1
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Lü Z, Dai X, Xu J, Liu Z, Guo Y, Gao Z, Meng F. Medicinal chemistry strategies toward broad-spectrum antiviral agents to prevent next pandemics. Eur J Med Chem 2024; 271:116442. [PMID: 38685143 DOI: 10.1016/j.ejmech.2024.116442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 04/02/2024] [Accepted: 04/19/2024] [Indexed: 05/02/2024]
Abstract
The pandemic and tremendous impact of severe acute respiratory syndrome coronavirus 2 alert us, despite great achievements in prevention and control of infectious diseases, we still lack universal and powerful antiviral strategies to rapidly respond to the potential threat of serious infectious disease. Various highly contagious and pathogenic viruses, as well as other unknown viruses may appear or reappear in human society at any time, causing a catastrophic epidemic. Developing broad-spectrum antiviral drugs with high security and efficiency is of great significance for timely meeting public health emergency and protecting the lives and health of the people. Hence, in this review, we summarized diverse broad-spectrum antiviral targets and corresponding agents from a medicinal chemistry prospective, compared the pharmacological advantages and disadvantages of different targets, listed representative agents, showed their structures, pharmacodynamics and pharmacokinetics characteristics, and conducted a critical discussion on their development potential, in the hope of providing up-to-date guidance for the development of broad-spectrum antivirals and perspectives for applications of antiviral therapy.
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Affiliation(s)
- Zirui Lü
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China
| | - Xiandong Dai
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China
| | - Jianjie Xu
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China
| | - Zhenming Liu
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing, China
| | - Yongbiao Guo
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China
| | - Zhenhua Gao
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China
| | - Fanhua Meng
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China.
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2
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He M, Yan Y, Liu X, Li L, Yang B, Liu M, Yu Q, Wang E, Li P, Liu T, Wang G. A nanobody-mediated drug system against largemouth bass virus delivered by bacterial nanocellulose in Micropterus salmoides. Int J Biol Macromol 2024; 266:131146. [PMID: 38561116 DOI: 10.1016/j.ijbiomac.2024.131146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/22/2024] [Accepted: 03/24/2024] [Indexed: 04/04/2024]
Abstract
Diseases caused by pathogens severely hampered the development of aquaculture, especially largemouth bass virus (LMBV) has caused massive mortality and severe economic losses to the culture of largemouth bass (Micropterus salmoides). Considering the environmental hazards and human health, effective and environmentally friendly therapy strategy against LMBV is of vital importance and in pressing need. In the present study, a novel nanobody (NbE4) specific for LMBV was selected from a phage display nanobody library. Immunofluorescence and indirect ELISA showed that NbE4 could recognize LMBV virions and had strong binding capacity, but RT-qPCR evidenced that NBE4 did not render the virus uninfectious. Besides, antiviral drug ribavirin was used to construct a targeted drug system delivered by bacterial nanocellulose (BNC). RT-qPCR revealed that NbE4 could significantly enhance the antiviral activity of ribavirin in vitro and in vivo. The targeted drug delivery system (BNC-Ribavirin-NbE4, BRN) reduced the inflammatory response caused by LMBV infection and improved survival rate (BRN-L, 33.3 %; BRN-M, 46.7 %; BRN-H, 56.7 %)compared with control group (13.3 %), ribavirin group (RBV, 26.7 %) and BNC-ribavirin (BNC-R, 40.0 %), respectively. This research provided an effective antiviral strategy that improved the drug therapeutic effect and thus reduced the dosage.
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Affiliation(s)
- Maosheng He
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China; Engineering Research Center of the Innovation and Development of Green Fishery Drugs, Universities of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ying Yan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China; Northwest A&F University Shenzhen Research Institute, Shenzhen, Guangdong 518057, China; Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China; Engineering Research Center of the Innovation and Development of Green Fishery Drugs, Universities of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiang Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China; Engineering Research Center of the Innovation and Development of Green Fishery Drugs, Universities of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Linhan Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Bin Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China; Engineering Research Center of the Innovation and Development of Green Fishery Drugs, Universities of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingzhu Liu
- Guangxi Key Laboratory of Aquatic Biotechnology and Modern Ecological Aquaculture, Guangxi Engineering Research Center for Fishery Major Diseases Control and Efficient Healthy Breeding Industrial Technology (GERCFT), Guangxi Academy of Sciences, Nanning, Guangxi 530007, China
| | - Qing Yu
- Guangxi Key Laboratory of Aquatic Biotechnology and Modern Ecological Aquaculture, Guangxi Engineering Research Center for Fishery Major Diseases Control and Efficient Healthy Breeding Industrial Technology (GERCFT), Guangxi Academy of Sciences, Nanning, Guangxi 530007, China
| | - Erlong Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China; Northwest A&F University Shenzhen Research Institute, Shenzhen, Guangdong 518057, China; Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China; Engineering Research Center of the Innovation and Development of Green Fishery Drugs, Universities of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Pengfei Li
- Guangxi Key Laboratory of Aquatic Biotechnology and Modern Ecological Aquaculture, Guangxi Engineering Research Center for Fishery Major Diseases Control and Efficient Healthy Breeding Industrial Technology (GERCFT), Guangxi Academy of Sciences, Nanning, Guangxi 530007, China.
