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Starvaggi J, Previti S, Zappalà M, Ettari R. The Inhibition of NS2B/NS3 Protease: A New Therapeutic Opportunity to Treat Dengue and Zika Virus Infection. Int J Mol Sci 2024; 25:4376. [PMID: 38673962 PMCID: PMC11050111 DOI: 10.3390/ijms25084376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 04/12/2024] [Accepted: 04/14/2024] [Indexed: 04/28/2024] Open
Abstract
In the global pandemic scenario, dengue and zika viruses (DENV and ZIKV, respectively), both mosquito-borne members of the flaviviridae family, represent a serious health problem, and considering the absence of specific antiviral drugs and available vaccines, there is a dire need to identify new targets to treat these types of viral infections. Within this drug discovery process, the protease NS2B/NS3 is considered the primary target for the development of novel anti-flavivirus drugs. The NS2B/NS3 is a serine protease that has a dual function both in the viral replication process and in the elusion of the innate immunity. To date, two main classes of NS2B/NS3 of DENV and ZIKV protease inhibitors have been discovered: those that bind to the orthosteric site and those that act at the allosteric site. Therefore, this perspective article aims to discuss the main features of the use of the most potent NS2B/NS3 inhibitors and their impact at the social level.
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Affiliation(s)
| | | | | | - Roberta Ettari
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d’Alcontres 31, 98166 Messina, Italy; (J.S.); (S.P.); (M.Z.)
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2
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Purohit P, Barik D, Dansana J, Meher BR. Investigating Lycotoxin-An1a (An1a), a defense antiviral peptide from Alopecosa nagpag venom as prospective anti-dengue agent against DENV-2 NS2B-NS3 protease. Comput Biol Chem 2024; 108:108005. [PMID: 38157660 DOI: 10.1016/j.compbiolchem.2023.108005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 12/02/2023] [Accepted: 12/13/2023] [Indexed: 01/03/2024]
Abstract
Dengue fever is a global health concern with no effective therapy. Screening synthetic chemicals, animal-originated compounds, and phytocompounds against Dengue virus (DENV) targets has failed to find dengue antivirals. The current study examines animal drugs as antagonists against NS2B-NS3Pro, one of DENV's most promising therapeutic targets for dengue fever. Antiviral-Lycotoxin-An1a (An1a), a defence antiviral peptide isolated from the venom of Alopecosa nagpag, a toxic spider. Based on prior in vitro research, it was discovered that the venom peptide suppresses the action of DENV-2 NS2B-NS3Pro. An1a peptide with NS2B-NS3Pro wild type (WT) and two mutants (H51N and S135A) was tested for anti-dengue characteristics using in silico analysis. The WT NS2B-NS3Pro has a catalytic triad of His51, Asp75, and Ser135 in the active site, but the mutants have N51 instead of His51 and Ala135 instead of Ser135. The dynamic sites of the three proteases (WT, H51N, S135A) and the peptide toxin (An1a) were taken into account to achieve molecular docking of An1a with WT NS2B-NS3Pro in conjunction with H51N and S135A. Cluspro-2 performs rigid-flexible docking to predict peptide binding affinity, effectiveness, and inhibitory consistency. Since the ligand had a higher binding affinity, docking score, and molecular interaction network, MD simulations and MM-GBSA free energy calculations were used to investigate the stability of the three protein-peptide complexes. The computer-aided screening and manufacture of spider venom-based anti-dengue medicines yielded intriguing results in the preliminary studies. This study is significant in defining the ideal therapeutic candidate against dengue infections.
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Affiliation(s)
- Priyanka Purohit
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, Odisha760007, India
| | - Debashis Barik
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, Odisha760007, India
| | - Jarmani Dansana
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, Odisha760007, India
| | - Biswa Ranjan Meher
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, Odisha760007, India.
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3
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Rabaan AA, AlShehail BM, Halwani MA, Alshengeti A, Najim MA, Garout M, Bajunaid HA, Alshamrani SA, Al Fares MA, Alissa M, Alwashmi ASS. Investigation of Zika virus methyl transferase inhibitors using steered molecular dynamics. J Biomol Struct Dyn 2024; 42:1711-1724. [PMID: 37325855 DOI: 10.1080/07391102.2023.2224882] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 04/05/2023] [Indexed: 06/17/2023]
Abstract
Zika virus (ZIKV) spread is considered a major public health threat by the World Health Organization (WHO). There are no vaccines or drugs available to control the infection of the Zika virus, therefore a highly effective medicinal molecule is urgently required. In this study, a computationally intensive investigation was performed to identify a potent natural compound that could inhibit the ZIKV NS5 methyltransferase. This research approach is based on target-based drug identification principles where the native inhibitor SAH (S-adenosylhomocysteine) of ZIKV NS5 methyltransferase was selected as a reference. High-throughput virtual screening and tanimoto similarity coefficient were applied to the natural compound library for ranking the potential candidates. The top five compounds were selected for interaction analysis, MD simulation, total binding free energy through MM/GBSA, and steered MD simulation. Among these compounds, Adenosine 5'-monophosphate monohydrate, Tubercidin, and 5-Iodotubercidin showed stable binding to the protein compared to the native compound, SAH. These three compounds also showed less fluctuations in RMSF in contrast to native compound. Additionally, the same interacting residues observed in SAH also made strong interactions with these three compounds. Adenosine 5'-monophosphate monohydrate and 5-Iodotubercidin had greater total binding free energies than the reference ligand. Moreover, the dissociation resistance of all three compounds was equivalent to that of the reference ligand. This study suggested binding properties of three-hit compounds that could be used to develop drugs against Zika virus infections.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur, Pakistan
| | - Bashayer M AlShehail
- Pharmacy Practice Department, College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Muhammad A Halwani
- Department of Medical Microbiology, Faculty of Medicine, Al Baha University, Saudi Arabia
| | - Amer Alshengeti
- Department of Pediatrics, College of Medicine, Taibah University, Al-Madinah, Saudi Arabia
- Department of Infection Prevention and Control, Prince Mohammad Bin Abdulaziz Hospital, National Guard Health Affairs, Al-Madinah, Saudi Arabia
| | - Mustafa A Najim
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Taibah University, Madinah, Saudi Arabia
| | - Mohammed Garout
- Department of Community Medicine and Health Care for Pilgrims, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Huda A Bajunaid
- Makkah Specialized Laboratory, Fakeeh Care group, Hadda, Saudi Arabia
| | - Saleh A Alshamrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Mona A Al Fares
- Department of Internal Medicine, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Mohammed Alissa
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Ameen S S Alwashmi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
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4
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Serafim MSM, Kronenberger T, Rocha REO, Rosa ADRA, Mello TLG, Poso A, Ferreira RS, Abrahão JS, Kroon EG, Mota BEF, Maltarollo VG. Aminopyrimidine Derivatives as Multiflavivirus Antiviral Compounds Identified from a Consensus Virtual Screening Approach. J Chem Inf Model 2024; 64:393-411. [PMID: 38194508 DOI: 10.1021/acs.jcim.3c01505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Around three billion people are at risk of infection by the dengue virus (DENV) and potentially other flaviviruses. Worldwide outbreaks of DENV, Zika virus (ZIKV), and yellow fever virus (YFV), the lack of antiviral drugs, and limitations on vaccine usage emphasize the need for novel antiviral research. Here, we propose a consensus virtual screening approach to discover potential protease inhibitors (NS3pro) against different flavivirus. We employed an in silico combination of a hologram quantitative structure-activity relationship (HQSAR) model and molecular docking on characterized binding sites followed by molecular dynamics (MD) simulations, which filtered a data set of 7.6 million compounds to 2,775 hits. Lastly, docking and MD simulations selected six final potential NS3pro inhibitors with stable interactions along the simulations. Five compounds had their antiviral activity confirmed against ZIKV, YFV, DENV-2, and DENV-3 (ranging from 4.21 ± 0.14 to 37.51 ± 0.8 μM), displaying aggregator characteristics for enzymatic inhibition against ZIKV NS3pro (ranging from 28 ± 7 to 70 ± 7 μM). Taken together, the compounds identified in this approach may contribute to the design of promising candidates to treat different flavivirus infections.
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Affiliation(s)
- Mateus Sá Magalhães Serafim
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
- Excellence Cluster "Controlling Microbes to Fight Infections" (CMFI), Tübingen 72076, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio 70211, Finland
| | - Rafael Eduardo Oliveira Rocha
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Amanda Del Rio Abreu Rosa
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Thaysa Lara Gonçalves Mello
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Antti Poso
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio 70211, Finland
- Department of Medical Oncology and Pneumology, University Hospital of Tübingen, Tübingen 70211, Germany
| | - Rafaela Salgado Ferreira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Jonatas Santos Abrahão
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Erna Geessien Kroon
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Bruno Eduardo Fernandes Mota
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Vinícius Gonçalves Maltarollo
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
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5
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Yao C, Ye G, Yang Q, Chen Z, Yang M. The Disulfide Bond-Mediated Cyclization of Oral Peptides. Curr Protein Pept Sci 2024; 25:438-442. [PMID: 38934364 DOI: 10.2174/0113892037280719231214095428] [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: 09/05/2023] [Revised: 11/02/2023] [Accepted: 11/20/2023] [Indexed: 06/28/2024]
Abstract
'Structure determines function' is a consensus in the current biological community, but the structural characteristics corresponding to a certain function have always been a hot field of scientific exploration. A peptide is a bio-active molecule that is between the size of an antibody and a small molecule. Still, the gastrointestinal barrier and the physicochemical properties of peptides have always limited the oral administration of peptides. Therefore, we analyze the main ways oral peptide conversion strategies of peptide modification and permeation enhancers. Based on our analysis of the structure of natural oral peptides, which can be absorbed through the gastrointestinal tract, we believe that the design strategy of natural stapled peptides based on disulfide bonds is good for oral peptide design. This cannot only be used to identify anti-gastrointestinal digestive structural proteins in nature but also provide a solid structural foundation for the construction of new oral peptide drugs.
