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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 2024:100164. [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] [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.
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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.
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2
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Shorkey SA, Zhang Y, Sharp J, Clingman S, Nguyen L, Chen J, Chen M. Tuning single-molecule ClyA nanopore tweezers for real-time tracking of the conformational dynamics of West Nile viral NS2B/NS3 protease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.594247. [PMID: 38798384 PMCID: PMC11118314 DOI: 10.1101/2024.05.14.594247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
The flaviviral NS2B/NS3 protease is a conserved enzyme required for flavivirus replication. Its highly dynamic conformation poses major challenges but also offers opportunities for antiviral inhibition. Here, we established a nanopore tweezers-based platform to monitor NS2B/NS3 conformational dynamics in real-time. Molecular simulations coupled with electrophysiology revealed that the protease could be captured in the middle of the ClyA nanopore lumen, stabilized mainly by dynamic electrostatic interactions. We designed a new Salmonella typhi ClyA nanopore with enhanced nanopore/protease interaction that can resolve the open and closed states at the single-molecule level for the first time. We demonstrated that the tailored ClyA could track the conformational transitions of the West Nile NS2B/NS3 protease and unravel the conformational energy landscape of various protease constructs through population and kinetic analysis. The new ClyA-protease platform paves a way to high-throughput screening strategies for discovering new allosteric inhibitors that target the NS2B and NS3 interface.
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3
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Zhang B, Yu J, Zhu G, Huang Y, Zhang K, Xiao X, He W, Yuan J, Gao X. Dapoxetine, a Selective Serotonin Reuptake Inhibitor, Suppresses Zika Virus Infection In Vitro. Molecules 2023; 28:8142. [PMID: 38138628 PMCID: PMC10745718 DOI: 10.3390/molecules28248142] [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: 10/30/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023] Open
Abstract
Zika virus (ZIKV) belongs to the Flavivirus genus of the Flaviviridae family, and is a pathogen posing a significant threat to human health. Currently, there is a lack of internationally approved antiviral drugs for the treatment of ZIKV infection, and symptomatic management remains the primary clinical approach. Consequently, the exploration of safe and effective anti-ZIKV drugs has emerged as a paramount imperative in ZIKV control efforts. In this study, we performed a screening of a compound library consisting of 1789 FDA-approved drugs to identify potential agents with anti-ZIKV activity. We have identified dapoxetine, an orally administered selective serotonin reuptake inhibitor (SSRI) commonly employed for the clinical management of premature ejaculation (PE), as a potential inhibitor of ZIKV RNA-dependent RNA polymerase (RdRp). Consequently, we conducted surface plasmon resonance (SPR) analysis to validate the specific binding of dapoxetine to ZIKV RdRp, and further evaluated its inhibitory effect on ZIKV RdRp synthesis using the ZIKV Gluc reporter gene assay. Furthermore, we substantiated the efficacy of dapoxetine in suppressing intracellular replication of ZIKV, thereby demonstrating a concentration-dependent antiviral effect (EC50 values ranging from 4.20 μM to 12.6 μM) and negligible cytotoxicity (CC50 > 50 μM) across diverse cell lines. Moreover, cell fluorescence staining and Western blotting assays revealed that dapoxetine effectively reduced the expression of ZIKV proteins. Collectively, our findings suggest that dapoxetine exhibits anti-ZIKV effects by inhibiting ZIKV RdRp activity, positioning it as a potential candidate for clinical therapeutic intervention against ZIKV infection.
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Affiliation(s)
- Bingzhi Zhang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China;
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China; (J.Y.); (G.Z.); (X.X.)
| | - Jianchen Yu
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China; (J.Y.); (G.Z.); (X.X.)
| | - Ge Zhu
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China; (J.Y.); (G.Z.); (X.X.)
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Yun Huang
- School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China;
| | - Kexin Zhang
- School of Public Health, Sun Yat-sen University, Guangzhou 510080, China;
| | - Xuhan Xiao
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China; (J.Y.); (G.Z.); (X.X.)
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Wenxuan He
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China;
| | - Jie Yuan
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China; (J.Y.); (G.Z.); (X.X.)
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Xiaoxia Gao
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China;
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4
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Li Q, Ng HQ, Loh YR, Kang C. Backbone 1H, 15N and 13C resonance assignments for dengue NS2B without the NS3 protease cofactor region in detergent micelles. BIOMOLECULAR NMR ASSIGNMENTS 2023; 17:205-209. [PMID: 37405583 DOI: 10.1007/s12104-023-10142-6] [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: 05/19/2023] [Accepted: 06/23/2023] [Indexed: 07/06/2023]
Abstract
Dengue virus is an important human pathogen affecting people especially in tropical and subtropical regions. Its genome encodes seven non-structural proteins that are important for viral assembly and replication. Dengue NS2B is a membrane protein containing four transmembrane helices and involved in protein-protein interactions. Its transmembrane helices are critical for location of NS2B on the cell membrane while one cytoplasmic region composed of approximately 40 amino acids serves as a cofactor of viral NS3 protease by forming a tight complex with the N-terminal region of NS3. Here, we report the backbone resonance assignments for a dengue NS2B construct referred to as mini-NS2B containing only the transmembrane regions without NS3 cofactor region in detergent micelles. Mini-NS2B exhibits well-dispersed cross-peaks in the 1H-15N-HSQC spectrum and contains four helices in solution. The available mini-NS2B and its assignment will be useful for determining the structure of NS2B and identifying small molecules binding to the transmembrane regions.
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Affiliation(s)
- Qingxin Li
- Guangdong Provincial Engineering Laboratory of Biomass High Value Utilization, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Hui Qi Ng
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - Ying Ru Loh
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore
| | - CongBao Kang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, Chromos, #05-01, Singapore, 138670, Singapore.
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5
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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.
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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
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6
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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.
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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
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7
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Zhu Y, Yu J, Chen T, Liu W, Huang Y, Li J, Zhang B, Zhu G, He Z, Long Y, Yuan J. Design, synthesis, and biological evaluation of a series of new anthraquinone derivatives as anti-ZIKV agents. Eur J Med Chem 2023; 258:115620. [PMID: 37421888 DOI: 10.1016/j.ejmech.2023.115620] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/10/2023]
Abstract
The major severe complications linked to Zika virus (ZIKV) cause the global public health problems, including microcephaly and other congenital abnormalities in newborns, and Guillain-Barré syndrome, meningoencephalitis, multi-organ failure in adults. However, neither approved vaccines nor drugs are available for ZIKV. In this study, we describe the design, synthesis and the anti-ZIKV activities of a series of anthraquinone analogs. Most of the newly synthesized compounds demonstrated moderate to excellent potency against ZIKV. Among all, compound 22, showed the most potent anti-ZIKV activity (EC50 value from 1.33 μM to 5.72 μM) with low cytotoxicity (CC50>50 μM) in multiple cellular model. Importantly, 22 significantly improved the survival of ZIKV-infected mice (Ifnar1-/-), alleviated ZIKV-associated pathological damages and suppressed the excessive inflammatory response and pyroptosis induced by ZIKV in vivo and in vitro. Furthermore, the molecular docking simulation analysis and the surface plasmon resonance results demonstrated the direct binding between 22 and ZIKV RdRp, and the mechanistic study revealed that 22 suppressed viral RNA synthesis by ZIKV NS5 in cells. Taken together, this study highlights that 22 may be a novel anti-ZIKV drug candidate and provides treatment options for ZIKV-associated diseases.
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Affiliation(s)
- Yujia Zhu
- School of Public Health, Sun Yat-sen University, Guangzhou, 510080, Guangdong, China.
| | - Jianchen Yu
- School of Chemistry, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, South China Normal University, Guangzhou, 510006, China; Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China.
| | - Tao Chen
- School of Chemistry, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, South China Normal University, Guangzhou, 510006, China
| | - Wenbin Liu
- School of Chemistry, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, South China Normal University, Guangzhou, 510006, China.
| | - Yun Huang
- School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Junsen Li
- School of Chemistry, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, South China Normal University, Guangzhou, 510006, China
| | - Bingzhi Zhang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China.
| | - Ge Zhu
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Zhenjian He
- School of Public Health, Sun Yat-sen University, Guangzhou, 510080, Guangdong, China; Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China.
| | - Yuhua Long
- School of Chemistry, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, South China Normal University, Guangzhou, 510006, China.
| | - Jie Yuan
- School of Public Health, Sun Yat-sen University, Guangzhou, 510080, Guangdong, China; Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
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8
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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.
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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.
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9
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Huang Z, Zhang Y, Li H, Zhu J, Song W, Chen K, Zhang Y, Lou Y. Vaccine development for mosquito-borne viral diseases. Front Immunol 2023; 14:1161149. [PMID: 37251387 PMCID: PMC10213220 DOI: 10.3389/fimmu.2023.1161149] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/13/2023] [Indexed: 05/31/2023] Open
Abstract
Mosquito-borne viral diseases are a group of viral illnesses that are predominantly transmitted by mosquitoes, including viruses from the Togaviridae and Flaviviridae families. In recent years, outbreaks caused by Dengue and Zika viruses from the Flaviviridae family, and Chikungunya virus from the Togaviridae family, have raised significant concerns for public health. However, there are currently no safe and effective vaccines available for these viruses, except for CYD-TDV, which has been licensed for Dengue virus. Efforts to control the transmission of COVID-19, such as home quarantine and travel restrictions, have somewhat limited the spread of mosquito-borne viral diseases. Several vaccine platforms, including inactivated vaccines, viral-vector vaccines, live attenuated vaccines, protein vaccines, and nucleic acid vaccines, are being developed to combat these viruses. This review analyzes the various vaccine platforms against Dengue, Zika, and Chikungunya viruses and provides valuable insights for responding to potential outbreaks.
