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Nguyen H, Nguyen HL, Li MS. Binding of SARS-CoV-2 Nonstructural Protein 1 to 40S Ribosome Inhibits mRNA Translation. J Phys Chem B 2024; 128:7033-7042. [PMID: 39007765 DOI: 10.1021/acs.jpcb.4c01391] [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: 07/16/2024]
Abstract
Experimental evidence has established that SARS-CoV-2 NSP1 acts as a factor that restricts cellular gene expression and impedes mRNA translation within the ribosome's 40S subunit. However, the precise molecular mechanisms underlying this phenomenon have remained elusive. To elucidate this issue, we employed a combination of all-atom steered molecular dynamics and coarse-grained alchemical simulations to explore the binding affinity of mRNA to the 40S ribosome, both in the presence and absence of SARS-CoV-2 NSP1. Our investigations revealed that the binding of SARS-CoV-2 NSP1 to the 40S ribosome leads to a significant enhancement in the binding affinity of mRNA. This observation, which aligns with experimental findings, strongly suggests that SARS-CoV-2 NSP1 has the capability to inhibit mRNA translation. Furthermore, we identified electrostatic interactions between mRNA and the 40S ribosome as the primary driving force behind mRNA translation. Notably, water molecules were found to play a pivotal role in stabilizing the mRNA-40S ribosome complex, underscoring their significance in this process. We successfully pinpointed the specific SARS-CoV-2 NSP1 residues that play a critical role in triggering the translation arrest.
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Affiliation(s)
- Hung Nguyen
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Hoang Linh Nguyen
- Institute of Fundamental and Applied Sciences, Duy Tan University, Ho Chi Minh City 700000, Vietnam
- Faculty of Environmental and Natural Sciences, Duy Tan University, Da Nang City 550000, Vietnam
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland
- Quang Trung Software City, Life Science Lab, Institute for Computational Science and Technology, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 729110, Vietnam
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2
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Nguyen H, Li MS. Antibody-nanobody combination increases their neutralizing activity against SARS-CoV-2 and nanobody H11-H4 is effective against Alpha, Kappa and Delta variants. Sci Rep 2022; 12:9701. [PMID: 35690632 PMCID: PMC9188278 DOI: 10.1038/s41598-022-14263-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/03/2022] [Indexed: 11/14/2022] Open
Abstract
The global spread of COVID-19 is devastating health systems and economies worldwide. While the use of vaccines has yielded encouraging results, the emergence of new variants of SARS-CoV-2 shows that combating COVID-19 remains a big challenge. One of the most promising treatments is the use of not only antibodies, but also nanobodies. Recent experimental studies revealed that the combination of antibody and nanobody can significantly improve their neutralizing ability through binding to the SARS-CoV-2 spike protein, but the molecular mechanisms underlying this observation remain largely unknown. In this work, we investigated the binding affinity of the CR3022 antibody and H11-H4 nanobody to the SARS-CoV-2 receptor binding domain (RBD) using molecular modeling. Both all-atom steered molecular dynamics simulations and coarse-grained umbrella sampling showed that, consistent with the experiment, CR3022 associates with RBD more strongly than H11-H4. We predict that the combination of CR3022 and H11-H4 considerably increases their binding affinity to the spike protein. The electrostatic interaction was found to control the association strength of CR3022, but the van der Waals interaction dominates in the case of H11-H4. However, our study for a larger set of nanobodies and antibodies showed that the relative role of these interactions depends on the specific complex. Importantly, we showed Beta, Gamma, Lambda, and Mu variants reduce the H11-H4 activity while Alpha, Kappa and Delta variants increase its neutralizing ability, which is in line with experiment reporting that the nanobody elicited from the llama is very promising for fighting against the Delta variant.
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Affiliation(s)
- Hung Nguyen
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668, Warsaw, Poland
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668, Warsaw, Poland. .,Life Science Lab, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam.
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3
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Nature of bilayer lipids affects membranes deformation and pore resealing during nanoparticle penetration. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2022; 132:112530. [DOI: 10.1016/j.msec.2021.112530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 10/17/2021] [Accepted: 10/30/2021] [Indexed: 01/31/2023]
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Nguyen H, Lan PD, Nissley DA, O’Brien EP, Li MS. Electrostatic Interactions Explain the Higher Binding Affinity of the CR3022 Antibody for SARS-CoV-2 than the 4A8 Antibody. J Phys Chem B 2021; 125:7368-7379. [PMID: 34228472 PMCID: PMC8276604 DOI: 10.1021/acs.jpcb.1c03639] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/30/2021] [Indexed: 12/23/2022]
Abstract
A structural understanding of the mechanism by which antibodies bind SARS-CoV-2 at the atomic level is highly desirable as it can tell the development of more effective antibodies to treat Covid-19. Here, we use steered molecular dynamics (SMD) and coarse-grained simulations to estimate the binding affinity of the monoclonal antibodies CR3022 and 4A8 to the SARS-CoV-2 receptor-binding domain (RBD) and SARS-CoV-2 N-terminal domain (NTD). Consistent with experiments, our SMD and coarse-grained simulations both indicate that CR3022 has a higher affinity for SARS-CoV-2 RBD than 4A8 for the NTD, and the coarse-grained simulations indicate the former binds three times stronger to its respective epitope. This finding shows that CR3022 is a candidate for Covid-19 therapy and is likely a better choice than 4A8. Energetic decomposition of the interaction energies between these two complexes reveals that electrostatic interactions explain the difference in the observed binding affinity between the two complexes. This result could lead to a new approach for developing anti-Covid-19 antibodies in which good candidates must contain charged amino acids in the area of contact with the virus.
