1
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Nam KH. Structural and bioinformatics analysis of single-domain substrate-binding protein from Rhodothermus marinus. Biochem Biophys Rep 2024; 37:101611. [PMID: 38269326 PMCID: PMC10805632 DOI: 10.1016/j.bbrep.2023.101611] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 01/26/2024] Open
Abstract
Substrate-binding proteins (SBPs) are key elements in determining the substrate specificity and high affinity of the ATP-binding cassette uptake system. A typical SBP has two domains that recognize substrates and are responsible for the specific substrate delivery. Conversely, in GenBank, genes for SBPs constituting a single domain SBP are often found in vicinity of a methyl-accepting chemotaxis protein gene. However, the molecular function and mechanism of single domain SBPs are not fully elucidated. To understand their molecular functions, we performed a crystallographic study of single domain SBP from Rhodothermus marinus (RmSBP). RmSBP crystals were soaked in solution containing NaBr or HgCl2 and their structures determined at 1.75 and 2.3 Å resolution, respectively. RmSBP soaked in NaBr exhibited disorder of the α2-helix, β5-to β6-strand loop, and C-terminus region, showing the structural dynamic region of RmSBP. RmSBP soaked in HgCl2 showed that Hg2+ bound to Cys145 located between the α5-and α6-helices. The structural properties of RmSBP were compared with those of single domain SBP homologs. These results will contribute to continued identification of the molecular function and mechanism of single domain SBPs.
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Affiliation(s)
- Ki Hyun Nam
- College of General Education, Kookmin University, Seoul, 20707, Republic of Korea
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2
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Gao K, Wang R, Chen J, Cheng L, Frishcosy J, Huzumi Y, Qiu Y, Schluckbier T, Wei X, Wei GW. Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. Chem Rev 2022; 122:11287-11368. [PMID: 35594413 PMCID: PMC9159519 DOI: 10.1021/acs.chemrev.1c00965] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein-protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.
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Affiliation(s)
- Kaifu Gao
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Rui Wang
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiahui Chen
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Limei Cheng
- Clinical
Pharmacology and Pharmacometrics, Bristol
Myers Squibb, Princeton, New Jersey 08536, United States
| | - Jaclyn Frishcosy
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuta Huzumi
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuchi Qiu
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tom Schluckbier
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Xiaoqi Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Guo-Wei Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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3
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Velu P, Rathinavel T, Kumarasamy S, Iqbal MN, Noor H, Ikram A, Rajamanickam K, Shanmugam G. Whole genome analysis and homology modeling of SARS-CoV-2 Indian isolate reveals potent FDA approved drug choice for treating COVID-19. J Biomol Struct Dyn 2022; 41:2772-2788. [PMID: 35139758 DOI: 10.1080/07391102.2022.2038272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Coronaviruses have caused enough devastation in the last two decades. These viruses have some rare features while sharing some common features. Novel coronavirus disease (nCoV-19) caused an outbreak with a fatality rate of 5%. It emerged from China and spread into many countries. The present research focused on genome analysis of Indian nCoV-19 Isolate and its translational product subjected to homology modeling and its subsequent molecular simulations to find out potent FDA approved drug for treating COVID-19. Phylogenetic analysis of SARS-CoV-2 Indian isolate shows close resemblance with 17 countries SARS-CoV-2 isolates. Homology modeling of four non-structural proteins translational product of Indian SARS-CoV-2 genome shows high similarity and allowed regions with the existing PDB deposited SARS-CoV-2 target proteins. Finally, these four generated proteins show more affinity with cobicistat, remdesivir and indinavir out of 14 screened FDA approved drugs in molecular docking which is further proven by molecular dynamics simulation and MMGBSA analysis of target ligand complex with best simulation trajectories. Overall our present research findings is that three proposed drugs namely cobicistat, remdesivir and indinavir showed higher interaction with the model SARS-CoV-2 viral target proteins from the Indian nCoV-19 isolate. These compounds could be used as a starting point for the creation of active antiviral drugs to combat the deadly COVID-19 virus during global pandemic and its subsequent viral infection waves across the globe.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Periyannan Velu