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Affiliation(s)
- Zhiwei Huang
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yuxuan Zhang
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Hongyu Li
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Jiajie Zhu
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Wanchen Song
- School of Medical Technology and Information Engineering, Zhejiang Chinese Medical University, Hangzhou, China
| | - Keda Chen
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Yanjun Zhang
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Yongliang Lou
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
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10
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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.
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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.
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11
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Gbore DJ, Zakari S, Yusuf L. In silico studies of bioactive compounds from Alpinia officinarum as inhibitors of Zika virus protease. INFORMATICS IN MEDICINE UNLOCKED 2023. [DOI: 10.1016/j.imu.2023.101214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023] Open
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12
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Murali A, Kumar S, Akshaya S, Singh SK. Drug repurposing toward the inhibition of RNA-dependent RNA polymerase of various flaviviruses through computational study. J Cell Biochem 2023; 124:127-145. [PMID: 36502494 DOI: 10.1002/jcb.30352] [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: 06/27/2022] [Revised: 11/08/2022] [Accepted: 11/15/2022] [Indexed: 12/14/2022]
Abstract
Numerous pathogens affecting human is present in the flavivirus family namely west nile, dengue, yellow fever, and zika which involves in development of global burden and distressing the environment economically. Till date, no approved drugs are available for targeting these viruses. The threat which urged the identification of small molecules for the inhibition of these viruses is the spreading of serious viral diseases. The recent outbreak of zika and dengue infections postured a solemn risk to worldwide public well-being. RNA-dependent RNA polymerase (RdRp) is the supreme adaptable enzymes of all the RNA viruses which is responsible for the replication and transcription of genome among the structural and nonstructural proteins of flaviviruses. It is understood that the RdRp of the flaviviruses are similar stating that the japanese encephalitis and west nile shares 70% identity with zika whereas the dengue serotype 2 and 3 shares the identity of 76% and 81%, respectively. In this study, we investigated the binding site of four flaviviral RdRp and provided insights into various interaction of the molecules using the computational approach. Our study helps in recognizing the potent compounds that could inhibit the viral protein as a common inhibitor. Additionally, with the conformational stability analysis, we proposed the possible mechanism of inhibition of the identified common small molecule toward RdRp of flavivirus. Finally, this study could be an initiative for the identification of common inhibitors and can be explored further for understanding the mechanism of action through in vitro studies for the study on efficacy.
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Affiliation(s)
- Aarthy Murali
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Sushil Kumar
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | | | - Sanjeev K Singh
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
- Department of Data Sciences, Centre of Biomedical Research, Sanjay Gandhi Post Institute of Medical Sciences Campus, Lucknow, India
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13
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Kandagalla S, Novak J, Shekarappa SB, Grishina MA, Potemkin VA, Kumbar B. Exploring potential inhibitors against Kyasanur forest disease by utilizing molecular dynamics simulations and ensemble docking. J Biomol Struct Dyn 2022; 40:13547-13563. [PMID: 34662258 DOI: 10.1080/07391102.2021.1990131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Kyasanur forest disease (KFD) is a tick-borne, neglected tropical disease, caused by KFD virus (KFDV) which belongs to Flavivirus (Flaviviridae family). This emerging viral disease is a major threat to humans. Currently, vaccination is the only controlling method against the KFDV, and its effectiveness is very low. An effective control strategy is required to combat this emerging tropical disease using the existing resources. In this regard, in silico drug repurposing method offers an effective strategy to find suitable antiviral drugs against KFDV proteins. Drug repurposing is an effective strategy to identify new use for approved or investigational drugs that are outside the scope of their initial usage and the repurposed drugs have lower risk and higher safety compared to de novo developed drugs, because their toxicity and safety issues are profoundly investigated during the preclinical trials in human/other models. In the present work, we evaluated the effectiveness of the FDA approved and natural compounds against KFDV proteins using in silico molecular docking and molecular simulations. At present, no experimentally solved 3D structures for the KFD viral proteins are available in Protein Data Bank and hence their homology model was developed and used for the analysis. The present analysis successfully developed the reliable homology model of NS3 of KFDV, in terms of geometry and energy contour. Further, in silico molecular docking and molecular dynamics simulations successfully presented four FDA approved drugs and one natural compound against the NS3 homology model of KFDV. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shivananda Kandagalla
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Jurica Novak
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Sharath Belenahalli Shekarappa
- Department of PG Studies and Research in Biotechnology and Bioinformatics, Kuvempu University, Shivamogga, Karnataka, India
| | - Maria A Grishina
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Vladimir A Potemkin
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Bhimanagoud Kumbar
- Department of PG Studies and Research in Biotechnology and Bioinformatics, Kuvempu University, Shivamogga, Karnataka, India.,ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, Karnataka, India
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14
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Discovery of dehydroandrographolide derivatives with C19 hindered ether as potent anti-ZIKV agents with inhibitory activities to MTase of ZIKV NS5. Eur J Med Chem 2022; 243:114710. [DOI: 10.1016/j.ejmech.2022.114710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/20/2022] [Accepted: 08/21/2022] [Indexed: 11/22/2022]
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15
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Viral proteases as therapeutic targets. Mol Aspects Med 2022; 88:101159. [PMID: 36459838 PMCID: PMC9706241 DOI: 10.1016/j.mam.2022.101159] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 11/30/2022]
Abstract
Some medically important viruses-including retroviruses, flaviviruses, coronaviruses, and herpesviruses-code for a protease, which is indispensable for viral maturation and pathogenesis. Viral protease inhibitors have become an important class of antiviral drugs. Development of the first-in-class viral protease inhibitor saquinavir, which targets HIV protease, started a new era in the treatment of chronic viral diseases. Combining several drugs that target different steps of the viral life cycle enables use of lower doses of individual drugs (and thereby reduction of potential side effects, which frequently occur during long term therapy) and reduces drug-resistance development. Currently, several HIV and HCV protease inhibitors are routinely used in clinical practice. In addition, a drug including an inhibitor of SARS-CoV-2 main protease, nirmatrelvir (co-administered with a pharmacokinetic booster ritonavir as Paxlovid®), was recently authorized for emergency use. This review summarizes the basic features of the proteases of human immunodeficiency virus (HIV), hepatitis C virus (HCV), and SARS-CoV-2 and discusses the properties of their inhibitors in clinical use, as well as development of compounds in the pipeline.
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16
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Dos Santos Nascimento IJ, da Silva Rodrigues ÉE, da Silva MF, de Araújo-Júnior JX, de Moura RO. Advances in Computational Methods to Discover New NS2B-NS3 Inhibitors Useful Against Dengue and Zika Viruses. Curr Top Med Chem 2022; 22:2435-2462. [PMID: 36415099 DOI: 10.2174/1568026623666221122121330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/20/2022] [Accepted: 09/27/2022] [Indexed: 11/24/2022]
Abstract
The Flaviviridae virus family consists of the genera Hepacivirus, Pestivirus, and Flavivirus, with approximately 70 viral types that use arthropods as vectors. Among these diseases, dengue (DENV) and zika virus (ZIKV) serotypes stand out, responsible for thousands of deaths worldwide. Due to the significant increase in cases, the World Health Organization (WHO) declared DENV a potential threat for 2019 due to being transmitted by infected travelers. Furthermore, ZIKV also has a high rate of transmissibility, highlighted in the outbreak in 2015, generating consequences such as Guillain-Barré syndrome and microcephaly. According to clinical outcomes, those infected with DENV can be asymptomatic, and in other cases, it can be lethal. On the other hand, ZIKV has severe neurological symptoms in newborn babies and adults. More serious symptoms include microcephaly, brain calcifications, intrauterine growth restriction, and fetal death. Despite these worrying data, no drug or vaccine is approved to treat these diseases. In the drug discovery process, one of the targets explored against these diseases is the NS2B-NS3 complex, which presents the catalytic triad His51, Asp75, and Ser135, with the function of cleaving polyproteins, with specificity for basic amino acid residues, Lys- Arg, Arg-Arg, Arg-Lys or Gln-Arg. Since NS3 is highly conserved in all DENV serotypes and plays a vital role in viral replication, this complex is an excellent drug target. In recent years, computer-aided drug discovery (CADD) is increasingly essential in drug discovery campaigns, making the process faster and more cost-effective, mainly explained by discovering new drugs against DENV and ZIKV. Finally, the main advances in computational methods applied to discover new compounds against these diseases will be presented here. In fact, molecular dynamics simulations and virtual screening is the most explored approach, providing several hit and lead compounds that can be used in further optimizations. In addition, fragment-based drug design and quantum chemistry/molecular mechanics (QM/MM) provides new insights for developing anti-DENV/ZIKV drugs. We hope that this review offers further helpful information for researchers worldwide and stimulates the use of computational methods to find a promising drug for treating DENV and ZIKV.
