Insight into TPMT*23 Mutation Mis-folding Using Molecular Dynamics Simulation and Protein Structure Analysis
Sofiene Larif, Chaker Ben Salem, Zohra Soua, Houssem Hmouda, Kamel Bouraoui [1]
Molecular Tour
Thiopurine antimetabolite pharmacologic class is one of the therapeutic arsenals available today for treatment of acute lymphoblastic, myeloblastic leukemia, as well as palliative chemotherapy, and some autoimmune diseases such as inflammatory bowel disease, rheumatoid arthritis, and organ transplantation.
TPMT enzyme is responsible for purine analogs deactivation by a methylation mechanism. Using the S-adenosylmethionine (SAM) as co-substrate, the transfers of methyl group from SAM to the thiopurine molecule transform this latter to thiopurine S-methylether, and transform SAM to S-adenosylhomocysteine (SAH). Human TPMT structure shows a monomeric protein composed by nine β sheets core surrounded by nine α helices . This protein has two site receptors; one of them is for the co-substrate SAM, surrounded by residues in helices α1, α5, α6, β strands 1 and 2. The second site is thiopurine receptor surrounded by residues in helices α1, α6, α9 and the β7-α8 loop. In TPMT structure, it has been described that substrate can diffuse through an internal channel linked to the SAM binding pocket.
SAM water channel entrance were identified as residues Leu24, Thr25, Leu26, Ser134, Phe136, Asn159 and Asp162. The thiopurine water channel entrance is bordered by residues Trp29, Lys32, Lys37, Ala39, Phe40, Pro195, Pro196, Arg226 and Trp230.
This enzyme activity is affected among other factors by Genetic polymorphisms. The single nucleotide polymorphism (SNP) C500G is located on allele TPMT*23. The produced protein is affected by mutation of Alanine to Glycine amino-acid at position 167.
Changes inflicted by mutation on solvent (SASA) can disturb TPMT substrate binding. The suggested mechanisms involve an increase in solvent exposure prohibiting the binding of the co-substrate SAM, and or, a decrease in accessibility to thiopurine site.
Both thiopurine and SAM tunnels entrances continue to exist during simulations. Furthermore, the shape of the SAM entrance was unchanged in the WT, but deformed in the mutant TPMT.
Buried tunnel connecting ligand to co-substrate sites has not been detected in WT simulations while it exists in mutated protein.
Our suggested hypothesis is that enzyme reaction is activated by thiopurine drug binding to it's site, which probably induces structural modifications that opens the SAM tunnel, but further investigations should be addressed.
