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Tomoda T, Nishimura A, Kamiya T, Inoue K, Katano H, Iida S, Hoshino A, Isoda T, Imai K, Kajiwara M, Takagi M, Kanegane H, Hanaoka N, Morio T. Immune reconstitution and cidofovir administration rescue human adenovirus hepatitis after allogeneic hematopoietic cell transplantation. Transpl Immunol 2024; 86:102093. [PMID: 39032616 DOI: 10.1016/j.trim.2024.102093] [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: 04/11/2024] [Revised: 07/09/2024] [Accepted: 07/17/2024] [Indexed: 07/23/2024]
Abstract
Human adenovirus infection (HAdV) may be fatal in patients undergoing allogeneic hematopoietic cell transplantation (HCT). Cidofovir is effective in only a part of the post-HCT HAdV infection. Therefore, posttransplant immune reconstitution is important for HAdV clearance. We describe the detailed immune reconstitution and response of adenovirus-specific T cells in a patient with inborn errors of immunity who had disseminated HAdV infection with hepatitis post-HCT and was treated with cidofovir. Though the patient received cidofovir for only 19 days starting from Day 72 after HCT because of renal dysfunction, we observed T-cell reconstitution, a decrease in HAdV copy number, and amelioration of the symptoms of HAdV infection after Day 90. We initially observed expanded NK and CD8+CD45RO+ memory subsets and later gradual increase of naïve T cells eveloped after cessation of cidofovir treatment. An increase in adenovirus-specific IFN-γ secretion from 2 to 4 months after HCT was confirmed by ELISpot assay. The progression of immune reconstitution and cidofovir treatment are considered to have contributed to survival in this patient. Optimization of transplantation methods, prompt appropriate antiviral medication, and virus-specific T-cell therapy would be necessary as the better strategy for systemic HAdV infection.
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Affiliation(s)
- Takahiro Tomoda
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan; Center for Transfusion Medicine and Cell Therapy, Tokyo Medical and Dental University (TMDU) Hospital, Tokyo, Japan
| | - Akira Nishimura
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Takahiro Kamiya
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan; Clinical Research Center, Tokyo Medical and Dental University (TMDU) Hospital, Tokyo, Japan.
| | - Kumi Inoue
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Harutaka Katano
- Department of Pathology, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Shun Iida
- Department of Pathology, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan
| | - Akihiro Hoshino
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan; Department of Child Health and Development, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Takeshi Isoda
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Kohsuke Imai
- Department of Pediatrics, National Defense Medical College, Tokorozawa, Japan
| | - Michiko Kajiwara
- Center for Transfusion Medicine and Cell Therapy, Tokyo Medical and Dental University (TMDU) Hospital, Tokyo, Japan
| | - Masatoshi Takagi
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Hirokazu Kanegane
- Department of Child Health and Development, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Nozomu Hanaoka
- Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tomohiro Morio
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
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2
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Snyder LR, Kilde I, Nemudryi A, Wiedenheft B, Koutmos M, Koutmou KS. Adenosine modifications impede SARS-CoV-2 RNA-dependent RNA transcription. RNA (NEW YORK, N.Y.) 2024; 30:1141-1150. [PMID: 38942480 PMCID: PMC11331411 DOI: 10.1261/rna.079991.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 05/20/2024] [Indexed: 06/30/2024]
Abstract
SARS-CoV-2, the causative virus of the COVID-19 pandemic, follows SARS and MERS as recent zoonotic coronaviruses causing severe respiratory illness and death in humans. The recurrent impact of zoonotic coronaviruses demands a better understanding of their fundamental molecular biochemistry. Nucleoside modifications, which modulate many steps of the RNA life cycle, have been found in SARS-CoV-2 RNA, although whether they confer a pro- or antiviral effect is unknown. Regardless, the viral RNA-dependent RNA polymerase will encounter these modifications as it transcribes through the viral genomic RNA. We investigated the functional consequences of nucleoside modification on the pre-steady state kinetics of SARS-CoV-2 RNA-dependent RNA transcription using an in vitro reconstituted transcription system with modified RNA templates. Our findings show that N 6-methyladenosine and 2'-O-methyladenosine modifications slow the rate of viral transcription at magnitudes specific to each modification, which has the potential to impact SARS-CoV-2 genome maintenance.
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Affiliation(s)
- Laura R Snyder
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Ingrid Kilde
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Artem Nemudryi
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana 59717, USA
| | - Blake Wiedenheft
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana 59717, USA
| | - Markos Koutmos
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Kristin S Koutmou
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
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De Clercq E, Li G, Zhang Y, Huang J, Tan L. Unachieved antiviral strategies with acyclic nucleoside phosphonates: Dedicated to the memory of dr. Salvatore "Sam" Joseph Enna. Biochem Pharmacol 2024:116448. [PMID: 39043335 DOI: 10.1016/j.bcp.2024.116448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 07/16/2024] [Accepted: 07/19/2024] [Indexed: 07/25/2024]
Abstract
Many acyclic nucleoside phosphonates such as cidofovir, adefovir dipivoxil, tenofovir disoproxil fumarate, and tenofovir alafenamide have been marketed for the treatment or prophylaxis of infectious diseases. Here, this review highlights potent acyclic nucleoside phosphonates for their potential in the treatment of retrovirus (e.g., human immunodeficiency virus) and DNA virus (e.g., adeno-, papilloma-, herpes- and poxvirus) infections. If properly assessed and/or optimized, some potent acyclic nucleoside phosphonates can be possibly applied in the control of current and emerging infectious diseases.
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Affiliation(s)
- Erik De Clercq
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Leuven 3000, Belgium
| | - Guangdi Li
- Xiangya School of Public Health, Central South University, Changsha 410078, China
| | - Yun Zhang
- Huaihua City Maternal and Child Health Care Hospital, Huaihua 418000, China
| | - Jie Huang
- Xiangya School of Public Health, Central South University, Changsha 410078, China
| | - Li Tan
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Hunan Clinical Molecular Diagnosis Center, Molecular Diagnostic Technology Hunan Engineering Research Center, Clinical Medical Research Center for Molecular Diagnosis of Infectious Diseases in Hunan Province, Changsha 410011, China.
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4
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Rabie AM, Eltayb WA. Potent Dual Polymerase/Exonuclease Inhibitory Activities of Antioxidant Aminothiadiazoles Against the COVID-19 Omicron Virus: A Promising In Silico/In Vitro Repositioning Research Study. Mol Biotechnol 2024; 66:592-611. [PMID: 36690820 PMCID: PMC9870775 DOI: 10.1007/s12033-022-00551-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 08/10/2022] [Indexed: 01/25/2023]
Abstract
Recently, natural and synthetic nitrogenous heterocyclic antivirals topped the scene as first choices for the treatment of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and their accompanying disease, the coronavirus disease 2019 (COVID-19). Meanwhile, the mysterious evolution of a new strain of SARS-CoV-2, the Omicron variant and its sublineages, caused a new defiance in the continual COVID-19 battle. Hitting the two principal coronaviral-2 multiplication enzymes RNA-dependent RNA polymerase (RdRp) and 3'-to-5' exoribonuclease (ExoN) synchronously using the same ligand is a highly effective novel dual pathway to hinder SARS-CoV-2 reproduction and stop COVID-19 progression irrespective of the SARS-CoV-2 variant type since RdRps and ExoNs are widely conserved among all SARS-CoV-2 strains. Herein, the present computational/biological study screened our previous small libraries of nitrogenous heterocyclic compounds, searching for the most ideal drug candidates predictably able to efficiently act through this double approach. Theoretical filtration gave rise to three promising antioxidant nitrogenous heterocyclic compounds of the 1,3,4-thiadiazole type, which are CoViTris2022, Taroxaz-26, and ChloViD2022. Further experimental evaluation proved for the first time, utilizing the in vitro anti-RdRp/ExoN and anti-SARS-CoV-2 bioassays, that ChloViD2022, CoViTris2022, and Taroxaz-26 could effectively inhibit the replication of the new virulent strains of SARS-CoV-2 with extremely minute in vitro anti-RdRp and anti-SARS-CoV-2 EC50 values of 0.17 and 0.41 μM for ChloViD2022, 0.21 and 0.69 μM for CoViTris2022, and 0.23 and 0.73 μM for Taroxaz-26, respectively, transcending the anti-COVID-19 drug molnupiravir. The preliminary in silico outcomes greatly supported these biochemical results, proposing that the three molecules potently strike the key catalytic pockets of the SARS-CoV-2 (Omicron variant) RdRp's and ExoN's vital active sites. Moreover, the idealistic pharmacophoric hallmarks of CoViTris2022, Taroxaz-26, and ChloViD2022 molecules relatively make them typical dual-action inhibitors of SARS-CoV-2 replication and proofreading, with their highly flexible structures open for various kinds of chemical derivatization. To cut it short, the present pivotal findings of this comprehensive work disclosed the promising repositioning potentials of the three 2-aminothiadiazoles, CoViTris2022, Taroxaz-26, and ChloViD2022, to successfully interfere with the crucial biological interactions of the coronaviral-2 polymerase/exoribonuclease with the four principal RNA nucleotides, and, as a result, cure COVID-19 infection, encouraging us to rapidly start the three drugs' broad preclinical/clinical anti-COVID-19 evaluations.
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Affiliation(s)
- Amgad M Rabie
- Dr. Amgad Rabie's Research Lab. for Drug Discovery (DARLD), Mansoura City, Mansoura, 35511, Dakahlia Governorate, Egypt.
- Head of Drug Discovery & Clinical Research Department, Dikernis General Hospital (DGH), Magliss El-Madina Street, Dikernis City, Dikernis, 35744, Dakahlia Governorate, Egypt.
| | - Wafa A Eltayb
- Biotechnology Department, Faculty of Science and Technology, Shendi University, Shendi, Nher Anile, Sudan.
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Velásquez PA, Hernandez JC, Galeano E, Hincapié-García J, Rugeles MT, Zapata-Builes W. Effectiveness of Drug Repurposing and Natural Products Against SARS-CoV-2: A Comprehensive Review. Clin Pharmacol 2024; 16:1-25. [PMID: 38197085 PMCID: PMC10773251 DOI: 10.2147/cpaa.s429064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 11/14/2023] [Indexed: 01/11/2024] Open
Abstract
The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a betacoronavirus responsible for the COVID-19 pandemic, causing respiratory disorders, and even death in some individuals, if not appropriately treated in time. To face the pandemic, preventive measures have been taken against contagions and the application of vaccines to prevent severe disease and death cases. For the COVID-19 treatment, antiviral, antiparasitic, anticoagulant and other drugs have been reused due to limited specific medicaments for the disease. Drug repurposing is an emerging strategy with therapies that have already tested safe in humans. One promising alternative for systematic experimental screening of a vast pool of compounds is computational drug repurposing (in silico assay). Using these tools, new uses for approved drugs such as chloroquine, hydroxychloroquine, ivermectin, zidovudine, ribavirin, lamivudine, remdesivir, lopinavir and tenofovir/emtricitabine have been conducted, showing effectiveness in vitro and in silico against SARS-CoV-2 and some of these, also in clinical trials. Additionally, therapeutic options have been sought in natural products (terpenoids, alkaloids, saponins and phenolics) with promising in vitro and in silico results for use in COVID-19 disease. Among these, the most studied are resveratrol, quercetin, hesperidin, curcumin, myricetin and betulinic acid, which were proposed as SARS-CoV-2 inhibitors. Among the drugs reused to control the SARS-CoV2, better results have been observed for remdesivir in hospitalized patients and outpatients. Regarding natural products, resveratrol, curcumin, and quercetin have demonstrated in vitro antiviral activity against SARS-CoV-2 and in vivo, a nebulized formulation has demonstrated to alleviate the respiratory symptoms of COVID-19. This review shows the evidence of drug repurposing efficacy and the potential use of natural products as a treatment for COVID-19. For this, a search was carried out in PubMed, SciELO and ScienceDirect databases for articles about drugs approved or under study and natural compounds recognized for their antiviral activity against SARS-CoV-2.
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Affiliation(s)
- Paula Andrea Velásquez
- Grupo Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia, Medellín, Colombia
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Juan C Hernandez
- Grupo Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia, Medellín, Colombia
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Elkin Galeano
- Grupo Productos Naturales Marinos, Departamento de Farmacia, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Jaime Hincapié-García
- Grupo de investigación, Promoción y prevención farmacéutica, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia UdeA, Medellín, Colombia
| | - María Teresa Rugeles
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Wildeman Zapata-Builes
- Grupo Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia, Medellín, Colombia
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
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6
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Gallardo-Toledo E, Neary M, Sharp J, Herriott J, Kijak E, Bramwell C, Curley P, Arshad U, Pertinez H, Rajoli RKR, Valentijn A, Cox H, Tatham L, Kipar A, Stewart JP, Owen A. Chemoprophylactic Assessment of Combined Intranasal SARS-CoV-2 Polymerase and Exonuclease Inhibition in Syrian Golden Hamsters. Viruses 2023; 15:2161. [PMID: 38005839 PMCID: PMC10675045 DOI: 10.3390/v15112161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023] Open
Abstract
Pibrentasvir (PIB) has been demonstrated to block exonuclease activity of the SARS-CoV-2 polymerase, protecting favipiravir (FVP) and remdesivir (RDV) from post-incorporation excision and eliciting antiviral synergy in vitro. The present study investigated the chemoprophylactic efficacy of PIB, FVP, RDV, FVP with PIB, or RDV with PIB dosed intranasally twice a day, using a Syrian golden hamster contact transmission model. Compared to the saline control, viral RNA levels were significantly lower in throat swabs in FVP (day 7), RDV (day 3, 5, 7), and RDV+PIB (day 3, 5) treatment groups. Similarly, findings were evident for nasal turbinate after PIB and RDV treatment, and lungs after PIB, FVP, and FVP+PIB treatment at day 7. Lung viral RNA levels after RDV and RDV+PIB treatment were only detectable in two animals per group, but the overall difference was not statistically significant. In situ examination of the lungs confirmed SARS-CoV-2 infection in all animals, except for one in each of the RDV and RDV+PIB treatment groups, which tested negative in all virus detection approaches. Overall, prevention of transmission was observed in most animals treated with RDV, while other agents reduced the viral load following contact transmission. No benefit of combining FVP or RDV with PIB was observed.