| | - Tianqiang Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China; Northwest A&F University Shenzhen Research Institute, Shenzhen, Guangdong 518057, China; Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China; Engineering Research Center of the Innovation and Development of Green Fishery Drugs, Universities of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Gaoxue Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China; Engineering Research Center of the Innovation and Development of Green Fishery Drugs, Universities of Shaanxi Province, Northwest A&F University, Yangling, Shaanxi 712100, China.
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3
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Abdullah Z, Chee HY, Yusof R, Mohd Fauzi F. Finding Lead Compounds for Dengue Antivirals from a Collection of Old Drugs through In Silico Target Prediction and Subsequent In Vitro Validation. ACS OMEGA 2023; 8:32483-32497. [PMID: 37720780 PMCID: PMC10500654 DOI: 10.1021/acsomega.3c02607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 07/14/2023] [Indexed: 09/19/2023]
Abstract
Dengue virus (DENV) infection is one of the most widely spread flavivirus infections. Despite the fatality it could cause, no antiviral treatment is currently available to treat the disease. Hence, this study aimed to repurpose old drugs as novel DENV NS3 inhibitors. Ligand-based (L-B) and proteochemometric (PCM) prediction models were built using 62,354 bioactivity data to screen for potential NS3 inhibitors. Selected drugs were then subjected to the foci forming unit reduction assay (FFURA) and protease inhibition assay. Finally, molecular docking was performed to validate these results. The in silico studies revealed that both models performed well in the internal and external validations. However, the L-B model showed better accuracy in the external validation in terms of its sensitivity (0.671). In the in vitro validation, all drugs (zileuton, trimethadione, and linalool) were able to moderately inhibit the viral activities at the highest concentration tested. Zileuton showed comparable results with linalool when tested at 2 mM against the DENV NS3 protease, with a reduction of protease activity at 17.89 and 18.42%, respectively. Two new compounds were also proposed through the combination of the selected drugs, which are ziltri (zilueton + trimethadione) and zilool (zileuton + linalool). The molecular docking study confirms the in vitro observations where all drugs and proposed compounds were able to achieve binding affinity ≥ -4.1 kcal/mol, with ziltri showing the highest affinity at -7.7 kcal/mol, surpassing the control, panduratin A. The occupation of both S1 and S2 subpockets of NS2B-NS3 may be essential and a reason for the lower binding energy shown by the proposed compounds compared to the screened drugs. Based on the results, this study provided five potential new lead compounds (ziltri, zilool, zileuton, linalool, and trimethadione) for DENV that could be modified further.
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Affiliation(s)
- Zafirah
Liyana Abdullah
- Department
of Pharmaceutical Life Sciences, Faculty of Pharmacy, Universiti Teknologi MARA Selangor, Puncak Alam Campus, 42300 Bandar Puncak Alam, Selangor, Malaysia
| | - Hui-Yee Chee
- Department
of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Rohana Yusof
- Department
of Molecular Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Fazlin Mohd Fauzi
- Department
of Pharmacology and Pharmaceutical Chemistry, Faculty of Pharmacy, UiTM Selangor, Puncak Alam Campus, 42300 Bandar Puncak Alam, Selangor, Malaysia
- Collaborative
Drug Discovery Research, Faculty of Pharmacy, Universiti Teknologi MARA Selangor, Puncak Alam Campus, 42300 Bandar Puncak Alam, Selangor, Malaysia
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4
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De Castro F, Stefàno E, De Luca E, Benedetti M, Fanizzi FP. Platinum-Nucleos(t)ide Compounds as Possible Antimetabolites for Antitumor/Antiviral Therapy: Properties and Perspectives. Pharmaceutics 2023; 15:pharmaceutics15030941. [PMID: 36986802 PMCID: PMC10058173 DOI: 10.3390/pharmaceutics15030941] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/06/2023] [Accepted: 03/12/2023] [Indexed: 03/16/2023] Open
Abstract
Nucleoside analogues (NAs) are a family of compounds which include a variety of purine and pyrimidine derivatives, widely used as anticancer and antiviral agents. For their ability to compete with physiological nucleosides, NAs act as antimetabolites exerting their activity by interfering with the synthesis of nucleic acids. Much progress in the comprehension of their molecular mechanisms has been made, including providing new strategies for potentiating anticancer/antiviral activity. Among these strategies, new platinum-NAs showing a good potential to improve the therapeutic indices of NAs have been synthesized and studied. This short review aims to describe the properties and future perspectives of platinum-NAs, proposing these complexes as a new class of antimetabolites.
