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Kovalishyn V, Severin O, Kachaeva M, Kobzar O, Keith KA, Harden EA, Hartline CB, James SH, Vovk A, Brovarets V. In Silico Design and Experimental Validation of Novel Oxazole Derivatives Against Varicella zoster virus. Mol Biotechnol 2024; 66:707-717. [PMID: 36709460 DOI: 10.1007/s12033-023-00670-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/14/2023] [Indexed: 01/30/2023]
Abstract
Varicella zoster virus (VZV) infection causes severe disease such as chickenpox, shingles, and postherpetic neuralgia, often leading to disability. Reactivation of latent VZV is associated with a decrease in specific cellular immunity in the elderly and in patients with immunodeficiency. However, due to the limited efficacy of existing therapy and the emergence of antiviral resistance, it has become necessary to develop new and effective antiviral drugs for the treatment of diseases caused by VZV, particularly in the setting of opportunistic infections. The goal of this work is to identify potent oxazole derivatives as anti-VZV agents by machine learning, followed by their synthesis and experimental validation. Predictive QSAR models were developed using the Online Chemical Modeling Environment (OCHEM). Data on compounds exhibiting antiviral activity were collected from the ChEMBL and uploaded in the OCHEM database. The predictive ability of the models was tested by cross-validation, giving coefficient of determination q2 = 0.87-0.9. The validation of the models using an external test set proves that the models can be used to predict the antiviral activity of newly designed and known compounds with reasonable accuracy within the applicability domain (q2 = 0.83-0.84). The models were applied to screen a virtual chemical library with expected activity of compounds against VZV. The 7 most promising oxazole derivatives were identified, synthesized, and tested. Two of them showed activity against the VZV Ellen strain upon primary in vitro antiviral screening. The synthesized compounds may represent an interesting starting point for further development of the oxazole derivatives against VZV. The developed models are available online at OCHEM http://ochem.eu/article/145978 and can be used to virtually screen for potential compounds with anti-VZV activity.
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Affiliation(s)
- Vasyl Kovalishyn
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Science of Ukraine, Kyiv, 02094, Ukraine.
| | - Oleksandr Severin
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Science of Ukraine, Kyiv, 02094, Ukraine
| | - Maryna Kachaeva
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Science of Ukraine, Kyiv, 02094, Ukraine
| | - Oleksandr Kobzar
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Science of Ukraine, Kyiv, 02094, Ukraine
| | - Kathy A Keith
- Department of Pediatrics, Division of Pediatric Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, 35233, USA
| | - Emma A Harden
- Department of Pediatrics, Division of Pediatric Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, 35233, USA
| | - Caroll B Hartline
- Department of Pediatrics, Division of Pediatric Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, 35233, USA
| | - Scott H James
- Department of Pediatrics, Division of Pediatric Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, 35233, USA
| | - Andriy Vovk
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Science of Ukraine, Kyiv, 02094, Ukraine
| | - Volodymyr Brovarets
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry of the National Academy of Science of Ukraine, Kyiv, 02094, Ukraine
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Shi W, Li T, Li H, Ren J, Lv M, Wang Q, He Y, Yu Y, Liu L, Jin S, Chen H. Bioinformatics approach to identify the hub gene associated with COVID-19 and idiopathic pulmonary fibrosis. IET Syst Biol 2023; 17:336-351. [PMID: 37814484 PMCID: PMC10725713 DOI: 10.1049/syb2.12080] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 09/26/2023] [Accepted: 09/26/2023] [Indexed: 10/11/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) has developed into a global health crisis. Pulmonary fibrosis, as one of the complications of SARS-CoV-2 infection, deserves attention. As COVID-19 is a new clinical entity that is constantly evolving, and many aspects of disease are remain unknown. The datasets of COVID-19 and idiopathic pulmonary fibrosis were obtained from the Gene Expression Omnibus. The hub genes were screened out using the Random Forest (RF) algorithm depending on the severity of patients with COVID-19. A risk prediction model was developed to assess the prognosis of patients infected with SARS-CoV-2, which was evaluated by another dataset. Six genes (named NELL2, GPR183, S100A8, ALPL, CD177, and IL1R2) may be associated with the development of PF in patients with severe SARS-CoV-2 infection. S100A8 is thought to be an important target gene that is closely associated with COVID-19 and pulmonary fibrosis. Construction of a neural network model was successfully predicted the prognosis of patients with COVID-19. With the increasing availability of COVID-19 datasets, bioinformatic methods can provide possible predictive targets for the diagnosis, treatment, and prognosis of the disease and show intervention directions for the development of clinical drugs and vaccines.
