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Sureshan M, Brintha S, Jothi A. Identification of Mulberrofuran as a potent inhibitor of hepatitis A virus 3C pro and RdRP enzymes through structure-based virtual screening, dynamics simulation, and DFT studies. Mol Divers 2024; 28:1609-1628. [PMID: 37386350 DOI: 10.1007/s11030-023-10679-7] [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: 04/25/2023] [Accepted: 06/16/2023] [Indexed: 07/01/2023]
Abstract
Hepatitis is a medical condition characterized by inflammation of the liver. It is commonly caused by the hepatitis viruses A, B, C, D, and E. Hepatitis A virus (HAV) is highly contagious and can spread from infected individuals, through contaminated food, blood, or can also be water-borne. As per the statistics of World Health Organization (WHO), HAV infects about 1.4 million individuals each year globally. In this research work, we have focused on identifying natural product-based potential inhibitors for the two major enzymes of HAV namely 3C proteinase (3Cpro) and RNA-directed RNA polymerase (RdRP). The enzyme 3Cpro plays an important role in proteolytic activity that promotes viral maturation and infectivity. RNA-directed RNA polymerase facilitate viral replication and transcription. Structure-based virtual screening was carried out using NPACT database that contains a collection of 1574 curated plant-derived natural compounds that are validated by experiments. The screening procedure identified the phytochemical Mulberrofuran W, which could bind to both the targets 3Cpro and RdRP. The phytochemical Mulberrofuran W also had better binding affinity compared to the control compounds atropine and pyridinyl ester, which are previously identified inhibitors of HAV 3Cpro and RdRP, respectively. The Mulberrofuran W bound 3Cpro and RdRP complexes were subjected to 200 ns molecular dynamics simulations and were found to be stable and interacting with the active site of the enzymes throughout the course of complex MD simulations. In addition to DFT, MMGBSA studies were also performed to validate the identified potential inhibitor further. The identified phytochemical Mulberrofuran W can be considered as a new potential drug candidate and could be taken up for experimental evaluation against HAV infection.
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Affiliation(s)
- Muthusamy Sureshan
- Department of Bioinformatics, School of Chemical & Biotechnology, SASTRA Deemed University, Thanjavur, 613401, India
| | - Sathishkumar Brintha
- Department of Bioinformatics, School of Chemical & Biotechnology, SASTRA Deemed University, Thanjavur, 613401, India
| | - Arunachalam Jothi
- Department of Bioinformatics, School of Chemical & Biotechnology, SASTRA Deemed University, Thanjavur, 613401, India.
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Gayatri, Brewitz L, Ibbotson L, Salah E, Basak S, Choudhry H, Schofield CJ. Thiophene-fused γ-lactams inhibit the SARS-CoV-2 main protease via reversible covalent acylation. Chem Sci 2024; 15:7667-7678. [PMID: 38784729 PMCID: PMC11110133 DOI: 10.1039/d4sc01027b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 04/15/2024] [Indexed: 05/25/2024] Open
Abstract
Enzyme inhibitors working by O-acylation of nucleophilic serine residues are of immense medicinal importance, as exemplified by the β-lactam antibiotics. By contrast, inhibition of nucleophilic cysteine enzymes by S-acylation has not been widely exploited for medicinal applications. The SARS-CoV-2 main protease (Mpro) is a nucleophilic cysteine protease and a validated therapeutic target for COVID-19 treatment using small-molecule inhibitors. The clinically used Mpro inhibitors nirmatrelvir and simnotrelvir work via reversible covalent reaction of their electrophilic nitrile with the Mpro nucleophilic cysteine (Cys145). We report combined structure activity relationship and mass spectrometric studies revealing that appropriately functionalized γ-lactams can potently inhibit Mpro by reversible covalent reaction with Cys145 of Mpro. The results suggest that γ-lactams have potential as electrophilic warheads for development of covalently reacting small-molecule inhibitors of Mpro and, by implication, other nucleophilic cysteine enzymes.
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Affiliation(s)
- Gayatri
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford UK
| | - Lennart Brewitz
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford UK
| | - Lewis Ibbotson
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford UK
| | - Eidarus Salah
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford UK
| | - Shyam Basak
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford UK
| | - Hani Choudhry
- Department of Biochemistry, Center for Artificial Intelligence in Precision Medicines, King Abdulaziz University Jeddah Saudi Arabia
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford UK
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K AK, Mahesh Y, Panwar J, Gupta S. Remediation of multifarious metal ions and molecular docking assessment for pathogenic microbe disinfection in aqueous solution by waste-derived Ca-MOF. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:21545-21567. [PMID: 38393560 DOI: 10.1007/s11356-024-32311-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 01/29/2024] [Indexed: 02/25/2024]
Abstract
The present study demonstrates an eco-friendly and cost-effective synthesis of calcium terephthalate metal-organic frameworks (Ca-MOF). The Ca-MOF were composed of metal ions (Ca2+) and organic ligands (terephthalic acid; TPA); the former was obtained from egg shells, and the latter was obtained from processing waste plastic bottles. Detailed characterization using standard techniques confirmed the synthesis of Ca-MOF with an average particle size of 461.9 ± 15 nm. The synthesized Ca-MOF was screened for its ability to remove multiple metal ions from an aqueous solution. Based on the maximum sorption capacity, Pb2+, Cd2+, and Cu2+ ions were selected for individual parametric batch studies. The obtained results were interpreted using standard isotherms and kinetic models. The maximum sorption capacity (qm) obtained from the Langmuir model was found to be 644.07 ± 47, 391.4 ± 26, and 260.5 ± 14 mg g-1 for Pb2+, Cd2+, and Cu2+, respectively. Moreover, Ca-MOF also showed an excellent ability to remove all three metal ions simultaneously from a mixed solution. The metal nodes and bonded TPA from Ca-MOF were dissociated by the acid dissolution method, which protonated and isolated TPA for reuse. Further, the crystal structure of Ca-MOF was prepared and docked with protein targets of selected pathogenic water-borne microbes, which showed its disinfection potential. Overall, multiple metal sorption capability, regeneration studies, and broad-spectrum antimicrobial activity confirmed the versatility of synthesized Ca-MOF for industrial wastewater treatment.
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Affiliation(s)
- Anil Kumar K
- Department of Chemical Engineering, Birla Institute of Technology and Science, Pilani, 333031, India
| | - Yeshwanth Mahesh
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jitendra Panwar
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, 333031, India
| | - Suresh Gupta
- Department of Chemical Engineering, Birla Institute of Technology and Science, Pilani, 333031, India.