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Affiliation(s)
- Igor José Dos Santos Nascimento
- Department of Pharmacy, Estácio of Alagoas College, Maceió, Brazil.,Department of Pharmacy, Cesmac University Center, Maceió, Brazil.,Department of Pharmacy, Drug Development and Synthesis Laboratory, State University of Paraíba, Campina Grande, Brazil
| | | | - Manuele Figueiredo da Silva
- Laboratory of Medicinal Chemistry, Pharmaceutical Sciences Institute, Federal University of Alagoas, Maceió, Brazil
| | - João Xavier de Araújo-Júnior
- Laboratory of Medicinal Chemistry, Pharmaceutical Sciences Institute, Federal University of Alagoas, Maceió, Brazil
| | - Ricardo Olimpio de Moura
- Department of Pharmacy, Drug Development and Synthesis Laboratory, State University of Paraíba, Campina Grande, Brazil
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17
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Structure-based design of a novel inhibitor of the ZIKA virus NS2B/NS3 protease. Bioorg Chem 2022; 128:106109. [DOI: 10.1016/j.bioorg.2022.106109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/02/2022] [Accepted: 08/19/2022] [Indexed: 11/24/2022]
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18
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Jonniya NA, Kar P. Functional Loop Dynamics and Characterization of the Inactive State of the NS2B-NS3 Dengue Protease due to Allosteric Inhibitor Binding. J Chem Inf Model 2022; 62:3800-3813. [PMID: 35950997 DOI: 10.1021/acs.jcim.2c00461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dengue virus, a flavivirus that causes dengue shock syndrome and dengue hemorrhagic fever, is currently prevalent worldwide. A two-component protease (NS2B-NS3) is essential for maturation, representing an important target for designing anti-flavivirus drugs. Previously, consideration has been centered on developing active-site inhibitors of NS2B-NS3pro. However, the flat and charged nature of its active site renders difficulties in developing inhibitors, suggesting an alternative strategy for identifying allosteric inhibitors. The allosterically sensitive site of the dengue protease is located near Ala125, between the 120s loop and 150s loop. Using atomistic molecular dynamics simulations, we have explored the protease's conformational dynamics upon binding of an allosteric inhibitor. Furthermore, characterization of the inherent flexible loops (71-75s loop, 120s loop, and 150s loop) is carried out for allosteric-inhibitor-bound wild-type and mutant A125C variants and a comparison is performed with its unbound state to extract the structural changes describing the inactive state of the protease. Our study reveals that compared to the unliganded system, the inhibitor-bound system shows large structural changes in the 120s loop and 150s loop in contrast to the rigid 71-75s loop. The unliganded system shows a closed-state pocket in contrast to the open state for the wild-type complex that locks the protease into the open and inactive-state conformations. However, the mutant complex fluctuates between open and closed states. Also, we tried to see how mutation and binding of an allosteric inhibitor perturb the connectivity in a protein structure network (PSN) at contact levels. Altogether, our study reveals the mechanism of conformational rearrangements of loops at the molecular level, locking the protein in an inactive conformation, which may be useful for developing allosteric inhibitors.
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Affiliation(s)
- Nisha Amarnath Jonniya
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Indore, Madhya Pradesh 453552, India
| | - Parimal Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Indore, Madhya Pradesh 453552, India
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19
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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.
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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
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20
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Gao Y, Tai W, Wang X, Jiang S, Debnath AK, Du L, Chen S. A gossypol derivative effectively protects against Zika and dengue virus infection without toxicity. BMC Biol 2022; 20:143. [PMID: 35706035 PMCID: PMC9202104 DOI: 10.1186/s12915-022-01344-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 06/07/2022] [Indexed: 11/28/2022] Open
Abstract
Background Zika virus (ZIKV) and dengue virus (DENV) cause microcephaly and dengue hemorrhagic fever, respectively, leading to severe problems. No effective antiviral agents are approved against infections of these flaviviruses, calling for the need to develop potent therapeutics. We previously identified gossypol as an effective inhibitor against ZIKV and DENV infections, but this compound is toxic and not suitable for in vivo treatment. Results In this study, we showed that gossypol derivative ST087010 exhibited potent and broad-spectrum in vitro inhibitory activity against infections of at least ten ZIKV strains isolated from different hosts, time periods, and countries, as well as DENV-1-4 serotypes, and significantly reduced cytotoxicity compared to gossypol. It presented broad-spectrum in vivo protective efficacy, protecting ZIKV-infected Ifnar1−/− mice from lethal challenge, with increased survival and reduced weight loss. Ifnar1−/− mice treated with this gossypol derivative decreased viral titers in various tissues, including the brain and testis, after infection with ZIKV at different human isolates. Moreover, ST087010 potently blocked ZIKV vertical transmission in pregnant Ifnar1−/− mice, preventing ZIKV-caused fetal death, and it was safe for pregnant mice and their pups. It also protected DENV-2-challenged Ifnar1−/− mice against viral replication by reducing the viral titers in the brain, kidney, heart, and sera. Conclusions Overall, our data indicate the potential for further development of this gossypol derivative as an effective and safe broad-spectrum therapeutic agent to treat ZIKV and DENV diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01344-w.
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Affiliation(s)
- Yaning Gao
- Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China.,Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, 10065, USA
| | - Wanbo Tai
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, 10065, USA
| | - Xinyi Wang
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, 10065, USA
| | - Shibo Jiang
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, 10065, USA.,Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Asim K Debnath
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, 10065, USA.
| | - Lanying Du
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, 10065, USA.
| | - Shizhong Chen
- Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China.
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21
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Naz F, Malik A, Riaz M, Mahmood Q, Mehmood MH, Rasool G, Mahmood Z, Abbas M. Bromocriptine Therapy: Review of mechanism of action, safety and tolerability. Clin Exp Pharmacol Physiol 2022; 49:903-922. [DOI: 10.1111/1440-1681.13678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Faiza Naz
- Punjab University College of Pharmacy University of the Punjab Lahore Pakistan
| | - Abdul Malik
- College of Pharmacy University of Sargodha Sargodha Pakistan
| | - Muhammad Riaz
- Department of Allied Health Sciences University of Sargodha Sargodha Pakistan
| | - Qaisar Mahmood
- College of Pharmacy University of Sargodha Sargodha Pakistan
| | - Malik Hassan Mehmood
- Department of Pharmacology, Faculty of Pharmaceutical Sciences Government College University Faisalabad Pakistan
| | - Ghulam Rasool
- Department of Allied Health Sciences University of Sargodha Sargodha Pakistan
| | - Zahed Mahmood
- Department of Biochemistry Government College University Faisalabad Pakistan
| | - Mazhar Abbas
- Department of Biochemistry College of Veterinary and Animal Sciences, University of Veterinary and Animal Sciences (Jhang Campus) Lahore Pakistan
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22
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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.
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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.
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23
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Yu Y, Gao C, Wen C, Zou P, Qi X, Cardona CJ, Xing Z. Intrinsic features of Zika Virus non-structural proteins NS2A and NS4A in the regulation of viral replication. PLoS Negl Trop Dis 2022; 16:e0010366. [PMID: 35522620 PMCID: PMC9075646 DOI: 10.1371/journal.pntd.0010366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 03/28/2022] [Indexed: 12/12/2022] Open
Abstract
Zika virus (ZIKV) is a mosquito-borne flavivirus and can cause neurodevelopmental disorders in fetus. As a neurotropic virus, ZIKV persistently infects neural tissues during pregnancy but the viral pathogenesis remains largely unknown. ZIKV has a positive-sense and single-stranded RNA genome, which encodes 7 non-structural (NS) proteins, participating in viral replication and dysregulation of host immunity. Like those in many other viruses, NS proteins are considered to be products evolutionarily beneficiary to viruses and some are virulence factors. However, we found that some NS proteins encoded by ZIKV genome appeared to function against the viral replication. In this report we showed that exogenously expressed ZIKV NS2A and NS4A inhibited ZIKV infection by inhibiting viral RNA replication in microglial cells and astrocytes. To understand how viral NS proteins suppressed viral replication, we analyzed the transcriptome of the microglial cells and astrocytes and found that expression of NS4A induced the upregulation of ISGs, including MX1/2, OAS1/2/3, IFITM1, IFIT1, IFI6, IFI27, ISG15 or BST2 through activating the ISGF3 signaling pathway. Upregulation of these ISGs seemed to be related to the inhibition of ZIKV replication, since the anti-ZIKV function of NS4A was partially attenuated when the cells were treated with Abrocitinib, an inhibitor of the ISGF3 signaling pathway, or were knocked down with STAT2. Aborting the protein expression of NS4A, but not its nucleic acid, eliminated the antiviral activity of NS4A effectively. Dynamic expression of viral NS proteins was examined in ZIKV-infected microglial cells and astrocytes, which showed comparatively NS4A occurred later than other NS proteins during the infection. We hypothesize that NS4A may possess intrinsic features to serve as a unique type of pathogen associated molecular pattern (PAMP), detectable by the cells to induce an innate immune response, or function with other mechanisms, to restrict the viral replication to a certain level as a negative feedback, which may help ZIKV maintain its persistent infection in fetal neural tissues. The birth of microcephaly infants due to ZIKV infection in pregnant women is related to ZIKV persistent infection. However, it is unclear how ZIKV maintains its persistent infection. In this work, we observed the delayed appearance of ZIKV NS4A protein in neuroglia including microglia and astrocytes compared with other non-structural proteins. Subsequently, we revealed that ZIKV NS4A inhibited viral RNA replication by activating the ISGF3 signaling pathway and inducing the production of ISGs. Aborting NS4A protein expression totally rescued ZIKV viral replication. Our study, combined with the previous findings, suggests that viral non-structural proteins may regulate viral replication, thus perpetuating ZIKV infection. Our hypothesis provides a mechanism for ZIKV to maintain its status of a persistent infection during viral infection in fetus, which can shed lights on our further understanding of viral neuropathogenesis in ZIKV infection.
