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Hassan SS, Kodakandla V, Redwan EM, Lundstrom K, Choudhury PP, Serrano-Aroca Á, Azad GK, Aljabali AAA, Palu G, Abd El-Aziz TM, Barh D, Uhal BD, Adadi P, Takayama K, Bazan NG, Tambuwala M, Sherchan SP, Lal A, Chauhan G, Baetas-da-Cruz W, Uversky VN. Non-uniform aspects of the SARS-CoV-2 intraspecies evolution reopen question of its origin. Int J Biol Macromol 2022; 222:972-993. [PMID: 36174872 PMCID: PMC9511875 DOI: 10.1016/j.ijbiomac.2022.09.184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 05/04/2022] [Accepted: 09/20/2022] [Indexed: 12/01/2022]
Abstract
Several hypotheses have been presented on the origin of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) from its identification as the agent causing the current coronavirus disease 19 (COVID-19) pandemic. So far, no solid evidence has been found to support any hypothesis on the origin of this virus, and the issue continue to resurface over and over again. Here we have unfolded a pattern of distribution of several mutations in the SARS-CoV-2 proteins in 24 geo-locations across different continents. The results showed an evenly uneven distribution of the unique protein variants, distinct mutations, unique frequency of common conserved residues, and mutational residues across these 24 geo-locations. Furthermore, ample mutations were identified in the evolutionarily conserved invariant regions in the SARS-CoV-2 proteins across almost all geo-locations studied. This pattern of mutations potentially breaches the law of evolutionary conserved functional units of the beta-coronavirus genus. These mutations may lead to several novel SARS-CoV-2 variants with a high degree of transmissibility and virulence. A thorough investigation on the origin and characteristics of SARS-CoV-2 needs to be conducted in the interest of science and for the preparation of meeting the challenges of potential future pandemics.
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Affiliation(s)
- Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur, 721140, West Bengal, India.
| | - Vaishnavi Kodakandla
- Department of Life sciences, Sophia College For Women, University of Mumbai, Bhulabhai Desai Road, Mumbai 400026, India
| | - Elrashdy M Redwan
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications, New Borg EL-Arab 21934, Alexandria, Egypt.
| | | | - Pabitra Pal Choudhury
- Indian Statistical Institute, Applied Statistics Unit, 203 B T Road, Kolkata 700108, India
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigacion Traslacional San Alberto Magno, Universidad Cat'olica de Valencia San Vicente Martir, c/Guillem de Castro, 94, 46001 Valencia, Valencia, Spain.
| | | | - Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Yarmouk University, Faculty of Pharmacy, Irbid 566, Jordan.
| | - Giorgio Palu
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121 Padova, Italy.
| | - Tarek Mohamed Abd El-Aziz
- Zoology Department, Faculty of Science, Minia University, El-Minia 61519, Egypt; Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229-3900, USA.
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, WB, India; Departamento de Geńetica, Ecologia e Evolucao, Instituto de Cíencias Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Bruce D Uhal
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA
| | - Parise Adadi
- Department of Food Science, University of Otago, Dunedin 9054, New Zealand
| | - Kazuo Takayama
- Center for iPS Cell Research and Application, Kyoto University, Kyoto 6068507, Japan.
| | - Nicolas G Bazan
- Neuroscience Center of Excellence, School of Medicine, LSU Health New Orleans, New Orleans, LA 70112, USA.
| | - Murtaza Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK.
| | - Samendra P Sherchan
- Lincoln Medical School, University of Lincoln, Brayford Pool Campus, Lincoln LN6 7TS, UK.
| | - Amos Lal
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN, USA
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501 Sur, 64849 Monterrey, Nuevo León, Mexico.
| | - Wagner Baetas-da-Cruz
- Translational Laboratory in Molecular Physiology, Centre for Experimental Surgery, College of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Vladimir N Uversky
- Department of Molecular Medicineand USF Health Byrd Alzheimer's Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny 141700, Russia.
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Das JK, Heryakusuma C, Susanti D, Choudhury PP, Mukhopadhyay B. Reduced Protein Sequence Patterns in Identifying Key Structural Elements of Dissimilatory Sulfite Reductase Homologs. Comput Biol Chem 2022; 98:107691. [DOI: 10.1016/j.compbiolchem.2022.107691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 04/26/2022] [Accepted: 04/26/2022] [Indexed: 11/03/2022]
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3
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Hassan SS, Kodakandla V, Redwan EM, Lundstrom K, Pal Choudhury P, Abd El-Aziz TM, Takayama K, Kandimalla R, Lal A, Serrano-Aroca Á, Azad GK, Aljabali AA, Palù G, Chauhan G, Adadi P, Tambuwala M, Brufsky AM, Baetas-da-Cruz W, Barh D, Azevedo V, Bazan NG, Andrade BS, Santana Silva RJ, Uversky VN. An issue of concern: unique truncated ORF8 protein variants of SARS-CoV-2. PeerJ 2022; 10:e13136. [PMID: 35341060 PMCID: PMC8944340 DOI: 10.7717/peerj.13136] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/27/2022] [Indexed: 01/12/2023] Open
Abstract
Open reading frame 8 (ORF8) shows one of the highest levels of variability among accessory proteins in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of Coronavirus Disease 2019 (COVID-19). It was previously reported that the ORF8 protein inhibits the presentation of viral antigens by the major histocompatibility complex class I (MHC-I), which interacts with host factors involved in pulmonary inflammation. The ORF8 protein assists SARS-CoV-2 in evading immunity and plays a role in SARS-CoV-2 replication. Among many contributing mutations, Q27STOP, a mutation in the ORF8 protein, defines the B.1.1.7 lineage of SARS-CoV-2, engendering the second wave of COVID-19. In the present study, 47 unique truncated ORF8 proteins (T-ORF8) with the Q27STOP mutations were identified among 49,055 available B.1.1.7 SARS-CoV-2 sequences. The results show that only one of the 47 T-ORF8 variants spread to over 57 geo-locations in North America, and other continents, which include Africa, Asia, Europe and South America. Based on various quantitative features, such as amino acid homology, polar/non-polar sequence homology, Shannon entropy conservation, and other physicochemical properties of all specific 47 T-ORF8 protein variants, nine possible T-ORF8 unique variants were defined. The question as to whether T-ORF8 variants function similarly to the wild type ORF8 is yet to be investigated. A positive response to the question could exacerbate future COVID-19 waves, necessitating severe containment measures.
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Affiliation(s)
- Sk. Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, India
| | - Vaishnavi Kodakandla
- Department of Life sciences, Sophia College For Women, University of Mumbai, Mumbai, India
| | - Elrashdy M. Redwan
- Faculty of Science, Department of Biological Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | | | - Tarek Mohamed Abd El-Aziz
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Ramesh Kandimalla
- Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad, India
| | - Amos Lal
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic Rochester, Rochester, NY, United States
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigacion Traslacional San Alberto Magno, Universidad Catolica de Valencia San Vicente Martir, Valencia, Spain
| | | | - Alaa A.A. Aljabali
- Department of Pharmaceutics and Pharmaceutical, Yarmouk University, Irbid, Jordan
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnologico de Monterrey, Monterrey, Mexico
| | - Parise Adadi
- Department of Food Science, University of Otago, University of Otago, Dunedin, New Zealand
| | - Murtaza Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine, UK
| | - Adam M. Brufsky
- Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Wagner Baetas-da-Cruz
- Translational Laboratory in Molecular Physiology, Centre for Experimental Surgery, College of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and 46 Applied Biotechnology (IIOAB), Nonakuri, India
| | - Vasco Azevedo
- Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Nikolas G. Bazan
- Neuroscience Center of Excellence, School of Medicine, LSU Health New Orleans, New Orleans, LA, United States
| | - Bruno Silva Andrade
- Laboratório de Bioinformática e Química Computacional, Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Jequié, Brazil
| | - Raner José Santana Silva
- Departamento de Ciencias Biologicas (DCB), Programa de Pos-Graduacao em Genetica e Biologia Molecular (PPGGBM), Universidade Estadual de Santa Cruz (UESC), Ilheus, Brazil
| | - Vladimir N. Uversky
- Department of Molecular Medicine, University of South Florida, Tampa, FL, United States
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4
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Hassan SS, Basu P, Redwan EM, Lundstrom K, Choudhury PP, Serrano-Aroca Á, Azad GK, Aljabali AAA, Palu G, Abd El-Aziz TM, Barh D, Uhal BD, Adadi P, Takayama K, Bazan NG, Tambuwala MM, Lal A, Chauhan G, Baetas-da-Cruz W, Sherchan SP, Uversky VN. Periodically aperiodic pattern of SARS-CoV-2 mutations underpins the uncertainty of its origin and evolution. Environ Res 2022; 204:112092. [PMID: 34562480 PMCID: PMC8457672 DOI: 10.1016/j.envres.2021.112092] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 05/20/2023]
Abstract
Various lineages of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) have contributed to prolongation of the Coronavirus Disease 2019 (COVID-19) pandemic. Several non-synonymous mutations in SARS-CoV-2 proteins have generated multiple SARS-CoV-2 variants. In our previous report, we have shown that an evenly uneven distribution of unique protein variants of SARS-CoV-2 is geo-location or demography-specific. However, the correlation between the demographic transmutability of the SARS-CoV-2 infection and mutations in various proteins remains unknown due to hidden symmetry/asymmetry in the occurrence of mutations. This study tracked how these mutations are emerging in SARS-CoV-2 proteins in six model countries and globally. In a geo-location, considering the mutations having a frequency of detection of at least 500 in each SARS-CoV-2 protein, we studied the country-wise percentage of invariant residues. Our data revealed that since October 2020, highly frequent mutations in SARS-CoV-2 have been observed mostly in the Open Reading Frame (ORF) 7b and ORF8, worldwide. No such highly frequent mutations in any of the SARS-CoV-2 proteins were found in the UK, India, and Brazil, which does not correlate with the degree of transmissibility of the virus in India and Brazil. However, we have found a signature that SARS-CoV-2 proteins were evolving at a higher rate, and considering global data, mutations are detected in the majority of the available amino acid locations. Fractal analysis of each protein's normalized factor time series showed a periodically aperiodic emergence of dominant variants for SARS-CoV-2 protein mutations across different countries. It was noticed that certain high-frequency variants have emerged in the last couple of months, and thus the emerging SARS-CoV-2 strains are expected to contain prevalent mutations in the ORF3a, membrane, and ORF8 proteins. In contrast to other beta-coronaviruses, SARS-CoV-2 variants have rapidly emerged based on demographically dependent mutations. Characterization of the periodically aperiodic nature of the demographic spread of SARS-CoV-2 variants in various countries can contribute to the identification of the origin of SARS-CoV-2.
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Affiliation(s)
- Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur, 721140, West Bengal, India.
| | - Pallab Basu
- School of Physics, University of the Witwatersrand, Johannesburg, Braamfontein 2000, 721140, South Africa.
| | - Elrashdy M Redwan
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications, New Borg EL-Arab, 21934, Alexandria, Egypt.
| | | | - Pabitra Pal Choudhury
- Indian Statistical Institute, Applied Statistics Unit, 203 B T Road, Kolkata, 700108, India.
| | - Ángel Serrano-Aroca
- Biomaterials & Bioengineering Lab, Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia, San Vicente Mártir, Valencia 46001, Spain.
| | | | - Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Yarmouk University, Faculty of Pharmacy, Irbid, 566, Jordan.
| | - Giorgio Palu
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121, Padova, Italy.
| | - Tarek Mohamed Abd El-Aziz
- Zoology Department, Faculty of Science, Minia University, El-Minia, 61519, Egypt; Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229-3900, USA.
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, WB, India; Departamento de Geńetica, Ecologia e Evolucao, Instituto de Cîencias Bioĺogicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
| | - Bruce D Uhal
- Department of Physiology, Michigan State University, East Lansing, MI, 48824, USA.
| | - Parise Adadi
- Department of Food Science, University of Otago, Dunedin, 9054, New Zealand.
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, 6068507, Japan.
| | - Nicolas G Bazan
- Neuroscience Center of Excellence, School of Medicine, LSU Health New Orleans, New Orleans, LA, 70112, USA.
| | - Murtaza M Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine, BT52 1SA, Northern Ireland, UK.
| | - Amos Lal
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN, USA.