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Affiliation(s)
- Chenguang Yao
- Sino-German Biomedical Center, Hubei Provincial Key Laboratory of Industrial Microbiology, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), National 111 Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, 430068, China
| | - Guoguo Ye
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, Division of Infectious Disease, The Third People's Hospital of Shenzhen, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Qin Yang
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhenwang Chen
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Minghui Yang
- School of Life Science, Advanced Research Institute of Multidisciplinary Sciences; Key Laboratory of Molecular Medicine and Biotherapy, Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Beijing Institute of Technology, Beijing, 100081, China
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6
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Tang K, Wang S, Gao W, Song Y, Yu B. Harnessing the cyclization strategy for new drug discovery. Acta Pharm Sin B 2022; 12:4309-4326. [PMID: 36562004 PMCID: PMC9764076 DOI: 10.1016/j.apsb.2022.09.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/07/2022] [Accepted: 09/23/2022] [Indexed: 12/25/2022] Open
Abstract
The design of new ligands with high affinity and specificity against the targets of interest has been a central focus in drug discovery. As one of the most commonly used methods in drug discovery, the cyclization represents a feasible strategy to identify new lead compounds by increasing structural novelty, scaffold diversity and complexity. Such strategy could also be potentially used for the follow-on drug discovery without patent infringement. In recent years, the cyclization strategy has witnessed great success in the discovery of new lead compounds against different targets for treating various diseases. Herein, we first briefly summarize the use of the cyclization strategy in the discovery of new small-molecule lead compounds, including the proteolysis targeting chimeras (PROTAC) molecules. Particularly, we focus on four main strategies including fused ring cyclization, chain cyclization, spirocyclization and macrocyclization and highlight the use of the cyclization strategy in lead generation. Finally, the challenges including the synthetic intractability, relatively poor pharmacokinetics (PK) profiles and the absence of the structural information for rational structure-based cyclization are also briefly discussed. We hope this review, not exhaustive, could provide a timely overview on the cyclization strategy for the discovery of new lead compounds.
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7
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Gary S, Bloom S. Peptide Carbocycles: From -SS- to -CC- via a Late-Stage "Snip-and-Stitch". ACS CENTRAL SCIENCE 2022; 8:1537-1547. [PMID: 36439308 PMCID: PMC9686213 DOI: 10.1021/acscentsci.2c00456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Indexed: 05/28/2023]
Abstract
One way to improve the therapeutic potential of peptides is through cyclization. This is commonly done using a disulfide bond between two cysteine residues in the peptide. However, disulfide bonds are susceptible to reductive cleavage, and this can deactivate the peptide and endanger endogenous proteins through covalent modification. Substituting disulfide bonds with more chemically robust carbon-based linkers has proven to be an effective strategy to better develop cyclic peptides as drugs, but finding the optimal carbon replacement is synthetically laborious. We report a new late-stage platform wherein a single disulfide bond in a cyclic peptide can serve as the progenitor for any number of new carbon-rich groups, derived from organodiiodides, using a Zn:Cu couple and a hydrosilane. We show that this platform can furnish entirely new carbocyclic scaffolds with enhanced permeability and structural integrity and that the stereochemistry of the new cycles can be biased by a judicious choice in silane.
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Affiliation(s)
- Samuel Gary
- Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas66045, United States
| | - Steven Bloom
- Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas66045, United States
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Saqallah FG, Abbas MA, Wahab HA. Recent advances in natural products as potential inhibitors of dengue virus with a special emphasis on NS2b/NS3 protease. PHYTOCHEMISTRY 2022; 202:113362. [PMID: 35948138 DOI: 10.1016/j.phytochem.2022.113362] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/18/2022] [Accepted: 07/31/2022] [Indexed: 06/15/2023]
Abstract
Dengue virus (DENV) is an arbovirus widespread through tropical and subtropical areas. It is transmitted to humans through Aedes mosquitoes. Infections with DENV can lead to a series of complications, including dengue fever, dengue haemorrhagic fever, or dengue shock syndrome, which might manifest through secondary infections because of a vulnerable immune system. To date, only one tetravalent DENV vaccine is approved to be administered to children whom have been previously DENV-infected and between 9 and 16 years of age. One of the key targets in discovering DENV antiviral agents is the NS2b/NS3 protease. This protease is a crucial enzyme complex for the proteolytic and cleavage activities of the translated polyprotein during DENV life cycle. Several studies were conducted to discover potential antivirals from natural sources or synthetic compounds and peptides. In this review, we describe the recent studies from the past five years dealing with isolated natural products as potential inhibitors of DENV with a greater focus on inhibiting the NS2b/NS3 protease. This review describes recent discoveries in anti-DENV potential of isolated phytochemicals belonging to different groups including fatty acids, glucosides, terpenes and terpenoids, flavonoids, phenolics, chalcones, acetamides, and peptides. Curcumin, quercetin, and myricetin were found to act as non-competitive inhibitors for the NS2b/NS3 protease enzyme. In some studies, the molecular targets of some of these compounds are yet to be identified using in-silico and in-vitro approaches. So far, none of the isolated natural products was tested clinically for the management of DENV infections. The discussed studies demonstrate that natural products are a rich source of potential anti-DENV compounds. However, not all of these compounds were studied for their kinetic molecular mechanism and type of inhibition. In-silico studies provided an ample number of phytochemical hits to be tested experimentally as DENV protease inhibitors. In conclusion, derivatives of these natural products can be designed and synthesised, which could enhance their specificity and efficacy towards the protease. Other sources of natural products, such as fungi, bacterial toxins, marine organisms, and animals, should also be explored towards discovering more potential and effective DENV NS2b/NS3 protease inhibitors.
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Affiliation(s)
- Fadi G Saqallah
- Pharmaceutical Design and Simulation (PhDS) Laboratory, School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia; Discipline of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia.
| | - Manal A Abbas
- Department of Medical Laboratory Sciences, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, 19328, Amman, Jordan; Pharmacological and Diagnostic Research Lab, Al-Ahliyya Amman University, 19328, Amman, Jordan.
| | - Habibah A Wahab
- Pharmaceutical Design and Simulation (PhDS) Laboratory, School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia; Discipline of Pharmaceutical Technology, School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia.
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Proteochemometric Method for pIC50 Prediction of Flaviviridae. BIOMED RESEARCH INTERNATIONAL 2022; 2022:7901791. [PMID: 36158882 PMCID: PMC9499780 DOI: 10.1155/2022/7901791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/18/2022] [Indexed: 11/17/2022]
Abstract
Viruses remain an area of concern despite constant development of antiviral drugs and therapies. One of the contributors is the Flaviviridae family of viruses causing diseases that need attention. Among other anitviral methods, antiviral peptides are being studied as viable candidates. Although antiviral peptides (AVPs) are emerging as potential therapeutics, it is important to assess the efficacy of a given peptide in terms of its bioactivity. Experimental identification of the bioactivity of each potential peptide is an expensive and time consuming task. Computational methods like proteochemometric modeling (PCM) is a promising method for prediction of bioactivity (pIC50) based on peptide and target sequence pair. In this study, we propose a prediction of pIC50 of AVP against the Flaviviridae family that may help make the decision to choose a peptide with desired efficacy. The peptides data was collected from a public database and target sequences were manually curated from literature. Features are calculated using peptide and target sequence PCM descriptors which consist of individual and cross-term features of peptide and respective target. The resultant R2 and MAPE values are 0.85 and 8.44%, respectively, for prediction of pIC50 value of AVPs.
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Hooda P, Chaudhary M, Parvez MK, Sinha N, Sehgal D. Inhibition of Hepatitis E Virus Replication by Novel Inhibitor Targeting Methyltransferase. Viruses 2022; 14:v14081778. [PMID: 36016400 PMCID: PMC9415367 DOI: 10.3390/v14081778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/07/2022] [Accepted: 08/11/2022] [Indexed: 11/17/2022] Open
Abstract
Hepatitis E Virus (HEV) is a quasi-enveloped virus having a single-stranded, positive-sense RNA genome (~7.2 kb), flanked with a 5′ methylated cap and a 3′ polyadenylated tail. The HEV open reading frame 1 (ORF1) encodes a 186-kDa polyprotein speculated to get processed and produce Methyltransferase (MTase), one of the four essential replication enzymes. In this study, we report the identification of the MTase inhibitor, which may potentially deplete its enzymatic activity, thus causing the cessation of viral replication. Using in silico screening through docking, we identified ten putative compounds, which were tested for their anti-MTase activity. This resulted in the identification of 3-(4-Hydroxyphenyl)propionic acid (HPPA), with an IC50 value of 0.932 ± 0.15 μM, which could be perceived as an effective HEV inhibitor. Furthermore, the compound was tested for inhibition of HEV replication in the HEV culture system. The viral RNA copies were markedly decreased from ~3.2 × 106 in untreated cells to ~4.3 × 102.8 copies in 800 μM HPPA treated cells. Therefore, we propose HPPA as a potential drug-like inhibitor against HEV-MTase, which would need further validation through in vivo analysis using animal models and the administration of Pharmacokinetic and Pharmacodynamic (PK/PD) studies.
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Affiliation(s)
- Preeti Hooda
- Virology Laboratory, Department of Life Sciences, Shiv Nadar University, Gautam Budh Nagar, Greater Noida 201314, India
| | - Meenakshi Chaudhary
- Virology Laboratory, Department of Life Sciences, Shiv Nadar University, Gautam Budh Nagar, Greater Noida 201314, India
| | - Mohammad K. Parvez
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
- Correspondence: (M.K.P.); (D.S.)
| | - Neha Sinha
- Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Deepak Sehgal
- Virology Laboratory, Department of Life Sciences, Shiv Nadar University, Gautam Budh Nagar, Greater Noida 201314, India
- Correspondence: (M.K.P.); (D.S.)
