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Chen Z, Chen J, Zhang G, Xiao X, Liu D, Lai W, Peng J. Dual-assist heterologous antigens screening: An effective strategy to improve the sensitivity of lateral flow immunoassay. Food Chem 2024; 463:141131. [PMID: 39276540 DOI: 10.1016/j.foodchem.2024.141131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Revised: 08/26/2024] [Accepted: 09/02/2024] [Indexed: 09/17/2024]
Abstract
Heterologous strategy has promising applications in improving the sensitivity of competitive immunoassay. In this study, the potential heterologous coating antigens (HEA) were screened from eight imidacloprid (IMI) structural analogs based on the cross-reactivity (CR) of a prepared antibody. Computer-aided molecular modeling was used to predict the optimal HEA. Compared with the homologous coating antigen (HOA), the predicted HEA prepared from acetamiprid (CR = 0.23 %) increased the detection sensitivity of the enzyme-linked immunoassay and colloidal gold nanoparticle-based lateral flow immunoassay (HOA-Au-LFIA) by 5.6 and 4.1 times, respectively. Subsequently, the HEA and aggregation-induced emission fluorescent labels were integrated into a lateral flow immunoassay platform (HEA-AIE-LFIA). The limit of detection was 0.12 ng mL-1 for HEA-AIE-LFIA, which was 7.7-fold lower than that of HOA-Au-LFIA. Furthermore, HEA-AIE-LFIA was applied to detect IMI in food samples with excellent recoveries (86.41 %-111.25 %). Overall, this strategy of screening for superior HEA has great potential for improving LFIA sensitivity.
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Affiliation(s)
- Zhenzhen Chen
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China
| | - Jiawei Chen
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China
| | - Gan Zhang
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China
| | - Xiaoyue Xiao
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China
| | - Daofeng Liu
- Jiangxi Provincial Center for Disease Control and Prevention, Nanchang, 330029, China
| | - Weihua Lai
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China
| | - Juan Peng
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China.
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2
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Kousaka S, Ishikawa T. Quantum Chemistry-Based Protein-Protein Docking without Empirical Parameters. J Chem Theory Comput 2024; 20:5164-5175. [PMID: 38845143 DOI: 10.1021/acs.jctc.4c00531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
This study developed a novel protein-protein docking approach based on quantum chemistry. To judge the appropriateness of complex structures, we introduced two criterion values, EV1 and EV2, computed using the fragment molecular orbital method without any empirical parameters. These criterion values enable us to search complex structures in which patterns of the electrostatic potential of the two proteins are optimally aligned at their interface. The performance of our method was validated using 53 complexes in a benchmark set provided for protein-protein docking. When employing bound state structures, docking success rates reached 64% for EV1 and 76% for EV2. On the other hand, when employing unbound state structures, docking success rates reached 13% for EV1 and 17% for EV2.
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Affiliation(s)
- Sumire Kousaka
- Department of Chemistry, Biotechnology, and Chemical Engineering, Graduate School of Science and Engineering, Kagoshima University, 1-21-40 Korimoto, Kagoshima 890-0065, Japan
| | - Takeshi Ishikawa
- Department of Chemistry, Biotechnology, and Chemical Engineering, Graduate School of Science and Engineering, Kagoshima University, 1-21-40 Korimoto, Kagoshima 890-0065, Japan
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3
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Hristova SH, Zhivkov AM. Three-Dimensional Structural Stability and Local Electrostatic Potential at Point Mutations in Spike Protein of SARS-CoV-2 Coronavirus. Int J Mol Sci 2024; 25:2174. [PMID: 38396850 PMCID: PMC10889838 DOI: 10.3390/ijms25042174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
The contagiousness of SARS-CoV-2 β-coronavirus is determined by the virus-receptor electrostatic association of its positively charged spike (S) protein with the negatively charged angiotensin converting enzyme-2 (ACE2 receptor) of the epithelial cells. If some mutations occur, the electrostatic potential on the surface of the receptor-binding domain (RBD) could be altered, and the S-ACE2 association could become stronger or weaker. The aim of the current research is to investigate whether point mutations can noticeably alter the electrostatic potential on the RBD and the 3D stability of the S1-subunit of the S-protein. For this purpose, 15 mutants with different hydrophilicity and electric charge (positive, negative, or uncharged) of the substituted and substituting amino acid residues, located on the RBD at the S1-ACE2 interface, are selected, and the 3D structure of the S1-subunit is reconstructed on the base of the crystallographic structure of the S-protein of the wild-type strain and the amino acid sequence of the unfolded polypeptide chain of the mutants. Then, the Gibbs free energy of folding, isoelectric point, and pH-dependent surface electrostatic potential of the S1-subunit are computed using programs for protein electrostatics. The results show alterations in the local electrostatic potential in the vicinity of the mutant amino acid residue, which can influence the S-ACE2 association. This approach allows prediction of the relative infectivity, transmissibility, and contagiousness (at equal social immune status) of new SARS-CoV-2 mutants by reconstruction of the 3D structure of the S1-subunit and calculation of the surface electrostatic potential.