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Affiliation(s)
- Eduardo Gallardo-Toledo
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK; (E.G.-T.); (J.H.); (E.K.); (C.B.); (H.C.); (L.T.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L69 3BX, UK
| | - Megan Neary
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK; (E.G.-T.); (J.H.); (E.K.); (C.B.); (H.C.); (L.T.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L69 3BX, UK
| | - Joanne Sharp
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK; (E.G.-T.); (J.H.); (E.K.); (C.B.); (H.C.); (L.T.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L69 3BX, UK
| | - Joanne Herriott
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK; (E.G.-T.); (J.H.); (E.K.); (C.B.); (H.C.); (L.T.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L69 3BX, UK
| | - Edyta Kijak
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK; (E.G.-T.); (J.H.); (E.K.); (C.B.); (H.C.); (L.T.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L69 3BX, UK
| | - Chloe Bramwell
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK; (E.G.-T.); (J.H.); (E.K.); (C.B.); (H.C.); (L.T.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L69 3BX, UK
| | - Paul Curley
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK; (E.G.-T.); (J.H.); (E.K.); (C.B.); (H.C.); (L.T.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L69 3BX, UK
| | - Usman Arshad
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK; (E.G.-T.); (J.H.); (E.K.); (C.B.); (H.C.); (L.T.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L69 3BX, UK
| | - Henry Pertinez
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK; (E.G.-T.); (J.H.); (E.K.); (C.B.); (H.C.); (L.T.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L69 3BX, UK
| | - Rajith K. R. Rajoli
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK; (E.G.-T.); (J.H.); (E.K.); (C.B.); (H.C.); (L.T.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L69 3BX, UK
| | - Anthony Valentijn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK; (E.G.-T.); (J.H.); (E.K.); (C.B.); (H.C.); (L.T.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L69 3BX, UK
| | - Helen Cox
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK; (E.G.-T.); (J.H.); (E.K.); (C.B.); (H.C.); (L.T.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L69 3BX, UK
| | - Lee Tatham
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK; (E.G.-T.); (J.H.); (E.K.); (C.B.); (H.C.); (L.T.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L69 3BX, UK
| | - Anja Kipar
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 3BX, UK
- Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland
| | - James P. Stewart
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 3BX, UK
| | - Andrew Owen
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK; (E.G.-T.); (J.H.); (E.K.); (C.B.); (H.C.); (L.T.)
- Centre of Excellence in Long-Acting Therapeutics (CELT), University of Liverpool, Liverpool L69 3BX, UK
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7
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Noser AA, Ibrahim SA, Saad-Allah KM, Salem MM, Baren MH. Facile One-Pot Three Component Synthesis, Characterization, and Molecular Docking Simulations of Novel α-Aminophosphonate Derivatives Based Pyrazole Moiety as Potential Antimicrobial Agent. Chem Biodivers 2023; 20:e202301035. [PMID: 37647333 DOI: 10.1002/cbdv.202301035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/01/2023]
Abstract
An efficient method has been developed for the synthesis of novel α-aminophosphonates (AAP) (3 a-m) through a one-pot three-component reaction of 1,3-disubstituted-1H-pyrazol-5-amine, aromatic aldehydes, and phosphite using lithium perchlorate as catalyst. All newly synthesized compounds were characterized via different spectroscopic techniques. The synthesized compounds' mode of action was investigated using molecular docking against the outer membrane protein A (OMPA) and exo-1,3-β-glucanase, with interpreting their pharmacokinetics aspects. The results of the antimicrobial effectiveness of these compounds revealed a broad spectrum of their biocidal activity and this in-vitro study was in line with the in- silico results. Additionally, it has been demonstrated that these compounds exhibited a minimum inhibitory concentration (MIC) with significant activity at low concentrations (7.5-30.0 mg/mL). Further, the radical scavenging (DPPH* ) activity of the synthesized compounds fluctuated, with compounds 3 h, 3 a, and 3 f showing the highest antioxidant activity. Overall, the formulated compounds can be employed as antimicrobial and antioxidant agents in medical applications.
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Affiliation(s)
- Ahmed A Noser
- Organic Chemistry, Chemistry Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Seham A Ibrahim
- Organic Chemistry, Chemistry Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Khalil M Saad-Allah
- Botany Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Maha M Salem
- Biochemistry Division, Chemistry Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt
| | - Mohamed H Baren
- Organic Chemistry, Chemistry Department, Faculty of Science, Tanta University, Tanta, 31527, Egypt
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8
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Russel NS, Kodali G, Stanley RJ, Narayanan M. Screening for Novel Fluorescent Nucleobase Analogues Using Computational and Experimental Methods: 2-Amino-6-chloro-8-vinylpurine (2A6Cl8VP) as a Case Study. J Phys Chem B 2023; 127:7858-7871. [PMID: 37698525 DOI: 10.1021/acs.jpcb.3c03618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
Novel fluorescent nucleic acid base analogues (FBAs) with improved optical properties are needed in a variety of biological applications. 2-Amino-6-chloro-8-vinylpurine (2A6Cl8VP) is structural analogue of two existing highly fluorescent FBAs, 2-aminopurine (2AP) and 8-vinyladenine (8VA), and can therefore be expected to have similar base pairing as well as better optical properties compared to its counterparts. In order to determine the absorption and fluorescence properties of 2A6Cl8VP, as a first step, we used TD-DFT calculations and the polarizable continuum model for simulating the solvents and computationally predicted absorption and fluorescence maxima. To test the computational predictions, we also synthesized 2A6Cl8VP and measured its UV/vis absorbance, fluorescence emission, and fluorescence lifetime. The computationally predicted absorbance and fluorescence maxima of 2A6Cl8VP are in reasonable agreement to the experimental values and are significantly redshifted compared to 2AP and 8VA, allowing for its specific excitation. The fluorescence quantum yield of 2A6Cl8VP, however, is significantly lower than those of 2AP and 8VA. Overall, 2A6Cl8VP is a novel fluorescent nucleobase analogue, which can be useful in studying structural, biophysical, and biochemical applications.
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Affiliation(s)
- Nadim Shahriar Russel
- Department of Chemistry, Temple University, 1901 N. Broad Street, Philadelphia, Pennsylvania 19122, United States
| | - Goutham Kodali
- GlowDNA LLC., Malvern, Pennsylvania 19355, United States
| | - Robert J Stanley
- Department of Chemistry, Temple University, 1901 N. Broad Street, Philadelphia, Pennsylvania 19122, United States
| | - Madhavan Narayanan
- Department of Physical Sciences, Benedictine University, 5700 College Rd, Lisle, Illinois 60532, United States
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9
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Tucci AR, da Rosa RM, Rosa AS, Augusto Chaves O, Ferreira VNS, Oliveira TKF, Coutinho Souza DD, Borba NRR, Dornelles L, Rocha NS, Mayer JCP, da Rocha JBT, Rodrigues OED, Miranda MD. Antiviral Effect of 5'-Arylchalcogeno-3-aminothymidine Derivatives in SARS-CoV-2 Infection. Molecules 2023; 28:6696. [PMID: 37764472 PMCID: PMC10537738 DOI: 10.3390/molecules28186696] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/04/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
The understanding that zidovudine (ZDV or azidothymidine, AZT) inhibits the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 and that chalcogen atoms can increase the bioactivity and reduce the toxicity of AZT has directed our search for the discovery of novel potential anti-coronavirus compounds. Here, the antiviral activity of selenium and tellurium containing AZT derivatives in human type II pneumocytes cell model (Calu-3) and monkey kidney cells (Vero E6) infected with SARS-CoV-2, and their toxic effects on these cells, was evaluated. Cell viability analysis revealed that organoselenium (R3a-R3e) showed lower cytotoxicity than organotellurium (R3f, R3n-R3q), with CC50 ≥ 100 µM. The R3b and R3e were particularly noteworthy for inhibiting viral replication in both cell models and showed better selectivity index. In Vero E6, the EC50 values for R3b and R3e were 2.97 ± 0.62 µM and 1.99 ± 0.42 µM, respectively, while in Calu-3, concentrations of 3.82 ± 1.42 µM and 1.92 ± 0.43 µM (24 h treatment) and 1.33 ± 0.35 µM and 2.31 ± 0.54 µM (48 h) were observed, respectively. The molecular docking calculations were carried out to main protease (Mpro), papain-like protease (PLpro), and RdRp following non-competitive, competitive, and allosteric inhibitory approaches. The in silico results suggested that the organoselenium is a potential non-competitive inhibitor of RdRp, interacting in the allosteric cavity located in the palm region. Overall, the cell-based results indicated that the chalcogen-zidovudine derivatives were more potent than AZT in inhibiting SARS-CoV-2 replication and that the compounds R3b and R3e play an important inhibitory role, expanding the knowledge about the promising therapeutic capacity of organoselenium against COVID-19.
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Affiliation(s)
- Amanda Resende Tucci
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (A.S.R.); (V.N.S.F.); (T.K.F.O.); (D.D.C.S.); (N.R.R.B.)
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
| | - Raquel Mello da Rosa
- LabSelen-NanoBio—Departamento de Química, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil; (R.M.d.R.); (L.D.); (N.S.R.); (J.C.P.M.)
| | - Alice Santos Rosa
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (A.S.R.); (V.N.S.F.); (T.K.F.O.); (D.D.C.S.); (N.R.R.B.)
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
| | - Otávio Augusto Chaves
- CQC-IMS, Departamento de Química, Universidade de Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
- Laboratório de Imunofarmacologia, Centro de Pesquisa, Inovação e Vigilância em COVID-19 e Emergências Sanitárias (CPIV), Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-900, RJ, Brazil
| | - Vivian Neuza Santos Ferreira
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (A.S.R.); (V.N.S.F.); (T.K.F.O.); (D.D.C.S.); (N.R.R.B.)
| | - Thamara Kelcya Fonseca Oliveira
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (A.S.R.); (V.N.S.F.); (T.K.F.O.); (D.D.C.S.); (N.R.R.B.)
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
| | - Daniel Dias Coutinho Souza
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (A.S.R.); (V.N.S.F.); (T.K.F.O.); (D.D.C.S.); (N.R.R.B.)
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
| | - Nathalia Roberto Resende Borba
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (A.S.R.); (V.N.S.F.); (T.K.F.O.); (D.D.C.S.); (N.R.R.B.)
| | - Luciano Dornelles
- LabSelen-NanoBio—Departamento de Química, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil; (R.M.d.R.); (L.D.); (N.S.R.); (J.C.P.M.)
| | - Nayra Salazar Rocha
- LabSelen-NanoBio—Departamento de Química, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil; (R.M.d.R.); (L.D.); (N.S.R.); (J.C.P.M.)
| | - João Candido Pilar Mayer
- LabSelen-NanoBio—Departamento de Química, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil; (R.M.d.R.); (L.D.); (N.S.R.); (J.C.P.M.)
| | - João B. Teixeira da Rocha
- Programa de Pós-Graduação em Bioquímica Toxicológica, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil;
| | - Oscar Endrigo D. Rodrigues
- LabSelen-NanoBio—Departamento de Química, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil; (R.M.d.R.); (L.D.); (N.S.R.); (J.C.P.M.)
| | - Milene Dias Miranda
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (A.S.R.); (V.N.S.F.); (T.K.F.O.); (D.D.C.S.); (N.R.R.B.)
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
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10
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Takács G, Havasi D, Sándor M, Dohánics Z, Balogh GT, Kiss R. DIY Virtual Chemical Libraries - Novel Starting Points for Drug Discovery. ACS Med Chem Lett 2023; 14:1188-1197. [PMID: 37736187 PMCID: PMC10510501 DOI: 10.1021/acsmedchemlett.3c00146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 08/28/2023] [Indexed: 09/23/2023] Open
Abstract
The advancement of in silico technologies such as library enumeration and synthetic feasibility prediction has made drug discovery pipelines rely more and more on virtual libraries, which provide a significantly larger pool of compounds than in-stock supplier catalogs. Virtual libraries from external sources, however, may be associated with long delivery time and high cost. In this study, we present a Do-It-Yourself (DIY) combinatorial chemistry library containing over 14 million almost completely novel products built from 1000 low-cost building blocks based on robust reactions frequently applied at medicinal chemistry laboratories. The applicability of the DIY library for various drug discovery approaches is demonstrated by extensive physicochemical property, structural diversity profiling, and the generation of focused libraries. We found that internally built DIY chemical libraries present a viable alternative of external virtual catalogs by providing access to a large number of low-cost and quickly accessible potential chemical starting points for drug discovery.
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Affiliation(s)
- Gergely Takács
- Department
of Chemical and Environmental Process Engineering, Faculty of Chemical
Technology and Biotechnology, Budapest University
of Technology and Economics, Műegyetem rakpart 3, Budapest 1111, Hungary
- Mcule.com
Kft, Bartók Béla
út 105-113, Budapest 1115, Hungary
| | - Dávid Havasi
- Department
of Chemical and Environmental Process Engineering, Faculty of Chemical
Technology and Biotechnology, Budapest University
of Technology and Economics, Műegyetem rakpart 3, Budapest 1111, Hungary
- Mcule.com
Kft, Bartók Béla
út 105-113, Budapest 1115, Hungary
| | - Márk Sándor
- Mcule.com
Kft, Bartók Béla
út 105-113, Budapest 1115, Hungary
| | - Zsolt Dohánics
- Mcule.com
Kft, Bartók Béla
út 105-113, Budapest 1115, Hungary
| | - György T. Balogh
- Department
of Chemical and Environmental Process Engineering, Faculty of Chemical
Technology and Biotechnology, Budapest University
of Technology and Economics, Műegyetem rakpart 3, Budapest 1111, Hungary
- Department
of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Semmelweis University, Hőgyes Endre utca 7-9, Budapest 1092, Hungary
| | - Róbert Kiss
- Mcule.com
Kft, Bartók Béla
út 105-113, Budapest 1115, Hungary
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11
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Xu T, Zhang L. Current understanding of nucleoside analogs inhibiting the SARS-CoV-2 RNA-dependent RNA polymerase. Comput Struct Biotechnol J 2023; 21:4385-4394. [PMID: 37711189 PMCID: PMC10498173 DOI: 10.1016/j.csbj.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/16/2023] Open
Abstract
Since the outbreak of the COVID-19 pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA-dependent RNA polymerase (RdRp) has become a main target for antiviral therapeutics due to its essential role in viral replication and transcription. Thus, nucleoside analogs structurally resemble the natural RdRp substrate and hold great potential as inhibitors. Until now, extensive experimental investigations have been performed to explore nucleoside analogs to inhibit the RdRp, and concerted efforts have been made to elucidate the underlying molecular mechanisms further. This review begins by discussing the nucleoside analogs that have demonstrated inhibition in the experiments. Second, we examine the current understanding of the molecular mechanisms underlying the action of nucleoside analogs on the SARS-CoV-2 RdRp. Recent findings in structural biology and computational research are presented through the classification of inhibitory mechanisms. This review summarizes previous experimental findings and mechanistic investigations of nucleoside analogs inhibiting SARS-CoV-2 RdRp. It would guide the rational design of antiviral medications and research into viral transcriptional mechanisms.
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Affiliation(s)
- Tiantian Xu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lu Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Fujian 361005, China
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12
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Luxenburger H, Thimme R. SARS-CoV-2 and the liver: clinical and immunological features in chronic liver disease. Gut 2023; 72:1783-1794. [PMID: 37316169 PMCID: PMC10423489 DOI: 10.1136/gutjnl-2023-329623] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/24/2023] [Indexed: 06/16/2023]
Abstract
SARS-CoV-2 infection may affect the liver in healthy individuals but also influences the course of COVID-19 in patients with chronic liver disease (CLD). As described in healthy individuals, a strong SARS-CoV-2-specific adaptive immune response is important for the outcome of COVID-19, however, knowledge on the adaptive immune response in CLD is limited.Here, we review the clinical and immunological features of SARS-CoV-2 infection in individuals with CLD. Acute liver injury occurs in many cases of SARS-CoV-2 infection and may be induced by multiple factors, such as cytokines, direct viral infection or toxic effects of COVID-19 drugs. In individuals with CLD, SARS-CoV-2 infection may have a more severe course and promote decompensation and particularly in patients with cirrhosis. Compared with healthy individuals, the SARS-CoV-2-specific adaptive immune responses is impaired in patients with CLD after both, natural infection and vaccination but improves at least partially after booster vaccination.Following SARS-CoV-2 vaccination, rare cases of acute vaccine-induced liver injury and the development of autoimmune-like hepatitis have been reported. However, the concomitant elevation of liver enzymes is reversible under steroid treatment.
