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Potential of cell-penetrating peptides (CPPs) in delivery of antiviral therapeutics and vaccines. Eur J Pharm Sci 2021; 169:106094. [PMID: 34896590 DOI: 10.1016/j.ejps.2021.106094] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 12/12/2022]
Abstract
Viral infections are a great threat to human health. Currently, there are no effective vaccines and antiviral drugs against the majority of viral diseases, suggesting the need to develop novel and effective antiviral agents. Since the intracellular delivery of antiviral agents, particularly the impermeable molecules, such as peptides, proteins, and nucleic acids, are essential to exert their therapeutic effects, using a delivery system is highly required. Among various delivery systems, cell-penetrating peptides (CPPs), a group of short peptides with the unique ability of crossing cell membrane, offer great potential for the intracellular delivery of various biologically active cargoes. The results of numerous in vitro and in vivo studies with CPP conjugates demonstrate their promise as therapeutic agents in various medical fields including antiviral therapy. The CPP-mediated delivery of various antiviral agents including peptides, proteins, nucleic acids, and nanocarriers have been associated with therapeutic efficacy both in vitro and in vivo. This review describes various aspects of viruses including their biology, pathogenesis, and therapy and briefly discusses the concept of CPP and its potential in drug delivery. Particularly, it will highlight a variety of CPP applications in the management of viral infections.
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Rahbar MR, Jahangiri A, Khalili S, Zarei M, Mehrabani-Zeinabad K, Khalesi B, Pourzardosht N, Hessami A, Nezafat N, Sadraei S, Negahdaripour M. Hotspots for mutations in the SARS-CoV-2 spike glycoprotein: a correspondence analysis. Sci Rep 2021; 11:23622. [PMID: 34880279 PMCID: PMC8654821 DOI: 10.1038/s41598-021-01655-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 11/01/2021] [Indexed: 12/19/2022] Open
Abstract
Spike glycoprotein (Sgp) is liable for binding of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to the host receptors. Since Sgp is the main target for vaccine and drug designing, elucidating its mutation pattern could help in this regard. This study is aimed at investigating the correspondence of specific residues to the SgpSARS-CoV-2 functionality by explorative interpretation of sequence alignments. Centrality analysis of the Sgp dissects the importance of these residues in the interaction network of the RBD-ACE2 (receptor-binding domain) complex and furin cleavage site. Correspondence of RBD to threonine500 and asparagine501 and furin cleavage site to glutamine675, glutamine677, threonine678, and alanine684 was observed; all residues are exactly located at the interaction interfaces. The harmonious location of residues dictates the RBD binding property and the flexibility, hydrophobicity, and accessibility of the furin cleavage site. These species-specific residues can be assumed as real targets of evolution, while other substitutions tend to support them. Moreover, all these residues are parts of experimentally identified epitopes. Therefore, their substitution may affect vaccine efficacy. Higher rate of RBD maintenance than furin cleavage site was predicted. The accumulation of substitutions reinforces the probability of the multi-host circulation of the virus and emphasizes the enduring evolutionary events.
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Affiliation(s)
- Mohammad Reza Rahbar
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abolfazl Jahangiri
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Saeed Khalili
- Department of Biology Sciences, Shahid Rajaee Teacher Training University, Tehran, Iran
| | - Mahboubeh Zarei
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Kamran Mehrabani-Zeinabad
- Department of Biostatistics, Faculty of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Bahman Khalesi
- Department of Research and Production of Poultry Viral Vaccine, Razi Vaccine, and Serum Research Institute, Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Navid Pourzardosht
- Cellular and Molecular Research Center, Faculty of Medicine, Guilan University of Medical Sciences, Rasht, Iran
- Biochemistry Department, Guilan University of Medical Sciences, Rasht, Iran
| | - Anahita Hessami
- School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Navid Nezafat
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Saman Sadraei
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Manica Negahdaripour
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, P.O. Box 71345-1583, Shiraz, Iran.
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Li J, Boix E. Host Defence RNases as Antiviral Agents against Enveloped Single Stranded RNA Viruses. Virulence 2021; 12:444-469. [PMID: 33660566 PMCID: PMC7939569 DOI: 10.1080/21505594.2021.1871823] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/26/2020] [Accepted: 12/30/2020] [Indexed: 02/06/2023] Open
Abstract
Owing to the recent outbreak of Coronavirus Disease of 2019 (COVID-19), it is urgent to develop effective and safe drugs to treat the present pandemic and prevent other viral infections that might come in the future. Proteins from our own innate immune system can serve as ideal sources of novel drug candidates thanks to their safety and immune regulation versatility. Some host defense RNases equipped with antiviral activity have been reported over time. Here, we try to summarize the currently available information on human RNases that can target viral pathogens, with special focus on enveloped single-stranded RNA (ssRNA) viruses. Overall, host RNases can fight viruses by a combined multifaceted strategy, including the enzymatic target of the viral genome, recognition of virus unique patterns, immune modulation, control of stress granule formation, and induction of autophagy/apoptosis pathways. The review also includes a detailed description of representative enveloped ssRNA viruses and their strategies to interact with the host and evade immune recognition. For comparative purposes, we also provide an exhaustive revision of the currently approved or experimental antiviral drugs. Finally, we sum up the current perspectives of drug development to achieve successful eradication of viral infections.
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Affiliation(s)
- Jiarui Li
- Dpt. Of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma De Barcelona, Spain
| | - Ester Boix
- Dpt. Of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma De Barcelona, Spain
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Kuroki A, Tay J, Lee GH, Yang YY. Broad-Spectrum Antiviral Peptides and Polymers. Adv Healthc Mater 2021; 10:e2101113. [PMID: 34599850 DOI: 10.1002/adhm.202101113] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 09/13/2021] [Indexed: 12/18/2022]
Abstract
As the human cost of the pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still being witnessed worldwide, the development of broad-spectrum antiviral agents against emerging and re-emerging viruses is seen as a necessity to hamper the spread of infections. Various targets during the viral life-cycle can be considered to inhibit viral infection, from viral attachment to viral fusion or replication. Macromolecules represent a particularly attractive class of therapeutics due to their multivalency and versatility. Although several antiviral macromolecules hold great promise in clinical applications, the emergence of resistance after prolonged exposure urges the need for improved solutions. In the present article, the recent advancement in the discovery of antiviral peptides and polymers with diverse structural features and antiviral mechanisms is reviewed. Future perspectives, such as, the development of virucidal peptides/polymers and their coatings against SARS-CoV-2 infection, standardization of antiviral testing protocols, and use of artificial intelligence or machine learning as a tool to accelerate the discovery of antiviral macromolecules, are discussed.
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Affiliation(s)
- Agnès Kuroki
- Yong Loo Lin School of Medicine National University of Singapore Singapore 117597 Singapore
- Institute of Bioengineering and Bioimaging 31 Biopolis Ways, The Nanos Singapore 138669 Singapore
| | - Joyce Tay
- Institute of Bioengineering and Bioimaging 31 Biopolis Ways, The Nanos Singapore 138669 Singapore
| | - Guan Huei Lee
- Yong Loo Lin School of Medicine National University of Singapore Singapore 117597 Singapore
| | - Yi Yan Yang
- Institute of Bioengineering and Bioimaging 31 Biopolis Ways, The Nanos Singapore 138669 Singapore
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Bayoumi M, Munir M. Potential Use of CRISPR/Cas13 Machinery in Understanding Virus-Host Interaction. Front Microbiol 2021; 12:743580. [PMID: 34899631 PMCID: PMC8664230 DOI: 10.3389/fmicb.2021.743580] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 10/25/2021] [Indexed: 12/20/2022] Open
Abstract
Prokaryotes have evolutionarily acquired an immune system to fend off invading mobile genetic elements, including viral phages and plasmids. Through recognizing specific sequences of the invading nucleic acid, prokaryotes mediate a subsequent degradation process collectively referred to as the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated (Cas) (CRISPR-Cas) system. The CRISPR-Cas systems are divided into two main classes depending on the structure of the effector Cas proteins. Class I systems have effector modules consisting of multiple proteins, while class II systems have a single multidomain effector. Additionally, the CRISPR-Cas systems can also be categorized into types depending on the spacer acquisition components and their evolutionary features, namely, types I-VI. Among CRISPR/Cas systems, Cas9 is one of the most common multidomain nucleases that identify, degrade, and modulate DNA. Importantly, variants of Cas proteins have recently been found to target RNA, especially the single-effector Cas13 nucleases. The Cas13 has revolutionized our ability to study and perturb RNAs in endogenous microenvironments. The Cas13 effectors offer an excellent candidate for developing novel research tools in virological and biotechnological fields. Herein, in this review, we aim to provide a comprehensive summary of the recent advances of Cas13s for targeting viral RNA for either RNA-mediated degradation or CRISPR-Cas13-based diagnostics. Additionally, we aim to provide an overview of the proposed applications that could revolutionize our understanding of viral-host interactions using Cas13-mediated approaches.
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Affiliation(s)
- Mahmoud Bayoumi
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster, United Kingdom
- Virology Department, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Muhammad Munir
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster, United Kingdom
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Troost-Kind B, van Hemert MJ, van de Pol D, van der Ende-Metselaar H, Merits A, Borggrewe M, Rodenhuis-Zybert IA, Smit JM. Tomatidine reduces Chikungunya virus progeny release by controlling viral protein expression. PLoS Negl Trop Dis 2021; 15:e0009916. [PMID: 34762680 PMCID: PMC8664216 DOI: 10.1371/journal.pntd.0009916] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 12/10/2021] [Accepted: 10/16/2021] [Indexed: 12/13/2022] Open
Abstract
Tomatidine, a natural steroidal alkaloid from unripe green tomatoes has been shown to exhibit many health benefits. We recently provided in vitro evidence that tomatidine reduces the infectivity of Dengue virus (DENV) and Chikungunya virus (CHIKV), two medically important arthropod-borne human infections for which no treatment options are available. We observed a potent antiviral effect with EC50 values of 0.82 μM for DENV-2 and 1.3 μM for CHIKV-LR. In this study, we investigated how tomatidine controls CHIKV infectivity. Using mass spectrometry, we identified that tomatidine induces the expression of p62, CD98, metallothionein and thioredoxin-related transmembrane protein 2 in Huh7 cells. The hits p62 and CD98 were validated, yet subsequent analysis revealed that they are not responsible for the observed antiviral effect. In parallel, we sought to identify at which step of the virus replication cycle tomatidine controls virus infectivity. A strong antiviral effect was seen when in vitro transcribed CHIKV RNA was transfected into Huh7 cells treated with tomatidine, thereby excluding a role for tomatidine during CHIKV cell entry. Subsequent determination of the number of intracellular viral RNA copies and viral protein expression levels during natural infection revealed that tomatidine reduces the RNA copy number and viral protein expression levels in infected cells. Once cells are infected, tomatidine is not able to interfere with active RNA replication yet it can reduce viral protein expression. Collectively, the results delineate that tomatidine controls viral protein expression to exert its antiviral activity. Lastly, sequential passaging of CHIKV in presence of tomatidine did not lead to viral resistance. Collectively, these results further emphasize the potential of tomatidine as an antiviral treatment towards CHIKV infection. Chikungunya fever is a debilitating disease caused by the mosquito-borne Chikungunya virus. Over the past two decades the geographical spread of the virus and its mosquito vector has drastically increased thereby causing millions of infections. To date there is no antiviral drug and no vaccine available to treat/prevent Chikungunya virus infection. We recently showed that the natural steroidal alkaloid tomatidine has potent antiviral activity towards Chikungunya virus at submicromolar concentrations. In this study we dissected how tomatidine reduces the production of Chikungunya virus particles. We show that tomatidine lowers viral protein expression and we hypothesize that the effect of tomatidine on viral protein translation hampers the production of progeny viral RNA copies / number of infected cells thereby leading to a reduced production of secreted virus particles. Also, we show that Chikungunya virus does not readily become resistant to tomatidine. Collectively, we deciphered the mechanism by which tomatidine exerts antiviral activity to Chikungunya virus and our results strengthen the potential of tomatidine as an antiviral treatment strategy towards Chikungunya virus.
