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Dutta M, Acharya P. Cryo-electron microscopy in the study of virus entry and infection. Front Mol Biosci 2024; 11:1429180. [PMID: 39114367 PMCID: PMC11303226 DOI: 10.3389/fmolb.2024.1429180] [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: 05/07/2024] [Accepted: 06/12/2024] [Indexed: 08/10/2024] Open
Abstract
Viruses have been responsible for many epidemics and pandemics that have impacted human life globally. The COVID-19 pandemic highlighted both our vulnerability to viral outbreaks, as well as the mobilization of the scientific community to come together to combat the unprecedented threat to humanity. Cryo-electron microscopy (cryo-EM) played a central role in our understanding of SARS-CoV-2 during the pandemic and continues to inform about this evolving pathogen. Cryo-EM with its two popular imaging modalities, single particle analysis (SPA) and cryo-electron tomography (cryo-ET), has contributed immensely to understanding the structure of viruses and interactions that define their life cycles and pathogenicity. Here, we review how cryo-EM has informed our understanding of three distinct viruses, of which two - HIV-1 and SARS-CoV-2 infect humans, and the third, bacteriophages, infect bacteria. For HIV-1 and SARS-CoV-2 our focus is on the surface glycoproteins that are responsible for mediating host receptor binding, and host and cell membrane fusion, while for bacteriophages, we review their structure, capsid maturation, attachment to the bacterial cell surface and infection initiation mechanism.
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Affiliation(s)
- Moumita Dutta
- Duke Human Vaccine Institute, Durham, NC, United States
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Durham, NC, United States
- Department of Surgery, Durham, NC, United States
- Department of Biochemistry, Duke University, Durham, NC, United States
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Zhu KF, Yuan C, Du YM, Sun KL, Zhang XK, Vogel H, Jia XD, Gao YZ, Zhang QF, Wang DP, Zhang HW. Applications and prospects of cryo-EM in drug discovery. Mil Med Res 2023; 10:10. [PMID: 36872349 PMCID: PMC9986049 DOI: 10.1186/s40779-023-00446-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 02/14/2023] [Indexed: 03/07/2023] Open
Abstract
Drug discovery is a crucial part of human healthcare and has dramatically benefited human lifespan and life quality in recent centuries, however, it is usually time- and effort-consuming. Structural biology has been demonstrated as a powerful tool to accelerate drug development. Among different techniques, cryo-electron microscopy (cryo-EM) is emerging as the mainstream of structure determination of biomacromolecules in the past decade and has received increasing attention from the pharmaceutical industry. Although cryo-EM still has limitations in resolution, speed and throughput, a growing number of innovative drugs are being developed with the help of cryo-EM. Here, we aim to provide an overview of how cryo-EM techniques are applied to facilitate drug discovery. The development and typical workflow of cryo-EM technique will be briefly introduced, followed by its specific applications in structure-based drug design, fragment-based drug discovery, proteolysis targeting chimeras, antibody drug development and drug repurposing. Besides cryo-EM, drug discovery innovation usually involves other state-of-the-art techniques such as artificial intelligence (AI), which is increasingly active in diverse areas. The combination of cryo-EM and AI provides an opportunity to minimize limitations of cryo-EM such as automation, throughput and interpretation of medium-resolution maps, and tends to be the new direction of future development of cryo-EM. The rapid development of cryo-EM will make it as an indispensable part of modern drug discovery.
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Affiliation(s)
- Kong-Fu Zhu
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055 Guangdong China
| | - Chuang Yuan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University, Beijing, 100191 China
| | - Yong-Ming Du
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105 USA
| | - Kai-Lei Sun
- Center for Protein Science and Crystallography, School of Life Sciences, Faculty of Science, Chinese University of Hong Kong, Hong Kong, 999077 China
| | - Xiao-Kang Zhang
- Interdisciplinary Center for Brain Information, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 Guangdong China
- Faculty of Life and Health Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 Guangdong China
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, 518055 Guangdong China
| | - Horst Vogel
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 Guangdong China
| | - Xu-Dong Jia
- State Key Lab for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Yuan-Zhu Gao
- Cryo-EM Facility Center, Southern University of Science and Technology, Shenzhen, 518055 Guangdong China
| | - Qin-Fen Zhang
- State Key Lab for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Da-Ping Wang
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055 Guangdong China
- Department of Orthopedics, Shenzhen Intelligent Orthopaedics and Biomedical Innovation Platform, Guangdong Provincial Research Center for Artificial Intelligence and Digital Orthopedic Technology, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, 518000 Guangdong China
| | - Hua-Wei Zhang
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055 Guangdong China
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Southern University of Science and Technology, Shenzhen, 518055 Guangdong China