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Moharana M, Pattanayak SK, Khan F. Bioactive compounds from Pandanous fascicularis as potential therapeutic candidate to tackle hepatitis a inhibition: Docking and molecular dynamics simulation study. J Biomol Struct Dyn 2023; 41:10478-10494. [PMID: 36541128 DOI: 10.1080/07391102.2022.2158940] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 12/10/2022] [Indexed: 12/24/2022]
Abstract
Due to extensive pharmacological research, medicinal plants the underpinning of indigenous herbal serve as a possible source of key compounds for the development of new drugs. Hepatitis A, one of the most widespread infectious diseases associated with global public health issues. The transmission of hepatitis A virus (HAV) occurs, through personal contact, as well as contaminated food/water. The HAV 3C cysteine protease is a non-structural protein, plays pivotal role in proliferation and viral replication. Significant phytochemicals of Pandanous fascicularis include phytosterol, kobusin, epipinoresinol, and ceroptene, which have a wide variety of biological functions. Through ADMET investigation, we have screened fifteen phytochemicals for this study. Additionally, using molecular docking, these phytochemicals were docked with the HAV 3C protease which signifies the phytochemicals phytosterol, kobusin, epipinoresinol, and ceroptene have a significant capability to bind with hepatitis A virus protein.The docking study was further accompanied by analyzes RMSD, RMSF, Rg, SASA, H-bond number, and principal component analysis through 100 ns MD simulations. The molecular dynamics study reveals that, all four phytochemicals possess considerable binding efficacy with hepatitis A virus protein. Based on our computational study and MMGBSA calculations, phytosterol, kobusin and epipinoresinol phytochemicals may be a potential drug candidate for inhibition of hepatitis A. The potential therapeutic characteristics of the phytochemicals against hepatitis A inhibition offer additional support for the in vitro and in vivo studies in future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Maheswata Moharana
- Department of Chemistry, National Institute of Technology, Raipur, India
| | | | - Fahmida Khan
- Department of Chemistry, National Institute of Technology, Raipur, India
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Soleman DM, Eldahshan OA, Ibrahim MH, Ogaly HA, Galal HM, Batiha GES, Elkousy RH. GC/MS Analysis, Cytotoxicity, and Antiviral Activities of Annona glabra Hexane Extract Supported by In Silico Study. Molecules 2023; 28:molecules28041628. [PMID: 36838616 PMCID: PMC9966597 DOI: 10.3390/molecules28041628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/22/2023] [Accepted: 01/31/2023] [Indexed: 02/10/2023] Open
Abstract
Annona glabra Linn is employed in conventional medicine to treat a number of human disorders, including cancer and viruses. In the present investigation, the significant phytochemical components of Annona glabra hexane extract were identified using gas chromatography-mass spectrometry (GC-MS) analysis. Three major compounds were identified in the hexane extract: tritriacontane (30.23%), 13, 17-dimethyl-tritriacontane (22.44%), and limonene (18.97%). MTT assay was used to assess the cytotoxicity of the extract on six human cancer cell lines including liver (HepG-2), pancreas (PANC-1), lung (A-549), breast (MCF-7, HTB-22), prostate (PC-3), and colon (CACO-2, ATB-37). The extract exhibited significant cytotoxic activity against both CACO-2 and A-549 cancer cell lines (IC50 = 47 ± 0.74 μg/mL and 56.82 ± 0.92 μg/mL) in comparison with doxorubicin (IC50 = 31.91 ± 0.81 μg/mL and 23.39 ± 0.43 μg/mL) and of SI of 3.8 and 3.1, respectively. It also induced moderate-to-weak activities against the other cancerous cell lines: PC-3, PANC-1, MCF-7, and HepG-2 (IC50 = 81.86 ± 3.26, 57.34 ± 0.77, 80.31 ± 4.13, and 57.01 ± 0.85 μg/mL) in comparison to doxorubicin (IC50 = 32.9 ± 1.74, 19.07 ± 0.2, 15.48 ± 0.84 and 5.4 ± 0.22 μg/mL, respectively) and SI of 2.2, 3.1, 2.2, and 3.1, respectively. In vitro anti-HSV1 (Herpes simplex 1 virus) and HAV (Hepatitis A virus) activity was evaluated using MTT colorimetric assay with three different protocols to test protective, anti-replicative, and anti-infective antiviral activities, and three separate replications of each experiment were conducted. The plant extract showed promising protective and virucidal activity against HSV1 with no significant difference with acyclovir (79.55 ± 1.67 vs. 68.44 ± 7.62 and 70.91 ± 7.02 vs. 83.76 ± 5.67), while it showed mild protective antiviral activity against HAV (48.08 ±3.46) with no significant difference vs. acyclovir (36.89 ± 6.61). The selected main compounds were examined for their bioactivity through in silico molecular docking, which exhibited that limonene could possess the strongest antiviral properties. These findings support Annona glabra's conventional use, which is an effective source of antiviral and anticancer substances that could be used in pharmaceuticals.
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Affiliation(s)
- Dalia M. Soleman
- Department of Pharmacognosy, Faculty of Pharmacy, Misr International University, Cairo P.O. Box 41611, Egypt
| | - Omayma A. Eldahshan
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt
- Center for Drug Discovery Research and Development, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt
- Correspondence: (O.A.E.); (R.H.E.)
| | - Mona H. Ibrahim
- Department of Pharmaceutical Medicinal Chemistry and Drug Design, Faculty of Pharmacy (for Girls), Al-Azhar University, Nasr City, Cairo 11651, Egypt
| | - Hanan A. Ogaly
- Chemistry Department, College of Science, King Khalid University, Abha 61421, Saudi Arabia
- Biochemistry and Molecular Biology Department, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt
| | - Heba M. Galal
- Department of Medical Physiology, College of Medicine, Jouf University, Sakaka 72388, Saudi Arabia
- Department of Medical Physiology, Faculty of Medicine, Assiut University, Assiut 71515, Egypt
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour 22511, Egypt
| | - Rawah H. Elkousy
- Department of Pharmacognosy, Faculty of Pharmacy (for Girls), Al-Azhar University, Nasr City, Cairo 11651, Egypt
- Correspondence: (O.A.E.); (R.H.E.)
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Hepatitis A: Viral Structure, Classification, Life Cycle, Clinical Symptoms, Diagnosis Error, and Vaccination. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2023; 2023:4263309. [PMID: 36644336 PMCID: PMC9833905 DOI: 10.1155/2023/4263309] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 12/14/2022] [Accepted: 12/21/2022] [Indexed: 01/06/2023]
Abstract
Hepatitis A virus (HAV) is one of the well-known viruses that cause hepatitis all around the globe. Although this illness has decreased in developed countries due to extensive immunization, numerous developing and under-developed countries are struggling with this virus. HAV infection can be spread by oral-fecal contact, and there are frequent epidemics through nutrition. Improvements in socioeconomic and sanitary circumstances have caused a shift in the disease's prevalence worldwide. Younger children are usually asymptomatic, but as they become older, the infection symptoms begin to appear. Symptoms range from slight inflammation and jaundice to acute liver failure in older individuals. While an acute infection may be self-limiting, unrecognized persistent infections, and the misapplication of therapeutic methods based on clinical guidelines are linked to a higher incidence of cirrhosis, hepatocellular carcinoma, and mortality. Fortunately, most patients recover within two months of infection, though 10-15% of patients will relapse within the first six months. A virus seldom leads to persistent infection or liver damage. The mainstay of therapy is based on supportive care. All children from 12-23 months, as well as some susceptible populations, should receive routine vaccinations, according to the Centers for Disease Control and Prevention and the American Academy of Pediatrics. Laboratory diagnosis of HAV is based on antigen detection, checking liver enzyme levels, and antibody screening. Furthermore, polymerase chain reaction (PCR) technology has identified HAV in suspected nutrition sources; therefore, this technique is used for preventative measures and food-related laws.
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Sasaki-Tanaka R, Nagulapalli Venkata KC, Okamoto H, Moriyama M, Kanda T. Evaluation of Potential Anti-Hepatitis A Virus 3C Protease Inhibitors Using Molecular Docking. Int J Mol Sci 2022; 23:6044. [PMID: 35682728 PMCID: PMC9181686 DOI: 10.3390/ijms23116044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 05/26/2022] [Accepted: 05/26/2022] [Indexed: 12/05/2022] Open
Abstract
Hepatitis A virus (HAV) infection is a major cause of acute hepatitis worldwide and occasionally causes acute liver failure and can lead to death in the absence of liver transplantation. Although HAV vaccination is available, the prevalence of HAV vaccination is not adequate in some countries. Additionally, the improvements in public health reduced our immunity to HAV infection. These situations motivated us to develop potentially new anti-HAV therapeutic options. We carried out the in silico screening of anti-HAV compounds targeting the 3C protease enzyme using the Schrodinger Modeling software from the antiviral library of 25,000 compounds to evaluate anti-HAV 3C protease inhibitors. Additionally, in vitro studies were introduced to examine the inhibitory effects of HAV subgenomic replicon replication and HAV HA11-1299 genotype IIIA replication in hepatoma cell lines using luciferase assays and real-time RT-PCR. In silico studies enabled us to identify five lead candidates with optimal binding interactions in the active site of the target HAV 3C protease using the Schrodinger Glide program. In vitro studies substantiated our hypothesis from in silico findings. One of our lead compounds, Z10325150, showed 47% inhibitory effects on HAV genotype IB subgenomic replicon replication and 36% inhibitory effects on HAV genotype IIIA HA11-1299 replication in human hepatoma cell lines, with no cytotoxic effects at concentrations of 100 μg/mL. The effects of the combination therapy of Z10325150 and RNA-dependent RNA polymerase inhibitor, favipiravir on HAV genotype IB HM175 subgenomic replicon replication and HAV genotype IIIA HA11-1299 replication showed 64% and 48% inhibitory effects of HAV subgenomic replicon and HAV replication, respectively. We identified the HAV 3C protease inhibitor Z10325150 through in silico screening and confirmed the HAV replication inhibitory activity in human hepatocytes. Z10325150 may offer the potential for a useful HAV inhibitor in severe hepatitis A.
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Affiliation(s)
- Reina Sasaki-Tanaka
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-kamicho, Itabashi-ku, Tokyo 173-8610, Japan; (M.M.); (T.K.)
| | - Kalyan C. Nagulapalli Venkata
- Department of Pharmaceutical and Administrative Sciences, Saint Louis College of Pharmacy, University of Health Sciences and Pharmacy, St. Louis, MO 63010, USA;
| | - Hiroaki Okamoto
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, 3311-1 Yakushiji, Shimotsuke-shi, Tochigi 329-0498, Japan;
| | - Mitsuhiko Moriyama
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-kamicho, Itabashi-ku, Tokyo 173-8610, Japan; (M.M.); (T.K.)
| | - Tatsuo Kanda
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-kamicho, Itabashi-ku, Tokyo 173-8610, Japan; (M.M.); (T.K.)