- Department of Biotechnology and Biochemistry, Annamalai University, Chidambaram, Tamil Nadu, India
| | | | - Suresh Kumarasamy
- PG and Research Centre in Biotechnology, MGR College, Adhiyamaan Educational Research Institute, Hosur, Tamil Nadu, India
| | - Muhammad Nasir Iqbal
- Department of Biosciences, COMSATS University, Islamabad Campus, Islamabad, Pakistan
| | - Hasnat Noor
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Ayesha Ikram
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Karthika Rajamanickam
- Department of Biotechnology, Vivekanandha College of Arts and Sciences for Women (Autonomous), Namakkal, Tamil Nadu, India
| | - Gnanendra Shanmugam
- Department of Biotechnology, Mahendra Arts and Science College, Namakkal, Tamil Nadu, India
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4
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In Silico Modeling as a Perspective in Developing Potential Vaccine Candidates and Therapeutics for COVID-19. COATINGS 2021. [DOI: 10.3390/coatings11111273] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The potential of computational models to identify new therapeutics and repurpose existing drugs has gained significance in recent times. The current ‘COVID-19’ pandemic caused by the new SARS CoV2 virus has affected over 200 million people and caused over 4 million deaths. The enormity and the consequences of this viral infection have fueled the research community to identify drugs or vaccines through a relatively expeditious process. The availability of high-throughput datasets has cultivated new strategies for drug development and can provide the foundation towards effective therapy options. Molecular modeling methods using structure-based or computer-aided virtual screening can potentially be employed as research guides to identify novel antiviral agents. This review focuses on in-silico modeling of the potential therapeutic candidates against SARS CoVs, in addition to strategies for vaccine design. Here, we particularly focus on the recently published SARS CoV main protease (Mpro) active site, the RNA-dependent RNA polymerase (RdRp) of SARS CoV2, and the spike S-protein as potential targets for vaccine development. This review can offer future perspectives for further research and the development of COVID-19 therapies via the design of new drug candidates and multi-epitopic vaccines and through the repurposing of either approved drugs or drugs under clinical trial.
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5
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COVID-19 and Cancer Therapy: Interrelationships and Management of Cancer Cases in the Era of COVID-19. J CHEM-NY 2021. [DOI: 10.1155/2021/9923518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The COVID-19 global epidemic poses this generation’s biggest worldwide public health challenge probably since the 1918 influenza epidemic. Recent reports on two new variants have triggered a dramatic upsurge in research to understand the pandemic, primarily focussing on the virology, triggers, clinical characteristics, and diagnostic tests including the prevention and management of the novel coronavirus. Whilst such studies are important in managing the present medical emergency, there is a need for further work to include interdependencies between the epidemic and other illnesses. This will help in developing effective approaches to treat and manage associated diseases in both the short and the long term. In this regard, people living with cancer are a subgroup that is highly vulnerable to respiratory infections and acute pneumonitis similar to the one caused by the COVID-19 virus. This is because the state of their immunity is compromised due to malignancy and the adverse effects of anticancer treatments. With annual cancer projections rising globally and an estimated 70 percent of all cancer-related deaths occurring in low- and middle-income countries, the patient population with impaired immune systems that could be adversely impacted by COVID-19 is only anticipated to rise. In this review, we delve into the challenges and health risks facing cancer patients and cancer treatment in the COVID-19 context, with suggestions into viable measures which can be taken to minimize exposure to the risk of contracting COVID-19 for this vulnerable subgroup. New mutations and the prospects offered by vaccines development and how they relate to this class of patients are also discussed.