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Affiliation(s)
- Berit Troost-Kind
- Department of Medical Microbiology and Infection Prevention, University of Groningen; University Medical Center Groningen; Groningen, the Netherlands
| | - Martijn J. van Hemert
- Department of Medical Microbiology, Molecular Virology Laboratory, Leiden University Medical Center, Leiden, the Netherlands
| | - Denise van de Pol
- Department of Medical Microbiology and Infection Prevention, University of Groningen; University Medical Center Groningen; Groningen, the Netherlands
| | - Heidi van der Ende-Metselaar
- Department of Medical Microbiology and Infection Prevention, University of Groningen; University Medical Center Groningen; Groningen, the Netherlands
| | - Andres Merits
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Malte Borggrewe
- Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, University of Groningen; University Medical Center Groningen; Groningen, the Netherlands
| | - Izabela A. Rodenhuis-Zybert
- Department of Medical Microbiology and Infection Prevention, University of Groningen; University Medical Center Groningen; Groningen, the Netherlands
| | - Jolanda M. Smit
- Department of Medical Microbiology and Infection Prevention, University of Groningen; University Medical Center Groningen; Groningen, the Netherlands
- * E-mail:
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Janissen R, Woodman A, Shengjuler D, Vallet T, Lee KM, Kuijpers L, Moustafa IM, Fitzgerald F, Huang PN, Perkins AL, Harki DA, Arnold JJ, Solano B, Shih SR, Vignuzzi M, Cameron CE, Dekker NH. Induced intra- and intermolecular template switching as a therapeutic mechanism against RNA viruses. Mol Cell 2021; 81:4467-4480.e7. [PMID: 34687604 PMCID: PMC8628313 DOI: 10.1016/j.molcel.2021.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/25/2021] [Accepted: 10/02/2021] [Indexed: 12/12/2022]
Abstract
Viral RNA-dependent RNA polymerases (RdRps) are a target for broad-spectrum antiviral therapeutic agents. Recently, we demonstrated that incorporation of the T-1106 triphosphate, a pyrazine-carboxamide ribonucleotide, into nascent RNA increases pausing and backtracking by the poliovirus RdRp. Here, by monitoring enterovirus A-71 RdRp dynamics during RNA synthesis using magnetic tweezers, we identify the "backtracked" state as an intermediate used by the RdRp for copy-back RNA synthesis and homologous recombination. Cell-based assays and RNA sequencing (RNA-seq) experiments further demonstrate that the pyrazine-carboxamide ribonucleotide stimulates these processes during infection. These results suggest that pyrazine-carboxamide ribonucleotides do not induce lethal mutagenesis or chain termination but function by promoting template switching and formation of defective viral genomes. We conclude that RdRp-catalyzed intra- and intermolecular template switching can be induced by pyrazine-carboxamide ribonucleotides, defining an additional mechanistic class of antiviral ribonucleotides with potential for broad-spectrum activity.
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Affiliation(s)
- Richard Janissen
- Department of Bionanoscience, Kavli Institute of Nanoscience, 2629 HZ Delft, the Netherlands
| | - Andrew Woodman
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, PA 16801, USA
| | - Djoshkun Shengjuler
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Thomas Vallet
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Kuo-Ming Lee
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, 33302 Taoyuan, Taiwan
| | - Louis Kuijpers
- Department of Bionanoscience, Kavli Institute of Nanoscience, 2629 HZ Delft, the Netherlands
| | - Ibrahim M Moustafa
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, PA 16801, USA
| | - Fiona Fitzgerald
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, PA 16801, USA
| | - Peng-Nien Huang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, 33302 Taoyuan, Taiwan
| | - Angela L Perkins
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Daniel A Harki
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA; Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jamie J Arnold
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, PA 16801, USA
| | - Belén Solano
- Department of Bionanoscience, Kavli Institute of Nanoscience, 2629 HZ Delft, the Netherlands
| | - Shin-Ru Shih
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, 33302 Taoyuan, Taiwan
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Craig E Cameron
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, State College, PA 16801, USA.
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, 2629 HZ Delft, the Netherlands.
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Highly Potent Host-Specific Small-Molecule Inhibitor of Paramyxovirus and Pneumovirus Replication with High Resistance Barrier. mBio 2021; 12:e0262121. [PMID: 34724816 PMCID: PMC8561388 DOI: 10.1128/mbio.02621-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Multiple enveloped RNA viruses of the family Paramyxoviridae and Pneumoviridae, like measles virus (MeV), Nipah virus (NiV), canine distemper virus (CDV), or respiratory syncytial virus (RSV), are of high clinical relevance. Each year a huge number of lives are lost as a result of these viral infections. Worldwide, MeV infection alone is responsible for over a hundred thousand deaths each year despite available vaccine. Therefore, there is an urgent need for treatment options to counteract these viral infections. The development of antiviral drugs in general stands as a huge challenge due to the rapid emergence of viral escape mutants. Here, we disclose the discovery of a small-molecule antiviral, compound 1 (ZHAWOC9045), active against several pneumo-/paramyxoviruses, including MeV, NiV, CDV, RSV, and parainfluenza virus type 5 (PIV-5). A series of mechanistic characterizations revealed that compound 1 targets a host factor which is indispensable for viral genome replication. Drug resistance profiling against a paramyxovirus model (CDV) demonstrated no detectable adaptation despite prolonged time of investigation, thereby mitigating the rapid emergence of escape variants. Furthermore, a thorough structure-activity relationship analysis of compound 1 led to the invention of 100-times-more potent-derivatives, e.g., compound 2 (ZHAWOC21026). Collectively, we present in this study an attractive host-directed pneumoviral/paramyxoviral replication inhibitor with potential therapeutic application.
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Aroso RT, Schaberle FA, Arnaut LG, Pereira MM. Photodynamic disinfection and its role in controlling infectious diseases. Photochem Photobiol Sci 2021; 20:1497-1545. [PMID: 34705261 PMCID: PMC8548867 DOI: 10.1007/s43630-021-00102-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 09/03/2021] [Indexed: 12/23/2022]
Abstract
Photodynamic therapy is witnessing a revival of its origins as a response to the rise of multi-drug resistant infections and the shortage of new classes of antibiotics. Photodynamic disinfection (PDDI) of microorganisms is making progresses in preclinical models and in clinical cases, and the perception of its role in the clinical armamentarium for the management of infectious diseases is changing. We review the positioning of PDDI from the perspective of its ability to respond to clinical needs. Emphasis is placed on the pipeline of photosensitizers that proved effective to inactivate biofilms, showed efficacy in animal models of infectious diseases or reached clinical trials. Novel opportunities resulting from the COVID-19 pandemic are briefly discussed. The molecular features of promising photosensitizers are emphasized and contrasted with those of photosensitizers used in the treatment of solid tumors. The development of photosensitizers has been accompanied by the fabrication of a variety of affordable and customizable light sources. We critically discuss the combination between photosensitizer and light source properties that may leverage PDDI and expand its applications to wider markets. The success of PDDI in the management of infectious diseases will ultimately depend on the efficacy of photosensitizers, affordability of the light sources, simplicity of the procedures, and availability of fast and efficient treatments.
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Affiliation(s)
- Rafael T Aroso
- Chemistry Department, University of Coimbra, 3004-535, Coimbra, Portugal
| | - Fábio A Schaberle
- Chemistry Department, University of Coimbra, 3004-535, Coimbra, Portugal
| | - Luís G Arnaut
- Chemistry Department, University of Coimbra, 3004-535, Coimbra, Portugal.
| | - Mariette M Pereira
- Chemistry Department, University of Coimbra, 3004-535, Coimbra, Portugal.
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Cakir M, Obernier K, Forget A, Krogan NJ. Target Discovery for Host-Directed Antiviral Therapies: Application of Proteomics Approaches. mSystems 2021; 6:e0038821. [PMID: 34519533 PMCID: PMC8547474 DOI: 10.1128/msystems.00388-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Current epidemics, such as AIDS or flu, and the emergence of new threatening pathogens, such as the one causing the current coronavirus disease 2019 (COVID-19) pandemic, represent major global health challenges. While vaccination is an important part of the arsenal to counter the spread of viral diseases, it presents limitations and needs to be complemented by efficient therapeutic solutions. Intricate knowledge of host-pathogen interactions is a powerful tool to identify host-dependent vulnerabilities that can be exploited to dampen viral replication. Such host-directed antiviral therapies are promising and are less prone to the development of drug-resistant viral strains. Here, we first describe proteomics-based strategies that allow the rapid characterization of host-pathogen interactions. We then discuss how such data can be exploited to help prioritize compounds with potential host-directed antiviral activity that can be tested in preclinical models.
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Affiliation(s)
- Merve Cakir
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, USA
| | - Kirsten Obernier
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, USA
| | - Antoine Forget
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, USA
| | - Nevan J. Krogan
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, USA
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Paradowska E, Studzińska M, Jabłońska A, Lozovski V, Rusinchuk N, Mukha I, Vitiuk N, Leśnikowski ZJ. Antiviral Effect of Nonfunctionalized Gold Nanoparticles against Herpes Simplex Virus Type-1 (HSV-1) and Possible Contribution of Near-Field Interaction Mechanism. Molecules 2021; 26:molecules26195960. [PMID: 34641506 PMCID: PMC8512028 DOI: 10.3390/molecules26195960] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 11/16/2022] Open
Abstract
The antiviral activity of nonfunctionalized gold nanoparticles (AuNPs) against herpes simplex virus type-1 (HSV-1) in vitro was revealed in this study. We found that AuNPs are capable of reducing the cytopathic effect (CPE) of HSV-1 in Vero cells in a dose- and time-dependent manner when used in pretreatment mode. The demonstrated antiviral activity was within the nontoxic concentration range of AuNPs. Interestingly, we noted that nanoparticles with smaller sizes reduced the CPE of HSV-1 more effectively than larger ones. The observed phenomenon can be tentatively explained by the near-field action of nanoparticles at the virus envelope. These results show that AuNPs can be considered as potential candidates for the treatment of HSV-1 infections.
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Affiliation(s)
- Edyta Paradowska
- Institute of Medical Biology, Polish Academy of Sciences, 106 Lodowa St., 93-232 Łódź, Poland; (E.P.); (M.S.); (A.J.)
| | - Mirosława Studzińska
- Institute of Medical Biology, Polish Academy of Sciences, 106 Lodowa St., 93-232 Łódź, Poland; (E.P.); (M.S.); (A.J.)
| | - Agnieszka Jabłońska
- Institute of Medical Biology, Polish Academy of Sciences, 106 Lodowa St., 93-232 Łódź, Poland; (E.P.); (M.S.); (A.J.)
| | - Valeri Lozovski
- Institute of High Technologies, Taras Shevchenko National University of Kyiv, 64/13 Volodymyrska St., 01033 Kyiv, Ukraine;
- Correspondence: (V.L.); (Z.J.L.)
| | - Natalia Rusinchuk
- Institute of High Technologies, Taras Shevchenko National University of Kyiv, 64/13 Volodymyrska St., 01033 Kyiv, Ukraine;
| | - Iuliia Mukha
- Chuiko Institute of Surface Chemistry of National Academy of Sciences of Ukraine, 17 General Naumov St., 03164 Kyiv, Ukraine; (I.M.); (N.V.)
| | - Nadiia Vitiuk
- Chuiko Institute of Surface Chemistry of National Academy of Sciences of Ukraine, 17 General Naumov St., 03164 Kyiv, Ukraine; (I.M.); (N.V.)
| | - Zbigniew J. Leśnikowski
- Institute of Medical Biology, Polish Academy of Sciences, 106 Lodowa St., 93-232 Łódź, Poland; (E.P.); (M.S.); (A.J.)