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Affiliation(s)
- Wenchao Shi
- Department of RespirationThe Fourth Affiliated Hospital of Harbin Medical UniversityHarbin Medical UniversityHarbinHeilongjiangChina
| | - Tinghui Li
- Department of RespirationHainan Cancer HospitalHaikouHainanChina
| | - Huiwen Li
- Department of RespirationThe Second Affiliated Hospital of Harbin Medical UniversityHarbin Medical UniversityHarbinHeilongjiangChina
| | - Juan Ren
- Department of RespirationThe Second Affiliated Hospital of Harbin Medical UniversityHarbin Medical UniversityHarbinHeilongjiangChina
| | - Meiyu Lv
- Department of RespirationThe Fourth Affiliated Hospital of Harbin Medical UniversityHarbin Medical UniversityHarbinHeilongjiangChina
| | - Qi Wang
- Department of RespirationThe Second Affiliated Hospital of Harbin Medical UniversityHarbin Medical UniversityHarbinHeilongjiangChina
| | - Yaowu He
- Department of RespirationThe Second Affiliated Hospital of Harbin Medical UniversityHarbin Medical UniversityHarbinHeilongjiangChina
| | - Yao Yu
- Department of RespirationThe Second Affiliated Hospital of Harbin Medical UniversityHarbin Medical UniversityHarbinHeilongjiangChina
| | - Lijie Liu
- Department of RespirationThe Fourth Affiliated Hospital of Harbin Medical UniversityHarbin Medical UniversityHarbinHeilongjiangChina
| | - Shoude Jin
- Department of RespirationThe Fourth Affiliated Hospital of Harbin Medical UniversityHarbin Medical UniversityHarbinHeilongjiangChina
| | - Hong Chen
- Department of RespirationThe Second Affiliated Hospital of Harbin Medical UniversityHarbin Medical UniversityHarbinHeilongjiangChina
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Advances and Perspectives in the Management of Varicella-Zoster Virus Infections. Molecules 2021; 26:molecules26041132. [PMID: 33672709 PMCID: PMC7924330 DOI: 10.3390/molecules26041132] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/10/2021] [Accepted: 02/12/2021] [Indexed: 02/06/2023] Open
Abstract
Varicella-zoster virus (VZV), a common and ubiquitous human-restricted pathogen, causes a primary infection (varicella or chickenpox) followed by establishment of latency in sensory ganglia. The virus can reactivate, causing herpes zoster (HZ, shingles) and leading to significant morbidity but rarely mortality, although in immunocompromised hosts, VZV can cause severe disseminated and occasionally fatal disease. We discuss VZV diseases and the decrease in their incidence due to the introduction of live-attenuated vaccines to prevent varicella or HZ. We also focus on acyclovir, valacyclovir, and famciclovir (FDA approved drugs to treat VZV infections), brivudine (used in some European countries) and amenamevir (a helicase-primase inhibitor, approved in Japan) that augur the beginning of a new era of anti-VZV therapy. Valnivudine hydrochloride (FV-100) and valomaciclovir stearate (in advanced stage of development) and several new molecules potentially good as anti-VZV candidates described during the last year are examined. We reflect on the role of antiviral agents in the treatment of VZV-associated diseases, as a large percentage of the at-risk population is not immunized, and on the limitations of currently FDA-approved anti-VZV drugs. Their low efficacy in controlling HZ pain and post-herpetic neuralgia development, and the need of multiple dosing regimens requiring daily dose adaptation for patients with renal failure urges the development of novel anti-VZV drugs.
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Skácel J, Dračínský M, Janeba Z. Synthesis of Tetrasubstituted Thiophenes via Direct Metalation. J Org Chem 2020; 85:788-797. [PMID: 31859495 DOI: 10.1021/acs.joc.9b02803] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Thiophene moiety can be derivatized by various synthetic procedures. The most convenient method seems to be derivatization via direct metalation, but synthesis of polysubstituted thiophenes bearing reactive groups is difficult because of high reactivity of organometallic reagents. This work reports the preparation of complex heterocyclic compounds using direct metalation of thiophenes with various reagents (Knochel-Hauser bases, LDA) as an efficient synthetic tool.
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Affiliation(s)
- Jan Skácel
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo nám. 2 , CZ-16610 Prague 6 , Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo nám. 2 , CZ-16610 Prague 6 , Czech Republic
| | - Zlatko Janeba
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo nám. 2 , CZ-16610 Prague 6 , Czech Republic
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