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Stewart LR, Willman M, Marty D, Cole AE, Willie K. Critical residues for proteolysis activity of maize chlorotic dwarf virus (MCDV) 3C-like protease and comparison of activity of orthologous waikavirus proteases. Virology 2021; 567:57-64. [PMID: 34998226 DOI: 10.1016/j.virol.2021.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 11/17/2022]
Abstract
Maize chlorotic dwarf virus (MCDV) encodes a 3C-like protease that cleaves the N-terminal polyprotein (R78) as previously demonstrated. Here, we examined amino acid residues required for catalytic activity of the protease, including those in the predicted catalytic triad, amino acid residues H2667, D2704, and C2798, as well as H2817 hypothesized to be important in substrate binding. These and other residues were targeted for mutagenesis and tested for proteolytic cleavage activity on the N-terminal 78 kDa MCDV-S polyprotein substrate to identify mutants that abolished catalytic activity. Mutations that altered the predicted catalytic triad residues and H2817 disrupted MCDV-S protease activity, as did mutagenesis of a conserved tyrosine residue, Y2774. The protease activity and R78 cleavage of orthologs from divergent MCDV isolates MCDV-Tn and MCDV-M1, and other waikavirus species including rice tungro spherical virus (RTSV) and bellflower vein chlorosis virus (BVCV) were also examined.
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Affiliation(s)
- Lucy R Stewart
- USDA ARS Foreign Disease-Weed Science Research Unit, Frederick, MD, 21702, USA.
| | - Matthew Willman
- USDA ARS Corn, Soybean and Wheat Quality Research Unit, Wooster, OH, 44691, USA
| | - DeeMarie Marty
- USDA ARS Corn, Soybean and Wheat Quality Research Unit, Wooster, OH, 44691, USA
| | | | - Kristen Willie
- USDA ARS Corn, Soybean and Wheat Quality Research Unit, Wooster, OH, 44691, USA
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Ekanayaka P, Shin SH, Weeratunga P, Lee H, Kim TH, Chathuranga K, Subasinghe A, Park JH, Lee JS. Foot-and-Mouth Disease Virus 3C Protease Antagonizes Interferon Signaling and C142T Substitution Attenuates the FMD Virus. Front Microbiol 2021; 12:737031. [PMID: 34867853 PMCID: PMC8639872 DOI: 10.3389/fmicb.2021.737031] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/28/2021] [Indexed: 12/24/2022] Open
Abstract
3C protease (3Cpro), a chymotrypsin-like cysteine protease encoded by the foot-and-mouth disease virus (FMDV), plays an essential role in processing the FMDV P1 polyprotein into individual viral capsid proteins in FMDV replication. Previously, it has been shown that 3Cpro is involved in the blockage of the host type-I interferon (IFN) responses by FMDV. However, the underlying mechanisms are poorly understood. Here, we demonstrated that the protease activity of 3Cpro contributed to the degradation of RIG-I and MDA5, key cytosolic sensors of the type-I IFN signaling cascade in proteasome, lysosome and caspase-independent manner. And also, we examined the degradation ability on RIG-I and MDA5 of wild-type FMDV 3Cpro and FMDV 3Cpro C142T mutant which is known to significantly alter the enzymatic activity of 3Cpro. The results showed that the FMDV 3Cpro C142T mutant dramatically reduce the degradation of RIG-I and MDA5 due to weakened protease activity. Thus, the protease activity of FMDV 3Cpro governs its RIG-I and MDA5 degradation ability and subsequent negative regulation of the type-I IFN signaling. Importantly, FMD viruses harboring 3Cpro C142T mutant showed the moderate attenuation of FMDV in a pig model. In conclusion, our results indicate that a novel mechanism evolved by FMDV 3Cpro to counteract host type-I IFN responses and a rational approach to virus attenuation that could be utilized for future vaccine development.
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Affiliation(s)
- Pathum Ekanayaka
- College of Veterinary Medicine, Chungnam National University, Daejeon, South Korea
| | - Sung Ho Shin
- Animal and Plant Quarantine Agency, Gyeongsangbuk-do, South Korea
| | - Prasanna Weeratunga
- College of Veterinary Medicine, Chungnam National University, Daejeon, South Korea
| | - Hyuncheol Lee
- College of Veterinary Medicine, Chungnam National University, Daejeon, South Korea
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, United States
| | - Tae-Hwan Kim
- College of Veterinary Medicine, Chungnam National University, Daejeon, South Korea
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Kiramage Chathuranga
- College of Veterinary Medicine, Chungnam National University, Daejeon, South Korea
| | - Ashan Subasinghe
- College of Veterinary Medicine, Chungnam National University, Daejeon, South Korea
| | - Jong-Hyeon Park
- Animal and Plant Quarantine Agency, Gyeongsangbuk-do, South Korea
| | - Jong-Soo Lee
- College of Veterinary Medicine, Chungnam National University, Daejeon, South Korea
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Kanda T, Sasaki R, Masuzaki R, Moriyama M. Artificial intelligence and machine learning could support drug development for hepatitis A virus internal ribosomal entry sites. Artif Intell Gastroenterol 2021; 2:1-9. [DOI: 10.35712/aig.v2.i1.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/29/2020] [Accepted: 02/12/2021] [Indexed: 02/06/2023] Open
Abstract
Hepatitis A virus (HAV) infection is still an important health issue worldwide. Although several effective HAV vaccines are available, it is difficult to perform universal vaccination in certain countries. Therefore, it may be better to develop antivirals against HAV for the prevention of severe hepatitis A. We found that several drugs potentially inhibit HAV internal ribosomal entry site-dependent translation and HAV replication. Artificial intelligence and machine learning could also support screening of anti-HAV drugs, using drug repositioning and drug rescue approaches.
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Affiliation(s)
- Tatsuo Kanda
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, Itabashi-ku 173-8610, Tokyo, Japan
| | - Reina Sasaki
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, Itabashi-ku 173-8610, Tokyo, Japan
| | - Ryota Masuzaki
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, Itabashi-ku 173-8610, Tokyo, Japan
| | - Mitsuhiko Moriyama
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, Itabashi-ku 173-8610, Tokyo, Japan
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Wątły J, Miller A, Kozłowski H, Rowińska-Żyrek M. Peptidomimetics - An infinite reservoir of metal binding motifs in metabolically stable and biologically active molecules. J Inorg Biochem 2021; 217:111386. [PMID: 33610030 DOI: 10.1016/j.jinorgbio.2021.111386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 01/14/2021] [Accepted: 01/27/2021] [Indexed: 12/12/2022]
Abstract
The involvement of metal ions in interactions with therapeutic peptides is inevitable. They are one of the factors able to fine-tune the biological properties of antimicrobial peptides, a promising group of drugs with one large drawback - a problematic metabolic stability. Appropriately chosen, proteolytically stable peptidomimetics seem to be a reasonable solution of the problem, and the use of D-, β-, γ-amino acids, unnatural amino acids, azapeptides, peptoids, cyclopeptides and dehydropeptides is an infinite reservoir of metal binding motifs in metabolically stable, well-designed, biologically active molecules. Below, their specific structural features, metal-chelating abilities and antimicrobial potential are discussed.
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Affiliation(s)
- Joanna Wątły
- Faculty of Chemistry, University of Wroclaw, Joliot - Curie 14, Wroclaw 50-383, Poland.
| | - Adriana Miller
- Faculty of Chemistry, University of Wroclaw, Joliot - Curie 14, Wroclaw 50-383, Poland
| | - Henryk Kozłowski
- Faculty of Chemistry, University of Wroclaw, Joliot - Curie 14, Wroclaw 50-383, Poland; Department of Health Sciences, University of Opole, Katowicka 68, Opole 45-060, Poland
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Kassem AF, Batran RZ, Abbas EMH, Elseginy SA, Shaheen MNF, Elmahdy EM. New 4-phenylcoumarin derivatives as potent 3C protease inhibitors: Design, synthesis, anti-HAV effect and molecular modeling. Eur J Med Chem 2019; 168:447-460. [PMID: 30844608 DOI: 10.1016/j.ejmech.2019.02.048] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/31/2019] [Accepted: 02/14/2019] [Indexed: 12/30/2022]
Abstract
A new series of 4-phenylcoumarin derivatives was synthesized starting from (2-oxo-4-phenyl-2H-chromen-7-yloxy) acetic acid hydrazide 3. Evaluation of the target compounds for their antiviral activity against hepatitis A virus revealed that the ethylthiosemicarbazide derivative 7b was the most potent virucidal agent (IC50 = 3.1 μg/ml, TI = 83). The Schiff's bases 14c and 14b demonstrated the highest virustatic effects against viral adsorption and replication, respectively (14c; IC50 = 8.5 μg/ml, TI = 88 and 14b; IC50 = 10.7 μg/ml, TI = 91). Furthermore, compounds 7b, 14b and 14c were tested against HAV 3C protease and showed significant inhibition effects (Ki = 1.903, 0.104 and 0.217 μM, respectively). The remarkable inhibitory effect expressed by the three target compounds against HAV 3C protease prompted us to expand our research on HRV 3C protease, a structurally related enzyme of the same family, and interestingly, the three target compounds displayed significant inhibitory effect against HRV 3C protease (IC50 = 16.10, 4.13 and 6.30 μM, respectively). Moreover, the active compounds 7b, 14b and 14c were docked within the pocket site of HAV 3C protease (PDB code: 2HAL) illustrating a strong H-profile with the key amino acids Gly170 and Cys172 similar to the co-crystallized ligand. Furthermore, 3D-pharmacophore and quantitative structure activity relationship (QSAR) models were generated to explore the structural requirements for the observed antiviral activity.