- Correspondence: (V.L.); (Z.J.L.)
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The information continuum model of evolution. Biosystems 2021; 209:104510. [PMID: 34416317 DOI: 10.1016/j.biosystems.2021.104510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/12/2021] [Accepted: 08/12/2021] [Indexed: 12/13/2022]
Abstract
Most biologists agree that evolution is contingent on inherited information shaped by natural selection. This apparent consensus could be taken to indicate agreement on the forces shaping evolution, but vivid discussions reveal divergences on how evolution is perceived. The predominant Modern Synthesis (MS) paradigm holds the position that evolution occurs through random changes acting on genomic inheritance. However, studies from recent decades have revealed that evolutionary inheritance also includes DNA-methylation, RNA, symbionts, and culture, among other factors. This has fueled a demand of a broader evolutionary perspective, for example from the proponents of the Extended Evolutionary Synthesis (EES). Despite fundamental disagreements the different views agree that natural selection happens through dissimilar perpetuation of inheritable information. Yet, neither the MS, nor the ESS dwell extensively on the nature of hereditary information. We do - and conclude that information in and of itself is immaterial. We then argue that the quality upon which natural selection acts henceforth is also immaterial. Based on these notions, we arrive at the information-centric Information Continuum Model (ICM) of evolution. The ICM asserts that hereditary information is embedded in diverse physical forms (DNA, RNA, symbionts etc.) representing a continuum of evolutionary qualities, and that information may migrate between these physical forms. The ICM leaves theoretical exploration of evolution unrestricted by the limitations imposed by the individual physical forms wherein the hereditary information is embedded (e.g. genomes). ICM bestows us with a simple heuristic model that adds explanatory dimensions to be considered in the evolution of biological systems.
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63
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Abstract
In recognition that evolutionary theory is critical for understanding modern human health, eLife is publishing a special issue on evolutionary medicine to showcase recent research in this growing and increasingly interdisciplinary field.
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Affiliation(s)
- George H Perry
- Departments of Anthropology and Biology, and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, United States
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64
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Abstract
Abstract The emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) or 2019 Novel Coronavirus (2019-nCoV) has put the entire globe into unrest, primarily due to unavailability of specific drug against the viral proteins. In the last two decades the world has withstood many contagious disease crashes. SARS-CoV-2 has put the world and the mankind in danger. It is spreading unstoppably all over the world. The virus is evolving and thus the pathogenicity of SARS-CoV-2 strains has been different and making it difficult to develop a broad-spectrum anti-viral molecule that would be effective against all the SARS-CoV-2 variants. This imperative situation demands development of molecules for effective treatment against SARS-CoV-2. The phytomolecules or the bioactive molecules of plants could be a great alternative to combat SARS-CoV-2. The bioactive molecules with their antiviral properties and the secondary metabolites may effectively deactivate the functioning of viral proteins. The structural configuration of 2019-nCoV proteins and genomic information are available, thus contributing immensely for fast molecular docking studies and hence, enables screening of numerous accessible phytomolecules. In the current study, we have essentially highlighted common phytomolecules against the known viral proteins and described the mode of action of few plant-derived molecules which have the potential to suppress the activity of the viral proteins. Graphic abstract ![]()
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Kaminski MM, Abudayyeh OO, Gootenberg JS, Zhang F, Collins JJ. CRISPR-based diagnostics. Nat Biomed Eng 2021; 5:643-656. [PMID: 34272525 DOI: 10.1038/s41551-021-00760-7] [Citation(s) in RCA: 442] [Impact Index Per Article: 147.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 06/02/2021] [Indexed: 02/02/2023]
Abstract
The accurate and timely diagnosis of disease is a prerequisite for efficient therapeutic intervention and epidemiological surveillance. Diagnostics based on the detection of nucleic acids are among the most sensitive and specific, yet most such assays require costly equipment and trained personnel. Recent developments in diagnostic technologies, in particular those leveraging clustered regularly interspaced short palindromic repeats (CRISPR), aim to enable accurate testing at home, at the point of care and in the field. In this Review, we provide a rundown of the rapidly expanding toolbox for CRISPR-based diagnostics, in particular the various assays, preamplification strategies and readouts, and highlight their main applications in the sensing of a wide range of molecular targets relevant to human health.
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Affiliation(s)
- Michael M Kaminski
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Omar O Abudayyeh
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA.,Massachusetts Consortium for Pathogen Readiness, Boston, MA, USA
| | - Jonathan S Gootenberg
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA.,Massachusetts Consortium for Pathogen Readiness, Boston, MA, USA
| | - Feng Zhang
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA.,Massachusetts Consortium for Pathogen Readiness, Boston, MA, USA.,Howard Hughes Medical Institute, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA.,Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - James J Collins
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Biological Engineering, MIT, Cambridge, MA, USA. .,Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA. .,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
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66
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Miljanovic D, Milicevic O, Loncar A, Abazovic D, Despot D, Banko A. The First Molecular Characterization of Serbian SARS-CoV-2 Isolates From a Unique Early Second Wave in Europe. Front Microbiol 2021; 12:691154. [PMID: 34220784 PMCID: PMC8250835 DOI: 10.3389/fmicb.2021.691154] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 05/19/2021] [Indexed: 12/23/2022] Open
Abstract
March 6, 2020 is considered as the official date of the beginning of the COVID-19 epidemic in Serbia. In late spring and early summer 2020, Europe recorded a decline in the rate of SARS-CoV-2 infection and subsiding of the first wave. This trend lasted until the fall, when the second wave of the epidemic began to appear. Unlike the rest of Europe, Serbia was hit by the second wave of the epidemic a few months earlier. Already in June 2020, newly confirmed cases had risen exponentially. As the COVID-19 pandemic is the first pandemic in which there has been instant sharing of genomic information on isolates around the world, the aim of this study was to analyze whole SARS-CoV-2 viral genomes from Serbia, to identify circulating variants/clade/lineages, and to explore site-specific mutational patterns in the unique early second wave of the European epidemic. This analysis of Serbian isolates represents the first publication from Balkan countries, which demonstrates the importance of specificities of local transmission especially when preventive measures differ among countries. One hundred forty-eight different genome variants among 41 Serbian isolates were detected in this study. One unique and seven extremely rare mutations were identified, with locally specific continuous dominance of the 20D clade. At the same time, amino acid substitutions of newly identified variants of concern were found in our isolates from October 2020. Future research should be focused on functional characterization of novel mutations in order to understand the exact role of these variations.
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Affiliation(s)
- Danijela Miljanovic
- Virology Laboratory, Faculty of Medicine, Institute of Microbiology and Immunology, University of Belgrade, Belgrade, Serbia
| | - Ognjen Milicevic
- Faculty of Medicine, Institute for Medical Statistics and Informatics, University of Belgrade, Belgrade, Serbia
| | - Ana Loncar
- Laboratory of Molecular Microbiology, Institute for Biocides and Medical Ecology, Belgrade, Serbia
| | - Dzihan Abazovic
- Biocell Hospital, Belgrade, Serbia
- Emergency Medical Centre of Montenegro, Podgorica, Montenegro
| | - Dragana Despot
- Laboratory of Molecular Microbiology, Institute for Biocides and Medical Ecology, Belgrade, Serbia
| | - Ana Banko
- Virology Laboratory, Faculty of Medicine, Institute of Microbiology and Immunology, University of Belgrade, Belgrade, Serbia
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67
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Abstract
Recent field trials have demonstrated that dengue incidence can be substantially reduced by introgressing strains of the endosymbiotic bacterium Wolbachia into Aedes aegypti mosquito populations. This strategy relies on Wolbachia reducing the susceptibility of Ae. aegypti to disseminated infection by positive-sense RNA viruses like dengue. However, RNA viruses are well known to adapt to antiviral pressures. Here, we review the viral infection stages where selection for Wolbachia-resistant virus variants could occur. We also consider the genetic constraints imposed on viruses that alternate between vertebrate and invertebrate hosts, and the likely selection pressures to which dengue virus might adapt in order to be effectively transmitted by Ae. aegypti that carry Wolbachia. While there are hurdles to dengue viruses developing resistance to Wolbachia, we suggest that long-term surveillance for resistant viruses should be an integral component of Wolbachia-introgression biocontrol programs.
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Affiliation(s)
| | - Heather A. Flores
- Institute of Vector-Borne Disease, Monash University, Clayton, Victoria, Australia
| | - Cameron P. Simmons
- World Mosquito Program, Institute of Vector-Borne Disease, Monash University, Clayton, Victoria, Australia
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Johanna E. Fraser
- Institute of Vector-Borne Disease, Monash University, Clayton, Victoria, Australia
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
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68
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Wolf JJ, Xia C, Studstill CJ, Ngo H, Brody SL, Anderson PE, Hahm B. Influenza A virus NS1 induces degradation of sphingosine 1-phosphate lyase to obstruct the host innate immune response. Virology 2021; 558:67-75. [PMID: 33730651 PMCID: PMC8109848 DOI: 10.1016/j.virol.2021.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/11/2021] [Accepted: 02/17/2021] [Indexed: 12/14/2022]
Abstract
The type I interferon (IFN)-mediated innate immune response is one of the central obstacles influenza A virus (IAV) must overcome in order to successfully replicate within the host. We have previously shown that sphingosine 1-phosphate (S1P) lyase (SPL) enhances IKKϵ-mediated type I IFN responses. Here, we demonstrate that the nonstructural protein 1 (NS1) of IAV counteracts the SPL-mediated antiviral response by inducing degradation of SPL. SPL was ubiquitinated and downregulated upon IAV infection or NS1 expression, whereas NS1-deficient IAV failed to elicit SPL ubiquitination or downregulation. Transiently overexpressed SPL increased phosphorylation of IKKϵ, resulting in enhanced expression of type I IFNs. However, this induction was markedly inhibited by IAV NS1. Collectively, this study reveals a novel strategy employed by IAV to subvert the type I IFN response, providing new insights into the interplay between IAV and host innate immunity.
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Affiliation(s)
- Jennifer J Wolf
- Department of Surgery, University of Missouri, Columbia, MO, 65212, USA; Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, 65212, USA
| | - Chuan Xia
- Department of Surgery, University of Missouri, Columbia, MO, 65212, USA; Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, 65212, USA; Present Address: State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Caleb J Studstill
- Department of Surgery, University of Missouri, Columbia, MO, 65212, USA; Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, 65212, USA
| | - Hanh Ngo
- Department of Surgery, University of Missouri, Columbia, MO, 65212, USA; Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, 65212, USA
| | - Steven L Brody
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Paul E Anderson
- Laboratory for Infectious Disease Research, University of Missouri, Columbia, MO, 65212, USA
| | - Bumsuk Hahm
- Department of Surgery, University of Missouri, Columbia, MO, 65212, USA; Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, 65212, USA.