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5
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Naidu SAG, Mustafa G, Clemens RA, Naidu AS. Plant-Derived Natural Non-Nucleoside Analog Inhibitors (NNAIs) against RNA-Dependent RNA Polymerase Complex (nsp7/nsp8/nsp12) of SARS-CoV-2. J Diet Suppl 2023; 20:254-283. [PMID: 34850656 DOI: 10.1080/19390211.2021.2006387] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The emergence of fast-spreading SARS-CoV-2 mutants has sparked a new phase of COVID-19 pandemic. There is a dire necessity for antivirals targeting highly conserved genomic domains on SARS-CoV-2 that are less prone to mutation. The nsp12, also known as the RNA-dependent RNA-polymerase (RdRp), the core component of 'SARS-CoV-2 replication-transcription complex', is a potential well-conserved druggable antiviral target. Several FDA-approved RdRp 'nucleotide analog inhibitors (NAIs)' such as remdesivir, have been repurposed to treat COVID-19 infections. The NAIs target RdRp protein translation and competitively block the nucleotide insertion into the RNA chain, resulting in the inhibition of viral replication. However, the replication proofreading function of nsp14-ExoN could provide resistance to SARS-CoV-2 against many NAIs. Conversely, the 'non-nucleoside analog inhibitors (NNAIs)' bind to allosteric sites on viral polymerase surface, change the redox state; thereby, exert antiviral activity by altering interactions between the enzyme substrate and active core catalytic site of the RdRp. NNAIs neither require metabolic activation (unlike NAIs) nor compete with intracellular pool of nucleotide triphosphates (NTPs) for anti-RdRp activity. The NNAIs from phytonutrient origin are potential antiviral candidates compared to their synthetic counterparts. Several in-silico studies reported the antiviral spectrum of natural phytonutrient-NNAIs such as Suramin, Silibinin (flavonolignan), Theaflavin (tea polyphenol), Baicalein (5,6,7-trihydroxyflavone), Corilagin (gallotannin), Hesperidin (citrus bioflavonoid), Lycorine (pyrrolidine alkaloid), with superior redox characteristics (free binding energy, hydrogen-bonds, etc.) than antiviral drugs (i.e. remdesivir, favipiravir). These phytonutrient-NNAIs also exert anti-inflammatory, antioxidant, immunomodulatory and cardioprotective functions, with multifunctional therapeutic benefits in the clinical management of COVID-19.
