1
|
Zhou P, Zhang Q, Yang Y, Wu W, Chen D, Zheng Z, Jongkaewwattana A, Jin H, Zhou H, Luo R. Cleavage of SQSTM1/p62 by the Zika virus protease NS2B3 prevents autophagic degradation of viral NS3 and NS5 proteins. Autophagy 2024:1-16. [PMID: 39128850 DOI: 10.1080/15548627.2024.2390810] [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: 03/23/2024] [Revised: 07/31/2024] [Accepted: 08/07/2024] [Indexed: 08/13/2024] Open
Abstract
Macroautophagy/autophagy plays a crucial role in inhibiting viral replication and regulating the host's immune response. The autophagy receptor SQSTM1/p62 (sequestosome 1) restricts viral replication by directing specific viral proteins to phagophores for degradation. In this study, we investigate the reciprocal relationship between Zika virus (ZIKV) and selective autophagy mediated by SQSTM1/p62. We show that NS2B3 protease encoded by ZIKV cleaves human SQSTM1/p62 at arginine 265 (R265). This cleavage also occurs with endogenous SQSTM1 in ZIKV-infected cells. Furthermore, overexpression of SQSTM1 inhibits ZIKV replication in A549 cells, while its absence increases viral titer. We have also shown that SQSTM1 impedes ZIKV replication by interacting with NS3 and NS5 and directing them to autophagic degradation, and that NS2B3-mediated cleavage could potentially alter this antiviral function of SQSTM1. Taken together, our study highlights the role of SQSTM1-mediated selective autophagy in the host's antiviral defense against ZIKV and uncovers potential viral evasion strategies that exploit the host's autophagic machinery to ensure successful infection.Abbreviation: Cas9: CRISPR-associated protein 9; Co-IP: co-immunoprecipitation; CRISPR: clustered regularly interspaced short palindromic repeats; DENV: dengue virus; GFP: green fluorescent protein; IFA: indirect immunofluorescence assay; KIR: KEAP1-interacting region; KO: knockout; LIR: MAP1LC3/LC3-interacting region; mAb: monoclonal antibody; NBR1: NBR1 autophagy cargo receptor; OPTN: optineurin; pAb: polyclonal antibody; PB1: Phox/BEM1 domain; R265A, a SQSTM1 construct with the arginine (R) residue at position 265 replaced with glutamic acid (A); SQSTM1: sequestosome 1; SQSTM1-C, C-terminal fragment of SQSTM1; SQSTM1-N, N-terminal fragment of SQSTM1; SVV: Seneca Valley virus; TAX1BP1: Tax1 binding protein 1; TBD: TRAF6-binding domain; TCID50: 50% tissue culture infective dose; UBA: ubiquitin-associated domain; Ub: ubiquitin; WT: wild type; ZIKV: Zika virus; ZZ: ZZ-type zinc finger domain.
Collapse
Affiliation(s)
- Peng Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Wuhan, China
| | - Qingxiang Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Wuhan, China
| | - Yueshan Yang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Wuhan, China
| | - Wanrong Wu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Wuhan, China
| | - Dong Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Wuhan, China
| | - Zhenhua Zheng
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Anan Jongkaewwattana
- Virology and Cell Technology Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Klong Nueng, Thailand
| | - Hui Jin
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Wuhan, China
| | - Hongbo Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Wuhan, China
| | - Rui Luo
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Wuhan, China
| |
Collapse
|
2
|
Ullah S, Ullah F, Rahman W, Ullah A, Haider S, Yueguang C. Elucidating the inhibitory mechanism of Zika virus NS2B-NS3 protease with dipeptide inhibitors: Insights from molecular docking and molecular dynamics simulations. PLoS One 2024; 19:e0307902. [PMID: 39116118 PMCID: PMC11309477 DOI: 10.1371/journal.pone.0307902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 07/13/2024] [Indexed: 08/10/2024] Open
Abstract
Microcephaly, Guillain-Barré syndrome, and potential sexual transmission stand as prominent complications associated with Zika virus (ZIKV) infection. The absence of FDA-approved drugs or vaccines presents a substantial obstacle in combatting the virus. Furthermore, the inclusion of pregnancy in the pharmacological screening process complicates and extends the endeavor to ensure molecular safety and minimal toxicity. Given its pivotal role in viral assembly and maturation, the NS2B-NS3 viral protease emerges as a promising therapeutic target against ZIKV. In this context, a dipeptide inhibitor was specifically chosen as a control against 200 compounds for docking analysis. Subsequent molecular dynamics simulations extending over 200 ns were conducted to ascertain the stability of the docked complex and confirm the binding of the inhibitor at the protein's active site. The simulation outcomes exhibited conformity to acceptable thresholds, encompassing parameters such as root mean square deviation (RMSD), root mean square fluctuation (RMSF), ligand-protein interaction analysis, ligand characterization, and surface area analysis. Notably, analysis of ligand angles bolstered the identification of prospective ligands capable of inhibiting viral protein activity and impeding virus dissemination. In this study, the integration of molecular docking and dynamics simulations has pinpointed the dipeptide inhibitor as a potential candidate ligand against ZIKV protease, thereby offering promise for therapeutic intervention against the virus.
Collapse
Affiliation(s)
- Shahid Ullah
- S-Khan Lab, Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Farhan Ullah
- S-Khan Lab, Mardan, Khyber Pakhtunkhwa, Pakistan
| | | | - Anees Ullah
- S-Khan Lab, Mardan, Khyber Pakhtunkhwa, Pakistan
| | | | - Cao Yueguang
- Huazhong University of Science and Technology Union Shenzhen Hospital, Nanshan, Shenzhen, China
| |
Collapse
|
3
|
Anindita PD, Otsuka Y, Lattmann S, Ngo KH, Liew CW, Kang C, Harris RS, Scampavia L, Spicer TP, Luo D. A high-throughput cell-based screening method for Zika virus protease inhibitor discovery. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100164. [PMID: 38796112 DOI: 10.1016/j.slasd.2024.100164] [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: 03/18/2024] [Revised: 05/03/2024] [Accepted: 05/23/2024] [Indexed: 05/28/2024]
Abstract
Zika virus (ZIKV) continues to pose a significant global public health threat, with recurring regional outbreaks and potential for pandemic spread. Despite often being asymptomatic, ZIKV infections can have severe consequences, including neurological disorders and congenital abnormalities. Unfortunately, there are currently no approved vaccines or antiviral drugs for the prevention or treatment of ZIKV. One promising target for drug development is the ZIKV NS2B-NS3 protease due to its crucial role in the virus life cycle. In this study, we established a cell-based ZIKV protease inhibition assay designed for high-throughput screening (HTS). Our assay relies on the ZIKV protease's ability to cleave a cyclised firefly luciferase fused to a natural cleavage sequence between NS2B and NS3 protease within living cells. We evaluated the performance of our assay in HTS setting using the pharmacologic controls (JNJ-40418677 and MK-591) and by screening a Library of Pharmacologically Active Compounds (LOPAC). The results confirmed the feasibility of our assay for compound library screening to identify potential ZIKV protease inhibitors.
Collapse
Affiliation(s)
- Paulina Duhita Anindita
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Yuka Otsuka
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, FL, United States
| | - Simon Lattmann
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Khac Huy Ngo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - Chong Wai Liew
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
| | - CongBao Kang
- Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, United States; Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, United States
| | - Louis Scampavia
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, FL, United States
| | - Timothy P Spicer
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, FL, United States.
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore; National Centre for Infectious Diseases, Singapore, Singapore.
| |
Collapse
|
4
|
Behnam MAM, Klein CD. Alternate recognition by dengue protease: Proteolytic and binding assays provide functional evidence beyond an induced-fit. Biochimie 2024:S0300-9084(24)00138-X. [PMID: 38871044 DOI: 10.1016/j.biochi.2024.06.002] [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: 04/15/2024] [Revised: 05/31/2024] [Accepted: 06/10/2024] [Indexed: 06/15/2024]
Abstract
Proteases are key enzymes in viral replication, and interfering with these targets is the basis for therapeutic interventions. We previously introduced a hypothesis about conformational selection in the protease of dengue virus and related flaviviruses, based on conformational plasticity noted in X-ray structures. The present work presents the first functional evidence for alternate recognition by the dengue protease, in a mechanism based primarily on conformational selection rather than induced-fit. Recognition of distinct substrates and inhibitors in proteolytic and binding assays varies to a different extent, depending on factors reported to influence the protease structure. The pH, salinity, buffer type, and temperature cause a change in binding, proteolysis, or inhibition behavior. Using representative inhibitors with distinct structural scaffolds, we identify two contrasting binding profiles to dengue protease. Noticeable effects are observed in the binding assay upon inclusion of a non-ionic detergent in comparison to the proteolytic assay. The findings highlight the impact of the selection of testing conditions on the observed ligand affinity or inhibitory potency. From a broader scope, the dengue protease presents an example, where the induced-fit paradigm appears insufficient to explain binding events with the biological target. Furthermore, this protein reveals the complexity of comparing or combining biochemical assay data obtained under different conditions. This can be particularly critical for artificial intelligence (AI) approaches in drug discovery that rely on large datasets of compounds activity, compiled from different sources using non-identical testing procedures. In such cases, mismatched results will compromise the model quality and its predictive power.
Collapse
Affiliation(s)
- Mira A M Behnam
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Christian D Klein
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany.
| |
Collapse
|
5
|
Voss S, Rademann J, Nitsche C. Characterisation of ten NS2B-NS3 proteases: Paving the way for pan-flavivirus drugs. Antiviral Res 2024; 226:105878. [PMID: 38582134 DOI: 10.1016/j.antiviral.2024.105878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/29/2024] [Accepted: 03/31/2024] [Indexed: 04/08/2024]
Abstract
Flaviviruses can cause severe illness in humans. Effective and safe vaccines are available for some species; however, for many flaviviruses disease prevention or specific treatments remain unavailable. The viral replication cycle depends on the proteolytic activity of the NS2B-NS3 protease, which releases functional viral proteins from a non-functional polyprotein precursor, rendering the protease a promising drug target. In this study, we characterised recombinant NS2B-NS3 proteases from ten flaviviruses including three unreported proteases from the Usutu, Kyasanur forest disease and Powassan viruses. All protease constructs comprise a covalent Gly4-Ser-Gly4 linker connecting the NS3 serine protease domain with its cofactor NS2B. We conducted a comprehensive cleavage site analysis revealing areas of high conversion. While all proteases were active in enzymatic assays, we noted a 1000-fold difference in catalytic efficiency across proteases from different flaviviruses. Two bicyclic peptide inhibitors displayed anti-pan-flaviviral protease activity with inhibition constants ranging from 10 to 1000 nM.
Collapse
Affiliation(s)
- Saan Voss
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Jörg Rademann
- Department of Biology, Chemistry and Pharmacy, Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia.
| |
Collapse
|
6
|
Huber S, Braun NJ, Schmacke LC, Murra R, Bender D, Hildt E, Heine A, Steinmetzer T. Synthesis and structural characterization of new macrocyclic inhibitors of the Zika virus NS2B-NS3 protease. Arch Pharm (Weinheim) 2024:e2400250. [PMID: 38809037 DOI: 10.1002/ardp.202400250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 05/06/2024] [Indexed: 05/30/2024]
Abstract
Three new series of macrocyclic active site-directed inhibitors of the Zika virus (ZIKV) NS2B-NS3 protease were synthesized. First, attempts were made to replace the basic P3 lysine residue of our previously described inhibitors with uncharged and more hydrophobic residues. This provided numerous compounds with inhibition constants between 30 and 50 nM. A stronger reduction of the inhibitory potency was observed when the P2 lysine was replaced by neutral residues, all of these inhibitors possess Ki values >1 µM. However, it is possible to replace the P2 lysine with the less basic 3-aminomethylphenylalanine, which provides a similarly potent inhibitor of the ZIKV protease (Ki = 2.69 nM). Crystal structure investigations showed that the P2 benzylamine structure forms comparable interactions with the protease as lysine. Twelve additional structures of these inhibitors in complex with the protease were determined, which explain many, but not all, SAR data obtained in this study. All individual modifications in the P2 or P3 position resulted in inhibitors with low antiviral efficacy in cell culture. Therefore, a third inhibitor series with combined modifications was synthesized; all of them contain a more hydrophobic d-cyclohexylalanine in the linker segment. At a concentration of 40 µM, two of these compounds possess similar antiviral potency as ribavirin at 100 µM. Due to their reliable crystallization in complex with the ZIKV protease, these cyclic compounds are very well suited for a rational structure-based development of improved inhibitors.
Collapse
Affiliation(s)
- Simon Huber
- Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marburg, Germany
| | - Niklas J Braun
- Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marburg, Germany
| | - Luna C Schmacke
- Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marburg, Germany
| | - Robin Murra
- Department of Virology, Paul-Ehrlich-Institut, Federal Institute for Vaccines and Biomedicines, Langen, Germany
| | - Daniela Bender
- Department of Virology, Paul-Ehrlich-Institut, Federal Institute for Vaccines and Biomedicines, Langen, Germany
| | - Eberhard Hildt
- Department of Virology, Paul-Ehrlich-Institut, Federal Institute for Vaccines and Biomedicines, Langen, Germany
| | - Andreas Heine
- Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marburg, Germany
| | - Torsten Steinmetzer
- Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marburg, Germany
| |
Collapse
|
7
|
Cheng Y, Wang R, Wu Q, Chen J, Wang A, Wu Z, Sun F, Zhu S. Advancements in Research on Duck Tembusu Virus Infections. Viruses 2024; 16:811. [PMID: 38793692 PMCID: PMC11126125 DOI: 10.3390/v16050811] [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: 04/02/2024] [Revised: 05/14/2024] [Accepted: 05/17/2024] [Indexed: 05/26/2024] Open
Abstract
Duck Tembusu Virus (DTMUV) is a pathogen of the Flaviviridae family that causes infections in poultry, leading to significant economic losses in the duck farming industry in recent years. Ducks infected with this virus exhibit clinical symptoms such as decreased egg production and neurological disorders, along with serious consequences such as ovarian hemorrhage, organ enlargement, and necrosis. Variations in morbidity and mortality rates exist across different age groups of ducks. It is worth noting that DTMUV is not limited to ducks alone; it can also spread to other poultry such as chickens and geese, and antibodies related to DTMUV have even been found in duck farm workers, suggesting a potential risk of zoonotic transmission. This article provides a detailed overview of DTMUV research, delving into its genomic characteristics, vaccines, and the interplay with host immune responses. These in-depth research findings contribute to a more comprehensive understanding of the virus's transmission mechanism and pathogenic process, offering crucial scientific support for epidemic prevention and control.
