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Fabiani M, Castro EF, Battini L, Rosas RA, Gärtner B, Bollini M, Cavallaro LV. Two thiosemicarbazones derived from 1-indanone as potent non-nucleoside inhibitors of bovine viral diarrhea virus of different genotypes and biotypes. Virology 2024; 598:110189. [PMID: 39089051 DOI: 10.1016/j.virol.2024.110189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 07/10/2024] [Accepted: 07/21/2024] [Indexed: 08/03/2024]
Abstract
Bovine viral diarrhea virus (BVDV) is a widespread pathogen of cattle and other mammals that causes major economic losses in the livestock industry. N4-TSC and 6NO2-TSC are two thiosemicarbazones derived from 1-indanone that exhibit anti-BVDV activity in vitro. These compounds selectively inhibit BVDV and are effective against both cytopathic and non-cytopathic BVDV-1 and BVDV-2 strains. We confirmed that N4-TSC acts at the onset of viral RNA synthesis, as previously reported for 6NO2-TSC. Moreover, resistance selection and characterization showed that N4-TSCR mutants were highly resistant to N4-TSC but remained susceptible to 6NO2-TSC. In contrast, 6NO2-TSCR mutants were resistant to both compounds. Additionally, mutations N264D and A392E were found in the viral RNA-dependent RNA polymerase (RdRp) of N4-TSCR mutants, whereas I261 M was found in 6NO2-TSCR mutants. These mutations lay in a hydrophobic pocket within the fingertips region of BVDV RdRp that has been described as a "hot spot" for BVDV non-nucleoside inhibitors.
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Affiliation(s)
- Matías Fabiani
- Cátedra de Virología, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina; Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.
| | - Eliana F Castro
- Cátedra de Virología, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Leandro Battini
- Laboratorio de Química Medicinal, Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Rocío A Rosas
- Cátedra de Virología, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina; Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Benjamin Gärtner
- Cátedra de Virología, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Mariela Bollini
- Laboratorio de Química Medicinal, Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Lucía V Cavallaro
- Cátedra de Virología, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina; Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.
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Template Entrance Channel as Possible Allosteric Inhibition and Resistance Site for Quinolines Tricyclic Derivatives in RNA Dependent RNA Polymerase of Bovine Viral Diarrhea Virus. Pharmaceuticals (Basel) 2023; 16:ph16030376. [PMID: 36986476 PMCID: PMC10058290 DOI: 10.3390/ph16030376] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/16/2023] [Accepted: 02/25/2023] [Indexed: 03/06/2023] Open
Abstract
The development of potent non-nucleoside inhibitors (NNIs) could be an alternate strategy to combating infectious bovine viral diarrhea virus (BVDV), other than the traditional vaccination. RNA-dependent RNA polymerase (RdRp) is an essential enzyme for viral replication; therefore, it is one of the primary targets for countermeasures against infectious diseases. The reported NNIs, belonging to the classes of quinolines (2h: imidazo[4,5-g]quinolines and 5m: pyrido[2,3-g] quinoxalines), displayed activity in cell-based and enzyme-based assays. Nevertheless, the RdRp binding site and microscopic mechanistic action are still elusive, and can be explored at a molecular level. Here, we employed a varied computational arsenal, including conventional and accelerated methods, to identify quinoline compounds’ most likely binding sites. Our study revealed A392 and I261 as the mutations that can render RdRp resistant against quinoline compounds. In particular, for ligand 2h, mutation of A392E is the most probable mutation. The loop L1 and linker of the fingertip is recognized as a pivotal structural determinant for the stability and escape of quinoline compounds. Overall, this work demonstrates that the quinoline inhibitors bind at the template entrance channel, which is governed by conformational dynamics of interactions with loops and linker residues, and reveals structural and mechanistic insights into inhibition phenomena, for the discovery of improved antivirals.