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Affiliation(s)
- Yufeng Yu
- Shanxi Provincial Key Laboratory for Functional Proteins, School of Basic Medical Sciences, Shanxi Medical University, Taiyuan, Shanxi, China
- * E-mail: (YY); (ZX)
| | - Chengfeng Gao
- Jiangsu Key Laboratory of Molecular Medicine, Medical school, Nanjing University, Nanjing, Jiangsu, China
| | - Chunxia Wen
- Jiangsu Key Laboratory of Molecular Medicine, Medical school, Nanjing University, Nanjing, Jiangsu, China
| | - Peng Zou
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Xian Qi
- Department of Acute Infectious Diseases Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, Jiangsu, China
| | - Carol J. Cardona
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine, University of Minnesota at Twin Cities, Saint Paul, Minnesota, United States of America
| | - Zheng Xing
- Jiangsu Key Laboratory of Molecular Medicine, Medical school, Nanjing University, Nanjing, Jiangsu, China
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine, University of Minnesota at Twin Cities, Saint Paul, Minnesota, United States of America
- * E-mail: (YY); (ZX)
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24
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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.
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25
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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.
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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.
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26
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Pant S, Bhattacharya G, Jena NR. Structures and dynamics of peptide and peptidomimetic inhibitors bound to the NS2B-NS3 protease of the ZIKA virus. J Biomol Struct Dyn 2022; 41:3076-3088. [PMID: 35238272 DOI: 10.1080/07391102.2022.2045223] [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: 10/18/2022]
Abstract
Infections caused by the Zika virus (ZIKV) have detrimental effects on human health, in particular on infants. As no potent drug or vaccine is available to date to contain this viral disease, it is necessary to design inhibitors that can target the NS2B-NS3 protease of the ZIKV, which is mainly responsible for the proliferation of the virus inside the host cells . Here, molecular dynamics (MD) simulation and molecular mechanics energies combined with the generalized Born and surface area continuum solvation model (MM/GBSA) are used to understand the binding modes and stabilities of R, KR, KKR, WKR, WKKR, YKKR, and FKKR peptide inhibitors bound to the NS3-NS2B protease. The results are compared with the corresponding results obtained for covalent (compound 1) and non-covalent (compound 4*) peptidomimetic inhibitors . It is revealed that peptide inhibitors can bind strongly with the ZIKV protease with the ΔGbind ranging from -12 kcal/mol to -73 kcal/mol. Among these peptides, YKKR is found to make the most stable complex with the protease and fully occupy the electrostatically active substrate binding site. Hence, it would inhibit the protease activities of ZIKV strongly. The residue-wise decomposition of ΔGbind indicates that Asp75, Asp129, Tyr130, Ser135, Gly151, Asn152, Glys153, and Tyr161 of NS3 and Ser81, Asp83, and Phe84 of NS2B play a prominent role in the inhibitor binding. Therefore, any future design of inhibitors should be aimed to target these residues.
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Affiliation(s)
- S Pant
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - G Bhattacharya
- Discipline of Natural Sciences, Indian Institute of Information Technology, Design and Manufacturing, Jabalpur, India
| | - N R Jena
- Discipline of Natural Sciences, Indian Institute of Information Technology, Design and Manufacturing, Jabalpur, India
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27
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Li Q, Kang C. Structures and Dynamics of Dengue Virus Nonstructural Membrane Proteins. MEMBRANES 2022; 12:membranes12020231. [PMID: 35207152 PMCID: PMC8880049 DOI: 10.3390/membranes12020231] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/11/2022] [Accepted: 02/15/2022] [Indexed: 02/01/2023]
Abstract
Dengue virus is an important human pathogen threating people, especially in tropical and sub-tropical regions. The viral genome has one open reading frame and encodes one polyprotein which can be processed into structural and nonstructural (NS) proteins. Four of the seven nonstructural proteins, NS2A, NS2B, NS4A and NS4B, are membrane proteins. Unlike NS3 or NS5, these proteins do not harbor any enzymatic activities, but they play important roles in viral replication through interactions with viral or host proteins to regulate important pathways and enzymatic activities. The location of these proteins on the cell membrane and the functional roles in viral replication make them important targets for antiviral development. Indeed, NS4B inhibitors exhibit antiviral activities in different assays. Structural studies of these proteins are hindered due to challenges in crystallization and the dynamic nature of these proteins. In this review, the function and membrane topologies of dengue nonstructural membrane proteins are presented. The roles of solution NMR spectroscopy in elucidating the structure and dynamics of these proteins are introduced. The success in the development of NS4B inhibitors proves that this class of proteins is an attractive target for antiviral development.
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Affiliation(s)
- Qingxin Li
- Guangdong Provincial Engineering Laboratory of Biomass High Value Utilization, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou 510316, China
- Correspondence: (Q.L.); (C.K.)
| | - Congbao Kang
- Experimental Drug Development Centre, Agency for Science, Technology and Research, 10 Biopolis Road, #5-01, Singapore 138670, Singapore
- Correspondence: (Q.L.); (C.K.)
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28
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Miao J, Yuan H, Rao J, Zou J, Yang K, Peng G, Cao S, Chen H, Song Y. Identification of a small compound that specifically inhibits Zika virus in vitro and in vivo by targeting the NS2B-NS3 protease. Antiviral Res 2022; 199:105255. [PMID: 35143853 DOI: 10.1016/j.antiviral.2022.105255] [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: 07/13/2021] [Revised: 01/14/2022] [Accepted: 01/25/2022] [Indexed: 11/02/2022]
Abstract
Zika virus (ZIKV) has rapid become a global threat, but no ZIKV-specific vaccines or drugs are currently available. In this study, inhibitors of ZIKV NS2B-NS3 protease were screened from a library containing 4,452 compound fragments. One of the compounds, 6-bromo-1,2-naphthalenedione, exhibited high specific inhibition against ZIKV NS2B-NS3 protease, but had no inhibitory effects against other viral proteases. A microscale thermophoresis (MST) assay confirmed that the compound bound to ZIKV NS2B-NS3 protein with a binding constant (Kd) of 12.26 μM. Indirect immunofluorescence assays, Western blots, and plaque assays indicated that the compound inhibited virus replication in cells. Virus titer was reduced by more than 75% when the compound was present at 1 μM. A time-of-addition assay showed that inhibition occurred at the virus replication stage, but not at the adsorption or invasion stages. The half cytotoxicity concentration (CC50) of the compound on HeLa, Vero, and BHK-21 cells were 445.44 μM, 123.87 μM, and 123.64 μM, respectively. In vivo tests using infected AG129 mice demonstrated that treatment with the compound reduced mortality by up to 60%. Mice treated with the compound showed a reduction in histopathological lesions in brain, testis, and ovary. Viral RNA, IL-1β, and IL-6 mRNA levels decreased significantly in these tissues. In summary, this study has identified a small compound with high and specific inhibitory effects on ZIKV. The compound can be used as a therapeutic agent and is also an ideal starting point for drug optimization.
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Affiliation(s)
- Juan Miao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; College of Animal Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Honggen Yuan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; College of Animal Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jingwei Rao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; College of Animal Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jiahui Zou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; College of Animal Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kelu Yang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; College of Animal Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guiqing Peng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; College of Animal Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shengbo Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; College of Animal Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; College of Animal Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yunfeng Song
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; College of Animal Science, Huazhong Agricultural University, Wuhan, 430070, China.
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29
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Yang X, Gao GF, Liu WJ. Powassan virus: A tick borne flavivirus infecting humans. BIOSAFETY AND HEALTH 2022. [DOI: 10.1016/j.bsheal.2021.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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30
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Abstract
Viral proteases are diverse in structure, oligomeric state, catalytic mechanism, and substrate specificity. This chapter focuses on proteases from viruses that are relevant to human health: human immunodeficiency virus subtype 1 (HIV-1), hepatitis C (HCV), human T-cell leukemia virus type 1 (HTLV-1), flaviviruses, enteroviruses, and coronaviruses. The proteases of HIV-1 and HCV have been successfully targeted for therapeutics, with picomolar FDA-approved drugs currently used in the clinic. The proteases of HTLV-1 and the other virus families remain emerging therapeutic targets at different stages of the drug development process. This chapter provides an overview of the current knowledge on viral protease structure, mechanism, substrate recognition, and inhibition. Particular focus is placed on recent advances in understanding the molecular basis of diverse substrate recognition and resistance, which is essential toward designing novel protease inhibitors as antivirals.
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Affiliation(s)
- Jacqueto Zephyr
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, United States
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, United States
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, United States.
