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Yang Z, Fu X, Zhao Y, Li X, Long J, Zhang L. Molecular insights into the inhibition mechanism of harringtonine against essential proteins associated with SARS-CoV-2 entry. Int J Biol Macromol 2023; 240:124352. [PMID: 37054859 PMCID: PMC10085973 DOI: 10.1016/j.ijbiomac.2023.124352] [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: 02/06/2023] [Revised: 03/11/2023] [Accepted: 04/03/2023] [Indexed: 04/15/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has recently posed a serious threat to global public health. Harringtonine (HT), as a small-molecule antagonist, has antiviral activity against a variety of viruses. There is evidence that HT can inhibit the SARS-CoV-2 entry into host cells by blocking the Spike protein and transmembrane protease serine 2 (TMPRSS2). However, the molecular mechanism underlying the inhibition effect of HT is largely elusive. Here, docking and all-atom molecular dynamic simulations were used to investigate the mechanism of HT against the receptor binding domain (RBD) of Spike, TMPRSS2, as well as the complex of RBD and angiotensin-converting enzyme 2 complex (RBD-ACE2). The results reveal that HT binds to all proteins primarily through hydrogen bond and hydrophobic interactions. Binding with HT influences the structural stability and dynamic motility processes of each protein. The interactions of HT with residues N33, H34 and K353 of ACE2, and residue K417 and Y453 of RBD contribute to disrupting the binding affinity between RBD and ACE2, which may hinder the virus entry into host cells. Our research provides molecular insights into the inhibition mechanism of HT against SARS-CoV-2 associated proteins, which will help for the novel antiviral drugs development.
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Affiliation(s)
- Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China; School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China.
| | - Xinyue Fu
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Yizhen Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Xuhua Li
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China.
| | - Jiangang Long
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
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Yu W, Zhong N, Li X, Ren J, Wang Y, Li C, Yao G, Zhu R, Wang X, Jia Z, Wu C, Chen R, Zheng W, Liao H, Wu X, Yuan X. Structure Based Affinity Maturation and Characterizing of SARS-CoV Antibody CR3022 against SARS-CoV-2 by Computational and Experimental Approaches. Viruses 2022; 14:v14020186. [PMID: 35215781 PMCID: PMC8875849 DOI: 10.3390/v14020186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/11/2022] [Accepted: 01/17/2022] [Indexed: 12/25/2022] Open
Abstract
The COVID-19 epidemic is raging around the world. Neutralizing antibodies are powerful tools for the prevention and treatment of SARS-CoV-2 infection. Antibody CR3022, a SARS-CoV neutralizing antibody, was found to cross-react with SARS-CoV-2, but its affinity was lower than that of its binding with SARS-CoV, which greatly limited the further development of CR3022 against SARS-CoV-2. Therefore, it is necessary to improve its affinity to SARS-CoV-2 in vitro. In this study, the structure-based molecular simulations were utilized to virtually mutate the possible key residues in the complementarity-determining regions (CDRs) of the CR3022 antibody. According to the criteria of mutation energy, the mutation sites that have the potential to impact the antibody affinity were then selected. Then optimized CR3022 mutants with the enhanced affinity were further identified and verified by enzyme-linked immunosorbent assay (ELISA), surface plasma resonance (SPR) and autoimmune reactivity experiments. Finally, molecular dynamics (MD) simulation and binding free energy calculation (MM/PBSA) were performed on the wild-type CR3022 and its two double-site mutants to understand in more detail the contribution of these sites to the higher affinity. It was found that the binding affinity of the CR3022 antibody could be significantly enhanced more than ten times after the introduction of the S103F/Y mutation in HCDR–3 and the S33R mutation in LCDR–1. The additional hydrogen-bonding, hydrophobic interactions, as well as salt-bridges formed between the modified double-site mutated antibody and SARS-CoV-2 RBD were identified. The computational and experimental results clearly demonstrated that the affinity of the modified antibody has been greatly enhanced. This study indicates that CR3022 as a neutralizing antibody recognizing the conserved region of RBD against SARS-CoV with cross-reactivity with SARS-CoV-2, a different member in a large family of coronaviruses, could be improved by the computational and experimental approaches which provided insights for developing antibody drugs against SARS-CoV-2.
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Affiliation(s)
- Wei Yu
- Institute of Biomedicine, Jinan University, Guangzhou 510632, China; (W.Y.); (N.Z.); (X.L.); (J.R.); (Y.W.); (C.L.)
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, Huaibei 235000, China; (G.Y.); (R.Z.)
| | - Nan Zhong
- Institute of Biomedicine, Jinan University, Guangzhou 510632, China; (W.Y.); (N.Z.); (X.L.); (J.R.); (Y.W.); (C.L.)
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou 510632, China
| | - Xin Li
- Institute of Biomedicine, Jinan University, Guangzhou 510632, China; (W.Y.); (N.Z.); (X.L.); (J.R.); (Y.W.); (C.L.)
- National Engineering Research Center of Genetic Medicine, Guangzhou 510632, China
| | - Jiayi Ren
- Institute of Biomedicine, Jinan University, Guangzhou 510632, China; (W.Y.); (N.Z.); (X.L.); (J.R.); (Y.W.); (C.L.)
- School of Health, Zhuhai College of Science and Technology, Zhuhai 519041, China
| | - Yueming Wang
- Institute of Biomedicine, Jinan University, Guangzhou 510632, China; (W.Y.); (N.Z.); (X.L.); (J.R.); (Y.W.); (C.L.)
- Zhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, China; (X.W.); (Z.J.); (C.W.); (R.C.); (W.Z.)
| | - Chengming Li
- Institute of Biomedicine, Jinan University, Guangzhou 510632, China; (W.Y.); (N.Z.); (X.L.); (J.R.); (Y.W.); (C.L.)
- Zhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, China; (X.W.); (Z.J.); (C.W.); (R.C.); (W.Z.)
| | - Gui Yao
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, Huaibei 235000, China; (G.Y.); (R.Z.)
| | - Rui Zhu
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, Huaibei 235000, China; (G.Y.); (R.Z.)
| | - Xiaoli Wang
- Zhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, China; (X.W.); (Z.J.); (C.W.); (R.C.); (W.Z.)
| | - Zhenxing Jia
- Zhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, China; (X.W.); (Z.J.); (C.W.); (R.C.); (W.Z.)
| | - Changwen Wu
- Zhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, China; (X.W.); (Z.J.); (C.W.); (R.C.); (W.Z.)
| | - Rongfeng Chen
- Zhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, China; (X.W.); (Z.J.); (C.W.); (R.C.); (W.Z.)
| | - Weihong Zheng
- Zhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, China; (X.W.); (Z.J.); (C.W.); (R.C.); (W.Z.)
| | - Huaxin Liao
- Institute of Biomedicine, Jinan University, Guangzhou 510632, China; (W.Y.); (N.Z.); (X.L.); (J.R.); (Y.W.); (C.L.)
- Zhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, China; (X.W.); (Z.J.); (C.W.); (R.C.); (W.Z.)
- Correspondence: (H.L.); (X.W.); (X.Y.); Tel.: +86-756-726-3999 (X.Y.)
| | - Xiaomin Wu
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, Huaibei 235000, China; (G.Y.); (R.Z.)
- Correspondence: (H.L.); (X.W.); (X.Y.); Tel.: +86-756-726-3999 (X.Y.)
| | - Xiaohui Yuan
- Institute of Biomedicine, Jinan University, Guangzhou 510632, China; (W.Y.); (N.Z.); (X.L.); (J.R.); (Y.W.); (C.L.)
- Zhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, China; (X.W.); (Z.J.); (C.W.); (R.C.); (W.Z.)
- Correspondence: (H.L.); (X.W.); (X.Y.); Tel.: +86-756-726-3999 (X.Y.)
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Yu W, Wu X, Zhao Y, Chen C, Yang Z, Zhang X, Ren J, Wang Y, Wu C, Li C, Chen R, Wang X, Zheng W, Liao H, Yuan X. Computational Simulation of HIV Protease Inhibitors to the Main Protease (Mpro) of SARS-CoV-2: Implications for COVID-19 Drugs Design. Molecules 2021; 26:7385. [PMID: 34885967 PMCID: PMC8659229 DOI: 10.3390/molecules26237385] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/03/2021] [Indexed: 12/23/2022] Open
Abstract
SARS-CoV-2 is highly homologous to SARS-CoV. To date, the main protease (Mpro) of SARS-CoV-2 is regarded as an important drug target for the treatment of Coronavirus Disease 2019 (COVID-19). Some experiments confirmed that several HIV protease inhibitors present the inhibitory effects on the replication of SARS-CoV-2 by inhibiting Mpro. However, the mechanism of action has still not been studied very clearly. In this work, the interaction mechanism of four HIV protease inhibitors Darunavir (DRV), Lopinavir (LPV), Nelfinavir (NFV), and Ritonavire (RTV) targeting SARS-CoV-2 Mpro was explored by applying docking, molecular dynamics (MD) simulations, and MM-GBSA methods using the broad-spectrum antiviral drug Ribavirin (RBV) as the negative and nonspecific control. Our results revealed that LPV, RTV, and NFV have higher binding affinities with Mpro, and they all interact with catalytic residues His41 and the other two key amino acids Met49 and Met165. Pharmacophore model analysis further revealed that the aromatic ring, hydrogen bond donor, and hydrophobic group are the essential infrastructure of Mpro inhibitors. Overall, this study applied computational simulation methods to study the interaction mechanism of HIV-1 protease inhibitors with SARS-CoV-2 Mpro, and the findings provide useful insights for the development of novel anti-SARS-CoV-2 agents for the treatment of COVID-19.
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Affiliation(s)
- Wei Yu
- Institute of Biomedicine, Jinan University, Guangzhou 510632, China; (W.Y.); (C.C.); (Y.W.); (C.W.); (C.L.)
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China; (Y.Z.); (Z.Y.)
| | - Xiaomin Wu
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, Huaibei 235000, China; (X.W.); (X.Z.)
| | - Yizhen Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China; (Y.Z.); (Z.Y.)
| | - Chun Chen
- Institute of Biomedicine, Jinan University, Guangzhou 510632, China; (W.Y.); (C.C.); (Y.W.); (C.W.); (C.L.)
| | - Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China; (Y.Z.); (Z.Y.)
| | - Xiaochun Zhang
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, Huaibei 235000, China; (X.W.); (X.Z.)
| | - Jiayi Ren
- Zhuhai College of Science and Technology, Zhuhai 519041, China;
| | - Yueming Wang
- Institute of Biomedicine, Jinan University, Guangzhou 510632, China; (W.Y.); (C.C.); (Y.W.); (C.W.); (C.L.)
- Zhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, China; (R.C.); (X.W.); (W.Z.)
| | - Changwen Wu
- Institute of Biomedicine, Jinan University, Guangzhou 510632, China; (W.Y.); (C.C.); (Y.W.); (C.W.); (C.L.)
- Zhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, China; (R.C.); (X.W.); (W.Z.)
| | - Chengming Li
- Institute of Biomedicine, Jinan University, Guangzhou 510632, China; (W.Y.); (C.C.); (Y.W.); (C.W.); (C.L.)
- Zhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, China; (R.C.); (X.W.); (W.Z.)
| | - Rongfeng Chen
- Zhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, China; (R.C.); (X.W.); (W.Z.)
| | - Xiaoli Wang
- Zhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, China; (R.C.); (X.W.); (W.Z.)
| | - Weihong Zheng
- Zhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, China; (R.C.); (X.W.); (W.Z.)
| | - Huaxin Liao
- Institute of Biomedicine, Jinan University, Guangzhou 510632, China; (W.Y.); (C.C.); (Y.W.); (C.W.); (C.L.)
- Zhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, China; (R.C.); (X.W.); (W.Z.)
| | - Xiaohui Yuan
- Institute of Biomedicine, Jinan University, Guangzhou 510632, China; (W.Y.); (C.C.); (Y.W.); (C.W.); (C.L.)
- Zhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, China; (R.C.); (X.W.); (W.Z.)
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4
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Yang Z, Li G, Zhao Y, Zhang L, Yuan X, Meng L, Liu H, Han Y, Jia L, Zhang S. Molecular Insights into the Recruiting Between UCP2 and DDX5/UBAP2L in the Metabolic Plasticity of Non-Small-Cell Lung Cancer. J Chem Inf Model 2021; 61:3978-3987. [PMID: 34308648 DOI: 10.1021/acs.jcim.1c00138] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Mitochondrial uncoupling protein 2 (UCP2) is distributed in tumor cells with a link to the support of systemic metabolic deregulation, and the downregulation of UCP2 has been unveiled as a biomarker of oncogenesis and chemoresistance in non-small-cell lung cancer (NSCLC) cells. However, the underlying mechanism of how UCP2 cooperates with other proteins in this metabolic reprogramming remains largely unsolved. We employed a combined computational and experimental strategy to explore into the recruiting of DDX5 with other proteins, and we unraveled the underlying structural mechanisms. We found that recruiting by ATP-dependent RNA helicase DDX5 (DDX5)/ubiquitin-associated protein 2-like (UBAP2L) might help UCP2 to play the pathological roles in NSCLC cells. According to the view of thermodynamics in physics, UCP2 tends to recruit DDX5 rather than UBAP2L, as shown by the ensemble-based docking, molecular dynamics simulations and molecular mechanics generalized Born surface area (MM/GBSA) approach. Cellular immunofluorescence assays further demonstrated that UCP2 associate with DDX5, and the recruiting of DDX5 with UCP2 at least partially contribute to the metabolic plasticity of NSCLCs via the AKT/mTOR pathway. Our study proposed an efficient way for detecting the protein-protein association via the experimentally validated molecular simulation. Our results shed light on the functional annotation of UCP and DDX family proteins in dysregulated metabolism, and the identification of candidate therapeutic targets for NSCLC.
