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Hasan M, He Z, Jia M, Leung ACF, Natarajan K, Xu W, Yap S, Zhou F, Chen S, Su H, Zhu K, Su H. Dynamic expedition of leading mutations in SARS-CoV-2 spike glycoproteins. Comput Struct Biotechnol J 2024; 23:2407-2417. [PMID: 38882678 PMCID: PMC11176665 DOI: 10.1016/j.csbj.2024.05.037] [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: 02/10/2024] [Revised: 05/21/2024] [Accepted: 05/21/2024] [Indexed: 06/18/2024] Open
Abstract
The continuous evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which caused the recent pandemic, has generated countless new variants with varying fitness. Mutations of the spike glycoprotein play a particularly vital role in shaping its evolutionary trajectory, as they have the capability to alter its infectivity and antigenicity. We present a time-resolved statistical method, Dynamic Expedition of Leading Mutations (deLemus), to analyze the evolutionary dynamics of the SARS-CoV-2 spike glycoprotein. The proposed L -index of the deLemus method is effective in quantifying the mutation strength of each amino acid site and outlining evolutionarily significant sites, allowing the comprehensive characterization of the evolutionary mutation pattern of the spike glycoprotein.
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Affiliation(s)
- Muhammad Hasan
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Zhouyi He
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Mengqi Jia
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Alvin C F Leung
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | | | - Wentao Xu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Shanqi Yap
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Feng Zhou
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Shihong Chen
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Hailei Su
- Bengbu Hospital of Traditional Chinese Medicine, 4339 Huai-shang Road, Anhui 233080, China
| | - Kaicheng Zhu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Haibin Su
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
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Gerashchenko GV, Hryshchenko NV, Melnichuk NS, Marchyshak TV, Chernushyn SY, Demchyshina IV, Chernenko LM, Kuzin IV, Tkachuk ZY, Kashuba VI, Tukalo MA. Genetic characteristics of SARS-CoV-2 virus variants observed upon three waves of the COVID-19 pandemic in Ukraine between February 2021-January 2022. Heliyon 2024; 10:e25618. [PMID: 38380034 PMCID: PMC10877268 DOI: 10.1016/j.heliyon.2024.e25618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 12/06/2023] [Accepted: 01/31/2024] [Indexed: 02/22/2024] Open
Abstract
The aim of our study was to identify and characterize the SARS-CoV-2 variants in COVID-19 patients' samples collected from different regions of Ukraine to determine the relationship between SARS-CoV-2 phylogenetics and COVID-19 epidemiology. Patients and methods Samples were collected from COVID-19 patients during 2021 and the beginning of 2022 (401 patients). The SARS-CoV-2 genotyping was performed by parallel whole genome sequencing. Results The obtained SARS-CoV-2 genotypes showed that three waves of the COVID-19 pandemic in Ukraine were represented by three main variants of concern (VOC), named Alpha, Delta and Omicron; each VOC successfully replaced the earlier variant. The VOC Alpha strain was presented by one B.1.1.7 lineage, while VOC Delta showed a spectrum of 25 lineages that had different prevalence in 19 investigated regions of Ukraine. The VOC Omicron in the first half of the pandemic was represented by 13 lines that belonged to two different clades representing B.1 and B.2 Omicron strains. Each of the three epidemic waves (VOC Alpha, Delta, and Omicron) demonstrated their own course of disease, associated with genetic changes in the SARS-CoV-2 genome. The observed epidemiological features are associated with the genetic characteristics of the different VOCs, such as point mutations, deletions and insertions in the viral genome. A phylogenetic and transmission analysis showed the different mutation rates; there were multiple virus sources with a limited distribution between regions. Conclusions The evolution of SARS-CoV-2 virus and high levels of morbidity due to COVID-19 are still registered in the world. Observed multiple virus sourses with the limited distribution between regions indicates the high efficiency of the anti-epidemic policy pursued by the Ministry of Health of Ukraine to prevent the spread of the epidemic, despite the low level of vaccination of the Ukrainian population.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Zenovii Yu Tkachuk
- Institute of Molecular Biology and Genetics of NAS of Ukraine, Kyiv, Ukraine
| | - Vladimir I. Kashuba
- Institute of Molecular Biology and Genetics of NAS of Ukraine, Kyiv, Ukraine
| | - Mykhailo A. Tukalo
- Institute of Molecular Biology and Genetics of NAS of Ukraine, Kyiv, Ukraine
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Tanino Y, Nishioka K, Yamamoto C, Watanabe Y, Daidoji T, Kawamoto M, Uda S, Kirito S, Nakagawa Y, Kasamatsu Y, Kawahara Y, Sakai Y, Nobori S, Inaba T, Ota B, Fujita N, Hoshino A, Nukui Y, Nakaya T. Emergence of SARS-CoV-2 with Dual-Drug Resistant Mutations During a Long-Term Infection in a Kidney Transplant Recipient. Infect Drug Resist 2024; 17:531-541. [PMID: 38348230 PMCID: PMC10860503 DOI: 10.2147/idr.s438915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/22/2024] [Indexed: 02/15/2024] Open
Abstract