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501 Sur, 64849, Monterrey, Nuevo Léon, Mexico.
| | - Wagner Baetas-da-Cruz
- Translational Laboratory in Molecular Physiology, Centre for Experimental Surgery, College of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, New Orleans, LA, 70112, USA.
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA; Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny, 141700, Russia.
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5
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Hassan SS, Kodakandla V, Redwan EM, Lundstrom K, Pal Choudhury P, Abd El-Aziz TM, Takayama K, Kandimalla R, Lal A, Serrano-Aroca Á, Azad GK, Aljabali AAA, Palù G, Chauhan G, Adadi P, Tambuwala M, Brufsky AM, Baetas-da-Cruz W, Barh D, Azevedo V, Bazan NG, Andrade BS, Santana Silva RJ, Uversky VN. An issue of concern: unique truncated ORF8 protein variants of SARS-CoV-2. PeerJ 2022. [PMID: 35341060 DOI: 10.1101/2021.05.25.445557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023] Open
Abstract
Open reading frame 8 (ORF8) shows one of the highest levels of variability among accessory proteins in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of Coronavirus Disease 2019 (COVID-19). It was previously reported that the ORF8 protein inhibits the presentation of viral antigens by the major histocompatibility complex class I (MHC-I), which interacts with host factors involved in pulmonary inflammation. The ORF8 protein assists SARS-CoV-2 in evading immunity and plays a role in SARS-CoV-2 replication. Among many contributing mutations, Q27STOP, a mutation in the ORF8 protein, defines the B.1.1.7 lineage of SARS-CoV-2, engendering the second wave of COVID-19. In the present study, 47 unique truncated ORF8 proteins (T-ORF8) with the Q27STOP mutations were identified among 49,055 available B.1.1.7 SARS-CoV-2 sequences. The results show that only one of the 47 T-ORF8 variants spread to over 57 geo-locations in North America, and other continents, which include Africa, Asia, Europe and South America. Based on various quantitative features, such as amino acid homology, polar/non-polar sequence homology, Shannon entropy conservation, and other physicochemical properties of all specific 47 T-ORF8 protein variants, nine possible T-ORF8 unique variants were defined. The question as to whether T-ORF8 variants function similarly to the wild type ORF8 is yet to be investigated. A positive response to the question could exacerbate future COVID-19 waves, necessitating severe containment measures.
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Affiliation(s)
- Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, India
| | - Vaishnavi Kodakandla
- Department of Life sciences, Sophia College For Women, University of Mumbai, Mumbai, India
| | - Elrashdy M Redwan
- Faculty of Science, Department of Biological Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | | | - Tarek Mohamed Abd El-Aziz
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Ramesh Kandimalla
- Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad, India
| | - Amos Lal
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic Rochester, Rochester, NY, United States
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigacion Traslacional San Alberto Magno, Universidad Catolica de Valencia San Vicente Martir, Valencia, Spain
| | | | - Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical, Yarmouk University, Irbid, Jordan
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnologico de Monterrey, Monterrey, Mexico
| | - Parise Adadi
- Department of Food Science, University of Otago, University of Otago, Dunedin, New Zealand
| | - Murtaza Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine, UK
| | - Adam M Brufsky
- Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Wagner Baetas-da-Cruz
- Translational Laboratory in Molecular Physiology, Centre for Experimental Surgery, College of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and 46 Applied Biotechnology (IIOAB), Nonakuri, India
| | - Vasco Azevedo
- Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Nikolas G Bazan
- Neuroscience Center of Excellence, School of Medicine, LSU Health New Orleans, New Orleans, LA, United States
| | - Bruno Silva Andrade
- Laboratório de Bioinformática e Química Computacional, Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Jequié, Brazil
| | - Raner José Santana Silva
- Departamento de Ciencias Biologicas (DCB), Programa de Pos-Graduacao em Genetica e Biologia Molecular (PPGGBM), Universidade Estadual de Santa Cruz (UESC), Ilheus, Brazil
| | - Vladimir N Uversky
- Department of Molecular Medicine, University of South Florida, Tampa, FL, United States
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6
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Hassan SS, Lundstrom K, Serrano-Aroca Á, Adadi P, Aljabali AAA, Redwan EM, Lal A, Kandimalla R, El-Aziz TMA, Pal Choudhury P, Azad GK, Sherchan SP, Chauhan G, Tambuwala M, Takayama K, Barh D, Palu G, Basu P, Uversky VN. Emergence of unique SARS-CoV-2 ORF10 variants and their impact on protein structure and function. Int J Biol Macromol 2022; 194:128-143. [PMID: 34863825 PMCID: PMC8635690 DOI: 10.1016/j.ijbiomac.2021.11.151] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 11/18/2021] [Accepted: 11/22/2021] [Indexed: 02/07/2023]
Abstract
The devastating impact of the ongoing coronavirus disease 2019 (COVID-19) on public health, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has made targeting the COVID-19 pandemic a top priority in medical research and pharmaceutical development. Surveillance of SARS-CoV-2 mutations is essential for the comprehension of SARS-CoV-2 variant diversity and their impact on virulence and pathogenicity. The SARS-CoV-2 open reading frame 10 (ORF10) protein interacts with multiple human proteins CUL2, ELOB, ELOC, MAP7D1, PPT1, RBX1, THTPA, TIMM8B, and ZYG11B expressed in lung tissue. Mutations and co-occurring mutations in the emerging SARS-CoV-2 ORF10 variants are expected to impact the severity of the virus and its associated consequences. In this article, we highlight 128 single mutations and 35 co-occurring mutations in the unique SARS-CoV-2 ORF10 variants. The possible predicted effects of these mutations and co-occurring mutations on the secondary structure of ORF10 variants and host protein interactomes are presented. The findings highlight the possible effects of mutations and co-occurring mutations on the emerging 140 ORF10 unique variants from secondary structure and intrinsic protein disorder perspectives.
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Affiliation(s)
- Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur 721140, West Bengal, India.
| | | | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigacion Traslacional San Alberto Magno, Universidad Catolica de Valencia San Vicente Martir, c/Guillem de Castro, 94, 46001 Valencia, Valencia, Spain.
| | - Parise Adadi
- Department of Food Science, University of Otago, Dunedin 9054, New Zealand
| | - Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Yarmouk University, Faculty of Pharmacy, Irbid 566, Jordan.
| | - Elrashdy M Redwan
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications, New Borg EL-Arab 21934, Alexandria, Egypt.
| | - Amos Lal
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN, USA
| | - Ramesh Kandimalla
- Applied Biology, CSIR-Indian Institute of Chemical Technology, Uppal Road, Tarnaka, Hyderabad 500007, Telangana, India; Department of Biocemistry, Kakatiya Medical College, Warangal, Telangana, India
| | - Tarek Mohamed Abd El-Aziz
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX 78229-3900, USA; Zoology Department, Faculty of Science, Minia University, El-Minia 61519, Egypt.
| | - Pabitra Pal Choudhury
- Indian Statistical Institute, Applied Statistics Unit, 203 B T Road, Kolkata 700108, India.
| | | | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, New Orleans, LA, 70112, USA.
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnologico de Monterrey, 64849 Monterrey, Nuevo Leon, Mexico.
| | - Murtaza Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK.
| | - Kazuo Takayama
- Center for iPS Cell Research and Application, Kyoto University, Kyoto 6068507, Japan.
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur 721172, West Bengal, India; Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil.
| | - Giorgio Palu
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121 Padova, Italy.
| | - Pallab Basu
- School of Physics, University of the Witwatersrand, Johannesburg, Braamfontein 2000, 721140, South Africa.
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
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7
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Hassan SS, Lundstrom K, Barh D, Silva RJS, Andrade BS, Azevedo V, Choudhury PP, Palu G, Uhal BD, Kandimalla R, Seyran M, Lal A, Sherchan SP, Azad GK, Aljabali AAA, Brufsky AM, Serrano-Aroca Á, Adadi P, Abd El-Aziz TM, Redwan EM, Takayama K, Rezaei N, Tambuwala M, Uversky VN. Implications derived from S-protein variants of SARS-CoV-2 from six continents. Int J Biol Macromol 2021; 191:934-955. [PMID: 34571123 PMCID: PMC8462006 DOI: 10.1016/j.ijbiomac.2021.09.080] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/13/2021] [Accepted: 09/13/2021] [Indexed: 01/19/2023]
Abstract
The spike (S) protein is a critical determinant of the infectivity and antigenicity of SARS-CoV-2. Several mutations in the S protein of SARS-CoV-2 have already been detected, and their effect in immune system evasion and enhanced transmission as a cause of increased morbidity and mortality are being investigated. From pathogenic and epidemiological perspectives, S proteins are of prime interest to researchers. This study focused on the unique variants of S proteins from six continents: Asia, Africa, Europe, Oceania, South America, and North America. In comparison to the other five continents, Africa had the highest percentage of unique S proteins (29.1%). The phylogenetic relationship implies that unique S proteins from North America are significantly different from those of the other five continents. They are most likely to spread to the other geographic locations through international travel or naturally by emerging mutations. It is suggested that restriction of international travel should be considered, and massive vaccination as an utmost measure to combat the spread of the COVID-19 pandemic. It is also further suggested that the efficacy of existing vaccines and future vaccine development must be reviewed with careful scrutiny, and if needed, further re-engineered based on requirements dictated by new emerging S protein variants.
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Affiliation(s)
- Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur 721140, West Bengal, India.
| | | | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, WB, India; Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil.
| | - Raner Jośe Santana Silva
- Department of Biological Sciences (DCB), Graduate Program in Genetics and Molecular Biology (PPGGBM), State University of Santa Cruz (UESC), Rodovia Ilheus-Itabuna, km 16, 45662-900 Ilheus, BA, Brazil
| | - Bruno Silva Andrade
- Laboratory of Bioinformatics and Computational Chemistry, Department of Biological Sciences, State University of Southwest Bahia (UESB), Jequié 45206-190, Brazil.
| | - Vasco Azevedo
- Laborat'orio de Geńetica Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciˆencias Biol'ogicas, Universidade Federal de Minas Gerais, Belo Horizonte CEP 31270-901, Brazil.
| | - Pabitra Pal Choudhury
- Applied Statistics Unit, Indian Statistical Institute, 203 B T Road, Kolkata 700108, India
| | - Giorgio Palu
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121 Padova, Italy.
| | - Bruce D Uhal
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA
| | - Ramesh Kandimalla
- Applied Biology, CSIR-Indian Institute of Chemical Technology, Uppal Road, Tarnaka, Hyderabad 500007, India; Department of Biochemistry, Kakatiya Medical College, Warangal, Telangana, India
| | - Murat Seyran
- Doctoral Studies in Natural and Technical Sciences (SPL 44), University of Vienna, W¨ahringer Straße, A-1090 Vienna, Austria
| | - Amos Lal
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN, USA
| | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, New Orleans, LA 70112, USA.
| | | | - Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Yarmouk University, Faculty of Pharmacy, Irbid 566, Jordan.
| | - Adam M Brufsky
- University of Pittsburgh School of Medicine, Department of Medicine, Division of Hematology/Oncology, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigaci'on Traslacional San Alberto Magno, Universidad Cat́olica de Valencia San Vicente Ḿartir, c/Guillem de Castro, 94, 46001 Valencia, Spain.
| | - Parise Adadi
- Department of Food Science, University of Otago, Dunedin 9054, New Zealand
| | - Tarek Mohamed Abd El-Aziz
- Zoology Department, Faculty of Science, Minia University, El-Minia 61519, Egypt; Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229-3900, USA.
| | - Elrashdy M Redwan
- Faculty of Science, Department of Biological Science, King Abdulazizi University, Jeddah 21589, Saudi Arabia; Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City for Scientific Research and Technology Applications, New Borg El-Arab, Alexandria 21934, Egypt.
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan.
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran; Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Stockholm, Sweden.
| | - Murtaza Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK.
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny, 141700, Russia.