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6
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Degueldre C. Single virus inductively coupled plasma mass spectroscopy analysis: A comprehensive study. Talanta 2021; 228:122211. [PMID: 33773712 DOI: 10.1016/j.talanta.2021.122211] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 11/18/2022]
Abstract
The characterisation of individual nanoparticles by single particle ICP-MS (SP-ICP-MS) has paved the way for the analysis of smallest biological systems. This study suggests to adapting this method for single viruses (SV) identification and counting. With high resolution multi-channel sector field (MC SF) ICP-MS records in SV detection mode, the counting of master and key ions can allow analysis and identification of single viruses. The counting of 2-500 virial units can be performed in 20 s. Analyses are proposed to be carried out in Ar torch for master ions: 12C+, 13C+, 14N+, 15N+, and key ions 31P+, 32S+, 33S+ and 34S+. All interferences are discussed in detail. The use of high resolution SF ICP-MS is recommended while options with anaerobic/aerobic atmospheres are explored to upgrade the analysis when using quadrupole ICP-MS. Application for two virus types (SARS-COV2 and bacteriophage T5) is investigated using time scan and fixed mass analysis for the selected virus ions allowing characterisation of the species using the N/C, P/C and S/C molar ratio's and quantification of their number concentration.
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Affiliation(s)
- Claude Degueldre
- Engineering Department, Lancaster University, Lancaster, LA1 4YW, UK.
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7
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Sakr MM, Elsayed NS, El-Housseiny GS. Latest updates on SARS-CoV-2 genomic characterization, drug, and vaccine development; a comprehensive bioinformatics review. Microb Pathog 2021; 154:104809. [PMID: 33647446 PMCID: PMC7910145 DOI: 10.1016/j.micpath.2021.104809] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/18/2021] [Accepted: 02/14/2021] [Indexed: 02/07/2023]
Abstract
Amid the COVID-19 outbreak, several bioinformatic analyses have been conducted on SARS-CoV-2 virus genome. Numerous studies rushed to fill the gap about this novel virus. Comparison with other related sequences, structural predictions of the produced proteins, determination of variations in amino acid residues and depiction of possible drug and vaccine targets have been the focus of scientific research from the beginning of this year. In addition to discussing the viral taxonomy, clinical features, life cycle, and genome organization, this review will focus on the recent updates in genome and viral proteins characterization and potential therapeutic and vaccine candidates developed so far. Comparative studies with related genomes and proteins provide understanding for the viral molecular mechanisms and suggest targets for therapeutics and vaccinology trials to stop the escalation of this new virus. This pandemic, with its resulting social and economic afflictions, will definitely have significant marks on our lives in the following years.
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Affiliation(s)
- Masarra M Sakr
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Organization of African Unity St., 11566, Abbassia, Cairo, Egypt
| | - Noha S Elsayed
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Organization of African Unity St., 11566, Abbassia, Cairo, Egypt.
| | - Ghadir S El-Housseiny
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Organization of African Unity St., 11566, Abbassia, Cairo, Egypt
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8
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Structural Flexibility of Peripheral Loops and Extended C-terminal Domain of Short Length Substrate Binding Protein from Rhodothermus marinus. Protein J 2021; 40:184-191. [PMID: 33651244 PMCID: PMC7923407 DOI: 10.1007/s10930-021-09970-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2021] [Indexed: 11/15/2022]
Abstract
Substrate binding proteins (SBPs) bind to specific ligands in the periplasmic regions of cells and then bind to membrane proteins to participate in transport or signal transduction. Typically, SBPs consist of two α/β domains and recognize the substrate by a flexible hinge region between the two domains. Conversely, the short-length SBPs are often observed in protein databases, which are located around methyl-accepting chemotaxis protein genes. We previously determined the crystal structure of Rhodothermus marinus SBP (named as RmSBP), consisting of a single α/β domain; however, the substrate recognition mechanism is still unclear. To better understand the functions of short length RmSBP, we performed a comprehensive study, involving comparative structure analysis, computational substrate docking, and X-ray crystallographic data. RmSBP shares a high level of similarity in the α/β domain region with other SBPs, but it has a distinct topology in the C-terminal domain. The substrate binding model suggested that conformational changes in the peripheral region of RmSBP was required to recognize the substrate. We determined the crystal structures of RmSBP at pH 5.5, 6.0, and 7.5. RmSBP showed structural flexibility in the β1–α2 loop, β5–β6 loop, and extended C-terminal domains, based on the electron density map and temperature B-factor analysis. These results provide information that will further our understanding on the functions of the short length SBP.