Introduction Various therapeutic agents are being developed for the treatment of coronavirus disease 2019 (COVID-19). Therefore, it is crucial to accumulate information regarding the features of drug-resistant viruses to these antiviral drugs. Methods We investigated the emergence of dual-drug resistance in a kidney transplant recipient who received sotrovimab (from day 0) and remdesivir (RDV) (from day 8 to day 17). We sequenced the whole viral genomes from nasopharyngeal swabs taken on day 0 and seven points after starting treatment (on days 12, 19, 23, 37, 43, 48, and 58). The genetic traits of the wild-type (day 0) and descendant viruses (after day 12) were determined by comparing the genomes with those of a Wuhan strain and the day 0 wild-type strain, respectively. Three viral isolates (from samples collected on days 0, 23, and 37) were investigated for their escape ability and growth kinetics in vitro. Results The sotrovimab resistant mutation (S:E340K) and the RDV resistant mutation RdRp:V792I (nt: G15814A) emerged within 12 days (day 12) and 11 days (day 19) after the treatment, respectively. The day 23 isolate harboring S:E340K/RdRp:V791I was resistant to both sotrovimab and RDV, showing 364- and 2.73-fold higher resistance respectively, compared with the wild-type. Moreover, compared with the day 23 isolate, the day 37 isolate accumulated multiple additional mutations and had a higher level of resistance to both drugs. Conclusion Drug-resistant variants with double mutations (S:E340K/RdRp:V791I) became dominant within 23 days after starting treatment, suggesting that even a combination therapy involving sotrovimab and RDV, dual-drug resistant viruses may emerge rapidly in immunocompromised patients. The dual-resistant variants had lower virus yields than those of the wild-type virus in vitro, suggesting that they paid a fitness cost.
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Affiliation(s)
- Yoko Tanino
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Department of Infection Control and Laboratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Keisuke Nishioka
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Chie Yamamoto
- Department of Infection Control and Laboratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yohei Watanabe
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, Japan
- JST, MIRAI, Tokyo, Japan
| | - Tomo Daidoji
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, Japan
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido, Japan
| | - Masataka Kawamoto
- Department of Forensics Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Sayaka Uda
- Department of Pulmonary Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Shoko Kirito
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yuta Nakagawa
- Department of Infection Control and Laboratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yu Kasamatsu
- Department of Infection Control and Laboratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yoshiyuki Kawahara
- Kyoto Prefectural Institute of Public Health and Environment, Kyoto, Japan
| | - Yuri Sakai
- Kyoto Prefectural Institute of Public Health and Environment, Kyoto, Japan
| | - Shuji Nobori
- Department of Organ Transplantation and General Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tohru Inaba
- Department of Infection Control and Laboratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Bon Ota
- Department of Emergency Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Naohisa Fujita
- Kyoto Prefectural Institute of Public Health and Environment, Kyoto, Japan
| | - Atsushi Hoshino
- Department of Cardiovascular Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yoko Nukui
- Department of Infection Control and Laboratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Takaaki Nakaya
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, Japan
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Russo E, Corrao S, Di Gaudio F, Alberti G, Caprnda M, Kubatka P, Kruzliak P, Miceli V, Conaldi PG, Borlongan CV, La Rocca G. Facing the Challenges in the COVID-19 Pandemic Era: From Standard Treatments to the Umbilical Cord-Derived Mesenchymal Stromal Cells as a New Therapeutic Strategy. Cells 2023; 12:1664. [PMID: 37371134 DOI: 10.3390/cells12121664] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/10/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which counts more than 650 million cases and more than 6.6 million of deaths worldwide, affects the respiratory system with typical symptoms such as fever, cough, sore throat, acute respiratory distress syndrome (ARDS), and fatigue. Other nonpulmonary manifestations are related with abnormal inflammatory response, the "cytokine storm", that could lead to a multiorgan disease and to death. Evolution of effective vaccines against SARS-CoV-2 provided multiple options to prevent the infection, but the treatment of the severe forms remains difficult to manage. The cytokine storm is usually counteracted with standard medical care and anti-inflammatory drugs, but researchers moved forward their studies on new strategies based on cell therapy approaches. The perinatal tissues, such as placental membranes, amniotic fluid, and umbilical cord derivatives, are enriched in mesenchymal stromal cells (MSCs) that exert a well-known anti-inflammatory role, immune response modulation, and tissue repair. In this review, we focused on umbilical-cord-derived MSCs (UC-MSCs) used in in vitro and in vivo studies in order to evaluate the weakening of the severe symptoms, and on recent clinical trials from different databases, supporting the favorable potential of UC-MSCs as therapeutic strategy.
