1
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Tiemann JKS, Szczuka M, Bouarroudj L, Oussaren M, Garcia S, Howard RJ, Delemotte L, Lindahl E, Baaden M, Lindorff-Larsen K, Chavent M, Poulain P. MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.02.538537. [PMID: 37205542 PMCID: PMC10187166 DOI: 10.1101/2023.05.02.538537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The rise of open science and the absence of a global dedicated data repository for molecular dynamics (MD) simulations has led to the accumulation of MD files in generalist data repositories, constituting the dark matter of MD - data that is technically accessible, but neither indexed, curated, or easily searchable. Leveraging an original search strategy, we found and indexed about 250,000 files and 2,000 datasets from Zenodo, Figshare and Open Science Framework. With a focus on files produced by the Gromacs MD software, we illustrate the potential offered by the mining of publicly available MD data. We identified systems with specific molecular composition and were able to characterize essential parameters of MD simulation such as temperature and simulation length, and could identify model resolution, such as all-atom and coarse-grain. Based on this analysis, we inferred metadata to propose a search engine prototype to explore the MD data. To continue in this direction, we call on the community to pursue the effort of sharing MD data, and to report and standardize metadata to reuse this valuable matter.
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2
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Belghit H, Spivak M, Dauchez M, Baaden M, Jonquet-Prevoteau J. From complex data to clear insights: visualizing molecular dynamics trajectories. FRONTIERS IN BIOINFORMATICS 2024; 4:1356659. [PMID: 38665177 PMCID: PMC11043564 DOI: 10.3389/fbinf.2024.1356659] [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: 12/15/2023] [Accepted: 03/14/2024] [Indexed: 04/28/2024] Open
Abstract
Advances in simulations, combined with technological developments in high-performance computing, have made it possible to produce a physically accurate dynamic representation of complex biological systems involving millions to billions of atoms over increasingly long simulation times. The analysis of these computed simulations is crucial, involving the interpretation of structural and dynamic data to gain insights into the underlying biological processes. However, this analysis becomes increasingly challenging due to the complexity of the generated systems with a large number of individual runs, ranging from hundreds to thousands of trajectories. This massive increase in raw simulation data creates additional processing and visualization challenges. Effective visualization techniques play a vital role in facilitating the analysis and interpretation of molecular dynamics simulations. In this paper, we focus mainly on the techniques and tools that can be used for visualization of molecular dynamics simulations, among which we highlight the few approaches used specifically for this purpose, discussing their advantages and limitations, and addressing the future challenges of molecular dynamics visualization.
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Affiliation(s)
- Hayet Belghit
- Université de Reims Champagne-Ardenne, CNRS, MEDYC, Reims, France
| | - Mariano Spivak
- Université Paris Cité, CNRS, Laboratoire de Biochimie Théorique, Paris, France
| | - Manuel Dauchez
- Université de Reims Champagne-Ardenne, CNRS, MEDYC, Reims, France
| | - Marc Baaden
- Université Paris Cité, CNRS, Laboratoire de Biochimie Théorique, Paris, France
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3
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Yu I, Mori T, Matsuoka D, Surblys D, Sugita Y. SPANA: Spatial decomposition analysis for cellular-scale molecular dynamics simulations. J Comput Chem 2024; 45:498-505. [PMID: 37966727 DOI: 10.1002/jcc.27260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/31/2023] [Accepted: 11/02/2023] [Indexed: 11/16/2023]
Abstract
The rapid increase in computational power with the latest supercomputers has enabled atomistic molecular dynamics (MDs) simulations of biomolecules in biological membrane, cytoplasm, and other cellular environments. These environments often contain a million or more atoms to be simulated simultaneously. Therefore, their trajectory analyses involve heavy computations that can become a bottleneck in the computational studies. Spatial decomposition analysis (SPANA) is a set of analysis tools in the Generalized-Ensemble Simulation System (GENESIS) software package that can carry out MD trajectory analyses of large-scale biological simulations using multiple CPU cores in parallel. SPANA applies the spatial decomposition of a large biological system to distribute structural and dynamical analyses into individual CPU cores, which reduces the computational time and the memory size, significantly. SPANA opens new possibilities for detailed atomistic analyses of biomacromolecules as well as solvent water molecules, ions, and metabolites in MD simulation trajectories of very large biological systems containing more than millions of atoms in cellular environments.
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Affiliation(s)
- Isseki Yu
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- Department of Bioinformatics, Maebashi Institute of Technology, Maebashi, Gunma, Japan
| | - Takaharu Mori
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
| | - Daisuke Matsuoka
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
| | - Donatas Surblys
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo, Japan
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4
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Caparotta M, Perez A. Advancing Molecular Dynamics: Toward Standardization, Integration, and Data Accessibility in Structural Biology. J Phys Chem B 2024; 128:2219-2227. [PMID: 38418288 DOI: 10.1021/acs.jpcb.3c04823] [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: 03/01/2024]
Abstract
Molecular dynamics (MD) simulations have become a valuable tool in structural biology, offering insights into complex biological systems that are difficult to obtain through experimental techniques alone. The lack of available data sets and structures in most published computational work has limited other researchers' use of these models. In recent years, the emergence of online sharing platforms and MD database initiatives favor the deposition of ensembles and structures to accompany publications, favoring reuse of the data sets. However, the lack of uniform metadata collection, formats, and what data are deposited limits the impact and its use by different communities that are not necessarily experts in MD. This Perspective highlights the need for standardization and better resource sharing for processing and interpreting MD simulation results, akin to efforts in other areas of structural biology. As the field moves forward, we will see an increase in popularity and benefits of MD-based integrative approaches combining experimental data and simulations through probabilistic reasoning, but these too are limited by uniformity in experimental data availability and choices on how the data are modeled that are not trivial to decipher from papers. Other fields have addressed similar challenges comprehensively by establishing task forces with different degrees of success. The large scope and number of communities to represent the breadth of types of MD simulations complicates a parallel approach that would fit all. Thus, each group typically decides what data and which format to upload on servers like Zenodo. Uploading data with FAIR (findable, accessible, interoperable, reusable) principles in mind including optimal metadata collection will make the data more accessible and actionable by the community. Such a wealth of simulation data will foster method development and infrastructure advancements, thus propelling the field forward.
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Affiliation(s)
- Marcelo Caparotta
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, Florida 32611, United States
| | - Alberto Perez
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, Florida 32611, United States
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5
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Ray D, Parrinello M. Data-driven classification of ligand unbinding pathways. Proc Natl Acad Sci U S A 2024; 121:e2313542121. [PMID: 38412121 DOI: 10.1073/pnas.2313542121] [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: 08/07/2023] [Accepted: 01/26/2024] [Indexed: 02/29/2024] Open
Abstract
Studying the pathways of ligand-receptor binding is essential to understand the mechanism of target recognition by small molecules. The binding free energy and kinetics of protein-ligand complexes can be computed using molecular dynamics (MD) simulations, often in quantitative agreement with experiments. However, only a qualitative picture of the ligand binding/unbinding paths can be obtained through a conventional analysis of the MD trajectories. Besides, the higher degree of manual effort involved in analyzing pathways limits its applicability in large-scale drug discovery. Here, we address this limitation by introducing an automated approach for analyzing molecular transition paths with a particular focus on protein-ligand dissociation. Our method is based on the dynamic time-warping algorithm, originally designed for speech recognition. We accurately classified molecular trajectories using a very generic descriptor set of contacts or distances. Our approach outperforms manual classification by distinguishing between parallel dissociation channels, within the pathways identified by visual inspection. Most notably, we could compute exit-path-specific ligand-dissociation kinetics. The unbinding timescale along the fastest path agrees with the experimental residence time, providing a physical interpretation to our entirely data-driven protocol. In combination with appropriate enhanced sampling algorithms, this technique can be used for the initial exploration of ligand-dissociation pathways as well as for calculating path-specific thermodynamic and kinetic properties.
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Affiliation(s)
- Dhiman Ray
- Simulations Research Line, Italian Institute of Technology, Via Enrico Melen 83, Genova GE 16152, Italy
| | - Michele Parrinello
- Simulations Research Line, Italian Institute of Technology, Via Enrico Melen 83, Genova GE 16152, Italy
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6
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Maity S, Acharya A. Many Roles of Carbohydrates: A Computational Spotlight on the Coronavirus S Protein Binding. ACS APPLIED BIO MATERIALS 2024; 7:646-656. [PMID: 36947738 PMCID: PMC10880061 DOI: 10.1021/acsabm.2c01064] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/08/2023] [Indexed: 03/24/2023]
Abstract
Glycosylation is one of the post-translational modifications with more than 50% of human proteins being glycosylated. The exact nature and chemical composition of glycans are inaccessible to X-ray or cryo-electron microscopy imaging techniques. Therefore, computational modeling studies and molecular dynamics must be used as a "computational microscope". The spike (S) protein of SARS-CoV-2 is heavily glycosylated, and a few glycans play a more functional role "beyond shielding". In this mini-review, we discuss computational investigations of the roles of specific S-protein and ACE2 glycans in the overall ACE2-S protein binding. We highlight different functions of specific glycans demonstrated in myriad computational models and simulations in the context of the SARS-CoV-2 virus binding to the receptor. We also discuss interactions between glycocalyx and the S protein, which may be utilized to design prophylactic polysaccharide-based therapeutics targeting the S protein. In addition, we underline the recent emergence of coronavirus variants and their impact on the S protein and its glycans.
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Affiliation(s)
- Suman Maity
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
| | - Atanu Acharya
- Department
of Chemistry, Syracuse University, Syracuse, New York 13244, United States
- BioInspired
Syracuse, Syracuse University, Syracuse, New York 13244, United States
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7
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Jin Z, Wei Z. Molecular simulation for food protein-ligand interactions: A comprehensive review on principles, current applications, and emerging trends. Compr Rev Food Sci Food Saf 2024; 23:e13280. [PMID: 38284571 DOI: 10.1111/1541-4337.13280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 11/19/2023] [Accepted: 11/22/2023] [Indexed: 01/30/2024]
Abstract
In recent years, investigations on molecular interaction mechanisms between food proteins and ligands have attracted much interest. The interaction mechanisms can supply much useful information for many fields in the food industry, including nutrient delivery, food processing, auxiliary detection, and others. Molecular simulation has offered extraordinary insights into the interaction mechanisms. It can reflect binding conformation, interaction forces, binding affinity, key residues, and other information that physicochemical experiments cannot reveal in a fast and detailed manner. The simulation results have proven to be consistent with the results of physicochemical experiments. Molecular simulation holds great potential for future applications in the field of food protein-ligand interactions. This review elaborates on the principles of molecular docking and molecular dynamics simulation. Besides, their applications in food protein-ligand interactions are summarized. Furthermore, challenges, perspectives, and trends in molecular simulation of food protein-ligand interactions are proposed. Based on the results of molecular simulation, the mechanisms of interfacial behavior, enzyme-substrate binding, and structural changes during food processing can be reflected, and strategies for hazardous substance detection and food flavor adjustment can be generated. Moreover, molecular simulation can accelerate food development and reduce animal experiments. However, there are still several challenges to applying molecular simulation to food protein-ligand interaction research. The future trends will be a combination of international cooperation and data sharing, quantum mechanics/molecular mechanics, advanced computational techniques, and machine learning, which contribute to promoting food protein-ligand interaction simulation. Overall, the use of molecular simulation to study food protein-ligand interactions has a promising prospect.