Collapse
Affiliation(s)
- Yuting Cheng
- Engineering Technology Research Center for Modern Animal Science and Novel Veterinary Pharmaceutic Development, Jiangsu Key Laboratory of Veterinary Bio-Pharmaceutical High Technology Research, Jiangsu Agri-Animal Husbandry Vocational College, Taizhou 225300, China; (Y.C.)
| | - Ruoheng Wang
- Engineering Technology Research Center for Modern Animal Science and Novel Veterinary Pharmaceutic Development, Jiangsu Key Laboratory of Veterinary Bio-Pharmaceutical High Technology Research, Jiangsu Agri-Animal Husbandry Vocational College, Taizhou 225300, China; (Y.C.)
| | - Qingguo Wu
- Engineering Technology Research Center for Modern Animal Science and Novel Veterinary Pharmaceutic Development, Jiangsu Key Laboratory of Veterinary Bio-Pharmaceutical High Technology Research, Jiangsu Agri-Animal Husbandry Vocational College, Taizhou 225300, China; (Y.C.)
| | - Jinying Chen
- Engineering Technology Research Center for Modern Animal Science and Novel Veterinary Pharmaceutic Development, Jiangsu Key Laboratory of Veterinary Bio-Pharmaceutical High Technology Research, Jiangsu Agri-Animal Husbandry Vocational College, Taizhou 225300, China; (Y.C.)
| | - Anping Wang
- Engineering Technology Research Center for Modern Animal Science and Novel Veterinary Pharmaceutic Development, Jiangsu Key Laboratory of Veterinary Bio-Pharmaceutical High Technology Research, Jiangsu Agri-Animal Husbandry Vocational College, Taizhou 225300, China; (Y.C.)
| | - Zhi Wu
- Engineering Technology Research Center for Modern Animal Science and Novel Veterinary Pharmaceutic Development, Jiangsu Key Laboratory of Veterinary Bio-Pharmaceutical High Technology Research, Jiangsu Agri-Animal Husbandry Vocational College, Taizhou 225300, China; (Y.C.)
| | - Fang Sun
- Department of Biochemistry and Molecular Biology, College of Basic Medicine, Hubei University of Medicine, Shiyan 442000, China
| | - Shanyuan Zhu
- Engineering Technology Research Center for Modern Animal Science and Novel Veterinary Pharmaceutic Development, Jiangsu Key Laboratory of Veterinary Bio-Pharmaceutical High Technology Research, Jiangsu Agri-Animal Husbandry Vocational College, Taizhou 225300, China; (Y.C.)
| |
Collapse
|
8
|
Qianzhu H, Abdelkader EH, Otting G, Huber T. Genetic Encoding of Fluoro-l-tryptophans for Site-Specific Detection of Conformational Heterogeneity in Proteins by NMR Spectroscopy. J Am Chem Soc 2024; 146:13641-13650. [PMID: 38687675 DOI: 10.1021/jacs.4c03743] [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: 05/02/2024]
Abstract
The substitution of a single hydrogen atom in a protein by fluorine yields a site-specific probe for sensitive detection by 19F nuclear magnetic resonance (NMR) spectroscopy, where the absence of background signal from the protein facilitates the detection of minor conformational species. We developed genetic encoding systems for the site-selective incorporation of 4-fluorotryptophan, 5-fluorotryptophan, 6-fluorotryptophan, and 7-fluorotryptophan in response to an amber stop codon and used them to investigate conformational heterogeneity in a designed amino acid binding protein and in flaviviral NS2B-NS3 proteases. These proteases have been shown to present variable conformations in X-ray crystal structures, including flips of the indole side chains of tryptophan residues. The 19F NMR spectra of different fluorotryptophan isomers installed at the conserved site of Trp83 indicate that the indole ring flip is common in flaviviral NS2B-NS3 proteases in the apo state and suppressed by an active-site inhibitor.
Collapse
Affiliation(s)
- Haocheng Qianzhu
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Elwy H Abdelkader
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| |
Collapse
|
9
|
Pereira F, Bedda L, Tammam MA, Alabdullah AK, Arafa R, El-Demerdash A. Investigating the antiviral therapeutic potentialities of marine polycyclic lamellarin pyrrole alkaloids as promising inhibitors for SARS-CoV-2 and Zika main proteases (Mpro). J Biomol Struct Dyn 2024; 42:3983-4001. [PMID: 37232419 DOI: 10.1080/07391102.2023.2217513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 05/18/2023] [Indexed: 05/27/2023]
Abstract
The new coronavirus variant (SARS-CoV-2) and Zika virus are two world-wide health pandemics. Along history, natural products-based drugs have always crucially recognized as a main source of valuable medications. Considering the SARS-CoV-2 and Zika main proteases (Mpro) as the re-production key element of the viral cycle and its main target, herein we report an intensive computer-aided virtual screening for a focused list of 39 marine lamellarins pyrrole alkaloids, against SARS-CoV-2 and Zika main proteases (Mpro) using a set of combined modern computational methodologies including molecular docking (MDock), molecule dynamic simulations (MDS) and structure-activity relationships (SARs) as well. Indeed, the molecular docking studies had revealed four promising marine alkaloids including [lamellarin H (14)/K (17)] and [lamellarin S (26)/Z (39)], according to their notable ligand-protein energy scores and relevant binding affinities with the SARS-CoV-2 and Zika (Mpro) pocket residues, respectively. Consequentially, these four chemical hits were further examined thermodynamically though investigating their MD simulations at 100 ns, where they showed prominent stability within the accommodated (Mpro) pockets. Moreover, in-deep SARs studies suggested the crucial roles of the rigid fused polycyclic ring system, particularly aromatic A- and F- rings, position of the phenolic -OH and δ-lactone functionalities as essential structural and pharmacophoric features. Finally, these four promising lamellarins alkaloids were investigated for their in-silico ADME using the SWISS ADME platform, where they displayed appropriated drug-likeness properties. Such motivating outcomes are greatly recommending further in vitro/vivo examinations regarding those lamellarins pyrrole alkaloids (LPAs).Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Florbela Pereira
- LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, Caparica, Portugal
| | - Loay Bedda
- Drug Design and Discovery Laboratory, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Mohamed A Tammam
- Department of Biochemistry, Faculty of Agriculture, Fayoum University, Fayoum, Egypt
| | | | - Reem Arafa
- Drug Design and Discovery Laboratory, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Amr El-Demerdash
- Division of Organic Chemistry, Department of Chemistry, Faculty of Sciences, Mansoura University, Mansoura, Egypt
- Department of Biochemistry and Metabolism, the John Innes Centre, Norwich Research Park, Norwich, UK
| |
Collapse
|
10
|
Ni X, Godoy AS, Marples PG, Fairhead M, Balcomb BH, Ferla MP, Tomlinson CWE, Wang S, Giroud C, Aschenbrenner JC, Lithgo RM, Winokan M, Chandran AV, Thompson W, Xavier MA, Williams EP, Walsh M, Fearon D, Koekemoer L, von Delft F. Crystallographic fragment screening delivers diverse chemical scaffolds for Zika virus NS2B-NS3 protease inhibitor development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.591502. [PMID: 38746305 PMCID: PMC11092485 DOI: 10.1101/2024.04.29.591502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Zika virus (ZIKV) infections cause microcephaly in new-borns and Guillain-Barre syndrome in adults raising a significant global public health concern, yet no vaccines or antiviral drugs have been developed to prevent or treat ZIKV infections. The viral protease NS3 and its co-factor NS2B are essential for the cleavage of the Zika polyprotein precursor into individual structural and non-structural proteins and is therefore an attractive drug target. Generation of a robust crystal system of co-expressed NS2B-NS3 protease has enabled us to perform a crystallographic fragment screening campaign with 1076 fragments. 48 binders with diverse chemical scaffolds were identified in the active site of the protease, with another 6 fragment hits observed in a potential allosteric binding site. Our work provides potential starting points for the development of potent NS2B-NS3 protease inhibitors. Furthermore, we have structurally characterized a potential allosteric binding pocket, identifying opportunities for allosteric inhibitor development.
Collapse
|
11
|
Starvaggi J, Previti S, Zappalà M, Ettari R. The Inhibition of NS2B/NS3 Protease: A New Therapeutic Opportunity to Treat Dengue and Zika Virus Infection. Int J Mol Sci 2024; 25:4376. [PMID: 38673962 PMCID: PMC11050111 DOI: 10.3390/ijms25084376] [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: 03/17/2024] [Revised: 04/12/2024] [Accepted: 04/14/2024] [Indexed: 04/28/2024] Open
Abstract
In the global pandemic scenario, dengue and zika viruses (DENV and ZIKV, respectively), both mosquito-borne members of the flaviviridae family, represent a serious health problem, and considering the absence of specific antiviral drugs and available vaccines, there is a dire need to identify new targets to treat these types of viral infections. Within this drug discovery process, the protease NS2B/NS3 is considered the primary target for the development of novel anti-flavivirus drugs. The NS2B/NS3 is a serine protease that has a dual function both in the viral replication process and in the elusion of the innate immunity. To date, two main classes of NS2B/NS3 of DENV and ZIKV protease inhibitors have been discovered: those that bind to the orthosteric site and those that act at the allosteric site. Therefore, this perspective article aims to discuss the main features of the use of the most potent NS2B/NS3 inhibitors and their impact at the social level.
Collapse
Affiliation(s)
| | | | | | - Roberta Ettari
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres 31, 98166 Messina, Italy; (J.S.); (S.P.); (M.Z.)
| |
Collapse
|
12
|
Hasan ME, Samir A, Khalil MM, Shafaa MW. Bioinformatics approach for prediction and analysis of the Non-Structural Protein 4B (NSP4B) of the Zika virus. J Genet Eng Biotechnol 2024; 22:100336. [PMID: 38494248 PMCID: PMC10860876 DOI: 10.1016/j.jgeb.2023.100336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
BACKGROUND The Nonstructural Protein (NSP) 4B of Zika virus of 251 amino acids from (ZIKV/Human/POLG_ZIKVF) with accession number (A0A024B7W1), Induces the production of Endoplasmic Reticulum ER-derived membrane vesicles, which are the sites of viral replication. To understand the physical basis of how proteins fold in nature and to solve the challenge of protein structure prediction, Ab-initio and comparative modeling are crucial tools. RESULTS The systematic in silico technique, ThreaDom, had only predicted one domain (4 - 190) of NSP4B. I-TASSER, and Alphafold were ranked as the best servers for full-length 3-D protein structure predictions of NSP4B, where the predicted models were evaluated quantitatively using benchmarked metrics including C-score (-3.43), TM-score (0.77949), RMSD (2.73), and Z-score (1.561). The functional and protein binding motifs were realized using motif databases, secondary and surface accessibility predictions combined with Post-Translational Modification Sites (PTMs) prediction. Two highly conserved protein-binding motifs (Flavi NS4B and Bacillus papRprotein), together with three (PTMs) (Casein Kinase II, Myristyl site, and ASN-Glycosylation site) were predicted utilizing the Motif scan and Scanprosite servers. These patterns and PTMs were associated with NSP4B's role in triggering the development of the viral replication complex and its participation in the localization of NS3 and NS5 on the membrane. Only one hit from Structural Classification of Protein (SCOP) matched the protein sequence at positions 10 to 397 and was categorized six-hairpin glycosidases superfamily according to CATH (Class, Architecture, Topology, and Homology). Integrating this NSP4B information with the templates' SCOP and CATH annotations achieves it easier to attribute structure-function/evolution links to both previously known and recently discovered protein structures.
Collapse
Affiliation(s)
- Mohamed E Hasan
- Bioinformatics Department, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City 32897, Egypt.
| | - Aya Samir
- Physics Department, Medical Biophysics Division, Faculty of Science, Helwan University, Cairo, Egypt
| | - Magdy M Khalil
- Physics Department, Medical Biophysics Division, Faculty of Science, Helwan University, Cairo, Egypt; School of Biotechnology, Badr University in Cairo, Egypt
| | - Medhat W Shafaa
- Physics Department, Medical Biophysics Division, Faculty of Science, Helwan University, Cairo, Egypt
| |
Collapse
|
13
|
Borges PHO, Ferreira SB, Silva FP. Recent Advances on Targeting Proteases for Antiviral Development. Viruses 2024; 16:366. [PMID: 38543732 PMCID: PMC10976044 DOI: 10.3390/v16030366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/21/2024] [Accepted: 02/24/2024] [Indexed: 05/23/2024] Open
Abstract
Viral proteases are an important target for drug development, since they can modulate vital pathways in viral replication, maturation, assembly and cell entry. With the (re)appearance of several new viruses responsible for causing diseases in humans, like the West Nile virus (WNV) and the recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), understanding the mechanisms behind blocking viral protease's function is pivotal for the development of new antiviral drugs and therapeutical strategies. Apart from directly inhibiting the target protease, usually by targeting its active site, several new pathways have been explored to impair its activity, such as inducing protein aggregation, targeting allosteric sites or by inducing protein degradation by cellular proteasomes, which can be extremely valuable when considering the emerging drug-resistant strains. In this review, we aim to discuss the recent advances on a broad range of viral proteases inhibitors, therapies and molecular approaches for protein inactivation or degradation, giving an insight on different possible strategies against this important class of antiviral target.
