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Das T, Mukerjee N, Ghosh A, Lorenzo JM, Dhama K, Dey A. Growing risk of aristolochic acid nephropathy in the era of COVID-19 - Correspondence. Int J Surg 2022; 108:106992. [PMID: 36372186 PMCID: PMC9650990 DOI: 10.1016/j.ijsu.2022.106992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/06/2022] [Indexed: 11/13/2022]
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2
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Design of siRNA molecules for silencing of membrane glycoprotein, nucleocapsid phosphoprotein, and surface glycoprotein genes of SARS-CoV2. J Genet Eng Biotechnol 2022; 20:65. [PMID: 35482116 PMCID: PMC9047631 DOI: 10.1186/s43141-022-00346-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 04/18/2022] [Indexed: 12/24/2022]
Abstract
The global COVID-19 pandemic caused by SARS-CoV2 infected millions of people and resulted in more than 4 million deaths worldwide. Apart from vaccines and drugs, RNA silencing is a novel approach for treating COVID-19. In the present study, siRNAs were designed for the conserved regions targeting three structural genes, M, N, and S, from forty whole-genome sequences of SARS-CoV2 using four different software, RNAxs, siDirect, i-Score Designer, and OligoWalk. Only siRNAs which were predicted in common by all the four servers were considered for further shortlisting. A multistep filtering approach has been adopted in the present study for the final selection of siRNAs by the usage of different online tools, viz., siRNA scales, MaxExpect, DuplexFold, and SMEpred. All these web-based tools consider several important parameters for designing functional siRNAs, e.g., target-site accessibility, duplex stability, position-specific nucleotide preference, inhibitory score, thermodynamic parameters, GC content, and efficacy in cleaving the target. In addition, a few parameters like GC content and dG value of the entire siRNA were also considered for shortlisting of the siRNAs. Antisense strands were subjected to check for any off-target similarities using BLAST. Molecular docking was carried out to study the interactions of guide strands with AGO2 protein. A total of six functional siRNAs (two for each gene) have been finally selected for targeting M, N, and S genes of SARS-CoV2. The siRNAs have not shown any off-target effects, interacted with the domain(s) of AGO2 protein, and were efficacious in cleaving the target mRNA. However, the siRNAs designed in the present study need to be tested in vitro and in vivo in the future.
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Ahmadi E, Bagherpour Z, Zarei E, Omidkhoda A. Pathological effects of SARS-CoV-2 on hematological and immunological cells: Alterations in count, morphology, and function. Pathol Res Pract 2022; 231:153782. [PMID: 35121363 PMCID: PMC8800420 DOI: 10.1016/j.prp.2022.153782] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 01/22/2022] [Accepted: 01/25/2022] [Indexed: 01/08/2023]
Abstract
The novel Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), the causative agent of COVID-19 outbreak, spread rapidly and infected more than 140 million people with more than three million victims worldwide. The SARS-CoV-2 causes destructive changes in the immunological and hematological system of the host. These alterations appear to play a critical role in disease pathology and the emerging of clinical manifestations. In this review, we aimed to discuss the effect of COVID-19 on the count, function and morphology of immune and blood cells and the role of these changes in the pathophysiology of the disease. Knowledge of these changes may help with better management and treatment of COVID-19 patients.
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Affiliation(s)
- Ehsan Ahmadi
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| | - Zahra Bagherpour
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran.
| | - Elmira Zarei
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran.
| | - Azadeh Omidkhoda
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran.
