1
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Choudhury A, Ojha PK, Ray S. Hazards of antiviral contamination in water: Dissemination, fate, risk and their impact on fish. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135087. [PMID: 38964042 DOI: 10.1016/j.jhazmat.2024.135087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/14/2024] [Accepted: 07/01/2024] [Indexed: 07/06/2024]
Abstract
Antiviral drugs are a cornerstone in the first line of antiviral therapy and their demand rises consistently with increments in viral infections and successive outbreaks. The drugs enter the waters due to improper disposal methods or via human excreta following their consumption; consequently, many of them are now classified as emerging pollutants. Hereby, we review the global dissemination of these medications throughout different water bodies and thoroughly investigate the associated risk they pose to the aquatic fauna, particularly our vertebrate relative fish, which has great economic and dietary importance and subsequently serves as a major doorway to the human exposome. Our risk assessment identifies eleven such drugs that presently pose high to moderate levels of risk to the fish. The antiviral drugs are likely to induce oxidative stress, alter the behaviour, affect different physiological processes and provoke various toxicological mechanisms. Many of the compounds exhibit elevated bioaccumulation potential, while, some have an increased tendency to leach through soil and contaminate the groundwater. Eight antiviral medications show a highly recalcitrant nature and would impact the aquatic life consistently in the long run and continue to influence the human exposome. Thereby, we call for urgent ecopharmacovigilance measures and modification of current water treatment methods.
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Affiliation(s)
- Abhigyan Choudhury
- Aquatic Toxicology Laboratory, Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700019, West Bengal, India
| | - Probir Kumar Ojha
- Drug Discovery and Development (DDD) Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India.
| | - Sajal Ray
- Aquatic Toxicology Laboratory, Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700019, West Bengal, India.
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2
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Hussain T, Zhao Z, Murphy B, Taylor ZE, Gudorf JA, Klein S, Barnes LF, VanNieuwenhze M, Jarrold MF, Zlotnick A. Chemically Tagging Cargo for Specific Packaging inside and on the Surface of Virus-like Particles. ACS NANO 2024. [PMID: 39087909 DOI: 10.1021/acsnano.4c02056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2024]
Abstract
Virus-like particles (VLPs) have untapped potential for packaging and delivery of macromolecular cargo. To be a broadly useful platform, there needs to be a strategy for attaching macromolecules to the inside or the outside of the VLP with minimal modification of the platform or cargo. Here, we repurpose antiviral compounds that bind to hepatitis B virus (HBV) capsids to create a chemical tag to noncovalently attach cargo to the VLP. Our tag consists of a capsid assembly modulator, HAP13, connected to a linker terminating in maleimide. Our cargo is a green fluorescent protein (GFP) with a single addressable cysteine, a feature that can be engineered in many proteins. The HAP-GFP construct maintained HAP's intrinsic ability to bind HBV capsids and accelerate assembly. We investigated the capacity of HAP-GFP to coassemble with HBV capsid protein and bind to preassembled capsids. HAP-GFP binding was concentration-dependent, sensitive to capsid stability, and dependent on linker length. Long linkers had the greatest activity to bind capsids, while short linkers impeded assembly and damaged intact capsids. In coassembly reactions, >20 HAP-GFP molecules were presented on the outside and inside of the capsid, concentrating the cargo by more than 100-fold compared to bulk solution. We also tested an HAP-GFP with a cleavable linker so that external GFP molecules could be removed, resulting in exclusive internal packaging. These results demonstrate a generalizable strategy for attaching cargo to a VLP, supporting development of HBV as a modular VLP platform.
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Affiliation(s)
- Tariq Hussain
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Zhongchao Zhao
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Brennan Murphy
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Zachary E Taylor
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Jessica A Gudorf
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Shelby Klein
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Lauren F Barnes
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Michael VanNieuwenhze
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Martin F Jarrold
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Adam Zlotnick
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
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3
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Hsieh YC, Delarue M, Orland H, Koehl P. Analyzing the Geometry and Dynamics of Viral Structures: A Review of Computational Approaches Based on Alpha Shape Theory, Normal Mode Analysis, and Poisson-Boltzmann Theories. Viruses 2023; 15:1366. [PMID: 37376665 DOI: 10.3390/v15061366] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
The current SARS-CoV-2 pandemic highlights our fragility when we are exposed to emergent viruses either directly or through zoonotic diseases. Fortunately, our knowledge of the biology of those viruses is improving. In particular, we have more and more structural information on virions, i.e., the infective form of a virus that includes its genomic material and surrounding protective capsid, and on their gene products. It is important to have methods that enable the analyses of structural information on such large macromolecular systems. We review some of those methods in this paper. We focus on understanding the geometry of virions and viral structural proteins, their dynamics, and their energetics, with the ambition that this understanding can help design antiviral agents. We discuss those methods in light of the specificities of those structures, mainly that they are huge. We focus on three of our own methods based on the alpha shape theory for computing geometry, normal mode analyses to study dynamics, and modified Poisson-Boltzmann theories to study the organization of ions and co-solvent and solvent molecules around biomacromolecules. The corresponding software has computing times that are compatible with the use of regular desktop computers. We show examples of their applications on some outer shells and structural proteins of the West Nile Virus.
