scholarly journals PERBANDINGAN INHIBISI BRUSEIN D TERHADAP PROTEIN NFKB PADA SEL KANKER PANKREAS SECARA FLEKSIBEL DAN RIGID DOCKING

2017 ◽  
Vol 2 (2) ◽  
pp. 55-62
Author(s):  
Harry Noviardi ◽  
◽  
Armi Wulanawati ◽  
Muhammad Sholehuddin malik Ibrohim ◽  
Keyword(s):  
Rigid Docking

scholarly journals Structural insights and evaluation of the potential impact of missense variants on the interactions of SLIT2 with ROBO1/4 in cancer progression

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Debmalya Sengupta ◽  
Gairika Bhattacharya ◽  
Sayak Ganguli ◽  
Mainak Sengupta
Keyword(s):  
Lung Cancer ◽  
Cancer Progression ◽  
Structural Parameters ◽  
Homology Modelling ◽  
Missense Variants ◽  
Potential Impact ◽  
The Impact ◽  
Structural Insights ◽  
Rigid Docking

AbstractThe cognate interaction of ROBO1/4 with its ligand SLIT2 is known to be involved in lung cancer progression. However, the precise role of genetic variants, disrupting the molecular interactions is less understood. All cancer-associated missense variants of ROBO1/4 and SLIT2 from COSMIC were screened for their pathogenicity. Homology modelling was done in Modeller 9.17, followed by molecular simulation in GROMACS. Rigid docking was performed for the cognate partners in PatchDock with refinement in HADDOCK server. Post-docking alterations in conformational, stoichiometric, as well as structural parameters, were assessed. The disruptive variants were ranked using a weighted scoring scheme. In silico prioritisation of 825 variants revealed 379 to be potentially pathogenic out of which, about 12% of the variants, i.e. ROBO1 (14), ROBO4 (8), and SLIT2 (23) altered the cognate docking. Six variants of ROBO1 and 5 variants of ROBO4 were identified as "high disruptors" of interactions with SLIT2 wild type. Likewise, 17 and 13 variants of SLIT2 were found to be "high disruptors" of its interaction with ROBO1 and ROBO4, respectively. Our study is the first report on the impact of cancer-associated missense variants on ROBO1/4 and SLIT2 interactions that might be the drivers of lung cancer progression.

Parallel cascade selection molecular dynamics to screen for protein complexes generated by rigid docking

2019 ◽  
Vol 92 ◽  
pp. 94-99
Author(s):  
Ryuhei Harada ◽  
Ryunosuke Yoshino ◽  
Hiroaki Nishizawa ◽  
Yasuteru Shigeta
Keyword(s):  
Molecular Dynamics ◽  
Protein Complexes ◽  
Rigid Docking

scholarly journals How ‘Protein-Docking’ Translates into the New Emerging Field of Docking Small Molecules to Nucleic Acids?

Molecules ◽  
2020 ◽  
Vol 25 (12) ◽  
pp. 2749
Author(s):  
Francesca Tessaro ◽  
Leonardo Scapozza
Keyword(s):  
Molecular Docking ◽  
Nucleic Acid ◽  
Nucleic Acids ◽  
Small Molecules ◽  
Viral Infections ◽  
Therapeutic Potential ◽  
Mrna Level ◽  
Protein Docking ◽  
Structural Nature ◽  
Rigid Docking

In this review, we retraced the ‘40-year evolution’ of molecular docking algorithms. Over the course of the years, their development allowed to progress from the so-called ‘rigid-docking’ searching methods to the more sophisticated ‘semi-flexible’ and ‘flexible docking’ algorithms. Together with the advancement of computing architecture and power, molecular docking’s applications also exponentially increased, from a single-ligand binding calculation to large screening and polypharmacology profiles. Recently targeting nucleic acids with small molecules has emerged as a valuable therapeutic strategy especially for cancer treatment, along with bacterial and viral infections. For example, therapeutic intervention at the mRNA level allows to overcome the problematic of undruggable proteins without modifying the genome. Despite the promising therapeutic potential of nucleic acids, molecular docking programs have been optimized mostly for proteins. Here, we have analyzed literature data on nucleic acid to benchmark some of the widely used docking programs. Finally, the comparison between proteins and nucleic acid targets docking highlighted similarity and differences, which are intrinsically related to their chemical and structural nature.

In-silico Study of Sulfonylurea Family Members’ Binding Site with their Receptor Kir6.2\SUR1

2018 ◽  
Author(s):  
Farah Yousef ◽  
Oussama Mansour ◽  
Jehad Herbali
Keyword(s):  
In Silico ◽  
Type Ii Diabetes ◽  
Family Members ◽  
Data Bank ◽  
Type Ii Diabetes Mellitus ◽  
Structure Activity ◽  
Sulfonyl Urea ◽  
In Silico Study ◽  
Urea Group ◽  
Rigid Docking

Sulfonylurea family members have been used as a second preferred line in the treatment of Type II Diabetes Mellitus (TIIDM) for decades. Only one crystal structure for its receptor Kir6.2\SUR1 binding with one of sulfonylurea member; Glibenclamide (GBM), is available in Protein Data Bank (PDB) database. The aim of this manuscript is to study in-silico other sulfonylurea family members’ interactions with their receptor Kir6.2\SUR1 using a docking software in the default settings. We have checked the validity of the software for the study. Then, we have applied a rigid docking on 14 compounds of sulfonyl urea group which they have anti-hyperglycemia activity. Next, we have compared their interactions to GBM interactions with Kir6.2\SUR1.  As a result, many compounds of this family had bound to Kir6.2\SUR1 receptor in the same pocket as GBM. These results confirmed a perspective we have discussed about sulfonylurea structure activity relationship.

Sign in / Sign up

Export Citation Format

Share Document