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He D, Li X, Wang S, Wang C, Liu X, Zhang Y, Cui Y, Yu S. Mechanism of drug resistance of BVDV induced by F224S mutation in RdRp: A case study of VP32947. Comput Biol Chem 2022; 99:107715. [PMID: 35751995 DOI: 10.1016/j.compbiolchem.2022.107715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 06/04/2022] [Accepted: 06/16/2022] [Indexed: 11/19/2022]
Abstract
Bovine viral diarrhea virus (BVDV) is an enveloped virus with an RNA genome, causing serious economic losses to the areas dominated by livestock industry. Currently, although several compounds with biological activities of inhibiting virus replication have been reported, amino acid mutations (especially F224S mutation) frequently occurring in the RNA-dependent RNA polymerase (RdRp) have greatly reduce their value of further research. In this study, we introduced an effective and rapid in silico strategy to explore the differences in the binding modes of VP32947 between the wild/mutant-type RdRp at the molecular level, and further explained the main reasons for the variations in the inhibitory activities of VP32947 against the two types of enzymes. Firstly, the binding site of VP32947 in the finger domain was determined based on the previously reported experimental data, and the initial conformation of VP32947 in the wild RdRp was constructed using molecular docking. Then, the mutant research system was obtained directly by artificial mutation strategy. Afterwards, the built research systems were subjected to microsecond-timescale molecular dynamic simulation, and the conformational and energic profile analyses were performed according to the simulation trajectories. It was found that after 1 μs simulation, VP32947 in the mutant system was transferred to the left side of Loop α, and its interactions with the residues in the loop region were weakened. However, VP32947 in the wild system remained at the right side of Loop α, and could have a good fit with the sub-pocket formed by F224, I261, P262, N264, S532, which was conducive to maintaining its stable binding conformation in the wild RdRp. The illustration of the difference in the binding mechanisms of VP32947 in the wild/mutant RdRp would provide a theoretical basis for the rational design of innovative inhibitors based on the enzyme.
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Affiliation(s)
- Dian He
- Gansu Province Livestock Embryo Engineering Research Center, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, PR China.
| | - Xuedong Li
- College of Pharmacy, Hebei Medical University, Shijiazhuang 050017, PR China
| | - Songsong Wang
- College of Pharmacy, Hebei Medical University, Shijiazhuang 050017, PR China
| | - Chengzhao Wang
- College of Pharmacy, Hebei Medical University, Shijiazhuang 050017, PR China
| | - Xingang Liu
- College of Pharmacy, Hebei Medical University, Shijiazhuang 050017, PR China
| | - Yang Zhang
- College of Pharmacy, Hebei Medical University, Shijiazhuang 050017, PR China.
| | - Yan Cui
- Gansu Province Livestock Embryo Engineering Research Center, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Sijiu Yu
- Gansu Province Livestock Embryo Engineering Research Center, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, PR China.
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Abstract
Bovine viral diarrhea virus (BVDV) belongs to the family Flaviviridae genus pestivirus. The viral genome is a single-stranded, positive-sense RNA that encodes four structural proteins (i.e., C, Erns, E1, and E2) and eight non-structural proteins (NSPs) (i.e., Npro, p7, NS2, NS3, NS4A, NS4B, NS5A, and NS5B). Cattle infected with BVDV exhibit a number of different clinical signs including diarrhea, abortion, and other reproductive disorders which have a serious impact on the cattle industry worldwide. Research on BVDV mainly focuses on its structural protein, however, progress in understanding the functions of the NSPs of BVDV has also been made in recent decades. The knowledge gained on the BVDV non-structural proteins is helpful to more fully understand the viral replication process and the molecular mechanism of viral persistent infection. This review focuses on the functions of BVDV NSPs and provides references for the identification of BVDV, the diagnosis and prevention of Bovine viral diarrhea mucosal disease (BVD-MD), and the development of vaccines.