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69
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Willis JA, Cheburkanov V, Kassab G, Soares JM, Blanco KC, Bagnato VS, Yakovlev VV. Photodynamic viral inactivation: Recent advances and potential applications. APPLIED PHYSICS REVIEWS 2021; 8:021315. [PMID: 34084253 PMCID: PMC8132927 DOI: 10.1063/5.0044713] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/13/2021] [Indexed: 05/04/2023]
Abstract
Antibiotic-resistant bacteria, which are growing at a frightening rate worldwide, has put the world on a long-standing alert. The COVID-19 health crisis reinforced the pressing need to address a fast-developing pandemic. To mitigate these health emergencies and prevent economic collapse, cheap, practical, and easily applicable infection control techniques are essential worldwide. Application of light in the form of photodynamic action on microorganisms and viruses has been growing and is now successfully applied in several areas. The efficacy of this approach has been demonstrated in the fight against viruses, prompting additional efforts to advance the technique, including safety use protocols. In particular, its application to suppress respiratory tract infections and to provide decontamination of fluids, such as blood plasma and others, can become an inexpensive alternative strategy in the fight against viral and bacterial infections. Diverse early treatment methods based on photodynamic action enable an accelerated response to emerging threats prior to the availability of preventative drugs. In this review, we evaluate a vast number of photodynamic demonstrations and first-principle proofs carried out on viral control, revealing its potential and encouraging its rapid development toward safe clinical practice. This review highlights the main research trends and, as a futuristic exercise, anticipates potential situations where photodynamic treatment can provide a readily available solution.
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Affiliation(s)
- Jace A. Willis
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas, USA
| | - Vsevolod Cheburkanov
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas, USA
| | - Giulia Kassab
- São Carlos Institute of Physics, University of São Paulo, São Carlos, São Paulo, Brazil
| | - Jennifer M. Soares
- São Carlos Institute of Physics, University of São Paulo, São Carlos, São Paulo, Brazil
| | - Kate C. Blanco
- São Carlos Institute of Physics, University of São Paulo, São Carlos, São Paulo, Brazil
| | | | - Vladislav V. Yakovlev
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas, USA
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70
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Bharti S, Mukherji S, Mukherji S. Antiviral application of colloidal and immobilized silver nanoparticles. NANOTECHNOLOGY 2021; 32:205102. [PMID: 33561842 DOI: 10.1088/1361-6528/abe489] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
This study explored the application of colloidal and immobilized silver nanoparticles (AgNPs) for inactivation of bacteriophages. Coliphages that are commonly used as indicators for enteric viruses, were used in this study. Colloidal AgNPs were synthesized via a chemical reduction approach using sodium borohydride as reducing agent and trisodium citrate as stabilizing agent. AgNP-immobilized glass substrate was prepared by immobilizing AgNPs on amine-functionalized glass substrate by post-immobilization method. The AgNP-immobilized glass substrate was also tested so as to minimize the release of AgNPs in the treated water. The characterization of AgNPs and the AgNP-immobilized glass surface was done using field emission gun-transmission electron microscopy and scanning electron microscopy. Studies conducted with varying concentrations of colloidal AgNPs displayed good antiviral activity for MS2 and T4 bacteriophage. Colloidal AgNPs at a dose of 60 μg ml-1 could completely inactivate MS2 and T4 bacteriophage within 30 and 50 min with an initial concentration of 103 PFU ml-1. Contaminated water (100 ml) in an unstirred batch reactor with an initial bacteriophage concentration of 103 PFU ml-1 could be inactivated by the AgNP-immobilized glass substrate (1 cm × 1 cm, containing 3.7 μg cm-2 silver) suspended centrally in the batch reactor. Complete 3-Log bacteriophage inactivation was achieved within 70 and 80 min for MS2 and T4 bacteriophage, respectively, while the aqueous silver concentration was less than 25 μg l-1. This is significantly lower than the recommended standard for silver in drinking water (i.e. 100 μg l-1, US EPA). Thus, AgNP-immobilized glass may have good potential for generating virus-free drinking water.
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Affiliation(s)
- Sharda Bharti
- Environmental Science and Engineering Department, IIT Bombay, Mumbai, 400076, India
| | - Soumyo Mukherji
- Department of Bioscience and Bioengineering, IIT Bombay, Mumbai, 400076, India
| | - Suparna Mukherji
- Environmental Science and Engineering Department, IIT Bombay, Mumbai, 400076, India
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71
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Sangtani R, Ghosh A, Jha HC, Parmar HS, Bala K. Potential of algal metabolites for the development of broad-spectrum antiviral therapeutics: Possible implications in COVID-19 therapy. Phytother Res 2021; 35:2296-2316. [PMID: 33210447 PMCID: PMC7753317 DOI: 10.1002/ptr.6948] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 10/26/2020] [Accepted: 10/30/2020] [Indexed: 01/25/2023]
Abstract
Covid-19 pandemic severely affected human health worldwide. Till October 19, 2020, total confirmed patients of COVID-19 are 39,944,882, whereas 1,111,998 people died across the globe. Till to date, we do not have any specific medicine and/or vaccine to treat COVID-19; however, research is still going on at war footing. So far vaccine development is concerned, here it is noteworthy that till now three major variants (named A, B, and C) of severe acute respiratory syndrome-coronavirus2 (SARS-CoV-2) have been recognized. Increased mutational rate and formation of new viral variants may increase the attrition rate of vaccines and/or candidate chemotherapies. Herbal remedies are chemical cocktails, thus open another avenue for effective antiviral therapeutics development. In fact, India is a large country, which is densely populated, but the overall severity of COVID-19 per million populations is lesser than any other country of the world. One of the major reasons for the aforesaid difference is the use of herbal remedies by the Government of India as a preventive measure for COVID-19. Therefore, the present review focuses on the epidemiology and molecular pathogenesis of COVID-19 and explores algal metabolites for their antiviral properties.
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Affiliation(s)
- Rimjhim Sangtani
- Discipline of Biosciences and Biomedical EngineeringIndian Institute of TechnologyIndoreIndia
| | - Atreyee Ghosh
- Discipline of Biosciences and Biomedical EngineeringIndian Institute of TechnologyIndoreIndia
| | - Hem C. Jha
- Discipline of Biosciences and Biomedical EngineeringIndian Institute of TechnologyIndoreIndia
| | | | - Kiran Bala
- Discipline of Biosciences and Biomedical EngineeringIndian Institute of TechnologyIndoreIndia
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72
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Luzon-Hidalgo R, Risso VA, Delgado A, Andrés-León E, Ibarra-Molero B, Sanchez-Ruiz JM. Evidence for a role of phenotypic mutations in virus adaptation. iScience 2021; 24:102257. [PMID: 33817569 PMCID: PMC8010470 DOI: 10.1016/j.isci.2021.102257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 01/22/2021] [Accepted: 02/26/2021] [Indexed: 12/12/2022] Open
Abstract
Viruses interact extensively with the host molecular machinery, but the underlying mechanisms are poorly understood. Bacteriophage T7 recruits the small protein thioredoxin of the Escherichia coli host as an essential processivity factor for the viral DNA polymerase. We challenged the phage to propagate in a host in which thioredoxin had been extensively modified to hamper its recruitment. The virus adapted to the engineered host without losing the capability to propagate in the original host, but no genetic mutations were fixed in the thioredoxin binding domain of the viral DNA polymerase. Virus adaptation correlated with mutations in the viral RNA polymerase, supporting that promiscuous thioredoxin recruitment was enabled by phenotypic mutations caused by transcription errors. These results point to a mechanism of virus adaptation that may play a role in cross-species transmission. We propose that phenotypic mutations may generally contribute to the capability of viruses to evade antiviral strategies. Phage adapts to a host modified to hinder the essential recruitment of a host protein No genetic mutations are fixed at the engineered virus-host interaction interface Adaptation is likely linked to phenotypic mutations caused by transcription errors Sub-genomic RNAs may enable this kind of adaptation mechanism in coronaviruses
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Affiliation(s)
- Raquel Luzon-Hidalgo
- Departamento de Quimica Fisica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, Granada 18071, Spain
| | - Valeria A Risso
- Departamento de Quimica Fisica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, Granada 18071, Spain
| | - Asuncion Delgado
- Departamento de Quimica Fisica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, Granada 18071, Spain
| | - Eduardo Andrés-León
- Unidad de Bioinformática. Instituto de Parasitología y Biomedicina "López Neyra", CSIC, Armilla, Granada 18016, Spain
| | - Beatriz Ibarra-Molero
- Departamento de Quimica Fisica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, Granada 18071, Spain
| | - Jose M Sanchez-Ruiz
- Departamento de Quimica Fisica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, Granada 18071, Spain
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Rajput A, Kumar A, Megha K, Thakur A, Kumar M. DrugRepV: a compendium of repurposed drugs and chemicals targeting epidemic and pandemic viruses. Brief Bioinform 2021; 22:1076-1084. [PMID: 33480398 PMCID: PMC7929368 DOI: 10.1093/bib/bbaa421] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 12/04/2020] [Accepted: 12/19/2020] [Indexed: 12/16/2022] Open
Abstract
Viruses are responsible for causing various epidemics and pandemics with a high mortality rate e.g. ongoing SARS-CoronaVirus-2 crisis. The discovery of novel antivirals remains a challenge but drug repurposing is emerging as a potential solution to develop antivirals in a cost-effective manner. In this regard, we collated the information of repurposed drugs tested for antiviral activity from literature and presented it in the form of a user-friendly web server named ‘DrugRepV’. The database contains 8485 entries (3448 unique) with biological, chemical, clinical and structural information of 23 viruses responsible to cause epidemics/pandemics. The database harbors browse and search options to explore the repurposed drug entries. The data can be explored by some important fields like drugs, viruses, drug targets, clinical trials, assays, etc. For summarizing the data, we provide overall statistics of the repurposed candidates. To make the database more informative, it is hyperlinked to various external repositories like DrugBank, PubChem, NCBI-Taxonomy, Clinicaltrials.gov, World Health Organization and many more. ‘DrugRepV’ database (https://bioinfo.imtech.res.in/manojk/drugrepv/) would be highly useful to the research community working to develop antivirals.
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Affiliation(s)
- Akanksha Rajput
- Virology Unit and Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39A, Chandigarh-160036, India
| | - Archit Kumar
- Virology Unit and Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39A, Chandigarh-160036, India
| | - Kirti Megha
- Virology Unit and Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39A, Chandigarh-160036, India
| | - Anamika Thakur
- Virology Unit and Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39A, Chandigarh-160036, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Manoj Kumar
- Virology Unit and Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39A, Chandigarh-160036, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
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Mercatelli D, Holding AN, Giorgi FM. Web tools to fight pandemics: the COVID-19 experience. Brief Bioinform 2021; 22:690-700. [PMID: 33057582 PMCID: PMC7665357 DOI: 10.1093/bib/bbaa261] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/26/2020] [Accepted: 09/13/2020] [Indexed: 01/30/2023] Open
Abstract
The current outbreak of COVID-19 has generated an unprecedented scientific response worldwide, with the generation of vast amounts of publicly available epidemiological, biological and clinical data. Bioinformatics scientists have quickly produced online methods to provide non-computational users with the opportunity of analyzing such data. In this review, we report the results of this effort, by cataloguing the currently most popular web tools for COVID-19 research and analysis. Our focus was driven on tools drawing data from the fields of epidemiology, genomics, interactomics and pharmacology, in order to provide a meaningful depiction of the current state of the art of COVID-19 online resources.