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4
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AI-powered drug repurposing for developing COVID-19 treatments. REFERENCE MODULE IN BIOMEDICAL SCIENCES 2022. [PMCID: PMC8865759 DOI: 10.1016/b978-0-12-824010-6.00005-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Emerging infectious diseases are an ever-present threat to public health, and COVID-19 is the most recent example. There is an urgent need to develop a robust framework to combat the disease with safe and effective therapeutic options. Compared to de novo drug discovery, drug repurposing may offer a lower-cost and faster drug discovery paradigm to explore potential treatment options of existing drugs. This chapter elucidates the advantages of artificial intelligence (AI) in enhancing the drug repurposing process from a data science perspective, using COVID-19 as an example. First, we elaborate on how AI-powered drug repurposing benefits from the accumulated data and knowledge of COVID-19 natural history and pathogenesis. Second, we summarize the pros and cons of AI-powered drug repurposing strategies to facilitate fit-for-purpose selection. Finally, we outline challenges of AI-powered drug repurposing from a regulatory perspective and suggest some potential solutions. AI-powered drug purposing is promising for emerging treatments for COVID-19 infection. Accumulated biological data profiles facilitate AI-based drug repurposing efforts for development of COVID-19 therapies. The ‘fit-for-purpose selection of AI-powered drug repurposing strategies is key to uncovering hidden information among drugs, targets, and diseases. Efforts from different stakeholders boost the adoption of AI-powered drug repurposing in the regulatory setting.
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Prasad A, Prasad M. Research and leaders: a twisted tale! Trends Genet 2021; 37:863-864. [PMID: 34218957 PMCID: PMC8436586 DOI: 10.1016/j.tig.2021.06.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 06/17/2021] [Accepted: 06/17/2021] [Indexed: 11/30/2022]
Abstract
Good leadership is important for the efficient functioning of an organization. PhD and postdoctoral research is a mentally challenging job, and a good mentor must be able to both treat students with compassion and provide motivation. Coronavirus disease 2019 (COVID-19) has resulted in the decline of the mental health of a large fraction of mentees.
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Affiliation(s)
- Ashish Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India; Department of Plant Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India.
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Singh R, Singh PK, Kumar R, Kabir MT, Kamal MA, Rauf A, Albadrani GM, Sayed AA, Mousa SA, Abdel-Daim MM, Uddin MS. Multi-Omics Approach in the Identification of Potential Therapeutic Biomolecule for COVID-19. Front Pharmacol 2021; 12:652335. [PMID: 34054532 PMCID: PMC8149611 DOI: 10.3389/fphar.2021.652335] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 04/21/2021] [Indexed: 02/05/2023] Open
Abstract
COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It has a disastrous effect on mankind due to the contagious and rapid nature of its spread. Although vaccines for SARS-CoV-2 have been successfully developed, the proven, effective, and specific therapeutic molecules are yet to be identified for the treatment. The repurposing of existing drugs and recognition of new medicines are continuously in progress. Efforts are being made to single out plant-based novel therapeutic compounds. As a result, some of these biomolecules are in their testing phase. During these efforts, the whole-genome sequencing of SARS-CoV-2 has given the direction to explore the omics systems and approaches to overcome this unprecedented health challenge globally. Genome, proteome, and metagenome sequence analyses have helped identify virus nature, thereby assisting in understanding the molecular mechanism, structural understanding, and disease propagation. The multi-omics approaches offer various tools and strategies for identifying potential therapeutic biomolecules for COVID-19 and exploring the plants producing biomolecules that can be used as biopharmaceutical products. This review explores the available multi-omics approaches and their scope to investigate the therapeutic promises of plant-based biomolecules in treating SARS-CoV-2 infection.
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Affiliation(s)
- Rachana Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, India
| | - Pradhyumna Kumar Singh
- Plant Molecular Biology and Biotechnology Division, Council of Scientific and Industrial Research- National Botanical Research Institute (CSIR-NBRI), Lucknow, India
| | - Rajnish Kumar
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, India
| | | | - Mohammad Amjad Kamal
- West China School of Nursing/Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Enzymoics, Novel Global Community Educational Foundation, Hebersham, NSW, Australia
| | - Abdur Rauf
- Department of Chemistry, University of Swabi, Khyber Pakhtunkhwa, Pakistan
| | - Ghadeer M. Albadrani
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Amany A. Sayed
- Zoology Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Shaker A. Mousa
- Pharmaceutical Research Institute, Albany College of Pharmacy and Health Sciences, Rensselaer, NY, United States
| | - Mohamed M. Abdel-Daim
- Pharmacology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Md. Sahab Uddin
- Department of Pharmacy, Southeast University, Dhaka, Bangladesh
- Pharmakon Neuroscience Research Network, Dhaka, Bangladesh
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7
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Host-virus interactions mediated by long non-coding RNAs. Virus Res 2021; 298:198402. [PMID: 33771610 DOI: 10.1016/j.virusres.2021.198402] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 11/21/2022]
Abstract
Viruses are obligate pathogens that cause a wide range of diseases across all kingdoms of life. They have a colossal impact on the economy and healthcare infrastructure world-wide. Plants and animals have developed sophisticated molecular mechanisms to defend themselves against viruses and viruses in turn hijack host mechanisms to ensure their survival inside their hosts. Long non-coding (lnc) RNAs have emerged as important macromolecules that regulate plant-virus and animal-virus interactions. Both pro-viral and anti-viral lncRNAs have been reported and they show immense potential to be used as markers and in therapeutics. The current review is focussed on the recent developments that have been made in viral interactions of animals and plants.