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Affiliation(s)
- Yin-Chen Hsieh
- Institute for Arctic and Marine Biology, Department of Biosciences, Fisheries, and Economics, UiT The Arctic University of Norway, 9037 Tromso, Norway
| | - Marc Delarue
- Institut Pasteur, Université Paris-Cité and CNRS, UMR 3528, Unité Architecture et Dynamique des Macromolécules Biologiques, 75015 Paris, France
| | - Henri Orland
- Institut de Physique Théorique, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Patrice Koehl
- Department of Computer Science, University of California, Davis, CA 95616, USA
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4
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Lynch DL, Pavlova A, Fan Z, Gumbart JC. Understanding Virus Structure and Dynamics through Molecular Simulations. J Chem Theory Comput 2023. [PMID: 37192279 DOI: 10.1021/acs.jctc.3c00116] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Viral outbreaks remain a serious threat to human and animal populations and motivate the continued development of antiviral drugs and vaccines, which in turn benefits from a detailed understanding of both viral structure and dynamics. While great strides have been made in characterizing these systems experimentally, molecular simulations have proven to be an essential, complementary approach. In this work, we review the contributions of molecular simulations to the understanding of viral structure, functional dynamics, and processes related to the viral life cycle. Approaches ranging from coarse-grained to all-atom representations are discussed, including current efforts at modeling complete viral systems. Overall, this review demonstrates that computational virology plays an essential role in understanding these systems.
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Affiliation(s)
- Diane L Lynch
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Zixing Fan
- Interdisciplinary Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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5
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McFadden WM, Sarafianos SG. Targeting the HIV-1 and HBV Capsids, an EnCore. Viruses 2023; 15:896. [PMID: 37112877 PMCID: PMC10146275 DOI: 10.3390/v15040896] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 03/25/2023] [Indexed: 04/03/2023] Open
Abstract
Not many structures are common among all viruses: only nucleic acid and a protein coat [...].
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Affiliation(s)
- William M. McFadden
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Stefan G. Sarafianos
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
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6
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Targeting Human Proteins for Antiviral Drug Discovery and Repurposing Efforts: A Focus on Protein Kinases. Viruses 2023; 15:v15020568. [PMID: 36851782 PMCID: PMC9966946 DOI: 10.3390/v15020568] [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: 01/11/2023] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/22/2023] Open
Abstract
Despite the great technological and medical advances in fighting viral diseases, new therapies for most of them are still lacking, and existing antivirals suffer from major limitations regarding drug resistance and a limited spectrum of activity. In fact, most approved antivirals are directly acting antiviral (DAA) drugs, which interfere with viral proteins and confer great selectivity towards their viral targets but suffer from resistance and limited spectrum. Nowadays, host-targeted antivirals (HTAs) are on the rise, in the drug discovery and development pipelines, in academia and in the pharmaceutical industry. These drugs target host proteins involved in the virus life cycle and are considered promising alternatives to DAAs due to their broader spectrum and lower potential for resistance. Herein, we discuss an important class of HTAs that modulate signal transduction pathways by targeting host kinases. Kinases are considered key enzymes that control virus-host interactions. We also provide a synopsis of the antiviral drug discovery and development pipeline detailing antiviral kinase targets, drug types, therapeutic classes for repurposed drugs, and top developing organizations. Furthermore, we detail the drug design and repurposing considerations, as well as the limitations and challenges, for kinase-targeted antivirals, including the choice of the binding sites, physicochemical properties, and drug combinations.
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7
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Starr CA, Nair S, Huang SY, Hagan MF, Jacobson SC, Zlotnick A. Engineering Metastability into a Virus-like Particle to Enable Triggered Dissociation. J Am Chem Soc 2023; 145:2322-2331. [PMID: 36651799 PMCID: PMC10018796 DOI: 10.1021/jacs.2c10937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
For a virus-like particle (VLP) to serve as a delivery platform, the VLP must be able to release its cargo in response to a trigger. Here, we use a chemical biology approach to destabilize a self-assembling capsid for a subsequent triggered disassembly. We redesigned the dimeric hepatitis B virus (HBV) capsid protein (Cp) with two differentially addressable cysteines, C150 for reversibly crosslinking the capsid and C124 to react with a destabilizing moiety. The resulting construct, Cp150-V124C, assembles into icosahedral, 120-dimer VLPs that spontaneously crosslink via the C-terminal C150, leaving C124 buried at a dimer-dimer interface. The VLP is driven into a metastable state when C124 is reacted with the bulky fluorophore, maleimidyl BoDIPY-FL. The resulting VLP is stable until exposed to modest, physiologically relevant concentrations of reducing agent. We observe dissociation with FRET relaxation of polarization, size exclusion chromatography, and resistive-pulse sensing. Dissociation is slow, minutes to hours, with a characteristic lag phase. Mathematical modeling based on the presence of a nucleation step predicts disassembly dynamics that are consistent with experimental observations. VLPs transfected into hepatoma cells show similar dissociation behavior. These results suggest a generalizable strategy for designing a VLP that can release its contents in an environmentally responsive reaction.
