3 research outputs found
PARCE: Protocol for Amino acid Refinement through Computational Evolution
The in silico design of peptides and proteins as binders is useful for
diagnosis and therapeutics due to their low adverse effects and major
specificity. To select the most promising candidates, a key matter is to
understand their interactions with protein targets. In this work, we present
PARCE, an open source Protocol for Amino acid Refinement through Computational
Evolution that implements an advanced and promising method for the design of
peptides and proteins. The protocol performs a random mutation in the binder
sequence, then samples the bound conformations using molecular dynamics
simulations, and evaluates the protein-protein interactions from multiple
scoring. Finally, it accepts or rejects the mutation by applying a consensus
criterion based on binding scores. The procedure is iterated with the aim to
explore efficiently novel sequences with potential better affinities toward
their targets. We also provide a tutorial for running and reproducing the
methodology
Identification of Novel Potential Inhibitors of Pteridine Reductase 1 in Trypanosoma brucei via Computational Structure-Based Approaches and in Vitro Inhibition Assays
Pteridine reductase 1 (PTR1) is a trypanosomatid multifunctional enzyme that provides a mechanism for escape of dihydrofolate reductase (DHFR) inhibition. This is because PTR1 can reduce pterins and folates. Trypanosomes require folates and pterins for survival and are unable to synthesize them de novo. Currently there are no anti-folate based Human African Trypanosomiasis (HAT) chemotherapeutics in use. Thus, successful dual inhibition of Trypanosoma brucei dihydrofolate reductase (TbDHFR) and Trypanosoma brucei pteridine reductase 1 (TbPTR1) has implications in the exploitation of anti-folates. We carried out molecular docking of a ligand library of 5742 compounds against TbPTR1 and identified 18 compounds showing promising binding modes. The protein-ligand complexes were subjected to molecular dynamics to characterize their molecular interactions and energetics, followed by in vitro testing. In this study, we identified five compounds which showed low micromolar Trypanosome growth inhibition in in vitro experiments that might be acting by inhibition of TbPTR1. Compounds RUBi004, RUBi007, RUBi014, and RUBi018 displayed moderate to strong antagonism (mutual reduction in potency) when used in combination with the known TbDHFR inhibitor, WR99210. This gave an indication that the compounds might inhibit both TbPTR1 and TbDHFR. RUBi016 showed an additive effect in the isobologram assay. Overall, our results provide a basis for scaffold optimization for further studies in the development of HAT anti-folates