Collapse
Affiliation(s)
- Pedro Henrique Oliveira Borges
- Laboratory of Organic Synthesis and Biological Prospecting, Chemistry Institute, Federal University of Rio de Janeiro, Rio de Janeiro 21941-909, Brazil;
- Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-900, Brazil
| | - Sabrina Baptista Ferreira
- Laboratory of Organic Synthesis and Biological Prospecting, Chemistry Institute, Federal University of Rio de Janeiro, Rio de Janeiro 21941-909, Brazil;
| | - Floriano Paes Silva
- Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-900, Brazil
| |
Collapse
|
14
|
Cruz KG, Eron MH, Makhaik S, Savinov S, Hardy JA. A Non-Active-Site Inhibitor with Selectivity for Zika Virus NS2B-NS3 Protease. ACS Infect Dis 2024; 10:412-425. [PMID: 38265226 PMCID: PMC11099878 DOI: 10.1021/acsinfecdis.3c00330] [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] [Indexed: 01/25/2024]
Abstract
Flavivirus infection usually results in fever accompanied by headache, arthralgia, and, in some cases, rash. Although the symptoms are mild, full recovery can take several months. Flaviviruses encode seven nonstructural proteins that represent potential drug targets for this viral family. Focusing on the Zika virus NS2B-NS3 protease, we uncovered a unique inhibitor, MH1, composed of aminothiazolopyridine and benzofuran moieties. MH1 inhibits ZVP with a biochemical IC50 of 440 nM and effectively blocks cleavage of ZVP substrates in cells. Surprisingly, MH1 inhibits the other flaviviral proteases at least 18-fold more weakly. This same phenomenon was observed in assays of the viral cytopathic effect, where only Zika virus showed sensitivity to MH1. This selectivity was unexpected since flaviviral proteases have high similarity in sequence and protein structure. MH1 binds at an allosteric site, as demonstrated by its ability to stabilize ZVP synergistically with an active site inhibitor. To understand its selectivity, we constructed a series of hybrid proteases composed of select segments of ZVP, which is sensitive to MH1, and dengue virus protease, which is essentially insensitive to MH1. Our results suggest that MH1 binds to the NS3 protease domain, disrupting its interaction with NS2B. These interactions are essential for substrate binding and cleavage. In particular, the unique dynamic properties of NS2B from Zika seem to be required for the function of MH1. Insights into the mechanism of MH1 function will aid us in developing non-active-site-directed, pan-flaviviral inhibitors, by highlighting the importance of evaluating and considering the dynamics of the NS2B regions.
Collapse
Affiliation(s)
| | | | - Sparsh Makhaik
- Department of Chemistry, University of Massachusetts Amherst, MA, US 01002
| | | | - Jeanne A. Hardy
- Department of Chemistry, University of Massachusetts Amherst, MA, US 01002
| |
Collapse
|
15
|
Savino DF, Silva JV, da Silva Santos S, Lourenço FR, Giarolla J. How do physicochemical properties contribute to inhibitory activity of promising peptides against Zika Virus NS3 protease? J Mol Model 2024; 30:54. [PMID: 38289526 DOI: 10.1007/s00894-024-05843-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 01/09/2024] [Indexed: 02/01/2024]
Abstract
CONTEXT AND RESULTS Flavivirus diseases' cycles, especially Dengue and Yellow Fever, can be observed all over Brazilian territory, representing a great health concern. Additionally, there are no drugs available in therapy. In this scenario, in silico methodologies were applied to obtain physicochemical properties, as well as to better understand the ligand-biological target interaction mode of 20 previously reported NS2B/NS3 protease inhibitors of Dengue virus. Since catalytic site of flavivirus hold similarities, such as the same catalytic triad (His51, Asp75 e Ser135), the ability of this series of molecules to fit in Zika NS3 domains can be achieved. We performed an exploratory data analysis, using statistical methodologies, such as PCA (Principal Component Analysis) and HCA (Hierarchical Component Analysis), to assist the comprehension of how physicochemical properties impact the interaction observed by the docking studies, as well as to build a correlation between the respective ranked characteristics. Based on these previous studies, peptides were selected for the dynamics simulations, which were useful to better understand the ligand-protein interactions. Information relating to, for instance, energy, ΔG, average number of hydrogen bonds and distance from Ser135 (one of the main amino acids in the catalytic pocket) were discussed. In this sense, peptides 15 (considering ΔG value and Hbond number), 7 (ΔG and energy) and 1, 6, 7 and 15 (the proximity to Ser135 throughout the dynamics simulation) were highlighted as promising. Those interesting results could contribute to future studies regarding Zika virus drug design, since this infection represents a great concern in neglected populations. METHODS The models were constructed in the ChemDraw software. The ligand parametrization was performed in the CHEM3D 17.0, UCSF Chimera. Docking simulations were carried out in the GOLD software, after the redocking validation. We used ASP as the function score. Additionally, for dynamics simulations we applied GROMACS software, exploring, mainly, free binding energy calculations. Exploratory analysis was carried out in Minitab 17.3.1 statistical software. Prior to the exploratory analysis, data of quantum chemical properties of the peptides were collected in Microsoft Excel spreadsheet and organized to obtain Hierarchical Cluster Analysis (HCA) and Principal Component Analysis (PCA).
Collapse
Affiliation(s)
- Débora Feliciano Savino
- Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo (USP), Professor Lineu Prestes Avenue, 580, Building 13, São Paulo, SP, 05508-900, Brazil
| | - João Vitor Silva
- Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo (USP), Professor Lineu Prestes Avenue, 580, Building 13, São Paulo, SP, 05508-900, Brazil
| | - Soraya da Silva Santos
- Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo (USP), Professor Lineu Prestes Avenue, 580, Building 13, São Paulo, SP, 05508-900, Brazil
| | - Felipe Rebello Lourenço
- Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo (USP), Professor Lineu Prestes Avenue, 580, Building 13, São Paulo, SP, 05508-900, Brazil
| | - Jeanine Giarolla
- Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo (USP), Professor Lineu Prestes Avenue, 580, Building 13, São Paulo, SP, 05508-900, Brazil.
| |
Collapse
|
16
|
Serafim MSM, Kronenberger T, Rocha REO, Rosa ADRA, Mello TLG, Poso A, Ferreira RS, Abrahão JS, Kroon EG, Mota BEF, Maltarollo VG. Aminopyrimidine Derivatives as Multiflavivirus Antiviral Compounds Identified from a Consensus Virtual Screening Approach. J Chem Inf Model 2024; 64:393-411. [PMID: 38194508 DOI: 10.1021/acs.jcim.3c01505] [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: 01/11/2024]
Abstract
Around three billion people are at risk of infection by the dengue virus (DENV) and potentially other flaviviruses. Worldwide outbreaks of DENV, Zika virus (ZIKV), and yellow fever virus (YFV), the lack of antiviral drugs, and limitations on vaccine usage emphasize the need for novel antiviral research. Here, we propose a consensus virtual screening approach to discover potential protease inhibitors (NS3pro) against different flavivirus. We employed an in silico combination of a hologram quantitative structure-activity relationship (HQSAR) model and molecular docking on characterized binding sites followed by molecular dynamics (MD) simulations, which filtered a data set of 7.6 million compounds to 2,775 hits. Lastly, docking and MD simulations selected six final potential NS3pro inhibitors with stable interactions along the simulations. Five compounds had their antiviral activity confirmed against ZIKV, YFV, DENV-2, and DENV-3 (ranging from 4.21 ± 0.14 to 37.51 ± 0.8 μM), displaying aggregator characteristics for enzymatic inhibition against ZIKV NS3pro (ranging from 28 ± 7 to 70 ± 7 μM). Taken together, the compounds identified in this approach may contribute to the design of promising candidates to treat different flavivirus infections.
Collapse
Affiliation(s)
- Mateus Sá Magalhães Serafim
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
- Excellence Cluster "Controlling Microbes to Fight Infections" (CMFI), Tübingen 72076, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio 70211, Finland
| | - Rafael Eduardo Oliveira Rocha
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Amanda Del Rio Abreu Rosa
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Thaysa Lara Gonçalves Mello
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Antti Poso
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio 70211, Finland
- Department of Medical Oncology and Pneumology, University Hospital of Tübingen, Tübingen 70211, Germany
| | - Rafaela Salgado Ferreira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Jonatas Santos Abrahão
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Erna Geessien Kroon
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Bruno Eduardo Fernandes Mota
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Vinícius Gonçalves Maltarollo
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| |
Collapse
|
17
|
Medrano FJ, de la Hoz-Rodríguez S, Martí S, Arafet K, Schirmeister T, Hammerschmidt SJ, Müller C, González-Martínez Á, Santillana E, Ziebuhr J, Romero A, Zimmer C, Weldert A, Zimmermann R, Lodola A, Świderek K, Moliner V, González FV. Peptidyl nitroalkene inhibitors of main protease rationalized by computational and crystallographic investigations as antivirals against SARS-CoV-2. Commun Chem 2024; 7:15. [PMID: 38238420 PMCID: PMC10796436 DOI: 10.1038/s42004-024-01104-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 01/09/2024] [Indexed: 01/22/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic continues to represent a global public health issue. The viral main protease (Mpro) represents one of the most attractive targets for the development of antiviral drugs. Herein we report peptidyl nitroalkenes exhibiting enzyme inhibitory activity against Mpro (Ki: 1-10 μM) good anti-SARS-CoV-2 infection activity in the low micromolar range (EC50: 1-12 μM) without significant toxicity. Additional kinetic studies of compounds FGA145, FGA146 and FGA147 show that all three compounds inhibit cathepsin L, denoting a possible multitarget effect of these compounds in the antiviral activity. Structural analysis shows the binding mode of FGA146 and FGA147 to the active site of the protein. Furthermore, our results illustrate that peptidyl nitroalkenes are effective covalent reversible inhibitors of the Mpro and cathepsin L, and that inhibitors FGA145, FGA146 and FGA147 prevent infection against SARS-CoV-2.
Collapse
Affiliation(s)
- Francisco J Medrano
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain.
| | | | - Sergio Martí
- Departament de Química Física i Analítica, Universitat Jaume I, 12071, Castelló, Spain
| | - Kemel Arafet
- Departament de Química Física i Analítica, Universitat Jaume I, 12071, Castelló, Spain
| | - Tanja Schirmeister
- Institute of Pharmaceutical and BiomedicalSciences, Johannes Gutenberg-University Mainz, Staudinger Weg 5, 55128, Mainz, Germany
| | - Stefan J Hammerschmidt
- Institute of Pharmaceutical and BiomedicalSciences, Johannes Gutenberg-University Mainz, Staudinger Weg 5, 55128, Mainz, Germany
| | - Christin Müller
- Institute of Medical Virology, Justus Liebig University Giessen, Schubertstrasse 81, 35392, Giessen, Germany
| | - Águeda González-Martínez
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Elena Santillana
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - John Ziebuhr
- Institute of Medical Virology, Justus Liebig University Giessen, Schubertstrasse 81, 35392, Giessen, Germany
| | - Antonio Romero
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Collin Zimmer
- Institute of Pharmaceutical and BiomedicalSciences, Johannes Gutenberg-University Mainz, Staudinger Weg 5, 55128, Mainz, Germany
| | - Annabelle Weldert
- Institute of Pharmaceutical and BiomedicalSciences, Johannes Gutenberg-University Mainz, Staudinger Weg 5, 55128, Mainz, Germany
| | - Robert Zimmermann
- Institute of Pharmaceutical and BiomedicalSciences, Johannes Gutenberg-University Mainz, Staudinger Weg 5, 55128, Mainz, Germany
| | - Alessio Lodola
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parma, Italy
| | - Katarzyna Świderek
- Departament de Química Física i Analítica, Universitat Jaume I, 12071, Castelló, Spain
| | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I, 12071, Castelló, Spain.
| | - Florenci V González
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, 12071, Castelló, Spain.
| |
Collapse
|
18
|
Wahaab A, Zhang Y, Rasgon JL, Kang L, Hameed M, Li C, Anwar MN, Zhang Y, Shoaib A, Liu K, Lee B, Wei J, Qiu Y, Ma Z. NS2B-D55E and NS2B-E65D Variations are Responsible for Differences in NS2B-NS3 Protease Activities Between Japanese Encephalitis Virus Genotype I and III in Fluorogenic Peptide Model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.08.570834. [PMID: 38105993 PMCID: PMC10723430 DOI: 10.1101/2023.12.08.570834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Japanese Encephalitis Virus (JEV) NS2B-NS3 is a protein complex composed of NS3 proteases and a NS2B cofactor. The N-terminal protease domain (180 residues) of NS3 (NS3(pro)) interacts directly with a central 40-amino acid hydrophilic domain of NS2B (NS2B(H)) to form an active serine protease. In this study, the recombinant NS2B(H)-NS3(pro) proteases were prepared in E. coli and used to compare the enzymatic activity between genotype I (GI) and III (GIII) NS2B-NS3 proteases. The GI NS2B(H)-NS3(pro) was able to cleave the sites at internal C, NS2A/NS2B, NS2B/NS3 and NS3/NS4A junctions that were identical to the sites proteolytically processed by GIII NS2B(H)-NS3(pro). Analysis of the enzymatic activity of recombinant NS2B(H)-NS3(pro) proteases using a model of fluorogenic peptide substrate revealed that the proteolytical processing activity of GIII NS2B(H)-NS3(pro) was significantly higher than that of GI NS2B(H)-NS3(pro). There were eight amino acid variations between GI and GIII NS2B(H)-NS3(pro), which may be responsible for the difference in enzymatic activities between GI and GIII proteases. Therefore, recombinant mutants were generated by exchanging NS2B(H) and NS3(pro) domains between GI and GIII NS2B(H)-NS3(pro) and subjected to protease activity analysis. Substitution of NS2B(H) significantly altered the protease activities, as compared to the parental NS2B(H)-NS3(pro), suggesting that NS2B(H) played an essential role in regulation of NS3(pro) protease activity. To further identify the amino acids responsible for the difference in protease activities, multiple substitution mutants including the individual and combined mutations at the variant residue 55 and 65 of NS2B(H) were generated and subjected to protease activity analysis. Replacement of NS2B-55 and NS2B-65 of GI to GIII significantly increased the enzymatic activity of GI NS2B(H)-NS3(pro) protease, whereas mutation of NS2B-55 and NS2B-65 of GIII to GI remarkably reduced the enzymatic activity of GIII NS2B(H)-NS3(pro) protease. Overall, these data demonstrated that NS2B-55 and NS2B-65 variations in hydrophilic domain of NS2B co-contributed to the difference in NS2B(H)-NS3(pro) protease activities between GI and GIII. These observations gain an insight into the role of NS2B in regulation of NS3 protease activities, which is useful for understanding the replication of JEV GI and GIII viruses.
