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Akuma DC, Wodzanowski KA, Schwartz Wertman R, Exconde PM, Vázquez Marrero VR, Odunze CE, Grubaugh D, Shin S, Taabazuing C, Brodsky IE. Catalytic activity and autoprocessing of murine caspase-11 mediate noncanonical inflammasome assembly in response to cytosolic LPS. eLife 2024; 13:e83725. [PMID: 38231198 PMCID: PMC10794067 DOI: 10.7554/elife.83725] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/06/2023] [Indexed: 01/18/2024] Open
Abstract
Inflammatory caspases are cysteine protease zymogens whose activation following infection or cellular damage occurs within supramolecular organizing centers (SMOCs) known as inflammasomes. Inflammasomes recruit caspases to undergo proximity-induced autoprocessing into an enzymatically active form that cleaves downstream targets. Binding of bacterial LPS to its cytosolic sensor, caspase-11 (Casp11), promotes Casp11 aggregation within a high-molecular-weight complex known as the noncanonical inflammasome, where it is activated to cleave gasdermin D and induce pyroptosis. However, the cellular correlates of Casp11 oligomerization and whether Casp11 forms an LPS-induced SMOC within cells remain unknown. Expression of fluorescently labeled Casp11 in macrophages revealed that cytosolic LPS induced Casp11 speck formation. Unexpectedly, catalytic activity and autoprocessing were required for Casp11 to form LPS-induced specks in macrophages. Furthermore, both catalytic activity and autoprocessing were required for Casp11 speck formation in an ectopic expression system, and processing of Casp11 via ectopically expressed TEV protease was sufficient to induce Casp11 speck formation. These data reveal a previously undescribed role for Casp11 catalytic activity and autoprocessing in noncanonical inflammasome assembly, and shed new light on the molecular requirements for noncanonical inflammasome assembly in response to cytosolic LPS.
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Affiliation(s)
- Daniel C Akuma
- Department of Pathobiology, University of Pennsylvania School of Veterinary MedicinePhiladelphiaUnited States
| | - Kimberly A Wodzanowski
- Department of Microbiology, University of Pennsylvania Perelman School of MedicinePhiladelphiaUnited States
| | - Ronit Schwartz Wertman
- Department of Pathobiology, University of Pennsylvania School of Veterinary MedicinePhiladelphiaUnited States
| | - Patrick M Exconde
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of MedicinePhiladelphiaUnited States
| | - Víctor R Vázquez Marrero
- Department of Microbiology, University of Pennsylvania Perelman School of MedicinePhiladelphiaUnited States
| | | | - Daniel Grubaugh
- Department of Pathobiology, University of Pennsylvania School of Veterinary MedicinePhiladelphiaUnited States
| | - Sunny Shin
- Department of Microbiology, University of Pennsylvania Perelman School of MedicinePhiladelphiaUnited States
| | - Cornelius Taabazuing
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of MedicinePhiladelphiaUnited States
| | - Igor E Brodsky
- Department of Pathobiology, University of Pennsylvania School of Veterinary MedicinePhiladelphiaUnited States
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2
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Sundar S, Piramanayagam S, Natarajan J. A review on structural genomics approach applied for drug discovery against three vector-borne viral diseases: Dengue, Chikungunya and Zika. Virus Genes 2022; 58:151-171. [PMID: 35394596 DOI: 10.1007/s11262-022-01898-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 03/22/2022] [Indexed: 12/22/2022]
Abstract
Structural genomics involves the advent of three-dimensional structures of the genome encoded proteins through various techniques available. Numerous structural genomics research groups have been developed across the globe and they contribute enormously to the identification of three-dimensional structures of various proteins. In this review, we have discussed the applications of the structural genomics approach towards the discovery of potential lead-like molecules against the genomic drug targets of three vector-borne diseases, namely, Dengue, Chikungunya and Zika. Currently, all these three diseases are associated with the most important global public health problems and significant economic burden in tropical countries. Structural genomics has accelerated the identification of novel drug targets and inhibitors for the treatment of these diseases. We start with the current development status of the drug targets and antiviral drugs against these three diseases and conclude by describing challenges that need to be addressed to overcome the shortcomings in the process of drug discovery.
