ITC and SPR Analysis Using Dynamic Approach

2019 ◽  
Author(s):  
Ganesh Kumar Krishnamoorthy ◽  
Prashanth Alluvada ◽  
Shahul Hameed ◽  
Timothy Kwa ◽  
Janarthanan Krishnamoorthy
Keyword(s):  
Binding Sites ◽  
Isothermal Calorimetry ◽  
Dynamic Approach ◽  
Ligand Interaction ◽  
Experimental Profile ◽  
Kinetic Rate Constants ◽  
Instrument Response ◽  
Sequential Binding ◽  
Protein Ligand Interaction ◽  
Two State Model

ABSTRACTBiophysical techniques such as Isothermal Calorimetry (ITC) and Surface Plasmon Resonance (SPR) are routinely used to ascertain the global binding mechanisms of protein-protein or protein-ligand interaction. Recently, Dumas etal, have explicitly modelled the instrument response of the ligand dilution and analysed the ITC thermogram to obtain kinetic rate constants. Adopting a similar approach, we have integrated the dynamic instrument response with the binding mechanism to simulate the ITC profiles of equivalent and independent binding sites, equivalent and sequential binding sites and aggregating systems. The results were benchmarked against the standard commercial software Origin-ITC. Further, the experimental ITC chromatograms of 2’-CMP + RNASE and BH3I-1 + hBCLXL interactions were analysed and shown to be comparable with that of the conventional analysis. Dynamic approach was applied to simulate the SPR profiles of a two-state model, and could reproduce the experimental profile accurately.

Conformation of Albumin Binding Sites are Disturbed in Schizophrenia

2009 ◽  
Vol 24 (S1) ◽  
pp. 1-1
Author(s):  
M. Uzbekov ◽  
Y. Gryzunov ◽  
E. Misionzhnik ◽  
T. Syrejshchikova ◽  
G. Dobretsov ◽  
...  
Keyword(s):  
Binding Sites ◽  
Conformational State ◽  
Albumin Binding ◽  
Nitrate Anion ◽  
Specific Probe ◽  
Serum Samples ◽  
Ligand Interaction ◽  
Schizophrenic Patients ◽  
Protein Ligand Interaction ◽  
Fluorescent Fraction

Aim:Investigate some properties of albumin binding sites in schizophrenic patients.Methods:Properties of serum albumin binding sites were studied using quenching of fluorescence of probe K-35 (N-carboxyphenylimide of dimethylaminonaphthalic acid) with nitrate anion. Serum samples were collected from 24 schizophrenic patients and 24 healthy volunteers.Results:In the absence of quencher specific probe fluorescence in patients was 1,4 times higher than in controls. Fluorescent quenching constant for probe bound to albumin was 2,5 L/mol in patients versus 4,6 L/mol in volunteers (p< 0,01). Fluorescent fraction assessable to quenching was significantly lower in patients than in volunteers. Fluorescent decay studies on S-60 synchrotron have revealed in patient's albumin the redistribution between long-lived and short-lived molecules of the probe with increase of the latter. There were found decrease of albumin accessible SH-groups in schizophrenic patients as compared with volunteers.Conclusions:In schizophrenic patients conformational state of albumin binding sites is significantly disturbed that can lead to changes in protein-ligand interaction and to damage of main albumin functions (transport and detoxification) and aggravation of endotoxicosis.

scholarly journals Two Rules on the Protein-Ligand Interaction

2008 ◽  
Author(s):  
Xiaodong Pang ◽  
Linxiang Zhou ◽  
Lily Zhang ◽  
Lina Xu ◽  
Xinyi Zhang
Keyword(s):  
Ligand Interaction ◽  
Protein Ligand Interaction

scholarly journals Protein-ligand free energies of binding from full-protein DFT calculations: convergence and choice of exchange-correlation functional

2021 ◽  
Author(s):  
Lennart Gundelach ◽  
Christofer S Tautermann ◽  
Thomas Fox ◽  
Chris-Kriton Skylaris
Keyword(s):  
Drug Discovery ◽  
Ligand Binding ◽  
Dft Calculations ◽  
Quantum Mechanical ◽  
Free Energies ◽  
Ligand Interaction ◽  
Exchange Correlation ◽  
Ligand Free ◽  
Protein Ligand Interaction ◽  
Binding Free Energies

The accurate prediction of protein-ligand binding free energies with tractable computational methods has the potential to revolutionize drug discovery. Modeling the protein-ligand interaction at a quantum mechanical level, instead of...