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31
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Moraes TFS, Ferraz AC, da Cruz Nizer WS, Tótola AH, Soares DBS, Duarte LP, Vieira-Filho SA, Magalhães CLB, de Magalhães JC. A methanol extract and N,N-dimethyltryptamine from Psychotria viridis Ruiz & Pav. inhibit Zika virus infection in vitro. Arch Virol 2021; 166:3275-3287. [PMID: 34536126 DOI: 10.1007/s00705-021-05230-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/19/2021] [Indexed: 10/20/2022]
Abstract
Zika virus (ZIKV) is a public health problem due to its association with serious fetal and neurological complications and the lack of antiviral agents and licensed vaccines against this virus. Surveillance studies have alerted about the potential occurrence of a new South American epidemic episode due to the recent circulation of an African ZIKV strain detected in Brazil. Therefore, it is essential to discover antiviral agents, including natural substances, that are capable of neutralizing the action of ZIKV. Several Psychotria species have antimicrobial and anti-inflammatory properties. Thus, a methanol extract and dimethyltryptamine from Psychotria viridis were evaluated for their ability to inhibit ZIKV infection in vitro by measuring the effective concentration that protects 50% of cells and investigating their possible mechanisms of action. The tested samples showed antiviral activity against ZIKV. The extract showed virucidal activity, affecting viral and non-cellular elements, inactivating the virus before infection or when it becomes extracellular after the second cycle of infection. It was also observed that both extract and dimethyltryptamine could inhibit the virus at intracellular stages of the viral cycle. In addition to dimethyltryptamine, it is believed that other compounds also contribute to the promising virucidal effect observed for the methanol extract. To our knowledge, this is the first report of the activity of a methanolic extract and dimethyltryptamine from Psychotria viridis against cellular ZIKV infection. These two samples, extracted from natural sources, are potential candidates for use as antiviral drugs to inhibit ZIKV infections.
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Affiliation(s)
- Thaís F S Moraes
- Department of Chemistry, Biotechnology and Bioprocess Engineering, Universidade Federal de São João del-Rei, Rodovia MG 443, Km7, Ouro Branco, MG, 36420-000, Brazil.,Department of Microbiology, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, Belo Horizonte, MG, 31270-901, Brazil
| | - Ariane C Ferraz
- Department of Chemistry, Biotechnology and Bioprocess Engineering, Universidade Federal de São João del-Rei, Rodovia MG 443, Km7, Ouro Branco, MG, 36420-000, Brazil.,Department of Biological Sciences, Universidade Federal de Ouro Preto, Campus Morro do Cruzeiro, Ouro Prêto, MG, 35400-000, Brazil
| | - Waleska S da Cruz Nizer
- Department of Chemistry, Biotechnology and Bioprocess Engineering, Universidade Federal de São João del-Rei, Rodovia MG 443, Km7, Ouro Branco, MG, 36420-000, Brazil.,Department of Health Sciences, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Antônio H Tótola
- Department of Chemistry, Biotechnology and Bioprocess Engineering, Universidade Federal de São João del-Rei, Rodovia MG 443, Km7, Ouro Branco, MG, 36420-000, Brazil
| | - Débora B S Soares
- Department of Chemistry, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Lucienir P Duarte
- Department of Chemistry, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Sidney A Vieira-Filho
- Department of Pharmacy, Pharmacy's School, Universidade Federal de Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, MG, 35400-000, Brazil
| | - Cintia L B Magalhães
- Department of Biological Sciences, Universidade Federal de Ouro Preto, Campus Morro do Cruzeiro, Ouro Prêto, MG, 35400-000, Brazil
| | - José C de Magalhães
- Department of Chemistry, Biotechnology and Bioprocess Engineering, Universidade Federal de São João del-Rei, Rodovia MG 443, Km7, Ouro Branco, MG, 36420-000, Brazil.
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32
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Structure and Dynamics of Zika Virus Protease and Its Insights into Inhibitor Design. Biomedicines 2021; 9:biomedicines9081044. [PMID: 34440248 PMCID: PMC8394600 DOI: 10.3390/biomedicines9081044] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/04/2021] [Accepted: 08/16/2021] [Indexed: 12/16/2022] Open
Abstract
Zika virus (ZIKV)—a member of the Flaviviridae family—is an important human pathogen. Its genome encodes a polyprotein that can be further processed into structural and non-structural proteins. ZIKV protease is an important target for antiviral development due to its role in cleaving the polyprotein to release functional viral proteins. The viral protease is a two-component protein complex formed by NS2B and NS3. Structural studies using different approaches demonstrate that conformational changes exist in the protease. The structures and dynamics of this protease in the absence and presence of inhibitors were explored to provide insights into the inhibitor design. The dynamic nature of residues binding to the enzyme cleavage site might be important for the function of the protease. Due to the charges at the protease cleavage site, it is challenging to develop small-molecule compounds acting as substrate competitors. Developing small-molecule compounds to inhibit protease activity through an allosteric mechanism is a feasible strategy because conformational changes are observed in the protease. Herein, structures and dynamics of ZIKV protease are summarized. The conformational changes of ZIKV protease and other proteases in the same family are discussed. The progress in developing allosteric inhibitors is also described. Understanding the structures and dynamics of the proteases are important for designing potent inhibitors.
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33
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Could Probiotics and Postbiotics Function as "Silver Bullet" in the Post-COVID-19 Era? Probiotics Antimicrob Proteins 2021; 13:1499-1507. [PMID: 34386940 PMCID: PMC8360758 DOI: 10.1007/s12602-021-09833-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2021] [Indexed: 12/14/2022]
Abstract
We are currently experiencing the realities of the most severe pandemic within living memory, with major impacts on the health and economic well-being of our planet. The scientific community has demonstrated an unprecedented mobilization capability, with the rapid development of vaccines and drugs targeting the protection of human life and palliative measures for infected individuals. However, are we adequately prepared for ongoing defense against COVID-19 and its variants in the post-pandemic world? Moreover, are we equipped to provide a satisfactory quality of life for individuals who are recovering from COVID-19 disease? What are the possibilities for the acceleration of the recovery process? Here, we give special consideration to the potential and already-demonstrated role of probiotics and traditional medical approaches to the management of current and potential future encounters with our major virus adversaries.
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34
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Amidoxime prodrugs convert to potent cell-active multimodal inhibitors of the dengue virus protease. Eur J Med Chem 2021; 224:113695. [PMID: 34298282 DOI: 10.1016/j.ejmech.2021.113695] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 12/16/2022]
Abstract
The flavivirus genus of the Flaviviridae family comprises Dengue, Zika and West-Nile viruses which constitute unmet medical needs as neither appropriate antivirals nor safe vaccines are available. The dengue NS2BNS3 protease is one of the most promising validated targets for developing a dengue treatment however reported protease inhibitors suffer from toxicity and cellular inefficacy. Here we report SAR on our previously reported Zika-active carbazole scaffold, culminating prodrug compound SP-471P (EC50 1.10 μM, CC50 > 100 μM) that generates SP-471; one of the most potent, non-cytotoxic and cell-active protease inhibitors described in the dengue literature. In cell-based assays, SP-471P leads to inhibition of viral RNA replication and complete abolishment of infective viral particle production even when administered 6 h post-infection. Mechanistically, SP-471 appears to inhibit both normal intermolecular protease processes and intramolecular cleavage events at the NS2BNS3 junction, as well as at NS3 internal sites, all critical for virus replication. These render SP-471 a unique to date multimodal inhibitor of the dengue protease.
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35
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Zhao R, Wang M, Cao J, Shen J, Zhou X, Wang D, Cao J. Flavivirus: From Structure to Therapeutics Development. Life (Basel) 2021; 11:life11070615. [PMID: 34202239 PMCID: PMC8303334 DOI: 10.3390/life11070615] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/16/2021] [Accepted: 06/22/2021] [Indexed: 12/25/2022] Open
Abstract
Flaviviruses are still a hidden threat to global human safety, as we are reminded by recent reports of dengue virus infections in Singapore and African-lineage-like Zika virus infections in Brazil. Therapeutic drugs or vaccines for flavivirus infections are in urgent need but are not well developed. The Flaviviridae family comprises a large group of enveloped viruses with a single-strand RNA genome of positive polarity. The genome of flavivirus encodes ten proteins, and each of them plays a different and important role in viral infection. In this review, we briefly summarized the major information of flavivirus and further introduced some strategies for the design and development of vaccines and anti-flavivirus compound drugs based on the structure of the viral proteins. There is no doubt that in the past few years, studies of antiviral drugs have achieved solid progress based on better understanding of the flavivirus biology. However, currently, there are no fully effective antiviral drugs or vaccines for most flaviviruses. We hope that this review may provide useful information for future development of anti-flavivirus drugs and vaccines.
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Affiliation(s)
- Rong Zhao
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan 030001, China; (R.Z.); (M.W.); (J.C.); (J.S.)
- Department of Physiology, Shanxi Medical University, Taiyuan 030001, China
| | - Meiyue Wang
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan 030001, China; (R.Z.); (M.W.); (J.C.); (J.S.)
- Department of Physiology, Shanxi Medical University, Taiyuan 030001, China
| | - Jing Cao
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan 030001, China; (R.Z.); (M.W.); (J.C.); (J.S.)
- Department of Physiology, Shanxi Medical University, Taiyuan 030001, China
| | - Jing Shen
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan 030001, China; (R.Z.); (M.W.); (J.C.); (J.S.)
- Department of Physiology, Shanxi Medical University, Taiyuan 030001, China
| | - Xin Zhou
- Department of Medical Imaging, Shanxi Medical University, Taiyuan 030001, China;
| | - Deping Wang
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan 030001, China; (R.Z.); (M.W.); (J.C.); (J.S.)
