Mapping the Pathway and Dynamics of Bestatin Inhibition of the Plasmodium falciparum M1 Aminopeptidase PfA‐M1

Abstract

The M1 metallo‐aminopeptidase from Plasmodium falciparum, PfA‐M1, is an attractive drug target for the design of new antimalarials. Bestatin, a broad‐spectrum metalloprotease inhibitor, is a moderate inhibitor of PfA‐M1, and has been used to provide structure–activity relationships to inform drug design. The crystal structure of PfA‐M1 with bestatin bound within its active site has been determined; however, dynamics of the inhibitor and the association or dissociation pathway have yet to be characterized. Here we present an all‐atom molecular dynamics study where we have generated a hidden Markov state model from 2.3 μs of molecular dynamics simulation. Our hidden Markov state model identifies five macrostates that clearly show the events involved in bestatin dissociation from the PfA‐M1 active site. The results show for the first time that bestatin can escape the substrate specificity pockets of the enzyme, primarily due to weak interactions within the pockets. Our approach identifies relevant conformational sampling of the inhibitor inside the enzyme and the protein dynamics that could be exploited to produce potent and selective inhibitors that can differentiate between similar members of the M1 aminopeptidase superfamily.

Novel Human Aminopeptidase N Inhibitors: Discovery and Optimization of Subsite Binding Interactions

“…In the case of APN, the presence of zinc in the active site means that this problem cannot be computationally ignored. Recently, our team has produced the necessary parameters to use the zinc Amber force field (ZAFF) to simulate the active site of Pf A-M1. , We used this system to simulate our docking of APN bound to 1 . MD simulations ( n = 3) were performed for the duration of 50 ns, which should be sufficient to observe the movements of small molecules.…”

Insights into the Inhibitory Mechanisms of the Covalent Drugs for DNMT3A

“…The Cys710 and Glu756 were modeled in the protonated state, as treated in the former theoretical study of DNMT1 [ 35 ]. Similar to our previous study [ 49 , 50 , 51 , 52 , 53 , 54 ], the PDB2PQR server was used to determine the protonation states of amino acids under pH 7.0 for all MD systems [ 55 ]. The inputs for generating the parameters for the SAM, AZA, ZEB, 5m-dC-Cys, 5m-AZA-Cys, and 5m-ZEB-Cys, were all created by the Antechamber program of AmberTools 21 [ 56 , 57 ].…”

Driving antimalarial design through understanding of target mechanism

“…SAR studies of different inhibitors probing this pocket and the comparison of their crystal structures indicate that the spatial differences in the S1 0 cavity is the major contributor to the enzyme selectivity of PfA-M1 over other MAPs (PfA-M17) [94,95]. Computational studies have shown that measurements of pocket size from crystal structures are influenced by crystal packing [101]. These two facts highlight some of the challenges of compound design and the strong need to consider mechanism and how the target responds to inhibition.…”