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Affiliation(s)
- Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China.,MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Chemistry, Xi'an Jiaotong University, Xi'an 710049, China.,School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Guoyin Li
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou 466000, China.,State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an 710032, China
| | - Yizhen Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Xiaohui Yuan
- Institute of Biomedicine, Jinan University, Guangzhou 510632, China
| | - Lingjie Meng
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Chemistry, Xi'an Jiaotong University, Xi'an 710049, China.,Instrumental Analysis Center, Xi'an Jiao Tong University, Xi'an 710049, China
| | - Huadong Liu
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Yong Han
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an 710038, China
| | - Lintao Jia
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an 710032, China
| | - Shengli Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
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5
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Zang Y, Li X, Zhao Y, Wang H, Hao D, Zhang L, Yang Z, Yuan X, Zhang S. Molecular insights into the binding variance of the SARS-CoV-2 spike with human, cat and dog ACE2 proteins. Phys Chem Chem Phys 2021; 23:13752-13759. [PMID: 34132301 DOI: 10.1039/d1cp01611c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
SARS-CoV-2 has recently caused an epidemic in humans and poses a huge threat to global public health. As a primary receptor of SARS-CoV-2, angiotensin-converting enzyme 2 (ACE2) exists in different hosts that are in close contact with humans, especially cats and dogs. However, the underlying mechanism of how the spike receptor binding domain (RBD) of SARS-CoV-2 cooperates with human ACE2 (hACE2), cat ACE2 (cACE2) and dog ACE2 (dACE2) and the variation in binding remains largely unsolved. Therefore, we explored the binding behavior of the spike RBD with cACE2, dACE2 and hACE2 via all-atom molecular dynamics simulations. In accordance with the binding free energies and residue interactions, the spike RBD has respective binding specificities with cACE2, dACE2 and hACE2, and the binding affinities decrease in the order of hACE2, cACE2, dACE2, mainly due to changes in the amino acids Q24L, H34Y, and M82T in cACE2 or dACE2. Furthermore, alanine scanning analysis results validated some key residues of the spike RBD interact with ACE2 and provided clues to the variation of amino acid that could influence the transmissibility or immune responses of SARS-CoV-2. Decreasing dynamic correlations strengths of ACE2 with the RBD were found in all hACE2-RBD, cACE2-RBD and dACE2-RBD systems. The ACE2 protein shows variable motion modes across the zinc metallopeptidase domain, which induces different interactions between ACE2 and the RBD. Our studies reveal that the motion pattern of the zinc metallopeptidase domain is critical to the binding behavior of RBD with ACE2. These findings could aid our understanding of selective recognition involving various ACE2 with the SARS-CoV-2 spike and shed further light on the binding mechanisms.
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Affiliation(s)
- Yongjian Zang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China.
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Frota NF, Rebouças ADS, Fuzo CA, Lourenzoni MR. Alemtuzumab scFv fragments and CD52 interaction study through molecular dynamics simulation and binding free energy. J Mol Graph Model 2021; 107:107949. [PMID: 34089985 DOI: 10.1016/j.jmgm.2021.107949] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/14/2021] [Accepted: 05/20/2021] [Indexed: 11/30/2022]
Abstract
Specific antibody-antigen recognition is crucial for the immune response. Knowledge of molecular interaction details in the recognition process is fundamental for the rational design of antibodies with improved properties. We used state-of-the-art computer simulation tools to deepen the molecular-level understanding of the interactions between the monoclonal antibody Alemtuzumab and its antigen, the CD52 membrane receptor, of great biotechnological importance. Thus, we seek such responses by modeling the interaction of native and known mutants single-chain fragment variable (scFv) of Alemtuzumab with CD52 inserted in a membrane model to mimic the physiological conditions of antibody-antigen binding. Extensive molecular dynamics simulations of the interaction between Alemtuzumab's scFvs and CD52 promoted greater understanding of the structural and energetic bases, which can be translated into the biological action and affinity of this antibody. The quantification of the scFv-CD52 complexes binding free energy (ΔGbind) by Molecular Mechanics-Poisson-Boltzmann Surface Area (MM-PBSA) correlated with the experimental binding energies described before. Thus, the mutants D53K, K54D, and K56D resulted in less attractive ΔGbind, therefore lower scFv-CD52 affinity than the native scFv. On the other hand, K56D and K54D/K56D showed lower binding to CD52. These Results revealed that the model system mimicking an environment close to the physiological with the presence of the CD52 in a membrane model proved essential for this system's study. The present study allowed to unveil the molecular mechanisms involved in antigen-antibody interaction and the effects of mutations. Thus, these mechanisms may be explored in the Alemtuzumab variants' rational design with enhanced properties.
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Affiliation(s)
- Natália Fernandes Frota
- Research Group on Protein Engineering and Health Solutions (GEPeSS), Fundação Oswaldo Cruz Ceará (Fiocruz-CE), São José, Precabura, 61760000, Eusébio, Ceara, Brazil; Federal University of Ceara (UFC), Campus do Pici (Bloco 873), 60440-970, Fortaleza, Ceara Brazil
| | - Alison de Sousa Rebouças
- Research Group on Protein Engineering and Health Solutions (GEPeSS), Fundação Oswaldo Cruz Ceará (Fiocruz-CE), São José, Precabura, 61760000, Eusébio, Ceara, Brazil; Federal University of Ceara (UFC), Campus do Pici (Bloco 873), 60440-970, Fortaleza, Ceara Brazil
| | - Carlos Alessandro Fuzo
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Marcos Roberto Lourenzoni
- Research Group on Protein Engineering and Health Solutions (GEPeSS), Fundação Oswaldo Cruz Ceará (Fiocruz-CE), São José, Precabura, 61760000, Eusébio, Ceara, Brazil.