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11
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Animal venoms as a source of antiviral peptides active against arboviruses: a systematic review. Arch Virol 2022; 167:1763-1772. [PMID: 35723756 DOI: 10.1007/s00705-022-05494-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 04/04/2022] [Indexed: 11/02/2022]
Abstract
Arthropod-borne viruses (arboviruses), such as Zika virus (ZIKV), chikungunya virus (CHIKV), dengue virus (DENV), yellow fever virus (YFV), and West Nile virus (WNV), are pathogens of global importance. Therefore, there has been an increasing need for new drugs for the treatment of these viral infections. In this context, antimicrobial peptides (AMPs) obtained from animal venoms stand out as promising compounds because they exhibit strong antiviral activity against emerging arboviral pathogens. Thus, we systematically searched and critically analyzed in vitro and in vivo studies that evaluated the anti-arbovirus effect of peptide derivatives from toxins produced by vertebrates and invertebrates. Thirteen studies that evaluated the antiviral action of 10 peptides against arboviruses were included in this review. The peptides were derived from the venom of scorpions, spiders, wasps, snakes, sea snails, and frogs and were tested against DENV, ZIKV, YFV, WNV, and CHIKV. Despite the high structural variety of the peptides included in this study, their antiviral activity appears to be associated with the presence of positive charges, an excess of basic amino acids (mainly lysine), and a high isoelectric point (above 8). These peptides use different antiviral mechanisms, the most common of which is the inhibition of viral replication, release, entry, or fusion. Moreover, peptides with virucidal and cytoprotective (pre-treatment) effects were also identified. In conclusion, animal-venom-derived peptides stand out as a promising alternative in the search and development of prototype antivirals against arboviruses.
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Lee YCJ, Shirkey JD, Park J, Bisht K, Cowan AJ. An Overview of Antiviral Peptides and Rational Biodesign Considerations. BIODESIGN RESEARCH 2022; 2022:9898241. [PMID: 37850133 PMCID: PMC10521750 DOI: 10.34133/2022/9898241] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/04/2022] [Indexed: 10/19/2023] Open
Abstract
Viral diseases have contributed significantly to worldwide morbidity and mortality throughout history. Despite the existence of therapeutic treatments for many viral infections, antiviral resistance and the threat posed by novel viruses highlight the need for an increased number of effective therapeutics. In addition to small molecule drugs and biologics, antimicrobial peptides (AMPs) represent an emerging class of potential antiviral therapeutics. While AMPs have traditionally been regarded in the context of their antibacterial activities, many AMPs are now known to be antiviral. These antiviral peptides (AVPs) have been shown to target and perturb viral membrane envelopes and inhibit various stages of the viral life cycle, from preattachment inhibition through viral release from infected host cells. Rational design of AMPs has also proven effective in identifying highly active and specific peptides and can aid in the discovery of lead peptides with high therapeutic selectivity. In this review, we highlight AVPs with strong antiviral activity largely curated from a publicly available AMP database. We then compile the sequences present in our AVP database to generate structural predictions of generic AVP motifs. Finally, we cover the rational design approaches available for AVPs taking into account approaches currently used for the rational design of AMPs.
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Affiliation(s)
- Ying-Chiang J. Lee
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Jaden D. Shirkey
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Jongbeom Park
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Karishma Bisht
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Alexis J. Cowan
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
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13
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Antiviral Effects of Animal Toxins: Is There a Way to Drugs? Int J Mol Sci 2022; 23:ijms23073634. [PMID: 35408989 PMCID: PMC8998278 DOI: 10.3390/ijms23073634] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 12/18/2022] Open
Abstract
Viruses infect all types of organisms, causing viral diseases, which are very common in humans. Since viruses use the metabolic pathways of their host cells to replicate, they are difficult to eradicate without affecting the cells. The most effective measures against viral infections are vaccinations and antiviral drugs, which selectively inhibit the viral replication cycle. Both methods have disadvantages, which requires the development of new approaches to the treatment of viral diseases. In the study of animal venoms, it was found that, in addition to toxicity, venoms exhibit other types of biological activity, including an antiviral one, the first mention of which dates back to middle of the last century, but detailed studies of their antiviral activity have been conducted over the past 15 years. The COVID-19 pandemic has reinforced these studies and several compounds with antiviral activity have been identified in venoms. Some of them are very active and can be considered as the basis for antiviral drugs. This review discusses recent antiviral studies, the found compounds with high antiviral activity, and the possible mechanisms of their action. The prospects for using the animal venom components to create antiviral drugs, and the expected problems and possible solutions are also considered.
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14
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Sheikh M, Shilkar D, Sarkar B, Sinha BN, Jayprakash V. A Critical Observation on the Design and Development of Reported Peptide Inhibitors of DENV NS2B-NS3 Protease in the Last Two Decades. Mini Rev Med Chem 2021; 22:1108-1130. [PMID: 34720077 DOI: 10.2174/1389557521666211101154619] [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: 05/03/2021] [Revised: 07/09/2021] [Accepted: 09/10/2021] [Indexed: 11/22/2022]
Abstract
Dengue is one of the neglected tropical diseases, which remains a reason for concern as cases seem to rise every year. The failure of the only dengue vaccine, Dengvaxia®, has made the problem more severe and humanity has no immediate respite from this global burden. Dengue virus (DENV) NS2B-NS3 protease is an attractive target partly due to its role in polyprotein processing. Also, since it is among the most conserved domains in the viral genome, it could produce a broad scope of opportunities toward antiviral drug discovery in general. This review has made a detailed analysis of each case of the design and development of peptide inhibitors against DENV NS2B-NS3 protease in the last two decades. Also, we have discussed the reasons attributed to their inhibitory activity, and wherever possible, we have highlighted the concerns raised, challenges met, and suggestions to improve the inhibitory activity. Thus, we attempt to take the readers through the designing and development of reported peptide inhibitors and gain insight from these developments, which could further contribute toward strategizing the designing and development of peptide inhibitors of DENV protease with improved properties in the coming future.
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Affiliation(s)
- Murtuja Sheikh
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi 835215 (JH). India
| | - Deepak Shilkar
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi 835215 (JH). India
| | - Biswatrish Sarkar
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi 835215 (JH). India
| | - Barij Nayan Sinha
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi 835215 (JH). India
| | - Venkatesan Jayprakash
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi 835215 (JH). India
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15
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Dražić T, Kühl N, Gottscheber N, Hacker CN, Klein CD. The spectrum between substrates and inhibitors: Pinpointing the binding mode of dengue protease ligands with modulated basicity and hydrophobicity. Bioorg Med Chem 2021; 48:116412. [PMID: 34592636 DOI: 10.1016/j.bmc.2021.116412] [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] [Received: 07/07/2021] [Revised: 09/06/2021] [Accepted: 09/09/2021] [Indexed: 10/20/2022]
Abstract
Peptides can be inhibitors and substrates of proteases. The present study describes the inhibitor- vs. substrate-like properties of peptidic ligands of dengue protease which were designed to provide insight into their binding modes. Of particular interest was the localization of the cleavable peptide bond and the placement of hydrophobic elements in the binding site. The findings provide clues for the design of covalent inhibitors in which electrophilic functional groups bind to the catalytic serine, and in addition for the development of inhibitors that are less basic than the natural substrate and therefore have an improved pharmacokinetic profile. We observed a tendency of basic elements to favor a substrate-like binding mode, whereas hydrophobic elements decrease or eliminate enzymatic cleavage. This indicates a necessity to include basic elements which closely mimic the natural substrates into covalent inhibitors, posing a challenge from the chemical and pharmacokinetic perspective. However, hydrophobic elements may offer opportunities to develop non-covalent inhibitors with a favorable ADME profile and potentially improved target-binding kinetics.
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Affiliation(s)
- Tonko Dražić
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Nikos Kühl
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Nicole Gottscheber
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Christina N Hacker
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Christian D Klein
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany.
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16
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Song W, Zhang H, Zhang Y, Chen Y, Lin Y, Han Y, Jiang J. Identification and Characterization of Zika Virus NS5 Methyltransferase Inhibitors. Front Cell Infect Microbiol 2021; 11:665379. [PMID: 33898335 PMCID: PMC8058401 DOI: 10.3389/fcimb.2021.665379] [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: 02/08/2021] [Accepted: 03/19/2021] [Indexed: 01/19/2023] Open
Abstract
The recurring outbreak of Zika virus (ZIKV) worldwide makes an emergent demand for novel, safe and efficacious anti-ZIKV agents. ZIKV non-structural protein 5 (NS5) methyltransferase (MTase), which is essential for viral replication, is regarded as a potential drug target. In our study, a luminescence-based methyltransferase assay was used to establish the ZIKV NS5 MTase inhibitor screening model. Through screening a natural product library, we found theaflavin, a polyphenol derived from tea, could inhibit ZIKV NS5 MTase activity with a 50% inhibitory concentration (IC50) of 10.10 μM. Molecular docking and site-directed mutagenesis analyses identified D146 as the key amino acid in the interaction between ZIKV NS5 MTase and theaflavin. The SPR assay indicated that theaflavin had a stronger binding activity with ZIKV NS5 wild-type (WT)-MTase than it with D146A-MTase. Moreover, theaflavin exhibited a dose dependent inhibitory effect on ZIKV replication with a 50% effective concentration (EC50) of 8.19 μM. All these results indicate that theaflavin is likely to be a promising lead compound against ZIKV.