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Affiliation(s)
- Eleonora Russo
- Section of Histology and Embryology, Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, 90127 Palermo, Italy
| | - Simona Corrao
- Research Department, IRCCS ISMETT (Istituto Mediterraneo per per i Trapianti e Terapie Ad Alta Specializzazione), 90127 Palermo, Italy
| | | | - Giusi Alberti
- Section of Histology and Embryology, Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, 90127 Palermo, Italy
| | - Martin Caprnda
- 1st Department of Internal Medicine, Faculty of Medicine, Comenius University, University Hospital Bratislava, 81499 Bratislava, Slovakia
| | - Peter Kubatka
- Department of Medical Biology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03649 Martin, Slovakia
| | - Peter Kruzliak
- Research and Development Services, Pradlacka 18, 61300 Brno, Czech Republic
| | - Vitale Miceli
- Research Department, IRCCS ISMETT (Istituto Mediterraneo per per i Trapianti e Terapie Ad Alta Specializzazione), 90127 Palermo, Italy
| | - Pier Giulio Conaldi
- Research Department, IRCCS ISMETT (Istituto Mediterraneo per per i Trapianti e Terapie Ad Alta Specializzazione), 90127 Palermo, Italy
| | - Cesario Venturina Borlongan
- Department of Neurosurgery and Brain Repair, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Giampiero La Rocca
- Section of Histology and Embryology, Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, 90127 Palermo, Italy
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Godbold GD, Hewitt FC, Kappell AD, Scholz MB, Agar SL, Treangen TJ, Ternus KL, Sandbrink JB, Koblentz GD. Improved understanding of biorisk for research involving microbial modification using annotated sequences of concern. Front Bioeng Biotechnol 2023; 11:1124100. [PMID: 37180048 PMCID: PMC10167326 DOI: 10.3389/fbioe.2023.1124100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/11/2023] [Indexed: 05/15/2023] Open
Abstract
Regulation of research on microbes that cause disease in humans has historically been focused on taxonomic lists of 'bad bugs'. However, given our increased knowledge of these pathogens through inexpensive genome sequencing, 5 decades of research in microbial pathogenesis, and the burgeoning capacity of synthetic biologists, the limitations of this approach are apparent. With heightened scientific and public attention focused on biosafety and biosecurity, and an ongoing review by US authorities of dual-use research oversight, this article proposes the incorporation of sequences of concern (SoCs) into the biorisk management regime governing genetic engineering of pathogens. SoCs enable pathogenesis in all microbes infecting hosts that are 'of concern' to human civilization. Here we review the functions of SoCs (FunSoCs) and discuss how they might bring clarity to potentially problematic research outcomes involving infectious agents. We believe that annotation of SoCs with FunSoCs has the potential to improve the likelihood that dual use research of concern is recognized by both scientists and regulators before it occurs.
