scholarly journals Graphic representation of pharmacology: Development of an alternative model

2017 ◽  
Vol 7 (5) ◽  
pp. 201-206 ◽  
Author(s):  
Stephen R. Saklad
Keyword(s):  
Binding Affinity ◽  
Receptor Binding ◽  
Functional Data ◽  
Binding Affinities ◽  
Inverse Agonists ◽  
Receptor Sites ◽  
Binding Data ◽  
And Function ◽  
Pie Chart

Abstract Introduction: Providing clinicians with an easy to grasp and understandable representation of pharmacology is important to allow optimal clinical decisions to be made. Two of the most clinically relevant dimensions are receptor binding affinity and functional activity. The binding affinity for an agonist is described by the dissociation constant (KA), and an antagonist by the inhibition constant (Ki). Functionally, medications can act as superagonists, agonists, partial agonists, antagonists, partial inverse agonists, or inverse agonists at several receptor sites, transporters, or ion channels. Comprehending the differences between agents is complicated by the number and types of binding sites. Methods: Binding and functional data are obtained from primary literature, product labels, human cloned receptor binding, and other sources. Binding affinities are converted into ratios relative to the putative primary receptor for that category of agent. Antipsychotic binding is referenced to dopamine type 2 long (D2L) receptor binding. Binding affinity ratios (BARs) generate a 6-spoked diagram, with D2L as the hub. The most avidly bound sites are the spokes, and the disk diameter represents the BAR. Where functional data are available, they are shown as a pie chart shading the binding site's disk. Results: Binding and function diagrams are shown for the antipsychotics where binding data are available and are compared to previous methods of pharmacologic comparisons of antipsychotics. Discussion: Use of graphic models of psychotropic pharmacology improves clinician comprehension and may serve as an aid to improve rational therapeutics and patient outcomes.

scholarly journals E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies

2021 ◽  
Author(s):  
Wei Bu Wang ◽  
Yu Liang ◽  
Yu Qin Jin ◽  
Jing Zhang ◽  
Ji Guo Su ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Binding Affinity ◽  
Receptor Binding ◽  
Neutralizing Antibodies ◽  
Electrostatic Interactions ◽  
Tight Binding ◽  
Energy Calculation ◽  
Binding Affinities ◽  
Loop Region ◽  
Binding Interface

AbstractThe pandemic of the COVID-19 disease caused by SARS-CoV-2 has led to more than 100 million infections and over 2 million deaths worldwide. The progress in the developments of effective vaccines and neutralizing antibody therapeutics brings hopes to eliminate the threat of COVID-19. However, SARS-CoV-2 continues to mutate, and several new variants have been emerged. Among the various naturally-occurring mutations, the E484K mutation shared by both the 501Y.V2 and 501Y.V3 variants attracted serious concerns, which may potentially enhance the receptor binding affinity and reduce the immune response. In the present study, the molecular mechanism behind the impacts of E484K mutation on the binding affinity of the receptor-binding domain (RBD) with the receptor human angiotensin-converting enzyme 2 (hACE2) was investigated by using the molecular dynamics (MD) simulations combined with the molecular mechanics-generalized Born surface area (MMGBSA) method. Our results indicate that the E484K mutation results in more favorable electrostatic interactions compensating the burial of the charged and polar groups upon the binding of RBD with hACE2, which significantly improves the RBD-hACE2 binding affinity. Besides that, the E484K mutation also causes the conformational rearrangements of the loop region containing the mutant residue, which leads to more tight binding interface of RBD with hACE2 and formation of some new hydrogen bonds. The more tight binding interface and the new hydrogen bonds formation also contribute to the improved binding affinity of RBD to the receptor hACE2. In addition, six neutralizing antibodies and nanobodies complexed with RBD were selected to explore the effects of E484K mutation on the recognition of these antibodies to RBD. The simulation results show that the E484K mutation significantly reduces the binding affinities to RBD for most of the studied neutralizing antibodies, and the decrease in the binding affinities is mainly owing to the unfavorable electrostatic interactions caused by the mutation. Our studies revealed that the E484K mutation may improve the binding affinity between RBD and the receptor hACE2, implying more transmissibility of the E484K-containing variants, and weaken the binding affinities between RBD and the studied neutralizing antibodies, indicating reduced effectiveness of these antibodies. Our results provide valuable information for the effective vaccine development and antibody drugs design.

