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Saini S, Pareekh S, Kumar Y. Investigating the structural impact of Omicron RBD mutation on antibody escape and receptor management. J Biomol Struct Dyn 2024; 42:4668-4678. [PMID: 37334729 DOI: 10.1080/07391102.2023.2222174] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 06/01/2023] [Indexed: 06/20/2023]
Abstract
The SARS-CoV-2 Variant B.1.1.5291 evolved rapidly in late November 2021 from the existing mutants sparking fear worldwide owing to its infamous immune escape from a varied class of neutralising antibodies. To assess the structural behaviour of Omicron-Receptor Binding Domain (RBD) upon interacting with cross-reactive CR3022 antibody, we investigated the computational approach of structural engagement in B.1.1529 RBD and wild-type RBD with CR3022 antibody. The current study investigates the interacting interface between the RBDs and CR3022 to decipher the key residues accompanying the potential mutational landscape of SARS-CoV-2 variants. We conducted in-silico docking followed by molecular dynamics simulation analysis to examine the dynamic behaviour of protein-protein interactions. Furthermore, the study unleashed possible interactions post energy decomposition analysis via MM-GBSA. Conclusively, the mutational landscape of RBD eases in designing and discovering the effective neutralisation accompanied by development of a universal vaccine.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Samvedna Saini
- Department of Biological Sciences and Engineering (BSE), Netaji Subhas University of Technology (NSUT), New Delhi, India
| | - Savita Pareekh
- High Performance Computing (HPC) & AI Innovation Lab, Dell EMC, Bengaluru, India
| | - Yatender Kumar
- Department of Biological Sciences and Engineering (BSE), Netaji Subhas University of Technology (NSUT), New Delhi, India
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Saini S, Kumar Y. Structural and functional analysis of engineered antibodies for cancer immunotherapy: insights into protein compactness and solvent accessibility. J Biomol Struct Dyn 2024:1-14. [PMID: 38173178 DOI: 10.1080/07391102.2023.2300129] [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: 08/14/2023] [Accepted: 12/22/2023] [Indexed: 01/05/2024]
Abstract
Antibodies are crucial tools in various biomedical applications, including immunotherapy. In this study, we focused on designing and engineering antibodies to enhance their structural dynamics and functional properties. By employing advanced computational techniques and experimental validation, we gained crucial insights into the impact of specific mutations on the engineered antibodies. This study investigates the design and engineering of antibodies to improve their structural dynamics and functional properties. Structural attributes, such as protein compactness and solvent accessibility, were assessed, revealing interesting trends in anti-CD3 and anti-HER2 antibodies. Mutations in CD3 antibodies resulted in a more stable conformation, while mutant HER2 antibodies exhibited altered interaction with the target. Analysis of secondary structure assignments demonstrated significant changes in the folding and stability of the mutant antibodies compared to the wild-type counterparts. The conformational landscape of the engineered antibodies was explored, providing insights into folding pathways and binding mechanisms. Overall, the current study highlights the significance of antibody design and engineering in modulating structural dynamics and functional properties. The findings contribute to developing improved immunotherapeutic strategies by optimising antibody-based therapeutics for targeted diseases with enhanced efficacy and precision.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Samvedna Saini
- Department of Biological Sciences and Engineering (BSE), Netaji Subhas University of Technology (NSUT), New Delhi, India
| | - Yatender Kumar
- Department of Biological Sciences and Engineering (BSE), Netaji Subhas University of Technology (NSUT), New Delhi, India
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Ge Y, Yan H, Shi X, Wu Z, Wang Y, Zhang Z, Luo Q, Liu W, Liang L, Peng L, Hu J. Study on dietary intake, risk assessment, and molecular toxicity mechanism of benzo[α]pyrene in college students in China Bashu area. Food Sci Nutr 2022; 10:4155-4167. [PMID: 36514765 PMCID: PMC9731532 DOI: 10.1002/fsn3.3007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 07/05/2022] [Accepted: 07/14/2022] [Indexed: 12/16/2022] Open
Abstract
As an extremely strong polycyclic aromatic hydrocarbon carcinogen, benzo[α]pyrene (BaP) is often produced during food processing at high temperatures. Recently, food safety, as well as toxicity mechanism and risk assessment of BaP, has received extensive attention. We first constructed the database of BaP pollution concentration in Chinese daily food with over 104 data items; collected dietary intake data using online survey; then assessed dietary exposure risk; and finally revealed the possible toxicity mechanism through four comparative molecular dynamics (MD) simulations. The statistical results showed that the concentration of BaP in olive oil was the highest, followed by that in fried meat products. The margins of exposure and incremental lifetime cancer risk both indicated that the dietary exposure to BaP of the participants was generally safe, but there were still some people with certain carcinogenic risks. Specifically, the health risk of the core district population was higher than that of the noncore district in Bashu area, and the female postgraduate group was higher than the male group with bachelor degree or below. From MD trajectories, BaP binding does not affect the global motion of individual nucleic acid sequences, but local weak noncovalent interactions changed greatly; it also weakens molecular interactions of nucleic acid with Bacillus stearothermophilus DNA polymerase I large fragment (BF), and significantly changes the cavity structure of recognition interface. This work not only reveals the possible toxicity mechanism of BaP, but also provides theoretical guidance for the subsequent optimization of food safety standards and reference of rational diet.
