Steered molecular dynamics simulations reveal critical residues for (un)binding of substrates, inhibitors and a product to the malarial M1 aminopeptidase

• Published in: PLoS computational biology Vol. 14; no. 10; p. e1006525
• Main Authors: Moore, Daniel S, Brines, Conor, Jewhurst, Heather, Dalton, John P, Tikhonova, Irina G
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.10.2018; Public Library of Science (PLoS)
• Subjects: Amino acids; Aminopeptidase; Aminopeptidases - antagonists & inhibitors; Aminopeptidases - chemistry; Aminopeptidases - genetics; Aminopeptidases - metabolism; Aquatic insects; Binding; Bioassays; Biology; Biology and Life Sciences; Buried structures; Catalytic Domain; Computational Biology; Conformation; Crystal structure; Disease spread; Enzymes; Hemoglobin; Inhibitors; Ligands; Malaria; Medicine and Health Sciences; Migration; Molecular dynamics; Molecular Dynamics Simulation; Mosquitoes; Mutagenesis; Network analysis; Parasites; Peptides; Pharmacy; Physical Sciences; Plasmodium falciparum; Plasmodium falciparum - enzymology; Proteins; Protozoan Proteins - antagonists & inhibitors; Protozoan Proteins - chemistry; Protozoan Proteins - genetics; Protozoan Proteins - metabolism; Research and Analysis Methods; Residues; Simulation; Substrate inhibition; Substrates; Tropical diseases; Vector-borne diseases; United Kingdom > UK; Northern Ireland
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1006525

Malaria is a life-threatening disease spread by mosquitoes. Plasmodium falciparum M1 alanyl aminopeptidase (PfM1-AAP) is a promising target for the treatment of malaria. The recently solved crystal structures of PfM1-AAP revealed that the buried active site can be accessed through two channel openings: a short N-terminal channel with the length of 8 Å and a long C-terminal channel with the length of 30 Å. It is unclear, however, how substrates and inhibitors migrate to the active site and a product of cleavage leaves. Here, we study the molecular mechanism of substrate and inhibitor migration to the active site and the product release using steered molecular dynamics simulations. We identified a stepwise passage of substrates and inhibitors in the C-terminal channel of PfM1-AAP, involving (I) ligand recognition at the opening of the channel, (II) ionic translation to the 'water reservoir', (III) ligand reorientation in the 'water reservoir' and (IV) passage in a suitable conformation into the active site. Endorsed by enzymatic analysis of functional recombinant PfM1-AAP and mutagenesis studies, our novel ligand-residue binding network analysis has identified the functional residues controlling ligand migration within the C-terminal channel of PfM1-AAP. Furthermore, from unbinding simulations of the Arg product we propose a charge repulsion as the driving force to expel the product out from the N-terminal channel of PfM1-AAP. Our work paves the way towards the design of a novel class of PfM1-AAP inhibitors based on preventing substrate entry to the active site.