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Affiliation(s)
- Caleb A. Starr
- Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405 USA
| | - Smita Nair
- Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405 USA
- current address: Door Pharmaceuticals, Bloomington, IN 47401 USA
| | - Sheng-Yuan Huang
- Department of Chemistry, Indiana University, Bloomington, IN 47405 USA
| | - Michael F. Hagan
- Martin Fisher School of Physics, Brandeis University, Waltham, MA 02454 USA
| | | | - Adam Zlotnick
- Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405 USA
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8
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Molecular elucidation of drug-induced abnormal assemblies of the hepatitis B virus capsid protein by solid-state NMR. Nat Commun 2023; 14:471. [PMID: 36709212 PMCID: PMC9884277 DOI: 10.1038/s41467-023-36219-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 01/18/2023] [Indexed: 01/29/2023] Open
Abstract
Hepatitis B virus (HBV) capsid assembly modulators (CAMs) represent a recent class of anti-HBV antivirals. CAMs disturb proper nucleocapsid assembly, by inducing formation of either aberrant assemblies (CAM-A) or of apparently normal but genome-less empty capsids (CAM-E). Classical structural approaches have revealed the CAM binding sites on the capsid protein (Cp), but conformational information on the CAM-induced off-path aberrant assemblies is lacking. Here we show that solid-state NMR can provide such information, including for wild-type full-length Cp183, and we find that in these assemblies, the asymmetric unit comprises a single Cp molecule rather than the four quasi-equivalent conformers typical for the icosahedral T = 4 symmetry of the normal HBV capsids. Furthermore, while in contrast to truncated Cp149, full-length Cp183 assemblies appear, on the mesoscopic level, unaffected by CAM-A, NMR reveals that on the molecular level, Cp183 assemblies are equally aberrant. Finally, we use a eukaryotic cell-free system to reveal how CAMs modulate capsid-RNA interactions and capsid phosphorylation. Our results establish a structural view on assembly modulation of the HBV capsid, and they provide a rationale for recently observed differences between in-cell versus in vitro capsid assembly modulation.
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9
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de Araujo Dorneles ML, Cardoso-Lima R, Souza PFN, Santoro Rosa D, Magne TM, Santos-Oliveira R, Alencar LMR. Zika Virus (ZIKV): A New Perspective on the Nanomechanical and Structural Properties. Viruses 2022; 14:v14081727. [PMID: 36016349 PMCID: PMC9414353 DOI: 10.3390/v14081727] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/25/2022] [Accepted: 08/01/2022] [Indexed: 11/16/2022] Open
Abstract
Zika virus (ZIKV) is an arthropod-borne virus (arbovirus) from Flavivirus. In 2015, Brazil and other Latin American countries experienced an outbreak of ZIKV infections associated with severe neurological disorders such as Guillain–Barre syndrome (GBS), encephalopathy, and encephalitis. Here, a complete mechanical and structural analysis of the ZIKV has been performed using Atomic Force Microscopy (AFM). AFM analysis corroborated the virus mean size (~50 nm) and icosahedral geometry and revealed high mechanical resistance of both: the viral surface particle (~200 kPa) and its internal content (~800 kPa). The analysis demonstrated the detailed organization of the nucleocapsid structure (such as RNA strips). An interesting finding was the discovery that ZIKV has no surface self-assembling property. These results can contribute to the development of future treatment candidates and circumscribe the magnitude of viral transmission.
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Affiliation(s)
| | - Ruana Cardoso-Lima
- Laboratory of Biophysics and Nanosystems, Physics Department, Federal University of Maranhão, São Luís 65020070, Brazil
| | - Pedro Filho Noronha Souza
- Department of Biochemistry, Federal University of Ceará, Fortaleza 60440900, Brazil
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Fortaleza 60440900, Brazil
| | - Daniela Santoro Rosa
- Department of Microbiology, Immunology, and Parasitology, Federal University of São Paulo, São Paulo 04023062, Brazil
| | - Tais Monteiro Magne
- Brazilian Nuclear Energy Commission, Nuclear Engineering Institute, Rio de Janeiro 21941906, Brazil
| | - Ralph Santos-Oliveira
- Brazilian Nuclear Energy Commission, Nuclear Engineering Institute, Rio de Janeiro 21941906, Brazil
- Laboratory of Nanoradiopharmacy, Rio de Janeiro State University, Rio de Janeiro 23070200, Brazil
| | - Luciana Magalhães Rebelo Alencar
- Laboratory of Biophysics and Nanosystems, Physics Department, Federal University of Maranhão, São Luís 65020070, Brazil
- Correspondence:
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10
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Spunde K, Vigante B, Dubova UN, Sipola A, Timofejeva I, Zajakina A, Jansons J, Plotniece A, Pajuste K, Sobolev A, Muhamadejev R, Jaudzems K, Duburs G, Kozlovska T. Design and Synthesis of Hepatitis B Virus (HBV) Capsid Assembly Modulators and Evaluation of Their Activity in Mammalian Cell Model. Pharmaceuticals (Basel) 2022; 15:ph15070773. [PMID: 35890072 PMCID: PMC9317397 DOI: 10.3390/ph15070773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/15/2022] [Accepted: 06/17/2022] [Indexed: 12/02/2022] Open
Abstract
Capsid assembly modulators (CAMs) have emerged as a promising class of antiviral agents. We studied the effects of twenty-one newly designed and synthesized CAMs including heteroaryldihydropyrimidine compounds (HAPs), their analogs and standard compounds on hepatitis B virus (HBV) capsid assembly. Cytoplasmic expression of the HBV core (HBc) gene driven by the exogenously delivered recombinant alphavirus RNA replicon was used for high level production of the full-length HBc protein in mammalian cells. HBV capsid assembly was assessed by native agarose gel immunoblot analysis, electron microscopy and inhibition of virion secretion in HepG2.2.15 HBV producing cell line. Induced fit docking simulation was applied for modelling the structural relationships of the synthesized compounds and HBc. The most efficient were the HAP class compounds—dihydropyrimidine 5-carboxylic acid n-alkoxyalkyl esters, which induced the formation of incorrectly assembled capsid products and their accumulation within the cells. HBc product accumulation in the cells was not detected with the reference HAP compound Bay 41-4109, suggesting different modes of action. A significant antiviral effect and substantially reduced toxicity were revealed for two of the synthesized compounds. Two new HAP compounds revealed a significant antiviral effect and a favorable toxicity profile that allows these compounds to be considered promising leads and drug candidates for the treatment of HBV infection. The established alphavirus based HBc expression approach allows for the specific selection of capsid assembly modulators directly in the natural cell environment.