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Affiliation(s)
- Zihan Jin
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Zihao Wei
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao, China
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8
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Firouzi R, Ashouri M. Identification of Potential Anti‐COVID‐19 Drug Leads from Medicinal Plants through Virtual High‐Throughput Screening. ChemistrySelect 2023. [DOI: 10.1002/slct.202203865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Affiliation(s)
- Rohoullah Firouzi
- Department of Physical Chemistry Chemistry and Chemical Engineering Research Center of Iran Tehran Iran
| | - Mitra Ashouri
- Department of Physical Chemistry School of Chemistry College of Science University of Tehran Tehran Iran
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9
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Sahihi M, Faraudo J. Molecular Dynamics Simulations of Adsorption of SARS-CoV-2 Spike Protein on Polystyrene Surface. J Chem Inf Model 2022; 62:3814-3824. [PMID: 35926227 PMCID: PMC9364975 DOI: 10.1021/acs.jcim.2c00562] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
A prominent feature of coronaviruses is the presence
of a large
glycoprotein spike (S) protruding from the viral particle. The specific
interactions of a material with S determine key aspects such as its
possible role for indirect transmission or its suitability as a virucidal
material. Here, we consider all-atom molecular dynamics simulations
of the interaction between a polymer surface (polystyrene) and S in
its up and down conformations. Polystyrene is a commonly used plastic
found in electronics, toys, and many other common objects. Also, previous
atomic force microscopy (AFM) experiments showed substantial adhesion
of S over polystyrene, stronger than in other common materials. Our
results show that the main driving forces for the adsorption of the
S protein over polystyrene were hydrophobic and π–π
interactions with S amino acids and glycans. The interaction was stronger
for the case of S in the up conformation, which exposes one highly
flexible receptor binding domain (RBD) that adjusts its conformation
to interact with the polymer surface. In this case, the interaction
has similar contributions from the RBD and glycans. In the case of
S in the down conformation, the interaction with the polystyrene surface
was weaker and it was dominated by glycans located near the RBD. We
do not find significant structural changes in the conformation of
S, a result which is in deep contrast to our previous results with
another hydrophobic surface (graphite). Our results suggest that SARS-CoV-2
virions may adsorb strongly over plastic surfaces without significantly
affecting their infectivity.
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Affiliation(s)
- Mehdi Sahihi
- Institut de Ciencia de Materials de Barcelona (ICMAB-CSIC), Campus de la UAB, Bellaterra, E-08193 Barcelona, Spain
| | - Jordi Faraudo
- Institut de Ciencia de Materials de Barcelona (ICMAB-CSIC), Campus de la UAB, Bellaterra, E-08193 Barcelona, Spain
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10
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Folescu DE, Onufriev AV. A Closed-Form, Analytical Approximation for Apparent Surface Charge and Electric Field of Molecules. ACS OMEGA 2022; 7:26123-26136. [PMID: 35936397 PMCID: PMC9352323 DOI: 10.1021/acsomega.2c01484] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
Closed-form, analytical approximations for electrostatic properties of molecules are of unique value as these can provide computational speed, versatility, and physical insight. Here, we have derived a simple, closed-form formula for the apparent surface charge (ASC) as well as for the electric field generated by a molecular charge distribution in aqueous solution. The approximation, with no fitted parameters, was tested against numerical solutions of the Poisson equation, where it has produced a significant speed-up. For neutral small molecules, the hydration free energies estimated from the closed-form ASC formula are within 0.8 kcal/mol RMSD from the numerical Poisson reference; the electric field at the surface is in quantitative agreement with the reference. Performance of the approximation was also tested on larger structures, including a protein, a DNA fragment, and a viral receptor-target complex. For all structures tested, a near-quantitative agreement with the numerical Poisson reference was achieved, except in regions of high negative curvature, where the new approximation is still qualitatively correct. A unique efficiency feature of the proposed "source-based″ closed-form approximation is that the ASC and electric field can be estimated individually at any point or surface patch, without the need to obtain the full global solution. An open-source software implementation of the method is available: https://people.cs.vt.edu/~onufriev/CODES/aasc.zip.
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Affiliation(s)
- Dan E. Folescu
- Department
of Computer Science, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Alexey V. Onufriev
- Department
of Computer Science, Virginia Tech, Blacksburg, Virginia 24061, United States
- Department
of Physics, Virginia Tech, Blacksburg, Virginia 24061, United States
- Center
for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia 24061, United States
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11
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Structure and dynamics of SARS-CoV-2 proofreading exoribonuclease ExoN. Proc Natl Acad Sci U S A 2022; 119:2106379119. [PMID: 35165203 PMCID: PMC8892293 DOI: 10.1073/pnas.2106379119] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2022] [Indexed: 12/13/2022] Open
Abstract
High-fidelity replication of the large RNA genome of coronaviruses (CoVs) is mediated by a 3'-to-5' exoribonuclease (ExoN) in nonstructural protein 14 (nsp14), which excises nucleotides including antiviral drugs misincorporated by the low-fidelity viral RNA-dependent RNA polymerase (RdRp) and has also been implicated in viral RNA recombination and resistance to innate immunity. Here, we determined a 1.6-Å resolution crystal structure of severe acute respiratory syndrome CoV 2 (SARS-CoV-2) ExoN in complex with its essential cofactor, nsp10. The structure shows a highly basic and concave surface flanking the active site, comprising several Lys residues of nsp14 and the N-terminal amino group of nsp10. Modeling suggests that this basic patch binds to the template strand of double-stranded RNA substrates to position the 3' end of the nascent strand in the ExoN active site, which is corroborated by mutational and computational analyses. We also show that the ExoN activity can rescue a stalled RNA primer poisoned with sofosbuvir and allow RdRp to continue its extension in the presence of the chain-terminating drug, biochemically recapitulating proofreading in SARS-CoV-2 replication. Molecular dynamics simulations further show remarkable flexibility of multidomain nsp14 and suggest that nsp10 stabilizes ExoN for substrate RNA binding to support its exonuclease activity. Our high-resolution structure of the SARS-CoV-2 ExoN-nsp10 complex serves as a platform for future development of anticoronaviral drugs or strategies to attenuate the viral virulence.
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12
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Martin W, Sheynkman G, Lightstone FC, Nussinov R, Cheng F. Interpretable artificial intelligence and exascale molecular dynamics simulations to reveal kinetics: Applications to Alzheimer's disease. Curr Opin Struct Biol 2022; 72:103-113. [PMID: 34628220 PMCID: PMC8860862 DOI: 10.1016/j.sbi.2021.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 02/03/2023]
Abstract
The rapid increase in computing power, especially with the integration of graphics processing units, has dramatically increased the capabilities of molecular dynamics simulations. To date, these capabilities extend from running very long simulations (tens to hundreds of microseconds) to thousands of short simulations. However, the expansive data generated in these simulations must be made interpretable not only by the investigator who performs them but also by others as well. Here, we demonstrate how integrating learning techniques, such as artificial intelligence, machine learning, and neural networks, into analysis pipelines can reveal the kinetics of Alzheimer's disease (AD) protein aggregation. We review select AD targets, describe current simulation methods, and introduce learning concepts and their application in AD, highlighting limitations and potential solutions.
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Affiliation(s)
- William Martin
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Gloria Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, 22903, USA
| | - Felice C Lightstone
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Lab, Livermore, CA, 94550, USA
| | - Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD, 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Feixiong Cheng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA; Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, 44195, USA; Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
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13
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Roy R, Jonniya NA, Poddar S, Sk MF, Kar P. Unraveling the Molecular Mechanism of Recognition of Human Interferon-Stimulated Gene Product 15 by Coronavirus Papain-Like Proteases: A Multiscale Simulation Study. J Chem Inf Model 2021; 61:6038-6052. [PMID: 34784198 PMCID: PMC8610008 DOI: 10.1021/acs.jcim.1c00918] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Indexed: 12/21/2022]
Abstract
The papain-like protease (PLpro) of the coronavirus (CoV) family plays an essential role in processing the viral polyprotein and immune evasion. Additional proteolytic activities of PLpro include deubiquitination and deISGylation, which can reverse the post-translational modification of cellular proteins conjugated with ubiquitin or (Ub) or Ub-like interferon-stimulated gene product 15 (ISG15). These activities regulate innate immune responses against viral infection. Thus, PLpro is a potential antiviral target. Here, we have described the structural and energetic basis of recognition of PLpro by the human ISG15 protein (hISG15) using atomistic molecular dynamics simulation across the CoV family, i.e., MERS-CoV (MCoV), SARS-CoV (SCoV), and SARS-CoV-2 (SCoV2). The cumulative simulation length for all trajectories was 32.0 μs. In the absence of the complete crystal structure of complexes, protein-protein docking was used. A mutation (R167E) was introduced across all three PLpro to study the effect of mutation on the protein-protein binding. Our study reveals that the apo-ISG15 protein remains closed while it adopts an open conformation when bound to PLpro, although the degree of openness varies across the CoV family. The binding free energy analysis suggests that hISG15 binds more strongly with SCoV2-PLpro compared to SCoV or MCoV. The intermolecular electrostatic interaction drives the hISG15-PLpro complexation. Our study showed that SCoV or MCoV-PLpro binds more strongly with the C-domain of hISG15, while SCoV2-PLpro binds more favorably the N-domain of hISG15. Overall, our study explains the molecular basis of differential deISGylating activities of PLpro among the CoV family and the specificity of SCoV2-PLpro toward hISG15.
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Affiliation(s)
- Rajarshi Roy
- Department of Biosciences and Biomedical Engineering, Indian
Institute of Technology Indore, Khandwa Road, Simrol, Madhya Pradesh
453552, India
| | - Nisha Amarnath Jonniya
- Department of Biosciences and Biomedical Engineering, Indian
Institute of Technology Indore, Khandwa Road, Simrol, Madhya Pradesh
453552, India
| | - Sayan Poddar
- Department of Biosciences and Biomedical Engineering, Indian
Institute of Technology Indore, Khandwa Road, Simrol, Madhya Pradesh
453552, India
| | - Md Fulbabu Sk
- Department of Biosciences and Biomedical Engineering, Indian
Institute of Technology Indore, Khandwa Road, Simrol, Madhya Pradesh
453552, India
| | - Parimal Kar
- Department of Biosciences and Biomedical Engineering, Indian
Institute of Technology Indore, Khandwa Road, Simrol, Madhya Pradesh
453552, India
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14
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Emrani J, Ahmed M, Jeffers-Francis L, Teleha JC, Mowa N, Newman RH, Thomas MD. SARS-COV-2, infection, transmission, transcription, translation, proteins, and treatment: A review. Int J Biol Macromol 2021; 193:1249-1273. [PMID: 34756970 PMCID: PMC8552795 DOI: 10.1016/j.ijbiomac.2021.10.172] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 10/21/2021] [Indexed: 01/18/2023]
Abstract
In this review, we describe the key molecular entities involved in the process of infection by SARS-CoV-2, while also detailing how those key entities influence the spread of the disease. We further introduce the molecular mechanisms of preventive and treatment strategies including drugs, antibodies, and vaccines.