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Affiliation(s)
| | - Ghulam Mustafa
- Department of Biochemistry, Government College University, Faisalabad, Pakistan
| | - Roger A Clemens
- Department of International Regulatory Science, University of Southern California School of Pharmacy, Los Angeles, CA, USA
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6
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Ornelas MY, Thomas AY, Johnson Rosas LI, Scoville RO, Mehta AP. Synthetic Platforms for Characterizing and Targeting of SARS-CoV-2 Genome Capping Enzymes. ACS Synth Biol 2022; 11:3759-3771. [PMID: 36331143 PMCID: PMC9662071 DOI: 10.1021/acssynbio.2c00359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Indexed: 11/06/2022]
Abstract
Essential viral enzymes have been successfully targeted to combat the diseases caused by emerging pathogenic RNA viruses (e.g., viral RNA-dependent RNA polymerase). Because of the conserved nature of such viral enzymes, therapeutics targeting these enzymes have the potential to be repurposed to combat emerging diseases, e.g., remdesivir, which was initially developed as a potential Ebola treatment, then was repurposed for COVID-19. Our efforts described in this study target another essential and highly conserved, but relatively less explored, step in RNA virus translation and replication, i.e., capping of the viral RNA genome. The viral genome cap structure disguises the genome of most RNA viruses to resemble the mRNA cap structure of their host and is essential for viral translation, propagation, and immune evasion. Here, we developed a synthetic, phenotypic yeast-based complementation platform (YeRC0M) for molecular characterization and targeting of SARS-CoV-2 genome-encoded RNA cap-0 (guanine-N7)-methyltransferase (N7-MTase) enzyme (nsp14). In YeRC0M, the lack of yeast mRNA capping N7-MTase in yeast, which is an essential gene in yeast, is complemented by the expression of functional viral N7-MTase or its variants. Using YeRC0M, we first identified important protein domains and amino acid residues that are essential for SARS-CoV-2 nsp14 N7-MTase activity. We also expanded YeRC0M to include key nsp14 variants observed in emerging variants of SARS-CoV-2 (e.g., delta variant of SARS-CoV-2 encodes nsp14 A394V and nsp14 P46L). We also combined YeRC0M with directed evolution to identify attenuation mutations in SARS-CoV-2 nsp14. Because of the high sequence similarity of nsp14 in emerging coronaviruses, these observations could have implications on live attenuated vaccine development strategies. These data taken together reveal key domains in SARS-CoV-2 nsp14 that can be targeted for therapeutic strategies. We also anticipate that these readily tractable phenotypic platforms can also be used for the identification of inhibitors of viral RNA capping enzymes as antivirals.
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Affiliation(s)
- Marya Y. Ornelas
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, Illinois 61801, United States
| | - Angela Y. Thomas
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, Illinois 61801, United States
| | - L. Idalee Johnson Rosas
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, Illinois 61801, United States
| | - Riley O. Scoville
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, Illinois 61801, United States
| | - Angad P. Mehta
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, Illinois 61801, United States
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign
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7
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Selvavinayagam ST, Yong YK, Joseph N, Hemashree K, Tan HY, Zhang Y, Rajeshkumar M, Kumaresan A, Kalpana R, Kalaivani V, Monika AVD, Suvaithenamudhan S, Kannan M, Murugesan A, Narayanasamy K, Palani S, Larsson M, Shankar EM, Raju S. Low SARS-CoV-2 viral load among vaccinated individuals infected with Delta B.1.617.2 and Omicron BA.1.1.529 but not with Omicron BA.1.1 and BA.2 variants. Front Public Health 2022; 10:1018399. [PMID: 36211690 PMCID: PMC9540788 DOI: 10.3389/fpubh.2022.1018399] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 08/25/2022] [Indexed: 01/28/2023] Open
Abstract
The rapid spread of SARS-CoV-2 variants in the global population is indicative of the development of selective advantages in emerging virus strains. Here, we performed a case-control investigation of the clinical and demographic characteristics, clinical history, and virological markers to predict disease progression in hospitalized adults for COVID-19 between December 2021 and January 2022 in Chennai, India. COVID-19 diagnosis was made by a commercial TaqPath COVID-19 RT-PCR, and WGS was performed with the Ion Torrent Next Generation Sequencing System. High-quality (<5% of N) complete sequences of 73 Omicron B.1.1.529 variants were randomly selected for phylogenetic analysis. SARS-CoV-2 viral load, number of comorbidities, and severe disease presentation were independently associated with a shorter time-to-death. Strikingly, this was observed among individuals infected with Omicron BA.2 but not among those with the BA.1.1.529, BA.1.1, or the Delta B.1.617.2 variants. Phylogenetic analysis revealed severe cases predominantly clustering under the BA.2 lineage. Sequence analyses showed 30 mutation sites in BA.1.1.529 and 33 in BA.1.1. The mutations unique to BA.2 were T19I, L24S, P25del, P26del, A27S, V213G, T376A, D405N and R408S. Low SARS-CoV-2 viral load among vaccinated individuals infected with Delta B.1.617.2 and the Omicron BA.1.1.529 variant but not with Omicron BA.1.1 or BA.2 suggests that the newer strains are largely immune escape variants. The number of vaccine doses received was independently associated with increased odds of developing asymptomatic disease or recovery. We propose that the novel mutations reported herein could likely bear a significant impact on the clinical characteristics, disease progression, and epidemiological aspects of COVID-19. Surging rates of mutations and the emergence of eclectic variants of SARS-CoV-2 appear to impact disease dynamics.