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Affiliation(s)
| | | | | | | | - Stacy L. Agar
- Signature Science, LLC, Charlottesville, VA, United States
| | - Todd J. Treangen
- Department of Computer Science, Rice University, Houston, TX, United States
| | | | - Jonas B. Sandbrink
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Gregory D. Koblentz
- Schar School of Policy and Government, George Mason University, Arlington, VA, United States
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Orgera J, Kelley JJ, Bar O, Vaidhyanathan S, Grigoriev A. SARSNTdb database: Factors affecting SARS-CoV-2 sequence conservation. FRONTIERS IN VIROLOGY 2022. [DOI: 10.3389/fviro.2022.1028335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
SARSNTdb offers a curated, nucleotide-centric database for users of varying levels of SARS-CoV-2 knowledge. Its user-friendly interface enables querying coding regions and coordinate intervals to find out the various functional and selective constraints that act upon the corresponding nucleotides and amino acids. Users can easily obtain information about viral genes and proteins, functional domains, repeats, secondary structure formation, intragenomic interactions, and mutation prevalence. Currently, many databases are focused on the phylogeny and amino acid substitutions, mainly in the spike protein. We took a novel, more nucleotide-focused approach as RNA does more than just code for proteins and many insights can be gleaned from its study. For example, RNA-targeted drug therapies for SARS-CoV-2 are currently being developed and it is essential to understand the features only visible at that level. This database enables the user to identify regions that are more prone to forming secondary structures that drugs can target. SARSNTdb also provides illustrative mutation data from a subset of ~25,000 patient samples with a reliable read coverage across the whole genome (from different locations and time points in the pandemic. Finally, the database allows for comparing SARS-CoV-2 and SARS-CoV domains and sequences. SARSNTdb can serve the research community by being a curated repository for information that gives a jump start to analyze a mutation’s effect far beyond just determining synonymous/non-synonymous substitutions in protein sequences.
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Analysis of the mutation dynamics of SARS-CoV-2 genome in the samples from Georgia State of the United States. Gene 2022; 841:146774. [PMID: 35905853 PMCID: PMC9323210 DOI: 10.1016/j.gene.2022.146774] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/12/2022] [Accepted: 07/24/2022] [Indexed: 11/23/2022]
Abstract
BACKGROUND The COVID-19 is caused by a novel coronavirus SARS-CoV-2, which started from China. It spread rapidly throughout the world and was later declared a pandemic by the WHO. Over the course of time, SARS-CoV-2 has mutated for survival advantages, and this led to multiple variants. Multiple studies on mutations identification in SARS-CoV2 have been published covering extensive sample areas. The purpose of this study was to limit the sample area to the Georgia state in the U.S. and to analyze the genome sequences for mutation profiling across the genome and origin of variants. METHODS The genome sequences (n = 3,970) were obtained from the NCBI database as of June 12, 2021, with the filter of being complete sequenced genomes, homo-sapiens host, and only from Georgia State of the U.S. NextClade, an online tool was used for the analysis of the sequences using Wuhan-Hu-1/2019 as a reference genome. The algorithm was sequence alignment, translation, mutation calling, phylogenetic placement, clade assignment, and quality control (QC). Thirty-six samples with bad QC were removed from the mutational analysis. RESULTS A total 117,743 mutations in the nucleotides were identified (averaging 31.5 mutations per sample). The mutations A23403G, C3037T, C241T, and C14408T were detected in 98% of the samples. Also, a total of 75,517 mutations in the amino acid were identified (averaging 20.2 mutations per sample). The mutations D614G and P314L were identified in >97% samples whereas R203K, G204R, P681H, and N501Y were detected in >50% samples. Analysis also revealed 16 different clades with 20I (49.6%). Clades 20G (24.2%) and 20A (5.5%) being the most abundant, showed that SARS-CoV-2 in the Georgia State originated mainly from Southeast England, other parts of the U.S., and several countries in Western Europe. CONCLUSION Looking at the three most common variants in Georgia State of the U.S., we could determine the primary locations of transmission or origin for the virus, and our analyses indicates that majority of the cases originated from Southeast England (Clade 20I), the U.S. itself (Clade 20G), and from Western Europe (Clade 20C).