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Affiliation(s)
- Asmaa F Kassem
- Chemistry of Natural and Microbial Products Department, Pharmaceutical and Drug Industries Research Division, National Research Centre, 33 El Bohouth St., Dokki, Giza, p.o.box 12622, Egypt
| | - Rasha Z Batran
- Chemistry of Natural Compounds Department, Pharmaceutical and Drug Industries Research Division, National Research Centre, 33 El Bohouth St., Dokki, Giza, p.o. box 12622, Egypt.
| | - Eman M H Abbas
- Chemistry of Natural and Microbial Products Department, Pharmaceutical and Drug Industries Research Division, National Research Centre, 33 El Bohouth St., Dokki, Giza, p.o.box 12622, Egypt
| | - Samia A Elseginy
- Green Chemistry Department, Chemical Industries Research Division, National Research Centre, 33 El Bohouth St., Dokki, Giza, p.o. box 12622, Egypt
| | - Mohamed N F Shaheen
- Environmental Virology Laboratory, Water pollution Research Department, Environmental Research Division, National Research Centre, 33 El Bohouth St., Dokki, Giza, p.o. box 12622, Egypt
| | - Elmahdy M Elmahdy
- Environmental Virology Laboratory, Water pollution Research Department, Environmental Research Division, National Research Centre, 33 El Bohouth St., Dokki, Giza, p.o. box 12622, Egypt
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13
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Banerjee K, Bhat R, Rao VUB, Nain A, Rallapalli KL, Gangopadhyay S, Singh RP, Banerjee M, Jayaram B. Toward development of generic inhibitors against the 3C proteases of picornaviruses. FEBS J 2019; 286:765-787. [PMID: 30461192 PMCID: PMC7164057 DOI: 10.1111/febs.14707] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 09/20/2018] [Accepted: 11/16/2018] [Indexed: 12/25/2022]
Abstract
Development of novel antivirals, which requires knowledge of the viral life cycle in molecular detail, is a daunting task, involving extensive investments, and frequently resulting in failure. As there exist significant commonalities among virus families in the manner of host interaction, identifying and targeting common rather than specific features may lead to the development of broadly useful antivirals. Here, we have targeted the 3C protease of Hepatitis A Virus (HAV), a feco-orally transmitted virus of the family Picornaviridae, for identification of potential antivirals. The 3C protease is a viable drug target as it is required by HAV, as well as by other picornaviruses, for post-translational proteolysis of viral polyproteins and for inhibiting host innate immune pathways. Computational screening, followed by chemical synthesis and experimental validation resulted in identification of a few compounds which, at low micromolar concentrations, could inhibit HAV 3C activity. These compounds were further tested experimentally against the 3C protease of Human Rhinovirus, another member of the Picornaviridae family, with comparable results. Computational studies on 3C proteases from other members of the picornavirus family have indicated that the compounds identified could potentially be generic inhibitors for picornavirus 3C proteases.
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Affiliation(s)
- Kamalika Banerjee
- Kusuma School of Biological SciencesIndian Institute of TechnologyHauz KhasIndia
| | - Ruchika Bhat
- Department of ChemistryIndian Institute of TechnologyHauz KhasIndia
- Supercomputing Facility for Bioinformatics & Computational BiologyIndian Institute of TechnologyHauz KhasIndia
| | | | - Anshu Nain
- Kusuma School of Biological SciencesIndian Institute of TechnologyHauz KhasIndia
| | - Kartik Lakshmi Rallapalli
- Department of ChemistryIndian Institute of TechnologyHauz KhasIndia
- Present address:
Department of Chemistry and BiochemistryUniversity of California San Diego9500 Gilman DrLa JollaCA92093USA
| | - Sohona Gangopadhyay
- Department of ChemistryIndian Institute of TechnologyHauz KhasIndia
- Present address:
Chemical DivisionGeological Survey of India15‐16 Jhalana DungriWestern RegionJaipur302004India
| | - R. P. Singh
- Department of ChemistryIndian Institute of TechnologyHauz KhasIndia
| | - Manidipa Banerjee
- Kusuma School of Biological SciencesIndian Institute of TechnologyHauz KhasIndia
| | - Bhyravabhotla Jayaram
- Kusuma School of Biological SciencesIndian Institute of TechnologyHauz KhasIndia
- Department of ChemistryIndian Institute of TechnologyHauz KhasIndia
- Supercomputing Facility for Bioinformatics & Computational BiologyIndian Institute of TechnologyHauz KhasIndia
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14
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Yang J, Leen EN, Maree FF, Curry S. Crystal structure of the 3C protease from Southern African Territories type 2 foot-and-mouth disease virus. PeerJ 2016; 4:e1964. [PMID: 27168976 PMCID: PMC4860321 DOI: 10.7717/peerj.1964] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 04/02/2016] [Indexed: 11/23/2022] Open
Abstract
The replication of foot-and-mouth disease virus (FMDV) is dependent on the virus-encoded 3C protease (3Cpro). As in other picornaviruses, 3Cpro performs most of the proteolytic processing of the polyprotein expressed from the large open reading frame in the RNA genome of the virus. Previous work revealed that the 3Cpro from serotype A—one of the seven serotypes of FMDV—adopts a trypsin-like fold. On the basis of capsid sequence comparisons the FMDV serotypes are grouped into two phylogenetic clusters, with O, A, C, and Asia 1 in one, and the three Southern African Territories serotypes, (SAT-1, SAT-2 and SAT-3) in another, a grouping pattern that is broadly, but not rigidly, reflected in 3Cpro amino acid sequences. We report here the cloning, expression and purification of 3C proteases from four SAT serotype viruses (SAT2/GHA/8/91, SAT1/NIG/5/81, SAT1/UGA/1/97, and SAT2/ZIM/7/83) and the crystal structure at 3.2 Å resolution of 3Cpro from SAT2/GHA/8/91.
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Affiliation(s)
- Jingjie Yang
- Departmet of Life Sciences, Imperial College , London , United Kingdom
| | - Eoin N Leen
- Departmet of Life Sciences, Imperial College , London , United Kingdom
| | - Francois F Maree
- Transboundary Animal Disease Programme, Agricultural Research Council, Onderstepoort Veterinary Institute , Onderstepoort , South Africa
| | - Stephen Curry
- Departmet of Life Sciences, Imperial College , London , United Kingdom
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15
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Sun D, Chen S, Cheng A, Wang M. Roles of the Picornaviral 3C Proteinase in the Viral Life Cycle and Host Cells. Viruses 2016; 8:82. [PMID: 26999188 PMCID: PMC4810272 DOI: 10.3390/v8030082] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Revised: 02/27/2016] [Accepted: 03/07/2016] [Indexed: 12/12/2022] Open
Abstract
The Picornaviridae family comprises a large group of non-enveloped viruses that have a major impact on human and veterinary health. The viral genome contains one open reading frame encoding a single polyprotein that can be processed by viral proteinases. The crucial 3C proteinases (3C(pro)s) of picornaviruses share similar spatial structures and it is becoming apparent that 3C(pro) plays a significant role in the viral life cycle and virus host interaction. Importantly, the proteinase and RNA-binding activity of 3C(pro) are involved in viral polyprotein processing and the initiation of viral RNA synthesis. In addition, 3C(pro) can induce the cleavage of certain cellular factors required for transcription, translation and nucleocytoplasmic trafficking to modulate cell physiology for viral replication. Due to interactions between 3C(pro) and these essential factors, 3C(pro) is also involved in viral pathogenesis to support efficient infection. Furthermore, based on the structural conservation, the development of irreversible inhibitors and discovery of non-covalent inhibitors for 3C(pro) are ongoing and a better understanding of the roles played by 3C(pro) may provide insights into the development of potential antiviral treatments. In this review, the current knowledge regarding the structural features, multiple functions in the viral life cycle, pathogen host interaction, and development of antiviral compounds for 3C(pro) is summarized.
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Affiliation(s)
- Di Sun
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China.
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China.
| | - Shun Chen
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China.
