rifampin and other drugs in the TB drug resistance. Apart from the paucity of data elucidating the
structural mechanism of action of the synergistic interaction between Rifampin and DAAPI, previous
studies did not also utilize the X-ray crystal structure of Mtb RNAP due its unavailability.
This thesis used advanced computational tools to unravel molecular insights into the suppression of
the emergence of resistance to Rifampin by a novel Nα-aroyl-N-aryl-phenylalaninamides (AAPI)
prototype inhibitor, DAAPI, co-bound to Mtb RNAP with Rifampin. Our studies revealed co-binding
induced a stable Mtb RNAP protein structure, increased the degree of compactness of binding site
residues around Rifampin and subsequently improved the binding affinity of Rifampin.
Studies in this thesis further provide an atomistic mechanism behind Rifampin resistance when the
recently resolved crystal structure of Mycobacterium tuberculosis RNA polymerase is subjected to a
single active site mutation. We also identified and rationalized the structural interplay of this single
active site mutation upon co-binding of Rifampin with the novel inhibitor, DAAPI. Our findings
report that the mutation distorted the overall conformational landscape of Mycobacterium
tuberculosis RNA polymerase, resulting in a reduction of binding affinity of Rifampin and an overall
shift in the residue interaction network of Mycobacterium tuberculosis RNA polymerase and upon
single binding. Interestingly, co-binding with DAAPI, though impacted by the mutation exhibited
improved Rifampin binding interactions amidst a distorted residue interaction network.
Findings establish a structural mechanism by which the novel inhibitor DAAPI stabilizes
Mycobacterium tuberculosis RNA polymerase upon co-binding with Rifampin, thus suppressing
Rifampin resistance. We also provide vital conformational dynamics and structural mechanisms of
mutant enzyme-single ligand and mutant enzyme-dual ligand interactions which could potentially
shift the current therapeutic protocol of TB infections, thus aiding in the design of novel
Mycobacterium tuberculosis RNA polymerase inhibitors with improved therapeutic features against
the mutant proteins.
Description
Masters Degree. University of KwaZulu-Natal, Westville.