Understanding Noncovalent Interactions: Ligand Binding Energy and Catalytic Efficiency from Ligand-Induced Reductions in Motion within Receptors and Enzymes

ChemInform ◽  
2005 ◽  
Vol 36 (14) ◽  
Author(s):  
Dudley H. Williams ◽  
Elaine Stephens ◽  
Dominic P. O'Brien ◽  
Min Zhou
Keyword(s):  
Binding Energy ◽  
Ligand Binding ◽  
Noncovalent Interactions ◽  
Catalytic Efficiency

Search for approaches to improving the calculation accuracy of the protein—ligand binding energy by docking

2017 ◽  
Vol 66 (10) ◽  
pp. 1913-1924 ◽  
Author(s):  
A. V. Sulimov ◽  
D. C. Kutov ◽  
E. V. Katkova ◽  
O. A. Kondakova ◽  
V. B. Sulimov
Keyword(s):  
Binding Energy ◽  
Ligand Binding

scholarly journals Drug and Drug-like Molecule Binding to Interface of SARS-CoV-2 Sprotein:human ACE2 Complex: A Density Functional Theory Study

2020 ◽  
Author(s):  
CH Suresh
Keyword(s):  
Binding Energy ◽  
Density Functional ◽  
Rational Design ◽  
Noncovalent Interactions ◽  
Receptor Interaction ◽  
Site Model ◽  
Model Drug ◽  
Drug Receptor ◽  
Approved Drugs ◽  
Better Than

SARS-CoV-2 S-protein:human ACE2 complex models.<div>QM-MM optimized active site model of SARS-CoV-2 S-protein:human ACE2 interface.</div><div>ONIOM(B3LYP/6-31G*:PM7) method is the chosen QM-MM method. </div><div> DFT B3LYP/6-31G* level data on energetics is reported for drug-receptor interaction.</div><div>Several FDA approved drugs and traditional herbal isolates are modelled.</div><div>Used Gaussian16 to model the systems.</div><div><br></div><div><br></div><p>The interface cavity of SARS-CoV-2 S-protein:human ACE2 complex (<b>M</b>) for ligand (<b>L</b>) binding is modelled using a two layer ONIOM(B3LYP/6-31G*:PM7) method for sixteen traditional herbal isolates (THI) and nineteen drugs. The binding energy (E<sub>b</sub>) of <b>ML</b> complexes increased with increase in dipole moment of <b>L</b>s. E<sub>b</sub> better than -80.0 kcal/mol is observed for digallic acid and adenosine 3',5'-bisphosphate whereas myricetin, glucogallin, sapropterin, tetrahydrobiopterin, protirelin and fidarestat<b> </b>showed E<sub>b</sub> better than -60.0 kcal/mol. Multiple noncovalent interactions emanating from arginine, histidine, tyrosine, lysine, carboxylate and amide units (total around 6 - 8) of <b>L</b>, S-protein and ACE2 receptors provide the high binding energy. The sugar substitute aspartame modified with myricetin unit showed the best E<sub>b</sub> -91.7 kcal/mol. ONIOM-linked DFT study is effective, affordable and reliable for a quantum chemical rational design approach to model drug-receptor binding process for COVID-19 drug development which sheds light upon the noncovalent binding features of receptor cavity.</p>

scholarly journals Noncontiguous regions in the extracellular domain of EGF receptor define ligand-binding specificity.

1991 ◽  
Vol 2 (5) ◽  
pp. 337-345 ◽  
Author(s):  
I Lax ◽  
R Fischer ◽  
C Ng ◽  
J Segre ◽  
A Ullrich ◽  
...  
Keyword(s):  
Binding Energy ◽  
Ligand Binding ◽  
Binding Site ◽  
Binding Affinity ◽  
Egf Receptor ◽  
Binding Properties ◽  
Amino Terminal ◽  
High Affinity ◽  
Domain Iii ◽  
Domain I

Murine epidermal growth factor (EGF) binds with approximately 250-fold higher binding affinity to the human EGF receptor (EGFR) than to the chicken EGFR. This difference in binding affinity enabled the identification of a major ligand-binding domain for EGF by studying the binding properties of various chicken/human EGFR chimera expressed in transfected cells lacking endogenous EGFR. It was shown that domain III of EGFR is a major ligand-binding region. Here, we analyze the binding properties of novel chicken/human chimera to further delineate the contact sequences in domain III and to assess the role of other regions of EGFR for their contribution to the display of high-affinity EGF binding. The chimeric receptors include chicken EGFR containing domain I of the human EGFR, chicken receptor containing domain I and III of the human EGFR, and two chimeric chicken EGFR containing either the amino terminal or the carboxy terminal halves of domain III of human EGFR, respectively. In addition, the binding of various human-specific anti-EGFR monoclonal antibodies that interfere with EGF binding is also compared. It is concluded that noncontiguous regions of the EGFR contribute additively to the binding of EGF. Each of the two halves of domain III has a similar contribution to the binding energy, and the sum of both is close to that of the entire domain III. This suggests that the folding of domain III juxtaposes sequences that together constitute the ligand-binding site. Domain I also provides a contribution to the binding energy, and the added contributions of both domain I and III to the binding energy generate the high-affinity binding site typical of human EGFR.

scholarly journals In silico approach of receptor-ligand binding and interaction: Established phytoligands from Tagetes errecta Linn. against bacterial β-glucosidase receptor

2019 ◽  
Vol 9 (1-s) ◽  
pp. 125-131
Author(s):  
Madhumita Lahiri ◽  
Partha Talukdar ◽  
Soumendra Nath Talapatra
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Ligand Binding ◽  
Antimicrobial Agents ◽  
Volatile Oil ◽  
Competitive Inhibitor ◽  
Ornamental Plant ◽  
Binding Interaction ◽  
Receptor Ligand ◽  
Energy Value

The medicinal plant, Tagetes errecta Linn. is a common ornamental plant and leaves of this plant are containing phytochemicals (volatile oil) that inhibit the growth of bacteria, fungi and known natural antimicrobial agents. The objective of the present study was to detect receptor-ligand binding energy and interaction through molecular docking for phytoligands established in the leaves of T. errecta against β-glucosidase receptor (PDB ID: 3AHZ). Molecular docking was performed by using PyRx (Version 0.8) for the structure-based virtual screening and visualized the interaction in the molecular graphic laboratory (MGL) tool (Version 1.5.6). Among 25 phytochemicals and 2 synthetic compounds (Carbendazim and 2-Amino-2-hydroxymethyl-propane-1,3-diol), binding energy value was obtained highest in Bicyclogermacrene (-6.4 Kcal/mol) and lowest in Octanol (-4.4 Kcal/mol) and Carbendazim and 2-Amino-2-hydroxymethyl-propane-1,3-diol showed -6.7 Kcal/mol and -3.5 Kcal/mol all of these showed no hydrogen bonding. The binding interaction of target protein with this phytocompound found binding at the mouth of the active site may be treated as competitive inhibitor. In conclusion, phytocompound Bicyclogermacrene can be alternative of synthetic fungicide as per binding energy value and interaction. It is suggesting further pharmacological and toxicological assay with this phytocompound after isolation from ornamental plant (T. errecta).

scholarly journals Transduction of enzyme-ligand binding energy into catalytic driving force

FEBS Letters ◽  
1991 ◽  
Vol 294 (1-2) ◽  
pp. 1-5 ◽  
Author(s):  
Harvey F. Fisher ◽  
Narinder Singh
Keyword(s):  
Binding Energy ◽  
Ligand Binding ◽  
Driving Force
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