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Pathania S, Rawal RK, Singh PK. RdRp (RNA-dependent RNA polymerase): A key target providing anti-virals for the management of various viral diseases. J Mol Struct 2022; 1250:131756. [PMID: 34690363 PMCID: PMC8520695 DOI: 10.1016/j.molstruc.2021.131756] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/13/2021] [Accepted: 10/15/2021] [Indexed: 01/04/2023]
Abstract
With the arrival of the Covid-19 pandemic, anti-viral agents have regained center stage in the arena of medicine. Out of the various drug targets involved in managing RNA-viral infections, the one that dominates almost all RNA viruses is RdRp (RNA-dependent RNA polymerase). RdRp are proteins that are involved in the replication of RNA-based viruses. Inhibition of RdRps has been an integral approach for managing various viral infections such as dengue, influenza, HCV (Hepatitis), BVDV, etc. Inhibition of the coronavirus RdRp is currently rigorously explored for the treatment of Covid-19 related complications. So, keeping in view the importance and current relevance of this drug target, we have discussed the importance of RdRp in developing anti-viral agents against various viral diseases. Different reported inhibitors have also been discussed, and emphasis has been laid on highlighting the inhibitor's pharmacophoric features and SAR profile.
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Affiliation(s)
- Shelly Pathania
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga-142001, Punjab, India
| | - Ravindra K. Rawal
- Department of Chemistry, Maharishi Markandeshwar (Deemed to be University), Mullana-133207, Haryana, India,CSIR-North East Institute of Science and Technology, Jorhat-785006, Assam, India,Corresponding authors
| | - Pankaj Kumar Singh
- Faculty of Medicine, Integrative Physiology and Pharmacology, Institute of Biomedicine, University of Turku, Turku, FI-20014, Finland,Corresponding authors
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Newcomer BW. 75 years of bovine viral diarrhea virus: Current status and future applications of the use of directed antivirals. Antiviral Res 2021; 196:105205. [PMID: 34742739 DOI: 10.1016/j.antiviral.2021.105205] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 10/30/2021] [Accepted: 11/02/2021] [Indexed: 01/03/2023]
Abstract
Bovine viral diarrhea virus (BVDV) was first reported 75 years ago and remains a source of major financial and production losses in the North American cattle industry. Currently, control methods in North America primarily center around biosecurity and vaccination programs; however, despite high levels of vaccination, the virus persists in the cattle herd due at least in part to the often-insidious nature of disease and the constant viremia and viral shedding of persistently infected animals which act as a reservoir for the virus. Continued development of targeted antivirals represents an additional tool for the prevention of BVDV-associated losses. Currently, in vivo studies of BVDV antivirals are relatively limited and have primarily been directed at the RNA-dependent RNA polymerase which represents the viral target with the highest potential for commercial development. Additional live animal studies have explored the potential of exogenous interferon treatment. Future research of commercial antivirals must focus on the establishment and validation of in vivo efficacy for compounds with demonstrated antiviral potential. The areas which provide the most viable economic justification for the research and development of antivirals drugs are the fed cattle sector, outbreak control, and wildlife or animals of high genetic value. With further development, targeted antivirals represent an additional tool for the management and control of BVDV in North American cattle herds.
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Affiliation(s)
- Benjamin W Newcomer
- Veterinary Education, Research, & Outreach Program, Texas A&M and West Texas A&M Universities, Canyon, TX, 79016, USA.
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Bovine Viral Diarrhea Virus (BVDV): A Preliminary Study on Antiviral Properties of Some Aromatic and Medicinal Plants. Pathogens 2021; 10:pathogens10040403. [PMID: 33805453 PMCID: PMC8066157 DOI: 10.3390/pathogens10040403] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/19/2021] [Accepted: 03/25/2021] [Indexed: 12/18/2022] Open
Abstract
Plant products provide an alternative and successful source of lead compounds for the pharmaceutical industry. The present study was aimed to evaluate, in cell-based assays, the antiviral properties of essential oils obtained from plants that commonly grow in Sardinia, Italy, against a broad spectrum of RNA/DNA viruses. The essential oils of Helichrisumitalicum (Roth) G. Don ssp. microphyllum (Willd.) Nyman, Laurus nobilis L., Mirtuscommunis L., Pistacia lentiscus L., Salvia officinalis L., Saturejathymbra L., Lavandula angustifolia Mill., Foeniculum vulgare Mill., and Eucalyptus globulus Labill. were extracted by hydrodistillation and analyzed by gas chromatography mass spectrometry (GC–MS). Interestingly, the essential oil of Salvia officinalis showed moderate activity against bovine viral diarrhea virus (BVDV), an enveloped RNA virus belonging to the Flaviviridae family. BVDV is responsible for several clinical manifestations in bovines, including respiratory, gastroenteric, and reproductive diseases, with a significant economic impact. With the aim to individuate the constituent of the Salvia officinalis responsible for the biological activity, we tested the major components of the oil: camphene, β-pinene, limonene, 1,8-cineole, cis-thujone, camphor, (E)-caryophyllene, and α-humulene. Here, we describe α-humulene as an active component that is non-cytotoxic and active against BVDV (EC50 = 36 µM). Its antiviral effects were evaluated using virucidal cytopathic effect inhibition and viral yield reduction assays. This is the first scientific report showing the anti BVDV effects of Salvia officinalis essential oil and α-humulene as the main active component.