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Affiliation(s)
- Hendrik Luxenburger
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Robert Thimme
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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13
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Mukerjee N, Ghosh A. Revolutionizing viral disease treatment: PROTACs therapy could be the ultimate weapon of the future. J Med Virol 2023; 95:e28981. [PMID: 37515471 DOI: 10.1002/jmv.28981] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 05/22/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023]
Affiliation(s)
- Nobendu Mukerjee
- Department of Microbiology, West Bengal State University, Kolkata, West Bengal, India
| | - Arabinda Ghosh
- Department of Computational Biology and Biotechnology, Mahapurasha Srimanta Sankaradeva Viswavidyalaya, Guwahati, Assam, India
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14
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Abdalla M, Rabie AM. Dual computational and biological assessment of some promising nucleoside analogs against the COVID-19-Omicron variant. Comput Biol Chem 2023; 104:107768. [PMID: 36842392 PMCID: PMC9450471 DOI: 10.1016/j.compbiolchem.2022.107768] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/16/2022] [Accepted: 09/04/2022] [Indexed: 01/18/2023]
Abstract
Nucleoside analogs/derivatives (NAs/NDs) with potent antiviral activities are now deemed very convenient choices for the treatment of coronavirus disease 2019 (COVID-19) arisen by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. At the same time, the appearance of a new strain of SARS-CoV-2, the Omicron variant, necessitates multiplied efforts in fighting COVID-19. Counteracting the crucial SARS-CoV-2 enzymes RNA-dependent RNA polymerase (RdRp) and 3'-to-5' exoribonuclease (ExoN) jointly altogether using the same inhibitor is a quite successful new plan to demultiplicate SARS-CoV-2 particles and eliminate COVID-19 whatever the SARS-CoV-2 subtype is (due to the significant conservation nature of RdRps and ExoNs in the different SARS-CoV-2 strains). Successive in silico screening of known NAs finally disclosed six different promising NAs, which are riboprine/forodesine/tecadenoson/nelarabine/vidarabine/maribavir, respectively, that predictably can act through the planned dual-action mode. Further in vitro evaluations affirmed the anti-SARS-CoV-2/anti-COVID-19 potentials of these NAs, with riboprine and forodesine being at the top. The two NAs are able to effectively antagonize the replication of the new virulent SARS-CoV-2 strains with considerably minute in vitro anti-RdRp and anti-SARS-CoV-2 EC50 values of 189 and 408 nM for riboprine and 207 and 657 nM for forodesine, respectively, surpassing both remdesivir and the new anti-COVID-19 drug molnupiravir. Furthermore, the favorable structural characteristics of the two molecules qualify them for varied types of isosteric and analogistic chemical derivatization. In one word, the present important outcomes of this comprehensive dual study revealed the anticipating repurposing potentials of some known nucleosides, led by the two NAs riboprine and forodesine, to successfully discontinue the coronaviral-2 polymerase/exoribonuclease interactions with RNA nucleotides in the SARS-CoV-2 Omicron variant (BA.5 sublineage) and accordingly alleviate COVID-19 infections, motivating us to initiate the two drugs' diverse anti-COVID-19 pharmacological evaluations to add both of them betimes in the COVID-19 therapeutic protocols.
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Affiliation(s)
- Mohnad Abdalla
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 Cultural West Road, Shandong Province 250012, PR China.
| | - Amgad M. Rabie
- Dr. Amgad Rabie's Research Lab. for Drug Discovery (DARLD), Mansoura City 35511, Mansoura, Dakahlia Governorate, Egypt,Head of Drug Discovery & Clinical Research Department, Dikernis General Hospital (DGH), Magliss El-Madina Street, Dikernis City 35744, Dikernis, Dakahlia Governorate, Egypt,Correspondence to: 16 Magliss El-Madina Street, Dikernis City 35744, Dikernis, Dakahlia Governorate, Egypt
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15
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Tenofovir Disoproxil Fumarate Reduces the Severity of COVID-19 in Patients with Chronic Hepatitis B. Dig Dis Sci 2023; 68:2731-2737. [PMID: 36737575 PMCID: PMC9897881 DOI: 10.1007/s10620-022-07817-w] [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: 09/18/2022] [Accepted: 12/29/2022] [Indexed: 02/05/2023]
Abstract
BACKGROUND AND AIMS HIV-positive patients on tenofovir hydroxyl fumarate (TDF)/emtricitabine have a lower risk of COVID-19 and hospitalization than those given other treatments. Our aim was to analyze the severity of COVID-19 in patients with chronic hepatitis B (CHB) on TDF or entecavir (ETV). METHODS Spanish hospital databases (n = 28) including information regarding adult CHB patients on TDF or ETV for the period February 1st to November 30th 2020 were searched for COVID-19, defined as a positive SARS-CoV-2 polymerase chain reaction, and for severe COVID-19. RESULTS Of 4736 patients, 117 had COVID-19 (2.5%), 67 on TDF and 50 on ETV. Compared to patients on TDF, those on ETV showed (p < 0.05) greater rates of obesity, diabetes, ischemic cardiopathy, and hypertension. COVID-19 incidence was similar in both groups (2.3 vs. 2.6%). Compared to TDF, patients on ETV more often (p < 0.01) had severe COVID-19 (36 vs. 6%), required intensive care unit (ICU) (10% vs. 0) or ventilatory support (20 vs. 3%), were hospitalized for longer (10.8 ± 19 vs. 3.1 ± 7 days) or died (10 vs. 1.5%, p = 0.08). In an IPTW propensity score analysis adjusted for age, sex, obesity, comorbidities, and fibrosis stage, TDF was associated with a sixfold reduction in severe COVID-19 risk (adjusted-IPTW-OR 0.17, 95%CI 0.04-0.67, p = 0.01). CONCLUSION Compared to ETV, TDF seems to play a protective role in CHB patients with SARS-CoV-2 whereby the risk of severe COVID-19 is lowered.
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16
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Rabie AM, Eltayb WA. Strong Dual Antipolymerase/Antiexonuclease Actions of Some Aminothiadiazole Antioxidants: A Promising In-Silico/ In-Vitro Repurposing Research Study against the COVID-19 Omicron Virus (B.1.1.529.3 Lineage). ADVANCES IN REDOX RESEARCH 2023:100064. [PMID: 36776420 PMCID: PMC9907022 DOI: 10.1016/j.arres.2023.100064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 01/03/2023] [Accepted: 01/21/2023] [Indexed: 01/27/2023]
Abstract
Currently, nitrogen-containing heterocyclic virucides take the lead as top options for treating the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and their escorting disease, the coronavirus disease 2019 (COVID-19). But unfortunately, the sudden emergence of a new strain of SARS-CoV-2, the Omicron variant and its lineages, complicated matters in the incessant COVID-19 battle. Goaling the two paramount coronaviral-2 multiplication enzymes RNA-dependent RNA polymerase (RdRp) and 3'-to-5' exoribonuclease (ExoN) at synchronous times using single ligand is a quite effective new binary avenue to restrain SARS-CoV-2 reproduction and cease COVID-19 progression irrespective of the SARS-CoV-2 strain type, as RdRps and ExoNs are vastly conserved in all SARS-CoV-2 strains. The presented in-silico/in-vitro research winnowed our own small libraries of antioxidant nitrogenous heterocyclic compounds, inspecting for the utmost convenient drug candidates expectedly capable of effectively working through this dual tactic. Computational screening afforded three promising compounds of the antioxidant 1,3,4-thiadiazole class, which were named ChloViD2022, Taroxaz-26, and CoViTris2022. Subsequent biological examination, employing the in-vitro anti-RdRp/anti-ExoN and anti-SARS-CoV-2 assays, exclusively demonstrated that ChloViD2022, CoViTris2022, and Taroxaz-26 could efficiently block the replication of the new lineages of SARS-CoV-2 with considerably minute anti-RdRp and anti-SARS-CoV-2 EC50 values of about 0.18 and 0.44 μM for ChloViD2022, 0.22 and 0.72 μM for CoViTris2022, and 0.25 and 0.78 μM for Taroxaz-26, in the order, overtaking the standard anti-SARS-CoV-2 drug molnupiravir. These biochemical findings were optimally presupported by the results of the prior in-silico screening, suggesting that the three compounds might potently hit the catalytic active sites of the virus's RdRp and ExoN enzymes. Furthermore, the perfect pharmacophoric features of ChloViD2022, Taroxaz-26, and CoViTris2022 molecules make them typical dual inhibitors of SARS-CoV-2 replication and proofreading, with their relatively flexible structures eligible for diverse forms of chemical modification. In sum, the current important results of this thorough research work exposed the interesting repurposing potential of the three 2-amino-1,3,4-thiadiazole ligands, ChloViD2022, Taroxaz-26, and CoViTris2022, to effectively conflict with the vital biointeractions between the coronavirus's polymerase/exoribonuclease and the four essential RNA nucleotides, and, accordingly, arrest COVID-19 disease, persuading the relevant investigators to quickly begin the three agents' comprehensive preclinical and clinical anti-COVID-19 assessments.
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Affiliation(s)
- Amgad M Rabie
- Dr. Amgad Rabie's Research Lab. for Drug Discovery (DARLD), Mansoura City 35511, Mansoura, Dakahlia Governorate, Egypt
- Head of Drug Discovery & Clinical Research Department, Dikernis General Hospital (DGH), Magliss El-Madina Street, Dikernis City 35744, Dikernis, Dakahlia Governorate, Egypt
| | - Wafa A Eltayb
- Biotechnology Department, Faculty of Science and Technology, Shendi University, Shendi 11111, River Nile State, Sudan
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17
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Petushkov I, Esyunina D, Kulbachinskiy A. Effects of natural RNA modifications on the activity of SARS-CoV-2 RNA-dependent RNA polymerase. FEBS J 2023; 290:80-92. [PMID: 35916766 PMCID: PMC9538676 DOI: 10.1111/febs.16587] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/17/2022] [Accepted: 08/01/2022] [Indexed: 01/18/2023]
Abstract
RNA-dependent RNA polymerase (RdRp) plays a key role in the replication of RNA viruses, including SARS-CoV-2. Processive RNA synthesis by RdRp is crucial for successful genome replication and expression, especially in the case of very long coronaviral genomes. Here, we analysed the activity of SARS-CoV-2 RdRp (the nsp12-nsp7-nsp8 complex) on synthetic primer-templates of various structures, including substrates with mismatched primers or template RNA modifications. It has been shown that RdRp cannot efficiently extend RNA primers containing mismatches and has no intrinsic RNA cleavage activity to remove the primer 3'-end, thus necessitating the action of exoribonuclease for proofreading. Similar to DNA-dependent RNA polymerases, RdRp can perform processive pyrophosphorolysis of the nascent RNA product but this reaction is also blocked in the presence of mismatches. Furthermore, we have demonstrated that several natural post-transcriptional modifications in the RNA template, which do not prevent complementary interactions (N6-methyladenosine, 5-methylcytosine, inosine and pseudouridine), do not change RdRp processivity. At the same time, certain modifications of RNA bases and ribose residues strongly block RNA synthesis, either prior to nucleotide incorporation (3-methyluridine and 1-methylguanosine) or immediately after it (2'-O-methylation). The results demonstrate that the activity of SARS-CoV-2 RdRp can be strongly inhibited by common modifications of the RNA template suggesting a way to design novel antiviral compounds.
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Affiliation(s)
- Ivan Petushkov
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”MoscowRussia
| | - Daria Esyunina
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”MoscowRussia
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”MoscowRussia
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18
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Polo R, García-Albéniz X, Terán C, Morales M, Rial-Crestelo D, Garcinuño MA, García Del Toro M, Hita C, Gómez-Sirvent JL, Buzón L, Díaz de Santiago A, Arellano JP, Sanz J, Bachiller P, Alfaro EM, Díaz-Brito V, Masiá M, Hernández-Torres A, Guerra JM, Santos J, Arazo P, Muñoz L, Arribas JR, Martínez de Salazar P, Moreno S, Hernán MA, Del Amo J. Daily tenofovir disoproxil fumarate/emtricitabine and hydroxychloroquine for pre-exposure prophylaxis of COVID-19: a double-blind placebo-controlled randomized trial in healthcare workers. Clin Microbiol Infect 2023; 29:85-93. [PMID: 35940567 PMCID: PMC9352647 DOI: 10.1016/j.cmi.2022.07.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 07/06/2022] [Accepted: 07/09/2022] [Indexed: 12/27/2022]
Abstract
OBJECTIVES To assess the effect of hydroxychloroquine (HCQ) and Tenofovir disoproxil fumarate/emtricitabine (TDF/FTC) as pre-exposure prophylaxis on COVID-19 risk. METHODS EPICOS is a double-blind, placebo-controlled randomized trial conducted in Spain, Bolivia, and Venezuela. Healthcare workers with negative SARS-CoV-2 IgM/IgG test were randomly assigned to the following: daily TDF/FTC plus HCQ for 12 weeks, TDF/FTC plus HCQ placebo, HCQ plus TDF/FTC placebo, and TDF/FTC placebo plus HCQ placebo. Randomization was performed in groups of four. Primary outcome was laboratory-confirmed, symptomatic COVID-19. We also studied any (symptomatic or asymptomatic) COVID-19. We compared group-specific 14-week risks via differences and ratios with 95% CIs. RESULTS Of 1002 individuals screened, 926 (92.4%) were eligible and there were 14 cases of symptomatic COVID-19: 220 were assigned to the TDF/FTC plus HCQ group (3 cases), 231 to the TDF/FTC placebo plus HCQ group (3 cases), 233 to the TDF/FTC plus HCQ placebo group (3 cases), and 223 to the double placebo group (5 cases). Compared with the double placebo group, 14-week risk ratios (95% CI) of symptomatic COVID-19 were 0.39 (0.00-1.98) for TDF + HCQ, 0.34 (0.00-2.06) for TDF, and 0.49 (0.00-2.29) for HCQ. Corresponding risk ratios of any COVID-19 were 0.51 (0.21-1.00) for TDF + HCQ, 0.81 (0.44-1.49) for TDF, and 0.73 (0.41-1.38) for HCQ. Adverse events were generally mild. DISCUSSION The target sample size was not met. Our findings are compatible with both benefit and harm of pre-exposure prophylaxis with TDF/FTC and HCQ, alone or in combination, compared with placebo.
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Affiliation(s)
- Rosa Polo
- Division for HIV, STI, Viral Hepatitis and TB Control, Ministry of Health, Madrid, Spain
| | - Xabier García-Albéniz
- CAUSALab, Harvard T.H. Chan School of Public Health, Boston, MA, USA; RTI Health Solutions, Barcelona, Spain
| | - Carolina Terán
- Facultad de Medicina Universidad Mayor, Real y Pontificia de San Francisco Xavier de Chuquisaca, Hospital Santa Bárbara, Sucre, Bolivia
| | | | - David Rial-Crestelo
- Hospital Doce de Octubre, Madrid, Spain; CIBER de Enfermedades Infecciosas, Institute of Health Carlos III, Madrid, Spain
| | | | | | | | | | - Luis Buzón
- Hospital Universitario de Burgos, Burgos, Spain
| | | | | | - Jesus Sanz
- CIBER de Enfermedades Infecciosas, Institute of Health Carlos III, Madrid, Spain; Hospital Universitario de la Princesa, Madrid, Spain
| | | | | | | | - Mar Masiá
- CIBER de Enfermedades Infecciosas, Institute of Health Carlos III, Madrid, Spain; Hospital General Universitario de Elche, Alicante, Spain
| | | | | | - Jesús Santos
- Hospital Universitario Virgen de la Victoria de Málaga, Málaga, Spain
| | - Piedad Arazo
- Hospital Universitario Miguel Servet, Zaragoza, Spain
| | - Leopoldo Muñoz
- Complejo Hospitalario Universitario de Granada, Granada, Spain
| | - Jose Ramon Arribas
- CIBER de Enfermedades Infecciosas, Institute of Health Carlos III, Madrid, Spain; Hospital Universitario La Paz, IdiPAZ, Madrid, Spain
| | - Pablo Martínez de Salazar
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Santiago Moreno
- CIBER de Enfermedades Infecciosas, Institute of Health Carlos III, Madrid, Spain; Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Miguel A Hernán
- CAUSALab, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Departments of Epidemiology and Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Julia Del Amo
- Division for HIV, STI, Viral Hepatitis and TB Control, Ministry of Health, Madrid, Spain; CIBER de Enfermedades Infecciosas, Institute of Health Carlos III, Madrid, Spain.