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75
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The Worldwide Search for the New Mutations in the RNA-Directed RNA Polymerase Domain of SARS-CoV-2. MACEDONIAN VETERINARY REVIEW 2021. [DOI: 10.2478/macvetrev-2020-0036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an RNA virus, responsible for the current pandemic outbreak. In total, 200 genomes of the SARS-CoV-2 strains from four host organisms have been analyzed. To investigate the presence of the new mutations in the RNA-directed RNA Polymerase (RdRp) of SARS-CoV-2, we analyzed sequences isolated from different hosts, with particular emphasis on human isolates. We performed a search for the new mutations of the RdRp proteins and study how those newly identified mutations could influence RdRp protein stability. Our results revealed 25 mutations in Rhinolophus sinicus, 1 in Mustela lutreola, 6 in Homo sapiens, and none in Mus musculus RdRp proteins of the SARS-CoV-2 isolates. We found that P323L is the most common stabilising radical mutation in human isolates. Also, we described several unique mutations, specific for studied hosts. Therefore, our data suggest that new and emerging variants of the SARS-CoV-2 RdRp have to be considered for the development of effective therapeutic agents and treatments.
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76
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Kumar M, Mazumder P, Mohapatra S, Kumar Thakur A, Dhangar K, Taki K, Mukherjee S, Kumar Patel A, Bhattacharya P, Mohapatra P, Rinklebe J, Kitajima M, Hai FI, Khursheed A, Furumai H, Sonne C, Kuroda K. A chronicle of SARS-CoV-2: Seasonality, environmental fate, transport, inactivation, and antiviral drug resistance. JOURNAL OF HAZARDOUS MATERIALS 2021; 405:124043. [PMID: 33268203 PMCID: PMC7536132 DOI: 10.1016/j.jhazmat.2020.124043] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/11/2020] [Accepted: 09/17/2020] [Indexed: 05/08/2023]
Abstract
In this review, we present the environmental perspectives of the viruses and antiviral drugs related to SARS-CoV-2. The present review paper discusses occurrence, fate, transport, susceptibility, and inactivation mechanisms of viruses in the environment as well as environmental occurrence and fate of antiviral drugs, and prospects (prevalence and occurrence) of antiviral drug resistance (both antiviral drug resistant viruses and antiviral resistance in the human). During winter, the number of viral disease cases and environmental occurrence of antiviral drug surge due to various biotic and abiotic factors such as transmission pathways, human behaviour, susceptibility, and immunity as well as cold climatic conditions. Adsorption and persistence critically determine the fate and transport of viruses in the environment. Inactivation and disinfection of virus include UV, alcohol, and other chemical-base methods but the susceptibility of virus against these methods varies. Wastewater treatment plants (WWTPs) are major reserviors of antiviral drugs and their metabolites and transformation products. Ecotoxicity of antiviral drug residues against aquatic organisms have been reported, however more threatening is the development of antiviral resistance, both in humans and in wild animal reservoirs. In particular, emergence of antiviral drug-resistant viruses via exposure of wild animals to high loads of antiviral residues during the current pandemic needs further evaluation.
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Affiliation(s)
- Manish Kumar
- Discipline of Earth Science, Indian Institute of Technology Gandhinagar, Gujarat 382 355, India.
| | - Payal Mazumder
- Centre for the Environment, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Sanjeeb Mohapatra
- Environmnetal Science and Engineering Department, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Alok Kumar Thakur
- Discipline of Earth Science, Indian Institute of Technology Gandhinagar, Gujarat 382 355, India
| | - Kiran Dhangar
- Discipline of Earth Science, Indian Institute of Technology Gandhinagar, Gujarat 382 355, India
| | - Kaling Taki
- Discipline of Civil Engineering, Indian Institute of Technology Gandhinagar, Gujarat 382 355, India
| | - Santanu Mukherjee
- Discipline of Earth Science, Indian Institute of Technology Gandhinagar, Gujarat 382 355, India
| | - Arbind Kumar Patel
- Discipline of Earth Science, Indian Institute of Technology Gandhinagar, Gujarat 382 355, India
| | - Prosun Bhattacharya
- Department of Sustainable Development, Environmental Science and Engineering, KTH Royal Institute of Technology, Teknikringen 10B, SE-10044 Stockholm, Sweden
| | - Pranab Mohapatra
- Discipline of Civil Engineering, Indian Institute of Technology Gandhinagar, Gujarat 382 355, India
| | - Jörg Rinklebe
- Laboratory of Soil- and Groundwater-Management, School of Architecture and Civil Engineering, University of Wuppertal, Wuppertal 42285, Germany; Department of Environment, Energy and Geoinformatics, University of Sejong, Seoul, South Korea
| | - Masaaki Kitajima
- Division of Environmental Engineering, Hokkaido University, Hokkaido 060-8628, Japan
| | - Faisal I Hai
- Wollongong, Strategic Water Infrastructure Laboratory, School of Civil, Mining and Environmental Engineering, University of Wollongong, NSW 2522, Australia
| | - Anwar Khursheed
- Department of Civil Engineering, King Saud University, Riyadh, Saudi Arabia
| | - Hiroaki Furumai
- Research Centre for Water Environment Technology, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Christian Sonne
- Department of Bioscience, Aarhus University, Frederiksborgvej 399, PO Box 358, DK-4000 Roskilde, Denmark
| | - Keisuke Kuroda
- Department of Environmental and Civil Engineering, Toyama Prefectural University, Toyama 9390398, Japan
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Obajuluwa AO, Okiki PA, Obajuluwa TM, Afolabi OB. In-silico nucleotide and protein analyses of S-gene region in selected zoonotic coronaviruses reveal conserved domains and evolutionary emergence with trajectory course of viral entry from SARS-CoV-2 genomic data. Pan Afr Med J 2021; 37:285. [PMID: 33654512 PMCID: PMC7896521 DOI: 10.11604/pamj.2020.37.285.24663] [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: 06/29/2020] [Accepted: 07/20/2020] [Indexed: 11/24/2022] Open
Abstract
Introduction the recent zoonotic coronavirus virus outbreak of a novel type (COVID-19) has necessitated the adequate understanding of the evolutionary pathway of zoonotic viruses which adversely affects human populations for therapeutic constructs to combat the pandemic now and in the future. Methods we analyzed conserved domains of the severe acute respiratory coronavirus 2 (SARS-CoV-2) for possible targets of viral entry inhibition in host cells, evolutionary relationship of human coronavirus (229E) and zoonotic coronaviruses with SARS-CoV-2 as well as evolutionary relationship between selected SARS-CoV-2 genomic data. Results conserved domains with antagonistic action on host innate antiviral cellular mechanisms in SARS-CoV-2 include nsp 11, nsp 13 etc. Also, multiple sequence alignments of the spike (S) gene protein of selected candidate zoonotic coronaviruses alongside the S gene protein of the SARS-CoV-2 revealed closest evolutionary relationship (95.6%) with pangolin coronaviruses (S) gene. Clades formed between Wuhan SARS-CoV-2 phylogeny data and five others suggests viral entry trajectory while revealing genomic and protein SARS-CoV-2 data from Philippines as early ancestors. Conclusion phylogeny of SARS-CoV-2 genomic data suggests profiling in diverse populations with and without the outbreak alongside migration history and racial background for mutation tracking and dating of viral subtype divergence which is essential for effective management of present and future zoonotic coronavirus outbreaks.
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Affiliation(s)
- Adejoke Olukayode Obajuluwa
- Biotechnology Unit, Department of Biological Sciences, Afe Babalola University, Ado Ekiti, Ekiti State, Nigeria
| | - Pius Abimbola Okiki
- Biotechnology Unit, Department of Biological Sciences, Afe Babalola University, Ado Ekiti, Ekiti State, Nigeria
| | | | - Olakunle Bamikole Afolabi
- Biochemistry Unit, Department of Chemical Sciences, Afe Babalola University, Ado Ekiti, Ekiti State, Nigeria
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78
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Besednova NN, Andryukov BG, Zaporozhets TS, Kryzhanovsky SP, Fedyanina LN, Kuznetsova TA, Zvyagintseva TN, Shchelkanov MY. Antiviral Effects of Polyphenols from Marine Algae. Biomedicines 2021; 9:200. [PMID: 33671278 PMCID: PMC7921925 DOI: 10.3390/biomedicines9020200] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/12/2021] [Accepted: 02/14/2021] [Indexed: 02/07/2023] Open
Abstract
The disease-preventive and medicinal properties of plant polyphenolic compounds have long been known. As active ingredients, they are used to prevent and treat many noncommunicable diseases. In recent decades, marine macroalgae have attracted the attention of biotechnologists and pharmacologists as a promising and almost inexhaustible source of polyphenols. This heterogeneous group of compounds contains many biopolymers with unique structure and biological properties that exhibit high anti-infective activity. In the present review, the authors focus on the antiviral potential of polyphenolic compounds (phlorotannins) from marine algae and consider the mechanisms of their action as well as other biological properties of these compounds that have effects on the progress and outcome of viral infections. Effective nutraceuticals, to be potentially developed on the basis of algal polyphenols, can also be used in the complex therapy of viral diseases. It is necessary to extend in vivo studies on laboratory animals, which subsequently will allow proceeding to clinical tests. Polyphenolic compounds have a great potential as active ingredients to be used for the creation of new antiviral pharmaceutical substances.
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Affiliation(s)
- Natalya N. Besednova
- G.P. Somov Institute of Epidemiology and Microbiology, Russian Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 690087 Vladivostok, Russia; (B.G.A.); (T.S.Z.); (T.A.K.); (M.Y.S.)
| | - Boris G. Andryukov
- G.P. Somov Institute of Epidemiology and Microbiology, Russian Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 690087 Vladivostok, Russia; (B.G.A.); (T.S.Z.); (T.A.K.); (M.Y.S.)
- School of Biomedicine, Far Eastern Federal University (FEFU), 690091 Vladivostok, Russia;
| | - Tatyana S. Zaporozhets
- G.P. Somov Institute of Epidemiology and Microbiology, Russian Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 690087 Vladivostok, Russia; (B.G.A.); (T.S.Z.); (T.A.K.); (M.Y.S.)
| | - Sergey P. Kryzhanovsky
- Medical Association of the Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia;
| | - Ludmila N. Fedyanina
- School of Biomedicine, Far Eastern Federal University (FEFU), 690091 Vladivostok, Russia;
| | - Tatyana A. Kuznetsova
- G.P. Somov Institute of Epidemiology and Microbiology, Russian Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 690087 Vladivostok, Russia; (B.G.A.); (T.S.Z.); (T.A.K.); (M.Y.S.)
| | | | - Mikhail Yu. Shchelkanov
- G.P. Somov Institute of Epidemiology and Microbiology, Russian Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing, 690087 Vladivostok, Russia; (B.G.A.); (T.S.Z.); (T.A.K.); (M.Y.S.)
- School of Biomedicine, Far Eastern Federal University (FEFU), 690091 Vladivostok, Russia;
- Federal Scientific Center of the Eastern Asia Terrestrial Biodiversity, Far Eastern Branch of Russian Academy of Sciences, 690091 Vladivostok, Russia
- National Scientific Center of Marine Biology, Far Eastern Branch of Russian Academy of Sciences, 690091 Vladivostok, Russia
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79
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COVID-19 Crisis: How Can Plant Biotechnology Help? PLANTS 2021; 10:plants10020352. [PMID: 33673316 PMCID: PMC7917634 DOI: 10.3390/plants10020352] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 12/16/2022]
Abstract
The emergence of the COVID-19 pandemic has led to significant public health crisis all over the world. The rapid spreading nature and high mortality rate of COVID-19 places a huge pressure on scientists to develop effective diagnostics and therapeutics to control the pandemic. Some scientists working on plant biotechnology together with commercial enterprises for the emergency manufacturing of diagnostics and therapeutics have aimed to fulfill the rapid demand for SARS-CoV-2 protein antigen and antibody through a rapid, scalable technology known as transient/stable expression in plants. Plant biotechnology using transient/stable expression offers a rapid solution to address this crisis through the production of low-cost diagnostics, antiviral drugs, immunotherapy, and vaccines. Transient/stable expression technology for manufacturing plant-based biopharmaceuticals is already established at commercial scale. Here, current opinions regarding how plant biotechnology can help fight against COVID-19 through the production of low-cost diagnostics and therapeutics are discussed.