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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, 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, 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, China
| | - Ying Chen
- 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, 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, 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, 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, China
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17
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Ortet PC, Muellers SN, Viarengo-Baker LA, Streu K, Szymczyna BR, Beeler AB, Allen KN, Whitty A. Recapitulating the Binding Affinity of Nrf2 for KEAP1 in a Cyclic Heptapeptide, Guided by NMR, X-ray Crystallography, and Machine Learning. J Am Chem Soc 2021; 143:3779-3793. [DOI: 10.1021/jacs.0c09799] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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18
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Vishvakarma VK, Chandra R, Singh P. An Experimental and Theoretical Approach to Understand Fever, DENF & its Cure. Infect Disord Drug Targets 2020; 21:495-513. [PMID: 32888275 DOI: 10.2174/1871526520999200905122052] [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] [Received: 04/17/2020] [Revised: 06/21/2020] [Accepted: 07/17/2020] [Indexed: 11/22/2022]
Abstract
Fever is a response of a human body, due to an increase in the temperature, against certain stimuli. It may be associated with several reasons and one of the major causes of fever is a mosquito bite. Fever due to dengue virus (DENV) infection is being paid most attention out of several other fever types because of a large number of deaths reported worldwide. Dengue virus is transmitted by biting of the mosquitoes, Aedes aegypti and Aedes albopictus. DENV1, DENV2, DENV3 and DENV4 are the four serotypes of dengue virus and these serotypes have 65% similarities in their genomic structure. The genome of DENV is composed of single-stranded RNA and it encodes for the polyprotein. Structural and non-structural proteins (nsP) are the two major parts of polyprotein. Researchers have paid high attention to the non-structural protease (nsP) of DENV like nsP1, nsP2A, nsP2B, nsP3, nsP4A, nsP4B and nsP5. The NS2B-NS3 protease of DENV is the prime target of the researchers as it is responsible for the catalytic activity. In the present time, Dengvaxia (vaccine) is being recommended to patients suffering severely from DENV infection in few countries only. Till date, neither a vaccine nor an effective medicine is available to combat all four serotypes. This review describes the fever, its causes, and studies to cure the infection due to DENV using theoretical and experimental approaches.
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Affiliation(s)
- Vijay Kumar Vishvakarma
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India
| | - Ramesh Chandra
- Drug Discovery & Development Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Prashant Singh
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India
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19
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Shanmugam A, Ramakrishnan C, Velmurugan D, Gromiha MM. Identification of Potential Inhibitors for Targets Involved in Dengue Fever. Curr Top Med Chem 2020; 20:1742-1760. [PMID: 32552652 DOI: 10.2174/1568026620666200618123026] [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] [Received: 10/20/2019] [Revised: 11/05/2019] [Accepted: 01/10/2020] [Indexed: 01/16/2023]
Abstract
Lethality due to dengue infection is a global threat. Nearly 400 million people are affected every year, which approximately costs 500 million dollars for surveillance and vector control itself. Many investigations on the structure-function relationship of proteins expressed by the dengue virus are being made for more than a decade and had come up with many reports on small molecule drug discovery. In this review, we present a detailed note on viral proteins and their functions as well as the inhibitors discovered/designed so far using experimental and computational methods. Further, the phytoconstituents from medicinal plants, specifically the extract of the papaya leaves, neem and bael, which combat dengue infection via dengue protease, helicase, methyl transferase and polymerase are summarized.
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Affiliation(s)
- Anusuya Shanmugam
- Department of Pharmaceutical Engineering, Vinayaka Mission's Kirupananda Variyar Engineering College, Vinayaka Mission's Research Foundation (Deemed to be University), Salem - 636308, India
| | - Chandrasekaran Ramakrishnan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai - 600036, India
| | - Devadasan Velmurugan
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai - 600025, India
| | - M Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai - 600036, India
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20
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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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21
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Abdullah AA, Lee YK, Chin SP, Lim SK, Lee VS, Othman R, Othman S, Rahman NA, Yusof R, Heh CH. Discovery of Dengue Virus Inhibitors. Curr Med Chem 2020; 27:4945-5036. [PMID: 30514185 DOI: 10.2174/0929867326666181204155336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 11/11/2018] [Accepted: 11/22/2018] [Indexed: 11/22/2022]
Abstract
To date, there is still no approved anti-dengue agent to treat dengue infection in the market. Although the only licensed dengue vaccine, Dengvaxia is available, its protective efficacy against serotypes 1 and 2 of dengue virus was reported to be lower than serotypes 3 and 4. Moreover, according to WHO, the risk of being hospitalized and having severe dengue increased in seronegative individuals after they received Dengvaxia vaccination. Nevertheless, various studies had been carried out in search of dengue virus inhibitors. These studies focused on the structural (C, prM, E) and non-structural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B and NS5) of dengue virus as well as host factors as drug targets. Hence, this article provides an overall up-to-date review of the discovery of dengue virus inhibitors that are only targeting the structural and non-structural viral proteins as drug targets.
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Affiliation(s)
- Adib Afandi Abdullah
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
| | - Yean Kee Lee
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
| | - Sek Peng Chin
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
| | - See Khai Lim
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
| | - Vannajan Sanghiran Lee
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
| | - Rozana Othman
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
| | - Shatrah Othman
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
| | - Noorsaadah Abdul Rahman
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
| | - Rohana Yusof
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
| | - Choon Han Heh
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
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22
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Choi JS, Joo SH. Recent Trends in Cyclic Peptides as Therapeutic Agents and Biochemical Tools. Biomol Ther (Seoul) 2020; 28:18-24. [PMID: 31597413 PMCID: PMC6939695 DOI: 10.4062/biomolther.2019.082] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 08/09/2019] [Accepted: 08/12/2019] [Indexed: 12/26/2022] Open
Abstract
Notable progress has been made in the therapeutic and research applications of cyclic peptides since our previous review. New drugs based on cyclic peptides are entering the market, such as plecanatide, a cyclic peptide approved by the United States Food and Drug Administration in 2017 for the treatment of chronic idiopathic constipation. In this review, we discuss recent developments in stapled peptides, prepared with the use of chemical linkers, and bicyclic/tricyclic peptides with more than two rings. These have widespread applications for clinical and research purposes: imaging, diagnostics, improvement of oral absorption, enzyme inhibition, development of receptor agonist/antagonist, and the modulation of protein-protein interaction or protein-RNA interaction. Many cyclic peptides are expected to emerge as therapeutics and biochemical tools.
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Affiliation(s)
- Joon-Seok Choi
- College of Pharmacy, Daegu Catholic University, Gyeongsan 38430, Republic of Korea
| | - Sang Hoon Joo
- College of Pharmacy, Daegu Catholic University, Gyeongsan 38430, Republic of Korea
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23
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Faheem M, Barbosa Lima JC, Jamal SB, Silva PA, Barbosa JARG. An insight into dengue virus proteins as potential drug/vaccine targets. Future Virol 2019. [DOI: 10.2217/fvl-2019-0107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dengue virus (DENV) is an arbovirus that belongs to family flaviviridae. Its genome is composed of a single stranded RNA molecule that encodes a single polyprotein. The polyprotein is processed by viral and cellular proteases to generate ten viral proteins. There are four antigenically distinct serotypes of DENV (DENV1, DENV2, DENV3 and DENV4), which are genetically related. Although protein variability is a major problem in dengue treatment, the functional and structural studies of individual proteins are equally important in treatment development. The data accumulated on dengue proteins are significant to provide detailed understanding of viral infection, replication, host-immune evasion and pathogenesis. In this review, we summarized the detailed current knowledge about DENV proteins.
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Affiliation(s)
- Muhammad Faheem
- Laboratory of Biophysics, Department of Cellular Biology, University of Brasilia, Brasilia-DF 70910-900, Brazil
- Post-graduate program of Genomics Sciences & Biotechnology, Catholic University of Brasilia, Brasília-DF 70790-160, Brazil
| | - Jônatas Cunha Barbosa Lima
- Laboratory of Biophysics, Department of Cellular Biology, University of Brasilia, Brasilia-DF 70910-900, Brazil
| | - Syed Babar Jamal
- Department of Biological Sciences, National University of Medical Sciences, The Mall road, Rawalpindi, Punjab 46000, Pakistan
| | - Paula Andreia Silva
- Post-graduate program of Genomics Sciences & Biotechnology, Catholic University of Brasilia, Brasília-DF 70790-160, Brazil
| | - João Alexandre Ribeiro Gonçalves Barbosa
- Laboratory of Biophysics, Department of Cellular Biology, University of Brasilia, Brasilia-DF 70910-900, Brazil
- Post-graduate program of Genomics Sciences & Biotechnology, Catholic University of Brasilia, Brasília-DF 70790-160, Brazil
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24
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Peptide derivatives as inhibitors of NS2B-NS3 protease from Dengue, West Nile, and Zika flaviviruses. Bioorg Med Chem 2019; 27:3963-3978. [DOI: 10.1016/j.bmc.2019.07.038] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 07/18/2019] [Accepted: 07/22/2019] [Indexed: 12/19/2022]
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25
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Huang YW, Lee CT, Wang TC, Kao YC, Yang CH, Lin YM, Huang KS. The Development of Peptide-based Antimicrobial Agents against Dengue Virus. Curr Protein Pept Sci 2019; 19:998-1010. [PMID: 29852867 PMCID: PMC6446661 DOI: 10.2174/1389203719666180531122724] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 04/20/2018] [Accepted: 05/25/2018] [Indexed: 11/22/2022]
Abstract
Dengue fever has become an imminent threat to international public health because of global warming and climate change. The World Health Organization proclaimed that more than 50% of the world’s population is at risk of dengue virus (DENV) infection. Therefore, developing a clinically ap-proved vaccine and effective therapeutic remedy for treating dengue fever is imperative. Peptide drug de-velopment has become a novel pharmaceutical research field. This article reviews various peptides-based antimicrobial agents targeting three pathways involved in the DENV lifecycle. Specifically, they are peptide vaccines from immunomodulation, peptide drugs that inhibit virus entry, and peptide drugs that interfere with viral replication. Many antiviral peptide studies against DENV have been conducted in animal model trials, and progression to clinical trials for these promising peptide drugs is anticipated.
