Catalytic Mechanism of the Serine Hydroxymethyltransferase: A Computational ONIOM QM/MM Study

Serine hydroxymethyltransferase (SHMT) is an important drug target to fight malaria, which is one of the most devastating infectious diseases, with 216 million cases cited and accounting for similar to 450 000 deaths in 2016. In this paper, computational studies were performed to unveil the catalytic mechanism of SHMT using quantum mechanics/molecular mechanics (QM/MM) methodologies. This enzyme is responsible for the extraordinary cyclization of a tetrahydrofolate (THF) into 5,10-methylene-THF. This process is catalyzed by a pyridoxal-5'-phosphate (PLP) cofactor that binds L-serine and, from this, one molecule of L-glycine is produced. The results show that the catalytic process occurs in eight sequential steps that involve an a elimination, the cyclization of the 5-hydroxymethyl-THF intermediate into 5,10-methylene-THF, and the protonation of the quinonoid intermediate. According to the calculated energetic profile, the rate-limiting step of the full mechanism is the elimination of the hydroxymethyl group, from which results a formaldehyde intermediate that then becomes covalently bonded to the THF cofactor. The calculated barrier (DLPNO-CCSD(T)/CBS:ff99SB) for the rate-limiting step (18.0 kcal/mol) agrees very well with the experimental kinetic results (15.7-16.2 kcal/mol). The results also highlight the key role played by Glu57 during the full catalytic process and particularly in the first step of the mechanism that requires an anionic Glu57, contrasting with some proposals available in the literature for this step. It was also concluded that the cyclization of THF must occur in the enzyme, rather than in solution, as it has been proposed also in the past. Together, all of these results provide knowledge and insight on the catalytic mechanism of SHMT, which can now be used to develop inhibitors targeting SHMT and, therefore, antimalaria drugs.