- Department of Physiology, Shanxi Medical University, Taiyuan 030001, China
- Correspondence: (D.W.); (J.C.)
| | - Jimin Cao
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan 030001, China; (R.Z.); (M.W.); (J.C.); (J.S.)
- Department of Physiology, Shanxi Medical University, Taiyuan 030001, China
- Correspondence: (D.W.); (J.C.)
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36
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Molecular Insights into the Flavivirus Replication Complex. Viruses 2021; 13:v13060956. [PMID: 34064113 PMCID: PMC8224304 DOI: 10.3390/v13060956] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 05/17/2021] [Accepted: 05/17/2021] [Indexed: 12/11/2022] Open
Abstract
Flaviviruses are vector-borne RNA viruses, many of which are clinically relevant human viral pathogens, such as dengue, Zika, Japanese encephalitis, West Nile and yellow fever viruses. Millions of people are infected with these viruses around the world each year. Vaccines are only available for some members of this large virus family, and there are no effective antiviral drugs to treat flavivirus infections. The unmet need for vaccines and therapies against these flaviviral infections drives research towards a better understanding of the epidemiology, biology and immunology of flaviviruses. In this review, we discuss the basic biology of the flavivirus replication process and focus on the molecular aspects of viral genome replication. Within the virus-induced intracellular membranous compartments, flaviviral RNA genome replication takes place, starting from viral poly protein expression and processing to the assembly of the virus RNA replication complex, followed by the delivery of the progeny viral RNA to the viral particle assembly sites. We attempt to update the latest understanding of the key molecular events during this process and highlight knowledge gaps for future studies.
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37
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Kumar N, Sarma H, Sastry GN. Repurposing of approved drug molecules for viral infectious diseases: a molecular modelling approach. J Biomol Struct Dyn 2021; 40:8056-8072. [PMID: 33810775 DOI: 10.1080/07391102.2021.1905558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The identification of new viral drugs has become a task of paramount significance due to the frequent occurrence of viral infections and especially during the current pandemic. Despite the recent advancements, the development of antiviral drugs has not made parallel progress. Reduction of time frame and cost of the drug development process is the major advantage of drug repurposing. Therefore, in this study, a drug repurposing strategy using molecular modelling techniques, i.e. biological activity prediction, virtual screening, and molecular dynamics simulation was employed to find promising repurposing candidates for viral infectious diseases. The biological activities of non-redundant (4171) drug molecules were predicted using PASS analysis, and 1401 drug molecules were selected which showed antiviral activities in the analysis. These drug molecules were subjected to virtual screening against the selected non-structural viral proteins. A series of filters, i.e. top 10 drug molecules based on binding affinity, mean value of binding affinity, visual inspection of protein-drug complexes, and number of H-bond between protein and drug molecules were used to narrow down the drug molecules. Molecular dynamics simulation analysis was carried out to validate the intrinsic atomic interactions and binding conformations of protein-drug complexes. The binding free energies of drug molecules were assessed by employing MMPBSA analysis. Finally, nine drug molecules were prioritized, as promising repurposing candidates with the potential to inhibit the selected non-structural viral proteins.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nandan Kumar
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Hyderabad, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Himakshi Sarma
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, India
| | - G Narahari Sastry
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Hyderabad, India.,Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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38
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Lima CS, Mottin M, de Assis LR, Mesquita NCDMR, Sousa BKDP, Coimbra LD, Santos KBD, Zorn KM, Guido RVC, Ekins S, Marques RE, Proença-Modena JL, Oliva G, Andrade CH, Regasini LO. Flavonoids from Pterogyne nitens as Zika virus NS2B-NS3 protease inhibitors. Bioorg Chem 2021; 109:104719. [PMID: 33636437 PMCID: PMC8227833 DOI: 10.1016/j.bioorg.2021.104719] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 01/26/2021] [Accepted: 02/02/2021] [Indexed: 12/18/2022]
Abstract
Although the widespread epidemic of Zika virus (ZIKV) and its neurological complications are well-known there are still no approved drugs available to treat this arboviral disease or vaccine to prevent the infection. Flavonoids from Pterogyne nitens have already demonstrated anti-flavivirus activity, although their target is unknown. In this study, we virtually screened an in-house database of 150 natural and semi-synthetic compounds against ZIKV NS2B-NS3 protease (NS2B-NS3p) using docking-based virtual screening, as part of the OpenZika project. As a result, we prioritized three flavonoids from P. nitens, quercetin, rutin and pedalitin, for experimental evaluation. We also used machine learning models, built with Assay Central® software, for predicting the activity and toxicity of these flavonoids. Biophysical and enzymatic assays generally agreed with the in silico predictions, confirming that the flavonoids inhibited ZIKV protease. The most promising hit, pedalitin, inhibited ZIKV NS2B-NS3p with an IC50 of 5 μM. In cell-based assays, pedalitin displayed significant activity at 250 and 500 µM, with slight toxicity in Vero cells. The results presented here demonstrate the potential of pedalitin as a candidate for hit-to-lead (H2L) optimization studies towards the discovery of antiviral drug candidates to treat ZIKV infections.
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Affiliation(s)
- Caroline Sprengel Lima
- Laboratory of Antibiotics and Chemotherapeutics (LAQ), Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), São José do Rio Preto, SP, Brazil
| | - Melina Mottin
- Laboratory of Molecular Modeling and Drug Design (LabMol), Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Leticia Ribeiro de Assis
- Laboratory of Antibiotics and Chemotherapeutics (LAQ), Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), São José do Rio Preto, SP, Brazil
| | | | - Bruna Katiele de Paula Sousa
- Laboratory of Molecular Modeling and Drug Design (LabMol), Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Lais Durco Coimbra
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | - Karina Bispo-Dos- Santos
- Laboratory of Emerging Viruses (LEVE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Kimberley M Zorn
- Collaborations Pharmaceuticals, Inc., Raleigh, NC, United States
| | - Rafael V C Guido
- Institute of Physics of São Carlos, University of São Paulo, São Carlos, SP, Brazil
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., Raleigh, NC, United States
| | - Rafael Elias Marques
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | - José Luiz Proença-Modena
- Laboratory of Emerging Viruses (LEVE), Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Glaucius Oliva
- Institute of Physics of São Carlos, University of São Paulo, São Carlos, SP, Brazil
| | - Carolina Horta Andrade
- Laboratory of Molecular Modeling and Drug Design (LabMol), Faculdade de Farmácia, Universidade Federal de Goiás, Goiânia, GO, Brazil.
| | - Luis Octavio Regasini
- Laboratory of Antibiotics and Chemotherapeutics (LAQ), Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), São José do Rio Preto, SP, Brazil.
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Structure-Based Virtual Screening: Identification of a Novel NS2B-NS3 Protease Inhibitor with Potent Antiviral Activity against Zika and Dengue Viruses. Microorganisms 2021; 9:microorganisms9030545. [PMID: 33800763 PMCID: PMC8000814 DOI: 10.3390/microorganisms9030545] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/25/2021] [Accepted: 03/02/2021] [Indexed: 11/16/2022] Open
Abstract
Zika virus (ZIKV), which is associated with severe diseases in humans, has spread rapidly and globally since its emergence. ZIKV and dengue virus (DENV) are closely related, and antibody-dependent enhancement (ADE) of infection between cocirculating ZIKV and DENV may exacerbate disease. Despite these serious threats, there are currently no approved antiviral drugs against ZIKV and DENV. The NS2B-NS3 viral protease is an attractive antiviral target because it plays a pivotal role in polyprotein cleavage, which is required for viral replication. Thus, we sought to identify novel inhibitors of the NS2B-NS3 protease. To that aim, we performed structure-based virtual screening using 467,000 structurally diverse chemical compounds. Then, a fluorescence-based protease inhibition assay was used to test whether the selected candidates inhibited ZIKV protease activity. Among the 123 candidate inhibitors selected from virtual screening, compound 1 significantly inhibited ZIKV NS2B-NS3 protease activity in vitro. In addition, compound 1 effectively inhibited ZIKV and DENV infection of human cells. Molecular docking analysis suggested that compound 1 binds to the NS2B-NS3 protease of ZIKV and DENV. Thus, compound 1 could be used as a new therapeutic option for the development of more potent antiviral drugs against both ZIKV and DENV, reducing the risks of ADE.
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40
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Nie S, Yao Y, Wu F, Wu X, Zhao J, Hua Y, Wu J, Huo T, Lin YL, Kneubehl AR, Vogt MB, Ferreon J, Rico-Hesse R, Song Y. Synthesis, Structure-Activity Relationships, and Antiviral Activity of Allosteric Inhibitors of Flavivirus NS2B-NS3 Protease. J Med Chem 2021; 64:2777-2800. [PMID: 33596380 DOI: 10.1021/acs.jmedchem.0c02070] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Flaviviruses, including Zika, dengue, and West Nile viruses, are important human pathogens. The highly conserved NS2B-NS3 protease of Flavivirus is essential for viral replication and therefore a promising drug target. Through compound screening, followed by medicinal chemistry studies, a novel series of 2,5,6-trisubstituted pyrazine compounds are found to be potent, allosteric inhibitors of Zika virus protease (ZVpro) with IC50 values as low as 130 nM. Their structure-activity relationships are discussed. The ZVpro inhibitors also inhibit homologous proteases of dengue and West Nile viruses, and their inhibitory activities are correlated. The most potent compounds 47 and 103 potently inhibited Zika virus replication in cells with EC68 values of 300-600 nM and in a mouse model of Zika infection. These compounds represent novel pharmacological leads for drug development against Flavivirus infections.