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang, Chengdu 611130, China.
| | - Anchun Cheng
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China.
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang, Chengdu 611130, China.
| | - Mingshu Wang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China.
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China.
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Wenjiang, Chengdu 611130, China.
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16
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Kanda T, Nakamoto S, Wu S, Nakamura M, Jiang X, Haga Y, Sasaki R, Yokosuka O. Direct-acting Antivirals and Host-targeting Agents against the Hepatitis A Virus. J Clin Transl Hepatol 2015; 3:205-10. [PMID: 26623267 PMCID: PMC4663202 DOI: 10.14218/jcth.2015.00016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 06/10/2015] [Accepted: 06/11/2015] [Indexed: 12/16/2022] Open
Abstract
Hepatitis A virus (HAV) infection is a major cause of acute hepatitis and occasionally leads to acute liver failure in both developing and developed countries. Although effective vaccines for HAV are available, the development of new antivirals against HAV may be important for the control of HAV infection in developed countries where no universal vaccination program against HAV exists, such as Japan. There are two forms of antiviral agents against HAV: direct-acting antivirals (DAAs) and host-targeting agents (HTAs). Studies using small interfering ribonucleic acid (siRNA) have suggested that the HAV internal ribosomal entry site (IRES) is an attractive target for the control of HAV replication and infection. Among the HTAs, amantadine and interferon-lambda 1 (IL-29) inhibit HAV IRES-mediated translation and HAV replication. Janus kinase (JAK) inhibitors inhibit La protein expression, HAV IRES activity, and HAV replication. Based on this review, both DAAs and HTAs may be needed to control effectively HAV infection, and their use should continue to be explored.
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Affiliation(s)
- Tatsuo Kanda
- Correspondence to: Tatsuo Kanda, Department of Gastroenterology and Nephrology, Chiba University, Graduate School of Medicine, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan. Tel: +81-43-226-2086, Fax: +81-43-226-2088, E-mail:
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17
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Yin J, Bergmann EM. Hepatitis A Virus Picornain 3C. HANDBOOK OF PROTEOLYTIC ENZYMES 2013. [PMCID: PMC7149673 DOI: 10.1016/b978-0-12-382219-2.00540-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The third edition of the Handbook of Proteolytic Enzymes aims to be a comprehensive reference work for the enzymes that cleave proteins and peptides, and contains over 800 chapters. Each chapter is organized into sections describing the name and history, activity and specificity, structural chemistry, preparation, biological aspects, and distinguishing features for a specific peptidase. The subject of Chapter 540 is Hepatitis A Virus Picornain 3C. Keywords: β-barrel, β-ribbon, catalytic triad, cleavage site, hepatitis A virus, polyprotein processing, substrate specificity pocket, picornain 3C, picornavirus, viral cysteine proteinase.
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18
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Biochemical and mass spectrometric characterization of human N-acylethanolamine-hydrolyzing acid amidase inhibition. PLoS One 2012; 7:e43877. [PMID: 22952796 PMCID: PMC3432061 DOI: 10.1371/journal.pone.0043877] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 07/30/2012] [Indexed: 12/15/2022] Open
Abstract
The mechanism of inactivation of human enzyme N-acylethanolamine-hydrolyzing acid amidase (hNAAA), with selected inhibitors identified in a novel fluorescent based assay developed for characterization of both reversible and irreversible inhibitors, was investigated kinetically and using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). 1-Isothiocyanatopentadecane (AM9023) was found to be a potent, selective and reversible hNAAA inhibitor, while two others, 5-((biphenyl-4-yl)methyl)-N,N-dimethyl-2H-tetrazole-2-carboxamide (AM6701) and N-Benzyloxycarbonyl-L-serine β-lactone (N-Cbz-serine β-lactone), inhibited hNAAA in a covalent and irreversible manner. MS analysis of the hNAAA/covalent inhibitor complexes identified modification only of the N-terminal cysteine (Cys126) of the β-subunit, confirming a suggested mechanism of hNAAA inactivation by the β-lactone containing inhibitors. These experiments provide direct evidence of the key role of Cys126 in hNAAA inactivation by different classes of covalent inhibitors, confirming the essential role of cysteine for catalysis and inhibition in this cysteine N-terminal nucleophile hydrolase enzyme. They also provide a methodology for the rapid screening and characterization of large libraries of compounds as potential inhibitors of NAAA, and subsequent characterization or their mechanism through MALDI-TOF MS based bottom up-proteomics.
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19
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Leen EN, Baeza G, Curry S. Structure of a murine norovirus NS6 protease-product complex revealed by adventitious crystallisation. PLoS One 2012; 7:e38723. [PMID: 22685603 PMCID: PMC3369882 DOI: 10.1371/journal.pone.0038723] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 05/14/2012] [Indexed: 01/19/2023] Open
Abstract
Murine noroviruses have emerged as a valuable tool for investigating the molecular basis of infection and pathogenesis of the closely related human noroviruses, which are the major cause of non-bacterial gastroenteritis. The replication of noroviruses relies on the proteolytic processing of a large polyprotein precursor into six non-structural proteins (NS1–2, NS3, NS4, NS5, NS6pro, NS7pol) by the virally-encoded NS6 protease. We report here the crystal structure of MNV NS6pro, which has been determined to a resolution of 1.6 Å. Adventitiously, the crystal contacts are mediated in part by the binding of the C-terminus of NS6pro within the peptide-binding cleft of a neighbouring molecule. This insertion occurs for both molecules in the asymmetric unit of the crystal in a manner that is consistent with physiologically-relevant binding, thereby providing two independent views of a protease-peptide complex. Since the NS6pro C-terminus is formed in vivo by NS6pro processing, these crystal contacts replicate the protease-product complex that is formed immediately following cleavage of the peptide bond at the NS6-NS7 junction. The observed mode of binding of the C-terminal product peptide yields new insights into the structural basis of NS6pro specificity.
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Affiliation(s)
- Eoin N. Leen
- Department of Life Sciences, Imperial College, London, United Kingdom
| | - Gabriela Baeza
- Department of Life Sciences, Imperial College, London, United Kingdom
| | - Stephen Curry
- Department of Life Sciences, Imperial College, London, United Kingdom
- * E-mail:
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20
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Blaum BS, Wünsche W, Benie AJ, Kusov Y, Peters H, Gauss-Müller V, Peters T, Sczakiel G. Functional binding of hexanucleotides to 3C protease of hepatitis A virus. Nucleic Acids Res 2012; 40:3042-55. [PMID: 22156376 PMCID: PMC3326307 DOI: 10.1093/nar/gkr1152] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2010] [Revised: 11/09/2011] [Accepted: 11/10/2011] [Indexed: 12/01/2022] Open
Abstract
Oligonucleotides as short as 6 nt in length have been shown to bind specifically and tightly to proteins and affect their biological function. Yet, sparse structural data are available for corresponding complexes. Employing a recently developed hexanucleotide array, we identified hexadeoxyribonucleotides that bind specifically to the 3C protease of hepatitis A virus (HAV 3C(pro)). Inhibition assays in vitro identified the hexanucleotide 5'-GGGGGT-3' (G(5)T) as a 3C(pro) protease inhibitor. Using (1)H NMR spectroscopy, G(5)T was found to form a G-quadruplex, which might be considered as a minimal aptamer. With the help of (1)H, (15)N-HSQC experiments the binding site for G(5)T was located to the C-terminal β-barrel of HAV 3C(pro). Importantly, the highly conserved KFRDI motif, which has previously been identified as putative viral RNA binding site, is not part of the G(5)T-binding site, nor does G(5)T interfere with the binding of viral RNA. Our findings demonstrate that sequence-specific nucleic acid-protein interactions occur with oligonucleotides as small as hexanucleotides and suggest that these compounds may be of pharmaceutical relevance.