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Affiliation(s)
- Shobana Sundar
- Computational Biology Lab, Department of Bioinformatics, Bharathiar University, Coimbatore, India
| | | | - Jeyakumar Natarajan
- Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu, India.
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3
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Wahaab A, Mustafa BE, Hameed M, Stevenson NJ, Anwar MN, Liu K, Wei J, Qiu Y, Ma Z. Potential Role of Flavivirus NS2B-NS3 Proteases in Viral Pathogenesis and Anti-flavivirus Drug Discovery Employing Animal Cells and Models: A Review. Viruses 2021; 14:44. [PMID: 35062249 PMCID: PMC8781031 DOI: 10.3390/v14010044] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 02/07/2023] Open
Abstract
Flaviviruses are known to cause a variety of diseases in humans in different parts of the world. There are very limited numbers of antivirals to combat flavivirus infection, and therefore new drug targets must be explored. The flavivirus NS2B-NS3 proteases are responsible for the cleavage of the flavivirus polyprotein, which is necessary for productive viral infection and for causing clinical infections; therefore, they are a promising drug target for devising novel drugs against different flaviviruses. This review highlights the structural details of the NS2B-NS3 proteases of different flaviviruses, and also describes potential antiviral drugs that can interfere with the viral protease activity, as determined by various studies. Moreover, optimized in vitro reaction conditions for studying the NS2B-NS3 proteases of different flaviviruses may vary and have been incorporated in this review. The increasing availability of the in silico and crystallographic/structural details of flavivirus NS2B-NS3 proteases in free and drug-bound states can pave the path for the development of promising antiflavivirus drugs to be used in clinics. However, there is a paucity of information available on using animal cells and models for studying flavivirus NS2B-NS3 proteases, as well as on the testing of the antiviral drug efficacy against NS2B-NS3 proteases. Therefore, on the basis of recent studies, an effort has also been made to propose potential cellular and animal models for the study of flavivirus NS2B-NS3 proteases for the purposes of exploring flavivirus pathogenesis and for testing the efficacy of possible drugs targets, in vitro and in vivo.
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Affiliation(s)
- Abdul Wahaab
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (A.W.); (M.H.); (M.N.A.); (K.L.); (J.W.)
| | - Bahar E Mustafa
- Sub Campus Toba Tek Singh, University of Agriculture, Faisalabad 36050, Pakistan;
| | - Muddassar Hameed
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (A.W.); (M.H.); (M.N.A.); (K.L.); (J.W.)
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute, State University, Fralin Life Sciences Building, 360 W Campus Blacksburg, Blacksburg, VA 24061, USA
| | - Nigel J. Stevenson
- Royal College of Surgeons in Ireland, Medical University of Bahrain, Busaiteen, Adliya 15503, Bahrain;
- Viral Immunology Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 R590 Dublin, Ireland
| | - Muhammad Naveed Anwar
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (A.W.); (M.H.); (M.N.A.); (K.L.); (J.W.)
| | - Ke Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (A.W.); (M.H.); (M.N.A.); (K.L.); (J.W.)
| | - Jianchao Wei
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (A.W.); (M.H.); (M.N.A.); (K.L.); (J.W.)
| | - Yafeng Qiu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (A.W.); (M.H.); (M.N.A.); (K.L.); (J.W.)
| | - Zhiyong Ma
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (A.W.); (M.H.); (M.N.A.); (K.L.); (J.W.)