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Affiliation(s)
- Yutong Ge
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of AntibioticsChengdu UniversityChengduChina
| | - Hailian Yan
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of AntibioticsChengdu UniversityChengduChina
| | - Xiaodong Shi
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of AntibioticsChengdu UniversityChengduChina
| | - Zhixiang Wu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of AntibioticsChengdu UniversityChengduChina
| | - Yueteng Wang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of AntibioticsChengdu UniversityChengduChina
| | - Zelan Zhang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of AntibioticsChengdu UniversityChengduChina
| | - Qing Luo
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of AntibioticsChengdu UniversityChengduChina
| | - Wei Liu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of AntibioticsChengdu UniversityChengduChina
| | - Li Liang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of AntibioticsChengdu UniversityChengduChina
| | - Lianxin Peng
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of AntibioticsChengdu UniversityChengduChina
| | - Jianping Hu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of AntibioticsChengdu UniversityChengduChina
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Mukherjee C, Sengupta D, Maganti L, Mahendar M, Bhattacharyya D, Sengupta K. Slower diffusion and anomalous association of R453W lamin A protein alter nuclear architecture in AD-EDMD. RSC Adv 2022; 12:32129-32141. [DOI: 10.1039/d2ra05620h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/28/2022] [Indexed: 11/11/2022] Open
Abstract
Changes in the microdynamics landscape of Ig fold R453W modulate the mobility and assembly of full length lamin A.
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Affiliation(s)
- Chandrayee Mukherjee
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, A CI of Homi Bhabha National Institute, 1/AF Bidhannagar, Kolkata, 700064, West Bengal, India
| | - Duhita Sengupta
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, A CI of Homi Bhabha National Institute, 1/AF Bidhannagar, Kolkata, 700064, West Bengal, India
| | - Lakshmi Maganti
- Computational Science Division, Saha Institute of Nuclear Physics, A CI of Homi Bhabha National Institute, 1/AF Bidhannagar, Kolkata, 700064, West Bengal, India
| | - M. Mahendar
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, A CI of Homi Bhabha National Institute, 1/AF Bidhannagar, Kolkata, 700064, West Bengal, India
| | - Dhananjay Bhattacharyya
- Computational Science Division, Saha Institute of Nuclear Physics, A CI of Homi Bhabha National Institute, 1/AF Bidhannagar, Kolkata, 700064, West Bengal, India
| | - Kaushik Sengupta
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, A CI of Homi Bhabha National Institute, 1/AF Bidhannagar, Kolkata, 700064, West Bengal, India
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Metal binding mediated conformational change of XPA protein:a potential cytotoxic mechanism of nickel in the nucleotide excision repair. J Mol Model 2016; 22:156. [PMID: 27307058 DOI: 10.1007/s00894-016-3017-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/26/2016] [Indexed: 12/13/2022]
Abstract
Nucleotide excision repair (NER) is a pivotal life process for repairing DNA nucleotide mismatch caused by chemicals, metal ions, radiation, and other factors. As the initiation step of NER, the xeroderma pigmentosum complementation group A protein (XPA) recognizes damaged DNA molecules, and recruits the replication protein A (RPA), another important player in the NER process. The stability of the Zn(2+)-chelated Zn-finger domain of XPA center core portion (i.e., XPA98-210) is the foundation of its biological functionality, while the displacement of the Zn(2+) by toxic metal ions (such as Ni(2+), a known human carcinogen and allergen) may impair the effectiveness of NER and hence elevate the chance of carcinogenesis. In this study, we first calculated the force field parameters for the bonded model in the metal center of the XPA98-210 system, showing that the calculated results, including charges, bonds, angles etc., are congruent with previously reported results measured by spectrometry experiments and quantum chemistry computation. Then, comparative molecular dynamics simulations using these parameters revealed the changes in the conformation and motion mode of XPA98-210 Zn-finger after the substitution of Zn(2+) by Ni(2+). The results showed that Ni(2+) dramatically disrupted the relative positions of the four Cys residues in the Zn-finger structure, forcing them to collapse from a tetrahedron into an almost planar structure. Finally, we acquired the binding mode of XPA98-210 with its ligands RPA70N and DNA based on molecular docking and structural alignment. We found that XPA98-210's Zn-finger domain primarily binds to a V-shaped cleft in RPA70N, while the cationic band in its C-terminal subdomain participates in the recognition of damaged DNA. In addition, this article sheds light on the multi-component interaction pattern among XPA, DNA, and other NER-related proteins (i.e., RPA70N, RPA70A, RPA70B, RPA70C, RPA32, and RPA14) based on previously reported structural biology information. Thus, we derived a putative cytotoxic mechanism associated with the nickel ion, where the Ni(2+) disrupts the conformation of the XPA Zn-finger, directly weakening its interaction with RPA70N, and thus lowering the effectiveness of the NER process. In sum, this work not only provides a theoretical insight into the multi-protein interactions involved in the NER process and potential cytotoxic mechanism associated with Ni(2+) binding in XPA, but may also facilitate rational anti-cancer drug design based on the NER mechanism.