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19
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Rabie AM, Abdalla M. Evaluation of a series of nucleoside analogs as effective anticoronaviral-2 drugs against the Omicron-B.1.1.529/BA.2 subvariant: A repurposing research study. Med Chem Res 2022; 32:326-341. [PMID: 36593869 PMCID: PMC9797896 DOI: 10.1007/s00044-022-02970-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 09/06/2022] [Indexed: 12/30/2022]
Abstract
Mysterious evolution of a new strain of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the Omicron variant, led to a new challenge in the persistent coronavirus disease 2019 (COVID-19) battle. Objecting the conserved SARS-CoV-2 enzymes RNA-dependent RNA polymerase (RdRp) and 3'-to-5' exoribonuclease (ExoN) together using one ligand is a successful new tactic to stop SARS-CoV-2 multiplication and COVID-19 progression. The current comprehensive study investigated most nucleoside analogs (NAs) libraries, searching for the most ideal drug candidates expectedly able to act through this double tactic. Gradual computational filtration afforded six different promising NAs, riboprine/forodesine/tecadenoson/nelarabine/vidarabine/maribavir. Further biological assessment proved that riboprine and forodesine are able to powerfully inhibit the replication of the new virulent strains of SARS-CoV-2 with extremely minute in vitro anti-RdRp and anti-SARS-CoV-2 EC50 values of about 0.21 and 0.45 μM for riboprine and about 0.23 and 0.70 μM for forodesine, respectively, surpassing both remdesivir and the new anti-COVID-19 drug molnupiravir. These biochemical findings were supported by the prior in silico data. Additionally, the ideal pharmacophoric features of riboprine and forodesine molecules render them typical dual-action inhibitors of SARS-CoV-2 replication and proofreading. These findings suggest that riboprine and forodesine could serve as prospective lead compounds against COVID-19. Graphical abstract.
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Affiliation(s)
- Amgad M. Rabie
- Dr. Amgad Rabie’s Research Lab. for Drug Discovery (DARLD), Mansoura City 35511, Mansoura, Dakahlia Governorate Egypt
- Head of Drug Discovery & Clinical Research Department, Dikernis General Hospital (DGH), Magliss El-Madina Street, Dikernis City 35744, Dikernis, Dakahlia Governorate Egypt
| | - Mohnad Abdalla
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 Cultural West Road, Jinan, Shandong Province 250012 PR China
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20
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Guo J, Wang Y, Zhang M, Zheng H, Zang Q, Huang P, Wen L, Song D, Yang F, Dong R, Miao W. Human parvovirus B19 infection in hospitalized patients suspected of infection with pathogenic microorganism. Front Cell Infect Microbiol 2022; 12:1083839. [PMID: 36619750 PMCID: PMC9812433 DOI: 10.3389/fcimb.2022.1083839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
Background Human parvovirus B19 (HPV B19) is a single-stranded DNA virus. The detection rate of HPV B19 in the blood of healthy blood donors using PCR technology was reported to be 6.323/100000. However, that among hospitalized patients suspected of being infected with a pathogenic microorganism is unknown. Methods A retrospective analysis was conducted on 2,182 high-throughput NGS results for 1,484 inpatients admitted to the First Affiliated Hospital of Zhengzhou University from January 2020 to October 2021 who were suspected of being infected with a pathogenic microorganism, as well as on clinical data of some HPV B19-positive patients. Results Human parvovirus B19 was detected in 39 samples from 33 patients. The positivity rate was 2.22% among patients and 1.78% among samples. HPV B19 was detected in 20 cerebrospinal fluid samples, 13 blood samples, 3 alveolar lavage fluid samples, 2 tissue samples, and 1 throat swab. Based on clinical symptoms and NGS results, 16 patients were diagnosed with HPV B19 infection. The number of HPV B19 sequences in these patients was greater than 6, and the patients showed common symptoms such as fever (14 cases), anemia (11 cases), and severe nervous system symptoms such as meningoencephalitis (9 cases) and Guillain-Barré syndrome with peripheral motor and sensory nerve axon damage (4 cases). All 16 patients had experienced events likely to lead to decreased immunity (11 had a history of trauma/surgery/major disease, 4 had a history of precursor infection, and 3 had used immunosuppressants) and 7 had a history of blood transfusion during hospitalization. After treatment with antiviral drugs (12 cases) and intravenous human immunoglobulin (3 cases), of the 16 patients, 14 patients improved. Conclusion The HPV B19 infection rate in hospitalized patients suspected of microbial infection was 2.22%. Most patients with HPV B19 infection had a history of low immunity and blood transfusion. HPV B19 could be detected in various bodily fluids and tissues (especially cerebrospinal fluid) using NGS. Patients with severe HPV B19 infection may have nervous system damage such as Guillain-Barré syndrome and meningoencephalitis. Early diagnosis using NGS and treatment with antiviral drugs and immunoglobulin can improve prognosis.
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Affiliation(s)
- Junshuang Guo
- Neuro-Intensive Care Unit of the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China,Department of Immunology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Yating Wang
- Neuro-Intensive Care Unit of the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Mian Zhang
- General intensive care unit of Zhengzhou Seventh People’s Hospital, Zhengzhou, Henan, China
| | - Hongxiang Zheng
- General intensive care unit of Zhengzhou Seventh People’s Hospital, Zhengzhou, Henan, China
| | - Qiuling Zang
- Neuro-Intensive Care Unit of the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Peipei Huang
- Neuro-Intensive Care Unit of the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Lijun Wen
- Neuro-Intensive Care Unit of the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Dandan Song
- Neuro-Intensive Care Unit of the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Fan Yang
- Neuro-Intensive Care Unit of the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Ruirui Dong
- Neuro-Intensive Care Unit of the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Wang Miao
- Neuro-Intensive Care Unit of the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China,*Correspondence: Wang Miao,
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21
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Rabie AM, Abdalla M. Forodesine and Riboprine Exhibit Strong Anti-SARS-CoV-2 Repurposing Potential: In Silico and In Vitro Studies. ACS BIO & MED CHEM AU 2022; 2:565-585. [PMID: 37582236 PMCID: PMC9631343 DOI: 10.1021/acsbiomedchemau.2c00039] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/16/2022] [Accepted: 07/19/2022] [Indexed: 11/07/2022]
Abstract
Lately, nucleos(t)ide antivirals topped the scene as top options for the treatment of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Targeting the two broadly conserved SARS-CoV-2 enzymes, RNA-dependent RNA polymerase (RdRp) and 3'-to-5' exoribonuclease (ExoN), together using only one shot is a very successful new tactic to stop SARS-CoV-2 multiplication irrespective of the SARS-CoV-2 variant type. Herein, the current studies investigated most nucleoside analogue (NA) libraries, searching for the ideal drug candidates expectedly able to act through this double tactic. Gradual computational filtration gave rise to six different promising NAs along with their corresponding triphosphate (TP) nucleotides. The subsequent biological assessment proved for the first time that, among the six NAs, riboprine and forodesine are able to hyperpotently inhibit the replication of the Omicron strain of SARS-CoV-2 with extremely low in vitro anti-RdRp, anti-ExoN, and anti-SARS-CoV-2 EC50 values of about 0.18, 0.28, and 0.40 μM for riboprine and about 0.20, 0.31, and 0.65 μM for forodesine, respectively, surpassing remdesivir and molnupiravir. The significant probability that both compounds may also act as prodrugs for their final TP nucleotides in vivo pushed us to examine the same activities for forodesine-TP and riboprine-TP. Both nucleotides similarly displayed very promising results, respectively, which are much better than those for the two reference TP nucleotides, GS-443902 and β-d-N4-hydroxycytidine 5'-TP (NHC-TP). The prior in silico data supported these biochemical findings, suggesting that riboprine and forodesine molecules and their expected active TP metabolites strongly hit the key catalytic pockets of the SARS-CoV-2 RdRp's and ExoN's main active sites. In brief, the current important results of this comprehensive study revealed the interesting repurposing potentials of, mainly, the two bioactive nucleosides forodesine and riboprine and their TP nucleotides to effectively shut down the polymerase/exoribonuclease-RNA nucleotide interactions of SARS-CoV-2 and consequently treat COVID-19 infections.
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Affiliation(s)
- Amgad M. Rabie
- Dr.
Amgad Rabie’s Research Lab. for Drug Discovery (DARLD), Mansoura City35511,Mansoura, Dakahlia Governorate, Egypt
- Head
of Drug Discovery & Clinical Research Department, Dikernis General Hospital (DGH), Magliss El-Madina Street, Dikernis City35744,Dikernis, Dakahlia Governorate, Egypt
| | - Mohnad Abdalla
- Key
Laboratory of Chemical Biology (Ministry of Education), Department
of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College
of Medicine, Shandong University, 44 Cultural West Road, Jinan, Shandong Province250012, P. R. China
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22
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Zemskov DN, Balykova LA, Radaeva OA, Zaslavskaya KY, Bely PA, Semenova EV, Shirmankina MV, Koryanova KN. CURRENT ASPECTS OF ETIOTROPIC COVID-19 THERAPY. PHARMACY & PHARMACOLOGY 2022. [DOI: 10.19163/2307-9266-2022-10-5-432-445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Since the beginning of the pandemic, repeated attempts have been made to develop etiotropic therapy for a novel coronavirus infection. Hydroxychloroquine, lopinavir/ritonavir, etc. derivatives were used as antiviral agents, however, they demonstrated a low efficiency and an insufficient safety. In this connection, other groups of drugs with a more effective and safe pharmacological profile are currently being actively used.The aim of the study was to analyze the literature references on the efficacy and safety of antiviral drugs for the COVID-19 treatment.Materials and methods. When searching for the materials for the review article writing, such abstract databases as PubMed, Google Scholar, e-Library were used. The search was carried out on publications for the period from January 2020 to september 2022. The key queries were: COVID-19, etiotropic therapy; immunological drugs; antiviral drugs; interferons.Results. Currently, there are various degrees of effective etiotropic drugs for the treatment of COVID-19 patients. The review has considered a few groups of drugs that are of interest from the point of view of etiotropic therapy: immunological drugs (anticovid plasma, the drugs based on antiviral antibodies, the drugs of recombinant interferons-α2 and -β1, as well as interferon inducers, i.e., the drugs based on double-stranded RNA sodium salt, and others); drugs that block the penetration of the virus into the cell (umifenovir); the drugs that disrupt the process of the viral replication (favipiravir, remdesivir, molnupiravir, nirmatrelvir/ritonavir).Conclusion. Synthetic antivirals, in particular favipiravir, molnupiravir, remdesivir, and nirmatrelvir/ritonavir, have the largest evidence base for their efficacy and safety. The search for new effective and safe etiotropic drugs for the treatment of COVID-19, as well as the collection and analysis of post-registration data on the drugs already used in clinical practice, continues.
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Affiliation(s)
| | | | | | | | - P. A. Bely
- Evdokimov Moscow State Medical and Dental University
| | | | | | - K. N. Koryanova
- Pyatigorsk Medical and Pharmaceutical Institute – branch of Volgograd State Medical University
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23
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He YF, Jiang ZG, Wu N, Bian N, Ren JL. Correlation between COVID-19 and hepatitis B: A systematic review. World J Gastroenterol 2022; 28:6599-6618. [PMID: 36569273 PMCID: PMC9782843 DOI: 10.3748/wjg.v28.i46.6599] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/29/2022] [Accepted: 11/19/2022] [Indexed: 12/08/2022] Open
Abstract
BACKGROUND There is growing evidence that patients with coronavirus disease 2019 (COVID-19) frequently present with liver impairment. Hepatitis B virus (HBV) remains a major public health threat in current society. Both severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and HBV can cause liver damage, and current findings on whether HBV infection increases disease severity in COVID-19 patients are inconsistent, and whether SARS-CoV-2 infection accelerates hepatitis B progression or leads to a worse prognosis in hepatitis B patients has not been adequately elucidated. AIM To explore the complex relationship between COVID-19 and hepatitis B in order to inform the research and management of patients co-infected with SARS-CoV-2 and HBV. METHODS An experienced information specialist searched the literature in the following online databases: PubMed, China National Knowledge Infrastructure, Google Scholar, Scopus, Wiley, Web of Science, Cochrane, and ScienceDirect. The literature published from December 2019 to September 1, 2022 was included in the search. We also searched medRxiv and bioRxiv for gray literature and manually scanned references of included articles. Articles reporting studies conducted in humans discussing hepatitis B and COVID-19 were included. We excluded duplicate publications. News reports, reports, and other gray literature were included if they contained quantifiable evidence (case reports, findings, and qualitative analysis). Some topics that included HBV or COVID-19 samples but did not have quantitative evidence were excluded from the review. RESULTS A total of 57 studies were eligible and included in this review. They were from 11 countries, of which 33 (57.9%) were from China. Forty-two of the 57 studies reported abnormalities in liver enzymes, three mainly reported abnormalities in blood parameters, four indicated no significant liver function alterations, and another eight studies did not provide data on changes in liver function. Fifty-seven studies were retrospective and the total number of co-infections was 1932, the largest sample size was 7723, and the largest number of co-infections was 353. Most of the studies suggested an interaction between hepatitis B and COVID-19, while 12 studies clearly indicated no interaction between hepatitis B and COVID-19. Six of the 57 studies clearly reported HBV activation. Six studies were related to liver transplant patients. CONCLUSION There is some association between COVID-19 and hepatitis B. Future high-quality randomized trials are needed to further elucidate the interaction between COVID-19 and hepatitis B.