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4
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Structure and Dynamics of Zika Virus Protease and Its Insights into Inhibitor Design. Biomedicines 2021; 9:biomedicines9081044. [PMID: 34440248 PMCID: PMC8394600 DOI: 10.3390/biomedicines9081044] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/04/2021] [Accepted: 08/16/2021] [Indexed: 12/16/2022] Open
Abstract
Zika virus (ZIKV)—a member of the Flaviviridae family—is an important human pathogen. Its genome encodes a polyprotein that can be further processed into structural and non-structural proteins. ZIKV protease is an important target for antiviral development due to its role in cleaving the polyprotein to release functional viral proteins. The viral protease is a two-component protein complex formed by NS2B and NS3. Structural studies using different approaches demonstrate that conformational changes exist in the protease. The structures and dynamics of this protease in the absence and presence of inhibitors were explored to provide insights into the inhibitor design. The dynamic nature of residues binding to the enzyme cleavage site might be important for the function of the protease. Due to the charges at the protease cleavage site, it is challenging to develop small-molecule compounds acting as substrate competitors. Developing small-molecule compounds to inhibit protease activity through an allosteric mechanism is a feasible strategy because conformational changes are observed in the protease. Herein, structures and dynamics of ZIKV protease are summarized. The conformational changes of ZIKV protease and other proteases in the same family are discussed. The progress in developing allosteric inhibitors is also described. Understanding the structures and dynamics of the proteases are important for designing potent inhibitors.
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Bharadwaj S, Rao AK, Dwivedi VD, Mishra SK, Yadava U. Structure-based screening and validation of bioactive compounds as Zika virus methyltransferase (MTase) inhibitors through first-principle density functional theory, classical molecular simulation and QM/MM affinity estimation. J Biomol Struct Dyn 2020; 39:2338-2351. [PMID: 32216596 DOI: 10.1080/07391102.2020.1747545] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Recent Zika virus (ZIKV) outbreak and association with human diseases such as neurological disorders have raised global health concerns. However, in the absence of an approved anti-ZIKV drug has generated urgency for the drug development against ZIKV infection. Here, structure-based virtual screening of 8589 bioactive compounds, screened at the substrate-binding site of ZIKV nonstructural 5 (NS5)-based structure N-terminal methyltransferase (MTase) domain followed by ADMET (absorption, distribution, metabolism, excretion and toxicity) profiling concluded the four potential lead inhibitors, i.e. (4-acetylamino-benzenesulfonylamino)-acetic acid (F3342-0450), 3-(5-methylfuran-2-yl)-N-(4-sulfamoylphenyl)propanamide (F1736-0142), 8-(2-hydroxy-ethylamino)-1,3-dimethyl-7-(3-methyl-benzyl)-3,7-dihydro-purine-2,6-dione (F0886-0080) and N-[4-(aminosulfonyl)phenyl]-2,3-dihydro-1,4-benzodioxine-2-carboxamide (F0451-2187). Collectively, extra precision docking and Density Functional Theory(DFT) calculations studies identified the F3342-0450 molecule, having strong interactions on the active site of MTase, further supported by molecular dynamics simulation, binding affinity and hybrid QM/MM calculations, suggest a new drug molecule for the antiviral drug development against ZIKV infection. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shiv Bharadwaj
- Sabanci University Nanotechnology Research and Application Center, Istanbul, Turkey
| | - Akhilesh Kumar Rao
- Department of Physics, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, India
| | - Vivek Dhar Dwivedi
- Centre for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida, India
| | - Sarad Kumar Mishra
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, India
| | - Umesh Yadava
- Department of Physics, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, India
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6
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Dwivedi VD, Bharadwaj S, Afroz S, Khan N, Ansari MA, Yadava U, Tripathi RC, Tripathi IP, Mishra SK, Kang SG. Anti-dengue infectivity evaluation of bioflavonoid from Azadirachta indica by dengue virus serine protease inhibition. J Biomol Struct Dyn 2020; 39:1417-1430. [DOI: 10.1080/07391102.2020.1734485] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Vivek Dhar Dwivedi
- Faculty of Science and Environment, Mahatma Gandhi Chitrakoot Gramodaya Vishwavidyalaya, Chitrakoot, Satna, India
- Center for Bioinformatics, Computational and System Biology, Pathfinder Research and Training Foundation, India
| | - Shiv Bharadwaj
- Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, Republic of Korea
| | - Sumbul Afroz