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Affiliation(s)
- Karina Spunde
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (U.N.D.); (I.T.); (A.Z.); (J.J.); (T.K.)
- Correspondence: (K.S.); (B.V.)
| | - Brigita Vigante
- Latvian Institute of Organic Synthesis, LV-1006 Riga, Latvia; (A.S.); (A.P.); (K.P.); (A.S.); (R.M.); (K.J.); (G.D.)
- Correspondence: (K.S.); (B.V.)
| | - Unda Nelda Dubova
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (U.N.D.); (I.T.); (A.Z.); (J.J.); (T.K.)
| | - Anda Sipola
- Latvian Institute of Organic Synthesis, LV-1006 Riga, Latvia; (A.S.); (A.P.); (K.P.); (A.S.); (R.M.); (K.J.); (G.D.)
| | - Irena Timofejeva
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (U.N.D.); (I.T.); (A.Z.); (J.J.); (T.K.)
| | - Anna Zajakina
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (U.N.D.); (I.T.); (A.Z.); (J.J.); (T.K.)
| | - Juris Jansons
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (U.N.D.); (I.T.); (A.Z.); (J.J.); (T.K.)
| | - Aiva Plotniece
- Latvian Institute of Organic Synthesis, LV-1006 Riga, Latvia; (A.S.); (A.P.); (K.P.); (A.S.); (R.M.); (K.J.); (G.D.)
| | - Karlis Pajuste
- Latvian Institute of Organic Synthesis, LV-1006 Riga, Latvia; (A.S.); (A.P.); (K.P.); (A.S.); (R.M.); (K.J.); (G.D.)
| | - Arkadij Sobolev
- Latvian Institute of Organic Synthesis, LV-1006 Riga, Latvia; (A.S.); (A.P.); (K.P.); (A.S.); (R.M.); (K.J.); (G.D.)
| | - Ruslan Muhamadejev
- Latvian Institute of Organic Synthesis, LV-1006 Riga, Latvia; (A.S.); (A.P.); (K.P.); (A.S.); (R.M.); (K.J.); (G.D.)
| | - Kristaps Jaudzems
- Latvian Institute of Organic Synthesis, LV-1006 Riga, Latvia; (A.S.); (A.P.); (K.P.); (A.S.); (R.M.); (K.J.); (G.D.)
| | - Gunars Duburs
- Latvian Institute of Organic Synthesis, LV-1006 Riga, Latvia; (A.S.); (A.P.); (K.P.); (A.S.); (R.M.); (K.J.); (G.D.)
| | - Tatjana Kozlovska
- Latvian Biomedical Research and Study Centre, LV-1067 Riga, Latvia; (U.N.D.); (I.T.); (A.Z.); (J.J.); (T.K.)
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11
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Domínguez-Zotes S, Valbuena A, Mateu MG. Antiviral compounds modulate elasticity, strength and material fatigue of a virus capsid framework. Biophys J 2022; 121:919-931. [PMID: 35151634 PMCID: PMC8943814 DOI: 10.1016/j.bpj.2022.02.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/18/2022] [Accepted: 02/09/2022] [Indexed: 11/30/2022] Open
Abstract
This study investigates whether the biochemical and antiviral effects of organic compounds that bind different sites in the mature human immunodeficiency virus capsid may be related to the modulation of different mechanical properties of the protein lattice from which the capsid is built. Mechanical force was used as a probe to quantify, in atomic force microscopy experiments at physiological pH and ionic strength, ligand-mediated changes in capsid lattice elasticity, breathing, strength against local dislocation by mechanical stress, and resistance to material fatigue. The results indicate that the effects of the tested compounds on assembly or biochemical stability can be linked, from a physics-based perspective, to their interference with the mechanical behavior of the viral capsid framework. The antivirals CAP-1 and CAI-55 increased the intrinsic elasticity and breathing of the capsid protein lattice and may entropically decrease the probability of the capsid protein to assemble into a functionally competent conformation. Antiviral PF74 increased the resistance of the capsid protein lattice to disruption by mechanical stress and material fatigue and may enthalpically strengthen the basal capsid lattice against breakage and disintegration. This study provides proof of concept that the interrogation of the mechanical properties of the nanostructured protein material that makes a virus capsid may provide fundamental insights into the biophysical action of capsid-binding antiviral agents. The implications for drug design by specifically targeting the biomechanics of viruses are discussed.