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Josa-Laorden C, Crestelo-Vieitez A, García Andreu MDM, Rubio-Rivas M, Sánchez M, Toledo Samaniego N, Arnalich Fernández F, Iguaran Bermudez R, Fonseca Aizpuru EM, Vargas Núñez JA, Pesqueira Fontan PM, Serrano Ballesteros J, Freire Castro SJ, Pestaña Fernández M, Viana García A, Nuñez Rodriguez V, Giner-Galvañ V, Carrasco Sánchez FJ, Hernández Milián A, Cobos-Siles M, Napal Lecumberri JJ, Herrero García V, Pascual Pérez MDLR, Millán Núñez-Cortés J, Casas Rojo JM. Gender-Based Differences by Age Range in Patients Hospitalized with COVID-19: A Spanish Observational Cohort Study. J Clin Med 2021; 10:899. [PMID: 33668766 PMCID: PMC7956359 DOI: 10.3390/jcm10050899] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/05/2021] [Accepted: 02/13/2021] [Indexed: 12/19/2022] Open
Abstract
There is some evidence that male gender could have a negative impact on the prognosis and severity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. The aim of the present study was to compare the characteristics of coronavirus disease 2019 (COVID-19) between hospitalized men and women with confirmed SARS-CoV-2 infection. This multicenter, retrospective, observational study is based on the SEMI-COVID-19 Registry. We analyzed the differences between men and women for a wide variety of demographic, clinical, and treatment variables, and the sex distribution of the reported COVID-19 deaths, as well as intensive care unit (ICU) admission by age subgroups. This work analyzed 12,063 patients (56.8% men). The women in our study were older than the men, on average (67.9 vs. 65.7 years; p < 001). Bilateral condensation was more frequent among men than women (31.8% vs. 29.9%; p = 0.007). The men needed non-invasive and invasive mechanical ventilation more frequently (5.6% vs. 3.6%, p < 0.001, and 7.9% vs. 4.8%, p < 0.001, respectively). The most prevalent complication was acute respiratory distress syndrome, with severe cases in 19.9% of men (p < 0.001). In men, intensive care unit admission was more frequent (10% vs. 6.1%; p < 0.001) and the mortality rate was higher (23.1% vs. 18.9%; p < 0.001). Regarding mortality, the differences by gender were statistically significant in the age groups from 55 years to 89 years of age. A multivariate analysis showed that female sex was significantly and independently associated with a lower risk of mortality in our study. Male sex appears to be related to worse progress in COVID-19 patients and is an independent prognostic factor for mortality. In order to fully understand its prognostic impact, other factors associated with sex must be considered.
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Affiliation(s)
- Claudia Josa-Laorden
- Internal Medicine Department, Royo Villanova Hospital, Avenida San Gregorio 30, 50015 Zaragoza, Spain;
- Aragon Institute of Health Research, IIS-Aragon, 50009 Zaragoza, Spain
| | - Anxela Crestelo-Vieitez
- Internal Medicine Department, Royo Villanova Hospital, Avenida San Gregorio 30, 50015 Zaragoza, Spain;
| | | | - Manuel Rubio-Rivas
- Internal Medicine Department, Bellvitge University Hospital-IDIBELL, L’Hospitalet de Llobregat, 08901 Barcelona, Spain;
| | - Marcos Sánchez
- Internal Medicine Department, 12 de Octubre University Hospital, 28041 Madrid, Spain;
| | - Neera Toledo Samaniego
- Internal Medicine Department, Gregorio Marañon University Hospital, 28007 Madrid, Spain; (N.T.S.); (J.M.N.-C.)