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8
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Elrashdy F, Tambuwala MM, Hassan SS, Adadi P, Seyran M, Abd El-Aziz TM, Rezaei N, Lal A, Aljabali AAA, Kandimalla R, Bazan NG, Azad GK, Sherchan SP, Choudhury PP, Serrano-Aroca Á, Takayama K, Chauhan G, Pizzol D, Barh D, Panda PK, Mishra YK, Palù G, Lundstrom K, Redwan EM, Uversky VN. Autoimmunity roots of the thrombotic events after COVID-19 vaccination. Autoimmun Rev 2021; 20:102941. [PMID: 34508917 PMCID: PMC8426137 DOI: 10.1016/j.autrev.2021.102941] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 06/06/2021] [Indexed: 02/03/2023]
Abstract
Although vaccination represents the most promising way to stop or contain the coronavirus disease 2019 (COVID-19) pandemic and safety and effectiveness of available vaccines were proven, a small number of individuals who received anti-SARS-CoV-2 vaccines developed a prothrombotic syndrome. Vaccine-induced immune thrombotic thrombocytopenia (VITT) can be triggered by the adenoviral vector-based vaccine, whereas lipid nanoparticle-mRNA-based vaccines can induce rare cases of deep vein thrombosis (DVT). Although the main pathogenic mechanisms behind this rare phenomenon have not yet been identified, both host and vaccine factors might be involved, with pathology at least in part being related to the vaccine-triggered autoimmune reaction. In this review, we are considering some aspects related to pathogenesis, major risk factors, as well as peculiarities of diagnosis and treatment of this rare condition.
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Affiliation(s)
- Fatma Elrashdy
- Department of Endemic Medicine and Hepatogastroenterology, Kasr Alainy, Cairo University, Cairo, Egypt.
| | - Murtaza M Tambuwala
- School of Pharmacy and Pharmaceutical Sciences, Ulster University, Coleraine, BT52 1SA, Northern Ireland, United Kingdom.
| | - Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, 722140 Paschim Medinipur, West Bengal, India
| | - Parise Adadi
- Department of Food Science, University of Otago, Dunedin, New Zealand
| | - Murat Seyran
- Doctoral Student in Natural and Technical Sciences (SPL 44), University of Vienna, Währinger Straße, A-1090 Vienna, Austria.
| | - Tarek Mohamed Abd El-Aziz
- Zoology Department, Faculty of Science, Minia University, El-Minia 61519, Egypt; Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229-3900, USA.
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran; Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Stockholm, Sweden
| | - Amos Lal
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, USA
| | - Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Yarmouk University, Irbid 21163, P. O. BOX 566, Jordan.
| | - Ramesh Kandimalla
- Applied Biology, CSIR-Indian Institute of Chemical Technology, Uppal Road, Tarnaka, Hyderabad 500007, India; Department of Biochemistry, Kakatiya Medical College, Warangal, India
| | - Nicolas G Bazan
- Neuroscience Center of Excellence, School of Medicine, Louisiana State University Health New Orleans, New Orleans, Louisiana, 70112, USA.
| | | | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, New Orleans, LA 70112, USA.
| | - Pabitra Pal Choudhury
- Applied Statistics Unit, Indian Statistical Institute, Kolkata, 700108, West Bengal, India
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia San Vicente Mártir, c/Guillem de Castro 94, Valencia 46001, Spain.
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan.
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnológico de Monterrey, Av. Eugenio Garza Sada 2501 Sur, 64849 Monterrey, Nuevo León, Mexico.
| | - Damiano Pizzol
- Italian Agency for Development Cooperation -, Khartoum, Sudan Street 33, Al Amarat, Sudan
| | - Debmalya Barh
- Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, WB-721172, India; and Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil.
| | - Pritam Kumar Panda
- Condensed Matter Theory Group, Materials Theory Division, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden.
| | - Yogendra K Mishra
- University of Southern Denmark, Mads Clausen Institute, NanoSYD, Alsion 2, 6400 Sønderborg, Denmark.
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padova, Italy.
| | | | - Elrashdy M Redwan
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Vladimir N Uversky
- Department of Molecular Medicine, University of South Florida, Tampa, FL, United States.
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9
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Redwan EM, Alghamdi MF, El-Aziz TMA, Adadi P, Aljabali AAA, Attrish D, Azad GK, Baetas-da-Cruz W, Barh D, Bazan NG, Brufsky AM, Chauhan G, Hassan SKS, Kandimalla R, Lal A, Lundstrom K, Mishra YK, Choudhury PP, Palù G, Panda PK, Pizzol D, Rezaei N, Serrano-Aroca Á, Sherchan SP, Seyran M, Takayama K, Tambuwala MM, Uhal BD, Uversky VN. The mechanism behind flaring/triggering of autoimmunity disorders associated with COVID-19. Autoimmun Rev 2021; 20:102909. [PMID: 34274539 PMCID: PMC8282442 DOI: 10.1016/j.autrev.2021.102909] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 12/12/2022]
Affiliation(s)
- Elrashdy M Redwan
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah, Saudi Arabia; Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications, New Borg EL-Arab, 21934 Alexandria, Egypt.
| | - Mohammed F Alghamdi
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah, Saudi Arabia; Laboratory Department, University Medical Services Center, King Abdulaziz University, P.O. Box 80200, Jeddah 21589, Saudi Arabia.
| | - Tarek Mohamed Abd El-Aziz
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX 78229-3900, USA; Zoology Department, Faculty of Science, Minia University, El-Minia 61519, Egypt.
| | - Parise Adadi
- Department of Food Science, University of Otago, Dunedin 9054, New Zealand
| | - Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Yarmouk University-Faculty of Pharmacy, Irbid 566, Jordan.
| | - Diksha Attrish
- Dr. B R Ambedkar Center for Biomedical Research (ACBR), University of Delhi (North Camps), Delhi 110007, India
| | | | - Wagner Baetas-da-Cruz
- Translational Laboratory in Molecular Physiology, Centre for Experimental Surgery, College of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Debmalya Barh
- Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur WB-721172, India; Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Nicolas G Bazan
- Neuroscience Center of Excellence, School of Medicine, LSU Heath New Orleans, New Orleans 70112, USA.
| | - Adam M Brufsky
- University of Pittsburgh School of Medicine, Department of Medicine, Division of Hematology/Oncology, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnológico de Monterrey, Av. Eugenio Garza Sada 2501 Sur, 64849, Monterrey, NL, Mexico.
| | - S K Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur, 721140, West Bengal, India
| | - Ramesh Kandimalla
- CSIR-Indian Institute of Chemical Technology Uppal Road, Tarnaka, Hyderabad 500007, Department of Biochemistry, Kakatiya Medical College, Warangal, Telangana State, India
| | - Amos Lal
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Yogendra Kumar Mishra
- University of Southern Denmark, Mads Clausen Institute, NanoSYD, Alsion 2, 6400 Sønderborg, Denmark.
| | - Pabitra Pal Choudhury
- Applied Statistics Unit, Indian Statistical Institute, Kolkata 700108, West Bengal, India
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121, Padova, Italy.
| | - Pritam K Panda
- Condensed Matter Theory Group, Materials Theory Division, Department of Physics and Astronomy, Uppsala University, Box 516, 75120 Uppsala, Sweden.
| | - Damiano Pizzol
- Italian Agency for Development Cooperation - Khartoum, Sudan Street 33, Al Amarat, Sudan
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, University of Medical Sciences, Tehran, Iran; Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Stockholm, Sweden
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia San Vicente Mártir, 46001, Valencia, Spain.
| | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, New Orleans, LA 70112, USA.
| | - Murat Seyran
- Doctoral Student in Natural and Technical Sciences (SPL 44), University of Vienna, Währinger Straße, A-1090 Vienna, Austria; Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Austria.
| | - Kazuo Takayama
- Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8397, Japan.
| | - Murtaza M Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK.
| | - Bruce D Uhal
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA
| | - Vladimir N Uversky
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah, Saudi Arabia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
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10
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Lundstrom K, Barh D, Uhal BD, Takayama K, Aljabali AAA, Abd El-Aziz TM, Lal A, Redwan EM, Adadi P, Chauhan G, Sherchan SP, Azad GK, Rezaei N, Serrano-Aroca Á, Bazan NG, Hassan SS, Panda PK, Pal Choudhury P, Pizzol D, Kandimalla R, Baetas-da-Cruz W, Mishra YK, Palu G, Brufsky AM, Tambuwala MM, Uversky VN. COVID-19 Vaccines and Thrombosis-Roadblock or Dead-End Street? Biomolecules 2021; 11:1020. [PMID: 34356644 PMCID: PMC8301964 DOI: 10.3390/biom11071020] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/08/2021] [Accepted: 07/10/2021] [Indexed: 12/16/2022] Open
Abstract
Two adenovirus-based vaccines, ChAdOx1 nCoV-19 and Ad26.COV2.S, and two mRNA-based vaccines, BNT162b2 and mRNA.1273, have been approved by the European Medicines Agency (EMA), and are invaluable in preventing and reducing the incidence of coronavirus disease-2019 (COVID-19). Recent reports have pointed to thrombosis with associated thrombocytopenia as an adverse effect occurring at a low frequency in some individuals after vaccination. The causes of such events may be related to SARS-CoV-2 spike protein interactions with different C-type lectin receptors, heparan sulfate proteoglycans (HSPGs) and the CD147 receptor, or to different soluble splice variants of the spike protein, adenovirus vector interactions with the CD46 receptor or platelet factor 4 antibodies. Similar findings have been reported for several viral diseases after vaccine administration. In addition, immunological mechanisms elicited by viral vectors related to cellular delivery could play a relevant role in individuals with certain genetic backgrounds. Although rare, the potential COVID-19 vaccine-induced immune thrombotic thrombocytopenia (VITT) requires immediate validation, especially in risk groups, such as the elderly, chronic smokers, and individuals with pre-existing incidences of thrombocytopenia; and if necessary, a reformulation of existing vaccines.
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Affiliation(s)
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Purba Medinipur 721172, India
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Bruce D. Uhal
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA;
| | - Kazuo Takayama
- Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8397, Japan;
| | - Alaa A. A. Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Yarmouk University, P.O. Box 566, Irbid 21163, Jordan;
| | - Tarek Mohamed Abd El-Aziz
- Zoology Department, Faculty of Science, Minia University, El-Minia 61519, Egypt;
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Amos Lal
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN 55902, USA;
| | - Elrashdy M. Redwan
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Parise Adadi
- Department of Food Science, University of Otago, Dunedin 9054, New Zealand;
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnológico de Monterrey, Av. Eugenio Garza Sada 2501 Sur, Monterrey 64849, Mexico;
| | - Samendra P. Sherchan
- Department of Environmental Health Sciences, Tulane University, New Orleans, LA 70112, USA;
| | | | - Nima Rezaei
- Research Center for Immunodeficiency, Children’s Medical Center, Tehran University of Medical Sciences, Tehran 1416753955, Iran;
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), 17177 Stockholm, Sweden
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia San Vicente Mártir, c/Guillem de Castro 94, 46001 Valencia, Spain;
| | - Nicolas G. Bazan
- Neuroscience Center of Excellence, School of Medicine, LSU Health New Orleans, New Orleans, LA 70112, USA;
| | - Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram 721140, India;
| | - Pritam Kumar Panda
- Condensed Matter Theory Group, Materials Theory Division, Department of Physics and Astronomy, Uppsala University, Box 516, 75120 Uppsala, Sweden;
| | | | - Damiano Pizzol
- Italian Agency for Development Cooperation—Khartoum, Sudan Street 33, Al Amarat 11111, Sudan;
| | - Ramesh Kandimalla
- Applied Biology, CSIR-Indian Institute of Technology, Uppal Road, Tarnaka, Hyderabad 500007, India;
- Department of Biochemistry, Kakatiya Medical College, Warangal 506007, India
| | - Wagner Baetas-da-Cruz
- Translational Laboratory in Molecular Physiology, Centre for Experimental Surgery, College of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-901, Brazil;
| | - Yogendra Kumar Mishra
- Mads Clausen Institute, University of Southern Denmark, NanoSYD, Alsion 2, 6400 Sønderborg, Denmark;
| | - Giorgio Palu
- Department of Molecular Medicine, University of Padova, 35122 Padova, PD, Italy;
| | - Adam M. Brufsky
- UPMC Hillman Cancer Center, Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA;
| | - Murtaza M. Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine BT52 1SA, UK
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
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11
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Serrano-Aroca Á, Takayama K, Tuñón-Molina A, Seyran M, Hassan SS, Pal Choudhury P, Uversky VN, Lundstrom K, Adadi P, Palù G, Aljabali AAA, Chauhan G, Kandimalla R, Tambuwala MM, Lal A, Abd El-Aziz TM, Sherchan S, Barh D, Redwan EM, Bazan NG, Mishra YK, Uhal BD, Brufsky A. Carbon-Based Nanomaterials: Promising Antiviral Agents to Combat COVID-19 in the Microbial-Resistant Era. ACS Nano 2021; 15:8069-8086. [PMID: 33826850 PMCID: PMC8043205 DOI: 10.1021/acsnano.1c00629] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/02/2021] [Indexed: 05/04/2023]
Abstract
Therapeutic options for the highly pathogenic human severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing the current pandemic coronavirus disease (COVID-19) are urgently needed. COVID-19 is associated with viral pneumonia and acute respiratory distress syndrome causing significant morbidity and mortality. The proposed treatments for COVID-19 have shown little or no effect in the clinic so far. Additionally, bacterial and fungal pathogens contribute to the SARS-CoV-2-mediated pneumonia disease complex. The antibiotic resistance in pneumonia treatment is increasing at an alarming rate. Therefore, carbon-based nanomaterials (CBNs), such as fullerene, carbon dots, graphene, and their derivatives constitute a promising alternative due to their wide-spectrum antimicrobial activity, biocompatibility, biodegradability, and capacity to induce tissue regeneration. Furthermore, the antimicrobial mode of action is mainly physical (e.g., membrane distortion), characterized by a low risk of antimicrobial resistance. In this Review, we evaluated the literature on the antiviral activity and broad-spectrum antimicrobial properties of CBNs. CBNs had antiviral activity against 13 enveloped positive-sense single-stranded RNA viruses, including SARS-CoV-2. CBNs with low or no toxicity to humans are promising therapeutics against the COVID-19 pneumonia complex with other viruses, bacteria, and fungi, including those that are multidrug-resistant.
