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Algar‐Lizana S, Bonache MÁ, González‐Muñiz R. SARS-CoV-2 main protease inhibitors: What is moving in the field of peptides and peptidomimetics? J Pept Sci 2022; 29:e3467. [PMID: 36479966 PMCID: PMC9877768 DOI: 10.1002/psc.3467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/04/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022]
Abstract
The COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is still affecting people worldwide. Despite the good degree of immunological protection achieved through vaccination, there are still severe cases that require effective antivirals. In this sense, two specific pharmaceutical preparations have been marketed already, the RdRp polymerase inhibitor molnupiravir and the main viral protease inhibitor nirmatrelvir (commercialized as Paxlovid, a combination with ritonavir). Nirmatrelvir is a peptidomimetic acting as orally available, covalent, and reversible inhibitor of SARS-CoV-2 main viral protease. The success of this compound has revitalized the search for new peptide and peptidomimetic protease inhibitors. This highlight collects some selected examples among those recently published in the field of SARS-CoV-2.
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Tao J, Wang W, Weissman JL, Zhang Y, Chen S, Zhu Y, Zhang C, Hou S. Size-fractionated microbiome observed during an eight-month long sampling in Jiaozhou Bay and the Yellow Sea. Sci Data 2022; 9:605. [PMID: 36207335 PMCID: PMC9546851 DOI: 10.1038/s41597-022-01734-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/28/2022] [Indexed: 11/09/2022] Open
Abstract
Jiaozhou Bay is a typical semi-enclosed bay with a temperate climate imposed by strong anthropogenic influence. To investigate microbial biodiversity and ecosystem services in this highly dynamic coastal environment, we conducted a monthly microbial survey spanning eight months at two stations in the bay and the open Yellow Sea starting in April 2015. This report provides a comprehensive inventory of amplicon sequences and environmental microbial genomes from this survey. In total, 2,543 amplicon sequence variants were obtained with monthly relative abundance profiles in three size fractions (>2.7 μm, 2.7-0.7 μm, and 0.7-0.22 μm). Shotgun metagenomes yielded 915 high-quality metagenome-assembled genomes with ≥50% completeness and ≤5% contamination. These environmental genomes comprise 27 bacterial and 5 archaeal phyla. We expect this comprehensive dataset will facilitate a better understanding of coastal microbial ecology.
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Affiliation(s)
- Jianchang Tao
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518000, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.,Shanghai Sheshan National Geophysical Observatory, Shanghai Earthquake Agency, Shanghai, 200062, China
| | - Wenxiu Wang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518000, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.,Shanghai Sheshan National Geophysical Observatory, Shanghai Earthquake Agency, Shanghai, 200062, China
| | - J L Weissman
- Department of Biological Sciences-Marine and Environmental Biology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Yongyu Zhang
- Research Center for Marine Biology and Carbon Sequestration, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266000, China
| | - Songze Chen
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518000, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.,Shanghai Sheshan National Geophysical Observatory, Shanghai Earthquake Agency, Shanghai, 200062, China
| | - Yuanqing Zhu
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518000, China.,Shanghai Sheshan National Geophysical Observatory, Shanghai Earthquake Agency, Shanghai, 200062, China
| | - Chuanlun Zhang
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518000, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.,Shanghai Sheshan National Geophysical Observatory, Shanghai Earthquake Agency, Shanghai, 200062, China
| | - Shengwei Hou
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518000, China. .,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China. .,State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361102, China.
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Yang KS, Leeuwon SZ, Xu S, Liu WR. Evolutionary and Structural Insights about Potential SARS-CoV-2 Evasion of Nirmatrelvir. J Med Chem 2022; 65:8686-8698. [PMID: 35731933 PMCID: PMC9236210 DOI: 10.1021/acs.jmedchem.2c00404] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Indexed: 12/15/2022]
Abstract
The U.S. FDA approval of PAXLOVID, a combination therapy of nirmatrelvir and ritonavir has significantly boosted our morale in fighting the COVID-19 pandemic. Nirmatrelvir is an inhibitor of the main protease (MPro) of SARS-CoV-2. Since many SARS-CoV-2 variants that resist vaccines and antibodies have emerged, a concern of acquired viral resistance to nirmatrelvir naturally arises. Here, possible mutations in MPro to confer viral evasion of nirmatrelvir are analyzed and discussed from both evolutionary and structural standpoints. The analysis indicates that those mutations will likely reside in the whole aa45-51 helical region and residues including M165, L167, P168, R188, and Q189. Relevant mutations have also been observed in existing SARS-CoV-2 samples. Implications of this analysis to the fight against future drug-resistant viral variants and the development of broad-spectrum antivirals are discussed as well.
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Affiliation(s)
- Kai S. Yang
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 7743, USA
| | - Sunshine Z. Leeuwon
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 7743, USA
| | - Shiqing Xu
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 7743, USA
| | - Wenshe Ray Liu
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 7743, USA
- Institute of Biosciences and Technology and Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX 77030, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University, College Station, TX 77843, USA
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Lack of age-related respiratory changes in Daphnia. Biogerontology 2022; 23:85-97. [PMID: 34989913 DOI: 10.1007/s10522-021-09947-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 12/23/2021] [Indexed: 12/29/2022]
Abstract
Aging is a multifaceted process of accumulation of damage and waste in cells and tissues; age-related changes in mitochondria and in respiratory metabolism have the focus of aging research for decades. Studies of aging in nematodes, flies and mammals all revealed age-related decline in respiratory functions, with somewhat controversial causative role. Here we investigated age-related changes in respiration rates, lactate/pyruvate ratio, a commonly used proxy for NADH/NAD+ balance, and mitochondrial membrane potential in 4 genotypes of an emerging model organism for aging research, a cyclic parthenogen Daphnia magna. We show that total body weight-adjusted respiration rate decreased with age, although this decrease was small in magnitude and could be fully accounted for by the decrease in locomotion and feeding activity. Neither total respiration normalized by protein content, nor basal respiration rate measured in anaesthetized animals decreased with age. Lactate/pyruvate ratio and mitochondrial membrane potential (∆Ψmt) showed no age-related changes, with possible exceptions of ∆Ψmt in epipodites (excretory and gas exchange organs) in which ∆Ψmt decreased with age and in the optical lobe of the brain, in which ∆Ψmt showed a maximum at middle age. We conclude that actuarial senescence in Daphnia is not caused by a decline in respiratory metabolism and discuss possible mechanisms of maintaining mitochondrial healthspan throughout the lifespan.
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