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Affiliation(s)
- Santos Domínguez-Zotes
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
| | - Alejandro Valbuena
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain.
| | - Mauricio G Mateu
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain.
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12
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Briday M, Hallé F, Lecoq L, Radix S, Martin J, Montserret R, Dujardin M, Fogeron ML, Nassal M, Meier BH, Lomberget T, Böckmann A. Pharmacomodulation of a ligand targeting the HBV capsid hydrophobic pocket. Chem Sci 2022; 13:8840-8847. [PMID: 36042894 PMCID: PMC9358932 DOI: 10.1039/d2sc02420a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/06/2022] [Indexed: 11/21/2022] Open
Abstract
Hepatitis B virus (HBV) is a small enveloped retrotranscribing DNA virus and an important human pathogen. Its capsid-forming core protein (Cp) features a hydrophobic pocket proposed to be central notably in capsid envelopment. Indeed, mutations in and around this pocket can profoundly modulate, and even abolish, secretion of enveloped virions. We have recently shown that Triton X-100, a detergent used during Cp purification, binds to the hydrophobic pocket with micromolar affinity. We here performed pharmacomodulation of pocket binders through systematic modifications of the three distinct chemical moieties composing the Triton X-100 molecule. Using NMR and ITC, we found that the flat aromatic moiety is essential for binding, while the number of atoms of the aliphatic chain modulates binding affinity. The hydrophilic tail, in contrast, is highly tolerant to changes in both length and type. Our data provide essential information for designing a new class of HBV antivirals targeting capsid–envelope interactions. Small-molecule binding to the Hepatitis B virus core protein hydrophobic pocket, a possible strategy for targeting viral particle assembly.![]()
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Affiliation(s)
- Mathilde Briday
- Molecular Microbiology and Structural Biochemistry (MMSB) UMR 5086 CNRS/Université de Lyon, Labex Ecofect, 7 Passage du Vercors, 69367 Lyon, France
| | - François Hallé
- Université de Lyon, Université Lyon 1, CNRS UMR 5246 Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS), Faculté de Pharmacie-ISPB, 8 Avenue Rockefeller, FR-69373 Lyon Cedex 08, France
| | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry (MMSB) UMR 5086 CNRS/Université de Lyon, Labex Ecofect, 7 Passage du Vercors, 69367 Lyon, France
| | - Sylvie Radix
- Université de Lyon, Université Lyon 1, CNRS UMR 5246 Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS), Faculté de Pharmacie-ISPB, 8 Avenue Rockefeller, FR-69373 Lyon Cedex 08, France
| | - Juliette Martin
- Molecular Microbiology and Structural Biochemistry (MMSB) UMR 5086 CNRS/Université de Lyon, Labex Ecofect, 7 Passage du Vercors, 69367 Lyon, France
| | - Roland Montserret
- Molecular Microbiology and Structural Biochemistry (MMSB) UMR 5086 CNRS/Université de Lyon, Labex Ecofect, 7 Passage du Vercors, 69367 Lyon, France
| | - Marie Dujardin
- Molecular Microbiology and Structural Biochemistry (MMSB) UMR 5086 CNRS/Université de Lyon, Labex Ecofect, 7 Passage du Vercors, 69367 Lyon, France
| | - Marie-Laure Fogeron
- Molecular Microbiology and Structural Biochemistry (MMSB) UMR 5086 CNRS/Université de Lyon, Labex Ecofect, 7 Passage du Vercors, 69367 Lyon, France
| | - Michael Nassal
- Department of Medicine II/Molecular Biology, University Hospital Freiburg, Medical Center, University of Freiburg, Freiburg 79106, Germany
| | - Beat H. Meier
- Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland
| | - Thierry Lomberget
- Université de Lyon, Université Lyon 1, CNRS UMR 5246 Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS), Faculté de Pharmacie-ISPB, 8 Avenue Rockefeller, FR-69373 Lyon Cedex 08, France
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry (MMSB) UMR 5086 CNRS/Université de Lyon, Labex Ecofect, 7 Passage du Vercors, 69367 Lyon, France
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13
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In a flash of light: X-ray free electron lasers meet native mass spectrometry. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021; 39:89-99. [PMID: 34906329 DOI: 10.1016/j.ddtec.2021.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 06/14/2021] [Accepted: 07/13/2021] [Indexed: 01/02/2023]
Abstract
During the last years, X-ray free electron lasers (XFELs) have emerged as X-ray sources of unparalleled brightness, delivering extreme amounts of photons in femtosecond pulses. As such, they have opened up completely new possibilities in drug discovery and structural biology, including studying high resolution biomolecular structures and their functioning in a time resolved manner, and diffractive imaging of single particles without the need for their crystallization. In this perspective, we briefly review the operation of XFELs, their immediate uses for drug discovery and focus on the potentially revolutionary single particle diffractive imaging technique and the challenges which remain to be overcome to fully realize its potential to provide high resolution structures without the need for crystallization, freezing or the need to keep proteins stable at extreme concentrations for long periods of time. As the issues have been to a large extent sample delivery related, we outline a way for native mass spectrometry to overcome these and enable so far impossible research with a potentially huge impact on structural biology and drug discovery, such as studying structures of transient intermediate species in viral life cycles or during functioning of molecular machines.