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Affiliation(s)
- Jahangir Emrani
- Department of Chemistry, North Carolina A&T State University, Greensboro, NC 27411, United States of America.
| | - Maryam Ahmed
- Department of Biology, Appalachian State University, Boone, NC 28608, United States of America
| | - Liesl Jeffers-Francis
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, United States of America
| | - John C Teleha
- Department of Reference and Instruction, North Carolina A&T State University, Greensboro, NC 27411, United States of America
| | - Nathan Mowa
- Department of Biology, Appalachian State University, Boone, NC 28608, United States of America
| | - Robert H Newman
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, United States of America
| | - Misty D Thomas
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, United States of America
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15
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Torrens-Fontanals M, Peralta-García A, Talarico C, Guixà-González R, Giorgino T, Selent J. SCoV2-MD: a database for the dynamics of the SARS-CoV-2 proteome and variant impact predictions. Nucleic Acids Res 2021; 50:D858-D866. [PMID: 34761257 PMCID: PMC8689960 DOI: 10.1093/nar/gkab977] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/21/2021] [Accepted: 11/08/2021] [Indexed: 11/23/2022] Open
Abstract
SCoV2-MD (www.scov2-md.org) is a new
online resource that systematically organizes atomistic simulations of the
SARS-CoV-2 proteome. The database includes simulations produced by leading
groups using molecular dynamics (MD) methods to investigate the
structure-dynamics-function relationships of viral proteins. SCoV2-MD
cross-references the molecular data with the pandemic evolution by tracking all
available variants sequenced during the pandemic and deposited in the GISAID
resource. SCoV2-MD enables the interactive analysis of the deposited
trajectories through a web interface, which enables users to search by viral
protein, isolate, phylogenetic attributes, or specific point mutation. Each
mutation can then be analyzed interactively combining static (e.g. a variety of
amino acid substitution penalties) and dynamic (time-dependent data derived from
the dynamics of the local geometry) scores. Dynamic scores can be computed on
the basis of nine non-covalent interaction types, including steric properties,
solvent accessibility, hydrogen bonding, and other types of chemical
interactions. Where available, experimental data such as antibody escape and
change in binding affinities from deep mutational scanning experiments are also
made available. All metrics can be combined to build predefined or custom scores
to interrogate the impact of evolving variants on protein structure and
function. SCoV2-MD is a new online resource that systematically organizes atomistic
simulations of the SARS-CoV-2 proteome. The database includes simulations
produced by leading groups using molecular dynamics (MD) methods to investigate
the structure-dynamics-function relationships of viral proteins. SCoV2-MD
cross-references the molecular data with the pandemic evolution by tracking all
available variants sequenced during the pandemic and deposited in the GISAID
resource. SCoV2-MD enables the interactive analysis of the deposited
trajectories through a web interface, which enables users to search by viral
protein, isolate, phylogenetic attributes, or specific point mutation. Each
mutation can then be analyzed interactively combining static (e.g. a variety of
amino acid substitution penalties) and dynamic (time-dependent data derived from
the dynamics of the local geometry) scores.
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Affiliation(s)
- Mariona Torrens-Fontanals
- Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute-Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona 08003, Spain
| | - Alejandro Peralta-García
- Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute-Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona 08003, Spain
| | - Carmine Talarico
- EXSCALATE, Dompé Farmaceutici S.p.A., Via Tommaso De Amicis, 95, Napoli, 80131, Italy
| | - Ramon Guixà-González
- Laboratory of Biomolecular Research, Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland.,Condensed Matter Theory Group, Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
| | - Toni Giorgino
- Biophysics Institute (CNR-IBF), National Research Council of Italy, Milan 20133, Italy.,Department of Biosciences, University of Milan, Milan 20133, Italy
| | - Jana Selent
- Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute-Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona 08003, Spain
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16
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Casalino L, Dommer AC, Gaieb Z, Barros EP, Sztain T, Ahn SH, Trifan A, Brace A, Bogetti AT, Clyde A, Ma H, Lee H, Turilli M, Khalid S, Chong LT, Simmerling C, Hardy DJ, Maia JD, Phillips JC, Kurth T, Stern AC, Huang L, McCalpin JD, Tatineni M, Gibbs T, Stone JE, Jha S, Ramanathan A, Amaro RE. AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics. THE INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS 2021; 35:432-451. [PMID: 38603008 PMCID: PMC8064023 DOI: 10.1177/10943420211006452] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
We develop a generalizable AI-driven workflow that leverages heterogeneous HPC resources to explore the time-dependent dynamics of molecular systems. We use this workflow to investigate the mechanisms of infectivity of the SARS-CoV-2 spike protein, the main viral infection machinery. Our workflow enables more efficient investigation of spike dynamics in a variety of complex environments, including within a complete SARS-CoV-2 viral envelope simulation, which contains 305 million atoms and shows strong scaling on ORNL Summit using NAMD. We present several novel scientific discoveries, including the elucidation of the spike's full glycan shield, the role of spike glycans in modulating the infectivity of the virus, and the characterization of the flexible interactions between the spike and the human ACE2 receptor. We also demonstrate how AI can accelerate conformational sampling across different systems and pave the way for the future application of such methods to additional studies in SARS-CoV-2 and other molecular systems.
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Affiliation(s)
- Lorenzo Casalino
- University of California San Diego, La Jolla, CA, USA
- Authors with symbol indicate equal contribution
| | - Abigail C Dommer
- University of California San Diego, La Jolla, CA, USA
- Authors with symbol indicate equal contribution
| | - Zied Gaieb
- University of California San Diego, La Jolla, CA, USA
- Authors with symbol indicate equal contribution
| | | | - Terra Sztain
- University of California San Diego, La Jolla, CA, USA
| | - Surl-Hee Ahn
- University of California San Diego, La Jolla, CA, USA
| | - Anda Trifan
- Argonne National Lab, Lemont, IL, USA
- University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | | | - Austin Clyde
- Argonne National Lab, Lemont, IL, USA
- University of Chicago, Chicago, IL, USA
| | - Heng Ma
- Argonne National Lab, Lemont, IL, USA
| | | | | | | | | | | | - David J Hardy
- University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Julio Dc Maia
- University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | | | | | - Lei Huang
- Texas Advanced Computing Center, Austin, TX, USA
| | | | | | - Tom Gibbs
- NVIDIA Corporation, Santa Clara, CA, USA
| | - John E Stone
- University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Shantenu Jha
- Rutgers University, Piscataway, NJ, USA
- Brookhaven National Lab, Upton, NY, USA
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17
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Muratov EN, Amaro R, Andrade CH, Brown N, Ekins S, Fourches D, Isayev O, Kozakov D, Medina-Franco JL, Merz KM, Oprea TI, Poroikov V, Schneider G, Todd MH, Varnek A, Winkler DA, Zakharov AV, Cherkasov A, Tropsha A. A critical overview of computational approaches employed for COVID-19 drug discovery. Chem Soc Rev 2021; 50:9121-9151. [PMID: 34212944 PMCID: PMC8371861 DOI: 10.1039/d0cs01065k] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Indexed: 01/18/2023]
Abstract
COVID-19 has resulted in huge numbers of infections and deaths worldwide and brought the most severe disruptions to societies and economies since the Great Depression. Massive experimental and computational research effort to understand and characterize the disease and rapidly develop diagnostics, vaccines, and drugs has emerged in response to this devastating pandemic and more than 130 000 COVID-19-related research papers have been published in peer-reviewed journals or deposited in preprint servers. Much of the research effort has focused on the discovery of novel drug candidates or repurposing of existing drugs against COVID-19, and many such projects have been either exclusively computational or computer-aided experimental studies. Herein, we provide an expert overview of the key computational methods and their applications for the discovery of COVID-19 small-molecule therapeutics that have been reported in the research literature. We further outline that, after the first year the COVID-19 pandemic, it appears that drug repurposing has not produced rapid and global solutions. However, several known drugs have been used in the clinic to cure COVID-19 patients, and a few repurposed drugs continue to be considered in clinical trials, along with several novel clinical candidates. We posit that truly impactful computational tools must deliver actionable, experimentally testable hypotheses enabling the discovery of novel drugs and drug combinations, and that open science and rapid sharing of research results are critical to accelerate the development of novel, much needed therapeutics for COVID-19.
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Affiliation(s)
- Eugene N. Muratov
- UNC Eshelman School of Pharmacy, University of North CarolinaChapel HillNCUSA
| | - Rommie Amaro
- University of California in San DiegoSan DiegoCAUSA
| | | | | | - Sean Ekins
- Collaborations PharmaceuticalsRaleighNCUSA
| | - Denis Fourches
- Department of Chemistry, North Carolina State UniversityRaleighNCUSA
| | - Olexandr Isayev
- Department of Chemistry, Carnegie Melon UniversityPittsburghPAUSA
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook UniversityStony BrookNYUSA
| | | | - Kenneth M. Merz
- Department of Chemistry, Michigan State UniversityEast LansingMIUSA
| | - Tudor I. Oprea
- Department of Internal Medicine and UNM Comprehensive Cancer Center, University of New Mexico, AlbuquerqueNMUSA
- Department of Rheumatology and Inflammation Research, Gothenburg UniversitySweden
- Novo Nordisk Foundation Center for Protein Research, University of CopenhagenDenmark
| | | | - Gisbert Schneider
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of TechnologyZurichSwitzerland
| | | | - Alexandre Varnek
- Department of Chemistry, University of StrasbourgStrasbourgFrance
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido UniversitySapporoJapan
| | - David A. Winkler
- Monash Institute of Pharmaceutical Sciences, Monash UniversityMelbourneVICAustralia
- School of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe UniversityBundooraAustralia
- School of Pharmacy, University of NottinghamNottinghamUK
| | | | - Artem Cherkasov
- Vancouver Prostate Centre, University of British ColumbiaVancouverBCCanada
| | - Alexander Tropsha
- UNC Eshelman School of Pharmacy, University of North CarolinaChapel HillNCUSA
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18
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Sztain T, Ahn SH, Bogetti AT, Casalino L, Goldsmith JA, Seitz E, McCool RS, Kearns FL, Acosta-Reyes F, Maji S, Mashayekhi G, McCammon JA, Ourmazd A, Frank J, McLellan JS, Chong LT, Amaro RE. A glycan gate controls opening of the SARS-CoV-2 spike protein. Nat Chem 2021; 13:963-968. [PMID: 34413500 PMCID: PMC8488004 DOI: 10.1038/s41557-021-00758-3] [Citation(s) in RCA: 202] [Impact Index Per Article: 67.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 06/21/2021] [Indexed: 12/18/2022]
Abstract
SARS-CoV-2 infection is controlled by the opening of the spike protein receptor binding domain (RBD), which transitions from a glycan-shielded 'down' to an exposed 'up' state to bind the human angiotensin-converting enzyme 2 receptor and infect cells. While snapshots of the 'up' and 'down' states have been obtained by cryo-electron microscopy and cryo-electron tomagraphy, details of the RBD-opening transition evade experimental characterization. Here over 130 µs of weighted ensemble simulations of the fully glycosylated spike ectodomain allow us to characterize more than 300 continuous, kinetically unbiased RBD-opening pathways. Together with ManifoldEM analysis of cryo-electron microscopy data and biolayer interferometry experiments, we reveal a gating role for the N-glycan at position N343, which facilitates RBD opening. Residues D405, R408 and D427 also participate. The atomic-level characterization of the glycosylated spike activation mechanism provided herein represents a landmark study for ensemble pathway simulations and offers a foundation for understanding the fundamental mechanisms of SARS-CoV-2 viral entry and infection.
