Docking-Based Virtual Screening Enables Prioritizing Protein Kinase Inhibitors With In Vitro Phenotypic Activity Against Schistosoma mansoni

Abstract

Schistosomiasis is a parasitic neglected disease with praziquantel (PZQ) utilized as the main drug for treatment, despite its low effectiveness against early stages of the worm. To aid in the search for new drugs to tackle schistosomiasis, computer-aided drug design has been proved a helpful tool to enhance the search and initial identification of schistosomicidal compounds, allowing fast and cost-efficient progress in drug discovery. The combination of high-throughput in silico data followed by in vitro phenotypic screening assays allows the assessment of a vast library of compounds with the potential to inhibit a single or even several biological targets in a more time- and cost-saving manner. Here, we describe the molecular docking for in silico screening of predicted homology models of five protein kinases (JNK, p38, ERK1, ERK2, and FES) of Schistosoma mansoni against approximately 85,000 molecules from the Managed Chemical Compounds Collection (MCCC) of the University of Nottingham (UK). We selected 169 molecules predicted to bind to SmERK1, SmERK2, SmFES, SmJNK, and/or Smp38 for in vitro screening assays using schistosomula and adult worms. In total, 89 (52.6%) molecules were considered active in at least one of the assays. This approach shows a much higher efficiency when compared to using only traditional high-throughput in vitro screening assays, where initial positive hits are retrieved from testing thousands of molecules. Additionally, when we focused on compound promiscuity over selectivity, we were able to efficiently detect active compounds that are predicted to target all kinases at the same time. This approach reinforces the concept of polypharmacology aiming for “one drug-multiple targets”. Moreover, at least 17 active compounds presented satisfactory drug-like properties score when compared to PZQ, which allows for optimization before further in vivo screening assays. In conclusion, our data support the use of computer-aided drug design methodologies in conjunction with high-throughput screening approach.

Hypoxanthine guanine phosphoribosyl transferases SmHGPRTases functional roles in Schistosoma mansoni

“…Since transcriptomic data are a snapshot of transcription rates, generating an insight of general biological data that requires posterior refinement, thus, we aimed at corroborating previously data generated by transcriptomics approach, using molecules predicted to bind to the Smp38 ATP-binding site to confirm the regulation of SmHGPRTase expression. We observed significant changes in the parasite phenotype indicating that they can be promising protein inhibitors, even more by the fact that these kinases are unique members of their families in S. mansoni ( Rask-Andersen et al, 2014 ; Moreira et al, 2022 ). Besides that, we confirmed that Smp38 seems to regulate the expression of SmHGPRTase 1 .…”

“…Thus, schistosomula were exposed to Smp38 (NCC–00001994) predicted inhibitor ( Moreira et al, 2022 ). After 30 h of culture, as described by Moreira et al (2022) it was observed alterations in schistosomula phenotypes, like the presence of a dark middle-region and round bodies ( Figures 1A , B ). Additionally, the transcript levels of SmHGPRTase 1 , 2/4/5, and 3 were evaluated after the parasite exposure to the inhibitor.…”

“…After the in silico analysis, we sought to confirm whether SmHGPRTases are regulated by the Smp38 MAPK pathway as previously described ( Gava et al, 2019 ). Thus, schistosomula were exposed to Smp38 (NCC–00001994) predicted inhibitor ( Moreira et al, 2022 ). After 30 h of culture, as described by Moreira et al (2022) it was observed alterations in schistosomula phenotypes, like the presence of a dark middle-region and round bodies ( Figures 1A , B ).…”

“…According to Gava et al (2019) , the SmHGPRTase 1 expression is down-regulated in Smp38 knocked-down schistosomula. To experimentally verify that regulation, an inhibitor previously identified by our group to bind in the ATP binding site of Smp38 was used (inhibitor NCC – 00001994 from the Managed Chemical Compound Collection – MCCC; Moreira et al, 2022 ) The inhibitor NCC – 00001994 was used at a final concentration of 10 μM in cultures containing 5,000 schistosomula in 1 ml of Glasgow Minimum Essential Medium (GMEM; Sigma-Aldrich) supplemented with 20 mM HEPES (Sigma-Aldrich), 0.1% lactalbumin hydrolysate (Vetec), 0.1% D-glucose (Sigma-Aldrich), 0.5 μM hypoxanthine (Sigma-Aldrich), 1 μM hydrocortisone (Sigma-Aldrich), 0.5% MEM vitamin solution (Gibco), 5% Schneider (Gibco), 1% penicillin and streptomycin (Gibco), and 2% heat-inactivated fetal bovine serum (FBS; Gibco). Parasites cultured with 0.2% of dimethyl sulfoxide (DMSO; negative control) were used as controls.…”

Dual-targeting cyclic peptides of receptor-binding domain (RBD) and main protease (Mpro) as potential drug leads for the treatment of SARS-CoV-2 infection

“…Cyclic peptides have several favorable properties such as strong binding affinity, target selectivity, good biocompatibility and low toxicity, which make them an attractive modality for the development of therapeutics ( Kreutzer et al, 2021 ). Docking-based virtual screening (DBVS) is a fast and efficient technique that has great potential to identify novel active peptides in the pharmaceutical industry compared with traditional high-throughput screening ( Yang D. S. et al, 2020 ; Moreira et al, 2022 ). In addition, molecular dynamics (MD) simulation can greatly reflect the stability of protein-ligand interactions ( Zinovjev and van der Kamp, 2020 ).…”