1
|
Danda M, Klimešová A, Kušková K, Dostálková A, Pagáčová A, Prchal J, Kapisheva M, Ruml T, Rumlová M. Biochemical characterization of naturally occurring mutations in SARS-CoV-2 RNA-dependent RNA polymerase. Protein Sci 2024; 33:e5103. [PMID: 39145418 PMCID: PMC11325161 DOI: 10.1002/pro.5103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 06/06/2024] [Accepted: 06/21/2024] [Indexed: 08/16/2024]
Abstract
Since the emergence of SARS-CoV-2, mutations in all subunits of the RNA-dependent RNA polymerase (RdRp) of the virus have been repeatedly reported. Although RdRp represents a primary target for antiviral drugs, experimental studies exploring the phenotypic effect of these mutations have been limited. This study focuses on the phenotypic effects of substitutions in the three RdRp subunits: nsp7, nsp8, and nsp12, selected based on their occurrence rate and potential impact. We employed nano-differential scanning fluorimetry and microscale thermophoresis to examine the impact of these mutations on protein stability and RdRp complex assembly. We observed diverse impacts; notably, a single mutation in nsp8 significantly increased its stability as evidenced by a 13°C increase in melting temperature, whereas certain mutations in nsp7 and nsp8 reduced their binding affinity to nsp12 during RdRp complex formation. Using a fluorometric enzymatic assay, we assessed the overall effect on RNA polymerase activity. We found that most of the examined mutations altered the polymerase activity, often as a direct result of changes in stability or affinity to the other components of the RdRp complex. Intriguingly, a combination of nsp8 A21V and nsp12 P323L mutations resulted in a 50% increase in polymerase activity. To our knowledge, this is the first biochemical study to demonstrate the impact of amino acid mutations across all components constituting the RdRp complex in emerging SARS-CoV-2 subvariants.
Collapse
Affiliation(s)
- Matěj Danda
- Department of Biotechnology, University of Chemistry and Technology, Prague, Czech Republic
| | - Anna Klimešová
- Department of Biotechnology, University of Chemistry and Technology, Prague, Czech Republic
| | - Klára Kušková
- Department of Biotechnology, University of Chemistry and Technology, Prague, Czech Republic
| | - Alžběta Dostálková
- Department of Biotechnology, University of Chemistry and Technology, Prague, Czech Republic
| | - Aneta Pagáčová
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
| | - Jan Prchal
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
| | - Marina Kapisheva
- Department of Biotechnology, University of Chemistry and Technology, Prague, Czech Republic
| | - Tomáš Ruml
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
| | - Michaela Rumlová
- Department of Biotechnology, University of Chemistry and Technology, Prague, Czech Republic
| |
Collapse
|
2
|
Wang Y, Li L, Sutton AT, Tu Q, Zhao K, Wen E, Osborn J, Singh A, Gunsch MJ, Rustandi RR, Foley D, He Y. Development of a capillary zone electrophoresis method to monitor magnesium ion consumption during in vitro transcription for mRNA production. Anal Bioanal Chem 2024:10.1007/s00216-024-05242-8. [PMID: 38594392 DOI: 10.1007/s00216-024-05242-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 03/01/2024] [Accepted: 03/05/2024] [Indexed: 04/11/2024]
Abstract
Messenger RNA (mRNA) vaccines represent a landmark in vaccinology, especially with their success in COVID-19 vaccines, which have shown great promise for future vaccine development and disease prevention. As a platform technology, synthetic mRNA can be produced with high fidelity using in vitro transcription (IVT). Magnesium plays a vital role in the IVT process, facilitating the phosphodiester bond formation between adjacent nucleotides and ensuring accurate transcription to produce high-quality mRNA. The development of the IVT process has prompted key inquiries about in-process characterization of magnesium ion (Mg++) consumption, relating to the RNA polymerase (RNAP) activation, fed-batch mode production yield, and mRNA quality. Hence, it becomes crucial to monitor the free Mg++ concentration throughout the IVT process. However, no free Mg++ analysis method has been reported for complex IVT reactions. Here we report a robust capillary zone electrophoresis (CZE) method with indirect UV detection. The assay allows accurate quantitation of free Mg++ for the complex IVT reaction where it is essential to preserve IVT samples in their native-like state during analysis to avoid dissociation of bound Mg complexes. By applying this CZE method, the relationships between free Mg++ concentration, the mRNA yield, and dsRNA impurity level were investigated. Such mechanistic understanding facilitates informed decisions regarding the quantity and timing of feeding starting materials to increase the yield. Furthermore, this approach can serve as a platform method for analyzing the free Mg++ in complex sample matrices where preserving the native-like state of Mg++ binding is key for accurate quantitation.