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Affiliation(s)
- Terra Sztain
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA, USA
| | - Surl-Hee Ahn
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA, USA
| | - Anthony T Bogetti
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lorenzo Casalino
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA, USA
| | - Jory A Goldsmith
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Evan Seitz
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Ryan S McCool
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Fiona L Kearns
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA, USA
| | - Francisco Acosta-Reyes
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY, USA
| | - Suvrajit Maji
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY, USA
| | - Ghoncheh Mashayekhi
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA, USA.,Department of Pharmacology, University of California-San Diego, La Jolla, CA, USA
| | - Abbas Ourmazd
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Joachim Frank
- Department of Biological Sciences, Columbia University, New York, NY, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Lillian T Chong
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA, USA.
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19
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Agamennone M, Nicoli A, Bayer S, Weber V, Borro L, Gupta S, Fantacuzzi M, Di Pizio A. Protein-protein interactions at a glance: Protocols for the visualization of biomolecular interactions. Methods Cell Biol 2021; 166:271-307. [PMID: 34752337 DOI: 10.1016/bs.mcb.2021.06.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Protein-protein interactions (PPIs) play a key role in many biological processes and are intriguing targets for drug discovery campaigns. Advancements in experimental and computational techniques are leading to a growth of data accessibility, and, with it, an increased need for the analysis of PPIs. In this respect, visualization tools are essential instruments to represent and analyze biomolecular interactions. In this chapter, we reviewed some of the available tools, highlighting their features, and describing their functions with practical information on their usage.
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Affiliation(s)
| | - Alessandro Nicoli
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
| | - Sebastian Bayer
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
| | - Verena Weber
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
| | - Luca Borro
- Department of Imaging, Advanced Cardiovascular Imaging Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Shailendra Gupta
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
| | | | - Antonella Di Pizio
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany.
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20
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Sztain T, Amaro R, McCammon JA. Elucidation of Cryptic and Allosteric Pockets within the SARS-CoV-2 Main Protease. J Chem Inf Model 2021; 61:3495-3501. [PMID: 33939913 PMCID: PMC8117783 DOI: 10.1021/acs.jcim.1c00140] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Indexed: 01/09/2023]
Abstract
The SARS-CoV-2 pandemic has rapidly spread across the globe, posing an urgent health concern. Many quests to computationally identify treatments against the virus rely on in silico small molecule docking to experimentally determined structures of viral proteins. One limit to these approaches is that protein dynamics are often unaccounted for, leading to overlooking transient, druggable conformational states. Using Gaussian accelerated molecular dynamics to enhance sampling of conformational space, we identified cryptic pockets within the SARS-CoV-2 main protease, including some within regions far from the active site. These simulations sampled comparable dynamics and pocket volumes to conventional brute force simulations carried out on two orders of magnitude greater timescales.
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Affiliation(s)
| | - Rommie Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - J. Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093, United States
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21
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Zimmerman MI, Porter JR, Ward MD, Singh S, Vithani N, Meller A, Mallimadugula UL, Kuhn CE, Borowsky JH, Wiewiora RP, Hurley MFD, Harbison AM, Fogarty CA, Coffland JE, Fadda E, Voelz VA, Chodera JD, Bowman GR. SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome. Nat Chem 2021; 13:651-659. [PMID: 34031561 PMCID: PMC8249329 DOI: 10.1038/s41557-021-00707-0] [Citation(s) in RCA: 127] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 04/14/2021] [Indexed: 01/20/2023]
Abstract
SARS-CoV-2 has intricate mechanisms for initiating infection, immune evasion/suppression and replication that depend on the structure and dynamics of its constituent proteins. Many protein structures have been solved, but far less is known about their relevant conformational changes. To address this challenge, over a million citizen scientists banded together through the Folding@home distributed computing project to create the first exascale computer and simulate 0.1 seconds of the viral proteome. Our adaptive sampling simulations predict dramatic opening of the apo spike complex, far beyond that seen experimentally, explaining and predicting the existence of 'cryptic' epitopes. Different spike variants modulate the probabilities of open versus closed structures, balancing receptor binding and immune evasion. We also discover dramatic conformational changes across the proteome, which reveal over 50 'cryptic' pockets that expand targeting options for the design of antivirals. All data and models are freely available online, providing a quantitative structural atlas.
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Affiliation(s)
- Maxwell I Zimmerman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St Louis, MO, USA
| | - Justin R Porter
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St Louis, MO, USA
| | - Michael D Ward
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St Louis, MO, USA
| | - Sukrit Singh
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St Louis, MO, USA
| | - Neha Vithani
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St Louis, MO, USA
| | - Artur Meller
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St Louis, MO, USA
| | - Upasana L Mallimadugula
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St Louis, MO, USA
| | - Catherine E Kuhn
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St Louis, MO, USA
| | - Jonathan H Borowsky
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St Louis, MO, USA
| | - Rafal P Wiewiora
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, NY, New York, USA
- Computational and Systems Biology Program, Sloan Kettering Institute, NY, New York, USA
| | | | - Aoife M Harbison
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Ireland
| | - Carl A Fogarty
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Ireland
| | | | - Elisa Fadda
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Ireland
| | - Vincent A Voelz
- Department of Chemistry, Temple University, Philadelphia, PA, USA
| | - John D Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, NY, New York, USA
| | - Gregory R Bowman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA.
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St Louis, MO, USA.
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22
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Bottaro S, Bussi G, Lindorff-Larsen K. Conformational Ensembles of Noncoding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations. J Am Chem Soc 2021; 143:8333-8343. [PMID: 34039006 PMCID: PMC8188756 DOI: 10.1021/jacs.1c01094] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Indexed: 12/17/2022]
Abstract
The 5' untranslated region (UTR) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome is a conserved, functional and structured genomic region consisting of several RNA stem-loop elements. While the secondary structure of such elements has been determined experimentally, their three-dimensional structures are not known yet. Here, we predict structure and dynamics of five RNA stem loops in the 5'-UTR of SARS-CoV-2 by extensive atomistic molecular dynamics simulations, more than 0.5 ms of aggregate simulation time, in combination with enhanced sampling techniques. We compare simulations with available experimental data, describe the resulting conformational ensembles, and identify the presence of specific structural rearrangements in apical and internal loops that may be functionally relevant. Our atomic-detailed structural predictions reveal a rich dynamics in these RNA molecules, could help the experimental characterization of these systems, and provide putative three-dimensional models for structure-based drug design studies.
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Affiliation(s)
- Sandro Bottaro
- Structural
Biology and NMR Laboratory & Linderstrøm-Lang Centre for
Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Giovanni Bussi
- Scuola
Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136, Trieste, Italy
| | - Kresten Lindorff-Larsen
- Structural
Biology and NMR Laboratory & Linderstrøm-Lang Centre for
Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
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23
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Martinez X, Baaden M. UnityMol prototype for FAIR sharing of molecular-visualization experiences: from pictures in the cloud to collaborative virtual reality exploration in immersive 3D environments. Acta Crystallogr D Struct Biol 2021; 77:746-754. [PMID: 34076589 PMCID: PMC8171070 DOI: 10.1107/s2059798321002941] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 03/19/2021] [Indexed: 11/14/2022] Open
Abstract
Motivated by the current COVID-19 pandemic, which has spurred a substantial flow of structural data, the use of molecular-visualization experiences to make these data sets accessible to a broad audience is described. Using a variety of technology vectors related to the cloud, 3D and virtual reality gear, how to share curated visualizations of structural biology, modeling and/or bioinformatics data sets for interactive and collaborative exploration is examined. FAIR is discussed as an overarching principle for sharing such visualizations. Four initial example scenes related to recent COVID-19 structural data are provided, together with a ready-to-use (and share) implementation in the UnityMol software.
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Affiliation(s)
- Xavier Martinez
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 Rue Pierre et Marie Curie, 75005 Paris, France
- Institut de Biologie Physico-Chimique–Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Marc Baaden
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 Rue Pierre et Marie Curie, 75005 Paris, France
- Institut de Biologie Physico-Chimique–Fondation Edmond de Rothschild, PSL Research University, Paris, France
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24
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Sztain T, Ahn SH, Bogetti AT, Casalino L, Goldsmith JA, Seitz E, McCool RS, Kearns FL, Acosta-Reyes F, Maji S, Mashayekhi G, McCammon JA, Ourmazd A, Frank J, McLellan JS, Chong LT, Amaro RE. A glycan gate controls opening of the SARS-CoV-2 spike protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.02.15.431212. [PMID: 33619492 PMCID: PMC7899456 DOI: 10.1101/2021.02.15.431212] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
SARS-CoV-2 infection is controlled by the opening of the spike protein receptor binding domain (RBD), which transitions from a glycan-shielded "down" to an exposed "up" state in order to bind the human ACE2 receptor and infect cells. While snapshots of the "up" and "down" states have been obtained by cryoEM and cryoET, details of the RBD opening transition evade experimental characterization. Here, over 130 μs of weighted ensemble (WE) simulations of the fully glycosylated spike ectodomain allow us to characterize more than 300 continuous, kinetically unbiased RBD opening pathways. Together with ManifoldEM analysis of cryo-EM data and biolayer interferometry experiments, we reveal a gating role for the N-glycan at position N343, which facilitates RBD opening. Residues D405, R408, and D427 also participate. The atomic-level characterization of the glycosylated spike activation mechanism provided herein achieves a new high-water mark for ensemble pathway simulations and offers a foundation for understanding the fundamental mechanisms of SARS-CoV-2 viral entry and infection.