| | | | | | | | | | | | | | | | | | - Alba Viana García
- Internal Medicine Department, Dr. Peset University Hospital, 45017 Valencia, Spain;
| | | | - Vicente Giner-Galvañ
- General Internal Medicine Department, San Juan de Alicante University Hospital, 03550 Alicante, Spain;
- Department of Clinical Medicine, Faculty of Medicine, Miguel Hernández University, 03202 Alicante, Spain
| | | | | | - Marta Cobos-Siles
- Internal Medicine Department, Río Hortega University Hospital, Regional Health Management of Castilla y Leon (SACYL), 47012 Valladolid, Spain;
| | | | | | | | - Jesús Millán Núñez-Cortés
- Internal Medicine Department, Gregorio Marañon University Hospital, 28007 Madrid, Spain; (N.T.S.); (J.M.N.-C.)
| | - José Manuel Casas Rojo
- Internal Medicine Department, Infanta Cristina University Hospital, 28981 Madrid, Spain;
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9
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Naik RR, Shakya AK. Therapeutic Strategies in the Management of COVID-19. Front Mol Biosci 2021; 7:636738. [PMID: 33614709 PMCID: PMC7890447 DOI: 10.3389/fmolb.2020.636738] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 12/30/2020] [Indexed: 12/15/2022] Open
Abstract
Since December 2019, SARS-CoV-2 (COVID-19), novel corona virus has caused pandemic globally, with rise in the number of cases and death of the patients. Vast majority of the countries that are dealing with rise in the active cases and death of patients suffering from novel corona viruses COVID-19 are trying to content the virus by isolating the patients and treating them with the approved antiviral that have been previously used in treating SARS, MERS, and drugs that are used to treat other viral infections. Some of these are under clinical trials. At present there are no therapeutically effective antiviral present and there are no vaccines or drugs available that are clinically approved for treating the corona virus. The current strategy is to re-purpose the available drugs or antiviral that can minimise or reduce the burden of the health care emergencies. In this article the reuse of antiviral, US-FDA approved drugs, plant based therapeutic, anti-malarial, anti-parasitic, anti-HIV drugs and the traditional medicines that are being currently used in treating the symptoms of COVID-19 patients is discussed emphasis is also given on the treatment using monoclonal antibodies. The present article provides the therapeutic strategies that will qualify as one of the best available treatment for the better management of the COVID-19 patients in order to achieve medical benefits.
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Affiliation(s)
- Rajashri R. Naik
- Department of Biopharmaceutics and Clinical Pharmacy, Pharmacological and Diagnostic Research Center, Al-Ahliyya Amman University, Amman, Jordan
| | - Ashok K. Shakya
- Department of Pharmaceutical Sciences, Pharmacological and Diagnostic Research Center, Al-Ahliyya Amman University, Amman, Jordan
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10
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Singh R, Singh PK, Kumar R, Kabir MT, Kamal MA, Rauf A, Albadrani GM, Sayed AA, Mousa SA, Abdel-Daim MM, Uddin MS. Multi-Omics Approach in the Identification of Potential Therapeutic Biomolecule for COVID-19. Front Pharmacol 2021. [PMID: 34054532 DOI: 10.3389/fphar2021652335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023] Open
Abstract
COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It has a disastrous effect on mankind due to the contagious and rapid nature of its spread. Although vaccines for SARS-CoV-2 have been successfully developed, the proven, effective, and specific therapeutic molecules are yet to be identified for the treatment. The repurposing of existing drugs and recognition of new medicines are continuously in progress. Efforts are being made to single out plant-based novel therapeutic compounds. As a result, some of these biomolecules are in their testing phase. During these efforts, the whole-genome sequencing of SARS-CoV-2 has given the direction to explore the omics systems and approaches to overcome this unprecedented health challenge globally. Genome, proteome, and metagenome sequence analyses have helped identify virus nature, thereby assisting in understanding the molecular mechanism, structural understanding, and disease propagation. The multi-omics approaches offer various tools and strategies for identifying potential therapeutic biomolecules for COVID-19 and exploring the plants producing biomolecules that can be used as biopharmaceutical products. This review explores the available multi-omics approaches and their scope to investigate the therapeutic promises of plant-based biomolecules in treating SARS-CoV-2 infection.