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Bhowmick S, AlFaris NA, Zaidan ALTamimi J, ALOthman ZA, Patil PC, Aldayel TS, Wabaidur SM, Saha A. Identification of bio-active food compounds as potential SARS-CoV-2 PLpro inhibitors-modulators via negative image-based screening and computational simulations. Comput Biol Med 2022; 145:105474. [PMID: 35395517 PMCID: PMC8973019 DOI: 10.1016/j.compbiomed.2022.105474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/10/2022] [Accepted: 03/29/2022] [Indexed: 12/16/2022]
Abstract
Despite significant studies on the COVID-19 pandemic, scientists around the world are still battling to find a definitive therapy against the ongoing severe global health crisis. In this study, advanced computational approaches have been employed to identify bioactive food constituents as potential SARS-CoV-2 PLpro inhibitors-modulators. As a validated antiviral drug target, PLpro has gained tremendous attention for therapeutics developments. Therefore, targeting the multifunctional SARS-CoV-2 PLpro protein, ∼1039 bioactive dietary compounds have been screened extensively through novel techniques like negative image-based (NIB) screening and molecular docking approaches. In particular, the three different models of NIB screening have been generated and used to re-score the dietary compounds based on the negative image which is created by reversing the shape and electrostatics features of PLpro protein's ligand-binding cavity. Further, 100 ns molecular dynamics simulation has been performed and MM-GBSA based binding free energies have been estimated for the final proposed four dietary compounds (PC000550, PC000361, PC000558, and PC000573) as potential inhibitors/modulators of SARS-CoV-2 PLpro protein. Employed computational study outcome also has been compared with respect to the earlier experimentally investigated compound GRL0617 against SARS-CoV-2 PLpro protein, which suggests much greater interaction potential in terms of binding affinity and other energetic contributions for the proposed dietary compounds. Hence, the present study suggests that proposed dietary compounds can be suitable chemical entities for modulating the activity of PLpro protein or can be further utilized for optimizing or screening of novel chemical surrogates, however also needs experimental evaluation for entry in clinical studies for better assessment.
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Affiliation(s)
- Shovonlal Bhowmick
- Department of Chemical Technology, University of Calcutta, 92 A.P.C. Road, Kolkata, India
| | - Nora Abdullah AlFaris
- Nutrition and Food Science, Department of Physical Sport Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia,Corresponding author
| | - Jozaa Zaidan ALTamimi
- Nutrition and Food Science, Department of Physical Sport Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Zeid A. ALOthman
- Chemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Pritee Chunarkar Patil
- Department of Bioinformatics, Rajiv Gandhi Institute of IT and Biotechnology, Bharati Vidyapeeth Deemed University, Pune-Satara Road, Pune, India
| | - Tahany Saleh Aldayel
- Nutrition and Food Science, Department of Physical Sport Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | | | - Achintya Saha
- Department of Chemical Technology, University of Calcutta, 92 A.P.C. Road, Kolkata, India,Corresponding author
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Bhowmick S, Saha A, AlFaris NA, ALTamimi JZ, ALOthman ZA, Aldayel TS, Wabaidur SM, Islam MA. Identification of potent food constituents as SARS-CoV-2 papain-like protease modulators through advanced pharmacoinformatics approaches. J Mol Graph Model 2021; 111:108113. [PMID: 34959151 PMCID: PMC8688376 DOI: 10.1016/j.jmgm.2021.108113] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/05/2021] [Accepted: 12/18/2021] [Indexed: 12/15/2022]
Abstract
The current ongoing pandemic of COVID-19 urges immediate treatment measures for controlling the highly contagious SARS-CoV-2 infections. The papain-like protease (PLpro), which is released from nsp3, is presently being evaluated as a significant anti-viral drug target for COVID-19 therapy development. Particularly, PLpro is implicated in the cleavage of viral polyproteins and antagonizes the host innate immune response through its deubiquitinating and deISGylating actions, thus making it a high-profile antiviral therapeutic target. The present study reports a few specific food compounds that can bind tightly with the SARS-CoV-2 PLpro protein identified through extensive computational screening techniques. Precisely, extensive advanced computational approaches combining target-based virtual screening, particularly employing sub-structure based similarity search, molecular docking, molecular dynamics (MD) simulations, and MM-GBSA based binding free energy calculations have been employed for the identification of the most promising food compounds with substantial functional implications as SARS-CoV-2 PLpro protein inhibitors/modulators. Observations from the present research investigation also provide a deeper understanding of the binding modes of the proposed four food compounds with SARS-CoV-2 PLpro protein. In docking analyses, all compounds have established essential inter-molecular interaction profiles at the active site cavity of the SARS-CoV-2 PLpro protein. Similarly, the long-range 100 ns conventional MD simulation studies also provided an in-depth understanding of probable interactions and dynamic behaviour of the SARS-CoV-2 PLpro protein-food compound complexes. Binding free energies of all molecular systems revealed a strong interaction affinity of food compounds towards the SARS-CoV-2 PLpro protein. Moreover, clear-cut comparative analyses against the known standard inhibitor also suggest that proposed food compounds may act as potential active chemical entities for modulating the action of the SARS-CoV-2 PLpro protein.