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Affiliation(s)
- Terra Sztain
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, CA 92093
| | - Surl-Hee Ahn
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, CA 92093
| | | | - Lorenzo Casalino
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, CA 92093
| | - Jory A. Goldsmith
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Evan Seitz
- Department of Biological Sciences, Columbia University, New York, NY, 10032, USA
| | - Ryan S. McCool
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Fiona L. Kearns
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, CA 92093
| | - Francisco Acosta-Reyes
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Suvrajit Maji
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Ghoncheh Mashayekhi
- Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI 53211, USA
| | - J. Andrew McCammon
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, CA 92093
- Department of Pharmacology, UC San Diego, La Jolla, CA 92093
| | - Abbas Ourmazd
- Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI 53211, USA
| | - Joachim Frank
- Department of Biological Sciences, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Lillian T. Chong
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260
| | - Rommie E. Amaro
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, CA 92093
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25
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Machado MR, Pantano S. Fighting viruses with computers, right now. Curr Opin Virol 2021; 48:91-99. [PMID: 33975154 DOI: 10.1016/j.coviro.2021.04.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/20/2021] [Accepted: 04/06/2021] [Indexed: 10/21/2022]
Abstract
The synergistic conjunction of various technological revolutions with the accumulated knowledge and workflows is rapidly transforming several scientific fields. Particularly, Virology can now feed from accurate physical models, polished computational tools, and massive computational power to readily integrate high-resolution structures into biological representations of unprecedented detail. That preparedness allows for the first time to get crucial information for vaccine and drug design from in-silico experiments against emerging pathogens of worldwide concern at relevant action windows. The present work reviews some of the main milestones leading to these breakthroughs in Computational Virology, providing an outlook for future developments in capacity building and accessibility to computational resources.
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Affiliation(s)
- Matías R Machado
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo, 11400, Uruguay.
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo, 11400, Uruguay.
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26
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Forouzesh N, Mishra N. An Effective MM/GBSA Protocol for Absolute Binding Free Energy Calculations: A Case Study on SARS-CoV-2 Spike Protein and the Human ACE2 Receptor. Molecules 2021; 26:2383. [PMID: 33923909 PMCID: PMC8074138 DOI: 10.3390/molecules26082383] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/09/2021] [Accepted: 04/13/2021] [Indexed: 12/23/2022] Open
Abstract
The binding free energy calculation of protein-ligand complexes is necessary for research into virus-host interactions and the relevant applications in drug discovery. However, many current computational methods of such calculations are either inefficient or inaccurate in practice. Utilizing implicit solvent models in the molecular mechanics generalized Born surface area (MM/GBSA) framework allows for efficient calculations without significant loss of accuracy. Here, GBNSR6, a new flavor of the generalized Born model, is employed in the MM/GBSA framework for measuring the binding affinity between SARS-CoV-2 spike protein and the human ACE2 receptor. A computational protocol is developed based on the widely studied Ras-Raf complex, which has similar binding free energy to SARS-CoV-2/ACE2. Two options for representing the dielectric boundary of the complexes are evaluated: one based on the standard Bondi radii and the other based on a newly developed set of atomic radii (OPT1), optimized specifically for protein-ligand binding. Predictions based on the two radii sets provide upper and lower bounds on the experimental references: -14.7(ΔGbindBondi)<-10.6(ΔGbindExp.)<-4.1(ΔGbindOPT1) kcal/mol. The consensus estimates of the two bounds show quantitative agreement with the experiment values. This work also presents a novel truncation method and computational strategies for efficient entropy calculations with normal mode analysis. Interestingly, it is observed that a significant decrease in the number of snapshots does not affect the accuracy of entropy calculation, while it does lower computation time appreciably. The proposed MM/GBSA protocol can be used to study the binding mechanism of new variants of SARS-CoV-2, as well as other relevant structures.
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Affiliation(s)
- Negin Forouzesh
- Department of Computer Science, California State University, Los Angeles, CA 90032, USA
| | - Nikita Mishra
- Department of Chemistry and Biochemistry, California State University, Los Angeles, CA 90032, USA;
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27
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Yu A, Pak AJ, He P, Monje-Galvan V, Casalino L, Gaieb Z, Dommer AC, Amaro RE, Voth GA. A multiscale coarse-grained model of the SARS-CoV-2 virion. Biophys J 2021; 120:1097-1104. [PMID: 33253634 PMCID: PMC7695975 DOI: 10.1016/j.bpj.2020.10.048] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/27/2020] [Accepted: 10/30/2020] [Indexed: 01/01/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 pandemic. Computer simulations of complete viral particles can provide theoretical insights into large-scale viral processes including assembly, budding, egress, entry, and fusion. Detailed atomistic simulations are constrained to shorter timescales and require billion-atom simulations for these processes. Here, we report the current status and ongoing development of a largely "bottom-up" coarse-grained (CG) model of the SARS-CoV-2 virion. Data from a combination of cryo-electron microscopy (cryo-EM), x-ray crystallography, and computational predictions were used to build molecular models of structural SARS-CoV-2 proteins, which were then assembled into a complete virion model. We describe how CG molecular interactions can be derived from all-atom simulations, how viral behavior difficult to capture in atomistic simulations can be incorporated into the CG models, and how the CG models can be iteratively improved as new data become publicly available. Our initial CG model and the detailed methods presented are intended to serve as a resource for researchers working on COVID-19 who are interested in performing multiscale simulations of the SARS-CoV-2 virion.
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Affiliation(s)
- Alvin Yu
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Franck Institute, The University of Chicago, Chicago, Illinois
| | - Alexander J Pak
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Franck Institute, The University of Chicago, Chicago, Illinois
| | - Peng He
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Franck Institute, The University of Chicago, Chicago, Illinois
| | - Viviana Monje-Galvan
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Franck Institute, The University of Chicago, Chicago, Illinois
| | - Lorenzo Casalino
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | - Zied Gaieb
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | - Abigail C Dommer
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Franck Institute, The University of Chicago, Chicago, Illinois.
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28
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Oliveira ASF, Ibarra AA, Bermudez I, Casalino L, Gaieb Z, Shoemark DK, Gallagher T, Sessions RB, Amaro RE, Mulholland AJ. A potential interaction between the SARS-CoV-2 spike protein and nicotinic acetylcholine receptors. Biophys J 2021; 120:983-993. [PMID: 33609494 PMCID: PMC7889469 DOI: 10.1016/j.bpj.2021.01.037] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 01/08/2023] Open
Abstract
Changeux et al. (Changeux et al. C. R. Biol. 343:33-39.) recently suggested that the SARS-CoV-2 spike protein may interact with nicotinic acetylcholine receptors (nAChRs) and that such interactions may be involved in pathology and infectivity. This hypothesis is based on the fact that the SARS-CoV-2 spike protein contains a sequence motif similar to known nAChR antagonists. Here, we use molecular simulations of validated atomically detailed structures of nAChRs and of the spike to investigate the possible binding of the Y674-R685 region of the spike to nAChRs. We examine the binding of the Y674-R685 loop to three nAChRs, namely the human α4β2 and α7 subtypes and the muscle-like αβγδ receptor from Tetronarce californica. Our results predict that Y674-R685 has affinity for nAChRs. The region of the spike responsible for binding contains a PRRA motif, a four-residue insertion not found in other SARS-like coronaviruses. The conformational behavior of the bound Y674-R685 is highly dependent on the receptor subtype; it adopts extended conformations in the α4β2 and α7 complexes but is more compact when bound to the muscle-like receptor. In the α4β2 and αβγδ complexes, the interaction of Y674-R685 with the receptors forces the loop C region to adopt an open conformation, similar to other known nAChR antagonists. In contrast, in the α7 complex, Y674-R685 penetrates deeply into the binding pocket in which it forms interactions with the residues lining the aromatic box, namely with TrpB, TyrC1, and TyrC2. Estimates of binding energy suggest that Y674-R685 forms stable complexes with all three nAChR subtypes. Analyses of simulations of the glycosylated spike show that the Y674-R685 region is accessible for binding. We suggest a potential binding orientation of the spike protein with nAChRs, in which they are in a nonparallel arrangement to one another.
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Affiliation(s)
- A Sofia F Oliveira
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, United Kingdom; Bristol Synthetic Biology Centre, BrisSynBio, Bristol, United Kingdom
| | - Amaurys Avila Ibarra
- Research Software Engineering, Advanced Computing Research Centre, University of Bristol, Bristol, United Kingdom
| | - Isabel Bermudez
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Lorenzo Casalino
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | - Zied Gaieb
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | - Deborah K Shoemark
- School of Biochemistry, University of Bristol, Bristol, United Kingdom; Bristol Synthetic Biology Centre, BrisSynBio, Bristol, United Kingdom
| | - Timothy Gallagher
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, United Kingdom
| | | | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, United Kingdom.
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29
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Straub JE. New and notable: A multiscale coarse-grained model of the SARS-CoV-2 virion. Biophys J 2021; 120:975-976. [PMID: 33577762 PMCID: PMC7837621 DOI: 10.1016/j.bpj.2020.12.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 12/30/2020] [Indexed: 11/24/2022] Open
Affiliation(s)
- John E Straub
- Department of Chemistry, Boston University, Boston, Massachusetts.
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30
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Garay PG, Barrera EE, Klein F, Machado MR, Soñora M, Pantano S. The SIRAH-CoV-2 Initiative: A Coarse-Grained Simulations' Dataset of the SARS-CoV-2 Proteome. FRONTIERS IN MEDICAL TECHNOLOGY 2021; 3:644039. [PMID: 35047913 PMCID: PMC8757729 DOI: 10.3389/fmedt.2021.644039] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 01/20/2021] [Indexed: 12/03/2022] Open
Affiliation(s)
| | | | | | | | | | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Montevideo, Uruguay
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31
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Tong JB, Luo D, Xu HY, Bian S, Zhang X, Xiao XC, Wang J. A computational approach for designing novel SARS-CoV-2 M pro inhibitors: combined QSAR, molecular docking, and molecular dynamics simulation techniques. NEW J CHEM 2021. [DOI: 10.1039/d1nj02127c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The promising compound T21 for treating COVID-19 at the active site of SARS-CoV-2 Mpro.
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Affiliation(s)
- Jian-Bo Tong
- College of Chemistry and Chemical Engineering
- Shaanxi University of Science and Technology
- Xi’an 710021
- China
- Shaanxi Key Laboratory of Chemical Additives for Industry
| | - Ding Luo
- College of Chemistry and Chemical Engineering
- Shaanxi University of Science and Technology
- Xi’an 710021
- China
- Shaanxi Key Laboratory of Chemical Additives for Industry
| | - Hai-Yin Xu
- College of Chemistry and Chemical Engineering
- Shaanxi University of Science and Technology
- Xi’an 710021
- China
- Shaanxi Key Laboratory of Chemical Additives for Industry
| | - Shuai Bian
- College of Chemistry and Chemical Engineering
- Shaanxi University of Science and Technology
- Xi’an 710021
- China
- Shaanxi Key Laboratory of Chemical Additives for Industry
| | - Xing Zhang
- College of Chemistry and Chemical Engineering
- Shaanxi University of Science and Technology
- Xi’an 710021
- China
- Shaanxi Key Laboratory of Chemical Additives for Industry
| | - Xue-Chun Xiao
- College of Chemistry and Chemical Engineering
- Shaanxi University of Science and Technology
- Xi’an 710021
- China
- Shaanxi Key Laboratory of Chemical Additives for Industry
| | - Jie Wang
- College of Chemistry and Chemical Engineering
- Shaanxi University of Science and Technology
- Xi’an 710021
- China
- Shaanxi Key Laboratory of Chemical Additives for Industry
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32
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Barba LA. Trustworthy Computational Evidence Through Transparency and Reproducibility. Comput Sci Eng 2021; 23:58-64. [PMID: 35939272 PMCID: PMC9280797 DOI: 10.1109/mcse.2020.3048406] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/1899] [Accepted: 01/01/1899] [Indexed: 11/28/2022]
Abstract
Many high-performance computing applications are of high consequence to society. Global climate modeling is a historic example of this. In 2020, the societal issue of greatest concern, the still-raging COVID-19 pandemic, saw a legion of computational scientists turning their endeavors to new research projects in this direction. Applications of such high consequence highlight the need for building trustworthy computational models.