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Affiliation(s)
- Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de
Investigación Traslacional San Alberto Magno, Universidad
Católica de Valencia San Vicente Mártir, 46001 Valencia,
Spain
| | - Kazuo Takayama
- Center for iPS Cell Research and Application,
Kyoto University, Kyoto 606-8397,
Japan
| | - Alberto Tuñón-Molina
- Biomaterials and Bioengineering Lab, Centro de
Investigación Traslacional San Alberto Magno, Universidad
Católica de Valencia San Vicente Mártir, 46001 Valencia,
Spain
| | - Murat Seyran
- Doctoral studies in natural and technical sciences (SPL
44), University of Vienna, Währinger Straße, A-1090
Vienna, Austria
| | - Sk. Sarif Hassan
- Department of Mathematics, Pingla Thana
Mahavidyalaya, Maligram, Paschim Medinipur 721140, West Bengal,
India
| | - Pabitra Pal Choudhury
- Applied Statistics Unit, Indian
Statistical Institute, Kolkata 700108, West Bengal,
India
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of
Medicine, University of South Florida, Tampa, Florida 33612,
United States
| | | | - Parise Adadi
- Department of Food Science, University of
Otago, Dunedin 9054, New Zealand
| | - Giorgio Palù
- Department of Molecular Medicine,
University of Padova, Via Gabelli 63, 35121 Padova,
Italy
| | - Alaa A. A. Aljabali
- Department of Pharmaceutics and
Pharmaceutical Technology, Yarmouk University-Faculty of
Pharmacy, Irbid 21163, Jordan
| | - Gaurav Chauhan
- School of Engineering and Sciences,
Tecnológico de Monterrey, Av. Eugenio Garza Sada 2501
Sur, 64849 Monterrey, NL, Mexico
| | - Ramesh Kandimalla
- Applied Biology, CSIR-Indian
Institute of Chemical Technology, Uppal Road, Tarnaka, Hyderabad-500007,
India
- Department of Biochemistry,
Kakatiya Medical College, Warangal-506007, Telangana State,
India
| | - Murtaza M. Tambuwala
- School of Pharmacy and Pharmaceutical
Science, Ulster University, Coleraine BT52 1SA, Northern
Ireland, U.K.
| | - Amos Lal
- Department of Medicine, Division of Pulmonary and Critical
Care Medicine, Mayo Clinic, Rochester, Minnesota 55905,
United States
| | - Tarek Mohamed Abd El-Aziz
- Zoology Department, Faculty of Science,
Minia University, El-Minia 61519,
Egypt
- Department of Cellular and Integrative
Physiology, University of Texas Health Science Center at San
Antonio, San Antonio, Texas 78229-3900, United
States
| | - Samendra Sherchan
- Department of Environmental Health Sciences,
School of Public Health and Tropical Medicine, Tulane University of
Louisiana, New Orleans, Louisiana 70112, United
States
| | - Debmalya Barh
- Institute of Integrative
Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur,
WB-721172, India
| | - Elrashdy M. Redwan
- Biological Sciences Department,
Faculty of Science, King Abdulaziz University, P.O. Box 80203,
Jeddah 21589, Saudi Arabia
- Therapeutic and Protective Proteins
Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research
Institute, City for Scientific Research and Technology
Applications, New Borg El-Arab, Alexandria 21934,
Egypt
| | - Nicolas G. Bazan
- Neuroscience Center of Excellence,
School of Medicine, LSU Heath New Orleans, New Orleans,
Louisiana 70112, United States
| | - Yogendra Kumar Mishra
- University of Southern
Denmark, Mads Clausen Institute, NanoSYD, Alsion 2, 6400 Sønderborg,
Denmark
| | - Bruce D. Uhal
- Department of Physiology, Michigan State
University, East Lansing, Michigan 48824, United
States
| | - Adam Brufsky
- University of Pittsburgh
School of Medicine, Department of Medicine, Division of
Hematology/Oncology, UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania 15232,
United States
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12
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Hassan SS, Attrish D, Ghosh S, Choudhury PP, Roy B. Pathogenic perspective of missense mutations of ORF3a protein of SARS-CoV-2. Virus Res 2021; 300:198441. [PMID: 33940003 PMCID: PMC8086268 DOI: 10.1016/j.virusres.2021.198441] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 02/06/2023]
Abstract
One of the most important proteins for COVID-19 pathogenesis in SARS-CoV-2 is the ORF3a which is the largest accessory protein among others coded by the SARS-CoV-2 genome. The major roles of the protein include virulence, infectivity, ion channel activity, morphogenesis, and virus release. The coronavirus, SARS-CoV-2 is mutating rapidly, therefore, critical study of mutations in ORF3a is certainly important from the pathogenic perspective. Here, a sum of 175 non-synonymous mutations in the ORF3a of SARS-CoV-2 were identified from 7194 complete genomes of SARS-CoV-2 available from NCBI database. Effects of these mutations on structural stability, and functions of ORF3a were also studied. Broadly, three different classes of mutations, such as neutral, disease, and mixed (neutral and disease) types of mutations were observed. Consecutive phenomena of mutations in ORF3a protein were studied based on the timeline of detection of the mutations. Considering the amino acid compositions of the ORF3a protein, twenty clusters were detected using the K-means clustering method. The present findings on 175 novel mutations of ORF3a proteins will extend our knowledge on ORF3a, a vital accessory protein in SARS-CoV-2, to enlighten the pathogenicity of this life-threatening virus.
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Affiliation(s)
- Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram 721140, India.
| | - Diksha Attrish
- Dr. B. R. Ambedkar Centre For Biomedical Research (ACBR), University of Delhi (North Campus), Delhi 110007, India.
| | - Shinjini Ghosh
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata 700009, West Bengal, India.
| | - Pabitra Pal Choudhury
- Applied Statistics Unit, Indian Statistical Institute, Kolkata 700108, West Bengal, India.
| | - Bidyut Roy
- Human Genetics Unit, Indian Statistical Institute, Kolkata 700108, West Bengal, India.
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13
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Hassan SS, Attrish D, Ghosh S, Choudhury PP, Uversky VN, Aljabali AAA, Lundstrom K, Uhal BD, Rezaei N, Seyran M, Pizzol D, Adadi P, Soares A, Abd El-Aziz TM, Kandimalla R, Tambuwala MM, Azad GK, Sherchan SP, Baetas-da-Cruz W, Lal A, Palù G, Takayama K, Serrano-Aroca Á, Barh D, Brufsky AM. Notable sequence homology of the ORF10 protein introspects the architecture of SARS-CoV-2. Int J Biol Macromol 2021; 181:801-809. [PMID: 33862077 PMCID: PMC8051021 DOI: 10.1016/j.ijbiomac.2021.03.199] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 03/30/2021] [Accepted: 03/30/2021] [Indexed: 01/01/2023]
Abstract
The current Coronavirus Disease 19 (COVID-19) pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) shows similar pathology to MERS and SARS-CoV, with a current estimated fatality rate of 1.4%. Open reading frame 10 (ORF10) is a unique SARS-CoV-2 accessory protein, which contains eleven cytotoxic T lymphocyte (CTL) epitopes each of nine amino acids in length. Twenty-two unique SARS-CoV-2 ORF10 variants have been identified based on missense mutations found in sequence databases. Some of these mutations are predicted to decrease the stability of ORF10 in silico physicochemical and structural comparative analyses were carried out on SARS-CoV-2 and Pangolin-CoV ORF10 proteins, which share 97.37% amino acid (aa) homology. Though there is a high degree of ORF10 protein similarity of SARS-CoV-2 and Pangolin-CoV, there are differences of these two ORF10 proteins related to their sub-structure (loop/coil region), solubility, antigenicity and shift from strand to coil at aa position 26 (tyrosine). SARS-CoV-2 ORF10, which is apparently expressed in vivo since reactive T cell clones are found in convalescent patients should be monitored for changes which could correlate with the pathogenesis of COVID-19.
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Affiliation(s)
- Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram 721140, India.
| | - Diksha Attrish
- Dr. B. R. Ambedkar Centre For Biomedical Research (ACBR), University of Delhi (North Campus), Delhi 110007, India
| | - Shinjini Ghosh
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata 700009, West Bengal, India
| | - Pabitra Pal Choudhury
- Applied Statistics Unit, Indian Statistical Institute, Kolkata 700108, West Bengal, India
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
| | - Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Yarmouk University-Faculty of Pharmacy, Irbid 566, Jordan.
| | | | - Bruce D Uhal
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran; Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Stockholm, Sweden.
| | - Murat Seyran
- Doctoral Studies in Natural and Technical Sciences (SPL 44), University of Vienna, Austria
| | - Damiano Pizzol
- Italian Agency for Development Cooperation - Khartoum, Sudan Street 33, Al Amarat, Sudan
| | - Parise Adadi
- Department of Food Science, University of Otago, Dunedin 9054, New Zealand.
| | - Antonio Soares
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX 78229-3900, USA.
| | - Tarek Mohamed Abd El-Aziz
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX 78229-3900, USA; Zoology Department, Faculty of Science, Minia University, El-Minia 61519, Egypt.
| | - Ramesh Kandimalla
- CSIR-Indian Institute of Chemical Technology, Uppal Road, Tarnaka, Hyderabad 500007, Telangana State, India; Department of Biochemistry, Kakatiya Medical College, Warangal, Telangana State, India.
| | - Murtaza M Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK.
| | | | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, New Orleans, LA 70112, USA.
| | - Wagner Baetas-da-Cruz
- Translational Laboratory in Molecular Physiology, Centre for Experimental Surgery, College of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Amos Lal
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN, USA
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121 Padova, Italy.
| | - Kazuo Takayama
- Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8397, Japan.
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia, San Vicente Mártir 46001, Valencia, Spain.
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Purba Medinipur, India
| | - Adam M Brufsky
- University of Pittsburgh School of Medicine, Department of Medicine, Division of Hematology/Oncology, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
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14
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Hassan SS, Aljabali AAA, Panda PK, Ghosh S, Attrish D, Choudhury PP, Seyran M, Pizzol D, Adadi P, Abd El-Aziz TM, Soares A, Kandimalla R, Lundstrom K, Lal A, Azad GK, Uversky VN, Sherchan SP, Baetas-da-Cruz W, Uhal BD, Rezaei N, Chauhan G, Barh D, Redwan EM, Dayhoff GW, Bazan NG, Serrano-Aroca Á, El-Demerdash A, Mishra YK, Palu G, Takayama K, Brufsky AM, Tambuwala MM. A unique view of SARS-CoV-2 through the lens of ORF8 protein. Comput Biol Med 2021; 133:104380. [PMID: 33872970 PMCID: PMC8049180 DOI: 10.1016/j.compbiomed.2021.104380] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 01/07/2023]
Abstract
Immune evasion is one of the unique characteristics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) attributed to its ORF8 protein. This protein modulates the adaptive host immunity through down-regulation of MHC-1 (Major Histocompatibility Complex) molecules and innate immune responses by surpassing the host's interferon-mediated antiviral response. To understand the host's immune perspective in reference to the ORF8 protein, a comprehensive study of the ORF8 protein and mutations possessed by it have been performed. Chemical and structural properties of ORF8 proteins from different hosts, such as human, bat, and pangolin, suggest that the ORF8 of SARS-CoV-2 is much closer to ORF8 of Bat RaTG13-CoV than to that of Pangolin-CoV. Eighty-seven mutations across unique variants of ORF8 in SARS-CoV-2 can be grouped into four classes based on their predicted effects (Hussain et al., 2021) [1]. Based on the geo-locations and timescale of sample collection, a possible flow of mutations was built. Furthermore, conclusive flows of amalgamation of mutations were found upon sequence similarity analyses and consideration of the amino acid conservation phylogenies. Therefore, this study seeks to highlight the uniqueness of the rapidly evolving SARS-CoV-2 through the ORF8.