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Affiliation(s)
| | - Yean Kong Yong
- Laboratory Centre, Xiamen University Malaysia, Sepang, Malaysia
| | - Narcisse Joseph
- Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Kannan Hemashree
- Directorate of Public Health and Preventive Medicine, Chennai, India
| | - Hong Yien Tan
- Laboratory Centre, Xiamen University Malaysia, Sepang, Malaysia
- School of Traditional Chinese Medicine, Xiamen University Malaysia, Sepang, Malaysia
| | - Ying Zhang
- Chemical Engineering, Xiamen University Malaysia, Sepang, Malaysia
| | | | | | - Raghu Kalpana
- Directorate of Public Health and Preventive Medicine, Chennai, India
| | | | | | | | - Meganathan Kannan
- Blood and Vascular Biology, Department of Life Sciences, Central University of Tamil Nadu, Thiruvarur, India
| | - Amudhan Murugesan
- Department of Microbiology, The Government Theni Medical College and Hospital, Theni, India
| | | | - Sampath Palani
- Directorate of Public Health and Preventive Medicine, Chennai, India
| | - Marie Larsson
- Molecular Medicine and Virology, Department of Biomedicine and Clinical Sciences, Linkoping University, Linköping, Sweden
| | - Esaki M. Shankar
- Infection Biology, Department of Life Sciences, Central University of Tamil Nadu, Thiruvarur, India
| | - Sivadoss Raju
- Directorate of Public Health and Preventive Medicine, Chennai, India
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8
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Wang B, Svetlov D, Bartikofsky D, Wobus CE, Artsimovitch I. Going Retro, Going Viral: Experiences and Lessons in Drug Discovery from COVID-19. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123815. [PMID: 35744940 PMCID: PMC9228142 DOI: 10.3390/molecules27123815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/03/2022] [Accepted: 06/07/2022] [Indexed: 12/15/2022]
Abstract
The severity of the COVID-19 pandemic and the pace of its global spread have motivated researchers to opt for repurposing existing drugs against SARS-CoV-2 rather than discover or develop novel ones. For reasons of speed, throughput, and cost-effectiveness, virtual screening campaigns, relying heavily on in silico docking, have dominated published reports. A particular focus as a drug target has been the principal active site (i.e., RNA synthesis) of RNA-dependent RNA polymerase (RdRp), despite the existence of a second, and also indispensable, active site in the same enzyme. Here we report the results of our experimental interrogation of several small-molecule inhibitors, including natural products proposed to be effective by in silico studies. Notably, we find that two antibiotics in clinical use, fidaxomicin and rifabutin, inhibit RNA synthesis by SARS-CoV-2 RdRp in vitro and inhibit viral replication in cell culture. However, our mutagenesis studies contradict the binding sites predicted computationally. We discuss the implications of these and other findings for computational studies predicting the binding of ligands to large and flexible protein complexes and therefore for drug discovery or repurposing efforts utilizing such studies. Finally, we suggest several improvements on such efforts ongoing against SARS-CoV-2 and future pathogens as they arise.
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Affiliation(s)
- Bing Wang
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA;
| | | | - Dylan Bartikofsky
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA; (D.B.); (C.E.W.)
| | - Christiane E. Wobus
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA; (D.B.); (C.E.W.)
| | - Irina Artsimovitch
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA;
- Correspondence:
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9
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Schultz DC, Johnson RM, Ayyanathan K, Miller J, Whig K, Kamalia B, Dittmar M, Weston S, Hammond HL, Dillen C, Ardanuy J, Taylor L, Lee JS, Li M, Lee E, Shoffler C, Petucci C, Constant S, Ferrer M, Thaiss CA, Frieman MB, Cherry S. Pyrimidine inhibitors synergize with nucleoside analogues to block SARS-CoV-2. Nature 2022; 604:134-140. [PMID: 35130559 PMCID: PMC10377386 DOI: 10.1038/s41586-022-04482-x] [Citation(s) in RCA: 87] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/26/2022] [Indexed: 11/09/2022]
Abstract
The SARS-CoV-2 virus has infected more than 261 million people and has led to more than 5 million deaths in the past year and a half1 ( https://www.who.org/ ). Individuals with SARS-CoV-2 infection typically develop mild-to-severe flu-like symptoms, whereas infection of a subset of individuals leads to severe-to-fatal clinical outcomes2. Although vaccines have been rapidly developed to combat SARS-CoV-2, there has been a dearth of antiviral therapeutics. There is an urgent need for therapeutics, which has been amplified by the emerging threats of variants that may evade vaccines. Large-scale efforts are underway to identify antiviral drugs. Here we screened approximately 18,000 drugs for antiviral activity using live virus infection in human respiratory cells and validated 122 drugs with antiviral activity and selectivity against SARS-CoV-2. Among these candidates are 16 nucleoside analogues, the largest category of clinically used antivirals. This included the antivirals remdesivir and molnupiravir, which have been approved for use in COVID-19. RNA viruses rely on a high supply of nucleoside triphosphates from the host to efficiently replicate, and we identified a panel of host nucleoside biosynthesis inhibitors as antiviral. Moreover, we found that combining pyrimidine biosynthesis inhibitors with antiviral nucleoside analogues synergistically inhibits SARS-CoV-2 infection in vitro and in vivo against emerging strains of SARS-CoV-2, suggesting a clinical path forward.