Collapse
Affiliation(s)
- Abdul Wahaab
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
- The Department of Entomology, Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
| | - Yan Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Jason L. Rasgon
- The Department of Entomology, Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
| | - Lei Kang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Muddassar Hameed
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
- Department of Biomedical Science and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Chenxi Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Muhammad Naveed Anwar
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Yanbing Zhang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
- College of Animal Science and Technology, Shihezi University, Shihezi, 832003, China
| | - Anam Shoaib
- School of Behavior and Brain Sciences, University of Texas at Dallas, TX, United States
| | - Ke Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Beibei Lee
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Jianchao Wei
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Yafeng Qiu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Zhiyong Ma
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| |
Collapse
|
19
|
Chen X, Yan Y, Song H, Wang Z, Wang A, Yang J, Zhou R, Xu S, Yang S, Li W, Qin X, Dai Q, Liu M, Lv K, Cao R, Zhong W. Investigation of novel 5'-amino adenosine derivatives with potential anti-Zika virus activity. Eur J Med Chem 2023; 261:115852. [PMID: 37801825 DOI: 10.1016/j.ejmech.2023.115852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/26/2023] [Accepted: 09/29/2023] [Indexed: 10/08/2023]
Abstract
The Zika virus (ZIKV) infections remains a global health threat. However, no approved drug for treating ZIKV infection. We previously found TZY12-9, a 5'-amino NI analog, that showed anti-ZIKV activity without chemical phosphorylation. Here, a series of 5'-amino NI analogs were synthesized and evaluated. The compound XSJ2-46 exhibited potent in vitro activity without requiring chemical phosphorylation, favorable pharmacokinetic and acute toxicity profiles. Preliminary mechanisms of anti-ZIKV activity of XSJ2-46 were investigated via a series of ZIKV non-structural protein inhibition assays and host cell RNA-seq. XSJ2-46 acted at the replication stage of viral infection cycle, and exhibited reasonable inhibition of RNA-dependent RNA polymerases (RdRp) with an IC50 value of 8.78 μM, while not affecting MTase. RNA-seq analysis also revealed differential expression genes involved in cytokine and cytokine receptor pathway in ZIKV-infected U87 cells treated with XSJ2-46. Importantly, treatment with XSJ2-46 (10 mg/kg/day) significantly enhanced survival protection (70% survival) in ZIKV-infected ICR mice. Additionally, XSJ2-46 administration resulted in a significant decrease in serum levels of ZIKV viral RNA in the IFNα/β receptor-deficient (Ifnar-/-) A129 mouse model. Therefore, the remarkable in vitro and in vivo anti-ZIKV activity of compound XSJ2-46 highlights the promising research direction of utilizing the 5'-amino NI structure skeleton for developing antiviral NIs.
Collapse
Affiliation(s)
- Xingjuan Chen
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, Shannxi, 710072, China; National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Yunzheng Yan
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Huijuan Song
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Zhuang Wang
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, Shannxi, 710072, China; National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Apeng Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Jingjing Yang
- Song Li' Academician Workstation of Hainan University (School of Pharmaceutical Sciences), Sanya, Hainan, 572000, China
| | - Rui Zhou
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Shijie Xu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Shaokang Yang
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Wei Li
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Xiaoyu Qin
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Qingsong Dai
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Mingliang Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Kai Lv
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| | - Ruiyuan Cao
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China.
| | - Wu Zhong
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China.
| |
Collapse
|
20
|
Putri GN, Gudla CS, Singh M, Ng CH, Idris FFH, Oo Y, Tan JHY, Wong JFJ, Chu JJH, Selvam V, Selvaraj SS, Shandil RK, Narayanan S, Alonso S. Expanding the anti-flaviviral arsenal: Discovery of a baicalein-derived Compound with potent activity against DENV and ZIKV. Antiviral Res 2023; 220:105739. [PMID: 37944824 DOI: 10.1016/j.antiviral.2023.105739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 10/22/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023]
Abstract
With approximately 3.8 billion people at risk of infection in tropical and sub-tropical regions, Dengue ranks among the top ten threats worldwide. Despite the potential for severe disease manifestation and the economic burden it places on endemic countries, there is a lack of approved antiviral agents to effectively treat the infection. Flavonoids, including baicalein, have garnered attention for their antimicrobial properties. In this study, we took a rational and iterative approach to develop a series of baicalein derivatives with improved antiviral activity against Dengue virus (DENV). Compound 11064 emerged as a promising lead candidate, exhibiting antiviral activity against the four DENV serotypes and representative strains of Zika virus (ZIKV) in vitro, with attractive selectivity indices. Mechanistic studies revealed that Compound 11064 did not prevent DENV attachment at the cell surface, nor viral RNA synthesis and viral protein translation. Instead, the drug was found to impair the post-receptor binding entry steps (endocytosis and/or uncoating), as well as the late stage of DENV infection cycle, including virus assembly/maturation and/or exocytosis. The inability to raise DENV resistant mutants, combined with significant antiviral activity against an unrelated RNA virus (Enterovirus-A71) suggested that Compound 11064 targets the host rather than a viral protein, further supporting its broad-spectrum antiviral potential. Overall, Compound 11064 represents a promising antiviral candidate for the treatment of Dengue and Zika.
Collapse
Affiliation(s)
- Geraldine Nadya Putri
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School, National University of Singapore, Singapore; Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore
| | | | - Mayas Singh
- Foundation for Neglected Disease Research, Bangalore, Karnataka, India
| | - Chin Huan Ng
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School, National University of Singapore, Singapore; Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore
| | - Fakhriedzwan Fitri Haji Idris
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School, National University of Singapore, Singapore; Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore
| | - Yukei Oo
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School, National University of Singapore, Singapore; Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore
| | - Jasmine Hwee Yee Tan
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School, National University of Singapore, Singapore; Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore
| | - Joel Feng Jie Wong
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School, National University of Singapore, Singapore; Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore
| | - Justin Jang Hann Chu
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School, National University of Singapore, Singapore
| | - Vignesh Selvam
- Foundation for Neglected Disease Research, Bangalore, Karnataka, India
| | | | | | | | - Sylvie Alonso
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School, National University of Singapore, Singapore; Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore.
| |
Collapse
|
21
|
Abdelkader EH, Qianzhu H, Huber T, Otting G. Genetic Encoding of 7-Aza-l-tryptophan: Isoelectronic Substitution of a Single CH-Group in a Protein for a Nitrogen Atom for Site-Selective Isotope Labeling. ACS Sens 2023; 8:4402-4406. [PMID: 37890165 DOI: 10.1021/acssensors.3c01904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2023]
Abstract
Genetic encoding of a noncanonical amino acid (ncAA) in an in vivo expression system requires an aminoacyl-tRNA synthetase that specifically recognizes the ncAA, while the ncAA must not be recognized by the canonical protein expression machinery. We succeeded in genetically encoding 7-aza-tryptophan (7AW), which is isoelectronic with tryptophan. The system is fully orthogonal to protein expression in Escherichia coli, enabling high-yielding site-selective isotope labeling in vivo. 7AW is readily synthesized from serine and 7-aza-indole using a tryptophan synthetase β-subunit (TrpB) mutant, affording easy access to isotope-labeled 7AW. Using labeled 7AW produced from 15N/13C-labeled serine, we produced 7AW mutants of the 25 kDa Zika virus NS2B-NS3 protease. 15N-HSQC spectra display single cross-peaks at chemical shifts near those observed for the wild-type protein labeled with 15N/13C-tryptophan, confirming the structural integrity of the protein and yielding straightforward NMR resonance assignments for site-specific probing.
Collapse
Affiliation(s)
- Elwy H Abdelkader
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Haocheng Qianzhu
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| |
Collapse
|
22
|
Manzato VDM, Di Santo C, Torquato RJS, Coelho C, Gallo G, Hardy L, Würtele M, Tanaka AS. Boophilin D1, a Kunitz type protease inhibitor, as a source of inhibitors for the ZIKA virus NS2B-NS3 protease. Biochimie 2023; 214:96-101. [PMID: 37364769 DOI: 10.1016/j.biochi.2023.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 06/28/2023]
Abstract
Arboviruses are a global concern for a multitude of reasons, including their increased incidence and human mortality. Vectors associated with arboviruses include the mosquito Aedes sp., which is responsible for transmitting the Zika virus. Flaviviruses, like the Zika virus, present only one chymotrypsin-like serine protease (NS3) in their genome. Together with host enzymes, the NS2B co-factor NS3 protease complex are essential for the viral replication cycle by virus polyprotein processing. To search for Zika virus NS2B-NS3 protease (ZIKVPro) inhibitors, a phage display library was constructed using the Boophilin domain 1 (BoophD1), a thrombin inhibitor from the Kunitz family. A BoophilinD1 library mutated at positions P1-P4' was constructed, presenting a titer of 2.9x106 (cfu), and screened utilizing purified ZIKVPro. The results demonstrated at the P1-P4' positions the occurrence of 47% RALHA sequence (mut 12) and 11.8% RASWA sequence (mut14), SMRPT, or KALIP (wt) sequence. BoophD1-wt and mutants 12 and 14 were expressed and purified. The purified BoophD1 wt, mut 12 and 14, presented Ki values for ZIKVPro of 0.103, 0.116, and 0.101 μM, respectively. The BoophD1 mutant inhibitors inhibit the Dengue virus 2 protease (DENV2) with Ki values of 0.298, 0.271, and 0.379 μM, respectively. In conclusion, BoophD1 mut 12 and 14 selected for ZIKVPro demonstrated inhibitory activity like BoophD1-wt, suggesting that these are the strongest Zika inhibitors present in the BoophD1 mutated phage display library. Furthermore, BoophD1 mutants selected for ZIKVPro inhibit both Zika and Dengue 2 proteases making them potential pan-flavivirus inhibitors.
Collapse
Affiliation(s)
- Veronica de Moraes Manzato
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - Camila Di Santo
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - Ricardo Jose Soares Torquato
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - Camila Coelho
- Department of Science and Technology, Federal University of São Paulo (UNIFESP), São José dos Campos, SP, Brazil
| | - Gloria Gallo
- Department of Science and Technology, Federal University of São Paulo (UNIFESP), São José dos Campos, SP, Brazil
| | - Leon Hardy
- Department of Physics, University of South Florida, Tampa, USA
| | - Martin Würtele
- Department of Science and Technology, Federal University of São Paulo (UNIFESP), São José dos Campos, SP, Brazil
| | - Aparecida Sadae Tanaka
- Department of Biochemistry, Escola Paulista de Medicina, Federal University of São Paulo (UNIFESP), São Paulo, SP, Brazil; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular (INCT-EM), RJ, Brazil.
| |
Collapse
|
23
|
Shiryaev SA, Cieplak P, Cheltsov A, Liddington RC, Terskikh AV. Dual function of Zika virus NS2B-NS3 protease. PLoS Pathog 2023; 19:e1011795. [PMID: 38011215 PMCID: PMC10723727 DOI: 10.1371/journal.ppat.1011795] [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] [Received: 09/05/2023] [Revised: 12/15/2023] [Accepted: 11/02/2023] [Indexed: 11/29/2023] Open
Abstract
Zika virus (ZIKV) serine protease, indispensable for viral polyprotein processing and replication, is composed of the membrane-anchored NS2B polypeptide and the N-terminal domain of the NS3 polypeptide (NS3pro). The C-terminal domain of the NS3 polypeptide (NS3hel) is necessary for helicase activity and contains an ATP-binding site. We discovered that ZIKV NS2B-NS3pro binds single-stranded RNA with a Kd of ~0.3 μM, suggesting a novel function. We tested various structural modifications of NS2B-NS3pro and observed that constructs stabilized in the recently discovered "super-open" conformation do not bind RNA. Likewise, stabilizing NS2B-NS3pro in the "closed" (proteolytically active) conformation using substrate inhibitors abolished RNA binding. We posit that RNA binding occurs when ZIKV NS2B-NS3pro adopts the "open" conformation, which we modeled using highly homologous dengue NS2B-NS3pro crystallized in the open conformation. We identified two positively charged fork-like structures present only in the open conformation of NS3pro. These forks are conserved across Flaviviridae family and could be aligned with the positively charged grove on NS3hel, providing a contiguous binding surface for the negative RNA strand exiting helicase. We propose a "reverse inchworm" model for a tightly intertwined NS2B-NS3 helicase-protease machinery, which suggests that NS2B-NS3pro cycles between open and super-open conformations to bind and release RNA enabling long-range NS3hel processivity. The transition to the closed conformation, likely induced by the substrate, enables the classical protease activity of NS2B-NS3pro.
Collapse
Affiliation(s)
- Sergey A. Shiryaev
- Sanford-Burnham-Prebys Medical Discovery Institute, Infectious and Inflammatory Disease Center, La Jolla, California, United States of America
| | - Piotr Cieplak
- Sanford-Burnham-Prebys Medical Discovery Institute, Infectious and Inflammatory Disease Center, La Jolla, California, United States of America
| | - Anton Cheltsov
- Q-mol LLC, San Diego, California, United States of America
| | - Robert C. Liddington
- Sanford-Burnham-Prebys Medical Discovery Institute, Infectious and Inflammatory Disease Center, La Jolla, California, United States of America
| | - Alexey V. Terskikh
- Sanford-Burnham-Prebys Medical Discovery Institute, Infectious and Inflammatory Disease Center, La Jolla, California, United States of America
| |
Collapse
|
24
|
Hossain MS, Shovon MTI, Hasan MR, Hakim FT, Hasan MM, Esha SA, Tasnim S, Nazir MS, Akhter F, Ali MA, Halim MA. Therapeutic Potential of Antiviral Peptides against the NS2B/NS3 Protease of Zika Virus. ACS OMEGA 2023; 8:35207-35218. [PMID: 37779969 PMCID: PMC10536883 DOI: 10.1021/acsomega.3c04903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 09/01/2023] [Indexed: 10/03/2023]
Abstract
The NS2B/NS3 protease is highly conserved among various proteases of the Zika virus, making it an important therapeutic target for developing broad-spectrum antiviral drugs. The NS2B/NS3 protease is a crucial enzyme in the replication cycle of Zika virus and plays a significant role in viral maturation and assembly. Inhibiting the activity of this protease can potentially prevent viral replication, making it an attractive target for developing therapies against Zika virus infection. This work screens 429 antiviral peptides in comparison with substrate peptide against the NS2B/NS3 of Zika virus using molecular docking and molecular dynamics (MD) simulation. Based on the docking screening, MD simulation conducted for the best four peptides including AVP0239, AVP0642, AVP0660, and AVP2044, could be effective against NS2B/NS3. These results were compared with the control substrate peptide. Further analysis indicates that AVP0642 and AVP2044 are the most promising candidates. The interaction analysis showed that the catalytic site residues including His51, Asp75, Ser135 and other non-catalytic residues such as Asp129, Asp83, and Asp79 contribute substantial interactions. Hydrogen bonds (41%) and hydrophobic interactions (33%) are observed as the prominent non-covalent interaction prompting the peptide-protein complex formation. Furthermore, the structure-activity relationship (SAR) illustrates that positively charged (Lys, Arg) residues in the peptides dominate the interactions. This study provides the basis for developing novel peptide-based protease inhibitors for Zika virus.