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Affiliation(s)
- Yan-Fei He
- Health Management Center, The Sixth Medical Center, Chinese PLA General Hospital, Beijing 100048, China
| | - Zhi-Gang Jiang
- Department of Statistics, Zunyi Medical University, Guizhou 563006, Guizhou Province, China
| | - Ni Wu
- Health Management Center, The Sixth Medical Center, Chinese PLA General Hospital, Beijing 100048, China
| | - Ning Bian
- Health Management Center, The Sixth Medical Center, Chinese PLA General Hospital, Beijing 100048, China
| | - Jun-Lin Ren
- Department of Infection Control, The Sixth Medical Center, Chinese PLA General Hospital, Beijing 100048, China
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24
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Rabie AM, Abdalla M. A Series of Adenosine Analogs as the First Efficacious Anti-SARS-CoV-2 Drugs against the B.1.1.529.4 Lineage: A Preclinical Repurposing Research Study. ChemistrySelect 2022; 7:e202201912. [PMID: 36718467 PMCID: PMC9877610 DOI: 10.1002/slct.202201912] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 09/30/2022] [Indexed: 12/13/2022]
Abstract
Given the rapid progression of the coronavirus disease 2019 (COVID-19) pandemic, an ultrafast response was urgently required to handle this major public crisis. To contain the pandemic, investments are required to develop diagnostic tests, prophylactic vaccines, and novel therapies. Lately, nucleoside analog (NA) antivirals topped the scene as top options for the treatment of COVID-19 caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. Meanwhile, the continuous generation of new lineages of the SARS-CoV-2 Omicron variant caused a new challenge in the persistent COVID-19 battle. Hitting the two crucial SARS-CoV-2 enzymes RNA-dependent RNA polymerase (RdRp) and 3'-to-5' exoribonuclease (ExoN) collectively together using only one single ligand is a very successful new approach to stop SARS-CoV-2 multiplication and combat COVID-19 irrespective of the SARS-CoV-2 variant type because RdRps and ExoNs are broadly conserved among all SARS-CoV-2 strains. Herein, the current comprehensive study investigated most NAs libraries, searching for the most ideal drug candidates expectedly able to perfectly act through this double tactic. Gradual computational filtration gave rise to six different promising NAs, which are riboprine, forodesine, tecadenoson, nelarabine, vidarabine, and maribavir, respectively. Further biological assessment proved for the first time, using the in vitro anti-RdRp/ExoN and anti-SARS-CoV-2 bioassays, that riboprine and forodesine, among all the six tested NAs, are able to powerfully inhibit the replication of the new virulent strains of SARS-CoV-2 with extremely minute in vitro anti-RdRp and anti-SARS-CoV-2 EC50 values of about 0.22 and 0.49 μM for riboprine and about 0.25 and 0.73 μM for forodesine, respectively, surpassing both remdesivir and the new anti-COVID-19 drug molnupiravir. The prior in silico data supported these biochemical findings, suggesting that riboprine and forodesine molecules strongly hit the key catalytic pockets of the SARS-CoV-2 (Omicron variant) RdRp's and ExoN's main active sites. Additionally, the ideal pharmacophoric features of riboprine and forodesine molecules render them typical dual-action inhibitors of SARS-CoV-2 replication and proofreading, with their relatively flexible structures open for diverse types of chemical derivatization. In Brief, the current important results of this comprehensive study revealed the interesting repurposing potentials of, mainly, the two nucleosides riboprine and forodesine to effectively shut down the polymerase/exoribonuclease-RNA nucleotides interactions of the SARS-CoV-2 Omicron variant and consequently treat COVID-19 infections, motivating us to rapidly begin the two drugs' broad preclinical/clinical anti-COVID-19 bioevaluations, hoping to combine both drugs soon in the COVID-19 treatment protocols.
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Affiliation(s)
- Amgad M. Rabie
- Dr. Amgad Rabie's Research Lab. for Drug Discovery (DARLD)35511MansouraDakahlia GovernorateEgypt,Head of Drug Discovery & Clinical Research Department Dikernis General Hospital (DGH)Magliss El-Madina Street Dikernis35744DikernisDakahlia GovernorateEgypt
| | - Mohnad Abdalla
- Key Laboratory of Chemical Biology (Ministry of Education)Department of PharmaceuticsSchool of Pharmaceutical SciencesCheeloo College of MedicineShandong University44 Cultural West RoadShandong Province250012PR China
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25
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Nguyenla X, Wehri E, Van Dis E, Biering SB, Yamashiro LH, Zhu C, Stroumza J, Dugast-Darzacq C, Graham TGW, Wang X, Jockusch S, Tao C, Chien M, Xie W, Patel DJ, Meyer C, Garzia A, Tuschl T, Russo JJ, Ju J, Näär AM, Stanley S, Schaletzky J. Discovery of SARS-CoV-2 antiviral synergy between remdesivir and approved drugs in human lung cells. Sci Rep 2022; 12:18506. [PMID: 36323770 PMCID: PMC9628577 DOI: 10.1038/s41598-022-21034-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/21/2022] [Indexed: 11/07/2022] Open
Abstract
SARS coronavirus 2 (SARS-CoV-2) has caused an ongoing global pandemic with significant mortality and morbidity. At this time, the only FDA-approved therapeutic for COVID-19 is remdesivir, a broad-spectrum antiviral nucleoside analog. Efficacy is only moderate, and improved treatment strategies are urgently needed. To accomplish this goal, we devised a strategy to identify compounds that act synergistically with remdesivir in preventing SARS-CoV-2 replication. We conducted combinatorial high-throughput screening in the presence of submaximal remdesivir concentrations, using a human lung epithelial cell line infected with a clinical isolate of SARS-CoV-2. This identified 20 approved drugs that act synergistically with remdesivir, many with favorable pharmacokinetic and safety profiles. Strongest effects were observed with established antivirals, Hepatitis C virus nonstructural protein 5A (HCV NS5A) inhibitors velpatasvir and elbasvir. Combination with their partner drugs sofosbuvir and grazoprevir further increased efficacy, increasing remdesivir's apparent potency > 25-fold. We report that HCV NS5A inhibitors act on the SARS-CoV-2 exonuclease proofreader, providing a possible explanation for the synergy observed with nucleoside analog remdesivir. FDA-approved Hepatitis C therapeutics Epclusa® (velpatasvir/sofosbuvir) and Zepatier® (elbasvir/grazoprevir) could be further optimized to achieve potency and pharmacokinetic properties that support clinical evaluation in combination with remdesivir.
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Affiliation(s)
- Xammy Nguyenla
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA, 94720, USA
| | - Eddie Wehri
- The Henry Wheeler Center for Emerging and Neglected Diseases, 344 Li Ka Shing, Berkeley, CA, 94720, USA
| | - Erik Van Dis
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, Berkeley, CA, 94720, USA
| | - Scott B Biering
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA, 94720, USA
| | - Livia H Yamashiro
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA, 94720, USA
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, Berkeley, CA, 94720, USA
| | - Chi Zhu
- Department of Nutritional Sciences & Toxicology, University of California, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA
| | - Julien Stroumza
- The Henry Wheeler Center for Emerging and Neglected Diseases, 344 Li Ka Shing, Berkeley, CA, 94720, USA
| | - Claire Dugast-Darzacq
- Department of Molecular and Cell Biology, Division of Genetics, Genomics and Development, University of California, Berkeley, CA, 94720, USA
| | - Thomas G W Graham
- Department of Molecular and Cell Biology, Division of Genetics, Genomics and Development, University of California, Berkeley, CA, 94720, USA
| | - Xuanting Wang
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Steffen Jockusch
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Chuanjuan Tao
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Minchen Chien
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Wei Xie
- Laboratory of Structural Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Dinshaw J Patel
- Laboratory of Structural Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Cindy Meyer
- Laboratory of RNA Molecular Biology, Rockefeller University, New York, NY, 10065, USA
| | - Aitor Garzia
- Laboratory of RNA Molecular Biology, Rockefeller University, New York, NY, 10065, USA
| | - Thomas Tuschl
- Laboratory of RNA Molecular Biology, Rockefeller University, New York, NY, 10065, USA
| | - James J Russo
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Jingyue Ju
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
- Department of Molecular Pharmacology and Therapeutics, Columbia University, New York, NY, 10032, USA
| | - Anders M Näär
- Department of Nutritional Sciences & Toxicology, University of California, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA
| | - Sarah Stanley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA, 94720, USA.
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, Berkeley, CA, 94720, USA.
| | - Julia Schaletzky
- The Henry Wheeler Center for Emerging and Neglected Diseases, 344 Li Ka Shing, Berkeley, CA, 94720, USA.
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26
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Pourfarjam Y, Ma Z, Kim IK. ATP enhances the error-prone ribonucleotide incorporation by the SARS-CoV-2 RNA polymerase. Biochem Biophys Res Commun 2022; 625:53-59. [PMID: 35947915 PMCID: PMC9344795 DOI: 10.1016/j.bbrc.2022.07.087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 07/22/2022] [Accepted: 07/22/2022] [Indexed: 01/18/2023]
Abstract
The novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2 or COVID-19) has caused a global pandemic. The SARS-CoV-2 RNA genome is replicated by a conserved "core" replication-transcription complex (RTC) containing an error-prone RNA-dependent RNA polymerase holoenzyme (holo-RdRp, nsp12-nsp7-nsp8) and a RNA proofreading nuclease (nsp14-nsp10). Although structures and functions of SARS-CoV-2 holo-RdRp have been extensively studied and ribonucleotide-analog inhibitors, such as Remdesivir, have been treated for COVID-19 patients, the substrate and nucleotide specificity of SARS-CoV-2 holo-RdRp remain unknown. Here, our biochemical analysis of SARS-CoV-2 holo-RdRp reveals that it has a robust DNA-dependent RNA polymerase activity, in addition to its intrinsic RNA-dependent RNA polymerase activity. Strikingly, SARS-CoV-2 holo-RdRp fully extends RNAs with a low-fidelity even when only ATP and pyrimidine nucleotides, in particular CTP, are provided. This ATP-dependent error-prone ribonucleotide incorporation by SARS-CoV-2 holo-RdRp resists excision by the RNA proofreading nuclease in vitro. Our collective results suggest that a physiological concentration of ATP likely contributes to promoting the error-prone incorporation of ribonucleotides and ribonucleotide-analogs by SARS-CoV-2 holo-RdRp and provide a useful foundation to develop ribonucleotide analogs as an effective therapeutic strategy to combat coronavirus-mediated outbreak.
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Affiliation(s)
- Yasin Pourfarjam
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct, Cincinnati, OH, 45221, USA
| | - Zhijun Ma
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct, Cincinnati, OH, 45221, USA
| | - In-Kwon Kim
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct, Cincinnati, OH, 45221, USA.
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27
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The First 5′-Phosphorylated 1,2,3-Triazolyl Nucleoside Analogues with Uracil and Quinazoline-2,4-Dione Moieties: A Synthesis and Antiviral Evaluation. Molecules 2022; 27:molecules27196214. [PMID: 36234748 PMCID: PMC9573387 DOI: 10.3390/molecules27196214] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 09/12/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022] Open
Abstract
A series of 5′-phosphorylated (dialkyl phosphates, diaryl phosphates, phosphoramidates, H-phosphonates, phosphates) 1,2,3-triazolyl nucleoside analogues in which the 1,2,3-triazole-4-yl-β-D-ribofuranose fragment is attached via a methylene group or a butylene chain to the N-1 atom of the heterocycle moiety (uracil or quinazoline-2,4-dione) was synthesized. All compounds were evaluated for antiviral activity against influenza virus A/PR/8/34/(H1N1). Antiviral assays revealed three compounds, 13b, 14b, and 17a, which showed moderate activity against influenza virus A (H1N1) with IC50 values of 17.9 μM, 51 μM, and 25 μM, respectively. In the first two compounds, the quinazoline-2,4-dione moiety is attached via a methylene or a butylene linker, respectively, to the 1,2,3-triazole-4-yl-β-D-ribofuranosyl fragment possessing a 5′-diphenyl phosphate substituent. In compound 17a, the uracil moiety is attached via the methylene unit to the 1,2,3-triazole-4-yl-β-D-ribofuranosyl fragment possessing a 5′-(phenyl methoxy-L-alaninyl)phosphate substituent. The remaining compounds appeared to be inactive against influenza virus A/PR/8/34/(H1N1). The results of molecular docking simulations indirectly confirmed the literature data that the inhibition of viral replication is carried out not by nucleoside analogues themselves, but by their 5′-triphosphate derivatives.
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28
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Madariaga-Mazón A, Naveja JJ, Becerra A, Alberto Campillo-Balderas J, Hernández-Morales R, Jácome R, Lazcano A, Martinez-Mayorga K. Subtle structural differences of nucleotide analogs may impact SARS-CoV-2 RNA-dependent RNA polymerase and exoribonuclease activity. Comput Struct Biotechnol J 2022; 20:5181-5192. [PMID: 36097553 PMCID: PMC9452397 DOI: 10.1016/j.csbj.2022.08.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 08/05/2022] [Accepted: 08/27/2022] [Indexed: 11/17/2022] Open
Abstract
The rapid spread and public health impact of the novel SARS-CoV-2 variants that cause COVID-19 continue to produce major global impacts and social distress. Several vaccines were developed in record time to prevent and limit the spread of the infection, thus playing a pivotal role in controlling the pandemic. Although the repurposing of available drugs attempts to provide therapies of immediate access against COVID-19, there is still a need for developing specific treatments for this disease. Remdesivir, molnupiravir and Paxlovid remain the only evidence-supported antiviral drugs to treat COVID-19 patients, and only in severe cases. To contribute on the search of potential Covid-19 therapeutic agents, we targeted the viral RNA-dependent RNA polymerase (RdRp) and the exoribonuclease (ExoN) following two strategies. First, we modeled and analyzed nucleoside analogs sofosbuvir, remdesivir, favipiravir, ribavirin, and molnupiravir at three key binding sites on the RdRp-ExoN complex. Second, we curated and virtually screened a database containing 517 nucleotide analogs in the same binding sites. Finally, we characterized key interactions and pharmacophoric features presumably involved in viral replication halting at multiple sites. Our results highlight structural modifications that might lead to more potent SARS-CoV-2 inhibitors against an expansive range of variants and provide a collection of nucleotide analogs useful for screening campaigns.
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Affiliation(s)
- Abraham Madariaga-Mazón
- Instituto de Química Unidad Mérida, Universidad Nacional Autónoma de México, Carretera Mérida-Tetiz Km. 4.5, Ucú, Yucatán, Mexico.,Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas Unidad Mérida, Universidad Nacional Autónoma de México, Sierra Papacál Mérida, Yucatán 97302, Mexico
| | - José J Naveja
- Instituto de Química Unidad Mérida, Universidad Nacional Autónoma de México, Carretera Mérida-Tetiz Km. 4.5, Ucú, Yucatán, Mexico.,Institute for Molecular Biology and University Cancer Center (UCT) Mainz, Germany
| | - Arturo Becerra
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | | | - Rodrigo Jácome
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Antonio Lazcano
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico.,El Colegio Nacional, Mexico City, Mexico
| | - Karina Martinez-Mayorga
- Instituto de Química Unidad Mérida, Universidad Nacional Autónoma de México, Carretera Mérida-Tetiz Km. 4.5, Ucú, Yucatán, Mexico.,Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas Unidad Mérida, Universidad Nacional Autónoma de México, Sierra Papacál Mérida, Yucatán 97302, Mexico
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29
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Tanimoto S, Itoh SG, Okumura H. State-of-the-Art Molecular Dynamics Simulation Studies of RNA-Dependent RNA Polymerase of SARS-CoV-2. Int J Mol Sci 2022; 23:ijms231810358. [PMID: 36142270 PMCID: PMC9499461 DOI: 10.3390/ijms231810358] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/26/2022] [Accepted: 08/31/2022] [Indexed: 01/18/2023] Open
Abstract
Molecular dynamics (MD) simulations are powerful theoretical methods that can reveal biomolecular properties, such as structure, fluctuations, and ligand binding, at the level of atomic detail. In this review article, recent MD simulation studies on these biomolecular properties of the RNA-dependent RNA polymerase (RdRp), which is a multidomain protein, of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are presented. Although the tertiary structures of RdRps in SARS-CoV-2 and SARS-CoV are almost identical, the RNA synthesis activity of RdRp of SARS-CoV is higher than SARS-CoV-2. Recent MD simulations observed a difference in the dynamic properties of the two RdRps, which may cause activity differences. RdRp is also a drug target for Coronavirus disease 2019 (COVID-19). Nucleotide analogs, such as remdesivir and favipiravir, are considered to be taken up by RdRp and inhibit RNA replication. Recent MD simulations revealed the recognition mechanism of RdRp for these drug molecules and adenosine triphosphate (ATP). The ligand-recognition ability of RdRp decreases in the order of remdesivir, favipiravir, and ATP. As a typical recognition process, it was found that several lysine residues of RdRp transfer these ligand molecules to the binding site such as a “bucket brigade.” This finding will contribute to understanding the mechanism of the efficient ligand recognition by RdRp. In addition, various simulation studies on the complexes of SARS-CoV-2 RdRp with several nucleotide analogs are reviewed, and the molecular mechanisms by which these compounds inhibit the function of RdRp are discussed. The simulation studies presented in this review will provide useful insights into how nucleotide analogs are recognized by RdRp and inhibit the RNA replication.