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Affiliation(s)
- Hung Nguyen
- Institute
of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Pham Dang Lan
- Life
Science Lab, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
- Faculty
of Physics and Engineering Physics, VNUHCM-University
of Science, 227, Nguyen
Van Cu Street, District 5, Ho Chi Minh City, Vietnam
| | - Daniel A. Nissley
- Department
of Statistics, University of Oxford, Oxford
Protein Bioinformatics Group, Oxford OX1 2JD, United Kingdom
| | - Edward P. O’Brien
- Department
of Chemistry, Penn State University, University Park, Pennsylvania 16802, United States
- Bioinformatics
and Genomics Graduate Program, The Huck
Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802, United States
- Institute
for Computational and Data Sciences, Penn
State University, University Park, Pennsylvania 16802, United States
| | - Mai Suan Li
- Institute
of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland
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Nademi Y, Tang T, Uludağ H. Membrane lipids destabilize short interfering ribonucleic acid (siRNA)/polyethylenimine nanoparticles. NANOSCALE 2020; 12:1032-1045. [PMID: 31845926 DOI: 10.1039/c9nr08128c] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cell entry of polymeric nanoparticles (NPs) bearing polynucleotides is an important stage for successful gene delivery. In this work, we addressed the influence of cell membrane lipids on the integrity and configurational changes of NPs composed of short interfering ribonucleic acid (siRNA) and polyethylenimine. We focused on NPs derived from two different PEIs, unmodified low molecular weight PEI and linoleic acid (LA)-substituted PEI, and their interactions with two membrane lipids (zwitterionic 2-oleoyl-1-palmitoyl-sn-glycero-3-phosphocholine (POPC) and anionic 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-l-serine (POPS)). Our experiments showed that POPS liposomes interacted strongly with both types of NPs, which caused partial dissociation of the NPs. POPC liposomes, however, did not induce any dissociation. Consistent with the experiments, steered molecular dynamics simulations showed a stronger interaction between the NPs and the POPS membrane than between the NPs and the POPC membrane. Lipid substitution on the PEIs enhanced the stability of the NPs during membrane crossing; lipid association between PEIs of the LA-bearing NPs as well as parallel orientation of the siRNAs provided protection against their dissociation (unlike NPs from native PEI). Our observations provide valuable insight into the integrity and structural changes of PEI/siRNA NPs during membrane crossing which will help in the design of more effective carriers for nucleic acid delivery.
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Affiliation(s)
- Yousef Nademi
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Canada.
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Gong Q, Zhang H, Zhang H, Chen C. Calculating the absolute binding free energy of the insulin dimer in an explicit solvent. RSC Adv 2020; 10:790-800. [PMID: 35494470 PMCID: PMC9047981 DOI: 10.1039/c9ra08284k] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 12/23/2019] [Indexed: 12/23/2022] Open
Abstract
Insulin is a significant hormone in the regulation of glucose level in the blood. Its monomers bind to each other to form dimers or hexamers through a complex process. To study the binding of the insulin dimer, we first calculate its absolute binding free energy by the steered molecular dynamics method and the confinement method based on a fictitious thermodynamic cycle. After considering some special correction terms, the final calculated binding free energy at 298 K is −8.97 ± 1.41 kcal mol−1, which is close to the experimental value of −7.2 ± 0.8 kcal mol−1. Furthermore, we discuss the important residue–residue interactions between the insulin monomers, including hydrophobic interactions, π–π interactions and hydrogen bond interactions. The analysis reveals five key residues, VlaB12, TyrB16, PheB24, PheB25, and TyrB26, for the dimerization of the insulin. We also perform MM-PBSA calculations for the wild-type dimer and some mutants and study the roles of the key residues by the change of the binding energy of the insulin dimer. In this paper, we calculate the absolute binding free energy of an insulin dimer by steered MD method. The result of −8.97 kcal mol−1 is close to the experimental value −7.2 kcal mol−1. We also analyze the residue–residue interactions.![]()
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Affiliation(s)
- Qiankun Gong
- Biomolecular Physics and Modeling Group
- School of Physics
- Huazhong University of Science and Technology
- Wuhan 430074
- China
| | - Haomiao Zhang
- Biomolecular Physics and Modeling Group
- School of Physics
- Huazhong University of Science and Technology
- Wuhan 430074
- China
| | - Haozhe Zhang
