QSAR modeling and in silico design of small-molecule inhibitors targeting the interaction between E3 ligase VHL and HIF-1 $$\alpha $$ α

2017 ◽  
Vol 21 (3) ◽  
pp. 719-739
Author(s):  
Jing Pan ◽  
Yanmin Zhang ◽  
Ting Ran ◽  
Anyang Xu ◽  
Xin Qiao ◽  
...  
Keyword(s):  
Small Molecule ◽  
In Silico ◽  
Small Molecule Inhibitors ◽  
E3 Ligase ◽  
Qsar Modeling ◽  
In Silico Design

In silico design of small molecule inhibitors of CDK9/cyclin T1 interaction

2014 ◽  
Vol 50 ◽  
pp. 100-112 ◽  
Author(s):  
Jelena Randjelovic ◽  
Slavica Eric ◽  
Vladimir Savic
Keyword(s):  
Small Molecule ◽  
In Silico ◽  
Small Molecule Inhibitors ◽  
In Silico Design ◽  
Cyclin T1

scholarly journals High Throughput in Silico Identification of Novel Phytochemical Inhibitors for the Master Regulator of Inflammation (TNFα)

2021 ◽  
Author(s):  
Pratap Kumar Parida ◽  
Dipak Paul ◽  
Debamitra Chakravorty
Keyword(s):  
Small Molecule ◽  
High Throughput ◽  
In Silico ◽  
Small Molecule Inhibitors ◽  
Binding Free Energy ◽  
Natural Compounds ◽  
Free Energy Calculations ◽  
Compound Libraries ◽  
Relative Binding

<p><a>The over expression of Tumor necrosis factor-α (TNFα) has been implicated in a variety of disease and is classified as a therapeutic target for inflammatory diseases (Crohn disease, psoriasis, psoriatic arthritis, rheumatoid arthritis).Commercially available therapeutics are biologics which are associated with several risks and limitations. Small molecule inhibitors and natural compounds (saponins) were identified by researchers as lead molecules against TNFα, however, </a>they were often associated with high IC50 values which can lead to their failure in clinical trials. This warrants research related to identification of better small molecule inhibitors by screening of large compound libraries. Recent developments have demonstrated power of natural compounds as safe therapeutics, hence, in this work, we have identified TNFα phytochemical inhibitors using high throughput <i>in silico </i>screening approaches of 6000 phytochemicals followed by 200 ns molecular dynamics simulations and relative binding free energy calculations. The work yielded potent hits that bind to TNFα at its dimer interface. The mechanism targeted was inhibition of oligomerization of TNFα upon phytochemical binding to restrict its interaction with TNF-R1 receptor. MD simulation analysis resulted in identification of two phytochemicals that showed stable protein-ligand conformations over time. The two compounds were triterpenoids: Momordicilin and Nimbolin A with relative binding energy- calculated by MM/PBSA to be -190.5 kJ/Mol and -188.03 kJ/Mol respectively. Therefore, through this work it is being suggested that these phytochemicals can be used for further <i>in vitro</i> analysis to confirm their inhibitory action against TNFα or can be used as scaffolds to arrive at better drug candidates.</p>

scholarly journals Identification of small molecule inhibitors for influenza a virus using in silico and in vitro approaches

PLoS ONE ◽  
2017 ◽  
Vol 12 (3) ◽  
pp. e0173582 ◽  
Author(s):  
Juliann Nzembi Makau ◽  
Ken Watanabe ◽  
Takeshi Ishikawa ◽  
Satoshi Mizuta ◽  
Tsuyoshi Hamada ◽  
...  
Keyword(s):  
Influenza A Virus ◽  
Small Molecule ◽  
In Silico ◽  
Influenza A ◽  
Small Molecule Inhibitors

scholarly journals In silico design and synthesis of novel small molecule antibiotics targeting the T-box riboswitch

2020 ◽  
Author(s):  
Eric Parsons ◽  
Ben J Haines ◽  
Ali H. Aldhumani ◽  
Jennifer V. Hines ◽  
Dr. Stephen C. Bergmeier
Keyword(s):  
Small Molecule ◽  
In Silico ◽  
In Silico Design ◽  
T Box ◽  
Design And Synthesis

In silico design and in vitro assessment of anti-Helicobacter pylori compounds as potential small-molecule arginase inhibitors

2022 ◽  
Author(s):  
Ana Thereza Fiori-Duarte ◽  
João Paulo de Oliveira Guarnieri ◽  
Jessica Rodrigues Pereira de Oliveira Borlot ◽  
Marcelo Lancellotti ◽  
Ricardo Pereira Rodrigues ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Small Molecule ◽  
In Silico ◽  
In Silico Design ◽  
In Vitro Assessment ◽  
Arginase Inhibitors

Discovery of Small-Molecule Inhibitors of Ubiquitin Specific Protease 7 (USP7) Using Integrated NMR and in Silico Techniques

2017 ◽  
Vol 60 (24) ◽  
pp. 10056-10070 ◽  
Author(s):  
Paola Di Lello ◽  
Richard Pastor ◽  
Jeremy M. Murray ◽  
Robert A. Blake ◽  
Frederick Cohen ◽  
...  
Keyword(s):  
Small Molecule ◽  
In Silico ◽  
Small Molecule Inhibitors ◽  
Specific Protease ◽  
Ubiquitin Specific Protease

Identification of Non-Macrocyclic Small Molecule Inhibitors against the NS3/4A Serine Protease of Hepatitis C Virus through in Silico Screening

2012 ◽  
Vol 52 (8) ◽  
pp. 2245-2256 ◽  
Author(s):  
Rima Chaudhuri ◽  
Hyun Lee ◽  
Lena Truong ◽  
Jaime Torres ◽  
Kavankumar Patel ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Serine Protease ◽  
Small Molecule ◽  
In Silico ◽  
Small Molecule Inhibitors ◽  
In Silico Screening
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