Insights into the substrate binding mechanism of SULT1A1 through molecular dynamics with excited normal modes simulations

Abstract

Sulfotransferases (SULTs) are phase II drug-metabolizing enzymes catalyzing the sulfoconjugation from the co-factor 3′-phosphoadenosine 5′-phosphosulfate (PAPS) to a substrate. It has been previously suggested that a considerable shift of SULT structure caused by PAPS binding could control the capability of SULT to bind large substrates. We employed molecular dynamics (MD) simulations and the recently developed approach of MD with excited normal modes (MDeNM) to elucidate molecular mechanisms guiding the recognition of diverse substrates and inhibitors by SULT1A1. MDeNM allowed exploring an extended conformational space of PAPS-bound SULT1A1, which has not been achieved up to now by using classical MD. The generated ensembles combined with docking of 132 SULT1A1 ligands shed new light on substrate and inhibitor binding mechanisms. Unexpectedly, our simulations and analyses on binding of the substrates estradiol and fulvestrant demonstrated that large conformational changes of the PAPS-bound SULT1A1 could occur independently of the co-factor movements that could be sufficient to accommodate large substrates as fulvestrant. Such structural displacements detected by the MDeNM simulations in the presence of the co-factor suggest that a wider range of drugs could be recognized by PAPS-bound SULT1A1 and highlight the utility of including MDeNM in protein–ligand interactions studies where major rearrangements are expected.

Sampling of Protein Conformational Space Using Hybrid Simulations: A Critical Assessment of Recent Methods

“…Each excitation step is followed by a relaxation time. In line with other studies, we found that excitation energies of 2-3 K coupled with relaxation times ranging from 4 to 8 ps (Costa et al, 2015;Floquet et al, 2015;Dudas et al, 2020Dudas et al, , 2021aDudas et al, , 2021b) are broadly applicable. The number of cycles varies by system (Table 2).…”

“…Even though NMs are usually computed in vacuum, they are used as privileged directions in MD simulations with an explicit representation of the surrounding medium. MDeNM has demonstrated its power in conformational sampling in several studies revealing important protein functional movements (Dudas et al, 2020;Dudas et al, 2021a;Fagnen et al, 2020;Fagnen et al, 2021) and has also been successfully used in ensemble docking studies (Dudas et al, 2021b). CoMD provides a combination of ENM-NMA and targeted MD, coupled with energy minimization to adaptively generate a series of conformers.…”

Computational Analysis of Chemical Space of Natural Compounds Interacting with Sulfotransferases

“…Interestingly, the docking into the MD conformations allowed for the improvement of the Alpha HB and LondondG docking scores of sub-cluster 7.2, underlying the importance of taking into account the conformational changes of SULTs when exploring interactions with their ligands. Our recent study [25], using MD simulations with excited Normal Modes (MDeNM) [68], demonstrated that the natural flexibility of SULT1A1 provides a large opening of the key loops 1, 2, and 3, thus ensuring the recognition of diverse substrates and inhibitors by SULT1A1, the large inhibitor epigallocatechin gallate, in particular [20].…”

“…SULTs metabolize a wide variety of substrates, including endogenous compounds like steroids and polysaccharides, natural compounds [12,13] and drugs [8]. The molecular mechanisms involved in the substrate specificity of different SULT isoforms have been previously studied [14][15][16][17][18][19][20][21][22][23][24][25].…”

Evaluation of Phenol Sulfotransferase (SULT1A1) Ligand Binding Order

“…While it is not possible to review all reports here, appreciate that the study of SULT kinetics has generated an array of models. Steady state kinetic studies of various SULTs have yielded both sequential ordered [15,[20][21][22][23] and random [24][25][26][27][28] mechanisms. Isotope exchange at equilibrium was thought to prove an ordered mechanism [29], but this has been criticized as overlooking the formation of dead end complexes within a random scheme [30].…”