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9
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Kumar A, Prasoon P, Kumari C, Pareek V, Faiq MA, Narayan RK, Kulandhasamy M, Kant K. SARS-CoV-2-specific virulence factors in COVID-19. J Med Virol 2021; 93:1343-1350. [PMID: 33085084 DOI: 10.1002/jmv.26615] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/14/2020] [Accepted: 10/19/2020] [Indexed: 12/25/2022]
Abstract
The paucity of knowledge about severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific virulence factors has greatly hampered the therapeutic management of patients with coronavirus disease 2019 (COVID-19). Recently, a cluster of studies appeared, which presented empirical evidence for SARS-CoV-2-specific virulence factors that can explain key elements of COVID-19 pathology. These studies unravel multiple structural and nonstructural specifics of SARS-CoV-2, such as a unique FURIN cleavage site, papain-like protease (SCoV2-PLpro), ORF3b and nonstructural proteins, and dynamic conformational changes in the structure of spike protein during host cell fusion, which give it an edge in infectivity and virulence over previous coronaviruses causing pandemics. Investigators provided robust evidence that SARS-CoV-2-specific virulence factors may have an impact on viral infectivity and transmissibility and disease severity as well as the development of immunity against the infection, including response to the vaccines. In this article, we are presenting a summarized account of the newly reported studies.
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Affiliation(s)
- Ashutosh Kumar
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India
- Department of Anatomy, All India Institute of Medical Sciences (AIIMS), Patna, India
| | - Pranav Prasoon
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India
- Pittsburgh Center for Pain Research, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Chiman Kumari
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India
- Department of Anatomy, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Vikas Pareek
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India
- National Brain Research Center, Manesar, Haryana, India
| | - Muneeb A Faiq
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India
- New York University (NYU) Langone Health Center, NYU Robert I Grossman School of Medicine, New York, New York, USA
| | - Ravi K Narayan
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India
- Department of Anatomy, All India Institute of Medical Sciences (AIIMS), Patna, India
| | - Maheswari Kulandhasamy
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India
- Department of Biochemistry, Maulana Azad Medical College (MAMC), New Delhi, India
| | - Kamla Kant
- Etiologically Elusive Disorders Research Network (EEDRN), New Delhi, India
- Department of Microbiology, All India Institute of Medical Sciences (AIIMS), Bathinda, India
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10
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Genetic Diversity of SARS-CoV2 and Environmental Settings: Possible Association with Neurological Disorders. Mol Neurobiol 2021; 58:1917-1931. [PMID: 33404977 PMCID: PMC7786338 DOI: 10.1007/s12035-020-02239-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 11/25/2020] [Indexed: 01/22/2023]
Abstract
The new coronavirus (CoV), called novel coronavirus disease 2019 (COVID-19), belongs to the Coronaviridae family which was originated from the sea market in Wuhan city in China, at the end of the year 2019. COVID-19 and severe acute respiratory syndrome (SARS) are belonging to the same family (Coronaviridae). The current outbreak of COVID-19 creates public concern and threats all over the world and now it spreads out to more than 250 countries and territories. The researchers and scientists from all over the world are trying to find out the therapeutic strategies to abate the morbidity and mortality rate of the COVID-19 pandemic. The replication, spreading, and severity of SARS-CoV2 depend on environmental settings. Noteworthy, meteorological parameters are considered as crucial factors that affect respiratory infectious disorders, although the controversial effect of the meteorological parameter is exposed against COVID-19. Besides, COVID-19 accelerates the pathogenesis of the neurological disorders. However, the pathogenic mechanisms between COVID-19 and neurological disorders are still unclear. Hence, this review is focused on the genomics and ecology of SARS-CoV2 and elucidated the effects of climatic factors on the progression of COVID-19. This review also critically finds out the vulnerability between COVID-19 and neurological disorders based on the latest research data.