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Target SARS-CoV-2: computation of binding energies with drugs of dexamethasone/umifenovir by molecular dynamics using OPLS-AA force field. RESEARCH ON BIOMEDICAL ENGINEERING 2021. [PMCID: PMC7791166 DOI: 10.1007/s42600-020-00119-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Introduction In recent times, myriads of public have been infected with a novel SARS-CoV-2, and the fatality toll has reached thousands and been mounting step by step, which is a major crisis in the world. The challenge for this burning issue pertinent to repurposed medicines which prevent novel coronavirus is of immense concern for all scientists around the globe until the arrival of the vaccine. Methods Because of the global high priority rating on the search for the repurposed drugs which outfits clinical suitability to SARS-CoV-2, a unique theoretical methodology is proposed. The approach is based on explorations of biothermodynamics computed via molecular dynamics, root-mean-square deviation (RMSD), radius of gyration (Rg) and interactions. This unique methodology is tested for umifenovir/dexamethasone drugs on (SARS-CoV-2) main protease. Results This theoretical exploration not only suggested the presence of strong interactions between (SARS-CoV-2 + umifenovir/dexamethasone) but also emphasized the clinical suitability of dexamethasone over umifenovir to treat SARS-CoV-2. This supremacy of dexamethasone is well supported by the results of global clinical trials and COVID-19 therapeutic approved management guidelines of countries. Conclusions Thus, this work will pave a way for incremental advancement towards future design and development of more specific inhibitors for the treatment of SARS-CoV-2 infection in humans.
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Zang Y, Hao D, Wang H, Yang Z, Liu H, Zhang S. Structure-based methoxyflavone derivatives with potent inhibitory activity against various influenza neuraminidases. J Biomol Struct Dyn 2020; 38:4617-4624. [DOI: 10.1080/07391102.2019.1680436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Yongjian Zang
- School of Science, MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, Xi’an Jiaotong University, Xi’an, China
| | - Dongxiao Hao
- School of Science, MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, Xi’an Jiaotong University, Xi’an, China
| | - He Wang
- School of Science, MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, Xi’an Jiaotong University, Xi’an, China
| | - Zhiwei Yang
- School of Science, MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, Xi’an Jiaotong University, Xi’an, China
- School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Huadong Liu
- School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Shengli Zhang
- School of Science, MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, Xi’an Jiaotong University, Xi’an, China
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9
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Yang ZW, Zhao YZ, Zang YJ, Wang H, Zhu X, Meng LJ, Yuan XH, Zhang L, Zhang SL. Rapid Structure-Based Screening Informs Potential Agents for Coronavirus Disease (COVID-19) Outbreak. CHINESE PHYSICS LETTERS 2020; 37:058701. [PMID: 38619931 PMCID: PMC7351243 DOI: 10.1088/0256-307x/37/5/058701] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Indexed: 08/13/2023]
Abstract
Coronavirus Disease 2019 (COVID-19), caused by the novel coronavirus, has spread rapidly across China. Consequently, there is an urgent need to sort and develop novel agents for the prevention and treatment of viral infections. A rapid structure-based virtual screening is used for the evaluation of current commercial drugs, with structures of human angiotensin converting enzyme II (ACE2), and viral main protease, spike, envelope, membrane and nucleocapsid proteins. Our results reveal that the reported drugs Arbidol, Chloroquine and Remdesivir may hinder the entry and release of virions through the bindings with ACE2, spike and envelope proteins. Due to the similar binding patterns, NHC (β-d-N4-hydroxycytidine) and Triazavirin are also in prospects for clinical use. Main protease (3CLpro) is likely to be a feasible target of drug design. The screening results to target 3CL-pro reveal that Mitoguazone, Metformin, Biguanide Hydrochloride, Gallic acid, Caffeic acid, Sulfaguanidine and Acetylcysteine seem be possible inhibitors and have potential application in the clinical therapy of COVID-19.
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Affiliation(s)
- Zhi-Wei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Science, Xi'an Jiaotong University, Xi'an 710049
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049
| | - Yi-Zhen Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Science, Xi'an Jiaotong University, Xi'an 710049
| | - Yong-Jian Zang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Science, Xi'an Jiaotong University, Xi'an 710049
| | - He Wang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Science, Xi'an Jiaotong University, Xi'an 710049
| | - Xun Zhu
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Science, Xi'an Jiaotong University, Xi'an 710049
| | - Ling-Jie Meng
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Science, Xi'an Jiaotong University, Xi'an 710049
| | - Xiao-Hui Yuan
- Institute of Biomedicine, Jinan University, Guangzhou 510632
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Science, Xi'an Jiaotong University, Xi'an 710049
| | - Sheng-Li Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Science, Xi'an Jiaotong University, Xi'an 710049
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Crosstalk between the Akt/mTORC1 and NF-κB signaling pathways promotes hypoxia-induced pulmonary hypertension by increasing DPP4 expression in PASMCs. Acta Pharmacol Sin 2019; 40:1322-1333. [PMID: 31316183 DOI: 10.1038/s41401-019-0272-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 06/10/2019] [Accepted: 06/11/2019] [Indexed: 12/19/2022] Open
Abstract
Abnormal wound healing by pulmonary artery smooth muscle cells (PASMCs) promotes vascular remodeling in hypoxia-induced pulmonary hypertension (HPH). Increasing evidence shows that both the mammalian target of rapamycin complex 1 (mTORC1) and nuclear factor-kappa B (NF-κB) are involved in the development of HPH. In this study, we explored the crosstalk between mTORC1 and NF-κB in PASMCs cultured under hypoxic condition and in a rat model of hypoxia-induced pulmonary hypertension (HPH). We showed that hypoxia promoted wound healing of PASMCs, which was dose-dependently blocked by the mTORC1 inhibitor rapamycin (5-20 nM). In PASMCs, hypoxia activated mTORC1, which in turn promoted the phosphorylation of NF-κB. Molecular docking revealed that mTOR interacted with IκB kinases (IKKs) and that was validated by immunoprecipitation. In vitro kinase assays and mass spectrometry demonstrated that mTOR phosphorylated IKKα and IKKβ separately. Inhibition of mTORC1 decreased the level of phosphorylated IKKα/β, thus reducing the phosphorylation and transcriptional activity of NF-κB. Bioinformatics study revealed that dipeptidyl peptidase-4 (DPP4) was a target gene of NF-κB; DPP4 inhibitor, sitagliptin (10-500 μM) effectively inhibited the abnormal wound healing of PASMCs under hypoxic condition. In the rat model of HPH, we showed that NF-κB activation (at 3 weeks) was preceded by mTOR signaling activation (after 1 or 2 weeks) in lungs, and administration of sitagliptin (1-5 mg/kg every day, ig) produced preventive effects against the development of HPH. In conclusion, hypoxia activates the crosstalk between mTORC1 and NF-κB, and increased DPP4 expression in PASMCs that leads to vascular remodeling. Sitagliptin, a DPP4 inhibitor, exerts preventive effect against HPH.