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Affiliation(s)
- Svetlana H. Hristova
- Department of Medical Physics and Biophysics, Medical Faculty, Medical University—Sofia, Zdrave Street 2, 1431 Sofia, Bulgaria;
| | - Alexandar M. Zhivkov
- Scientific Research Center, “St. Kliment Ohridski” Sofia University, 8 Dragan Tsankov Blvd., 1164 Sofia, Bulgaria
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4
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Yuan Z, Chen X, Fan S, Chang L, Chu L, Zhang Y, Wang J, Li S, Xie J, Hu J, Miao R, Zhu L, Zhao Z, Li H, Li S. Binding Free Energy Calculation Based on the Fragment Molecular Orbital Method and Its Application in Designing Novel SHP-2 Allosteric Inhibitors. Int J Mol Sci 2024; 25:671. [PMID: 38203841 PMCID: PMC10779950 DOI: 10.3390/ijms25010671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
The accurate prediction of binding free energy is a major challenge in structure-based drug design. Quantum mechanics (QM)-based approaches show promising potential in predicting ligand-protein binding affinity by accurately describing the behavior and structure of electrons. However, traditional QM calculations face computational limitations, hindering their practical application in drug design. Nevertheless, the fragment molecular orbital (FMO) method has gained widespread application in drug design due to its ability to reduce computational costs and achieve efficient ab initio QM calculations. Although the FMO method has demonstrated its reliability in calculating the gas phase potential energy, the binding of proteins and ligands also involves other contributing energy terms, such as solvent effects, the 'deformation energy' of a ligand's bioactive conformations, and entropy. Particularly in cases involving ionized fragments, the calculation of solvation free energy becomes particularly crucial. We conducted an evaluation of some previously reported implicit solvent methods on the same data set to assess their potential for improving the performance of the FMO method. Herein, we develop a new QM-based binding free energy calculation method called FMOScore, which enhances the performance of the FMO method. The FMOScore method incorporates linear fitting of various terms, including gas-phase potential energy, deformation energy, and solvation free energy. Compared to other widely used traditional prediction methods such as FEP+, MM/PBSA, MM/GBSA, and Autodock vina, FMOScore showed good performance in prediction accuracies. By constructing a retrospective case study, it was observed that incorporating calculations for solvation free energy and deformation energy can further enhance the precision of FMO predictions for binding affinity. Furthermore, using FMOScore-guided lead optimization against Src homology-2-containing protein tyrosine phosphatase 2 (SHP-2), we discovered a novel and potent allosteric SHP-2 inhibitor (compound 8).
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Affiliation(s)
- Zhen Yuan
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China; (Z.Y.); (X.C.); (S.F.); (Z.Z.)
| | - Xingyu Chen
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China; (Z.Y.); (X.C.); (S.F.); (Z.Z.)
| | - Sisi Fan
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China; (Z.Y.); (X.C.); (S.F.); (Z.Z.)
| | - Longfeng Chang
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China; (Z.Y.); (X.C.); (S.F.); (Z.Z.)
| | - Linna Chu
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China; (Z.Y.); (X.C.); (S.F.); (Z.Z.)
| | - Ying Zhang
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China; (Z.Y.); (X.C.); (S.F.); (Z.Z.)
| | - Jie Wang
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China; (Z.Y.); (X.C.); (S.F.); (Z.Z.)
| | - Shuang Li
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China; (Z.Y.); (X.C.); (S.F.); (Z.Z.)
| | - Jinxin Xie
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China; (Z.Y.); (X.C.); (S.F.); (Z.Z.)
| | - Jianguo Hu
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China; (Z.Y.); (X.C.); (S.F.); (Z.Z.)
| | - Runyu Miao
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China; (Z.Y.); (X.C.); (S.F.); (Z.Z.)
| | - Lili Zhu
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China; (Z.Y.); (X.C.); (S.F.); (Z.Z.)
| | - Zhenjiang Zhao
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China; (Z.Y.); (X.C.); (S.F.); (Z.Z.)