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11
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Shin D, Mukherjee R, Grewe D, Bojkova D, Baek K, Bhattacharya A, Schulz L, Widera M, Mehdipour AR, Tascher G, Geurink PP, Wilhelm A, van der Heden van Noort GJ, Ovaa H, Müller S, Knobeloch KP, Rajalingam K, Schulman BA, Cinatl J, Hummer G, Ciesek S, Dikic I. Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity. Nature 2020; 587:657-662. [PMID: 32726803 PMCID: PMC7116779 DOI: 10.1038/s41586-020-2601-5] [Citation(s) in RCA: 694] [Impact Index Per Article: 173.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/23/2020] [Indexed: 01/01/2023]
Abstract
The papain-like protease PLpro is an essential coronavirus enzyme that is required for processing viral polyproteins to generate a functional replicase complex and enable viral spread1,2. PLpro is also implicated in cleaving proteinaceous post-translational modifications on host proteins as an evasion mechanism against host antiviral immune responses3-5. Here we perform biochemical, structural and functional characterization of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) PLpro (SCoV2-PLpro) and outline differences with SARS-CoV PLpro (SCoV-PLpro) in regulation of host interferon and NF-κB pathways. SCoV2-PLpro and SCoV-PLpro share 83% sequence identity but exhibit different host substrate preferences; SCoV2-PLpro preferentially cleaves the ubiquitin-like interferon-stimulated gene 15 protein (ISG15), whereas SCoV-PLpro predominantly targets ubiquitin chains. The crystal structure of SCoV2-PLpro in complex with ISG15 reveals distinctive interactions with the amino-terminal ubiquitin-like domain of ISG15, highlighting the high affinity and specificity of these interactions. Furthermore, upon infection, SCoV2-PLpro contributes to the cleavage of ISG15 from interferon responsive factor 3 (IRF3) and attenuates type I interferon responses. Notably, inhibition of SCoV2-PLpro with GRL-0617 impairs the virus-induced cytopathogenic effect, maintains the antiviral interferon pathway and reduces viral replication in infected cells. These results highlight a potential dual therapeutic strategy in which targeting of SCoV2-PLpro can suppress SARS-CoV-2 infection and promote antiviral immunity.
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Affiliation(s)
- Donghyuk Shin
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany
- Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Rukmini Mukherjee
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany
| | - Diana Grewe
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany
| | - Denisa Bojkova
- Institute of Medical Virology, University Hospital Frankfurt, Frankfurt, Germany
| | - Kheewoong Baek
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Anshu Bhattacharya
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany
| | - Laura Schulz
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Marek Widera
- Institute of Medical Virology, University Hospital Frankfurt, Frankfurt, Germany
| | - Ahmad Reza Mehdipour
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Georg Tascher
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Germany
| | - Paul P Geurink
- Oncode Institute and Department of Chemical Immunology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Alexander Wilhelm
- Institute of Medical Virology, University Hospital Frankfurt, Frankfurt, Germany
- Institute of Pharmaceutical Biology, Goethe-University, Frankfurt, Germany
| | | | - Huib Ovaa
- Oncode Institute and Department of Chemical Immunology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Stefan Müller
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Germany
| | - Klaus-Peter Knobeloch
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Krishnaraj Rajalingam
- Cell Biology Unit, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jindrich Cinatl
- Institute of Medical Virology, University Hospital Frankfurt, Frankfurt, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt, Germany
- Institute of Biophysics, Goethe University Frankfurt, Frankfurt, Germany
| | - Sandra Ciesek
- Institute of Medical Virology, University Hospital Frankfurt, Frankfurt, Germany
- Institute of Pharmaceutical Biology, Goethe-University, Frankfurt, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch Translational Medicine and Pharmacology, Frankfurt, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Germany.
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany.
- Max Planck Institute of Biophysics, Frankfurt, Germany.
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch Translational Medicine and Pharmacology, Frankfurt, Germany.