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33
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Novara FR. 10 Years of Open Access Society Publishing. ChemistryOpen 2020; 10:4-7. [PMID: 33377254 DOI: 10.1002/open.202000353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Indexed: 11/12/2022] Open
Abstract
That was ten, this is now! The Editor-in-Chief of ChemistryOpen Francesca Novara discusses what 2020 meant for the development of open science and ChemistryOpen and what is the landscape in which ChemistryOpen will celebrate its 10th anniversary.
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Affiliation(s)
- Francesca Rita Novara
- ChemistryOpen, co-owned and supported by Chemistry Europe Wiley-VCH, Boschstrasse 12, 69469, Weinheim, Germany
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34
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Affiliation(s)
- Adrian J Mulholland
- School of Chemistry, Cantock's Close, Bristol BS8 1TS, United Kingdom of Great Britain and Northern Ireland
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California San Diego, 3234 Urey Hall, no. 0340 9500 Gilman Drive, La Jolla, California 92093-0340, United States
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35
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Zuo YY, Uspal WE, Wei T. Airborne Transmission of COVID-19: Aerosol Dispersion, Lung Deposition, and Virus-Receptor Interactions. ACS NANO 2020; 14:16502-16524. [PMID: 33236896 PMCID: PMC7724984 DOI: 10.1021/acsnano.0c08484] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 11/19/2020] [Indexed: 05/02/2023]
Abstract
Coronavirus disease 2019 (COVID-19), due to infection by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is now causing a global pandemic. Aerosol transmission of COVID-19, although plausible, has not been confirmed by the World Health Organization (WHO) as a general transmission route. Considering the rapid spread of SARS-CoV-2, especially nosocomial outbreaks and other superspreading events, there is an urgent need to study the possibility of airborne transmission and its impact on the lung, the primary body organ attacked by the virus. Here, we review the complete pathway of airborne transmission of SARS-CoV-2 from aerosol dispersion in air to subsequent biological uptake after inhalation. In particular, we first review the aerodynamic and colloidal mechanisms by which aerosols disperse and transmit in air and deposit onto surfaces. We then review the fundamental mechanisms that govern regional deposition of micro- and nanoparticles in the lung. Focus is given to biophysical interactions between particles and the pulmonary surfactant film, the initial alveolar-capillary barrier and first-line host defense system against inhaled particles and pathogens. Finally, we summarize the current understanding about the structural dynamics of the SARS-CoV-2 spike protein and its interactions with receptors at the atomistic and molecular scales, primarily as revealed by molecular dynamics simulations. This review provides urgent and multidisciplinary knowledge toward understanding the airborne transmission of SARS-CoV-2 and its health impact on the respiratory system.
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Affiliation(s)
- Yi Y. Zuo
- Department of Mechanical Engineering,
University of Hawaii at Manoa,
Honolulu, Hawaii 96822, United States
- Department of Pediatrics, John A.
Burns School of Medicine, University of
Hawaii, Honolulu, Hawaii 96826, United
States
| | - William E. Uspal
- Department of Mechanical Engineering,
University of Hawaii at Manoa,
Honolulu, Hawaii 96822, United States
| | - Tao Wei
- Chemical Engineering Department,
Howard University, Washington, DC
20059, United States
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36
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Sehnal D, Svobodová R, Berka K, Rose AS, Burley SK, Velankar S, Koča J. High-performance macromolecular data delivery and visualization for the web. Acta Crystallogr D Struct Biol 2020; 76:1167-1173. [PMID: 33263322 PMCID: PMC7709201 DOI: 10.1107/s2059798320014515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/01/2020] [Indexed: 11/11/2022] Open
Abstract
Biomacromolecular structural data make up a vital and crucial scientific resource that has grown not only in terms of its amount but also in its size and complexity. Furthermore, these data are accompanied by large and increasing amounts of experimental data. Additionally, the macromolecular data are enriched with value-added annotations describing their biological, physicochemical and structural properties. Today, the scientific community requires fast and fully interactive web visualization to exploit this complex structural information. This article provides a survey of the available cutting-edge web services that address this challenge. Specifically, it focuses on data-delivery problems, discusses the visualization of a single structure, including experimental data and annotations, and concludes with a focus on the results of molecular-dynamics simulations and the visualization of structural ensembles.
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Affiliation(s)
- David Sehnal
- CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL–EBI), Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom
| | - Radka Svobodová
- CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Karel Berka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, Šlechtitelů 241/27, 779 00 Olomouc, Czech Republic
| | - Alexander S. Rose
- Research Collaboratory for Structural Bioinformatics (RCSB), San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, San Diego, CA 92093-0743, USA
| | - Stephen K. Burley
- RCSB Protein Data Bank, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854-8076, USA
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, 195 Little Albany Street, New Brunswick, NJ 08903-2681, USA
- RCSB Protein Data Bank, San Diego Supercomputer Center and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0654, USA
| | - Sameer Velankar
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL–EBI), Wellcome Genome Campus, Hinxton CB10 1SD, United Kingdom
| | - Jaroslav Koča
- CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
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37
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Ospanov M, León F, Jenis J, Khan IKA, Ibrahim MA. Challenges and future directions of potential natural products leads against 2019-nCoV outbreak. CURRENT PLANT BIOLOGY 2020; 24:100180. [PMID: 33052305 PMCID: PMC7543902 DOI: 10.1016/j.cpb.2020.100180] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/01/2020] [Accepted: 10/05/2020] [Indexed: 05/08/2023]
Abstract
Except for Remdesivir® no other drug or vaccine has yet been approved to treat the coronavirus disease (COVID-19) caused by the virus known as, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Remdesivir® an small molecule and nucleic acid analogue, it is used to treat adults and children with laboratory confirmed COVID-19, only administrated in hospital settings. Small molecules and particularly natural products count for almost fifty percent of the commercially available drugs, several of them are marketed antiviral agents and those can be a potential agent to treat COVID-19 infections. This short review rationalized different key natural products with known activity against coronaviruses as potential leads against COVID-19.
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Affiliation(s)
- Meirambek Ospanov
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, MS, 38677, USA
- The Research Center for Medicinal Plants, Al-Farabi Kazakh National University, Al-Farabi ave. 71, 050040, Almaty, Kazakhstan
| | - Francisco León
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, 29208, USA
| | - Janar Jenis
- The Research Center for Medicinal Plants, Al-Farabi Kazakh National University, Al-Farabi ave. 71, 050040, Almaty, Kazakhstan
| | - IKhlas A Khan
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, MS, 38677, USA
| | - Mohamed A Ibrahim
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, MS, 38677, USA
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Division, National Research Centre, Dokki, 12622, Cairo, Egypt
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38
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Casalino L, Dommer A, Gaieb Z, Barros EP, Sztain T, Ahn SH, Trifan A, Brace A, Bogetti A, Ma H, Lee H, Turilli M, Khalid S, Chong L, Simmerling C, Hardy DJ, Maia JDC, Phillips JC, Kurth T, Stern A, Huang L, McCalpin J, Tatineni M, Gibbs T, Stone JE, Jha S, Ramanathan A, Amaro RE. AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.11.19.390187. [PMID: 33236007 PMCID: PMC7685317 DOI: 10.1101/2020.11.19.390187] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2023]
Abstract
We develop a generalizable AI-driven workflow that leverages heterogeneous HPC resources to explore the time-dependent dynamics of molecular systems. We use this workflow to investigate the mechanisms of infectivity of the SARS-CoV-2 spike protein, the main viral infection machinery. Our workflow enables more efficient investigation of spike dynamics in a variety of complex environments, including within a complete SARS-CoV-2 viral envelope simulation, which contains 305 million atoms and shows strong scaling on ORNL Summit using NAMD. We present several novel scientific discoveries, including the elucidation of the spike's full glycan shield, the role of spike glycans in modulating the infectivity of the virus, and the characterization of the flexible interactions between the spike and the human ACE2 receptor. We also demonstrate how AI can accelerate conformational sampling across different systems and pave the way for the future application of such methods to additional studies in SARS-CoV-2 and other molecular systems.
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Affiliation(s)
| | | | | | | | | | | | - Anda Trifan
- Argonne National Lab
- University of Illinois at Urbana-Champaign
| | | | | | | | - Hyungro Lee
- Rutgers University & Brookhaven National Lab
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39
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Barros EP, Casalino L, Gaieb Z, Dommer AC, Wang Y, Fallon L, Raguette L, Belfon K, Simmerling C, Amaro RE. The flexibility of ACE2 in the context of SARS-CoV-2 infection. Biophys J 2020; 120:1072-1084. [PMID: 33189680 PMCID: PMC7661960 DOI: 10.1016/j.bpj.2020.10.036] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/22/2020] [Accepted: 10/27/2020] [Indexed: 12/13/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has swept over the world in the past months, causing significant loss of life and consequences to human health. Although numerous drug and vaccine development efforts are underway, there are many outstanding questions on the mechanism of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral association to angiotensin-converting enzyme 2 (ACE2), its main host receptor, and host cell entry. Structural and biophysical studies indicate some degree of flexibility in the viral extracellular spike glycoprotein and at the receptor-binding domain (RBD)-receptor interface, suggesting a role in infection. Here, we perform explicitly solvated, all-atom, molecular dynamics simulations of the glycosylated, full-length, membrane-bound ACE2 receptor in both an apo and spike RBD-bound state to probe the intrinsic dynamics of the ACE2 receptor in the context of the cell surface. A large degree of fluctuation in the full-length structure is observed, indicating hinge bending motions at the linker region connecting the head to the transmembrane helix while still not disrupting the ACE2 homodimer or ACE2-RBD interfaces. This flexibility translates into an ensemble of ACE2 homodimer conformations that could sterically accommodate binding of the spike trimer to more than one ACE2 homodimer and suggests a mechanical contribution of the host receptor toward the large spike conformational changes required for cell fusion. This work presents further structural and functional insights into the role of ACE2 in viral infection that can potentially be exploited for the rational design of effective SARS-CoV-2 therapeutics.
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Affiliation(s)
- Emilia P Barros
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - Lorenzo Casalino
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - Zied Gaieb
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - Abigail C Dommer
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - Yuzhang Wang
- Department of Chemistry, Stony Brook University, Stony Brook, New York
| | - Lucy Fallon
- Department of Chemistry, Stony Brook University, Stony Brook, New York
| | - Lauren Raguette
- Department of Chemistry, Stony Brook University, Stony Brook, New York
| | - Kellon Belfon
- Department of Chemistry, Stony Brook University, Stony Brook, New York
| | - Carlos Simmerling
- Department of Chemistry, Stony Brook University, Stony Brook, New York; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California.