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China; (Z.Y.); (X.C.); (S.F.); (Z.Z.)
- Innovation Center for AI and Drug Discovery, East China Normal University, Shanghai 200062, China
- Lingang Laboratory, Shanghai 200031, China
| | - Shiliang Li
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai 200237, China; (Z.Y.); (X.C.); (S.F.); (Z.Z.)
- Innovation Center for AI and Drug Discovery, East China Normal University, Shanghai 200062, China
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5
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Shen H, Yang H. Binding of synthetic nanobodies to the SARS-CoV-2 receptor-binding domain: the importance of salt bridges. Phys Chem Chem Phys 2023; 25:24129-24142. [PMID: 37655617 DOI: 10.1039/d3cp02628k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
In this study, five different SARS-CoV-2 receptor-binding domain (RBD) models were created based on the crystal structures of RBD complexes with two synthetic nanobodies (Sb16 and Sb45). Microsecond all-atom MD simulations revealed that Sb16 and Sb45 substantially stabilized the flexible RBD loop (residues GLU471-SER494) due to the salt bridges and hydrogen bonding interactions between RBD and the synthetic nanobodies. However, the calculation of binding free energy displayed that Sb45 had a higher binding affinity to RBD than Sb16, in agreement with the experimental result. This is because Sb45 has stronger electrostatic attraction to RBD as compared to Sb16. In particular, the salt bridge GLU484-ARG33 in Sb45-RBD is stronger than the GLU484-LYS32 in Sb16-RBD. Furthermore, by comparing the binding affinity of Sb16 for two RBD mutants (E484K and K417N), we found that E484K mutation substantially reduced the binding affinity to Sb16, and K417N mutation had no significant effect, qualitatively in agreement with experimental studies. According to the binding free energy calculation, the strong electrostatic repulsion between LYS32 and LYS484 caused by E484K mutation destroys the salt bridge between LYS32 and GLU484 in the RBD wild type (WT). In contrast, the binding of the K417N mutant to Sb16 effectively maintains the salt bridge between LYS32 and GLU484. Therefore, our research suggests that the salt bridges between RBD and synthetic nanobodies are crucial for binding synthetic nanobodies to RBD, and a SARS-CoV-2 variant can escape neutralization from nanobodies by creating electrostatic repulsion between them.
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Affiliation(s)
- Hujun Shen
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Education University, Guiyang, 550018, China.
| | - Hengxiu Yang
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Education University, Guiyang, 550018, China.
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6
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Hristova SH, Zhivkov AM. Omicron Coronavirus: pH-Dependent Electrostatic Potential and Energy of Association of Spike Protein to ACE2 Receptor. Viruses 2023; 15:1752. [PMID: 37632094 PMCID: PMC10460073 DOI: 10.3390/v15081752] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
The association of the S-protein of the SARS-CoV-2 beta coronavirus to ACE2 receptors of the human epithelial cells determines its contagiousness and pathogenicity. We computed the pH-dependent electric potential on the surface of the interacting globular proteins and pH-dependent Gibbs free energy at the association of the wild-type strain and the omicron variant. The calculated isoelectric points of the ACE2 receptor (pI 5.4) and the S-protein in trimeric form (pI 7.3, wild type), (pI 7.8, omicron variant), experimentally verified by isoelectric focusing, show that at pH 6-7, the S1-ACE2 association is conditioned by electrostatic attraction of the oppositely charged receptor and viral protein. The comparison of the local electrostatic potentials of the omicron variant and the wild-type strain shows that the point mutations alter the electrostatic potential in a relatively small area on the surface of the receptor-binding domain (RBD) of the S1 subunit. The appearance of seven charge-changing point mutations in RBD (equivalent to three additional positive charges) leads to a stronger S1-ACE2 association at pH 5.5 (typical for the respiratory tract) and a weaker one at pH 7.4 (characteristic of the blood plasma); this reveals the reason for the higher contagiousness but lower pathogenicity of the omicron variant in comparison to the wild-type strain.