scholarly journals A Theoretical Study of the Relationships between Electronic Structure and CB1 and CB2 Cannabinoid Receptor Binding Affinity in a Group of 1-Aryl-5-(1-H-pyrrol-1-yl)-1-H-pyrazole-3-carboxamides

2014 ◽  
Vol 2014 ◽  
pp. 1-15
Author(s):  
Francisco Salgado-Valdés ◽  
Juan S. Gómez-Jeria
Keyword(s):  
Binding Affinity ◽  
Receptor Binding ◽  
Theoretical Study ◽  
Cannabinoid Receptor ◽  
Geometry Optimization ◽  
Wave Functions ◽  
Binding Affinities ◽  
Full Geometry Optimization ◽  
Receptor Binding Affinity ◽  
Reactivity Indices

We report the results of a search for model-based relationships between hCB1 and hCB2 receptor binding affinity and molecular structure for a group of 1-aryl-5-(1-H-pyrrol-1-yl)-1-H-pyrazole-3-carboxamides. The wave functions and local atomic reactivity indices were obtained at the B3LYP/6-31G(d,p) levels of theory with full geometry optimization. Interaction pharmacophores were generated for both receptors. The main conclusions of this work are as follows. (1) We obtained statistically significant equations relating the variation of hCB1 and hCB2 receptor binding affinities with the variation of definite sets of local atomic reactivity indices. (2) The interaction of the molecules with the hCB1 and hCB2 receptors seems to be highly complex and mainly orbital controlled. (3) The interaction mechanisms seem to be different for each type of receptor. This study, contrarily to the statistically backed ones, is able to provide a microscopic insight of the mechanisms involved in the binding process.

Antiproliferative and antiviral effects of mutated IFN-alpha with increased IFN receptor binding affinity

2011 ◽  
Vol 49 (01) ◽  
Author(s):  
MF Sprinzl ◽  
L Bührer ◽  
D Strand ◽  
G Schreiber ◽  
PR Galle ◽  
...  
Keyword(s):  
Binding Affinity ◽  
Receptor Binding ◽  
Receptor Binding Affinity ◽  
Ifn Alpha ◽  
Antiviral Effects

scholarly journals SMPLIP-Score: predicting ligand binding affinity from simple and interpretable on-the-fly interaction fingerprint pattern descriptors

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Surendra Kumar ◽  
Mi-hyun Kim
Keyword(s):  
Ligand Binding ◽  
Binding Affinity ◽  
Scoring Functions ◽  
Binding Affinities ◽  
Ligand Interaction ◽  
Fingerprint Pattern ◽  
Comparable Performance ◽  
Direct Interpretation ◽  
Benchmark Datasets ◽  
Complex Features

AbstractIn drug discovery, rapid and accurate prediction of protein–ligand binding affinities is a pivotal task for lead optimization with acceptable on-target potency as well as pharmacological efficacy. Furthermore, researchers hope for a high correlation between docking score and pose with key interactive residues, although scoring functions as free energy surrogates of protein–ligand complexes have failed to provide collinearity. Recently, various machine learning or deep learning methods have been proposed to overcome the drawbacks of scoring functions. Despite being highly accurate, their featurization process is complex and the meaning of the embedded features cannot directly be interpreted by human recognition without an additional feature analysis. Here, we propose SMPLIP-Score (Substructural Molecular and Protein–Ligand Interaction Pattern Score), a direct interpretable predictor of absolute binding affinity. Our simple featurization embeds the interaction fingerprint pattern on the ligand-binding site environment and molecular fragments of ligands into an input vectorized matrix for learning layers (random forest or deep neural network). Despite their less complex features than other state-of-the-art models, SMPLIP-Score achieved comparable performance, a Pearson’s correlation coefficient up to 0.80, and a root mean square error up to 1.18 in pK units with several benchmark datasets (PDBbind v.2015, Astex Diverse Set, CSAR NRC HiQ, FEP, PDBbind NMR, and CASF-2016). For this model, generality, predictive power, ranking power, and robustness were examined using direct interpretation of feature matrices for specific targets.