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Affiliation(s)
- Bärbel S. Blaum
- Institute of Chemistry, Institute of Molecular Medicine, Institute for Virology and Cell Biology and Institute for Biochemistry, University of Luebeck, Center for Structural and Cell Biology in Medicine (CSCM), Ratzeburger Allee 160, D-23538 Luebeck, Germany
| | - Winfried Wünsche
- Institute of Chemistry, Institute of Molecular Medicine, Institute for Virology and Cell Biology and Institute for Biochemistry, University of Luebeck, Center for Structural and Cell Biology in Medicine (CSCM), Ratzeburger Allee 160, D-23538 Luebeck, Germany
| | - Andrew J. Benie
- Institute of Chemistry, Institute of Molecular Medicine, Institute for Virology and Cell Biology and Institute for Biochemistry, University of Luebeck, Center for Structural and Cell Biology in Medicine (CSCM), Ratzeburger Allee 160, D-23538 Luebeck, Germany
| | - Yuri Kusov
- Institute of Chemistry, Institute of Molecular Medicine, Institute for Virology and Cell Biology and Institute for Biochemistry, University of Luebeck, Center for Structural and Cell Biology in Medicine (CSCM), Ratzeburger Allee 160, D-23538 Luebeck, Germany
| | - Hannelore Peters
- Institute of Chemistry, Institute of Molecular Medicine, Institute for Virology and Cell Biology and Institute for Biochemistry, University of Luebeck, Center for Structural and Cell Biology in Medicine (CSCM), Ratzeburger Allee 160, D-23538 Luebeck, Germany
| | - Verena Gauss-Müller
- Institute of Chemistry, Institute of Molecular Medicine, Institute for Virology and Cell Biology and Institute for Biochemistry, University of Luebeck, Center for Structural and Cell Biology in Medicine (CSCM), Ratzeburger Allee 160, D-23538 Luebeck, Germany
| | - Thomas Peters
- Institute of Chemistry, Institute of Molecular Medicine, Institute for Virology and Cell Biology and Institute for Biochemistry, University of Luebeck, Center for Structural and Cell Biology in Medicine (CSCM), Ratzeburger Allee 160, D-23538 Luebeck, Germany
| | - Georg Sczakiel
- Institute of Chemistry, Institute of Molecular Medicine, Institute for Virology and Cell Biology and Institute for Biochemistry, University of Luebeck, Center for Structural and Cell Biology in Medicine (CSCM), Ratzeburger Allee 160, D-23538 Luebeck, Germany
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21
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Aronica LA, Caporusso AM, Evangelisti C, Botavina M, Alberto G, Martra G. Metal vapour derived supported rhodium nanoparticles in the synthesis of β-lactams and β-lactones derivatives. J Organomet Chem 2012. [DOI: 10.1016/j.jorganchem.2011.11.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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22
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Someya Y. From head to toe of the norovirus 3C-like protease. Biomol Concepts 2012; 3:41-56. [DOI: 10.1515/bmc.2011.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 11/02/2011] [Indexed: 01/25/2023] Open
Abstract
AbstractNoroviruses are major causative agents of viral gastroenteritis in humans. Currently, there are no therapeutic medications to treat noroviral infections, nor are there effective vaccines against these pathogens. The viral 3C-like protease is solely responsible for the maturation of viral protein components. The crystal structures of the proteases were resolved at high atomic resolution. The protease was also explored by means of mutagenesis. These studies revealed the active-site amino acid residues and factors determining and affecting substrate specificity as well as the principle of architecting the protease molecule. The possible mechanism of proteolysis was also suggested. Consideration of the data accumulated thus far will be useful for development of therapeutic drugs targeting the viral protease.
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Affiliation(s)
- Yuichi Someya
- 1Department of Virology II, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashi-Murayama, Tokyo 208-0011, Japan
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23
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Schultz-Cherry S. Astrovirus Structure and Assembly. ASTROVIRUS RESEARCH 2012. [PMCID: PMC7120587 DOI: 10.1007/978-1-4614-4735-1_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Recent structural studies on the astrovirus virion and viral proteins have yielded exciting new insights into the molecular mechanisms of the astrovirus life cycle. The 25 Å-resolution cryo-electron microscopy (Cryo-EM) reconstructions of the astrovirus virion reveal a solid capsid shell studded with spikes. Proteolytic maturation of the virus particle results in capsid conformational changes, most prominently at the spikes. High-resolution crystal structures of the human and avian astrovirus capsid spike domains have shed light on potential host receptors and species specificity. Together, both the structural studies on the astrovirus virion and capsid spike domains have revealed similarities to hepatitis E virus, suggesting an evolutionary relationship. The only other structural information on astrovirus is from the high-resolution crystal structure of the protease that is involved in nonstructural polyprotein processing. Overall, these structural studies have led a better understanding of the astrovirus life cycle, including astrovirus assembly, virus release, maturation, receptor binding, antibody neutralization, and nonstructural polyprotein processing.
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Affiliation(s)
- Stacey Schultz-Cherry
- , Infectious Diseases, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, 38105 Tennessee USA
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24
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Aubry S, Sasaki K, Eloy L, Aubert G, Retailleau P, Cresteil T, Crich D. Exploring the potential of the β-thiolactones in bioorganic chemistry. Org Biomol Chem 2011; 9:7134-43. [DOI: 10.1039/c1ob05967j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Solorzano C, Antonietti F, Duranti A, Tontini A, Rivara S, Lodola A, Vacondio F, Tarzia G, Piomelli D, Mor M. Synthesis and structure-activity relationships of N-(2-oxo-3-oxetanyl)amides as N-acylethanolamine-hydrolyzing acid amidase inhibitors. J Med Chem 2010; 53:5770-81. [PMID: 20604568 PMCID: PMC2932887 DOI: 10.1021/jm100582w] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The fatty acid ethanolamides (FAEs) are a family of bioactive lipid mediators that include the endogenous agonist of peroxisome proliferator-activated receptor-alpha, palmitoylethanolamide (PEA). FAEs are hydrolyzed intracellularly by either fatty acid amide hydrolase or N-acylethanolamine-hydrolyzing acid amidase (NAAA). Selective inhibition of NAAA by (S)-N-(2-oxo-3-oxetanyl)-3-phenylpropionamide [(S)-OOPP, 7a] prevents PEA degradation in mouse leukocytes and attenuates responses to proinflammatory stimuli. Starting from the structure of 7a, a series of beta-lactones was prepared and tested on recombinant rat NAAA to explore structure-activity relationships (SARs) for this class of inhibitors and improve their in vitro potency. Following the hypothesis that these compounds inhibit NAAA by acylation of the catalytic cysteine, we identified several requirements for recognition at the active site and obtained new potent inhibitors. In particular, (S)-N-(2-oxo-3-oxetanyl)biphenyl-4-carboxamide (7h) was more potent than 7a at inhibiting recombinant rat NAAA activity (7a, IC(50) = 420 nM; 7h, IC(50) = 115 nM) in vitro and at reducing carrageenan-induced leukocyte infiltration in vivo.
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Affiliation(s)
- Carlos Solorzano
- Department of Pharmacology, University of California, Irvine, 360 MSRII, Irvine CA 92697-4625, USA
| | - Francesca Antonietti
- Dipartimento di Scienze del Farmaco e della Salute, Università degli Studi di Urbino “Carlo Bo”, Piazza del Rinascimento 6, I-61029 Urbino, Italy
| | - Andrea Duranti
- Dipartimento di Scienze del Farmaco e della Salute, Università degli Studi di Urbino “Carlo Bo”, Piazza del Rinascimento 6, I-61029 Urbino, Italy
| | - Andrea Tontini
- Dipartimento di Scienze del Farmaco e della Salute, Università degli Studi di Urbino “Carlo Bo”, Piazza del Rinascimento 6, I-61029 Urbino, Italy
| | - Silvia Rivara
- Dipartimento Farmaceutico, Università degli Studi di Parma, viale G. P. Usberti 27/A I-43124 Parma, Italy
| | - Alessio Lodola
- Dipartimento Farmaceutico, Università degli Studi di Parma, viale G. P. Usberti 27/A I-43124 Parma, Italy
| | - Federica Vacondio
- Dipartimento Farmaceutico, Università degli Studi di Parma, viale G. P. Usberti 27/A I-43124 Parma, Italy
| | - Giorgio Tarzia
- Dipartimento di Scienze del Farmaco e della Salute, Università degli Studi di Urbino “Carlo Bo”, Piazza del Rinascimento 6, I-61029 Urbino, Italy
| | - Daniele Piomelli
- Department of Pharmacology, University of California, Irvine, 360 MSRII, Irvine CA 92697-4625, USA
- Department of Drug Discovery and Development, Italian Institute of Technology, via Morego 30, I-16163 Genova, Italy
| | - Marco Mor
- Dipartimento Farmaceutico, Università degli Studi di Parma, viale G. P. Usberti 27/A I-43124 Parma, Italy
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26
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Zunszain PA, Knox SR, Sweeney TR, Yang J, Roqué-Rosell N, Belsham GJ, Leatherbarrow RJ, Curry S. Insights into cleavage specificity from the crystal structure of foot-and-mouth disease virus 3C protease complexed with a peptide substrate. J Mol Biol 2010; 395:375-89. [PMID: 19883658 PMCID: PMC7099390 DOI: 10.1016/j.jmb.2009.10.048] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Revised: 10/16/2009] [Accepted: 10/19/2009] [Indexed: 11/07/2022]
Abstract
Picornavirus replication is critically dependent on the correct processing of a polyprotein precursor by 3C protease(s) (3C(pro)) at multiple specific sites with related but non-identical sequences. To investigate the structural basis of its cleavage specificity, we performed the first crystallographic structural analysis of non-covalent complexes of a picornavirus 3C(pro) with peptide substrates. The X-ray crystal structure of the foot-and-mouth disease virus 3C(pro), mutated to replace the catalytic Cys by Ala and bound to a peptide (APAKQ|LLNFD) corresponding to the P5-P5' region of the VP1-2A cleavage junction in the viral polyprotein, was determined up to 2.5 A resolution. Comparison with free enzyme reveals significant conformational changes in 3C(pro) on substrate binding that lead to the formation of an extended interface of contact primarily involving the P4-P2' positions of the peptide. Strikingly, the deep S1' specificity pocket needed to accommodate P1'-Leu only forms when the peptide binds. Substrate specificity was investigated using peptide cleavage assays to show the impact of amino acid substitutions within the P5-P4' region of synthetic substrates. The structure of the enzyme-peptide complex explains the marked substrate preferences for particular P4, P2 and P1 residue types, as well as the relative promiscuity at P3 and on the P' side of the scissile bond. Furthermore, crystallographic analysis of the complex with a modified VP1-2A peptide (APAKE|LLNFD) containing a Gln-to-Glu substitution reveals an identical mode of peptide binding and explains the ability of foot-and-mouth disease virus 3C(pro) to cleave sequences containing either P1-Gln or P1-Glu. Structure-based mutagenesis was used to probe interactions within the S1' specificity pocket and to provide direct evidence of the important contribution made by Asp84 of the Cys-His-Asp catalytic triad to proteolytic activity. Our results provide a new level of detail in our understanding of the structural basis of polyprotein cleavage by 3C(pro).