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Affiliation(s)
- Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, 721140, India
| | - Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Yarmouk University-Faculty of Pharmacy, Irbid, 566, Jordan
| | - Pritam Kumar Panda
- Condensed Matter Theory Group, Materials Theory Division, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20, Uppsala, Sweden
| | - Shinjini Ghosh
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, 700009, West Bengal, India
| | - Diksha Attrish
- Dr. B. R. Ambedkar Centre for Biomedical Research (ACBR), University of Delhi (North Campus), Delhi, 110007, India
| | - Pabitra Pal Choudhury
- Applied Statistics Unit, Indian Statistical Institute, Kolkata, 700108, West Bengal, India
| | - Murat Seyran
- Doctoral Studies in Natural and Technical Sciences (SPL 44), University of Vienna, Austria
| | - Damiano Pizzol
- Italian Agency for Development Cooperation - Khartoum, Sudan Street 33, Al Amarat, Sudan
| | - Parise Adadi
- Department of Food Science, University of Otago, Dunedin, 9054, New Zealand
| | - Tarek Mohamed Abd El-Aziz
- Zoology Department, Faculty of Science, Minia University, El-Minia, 61519, Egypt; Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX, 78229-3900, USA
| | - Antonio Soares
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX, 78229-3900, USA
| | - Ramesh Kandimalla
- CSIR-Indian Institute of Chemical Technology Uppal Road, Tarnaka, Hyderabad, 500007, Telangana State, India
| | | | - Amos Lal
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, New Orleans, LA, 70112, USA
| | - Wagner Baetas-da-Cruz
- Translational Laboratory in Molecular Physiology, Centre for Experimental Surgery, College of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Bruce D Uhal
- Department of Physiology, Michigan State University, East Lansing, MI, 48824, USA
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran and Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Stockholm, Sweden
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501, Sur, 64849, Monterrey, NL, Mexico Tecnológico De Monterrey, Campus Monterrey, Monterrey, Nuevo León, Mexico
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), PatnaPatna, India
| | - Elrashdy M Redwan
- King Abdulazizi University, Faculty of Science, Department of Biological Science, Saudi Arabia
| | - Guy W Dayhoff
- Department of Chemistry, College of Art and Sciences, University of South Florida, Tampa, FL, 33620, USA
| | - Nicolas G Bazan
- Neuroscience Center of Excellence, School of Medicine, Louisiana State University Health New Orleans, New Orleans, LA, 70112, USA
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Translational Research Centre San Alberto Magno, Catholic University of Valencia San Vicente Mártir, C/Guillem de Castro 94, 46001, Valencia, Spain
| | - Amr El-Demerdash
- Natural Products and Medicinal Chemistry Department, Institute de Chimie des Substances Naturelles, Gif-sur-Yvette, France
| | - Yogendra K Mishra
- University of Southern Denmark, Mads Clausen Institute, NanoSYD, Alsion 2, 6400 Sønderborg, Denmark
| | - Giorgio Palu
- Department of Molecular Medicine, University of Padova, Italy
| | - Kazuo Takayama
- Center for IPS Cell Research and Application, Kyoto University, Kyoto, 606-8397, Japan
| | - Adam M Brufsky
- University of Pittsburgh School of Medicine, Department of Medicine, Division of Hematology/Oncology, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Murtaza M Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK.
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15
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Seyran M, Hassan SS, Uversky VN, Pal Choudhury P, Uhal BD, Lundstrom K, Attrish D, Rezaei N, Aljabali AAA, Ghosh S, Pizzol D, Adadi P, El-Aziz TMA, Kandimalla R, Tambuwala MM, Lal A, Azad GK, Sherchan SP, Baetas-da-Cruz W, Palù G, Brufsky AM. Urgent Need for Field Surveys of Coronaviruses in Southeast Asia to Understand the SARS-CoV-2 Phylogeny and Risk Assessment for Future Outbreaks. Biomolecules 2021; 11:398. [PMID: 33803118 PMCID: PMC7999587 DOI: 10.3390/biom11030398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 02/19/2021] [Accepted: 02/20/2021] [Indexed: 02/06/2023] Open
Abstract
Phylogenetic analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is focused on a single isolate of bat coronaviruses (bat CoVs) which does not adequately represent genetically related coronaviruses (CoVs) [...].
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Affiliation(s)
- Murat Seyran
- Doctoral Studies in Natural and Technical Sciences (SPL 44), University of Vienna, Währinger Straße, A-1090 Vienna, Austria;
| | - Sk. Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur 721140, West Bengal, India;
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Pabitra Pal Choudhury
- Applied Statistics Unit, Indian Statistical Institute, Kolkata 700108, West Bengal, India;
| | - Bruce D. Uhal
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA;
| | | | - Diksha Attrish
- Dr. B R Ambedkar Center for Biomedical Research (ACBR), University of Delhi (North Camps), Delhi-110007, India;
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children’s Medical Center, Tehran, University of Medical Sciences, Tehran 1419733151, Iran;
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran 1419733151, Iran
| | - Alaa A. A. Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Yarmouk University-Faculty of Pharmacy, Irbid 566, Jordan;
| | - Shinjini Ghosh
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata 700009, West Bengal, India;
| | - Damiano Pizzol
- Italian Agency for Development Cooperation—Khartoum, Sudan Street 33, Al Amarat 13374, Sudan;
| | - Parise Adadi
- Department of Food Science, University of Otago, Dunedin 9054, New Zealand;
| | - Tarek Mohamed Abd El-Aziz
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX 78229-3900, USA;
- Zoology Department, Faculty of Science, Minia University, El-Minia 61519, Egypt
| | - Ramesh Kandimalla
- CSIR-Indian Institute of Chemical Technology Uppal Road, Tarnaka, Hyderabad 500007, Telangana State, India;
| | - Murtaza M. Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK;
| | - Amos Lal
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN 55905, USA;
| | | | - Samendra P. Sherchan
- Department of Environmental Health Sciences, Tulane University, New Orleans, LA 70112, USA;
| | - Wagner Baetas-da-Cruz
- Translational Laboratory in Molecular Physiology, Centre for Experimental Surgery, College of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941901, Brazil;
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121 Padova, Italy
| | - Adam M. Brufsky
- UPMC Hillman Cancer Center, Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA;
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16
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Hassan SS, Choudhury PP, Roy B. Rare mutations in the accessory proteins ORF6, ORF7b, and ORF10 of the SARS-CoV-2 genomes. Meta Gene 2021; 28:100873. [PMID: 33619452 PMCID: PMC7890336 DOI: 10.1016/j.mgene.2021.100873] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 02/11/2021] [Accepted: 02/15/2021] [Indexed: 02/03/2023] Open
Abstract
A total number of 3080 SARS-CoV-2 genomes from all continents are considered from the NCBI database. Every accessory protein ORF6, ORF7b, and ORF10 of SARS-CoV-2 possess a single missense mutation in less than 1.5% of the 3080 genomes. It has now been observed that different non-synonymous mutations occurred in these three accessory proteins. Most of these rare mutations are changing the amino acids such as hydrophilic to hydrophobic, acidic or basic to hydrophobic, and vice versa etc. So these highly conserved proteins might play an essential role in virus pathogenicity. This study opens a question whether it carries some messages about the virus rapid replications, and virulence.
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Affiliation(s)
- Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram 721140, India
| | - Pabitra Pal Choudhury
- Applied Statistics Unit, Indian Statistical Institute, Kolkata 700108, West Bengal, India
| | - Bidyut Roy
- Human Genetics Unit, Indian Statistical Institute, Kolkata 700108, West Bengal, India
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17
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Sengupta A, Hassan SS, Choudhury PP. Clade GR and clade GH isolates of SARS-CoV-2 in Asia show highest amount of SNPs. Infect Genet Evol 2021; 89:104724. [PMID: 33476804 PMCID: PMC7816605 DOI: 10.1016/j.meegid.2021.104724] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/04/2021] [Accepted: 01/11/2021] [Indexed: 02/06/2023]
Abstract
Clades are monophyletic groups composed of a common ancestor and all its lineal descendants. As the propensity of virulence of a disease depends upon the type of clade the virus belongs to and it causes different fatality rates of disease in different countries, so the clade-wise analysis of SARS-CoV-2 isolates collected from different countries can illuminate the actual evolutionary relationships between them. In this study, 1566 SARS-CoV-2 genome sequences across ten Asian countries are collected, clustered, and characterized based on the clade they belong to. The isolates are compared to the Wuhan reference sequence” hCoV-19/Wuhan/WIV04/19″ to identify the mutations that occurred at different protein regions. Structural changes in amino acids due to mutations lead to functional instability of the proteins. Detailed clade-wise functional assessments are carried out to quantify the stability and vulnerability of the mutations occurring in SARS-CoV-2 genomes which can shade light on personalized prevention and treatment of the disease and encourage towards the invention of clade-specific vaccines.
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Affiliation(s)
- Antara Sengupta
- Department of Computer Science and Engineering, University of Calcutta, West Bengal, India.
| | - Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur, West Bengal, India
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18
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Seyran M, Takayama K, Uversky VN, Lundstrom K, Palù G, Sherchan SP, Attrish D, Rezaei N, Aljabali AAA, Ghosh S, Pizzol D, Chauhan G, Adadi P, Mohamed Abd El-Aziz T, Soares AG, Kandimalla R, Tambuwala M, Hassan SS, Azad GK, Pal Choudhury P, Baetas-da-Cruz W, Serrano-Aroca Á, Brufsky AM, Uhal BD. The structural basis of accelerated host cell entry by SARS-CoV-2†. FEBS J 2020; 288:5010-5020. [PMID: 33264497 PMCID: PMC7753708 DOI: 10.1111/febs.15651] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 11/30/2020] [Indexed: 12/11/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is the causative agent of the pandemic coronavirus disease 2019 (COVID‐19) that exhibits an overwhelming contagious capacity over other human coronaviruses (HCoVs). This structural snapshot describes the structural bases underlying the pandemic capacity of SARS‐CoV‐2 and explains its fast motion over respiratory epithelia that allow its rapid cellular entry. Based on notable viral spike (S) protein features, we propose that the flat sialic acid‐binding domain at the N‐terminal domain (NTD) of the S1 subunit leads to more effective first contact and interaction with the sialic acid layer over the epithelium, and this, in turn, allows faster viral ‘surfing’ of the epithelium and receptor scanning by SARS‐CoV‐2. Angiotensin‐converting enzyme 2 (ACE‐2) protein on the epithelial surface is the primary entry receptor for SARS‐CoV‐2, and protein–protein interaction assays demonstrate high‐affinity binding of the spike protein (S protein) to ACE‐2. To date, no high‐frequency mutations were detected at the C‐terminal domain of the S1 subunit in the S protein, where the receptor‐binding domain (RBD) is located. Tight binding to ACE‐2 by a conserved viral RBD suggests the ACE2‐RBD interaction is likely optimal. Moreover, the viral S subunit contains a cleavage site for furin and other proteases, which accelerates cell entry by SARS‐CoV‐2. The model proposed here describes a structural basis for the accelerated host cell entry by SARS‐CoV‐2 relative to other HCoVs and also discusses emerging hypotheses that are likely to contribute to the development of antiviral strategies to combat the pandemic capacity of SARS‐CoV‐2.