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Affiliation(s)
- David C Schultz
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA.
| | - Robert M Johnson
- Department of Microbiology and Immunology, Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kasirajan Ayyanathan
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jesse Miller
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kanupriya Whig
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Brinda Kamalia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Mark Dittmar
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Stuart Weston
- Department of Microbiology and Immunology, Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Holly L Hammond
- Department of Microbiology and Immunology, Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Carly Dillen
- Department of Microbiology and Immunology, Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jeremy Ardanuy
- Department of Microbiology and Immunology, Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Louis Taylor
- Department of Microbiology and Immunology, Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jae Seung Lee
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Minghua Li
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Emily Lee
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Clarissa Shoffler
- Metabolomics Core, Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Christopher Petucci
- Metabolomics Core, Penn Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Marc Ferrer
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Christoph A Thaiss
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew B Frieman
- Department of Microbiology and Immunology, Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - Sara Cherry
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA.
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10
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Broad-Spectrum Antiviral Activity of the Amphibian Antimicrobial Peptide Temporin L and Its Analogs. Int J Mol Sci 2022; 23:ijms23042060. [PMID: 35216177 PMCID: PMC8878748 DOI: 10.3390/ijms23042060] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/08/2022] [Accepted: 02/11/2022] [Indexed: 12/04/2022] Open
Abstract
The COVID-19 pandemic has evidenced the urgent need for the discovery of broad-spectrum antiviral therapies that could be deployed in the case of future emergence of novel viral threats, as well as to back up current therapeutic options in the case of drug resistance development. Most current antivirals are directed to inhibit specific viruses since these therapeutic molecules are designed to act on a specific viral target with the objective of interfering with a precise step in the replication cycle. Therefore, antimicrobial peptides (AMPs) have been identified as promising antiviral agents that could help to overcome this limitation and provide compounds able to act on more than a single viral family. We evaluated the antiviral activity of an amphibian peptide known for its strong antimicrobial activity against both Gram-positive and Gram-negative bacteria, namely Temporin L (TL). Previous studies have revealed that TL is endowed with widespread antimicrobial activity and possesses marked haemolytic activity. Therefore, we analyzed TL and a previously identified TL derivative (Pro3, DLeu9 TL, where glutamine at position 3 is replaced with proline, and the D-Leucine enantiomer is present at position 9) as well as its analogs, for their activity against a wide panel of viruses comprising enveloped, naked, DNA and RNA viruses. We report significant inhibition activity against herpesviruses, paramyxoviruses, influenza virus and coronaviruses, including SARS-CoV-2. Moreover, we further modified our best candidate by lipidation and demonstrated a highly reduced cytotoxicity with improved antiviral effect. Our results show a potent and selective antiviral activity of TL peptides, indicating that the novel lipidated temporin-based antiviral agents could prove to be useful additions to current drugs in combatting rising drug resistance and epidemic/pandemic emergencies.
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11
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Lee CZ, Zoqratt MZHM, Phipps ME, Barr JJ, Lal SK, Ayub Q, Rahman S. The gut virome in two indigenous populations from Malaysia. Sci Rep 2022; 12:1824. [PMID: 35115615 PMCID: PMC8813915 DOI: 10.1038/s41598-022-05656-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 01/04/2022] [Indexed: 12/30/2022] Open
Abstract
The human gut contains a complex microbiota dominated by bacteriophages but also containing other viruses and bacteria and fungi. There are a growing number of techniques for the extraction, sequencing, and analysis of the virome but currently no standardized protocols. This study established an effective workflow for virome analysis to investigate the virome of stool samples from two understudied ethnic groups from Malaysia: the Jakun and Jehai Orang Asli. By using the virome extraction and analysis workflow with the Oxford Nanopore Technology, long-read sequencing successfully captured close to full-length viral genomes. The virome composition of the two indigenous Malaysian communities were remarkably different from those found in other parts of the world. Additionally, plant viruses found in the viromes of these individuals were attributed to traditional food-seeking methods. This study establishes a human gut virome workflow and extends insights into the healthy human gut virome, laying the groundwork for comparative studies.