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Ren J, Yuan X, Li J, Lin S, Yang B, Chen C, Zhao J, Zheng W, Liao H, Yang Z, Qu Z. Assessing the performance of the g_mmpbsa tools to simulate the inhibition of oseltamivir to influenza virus neuraminidase by molecular mechanics Poisson–Boltzmann surface area methods. J CHIN CHEM SOC-TAIP 2019. [DOI: 10.1002/jccs.201900148] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jiayi Ren
- Zhuhai CollegeJilin University Zhuhai China
| | - Xiaohui Yuan
- Institute of BiomedicineJinan University Guangzhou China
| | - Junqi Li
- Institute of BiomedicineJinan University Guangzhou China
- Guangdong Provincial Key Laboratory of Bioengineering Medicine Guangzhou China
| | - Shujian Lin
- Institute of BiomedicineJinan University Guangzhou China
- Guangdong Provincial Key Laboratory of Bioengineering Medicine Guangzhou China
| | - Bing Yang
- Institute of BiomedicineJinan University Guangzhou China
- Guangdong Provincial Key Laboratory of Bioengineering Medicine Guangzhou China
| | - Chun Chen
- Institute of BiomedicineJinan University Guangzhou China
- National Engineering Research Center of Genetic Medicine Guangzhou China
| | - Jian Zhao
- Zhuhai Trinomab Biotechnology Co. Ltd. Zhuhai China
| | | | - Huaxin Liao
- Guangdong Provincial Key Laboratory of Bioengineering Medicine Guangzhou China
- Zhuhai Trinomab Biotechnology Co. Ltd. Zhuhai China
| | - Zhiwei Yang
- School of ScienceXian Jiaotong University Xian China
| | - Zhangyi Qu
- Department of Microbiology, Public Health CollegeHarbin Medical University Harbin China
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12
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Yang Z, Zhao Y, Hao D, Ren S, Yuan X, Meng L, Zhang S. Bindings of PPARγ ligand-binding domain with 5-cholesten-3β, 25-diol, 3-sulfate: accurate prediction by molecular simulation. J Biomol Struct Dyn 2019; 38:1918-1926. [DOI: 10.1080/07391102.2019.1620129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Science, Xi’an Jiaotong University, Xi’an, China
- School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, China
| | - Yizhen Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Science, Xi’an Jiaotong University, Xi’an, China
| | - Dongxiao Hao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Science, Xi’an Jiaotong University, Xi’an, China
| | - Shunlin Ren
- Department of Medicine, Veterans Affairs McGuire Medical Center/Department of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Xiaohui Yuan
- Institute of Biomedicine, Jinan University, Guangzhou, China
| | - Lingjie Meng
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Science, Xi’an Jiaotong University, Xi’an, China
| | - Shengli Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Science, Xi’an Jiaotong University, Xi’an, China
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13
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Hao D, Yang Z, Gao T, Tian Z, Zhang L, Zhang S. Role of glycans in cholesteryl ester transfer protein revealed by molecular dynamics simulation. Proteins 2018; 86:882-891. [DOI: 10.1002/prot.25520] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 04/23/2018] [Accepted: 04/25/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Dongxiao Hao
- Department of Applied Physics, School of Science; Xi'an Jiaotong University; Xi'an 710049 China
| | - Zhiwei Yang
- Department of Applied Physics, School of Science; Xi'an Jiaotong University; Xi'an 710049 China
- Department of Applied Chemistry, School of Science; Xi'an Jiaotong University; Xi'an 710049 China
| | - Teng Gao
- Department of Applied Physics, School of Science; Xi'an Jiaotong University; Xi'an 710049 China
| | - Zhiqi Tian
- Department of Applied Physics, School of Science; Xi'an Jiaotong University; Xi'an 710049 China
| | - Lei Zhang
- Department of Applied Physics, School of Science; Xi'an Jiaotong University; Xi'an 710049 China
| | - Shengli Zhang
- Department of Applied Physics, School of Science; Xi'an Jiaotong University; Xi'an 710049 China
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14
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Xia J, Yang L, Dong L, Niu M, Zhang S, Yang Z, Wumaier G, Li Y, Wei X, Gong Y, Zhu N, Li S. Cefminox, a Dual Agonist of Prostacyclin Receptor and Peroxisome Proliferator-Activated Receptor-Gamma Identified by Virtual Screening, Has Therapeutic Efficacy against Hypoxia-Induced Pulmonary Hypertension in Rats. Front Pharmacol 2018. [PMID: 29527168 PMCID: PMC5829529 DOI: 10.3389/fphar.2018.00134] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Prostacyclin receptor (IP) and peroxisome proliferator-activated receptor-gamma (PPARγ) are both potential targets for treatment of pulmonary arterial hypertension (PAH). Expression of IP and PPARγ decreases in PAH, suggesting that screening of dual agonists of IP and PPARγ might be an efficient method for drug discovery. Virtual screening (VS) of potential IP-PPARγ dual-targeting agonists was performed in the ZINC database. Ten of the identified compounds were further screened, and cefminox was found to dramatically inhibit growth of PASMCs with no obvious cytotoxicity. Growth inhibition by cefminox was partially reversed by both the IP antagonist RO113842 and the PPARγ antagonist GW9662. Investigation of the underlying mechanisms of action demonstrated that cefminox inhibits the protein kinase B (Akt)/mammalian target of rapamycin (mTOR) signaling pathway through up-regulation of the expression of phosphatase and tensin homolog (PTEN, which is inhibited by GW9662), and enhances cyclic adenosine monophosphate (cAMP) production in PASMCs (which is inhibited by RO113842). In a rat model of hypoxia-induced pulmonary hypertension, cefminox displayed therapeutic efficacy not inferior to that of the prostacyclin analog iloprost or the PPARγ agonist rosiglitazone. Our results identified cefminox as a dual agonist of IP and PPARγ that significantly inhibits PASMC proliferation by up-regulation of PTEN and cAMP, suggesting that it has potential for treatment of PAH.