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Affiliation(s)
- Svetlana H. Hristova
- Department of Medical Physics and Biophysics, Medical Faculty, Medical University—Sofia, Zdrave Str. 2, 1431 Sofia, Bulgaria;
| | - Alexandar M. Zhivkov
- Institute of Physical Chemistry, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., bl. 11, 1113 Sofia, Bulgaria
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7
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Giron CC, Laaksonen A, Barroso da Silva FL. Differences between Omicron SARS-CoV-2 RBD and other variants in their ability to interact with cell receptors and monoclonal antibodies. J Biomol Struct Dyn 2023; 41:5707-5727. [PMID: 35815535 DOI: 10.1080/07391102.2022.2095305] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/23/2022] [Indexed: 12/23/2022]
Abstract
SARS-CoV-2 remains a health threat with the continuous emergence of new variants. This work aims to expand the knowledge about the SARS-CoV-2 receptor-binding domain (RBD) interactions with cell receptors and monoclonal antibodies (mAbs). By using constant-pH Monte Carlo simulations, the free energy of interactions between the RBD from different variants and several partners (Angiotensin-Converting Enzyme-2 (ACE2) polymorphisms and various mAbs) were predicted. Computed RBD-ACE2-binding affinities were higher for two ACE2 polymorphisms (rs142984500 and rs4646116) typically found in Europeans which indicates a genetic susceptibility. This is amplified for Omicron (BA.1) and its sublineages BA.2 and BA.3. The antibody landscape was computationally investigated with the largest set of mAbs so far in the literature. From the 32 studied binders, groups of mAbs were identified from weak to strong binding affinities (e.g. S2K146). These mAbs with strong binding capacity and especially their combination are amenable to experimentation and clinical trials because of their high predicted binding affinities and possible neutralization potential for current known virus mutations and a universal coronavirus.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Carolina Corrêa Giron
- Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
- Universidade Federal do Triângulo Mineiro, Hospital de Clínicas, Uberaba, MG, Brazil
| | - Aatto Laaksonen
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
- State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, Nanjing, PR China
- Centre of Advanced Research in Bionanoconjugates and Biopolymers, Petru Poni Institute of Macromolecular Chemistry, Iasi, Romania
- Department of Engineering Sciences and Mathematics, Division of Energy Science, Luleå University of Technology, Luleå, Sweden
- Department of Chemical and Geological Sciences, University of Cagliari, Monserrato, Italy
| | - Fernando Luís Barroso da Silva
- Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
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8
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Nakata H, Fedorov DG. Analytic Gradient for Time-Dependent Density Functional Theory Combined with the Fragment Molecular Orbital Method. J Chem Theory Comput 2023; 19:1276-1285. [PMID: 36753486 DOI: 10.1021/acs.jctc.2c01177] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The analytic energy gradient of energy with respect to nuclear coordinates is derived for the fragment molecular orbital (FMO) method combined with time-dependent density functional theory (TDDFT). The response terms arising from the use of a polarizable embedding are derived. The obtained analytic FMO-TDDFT gradient is shown to be accurate in comparison to both numerical FMO-TDDFT and unfragmented TDDFT gradients, at the level of two- and three-body expansions. The gradients are used for geometry optimizations, molecular dynamics, vibrational calculations, and simulations of IR and Raman spectra of excited states. The developed method is used to optimize the geometry of the ground and excited electronic states of the photoactive yellow protein (PDB: 2PHY).
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Affiliation(s)
- Hiroya Nakata
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | - Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, Umezono 1-1-1, Tsukuba 305-8568, Japan
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9
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Ciccozzi M, Pascarella S. Two sides of the same coin: the N-terminal and the receptor binding domains of SARS-CoV-2 Spike. Future Virol 2023:10.2217/fvl-2022-0181. [PMID: 36896145 PMCID: PMC9987531 DOI: 10.2217/fvl-2022-0181] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 01/31/2023] [Indexed: 03/08/2023]
Abstract
The SARS-CoV-2 Spike receptor binding domain and N-terminal domain interact with each other in an intricate mechanism. Mutations modulate the interplay between the Spike and host molecules. This editorial comments on the intricacies of SARS-CoV-2 Spike interactions.