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Affiliation(s)
- Shoichi Tanimoto
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8787, Aichi, Japan
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki 444-8787, Aichi, Japan
| | - Satoru G. Itoh
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8787, Aichi, Japan
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki 444-8787, Aichi, Japan
- Department of Structural Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki 444-8787, Aichi, Japan
| | - Hisashi Okumura
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8787, Aichi, Japan
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki 444-8787, Aichi, Japan
- Department of Structural Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki 444-8787, Aichi, Japan
- Correspondence:
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30
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Jena NR, Pant S, Srivastava HK. Artificially expanded genetic information systems (AEGISs) as potent inhibitors of the RNA-dependent RNA polymerase of the SARS-CoV-2. J Biomol Struct Dyn 2022; 40:6381-6397. [PMID: 33565387 PMCID: PMC7885727 DOI: 10.1080/07391102.2021.1883112] [Citation(s) in RCA: 4] [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: 08/01/2020] [Accepted: 01/25/2021] [Indexed: 01/18/2023]
Abstract
The recent outbreak of the SARS-CoV-2 infection has affected the lives and economy of more than 200 countries. The unavailability of virus-specific drugs has created an opportunity to identify potential therapeutic agents that can control the rapid transmission of this pandemic. Here, the mechanisms of the inhibition of the RNA-dependent RNA polymerase (RdRp), responsible for the replication of the virus in host cells, are examined by different ligands, such as Remdesivir (RDV), Remdesivir monophosphate (RMP), and several artificially expanded genetic information systems (AEGISs) including their different sequences by employing molecular docking, MD simulations, and MM/GBSA techniques. It is found that the binding of RDV to RdRp may block the RNA binding site. However, RMP would acquire a partially flipped conformation and may allow the viral RNA to enter into the binding site. The internal dynamics of RNA and RdRp may help RMP to regain its original position, where it may inhibit the RNA-chain elongation reaction. Remarkably, AEGISs are found to obstruct the binding site of RNA. It is shown that dPdZ, a two-nucleotide sequence containing P and Z would bind to RdRp very strongly and may occupy the positions of two nucleotides in the RNA strand, thereby denying access of the substrate-binding site to the viral RNA. Thus, it is proposed that the AEGISs may act as novel therapeutic candidates against the SARS-CoV-2. However, in vivo evaluations of their potencies and toxicities are needed before using them against COVID-19.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- N. R. Jena
- Discipline of Natural Sciences, Indian Institute of Information Technology, Design, and Manufacturing, Jabalpur, Madhya Pradesh, India
| | - Suyash Pant
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Kolkata, West Bengal, India
| | - Hemant Kumar Srivastava
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Changsari, Guwahati, Assam, India
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31
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Sarma H, Sastry GN. A Computational Study on the Interaction of NSP10 and NSP14: Unraveling the RNA Synthesis Proofreading Mechanism in SARS-CoV-2, SARS-CoV, and MERS-CoV. ACS OMEGA 2022; 7:30003-30022. [PMID: 36035077 PMCID: PMC9397572 DOI: 10.1021/acsomega.2c03007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
The interaction of exoribonuclease (ExoN) nonstructural protein (NSP14) with NSP10 co-factors is crucial for high-fidelity proofreading activity of coronavirus replication and transcription. Proofreading function is critical for maintaining the large genomes to ensure replication proficiency; therefore, while maintaining the viral replication fitness, quick resistance has been reported to the nucleotide analogue (NA) drugs. Therefore, targeting the NSP14 and NSP10 interacting interface with small molecules or peptides could be a better strategy to obstruct replication processes of coronaviruses (CoVs). A comparative study on the binding mechanism of NSP10 with the NSP14 ExoN domain of SARS-CoV-2, SARS-CoV, MERS-CoV, and four SARS-CoV-2 NSP14mutant complexes has been carried out. Protein-protein interaction (PPI) dynamics, per-residue binding free energy (BFE) analyses, and the identification of interface hotspot residues have been studied using molecular dynamics simulations and various computational tools. The BFE of the SARS-CoV NSP14-NSP10 complex was higher when compared to novel SARS-CoV-2 and MERS. However, SARS-CoV-2 NSP14mutant systems display a higher BFE as compared to the wild type (WT) but lower than SARS-CoV and MERS. Despite the high BFE, the SARS-CoV NSP14-NSP10 complex appears to be structurally more flexible in many regions especially the catalytic site, which is not seen in SARS-CoV-2 and its mutant or MERS complexes. The significantly high residue energy contribution of key interface residues and hotspots reveals that the high binding energy between NSP14 and NSP10 may enhance the functional activity of the proofreading complex, as the NSP10-NSP14 interaction is essential in maintaining the stability of the ExoN domain for the replicative fitness of CoVs. The factors discussed for SARS-CoV-2 complexes may be responsible for NSP14 ExoN having a high replication proficiency, significantly leading to the evolution of new variants of SARS-CoV-2. The NSP14 residues V66, T69, D126, and I201and eight residues of NSP10 (L16, F19, V21, V42, M44, H80, K93, and F96) are identified as common hotspots. Overall, the interface area, hotspot locations, bonded/nonbonded contacts, and energies between NSP14 and NSP10 may pave a way in designing potential inhibitors to disrupt NSP14-NSP10 interactions of CoVs especially SARS-CoV-2.
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Affiliation(s)
- Himakshi Sarma
- Advanced Computation and Data Sciences Division,
CSIR−North East Institute of Science and Technology,
Jorhat, Assam785006, India
| | - G. Narahari Sastry
- Advanced Computation and Data Sciences Division,
CSIR−North East Institute of Science and Technology,
Jorhat, Assam785006, India
- Academy of Scientific and Innovative
Research (AcSIR), Ghaziabad 201002, India
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32
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Luo X, Wang X, Yao Y, Gao X, Zhang L. Unveiling the "Template-Dependent" Inhibition on the Viral Transcription of SARS-CoV-2. J Phys Chem Lett 2022; 13:7197-7205. [PMID: 35912566 PMCID: PMC9363016 DOI: 10.1021/acs.jpclett.2c01314] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
Remdesivir is one nucleotide analogue prodrug capable to terminate RNA synthesis in SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) by two distinct mechanisms. Although the "delayed chain termination" mechanism has been extensively investigated, the "template-dependent" inhibitory mechanism remains elusive. In this study, we have demonstrated that remdesivir embedded in the template strand seldom directly disrupted the complementary NTP incorporation at the active site. Instead, the translocation of remdesivir from the +2 to the +1 site was hindered due to the steric clash with V557. Moreover, we have elucidated the molecular mechanism characterizing the drug resistance upon V557L mutation. Overall, our studies have provided valuable insight into the "template-dependent" inhibitory mechanism exerted by remdesivir on SARS-CoV-2 RdRp and paved venues for an alternative antiviral strategy for the COVID-19 pandemic. As the "template-dependent" inhibition occurs across diverse viral RdRps, our findings may also shed light on a common acting mechanism of inhibitors.
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Affiliation(s)
- Xueying Luo
- State
Key Laboratory of Structural Chemistry, Fujian Institute of Research
on the Structure of Matter, Chinese Academy
of Sciences, 350002 Fuzhou, Fujian, China
- University
of Chinese Academy of Sciences, 100049 Beijing, China
| | - Xiaowei Wang
- Department
of Chemical and Biological Engineering, Department of Mathematics, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Yuan Yao
- Department
of Mathematics, Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Xin Gao
- Computer
Science Program, Computer, Electrical and Mathematical Sciences and
Engineering (CEMSE) Division, King Abdullah
University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
- KAUST
Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Lu Zhang
- State
Key Laboratory of Structural Chemistry, Fujian Institute of Research
on the Structure of Matter, Chinese Academy
of Sciences, 350002 Fuzhou, Fujian, China
- University
of Chinese Academy of Sciences, 100049 Beijing, China
- Fujian Provincial
Key Laboratory of Theoretical and Computational Chemistry, 361005 Fujian, China
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33
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Tuberculosis and HIV responses threatened by nCOVID-19: A situation prompting an in silico investigation of reported MbtA inhibitors for combined inhibition of SARS-CoV-2 and HIV-TB co-infection. Struct Chem 2022. [DOI: 10.1007/s11224-022-02013-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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34
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Wang X, Tao C, Morozova I, Kalachikov S, Li X, Kumar S, Russo JJ, Ju J. Identifying Structural Features of Nucleotide Analogues to Overcome SARS-CoV-2 Exonuclease Activity. Viruses 2022; 14:1413. [PMID: 35891393 PMCID: PMC9324094 DOI: 10.3390/v14071413] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/24/2022] [Accepted: 06/25/2022] [Indexed: 01/27/2023] Open
Abstract
With the recent global spread of new SARS-CoV-2 variants, there remains an urgent need to develop effective and variant-resistant oral drugs. Recently, we reported in vitro results validating the use of combination drugs targeting both the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) and proofreading exonuclease (ExoN) as potential COVID-19 therapeutics. For the nucleotide analogues to be efficient SARS-CoV-2 inhibitors, two properties are required: efficient incorporation by RdRp and substantial resistance to excision by ExoN. Here, we have selected and evaluated nucleotide analogues with a variety of structural features for resistance to ExoN removal when they are attached at the 3' RNA terminus. We found that dideoxynucleotides and other nucleotides lacking both 2'- and 3'-OH groups were most resistant to ExoN excision, whereas those possessing both 2'- and 3'-OH groups were efficiently removed. We also found that the 3'-OH group in the nucleotide analogues was more critical than the 2'-OH for excision by ExoN. Since the functionally important sequences in Nsp14/10 are highly conserved among all SARS-CoV-2 variants, these identified structural features of nucleotide analogues offer invaluable insights for designing effective RdRp inhibitors that can be simultaneously efficiently incorporated by the RdRp and substantially resist ExoN excision. Such newly developed RdRp terminators would be good candidates to evaluate their ability to inhibit SARS-CoV-2 in cell culture and animal models, perhaps combined with additional exonuclease inhibitors to increase their overall effectiveness.
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Affiliation(s)
- Xuanting Wang
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY 10027, USA; (X.W.); (C.T.); (I.M.); (S.K.); (X.L.); (S.K.); (J.J.R.)
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA
| | - Chuanjuan Tao
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY 10027, USA; (X.W.); (C.T.); (I.M.); (S.K.); (X.L.); (S.K.); (J.J.R.)
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA
| | - Irina Morozova
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY 10027, USA; (X.W.); (C.T.); (I.M.); (S.K.); (X.L.); (S.K.); (J.J.R.)
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA
| | - Sergey Kalachikov
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY 10027, USA; (X.W.); (C.T.); (I.M.); (S.K.); (X.L.); (S.K.); (J.J.R.)
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA
| | - Xiaoxu Li
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY 10027, USA; (X.W.); (C.T.); (I.M.); (S.K.); (X.L.); (S.K.); (J.J.R.)
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA
| | - Shiv Kumar
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY 10027, USA; (X.W.); (C.T.); (I.M.); (S.K.); (X.L.); (S.K.); (J.J.R.)
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA
| | - James J. Russo
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY 10027, USA; (X.W.); (C.T.); (I.M.); (S.K.); (X.L.); (S.K.); (J.J.R.)
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA
| | - Jingyue Ju
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY 10027, USA; (X.W.); (C.T.); (I.M.); (S.K.); (X.L.); (S.K.); (J.J.R.)
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA
- Department of Molecular Pharmacology and Therapeutics, Columbia University, New York, NY 10032, USA
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35
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Munafò F, Donati E, Brindani N, Ottonello G, Armirotti A, De Vivo M. Quercetin and luteolin are single-digit micromolar inhibitors of the SARS-CoV-2 RNA-dependent RNA polymerase. Sci Rep 2022; 12:10571. [PMID: 35732785 PMCID: PMC9216299 DOI: 10.1038/s41598-022-14664-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 06/10/2022] [Indexed: 01/18/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly become a global health pandemic. Among the viral proteins, RNA-dependent RNA polymerase (RdRp) is responsible for viral genome replication and has emerged as one of the most promising targets for pharmacological intervention against SARS-CoV-2. To this end, we experimentally tested luteolin and quercetin for their ability to inhibit the RdRp enzyme. These two compounds are ancestors of flavonoid natural compounds known for a variety of basal pharmacological activities. Luteolin and quercetin returned a single-digit IC50 of 4.6 µM and 6.9 µM, respectively. Then, through dynamic docking simulations, we identified possible binding modes of these compounds to a recently published cryo-EM structure of RdRp. Collectively, these data indicate that these two compounds are a valid starting point for further optimization and development of a new class of RdRp inhibitors to treat SARS-CoV-2 and potentially other viral infections.
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Affiliation(s)
- Federico Munafò
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano Di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Elisa Donati
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano Di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Nicoletta Brindani
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano Di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Giuliana Ottonello
- Analytical Chemistry Facility, Istituto Italiano Di Tecnologia, via Morego, 30, 16163, Genoa, Italy
| | - Andrea Armirotti
- Analytical Chemistry Facility, Istituto Italiano Di Tecnologia, via Morego, 30, 16163, Genoa, Italy
| | - Marco De Vivo
- Molecular Modeling and Drug Discovery Lab, Istituto Italiano Di Tecnologia, via Morego 30, 16163, Genoa, Italy.
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36
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Rabie AM. Efficacious Preclinical Repurposing of the Nucleoside Analogue Didanosine against COVID-19 Polymerase and Exonuclease. ACS OMEGA 2022; 7:21385-21396. [PMID: 35785294 PMCID: PMC9244909 DOI: 10.1021/acsomega.1c07095] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/16/2022] [Indexed: 01/18/2023]
Abstract
![]()
Analogues and derivatives
of natural nucleosides/nucleotides are
considered among the most successful bioactive species of drug-like
compounds in modern medicinal chemistry, as they are well recognized
for their diverse and efficient pharmacological activities in humans,
especially as antivirals and antitumors. Coronavirus disease 2019
(COVID-19) is still almost incurable, with its infectious viral microbe,
the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2),
continuing to wreak devastation around the world. This global crisis
pushed all involved scientists, including drug discoverers and clinical
researchers, to try to find an effective and broad-spectrum anti-COVID-19
drug. Didanosine (2′,3′-dideoxyinosine, DDI) is a synthetic
inosine/adenosine/guanosine analogue and highly active antiretroviral
therapeutic agent used for the treatment of human immunodeficiency
virus infection and acquired immunodeficiency syndrome (HIV/AIDS).