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Affiliation(s)
- Shenyou Nie
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United States
| | - Yuan Yao
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United States
| | - Fangrui Wu
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United States
| | - Xiaowei Wu
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United States
| | - Jidong Zhao
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United States
| | - Yuanda Hua
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United States
| | - Jingyu Wu
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United States
| | - Tong Huo
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United States
| | - Yi-Lun Lin
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United States
| | - Alexander R Kneubehl
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United States
| | - Megan B Vogt
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United States.,Intragrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United States
| | - Josephine Ferreon
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United States
| | - Rebecca Rico-Hesse
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United States
| | - Yongcheng Song
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United States
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41
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Song W, Zhang H, Zhang Y, Li R, Han Y, Lin Y, Jiang J. Repurposing clinical drugs is a promising strategy to discover drugs against Zika virus infection. Front Med 2020; 15:404-415. [PMID: 33369711 PMCID: PMC7768800 DOI: 10.1007/s11684-021-0834-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 10/14/2020] [Indexed: 12/19/2022]
Abstract
Zika virus (ZIKV) is an emerging pathogen associated with neurological complications, such as Guillain-Barré syndrome in adults and microcephaly in fetuses and newborns. This mosquito-borne flavivirus causes important social and sanitary problems owing to its rapid dissemination. However, the development of antivirals against ZIKV is lagging. Although various strategies have been used to study anti-ZIKV agents, approved drugs or vaccines for the treatment (or prevention) of ZIKV infections are currently unavailable. Repurposing clinically approved drugs could be an effective approach to quickly respond to an emergency outbreak of ZIKV infections. The well-established safety profiles and optimal dosage of these clinically approved drugs could provide an economical, safe, and efficacious approach to address ZIKV infections. This review focuses on the recent research and development of agents against ZIKV infection by repurposing clinical drugs. Their characteristics, targets, and potential use in anti-ZIKV therapy are presented. This review provides an update and some successful strategies in the search for anti-ZIKV agents are given.
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Affiliation(s)
- Weibao Song
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Hongjuan Zhang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Yu Zhang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Rui Li
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Yanxing Han
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Yuan Lin
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| | - Jiandong Jiang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
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42
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Therapeutic candidates for the Zika virus identified by a high-throughput screen for Zika protease inhibitors. Proc Natl Acad Sci U S A 2020; 117:31365-31375. [PMID: 33229545 DOI: 10.1073/pnas.2005463117] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
When Zika virus emerged as a public health emergency there were no drugs or vaccines approved for its prevention or treatment. We used a high-throughput screen for Zika virus protease inhibitors to identify several inhibitors of Zika virus infection. We expressed the NS2B-NS3 Zika virus protease and conducted a biochemical screen for small-molecule inhibitors. A quantitative structure-activity relationship model was employed to virtually screen ∼138,000 compounds, which increased the identification of active compounds, while decreasing screening time and resources. Candidate inhibitors were validated in several viral infection assays. Small molecules with favorable clinical profiles, especially the five-lipoxygenase-activating protein inhibitor, MK-591, inhibited the Zika virus protease and infection in neural stem cells. Members of the tetracycline family of antibiotics were more potent inhibitors of Zika virus infection than the protease, suggesting they may have multiple mechanisms of action. The most potent tetracycline, methacycline, reduced the amount of Zika virus present in the brain and the severity of Zika virus-induced motor deficits in an immunocompetent mouse model. As Food and Drug Administration-approved drugs, the tetracyclines could be quickly translated to the clinic. The compounds identified through our screening paradigm have the potential to be used as prophylactics for patients traveling to endemic regions or for the treatment of the neurological complications of Zika virus infection.
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43
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Maiti BK, Govil N, Kundu T, Moura JJG. Designed Metal-ATCUN Derivatives: Redox- and Non-redox-Based Applications Relevant for Chemistry, Biology, and Medicine. iScience 2020; 23:101792. [PMID: 33294799 PMCID: PMC7701195 DOI: 10.1016/j.isci.2020.101792] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
The designed “ATCUN” motif (amino-terminal copper and nickel binding site) is a replica of naturally occurring ATCUN site found in many proteins/peptides, and an attractive platform for multiple applications, which include nucleases, proteases, spectroscopic probes, imaging, and small molecule activation. ATCUN motifs are engineered at periphery by conjugation to recombinant proteins, peptides, fluorophores, or recognition domains through chemically or genetically, fulfilling the needs of various biological relevance and a wide range of practical usages. This chemistry has witnessed significant growth over the last few decades and several interesting ATCUN derivatives have been described. The redox role of the ATCUN moieties is also an important aspect to be considered. The redox potential of designed M-ATCUN derivatives is modulated by judicious choice of amino acid (including stereochemistry, charge, and position) that ultimately leads to the catalytic efficiency. In this context, a wide range of M-ATCUN derivatives have been designed purposefully for various redox- and non-redox-based applications, including spectroscopic probes, target-based catalytic metallodrugs, inhibition of amyloid-β toxicity, and telomere shortening, enzyme inactivation, biomolecules stitching or modification, next-generation antibiotic, and small molecule activation.
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Affiliation(s)
- Biplab K Maiti
- National Institute of Technology Sikkim, Ravangla Campus, Barfung Block, Ravangla Sub Division, South Sikkim 737139, India
| | - Nidhi Govil
- National Institute of Technology Sikkim, Ravangla Campus, Barfung Block, Ravangla Sub Division, South Sikkim 737139, India
| | - Taraknath Kundu
- National Institute of Technology Sikkim, Ravangla Campus, Barfung Block, Ravangla Sub Division, South Sikkim 737139, India
| | - José J G Moura
- LAQV-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, 2829-516 Caparica, Portugal
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44
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Cui X, Zhou R, Huang C, Zhang R, Wang J, Zhang Y, Ding J, Li X, Zhou J, Cen S. Identification of Theaflavin-3,3'-Digallate as a Novel Zika Virus Protease Inhibitor. Front Pharmacol 2020; 11:514313. [PMID: 33192499 PMCID: PMC7609463 DOI: 10.3389/fphar.2020.514313] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 09/18/2020] [Indexed: 11/21/2022] Open
Abstract
Mounting evidence indicates that Zika virus (ZIKV) is closely related to neurological disorders such as microcephaly and Guillain-Barré syndrome. There are currently no effective vaccines and FDA-approved inhibitors against ZIKV infection. The flaviviral heterodimeric serine protease NS2B-NS3 plays an essential role in ZIKV maturation and replication, thus becoming a promising target in anti-ZIKV therapy. Herein, we developed a fluorescence-based screening assay to search for inhibitors targeting the ZIKV NS2B-NS3 protease (ZIKVpro), and identified theaflavin-3,3’-digallate (ZP10), a natural active compound derived from black tea, as a potent ZIKV protease inhibitor in vitro (IC50 = 2.3 μM). ZP10 exhibited dose-dependent inhibitory effect on ZIKV replication (EC50 = 7.65 μM). Western blot analysis suggested that ZP10 inhibited the cleavage processing of viral polyprotein precursor in cells either infected with ZIKV or expressing minimal self-cleaving proteinase NS2B-3 protease, resulting in inhibition of virus growth. Moreover, ZP10 was showed to directly bind to ZIKVpro, and a docking model further revealed that ZP10 interacted with several critical residues at the proteolytic cavity of the ZIKVpro. This study highlights that ZP10 has anti-ZIKV potency through ZIKVpro inhibition, which indicates its potential application in anti-ZIKV therapy.
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Affiliation(s)
- Xiangling Cui
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing, China
| | - Rui Zhou
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing, China
| | - Chenchao Huang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, Jinhua, China.,Drug Discovery & Innovation Center, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, China
| | - Rongyu Zhang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, Jinhua, China.,Drug Discovery & Innovation Center, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, China
| | - Jing Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing, China
| | - Yongxin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing, China
| | - Jiwei Ding
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing, China.,CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaoyu Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing, China
| | - Jinming Zhou
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing, China.,Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, Jinhua, China.,Drug Discovery & Innovation Center, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, China
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing, China.,CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Institute of Tropical Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, China
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45
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Li Z, Xu J, Lang Y, Fan X, Kuo L, D'Brant L, Hu S, Samrat SK, Trudeau N, Tharappel AM, Rugenstein N, Koetzner CA, Zhang J, Chen H, Kramer LD, Butler D, Zhang QY, Zhou J, Li H. JMX0207, a Niclosamide Derivative with Improved Pharmacokinetics, Suppresses Zika Virus Infection Both In Vitro and In Vivo. ACS Infect Dis 2020; 6:2616-2628. [PMID: 32866370 PMCID: PMC7559020 DOI: 10.1021/acsinfecdis.0c00217] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Flaviviruses causes significant human disease. Recent outbreaks of the Zika virus highlight the need to develop effective therapies for this class of viruses. Previously we identified niclosamide as a broad-spectrum inhibitor for flaviviruses by targeting the interface between viral protease NS3 and its cofactor NS2B. Here, we screened a small library of niclosamide derivatives and identified a new analogue with improved pharmacokinetic properties. Compound JMX0207 showed improved efficacy in inhibition of the molecular interaction between NS3 and NS2B, better inhibition of viral protease function, and enhanced antiviral efficacy in the cell-based antiviral assay. The derivative also significantly reduced Zika virus infection on 3D mini-brain organoids derived from pluripotent neural stem cells. Intriguingly, the compound significantly reduced viremia in a Zika virus (ZIKV) animal model. In summary, a niclosamide derivative, JMX0207, was identified, which shows improved pharmacokinetics and efficacy against Zika virus both in vitro and in vivo.