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Affiliation(s)
- Yen-Wei Huang
- The School of Chinese Medicine for Post-Baccalaureate, I-Shou University, Kaohsiung, Taiwan.,Department of Chinese Medicine, E-DA Hospital, Kaohsiung, Taiwan
| | - Chun-Ting Lee
- The School of Chinese Medicine for Post-Baccalaureate, I-Shou University, Kaohsiung, Taiwan.,Department of Chinese Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Ta-Chen Wang
- The School of Chinese Medicine for Post-Baccalaureate, I-Shou University, Kaohsiung, Taiwan.,Department of Chinese Medicine, E-DA Hospital, Kaohsiung, Taiwan
| | - Yun-Chung Kao
- The School of Chinese Medicine for Post-Baccalaureate, I-Shou University, Kaohsiung, Taiwan.,Department of Chinese Medicine, Kuanshan Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taitung, Taiwan
| | - Chih-Hui Yang
- Department of Biological Science and Technology, I-Shou University, Kaohsiung, Taiwan
| | - Yu-Mei Lin
- The School of Chinese Medicine for Post-Baccalaureate, I-Shou University, Kaohsiung, Taiwan
| | - Keng-Shiang Huang
- The School of Chinese Medicine for Post-Baccalaureate, I-Shou University, Kaohsiung, Taiwan
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26
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Majerová T, Novotný P, Krýsová E, Konvalinka J. Exploiting the unique features of Zika and Dengue proteases for inhibitor design. Biochimie 2019; 166:132-141. [PMID: 31077760 DOI: 10.1016/j.biochi.2019.05.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 05/01/2019] [Indexed: 02/07/2023]
Abstract
Zika and Dengue viruses have attracted substantial attention from researchers in light of recent outbreaks of Dengue fever and increases in cases of congenital microcephaly in areas with Zika incidence. This review summarizes the current state of knowledge about Zika and Dengue proteases. These enzymes have several interesting features: 1) NS3 serine protease requires the activating co-factor NS2B, which is anchored in the membrane of the endoplasmic reticulum; 2) NS2B displays extensive conformational dynamics; 3) NS3 is a multidomain protein with proteolytic, NTPase, RNA 5' triphosphatase and helicase activity and has many protein-protein interaction partners; 4) NS3 is autoproteolytically released from its precursor. Attempts to design tight-binding and specific active-site inhibitors are complicated by the facts that the substrate pocket of the NS2B-NS3 protease is flat and the active-site ligands are charged. The ionic character of potential active-site inhibitors negatively influences their cell permeability. Possibilities to block cis-autoprocessing of the protease precursor have recently been considered. Additionally, potential allosteric sites on NS2B-NS3 proteases have been identified and allosteric compounds have been designed to impair substrate binding and/or block the NS2B-NS3 interaction. Such compounds could be specific to viral proteases, without off-target effects on host serine proteases, and could have favorable pharmacokinetic profiles. This review discusses various groups of inhibitors of these proteases according to their mechanisms of action and chemical structures.
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Affiliation(s)
- Taťána Majerová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nám. 2, 16610, Prague 6, Czech Republic
| | - Pavel Novotný
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nám. 2, 16610, Prague 6, Czech Republic; Department of Biochemistry, Faculty of Science, Charles University in Prague, 12843, Prague, Czech Republic
| | - Eliška Krýsová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nám. 2, 16610, Prague 6, Czech Republic; Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, 12843, Prague, Czech Republic
| | - Jan Konvalinka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nám. 2, 16610, Prague 6, Czech Republic; Department of Biochemistry, Faculty of Science, Charles University in Prague, 12843, Prague, Czech Republic.
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27
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Zou J, Shi PY. Strategies for Zika drug discovery. Curr Opin Virol 2019; 35:19-26. [PMID: 30852345 DOI: 10.1016/j.coviro.2019.01.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/23/2019] [Accepted: 01/28/2019] [Indexed: 12/15/2022]
Abstract
Zika virus (ZIKV) can cause devastating congenital syndrome in fetuses from pregnant women and autoimmune disorder Guillain-Barré syndrome in adults. No clinically approved vaccine or drug is currently available for ZIKV. This unmet medical need has motivated a global effort to develop countermeasures. Several promising ZIKV vaccine candidates have already entered clinical trials. In contrast, antiviral development of ZIKV is lagging behind. Here, we review the overall strategies for ZIKV drug discovery, including (i) repurposing of clinically approved drugs, (ii) viral replication-based phenotypic screening for inhibitors, and (iii) targeted drug discovery of viral proteins. Along with vaccines, the development of antiviral treatment will provide a complementary means to control ZIKV infections.
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Affiliation(s)
- Jing Zou
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA; Department of Phamarcology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA; Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA.
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28
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Hariono M, Choi SB, Roslim RF, Nawi MS, Tan ML, Kamarulzaman EE, Mohamed N, Yusof R, Othman S, Abd Rahman N, Othman R, Wahab HA. Thioguanine-based DENV-2 NS2B/NS3 protease inhibitors: Virtual screening, synthesis, biological evaluation and molecular modelling. PLoS One 2019; 14:e0210869. [PMID: 30677071 PMCID: PMC6345492 DOI: 10.1371/journal.pone.0210869] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 01/03/2019] [Indexed: 12/25/2022] Open
Abstract
Dengue virus Type 2 (DENV-2) is predominant serotype causing major dengue epidemics. There are a number of studies carried out to find its effective antiviral, however to date, there is still no molecule either from peptide or small molecules released as a drug. The present study aims to identify small molecules inhibitor from National Cancer Institute database through virtual screening. One of the hits, D0713 (IC50 = 62 μM) bearing thioguanine scaffold was derivatised into 21 compounds and evaluated for DENV-2 NS2B/NS3 protease inhibitory activity. Compounds 18 and 21 demonstrated the most potent activity with IC50 of 0.38 μM and 16 μM, respectively. Molecular dynamics and MM/PBSA free energy of binding calculation were conducted to study the interaction mechanism of these compounds with the protease. The free energy of binding of 18 calculated by MM/PBSA is -16.10 kcal/mol compared to the known inhibitor, panduratin A (-11.27 kcal/mol), which corroborates well with the experimental observation. Results from molecular dynamics simulations also showed that both 18 and 21 bind in the active site and stabilised by the formation of hydrogen bonds with Asn174.
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Affiliation(s)
- Maywan Hariono
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Minden, Pulau Pinang, Malaysia
- Faculty of Pharmacy, Sanata Dharma University, Maguwoharjo, Sleman, Yogyakarta, Indonesia
| | - Sy Bing Choi
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Minden, Pulau Pinang, Malaysia
- School of Data Sciences, Perdana University, Blok B and d1, MARDI Complex, Jalan MAEPS Perdana, Serdang, Selangor
| | - Ros Fatihah Roslim
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Minden, Pulau Pinang, Malaysia
| | - Mohamed Sufian Nawi
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Minden, Pulau Pinang, Malaysia
- Department of Pharmaceutical Chemistry, Kulliyah of Pharmacy, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
| | - Mei Lan Tan
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, Pulau Pinang, Malaysia
| | | | - Nornisah Mohamed
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Minden, Pulau Pinang, Malaysia
| | - Rohana Yusof
- Department of Molecular Medicine, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Shatrah Othman
- Department of Chemistry, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Noorsaadah Abd Rahman
- Department of Chemistry, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Rozana Othman
- Department of Pharmacy, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Habibah A. Wahab
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Minden, Pulau Pinang, Malaysia
- Malaysian Institute of Pharmaceuticals and Nutraceuticals, Ministry of Science, Technology and Innovation, Halaman Bukit Gambir, Bayan Lepas, Pulau Pinang, Malaysia
- * E-mail: ,
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29
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Swain SP, Mohanty S. Imidazolidinones and Imidazolidine‐2,4‐diones as Antiviral Agents. ChemMedChem 2019; 14:291-302. [DOI: 10.1002/cmdc.201800686] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 12/18/2018] [Indexed: 01/12/2023]
Affiliation(s)
- Sharada Prasanna Swain
- Department of Process ChemistryDr. Reddy's Lab Ltd. CTO-III, IDA, Bollaram Hyderabad 502325 India
| | - Sandeep Mohanty
- Department of Process ChemistryDr. Reddy's Lab Ltd. CTO-III, IDA, Bollaram Hyderabad 502325 India
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30
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Tian YS, Zhou Y, Takagi T, Kameoka M, Kawashita N. Dengue Virus and Its Inhibitors: A Brief Review. Chem Pharm Bull (Tokyo) 2018; 66:191-206. [PMID: 29491253 DOI: 10.1248/cpb.c17-00794] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The global occurrence of viral infectious diseases poses a significant threat to human health. Dengue virus (DENV) infection is one of the most noteworthy of these infections. According to a WHO survey, approximately 400 million people are infected annually; symptoms deteriorate in approximately one percent of cases. Numerous foundational and clinical investigations on viral epidemiology, structure and function analysis, infection source and route, therapeutic targets, vaccines, and therapeutic drugs have been conducted by both academic and industrial researchers. At present, CYD-TDV or Dengvaxia® is the only approved vaccine, but potent inhibitors are currently under development. In this review, an overview of the viral life circle and the history of DENVs is presented, and the most recently reported antiviral candidates and newly discovered promising targets are focused and summarized. We believe that these successes and failures have enabled progress in anti-DENV drug discovery and hope that our review will stimulate further innovation in this area.