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Affiliation(s)
- Massimo Ciccozzi
- Medical Statistic & Molecular Epidemiology Unit, University of Biomedical Campus, Rome, Italy
| | - Stefano Pascarella
- Department of Biochemical Sciences 'A Rossi Fanelli', Sapienza Università di Roma, Rome, 00185, Italy
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10
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Ozono H, Mimoto K, Ishikawa T. Quantification and Neutralization of the Interfacial Electrostatic Potential and Visualization of the Dispersion Interaction in Visualization of the Interfacial Electrostatic Complementarity. J Phys Chem B 2022; 126:8415-8426. [PMID: 36257821 DOI: 10.1021/acs.jpcb.2c05033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Visualization of the interfacial electrostatic complementarity (VIINEC) is a quantum chemistry-based method to examine protein-protein interactions (PPI). In VIINEC, the electrostatic complementarity between proteins at the interface is visually and quantitatively evaluated using the partial electrostatic potential (pESP), which is defined based on the fragment molecular orbital method. In this work, new quantification and neutralization methods of the pESP were proposed together with a method to visualize the dispersion interaction. The reliability and efficiency of these methods were evaluated using 17 models of the complex. It was found that the quantification of the electrostatic complementarity with the pESP using the new neutralization method has a high correlation with the interaction energy, supporting the reliability of VIINEC. As an illustrative example, the PPI between a major histocompatibility complex class I molecule and a T-cell receptor was examined, which demonstrated the value of VIINEC in chemical and biological research.
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Affiliation(s)
- Hiroki Ozono
- Department of Chemistry, Biotechnology, and Chemical Engineering, Graduate School of Science and Engineering, Kagoshima University, 1-21-40 Korimoto, Kagoshima, Kagoshima890-0065, Japan
| | - Kento Mimoto
- Department of Chemistry, Biotechnology, and Chemical Engineering, Graduate School of Science and Engineering, Kagoshima University, 1-21-40 Korimoto, Kagoshima, Kagoshima890-0065, Japan
| | - Takeshi Ishikawa
- Department of Chemistry, Biotechnology, and Chemical Engineering, Graduate School of Science and Engineering, Kagoshima University, 1-21-40 Korimoto, Kagoshima, Kagoshima890-0065, Japan
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11
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Barroso da Silva FL, Giron CC, Laaksonen A. Electrostatic Features for the Receptor Binding Domain of SARS-COV-2 Wildtype and Its Variants. Compass to the Severity of the Future Variants with the Charge-Rule. J Phys Chem B 2022; 126:6835-6852. [PMID: 36066414 DOI: 10.1021/acs.jpcb.2c04225] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Electrostatic intermolecular interactions are important in many aspects of biology. We have studied the main electrostatic features involved in the interaction of the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein with the human receptor Angiotensin-converting enzyme 2 (ACE2). As the principal computational tool, we have used the FORTE approach, capable to model proton fluctuations and computing free energies for a very large number of protein-protein systems under different physical-chemical conditions, here focusing on the RBD-ACE2 interactions. Both the wild-type and all critical variants are included in this study. From our large ensemble of extensive simulations, we obtain, as a function of pH, the binding affinities, charges of the proteins, their charge regulation capacities, and their dipole moments. In addition, we have calculated the pKas for all ionizable residues and mapped the electrostatic coupling between them. We are able to present a simple predictor for the RBD-ACE2 binding based on the data obtained for Alpha, Beta, Gamma, Delta, and Omicron variants, as a linear correlation between the total charge of the RBD and the corresponding binding affinity. This "RBD charge rule" should work as a quick test of the degree of severity of the coming SARS-CoV-2 variants in the future.