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12
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Villas-Boas GR, Rescia VC, Paes MM, Lavorato SN, de Magalhães-Filho MF, Cunha MS, Simões RDC, de Lacerda RB, de Freitas-Júnior RS, Ramos BHDS, Mapeli AM, Henriques MDST, de Freitas WR, Lopes LAF, Oliveira LGR, da Silva JG, Silva-Filho SE, da Silveira APS, Leão KV, Matos MMDS, Fernandes JS, Cuman RKN, Silva-Comar FMDS, Comar JF, Brasileiro LDA, dos Santos JN, Oesterreich SA. The New Coronavirus (SARS-CoV-2): A Comprehensive Review on Immunity and the Application of Bioinformatics and Molecular Modeling to the Discovery of Potential Anti-SARS-CoV-2 Agents. Molecules 2020; 25:E4086. [PMID: 32906733 PMCID: PMC7571161 DOI: 10.3390/molecules25184086] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 02/07/2023] Open
Abstract
On March 11, 2020, the World Health Organization (WHO) officially declared the outbreak caused by the new coronavirus (SARS-CoV-2) a pandemic. The rapid spread of the disease surprised the scientific and medical community. Based on the latest reports, news, and scientific articles published, there is no doubt that the coronavirus has overloaded health systems globally. Practical actions against the recent emergence and rapid expansion of the SARS-CoV-2 require the development and use of tools for discovering new molecular anti-SARS-CoV-2 targets. Thus, this review presents bioinformatics and molecular modeling strategies that aim to assist in the discovery of potential anti-SARS-CoV-2 agents. Besides, we reviewed the relationship between SARS-CoV-2 and innate immunity, since understanding the structures involved in this infection can contribute to the development of new therapeutic targets. Bioinformatics is a technology that assists researchers in coping with diseases by investigating genetic sequencing and seeking structural models of potential molecular targets present in SARS-CoV2. The details provided in this review provide future points of consideration in the field of virology and medical sciences that will contribute to clarifying potential therapeutic targets for anti-SARS-CoV-2 and for understanding the molecular mechanisms responsible for the pathogenesis and virulence of SARS-CoV-2.
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Affiliation(s)
- Gustavo R. Villas-Boas
- Research Group on Development of Pharmaceutical Products (P&DProFar), Center for Biological and Health Sciences, Federal University of Western Bahia, Rua Bertioga, 892, Morada Nobre II, Barreiras CEP 47810-059, BA, Brazil; (V.C.R.); (M.M.P.); (S.N.L.); (M.F.d.M.-F.); (M.S.C.); (R.d.C.S.)
| | - Vanessa C. Rescia
- Research Group on Development of Pharmaceutical Products (P&DProFar), Center for Biological and Health Sciences, Federal University of Western Bahia, Rua Bertioga, 892, Morada Nobre II, Barreiras CEP 47810-059, BA, Brazil; (V.C.R.); (M.M.P.); (S.N.L.); (M.F.d.M.-F.); (M.S.C.); (R.d.C.S.)
| | - Marina M. Paes
- Research Group on Development of Pharmaceutical Products (P&DProFar), Center for Biological and Health Sciences, Federal University of Western Bahia, Rua Bertioga, 892, Morada Nobre II, Barreiras CEP 47810-059, BA, Brazil; (V.C.R.); (M.M.P.); (S.N.L.); (M.F.d.M.-F.); (M.S.C.); (R.d.C.S.)
| | - Stefânia N. Lavorato
- Research Group on Development of Pharmaceutical Products (P&DProFar), Center for Biological and Health Sciences, Federal University of Western Bahia, Rua Bertioga, 892, Morada Nobre II, Barreiras CEP 47810-059, BA, Brazil; (V.C.R.); (M.M.P.); (S.N.L.); (M.F.d.M.-F.); (M.S.C.); (R.d.C.S.)
| | - Manoel F. de Magalhães-Filho
- Research Group on Development of Pharmaceutical Products (P&DProFar), Center for Biological and Health Sciences, Federal University of Western Bahia, Rua Bertioga, 892, Morada Nobre II, Barreiras CEP 47810-059, BA, Brazil; (V.C.R.); (M.M.P.); (S.N.L.); (M.F.d.M.-F.); (M.S.C.); (R.d.C.S.)