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Affiliation(s)
- Yu-Shi Tian
- Graduate School of Pharmaceutical Sciences, Osaka University
| | - Yi Zhou
- Graduate School of Pharmaceutical Sciences, Osaka University
| | - Tatsuya Takagi
- Graduate School of Pharmaceutical Sciences, Osaka University
| | - Masanori Kameoka
- Department of International Health, Kobe University Graduate School of Health Sciences
| | - Norihito Kawashita
- Graduate School of Pharmaceutical Sciences, Osaka University.,Faculty of Sciences and Engineering, Kindai University
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31
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Gomes B, Augusto MT, Felício MR, Hollmann A, Franco OL, Gonçalves S, Santos NC. Designing improved active peptides for therapeutic approaches against infectious diseases. Biotechnol Adv 2018; 36:415-429. [PMID: 29330093 DOI: 10.1016/j.biotechadv.2018.01.004] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 12/13/2017] [Accepted: 01/06/2018] [Indexed: 12/25/2022]
Abstract
Infectious diseases are one of the main causes of human morbidity and mortality. In the last few decades, pathogenic microorganisms' resistance to conventional drugs has been increasing, and it is now pinpointed as a major worldwide health concern. The need to search for new therapeutic options, as well as improved treatment outcomes, has therefore increased significantly, with biologically active peptides representing a new alternative. A substantial research effort is being dedicated towards their development, especially due to improved biocompatibility and target selectivity. However, the inherent limitations of peptide drugs are restricting their application. In this review, we summarize the current status of peptide drug development, focusing on antiviral and antimicrobial peptide activities, highlighting the design improvements needed, and those already being used, to overcome the drawbacks of the therapeutic application of biologically active peptides.
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Affiliation(s)
- Bárbara Gomes
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Marcelo T Augusto
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Mário R Felício
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Axel Hollmann
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal; Laboratory of Molecular Microbiology, Institute of Basic and Applied Microbiology, National University of Quilmes, Bernal, Buenos Aires, Argentina; Laboratory of Biointerfaces and Biomimetic Systems, CITSE, National University of Santiago del Estero-CONICET, Santiago del Estero, Argentina
| | - Octávio L Franco
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; Programa de Pós-Graduação em Patologia Molecular, Universidade de Brasília, Brasília, DF, Brazil; S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
| | - Sónia Gonçalves
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Nuno C Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal.
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32
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Chew MF, Poh KS, Poh CL. Peptides as Therapeutic Agents for Dengue Virus. Int J Med Sci 2017; 14:1342-1359. [PMID: 29200948 PMCID: PMC5707751 DOI: 10.7150/ijms.21875] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 09/01/2017] [Indexed: 12/19/2022] Open
Abstract
Dengue is an important global threat caused by dengue virus (DENV) that records an estimated 390 million infections annually. Despite the availability of CYD-TDV as a commercial vaccine, its long-term efficacy against all four dengue virus serotypes remains unsatisfactory. There is therefore an urgent need for the development of antiviral drugs for the treatment of dengue. Peptide was once a neglected choice of medical treatment but it has lately regained interest from the pharmaceutical industry following pioneering advancements in technology. In this review, the design of peptide drugs, antiviral activities and mechanisms of peptides and peptidomimetics (modified peptides) action against dengue virus are discussed. The development of peptides as inhibitors for viral entry, replication and translation is also described, with a focus on the three main targets, namely, the host cell receptors, viral structural proteins and viral non-structural proteins. The antiviral peptides designed based on these approaches may lead to the discovery of novel anti-DENV therapeutics that can treat dengue patients.
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Affiliation(s)
- Miaw-Fang Chew
- Research Centre for Biomedical Sciences, Sunway University, Bandar Sunway, Selangor 47500, Malaysia
| | - Keat-Seong Poh
- Department of Surgery, Faculty of Medicine, University of Malaya, Jalan Universiti, Kuala Lumpur, 50603, Malaysia
| | - Chit-Laa Poh
- Research Centre for Biomedical Sciences, Sunway University, Bandar Sunway, Selangor 47500, Malaysia
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33
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Takagi Y, Matsui K, Nobori H, Maeda H, Sato A, Kurosu T, Orba Y, Sawa H, Hattori K, Higashino K, Numata Y, Yoshida Y. Discovery of novel cyclic peptide inhibitors of dengue virus NS2B-NS3 protease with antiviral activity. Bioorg Med Chem Lett 2017; 27:3586-3590. [PMID: 28539222 DOI: 10.1016/j.bmcl.2017.05.027] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 04/24/2017] [Accepted: 05/09/2017] [Indexed: 12/19/2022]
Abstract
NS2B-NS3 protease is an essential enzyme for the replication of dengue virus (DENV), which continues to be a serious threat to worldwide public health. We designed and synthesized a series of cyclic peptides mimicking the substrates of this enzyme, and assayed their activity against the DENV-2 NS2B-NS3 protease. The introduction of aromatic residues at the appropriate positions and conformational restriction generated the most promising cyclic peptide with an IC50 of 0.95μM against NS2B-NS3 protease. Cyclic peptides with proper positioning of additional arginines and aromatic residues exhibited antiviral activity against DENV. Furthermore, replacing the C-terminal amide bond of the polybasic amino acid sequence with an amino methylene moiety stabilized the cyclic peptides against hydrolysis by NS2B-NS3 protease, while maintaining their enzyme inhibitory activity and antiviral activity.
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Affiliation(s)
- Youhei Takagi
- Pharmaceutical Research Center, Shionogi & Co., Ltd., 3-1-1, Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Kouhei Matsui
- Pharmaceutical Research Center, Shionogi & Co., Ltd., 3-1-1, Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Haruaki Nobori
- Pharmaceutical Research Center, Shionogi & Co., Ltd., 3-1-1, Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Haruka Maeda
- Pharmaceutical Research Center, Shionogi & Co., Ltd., 3-1-1, Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Akihiko Sato
- Pharmaceutical Research Center, Shionogi & Co., Ltd., 3-1-1, Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Takeshi Kurosu
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yasuko Orba
- Division of Molecular Pathobiology, Center for Zoonosis Control, Hokkaido University, Kita-20, Nishi-10, Kita-ku, Sapporo 001-0020, Japan
| | - Hirofumi Sawa
- Division of Molecular Pathobiology, Center for Zoonosis Control, Hokkaido University, Kita-20, Nishi-10, Kita-ku, Sapporo 001-0020, Japan
| | - Kazunari Hattori
- Pharmaceutical Research Center, Shionogi & Co., Ltd., 3-1-1, Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Kenichi Higashino
- Pharmaceutical Research Center, Shionogi & Co., Ltd., 3-1-1, Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Yoshito Numata
- Pharmaceutical Research Center, Shionogi & Co., Ltd., 3-1-1, Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Yutaka Yoshida
- Pharmaceutical Research Center, Shionogi & Co., Ltd., 3-1-1, Futaba-cho, Toyonaka, Osaka 561-0825, Japan.
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34
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Tambunan USF, Nasution MAF, Azhima F, Parikesit AA, Toepak EP, Idrus S, Kerami D. Modification of S-Adenosyl-l-Homocysteine as Inhibitor of Nonstructural Protein 5 Methyltransferase Dengue Virus Through Molecular Docking and Molecular Dynamics Simulation. Drug Target Insights 2017; 11:1177392817701726. [PMID: 28469408 PMCID: PMC5404899 DOI: 10.1177/1177392817701726] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 03/01/2017] [Indexed: 01/01/2023] Open
Abstract
Dengue fever is still a major threat worldwide, approximately threatening two-fifths of the world's population in tropical and subtropical countries. Nonstructural protein 5 (NS5) methyltransferase enzyme plays a vital role in the process of messenger RNA capping of dengue by transferring methyl groups from S-adenosyl-l-methionine to N7 atom of the guanine bases of RNA and the RNA ribose group of 2'OH, resulting in S-adenosyl-l-homocysteine (SAH). The modification of SAH compound was screened using molecular docking and molecular dynamics simulation, along with computational ADME-Tox (absorption, distribution, metabolism, excretion, and toxicity) test. The 2 simulations were performed using Molecular Operating Environment (MOE) 2008.10 software, whereas the ADME-Tox test was performed using various software. The modification of SAH compound was done using several functional groups that possess different polarities and properties, resulting in 3460 ligands to be docked. After conducting docking simulation, we earned 3 best ligands (SAH-M331, SAH-M2696, and SAH-M1356) based on ΔGbinding and molecular interactions, which show better results than the standard ligands. Moreover, the results of molecular dynamics simulation show that the best ligands are still able to maintain the active site residue interaction with the binding site until the end of the simulation. After a series of molecular docking and molecular dynamics simulation were performed, we concluded that SAH-M1356 ligand is the most potential SAH-based compound to inhibit NS5 methyltransferase enzyme for treating dengue fever.
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Affiliation(s)
- Usman Sumo Friend Tambunan
- Bioinformatics Research Group, Department of Chemistry, Faculty of Mathematics and Natural Science, University of Indonesia, Depok, Indonesia
| | | | - Fauziah Azhima
- Bioinformatics Research Group, Department of Chemistry, Faculty of Mathematics and Natural Science, University of Indonesia, Depok, Indonesia
| | - Arli Aditya Parikesit
- Bioinformatics Research Group, Department of Chemistry, Faculty of Mathematics and Natural Science, University of Indonesia, Depok, Indonesia
| | - Erwin Prasetya Toepak
- Bioinformatics Research Group, Department of Chemistry, Faculty of Mathematics and Natural Science, University of Indonesia, Depok, Indonesia
| | - Syarifuddin Idrus
- Industrial Standardization Laboratory, Ministry of Industrial Affair, Ambon, Indonesia
| | - Djati Kerami
- Mathematics Computation Research Group, Department of Mathematics, Faculty of Mathematics and Natural Science, University of Indonesia, Depok, Indonesia
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35
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Lee H, Ren J, Nocadello S, Rice AJ, Ojeda I, Light S, Minasov G, Vargas J, Nagarathnam D, Anderson WF, Johnson ME. Identification of novel small molecule inhibitors against NS2B/NS3 serine protease from Zika virus. Antiviral Res 2016; 139:49-58. [PMID: 28034741 DOI: 10.1016/j.antiviral.2016.12.016] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 12/21/2016] [Accepted: 12/22/2016] [Indexed: 01/11/2023]
Abstract
Zika flavivirus infection during pregnancy appears to produce higher risk of microcephaly, and also causes multiple neurological problems such as Guillain-Barré syndrome. The Zika virus is now widespread in Central and South America, and is anticipated to become an increasing risk in the southern United States. With continuing global travel and the spread of the mosquito vector, the exposure is expected to accelerate, but there are no currently approved treatments against the Zika virus. The Zika NS2B/NS3 protease is an attractive drug target due to its essential role in viral replication. Our studies have identified several compounds with inhibitory activity (IC50) and binding affinity (KD) of ∼5-10 μM against the Zika NS2B-NS3 protease from testing 71 HCV NS3/NS4A inhibitors that were initially discovered by high-throughput screening of 40,967 compounds. Competition surface plasmon resonance studies and mechanism of inhibition analyses by enzyme kinetics subsequently determined the best compound to be a competitive inhibitor with a Ki value of 9.5 μM. We also determined the X-ray structure of the Zika NS2B-NS3 protease in a "pre-open conformation", a conformation never observed before for any flavivirus proteases. This provides the foundation for new structure-based inhibitor design.