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Affiliation(s)
- Shovonlal Bhowmick
- Department of Chemical Technology, University of Calcutta, 92, A.P.C. Road, Kolkata, 700009, India
| | - Achintya Saha
- Department of Chemical Technology, University of Calcutta, 92, A.P.C. Road, Kolkata, 700009, India.
| | - Nora Abdullah AlFaris
- Nutrition and Food Science, Department of Physical Sport Science, Princess Nourah bint Abdulrahman University, P. O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Jozaa Zaidan ALTamimi
- Nutrition and Food Science, Department of Physical Sport Science, Princess Nourah bint Abdulrahman University, P. O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Zeid A ALOthman
- Department of Chemistry, P.O. Box 2455, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Tahany Saleh Aldayel
- Nutrition and Food Science, Department of Physical Sport Science, Princess Nourah bint Abdulrahman University, P. O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Saikh Mohammad Wabaidur
- Department of Chemistry, P.O. Box 2455, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Md Ataul Islam
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom.
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10
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Wang X, Sahu KK, Cerny J. Coagulopathy, endothelial dysfunction, thrombotic microangiopathy and complement activation: potential role of complement system inhibition in COVID-19. J Thromb Thrombolysis 2021; 51:657-662. [PMID: 33063256 PMCID: PMC7561230 DOI: 10.1007/s11239-020-02297-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/26/2020] [Indexed: 12/18/2022]
Abstract
Coronavirus disease-2019 (COVID-19) is a rapidly evolving health crisis caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 is a novel disease entity and we are in a learning phase with regards to the pathogenesis, disease manifestations, and therapeutics. In addition to the primary lung injury, many patients especially the ones with moderate to severe COVID-19 display evidence of endothelial damage, complement activation, which leads to a pro-coagulable state. While there are still missing links in our understanding, the interplay of endothelium, complement system activation, and immune response to the SARS-CoV-2 virus is a surprisingly major factor in COVID-19 pathogenesis. One could envision COVID-19 becoming a novel hematological syndrome. This review is to discuss the available literature with regards to the involvement of the complement system, and coagulation cascade and their interaction with endothelium.
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Affiliation(s)
- Xin Wang
- Department of Medicine, UMass Memorial Health Care, University of Massachusetts Medical School, Worcester, MA USA
| | - Kamal Kant Sahu
- Department of Internal Medicine, Saint Vincent Hospital, Worcester, MA 01608 USA
| | - Jan Cerny
- Department of Medicine - Hematology, and Oncology, UMass Memorial Medical Center, University of Massachusetts Medical School, Worcester, MA USA
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Huang SW, Wang SF. SARS-CoV-2 Entry Related Viral and Host Genetic Variations: Implications on COVID-19 Severity, Immune Escape, and Infectivity. Int J Mol Sci 2021; 22:3060. [PMID: 33802729 PMCID: PMC8002537 DOI: 10.3390/ijms22063060] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/15/2021] [Accepted: 03/15/2021] [Indexed: 02/07/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved to display particular patterns of genetic diversity in the genome across geographical regions. These variations in the virus and genetic variation in human populations can determine virus transmissibility and coronavirus disease 2019 (COVID-19) severity. Genetic variations and immune differences in human populations could be the driving forces in viral evolution. Recently emerged SARS-CoV-2 variants show several mutations at the receptor binding domain in the spike (S) glycoprotein and contribute to immune escape and enhanced binding with angiotensin 1-converting enzyme 2 (ACE2). Since ACE2 and transmembrane protease serine 2 (TMPRSS2) play important roles in SARS-CoV-2 entry into the cell, genetic variation in these host entry-related proteins may be a driving force for positive selection in the SARS-CoV-2 S glycoprotein. Dendritic or liver/lymph cell-specific intercellular adhesion molecule (ICAM)-3-grabbing non-integrin is also known to play vital roles in several pathogens. Genetic variations of these host proteins may affect the susceptibility to SARS-CoV-2. This review summarizes the latest research to describe the impacts of genetic variation in the viral S glycoprotein and critical host proteins and aims to provide better insights for understanding transmission and pathogenesis and more broadly for developing vaccine/antiviral drugs and precision medicine strategies, especially for high risk populations with genetic risk variants.