scholarly journals Telomere Length and Oxidative Stress and Its Relation with Metabolic Syndrome Components in the Aging

Biology ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 253
Author(s):  
Graciela Gavia-García ◽  
Juana Rosado-Pérez ◽  
Taide Laurita Arista-Ugalde ◽  
Itzen Aguiñiga-Sánchez ◽  
Edelmiro Santiago-Osorio ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Metabolic Syndrome ◽  
Telomere Length ◽  
Scientific Evidence ◽  
Telomeric Dna ◽  
Biochemical Alterations ◽  
The Metabolic Syndrome ◽  
Age Related ◽  
And Function

A great amount of scientific evidence supports that Oxidative Stress (OxS) can contribute to telomeric attrition and also plays an important role in the development of certain age-related diseases, among them the metabolic syndrome (MetS), which is characterised by clinical and biochemical alterations such as obesity, dyslipidaemia, arterial hypertension, hyperglycaemia, and insulin resistance, all of which are considered as risk factors for type 2 diabetes mellitus (T2DM) and cardiovascular diseases, which are associated in turn with an increase of OxS. In this sense, we review scientific evidence that supports the association between OxS with telomere length (TL) dynamics and the relationship with MetS components in aging. It was analysed whether each MetS component affects the telomere length separately or if they all affect it together. Likewise, this review provides a summary of the structure and function of telomeres and telomerase, the mechanisms of telomeric DNA repair, how telomere length may influence the fate of cells or be linked to inflammation and the development of age-related diseases, and finally, how the lifestyles can affect telomere length.

Synthesis, receptor binding affinities and conformational properties of cyclic methylenedithioether analogues of angiotensin II

2001 ◽  
Vol 9 (3) ◽  
pp. 763-772 ◽  
Author(s):  
Susanna Lindman ◽  
Gunnar Lindeberg ◽  
Adolf Gogoll ◽  
Fred Nyberg ◽  
Anders Karlén ◽  
...  
Keyword(s):  
Angiotensin Ii ◽  
Receptor Binding ◽  
Binding Affinities ◽  
Conformational Properties

scholarly journals Design of peptides with strong binding affinity to poly(methyl methacrylate) resin by use of molecular simulation-based materials informatics

2021 ◽  
Author(s):  
Tomio Iwasaki ◽  
Masashi Maruyama ◽  
Tatsuya Niwa ◽  
Toshiki Sawada ◽  
Takeshi Serizawa
Keyword(s):  
Methyl Methacrylate ◽  
Binding Affinity ◽  
Molecular Simulation ◽  
Dynamics Simulation ◽  
Binding Affinities ◽  
Materials Informatics ◽  
Poly Methyl Methacrylate ◽  
Strong Binding ◽  
Experimental Values ◽  
Pmma Resin

AbstractPeptides with strong binding affinities for poly(methyl methacrylate) (PMMA) resin were designed by use of materials informatics technology based on molecular dynamics simulation for the purpose of covering the resin surface with adhesive peptides, which were expected to result in eco-friendly and biocompatible biomaterials. From the results of binding affinity obtained with this molecular simulation, it was confirmed that experimental values could be predicted with errors <10%. By analyzing the simulation data with the response-surface method, we found that three peptides (RWWRPWW, EWWRPWR, and RWWRPWR), which consist of arginine (R), tryptophan (W), and proline (P), have strong binding affinity to the PMMA resin. These amino acids were effective because arginine and tryptophan have strong binding affinities for methoxycarbonyl groups and methyl groups, which are the main constituents of the PMMA resin, and proline stabilizes the flat zigzag structures of the peptides in water. The strong binding affinities of the three peptides were confirmed by experiments (surface plasmon resonance methods).

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