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Affiliation(s)
- Murat Seyran
- Doctoral Studies in Natural and Technical Sciences (SPL 44), University of Vienna, Austria.,Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Vienna, Austria
| | - Kazuo Takayama
- Center for iPS Cell Research and Application, Kyoto University, Japan
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | | | - Giorgio Palù
- Department of Molecular Medicine, University of Padova, Italy
| | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, New Orleans, LA, USA
| | - Diksha Attrish
- Dr. B R Ambedkar Center for Biomedical Research (ACBR), University of Delhi (North Camps), Delhi, India
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Iran.,Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Stockholm, Sweden
| | - Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Yarmouk University, Irbid, Jordan
| | - Shinjini Ghosh
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
| | - Damiano Pizzol
- Italian Agency for Development Cooperation - Khartoum, Al Amarat, Sudan
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnologico de Monterrey, Mexico
| | - Parise Adadi
- Department of Food Science, University of Otago, Dunedin, New Zealand
| | - Tarek Mohamed Abd El-Aziz
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, TX, USA.,Zoology Department, Faculty of Science, Minia University, El-Minia, Egypt
| | - Antonio G Soares
- Zoology Department, Faculty of Science, Minia University, El-Minia, Egypt
| | - Ramesh Kandimalla
- Applied Biology, CSIR-Indian Institute of Chemical Technology, Tarnaka, India.,Department of Biochemistry, Kakatiya Medical College, Warangal, India
| | - Murtaza Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine, UK
| | - Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Paschim Medinipur, India
| | | | | | - Wagner Baetas-da-Cruz
- Translational Laboratory in Molecular Physiology, Centre for Experimental Surgery, College of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia San Vicente Mártir, Valencia, Spain
| | - Adam M Brufsky
- Department of Medicine, Division of Hematology/Oncology, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Bruce D Uhal
- Department of Physiology, Michigan State University, East Lansing, MI, USA
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Hassan SS, Ghosh S, Attrish D, Choudhury PP, Aljabali AAA, Uhal BD, Lundstrom K, Rezaei N, Uversky VN, Seyran M, Pizzol D, Adadi P, Soares A, El-Aziz TMA, Kandimalla R, Tambuwala MM, Azad GK, Sherchan SP, Baetas-da-Cruz W, Takayama K, Serrano-Aroca Á, Chauhan G, Palu G, Brufsky AM. Possible Transmission Flow of SARS-CoV-2 Based on ACE2 Features. Molecules 2020; 25:molecules25245906. [PMID: 33322198 PMCID: PMC7763092 DOI: 10.3390/molecules25245906] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/10/2020] [Accepted: 12/10/2020] [Indexed: 02/06/2023] Open
Abstract
Angiotensin-converting enzyme 2 (ACE2) is the cellular receptor for the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) that is engendering the severe coronavirus disease 2019 (COVID-19) pandemic. The spike (S) protein receptor-binding domain (RBD) of SARS-CoV-2 binds to the three sub-domains viz. amino acids (aa) 22–42, aa 79–84, and aa 330–393 of ACE2 on human cells to initiate entry. It was reported earlier that the receptor utilization capacity of ACE2 proteins from different species, such as cats, chimpanzees, dogs, and cattle, are different. A comprehensive analysis of ACE2 receptors of nineteen species was carried out in this study, and the findings propose a possible SARS-CoV-2 transmission flow across these nineteen species.
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Affiliation(s)
- Sk. Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram 721140, India;
| | - Shinjini Ghosh
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata 700009, India;
| | - Diksha Attrish
- Dr. B. R. Ambedkar Centre for Biomedical Research (ACBR), University of Delhi (North Campus), Delhi 110007, India;
| | - Pabitra Pal Choudhury
- Applied Statistics Unit, Indian Statistical Institute, Kolkata 700108, West Bengal, India;
| | - Alaa A. A. Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Yarmouk University-Faculty of Pharmacy, Irbid 566, Jordan;
| | - Bruce D. Uhal
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA;
| | | | - Nima Rezaei
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children’s Medical Center, Tehran University of Medical Sciences, Tehran 1416753955, Iran;
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), SE-123 Stockholm, Sweden
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Correspondence:
| | - Murat Seyran
- Doctoral studies in natural and technical sciences (SPL 44), University of Vienna, 1010 Wien, Austria;
| | - Damiano Pizzol
- Italian Agency for Development Cooperation—Khartoum, Sudan Street 33, Al Amarat, Khartoum 825109, Sudan;
| | - Parise Adadi
- Department of Food Science, University of Otago, Dunedin 9054, New Zealand;
| | - Antonio Soares
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX 77030, USA; (A.S.); (T.M.A.E.-A.)
| | - Tarek Mohamed Abd El-Aziz
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX 77030, USA; (A.S.); (T.M.A.E.-A.)
- Zoology Department, Faculty of Science, Minia University, El-Minia 61519, Egypt
| | - Ramesh Kandimalla
- Applied Biology, CSIR-Indian Institute of Chemical Technology Uppal Road, Tarnaka, Hyderabad 500007, India;
- Department of Biochemistry, Kakatiya Medical College, Warangal, Telangana 500022, India
| | - Murtaza M. Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK;
| | | | - Samendra P. Sherchan
- Department of Environmental Health Sciences, Tulane University, New Orleans, LA 70112, USA;
| | - Wagner Baetas-da-Cruz
- Translational Laboratory in Molecular Physiology, Centre for Experimental Surgery, College of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941901, Brazil;
| | - Kazuo Takayama
- Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8501, Japan;
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Translational Research Centre San Alberto Magno, Catholic University of Valencia San Vicente Mártir, c/Guillem de Castro 94, 46001 Valencia, Spain;
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501 Sur, Monterrey 64849, Nuevo León, Mexico;
| | - Giorgio Palu
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121 Padova, Italy;
| | - Adam M. Brufsky
- Division of Hematology/Oncology, Department of Medicine, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA;
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Hassan SS, Choudhury PP, Uversky VN, Dayhoff GW, Aljabali AAA, Uhal BD, Lundstrom K, Rezaei N, Seyran M, Pizzol D, Adadi P, Lal A, Soares A, Abd El-aziz TM, Kandimalla R, Tambuwala M, Azad GK, Sherchan SP, Baetas-da-cruz W, Takayama K, Serrano-aroca Á, Chauhan G, Palu G, Brufsky AM. Variability of Accessory Proteins Rules the SARS-CoV-2 Pathogenicity.. [DOI: 10.1101/2020.11.06.372227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
AbstractThe coronavirus disease 2019 (COVID-19) is caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) which is pandemic with an estimated fatality rate less than 1% is ongoing. SARS-CoV-2 accessory proteins ORF3a, ORF6, ORF7a, ORF7b, ORF8, and ORF10 with putative functions to manipulate host immune mechanisms such as interferons, immune signaling receptor NLRP3 (NOD-, LRR-, and pyrin domain-containing 3) inflammasome, inflammatory cytokines such as interleukin 1β(IL-1β) are critical in COVID-19 pathology. Outspread variations of each of the six accessory proteins of all complete proteomes (available as of October 26, 2020, in the National Center for Biotechnology Information depository) of SARS-CoV-2, were observed across six continents. Across all continents, the decreasing order of percentage of unique variations in the accessory proteins was found to be ORF3a>ORF8>ORF7a>ORF6>ORF10>ORF7b. The highest and lowest unique variations of ORF3a were observed in South America and Oceania, respectively. This finding suggests that the wide variations of accessory proteins seem to govern the pathogenicity of SARS-CoV-2, and consequently, certain propositions and recommendations can be made in the public interest.
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Hassan SS, Choudhury PP, Roy B. SARS-CoV2 envelope protein: non-synonymous mutations and its consequences. Genomics 2020; 112:3890-3892. [PMID: 32640274 PMCID: PMC7335631 DOI: 10.1016/j.ygeno.2020.07.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 06/30/2020] [Accepted: 07/01/2020] [Indexed: 01/09/2023]
Abstract
In the NCBI database, as on June 6, 2020, total number of available complete genome sequences of SARS-CoV2 across the world is 3617. The envelope (E) protein of SARS-CoV2 possesses several non-synonymous mutations over the transmembrane and C-terminus domains in 15 (0.414%) genomes among 3617 SARS-CoV2 genomes, analyzed. More precisely, 10(0.386%) out of 2588 genomes from the USA, 3(0.806%) from Asia, 1 (0.348%) from Europe and 1 (0.274%) from Oceania contained the missense mutations over the E-protein of SARS-CoV2 genomes. The C-terminus motif DLLV has been to DFLV and YLLV in the proteins from QJR88103 (Australia: Victoria) and QKI36831 (China: Guangzhou) respectively, which might affect the binding of this motif with the host protein PALS1.
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Affiliation(s)
- Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur, 721140, West Bengal, India.
| | - Pabitra Pal Choudhury
- Applied Statistics Unit, Indian Statistical Institute, Kolkata 700108, West Bengal, India.
| | - Bidyut Roy
- Human Genetics Unit, Indian Statistical Institute, Kolkata 700108, West Bengal, India.
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22
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Hassan SS, Choudhury PP, Roy B, Jana SS. Missense mutations in SARS-CoV2 genomes from Indian patients. Genomics 2020; 112:4622-4627. [PMID: 32822756 PMCID: PMC7434617 DOI: 10.1016/j.ygeno.2020.08.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/14/2020] [Accepted: 08/14/2020] [Indexed: 12/20/2022]
Abstract
The genetic diversity of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV2) in several countries sums up to worldwide genetic diversity. In this present study, variations in terms of missense mutations among the SARS-CoV2 genomes from 128 Indian patients, as of May 2020, are accounted and thereby some key findings with some hypotheses were made. These mutations across various genes of these genomes show wide genetic variations in sequence and rapid evolution of SARS-CoV2 virus. The presence of unique mutations in the studied SARS-CoV2 genomes may led to their attenuation. Few Genes such as ORF6, ORF10 are free from any mutations in the Indian context of 339 genomes observed as of 14th July 2020. Further, E protein contains only one mutation. This may suggest that designing a therapeutic approach against ORF6, ORF10 and E genes may have a beneficial effect in controlling COVID-19 pandemic especially in India.
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Affiliation(s)
- Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram 721140, India.
| | - Pabitra Pal Choudhury
- Applied Statistics Unit, Indian Statistical Institute, Kolkata 700108, West Bengal, India
| | - Bidyut Roy
- Human Genetics Unit, Indian Statistical Institute, Kolkata 700108, West Bengal, India.
| | - Siddhartha Sankar Jana
- School of Biological Sciences, Indian Association for the Cultivation of Science, West Bengal 700032, India.
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23
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Abstract
Envelope (E) protein is one of the structural viroporins (76-109 amino acids long) present in the coronavirus. Sixteen sequentially different E-proteins were observed from a total of 4917 available complete SARS-CoV-2 genomes as on 18th June 2020 in the NCBI database. The missense mutations over the envelope protein across various coronaviruses of the β-genus were analyzed to know the immediate parental origin of the envelope protein of SARS-CoV-2. The evolutionary origin is also endorsed by the phylogenetic analysis of the envelope proteins comparing sequence homology as well as amino acid conservations.
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Affiliation(s)
- Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur, 721140, West Bengal, India.
| | - Pabitra Pal Choudhury
- Applied Statistics Unit, Indian Statistical Institute, Kolkata 700108, West Bengal, India
| | - Bidyut Roy
- Human Genetics Unit, Indian Statistical Institute, Kolkata 700108, West Bengal, India.
