Molecular dynamics guided insight, binding free energy calculations and pharmacophore-based virtual screening for the identification of potential VEGFR2 inhibitors

2019 ◽  
Vol 39 (5-6) ◽  
pp. 415-433
Author(s):  
Ekta Rathi ◽  
Avinash Kumar ◽  
Suvarna G. Kini
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Virtual Screening ◽  
Binding Free Energy ◽  
Free Energy Calculations ◽  
Energy Calculations ◽  
Binding Free Energy Calculations

scholarly journals Structure-Based Virtual Screening, Molecular Dynamics and Binding Free Energy Calculations of Hit Candidates as ALK-5 Inhibitors

Molecules ◽  
2020 ◽  
Vol 25 (2) ◽  
pp. 264
Author(s):  
Sheila C. Araujo ◽  
Vinicius G. Maltarollo ◽  
Michell O. Almeida ◽  
Leonardo L. G. Ferreira ◽  
Adriano D. Andricopulo ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Virtual Screening ◽  
Anticancer Agents ◽  
Binding Free Energy ◽  
Free Energy Calculations ◽  
Energy Calculations ◽  
Cellular Events ◽  
Binding Free Energy Calculations ◽  
Alk 5

Activin-like kinase 5 (ALK-5) is involved in the physiopathology of several conditions, such as pancreatic carcinoma, cervical cancer and liver hepatoma. Cellular events that are landmarks of tumorigenesis, such as loss of cell polarity and acquisition of motile properties and mesenchymal phenotype, are associated to deregulated ALK-5 signaling. ALK-5 inhibitors, such as SB505154, GW6604, SD208, and LY2157299, have recently been reported to inhibit ALK-5 autophosphorylation and induce the transcription of matrix genes. Due to their ability to impair cell migration, invasion and metastasis, ALK-5 inhibitors have been explored as worthwhile hits as anticancer agents. This work reports the development of a structure-based virtual screening (SBVS) protocol aimed to prospect promising hits for further studies as novel ALK-5 inhibitors. From a lead-like subset of purchasable compounds, five molecules were identified as putative ALK-5 inhibitors. In addition, molecular dynamics and binding free energy calculations combined with pharmacokinetics and toxicity profiling demonstrated the suitability of these compounds to be further investigated as novel ALK-5 inhibitors.

Anti-dengue virus activity of scytovirin and evaluation of point mutation effects by molecular dynamics and binding free energy calculations

2017 ◽  
Vol 490 (3) ◽  
pp. 1033-1038 ◽  
Author(s):  
Andrei Santos Siqueira ◽  
Alex Ranieri Jerônimo Lima ◽  
Rafael Conceição de Souza ◽  
Alberdan Silva Santos ◽  
João Lídio da Silva Gonçalves Vianez Júnior ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Dengue Virus ◽  
Point Mutation ◽  
Binding Free Energy ◽  
Free Energy Calculations ◽  
Energy Calculations ◽  
Virus Activity ◽  
Binding Free Energy Calculations
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