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Affiliation(s)
- Fernando L Barroso da Silva
- Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. café, s/no-campus da USP, BR-14040-903 Ribeirão Preto, SP, Brazil.,Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Carolina Corrêa Giron
- Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. café, s/no-campus da USP, BR-14040-903 Ribeirão Preto, SP, Brazil.,Hospital de Clínicas, Universidade Federal do Triângulo Mineiro, Av. Getúlio Guaritá, 38025-440 Uberaba, MG, Brazil
| | - Aatto Laaksonen
- Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden.,State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, Nanjing, 210009, P. R. China.,Centre of Advanced Research in Bionanoconjugates and Biopolymers, Petru Poni Institute of Macromolecular Chemistry, Aleea Grigore Ghica-Voda, 41A, 700487 Iasi, Romania.,Department of Engineering Sciences and Mathematics, Division of Energy Science, Luleå University of Technology, SE-97187 Luleå, Sweden.,Department of Chemical and Geological Sciences, Campus Monserrato, University of Cagliari, SS 554 bivio per Sestu, 09042 Monserrato, Italy
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12
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Lima Neto JX, Vieira DS, de Andrade J, Fulco UL. Exploring the Spike-hACE 2 Residue-Residue Interaction in Human Coronaviruses SARS-CoV-2, SARS-CoV, and HCoV-NL63. J Chem Inf Model 2022; 62:2857-2868. [PMID: 35617018 PMCID: PMC9159508 DOI: 10.1021/acs.jcim.1c01544] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Indexed: 12/20/2022]
Abstract
Coronaviruses (CoVs) have been responsible for three major outbreaks since the beginning of the 21st century, and the emergence of the recent COVID-19 pandemic has resulted in considerable efforts to design new therapies against coronaviruses. Thus, it is crucial to understand the structural features of their major proteins related to the virus-host interaction. Several studies have shown that from the seven known CoV human pathogens, three of them use the human Angiotensin-Converting Enzyme 2 (hACE-2) to mediate their host's cell entry: SARS-CoV-2, SARS-CoV, and HCoV-NL63. Therefore, we employed quantum biochemistry techniques within the density function theory (DFT) framework and the molecular fragmentation with conjugate caps (MFCC) approach to analyze the interactions between the hACE-2 and the spike protein-RBD of the three CoVs in order to map the hot-spot residues that form the recognition surface for these complexes and define the similarities and differences in the interaction scenario. The total interaction energy evaluated showed a good agreement with the experimental binding affinity order: SARS-2 > SARS > NL63. A detailed investigation revealed the energetically most relevant regions of hACE-2 and the spike protein for each complex, as well as the key residue-residue interactions. Our results provide valuable information to deeply understand the structural behavior and binding site characteristics that could help to develop antiviral therapeutics that inhibit protein-protein interactions between CoVs S protein and hACE-2.
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Affiliation(s)
- José X. Lima Neto
- Departamento de Biofísica e Farmacologia,
Universidade Federal do Rio Grande do Norte, 59072-970
Natal-RN, Brazil
| | - Davi S. Vieira
- Instituto de Química, Universidade
Federal do Rio Grande do Norte, 59072-970 Natal-RN,
Brazil
| | - Jones de Andrade
- Department of Physical Chemistry,
Universidade Federal do Rio Grande do Sul, 91501-970 Porto
Alegre-RS, Brazil
| | - Umberto Laino Fulco
- Departamento de Biofísica e Farmacologia,
Universidade Federal do Rio Grande do Norte, 59072-970
Natal-RN, Brazil
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Santo KP, Neimark AV. Adsorption of Pulmonary and Exogeneous Surfactants on SARS-CoV-2 Spike Protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.05.04.490631. [PMID: 35547841 PMCID: PMC9094101 DOI: 10.1101/2022.05.04.490631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
COVID-19 is transmitted by inhaling SARS-CoV-2 virions, which are enveloped by a lipid bilayer decorated by a "crown" of Spike protein protrusions. In the respiratory tract, virions interact with surfactant films composed of phospholipids and cholesterol that coat lung airways. Here, we explore by using coarse-grained molecular dynamics simulations the physico-chemical mechanisms of surfactant adsorption on Spike proteins. With examples of zwitterionic dipalmitoyl phosphatidyl choline, cholesterol, and anionic sodium dodecyl sulphate, we show that surfactants form micellar aggregates that selectively adhere to the specific regions of S1 domain of the Spike protein that are responsible for binding with ACE2 receptors and virus transmission into the cells. We find high cholesterol adsorption and preferential affinity of anionic surfactants to Arginine and Lysine residues within S1 receptor binding motif. These findings have important implications for informing the search for extraneous therapeutic surfactants for curing and preventing COVID-19 by SARS-CoV-2 and its variants.
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