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Affiliation(s)
- Jingwen Xia
- Department of Pulmonary and Critical Care Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Li Yang
- Department of Anesthesiology, Chongqing Medical University, Chongqing, China
| | - Liang Dong
- Department of Pulmonary and Critical Care Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Mengjie Niu
- Department of Gastroenterology Medicine, Xi'an Third Hospital, Xi'an, China
| | - Shengli Zhang
- Department of Applied Physics, Xi'an Jiaotong University, Xi'an, China
| | - Zhiwei Yang
- Department of Applied Physics, Xi'an Jiaotong University, Xi'an, China
| | - Gulinuer Wumaier
- Department of Pulmonary and Critical Care Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Ying Li
- Department of Respiratory Medicine, Shaanxi Provincial Second People's Hospital, Xi'an, China
| | - Xiaomin Wei
- Department of Pulmonary and Critical Care Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Yi Gong
- Department of Pulmonary and Critical Care Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Ning Zhu
- Department of Pulmonary and Critical Care Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Shengqing Li
- Department of Pulmonary and Critical Care Medicine, Huashan Hospital, Fudan University, Shanghai, China
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15
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Xu S, Wang T, Yang Z, Li Y, Li W, Wang T, Wang S, Jia L, Zhang S, Li S. miR-26a desensitizes non-small cell lung cancer cells to tyrosine kinase inhibitors by targeting PTPN13. Oncotarget 2018; 7:45687-45701. [PMID: 27285768 PMCID: PMC5216753 DOI: 10.18632/oncotarget.9920] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 05/23/2016] [Indexed: 12/24/2022] Open
Abstract
Epidermal growth factor receptor (EGFR)-targeted tyrosine kinase inhibitors (TKIs) have emerged as first-line drugs for non-small cell lung cancers (NSCLCs). However, the resistance to TKIs represents the key limitation for their therapeutic efficacy. We found that miR-26a was upregulated in gefitinib-refractory NSCLCs; miR-26a is downstream of EGFR signaling and directly targets and silences protein tyrosine phosphatase non-receptor type 13 (PTPN13) to maintain the activation of Src, a dephosphorylation substrate of PTPN13, thus reinforcing EGFR pathway in a regulatory circuit. miR-26a inhibition significantly improved NSCLC responses to gefitinib. These data revealed a novel mechanism of NSCLC resistance to TKI treatment.
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Affiliation(s)
- Shudi Xu
- Department of Respiratory Medicine, Huashan Hospital, Fudan University, Shanghai, China.,Department of Respiratory Medicine, 9th Hospital of Xi'an, Xi'an, China
| | - Tao Wang
- Department of Neurology, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Zhiwei Yang
- Department of Applied Physics, Xi'an Jiaotong University, Xi'an, China
| | - Ying Li
- Department of Respiratory Medicine, Huashan Hospital, Fudan University, Shanghai, China.,Department of Respiratory Medicine, Shaanxi Provincial Second People's Hospital, Xi'an, China
| | - Weijie Li
- Department of Respiratory Medicine, Huashan Hospital, Fudan University, Shanghai, China.,Department of Respiratory Medicine, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Ting Wang
- Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - Shan Wang
- Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - Lintao Jia
- Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - Shengli Zhang
- Department of Applied Physics, Xi'an Jiaotong University, Xi'an, China
| | - Shengqing Li
- Department of Respiratory Medicine, Huashan Hospital, Fudan University, Shanghai, China
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16
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Yang Z, Cao Y, Hao D, Yuan X, Zhang L, Zhang S. Binding profiles of cholesterol ester transfer protein with current inhibitors: a look at mechanism and drawback. J Biomol Struct Dyn 2017; 36:2567-2580. [PMID: 28777919 DOI: 10.1080/07391102.2017.1363661] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Zhiwei Yang
- Department of Applied Physics, School of Science, Xi’an Jiaotong University, No. 28 Xianning West Road, Xi’an 710049, China
- Department of Applied Chemistry, School of Science, Xi’an Jiaotong University, Xi’an 710049, China
| | - Yang Cao
- Department of Applied Physics, School of Science, Xi’an Jiaotong University, No. 28 Xianning West Road, Xi’an 710049, China
| | - Dongxiao Hao
- Department of Applied Physics, School of Science, Xi’an Jiaotong University, No. 28 Xianning West Road, Xi’an 710049, China
| | - Xiaohui Yuan
- Institute of Biomedicine, Jinan University, Guangzhou 510632, China
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Jinan University, Guangzhou 510632, China
| | - Lei Zhang
- Department of Applied Physics, School of Science, Xi’an Jiaotong University, No. 28 Xianning West Road, Xi’an 710049, China
| | - Shengli Zhang
- Department of Applied Physics, School of Science, Xi’an Jiaotong University, No. 28 Xianning West Road, Xi’an 710049, China
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17
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Li Y, Yang Z, Li W, Xu S, Wang T, Wang T, Niu M, Zhang S, Jia L, Li S. TOPK promotes lung cancer resistance to EGFR tyrosine kinase inhibitors by phosphorylating and activating c-Jun. Oncotarget 2017; 7:6748-64. [PMID: 26745678 PMCID: PMC4872746 DOI: 10.18632/oncotarget.6826] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 12/31/2015] [Indexed: 12/16/2022] Open
Abstract
Tyrosine kinase inhibitors (TKIs) targeting the epidermal growth factor receptor (EGFR) have shown promising clinical efficacy in non-squamous non-small cell lung cancer (NSCLC); however, resistance is frequently observed in malignant cells, operating through a mechanism that remains largely unknown. The present study shows that T-lymphokine-activated killer cell-originated protein kinase (TOPK) is upregulated in NSCLC and excessively activated in TKI-refractory cells. TOPK dictates the responsiveness of lung cancers to the EGFR-targeted TKI gefitinib through the transcription factor AP-1 component c-Jun. TOPK binds directly to and phosphorylates c-Jun, which consequently activates the transcription of AP-1 target genes, including CCND1 and CDC2. TOPK silencing sensitizes EGFR-TKI-resistant lung cancer cells to gefitinib and increases gefitinib efficacy in preclinical lung adenocarcinoma xenograft models. These findings represent a novel mechanism of lung cancer resistance to TKIs and suggest that TOPK may have value both as a predictive biomarker and as a therapeutic target: TOPK-targeted therapy may synergize with EGFR-targeted therapy in lung cancers.
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Affiliation(s)
- Ying Li
- Department of Pulmonary and Critical Care Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Zhiwei Yang
- Department of Applied Physics, School of Science, Xi'an Jiaotong University, Xi'an, China.,Engineering Research Center of Forest Bio-preparation, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Weijie Li
- Department of Pulmonary and Critical Care Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Shudi Xu
- Department of Pulmonary and Critical Care Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, China.,Department of Pulmonary Medicine, Xi'an Ninth Hospital, Xi'an, China
| | - Tao Wang
- Department of Neurology, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Ting Wang
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - Mengjie Niu
- Department of Pulmonary and Critical Care Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Shengli Zhang
- Department of Applied Physics, School of Science, Xi'an Jiaotong University, Xi'an, China
| | - Lintao Jia
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - Shengqing Li
- Department of Pulmonary and Critical Care Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, China
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18
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Zwitterionic structures: from physicochemical properties toward computer-aided drug designs. Future Med Chem 2016; 8:2245-2262. [DOI: 10.4155/fmc-2016-0176] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Zwitterions, used widely in chemical, biological and medicinal fields, show distinct physicochemical properties relative to ordinary ampholytes, which largely decide their bioavailability and biological activities. In the present manuscript, these properties are discussed in order to facilitate our understanding of zwitterionic structures, followed by various examples of zwitterionic drugs and the critical role these properties play. We specifically focus our discussions on neuraminidase inhibitors (NAIs), which are used in the treatment and prevention of influenza, covering their computer-assisted design, transformation to zwitterionic isomers and interaction mechanisms of NAIs with proteins. The discovery and development of NAIs provide useful insights that may assist in the exploration of new zwitterionic drugs.