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Lundstrom K, Seyran M, Pizzol D, Adadi P, Mohamed Abd El-Aziz T, Hassan SS, Soares A, Kandimalla R, Tambuwala MM, Aljabali AAA, Kumar Azad G, Pal Choudhury P, Uversky VN, Sherchan SP, Uhal BD, Rezaei N, Brufsky AM. Viewpoint: Origin of SARS-CoV-2. Viruses 2020; 12:v12111203. [PMID: 33105685 PMCID: PMC7690418 DOI: 10.3390/v12111203] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/20/2020] [Accepted: 10/20/2020] [Indexed: 01/13/2023] Open
Abstract
The origin of the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) virus causing the COVID-19 pandemic has not yet been fully determined. Despite the consensus about the SARS-CoV-2 origin from bat CoV RaTG13, discrepancy to host tropism to other human Coronaviruses exist. SARS-CoV-2 also possesses some differences in its S protein receptor-binding domain, glycan-binding N-terminal domain and the surface of the sialic acid-binding domain. Despite similarities based on cryo-EM and biochemical studies, the SARS-CoV-2 shows higher stability and binding affinity to the ACE2 receptor. The SARS-CoV-2 does not appear to present a mutational “hot spot” as only the D614G mutation has been identified from clinical isolates. As laboratory manipulation is highly unlikely for the origin of SARS-CoV-2, the current possibilities comprise either natural selection in animal host before zoonotic transfer or natural selection in humans following zoonotic transfer. In the former case, despite SARS-CoV-2 and bat RaTG13 showing 96% identity some pangolin Coronaviruses exhibit very high similarity to particularly the receptor-binding domain of SARS-CoV-2. In the latter case, it can be hypothesized that the SARS-CoV-2 genome has adapted during human-to-human transmission and based on available data, the isolated SARS-CoV-2 genomes derive from a common origin. Before the origin of SARS-CoV-2 can be confirmed additional research is required
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Affiliation(s)
| | - Murat Seyran
- Doctoral Studies in Natural Sciences and Technology SPL44, University of Vienna, 1010 Vienna, Austria;
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Vienna, 1010 Vienna, Austria
| | - Damiano Pizzol
- Department of Global Health, Italian Agency for Development Cooperation—Khartoum, Al Amarat 111111, Sudan;
| | - Parise Adadi
- Department of Food Science, University of Otago, Dunedin 9054, New Zealand;
| | - Tarek Mohamed Abd El-Aziz
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229-3900, USA; (T.M.A.E.-A.); (A.S.)
- Zoology Department, Faculty of Science, Minia University, El-Minia 61519, Egypt
| | - Sk. Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur, West Bengal 721140, India;
| | - Antonio Soares
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229-3900, USA; (T.M.A.E.-A.); (A.S.)
| | - Ramesh Kandimalla
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500007, India;
- Department of Biochemistry, Kakatiya Medical College/MGM-Hospital, Hyderabad 500007, India
| | - Murtaza M. Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK;
| | - Alaa A. A. Aljabali
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Yarmouk University, Irbid 21163, Jordan;
| | | | - Pabitra Pal Choudhury
- Applied Statistics Unit, Indian Statistical Institute, Kolkata, West Bengal 700108, India;
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA;
| | - Samendra P. Sherchan
- Department of Environmental Health Sciences, Tulane University, New Orleans, LA 70112, USA;
| | - Bruce D. Uhal
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA;
| | - Nima Rezaei
- Center for Immunodeficiencies, Pediatrics Center of Excellence, Children’s Medical Center, Tehran University of Medical Sciences, Tehran 1419733151, Iran;
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran 1419733151, Iran
| | - Adam M. Brufsky
- UPMC Hillman Cancer Center, Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA;
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25
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Hassan SS, Attrish D, Ghosh S, Choudhury PP, Uversky VN, Uhal BD, Lundstrom K, Rezaei N, Aljabali AAA, Seyran M, Pizzol D, Adadi P, Abd El-aziz TM, Soares A, Kandimalla R, Tambuwala M, Lal A, Azad GK, Sherchan SP, Baetas-da-cruz W, Palù G, Brufsky AM. Notable sequence homology of the ORF10 protein introspects the architecture of SARS-COV-2.. [DOI: 10.1101/2020.09.06.284976] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
ABSTRACTThe global public health is endangered due to COVID-19 pandemic, which is caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). Despite having similar pathology to MERS and SARS-CoV, the infection fatality rate of SARS-CoV-2 is likely lower than 1%. SARS-CoV-2 has been reported to be uniquely characterized by the accessory protein ORF10, which contains eleven cytotoxic T lymphocyte (CTL) epitopes of nine amino acids length each, across various human leukocyte antigen (HLA) subtypes. In this study, all missense mutations found in sequence databases were examined across twnety-two unique SARS-CoV-2 ORF10 variants that could possibly alter viral pathogenicity. Some of these mutations decrease the stability of ORF10, e.g. I4L and V6I were found in the MoRF region of ORF10 which may also possibly contribute to Intrinsic protein disorder. Furthermore, a physicochemical and structural comparative analysis was carried out on SARS-CoV-2 and Pangolin-CoV ORF10 proteins, which share 97.37% amino acid homology. The high degree of physicochemical and structural similarity of ORF10 proteins of SARS-CoV-2 and Pangolin-CoV open questions about the architecture of SARS-CoV-2 due to the disagreement of these two ORF10 proteins over their sub-structure (loop/coil region), solubility, antigenicity and change from the strand to coil at amino acid position 26, where tyrosine is present. Altogether, SARS-CoV-2 ORF10 is a promising pharmaceutical target and a protein which should be monitored for changes which correlate to change pathogenesis and clinical course of COVID-19 infection.
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Hassan SS, Choudhury PP, Basu P, Jana SS. Molecular conservation and differential mutation on ORF3a gene in Indian SARS-CoV2 genomes. Genomics 2020; 112:3226-3237. [PMID: 32540495 PMCID: PMC7291963 DOI: 10.1016/j.ygeno.2020.06.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 06/06/2020] [Accepted: 06/08/2020] [Indexed: 01/28/2023]
Abstract
A global emergency due to the COVID-19 pandemic demands various studies related to genes and genomes of the SARS-CoV2. Among other important proteins, the role of accessory proteins are of immense importance in replication, regulation of infections of the coronavirus in the hosts. The largest accessory protein in the SARS-CoV2 genome is ORF3a which modulates the host response to the virus infection and consequently it plays an important role in pathogenesis. In this study, an attempt is made to decipher the conservation of nucleotides, dimers, codons and amino acids in the ORF3a genes across thirty-two genomes of Indian patients. ORF3a gene possesses single and double point mutations in Indian SARS-CoV2 genomes suggesting the change of SARS-CoV2's virulence property in Indian patients. We find that the parental origin of the ORF3a gene over the genomes of SARS-CoV2 and Pangolin-CoV is same from the phylogenetic analysis based on conservation of nucleotides and so on. This study highlights the accumulation of mutation on ORF3a in Indian SARS-CoV2 genomes which may provide the designing therapeutic approach against SARS-CoV2.
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Affiliation(s)
- Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram 721140, India.
| | - Pabitra Pal Choudhury
- Applied Statistics Unit, Indian Statistical Institute, Kolkata 700108, West Bengal, India.
| | - Pallab Basu
- Mandelstem Institute, School of Physics, University of the Witwatersrand, Johannesburg, South Africa.
| | - Siddhartha Sankar Jana
- School of Biological Sciences, Indian Association for the Cultivation of Science, West Bengal 700032, India.
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27
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Das JK, Choudhury PP, Chaturvedi N, Tayyab M, Hassan SS. Ranking and clustering of Drosophila olfactory receptors using mathematical morphology. Genomics 2019; 111:549-559. [DOI: 10.1016/j.ygeno.2018.03.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 02/12/2018] [Accepted: 03/07/2018] [Indexed: 11/26/2022]
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Das JK, Choudhury PP, Chaudhuri A, Hassan SS, Basu P. Analysis of Purines and Pyrimidines distribution over miRNAs of Human, Gorilla, Chimpanzee, Mouse and Rat. Sci Rep 2018; 8:9974. [PMID: 29967426 PMCID: PMC6028587 DOI: 10.1038/s41598-018-28289-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 06/19/2018] [Indexed: 12/18/2022] Open
Abstract
Meaningful words in English need vowels to break up the sounds that consonants make. The Nature has encoded her messages in RNA molecules using only four alphabets A, U, C and G in which the nine member double-ring bases (adenine (A) and Guanine (G)) are purines, while the six member single-ring bases (cytosine (C) and uracil (U)) are pyrimidines. Four bases A, U, C and G of RNA sequences are divided into three kinds of classifications according to their chemical properties. One of the three classifications, the purine-pyrimidine class is important. In understanding the distribution (organization) of purines and pyrimidines over some of the non-coding RNAs, all miRNAs of the three species (human, gorilla and chimpanzee) of Hominidae family and two species (mouse and rat) from of Muridae family are considered. The distribution of purines and pyrimidines over miRNA shows deviation from randomness. Based on the quantitative metrics (fractal dimension, Hurst exponent, Hamming distance, distance pattern of purine-pyrimidine, density distribution of purine-pyrimidine and Shannon entropy) five different clusters have been made for the five species. We have observed some couple of results including the closeness of different clusters among the five species.
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Affiliation(s)
- Jayanta Kumar Das
- Applied Statistics Unit, Indian Statistical Institute, 203 B.T. Road, Kolkata, 700108, West Bengal, India.
| | - Pabitra Pal Choudhury
- Applied Statistics Unit, Indian Statistical Institute, 203 B.T. Road, Kolkata, 700108, West Bengal, India
| | - Adwitiya Chaudhuri
- Department of Zoology, Pingla Thana Mahavidyalaya, Paschim Medinipur, 722140, West Bengal, India
| | - Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Paschim Medinipur, 722140, West Bengal, India
| | - Pallab Basu
- International Centre for Theoretical Sciences, TIFR, Bangalore, 560089, Karnataka, India
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29
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Rout RK, Pal Choudhury P, Maity SP, Daya Sagar BS, Hassan SS. Fractal and mathematical morphology in intricate comparison between tertiary protein structures. Computer Methods in Biomechanics and Biomedical Engineering: Imaging & Visualization 2018. [DOI: 10.1080/21681163.2016.1214850] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Ranjeet Kumar Rout
- Department of Computer Science and Engineering, National Institute of Technology, Jalandhar, India
| | | | - Santi Prasad Maity
- Information Technology, Indian Institute of Engineering Science and Technology, Shibpur, Howrah, India
| | - B. S. Daya Sagar
- Systems Science and Informatics Unit, Indian Statistical Institute (ISI), Bangalore, India
| | - Sk. Sarif Hassan
- Department of Mathematics, College of Engineering Studies, University of Petroleum and Energy Studies, Dehradun, India
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30
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Basak P, Maitra-Majee S, Das JK, Mukherjee A, Ghosh Dastidar S, Pal Choudhury P, Lahiri Majumder A. An evolutionary analysis identifies a conserved pentapeptide stretch containing the two essential lysine residues for rice L-myo-inositol 1-phosphate synthase catalytic activity. PLoS One 2017; 12:e0185351. [PMID: 28950028 PMCID: PMC5614600 DOI: 10.1371/journal.pone.0185351] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 09/11/2017] [Indexed: 12/11/2022] Open
Abstract
A molecular evolutionary analysis of a well conserved protein helps to determine the essential amino acids in the core catalytic region. Based on the chemical properties of amino acid residues, phylogenetic analysis of a total of 172 homologous sequences of a highly conserved enzyme, L-myo-inositol 1-phosphate synthase or MIPS from evolutionarily diverse organisms was performed. This study revealed the presence of six phylogenetically conserved blocks, out of which four embrace the catalytic core of the functional protein. Further, specific amino acid modifications targeting the lysine residues, known to be important for MIPS catalysis, were performed at the catalytic site of a MIPS from monocotyledonous model plant, Oryza sativa (OsMIPS1). Following this study, OsMIPS mutants with deletion or replacement of lysine residues in the conserved blocks were made. Based on the enzyme kinetics performed on the deletion/replacement mutants, phylogenetic and structural comparison with the already established crystal structures from non-plant sources, an evolutionarily conserved peptide stretch was identified at the active pocket which contains the two most important lysine residues essential for catalytic activity.
