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Updated: Dec 26, 2025
A High-throughput Compatible Assay to Evaluate Drug Efficacy against Macrophage Passaged Mycobacterium tuberculosis
Published on: March 24, 2017
Long-range replica exchange molecular dynamics guided drug repurposing against tyrosine kinase PtkA of Mycobacterium
Priya Nagpal1, Salma Jamal2, Hina Singh2
1School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India.
Abstract:
Tuberculosis (TB) is a leading cause of death worldwide and its impact has intensified due to the emergence of multi drug-resistant (MDR) and extensively drug-resistant (XDR) TB strains. Protein phosphorylation plays a vital role in the virulence of Mycobacterium tuberculosis (M.tb) mediated by protein kinases. Protein tyrosine phosphatase A (MptpA) undergoes phosphorylation by a unique tyrosine-specific kinase, protein tyrosine kinase A (PtkA), identified in the M.tb genome. PtkA phosphorylates PtpA on the tyrosine residues at positions 128 and 129, thereby increasing PtpA activity and promoting pathogenicity of MptpA. In the present study, we performed an extensive investigation of the conformational behavior of the intrinsically disordered domain (IDD) of PtkA using replica exchange molecular dynamics simulations. Long-term molecular dynamics (MD) simulations were performed to elucidate the role of IDD on the catalytic activity of kinase core domain (KCD) of PtkA. This was followed by identification of the probable inhibitors of PtkA using drug repurposing to block the PtpA-PtkA interaction. The inhibitory role of IDD on KCD has already been established; however, various analyses conducted in the present study showed that IDDPtkA had a greater inhibitory effect on the catalytic activity of KCDPtkA in the presence of the drugs esculin and inosine pranobex. The binding of drugs to PtkA resulted in formation of stable complexes, indicating that these two drugs are potentially useful as inhibitors of M.tb.
Insights
This study reveals that the intrinsically disordered domain of Mycobacterium tuberculosis protein tyrosine kinase A (PtkA) inhibits its catalytic activity. The drugs esculin and inosine pranobex enhance this inhibition, offering potential new treatments for drug-resistant tuberculosis.
Area of Science:
- Biochemistry
- Molecular Biology
- Drug Discovery
Background:
- Tuberculosis (TB) remains a global health crisis, exacerbated by multi-drug resistant (MDR) and extensively drug-resistant (XDR) strains.
- Protein phosphorylation by kinases is crucial for the virulence of Mycobacterium tuberculosis (M.tb).
- Protein tyrosine kinase A (PtkA) phosphorylates Protein tyrosine phosphatase A (MptpA), enhancing MptpA's pathogenicity.
Purpose of the Study:
- To investigate the conformational dynamics of PtkA's intrinsically disordered domain (IDD).
- To elucidate the role of PtkA's IDD in regulating the catalytic activity of its kinase core domain (KCD).
- To identify potential PtkA inhibitors through drug repurposing, targeting the PtpA-PtkA interaction.
Main Methods:
- Replica exchange molecular dynamics (REMD) simulations to study PtkA's IDD conformational behavior.
- Long-term molecular dynamics (MD) simulations to assess IDD's influence on PtkA's kinase core domain (KCD) activity.
- Drug repurposing screening to identify inhibitors of the PtpA-PtkA interaction.
Main Results:
- The intrinsically disordered domain (IDD) of PtkA exhibits significant inhibitory effects on the catalytic activity of its kinase core domain (KCD).
- The inhibitory effect of IDDPtkA on KCDPtkA was substantially enhanced in the presence of the drugs esculin and inosine pranobex.
- Binding analyses confirmed the formation of stable complexes between PtkA and these drugs, suggesting their potential as PtkA inhibitors.
Conclusions:
- The IDD of PtkA plays a critical role in regulating the kinase's activity.
- Esculin and inosine pranobex show promise as novel therapeutic agents by stabilizing inhibitory PtkA conformations.
- These findings offer a new strategy for developing treatments against drug-resistant TB by targeting PtkA.