| | - Mila S. Cunha
- Research Group on Development of Pharmaceutical Products (P&DProFar), Center for Biological and Health Sciences, Federal University of Western Bahia, Rua Bertioga, 892, Morada Nobre II, Barreiras CEP 47810-059, BA, Brazil; (V.C.R.); (M.M.P.); (S.N.L.); (M.F.d.M.-F.); (M.S.C.); (R.d.C.S.)
| | - Rafael da C. Simões
- Research Group on Development of Pharmaceutical Products (P&DProFar), Center for Biological and Health Sciences, Federal University of Western Bahia, Rua Bertioga, 892, Morada Nobre II, Barreiras CEP 47810-059, BA, Brazil; (V.C.R.); (M.M.P.); (S.N.L.); (M.F.d.M.-F.); (M.S.C.); (R.d.C.S.)
| | - Roseli B. de Lacerda
- Department of Pharmacology of the Biological Sciences Center, Federal University of Paraná, Jardim das Américas, Caixa. postal 19031, Curitiba CEP 81531-990, PR, Brazil;
| | - Renilson S. de Freitas-Júnior
- Clinical Health is Life-Integrated Health Center, Rua dos Andrades, 99, Barreirinhas, Barreiras CEP 47810-689, BA, Brazil;
| | - Bruno H. da S. Ramos
- Institute of the Spine and Pain Clinic, Rua Dr. Renato Gonçalves, 108, Renato Gonçalves, Barreiras CEP 47806-021, BA, Brazil;
| | - Ana M. Mapeli
- Research Group on Biomolecules and Catalyze, Center for Biological and Health Sciences, Federal University of Western Bahia, Rua Bertioga, 892, Morada Nobre II, Barreiras CEP 47810-059, BA, Brazil;
| | - Matheus da S. T. Henriques
- Laboratory of Pharmacology of Toxins (LabTox), Graduate Program in Pharmacology and Medicinal Chemistry (PPGFQM), Institute of Biomedical Sciences (ICB) Federal University of Rio de Janeiro (UFRJ), Avenida Carlos Chagas Filho, 373, Cidade Universitária, Rio de Janeiro CEP 21941-590, RJ, Brazil;
| | - William R. de Freitas
- Research Group on Biodiversity and Health (BIOSA), Center for Training in Health Sciences, Federal University of Southern Bahia, Praça Joana Angélica, 58, São José, Teixeira de Freitas, Teixeira de Freitas CEP 45988-058, Brazil;
| | - Luiz A. F. Lopes
- University Hospital of the Federal University of Grande Dourados (HU-UFGD), Federal University of Grande Dourados, Rua Ivo Alves da Rocha, 558, Altos do Indaiá, Dourados CEP 79823-501, MS, Brazil;
| | - Luiz G. R. Oliveira
- Nucleus of Studies on Infectious Agents and Vectors (Naive), Federal University of Western Bahia, Rua Bertioga, 892, Morada Nobre II, Barreiras CEP 47810-059, BA, Brazil;
| | - Jonatas G. da Silva
- Federal University of Western Bahia, Rua Bertioga, 892, Morada Nobre II, Barreiras CEP 47810-059, BA, Brazil; (J.G.d.S.); (K.V.L.); (J.S.F.)
| | - Saulo E. Silva-Filho
- Pharmaceutical Sciences, Food and Nutrition College, Federal University of Mato Grosso do Sul, Avenida Costa e Silva, s/nº, Bairro Universitário, Campo Grande CEP 79070-900, MS, Brazil;
| | - Ana P. S. da Silveira
- Faculty of Biological and Health Sciences, University Center Unigran Capital, Rua Balbina de Matos, 2121, Jd. University, Dourados CEP 79.824-900, MS, Brazil;
| | - Katyuscya V. Leão
- Federal University of Western Bahia, Rua Bertioga, 892, Morada Nobre II, Barreiras CEP 47810-059, BA, Brazil; (J.G.d.S.); (K.V.L.); (J.S.F.)