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Affiliation(s)
- Szu-Wei Huang
- Model Development Section, Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA;
| | - Sheng-Fan Wang
- Center for Tropical Medicine and Infectious Disease, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Clinical Microbiology Laboratory, Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
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Bayarri-Olmos R, Rosbjerg A, Johnsen LB, Helgstrand C, Bak-Thomsen T, Garred P, Skjoedt MO. The SARS-CoV-2 Y453F mink variant displays a pronounced increase in ACE-2 affinity but does not challenge antibody neutralization. J Biol Chem 2021; 296:100536. [PMID: 33716040 PMCID: PMC7948531 DOI: 10.1016/j.jbc.2021.100536] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/02/2021] [Accepted: 03/09/2021] [Indexed: 12/18/2022] Open
Abstract
Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 from humans to animals has been reported for many domesticated species, including farmed minks. The identification of novel spike gene mutations appearing in minks has raised major concerns about potential immune evasion and challenges for the global vaccine strategy. One genetic variant, known as "cluster five," arose among farmed minks in Denmark and resulted in a complete shutdown of the world's largest mink production. However, the functional properties of this new variant are not established. Here we present functional data on the cluster-five variant, which contains a mutation resulting in a Y453F residue change in the receptor-binding domain (RBD) of the spike protein. Using an ELISA-based angiotensin-converting enzyme-2/RBD inhibition assay, we show that the Y453F variant does not decrease established humoral immunity from previously infected individuals or affect the neutralizing antibody response in a vaccine mouse model based on the original Wuhan strain RBD or spike as antigens. However, biolayer interferometry analysis demonstrates that it binds the human angiotensin-converting enzyme-2 receptor with a 4-fold higher affinity than the original strain, suggesting an enhanced transmission capacity and a possible challenge for viral control. These results also indicate that the rise in the frequency of the cluster-five variant in mink farms might be a result of the fitness advantage conferred by the receptor adaptation rather than evading immune responses.
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MESH Headings
- Amino Acid Substitution
- Angiotensin-Converting Enzyme 2/chemistry
- Angiotensin-Converting Enzyme 2/genetics
- Angiotensin-Converting Enzyme 2/immunology
- Animals
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/metabolism
- Antibodies, Viral/chemistry
- Antibodies, Viral/metabolism
- COVID-19/epidemiology
- COVID-19/immunology
- COVID-19/transmission
- Convalescence
- Denmark/epidemiology
- Gene Expression
- HEK293 Cells
- Host-Pathogen Interactions/genetics
- Host-Pathogen Interactions/immunology
- Humans
- Immune Sera/chemistry
- Immunity, Innate
- Mink/virology
- Models, Molecular
- Mutation
- Pandemics
- Protein Binding
- Protein Structure, Secondary
- Recombinant Proteins/genetics
- Recombinant Proteins/immunology
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- SARS-CoV-2/pathogenicity
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Virus Internalization
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Affiliation(s)
- Rafael Bayarri-Olmos
- Laboratory of Molecular Medicine, Department of Clinical Immunology, University Hospital of Copenhagen, Copenhagen, Denmark
| | - Anne Rosbjerg
- Laboratory of Molecular Medicine, Department of Clinical Immunology, University Hospital of Copenhagen, Copenhagen, Denmark; Institute of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | - Peter Garred
- Laboratory of Molecular Medicine, Department of Clinical Immunology, University Hospital of Copenhagen, Copenhagen, Denmark
| | - Mikkel-Ole Skjoedt
- Laboratory of Molecular Medicine, Department of Clinical Immunology, University Hospital of Copenhagen, Copenhagen, Denmark; Institute of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.
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