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Affiliation(s)
- Chuen Zhang Lee
- School of Science, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | | | - Maude E Phipps
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Subang Jaya, Malaysia
| | - Jeremy J Barr
- School of Biological Sciences, Monash University, Melbourne, VIC, 3800, Australia
| | - Sunil K Lal
- School of Science, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Qasim Ayub
- School of Science, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
- Genomics Facility, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Sadequr Rahman
- School of Science, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia.
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Subang Jaya, Malaysia.
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12
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Nucleosides and emerging viruses: a new story. Drug Discov Today 2022; 27:1945-1953. [PMID: 35189369 PMCID: PMC8856764 DOI: 10.1016/j.drudis.2022.02.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/13/2022] [Accepted: 02/16/2022] [Indexed: 12/24/2022]
Abstract
With several US Food and Drug Administration (FDA)-approved drugs and high barriers to resistance, nucleoside and nucleotide analogs remain the cornerstone of antiviral therapies for not only herpesviruses, but also HIV and hepatitis viruses (B and C); however, with the exception of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), for which vaccines have been developed at unprecedented speed, there are no vaccines or small antivirals yet available for (re)emerging viruses, which are primarily RNA viruses. Thus, herein, we present an overview of ribonucleoside analogs recently developed and acting as inhibitors of the viral RNA-dependent RNA polymerase (RdRp). They are new lead structures that will be exploited for the discovery of new antiviral nucleosides.
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13
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Singla S, Goyal S. Antiviral activity of molnupiravir against COVID-19: a schematic review of evidences. BULLETIN OF THE NATIONAL RESEARCH CENTRE 2022; 46:62. [PMID: 35287311 PMCID: PMC8907909 DOI: 10.1186/s42269-022-00753-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/02/2022] [Indexed: 05/07/2023]
Abstract
BACKGROUND The study was aimed at encapsulating the evidence of in vitro and in vivo antiviral activities of molnupiravir and its active form against highly pathogenic SARS-CoV-2, the pathogen responsible for COVID-19, and finding out the efficacy and safety of molnupiravir in clinical trials. MAIN BODY Information on publications was explored on several databases, gray literature was reviewed, and the outcomes were discussed narratively. Molnupiravir's antiviral efficacy and associated mechanism of action have been verified in vitro against both non-COVID and multiple coronaviruses. Molnupiravir has been tried in preclinical investigations in numerous animal models against non-coronaviruses. Clinical studies in several countries are now being conducted to evaluate its antiviral efficacy in persons infected with COVID-19. The medication displays antiviral effect via generation of copying mistakes during viral RNA replication. CONCLUSIONS Molnupiravir is the first oral antiviral medicine to show considerable and convincing antiviral activity in vitro and in animal models. Molnupiravir stops the spread of SARS-CoV-2 in animals that have been infected and in cells grown in a lab. In a clinical research, early molnupiravir treatment reduced hospitalization and death risk in unvaccinated individuals with COVID-19. In the battle against SARS-CoV-2, it could be a potent weapon. However, its role in COVID-19 in moderate to severe cases is still up in the air, and more research is needed.