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80
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Abstract
Influenza poses a significant burden on society and health care systems. Although antivirals are an integral tool in effective influenza management, the potential for the emergence of antiviral-resistant viruses can lead to uncertainty and hesitation among front-line prescribers and policy makers. Here, we provide an overview of influenza antiviral resistance in context, exploring the key concepts underlying its development and clinical impact. Due to the acute nature of influenza in immunocompetent patients, resistant viruses that develop during antiviral treatment of a single patient ("treatment-emergent resistance") are usually cleared in a relatively short time, with no impact on future antiviral efficacy. In addition, although available data are limited by small numbers of patients, they show that antiviral treatment still provides clinical benefit to the patient within whom resistance emerges. In contrast, the sustained community transmission of resistant variants in the absence of treatment ("acquired resistance") is of greater concern and can potentially render front-line antivirals ineffective. Importantly, however, resistant viruses are usually associated with reduced fitness such that their widespread transmission is relatively rare. Influenza antivirals are an essential part of effective influenza management due to their ability to reduce the risk of complications and death in infected patients. Although antiviral resistance should be taken seriously and requires continuous careful monitoring, it is not comparable to antibiotic resistance in bacteria, which can become permanent and widespread, with far-reaching medical consequences. The benefits of antiviral treatment far outweigh concerns of potential resistance, which in the vast majority of cases does not have a significant clinical impact.
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81
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Dodge MJ, MacNeil KM, Tessier TM, Weinberg JB, Mymryk JS. Emerging antiviral therapeutics for human adenovirus infection: Recent developments and novel strategies. Antiviral Res 2021; 188:105034. [PMID: 33577808 DOI: 10.1016/j.antiviral.2021.105034] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 12/11/2022]
Abstract
Human adenoviruses (HAdV) are ubiquitous human pathogens that cause a significant burden of respiratory, ocular, and gastrointestinal illnesses. Although HAdV infections are generally self-limiting, pediatric and immunocompromised individuals are at particular risk for developing severe disease. Currently, no approved antiviral therapies specific to HAdV exist. Recent outbreaks underscore the need for effective antiviral agents to treat life-threatening infections. In this review we will focus on recent developments in search of potential therapeutic agents for controlling HAdV infections, with a focus on those targeting post-entry stages of the virus replicative cycle.
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Affiliation(s)
- Mackenzie J Dodge
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Katelyn M MacNeil
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Tanner M Tessier
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Jason B Weinberg
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA; Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Joe S Mymryk
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada; Department of Otolaryngology, Head & Neck Surgery, The University of Western Ontario, London, ON, Canada; Department of Oncology, The University of Western Ontario, London, ON, Canada; London Regional Cancer Program, Lawson Health Research Institute, London, ON, Canada.
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82
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Blanchard EL, Vanover D, Bawage SS, Tiwari PM, Rotolo L, Beyersdorf J, Peck HE, Bruno NC, Hincapie R, Michel F, Murray J, Sadhwani H, Vanderheyden B, Finn MG, Brinton MA, Lafontaine ER, Hogan RJ, Zurla C, Santangelo PJ. Treatment of influenza and SARS-CoV-2 infections via mRNA-encoded Cas13a in rodents. Nat Biotechnol 2021; 39:717-726. [PMID: 33536629 DOI: 10.1038/s41587-021-00822-w] [Citation(s) in RCA: 114] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 12/11/2022]
Abstract
Cas13a has been used to target RNA viruses in cell culture, but efficacy has not been demonstrated in animal models. In this study, we used messenger RNA (mRNA)-encoded Cas13a for mitigating influenza virus A and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in mice and hamsters, respectively. We designed CRISPR RNAs (crRNAs) specific for PB1 and highly conserved regions of PB2 of influenza virus, and against the replicase and nucleocapsid genes of SARS-CoV-2, and selected the crRNAs that reduced viral RNA levels most efficiently in cell culture. We delivered polymer-formulated Cas13a mRNA and the validated guides to the respiratory tract using a nebulizer. In mice, Cas13a degraded influenza RNA in lung tissue efficiently when delivered after infection, whereas in hamsters, Cas13a delivery reduced SARS-CoV-2 replication and reduced symptoms. Our findings suggest that Cas13a-mediated targeting of pathogenic viruses can mitigate respiratory infections.
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Affiliation(s)
- Emmeline L Blanchard
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Daryll Vanover
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Swapnil Subhash Bawage
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Pooja Munnilal Tiwari
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Laura Rotolo
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Jared Beyersdorf
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Hannah E Peck
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Nicholas C Bruno
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Robert Hincapie
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Frank Michel
- Department of Veterinary Biosciences and Diagnostic Imaging, College of Veterinary Medicine University of Georgia, Athens, GA, USA
| | - Jackelyn Murray
- Department of Infectious Diseases, College of Veterinary Medicine University of Georgia, Athens, GA, USA
| | - Heena Sadhwani
- Department of Biology, Georgia State University, Atlanta, GA, USA
| | - Bob Vanderheyden
- Analytics and Data Science Institute, Kennesaw State University, Kennesaw, GA, USA
| | - M G Finn
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Margo A Brinton
- Department of Biology, Georgia State University, Atlanta, GA, USA
| | - Eric R Lafontaine
- Department of Infectious Diseases, College of Veterinary Medicine University of Georgia, Athens, GA, USA
| | - Robert J Hogan
- Department of Veterinary Biosciences and Diagnostic Imaging, College of Veterinary Medicine University of Georgia, Athens, GA, USA.,Department of Infectious Diseases, College of Veterinary Medicine University of Georgia, Athens, GA, USA
| | - Chiara Zurla
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
| | - Philip J Santangelo
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
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Zhou J, Krishnan N, Jiang Y, Fang RH, Zhang L. Nanotechnology for virus treatment. NANO TODAY 2021; 36:101031. [PMID: 33519948 PMCID: PMC7836394 DOI: 10.1016/j.nantod.2020.101031] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 11/09/2020] [Accepted: 11/11/2020] [Indexed: 04/14/2023]
Abstract
The continued emergence of novel viruses poses a significant threat to global health. Uncontrolled outbreaks can result in pandemics that have the potential to overburden our healthcare and economic systems. While vaccination is a conventional modality that can be employed to promote herd immunity, antiviral vaccines can only be applied prophylactically and do little to help patients who have already contracted viral infections. During the early stages of a disease outbreak when vaccines are unavailable, therapeutic antiviral drugs can be used as a stopgap solution. However, these treatments do not always work against emerging viral strains and can be accompanied by adverse effects that sometimes outweigh the benefits. Nanotechnology has the potential to overcome many of the challenges facing current antiviral therapies. For example, nanodelivery vehicles can be employed to drastically improve the pharmacokinetic profile of antiviral drugs while reducing their systemic toxicity. Other unique nanomaterials can be leveraged for their virucidal or virus-neutralizing properties. In this review, we discuss recent developments in antiviral nanotherapeutics and provide a perspective on the application of nanotechnology to the SARS-CoV-2 outbreak and future virus pandemics.
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Affiliation(s)
- Jiarong Zhou
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Nishta Krishnan
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Yao Jiang
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Ronnie H Fang
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Liangfang Zhang
- Department of NanoEngineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
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84
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Bhattacharya R, Dev K, Sourirajan A. Antiviral activity of bioactive phytocompounds against coronavirus: An update. J Virol Methods 2021; 290:114070. [PMID: 33497729 PMCID: PMC7826042 DOI: 10.1016/j.jviromet.2021.114070] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 11/25/2020] [Accepted: 01/16/2021] [Indexed: 12/28/2022]
Abstract
Viral infections are one of the main cause of diseases worldwide due to the rising trends of migration, urbanization and global mobility of humans. The outbreak of corona virus diseases caused by SARS-CoV (year 2003), MERS-CoV (year 2012) and SARS-CoV-2 (year 2019) raised global health concerns. The side effects associated with the conventional drugs and increase in cases of anti-microbial resistance have led the researchers to switch to natural sources, especially plants, as they have immense potential to be used as antiviral agents. The aim of the article is to summarize the evidences of the bioactive phytocompounds from different plants as an effective alternative for the treatment of infections caused by coronaviruses. However, the use of most plant compounds succumbs to limitations due to lack of experimental evidences and safety studies. Therefore, further research and studies are required to validate their therapeutic uses for wide application of plant-based medicine, including anti-virals.
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Affiliation(s)
- Riya Bhattacharya
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Bajhol, PO Sultanpur, District Solan, 173229, Himachal Pradesh, India.
| | - Kamal Dev
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Bajhol, PO Sultanpur, District Solan, 173229, Himachal Pradesh, India.
| | - Anuradha Sourirajan
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Bajhol, PO Sultanpur, District Solan, 173229, Himachal Pradesh, India.
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85
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Knyazev S, Hughes L, Skums P, Zelikovsky A. Epidemiological data analysis of viral quasispecies in the next-generation sequencing era. Brief Bioinform 2021; 22:96-108. [PMID: 32568371 PMCID: PMC8485218 DOI: 10.1093/bib/bbaa101] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 04/24/2020] [Accepted: 05/04/2020] [Indexed: 01/04/2023] Open
Abstract
The unprecedented coverage offered by next-generation sequencing (NGS) technology has facilitated the assessment of the population complexity of intra-host RNA viral populations at an unprecedented level of detail. Consequently, analysis of NGS datasets could be used to extract and infer crucial epidemiological and biomedical information on the levels of both infected individuals and susceptible populations, thus enabling the development of more effective prevention strategies and antiviral therapeutics. Such information includes drug resistance, infection stage, transmission clusters and structures of transmission networks. However, NGS data require sophisticated analysis dealing with millions of error-prone short reads per patient. Prior to the NGS era, epidemiological and phylogenetic analyses were geared toward Sanger sequencing technology; now, they must be redesigned to handle the large-scale NGS datasets and properly model the evolution of heterogeneous rapidly mutating viral populations. Additionally, dedicated epidemiological surveillance systems require big data analytics to handle millions of reads obtained from thousands of patients for rapid outbreak investigation and management. We survey bioinformatics tools analyzing NGS data for (i) characterization of intra-host viral population complexity including single nucleotide variant and haplotype calling; (ii) downstream epidemiological analysis and inference of drug-resistant mutations, age of infection and linkage between patients; and (iii) data collection and analytics in surveillance systems for fast response and control of outbreaks.
