scholarly journals Methods for Effective Virtual Screening and Scaffold-Hopping in Chemical Compounds

2007 ◽  
Author(s):  
Nikil Wale ◽  
George Karypis ◽  
Ian A. Watson
Keyword(s):  
Virtual Screening ◽  
Chemical Compounds ◽  
Scaffold Hopping

Discovery of Novel Small Molecule Inhibitors of Dengue Viral NS2B-NS3 Protease Using Virtual Screening and Scaffold Hopping

2012 ◽  
Vol 55 (14) ◽  
pp. 6278-6293 ◽  
Author(s):  
Jing Deng ◽  
Ning Li ◽  
Hongchuan Liu ◽  
Zhili Zuo ◽  
Oi Wah Liew ◽  
...  
Keyword(s):  
Virtual Screening ◽  
Small Molecule ◽  
Small Molecule Inhibitors ◽  
Scaffold Hopping ◽  
Ns3 Protease

scholarly journals Indirect Similarity Based Methods for Effective Scaffold-Hopping in Chemical Compounds

2008 ◽  
Vol 48 (4) ◽  
pp. 730-741 ◽  
Author(s):  
Nikil Wale ◽  
Ian A. Watson ◽  
George Karypis
Keyword(s):  
Chemical Compounds ◽  
Scaffold Hopping

scholarly journals Identification of new SUMO activating enzyme 1 inhibitors using virtual screening and scaffold hopping

2016 ◽  
Vol 26 (4) ◽  
pp. 1218-1223 ◽  
Author(s):  
Ashutosh Kumar ◽  
Akihiro Ito ◽  
Mikako Hirohama ◽  
Minoru Yoshida ◽  
Kam Y.J. Zhang
Keyword(s):  
Virtual Screening ◽  
Scaffold Hopping

scholarly journals Attacking the SARS-CoV-2 Replication Machinery with the Pathogen Box’s Molecules

2020 ◽  
Author(s):  
Cleidy Osorio-Mogollon ◽  
Gustavo E. Olivos-Ramirez ◽  
Kewin Otazu ◽  
Manuel E. Chenet-Zuta ◽  
Georcki Ropon-Palacios ◽  
...  
Keyword(s):  
Virtual Screening ◽  
Drug Repositioning ◽  
Genetic Material ◽  
Chemical Compounds ◽  
Quick Response ◽  
Replication Machinery ◽  
Nonstructural Proteins ◽  
The World ◽  
Transcription And Replication ◽  
Positive Controls

The world is currently facing a pandemic caused by the new 2019 coronavirus disease (COVID-19), caused by SARS-CoV-2. Among the fundamental processes of this virus are viral transcription and replication. They allow the synthesis<br>of genetic material and the consequent multiplication of the virus to infect other cells or organisms. These are performed by a multi-subunit machinery of various nonstructural proteins (nsp); among which the RNA-dependent RNA<br>polymerase (RdRp or nsp12) is the most important, and, at the same time, conserved among coronaviruses. The structure of this protein (PDB ID: 6M71) was used as a target in the application of computational strategies for drug<br>search, like virtual screening and molecular docking. The region considered for virtual screening has three important amino acids for protein catalysis: T680 (located in Motif A), N691 and D623 (located in Motif B), where a grid box was located. In turn, applying the concept of drug repositioning is<br>considered as a quick response in the treatment of sudden outbreaks of diseases. Here, we used the Pathogen Box, a database of chemical compounds analyzed for the treatment against malaria, which were filtered under the criteria of selecting those that do not present any violation of Lipinski's<br>Rule of Five. At the same time, the Remdesivir, Beclabuvir and Sofosbuvir drug, previously used in <i>in silico</i> and clinical studies for inhibition of nsp12, were used as positive controls. The results showed a Top10 potential target inhibitors, with binding energy higher than those of the positive controls, of which TCMDC-134153 and TCMDC-135052, both with -7.53 kcal/mol, present interactions with the three important residues of the nsp12 catalytic site. These proposed ligands would be used for subsequent validation by molecular dynamics, where they can be<br>considered as drugs for the development of effective treatments against this new pandemic.

Identification of Novel Potential Inhibitors of the HIV-1 gp41 Protein by Virtual Screening and Molecular Modeling Methods

2015 ◽  
Vol 10 (2) ◽  
pp. 325-343 ◽  
Author(s):  
И.А. Кашин ◽  
I.A. Kashyn
Keyword(s):  
Virtual Screening ◽  
Chemical Compounds ◽  
External Region ◽  
Modeling Methods ◽  
Fusion Inhibitors ◽  
Neutralizing Monoclonal Antibody ◽  
Dynamics Simulations ◽  
Potential Inhibitors ◽  
Free Energy Of Binding ◽  
Hiv 1

Virtual screening of chemical compounds able to mimic pharmacophoric properties of broadly neutralizing monoclonal antibody 10E8 against HIV-1 was carried out. Evaluation of the efficacy of binding of these compounds to the membrane-proximal external region (MPER) of the HIV-1 gp41 protein critical for fusion of the virus membrane with a target cell was performed by molecular docking and molecular dynamics simulations. Eight chemical compounds exhibiting negative values of the free energy of binding to this functionally important site of HIV-1 were identified. The data obtained testify to the availability of these molecules in the studies aimed at the design of novel antiviral drugs presenting the HIV-1 fusion inhibitors that block the MPER region of the gp41 protein.

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