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Affiliation(s)
- Shivali Singla
- Department of Pharmaceutics, School of Pharmacy, Abhilashi University, Chail Chowk, HP 175028 India
| | - Sachin Goyal
- Department of Pharmaceutics, School of Pharmacy, Abhilashi University, Chail Chowk, HP 175028 India
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14
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De Castro F, De Luca E, Benedetti M, Fanizzi FP. Platinum compounds as potential antiviral agents. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214276] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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15
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Rajasekhar S, Das S, Balamurali MM, Chanda K. Therapeutic Inhibitory Activities of
N
‐Hydroxy Derived Cytidines: A Patent Overview. ChemistrySelect 2021. [DOI: 10.1002/slct.202102856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Sreerama Rajasekhar
- Department of Chemistry School of Advanced Sciences Vellore Institute of Technology Vellore 632014 India
| | - Soumyadip Das
- Department of Chemistry School of Advanced Sciences Vellore Institute of Technology Vellore 632014 India
| | - M. M. Balamurali
- Division of Chemistry School of Advanced Sciences Vellore Institute of Technology, Chennai campus Vandalur-Kelambakkam Road Chennai 600 127 Tamil Nadu India
| | - Kaushik Chanda
- Department of Chemistry School of Advanced Sciences Vellore Institute of Technology Vellore 632014 India
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16
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Novel Nonnucleoside Inhibitors of Zika Virus Polymerase Identified through the Screening of an Open Library of Antikinetoplastid Compounds. Antimicrob Agents Chemother 2021; 65:e0089421. [PMID: 34152807 PMCID: PMC8370225 DOI: 10.1128/aac.00894-21] [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: 01/22/2023] Open
Abstract
Zika virus (ZIKV) is a mosquito-borne pathogen responsible for neurological disorders (Guillain-Barré syndrome) and congenital malformations (microcephaly). Its ability to cause explosive epidemics, such as that of 2015 to 2016, urges the identification of effective antiviral drugs. Viral polymerase inhibitors constitute one of the most successful fields in antiviral research. Accordingly, the RNA-dependent RNA polymerase activity of flavivirus nonstructural protein 5 (NS5) provides a unique target for the development of direct antivirals with high specificity and low toxicity. Here, we describe the discovery and characterization of two novel nonnucleoside inhibitors of ZIKV polymerase. These inhibitors, TCMDC-143406 (compound 6) and TCMDC-143215 (compound 15) were identified through the screening of an open-resource library of antikinetoplastid compounds using a fluorescence-based polymerization assay based on ZIKV NS5. The two compounds inhibited ZIKV NS5 polymerase activity in vitro and ZIKV multiplication in cell culture (half-maximal effective concentrations [EC50] values of 0.5 and 2.6 μM for compounds 6 and 15, respectively). Both compounds also inhibited the replication of other pathogenic flaviviruses, namely, West Nile virus (WNV; EC50 values of 4.3 and 4.6 μM for compounds 6 and 15, respectively) and dengue virus 2 (DENV-2; EC50 values of 3.4 and 9.6 μM for compounds 6 and 15, respectively). Enzymatic assays confirmed that the polymerase inhibition was produced by a noncompetitive mechanism. Combinatorial assays revealed an antagonistic effect between both compounds, suggesting that they would bind to the same region of ZIKV polymerase. The nonnucleoside inhibitors of ZIKV polymerase here described could constitute promising lead compounds for the development of anti-ZIKV therapies and, eventually, broad-spectrum antiflavivirus drugs.
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17
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Narożna M, Rubiś B. Anti-SARS-CoV-2 Strategies and the Potential Role of miRNA in the Assessment of COVID-19 Morbidity, Recurrence, and Therapy. Int J Mol Sci 2021; 22:8663. [PMID: 34445368 PMCID: PMC8395427 DOI: 10.3390/ijms22168663] [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: 07/06/2021] [Revised: 08/07/2021] [Accepted: 08/08/2021] [Indexed: 02/06/2023] Open
Abstract
Recently, we have experienced a serious pandemic. Despite significant technological advances in molecular technologies, it is very challenging to slow down the infection spread. It appeared that due to globalization, SARS-CoV-2 spread easily and adapted to new environments or geographical or weather zones. Additionally, new variants are emerging that show different infection potential and clinical outcomes. On the other hand, we have some experience with other pandemics and some solutions in virus elimination that could be adapted. This is of high importance since, as the latest reports demonstrate, vaccine technology might not follow the new, mutated virus outbreaks. Thus, identification of novel strategies and markers or diagnostic methods is highly necessary. For this reason, we present some of the latest views on SARS-CoV-2/COVID-19 therapeutic strategies and raise a solution based on miRNA. We believe that in the face of the rapidly increasing global situation and based on analogical studies of other viruses, the possibility of using the biological potential of miRNA technology is very promising. It could be used as a promising diagnostic and prognostic factor, as well as a therapeutic target and tool.
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Affiliation(s)
- Maria Narożna
- Department of Pharmaceutical Biochemistry, Poznan University of Medical Sciences, 4 Święcickiego St., 60-781 Poznan, Poland;
| | - Błażej Rubiś
- Department of Clinical Chemistry and Molecular Diagnostics, Poznan University of Medical Sciences, 49 Przybyszewskiego St., 60-355 Poznan, Poland
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