| | - Maria M. de S. Matos
- Health Sciences at ABC Health University Center, Avenida Príncipe de Gales, 667, Bairro Princípe de Gales, Santo André CEP 09060-870, SP, Brazil;
| | - Jamille S. Fernandes
- Federal University of Western Bahia, Rua Bertioga, 892, Morada Nobre II, Barreiras CEP 47810-059, BA, Brazil; (J.G.d.S.); (K.V.L.); (J.S.F.)
| | - Roberto K. N. Cuman
- Department of Pharmacology and Therapeutics, State University of Maringá, Avenida Colombo, nº 5790, Jardim Universitário, Maringá CEP 87020-900, PR, Brazil; (R.K.N.C.); (F.M.d.S.S.-C.)
| | - Francielli M. de S. Silva-Comar
- Department of Pharmacology and Therapeutics, State University of Maringá, Avenida Colombo, nº 5790, Jardim Universitário, Maringá CEP 87020-900, PR, Brazil; (R.K.N.C.); (F.M.d.S.S.-C.)
| | - Jurandir F. Comar
- Department of Biochemistry, State University of Maringá, Avenida Colombo, nº 5790, Jardim Universitário, Maringá CEP 87020-900, PR, Brazil;
| | - Luana do A. Brasileiro
- Nacional Cancer Institute (INCA), Rua Visconde de Santa Isabel, 274, Rio de Janeiro CEP 20560-121, RJ, Brazil;
| | | | - Silvia A. Oesterreich
- Faculty of Health Sciences, Federal University of Grande Dourados, Dourados Rodovia Dourados, Itahum Km 12, Cidade Universitaria, Caixa postal 364, Dourados CEP 79804-970, Mato Grosso do Sul, Brazil;
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13
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Krupanidhi S, Abraham Peele K, Venkateswarulu TC, Ayyagari VS, Nazneen Bobby M, John Babu D, Venkata Narayana A, Aishwarya G. Screening of phytochemical compounds of Tinospora cordifolia for their inhibitory activity on SARS-CoV-2: an in silico study. J Biomol Struct Dyn 2020; 39:5799-5803. [PMID: 32627715 PMCID: PMC7441789 DOI: 10.1080/07391102.2020.1787226] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In the present study, we explored phytochemical constituents of Tinospora cordifolia in terms of its binding affinity targeting the active site pocket of the main protease (3CL pro) of SARS-CoV-2 using molecular docking study and assessed the stability of top docking complex of tinosponone and 3CL pro using molecular dynamics simulations with GROMACS 2020.2 version. Out of 11 curated screened compounds, we found the significant docking score for tinosponone, xanosporic acid, cardiofolioside B, tembetarine and berberine in Tinospora cordifolia. Based on the findings of the docking study, it was confirmed that tinosponone is the potent inhibitor of main protease of SARS-CoV-2 with the best binding affinity of −7.7 kcal/mol. Further, ADME along with toxicity analysis was studied to predict the pharmacokinetics and drug-likeness properties of five top hits compounds. The molecular dynamics simulation analysis confirmed the stability of tinosponone and 3CL pro complex with a random mean square deviation (RMSD) value of 0.1 nm. The computer-aided drug design approach proved that the compound tinosponone from T. cordifolia is a potent inhibitor of 3CL main protease of SARS-CoV-2. Further, the in vitro and in vivo-based testing will be required to confirm its inhibitory effect on SARS-CoV-2. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- S Krupanidhi
- Department of Bio-Technology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, Guntur, Andhra Pradesh, India
| | - K Abraham Peele
- Department of Bio-Technology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, Guntur, Andhra Pradesh, India
| | - T C Venkateswarulu
- Department of Bio-Technology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, Guntur, Andhra Pradesh, India
| | - Vijaya Sai Ayyagari
- Department of Bio-Technology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, Guntur, Andhra Pradesh, India
| | - Md Nazneen Bobby
- Department of Bio-Technology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, Guntur, Andhra Pradesh, India
| | - D John Babu
- Department of Bio-Technology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, Guntur, Andhra Pradesh, India
| | - A Venkata Narayana
- Department of Bio-Technology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, Guntur, Andhra Pradesh, India
| | - G Aishwarya
- Department of Bio-Technology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, Guntur, Andhra Pradesh, India
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