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Abed Y, Bouhy X, L'Huillier AG, Rhéaume C, Pizzorno A, Retamal M, Fage C, Dubé K, Joly MH, Beaulieu E, Mallett C, Kaiser L, Boivin G. The E119D neuraminidase mutation identified in a multidrug-resistant influenza A(H1N1)pdm09 isolate severely alters viral fitness in vitro and in animal models. Antiviral Res 2016; 132:6-12. [PMID: 27185624 DOI: 10.1016/j.antiviral.2016.05.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 05/12/2016] [Indexed: 10/21/2022]
Abstract
We recently isolated an influenza A(H1N1)pdm09 E119D/H275Y neuraminidase (NA) variant from an immunocompromised patient who received oseltamivir and zanamivir therapies. This variant demonstrated cross resistance to zanamivir, oseltamivir, peramivir and laninamivir. In this study, the viral fitness of the recombinant wild-type (WT), E119D and E119D/H275Y A(H1N1)pdm09 viruses was evaluated in vitro and in experimentally-infected C57BL/6 mice and guinea pigs. In replication kinetics experiments, viral titers obtained with the E119D and E119D/H275Y recombinants were up to 2- and 4-log lower compared to the WT virus in MDCK and ST6GalI-MDCK cells, respectively. Enzymatic studies revealed that the E119D mutation significantly decreased the surface NA activity. In experimentally-infected mice, a 50% mortality rate was recorded in the group infected with the WT recombinant virus whereas no mortality was observed in the E119D and E119D/H275Y groups. Mean lung viral titers on day 5 post-inoculation for the WT (1.2 ± 0.57 × 10(8) PFU/ml) were significantly higher than those of the E119D (9.75 ± 0.41 × 10(5) PFU/ml, P < 0.01) and the E119D/H275Y (1.47 ± 0.61 × 10(6) PFU/ml, P < 0.01) groups. In guinea pigs, comparable seroconversion rates and viral titers in nasal washes (NW) were obtained for the WT and mutant index and contact groups. However, the D119E reversion was observed in most NW samples of the E119D and E119D/H275Y animals. In conclusion, the E119D NA mutation that could emerge in A(H1N1)pdm09 viruses during zanamivir therapy has a significant impact on viral fitness and such mutant is unlikely to be highly transmissible.
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Affiliation(s)
- Yacine Abed
- CHUQ-CHUL and Laval University, Québec City, Québec, Canada
| | - Xavier Bouhy
- CHUQ-CHUL and Laval University, Québec City, Québec, Canada
| | | | | | | | - Miguel Retamal
- CHUQ-CHUL and Laval University, Québec City, Québec, Canada
| | - Clément Fage
- CHUQ-CHUL and Laval University, Québec City, Québec, Canada
| | | | | | | | | | - Laurent Kaiser
- Laboratory of Virology, University of Geneva Hospitals, Geneva, Switzerland
| | - Guy Boivin
- CHUQ-CHUL and Laval University, Québec City, Québec, Canada.
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20
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Yang Z, Wu F, Yuan X, Zhang L, Zhang S. Novel binding patterns between ganoderic acids and neuraminidase: Insights from docking, molecular dynamics and MM/PBSA studies. J Mol Graph Model 2016; 65:27-34. [PMID: 26905206 DOI: 10.1016/j.jmgm.2016.02.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 02/11/2016] [Accepted: 02/12/2016] [Indexed: 01/09/2023]
Abstract
Recently, ganoderic acids (GAs) give rise to the attractive candidates of novel neuraminidase (NA) inhibitors. However, there is still no evident conclusion about their binding patterns. To this end, docking, molecular dynamics and MM/PBSA methods were combined to study the binding profiles of GAs with the N1 protein and familiar H274Y and N294S mutations (A/Vietnam/1203/04 stain). It was found that the binding affinities of ganoderic acid DM and Z (ΔGbind, -16.83 and -10.99 kcal mol(-1)) are comparable to that of current commercial drug oseltamivir (-23.62 kcal mol(-1)). Electrostatic interaction is the main driving force, and should be one important factor to evaluate the binding quality and rational design of NA inhibitors. The 150-loop residues Asp151 and Arg152 played an important role in the binding processes. Further analysis revealed that ganoderic acid DM is a potential source of anti-influenza ingredient, with novel binding pattern and advantage over oseltamivir. It had steric hindrance on the 150 cavity of N1 protein, and exerted activities across the H274Y and N294S mutations. This work also pointed out how to effectively design dual-site NA inhibitors and reinforce their affinities. These findings should prove valuable for the in-depth understanding of interactions between NA and GAs, and warrant the experimental aspects to design novel anti-influenza drugs.
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Affiliation(s)
- Zhiwei Yang
- Department of Applied Physics, Xi'an Jiaotong University, Xi'an 710049, PR China; School of Basic Medical Sciences, Jiamusi University, Jiamusi 154007, PR China.
| | - Fei Wu
- School of Basic Medical Sciences, Jiamusi University, Jiamusi 154007, PR China
| | - Xiaohui Yuan
- Institute of Biomedicine, Jinan University, Guangzhou 510632, PR China
| | - Lei Zhang
- Department of Applied Physics, Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Shengli Zhang
- Department of Applied Physics, Xi'an Jiaotong University, Xi'an 710049, PR China.