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Affiliation(s)
- Patricia A Zunszain
- Biophysics Section, Blackett Laboratory, Imperial College, Exhibition Road, London SW7 2AZ, UK
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27
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Speroni S, Rohayem J, Nenci S, Bonivento D, Robel I, Barthel J, Luzhkov VB, Coutard B, Canard B, Mattevi A. Structural and biochemical analysis of human pathogenic astrovirus serine protease at 2.0 A resolution. J Mol Biol 2009; 387:1137-52. [PMID: 19249313 DOI: 10.1016/j.jmb.2009.02.044] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Revised: 02/13/2009] [Accepted: 02/18/2009] [Indexed: 11/29/2022]
Abstract
Astroviruses are single-stranded RNA viruses with a replication strategy based on the proteolytic processing of a polyprotein precursor and subsequent release of the viral enzymes of replication. So far, the catalytic properties of the astrovirus protease as well as its structure have remained uncharacterized. In this study, the three-dimensional crystal structure of the predicted protease of human pathogenic astrovirus has been solved to 2.0 A resolution. The protein displays the typical properties of trypsin-like enzymes but also several characteristic features: (i) a catalytic Asp-His-Ser triad in which the aspartate side chain is oriented away from the histidine, being replaced by a water molecule; (ii) a non-common conformation and composition of the S1 pocket; and (iii) the lack of the typical surface beta-ribbons together with a "featureless" shape of the substrate-binding site. Hydrolytic activity assays indicate that the S1 pocket recognises Glu and Asp side chains specifically, which, therefore, are predicted to occupy the P1 position on the substrate cleavage site. The positive electrostatic potential featured by the S1 region underlies this specificity. The comparative structural analysis highlights the peculiarity of the astrovirus protease, and differentiates it from the human and viral serine proteases.
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Affiliation(s)
- Silvia Speroni
- Department of Genetics and Microbiology, University of Pavia, via Ferrata 1, Pavia, 27100 Italy
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28
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Picornaviruses. VIRAL PROTEASES AND ANTIVIRAL PROTEASE INHIBITOR THERAPY 2009. [PMCID: PMC7122559 DOI: 10.1007/978-90-481-2348-3_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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29
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Huitema C, Zhang J, Yin J, James MNG, Vederas JC, Eltis LD. Heteroaromatic ester inhibitors of hepatitis A virus 3C proteinase: Evaluation of mode of action. Bioorg Med Chem 2008; 16:5761-77. [PMID: 18407505 PMCID: PMC7125897 DOI: 10.1016/j.bmc.2008.03.059] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2008] [Accepted: 03/24/2008] [Indexed: 11/23/2022]
Abstract
The related 3C and 3C-like proteinase (3C(pro) and 3CL(pro)) of picornaviruses and coronaviruses, respectively, are good drug targets. As part of an effort to generate broad-spectrum inhibitors of these enzymes, we screened a library of inhibitors based on a halopyridinyl ester from a previous study of the severe acute respiratory syndrome (SARS) 3CL proteinase against Hepatitis A virus (HAV) 3C(pro). Three of the compounds, which also had furan rings, inhibited the cleavage activity of HAV 3C(pro) with K(ic)s of 120-240nM. HPLC-based assays revealed that the inhibitors were slowly hydrolyzed by both HAV 3C(pro) and SARS 3CL(pro), confirming the identity of the expected products. Mass spectrometric analyses indicated that this hydrolysis proceeded via an acyl-enzyme intermediate. Modeling studies indicated that the halopyridinyl moiety of the inhibitor fits tightly into the S1-binding pocket, consistent with the lack of tolerance of the inhibitors to modification in this portion of the molecule. These compounds are among the most potent non-peptidic inhibitors reported to date against a 3C(pro).
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Affiliation(s)
- Carly Huitema
- Department of Microbiology, University of British Columbia, 2350 Health Science Mall, Vancouver, British Columbia, Canada V6T 1Z3
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30
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Yin J, Niu C, Cherney MM, Zhang J, Huitema C, Eltis LD, Vederas JC, James MN. A mechanistic view of enzyme inhibition and peptide hydrolysis in the active site of the SARS-CoV 3C-like peptidase. J Mol Biol 2007; 371:1060-74. [PMID: 17599357 PMCID: PMC7094781 DOI: 10.1016/j.jmb.2007.06.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Accepted: 05/30/2007] [Indexed: 11/22/2022]
Abstract
The 3C-like main peptidase 3CLpro is a viral polyprotein processing enzyme essential for the viability of the Severe Acute Respiratory Syndrome coronavirus (SARS-CoV). While it is generalized that 3CLpro and the structurally related 3Cpro viral peptidases cleave their substrates via a mechanism similar to that underlying the peptide hydrolysis by chymotrypsin-like serine proteinases (CLSPs), some of the hypothesized key intermediates have not been structurally characterized. Here, we present three crystal structures of SARS 3CLpro in complex with each of two members of a new class of peptide-based phthalhydrazide inhibitors. Both inhibitors form an unusual thiiranium ring with the nucleophilic sulfur atom of Cys145, trapping the enzyme's catalytic residues in configurations similar to the intermediate states proposed to exist during the hydrolysis of native substrates. Most significantly, our crystallographic data are consistent with a scenario in which a water molecule, possibly via indirect coordination from the carbonyl oxygen of Thr26, has initiated nucleophilic attack on the enzyme-bound inhibitor. Our data suggest that this structure resembles that of the proposed tetrahedral intermediate during the deacylation step of normal peptidyl cleavage.
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Affiliation(s)
- Jiang Yin
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, AB, Canada T6G 2H7
| | - Chunying Niu
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, AB, Canada T6G 2H7
| | - Maia M. Cherney
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, AB, Canada T6G 2H7
| | - Jianmin Zhang
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Carly Huitema
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Lindsay D. Eltis
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - John C. Vederas
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Michael N.G. James
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, AB, Canada T6G 2H7
- Alberta Synchrotron Institute, University of Alberta, Edmonton, AB, Canada T6G 2E1
- Corresponding author. Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, AB, Canada T6G 2H7.
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31
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Curry S, Roqué-Rosell N, Sweeney TR, Zunszain PA, Leatherbarrow RJ. Structural analysis of foot-and-mouth disease virus 3C protease: a viable target for antiviral drugs? Biochem Soc Trans 2007; 35:594-8. [PMID: 17511659 DOI: 10.1042/bst0350594] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Foot-and-mouth disease virus causes a major global agricultural problem that is difficult to control with existing vaccines. Structural analyses of the viral 3C protease not only have provided fresh insights into the catalytic mechanism of an unusual class of chymotrypsin-like cysteine proteases, but also are generating valuable information to drive the quest for effective antiviral therapies.
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Affiliation(s)
- S Curry
- Biophysics Section, Division of Cell and Molecular Biology, Blackett Laboratory, Imperial College, Exhibition Road, London SW7 2AZ, UK.