- Department of Biotechnology, School of Life Science, University of Hyderabad, India
| | - Nooruddin Khan
- Department of Biotechnology, School of Life Science, University of Hyderabad, India
| | | | - Umesh Yadava
- Department of Physics, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, India
| | - Ramesh Chandra Tripathi
- Faculty of Science and Environment, Mahatma Gandhi Chitrakoot Gramodaya Vishwavidyalaya, Chitrakoot, Satna, India
| | - Indra Prasad Tripathi
- Faculty of Science and Environment, Mahatma Gandhi Chitrakoot Gramodaya Vishwavidyalaya, Chitrakoot, Satna, India
| | - Sarad Kumar Mishra
- Department of Biotechnology, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, India
| | - Sang Gu Kang
- Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, Republic of Korea
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Fuzo CA, de Araujo LFL, Pontes RDS, Évora PM, Stabeli RG. Adjacent dimer epitope of envelope protein as an important region for Zika virus serum neutralization: a computational investigation. J Biomol Struct Dyn 2020; 39:1082-1092. [PMID: 32090677 DOI: 10.1080/07391102.2020.1728385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The recent emergence of Zika virus (ZIKV) has affected many countries, with severe clinical manifestations such as fetal microcephaly and Guillain-Barré syndrome. However, even though it is a major public health concern, there is no approved treatment available. Structural knowledge of the main neutralization regions of the envelope (E) protein of ZIKV and its interactions with neutralizing antibodies (nAbs) are crucial for the rational development of subunit vaccines and establishment of antibody-based interventions. In this study we screened from public data hot spot epitopes in conserved regions of ZIKV E protein that are nAbs targets. The result points to a conserved epitope located at domain II of the ZIKV E protein, namely adjacent dimer epitope, which is the ZIKV-117 and Z20 nAbs target. Although these two nAbs have been isolated from different donors, we have demonstrated, from structural and energetic details obtained by molecular dynamics of native and mutants, that hot spots residues of the epitope are the same for these nAbs, thereby indicating that they may share similar binding and neutralization mechanism. This convergence of information between these nAbs is important because both are potential targets for the development of therapies against ZIKV and only Z20 has its sequence and its complex structure with ZIKV E protein determined. Finally, these findings also contribute to existing knowledge, by fine mapping of the epitope/paratope residue pairs that are important for biotechnological development of therapies such as epitope mimetics for subunit vaccines and the rational design for antibody-based interventions against ZIKV. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Carlos Alessandro Fuzo
- Plataforma de Pesquisa em Medicina Translacional, Fundação Oswaldo Cruz - Fiocruz SP, São Paulo, Brazil.,Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Luiz Felipe Lemes de Araujo
- Plataforma de Pesquisa em Medicina Translacional, Fundação Oswaldo Cruz - Fiocruz SP, São Paulo, Brazil.,Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Rafael de Souza Pontes
- Plataforma de Pesquisa em Medicina Translacional, Fundação Oswaldo Cruz - Fiocruz SP, São Paulo, Brazil.,Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Patricia Martinez Évora
- Plataforma de Pesquisa em Medicina Translacional, Fundação Oswaldo Cruz - Fiocruz SP, São Paulo, Brazil.,Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Rodrigo Guerino Stabeli
- Plataforma de Pesquisa em Medicina Translacional, Fundação Oswaldo Cruz - Fiocruz SP, São Paulo, Brazil.,Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
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Voss S, Nitsche C. Inhibitors of the Zika virus protease NS2B-NS3. Bioorg Med Chem Lett 2020; 30:126965. [PMID: 31980339 DOI: 10.1016/j.bmcl.2020.126965] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 02/09/2023]
Abstract
In recent years, the Zika virus has emerged from a neglected flavivirus to a health-threatening pathogen that causes epidemic outbreaks associated with neurological disorders and congenital malformations. In addition to vaccine development, the discovery of specific antiviral agents has been pursued intensely. The Zika virus protease NS2B-NS3 catalyses the processing of the viral precursor polyprotein as an essential step during viral replication. Since the epidemic Zika virus outbreak in the Americas, several inhibitors of this protease have been reported. Substrate-derived peptides revealed important structural information about the active site, whilst more drug-like small molecules have been discovered as allosteric inhibitors.
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Affiliation(s)
- Saan Voss
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
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