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Affiliation(s)
- Hyun Lee
- Novalex Therapeutics, Inc., 2242 W Harrison Suite 201, Chicago, IL 60612, USA
| | - Jinhong Ren
- Center for Biomolecular Science, University of Illinois at Chicago, 900 S. Ashland, IL 60607, USA
| | - Salvatore Nocadello
- Center for Structural Genomics of Infectious Diseases (CSGID), Dept. of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL 60611, USA
| | - Amy J Rice
- Center for Biomolecular Science, University of Illinois at Chicago, 900 S. Ashland, IL 60607, USA; Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood Street, IL 60612, USA
| | - Isabel Ojeda
- Center for Biomolecular Science, University of Illinois at Chicago, 900 S. Ashland, IL 60607, USA; Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood Street, IL 60612, USA
| | - Samuel Light
- Center for Structural Genomics of Infectious Diseases (CSGID), Dept. of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL 60611, USA
| | - George Minasov
- Center for Structural Genomics of Infectious Diseases (CSGID), Dept. of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL 60611, USA
| | - Jason Vargas
- Center for Biomolecular Science, University of Illinois at Chicago, 900 S. Ashland, IL 60607, USA; Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood Street, IL 60612, USA
| | | | - Wayne F Anderson
- Center for Structural Genomics of Infectious Diseases (CSGID), Dept. of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL 60611, USA
| | - Michael E Johnson
- Novalex Therapeutics, Inc., 2242 W Harrison Suite 201, Chicago, IL 60612, USA.
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36
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Identification of fused bicyclic derivatives of pyrrolidine and imidazolidinone as dengue virus-2 NS2B-NS3 protease inhibitors. Eur J Med Chem 2016; 125:751-759. [PMID: 27721158 DOI: 10.1016/j.ejmech.2016.09.063] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 09/19/2016] [Accepted: 09/20/2016] [Indexed: 11/23/2022]
Abstract
A series of fused ring derivatives of pyrrolidine and imidazolidinone were designed, synthesized, characterized and assayed against the DENV-2 NS2B-NS3 protease and wild-type DENV-2 virus. The linear dipeptide compound 1 and the non-peptidic fused ring compound 2 show comparable activities against DENV-2 NS2B-NS3 protease and wild-type DENV-2 virus in a viral replication assay. The preliminary SAR reveals that a substituent and its stereochemistry at C-3 position, substitution (X) at N-2 arene and a linker (Y) between C-3 position and its attached arene are important for the fused-ring scaffold of pyrrolidino [1,2-c]imidazolidinone to block the active site of NS2B-NS3 protease. This promising structural core will facilitate the discovery of non-peptidic, potent NS2B-NS3 protease inhibitors to stop dengue virus infections.
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37
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Sato H, Yoshida M, Murase H, Nakagawa H, Doi T. Combinatorial Solid-Phase Synthesis and Biological Evaluation of Cyclodepsipeptide Destruxin B as a Negative Regulator for Osteoclast Morphology. ACS COMBINATORIAL SCIENCE 2016; 18:590-5. [PMID: 27490097 DOI: 10.1021/acscombsci.6b00076] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Combinatorial synthesis and biological evaluation of cyclodepsipeptide destruxin B have been achieved. The cyclization precursors were prepared by solid-phase peptide synthesis via a split and pool method utilizing SynPhase lanterns with colored tags and cogs, followed by cleavage from the polymer-support. Macrolactonization utilizing MNBA-DMAPO in solution-phase was successfully performed in parallel to afford the desired 64-member destruxin analogues in moderate to good yields. Biological evaluation of the synthesized analogues indicated that a MeAla residue for the building block A is required to induce the desired morphological changes in osteoclast-like multinuclear cells (OCLs), and introduction of the substituent at the R(4) position of a proline moiety is tolerated by the morphology and may enable the preparation of a molecular probe for the target identification in the osteoclasts.
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Affiliation(s)
- Hiroshi Sato
- Graduate
School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
- Mitsubishi Tanabe Pharma Corporation, 3-2-10, Dosho-machi, Chuo-ku, Osaka 541-8505, Japan
| | - Masahito Yoshida
- Graduate
School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Hayato Murase
- Department
of Applied Biological Chemistry, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Hiroshi Nakagawa
- Department
of Applied Biological Chemistry, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Takayuki Doi
- Graduate
School of Pharmaceutical Sciences, Tohoku University, 6-3 Aza-Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
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38
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Kuznetsova SS, Kolesanova EF, Talanova AV, Veselovsky AV. [Prospects for the design of new therapeutically significant protease inhibitors based on knottins and sunflower seed trypsin inhibitor (SFTI 1)]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2016; 62:353-68. [PMID: 27562989 DOI: 10.18097/pbmc20166204353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Plant seed knottins, mainly from the Cucurbitacea family, and sunflower seed trypsin inhibitor (SFTI 1) are the most low-molecular canonical peptide inhibitors of serine proteases. High efficiency of inhibition of various serine proteases, structure rigidity together with the possibility of limited variations of amino acid sequences, high chemical stability, lack of toxic properties, opportunity of production by either chemical synthesis or use of heterologous expression systems make these inhibitors attractive templates for design of new compounds for regulation of therapeutically significant serine protease activities. Hence the design of such compounds represents a prospective research field. The review considers structural characteristics of these inhibitors, their properties, methods of preparation and design of new analogs. Examples of successful employment of natural serine protease inhibitors belonging to knottin family and SFTI 1 as templates for the design of highly specific inhibitors of certain proteases are given.
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Affiliation(s)
| | | | - A V Talanova
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
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Boll E, Drobecq H, Lissy E, Cantrelle FX, Melnyk O. Kinetically Controlled Chemoselective Cyclization Simplifies the Access to Cyclic and Branched Peptides. Org Lett 2016; 18:3842-5. [DOI: 10.1021/acs.orglett.6b01847] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Emmanuelle Boll
- Université de Lille, CNRS, Institut Pasteur de Lille, UMR 8161, F-59000 Lille, France
| | - Hervé Drobecq
- Université de Lille, CNRS, Institut Pasteur de Lille, UMR 8161, F-59000 Lille, France
| | - Elizabeth Lissy
- Université de Lille, CNRS, Institut Pasteur de Lille, UMR 8161, F-59000 Lille, France
| | - François-Xavier Cantrelle
- Université de Lille, CNRS, UMR 8576, UGSF, Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Oleg Melnyk
- Université de Lille, CNRS, Institut Pasteur de Lille, UMR 8161, F-59000 Lille, France
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Timiri AK, Sinha BN, Jayaprakash V. Progress and prospects on DENV protease inhibitors. Eur J Med Chem 2016; 117:125-43. [DOI: 10.1016/j.ejmech.2016.04.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 03/28/2016] [Accepted: 04/04/2016] [Indexed: 12/17/2022]
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Yu S, Du T, Liu Z, Wu Q, Feng G, Dong M, Zhou X, Jiang L, Dai Q. Im10A, a short conopeptide isolated from Conus imperialis and possesses two highly concentrated disulfide bridges and analgesic activity. Peptides 2016; 81:15-20. [PMID: 27131596 DOI: 10.1016/j.peptides.2016.04.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/02/2016] [Accepted: 04/26/2016] [Indexed: 12/27/2022]
Abstract
In the present study, we isolated, synthesized and NMR structurally characterized a novel conopeptide Im10A consisting of 11 amino acids (NTICCEGCMCY-NH2) from Conus imperialis. Unlike other conopeptides with four cysteine residues, Im10A had only two residues in loop 1 and one residue in loop 2 (CC-loop1-C-loop2-C), which formed a stable disulfide connectivity "I-IV, II- III" (framework X) with a type I β-turn. Interestingly, Im10A exhibited 50.7% analgesic activity on rat partial sciatic nerve ligation (PNL) at 2h after Im10A administration. However, 10μM Im10A exhibited no apparent effect on neuronal nicotinic acetylcholine receptor, and it did not target DRG voltage-dependent sodium, potassium and calcium ion channels and opioid receptor. To our knowledge, Im10A had the most concentrated disulfide bridges among conopeptides with four cysteine residues. This finding provided a new motif for the future development of biomimetic compounds.
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Affiliation(s)
- Shuo Yu
- Beijing Institute of Biotechnology, Beijing 10071, PR China
| | - Tianpeng Du
- Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, State Key laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Science, Wuhan 430071, PR China
| | - Zhuguo Liu
- Beijing Institute of Biotechnology, Beijing 10071, PR China
| | - Qiaoling Wu
- Beijing Institute of Biotechnology, Beijing 10071, PR China
| | - Guixue Feng
- Beijing Institute of Biotechnology, Beijing 10071, PR China
| | - Mingxin Dong
- Beijing Institute of Biotechnology, Beijing 10071, PR China
| | - Xiaowei Zhou
- Beijing Institute of Biotechnology, Beijing 10071, PR China
| | - Ling Jiang
- Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, State Key laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Science, Wuhan 430071, PR China.
| | - Qiuyun Dai
- Beijing Institute of Biotechnology, Beijing 10071, PR China.