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de Pablo PJ, San Martín C. Seeing and touching adenovirus: complementary approaches for understanding assembly and disassembly of a complex virion. Curr Opin Virol 2021; 52:112-122. [PMID: 34906758 DOI: 10.1016/j.coviro.2021.11.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/09/2021] [Accepted: 11/11/2021] [Indexed: 12/24/2022]
Abstract
Understanding adenovirus assembly and disassembly poses many challenges due to the virion complexity. A distinctive feature of adenoviruses is the large amount of virus-encoded proteins packed together with the dsDNA genome. Cryo-electron microscopy (cryo-EM) structures are broadening our understanding of capsid variability along evolution, but little is known about the organization of the non-icosahedral nucleoproteic core and its influence in adenovirus function. Atomic force microscopy (AFM) probes the biomechanics of virus particles, while simultaneously inducing and monitoring their disassembly in real time. Synergistic combination of AFM with EM shows that core proteins play unexpected key roles in maturation and entry, and uncoating dynamics are finely tuned to ensure genome release at the appropriate time and place for successful infection.
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Affiliation(s)
- Pedro J de Pablo
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid and IFIMAC, 28049 Madrid, Spain.
| | - Carmen San Martín
- Departamento de Estructura de Macromoléculas, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, 28049 Madrid, Spain.
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15
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Niklasch M, Zimmermann P, Nassal M. The Hepatitis B Virus Nucleocapsid-Dynamic Compartment for Infectious Virus Production and New Antiviral Target. Biomedicines 2021; 9:1577. [PMID: 34829806 PMCID: PMC8615760 DOI: 10.3390/biomedicines9111577] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 12/11/2022] Open
Abstract
Hepatitis B virus (HBV) is a small enveloped DNA virus which replicates its tiny 3.2 kb genome by reverse transcription inside an icosahedral nucleocapsid, formed by a single ~180 amino acid capsid, or core, protein (Cp). HBV causes chronic hepatitis B (CHB), a severe liver disease responsible for nearly a million deaths each year. Most of HBV's only seven primary gene products are multifunctional. Though less obvious than for the multi-domain polymerase, P protein, this is equally crucial for Cp with its multiple roles in the viral life-cycle. Cp provides a stable genome container during extracellular phases, allows for directed intracellular genome transport and timely release from the capsid, and subsequent assembly of new nucleocapsids around P protein and the pregenomic (pg) RNA, forming a distinct compartment for reverse transcription. These opposing features are enabled by dynamic post-transcriptional modifications of Cp which result in dynamic structural alterations. Their perturbation by capsid assembly modulators (CAMs) is a promising new antiviral concept. CAMs inappropriately accelerate assembly and/or distort the capsid shell. We summarize the functional, biochemical, and structural dynamics of Cp, and discuss the therapeutic potential of CAMs based on clinical data. Presently, CAMs appear as a valuable addition but not a substitute for existing therapies. However, as part of rational combination therapies CAMs may bring the ambitious goal of a cure for CHB closer to reality.
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Affiliation(s)
| | | | - Michael Nassal
- Internal Medicine II/Molecular Biology, University Hospital Freiburg, Hugstetter Str. 55, D-79106 Freiburg, Germany; (M.N.); (P.Z.)
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Core Protein-Directed Antivirals and Importin β Can Synergistically Disrupt HBV Capsids. J Virol 2021; 96:e0139521. [PMID: 34705562 DOI: 10.1128/jvi.01395-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Viral structural proteins can have multiple activities. Antivirals that target structural proteins have potential to exhibit multiple antiviral mechanisms. Hepatitis B Virus (HBV) core protein (Cp) is involved in most stages of the viral lifecycle: it assembles into capsids, packages viral RNA, is a metabolic compartment for reverse transcription, interacts with nuclear trafficking machinery, and disassembles to release the viral genome into the nucleus. During nuclear localization, HBV capsids bind to host importins (e.g. Impβ) via Cp's C-terminal domain (CTD); the CTD is localized to the interior of the capsid and is transiently exposed on the exterior. We used HAP12 as a representative Cp Allosteric Modulators (CpAMs), a class of antivirals that inappropriately stimulates and misdirects HBV assembly and deforms capsids. CpAM impact on other aspects of the HBV lifecycle is poorly understood. We investigated how HAP12 influenced the interactions between empty or RNA-filled capsids with Impβ and trypsin in vitro. We showed that HAP12 can modulate CTD accessibility and capsid stability, depending on the saturation of HAP12-binding sites. We demonstrated that Impβ synergistically contributes to capsid disruption at high levels of HAP12 saturation, using electron microscopy to visualize disruption and rearrangement of Cp dimers into aberrant complexes. However, RNA-filled capsids resisted the destabilizing effects of HAP12 and Impβ. In summary, we show host protein-induced catalysis of capsid disruption, an unexpected additional mechanism of action for CpAMs. Potentially, untimely capsid disassembly can hamper the HBV lifecycle and also cause the virus to become vulnerable to host innate immune responses. IMPORTANCE The HBV core, an icosahedral complex of 120 copies of the homodimeric core (capsid) protein with or without packaged nucleic acid, is transported to the host nucleus by its interaction with host importin proteins. Importin-core interaction requires the core protein C-terminal domain, which is inside the capsid, to "flip" to the capsid exterior. Core-protein directed drugs that affect capsid assembly and stability have been developed recently. We show that these molecules can, synergistically with importins, disrupt capsids. This mechanism of action, synergism with host protein, has potential to disrupt the virus lifecycle and activate the innate immune system.
