scholarly journals Repurposing the antibacterial drugs for inhibition of SARS-CoV2-PLpro using molecular docking, MD simulation and binding energy calculation

2021 ◽  
Author(s):  
Rohit Patel ◽  
Jignesh Prajapati ◽  
Priyashi Rao ◽  
Rakesh M. Rawal ◽  
Meenu Saraf ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Md Simulation ◽  
Energy Calculation ◽  
Antibacterial Drugs ◽  
Binding Energy Calculation

scholarly journals Molecular Docking and Molecular Dynamics (MD) Simulation of Human Anti-Complement Factor H (CFH) Antibody Ab42 and CFH Polypeptide

2019 ◽  
Vol 20 (10) ◽  
pp. 2568 ◽  
Author(s):  
Bing Yang ◽  
Shu-Jian Lin ◽  
Jia-Yi Ren ◽  
Tong Liu ◽  
Yue-Ming Wang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Monoclonal Antibody ◽  
Molecular Docking ◽  
Md Simulation ◽  
Factor H ◽  
Complement Factor H ◽  
Energy Calculation ◽  
Complement Factor ◽  
Alanine Scanning ◽  
Computational Alanine Scanning

An understanding of the interaction between the antibody and its targeted antigen and knowing of the epitopes are critical for the development of monoclonal antibody drugs. Complement factor H (CFH) is implied to play a role in tumor growth and metastasis. An autoantibody to CHF is associated with anti-tumor cell activity. The interaction of a human monoclonal antibody Ab42 that was isolated from a cancer patient with CFH polypeptide (pCFH) antigen was analyzed by molecular docking, molecular dynamics (MD) simulation, free energy calculation, and computational alanine scanning (CAS). Experimental alanine scanning (EAS) was then carried out to verify the results of the theoretical calculation. Our results demonstrated that the Ab42 antibody interacts with pCFH by hydrogen bonds through the Tyr315, Ser100, Gly33, and Tyr53 residues on the complementarity-determining regions (CDRs), respectively, with the amino acid residues of Pro441, Ile442, Asp443, Asn444, Ile447, and Thr448 on the pCFH antigen. In conclusion, this study has explored the mechanism of interaction between Ab42 antibody and its targeted antigen by both theoretical and experimental analysis. Our results have important theoretical significance for the design and development of relevant antibody drugs.

scholarly journals Molecular Docking and Molecular Dynamics (MD) Simulation of Human Anti Complement Factor H (CFH) Antibody Ab42 and CFH Polypeptide (pCFH)

2018 ◽  
Author(s):  
Bing Yang ◽  
Jiayi Ren ◽  
Tong Liu ◽  
Shujian Lin ◽  
Yueming Wang ◽  
...  
Keyword(s):  
Monoclonal Antibody ◽  
Molecular Docking ◽  
Md Simulation ◽  
Factor H ◽  
Energy Calculation ◽  
Complement Factor ◽  
Alanine Scanning ◽  
Computational Alanine Scanning ◽  
Antigen Antibody ◽  
Antibody Interactions

The details of antigen-antibody interactions and the identification of epitopes are critical for the development of monoclonal antibody drugs. Ab42 is a native human-derived anti-CFH monoclonal antibody. In this study, the interaction between antigen pCFH and antibody (Ab42) was theoretically demonstrated by molecular docking and MD simulation, combined with free energy calculation and computational alanine scanning (CAS), and key amino acids and epitopes were identified. Experimental alanine scanning (EAS) was then carried out to verify the results of the calculation, and our results indicated that Ab42 antibody forms hydrogen bonds and interacts hydrophobically with pCFH through the Tyr315, Ser100, Gly33, and Tyr53 residues on its CDR, while the main pCFH epitopes are located at the six sites of Pro441, Ile442, Asp443, Asn444, Ile447, and Thr448. In conclusion, this study has explored the mechanism of antigen-antibody interaction from both theoretical and experimental aspects, and our results have important theoretical significance for the design and development of relevant antibody drugs.

scholarly journals Exciton and Bi-exciton Binding Energy Calculation in a Core Shell Quantum Dot

2021 ◽  
Vol 1080 (1) ◽  
pp. 012012
Author(s):  
Shivani Rana ◽  
Sanjib Kabi ◽  
Kamakhya Prakash Misra ◽  
Saikat Chattopadhyay
Keyword(s):  
Binding Energy ◽  
Quantum Dot ◽  
Exciton Binding Energy ◽  
Core Shell ◽  
Energy Calculation ◽  
Binding Energy Calculation

scholarly journals Exchange Perturbation Theory for Multiatomic Electron System and Its Application to Spin Arrangement in Manganite Chains

2011 ◽  
Vol 2011 ◽  
pp. 1-11 ◽  
Author(s):  
E. V. Orlenko ◽  
T. S. Orlova ◽  
F. E. Orlenko ◽  
G. G. Zegrya
Keyword(s):  
Perturbation Theory ◽  
Binding Energy ◽  
Electron System ◽  
Total Spin ◽  
Energy Calculation ◽  
First Principle ◽  
Hamiltonian Form ◽  
Spin Arrangement ◽  
Binding Energy Calculation ◽  
Good Agreement

A new methodology of binding energy calculation with respect to different spin arrangements for a multiatomic electron system is developed from the first principle in the frame of the exchange perturbation theory (EPT). We developed EPT formalism in the general form of the Rayleigh-Srchödinger expansion with a symmetric Hamiltonian, taking into account an exchange and nonadditive contributions of a superexchange interaction. The expressions of all corrections to the energy and wave function were reduced to the nonsymmetric Hamiltonian form. The EPT method is extended for the case of degeneracy in the total spin of a system. As an example of the application of the developed EPT formalism for the degeneracy case, spin arrangements were considered for the key –O– (: Mn3+ or Mn4+) fragments in manganites. In –O– for La1/3Ca2/3MnO3 are in good agreement the obtained estimations of Heisenberg parameter and binding energy with the available experimental data.

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