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86
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Jastrzębska AM, Vasilchenko AS. Smart and Sustainable Nanotechnological Solutions in a Battle against COVID-19 and Beyond: A Critical Review. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2021; 9:601-622. [PMID: 34192094 PMCID: PMC7805306 DOI: 10.1021/acssuschemeng.0c06565] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/14/2020] [Indexed: 05/05/2023]
Abstract
The variety of available biocidal features make nanomaterials promising for fighting infections. To effectively battle COVID-19, categorized as a pandemic by the World Health Organization (WHO), materials scientists and biotechnologists need to combine their knowledge to develop efficient antiviral nanomaterials. By design, nanostructured materials (spherical, two-dimensional, hybrid) can express a diverse bioactivity and unique combination of specific, nonspecific, and mixed mechanisms of antiviral action. It can be related to the material's specific features and their multiple functionalization strategies. This is a complex guiding approach in which an interaction target is constantly moving and quickly changing. On the other hand, in such a rush, sustainability may be put aside. Therefore, to elucidate the most promising nanotechnological solutions, we critically review available data within the frame of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other types of viruses. We highlight solutions that are, or could be, more sustainable and less toxic. In this regard, reduction of the number of synthetic routes, organic solvents, byproducts, and residues is highly recommended. Such efficient, green solutions may be further used for the prevention of virion-host interactions, treatment of the already developed infection, reducing inflammation, and finally, protecting healthcare professionals with masks, fabrics, equipment, and in other associated areas. Further translation into the market needs putting on the fast track with respect to principles of green chemistry, feasibility, safety, and the environment.
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Affiliation(s)
- Agnieszka M. Jastrzębska
- Warsaw
University of Technology, Faculty of Materials Science and Engineering, Wołoska 141, 02-507 Warsaw, Poland
| | - Alexey S. Vasilchenko
- Institute
of Environmental and Agricultural Biology (X-BIO), Tyumen State University, Tyumen, Russia
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87
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Abstract
It is well established that medicinal chemists should depart from the flat, sp2-dominated nature of traditional drugs and incorporate complexities of bioactive natural products, such as sp3-richness, 3D topology and chirality. There is a gray area, however, in the relevance of newly developed chemical scaffolds that exhibit these complexities but do not correlate to anything observed in nature. This can leave synthetic methodologists searching for structural similarities between their newly developed products and known natural products in search of justification. This article offers a perspective on how these types of complex 'abiotic' scaffolds can be appreciated purely on the basis of their structural novelty, and identifies the unique advantages arising when a complex chemical entity unrecognized by nature is introduced to biological systems.
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88
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Falanga A, Del Genio V, Galdiero S. Peptides and Dendrimers: How to Combat Viral and Bacterial Infections. Pharmaceutics 2021; 13:101. [PMID: 33466852 PMCID: PMC7830367 DOI: 10.3390/pharmaceutics13010101] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/08/2021] [Accepted: 01/12/2021] [Indexed: 12/15/2022] Open
Abstract
The alarming growth of antimicrobial resistance and recent viral pandemic events have enhanced the need for novel approaches through innovative agents that are mainly able to attach to the external layers of bacteria and viruses, causing permanent damage. Antimicrobial molecules are potent broad-spectrum agents with a high potential as novel therapeutics. In this context, antimicrobial peptides, cell penetrating peptides, and antiviral peptides play a major role, and have been suggested as promising solutions. Furthermore, dendrimers are to be considered as suitable macromolecules for the development of advanced nanosystems that are able to complement the typical properties of dendrimers with those of peptides. This review focuses on the description of nanoplatforms constructed with peptides and dendrimers, and their applications.
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Affiliation(s)
- Annarita Falanga
- Department of Agricultural Science, University of Naples “Federico II”, Via dell’Università 100, 80100 Portici, Italy
| | - Valentina Del Genio
- Department of Pharmacy, University of Naples “Federico II”, Via Domenico Montesano 49, 80131 Naples, Italy;
| | - Stefania Galdiero
- Department of Pharmacy, University of Naples “Federico II”, Via Domenico Montesano 49, 80131 Naples, Italy;
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89
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Abstract
Population genetic diversity plays a prominent role in viral evolution, pathogenesis, immune escape, and drug resistance. Different mechanisms are responsible for creating and maintaining genetic diversity in viruses, including error-prone replication, repair avoidance, and genome editing, among others. This diversity is subsequently modulated by natural selection and random genetic drift, whose action in turn depends on multiple factors including viral genetic architecture, viral demography, and ecology. Understanding these processes should contribute to the development of more efficient control and treatment strategies against viral pathogens.
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90
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Maheden K, Todd B, Gordon CJ, Tchesnokov EP, Götte M. Inhibition of viral RNA-dependent RNA polymerases with clinically relevant nucleotide analogs. Enzymes 2021; 49:315-354. [PMID: 34696837 PMCID: PMC8517576 DOI: 10.1016/bs.enz.2021.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The treatment of viral infections remains challenging, in particular in the face of emerging pathogens. Broad-spectrum antiviral drugs could potentially be used as a first line of defense. The RNA-dependent RNA polymerase (RdRp) of RNA viruses serves as a logical target for drug discovery and development efforts. Herein we discuss compounds that target RdRp of poliovirus, hepatitis C virus, influenza viruses, respiratory syncytial virus, and the growing data on coronaviruses. We focus on nucleotide analogs and mechanisms of action and resistance.
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Affiliation(s)
- Kieran Maheden
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada; School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada
| | - Brendan Todd
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada
| | - Calvin J Gordon
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada
| | - Egor P Tchesnokov
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada
| | - Matthias Götte
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, Canada; Li Ka Shing Institute of Virology at University of Alberta, Edmonton, AB, Canada.
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91
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Thi LAP, Panchangam SC, Do HT, Nguyen VH. Prospects and challenges of photocatalysis for degradation and mineralization of antiviral drugs. NANOSTRUCTURED PHOTOCATALYSTS 2021. [PMCID: PMC8237458 DOI: 10.1016/b978-0-12-823007-7.00012-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Among the outbreak of influenza and other pandemics such as SARS-CoV-2 recently over the globe, antiviral drugs were significantly concerned with controlling the disease and these pandemics. They have been developed for seven decades around more than 90 drugs categorized licensed to treat nine human infectious diseases. Based on their functional group, antiviral compounds will mitigate infectivity and symptoms and reduce the illness period by arresting the viral replication cycle at different stages. Antiviral drugs have been developed complexly and met many biothreat challenges due to their high biosafety level requirement. In recent years, the spreading of novel virus strains that are a threat to human life, the development in researching and manufacturing new types of antiviral drugs increases and the use by patients and clinicians have increased. Antiviral compounds have been reported only partly removed during wastewater treatment. They were available in wastewater treatment plant effluents and found in surface water from rivers and streams, underground water, and even in drinking water. Photocatalytic degradation of antiviral drugs was exploding to clear the environmental waters from the antiviral drugs. The principle of photocatalysis is based on the excitation of the catalyst material by irradiation of light. The catalyst produces free radicals under the action of photons, which will destroy the pollutants adsorbed on its surface. The photocatalytic degradation mechanism of antiviral drugs can be understood through decomposing in a heterogeneous photocatalytic system and which species are involved in the active decomposition of the drug and then photocatalytically degrading into intermediates or mineralization products. The intermediates and the reaction pathway of antiviral compound photocatalytic degradation are complicated. However, some of the degradation processes are complete, and inorganic compounds (CO2 and H2O) are their final products.
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92
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Elkhalifa D, Al-Hashimi I, Al Moustafa AE, Khalil A. A comprehensive review on the antiviral activities of chalcones. J Drug Target 2020; 29:403-419. [PMID: 33232192 DOI: 10.1080/1061186x.2020.1853759] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Some viral outbreaks have plagued the world since antiquity, including the most recent COVID-19 pandemic. The continuous spread and emergence of new viral diseases have urged the discovery of novel treatment options that can overcome the limitations of currently marketed antiviral drugs. Chalcones are natural open chain flavonoids that are found in various plants and can be synthesised in labs. Several studies have shown that these small organic molecules exert a number of pharmacological activities, including antiviral, anti-inflammatory, antimicrobial and anticancer. The purpose of this review is to provide a summary of the antiviral activities of chalcones and their derivatives on a set of human viral infections and their potential for targeting the most recent COVID-19 disease. Accordingly, we herein review chalcones activities on the following human viruses: Middle East respiratory syndrome coronavirus, severe acute respiratory syndrome coronavirus, human immunodeficiency, influenza, human rhinovirus, herpes simplex, dengue, human cytomegalovirus, hepatitis B and C, Rift Valley fever and Venezuelan equine encephalitis. We hope that this review will pave the way for the design and development of potentially potent and broad-spectrum chalcone based antiviral drugs.
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Affiliation(s)
- Dana Elkhalifa
- College of Pharmacy, QU Health, Qatar University, Doha, Qatar.,Department of Pharmacy, Aspetar Orthopedic and Sports Medicine Hospital, Doha, Qatar
| | | | - Ala-Eddin Al Moustafa
- College of Medicine, QU Health, Qatar University, Doha, Qatar.,Biomedical Research Centre, Qatar University, Doha, Qatar.,Oncology Department, McGill University, Montreal, Quebec, Canada.,Biomedical and Pharmaceutical Research Unit, QU Health, Qatar University, Doha, Qatar
| | - Ashraf Khalil
- College of Pharmacy, QU Health, Qatar University, Doha, Qatar.,Biomedical and Pharmaceutical Research Unit, QU Health, Qatar University, Doha, Qatar
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93
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Manfredonia I, Nithin C, Ponce-Salvatierra A, Ghosh P, Wirecki TK, Marinus T, Ogando NS, Snijder E, van Hemert MJ, Bujnicki JM, Incarnato D. Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements. Nucleic Acids Res 2020; 48:12436-12452. [PMID: 33166999 PMCID: PMC7736786 DOI: 10.1093/nar/gkaa1053] [Citation(s) in RCA: 157] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 10/13/2020] [Accepted: 10/22/2020] [Indexed: 01/25/2023] Open
Abstract
SARS-CoV-2 is a betacoronavirus with a linear single-stranded, positive-sense RNA genome, whose outbreak caused the ongoing COVID-19 pandemic. The ability of coronaviruses to rapidly evolve, adapt, and cross species barriers makes the development of effective and durable therapeutic strategies a challenging and urgent need. As for other RNA viruses, genomic RNA structures are expected to play crucial roles in several steps of the coronavirus replication cycle. Despite this, only a handful of functionally-conserved coronavirus structural RNA elements have been identified to date. Here, we performed RNA structure probing to obtain single-base resolution secondary structure maps of the full SARS-CoV-2 coronavirus genome both in vitro and in living infected cells. Probing data recapitulate the previously described coronavirus RNA elements (5' UTR and s2m), and reveal new structures. Of these, ∼10.2% show significant covariation among SARS-CoV-2 and other coronaviruses, hinting at their functionally-conserved role. Secondary structure-restrained 3D modeling of these segments further allowed for the identification of putative druggable pockets. In addition, we identify a set of single-stranded segments in vivo, showing high sequence conservation, suitable for the development of antisense oligonucleotide therapeutics. Collectively, our work lays the foundation for the development of innovative RNA-targeted therapeutic strategies to fight SARS-related infections.