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32
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Sweeney TR, Roqué-Rosell N, Birtley JR, Leatherbarrow RJ, Curry S. Structural and mutagenic analysis of foot-and-mouth disease virus 3C protease reveals the role of the beta-ribbon in proteolysis. J Virol 2007; 81:115-24. [PMID: 17065215 PMCID: PMC1797255 DOI: 10.1128/jvi.01587-06] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2006] [Accepted: 10/11/2006] [Indexed: 11/20/2022] Open
Abstract
The 3C protease (3C(pro)) from foot-and-mouth disease virus (FMDV), the causative agent of a widespread and economically devastating disease of domestic livestock, is a potential target for antiviral drug design. We have determined the structure of a new crystal form of FMDV 3C(pro), a chymotrypsin-like cysteine protease, which reveals features that are important for catalytic activity. In particular, we show that a surface loop which was disordered in previous structures adopts a beta-ribbon structure that is conformationally similar to equivalent regions on other picornaviral 3C proteases and some serine proteases. This beta-ribbon folds over the peptide binding cleft and clearly contributes to substrate recognition. Replacement of Cys142 at the tip of the beta-ribbon with different amino acids has a significant impact on enzyme activity and shows that higher activity is obtained with more hydrophobic side chains. Comparison of the structure of FMDV 3C(pro) with homologous enzyme-peptide complexes suggests that this correlation arises because the side chain of Cys142 contacts the hydrophobic portions of the P2 and P4 residues in the peptide substrate. Collectively, these findings provide compelling evidence for the role of the beta-ribbon in catalytic activity and provide valuable insights for the design of FMDV 3C(pro) inhibitors.
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Affiliation(s)
- Trevor R Sweeney
- Biophysics Section, Blackett Laboratory, Imperial College, London SW7 2AZ, United Kingdom
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33
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Mittl PR, Grütter MG. Opportunities for structure-based design of protease-directed drugs. Curr Opin Struct Biol 2006; 16:769-75. [PMID: 17112720 DOI: 10.1016/j.sbi.2006.10.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2006] [Revised: 10/06/2006] [Accepted: 10/25/2006] [Indexed: 01/09/2023]
Abstract
As a result of the recent enormous technological progress, experimental structure determination has become an integral part of the development of drugs against disease-related target proteins. The post-translational modification of proteins is an important regulatory process in living organisms; one such example is lytic processing by peptidases. Many different peptidases represent disease targets and are being used in structure-based drug design approaches. The development of drugs such as aliskiren and tipranavir, which inhibit renin and HIV protease, respectively, testifies to the success of this approach.
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Affiliation(s)
- Peer Re Mittl
- Institute for Biochemistry, University of Zürich, Winterthurer Strasse 190, 8057 Zürich, Switzerland
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34
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Yin J, Cherney MM, Bergmann EM, Zhang J, Huitema C, Pettersson H, Eltis LD, Vederas JC, James MNG. An episulfide cation (thiiranium ring) trapped in the active site of HAV 3C proteinase inactivated by peptide-based ketone inhibitors. J Mol Biol 2006; 361:673-86. [PMID: 16860823 PMCID: PMC7172884 DOI: 10.1016/j.jmb.2006.06.047] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2006] [Revised: 06/19/2006] [Accepted: 06/20/2006] [Indexed: 11/17/2022]
Abstract
We have solved the crystal and molecular structures of hepatitis A viral (HAV) 3C proteinase, a cysteine peptidase having a chymotrypsin-like protein fold, in complex with each of three tetrapeptidyl-based methyl ketone inhibitors to resolutions beyond 1.4 A, the highest resolution to date for a 3C or a 3C-Like (e.g. SARS viral main proteinase) peptidase. The residues of the beta-hairpin motif (residues 138-158), an extension of two beta-strands of the C-terminal beta-barrel of HAV 3C are critical for the interactions between the enzyme and the tetrapeptide portion of these inhibitors that are analogous to the residues at the P4 to P1 positions in the natural substrates of picornaviral 3C proteinases. Unexpectedly, the Sgamma of Cys172 forms two covalent bonds with each inhibitor, yielding an unusual episulfide cation (thiiranium ring) stabilized by a nearby oxyanion. This result suggests a mechanism of inactivation of 3C peptidases by methyl ketone inhibitors that is distinct from that occurring in the structurally related serine proteinases or in the papain-like cysteine peptidases. It also provides insight into the mechanisms underlying both the inactivation of HAV 3C by these inhibitors and on the proteolysis of natural substrates by this viral cysteine peptidase.
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Key Words
- hav, hepatitis a virus
- fmdv, foot-and-mouth disease virus
- tgev, transmissible gastroenteritis coronavirus
- sars, severe acute respiratory syndrome
- bbl, carboxylbenzyloxyl-l-serine-β-lactone
- cmk, chloromethylketone
- fmk, fluoromethylketone
- ac, acetyl
- qmm, n, n-dimethyl glutamine
- hepatitis a virus
- 3c proteinase
- inhibitor design
- methylketone
- episulfide
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Affiliation(s)
- Jiang Yin
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, AB, Canada T6G 2H7
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35
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Curry S, Roqué-Rosell N, Zunszain PA, Leatherbarrow RJ. Foot-and-mouth disease virus 3C protease: recent structural and functional insights into an antiviral target. Int J Biochem Cell Biol 2006; 39:1-6. [PMID: 16979372 PMCID: PMC7185863 DOI: 10.1016/j.biocel.2006.07.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2006] [Revised: 07/25/2006] [Accepted: 07/26/2006] [Indexed: 02/05/2023]
Abstract
The 3C protease from foot-and-mouth disease virus (FMDV 3C(pro)) is critical for viral pathogenesis, having vital roles in both the processing of the polyprotein precursor and RNA replication. Although recent structural and functional studies have revealed new insights into the mechanism and function of the enzyme, key questions remain that must be addressed before the potential of FMDV 3C(pro) as an antiviral drug target can be realised.
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Affiliation(s)
- Stephen Curry
- Biophysics Section, Division of Cell and Molecular Biology, Blackett Laboratory, Imperial College, Exhibition Road, London SW7 2AZ, UK.
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36
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Zeitler CE, Estes MK, Venkataram Prasad BV. X-ray crystallographic structure of the Norwalk virus protease at 1.5-A resolution. J Virol 2006; 80:5050-8. [PMID: 16641296 PMCID: PMC1472067 DOI: 10.1128/jvi.80.10.5050-5058.2006] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Norwalk virus (NV), a member of the Caliciviridae family, is the major cause of acute, epidemic, viral gastroenteritis. The NV genome is a positive sense, single-stranded RNA that encodes three open reading frames (ORFs). The first ORF produces a polyprotein that is processed by the viral cysteine protease into six nonstructural proteins. We have determined the structure of the NV protease to 1.5 and 2.2 A from crystals grown in the absence or presence, respectively, of the protease inhibitor AEBSF [4-(2-aminoethyl)-benzenesulfonyl fluoride]. The protease, which crystallizes as a stable dimer, exhibits a two-domain structure similar to those of other viral cysteine proteases with a catalytic triad composed of His 30, Glu 54, and Cys 139. The native structure of the protease reveals strong hydrogen bond interactions between His 30 and Glu 54, in the favorable syn configuration, indicating a role of Glu 54 during proteolysis. Mutation of this residue to Ala abolished the protease activity, in a fluorogenic peptide substrate assay, further substantiating the role of Glu 54 during proteolysis. These observations contrast with the suggestion, from a previous study of another norovirus protease, that this residue may not have a prominent role in proteolysis (K. Nakamura, Y. Someya, T. Kumasaka, G. Ueno, M. Yamamoto, T. Sato, N. Takeda, T. Miyamura, and N. Tanaka, J. Virol. 79:13685-13693, 2005). In the structure from crystals grown in the presence of AEBSF, Glu 54 undergoes a conformational change leading to disruption of the hydrogen bond interactions with His 30. Since AEBSF was not apparent in the electron density map, it is possible that these conformational changes are due to subtle changes in pH caused by its addition during crystallization.
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Affiliation(s)
- Corinne E Zeitler
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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37
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Abstract
Fungi and viruses encode a variety of peptidases having a plethora of functions. Many fungal peptidases are extracellular and are likely used to degrade proteins in their environment. Viral peptidases are processing enzymes, intimately involved in the virus infectious cycle. The viral RNA genome is translated by the host-cell machinery into a large polyprotein that is cleaved by the viral peptidases into mature capsid proteins, non-structural proteins and enzymes. I review the structure and catalytic mechanism of scytalidoglutamic peptidase isolated from the wood-destroying fungus Scytalidium lignicolum. This enzyme has a unique beta-sandwich fold and a novel catalytic mechanism based on a glutamate, a glutamine and a nucleophilic water molecule. Hepatitis A virus (HAV) 3C peptidase was the first structure identified for a viral 3C enzyme that exhibited the three-dimensional fold of the chymotrypsin family of serine peptidases but had a cysteine sulfur atom instead of the serine oxygen as the nucleophile. The structure of HAV 3C was unusual in that the Asp residue expected as the third member of the catalytic triad did not interact with the general base His. The present structure is of a beta-lactone-inhibited version of HAV 3C that has a restored catalytic triad.
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Affiliation(s)
- Michael N G James
- CIHR Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.
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