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21
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Singh A, Soliman ME. Understanding the cross-resistance of oseltamivir to H1N1 and H5N1 influenza A neuraminidase mutations using multidimensional computational analyses. DRUG DESIGN DEVELOPMENT AND THERAPY 2015; 9:4137-54. [PMID: 26257512 PMCID: PMC4527369 DOI: 10.2147/dddt.s81934] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This study embarks on a comprehensive description of the conformational contributions to resistance of neuraminidase (N1) in H1N1 and H5N1 to oseltamivir, using comparative multiple molecular dynamic simulations. The available data with regard to elucidation of the mechanism of resistance as a result of mutations in H1N1 and H5N1 neuraminidases is not well established. Enhanced post-dynamic analysis, such as principal component analysis, solvent accessible surface area, free binding energy calculations, and radius of gyration were performed to gain a precise insight into the binding mode and origin of resistance of oseltamivir in H1N1 and H5N1 mutants. Three significant features reflecting resistance in the presence of mutations H274Y and I222K, of the protein complexed with the inhibitor are: reduced flexibility of the α-carbon backbone; an improved ΔEele of ~15 (kcal/mol) for H1N1 coupled with an increase in ΔGsol (~13 kcal/mol) from wild-type to mutation; a low binding affinity in comparison with the wild-type of ~2 (kcal/mol) and ~7 (kcal/mol) with respect to each mutation for the H5N1 systems; and reduced hydrophobicity of the overall surface structure due to an impaired hydrogen bonding network. We believe the results of this study will ultimately provide a useful insight into the structural landscape of neuraminidase-associated binding of oseltamivir. Furthermore, the results can be used in the design and development of potent inhibitors of neuraminidases.
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Affiliation(s)
- Ashona Singh
- School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, South Africa
| | - Mahmoud E Soliman
- School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, South Africa
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Emergence of H7N9 Influenza A Virus Resistant to Neuraminidase Inhibitors in Nonhuman Primates. Antimicrob Agents Chemother 2015; 59:4962-73. [PMID: 26055368 DOI: 10.1128/aac.00793-15] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 06/01/2015] [Indexed: 01/05/2023] Open
Abstract
The number of patients infected with H7N9 influenza virus has been increasing since 2013. We examined the efficacy of neuraminidase (NA) inhibitors and the efficacy of a vaccine against an H7N9 influenza virus, A/Anhui/1/2013 (H7N9), isolated from a patient in a cynomolgus macaque model. NA inhibitors (oseltamivir and peramivir) barely reduced the total virus amount because of the emergence of resistant variants with R289K or I219T in NA [residues 289 and 219 in N9 of A/Anhui/1/2013 (H7N9) correspond to 292 and 222 in N2, respectively] in three of the six treated macaques, whereas subcutaneous immunization of an inactivated vaccine derived from A/duck/Mongolia/119/2008 (H7N9) prevented propagation of A/Anhui/1/2013 (H7N9) in all vaccinated macaques. The percentage of macaques in which variant H7N9 viruses with low sensitivity to the NA inhibitors were detected was much higher than that of macaques in which variant H5N1 highly pathogenic influenza virus was detected after treatment with one of the NA inhibitors in our previous study. The virus with R289K in NA was reported in samples from human patients, whereas that with I219T in NA was identified for the first time in this study using macaques, though no variant H7N9 virus was reported in previous studies using mice. Therefore, the macaque model enables prediction of the frequency of emerging H7N9 virus resistant to NA inhibitors in vivo. Since H7N9 strains resistant to NA inhibitors might easily emerge compared to other influenza viruses, monitoring of the emergence of variants is required during treatment of H7N9 influenza virus infection with NA inhibitors.
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L'Huillier AG, Abed Y, Petty TJ, Cordey S, Thomas Y, Bouhy X, Schibler M, Simon A, Chalandon Y, van Delden C, Zdobnov E, Boquete-Suter P, Boivin G, Kaiser L. E119D Neuraminidase Mutation Conferring Pan-Resistance to Neuraminidase Inhibitors in an A(H1N1)pdm09 Isolate From a Stem-Cell Transplant Recipient. J Infect Dis 2015; 212:1726-34. [PMID: 25985905 DOI: 10.1093/infdis/jiv288] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 05/08/2015] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND An influenza A(H1N1)pdm09 infection was diagnosed in a hematopoietic stem cell transplant recipient during conditioning regimen. He was treated with oral oseltamivir, later combined with intravenous zanamivir. The H275Y neuraminidase (NA) mutation was first detected, and an E119D NA mutation was identified during zanamivir therapy. METHODS Recombinant wild-type (WT) E119D and E119D/H275Y A(H1N1)pdm09 NA variants were generated by reverse genetics. Susceptibility to NA inhibitors (NAIs) was evaluated with a fluorometric assay using the 2'-(4-methylumbelliferyl)-α-D-N-acetylneuraminic acid (MUNANA) substrate. Susceptibility to favipiravir (T-705) was assessed using plaque reduction assays. The NA affinity and velocity values were determined with NA enzymatic studies. RESULTS We identified an influenza A(H1N1)pdm09 E119D mutant that exhibited a marked increase in the 50% inhibitory concentrations against all tested NAIs (827-, 25-, 286-, and 702-fold for zanamivir, oseltamivir, peramivir, and laninamivir, respectively). The double E119D/H275Y mutation further increased oseltamivir and peramivir 50% inhibitory concentrations by 790- and >5000-fold, respectively, compared with the WT. The mutant viruses remained susceptible to favipiravir. The NA affinity and velocity values of the E119D variant decreased by 8.1-fold and 4.5-fold, respectively, compared with the WT. CONCLUSIONS The actual emergence of a single NA mutation conferring pan-NAI resistance in the clinical setting reinforces the pressing need to develop new anti-influenza strategies.
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Affiliation(s)
- Arnaud G L'Huillier
- Laboratory of Virology, Divisions of Infectious Diseases and Laboratory Medicine
| | - Yacine Abed
- Centre Hospitalier Universitaire de Québec and Université Laval, Quebec City, Canada
| | - Tom J Petty
- Department of Genetic Medicine and Development, University of Geneva Medical School Swiss Institute of Bioinformatics, University of Geneva, Switzerland
| | - Samuel Cordey
- Laboratory of Virology, Divisions of Infectious Diseases and Laboratory Medicine
| | - Yves Thomas
- Laboratory of Virology, Divisions of Infectious Diseases and Laboratory Medicine
| | - Xavier Bouhy
- Centre Hospitalier Universitaire de Québec and Université Laval, Quebec City, Canada
| | - Manuel Schibler
- Laboratory of Virology, Divisions of Infectious Diseases and Laboratory Medicine
| | - Audrey Simon
- Division of Hematology, Department of Internal Medicine Specialties, University of Geneva Hospitals
| | - Yves Chalandon
- Division of Hematology, Department of Internal Medicine Specialties, University of Geneva Hospitals
| | - Christian van Delden
- Division of Infectious Diseases, Department of Internal Medicine Specialties, University of Geneva Hospitals
| | - Evgeny Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School Swiss Institute of Bioinformatics, University of Geneva, Switzerland
| | | | - Guy Boivin
- Centre Hospitalier Universitaire de Québec and Université Laval, Quebec City, Canada
| | - Laurent Kaiser
- Laboratory of Virology, Divisions of Infectious Diseases and Laboratory Medicine University of Geneva Medical School, University of Geneva, Switzerland
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