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Computational design of a full-length model of HIV-1 integrase: modeling of new inhibitors and comparison of their calculated binding energies with those previously studied. J Mol Model 2013; 19:4349-68. [PMID: 23907552 DOI: 10.1007/s00894-013-1943-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Accepted: 07/11/2013] [Indexed: 12/28/2022]
Abstract
A full-length model of integrase (IN) of the human immunodeficiency virus type 1 (HIV-1) was constructed based on the distinctly resolved X-ray crystal structures of its three domains, named N-terminal, catalytic core and C-terminal. Thirty-one already known inhibitors with varieties of structural differences as well as nine newly tested ones were docked into the catalytic core. The molecular dynamic (MD) and binding properties of these complexes were obtained by MD calculations. The binding energies calculated by molecular mechanic/Poisson Boltzmann solvation area were significantly correlationed with available IC50. Four inhibitors including two newly designed were also docked into the full-length model and their MD behaviors and binding properties were calculated. It was found that one of the newly designed compounds forms a better complex with HIV-1 IN compared to the rest including raltegravir. MD calculations were performed with AMBER suite of programs using ff99SB force field for the proteins and the general Amber force field for the ligands. In conclusion, the results have produced a promising standpoint not only in the construction of the full-length model but also in development of new drugs against it. However, the role of multimer formation and the involvement of DNAs, and their subsequent effect on the complexation and inhibition, are required to arrive at a conclusive decision.
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Hu J, Liu M, Tang D, Chang S. Substrate recognition and motion mode analyses of PFV integrase in complex with viral DNA via coarse-grained models. PLoS One 2013; 8:e54929. [PMID: 23365687 PMCID: PMC3554684 DOI: 10.1371/journal.pone.0054929] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 12/19/2012] [Indexed: 11/19/2022] Open
Abstract
HIV-1 integrase (IN) is an important target in the development of drugs against the AIDS virus. Drug design based on the structure of IN was markedly hampered due to the lack of three-dimensional structure information of HIV-1 IN-viral DNA complex. The prototype foamy virus (PFV) IN has a highly functional and structural homology with HIV-1 IN. Recently, the X-ray crystal complex structure of PFV IN with its cognate viral DNA has been obtained. In this study, both Gaussian network model (GNM) and anisotropy network model (ANM) have been applied to comparatively investigate the motion modes of PFV DNA-free and DNA-bound IN. The results show that the motion mode of PFV IN has only a slight change after binding with DNA. The motion of this enzyme is in favor of association with DNA, and the binding ability is determined by its intrinsic structural topology. Molecular docking experiments were performed to gain the binding modes of a series of diketo acid (DKA) inhibitors with PFV IN obtained from ANM, from which the dependability of PFV IN-DNA used in the drug screen for strand transfer (ST) inhibitors was confirmed. It is also found that the functional groups of keto-enol, bis-diketo, tetrazole and azido play a key role in aiding the recognition of viral DNA, and thus finally increase the inhibition capability for the corresponding DKA inhibitor. Our study provides some theoretical information and helps to design anti-AIDS drug based on the structure of IN.
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Affiliation(s)
- Jianping Hu
- Department of Chemistry and Life Science, Leshan Normal University, Leshan, China
| | - Ming Liu
- Beijing Institute of Biotechnology, Beijing, China
| | - Dianyong Tang
- Department of Chemistry and Life Science, Leshan Normal University, Leshan, China
| | - Shan Chang
- College of Informatics, South China Agricultural University, Guangzhou, China
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Wan H, Hu JP, Tian XH, Chang S. Molecular dynamics simulations of wild type and mutants of human complement receptor 2 complexed with C3d. Phys Chem Chem Phys 2013; 15:1241-51. [DOI: 10.1039/c2cp41388d] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Wang M, Yang J, Wang J, Wang X. Structural Effects of L16Q, S20G, and L16Q-S20G Mutations on hIAPP: A Comparative Molecular Dynamics Study. CHINESE J CHEM 2012. [DOI: 10.1002/cjoc.201100413] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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HU JP, LIU W, TANG DY, ZHANG YQ, CHANG S. Study on The Binding Mode and Mobility of HIV-1 Integrase With L708, 906 Inhibitor*. PROG BIOCHEM BIOPHYS 2011. [DOI: 10.3724/sp.j.1206.2010.00438] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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