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Affiliation(s)
- Zhong Li
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, New York 12208, United States
| | - Jimin Xu
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Yuekun Lang
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, New York 12208, United States
| | - Xiaoyu Fan
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Lili Kuo
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, New York 12208, United States
| | - Lianna D'Brant
- The Neural Stem Cell Institute, 1 Discovery Drive, Rensselaer, New York 12144, United States
| | - Saiyang Hu
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, New York 12208, United States
| | - Subodh Kumar Samrat
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, New York 12208, United States
| | - Nicole Trudeau
- The Neural Stem Cell Institute, 1 Discovery Drive, Rensselaer, New York 12144, United States
| | - Anil M Tharappel
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, New York 12208, United States
| | - Natasha Rugenstein
- The Neural Stem Cell Institute, 1 Discovery Drive, Rensselaer, New York 12144, United States
| | - Cheri A Koetzner
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, New York 12208, United States
| | - Jing Zhang
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, New York 12208, United States
| | - Haiying Chen
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Laura D Kramer
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, New York 12208, United States
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York 12201, United States
| | - David Butler
- The Neural Stem Cell Institute, 1 Discovery Drive, Rensselaer, New York 12144, United States
| | - Qing-Yu Zhang
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Hongmin Li
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, New York 12208, United States
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York 12201, United States
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46
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Karwal P, Vats ID, Sinha N, Singhal A, Sehgal T, Kumari P. Therapeutic Applications of Peptides against Zika Virus: A Review. Curr Med Chem 2020; 27:3906-3923. [DOI: 10.2174/0929867326666190111115132] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 11/22/2018] [Accepted: 12/28/2018] [Indexed: 01/27/2023]
Abstract
Zika Virus (ZIKV) belongs to the class of flavivirus that can be transmitted by Aedes
mosquitoes. The number of Zika virus caused cases of acute infections, neurological disorders and
congenital microcephaly are rapidly growing and therefore, in 2016, the World Health Organization
declared a global “Public Health Emergency of International Concern”. Anti-ZIKV therapeutic and
vaccine development strategies are growing worldwide in recent years, however, no specific and safe
treatment is available till date to save the human life. Currently, development of peptide therapeutics
against ZIKV has attracted rising attention on account of their high safety concern and low development
cost, in comparison to small therapeutic molecules and antibody-based anti-viral drugs. In present
review, an overview of ZIKV inhibition by peptide-based inhibitors including E-protein derived
peptides, antimicrobial peptides, frog skin peptides and probiotic peptides has been discussed. Peptides
inhibitors have also been reported to act against NS5, NS2B-NS3 protease and proteasome in
order to inhibit ZIKV infection. Recent advances in peptide-based therapeutics and vaccine have
been reviewed and their future promise against ZIKV infections has been explored.
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Affiliation(s)
- Preeti Karwal
- Department of Biochemistry, Deshbandhu College, University of Delhi, Delhi-110019, India
| | - Ishwar Dutt Vats
- Department of Chemistry, Deshbandhu College, University of Delhi, Delhi-110019, India
| | - Niharika Sinha
- Drug Development Laboratory Group, Gautam Buddha University, Noida, India
| | - Anchal Singhal
- Department of Chemistry, St. Joseph's College, Bengaluru, Karnataka, India
| | - Teena Sehgal
- Department of Chemistry, HMRITM, GGSIP University, New Delhi, India
| | - Pratibha Kumari
- Department of Chemistry, Deshbandhu College, University of Delhi, Delhi-110019, India
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47
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Pathak N, Kuo YP, Chang TY, Huang CT, Hung HC, Hsu JTA, Yu GY, Yang JM. Zika Virus NS3 Protease Pharmacophore Anchor Model and Drug Discovery. Sci Rep 2020; 10:8929. [PMID: 32488021 PMCID: PMC7265434 DOI: 10.1038/s41598-020-65489-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 04/29/2020] [Indexed: 11/28/2022] Open
Abstract
Zika virus (ZIKV) of the flaviviridae family, is the cause of emerging infections characterized by fever, Guillain-Barré syndrome (GBS) in adults and microcephaly in newborns. There exists an urgent unmet clinical need for anti-ZIKV drugs for the treatment of infected individuals. In the current work, we aimed at the promising virus drug target, ZIKV NS3 protease and constructed a Pharmacophore Anchor (PA) model for the active site. The PA model reveals a total of 12 anchors (E, H, V) mapped across the active site subpockets. We further identified five of these anchors to be critical core anchors (CEH1, CH3, CH7, CV1, CV3) conserved across flaviviral proteases. The ZIKV protease PA model was then applied in anchor-enhanced virtual screening yielding 14 potential antiviral candidates, which were tested by in vitro assays. We discovered FDA drugs Asunaprevir and Simeprevir to have potent anti-ZIKV activities with EC50 values 4.7 µM and 0.4 µM, inhibiting the viral protease with IC50 values 6.0 µM and 2.6 µM respectively. Additionally, the PA model anchors aided in the exploration of inhibitor binding mechanisms. In conclusion, our PA model serves as a promising guide map for ZIKV protease targeted drug discovery and the identified ‘previr’ FDA drugs are promising for anti-ZIKV treatments.
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Affiliation(s)
- Nikhil Pathak
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, 11529, Taiwan.,Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Yi-Ping Kuo
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, 35053, Taiwan
| | - Teng-Yuan Chang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, 35053, Taiwan
| | - Chin-Ting Huang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, 35053, Taiwan
| | - Hui-Chen Hung
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, 35053, Taiwan
| | - John Tsu-An Hsu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, 35053, Taiwan
| | - Guann-Yi Yu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, 35053, Taiwan
| | - Jinn-Moon Yang
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, 11529, Taiwan. .,Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 30010, Taiwan. .,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 30010, Taiwan.
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48
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Insights into Structures and Dynamics of Flavivirus Proteases from NMR Studies. Int J Mol Sci 2020; 21:ijms21072527. [PMID: 32260545 PMCID: PMC7177695 DOI: 10.3390/ijms21072527] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 03/29/2020] [Accepted: 03/31/2020] [Indexed: 12/29/2022] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy plays important roles in structural biology and drug discovery, as it is a powerful tool to understand protein structures, dynamics, and ligand binding under physiological conditions. The protease of flaviviruses is an attractive target for developing antivirals because it is essential for the maturation of viral proteins. High-resolution structures of the proteases in the absence and presence of ligands/inhibitors were determined using X-ray crystallography, providing structural information for rational drug design. Structural studies suggest that proteases from Dengue virus (DENV), West Nile virus (WNV), and Zika virus (ZIKV) exist in open and closed conformations. Solution NMR studies showed that the closed conformation is predominant in solution and should be utilized in structure-based drug design. Here, we reviewed solution NMR studies of the proteases from these viruses. The accumulated studies demonstrated that NMR spectroscopy provides additional information to understand conformational changes of these proteases in the absence and presence of substrates/inhibitors. In addition, NMR spectroscopy can be used for identifying fragment hits that can be further developed into potent protease inhibitors.
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49
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Identification and structural characterization of small molecule fragments targeting Zika virus NS2B-NS3 protease. Antiviral Res 2020; 175:104707. [PMID: 31953156 DOI: 10.1016/j.antiviral.2020.104707] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 01/06/2020] [Accepted: 01/08/2020] [Indexed: 11/23/2022]
Abstract
Zika virus (ZIKV) NS2B-NS3 protease is a validated antiviral target as it is essential for maturation of viral proteins. However, its negatively charged active site hinders the development of orthosteric small-molecule inhibitors. Fragment-based drug discovery (FBDD) is a powerful tool to generate novel chemical starting points against difficult drug targets. In this study, we scre ened a fragment compound library against the Zika protease using a primary thermal shift assay and identified twenty-two fragments which (bind to and) stabilize the protease. We then determined the X-ray crystal structures of two hits from different classes, all of which bind to the S1 pocket of the protease. We confirmed that these two fragments bind to the protease without inducing significant conformational changes using solution NMR spectroscopy. These fragment scaffolds serve as the starting point for subsequent lead compound development.
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50
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Voss S, Nitsche C. Inhibitors of the Zika virus protease NS2B-NS3. Bioorg Med Chem Lett 2020; 30:126965. [PMID: 31980339 DOI: 10.1016/j.bmcl.2020.126965] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 02/09/2023]
Abstract
In recent years, the Zika virus has emerged from a neglected flavivirus to a health-threatening pathogen that causes epidemic outbreaks associated with neurological disorders and congenital malformations. In addition to vaccine development, the discovery of specific antiviral agents has been pursued intensely. The Zika virus protease NS2B-NS3 catalyses the processing of the viral precursor polyprotein as an essential step during viral replication. Since the epidemic Zika virus outbreak in the Americas, several inhibitors of this protease have been reported. Substrate-derived peptides revealed important structural information about the active site, whilst more drug-like small molecules have been discovered as allosteric inhibitors.
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Affiliation(s)
- Saan Voss
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
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