- Biomolecular Physics and Modeling Group
- School of Physics
- Huazhong University of Science and Technology
- Wuhan 430074
- China
| | - Changjun Chen
- Biomolecular Physics and Modeling Group
- School of Physics
- Huazhong University of Science and Technology
- Wuhan 430074
- China
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Pham T, Nguyen HL, Phan-Toai T, Nguyen H. Investigation of Binding Affinity between Potential Antiviral Agents and PB2 Protein of Influenza A: Non-equilibrium Molecular Dynamics Simulation Approach. Int J Med Sci 2020; 17:2031-2039. [PMID: 32788882 PMCID: PMC7415388 DOI: 10.7150/ijms.46231] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 07/09/2020] [Indexed: 11/30/2022] Open
Abstract
The PB2 protein of the influenza virus RNA polymerase is a major virulence determinant of influenza viruses. It binds to the cap structure at the 5' end of host mRNA to generate short capped RNA fragments that are used as primers for viral transcription named cap-snatching. A large number of the compounds were shown to bind the minimal cap-binding domain of PB2 to inhibit the cap-snatching machinery. However, their binding in the context of an extended form of the PB2 protein has remained elusive. A previous study reported some promising compounds including azaindole and hydroxymethyl azaindole, which were analyzed here to predict binding affinity to PB2 protein using the steered molecular dynamics (SMD) and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) methods. The results show that the rupture force (Fmax) value of three complexes is in agreement with the binding free energy value (ΔGbind) estimated by the MM-PBSA method, whereas for the non-equilibrium pulling work (Wpull) value a small difference between A_PB2-4 and A_PB2-12 was observed. The binding affinity results indicate the A_PB2-12 complex is more favorable than the A_PB2-4 and A_PB2-16 complexes, which means the inhibitor (12) has the potential to be further developed as anti-influenza agents in the treatment of influenza A.
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Affiliation(s)
- Tri Pham
- Institute for Computational Science and Technology, Ho Chi Minh City, Vietnam.,VNUHCM-University of Technology, Ho Chi Minh City, Vietnam
| | - Hoang Linh Nguyen
- Institute for Computational Science and Technology, Ho Chi Minh City, Vietnam.,VNUHCM-University of Technology, Ho Chi Minh City, Vietnam
| | - Tuyn Phan-Toai
- Institute for Computational Science and Technology, Ho Chi Minh City, Vietnam
| | - Hung Nguyen
- Institute for Computational Science and Technology, Ho Chi Minh City, Vietnam
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Nademi Y, Tang T, Uludağ H. Steered molecular dynamics simulations reveal a self-protecting configuration of nanoparticles during membrane penetration. NANOSCALE 2018; 10:17671-17682. [PMID: 30206609 DOI: 10.1039/c8nr04287j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Cell entry of polynucleotide-based therapeutic agents can be facilitated by nanoparticle (NP) mediated delivery. In this work, using steered molecular dynamics simulations, we simulated the membrane penetration process of a NP formed by 2 short interfering RNA (siRNA) and 6 polyethylenimine (PEI) molecules. To the best of our knowledge, this is the first set of simulations that explore the direct penetration of an siRNA/PEI NP through a membrane at an all-atom scale. Three types of PEI molecules were used for NP formation: a native PEI, a PEI modified with caprylic acids and a PEI modified with linoleic acids. We found that hydrogen bond formation between the PEIs and the membrane did not lead to instability of the siRNA/PEI NPs during the internalization process. Instead, our results suggested adoption of a "self-protecting" configuration by the siRNA/PEI NP during membrane penetration, where the siRNA/PEI NP becomes more compact and siRNAs become aligned, leading to more stable configurations while detaching from the membrane. The siRNA/PEI NP modified with linoleic acid showed the smallest structural change due to its strong intra-particle lipid associations and the resulting rigidity, while NP modified with caprylic acid showed the largest structural changes. Our observations provide unique insight into the structural changes of siRNA/PEI NPs when crossing the cell membrane, which can be important for the design of new NP carriers for nucleic acid delivery.
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Affiliation(s)
- Yousef Nademi
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Canada.
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Nguyen H, Pham T, Nguyen HL, Phan T. Investigation of Binding Affinity Between Prokaryotic Proteins (AHU-IHF) and DNAs: Steered Molecular Dynamics Approach. Appl Biochem Biotechnol 2018; 186:834-846. [DOI: 10.1007/s12010-018-2735-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 03/12/2018] [Indexed: 11/29/2022]
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