This potent reverse-transcriptase inhibitor is characterized by proven
strong pharmacological effects against the viral genome, which may
successfully take part in the effective treatment of SARS-CoV-2/COVID-19.
Additionally, targeting the pivotal SARS-CoV-2 replication enzyme,
RNA-dependent RNA polymerase (RdRp), is a very successful tactic to
combat COVID-19 irrespective of the SARS-CoV-2 variant type because
RdRps are broadly conserved among all SARS-CoV-2 strains. Herein,
the current study proved for the first time, using the in
vitro antiviral evaluation, that DDI is capable of potently
inhibiting the replication of the novel virulent progenies of SARS-CoV-2
with quite tiny in vitro anti-SARS-CoV-2 and anti-RdRp
EC50 values of around 3.1 and 0.19 μM, respectively,
surpassing remdesivir together with its active metabolite (GS-441524).
Thereafter, the in silico computational interpretation
of the biological results supported that DDI strongly targets the
key pocket of the SARS-CoV-2 RdRp main catalytic active site. The
ideal pharmacophoric characteristics of the ligand DDI make it a typical
inhibiting agent of SARS-CoV-2 multiplication processes (including
high-fidelity proofreading), with its elastic structure open for many
kinds of derivatization. In brief, the present results further uphold
and propose the repurposing potentials of DDI against the different
types of COVID-19 and convincingly motivate us to quickly launch its
extensive preclinical/clinical pharmacological evaluations, hoping
to combine it in the COVID-19 therapeutic protocols soon.
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Affiliation(s)
- Amgad M. Rabie
- Dr. Amgad Rabie’s Research Lab. for Drug Discovery (DARLD), Mansoura 35511, Egypt
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
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37
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Jones AN, Mourão A, Czarna A, Matsuda A, Fino R, Pyrc K, Sattler M, Popowicz GM. Characterization of SARS-CoV-2 replication complex elongation and proofreading activity. Sci Rep 2022; 12:9593. [PMID: 35688849 PMCID: PMC9185715 DOI: 10.1038/s41598-022-13380-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 02/14/2022] [Indexed: 01/18/2023] Open
Abstract
The replication complex (RC) of SARS-CoV-2 was recently shown to be one of the fastest RNA-dependent RNA polymerases of any known coronavirus. With this rapid elongation, the RC is more prone to incorporate mismatches during elongation, resulting in a highly variable genomic sequence. Such mutations render the design of viral protein targets difficult, as drugs optimized for a given viral protein sequence can quickly become inefficient as the genomic sequence evolves. Here, we use biochemical experiments to characterize features of RNA template recognition and elongation fidelity of the SARS-CoV-2 RdRp, and the role of the exonuclease, nsp14. Our study highlights the 2'OH group of the RNA ribose as a critical component for RdRp template recognition and elongation. We show that RdRp fidelity is reduced in the presence of the 3' deoxy-terminator nucleotide 3'dATP, which promotes the incorporation of mismatched nucleotides (leading to U:C, U:G, U:U, C:U, and A:C base pairs). We find that the nsp10-nsp14 heterodimer is unable to degrade RNA products lacking free 2'OH or 3'OH ribose groups. Our results suggest the potential use of 3' deoxy-terminator nucleotides in RNA-derived oligonucleotide inhibitors as antivirals against SARS-CoV-2.
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Affiliation(s)
- Alisha N Jones
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Department of Chemistry, Bavarian NMR Center, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany
| | - André Mourão
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Department of Chemistry, Bavarian NMR Center, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany
| | - Anna Czarna
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Kraków, Poland
| | - Alex Matsuda
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Kraków, Poland
| | - Roberto Fino
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Department of Chemistry, Bavarian NMR Center, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany
| | - Krzysztof Pyrc
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Kraków, Poland.
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany. .,Department of Chemistry, Bavarian NMR Center, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany.
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany. .,Department of Chemistry, Bavarian NMR Center, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany.
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38
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Kaboudin B, Daliri P, Faghih S, Esfandiari H. Hydroxy- and Amino-Phosphonates and -Bisphosphonates: Synthetic Methods and Their Biological Applications. Front Chem 2022; 10:890696. [PMID: 35721002 PMCID: PMC9200139 DOI: 10.3389/fchem.2022.890696] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 04/28/2022] [Indexed: 12/02/2022] Open
Abstract
Phosphonates and bisphosphonates are stable analogs of phosphates and pyrophosphates that are characterized by one and two carbon–phosphorus bonds, respectively. Among the various phosphonates and bisphosphonates, hydroxy and amino substitutes are of interest as effective in medicinal and industrial chemistry. For example, hydroxy bisphosphonates have proven to be effective for the prevention of bone loss, especially in osteoporotic disease. On the other hand, different substitutions on the carbon atom connected to phosphorus have led to the synthesis of many different hydroxy- and amino-phosphonates and -bisphosphonates, each with its distinct physical, chemical, biological, therapeutic, and toxicological characteristics. Dialkyl or aryl esters of phosphonate and bisphosphonate compounds undergo the hydrolysis process readily and gave valuable materials with wide applications in pharmaceutical and agriculture. This review aims to demonstrate the ongoing preparation of various classes of hydroxy- and amino-phosphonates and -bisphosphonates. Furthermore, the current review summarizes and comprehensively describes articles on the biological applications of hydroxyl- and amino-phosphonates and -bisphosphonates from 2015 until today.
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39
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Li Y, Zhang D, Gao X, Wang X, Zhang L. 2'- and 3'-Ribose Modifications of Nucleotide Analogues Establish the Structural Basis to Inhibit the Viral Replication of SARS-CoV-2. J Phys Chem Lett 2022; 13:4111-4118. [PMID: 35503748 PMCID: PMC9088111 DOI: 10.1021/acs.jpclett.2c00087] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/27/2022] [Indexed: 05/12/2023]
Abstract
Inhibition of RNA-dependent RNA polymerase (RdRp) by nucleotide analogues with ribose modification provides a promising antiviral strategy for the treatment of SARS-CoV-2. Previous works have shown that remdesivir carrying 1'-substitution can act as a "delayed chain terminator", while nucleotide analogues with 2'-methyl group substitution could immediately terminate the chain extension. However, how the inhibition can be established by the 3'-ribose modification as well as other 2'-ribose modifications is not fully understood. Herein, we have evaluated the potential of several adenosine analogues with 2'- and/or 3'-modifications as obligate chain terminators by comprehensive structural analysis based on extensive molecular dynamics simulations. Our results suggest that 2'-modification couples with the protein environment to affect the structural stability, while 3'-hydrogen substitution inherently exerts "immediate termination" without compromising the structural stability in the active site. Our study provides an alternative promising modification scheme to orientate the further optimization of obligate terminators for SARS-CoV-2 RdRp.
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Affiliation(s)
- Yongfang Li
- State
Key Laboratory of Structural Chemistry, Fujian Institute of Research
on the Structure of Matter, Chinese Academy
of Sciences, 350002, Fuzhou, Fujian, China
- University
of Chinese Academy of Sciences, 100864, Beijing, China
| | - Dong Zhang
- State
Key Laboratory of Structural Chemistry, Fujian Institute of Research
on the Structure of Matter, Chinese Academy
of Sciences, 350002, Fuzhou, Fujian, China
- University
of Chinese Academy of Sciences, 100864, Beijing, China
| | - Xin Gao
- Computational
Bioscience Research Center (CBRC), Computer, Electrical and Mathematical
Sciences and Engineering Division, King
Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Xiaowei Wang
- Department
of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon 999077, Hong Kong
| | - Lu Zhang
- State
Key Laboratory of Structural Chemistry, Fujian Institute of Research
on the Structure of Matter, Chinese Academy
of Sciences, 350002, Fuzhou, Fujian, China
- University
of Chinese Academy of Sciences, 100864, Beijing, China
- Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry, 361005, Xiamen, Fujian, China
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40
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Delaugerre C, Assoumou L, Maylin S, Minier M, Gabassi A, Genin M, Beniguel L, Ghosn J, de Lamballerie X, El Mouhebb M, Costagliola D, Carrat F, Molina JM. SARS CoV-2 Seroprevalence Among HIV-Negative Participants Using Tenofovir/Emtricitabine Based PrEP in 2020 – A Sub-study of ANRS PREVENIR and INSERM SAPRIS-Sero Cohorts. Open Forum Infect Dis 2022; 9:ofac188. [PMID: 35791355 PMCID: PMC9047207 DOI: 10.1093/ofid/ofac188] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/09/2022] [Indexed: 11/12/2022] Open
Abstract
The potential preventive efficacy of tenofovir/emtricitabine on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection was assessed in human immunodeficiency virus preexposure prophylaxis (PrEP) users. Prevalence of SARS-CoV-2 immunoglobulin G between May and October 2020 was similar in PrEP users and in a matched population-based cohort, suggesting that tenofovir/emtricitabine has no role in reducing the risk of SARS-CoV-2 acquisition.
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Affiliation(s)
- Constance Delaugerre
- AP-HP, Service de Virologie, Hôpital Saint Louis, 75010 Paris, France
- Université de Paris, INSERM, U944, 75010 Paris, France
| | - Lambert Assoumou
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, 75013 Paris, France
| | - Sarah Maylin
- AP-HP, Service de Virologie, Hôpital Saint Louis, 75010 Paris, France
| | - Marine Minier
- AP-HP, Service de Virologie, Hôpital Saint Louis, 75010 Paris, France
| | - Audrey Gabassi
- AP-HP, Service de Virologie, Hôpital Saint Louis, 75010 Paris, France
| | - Michèle Genin
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, 75013 Paris, France
| | - Lydie Beniguel
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, 75013 Paris, France
| | - Jade Ghosn
- AP-HP, Service de Maladies infectieuses, Hôpital Bichat, IAME, INSERM, UMR 1137, Université de Paris, Paris, France
| | - Xavier de Lamballerie
- Unité des Virus Emergents, Université Aix Marseille, IRD 190, INSERM U1207, Marseille, France
| | - Mayssam El Mouhebb
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, 75013 Paris, France
| | - Dominique Costagliola
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, 75013 Paris, France
| | - Fabrice Carrat
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique, 75013 Paris, France
- AP-HP, Département de Santé Publique, Hôpital Saint-Antoine, Paris, France
| | - Jean-Michel Molina
- Université de Paris, INSERM, U944, 75010 Paris, France
- AP-HP, Service de Maladies Infectieuses, Hôpital Saint Louis, Paris, France
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41
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Costa SM, Saramago M, Matos RG, Arraiano CM, Viegas SC. How hydrolytic exoribonucleases impact human disease: Two sides of the same story. FEBS Open Bio 2022. [PMID: 35247037 DOI: 10.1002/2211-5463.13392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/16/2022] [Accepted: 03/03/2022] [Indexed: 11/05/2022] Open
Abstract
RNAs are extremely important molecules inside the cell which perform many different functions. For example, messenger RNAs, transfer RNAs, and ribosomal RNAs are involved in protein synthesis, whereas non-coding RNAs have numerous regulatory roles. Ribonucleases are the enzymes responsible for the processing and degradation of all types of RNAs, having multiple roles in every aspect of RNA metabolism. However, the involvement of RNases in disease is still not well understood. This review focuses on the involvement of the RNase II/RNB family of 3'-5' exoribonucleases in human disease. This can be attributed to direct effects, whereby mutations in the eukaryotic enzymes of this family (Dis3 (or Rrp44), Dis3L1 (or Dis3L), and Dis3L2) are associated with a disease, or indirect effects, whereby mutations in the prokaryotic counterparts of RNase II/RNB family (RNase II and/or RNase R) affect the physiology and virulence of several human pathogens. In this review, we will compare the structural and biochemical characteristics of the members of the RNase II/RNB family of enzymes. The outcomes of mutations impacting enzymatic function will be revisited, in terms of both the direct and indirect effects on disease. Furthermore, we also describe the SARS-CoV-2 viral exoribonuclease and its importance to combat COVID-19 pandemic. As a result, RNases may be a good therapeutic target to reduce bacterial and viral pathogenicity. These are the two perspectives on RNase II/RNB family enzymes that will be presented in this review.
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Affiliation(s)
- Susana M Costa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
| | - Margarida Saramago
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
| | - Rute G Matos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
| | - Sandra C Viegas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
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42
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Zang Q, Wang Y, Guo J, Long L, Zhang S, Cui C, Song D, Yu B, Tang F, Teng J, Miao W. Treatment of Severe Japanese Encephalitis Complicated With Hashimoto's Thyroiditis and Guillain-Barré Syndrome With Protein A Immunoadsorption: A Case Report. Front Immunol 2022; 12:807937. [PMID: 35069593 PMCID: PMC8777188 DOI: 10.3389/fimmu.2021.807937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/15/2021] [Indexed: 11/13/2022] Open
Abstract
A severely comatose female patient was diagnosed with Japanese encephalitis (JE). Her condition was complicated by Hashimoto’s thyroiditis (HT) and Guillain-Barré syndrome (GBS). After antiviral, glucocorticoid, and immunoglobulin treatment, the patient’s consciousness was restored, and she could breathe spontaneously. Following this, new-onset, primarily demyelinating GBS developed, which progressed to demyelination combined with axonal injury. The patient was switched to protein A immunoadsorption (PAIA) therapy, and her Hughes score decreased rapidly, from 4 to 1 after 6 months. This patient is the first to receive PAIA combined with an antiviral-glucocorticoid-immunoglobulin regimen to treat encephalitis, meningitis, HT, and GBS caused by JE infection, thereby reflecting the importance of clinical application of PAIA in the treatment of immunological complications of JE.
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Affiliation(s)
- Qiuling Zang
- Neuro-intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yating Wang
- Neuro-intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Junshuang Guo
- Neuro-intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Liyang Long
- Traditional Chinese Medicine Hospital of Qiandongnan Miao and Dong Autonomous Prefecture, Kaili, China
| | - Shuyu Zhang
- Neuro-intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Can Cui
- Neuro-intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Dandan Song
- Neuro-intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Boguang Yu
- Guangdong Provincial Key Laboratory of Hemoadsorption Technology, Guangzhou, China
| | - Fenlan Tang
- Guangdong Provincial Key Laboratory of Hemoadsorption Technology, Guangzhou, China
| | - Junfang Teng
- Neuro-intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wang Miao
- Neuro-intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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43
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Wang X, Sacramento CQ, Jockusch S, Chaves OA, Tao C, Fintelman-Rodrigues N, Chien M, Temerozo JR, Li X, Kumar S, Xie W, Patel DJ, Meyer C, Garzia A, Tuschl T, Bozza PT, Russo JJ, Souza TML, Ju J. Combination of antiviral drugs inhibits SARS-CoV-2 polymerase and exonuclease and demonstrates COVID-19 therapeutic potential in viral cell culture. Commun Biol 2022; 5:154. [PMID: 35194144 PMCID: PMC8863796 DOI: 10.1038/s42003-022-03101-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 02/02/2022] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2 has an exonuclease-based proofreader, which removes nucleotide inhibitors such as Remdesivir that are incorporated into the viral RNA during replication, reducing the efficacy of these drugs for treating COVID-19. Combinations of inhibitors of both the viral RNA-dependent RNA polymerase and the exonuclease could overcome this deficiency. Here we report the identification of hepatitis C virus NS5A inhibitors Pibrentasvir and Ombitasvir as SARS-CoV-2 exonuclease inhibitors. In the presence of Pibrentasvir, RNAs terminated with the active forms of the prodrugs Sofosbuvir, Remdesivir, Favipiravir, Molnupiravir and AT-527 were largely protected from excision by the exonuclease, while in the absence of Pibrentasvir, there was rapid excision. Due to its unique structure, Tenofovir-terminated RNA was highly resistant to exonuclease excision even in the absence of Pibrentasvir. Viral cell culture studies also demonstrate significant synergy using this combination strategy. This study supports the use of combination drugs that inhibit both the SARS-CoV-2 polymerase and exonuclease for effective COVID-19 treatment.