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3
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Trifan A, Gorgun D, Salim M, Li Z, Brace A, Zvyagin M, Ma H, Clyde A, Clark D, Hardy DJ, Burnley T, Huang L, McCalpin J, Emani M, Yoo H, Yin J, Tsaris A, Subbiah V, Raza T, Liu J, Trebesch N, Wells G, Mysore V, Gibbs T, Phillips J, Chennubhotla SC, Foster I, Stevens R, Anandkumar A, Vishwanath V, Stone JE, Tajkhorshid E, A. Harris S, Ramanathan A. Intelligent resolution: Integrating Cryo-EM with AI-driven multi-resolution simulations to observe the severe acute respiratory syndrome coronavirus-2 replication-transcription machinery in action. THE INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS 2022; 36:603-623. [PMID: 38464362 PMCID: PMC10923581 DOI: 10.1177/10943420221113513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) replication transcription complex (RTC) is a multi-domain protein responsible for replicating and transcribing the viral mRNA inside a human cell. Attacking RTC function with pharmaceutical compounds is a pathway to treating COVID-19. Conventional tools, e.g., cryo-electron microscopy and all-atom molecular dynamics (AAMD), do not provide sufficiently high resolution or timescale to capture important dynamics of this molecular machine. Consequently, we develop an innovative workflow that bridges the gap between these resolutions, using mesoscale fluctuating finite element analysis (FFEA) continuum simulations and a hierarchy of AI-methods that continually learn and infer features for maintaining consistency between AAMD and FFEA simulations. We leverage a multi-site distributed workflow manager to orchestrate AI, FFEA, and AAMD jobs, providing optimal resource utilization across HPC centers. Our study provides unprecedented access to study the SARS-CoV-2 RTC machinery, while providing general capability for AI-enabled multi-resolution simulations at scale.
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Affiliation(s)
- Anda Trifan
- Argonne National Laboratory
- University of Illinois Urbana-Champaign
| | - Defne Gorgun
- Argonne National Laboratory
- University of Illinois Urbana-Champaign
| | | | | | | | | | | | - Austin Clyde
- Argonne National Laboratory
- University of Chicago
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Ian Foster
- Argonne National Laboratory
- University of Chicago
| | - Rick Stevens
- Argonne National Laboratory
- University of Chicago
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Zhou W, Yadav GP, Yang X, Qin F, Li C, Jiang QX. Cryo-EM structure-based selection of computed ligand poses enables design of MTA-synergic PRMT5 inhibitors of better potency. Commun Biol 2022; 5:1054. [PMID: 36192627 PMCID: PMC9530242 DOI: 10.1038/s42003-022-03991-9] [Citation(s) in RCA: 1] [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: 11/28/2021] [Accepted: 09/13/2022] [Indexed: 12/31/2022] Open
Abstract
Projected potential of 2.5-4.0 Å cryo-EM structures for structure-based drug design is not well realized yet. Here we show that a 3.1 Å structure of PRMT5 is suitable for selecting computed poses of a chemical inhibitor and its analogs for enhanced potency. PRMT5, an oncogenic target for various cancer types, has many inhibitors manifesting little cooperativity with MTA, a co-factor analog accumulated in MTAP-/- cells. To achieve MTA-synergic inhibition, a pharmacophore from virtual screen leads to a specific inhibitor (11-2 F). Cryo-EM structures of 11-2 F / MTA-bound human PRMT5/MEP50 complex and its apo form resolved at 3.1 and 3.2 Å respectively show that 11-2 F in the catalytic pocket shifts the cofactor-binding pocket away by ~2.0 Å, contributing to positive cooperativity. Computational analysis predicts subtype specificity of 11-2 F among PRMTs. Structural analysis of ligands in the binding pockets is performed to compare poses of 11-2 F and its redesigned analogs and identifies three new analogs predicted to have significantly better potency. One of them, after synthesis, is ~4 fold more efficient in inhibiting PRMT5 catalysis than 11-2 F, with strong MTA-synergy. These data suggest the feasibility of employing near-atomic resolution cryo-EM structures and computational analysis of ligand poses for small molecule therapeutics.
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Affiliation(s)
- Wei Zhou
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, 32610, USA
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Gaya P Yadav
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
- Laboratory of Molecular Physiology and Biophysics, Hauptman-Woodward Medical Research Institute, Buffalo, NY, 14203, USA
- G.P.Y at the Department of Biochemistry and Biophysics, Texas A &M University, College Station, TX, 77843, USA
| | - Xiaozhi Yang
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, 32610, USA
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Feng Qin
- Department of Physiology and Biophysics, the State University of New York at Buffalo, Buffalo, NY, 14214, USA
| | - Chenglong Li
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, 32610, USA.
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA.
- Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL, 32610, USA.
| | - Qiu-Xing Jiang
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, 32610, USA.
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA.
- Laboratory of Molecular Physiology and Biophysics, Hauptman-Woodward Medical Research Institute, Buffalo, NY, 14203, USA.
- Department of Physiology and Biophysics, the State University of New York at Buffalo, Buffalo, NY, 14214, USA.
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