Collapse
Affiliation(s)
- Md. Shahadat Hossain
- Division
of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Center, BICCB, Tejgaon 1215, Dhaka, Bangladesh
| | - Md. Tanjil Islam Shovon
- Division
of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Center, BICCB, Tejgaon 1215, Dhaka, Bangladesh
| | - Md. Rafid Hasan
- Division
of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Center, BICCB, Tejgaon 1215, Dhaka, Bangladesh
| | - Fuad Taufiqul Hakim
- Division
of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Center, BICCB, Tejgaon 1215, Dhaka, Bangladesh
| | - Mohammad Mehedi Hasan
- Division
of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Center, BICCB, Tejgaon 1215, Dhaka, Bangladesh
| | - Sadia Afrose Esha
- Division
of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Center, BICCB, Tejgaon 1215, Dhaka, Bangladesh
| | - Sabiha Tasnim
- Division
of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Center, BICCB, Tejgaon 1215, Dhaka, Bangladesh
| | - Md. Shahoriar Nazir
- Division
of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Center, BICCB, Tejgaon 1215, Dhaka, Bangladesh
| | - Fahmida Akhter
- Division
of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Center, BICCB, Tejgaon 1215, Dhaka, Bangladesh
| | - Md Ackas Ali
- Department
of Chemistry and Biochemistry, Kennesaw
State University, Kennesaw, Georgia 30144, United States
| | - Mohammad A. Halim
- Department
of Chemistry and Biochemistry, Kennesaw
State University, Kennesaw, Georgia 30144, United States
| |
Collapse
|
25
|
Pant S, Jena NR. Repurposing of antiparasitic drugs against the NS2B-NS3 protease of the Zika virus. J Biomol Struct Dyn 2023:1-13. [PMID: 37747074 DOI: 10.1080/07391102.2023.2255648] [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: 02/23/2023] [Accepted: 08/28/2023] [Indexed: 09/26/2023]
Abstract
To date, no approved drugs are available to treat the Zika virus (ZIKV) infection. Therefore, it is necessary to urgently identify potential drugs against the ZIKV infection. Here, the repurposing of 30 antiparasitic drugs against the NS2B-NS3 protease of the ZIKV has been carried out by using combined docking and molecular dynamics- (MD) simulations. Based on the docking results, 5 drugs, such as Amodiaquine, Primaquine, Paromomycin, Dichlorophene, and Ivermectin were screened for further analysis by MD simulations and free energy calculations. Among these drugs, Amodiaquine and Dichlorophen are found to produce the most stable complexes and possess relative binding free energies of about -44.3 ± 3.7 kcal/mol and -41.1 ± 5.3 kcal/mol respectively. Therefore, they would act as potent small-molecule inhibitors of the ZIKV protease.However, evaluations of biological and safety activities of these drugs against the ZIKV protease are required before their clinical use.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- S Pant
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - N R Jena
- Discipline of Natural Sciences, Indian Institute of Information Technology, Design and Manufacturing, Jabalpur, India
| |
Collapse
|
26
|
Santos LH, Rocha REO, Dias DL, Ribeiro BMRM, Serafim MSM, Abrahão JS, Ferreira RS. Evaluating Known Zika Virus NS2B-NS3 Protease Inhibitor Scaffolds via In Silico Screening and Biochemical Assays. Pharmaceuticals (Basel) 2023; 16:1319. [PMID: 37765127 PMCID: PMC10537087 DOI: 10.3390/ph16091319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/04/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
The NS2B-NS3 protease (NS2B-NS3pro) is regarded as an interesting molecular target for drug design, discovery, and development because of its essential role in the Zika virus (ZIKV) cycle. Although no NS2B-NS3pro inhibitors have reached clinical trials, the employment of drug-like scaffolds can facilitate the screening process for new compounds. In this study, we performed a combination of ligand-based and structure-based in silico methods targeting two known non-peptide small-molecule scaffolds with micromolar inhibitory activity against ZIKV NS2B-NS3pro by a virtual screening (VS) of promising compounds. Based on these two scaffolds, we selected 13 compounds from an initial library of 509 compounds from ZINC15's similarity search. These compounds exhibited structural modifications that are distinct from previously known compounds yet keep pertinent features for binding. Despite promising outcomes from molecular docking and initial enzymatic assays against NS2B-NS3pro, confirmatory assays with a counter-screening enzyme revealed an artifactual inhibition of the assessed compounds. However, we report two compounds, 9 and 11, that exhibited antiviral properties at a concentration of 50 μM in cellular-based assays. Overall, this study provides valuable insights into the ongoing research on anti-ZIKV compounds to facilitate and improve the development of new inhibitors.
Collapse
Affiliation(s)
- Lucianna H. Santos
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil
| | - Rafael E. O. Rocha
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil
| | - Diego L. Dias
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil (M.S.M.S.)
| | - Beatriz M. R. M. Ribeiro
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil
| | - Mateus Sá M. Serafim
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil (M.S.M.S.)
| | - Jônatas S. Abrahão
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil (M.S.M.S.)
| | - Rafaela S. Ferreira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil
| |
Collapse
|
27
|
Leonard RA, Rao VN, Bartlett A, Froggatt HM, Luftig MA, Heaton BE, Heaton NS. A low-background, fluorescent assay to evaluate inhibitors of diverse viral proteases. J Virol 2023; 97:e0059723. [PMID: 37578235 PMCID: PMC10506478 DOI: 10.1128/jvi.00597-23] [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: 04/20/2023] [Accepted: 06/11/2023] [Indexed: 08/15/2023] Open
Abstract
Multiple coronaviruses (CoVs) can cause respiratory diseases in humans. While prophylactic vaccines designed to prevent infection are available for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), incomplete vaccine efficacy, vaccine hesitancy, and the threat of other pathogenic CoVs for which vaccines do not exist have highlighted the need for effective antiviral therapies. While antiviral compounds targeting the viral polymerase and protease are already in clinical use, their sensitivity to potential resistance mutations as well as their breadth against the full range of human and preemergent CoVs remain incompletely defined. To begin to fill that gap in knowledge, we report here the development of an improved, noninfectious, cell-based fluorescent assay with high sensitivity and low background that reports on the activity of viral proteases, which are key drug targets. We demonstrate that the assay is compatible with not only the SARS-CoV-2 Mpro protein but also orthologues from a range of human and nonhuman CoVs as well as clinically reported SARS-CoV-2 drug-resistant Mpro variants. We then use this assay to define the breadth of activity of two clinically used protease inhibitors, nirmatrelvir and ensitrelvir. Continued use of this assay will help define the strengths and limitations of current therapies and may also facilitate the development of next-generation protease inhibitors that are broadly active against both currently circulating and preemergent CoVs. IMPORTANCE Coronaviruses (CoVs) are important human pathogens with the ability to cause global pandemics. Working in concert with vaccines, antivirals specifically limit viral disease in people who are actively infected. Antiviral compounds that target CoV proteases are already in clinical use; their efficacy against variant proteases and preemergent zoonotic CoVs, however, remains incompletely defined. Here, we report an improved, noninfectious, and highly sensitive fluorescent method of defining the sensitivity of CoV proteases to small molecule inhibitors. We use this approach to assay the activity of current antiviral therapies against clinically reported SARS-CoV-2 protease mutants and a panel of highly diverse CoV proteases. Additionally, we show this system is adaptable to other structurally nonrelated viral proteases. In the future, this assay can be used to not only better define the strengths and limitations of current therapies but also help develop new, broadly acting inhibitors that more broadly target viral families.
Collapse
Affiliation(s)
- Rebecca A. Leonard
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Vishwas N. Rao
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Medical Scientist Training Program, Duke University School of Medicine, Durham, North Carolina, USA
| | - Alexandria Bartlett
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Heather M. Froggatt
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Micah A. Luftig
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Center for Virology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Brook E. Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Nicholas S. Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Center for Virology, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, USA
| |
Collapse
|
28
|
Maus H, Hammerschmidt SJ, Hinze G, Barthels F, Pérez Carrillo VH, Hellmich UA, Basché T, Schirmeister T. The effects of allosteric and competitive inhibitors on ZIKV protease conformational dynamics explored through smFRET, nanoDSF, DSF, and 19F NMR. Eur J Med Chem 2023; 258:115573. [PMID: 37379675 DOI: 10.1016/j.ejmech.2023.115573] [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: 02/13/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/30/2023]
Abstract
Zika and dengue viruses cause mosquito-borne diseases of high epidemic relevance. The viral NS2B-NS3 proteases play crucial roles in the pathogen replication cycle and are validated drug targets. They can adopt at least two conformations depending on the position of the NS2B cofactor. Recently, we reported ligand-induced conformational changes of dengue virus NS2B-NS3 protease by single-molecule Förster resonance energy transfer (smFRET). Here, we investigated the conformational dynamics of the homologous Zika virus protease through an integrated methodological approach combining smFRET, thermal shift assays (DSF and nanoDSF) and 19F NMR spectroscopy. Our results show that allosteric inhibitors favor the open conformation and competitive inhibitors stabilize the closed conformation of the Zika virus protease.
Collapse
Affiliation(s)
- Hannah Maus
- Institute of Pharmaceutical and Biomedical Sciences (IPBW), Johannes Gutenberg-University, Mainz, Germany
| | - Stefan J Hammerschmidt
- Institute of Pharmaceutical and Biomedical Sciences (IPBW), Johannes Gutenberg-University, Mainz, Germany
| | - Gerald Hinze
- Department of Chemistry, Johannes Gutenberg-University, Mainz, Germany
| | - Fabian Barthels
- Institute of Pharmaceutical and Biomedical Sciences (IPBW), Johannes Gutenberg-University, Mainz, Germany
| | - Victor H Pérez Carrillo
- Institute of Organic Chemistry & Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Jena, Germany
| | - Ute A Hellmich
- Institute of Organic Chemistry & Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Jena, Germany
| | - Thomas Basché
- Department of Chemistry, Johannes Gutenberg-University, Mainz, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences (IPBW), Johannes Gutenberg-University, Mainz, Germany.
| |
Collapse
|
29
|
Hu H, Feng Y, He ML. Targeting Type I Interferon Induction and Signaling: How Zika Virus Escapes from Host Innate Immunity. Int J Biol Sci 2023; 19:3015-3028. [PMID: 37416780 PMCID: PMC10321277 DOI: 10.7150/ijbs.83056] [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: 01/31/2023] [Accepted: 05/23/2023] [Indexed: 07/08/2023] Open
Abstract
Zika virus (ZIKV) infection causes neurological disorders and draws great attention. ZIKV infection can elicit a wide range of immune response. Type I interferons (IFNs) as well as its signaling cascade play crucial role in innate immunity against ZIKV infection and in turn ZIKV can antagonize them. ZIKV genome are mainly recognized by Toll-like receptors 3 (TLR3), TLR7/8 and RIG-I-like receptor 1 (RIG-1), which induces the expression of Type I IFNs and interferon-stimulated genes (ISGs). ISGs exert antiviral activity at different stages of the ZIKV life cycle. On the other hand, ZIKV takes multiple strategies to antagonize the Type Ⅰ IFN induction and its signaling pathway to establish a pathogenic infection, especially by using the viral nonstructural (NS) proteins. Most of the NS proteins can directly interact with the factors in the pathways to escape the innate immunity. In addition, structural proteins also participate in the innate immune evasion and activation of antibody-binding of blood dendritic cell antigen 2 (BDCA2) or inflammasome also be used to enhance ZIKV replication. In this review, we summarize the recent findings about the interaction between ZIKV infection and type I IFNs pathways and suggest potential strategies for antiviral drug development.
Collapse
Affiliation(s)
- Huan Hu
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Yaxiu Feng
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Ming-Liang He
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
- City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
| |
Collapse
|
30
|
van den Elsen K, Chew BLA, Ho JS, Luo D. Flavivirus nonstructural proteins and replication complexes as antiviral drug targets. Curr Opin Virol 2023; 59:101305. [PMID: 36870091 PMCID: PMC10023477 DOI: 10.1016/j.coviro.2023.101305] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 01/02/2023] [Accepted: 01/17/2023] [Indexed: 03/06/2023]
Abstract
Many flaviviruses are well-known pathogens, such as dengue, Zika, Japanese encephalitis, and yellow fever viruses. Among them, dengue viruses cause global epidemics and threaten billions of people. Effective vaccines and antivirals are in desperate need. In this review, we focus on the recent advances in understanding viral nonstructural (NS) proteins as antiviral drug targets. We briefly summarize the experimental structures and predicted models of flaviviral NS proteins and their functions. We highlight a few well-characterized inhibitors targeting these NS proteins and provide an update about the latest development. NS4B emerges as one of the most promising drug targets as novel inhibitors targeting NS4B and its interaction network are entering clinical studies. Studies aiming to elucidate the architecture and molecular basis of viral replication will offer new opportunities for novel antiviral discovery. Direct-acting agents against dengue and other pathogenic flaviviruses may be available very soon.