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Affiliation(s)
- Ilaria Manfredonia
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, the Netherlands
| | - Chandran Nithin
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Almudena Ponce-Salvatierra
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Pritha Ghosh
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Tomasz K Wirecki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Tycho Marinus
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, the Netherlands
| | - Natacha S Ogando
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Eric J Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Martijn J van Hemert
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Danny Incarnato
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, the Netherlands
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94
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Derilus D, Rahman MZ, Serrano AE, Massey SE. Proteome size reduction in Apicomplexans is linked with loss of DNA repair and host redundant pathways. INFECTION GENETICS AND EVOLUTION 2020; 87:104642. [PMID: 33296723 DOI: 10.1016/j.meegid.2020.104642] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 11/07/2020] [Accepted: 11/23/2020] [Indexed: 11/29/2022]
Abstract
Apicomplexans are alveolate parasites which include Plasmodium falciparum, the main cause of malaria, one of the world's biggest killers from infectious disease. Apicomplexans are characterized by a reduction in proteome size, which appears to result from metabolic and functional simplification, commensurate with their parasitic lifestyle. However, other factors may also help to explain gene loss such as population bottlenecks experienced during transmission, and the effect of reducing the overall genomic information content. The latter constitutes an 'informational constraint', which is proposed to exert a selective pressure to evolve and maintain genes involved in informational fidelity and error correction, proportional to the quantity of information in the genome (which approximates to proteome size). The dynamics of gene loss was examined in 41 Apicomplexan genomes using orthogroup analysis. We show that loss of genes involved in amino acid metabolism and steroid biosynthesis can be explained by metabolic redundancy with the host. We also show that there is a marked tendency to lose DNA repair genes as proteome size is reduced. This may be explained by a reduction in size of the informational constraint and can help to explain elevated mutation rates in pathogens with reduced genome size. Multiple Sequentially Markovian Coalescent (MSMC) analysis indicates a recent bottleneck, consistent with predictions generated using allele-based population genetics approaches, implying that relaxed selection pressure due to reduced population size might have contributed to gene loss. However, the non-randomness of pathways that are lost challenges this scenario. Lastly, we identify unique orthogroups in malaria-causing Plasmodium species that infect humans, with a high proportion of membrane associated proteins. Thus, orthogroup analysis appears useful for identifying novel candidate pathogenic factors in parasites, when there is a wide sample of genomes available.
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Affiliation(s)
- D Derilus
- Environmental Sciences Department, University of Puerto Rico-Rio Piedras, United States of America
| | - M Z Rahman
- Biology Department, University of Puerto Rico-Rio Piedras, United States of America
| | - A E Serrano
- Department of Microbiology, University of Puerto Rico-School of Medicine, Medical Sciences, United States of America
| | - S E Massey
- Biology Department, University of Puerto Rico-Rio Piedras, United States of America.
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95
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Al-Azzam S, Ding Y, Liu J, Pandya P, Ting JP, Afshar S. Peptides to combat viral infectious diseases. Peptides 2020; 134:170402. [PMID: 32889022 PMCID: PMC7462603 DOI: 10.1016/j.peptides.2020.170402] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/24/2020] [Accepted: 08/28/2020] [Indexed: 12/14/2022]
Abstract
Viral infectious diseases have resulted in millions of deaths throughout history and have created a significant public healthcare burden. Tremendous efforts have been placed by the scientific communities, health officials and government organizations to detect, treat, and prevent viral infection. However, the complicated life cycle and rapid genetic mutations of viruses demand continuous development of novel medicines with high efficacy and safety profiles. Peptides provide a promising outlook as a tool to combat the spread and re-emergence of viral infection. This article provides an overview of five viral infectious diseases with high global prevalence: influenza, chronic hepatitis B, acquired immunodeficiency syndrome, severe acute respiratory syndrome, and coronavirus disease 2019. The current and potential peptide-based therapies, vaccines, and diagnostics for each disease are discussed.
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Affiliation(s)
- Shams Al-Azzam
- Professional Scientific Services, Eurofins Lancaster Laboratories, Lancaster, PA, 17605, USA
| | - Yun Ding
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA
| | - Jinsha Liu
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA
| | - Priyanka Pandya
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA
| | - Joey Paolo Ting
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA
| | - Sepideh Afshar
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA.
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96
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Gelman R, Bayatra A, Kessler A, Schwartz A, Ilan Y. Targeting SARS-CoV-2 receptors as a means for reducing infectivity and improving antiviral and immune response: an algorithm-based method for overcoming resistance to antiviral agents. Emerg Microbes Infect 2020; 9:1397-1406. [PMID: 32490731 PMCID: PMC7473106 DOI: 10.1080/22221751.2020.1776161] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/25/2020] [Accepted: 05/25/2020] [Indexed: 01/08/2023]
Abstract
The ongoing severe acute respiratory syndrome pandemic caused by the novel coronavirus 2 (SARS-CoV-2) is associated with high morbidity and mortality rates, and it has created a pressing global need for effective antiviral therapies against it. COVID-19 disease pathogenesis is characterized by an initial virus-mediated phase, followed by inappropriate hyperactivation of the immune system leading to organ damage. Targeting of the SARS-CoV-2 viral receptors is being explored as a therapeutic option for these patients. In this paper, we summarize several potential receptors associated with the infectivity of SARS-CoV-2 and discuss their association with the immune-mediated inflammatory response. The potential for the development of resistance towards antiviral drugs is also presented. An algorithm-based platform to improve the efficacy of and overcome resistance to viral receptor blockers through the introduction of personalized variability is described. This method is designed to ensure sustained antiviral effectiveness when using SARS-CoV-2 receptor blockers.
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Affiliation(s)
- Ram Gelman
- Department of Medicine, Hebrew University-Hadassah Medical
Center, Jerusalem, Israel
| | - Areej Bayatra
- Department of Medicine, Hebrew University-Hadassah Medical
Center, Jerusalem, Israel
| | - Asa Kessler
- Department of Medicine, Hebrew University-Hadassah Medical
Center, Jerusalem, Israel
| | - Asaf Schwartz
- Department of Medicine, Hebrew University-Hadassah Medical
Center, Jerusalem, Israel
| | - Yaron Ilan
- Department of Medicine, Hebrew University-Hadassah Medical
Center, Jerusalem, Israel
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97
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An in silico approach to analyze HCV genotype-specific binding-site variation and its effect on drug-protein interaction. Sci Rep 2020; 10:20885. [PMID: 33257748 PMCID: PMC7705671 DOI: 10.1038/s41598-020-77720-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 09/18/2020] [Indexed: 01/06/2023] Open
Abstract
Genotype variation in viruses can affect the response of antiviral treatment. Several studies have established approaches to determine genotype-specific variations; however, analyses to determine the effect of these variations on drug–protein interactions remain unraveled. We present an in-silico approach to explore genotype-specific variations and their effect on drug–protein interaction. We have used HCV NS3 helicase and fluoroquinolones as a model for drug–protein interaction and have investigated the effect of amino acid variations in HCV NS3 of genotype 1a, 1b, 2b and 3a on NS3-fluoroquinolone interaction. We retrieved 687, 667, 101 and 248 nucleotide sequences of HCV NS3 genotypes 1a, 1b, 2b, and 3a, respectively, and translated these into amino acid sequences and used for genotype variation analysis, and also to construct 3D protein models for 2b and 3a genotypes. For 1a and 1b, crystal structures were used. Drug–protein interactions were determined using molecular docking analyses. Our results revealed that individual genotype-specific HCV NS3 showed substantial sequence heterogeneity that resulted in variations in docking interactions. We believe that our approach can be extrapolated to include other viruses to study the clinical significance of genotype-specific variations in drug–protein interactions.
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98
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Marinov R, Markova N, Krumova S, Yotovska K, Zaharieva MM, Genova-Kalou P. Antiviral properties of chalcones and their synthetic derivatives: a mini review. PHARMACIA 2020. [DOI: 10.3897/pharmacia.67.e53842] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Chalcones (natural or synthetic derivatives) are aromatic ketones possessing a central backbone that form a core for variety important compounds with different substitutions. Recent scientific advances show that chalcones exhibit different bio-medical activities, including antiviral, which is related to the variety substitutions. This review provides general information on the origin, sources, virucidal and direct antiviral properties of chalcones in vitro, as well as a brief overview of the possible application and molecular modes of action of these compounds. The antiviral effect of chalcones probably results from the disruption of the different stage of viral replication cycle, inhibition of viral or cell enzymes, induction of apoptosis and others. Structural requirements for antiviral activities vary according to the mechanisms of action. Based on the published information, it could be considered that synthetic chalcones are very perspective antiviral candidates and deserve further studies for elucidating of their pharmacological potential.
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99
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Davies JE, Behroozian S. An ancient solution to a modern problem. Mol Microbiol 2020; 113:546-549. [PMID: 32185831 DOI: 10.1111/mmi.14481] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/30/2020] [Accepted: 01/30/2020] [Indexed: 11/30/2022]
Abstract
The dearth of new antibiotics and escalating emergence of multidrug resistant bacteria have created a global healthcare crisis and highlight the drastic need for novel antimicrobial agents. Complementary and alternative strategies including the investigation of ancient medicinals could address this problem. Natural clay minerals with a long history of medicinal and biomedical applications have become an interest due to their broad-spectrum antimicrobial activity. Such untapped natural sources may provide new therapeutic agents in the battle against infectious diseases in the post-antibiotic era.
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Affiliation(s)
- Julian E Davies
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Shekooh Behroozian
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
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100
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Abo-Zeid Y, Williams GR, Touabi L, McLean GR. An investigation of rhinovirus infection on cellular uptake of poly (glycerol-adipate) nanoparticles. Int J Pharm 2020; 589:119826. [PMID: 32871219 PMCID: PMC7836899 DOI: 10.1016/j.ijpharm.2020.119826] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 07/24/2020] [Accepted: 08/24/2020] [Indexed: 12/26/2022]
Abstract
Viral infections represent 44% of newly emerging infections, and as is shown by the COVID-19 outbreak constitute a major risk to human health and wellbeing. Although there are many efficient antiviral agents, they still have drawbacks such as development of virus resistance and accumulation within off-target organs. Encapsulation of antiviral agents into nanoparticles (NPs) has been shown to improve bioavailability, control release, and reduce side effects. However, there is little quantitative understanding of how the uptake of NPs into virally infected cells compares to uninfected cells. In this work, the uptake of fluorescently labeled polymer NPs was investigated in several models of rhinovirus (RV) infected cells. Different multiplicities of RV infections (MOI) and timings of NPs uptake were also investigated. In some cases, RV infection resulted in a significant increase of NPs uptake, but this was not universally noted. For HeLa cells, RV-A16 and RV-A01 infection elevated NPs uptake upon increasing the incubation time, whereas at later timepoints (6 h) a reduced uptake was noted with RV-A01 infection (owing to decreased cell viability). Beas-2B cells exhibited more complex trends: decreases in NPs uptake (cf. uninfected cells) were observed at short incubation times following RV-A01 and RV-A16 infection. At later incubation times (4 h), we found a marked decrease of NPs uptake for RV-A01 infected cells but an increase in uptake with RV-A16 infected cells. Where increases in NPs uptake were found, they were very modest compared to results previously reported for a hepatitis C/ Huh7.5 cell line model. An increase in RV dose (MOI) was not associated with any notable change of NPs uptake. We argue that the diverse endocytic pathways among the different cell lines, together with changes in virus nature, size, and entry mechanism are responsible for these differences. These findings suggest that NPs entry into virally infected cells is a complex process, and further work is required to unravel the different factors which govern this. Undertaking this additional research will be crucial to develop potent nanomedicines for the delivery of antiviral agents.
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Affiliation(s)
- Yasmin Abo-Zeid
- Department of Pharmaceutics, Faculty of Pharmacy, Helwan University, Cairo, Egypt; UCL School of Pharmacy, University College London, 29 - 39 Brunswick Square, London WC1N 1AX, UK; Cellular and Molecular Immunology Research Centre, London Metropolitan University, 166-220 Holloway Road, London N7 8DB, UK.
| | - Gareth R Williams
- UCL School of Pharmacy, University College London, 29 - 39 Brunswick Square, London WC1N 1AX, UK.
| | - Lila Touabi
- Cellular and Molecular Immunology Research Centre, London Metropolitan University, 166-220 Holloway Road, London N7 8DB, UK.
| | - Gary R McLean
- Cellular and Molecular Immunology Research Centre, London Metropolitan University, 166-220 Holloway Road, London N7 8DB, UK; National Heart and Lung Institute, Imperial College London, Norfolk Place, London W2 1PG, UK.
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