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Grants
- P30 CA008748 NCI NIH HHS
- This work was supported by the Jack Ma Foundation, a gift from Columbia Engineering Member of the Board of Visitors Dr. Bing Zhao, and Fast Grants (to Jingyue Ju), the Maloris Foundation and the Memorial Sloan-Kettering Core Grant (P30CA008748) (to Dinshaw J. Patel), a grant from The JPB Foundation to Rockefeller University (to Thomas Tuschl). Funding was also provided by Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq, 441019/2020-0, 307162/2017-6), Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ, E-26/210.182/2020, E-26/201.067/2021, E-26/210.112/2020) and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES) - Finance Code 001 (to Thiago Moreno L. Souza and Patricia T. Bozza). CNPq, CAPES and FAPERJ also support the National Institutes of Science and Technology Program (INCT-IDPN, 465313/2014-0). Oswaldo Cruz Foundation/FIOCRUZ supports this study under the auspices of the Inova Program (B3-Bovespa funding, VGPDI-032-ARVC-20) (to Thiago Moreno L. Souza). Dr. Andre Sampaio from Farmanguinhos, platform RPT11M, is acknowledged for kindly donating the Calu-3 cells. We thank Dr. Andrew Owen from the University of Liverpool for insightful discussions.
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Affiliation(s)
- Xuanting Wang
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Carolina Q Sacramento
- Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
- National Institute for Science and Technology for Innovation on Diseases of Neglected Population (INCT/IDPN), Center for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Steffen Jockusch
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Otávio Augusto Chaves
- Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
- National Institute for Science and Technology for Innovation on Diseases of Neglected Population (INCT/IDPN), Center for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Chuanjuan Tao
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Natalia Fintelman-Rodrigues
- Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
- National Institute for Science and Technology for Innovation on Diseases of Neglected Population (INCT/IDPN), Center for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Minchen Chien
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Jairo R Temerozo
- Laboratory on Thymus Research, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
- National Institute for Science and Technology on Neuroimmunomodulation (INCT/NIM), Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Xiaoxu Li
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Shiv Kumar
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Wei Xie
- Laboratory of Structural Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Dinshaw J Patel
- Laboratory of Structural Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Cindy Meyer
- Laboratory of RNA Molecular Biology, Rockefeller University, New York, NY, 10065, USA
| | - Aitor Garzia
- Laboratory of RNA Molecular Biology, Rockefeller University, New York, NY, 10065, USA
| | - Thomas Tuschl
- Laboratory of RNA Molecular Biology, Rockefeller University, New York, NY, 10065, USA
| | - Patrícia T Bozza
- Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - James J Russo
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Thiago Moreno L Souza
- Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil.
- National Institute for Science and Technology for Innovation on Diseases of Neglected Population (INCT/IDPN), Center for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil.
| | - Jingyue Ju
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA.
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA.
- Department of Molecular Pharmacology and Therapeutics, Columbia University, New York, NY, 10032, USA.
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44
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del Amo J, Polo R, Moreno S, Jarrín I, Hernán MA. SARS-CoV-2 infection and coronavirus disease 2019 severity in persons with HIV on antiretroviral treatment. AIDS 2022; 36:161-168. [PMID: 34934017 PMCID: PMC8824311 DOI: 10.1097/qad.0000000000003132] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The relative susceptibility of people with HIV (PWH) to Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is debated. Numerous studies have been published with apparently contradictory findings, but comparisons are difficult because they have been conducted in populations with different characteristics (e.g. age, prevalence comorbidities) and have used different comparison groups (e.g. HIV-negative cohorts, coronavirus disease 2019 (COVID-19) hospitalized patients, general population), and because of challenges to measure the most important confounders. Here, we review the evidence regarding risk and severity of SARS-CoV-2 infection in PWH compared with persons without HIV. Publications originate largely from high-income settings where the majority of the PWH are on antiretroviral therapy (ART). Despite early evidence supporting higher frequency of SARS-CoV-2 testing in PWH on ART, HIV infection is not associated with SARS-CoV-2 infection, once confounding by socioeconomic characteristic is taken into account. Most publications identify increased COVID-19 severity in PWH compared with people without HIV from the general population or compared with COVID-19 hospitalized patients. The only study with an adequate comparison group to reduce confounding, has not identified differences in COVID-19 disease severity by HIV. Publications consistently identify that COVID-19 severity in PWH is not homogeneous and increases with age and baseline comorbidities. As PWH have a higher prevalence of comorbidities than people without HIV, examining their respective contribution to poor health outcomes is not straight forward as comorbidities could mediate the effect of HIV on COVID-19 outcomes.
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Affiliation(s)
- Julia del Amo
- National Plan on AIDS. Ministry of Health, Madrid, Spain
| | - Rosa Polo
- National Plan on AIDS. Ministry of Health, Madrid, Spain
| | - Santiago Moreno
- University Hospital Ramón y Cajal, Madrid, Spain
- HIV Network of Excellence (RIS), Madrid, Spain
| | - Inma Jarrín
- HIV Network of Excellence (RIS), Madrid, Spain
- National Center for Epidemiology, Institute of Health Carlos III, Madrid, Spain
| | - Miguel A. Hernán
- CAUSALab and Departments of Epidemiology and Biostatistics, Harvard School T.H. Chan of Public Health, Boston, MA, USA
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Structure and Properties of Copper Pyrophosphate by First-Principle Calculations. MATERIALS 2022; 15:ma15030842. [PMID: 35160787 PMCID: PMC8836541 DOI: 10.3390/ma15030842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 02/04/2023]
Abstract
Investigated the structural, electronic, and magnetic properties of copper pyrophosphate dihydrate (CuPPD) by the first-principle calculations based on the density functional theory (DFT). Simulations were performed with the generalized gradient approximation (GGA) of the exchange-correlation functional (Exc) supplemented by an on-site Coulomb self-interaction (U–Hubbard term). It was confirmed that the GGA method did not provide a satisfactory result in predicting the electronic energy band gap width (Eg) of the CuPPD crystals. Simultaneously, we measured the Eg of CuPPD nanocrystal placed inside mesoporous silica using the ultraviolet–visible spectroscopy (UV–VIS) technique. The proposed Hubbard correction for Cu-3d and O-2p states at U = 4.64 eV reproduces the experimental value of Eg = 2.34 eV. The electronic properties presented in this study and the results of UV–VIS investigations likely identify the semiconductor character of CuPPD crystal, which raises the prospect of using it as a component determining functional properties of nanomaterials, including quantum dots.
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46
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Wu J, Chen Z, Han X, Chen Q, Wang Y, Feng T. SARS-CoV-2 RNA-dependent RNA polymerase as a target for high-throughput drug screening. Future Virol 2022:10.2217/fvl-2021-0335. [PMID: 36794167 PMCID: PMC9910510 DOI: 10.2217/fvl-2021-0335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/06/2023] [Indexed: 02/05/2023]
Abstract
The ongoing COVID-19 pandemic caused by the SARS-CoV-2 has necessitated rapid development of drug screening tools. RNA-dependent RNA polymerase (RdRp) is a promising target due to its essential functions in replication and transcription of viral genome. To date, through minimal RNA synthesizing machinery established from cryo-electron microscopy structural data, there has been development of high-throughput screening assays for directly screening inhibitors that target the SARS-CoV-2 RdRp. Here, we analyze and present verified techniques that could be used to discover potential anti-RdRp agents or repurposing of approved drugs to target the SARS-CoV-2 RdRp. In addition, we highlight the characteristics and application value of cell-free or cell-based assays in drug discovery.
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Affiliation(s)
- Jiahui Wu
- 1Institute of Biology & Medical Sciences, Jiangsu Key Laboratory of Infection & Immunity, Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Zhiqiang Chen
- 1Institute of Biology & Medical Sciences, Jiangsu Key Laboratory of Infection & Immunity, Soochow University, Suzhou, 215123, Jiangsu Province, China,2Department of Nuclear Medicine, The First Affiliated Hospital of Soochow University, Suzhou, 215000, Jiangsu Province, China
| | - Xue Han
- 3Department of Clinical Laboratory, the Affiliated Hospital of Qingdao University, 59 Haier Road, Qingdao, 266000, Shandong Province, China
| | - Qiaoqiao Chen
- 1Institute of Biology & Medical Sciences, Jiangsu Key Laboratory of Infection & Immunity, Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Yintao Wang
- 1Institute of Biology & Medical Sciences, Jiangsu Key Laboratory of Infection & Immunity, Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Tingting Feng
- 1Institute of Biology & Medical Sciences, Jiangsu Key Laboratory of Infection & Immunity, Soochow University, Suzhou, 215123, Jiangsu Province, China,Author for correspondence: Tel.: +86 512 6588 2429;
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Dutta D, Liu J, Xiong H. NLRP3 inflammasome activation and SARS-CoV-2-mediated hyperinflammation, cytokine storm and neurological syndromes. INTERNATIONAL JOURNAL OF PHYSIOLOGY, PATHOPHYSIOLOGY AND PHARMACOLOGY 2022; 14:138-160. [PMID: 35891930 PMCID: PMC9301183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/02/2022] [Indexed: 04/13/2023]
Abstract
Despite the introduction of vaccines and drugs for SARS-CoV-2, the COVID-19 pandemic continues to spread throughout the world. In severe COVID-19 patients, elevated levels of proinflammatory cytokines have been detected in the blood, lung cells, and bronchoalveolar lavage, which is referred to as a cytokine storm, a consequence of overactivation of the NLR family pyrin domain-containing protein 3 (NLRP3) inflammasome and resultant excessive cytokine production. The hyperinflammatory response and cytokine storm cause multiorgan impairment including the central nervous system, in addition to a detriment to the respiratory system. Hyperactive NLRP3 inflammasome, due to dysregulated immune response, is the primary cause of COVID-19 severity. The severity could be enhanced due to viral evolution leading to the emergence of mutated variants of concern, such as delta and omicron. In this review, we elaborate on the inflammatory responses associated with the NLRP3 inflammasome activation in COVID-19 pathogenesis, the mechanisms for the NLRP3 inflammasome activation and pathway involved, cytokine storm, and neurological complications as long-term consequences of SARS-CoV-2 infection. Also discussed is the therapeutic potential of NLRP3 inflammasome inhibitors for the treatment of COVID-19.
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Affiliation(s)
- Debashis Dutta
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center Omaha, NE 68198-5880, USA
| | - Jianuo Liu
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center Omaha, NE 68198-5880, USA
| | - Huangui Xiong
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center Omaha, NE 68198-5880, USA
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Riccio AA, Sullivan ED, Copeland WC. Activation of the SARS-CoV-2 NSP14 3'-5' exoribonuclease by NSP10 and response to antiviral inhibitors. J Biol Chem 2021; 298:101518. [PMID: 34942146 PMCID: PMC8685350 DOI: 10.1016/j.jbc.2021.101518] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/15/2021] [Accepted: 12/17/2021] [Indexed: 12/22/2022] Open
Abstract
Understanding the core replication complex of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential to the development of novel coronavirus-specific antiviral therapeutics. Among the proteins required for faithful replication of the SARS-CoV-2 genome are nonstructural protein 14 (NSP14), a bifunctional enzyme with an N-terminal 3′-to-5′ exoribonuclease (ExoN) and a C-terminal N7-methyltransferase, and its accessory protein, NSP10. The difficulty in producing pure and high quantities of the NSP10/14 complex has hampered the biochemical and structural study of these important proteins. We developed a straightforward protocol for the expression and purification of both NSP10 and NSP14 from Escherichia coli and for the in vitro assembly and purification of a stoichiometric NSP10/14 complex with high yields. Using these methods, we observe that NSP10 provides a 260-fold increase in kcat/Km in the exoribonucleolytic activity of NSP14 and enhances protein stability. We also probed the effect of two small molecules on NSP10/14 activity, remdesivir monophosphate and the methyltransferase inhibitor S-adenosylhomocysteine. Our analysis highlights two important factors for drug development: first, unlike other exonucleases, the monophosphate nucleoside analog intermediate of remdesivir does not inhibit NSP14 activity; and second, S-adenosylhomocysteine modestly activates NSP14 exonuclease activity. In total, our analysis provides insights for future structure–function studies of SARS-CoV-2 replication fidelity for the treatment of coronavirus disease 2019.
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Affiliation(s)
- Amanda A Riccio
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709
| | - Eric D Sullivan
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709
| | - William C Copeland
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709.
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49
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Abstract
The development of effective antiviral therapy for COVID-19 is critical for those awaiting vaccination, as well as for those who do not respond robustly to vaccination. This review summarizes 1 year of progress in the race to develop antiviral therapies for COVID-19, including research spanning preclinical and clinical drug development efforts, with an emphasis on antiviral compounds that are in clinical development or that are high priorities for clinical development. The review is divided into sections on compounds that inhibit SARS-CoV-2 enzymes, including its polymerase and proteases; compounds that inhibit virus entry, including monoclonal antibodies; interferons; and repurposed drugs that inhibit host processes required for SARS-CoV-2 replication. The review concludes with a summary of the lessons to be learned from SARS-CoV-2 drug development efforts and the challenges to continued progress.
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Affiliation(s)
- Kaiming Tao
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, USA
| | - Philip L. Tzou
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, USA
| | - Janin Nouhin
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, USA
| | - Hector Bonilla
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, USA
| | - Prasanna Jagannathan
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, USA
| | - Robert W. Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, USA
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50
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Oka N, Kanda M, Furuzawa M, Arai W, Ando K. Serendipitous One-Step Synthesis of Cyclopentene Derivatives from 5'-Deoxy-5'-heteroarylsulfonylnucleosides as Nucleoside-Derived Julia-Kocienski Reagents. J Org Chem 2021; 86:16684-16698. [PMID: 34762430 DOI: 10.1021/acs.joc.1c01940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A serendipitous one-step transformation of 5'-deoxy-5'-heteroarylsulfonylnucleosides into cyclopentene derivatives is reported. This unique transformation likely proceeds via a domino reaction initiated by α-deprotonation of the heteroaryl sulfone and subsequent elimination reaction to generate a nucleobase and an α,β-unsaturated sulfone that contains a formyl group. The Michael addition of the nucleobase to the α,β-unsaturated sulfone and the subsequent intramolecular Julia-Kocienski reaction eventually generate the cyclopentene ring. Heteroarylthio and acylthio groups can be incorporated into the cyclopentene core in place of the nucleobase by conducting this reaction in the presence of a heteroarylthiol and a thiocarboxylic acid, respectively. cis,cis-Trisubstituted cyclopentene derivatives are obtained as a single stereoisomer from ribonucleoside-derived Julia-Kocienski sulfones.
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Affiliation(s)
- Natsuhisa Oka
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan.,Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN), Gifu University, Gifu 501-1193, Japan.,Institute for Glyco-core Research (iGCORE), Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Mayuka Kanda
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Minami Furuzawa
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Wakaba Arai
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Kaori Ando
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
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