Collapse
Affiliation(s)
- Kaïn van den Elsen
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore; Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK
| | - Bing Liang Alvin Chew
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Jun Sheng Ho
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 636921, Singapore
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore.
| |
Collapse
|
31
|
Bhattacharya M, Bhowmik D, Tian Y, He H, Zhu F, Yin Q. The Dengue virus protease NS2B3 cleaves cyclic GMP-AMP synthase to suppress cGAS activation. J Biol Chem 2023; 299:102986. [PMID: 36754281 PMCID: PMC10011430 DOI: 10.1016/j.jbc.2023.102986] [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: 08/11/2022] [Revised: 01/27/2023] [Accepted: 01/29/2023] [Indexed: 02/10/2023] Open
Abstract
Dengue virus (DENV) is one of the most prevalent mosquito-transmitted human viruses that causes significant morbidity and mortality worldwide. To persist in the cell and consequently cause disease, DENV is evolved with mechanisms to suppress the induction of type I interferons by antagonizing cGAS-STING signaling. Using recombinant proteins and in vitro cleavage assays, we have shown that the DENV protease NS2B3 is capable of cleaving cGAS in the N-terminal region without disrupting the C-terminal catalytic center. This generates two major cleavage products: cleavage product N-terminal (CP-N) and cleavage product C-terminal (CP-C). We observed reduction in DNA-binding affinity of CP-C as compared to full-length cGAS. Reduction in DNA-binding affinity is also correlated with the decrease in enzymatic activity of CP-C. CP-N, on the other hand, has almost comparable DNA-binding ability as that of the full-length cGAS. In fact, CP-N competitively inhibits cyclic GMP-AMP production by both full-length cGAS and CP-C. We hypothesize that high DNA-binding affinity of CP-N enables it to sequester the DNA from CP-C and noncleaved full-length cGAS and thus reduces the rate of enzyme activation and cyclic GMP-AMP synthesis. Furthermore, we found that NS2B3 physically interacts with full-length cGAS and CP-C, laying the basis for their shuttling to and eventual degradation in the autophagosome. Overall, our study highlights a multifaceted and effective strategy by which an RNA virus antagonizes cGAS-STING signaling which may be useful for the design of antivirals targeting viral proteases.
Collapse
Affiliation(s)
| | - Debipreeta Bhowmik
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Yuan Tian
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Huan He
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, USA
| | - Fanxiu Zhu
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Qian Yin
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, USA; Department of Biological Science, Florida State University, Tallahassee, Florida, USA.
| |
Collapse
|
32
|
Braun NJ, Huber S, Schmacke LC, Heine A, Steinmetzer T. Boroleucine-Derived Covalent Inhibitors of the ZIKV Protease. ChemMedChem 2023; 18:e202200336. [PMID: 36325810 PMCID: PMC10100045 DOI: 10.1002/cmdc.202200336] [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: 06/24/2022] [Revised: 11/02/2022] [Indexed: 11/06/2022]
Abstract
The Zika virus (ZIKV) remains a potential threat to the public health due to the lack of both an approved vaccination or a specific treatment. In this work, a series of peptidic inhibitors of the ZIKV protease with boroleucine as P1 residue was synthesized. The highest affinities with Ki values down to 8 nM were observed for compounds with basic residues in both P2 and P3 position and at the N-terminus. The low potency of reference compounds containing leucine, leucine-amide or isopentylamide as P1 residue suggested a covalent binding mode of the boroleucine-derived inhibitors. This was finally proven by crystal structure determination of the most potent inhibitor from this series in complex with the ZIKV protease.
Collapse
Affiliation(s)
- Niklas J Braun
- Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Simon Huber
- Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Luna C Schmacke
- Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Andreas Heine
- Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Torsten Steinmetzer
- Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| |
Collapse
|
33
|
Teramoto T, Choi KH, Padmanabhan R. Flavivirus proteases: The viral Achilles heel to prevent future pandemics. Antiviral Res 2023; 210:105516. [PMID: 36586467 PMCID: PMC10062209 DOI: 10.1016/j.antiviral.2022.105516] [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: 12/13/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/31/2022]
Abstract
Flaviviruses are important human pathogens and include dengue (DENV), West Nile (WNV), Yellow fever virus (YFV), Japanese encephalitis (JEV) and Zika virus (ZIKV). DENV, transmitted by mosquitoes, causes diseases ranging in severity from mild dengue fever with non-specific flu-like symptoms to fatal dengue hemorrhagic fever and dengue shock syndrome. DENV infections are caused by four serotypes, DENV1-4, which interact differently with antibodies in blood serum. The incidence of DENV infection has increased dramatically in recent decades and the CDC estimates 400 million dengue infections occur each year, resulting in ∼25,000 deaths mostly among children and elderly people. Similarly, ZIKV infections are caused by infected mosquito bites to humans, can be transmitted sexually and through blood transfusions. If a pregnant woman is infected, the virus can cross the placental barrier and can spread to her fetus, causing severe brain malformations in the child including microcephaly and other birth defects. It is noteworthy that the neurological manifestations of ZIKV were also observed in DENV endemic regions, suggesting that pre-existing antibody response to DENV could augment ZIKV infection. WNV, previously unknown in the US (and known to cause only mild disease in Middle East), first arrived in New York city in 1999 (NY99) and spread throughout the US and Canada by Culex mosquitoes and birds. WNV is now endemic in North America. Thus, emerging and re-emerging flaviviruses are significant threat to human health. However, vaccines are available for only a limited number of flaviviruses, and antiviral therapies are not available for any flavivirus. Hence, there is an urgent need to develop therapeutics that interfere with essential enzymatic steps, such as protease in the flavivirus lifecycle as these viruses possess significant threat to future pandemics. In this review, we focus on our E. coli expression of NS2B hydrophilic domain (NS2BH) covalently linked to NS3 protease domain (NS3Pro) in their natural context which is processed by the combined action of both subunits of the NS2B-NS3Pro precursor. Biochemical activities of the viral protease such as solubility and autoproteolysis of NS2BH-NS3Pro linkage depended on the C-terminal portion of NS2BH linked to the NS3Pro domain. Since 2008, we also focus on the use of the recombinant protease in high throughput screens and characterization of small molecular compounds identified in these screens.
Collapse
Affiliation(s)
- Tadahisa Teramoto
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC, 20057, USA.
| | - Kyung H Choi
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47406, USA.
| | - Radhakrishnan Padmanabhan
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC, 20057, USA.
| |
Collapse
|
34
|
Santos LH, Caffarena ER, Ferreira RS. pH and non-covalent ligand binding modulate Zika virus NS2B/NS3 protease binding site residues: Discoveries from MD and constant pH MD simulations. J Biomol Struct Dyn 2022; 40:10359-10372. [PMID: 34180376 DOI: 10.1080/07391102.2021.1943528] [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] [Indexed: 12/16/2022]
Abstract
Zika virus (ZIKV) is a global health concern and has been linked to severe neurological pathologies. Although no medication is available yet, many efforts to develop antivirals and host cell binding inhibitors led to attractive drug-like scaffolds, mainly targeting the nonstructural NS2B/NS3 protease (NS2B/NS3pro). NS2B/NS3pro active site has several titratable residues susceptible to pH changes and ligand binding; hence, understanding these residues' protonation is essential to drug design efforts targeting the active site. Here we use in silico methods to probe non-covalent binding and its effect on pKa shifts of the active site residues on a ligand-free protease and with a non-peptidic competitive inhibitor (Ki=13.5 µM). By applying constant pH molecular dynamics, we found that the catalytic residues of the unbound NS2B/NS3pro achieved the protonation needed for the serine protease mechanism over the pH value of 8.5. Nevertheless, the protease in the holo state achieved this same scenario at lower pH values. Also, non-covalent binding affected the catalytic triad (H51, D75, and S135) by stabilizing their distances and interaction network. Thus, NS2B/NS3pro residues configuration for activity might be both pH-dependent and influenced by ligand binding. However, compound presence within the binding site destabilized the NS2B, interfering with the closed and active conformation necessary for substrate binding and catalysis. Our outcomes provide valuable insights into non-covalent inhibitor behavior and its effect on protease active site residues, impacting optimization and design of novel compounds. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Lucianna H Santos
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ernesto R Caffarena
- Grupo de Biofísica Computacional e Modelagem Molecular, Programa de Computação Científica, Fiocruz, Rio de Janeiro, Brazil
| | - Rafaela S Ferreira
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| |
Collapse
|
35
|
Hammerschmidt SJ, Huber S, Braun NJ, Lander M, Steinmetzer T, Kersten C. Thermodynamic characterization of a macrocyclic Zika virus NS2B/NS3 protease inhibitor and its acyclic analogs. Arch Pharm (Weinheim) 2022; 356:e2200518. [PMID: 36480352 DOI: 10.1002/ardp.202200518] [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: 10/02/2022] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 12/13/2022]
Abstract
Cyclization of small molecules is a widely applied strategy in drug design for ligand optimization to improve affinity, as it eliminates the putative need for structural preorganization of the ligand before binding, or to improve pharmacokinetic properties. In this work, we provide a deeper insight into the binding thermodynamics of a macrocyclic Zika virus NS2B/NS3 protease inhibitor and its linear analogs. Characterization of the thermodynamic binding profiles by isothermal titration calorimetry experiments revealed an unfavorable entropy of the macrocycle compared to the open linear reference ligands. Molecular dynamic simulations and X-ray crystal structure analysis indicated only minor benefits from macrocyclization to fixate a favorable conformation, while linear ligands retained some flexibility even in the protein-bound complex structure, possibly explaining the initially surprising effect of a higher entropic penalty for the macrocyclic ligand.
Collapse
Affiliation(s)
- Stefan J Hammerschmidt
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Mainz, Germany
| | - Simon Huber
- Institute of Pharmaceutical Chemistry, Philipps-University, Marburg, Germany
| | - Niklas J Braun
- Institute of Pharmaceutical Chemistry, Philipps-University, Marburg, Germany
| | - Marc Lander
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Mainz, Germany
| | - Torsten Steinmetzer
- Institute of Pharmaceutical Chemistry, Philipps-University, Marburg, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Mainz, Germany
| |
Collapse
|
36
|
Ci Y, Yao B, Yue K, Yang Y, Xu C, Li DF, Qin CF, Shi L. Bortezomib inhibits ZIKV/DENV by interfering with viral polyprotein cleavage via the ERAD pathway. Cell Chem Biol 2022; 30:527-539.e5. [DOI: 10.1016/j.chembiol.2022.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 09/08/2022] [Accepted: 09/30/2022] [Indexed: 11/09/2022]
|
37
|
de Paula Junior VF, van Tilburg MF, Morais PA, Júnior FFM, Lima EG, Oliveira VTDS, Guedes MIF, Caetano EWS, Freire VN. Quantum Biochemistry and MM-PBSA Description of the ZIKV NS2B-NS3 Protease: Insights into the Binding Interactions beyond the Catalytic Triad Pocket. Int J Mol Sci 2022; 23:ijms231710088. [PMID: 36077486 PMCID: PMC9456192 DOI: 10.3390/ijms231710088] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/17/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
The Zika virus protease NS2B-NS3 has a binding site formed with the participation of a H51-D75-S135 triad presenting two forms, active and inactive. Studies suggest that the inactive conformation is a good target for the design of inhibitors. In this paper, we evaluated the co-crystallized structures of the protease with the inhibitors benzoic acid (5YOD) and benzimidazole-1-ylmethanol (5H4I). We applied a protocol consisting of two steps: first, classical molecular mechanics energy minimization followed by classical molecular dynamics were performed, obtaining stabilized molecular geometries; second, the optimized/relaxed geometries were used in quantum biochemistry and molecular mechanics/Poisson-Boltzmann surface area (MM-PBSA) calculations to estimate the ligand interactions with each amino acid residue of the binding pocket. We show that the quantum-level results identified essential residues for the stabilization of the 5YOD and 5H4I complexes after classical energy minimization, matching previously published experimental data. The same success, however, was not observed for the MM-PBSA simulations. The application of quantum biochemistry methods seems to be more promising for the design of novel inhibitors acting on NS2B-NS3.
Collapse
Affiliation(s)
- Valdir Ferreira de Paula Junior
- Biotechnology & Molecular Biology Laboratory, State University of Ceará, Fortaleza 60714-903, Brazil
- Correspondence: ; Tel.: +55-859-8541-8255
| | | | - Pablo Abreu Morais
- Federal Institute of Education, Science and Technology of Ceará, Campus Horizonte, Horizonte 62884-105, Brazil
| | - Francisco Franciné Maia Júnior
- Departamento de Ciências Naturais, Matemática e Estatística, Universidade Federal Rural do Semi-Árido, Mossoró 59625-900, Brazil
| | - Elza Gadelha Lima
- Laboratório Central de Saúde Pública do Ceará (LACEN), Fortaleza 60120-002, Brazil
| | | | | | | | | |
Collapse
|
38
|
Zu S, Li C, Li L, Deng YQ, Chen X, Luo D, Ye Q, Huang YJ, Li XF, Zhang RR, Sun N, Zhang X, Aliyari SR, Nielsen-Saines K, Jung JU, Yang H, Qin CF, Cheng G. TRIM22 suppresses Zika virus replication by targeting NS1 and NS3 for proteasomal degradation. Cell Biosci 2022; 12:139. [PMID: 36042495 PMCID: PMC9429444 DOI: 10.1186/s13578-022-00872-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/03/2022] [Indexed: 12/03/2022] Open
Abstract
Background Recognition of viral invasion by innate antiviral immune system triggers activation of the type I interferon (IFN-I) and proinflammatory signaling pathways. Subsequently, IFN-I induction regulates expression of a group of genes known as IFN-I-stimulated genes (ISGs) to block viral infection. The tripartite motif containing 22 (TRIM22) is an ISG with strong antiviral functions. Results Here we have shown that the TRIM22 has been strongly upregulated both transcriptionally and translationally upon Zika virus (ZIKV) infection. ZIKV infection is associated with a wide range of clinical manifestations in human from mild to severe symptoms including abnormal fetal brain development. We found that the antiviral function of TRIM22 plays a crucial role in counterattacking ZIKV infection. Overexpression of TRIM22 protein inhibited ZIKV growth whereas deletion of TRIM22 in host cells increased ZIKV infectivity. Mechanistically, TRIM22, as a functional E3 ubiquitin ligase, promoted the ubiquitination and degradation of ZIKV nonstructural protein 1 (NS1) and nonstructural protein 3 (NS3). Further studies showed that the SPRY domain and Ring domain of TRIM22 played important roles in protein interaction and degradation, respectively. In addition, we found that TRIM22 also inhibited other flaviviruses infection including dengue virus (DENV) and yellow fever virus (YFV). Conclusion Thus, TRIM22 is an ISG with important role in host defense against flaviviruses through binding and degradation of the NS1 and NS3 proteins. Supplementary Information The online version contains supplementary material available at 10.1186/s13578-022-00872-w.