scholarly journals Fragment-centric topographic mapping method guides the understanding of ABCG2-inhibitor interactions

RSC Advances ◽  
2019 ◽  
Vol 9 (14) ◽  
pp. 7757-7766 ◽  
Author(s):  
Yao Wu ◽  
Xin-Ying Gao ◽  
Xin-Hui Chen ◽  
Shao-Long Zhang ◽  
Wen-Juan Wang ◽  
...  
Keyword(s):  
Mapping Method ◽  
Topographic Mapping ◽  
Ligand Interaction ◽  
Mapping Tool ◽  
Protein Ligand Interaction ◽  
Insight Into ◽  
Computational Strategy

Our study gains insight into the development of novel specific ABCG2 inhibitors, and develops a comprehensive computational strategy to understand protein ligand interaction with the help of AlphaSpace, a fragment-centric topographic mapping tool.

Structural bioinformatics used to predict the protein targets of remdesivir and flavones in SARS-CoV-2 infection

2021 ◽  
Vol 17 ◽  
Author(s):  
Avram Speranta ◽  
Laura Manoliu ◽  
Catalina Sogor ◽  
Maria Mernea ◽  
Corina Duda Seiman ◽  
...  
Keyword(s):  
Human Body ◽  
Specific Treatment ◽  
Structural Similarity ◽  
Web Tool ◽  
Ligand Interaction ◽  
Protein Targets ◽  
Synthetic Compounds ◽  
Associated Proteins ◽  
Functional Features ◽  
Protein Ligand Interaction

Background: During the current SARS-CoV-2 pandemic, the identification of effective antiviral drugs is crucial. Unfortunately, no specific treatment or vaccine is available to date. Objective: Here, we aimed to predict the interactions between SARS-CoV-2 proteins and protein targets from the human body for some flavone molecules (kaempferol, morin, pectolinarin, myricitrin, and herbacetin) in comparison to synthetic compounds (hydroxychloroquine, remdesivir, ribavirin, ritonavir, AMD-070, favipiravir). Methods: Using MOE software and advanced bioinformatics and cheminformatics portals, we conducted an extensive analysis based on various structural and functional features of compounds, such as their amphiphilic field, flexibility, and steric features. The structural similarity analysis of natural and synthetic compounds was performed using Tanimoto coefficients. The interactions of some compounds with SARS-CoV-2 3CLprotease or RNA-dependent RNA polymerase were described using 2D protein-ligand interaction diagrams based on known crystal structures. The potential targets of considered compounds were identified using the SwissTargetPrediction web tool. Results: Our results showed that remdesivir, pectolinarin, and ritonavir present a strong structural similarity which may be correlated to their similar biological activity. As common molecular targets of compounds in the human body, ritonavir, kaempferol, morin, and herbacetin can activate multidrug resistance-associated proteins, while remdesivir, ribavirin, and pectolinarin appear as ligands for adenosine receptors. Conclusion: Our evaluation recommends remdesivir, pectolinarin, and ritonavir as promising anti-SARS-CoV-2 agents.

Spiro-acridine inhibiting tyrosinase enzyme: Kinetic, protein-ligand interaction and molecular docking studies

2019 ◽  
Vol 122 ◽  
pp. 289-297 ◽  
Author(s):  
Thaís Meira Menezes ◽  
Sinara Mônica Vitalino de Almeida ◽  
Ricardo Olímpio de Moura ◽  
Gustavo Seabra ◽  
Maria do Carmo Alves de Lima ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Docking Studies ◽  
Enzyme Kinetic ◽  
Ligand Interaction ◽  
Molecular Docking Studies ◽  
Protein Ligand Interaction ◽  
Tyrosinase Enzyme

Protein–ligand interaction study of signal transducer smoothened protein with different drugs: molecular docking and QM/MM calculations

RSC Advances ◽  
2015 ◽  
Vol 5 (84) ◽  
pp. 68829-68838 ◽  
Author(s):  
Hossein Farrokhpour ◽  
Vahid Pakatchian ◽  
Abdolreza Hajipour ◽  
Fatemeh Abyar ◽  
Alireza Najafi Chermahini ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Antitumor Agent ◽  
Signal Transducer ◽  
Interaction Study ◽  
Ligand Interaction ◽  
Protein Ligand Interaction

A part of signal transducer smoothened (SMO) protein including antitumor agent LY2940680. The site of this antitumor was considered for the docking of 716 ligands.

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