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40
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Francés-Monerris A, Hognon C, Miclot T, García-Iriepa C, Iriepa I, Terenzi A, Grandemange S, Barone G, Marazzi M, Monari A. Molecular Basis of SARS-CoV-2 Infection and Rational Design of Potential Antiviral Agents: Modeling and Simulation Approaches. J Proteome Res 2020; 19:4291-4315. [PMID: 33119313 PMCID: PMC7640986 DOI: 10.1021/acs.jproteome.0c00779] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Indexed: 01/18/2023]
Abstract
The emergence in late 2019 of the coronavirus SARS-CoV-2 has resulted in the breakthrough of the COVID-19 pandemic that is presently affecting a growing number of countries. The development of the pandemic has also prompted an unprecedented effort of the scientific community to understand the molecular bases of the virus infection and to propose rational drug design strategies able to alleviate the serious COVID-19 morbidity. In this context, a strong synergy between the structural biophysics and molecular modeling and simulation communities has emerged, resolving at the atomistic level the crucial protein apparatus of the virus and revealing the dynamic aspects of key viral processes. In this Review, we focus on how in silico studies have contributed to the understanding of the SARS-CoV-2 infection mechanism and the proposal of novel and original agents to inhibit the viral key functioning. This Review deals with the SARS-CoV-2 spike protein, including the mode of action that this structural protein uses to entry human cells, as well as with nonstructural viral proteins, focusing the attention on the most studied proteases and also proposing alternative mechanisms involving some of its domains, such as the SARS unique domain. We demonstrate that molecular modeling and simulation represent an effective approach to gather information on key biological processes and thus guide rational molecular design strategies.
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Affiliation(s)
- Antonio Francés-Monerris
- Université
de Lorraine and CNRS, LPCT UMR 7019, F-54000 Nancy, France
- Departament
de Química Física, Universitat
de València, 46100 Burjassot, Spain
| | - Cécilia Hognon
- Université
de Lorraine and CNRS, LPCT UMR 7019, F-54000 Nancy, France
| | - Tom Miclot
- Université
de Lorraine and CNRS, LPCT UMR 7019, F-54000 Nancy, France
- Department
of Biological, Chemical and Pharmaceutical Sciences and Technologies, Università degli Studi di Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
| | - Cristina García-Iriepa
- Department
of Analytical Chemistry, Physical Chemistry and Chemical Engineering, Universidad de Alcalá, Ctra. Madrid-Barcelona, Km 33,600, 28871 Alcalá de Henares, Madrid, Spain
- Chemical
Research Institute “Andrés M. del Río”
(IQAR), Universidad de Alcalá, 28871 Alcalá de
Henares, Madrid, Spain
| | - Isabel Iriepa
- Chemical
Research Institute “Andrés M. del Río”
(IQAR), Universidad de Alcalá, 28871 Alcalá de
Henares, Madrid, Spain
- Department
of Organic and Inorganic Chemistry, Universidad
de Alcalá, Ctra.
Madrid-Barcelona, Km 33,600, 28871 Alcalá de Henares, Madrid, Spain
| | - Alessio Terenzi
- Department
of Biological, Chemical and Pharmaceutical Sciences and Technologies, Università degli Studi di Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
| | | | - Giampaolo Barone
- Department
of Biological, Chemical and Pharmaceutical Sciences and Technologies, Università degli Studi di Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
| | - Marco Marazzi
- Department
of Analytical Chemistry, Physical Chemistry and Chemical Engineering, Universidad de Alcalá, Ctra. Madrid-Barcelona, Km 33,600, 28871 Alcalá de Henares, Madrid, Spain
- Chemical
Research Institute “Andrés M. del Río”
(IQAR), Universidad de Alcalá, 28871 Alcalá de
Henares, Madrid, Spain
| | - Antonio Monari
- Université
de Lorraine and CNRS, LPCT UMR 7019, F-54000 Nancy, France
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41
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Abstract
COVID19 has changed life for people worldwide. Despite lockdowns globally, computational research has pressed on, working remotely and collaborating virtually on research questions in COVID19 and the virus it is caused by, SARS-CoV-2. Molecular simulations can help to characterize the function of viral and host proteins and have the potential to contribute to the search for vaccines and treatments. Changes in the modus operandi of research groups include broader adoption of the use of preprint servers, earlier and more open sharing of methods, models, and data, the use of social media to rapidly disseminate information, online seminars, and cloud-based virtual collaboration. Research funders and computing providers worldwide recognized the need to provide rapid and significant access to computational architectures. In this review, we discuss how the interplay of all of these factors is influencing the impact - both potential and realized - of biomolecular simulations in the fight against SARS-CoV-2.
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42
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Casalino L, Gaieb Z, Goldsmith JA, Hjorth CK, Dommer AC, Harbison AM, Fogarty CA, Barros EP, Taylor BC, McLellan JS, Fadda E, Amaro RE. Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein. ACS CENTRAL SCIENCE 2020; 6:1722-1734. [PMID: 33140034 PMCID: PMC7523240 DOI: 10.1021/acscentsci.0c01056] [Citation(s) in RCA: 578] [Impact Index Per Article: 144.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Indexed: 05/04/2023]
Abstract
The ongoing COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in more than 28,000,000 infections and 900,000 deaths worldwide to date. Antibody development efforts mainly revolve around the extensively glycosylated SARS-CoV-2 spike (S) protein, which mediates host cell entry by binding to the angiotensin-converting enzyme 2 (ACE2). Similar to many other viral fusion proteins, the SARS-CoV-2 spike utilizes a glycan shield to thwart the host immune response. Here, we built a full-length model of the glycosylated SARS-CoV-2 S protein, both in the open and closed states, augmenting the available structural and biological data. Multiple microsecond-long, all-atom molecular dynamics simulations were used to provide an atomistic perspective on the roles of glycans and on the protein structure and dynamics. We reveal an essential structural role of N-glycans at sites N165 and N234 in modulating the conformational dynamics of the spike's receptor binding domain (RBD), which is responsible for ACE2 recognition. This finding is corroborated by biolayer interferometry experiments, which show that deletion of these glycans through N165A and N234A mutations significantly reduces binding to ACE2 as a result of the RBD conformational shift toward the "down" state. Additionally, end-to-end accessibility analyses outline a complete overview of the vulnerabilities of the glycan shield of the SARS-CoV-2 S protein, which may be exploited in the therapeutic efforts targeting this molecular machine. Overall, this work presents hitherto unseen functional and structural insights into the SARS-CoV-2 S protein and its glycan coat, providing a strategy to control the conformational plasticity of the RBD that could be harnessed for vaccine development.
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Affiliation(s)
- Lorenzo Casalino
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California 92093, United States
| | - Zied Gaieb
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California 92093, United States
| | - Jory A. Goldsmith
- Department
of Molecular Biosciences, The University
of Texas at Austin, Austin, Texas 78712, United States
| | - Christy K. Hjorth
- Department
of Molecular Biosciences, The University
of Texas at Austin, Austin, Texas 78712, United States
| | - Abigail C. Dommer
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California 92093, United States
| | - Aoife M. Harbison
- Department
of Chemistry and Hamilton Institute, Maynooth
University, Dublin, Ireland
| | - Carl A. Fogarty
- Department
of Chemistry and Hamilton Institute, Maynooth
University, Dublin, Ireland
| | - Emilia P. Barros
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California 92093, United States
| | - Bryn C. Taylor
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California 92093, United States
- Biomedical
Sciences Graduate Program, University of
California San Diego, La Jolla, California 92093, United States
| | - Jason S. McLellan
- Department
of Molecular Biosciences, The University
of Texas at Austin, Austin, Texas 78712, United States
| | - Elisa Fadda
- Department
of Chemistry and Hamilton Institute, Maynooth
University, Dublin, Ireland
| | - Rommie E. Amaro
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California 92093, United States
- Biomedical
Sciences Graduate Program, University of
California San Diego, La Jolla, California 92093, United States
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43
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Komatsu TS, Okimoto N, Koyama YM, Hirano Y, Morimoto G, Ohno Y, Taiji M. Drug binding dynamics of the dimeric SARS-CoV-2 main protease, determined by molecular dynamics simulation. Sci Rep 2020; 10:16986. [PMID: 33046764 PMCID: PMC7550358 DOI: 10.1038/s41598-020-74099-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 09/24/2020] [Indexed: 11/14/2022] Open
Abstract
We performed molecular dynamics simulation of the dimeric SARS-CoV-2 (severe acute respiratory syndrome corona virus 2) main protease (Mpro) to examine the binding dynamics of small molecular ligands. Seven HIV inhibitors, darunavir, indinavir, lopinavir, nelfinavir, ritonavir, saquinavir, and tipranavir, were used as the potential lead drugs to investigate access to the drug binding sites in Mpro. The frequently accessed sites on Mpro were classified based on contacts between the ligands and the protein, and the differences in site distributions of the encounter complex were observed among the ligands. All seven ligands showed binding to the active site at least twice in 28 simulations of 200 ns each. We further investigated the variations in the complex structure of the active site with the ligands, using microsecond order simulations. Results revealed a wide variation in the shapes of the binding sites and binding poses of the ligands. Additionally, the C-terminal region of the other chain often interacted with the ligands and the active site. Collectively, these findings indicate the importance of dynamic sampling of protein-ligand complexes and suggest the possibilities of further drug optimisations.
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Affiliation(s)
- Teruhisa S Komatsu
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan.
| | - Noriaki Okimoto
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
- Drug Discovery Molecular Simulation Platform Unit, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Yohei M Koyama
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Yoshinori Hirano
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
- Drug Discovery Molecular Simulation Platform Unit, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Gentaro Morimoto
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
- Drug Discovery Molecular Simulation Platform Unit, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Yousuke Ohno
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Makoto Taiji
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan.
- Drug Discovery Molecular Simulation Platform Unit, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan.
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44
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Zimmerman MI, Porter JR, Ward MD, Singh S, Vithani N, Meller A, Mallimadugula UL, Kuhn CE, Borowsky JH, Wiewiora RP, Hurley MFD, Harbison AM, Fogarty CA, Coffland JE, Fadda E, Voelz VA, Chodera JD, Bowman GR. SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.06.27.175430. [PMID: 32637963 PMCID: PMC7337393 DOI: 10.1101/2020.06.27.175430] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
SARS-CoV-2 has intricate mechanisms for initiating infection, immune evasion/suppression, and replication, which depend on the structure and dynamics of its constituent proteins. Many protein structures have been solved, but far less is known about their relevant conformational changes. To address this challenge, over a million citizen scientists banded together through the Folding@home distributed computing project to create the first exascale computer and simulate an unprecedented 0.1 seconds of the viral proteome. Our simulations capture dramatic opening of the apo Spike complex, far beyond that seen experimentally, which explains and successfully predicts the existence of 'cryptic' epitopes. Different Spike homologues modulate the probabilities of open versus closed structures, balancing receptor binding and immune evasion. We also observe dramatic conformational changes across the proteome, which reveal over 50 'cryptic' pockets that expand targeting options for the design of antivirals. All data and models are freely available online, providing a quantitative structural atlas.