Collapse
Affiliation(s)
- Ying Wang
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ, 07065, USA.
| | - Li Li
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ, 07065, USA.
| | - Adam T Sutton
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ, 07065, USA
| | - Qiang Tu
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ, 07065, USA
| | - Kaixi Zhao
- Process Research and Development, Merck & Co., Inc., Rahway, NJ, 07065, USA
| | - Emily Wen
- Process Research and Development, Merck & Co., Inc., Rahway, NJ, 07065, USA
| | - James Osborn
- Process Research and Development, Merck & Co., Inc., Rahway, NJ, 07065, USA
| | - Andrew Singh
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ, 07065, USA
| | - Matthew J Gunsch
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ, 07065, USA
| | | | - David Foley
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ, 07065, USA
| | - Yu He
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ, 07065, USA
| |
Collapse
|
3
|
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.
Collapse
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
| | | |
Collapse
|
4
|
In-depth analysis of the interactions of various aryl hydrocarbon receptor ligands from a computational perspective. J Mol Graph Model 2023; 118:108339. [PMID: 36183684 DOI: 10.1016/j.jmgm.2022.108339] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 09/01/2022] [Accepted: 09/17/2022] [Indexed: 11/21/2022]
Abstract
Aryl hydrocarbon receptor (AhR) is a ligand-dependent transcription factor that acts as a machinery that controls the expression of many genes, including cytochrome P450 CYP1A1, CYP1A2 and CYP1B1. It plays a principal role in numerous biological and toxicological functions, making it a promising target for developing therapeutic agents. Several novel small molecules targeting the AhR signaling pathway are currently under investigation as antitumor agents. Some have already advanced into clinical trials in patients with various tumors. Activation of AhR by diverse chemicals either endogenous or exogenous is initiated by the binding of these ligands to the PAS-B domain, which modulates AhR functions. There is, however, limited information about how various ligands interact with the PAS-B domain for activating or inhibiting the AhR. To better understand the mode of action of AhR agonists/antagonists. The current work proposes a combination of several computational tools to build dynamical models for the PAS-B domain bound to different ligands in mouse and human. Our findings reveal the essential roles of specific PAS-B residues (e.g., S365, V381& Q383), which mediate the AhR ligand-binding process. Our results also explain how these residues regulate the promiscuity of AhR in accommodating various chemicals in its binding PAS-B ligand-binding pocket.
Collapse
|
5
|
Wang B, Svetlov D, Bartikofsky D, Wobus CE, Artsimovitch I. Going Retro, Going Viral: Experiences and Lessons in Drug Discovery from COVID-19. Molecules 2022; 27:3815. [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/03/2022] [Accepted: 06/07/2022] [Indexed: 12/15/2022] Open
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.
Collapse
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;
| |
Collapse
|
6
|
Faisal S, Badshah SL, Kubra B, Sharaf M, Emwas AH, Jaremko M, Abdalla M. Computational Study of SARS-CoV-2 RNA Dependent RNA Polymerase Allosteric Site Inhibition. Molecules 2021; 27:223. [PMID: 35011458 PMCID: PMC8746673 DOI: 10.3390/molecules27010223] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 12/25/2021] [Accepted: 12/26/2021] [Indexed: 01/12/2023] Open
Abstract
The COVID-19 pandemic has caused millions of fatalities since 2019. Despite the availability of vaccines for this disease, new strains are causing rapid ailment and are a continuous threat to vaccine efficacy. Here, molecular docking and simulations identify strong inhibitors of the allosteric site of the SARS-CoV-2 virus RNA dependent RNA polymerase (RdRp). More than one hundred different flavonoids were docked with the SARS-CoV-2 RdRp allosteric site through computational screening. The three top hits were Naringoside, Myricetin and Aureusidin 4,6-diglucoside. Simulation analyses confirmed that they are in constant contact during the simulation time course and have strong association with the enzyme's allosteric site. Absorption, distribution, metabolism, excretion and toxicity (ADMET) data provided medicinal information of these top three hits. They had good human intestinal absorption (HIA) concentrations and were non-toxic. Due to high mutation rates in the active sites of the viral enzyme, these new allosteric site inhibitors offer opportunities to drug SARS-CoV-2 RdRp. These results provide new information for the design of novel allosteric inhibitors against SARS-CoV-2 RdRp.
Collapse
Affiliation(s)
- Shah Faisal
- Department of Chemistry, Islamia College University Peshawar, Peshawar 25120, Pakistan; (S.F.); (B.K.)
| | - Syed Lal Badshah
- Department of Chemistry, Islamia College University Peshawar, Peshawar 25120, Pakistan; (S.F.); (B.K.)
| | - Bibi Kubra
- Department of Chemistry, Islamia College University Peshawar, Peshawar 25120, Pakistan; (S.F.); (B.K.)
| | - Mohamed Sharaf
- Department of Biochemistry and Molecular Biology, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China;
- Department of Biochemistry, Faculty of Agriculture, AL-Azhar University, Nasr City, Cairo 11751, Egypt
| | - Abdul-Hamid Emwas
- Core Labs, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia;
| | - Mariusz Jaremko
- Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Mohnad Abdalla
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 Cultural West Road, Jinan 250012, China
| |
Collapse
|