Collapse
|
39
|
Kumar A, Kumar D, Jose J, Giri R, Mysorekar IU. Drugs to limit Zika virus infection and implication for maternal-fetal health. FRONTIERS IN VIROLOGY 2022; 2. [PMID: 37064602 PMCID: PMC10104533 DOI: 10.3389/fviro.2022.928599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Although the placenta has robust defense mechanisms that protect the fetus from a viral infection, some viruses can manipulate or evade these mechanisms and disrupt physiology or cross the placental barrier. It is well established that the Zika virus is capable of vertical transmission from mother to fetus and can cause malformation of the fetal central nervous system (i.e., microcephaly), as well as Guillain-Barre syndrome in adults. This review seeks to gather and assess the contributions of translational research associated with Zika virus infection, including maternal-fetal vertical transmission of the virus. Nearly 200 inhibitors that have been evaluated in vivo and/or in vitro for their therapeutic properties against the Zika virus are summarized in this review. We also review the status of current vaccine candidates. Our main objective is to provide clinically relevant information that can guide future research directions and strategies for optimized treatment and preventive care of infections caused by Zika virus or similar pathogens.
Collapse
Affiliation(s)
- Ankur Kumar
- Department of Medicine, Section of Infectious Diseases, Baylor College of Medicine, Houston, TX, United States
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO-Kamand, Mandi, India
| | - Deepak Kumar
- Department of Medicine, Section of Infectious Diseases, Baylor College of Medicine, Houston, TX, United States
| | - Joyce Jose
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, State College, United States
| | - Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO-Kamand, Mandi, India
| | - Indira U. Mysorekar
- Department of Medicine, Section of Infectious Diseases, Baylor College of Medicine, Houston, TX, United States
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- CORRESPONDENCE Indira U. Mysorekar,
| |
Collapse
|
40
|
Tembusu Virus Nonstructural Protein 2B Antagonizes Type I Interferon Production by Targeting MAVS for Degradation. J Virol 2022; 96:e0081622. [PMID: 35867574 PMCID: PMC9327690 DOI: 10.1128/jvi.00816-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Tembusu virus (TMUV) is a newly emerged avian flavivirus that has caused severe egg-drop syndrome and fatal encephalitis in domestic ducks. It has spread widely throughout the main duck-producing areas in Asia, resulting in substantial economic losses to the duck industry. Previous studies have reported that TMUV has evolved several strategies to counteract the duck's innate immune responses to successfully establish infection in its host cells. However, the mechanisms underlying this phenomenon have not been elucidated. Here, we discovered that TMUV-encoded NS2B is a negative regulator of poly(I:C)-induced duck interferon-β (IFN-β) expression. Mechanistically, TMUV NS2B was found to interact specifically with the mitochondrial antiviral-signaling protein (duMAVS). Consequently, duMAVS was degraded through the K48-linked ubiquitination and proteasomal pathway, leading to the interruption of the RIG-I-like receptor (RLR) signaling. Further analyses also identified K321, K354, K398, and K411 as crucial residues for NS2B-mediated ubiquitination and degradation of duMAVS. Additionally, we demonstrated that NS2B functions by recruiting the E3 ubiquitin ligase duck membrane-associated RING-CH-type finger 5 (duMARCH5) to modify duMAVS via polyubiquitination, blocking the duMAVS-mediated innate immune response and promoting TMUV replication. Taken together, our findings revealed a novel mechanism by which TMUV evades the duck's antiviral innate immune responses. IMPORTANCE Tembusu virus (TMUV), an emerging pathogenic flavivirus, has spread to most duck farming areas in Asia since 2010, causing significant economic losses to the duck industry. Recently, TMUV has expanded its host range and may pose a potential threat to mammals, including humans. Understanding the interaction between TMUV and its host is essential for the development of effective vaccines and therapeutics. Here, we show that NS2B encoded by TMUV inhibits IFN production by interacting with duck MAVS (duMAVS) to mediate ubiquitination and proteasomal degradation. Further studies suggest that the E3 ubiquitin ligase duck membrane-associated RING-CH-type finger 5 (duMARCH5) is recruited by NS2B to mediate proteasomal degradation of duMAVS. As a result, the innate immune response triggered by the RIG-I-like receptor (RLR) is disrupted, facilitating viral replication. Overall, our results reveal a novel mechanism by which TMUV evades host innate immunity and provide new therapeutic strategies to prevent TMUV infection.
Collapse
|
41
|
Pant S, Jena NR. C-Terminal Extended Hexapeptides as Potent Inhibitors of the NS2B-NS3 Protease of the ZIKA Virus. Front Med (Lausanne) 2022; 9:921060. [PMID: 35872792 PMCID: PMC9306491 DOI: 10.3389/fmed.2022.921060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/07/2022] [Indexed: 11/30/2022] Open
Abstract
The Zika virus (ZIKV) protease is an attractive drug target for the design of novel inhibitors to control the ZIKV infection. As the protease substrate-binding site contains acidic residues, inhibitors with basic residues can be beneficial for the inhibition of protease activities. Molecular dynamics (MD) simulation and molecular mechanics with generalized Born and surface area solvation (MM/GBSA) techniques are employed herein to design potent peptide inhibitors and to understand the nature of the basic residues that can potentially stabilize the acidic residues of the protease substrate-binding site. It is found that the inclusion of K, R, and K at P1, P2, and P3 positions, respectively, and Y at the P4 position (YKRK) would generate a highly stable tetrapeptide-protease complex with a ΔGbind of ~ −80 kcal/mol. We have also shown that the C-terminal extension of this and the second most stable tetrapeptide (YRRR) with small polar residues, such as S and T would generate even more stable hexapeptide-protease complexes. The modes of interactions of these inhibitors are discussed in detail, which are in agreement with earlier experimental studies. Thus, this study is expected to aid in the design of novel antiviral drugs against the ZIKV.
Collapse
Affiliation(s)
- Suyash Pant
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Nihar R. Jena
- Discipline of Natural Sciences, Indian Institute of Information Technology, Design and Manufacturing, Jabalpur, India
- *Correspondence: Nihar R. Jena
| |
Collapse
|
42
|
Dynamic Interactions of Post Cleaved NS2B Cofactor and NS3 Protease Identified by Integrative Structural Approaches. Viruses 2022; 14:v14071440. [PMID: 35891424 PMCID: PMC9323329 DOI: 10.3390/v14071440] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/17/2022] [Accepted: 06/20/2022] [Indexed: 02/04/2023] Open
Abstract
Diseases caused by flaviviruses such as dengue virus (DENV) and West Nile Virus (WNV), are a serious threat to public health. The flavivirus single-stranded RNA genome is translated into a polyprotein which is cleaved into three structural proteins and seven non-structural proteins by the viral and cellular proteases. Non-structural (NS) protein 3 is a multifunctional protein that has N-terminal protease and C-terminal helicase domains. The NS3 protease requires co-factor NS2B for enzymatic activity and folding. Due to its essential role in viral replication, NS2B-NS3 protease is an attractive target for antiviral drugs. Despite the availability of crystal structures, dynamic interactions of the N- and C-termini of NS2B co-factor have been elusive due to their flexible fold. In this study, we employ integrative structural approaches combined with biochemical assays to elucidate the dynamic interactions of the flexible DENV4 NS2B and NS3 N- and C-termini. We captured the crystal structure of self-cleaved DENV4 NS2B47NS3 protease in post cleavage state. The intermediate conformation adopted in the reported structure can be targeted by allosteric inhibitors. Comparison of our new findings from DENV4 against previously studied ZIKV NS2B-NS3 proteins reveals differences in NS2B-NS3 function between the two viruses. No inhibition of protease activity was observed for unlinked DENV NS2B-NS3 in presence of the cleavage site while ZIKV NS2B-NS3 cleavage inhibits protease activity. Another difference is that binding of the NS2B C-terminus to DENV4 eNS2B47NS3Pro active site is mediated via interactions with P4-P6 residues while for ZIKV, the binding of NS2B C-terminus to active site is mediated by P1-P3 residues. The mapping of NS2B N- and C-termini with NS3 indicates that these intermolecular interactions occur mainly on the beta-barrel 2 of the NS3 protease domain. Our integrative approach enables a comprehensive understanding of the folding and dynamic interactions of DENV NS3 protease and its cofactor NS2B.
Collapse
|
43
|
Eberle RJ, Olivier DS, Amaral MS, Pacca CC, Nogueira ML, Arni RK, Willbold D, Coronado MA. Riboflavin, a Potent Neuroprotective Vitamin: Focus on Flavivirus and Alphavirus Proteases. Microorganisms 2022; 10:1331. [PMID: 35889050 PMCID: PMC9315535 DOI: 10.3390/microorganisms10071331] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/24/2022] [Accepted: 06/29/2022] [Indexed: 12/01/2022] Open
Abstract
Several neurotropic viruses are members of the flavivirus and alphavirus families. Infections caused by these viruses may cause long-term neurological sequelae in humans. The continuous emergence of infections caused by viruses around the world, such as the chikungunya virus (CHIKV) (Alphavirus genus), the zika virus (ZIKV) and the yellow fever virus (YFV) (both of the Flavivirus genus), warrants the development of new strategies to combat them. Our study demonstrates the inhibitory potential of the water-soluble vitamin riboflavin against NS2B/NS3pro of ZIKV and YFV and nsP2pro of CHIKV. Riboflavin presents a competitive inhibition mode with IC50 values in the medium µM range of 79.4 ± 5.0 µM for ZIKV NS2B/NS3pro and 45.7 ± 2.9 μM for YFV NS2B/NS3pro. Against CHIKV nsP2pro, the vitamin showed a very strong effect (93 ± 5.7 nM). The determined dissociation constants (KD) are significantly below the threshold value of 30 µM. The ligand binding increases the thermal stability between 4 °C and 8 °C. Unexpectedly, riboflavin showed inhibiting activity against another viral protein; the molecule was also able to inhibit the viral entry of CHIKV. Molecular dynamics simulations indicated great stability of riboflavin in the protease active site, which validates the repurposing of riboflavin as a promising molecule in drug development against the viruses presented here.
Collapse
Affiliation(s)
- Raphael J. Eberle
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany;
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße, 40225 Düsseldorf, Germany
| | - Danilo S. Olivier
- Center of Integrated Sciences, Campus Cimba, Federal University of Tocantins, Araguaína 77824-838, TO, Brazil;
| | - Marcos S. Amaral
- Institute of Physics, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil;
| | - Carolina C. Pacca
- Instituto Superior de Educação Ceres, FACERES Medical School, São José do Rio Preto 15090-305, SP, Brazil;
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto-FAMERP, São José do Rio Preto 15090-000, SP, Brazil;
| | - Mauricio L. Nogueira
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto-FAMERP, São José do Rio Preto 15090-000, SP, Brazil;
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Raghuvir K. Arni
- Multiuser Center for Biomolecular Innovation, Department of Physics, IBILCE, São Paulo State University, São Jose do Rio Preto 15054-000, SP, Brazil;
| | - Dieter Willbold
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany;
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße, 40225 Düsseldorf, Germany
- JuStruct: Jülich Centre for Structural Biology, Forchungszentrum Jülich, 52428 Jülich, Germany
| | - Monika A. Coronado
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany;
| |
Collapse
|
44
|
Mirza MU, Alanko I, Vanmeert M, Muzzarelli KM, Salo-Ahen OMH, Abdullah I, Kovari IA, Claes S, De Jonghe S, Schols D, Schinazi RF, Kovari LC, Trant JF, Ahmad S, Froeyen M. The discovery of Zika virus NS2B-NS3 inhibitors with antiviral activity via an integrated virtual screening approach. Eur J Pharm Sci 2022; 175:106220. [PMID: 35618201 DOI: 10.1016/j.ejps.2022.106220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/18/2022] [Accepted: 05/23/2022] [Indexed: 11/15/2022]
Abstract
With expanding recent outbreaks and a lack of treatment options, the Zika virus (ZIKV) poses a severe health concern. The availability of ZIKV NS2B-NS3 co-crystallized structures paved the way for rational drug discovery. A computer-aided structure-based approach was used to screen a diverse library of compounds against ZIKV NS2B-NS3 protease. The top hits were selected based on various binding free energy calculations followed by per-residue decomposition analysis. The selected hits were then evaluated for their biological potential with ZIKV protease inhibition assay and antiviral activity. Among 26 selected compounds, 8 compounds showed promising activity against ZIKV protease with a percentage inhibition of greater than 25 and 3 compounds displayed ∼50% at 10 µM, which indicates an enrichment rate of approximately 36% (threshold IC50 < 10 µM) in the ZIKV-NS2B-NS3 protease inhibition assay. Of these, only one compound (23) produced whole-cell anti-ZIKV activity, and the binding mode of 23 was extensively analyzed through long-run molecular dynamics simulations. The current study provides a promising starting point for the further development of novel compounds against ZIKV.