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Fernández GA, Castro EF, Rosas RA, Fidalgo DM, Adler NS, Battini L, España de Marco MJ, Fabiani M, Bruno AM, Bollini M, Cavallaro LV. Design and Optimization of Quinazoline Derivatives: New Non-nucleoside Inhibitors of Bovine Viral Diarrhea Virus. Front Chem 2020; 8:590235. [PMID: 33425849 PMCID: PMC7793975 DOI: 10.3389/fchem.2020.590235] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/09/2020] [Indexed: 01/30/2023] Open
Abstract
Bovine viral diarrhea virus (BVDV) belongs to the Pestivirus genus (Flaviviridae). In spite of the availability of vaccines, the virus is still causing substantial financial losses to the livestock industry. In this context, the use of antiviral agents could be an alternative strategy to control and reduce viral infections. The viral RNA-dependent RNA polymerase (RdRp) is essential for the replication of the viral genome and constitutes an attractive target for the identification of antiviral compounds. In a previous work, we have identified potential molecules that dock into an allosteric binding pocket of BVDV RdRp via a structure-based virtual screening approach. One of them, N-(2-morpholinoethyl)-2-phenylquinazolin-4-amine [1, 50% effective concentration (EC50) = 9.7 ± 0.5 μM], was selected to perform different chemical modifications. Among 24 derivatives synthesized, eight of them showed considerable antiviral activity. Molecular modeling of the most active compounds showed that they bind to a pocket located in the fingers and thumb domains in BVDV RdRp, which is different from that identified for other non-nucleoside inhibitors (NNIs) such as thiosemicarbazone (TSC). We selected compound 2-[4-(2-phenylquinazolin-4-yl)piperazin-1-yl]ethanol (1.9; EC50 = 1.7 ± 0.4 μM) for further analysis. Compound 1.9 was found to inhibit the in vitro replication of TSC-resistant BVDV variants, which carry the N264D mutation in the RdRp. In addition, 1.9 presented adequate solubility in different media and a high-stability profile in murine and bovine plasma.
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Affiliation(s)
- Gabriela A Fernández
- Laboratorio de Química Medicinal, Centro de Investigaciones en Bionanociencias (CIBION)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Eliana F Castro
- Centro de Investigaciones en Ciencias Veterinarias y Agronómicas, Instituto de Virología e Innovaciones Tecnológicas, Instituto Nacional de Tecnología Agropecuaria, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Rocío A Rosas
- Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra Virología, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Daniela M Fidalgo
- Laboratorio de Química Medicinal, Centro de Investigaciones en Bionanociencias (CIBION)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Natalia S Adler
- Laboratorio de Química Medicinal, Centro de Investigaciones en Bionanociencias (CIBION)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Leandro Battini
- Laboratorio de Química Medicinal, Centro de Investigaciones en Bionanociencias (CIBION)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Maria J España de Marco
- Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Matias Fabiani
- Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra Virología, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Ana M Bruno
- Departamento de Química Orgánica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mariela Bollini
- Laboratorio de Química Medicinal, Centro de Investigaciones en Bionanociencias (CIBION)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Lucia V Cavallaro
- Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra Virología, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Universidad de Buenos Aires, Buenos Aires, Argentina
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