10779/crick.12607946.v1 Simone Brogi Simone Brogi Simone Giovani Simone Giovani Margherita Brindisi Margherita Brindisi Sandra Gemma Sandra Gemma Ettore Novellino Ettore Novellino Giuseppe Campiani Giuseppe Campiani Michael J Blackman Michael J Blackman Stefania Butini Stefania Butini In silico study of subtilisin-like protease 1 (SUB1) from different Plasmodium species in complex with peptidyl-difluorostatones and characterization of potent pan-SUB1 inhibitors The Francis Crick Institute 2020 Difluorostatone-based inhibitors Homology modeling Malaria Molecular docking Pharmacophore modeling Subtilisin-like protease Amino Acid Sequence Antimalarials Binding Sites Computer Simulation Enzyme Inhibitors Ligands Models, Molecular Molecular Conformation Molecular Docking Simulation Molecular Dynamics Simulation Molecular Sequence Data Plasmodium Protein Binding Protozoan Proteins Quantitative Structure-Activity Relationship Sequence Alignment Subtilisins Blackman FC001043 0307 Theoretical and Computational Chemistry 0601 Biochemistry and Cell Biology 0803 Computer Software Biophysics Medicinal & Biomolecular Chemistry 2020-07-15 10:02:37 Journal contribution https://crick.figshare.com/articles/journal_contribution/In_silico_study_of_subtilisin-like_protease_1_SUB1_from_different_Plasmodium_species_in_complex_with_peptidyl-difluorostatones_and_characterization_of_potent_pan-SUB1_inhibitors/12607946 Plasmodium falciparum subtilisin-like protease 1 (SUB1) is a novel target for the development of innovative antimalarials. We recently described the first potent difluorostatone-based inhibitors of the enzyme ((4S)-(N-((N-acetyl-l-lysyl)-l-isoleucyl-l-threonyl-l-alanyl)-2,2-difluoro-3-oxo-4-aminopentanoyl)glycine (1) and (4S)-(N-((N-acetyl-l-isoleucyl)-l-threonyl-l-alanylamino)-2,2-difluoro-3-oxo-4-aminopentanoyl)glycine (2)). As a continuation of our efforts towards the definition of the molecular determinants of enzyme-inhibitor interaction, we herein propose the first comprehensive computational investigation of the SUB1 catalytic core from six different Plasmodium species, using homology modeling and molecular docking approaches. Investigation of the differences in the binding sites as well as the interactions of our inhibitors 1,2 with all SUB1 orthologues, allowed us to highlight the structurally relevant regions of the enzyme that could be targeted for developing pan-SUB1 inhibitors. According to our in silico predictions, compounds 1,2 have been demonstrated to be potent inhibitors of SUB1 from all three major clinically relevant Plasmodium species (P. falciparum, P. vivax, and P. knowlesi). We next derived multiple structure-based pharmacophore models that were combined in an inclusive pan-SUB1 pharmacophore (SUB1-PHA). This latter was validated by applying in silico methods, showing that it may be useful for the future development of potent antimalarial agents.