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Affiliation(s)
- Papri Basak
- Division of Plant Biology, Bose Institute (Centenary Campus), Kolkata, West Bengal, India
| | - Susmita Maitra-Majee
- Division of Plant Biology, Bose Institute (Centenary Campus), Kolkata, West Bengal, India
| | - Jayanta Kumar Das
- Applied Statistics Unit, Indian Statistical Institute, Kolkata, West Bengal, India
| | - Abhishek Mukherjee
- Division of Plant Biology, Bose Institute (Centenary Campus), Kolkata, West Bengal, India
| | | | | | - Arun Lahiri Majumder
- Division of Plant Biology, Bose Institute (Centenary Campus), Kolkata, West Bengal, India
- * E-mail:
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Das JK, Pal Choudhury P. Chemical property based sequence characterization of PpcA and its homolog proteins PpcB-E: A mathematical approach. PLoS One 2017; 12:e0175031. [PMID: 28362850 PMCID: PMC5376323 DOI: 10.1371/journal.pone.0175031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/20/2017] [Indexed: 11/19/2022] Open
Abstract
Periplasmic c7 type cytochrome A (PpcA) protein is determined in Geobacter sulfurreducens along with its other four homologs (PpcB-E). From the crystal structure viewpoint the observation emerges that PpcA protein can bind with Deoxycholate (DXCA), while its other homologs do not. But it is yet to be established with certainty the reason behind this from primary protein sequence information. This study is primarily based on primary protein sequence analysis through the chemical basis of embedded amino acids. Firstly, we look for the chemical group specific score of amino acids. Along with this, we have developed a new methodology for the phylogenetic analysis based on chemical group dissimilarities of amino acids. This new methodology is applied to the cytochrome c7 family members and pinpoint how a particular sequence is differing with others. Secondly, we build a graph theoretic model on using amino acid sequences which is also applied to the cytochrome c7 family members and some unique characteristics and their domains are highlighted. Thirdly, we search for unique patterns as subsequences which are common among the group or specific individual member. In all the cases, we are able to show some distinct features of PpcA that emerges PpcA as an outstanding protein compared to its other homologs, resulting towards its binding with deoxycholate. Similarly, some notable features for the structurally dissimilar protein PpcD compared to the other homologs are also brought out. Further, the five members of cytochrome family being homolog proteins, they must have some common significant features which are also enumerated in this study.
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Affiliation(s)
- Jayanta Kumar Das
- Applied Statistics Unit, Indian Statistical Institute, 203 B.T Road, Kolkata-700108, West Bengal, India
| | - Pabitra Pal Choudhury
- Applied Statistics Unit, Indian Statistical Institute, 203 B.T Road, Kolkata-700108, West Bengal, India
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Das JK, Das P, Ray KK, Choudhury PP, Jana SS. Mathematical Characterization of Protein Sequences Using Patterns as Chemical Group Combinations of Amino Acids. PLoS One 2016; 11:e0167651. [PMID: 27930687 PMCID: PMC5145171 DOI: 10.1371/journal.pone.0167651] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 11/17/2016] [Indexed: 01/08/2023] Open
Abstract
Comparison of amino acid sequence similarity is the fundamental concept behind the protein phylogenetic tree formation. By virtue of this method, we can explain the evolutionary relationships, but further explanations are not possible unless sequences are studied through the chemical nature of individual amino acids. Here we develop a new methodology to characterize the protein sequences on the basis of the chemical nature of the amino acids. We design various algorithms for studying the variation of chemical group transitions and various chemical group combinations as patterns in the protein sequences. The amino acid sequence of conventional myosin II head domain of 14 family members are taken to illustrate this new approach. We find two blocks of maximum length 6 aa as 'FPKATD' and 'Y/FTNEKL' without repeating the same chemical nature and one block of maximum length 20 aa with the repetition of chemical nature which are common among all 14 members. We also check commonality with another motor protein sub-family kinesin, KIF1A. Based on our analysis we find a common block of length 8 aa both in myosin II and KIF1A. This motif is located in the neck linker region which could be responsible for the generation of mechanical force, enabling us to find the unique blocks which remain chemically conserved across the family. We also validate our methodology with different protein families such as MYOI, Myosin light chain kinase (MLCK) and Rho-associated protein kinase (ROCK), Na+/K+-ATPase and Ca2+-ATPase. Altogether, our studies provide a new methodology for investigating the conserved amino acids' pattern in different proteins.
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Affiliation(s)
- Jayanta Kumar Das
- Applied Statistics Unit, Indian Statistical Institute, 203 B.T Road, Kolkata-700108, West Bengal, India
| | - Provas Das
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Kolkata-700032, West Bengal, India
| | - Korak Kumar Ray
- Department of Chemistry, Indian Institute of Technology-Bombay, IIT Bombay, Powai, Mumbai-400076, Maharashtra, India
| | - Pabitra Pal Choudhury
- Applied Statistics Unit, Indian Statistical Institute, 203 B.T Road, Kolkata-700108, West Bengal, India
| | - Siddhartha Sankar Jana
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Kolkata-700032, West Bengal, India
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Yadav U, Choudhury PP. Biodegradation of sulfosulphuron in agricultural soil by Trichoderma sp. Lett Appl Microbiol 2014; 59:479-86. [PMID: 25041702 DOI: 10.1111/lam.12306] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 06/05/2014] [Accepted: 07/04/2014] [Indexed: 11/30/2022]
Abstract
UNLABELLED Sulfosulphuron-degrading fungus was isolated by enrichment technique from the sulfosulphuron-contaminated soil of wheat rhizosphere. To assess the biodegradation potential of isolated Trichoderma sp., minimal potato dextrose agar broth with different levels of sulfosulphuron (up to 2 g l(-1) ) was evaluated in the growth and biotransformation experiments. ESI LC-MS/MS analysis revealed the presence of degradation products 2-amino-4,6-dimethoxypyrimidine (I) and 2-ethylsulfonyl imidazo{1,2-a} pyridine-3-sulfonamide-2-ethylsulfonyl imidazo{1,2-a} pyridine-3-sulfonamide (II) indicating the cleavage of the urea bridge and the presence of the by-product N-(4,6-dimethoxypyrimidin-2-yl)urea (III) indicating the degradation of sulfonylamide linkage. Two other metabolites, N-(4,6-dimethoxypyrimidin-2-yl)-N'-hydroxyurea (IV) and N, N'-bis(4,6-dimethoxypyrimidin-2-yl)urea (V), were also identified. From the previous reports, it was found that the degradation of sulfonyl urea herbicides took place through the chemical degradation of the sulfonylurea bridge followed by microbial degradation. During this investigation, Trichoderma sp. grew well with and degraded sulfosulphuron via both the decarboxylation on the sulphonyl urea bridge and the hydrolytic cleavage of the sulfonylamide linkage as demonstrated by the formation of metabolites. Trichoderma is nonphytopathogenic in nature, and some species of it restrict the growth of soil-dwelling phytopathogens. Therefore, it is a promising candidate for the decontamination of soil from sulfosulphuron residues. SIGNIFICANCE AND IMPACT OF THE STUDY The degradation of sulfosulphuron by any individual fungus is being reported for the first time. Trichoderma sp. isolated from wheat-rhizospheric soil could survive in minimal broth rich in sulfosulphuron. Previous reports have described the complete degradation of any sulfonyl urea herbicides by micro-organisms only after the pH-dependent chemical hydrolysis of the sulfonyl urea bridge of the herbicide. This study demonstrates the novel result that the Trichoderma sp. utilized the sulfosulphuron as a sole carbon source and degraded it by cleaving sulfonyl urea bridge and sulfonylamide linkage. Thus, the application of Trichoderma sp., which is nonphytopathogenic, has the potential to decontaminate agricultural soil from sulfosulphuron load.
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Affiliation(s)
- U Yadav
- Govt. M. H. Autonomous College of Home Science and Science for Women, Rani Durgavati Vishwavidayalaya, Jabalpur, MP, India
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Hassan SS, Choudhury PP, Goswami A. Underlying mathematics in diversification of human olfactory receptors in different loci. Interdiscip Sci 2014; 5:270-3. [PMID: 24402819 DOI: 10.1007/s12539-013-0176-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Revised: 03/13/2012] [Accepted: 01/22/2013] [Indexed: 11/27/2022]
Abstract
As per conservative estimate, approximately 51-105 Olfactory Receptors (ORs) loci are present in human genome occurring in clusters. These clusters are apparently unevenly spread as mosaics over 21 pairs of human chromosomes. Olfactory Receptor (OR) gene families which are thought to have expanded for the need to provide recognition capability for a huge number of pure and complex odorants, form the largest known multigene family in the human genome. Recent studies have shown that 388 full length and 414 OR pseudo-genes are present in these OR genomic clusters. In this paper, the authors report a classification method for all human ORs based on their sequential quantitative information like presence of poly strings of nucleotides bases, long range correlation and so on. An L-System generated sequence has been taken as an input into a star-model of specific subfamily members and resultant sequence has been mapped to a specific OR based on the classification scheme using fractal parameters like Hurst exponent and fractal dimensions.
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Affiliation(s)
- Sk Sarif Hassan
- Applied Statistics Unit, Indian Statistical Institute, Kolkata, 700108, India,
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Hassan SS, Pal Choudhury P, Dayasagar BS, Chakraborty S, Guha R, Goswami A. Understanding Genomic Evolution of Olfactory Receptors through Fractal and Mathematical Morphology. ACTA ACUST UNITED AC 2011. [DOI: 10.1038/npre.2011.5674.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
AbstractFractals and Mathematical Morphology are immensely used to study many problems in different branches of science and technology including the domain of Biology. There are many more unrevealed facts and figures of genes and genome in Computational Biology. In this paper, our objective is to explore how the evolutionary network is associated among Human, Chimpanzee and Mouse with regards to their genomic information. We are about to explore their genomic evolution through the quantitative measures of fractals and morphology. We have considered olfactory receptors for our case study. These olfactory receptors do function in different species with subtle differences in the structures of DNA sequences. Those subtle differences can be exposed through intricate details of Fractals and Mathematical Morphology.
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Hassan SS, Choudhury PP, Pal A, Brahmachary RL, Goswami A. Designing exons for human olfactory receptor gene subfamilies using a mathematical paradigm. J Biosci 2011; 35:389-93. [PMID: 20826948 DOI: 10.1007/s12038-010-0044-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Ligands for only two human olfactory receptors are known. One of them, OR1D2, binds to Bourgeonal, a volatile chemical constituent of the fragrance of the mythical flower, Lily of the valley or Our Lady's tears, Convallaria majalis (also the national flower of Finland). OR1D2, OR1D4 and OR1D5 are three full-length olfactory receptors present in an olfactory locus in the human genome. These receptors are more than 80% identical in DNA sequences and have 108 base pair mismatches among them. Apparently, these mismatch positions show no striking pattern using computer pattern recognition tools. In an attempt to find a mathematical rule in those mismatches, we find that an L-system generated sequence can be inserted into the OR1D2 subfamily-specific star model and novel full-length olfactory receptors can be generated. This remarkable mathematical principle could be utilized for making new subfamily olfactory receptor members from any olfactory receptor subfamily. The aroma and electronic nose industry might utilize this rule in future.
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Affiliation(s)
- Sk Sarif Hassan
- Applied Statistics Unit, Indian Statistical Institute, 203 B T Road, Calcutta 700 108, India
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Hassan SS, Pal Choudhury P, Goswami A. Underlying Mathematics in Diversification of Human Olfactory Receptors in Different Loci. ACTA ACUST UNITED AC 2011. [DOI: 10.1038/npre.2010.5475.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
AbstractAs per conservative estimate, approximately (51-105) Olfactory Receptors (ORs) loci are present in human genome occurring in clusters. These clusters are apparently unevenly spread as mosaics over 21 pair of human chromosomes. Olfactory Receptor (OR) gene families which are thought to have expanded for the need to provide recognition capability for huge number of pure and complex odorants. ORs form the largest known multi-gene family in the human genome. Recent studies have shown that 388 full length and 414 OR pseudo-genes are present in these OR genomic clusters. In this paper, the authors report a classification method for all human ORs based on their sequential quantitative information like presence of poly strings of nucleotides bases, long range correlation and so on. An L-System generated sequence has been taken as an input into a star-model of specific subfamily members and resultant sequence has been mapped to a specific OR based on the classification scheme using fractal parameters like Hurst exponent and fractal dimensions.
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Goswami A, Pal Choudhury P, Pal A, Brahmachary RL, Hassan S. L-Systems: a mathematical paradigm for designing full length human genes and genomes. Genome Biol 2010. [PMCID: PMC3026243 DOI: 10.1186/gb-2010-11-s1-p15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Choudhury PP, Chowdhury AR. Economic return to the previous state for any nearest neighbourhood reversible autonomous finite state machines. Inf Sci (N Y) 2000. [DOI: 10.1016/s0020-0255(00)00011-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Abstract
A rapid reversed-phase HPLC method was developed for simultaneously determination of chlorimuron-ethyl and its metabolites such as ethyl-2-aminosulfonyl benzoate, 4-methoxy-6-chloro-2-amino pyrimidine and saccharin in soil and water systems by using RP18 column and methanol-water (70:30 v/v) solvent system with detection at 230 nm. The recoveries of chlorimuron-ethyl and its metabolites ranged from 80 to 95%.
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Affiliation(s)
- P P Choudhury
- Division of Agricultural Chemicals, Indian Agricultural Research Institute, New Delhi, India
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