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17
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Sornsuwan K, Thongkhum W, Pamonsupornwichit T, Carraway TS, Soponpong S, Sakkhachornphop S, Tayapiwatana C, Yasamut U. Performance of Affinity-Improved DARPin Targeting HIV Capsid Domain in Interference of Viral Progeny Production. Biomolecules 2021; 11:biom11101437. [PMID: 34680070 PMCID: PMC8533564 DOI: 10.3390/biom11101437] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/17/2021] [Accepted: 09/28/2021] [Indexed: 01/22/2023] Open
Abstract
Previously, a designed ankyrin repeat protein, AnkGAG1D4, was generated for intracellular targeting of the HIV-1 capsid domain. The efficiency was satisfactory in interfering with the HIV assembly process. Consequently, improved AnkGAG1D4 binding affinity was introduced by substituting tyrosine (Y) for serine (S) at position 45. However, the intracellular anti-HIV-1 activity of AnkGAG1D4-S45Y has not yet been validated. In this study, the performance of AnkGAG1D4 and AnkGAG1D4-S45Y in inhibiting wild-type HIV-1 and HIV-1 maturation inhibitor-resistant replication in SupT1 cells was evaluated. HIV-1 p24 and viral load assays were used to verify the biological activity of AnkGAG1D4 and AnkGAG1D4-S45Y as assembly inhibitors. In addition, retardation of syncytium formation in infected SupT1 cells was observed. Of note, the defense mechanism of both ankyrins did not induce the mutation of target amino acids in the capsid domain. The present data show that the potency of AnkGAG1D4-S45Y was superior to AnkGAG1D4 in interrupting either HIV-1 wild-type or the HIV maturation inhibitor-resistant strain.
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Affiliation(s)
- Kanokporn Sornsuwan
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
- Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Weeraya Thongkhum
- Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
- Center of Innovative Immunodiagnostic Development, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Thanathat Pamonsupornwichit
- Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Tanawan Samleerat Carraway
- Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Suthinee Soponpong
- Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
- Center of Innovative Immunodiagnostic Development, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | | | - Chatchai Tayapiwatana
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
- Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
- Center of Innovative Immunodiagnostic Development, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Umpa Yasamut
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
- Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
- Center of Innovative Immunodiagnostic Development, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
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Sabnis RW. Combination Therapy of RNA Interference and Small Molecules for Treating Hepatitis B Virus Infection. ACS Med Chem Lett 2021; 12:858-859. [PMID: 34141056 PMCID: PMC8201480 DOI: 10.1021/acsmedchemlett.1c00103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Indexed: 11/28/2022] Open
Affiliation(s)
- Ram W. Sabnis
- Smith, Gambrell & Russell
LLP, 1230 Peachtree Street NE, Suite 3100, Atlanta, Georgia 30309, United States
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19
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Conformational Plasticity of Hepatitis B Core Protein Spikes Promotes Peptide Binding Independent of the Secretion Phenotype. Microorganisms 2021; 9:microorganisms9050956. [PMID: 33946808 PMCID: PMC8145704 DOI: 10.3390/microorganisms9050956] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 12/31/2022] Open
Abstract
Hepatitis B virus is a major human pathogen, which forms enveloped virus particles. During viral maturation, membrane-bound hepatitis B surface proteins package hepatitis B core protein capsids. This process is intercepted by certain peptides with an “LLGRMKG” motif that binds to the capsids at the tips of dimeric spikes. With microcalorimetry, electron cryo microscopy and peptide microarray-based screens, we have characterized the structural and thermodynamic properties of peptide binding to hepatitis B core protein capsids with different secretion phenotypes. The peptide “GSLLGRMKGA” binds weakly to hepatitis B core protein capsids and mutant capsids with a premature (F97L) or low-secretion phenotype (L60V and P5T). With electron cryo microscopy, we provide novel structures for L60V and P5T and demonstrate that binding occurs at the tips of the spikes at the dimer interface, splaying the helices apart independent of the secretion phenotype. Peptide array screening identifies “SLLGRM” as the core binding motif. This shortened motif binds only to one of the two spikes in the asymmetric unit of the capsid and induces a much smaller conformational change. Altogether, these comprehensive studies suggest that the tips of the spikes act as an autonomous binding platform that is unaffected by mutations that affect secretion phenotypes.