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Affiliation(s)
- Maxwell I. Zimmerman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Justin R. Porter
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Michael D. Ward
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Sukrit Singh
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Neha Vithani
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Artur Meller
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Upasana L. Mallimadugula
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Catherine E. Kuhn
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Jonathan H. Borowsky
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Rafal P. Wiewiora
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Computational and Systems Biology Program, Sloan Kettering Institute, New York, New York 10065, United States
| | - Matthew F. D. Hurley
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Aoife M Harbison
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Kildare, Ireland
| | - Carl A Fogarty
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Kildare, Ireland
| | | | - Elisa Fadda
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Kildare, Ireland
| | - Vincent A. Voelz
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - John D. Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, New York, New York 10065, United States
| | - Gregory R. Bowman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, Missouri 63130, United States
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45
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Yu A, Pak AJ, He P, Monje-Galvan V, Casalino L, Gaieb Z, Dommer AC, Amaro RE, Voth GA. A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 33024966 DOI: 10.1101/2020.10.02.323915] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 pandemic. Computer simulations of complete viral particles can provide theoretical insights into large-scale viral processes including assembly, budding, egress, entry, and fusion. Detailed atomistic simulations, however, are constrained to shorter timescales and require billion-atom simulations for these processes. Here, we report the current status and on-going development of a largely "bottom-up" coarse-grained (CG) model of the SARS-CoV-2 virion. Structural data from a combination of cryo-electron microscopy (cryo-EM), x-ray crystallography, and computational predictions were used to build molecular models of structural SARS-CoV-2 proteins, which were then assembled into a complete virion model. We describe how CG molecular interactions can be derived from all-atom simulations, how viral behavior difficult to capture in atomistic simulations can be incorporated into the CG models, and how the CG models can be iteratively improved as new data becomes publicly available. Our initial CG model and the detailed methods presented are intended to serve as a resource for researchers working on COVID-19 who are interested in performing multiscale simulations of the SARS-CoV-2 virion. Significance Statement This study reports the construction of a molecular model for the SARS-CoV-2 virion and details our multiscale approach towards model refinement. The resulting model and methods can be applied to and enable the simulation of SARS-CoV-2 virions.
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46
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Khrenova MG, Tsirelson VG, Nemukhin AV. Dynamical properties of enzyme-substrate complexes disclose substrate specificity of the SARS-CoV-2 main protease as characterized by the electron density descriptors. Phys Chem Chem Phys 2020; 22:19069-19079. [PMID: 32812956 DOI: 10.1039/d0cp03560b] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A dynamical approach is proposed to discriminate between reactive (rES) and nonreactive (nES) enzyme-substrate complexes taking the SARS-CoV-2 main protease (Mpro) as an important example. Molecular dynamics simulations with the quantum mechanics/molecular mechanics potentials (QM(DFT)/MM-MD) followed by the electron density analysis are employed to evaluate geometry and electronic properties of the enzyme with different substrates along MD trajectories. We demonstrate that mapping the Laplacian of the electron density and the electron localization function provides easily visible images of the substrate activation that allow one to distinguish rES and nES. The computed fractions of reactive enzyme-substrate complexes along MD trajectories well correlate with the findings of recent experimental studies on the substrate specificity of Mpro. The results of our simulations demonstrate the role of the theory level used in QM subsystems for a proper description of the nucleophilic attack of the catalytic cysteine residue in Mpro. The activation of the carbonyl group of a substrate is correctly characterized with the hybrid DFT functional PBE0, whereas the use of a GGA-type PBE functional, that lacks the admixture of the Hartree-Fock exchange fails to describe activation.
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Affiliation(s)
- Maria G Khrenova
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Leninsky Prospect, 33, bld. 2, Moscow, 119071, Russia and Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Vladimir G Tsirelson
- Mendeleev University of Chemical Technology, Miusskaya Square, 9, Moscow, 125047, Russia
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia. and Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119334, Russia
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47
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Casalino L, Gaieb Z, Goldsmith JA, Hjorth CK, Dommer AC, Harbison AM, Fogarty CA, Barros EP, Taylor BC, McLellan JS, Fadda E, Amaro RE. Beyond Shielding: The Roles of Glycans in SARS-CoV-2 Spike Protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.06.11.146522. [PMID: 32577644 PMCID: PMC7302197 DOI: 10.1101/2020.06.11.146522] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
The ongoing COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in more than 15,000,000 infections and 600,000 deaths worldwide to date. Antibody development efforts mainly revolve around the extensively glycosylated SARS-CoV-2 spike (S) protein, which mediates the host cell entry by binding to the angiotensin-converting enzyme 2 (ACE2). Similar to many other viruses, the SARS-CoV-2 spike utilizes a glycan shield to thwart the host immune response. Here, we built a full-length model of glycosylated SARS-CoV-2 S protein, both in the open and closed states, augmenting the available structural and biological data. Multiple microsecond-long, all-atom molecular dynamics simulations were used to provide an atomistic perspective on the roles of glycans, and the protein structure and dynamics. We reveal an essential structural role of N-glycans at sites N165 and N234 in modulating the conformational dynamics of the spike's receptor binding domain (RBD), which is responsible for ACE2 recognition. This finding is corroborated by biolayer interferometry experiments, which show that deletion of these glycans through N165A and N234A mutations significantly reduces binding to ACE2 as a result of the RBD conformational shift towards the "down" state. Additionally, end-to-end accessibility analyses outline a complete overview of the vulnerabilities of the glycan shield of SARS-CoV-2 S protein, which may be exploited by therapeutic efforts targeting this molecular machine. Overall, this work presents hitherto unseen functional and structural insights into the SARS-CoV-2 S protein and its glycan coat, providing a strategy to control the conformational plasticity of the RBD that could be harnessed for vaccine development.
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Affiliation(s)
- Lorenzo Casalino
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Zied Gaieb
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Jory A. Goldsmith
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Christy K. Hjorth
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Abigail C. Dommer
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Aoife M. Harbison
- Department of Chemistry and Hamilton Institute, Maynooth University, Dublin, Ireland
| | - Carl A. Fogarty
- Department of Chemistry and Hamilton Institute, Maynooth University, Dublin, Ireland
| | - Emilia P. Barros
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Bryn C. Taylor
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, 92093, USA
| | | | - Elisa Fadda
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
- Department of Chemistry and Hamilton Institute, Maynooth University, Dublin, Ireland
| | - Rommie E. Amaro
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, 92093, USA
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48
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Li Z, Hirst JD. Computed optical spectra of SARS-CoV-2 proteins. Chem Phys Lett 2020; 758:137935. [PMID: 33518776 PMCID: PMC7836526 DOI: 10.1016/j.cplett.2020.137935] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 08/22/2020] [Accepted: 08/25/2020] [Indexed: 02/03/2023]
Abstract
Calculated circular dichroism spectra in the far- and near-UV spectra. Calculated infra-red (IR) spectra in the amide I region. Based on experimental structures and computational models of SARS-CoV-2 proteins. Near-UV CD spectra offer greatest sensitivity to conformation.
Treatment for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes Covid-19, may well be predicated on knowledge of the structures of protein of this virus. However, often these cannot be determined easily or quickly. Herein, we provide calculated circular dichroism (CD) spectra in the far- and near-UV, and infra-red (IR) spectra in the amide I region for experimental structures and computational models of SARS-CoV-2 proteins. The near-UV CD spectra offer greatest sensitivity in assessing the accuracy of models.
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Affiliation(s)
- Zhuo Li
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
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49
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Forouzesh N, Onufriev AV. MMGB/SA Consensus Estimate of the Binding Free Energy Between the Novel Coronavirus Spike Protein to the Human ACE2 Receptor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.08.25.267625. [PMID: 32869029 PMCID: PMC7457614 DOI: 10.1101/2020.08.25.267625] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The ability to estimate protein-protein binding free energy in a computationally efficient via a physics-based approach is beneficial to research focused on the mechanism of viruses binding to their target proteins. Implicit solvation methodology may be particularly useful in the early stages of such research, as it can offer valuable insights into the binding process, quickly. Here we evaluate the potential of the related molecular mechanics generalized Born surface area (MMGB/SA) approach to estimate the binding free energy ΔGbind between the SARS-CoV-2 spike receptor-binding domain and the human ACE2 receptor. The calculations are based on a recent flavor of the generalized Born model, GBNSR6. Two estimates of ΔGbind are performed: one based on standard bondi radii, and the other based on a newly developed set of atomic radii (OPT1), optimized specifically for protein-ligand binding. We take the average of the resulting two ΔGbind values as the consensus estimate. For the well-studied Ras-Raf protein-protein complex, which has similar binding free energy to that of the SARS-CoV-2/ACE2 complex, the consensus ΔGbind = -11.8 ± 1 kcal/mol, vs. experimental -9.7 ± 0.2 kcal/mol. The consensus estimates for the SARS-CoV-2/ACE2 complex is ΔGbind = -9.4 ± 1.5 kcal/mol, which is in near quantitative agreement with experiment (-10.6 kcal/mol). The availability of a conceptually simple MMGB/SA-based protocol for analysis of the SARS-CoV-2 /ACE2 binding may be beneficial in light of the need to move forward fast.
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Affiliation(s)
- Negin Forouzesh
- Department of Computer Science, California State University, Los Angeles, Los Angeles, CA 90032, USA
| | - Alexey V Onufriev
- Department of Computer Science, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061, USA
- Department of Physics, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061, USA
- Center for Soft Matter and Biological Physics, Virginia Polytechnic Institute & State University, Blacksburg, VA 24061, USA
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Laskar P, Yallapu MM, Chauhan SC. "Tomorrow Never Dies": Recent Advances in Diagnosis, Treatment, and Prevention Modalities against Coronavirus (COVID-19) amid Controversies. Diseases 2020; 8:E30. [PMID: 32781617 PMCID: PMC7563589 DOI: 10.3390/diseases8030030] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/30/2020] [Accepted: 08/04/2020] [Indexed: 02/06/2023] Open
Abstract
The outbreak of novel coronavirus disease (2019-nCoV or COVID-19) is responsible for severe health emergency throughout the world. The attack of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is found to be responsible for COVID-19. The World Health Organization has declared the ongoing global public health emergency as a pandemic. The whole world fights against this invincible enemy in various capacities to restore economy, lifestyle, and safe life. Enormous amount of scientific research work(s), administrative strategies, and economic measurements are in place to create a successful step against COVID-19. Furthermore, differences in opinion, facts, and implementation methods laid additional layers of complexities in this battle against survival. Thus, a timely overview of the recent, important, and overall inclusive developments against this pandemic is a pressing need for better understanding and dealing with COVID-19. In this review, we have systematically summarized the epidemiological studies, clinical features, biological properties, diagnostic methods, treatment modalities, and preventive measurements related to COVID-19.
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Affiliation(s)
- Partha Laskar
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK;
| | - Murali M. Yallapu
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Subhash C. Chauhan
- Department of Immunology and Microbiology, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
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