How to Computationally Stack the Deck for Hit-to-Lead Generation: In Silico Molecular Interaction Energy Profiling for de Novo siRNA Guide Strand Surrogate Selection

2019 ◽  
Vol 59 (5) ◽  
pp. 1897-1908 ◽  
Author(s):  
Paulette A. Greenidge ◽  
Marcel J. J. Blommers ◽  
John P. Priestle ◽  
Jürg Hunziker
Keyword(s):  
Interaction Energy ◽  
Molecular Interaction ◽  
In Silico ◽  
De Novo ◽  
Guide Strand ◽  
Lead Generation ◽  
Surrogate Selection ◽  
Energy Profiling

scholarly journals In Silico Chromatography: Modeling a New Support for Alkyl-Bonded Phases and a Solvent Phase

2017 ◽  
Vol 2 (2) ◽  
pp. 111-117 ◽  
Author(s):  
Toshihiko Hanai
Keyword(s):  
Hydrogen Bonding ◽  
Interaction Energy ◽  
Silica Gel ◽  
Molecular Interactions ◽  
Molecular Interaction ◽  
In Silico ◽  
Van Der Waals ◽  
Silica Gels ◽  
Electrostatic Energy ◽  
Acidic Drugs

Chromatography is a tool to measure molecular interactions, and computational chemistry is a tool to explain molecular interactions. Therefore, reversed-phase liquid chromatography of acidic drugs using a pentyl- and an octyl-bonded silica gels was quantitatively analyzed in silico. A model pentyl- and an octyl-bonded silica gel and a methanol phases were constructed for docking with acidic drugs. Molecular interaction energy values based on van der Waals energy were obtained after docking an acidic drug into the model pentyl- or octyl-phases. Solvent effects, hydrogen bonding, and electrostatic energy values were obtained after docking an acidic drug onto the model methanol phase. Chromatographically measured log k values were correlated with the sum of van der Waals, hydrogen bonding, and electrostatic energy values. The correlation coefficient between the log k values measured using the pentyl-bonded silica gel phase and the molecular interaction energy values was 0.95 (n = 20); that between the log k values measured using the octyl-bonded silica gel and the molecular interaction energy values was 0.95 (n = 20).

In silico Screening and Molecular Interaction Studies of Tetrahydrocannabinol and its Derivatives with Acetylcholine Binding Protein

2018 ◽  
Vol 12 (2) ◽  
pp. 181-190 ◽  
Author(s):  
Priya P. Panigrahi ◽  
Ramit Singla ◽  
Ankush Bansal ◽  
Moacyr Comar Junior ◽  
Vikas Jaitak ◽  
...  
Keyword(s):  
Molecular Interaction ◽  
In Silico ◽  
Binding Protein ◽  
In Silico Screening ◽  
Acetylcholine Binding Protein ◽  
Interaction Studies

Towards the de novo design of DNA based catalytic sites using a combined NMR and in silico approach

2014 ◽  
Author(s):  
Dieter Buyst ◽  
V. Gheerardijn ◽  
J. Van Den Begin ◽  
A. Madder ◽  
J. C. Martins
Keyword(s):  
In Silico ◽  
De Novo ◽  
De Novo Design ◽  
Catalytic Sites
Sign in / Sign up

Export Citation Format

Share Document