Collapse
Affiliation(s)
- Muhammad Usman Mirza
- KU Leuven, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, Medicinal Chemistry, Herestraat 49, box 1041, Leuven 3000, Belgium; Department of Chemistry and Biochemistry, University of Windsor, Windsor N9B 3P4, ON, Canada
| | - Ida Alanko
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, FI-20520 Turku, Finland; Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, FI-20520 Turku, Finland
| | - Michiel Vanmeert
- KU Leuven, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, Medicinal Chemistry, Herestraat 49, box 1041, Leuven 3000, Belgium
| | - Kendall M Muzzarelli
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit 48201, MI, USA
| | - Outi M H Salo-Ahen
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, FI-20520 Turku, Finland; Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, FI-20520 Turku, Finland
| | - Iskandar Abdullah
- Drug Design Development Research Group, Department of Chemistry, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Iulia A Kovari
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit 48201, MI, USA
| | - Sandra Claes
- KU Leuven, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Herestraat 49, box 1043, Leuven, Belgium
| | - Steven De Jonghe
- KU Leuven, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Herestraat 49, box 1043, Leuven, Belgium
| | - Dominique Schols
- KU Leuven, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Herestraat 49, box 1043, Leuven, Belgium
| | - Raymond F Schinazi
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta 30322, GA, USA
| | - Ladislau C Kovari
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit 48201, MI, USA
| | - John F Trant
- Department of Chemistry and Biochemistry, University of Windsor, Windsor N9B 3P4, ON, Canada
| | - Sarfraz Ahmad
- Drug Design Development Research Group, Department of Chemistry, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Matheus Froeyen
- KU Leuven, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, Medicinal Chemistry, Herestraat 49, box 1041, Leuven 3000, Belgium.
| |
Collapse
|
45
|
Huber S, Braun NJ, Schmacke LC, Quek JP, Murra R, Bender D, Hildt E, Luo D, Heine A, Steinmetzer T. Structure-Based Optimization and Characterization of Macrocyclic Zika Virus NS2B-NS3 Protease Inhibitors. J Med Chem 2022; 65:6555-6572. [PMID: 35475620 DOI: 10.1021/acs.jmedchem.1c01860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Zika virus (ZIKV) is a human pathogenic arbovirus. So far, neither a specific treatment nor a vaccination against ZIKV infections has been approved. Starting from our previously described lead structure, a series of 29 new macrocyclic inhibitors of the Zika virus protease containing different linker motifs have been synthesized. By selecting hydrophobic d-amino acids as part of the linker, numerous inhibitors with Ki values < 5 nM were obtained. For 12 inhibitors, crystal structures in complex with the ZIKV protease up to 1.30 Å resolution were determined, which contribute to the understanding of the observed structure-activity relationship (SAR). In immunofluorescence assays, an antiviral effect was observed for compound 26 containing a d-homocyclohexylalanine residue in its linker segment. Due to its excellent selectivity profile and low cytotoxicity, this inhibitor scaffold could be a suitable starting point for the development of peptidic drugs against the Zika virus and related flaviviruses.
Collapse
Affiliation(s)
- Simon Huber
- Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Niklas J Braun
- Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Luna C Schmacke
- Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Jun Ping Quek
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921.,NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921
| | - Robin Murra
- Federal Institute for Vaccines and Biomedicines, Department of Virology, Paul-Ehrlich-Institut, Paul-Ehrlich-Straße 51-59, 63225 Langen, Germany
| | - Daniela Bender
- Federal Institute for Vaccines and Biomedicines, Department of Virology, Paul-Ehrlich-Institut, Paul-Ehrlich-Straße 51-59, 63225 Langen, Germany
| | - Eberhard Hildt
- Federal Institute for Vaccines and Biomedicines, Department of Virology, Paul-Ehrlich-Institut, Paul-Ehrlich-Straße 51-59, 63225 Langen, Germany
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921.,NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Andreas Heine
- Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Torsten Steinmetzer
- Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| |
Collapse
|
46
|
Yan Y, Yang J, Xiao D, Yin J, Song M, Xu Y, Zhao L, Dai Q, Li Y, Wang C, Wang Z, Ren X, Yang X, Ni J, Liu M, Guo X, Li W, Chen X, Liu Z, Cao R, Zhong W. Nafamostat mesylate as a broad-spectrum candidate for the treatment of flavivirus infections by targeting envelope proteins. Antiviral Res 2022; 202:105325. [PMID: 35460703 DOI: 10.1016/j.antiviral.2022.105325] [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: 01/16/2022] [Revised: 04/13/2022] [Accepted: 04/16/2022] [Indexed: 01/24/2023]
Abstract
Epidemics caused by flaviviruses occur globally; however, no antiviral drugs treating flaviviruses infections have yet been developed. Nafamostat (NM) is a protease inhibitor approved for pancreatitis and anti-coagulation. The anti-flavivirus potential of NM has yet to be determined. Here, utilizing in vitro and in vivo infection assays, we present that NM effectively inhibits Zika virus (ZIKV) and other flaviviruses in vitro. NM inhibited the production of ZIKV viral RNA and proteins originating from Asia and African lineage in human-, mouse- and monkey-derived cell lines and the in vivo anti-ZIKV efficacy of NM was verified. Mode-of-action analysis using time-of-drug-addition assay, infectivity inhibition assay, surface plasmon resonance assay, and molecular docking revealed that NM interacted with viral particles and blocked the early stage of infection by targeting the domain III of ZIKV envelope protein. Analysing the anti-flavivirus effects of NM-related compounds suggested that the antiviral effect depended on the unique structure of NM. These findings suggest the potential use of NM as an anti-flavivirus candidate, and a novel drug design approach targeting the flavivirus envelope protein.
Collapse
Affiliation(s)
- Yunzheng Yan
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Jingjing Yang
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China; School of Pharmaceutical Sciences, Hainan University, Haikou, 570228, China
| | - Dian Xiao
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Jiye Yin
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Mengwen Song
- Beijing Institute of Basic Medical Sciences, Beijing, 100850, China
| | - Yijie Xu
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Lei Zhao
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Qingsong Dai
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Yuexiang Li
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Cui Wang
- Beijing Institute of Basic Medical Sciences, Beijing, 100850, China
| | - Zhuang Wang
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China; Institute of Medical Research, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Xiaofeng Ren
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Xiaotong Yang
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Jie Ni
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Miaomiao Liu
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Xiaojia Guo
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Wei Li
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Xingjuan Chen
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China; Institute of Medical Research, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Zhiqiang Liu
- Beijing Institute of Basic Medical Sciences, Beijing, 100850, China
| | - Ruiyuan Cao
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China.
| | - Wu Zhong
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China.
| |
Collapse
|
47
|
Discovery of Bispecific Lead Compounds from Azadirachta indica against ZIKA NS2B-NS3 Protease and NS5 RNA Dependent RNA Polymerase Using Molecular Simulations. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27082562. [PMID: 35458761 PMCID: PMC9025849 DOI: 10.3390/molecules27082562] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 12/30/2022]
Abstract
Zika virus (ZIKV) has been characterized as one of many potential pathogens and placed under future epidemic outbreaks by the WHO. However, a lack of potential therapeutics can result in an uncontrolled pandemic as with other human pandemic viruses. Therefore, prioritized effective therapeutics development has been recommended against ZIKV. In this context, the present study adopted a strategy to explore the lead compounds from Azadirachta indica against ZIKV via concurrent inhibition of the NS2B-NS3 protease (ZIKVpro) and NS5 RNA dependent RNA polymerase (ZIKVRdRp) proteins using molecular simulations. Initially, structure-based virtual screening of 44 bioflavonoids reported in Azadirachta indica against the crystal structures of targeted ZIKV proteins resulted in the identification of the top four common bioflavonoids, viz. Rutin, Nicotiflorin, Isoquercitrin, and Hyperoside. These compounds showed substantial docking energy (−7.9 to −11.01 kcal/mol) and intermolecular interactions with essential residues of ZIKVpro (B:His51, B:Asp75, and B:Ser135) and ZIKVRdRp (Asp540, Ile799, and Asp665) by comparison to the reference compounds, O7N inhibitor (ZIKVpro) and Sofosbuvir inhibitor (ZIKVRdRp). Besides, long interval molecular dynamics simulation (500 ns) on the selected docked poses reveals stability of the respective docked poses contributed by intermolecular hydrogen bonds and hydrophobic interactions. The predicted complex stability was further supported by calculated end-point binding free energy using molecular mechanics generalized born surface area (MM/GBSA) method. Consequently, the identified common bioflavonoids are recommended as promising therapeutic inhibitors of ZIKVpro and ZIKVRdRp against ZIKV for further experimental assessment.
Collapse
|
48
|
Regla-Nava JA, Wang YT, Fontes-Garfias CR, Liu Y, Syed T, Susantono M, Gonzalez A, Viramontes KM, Verma SK, Kim K, Landeras-Bueno S, Huang CT, Prigozhin DM, Gleeson JG, Terskikh AV, Shi PY, Shresta S. A Zika virus mutation enhances transmission potential and confers escape from protective dengue virus immunity. Cell Rep 2022; 39:110655. [PMID: 35417697 PMCID: PMC9093040 DOI: 10.1016/j.celrep.2022.110655] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 02/08/2022] [Accepted: 03/18/2022] [Indexed: 12/14/2022] Open
Abstract
Zika virus (ZIKV) and dengue virus (DENV) are arthropod-borne pathogenic flaviviruses that co-circulate in many countries. To understand some of the pressures that influence ZIKV evolution, we mimic the natural transmission cycle by repeating serial passaging of ZIKV through cultured mosquito cells and either DENV-naive or DENV-immune mice. Compared with wild-type ZIKV, the strains passaged under both conditions exhibit increased pathogenesis in DENV-immune mice. Application of reverse genetics identifies an isoleucine-to-valine mutation (I39V) in the NS2B proteins of both passaged strains that confers enhanced fitness and escape from pre-existing DENV immunity. Introduction of I39V or I39T, a naturally occurring homologous mutation detected in recent ZIKV isolates, increases the replication of wild-type ZIKV in human neuronal precursor cells and laboratory-raised mosquitoes. Our data indicate that ZIKV strains with enhanced transmissibility and pathogenicity can emerge in DENV-naive or -immune settings, and that NS2B-I39 mutants may represent ZIKV variants of interest.
Collapse
Affiliation(s)
- Jose Angel Regla-Nava
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Ying-Ting Wang
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Camila R Fontes-Garfias
- Department of Biochemistry and Molecular Biology, Sealy Institute for Drug Discovery, Department of Pharmacology and Toxicology and Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Yang Liu
- Department of Biochemistry and Molecular Biology, Sealy Institute for Drug Discovery, Department of Pharmacology and Toxicology and Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Thasneem Syed
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Mercylia Susantono
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Andrew Gonzalez
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Karla M Viramontes
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Shailendra Kumar Verma
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Kenneth Kim
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Sara Landeras-Bueno
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Chun-Teng Huang
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Daniil M Prigozhin
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Joseph G Gleeson
- Howard Hughes Medical Institute, Rady Children's Institute of Genomic Medicine, Department of Neurosciences, University of California, San Diego, San Diego, CA 92093, USA
| | - Alexey V Terskikh
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, Sealy Institute for Drug Discovery, Department of Pharmacology and Toxicology and Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Sujan Shresta
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA.
| |
Collapse
|
49
|
Li Z, Xu J, Lang Y, Wu X, Hu S, Samrat SK, Tharappel AM, Kuo L, Butler D, Song Y, Zhang QY, Zhou J, Li H. In vitro and in vivo characterization of erythrosin B and derivatives against Zika virus. Acta Pharm Sin B 2022; 12:1662-1670. [PMID: 35847519 PMCID: PMC9279632 DOI: 10.1016/j.apsb.2021.10.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 01/03/2023] Open
Abstract
Zika virus (ZIKV) causes significant human diseases without specific therapy. Previously we found erythrosin B, an FDA-approved food additive, inhibited viral NS2B−NS3 interactions, leading to inhibition of ZIKV infection in cell culture. In this study, we performed pharmacokinetic and in vivo studies to demonstrate the efficacy of erythrosin B against ZIKV in 3D mini-brain organoid and mouse models. Our results showed that erythrosin B is very effective in abolishing ZIKV replication in the 3D organoid model. Although pharmacokinetics studies indicated that erythrosin B had a low absorption profile, mice challenged by a lethal dose of ZIKV showed a significantly improved survival rate upon oral administration of erythrosin B, compared to vehicle control. Limited structure−activity relationship studies indicated that most analogs of erythrosin B with modifications on the xanthene ring led to loss or reduction of inhibitory activities towards viral NS2B−NS3 interactions, protease activity and antiviral efficacy. In contrast, introducing chlorine substitutions on the isobenzofuran ring led to slightly increased activities, suggesting that the isobenzofuran ring is well tolerated for modifications. Cytotoxicity studies indicated that all derivatives are nontoxic to human cells. Overall, our studies demonstrated erythrosin B is an effective antiviral against ZIKV both in vitro and in vivo.
Collapse
|
50
|
Penna BR, de Oliveira DMP, Anobom CD, Valente AP. Backbone 1H, 15N, and 13C resonance assignments of the non-structural protein NS2B of Zika virus. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:31-35. [PMID: 34817802 DOI: 10.1007/s12104-021-10055-2] [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: 08/05/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
Zika virus (ZIKV) emerged as a global public health concern due to its relationship with severe neurological disorders. Non-structural (NS) proteins of ZIKV are essential for viral replication, regulatory function, and subversion of host responses. NS2B is a membrane protein responsible for the regulation of viral protease activity. This protein has transmembrane domains critical for the localization of viral protease to the endoplasmic reticulum membrane and a hydrophilic domain essential for folding, recruitment, and protease activity. Therefore, NS2B is considered a cofactor of viral protease which processes viral polyprotein and is essential for virus replication, making it an attractive antiviral drug target. Here, we report the backbone 1H, 15N, 13C resonance assignments of the full-length NS2B by high-resolution NMR. The backbone assignment will be necessary for determining the three-dimensional structure and backbone dynamics of NS2B, interaction mapping and screening potential of antiviral drugs against ZIKV and related pathogenic flaviviruses.
Collapse
Affiliation(s)
- Beatriz Rosa Penna
- Institute of Medical Biochemistry (IBqM), National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- National Center of Nuclear Magnetic Resonance (CNRMN), Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Danielle Maria P de Oliveira
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Cristiane Dinis Anobom
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ana Paula Valente
- Institute of Medical Biochemistry (IBqM), National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
- National Center of Nuclear Magnetic Resonance (CNRMN), Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
| |
Collapse
|