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Abstract
INTRODUCTION Flaviviruses are major causes of infectious disease. The vast global, social and economic impact due to morbidity and mortality associated with diseases caused by these viruses urgently demands effective therapeutic interventions. There is currently no specific antiviral therapy available for the effective clinical treatment of infections by any of the flaviviridae. Development of more effective vaccines and antiviral agents for the prevention and treatment of most flavivirus infections remains a clear public health priority in the 21st century. AREAS COVERED This review describes some of the recent discoveries in the field of flavivirus inhibitor development, with a particular focus on targeting viral proteins. Emphasis is placed on the advances published during the 2012-2015 period. EXPERT OPINION The field of drug discovery targeting viral proteins has progressed slowly in recent years. New information, particularly on structures, location and mechanisms of action of established protein targets have been reported. There have also been studies on repurposing known drugs as templates for targeting flavivirus proteins and these hits could be promising templates for developing new more potent inhibitors. Further research should be conducted to improve in vitro assays that better reflect the conditions found in cellular environments.
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Affiliation(s)
- W Mei Kok
- a Division of Chemistry and Structural Biology, Institute for Molecular Bioscience , The University of Queensland , Brisbane , Australia
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Abstract
The dengue virus and related flaviviruses are an increasing global health threat. In this perspective, we comment on and review medicinal chemistry efforts aimed at the prevention or treatment of dengue infections. We include target-based approaches aimed at viral or host factors and results from phenotypic screenings in cellular assay systems for viral replication. This perspective is limited to the discussion of results that provide explicit chemistry or structure-activity relationship (SAR), or appear to be of particular interest to the medicinal chemist for other reasons. The discovery and development efforts discussed here may at least partially be extrapolated toward other emerging flaviviral infections, such as West Nile virus. Therefore, this perspective, although not aimed at flaviviruses in general, should also be able to provide an overview of the medicinal chemistry of these closely related infectious agents.
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Affiliation(s)
- Mira A M Behnam
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University , Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Christoph Nitsche
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University , Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Veaceslav Boldescu
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University , Im Neuenheimer Feld 364, 69120 Heidelberg, Germany.,Laboratory of Organic Synthesis, Institute of Chemistry of the Academy of Sciences of Moldova , Academiei 3, 2028 Chisinau, Moldova
| | - Christian D Klein
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University , Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
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Policresulen, a novel NS2B/NS3 protease inhibitor, effectively inhibits the replication of DENV2 virus in BHK-21 cells. Acta Pharmacol Sin 2015; 36:1126-36. [PMID: 26279156 DOI: 10.1038/aps.2015.56] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 05/08/2015] [Indexed: 12/17/2022] Open
Abstract
AIM Dengue is a severe epidemic disease caused by dengue virus (DENV) infection, for which no effective treatment is available. The protease complex, consisting of nonstructural protein 3 (NS3) and its cofactor NS2B, plays a pivotal role in the replication of DENV, thus may be a potential target for anti-DENV drugs. Here, we report a novel inhibitor of DENV2 NS2B/NS3 protease and its antiviral action. METHODS An enzymatic inhibition assay was used for screening DENV2 NS2B/NS3 inhibitors. Cytotoxicity to BHK-21 cells was assessed with MTT assay. Antiviral activity was evaluated in BHK-21 cells transfected with Rlu-DENV-Rep. The molecular mechanisms of the antiviral action was analyzed using surface plasmon resonance, ultraviolet-visible spectral analysis and differential scanning calorimetry assays, as well as molecular docking analysis combined with site-directed mutagenesis. RESULTS In our in-house library of old drugs (~1000 compounds), a topical hemostatic and antiseptic 2-hydroxy-3,5-bis[(4-hydroxy-2-methyl-5-sulfophenyl)methyl]-4-methyl-benzene-sulfonic acid (policresulen) was found to be a potent inhibitor of DENV2 NS2B/NS3 protease with IC50 of 0.48 μg/mL. Furthermore, policresulen inhibited DENV2 replication in BHK-21 cells with IC50 of 4.99 μg/mL, whereas its IC50 for cytotoxicity to BHK-21 cells was 459.45 μg/mL. Policresulen acted as a competitive inhibitor of the protease, and slightly affected the protease stability. Using biophysical technology-based assays and molecular docking analysis combined with site-directed mutagenesis, we demonstrated that the residues Gln106 and Arg133 of DENV2 NS2B/NS3 protease directly interacted with policresulen via hydrogen bonding. CONCLUSION Policresulen is a potent inhibitor of DENV2 NS2B/NS3 protease that inhibits DENV2 replication in BHK-21 cells. The binding mode of the protease and policresulen provides useful hints for designing new type of inhibitors against the protease.
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Antiviral activities of 15 dengue NS2B-NS3 protease inhibitors using a human cell-based viral quantification assay. Antiviral Res 2015; 118:68-74. [DOI: 10.1016/j.antiviral.2015.03.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 03/19/2015] [Accepted: 03/20/2015] [Indexed: 12/25/2022]
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Li L, Basavannacharya C, Chan KWK, Shang L, Vasudevan SG, Yin Z. Structure-guided Discovery of a Novel Non-peptide Inhibitor of Dengue Virus NS2B-NS3 Protease. Chem Biol Drug Des 2015; 86:255-64. [DOI: 10.1111/cbdd.12500] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 12/15/2014] [Accepted: 12/17/2014] [Indexed: 12/19/2022]
Affiliation(s)
- Linfeng Li
- College of Pharmacy; State Key Laboratory of Elemento-Organic Chemistry; Nankai University; Tianjin 300071 China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Tianjin 300071 China
| | - Chandrakala Basavannacharya
- Duke-NUS Graduate Medical School; Program in Emerging Infectious Diseases; 8 College Road Singapore 169857 Singapore
| | - Kitti Wing Ki Chan
- Duke-NUS Graduate Medical School; Program in Emerging Infectious Diseases; 8 College Road Singapore 169857 Singapore
| | - Luqing Shang
- College of Pharmacy; State Key Laboratory of Elemento-Organic Chemistry; Nankai University; Tianjin 300071 China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Tianjin 300071 China
| | - Subhash G. Vasudevan
- Duke-NUS Graduate Medical School; Program in Emerging Infectious Diseases; 8 College Road Singapore 169857 Singapore
| | - Zheng Yin
- College of Pharmacy; State Key Laboratory of Elemento-Organic Chemistry; Nankai University; Tianjin 300071 China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin); Tianjin 300071 China
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Boll E, Ebran JP, Drobecq H, El-Mahdi O, Raibaut L, Ollivier N, Melnyk O. Access to large cyclic peptides by a one-pot two-peptide segment ligation/cyclization process. Org Lett 2014; 17:130-3. [PMID: 25506740 DOI: 10.1021/ol503359w] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The use of the N-acetoacetyl protecting group for N-terminal cysteine residue enabled creation of an efficient and mild one-pot native chemical ligation/SEA ligation sequence giving access to large cyclic peptides.
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Affiliation(s)
- Emmanuelle Boll
- UMR CNRS 8161, Université de Lille, Pasteur Institute of Lille 59021 Lille, France
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Ma X, Jia J, Cao R, Wang X, Fei H. Histidine-iridium(III) coordination-based peptide luminogenic cyclization and cyclo-RGD peptides for cancer-cell targeting. J Am Chem Soc 2014; 136:17734-7. [PMID: 25486120 DOI: 10.1021/ja511656q] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In the field of peptide drug discovery, structural constraining and fluorescent labeling are two sought-after techniques important for both basic research and pharmaceutical development. In this work, we describe an easy-to-use approach for simultaneous peptide cyclization and luminescent labeling based on iridium(III)-histidine coordination (Ir-HH cyclization). Using a series of model peptides with histidine flanking each terminus, the binding activity and reaction kinetics of Ir-HH cyclization of different ring sizes were characterized. In the series, Ir-HAnH (n = 2, 3) with moderate ring sizes provides appropriate flexibility and proper distance between histidines for cyclic formation, which leads to the best binding affinity and structural stability in physiological conditions, as compared to other Ir-HH-cyclized peptides with smaller (n = 0, 1) or larger (n = 4, 5) ring sizes. Ir-HRGDH, an Ir-HH-cyclized peptide containing integrin targeting motif Arg-Gly-Asp (RGD), showed better targeting affinity than its linear form and enhanced membrane permeability in comparison with fluorescein-labeled cyclic RGDyK peptide. Cell death inducing peptide KLA-linked Ir-HRGDH (Ir-HRGDH-KLA) showed dramatically enhanced cytotoxicity and high selectivity for cancer cells versus noncancer cells. These data demonstrate that the method conveniently combines structural constraining of peptides with luminescent imaging capabilities, which facilitates functional and intracellular characterization of potential peptide-based drug leads, thus introducing a new tool to meet emerging needs in medicinal research.
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Affiliation(s)
- Xiaochuan Ma
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Key Laboratory for Nanotheranostics, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences , Suzhou 215123, China
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Liu H, Wu R, Sun Y, Ye Y, Chen J, Luo X, Shen X, Liu H. Identification of novel thiadiazoloacrylamide analogues as inhibitors of dengue-2 virus NS2B/NS3 protease. Bioorg Med Chem 2014; 22:6344-52. [DOI: 10.1016/j.bmc.2014.09.057] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 09/24/2014] [Accepted: 09/26/2014] [Indexed: 10/24/2022]
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50
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Nitsche C, Holloway S, Schirmeister T, Klein CD. Biochemistry and medicinal chemistry of the dengue virus protease. Chem Rev 2014; 114:11348-81. [PMID: 25268322 DOI: 10.1021/cr500233q] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Christoph Nitsche
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University , Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
| | - Steven Holloway
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz , Staudingerweg 5, D-55128 Mainz, Germany
| | - Tanja Schirmeister
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz , Staudingerweg 5, D-55128 Mainz, Germany
| | - Christian D Klein
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University , Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
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