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20
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Pérez-Segura C, Goh BC, Hadden-Perilla JA. All-Atom MD Simulations of the HBV Capsid Complexed with AT130 Reveal Secondary and Tertiary Structural Changes and Mechanisms of Allostery. Viruses 2021; 13:564. [PMID: 33810481 PMCID: PMC8065791 DOI: 10.3390/v13040564] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/15/2021] [Accepted: 03/23/2021] [Indexed: 12/18/2022] Open
Abstract
The hepatitis B virus (HBV) capsid is an attractive drug target, relevant to combating viral hepatitis as a major public health concern. Among small molecules known to interfere with capsid assembly, the phenylpropenamides, including AT130, represent an important antiviral paradigm based on disrupting the timing of genome packaging. Here, all-atom molecular dynamics simulations of an intact AT130-bound HBV capsid reveal that the compound increases spike flexibility and improves recovery of helical secondary structure in the spike tips. Regions of the capsid-incorporated dimer that undergo correlated motion correspond to established sub-domains that pivot around the central chassis. AT130 alters patterns of correlated motion and other essential dynamics. A new conformational state of the dimer is identified, which can lead to dramatic opening of the intradimer interface and disruption of communication within the spike tip. A novel salt bridge is also discovered, which can mediate contact between the spike tip and fulcrum even in closed conformations, revealing a mechanism of direct communication across these sub-domains. Altogether, results describe a dynamical connection between the intra- and interdimer interfaces and enable mapping of allostery traversing the entire core protein dimer.
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Affiliation(s)
- Carolina Pérez-Segura
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA;
| | - Boon Chong Goh
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-Massachusetts Institute of Technology Alliance for Research and Technology Centre, Singapore 138602, Singapore;
| | - Jodi A. Hadden-Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA;
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21
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Johnson JE, Olson AJ. Icosahedral virus structures and the protein data bank. J Biol Chem 2021; 296:100554. [PMID: 33744290 PMCID: PMC8081926 DOI: 10.1016/j.jbc.2021.100554] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 11/30/2022] Open
Abstract
The structural study of icosahedral viruses has a long and impactful history in both crystallographic methodology and molecular biology. The evolution of the Protein Data Bank has paralleled and supported these studies providing readily accessible formats dealing with novel features associated with viral particle symmetries and subunit interactions. This overview describes the growth in size and complexity of icosahedral viruses from the first early studies of small RNA plant viruses and human picornaviruses up to the larger and more complex bacterial phage, insect, and human disease viruses such as Zika, hepatitis B, Adeno and Polyoma virus. The analysis of icosahedral viral capsid protein domain folds has shown striking similarities, with the beta jelly roll motif observed across multiple evolutionarily divergent species. The icosahedral symmetry of viruses drove the development of noncrystallographic symmetry averaging as a powerful phasing method, and the constraints of maintaining this symmetry resulted in the concept of quasi-equivalence in viral structures. Symmetry also played an important early role in demonstrating the power of cryo-electron microscopy as an alternative to crystallography in generating atomic resolution structures of these viruses. The Protein Data Bank has been a critical resource for assembling and disseminating these structures to a wide community, and the virus particle explorer (VIPER) was developed to enable users to easily generate and view complete viral capsid structures from their asymmetric building blocks. Finally, we share a personal perspective on the early use of computer graphics to communicate the intricacies, interactions, and beauty of these virus structures.
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Affiliation(s)
- John E Johnson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA.
| | - Arthur J Olson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
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22
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Addressing Antiretroviral Drug Resistance with Host-Targeting Drugs-First Steps towards Developing a Host-Targeting HIV-1 Assembly Inhibitor. Viruses 2021; 13:v13030451. [PMID: 33802145 PMCID: PMC8001593 DOI: 10.3390/v13030451] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/02/2021] [Accepted: 03/02/2021] [Indexed: 12/13/2022] Open
Abstract
The concerning increase in HIV-1 resistance argues for prioritizing the development of host-targeting antiviral drugs because such drugs can offer high genetic barriers to the selection of drug-resistant viral variants. Targeting host proteins could also yield drugs that act on viral life cycle events that have proven elusive to inhibition, such as intracellular events of HIV-1 immature capsid assembly. Here, we review small molecule inhibitors identified primarily through HIV-1 self-assembly screens and describe how all act either narrowly post-entry or broadly on early and late events of the HIV-1 life cycle. We propose that a different screening approach could identify compounds that specifically inhibit HIV-1 Gag assembly, as was observed when a potent rabies virus inhibitor was identified using a host-catalyzed rabies assembly screen. As an example of this possibility, we discuss an antiretroviral small molecule recently identified using a screen that recapitulates the host-catalyzed HIV-1 capsid assembly pathway. This chemotype potently blocks HIV-1 replication in T cells by specifically inhibiting immature HIV-1 capsid assembly but fails to select for resistant viral variants over 37 passages, suggesting a host protein target. Development of such small molecules could yield novel host-targeting antiretroviral drugs and provide insight into chronic diseases resulting from dysregulation of host machinery targeted by these drugs.
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