scholarly journals Discover Novel Covalent Inhibitors Targeting FLT3 through Hybrid Virtual Screening Strategy

2021 ◽  
Vol 44 (12) ◽  
pp. 1872-1877
Author(s):  
Shengquan Hu ◽  
Jing Liu ◽  
Sikang Chen ◽  
Jian Gao ◽  
Yubo Zhou ◽  
...  
2019 ◽  
Author(s):  
Edward A. Valera-Vera ◽  
Melisa Sayé ◽  
Chantal Reigada ◽  
Mariana R. Miranda ◽  
Claudio A. Pereira

AbstractEnolase is a glycolytic enzyme that catalyzes the interconversion between 2-phosphoglycerate and phosphoenolpyruvate. In trypanosomatids enolase was proposed as a key enzyme afterin silicoandin vivoanalysis and it was validated as a protein essential for the survival of the parasite. Therefore, enolase constitutes an interesting enzyme target for the identification of drugs against Chagas disease. In this work, a combined virtual screening strategy was implemented, employing similarity virtual screening, molecular docking and molecular dynamics. First, two known enolase inhibitors and the enzyme substrates were used as queries for the similarity screening on the Sweetlead database using five different algorithms. Compounds retrieved in the top 10 of at least three search algorithms were selected for further analysis, resulting in six compounds of medical use (etidronate, pamidronate, fosfomycin, acetohydroximate, triclofos, and aminohydroxybutyrate). Molecular docking simulations predicted acetohydroxamate and triclofos would not bind to the active site of the enzyme, and a re-scoring of the obtained poses signaled fosfomycin and aminohydroxybutyrate as bad enzyme binders. Docking poses obtained for etidronate, pamidronate, and PEP, were used for molecular dynamics calculations to describe their mode of binding. From the obtained results, we propose etidronate as a possibleTcENO inhibitor, and describe desirable and undesirable molecular motifs to be taken into account in the repurposing or design of drugs aiming this enzyme active site.


2019 ◽  
Vol 11 (8) ◽  
pp. 801-816 ◽  
Author(s):  
Dong Wang ◽  
Zhaoyang Li ◽  
Yi Liu ◽  
Mo Chen ◽  
Nianhang Chen ◽  
...  

2019 ◽  
Vol 184 ◽  
pp. 111750 ◽  
Author(s):  
Yi Zou ◽  
Yue Hu ◽  
Shushan Ge ◽  
Yingbo Zheng ◽  
Yuezhen Li ◽  
...  

RSC Advances ◽  
2020 ◽  
Vol 10 (46) ◽  
pp. 27752-27763
Author(s):  
Ying Yang ◽  
Lei Zhang ◽  
Jinying Tian ◽  
Fei Ye ◽  
Zhiyan Xiao

A new chemotype of XO inhibitor with the IC50 of 2.6 μM was identified by a hierarchical virtual screening strategy.


2020 ◽  
Author(s):  
Rupesh Agarwal ◽  
Barbara A. Bensing ◽  
Dehui Mi ◽  
Paige N. Vinson ◽  
Jerome Baudry ◽  
...  

AbstractInfective endocarditis (IE) is a cardiovascular disease often caused by bacteria of the viridans group of streptococci, which includes Streptococcus gordonii and Streptococcus sanguinis. Previous research has found that a serine-rich repeat (SRR) proteins on the S. gordonii bacterial surface play a critical role in pathogenesis by facilitating bacterial attachment to sialyated glycans displayed on human platelets. Despite its important role in disease progression, there are currently no anti-adhesive drugs available on the market. Here, we performed structure-based virtual screening using an ensemble docking approach followed by consensus scoring to identify novel inhibitors against the sialoglycan binding domain of the SRR adhesin protein Hsa from the S. gordonii strain DL1. In silico cross screening against the glycan binding domains of closely related SRR proteins from five other S. gordonii or S. sanguinis strains was also performed to further reduce false positives. Using our in silico screening strategy we successfully predicted nine compounds which were able to displace the native ligand (sialyl-T antigen) in an in vitro assay and bind competitively to adhesin protein Hsa (∼20% hit rate).


2019 ◽  
Vol 15 (3) ◽  
pp. 193-205 ◽  
Author(s):  
Wei-Neng Zhou ◽  
Yan-Min Zhang ◽  
Xin Qiao ◽  
Jing Pan ◽  
Ling-Feng Yin ◽  
...  

Introduction: Acetyl-CoA Carboxylases (ACC) have been an important target for the therapy of metabolic syndrome, such as obesity, hepatic steatosis, insulin resistance, dyslipidemia, non-alcoholic fatty liver disease (NAFLD), non-alcoholic steatohepatitis (NASH), type 2 diabetes (T2DM), and some other diseases. Methods: In this study, virtual screening strategy combined with Bayesian categorization modeling, molecular docking and binding site analysis with protein ligand interaction fingerprint (PLIF) was adopted to validate some potent ACC inhibitors. First, the best Bayesian model with an excellent value of Area Under Curve (AUC) value (training set AUC: 0.972, test set AUC: 0.955) was used to screen compounds of validation library. Then the compounds screened by best Bayesian model were further screened by molecule docking again. Results: Finally, the hit compounds evaluated with four percentages (1%, 2%, 5%, 10%) were verified to reveal enrichment rates for the compounds. The combination of the ligandbased Bayesian model and structure-based virtual screening resulted in the identification of top four compounds which exhibited excellent IC 50 values against ACC in top 1% of the validation library. Conclusion: In summary, the whole strategy is of high efficiency, and would be helpful for the discovery of ACC inhibitors and some other target inhibitors.</P>


2020 ◽  
Vol 88 (4) ◽  
pp. 54
Author(s):  
Alfredo Juárez-Saldívar ◽  
Edgar E. Lara-Ramírez ◽  
Francisco Reyes-Espinosa ◽  
Alma D. Paz-González ◽  
Juan Carlos Villalobos-Rocha ◽  
...  

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a coronavirus that causes the pandemic Coronavirus Disease 2019 (COVID-19). There is no current specific treatment for this new coronavirus. In this study, we employed a virtual screening repurposing strategy to search for potential SARS-CoV-2 Mpro inhibitors. The databases PDB, ChEMBL, BindingDB and DrugBank were queried with several filtering steps based on ligand-based and structure-based approaches. As a result, we obtained 58 molecules (37 from ChEMBL and 21 from DrugBank) that potentially inhibit SARS-CoV-2 Mpro. These molecules have on their chemical structure functional groups that favor stronger docking scores than the inhibitor N3. Several of these molecules are reported experimentally as SARS-CoV Mpro inhibitors. Hence, a combined virtual screening strategy allowed finding chemical compounds with a high potential for the inhibition of SARS-CoV-2 Mpro.


2017 ◽  
Vol 18 (1) ◽  
pp. 137 ◽  
Author(s):  
Huabin Hu ◽  
Jie Xia ◽  
Dongmei Wang ◽  
Xiang Wang ◽  
Song Wu

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