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Affiliation(s)
- Rachana Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, India
| | - Pradhyumna Kumar Singh
- Plant Molecular Biology and Biotechnology Division, Council of Scientific and Industrial Research- National Botanical Research Institute (CSIR-NBRI), Lucknow, India
| | - Rajnish Kumar
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, India
| | | | - Mohammad Amjad Kamal
- West China School of Nursing/Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Enzymoics, Novel Global Community Educational Foundation, Hebersham, NSW, Australia
| | - Abdur Rauf
- Department of Chemistry, University of Swabi, Khyber Pakhtunkhwa, Pakistan
| | - Ghadeer M Albadrani
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Amany A Sayed
- Zoology Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Shaker A Mousa
- Pharmaceutical Research Institute, Albany College of Pharmacy and Health Sciences, Rensselaer, NY, United States
| | - Mohamed M Abdel-Daim
- Pharmacology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Md Sahab Uddin
- Department of Pharmacy, Southeast University, Dhaka, Bangladesh
- Pharmakon Neuroscience Research Network, Dhaka, Bangladesh
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11
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Ayyagari VS, T C V, K AP, Srirama K. Design of a multi-epitope-based vaccine targeting M-protein of SARS-CoV2: an immunoinformatics approach. J Biomol Struct Dyn 2020; 40:2963-2977. [PMID: 33252008 PMCID: PMC7754933 DOI: 10.1080/07391102.2020.1850357] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In the present study, one of the targets present on the envelopes of coronaviruses, membrane glycoprotein (M) was chosen for the design of a multi-epitope vaccine by Immunoinformatics approach. The B-cell and T-cell epitopes used for the construction of vaccine were antigenic, nonallergic and nontoxic. An adjuvant, β-defensin and PADRE sequence were included at the N-terminal end of the vaccine. All the epitopes were joined by linkers for decreasing the junctional immunogenicity. Various physicochemical parameters of the vaccine were evaluated. Secondary and tertiary structures were predicted for the vaccine construct. The tertiary structure was further refined, and various parameters related to the refinement of the protein structure were validated by using different tools. Humoral immunity induced by B-cells relies upon the identification of antigenic determinants on the surface of the vaccine construct. In this regard, the vaccine construct was found to consist of several B-cell epitopes in its three-dimensional conformation. Molecular docking of the vaccine was carried out with TLR-3 receptor to study their binding and its strength. Further, protein-protein interactions in the docked complex were visualized using LigPlot+. Population coverage analysis had shown that the multi-epitope vaccine covers 94.06% of the global population. The vaccine construct was successfully cloned in silico into pET-28a (+). Immune simulation studies showed the induction of primary, secondary and tertiary immune responses marked by the increased levels of antibodies, INF-γ, IL-2, TGF-β, B- cells, CD4+ and CD8+ cells. Finally, the vaccine construct was able to elicit immune response as desired.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vijaya Sai Ayyagari
- Department of Biotechnology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, Guntur, Andhra Pradesh, India
| | - Venkateswarulu T C
- Department of Biotechnology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, Guntur, Andhra Pradesh, India
| | - Abraham Peele K
- Department of Biotechnology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, Guntur, Andhra Pradesh, India
| | - Krupanidhi Srirama
- Department of Biotechnology, Vignan's Foundation for Science, Technology & Research, Vadlamudi, Guntur, Andhra Pradesh, India
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12
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Sharma N, Muthamilarasan M, Prasad A, Prasad M. Genomics approaches to synthesize plant-based biomolecules for therapeutic applications to combat SARS-CoV-2. Genomics 2020; 112:4322-4331. [PMID: 32717321 PMCID: PMC7381398 DOI: 10.1016/j.ygeno.2020.07.033] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/10/2020] [Accepted: 07/20/2020] [Indexed: 12/22/2022]
Abstract
COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is devastative to the humankind for which neither vaccines nor precise therapeutic molecules for treatment are identified. The search for new drugs and repurposing of existing drugs are being performed; however, at the same time, research on plants to identify novel therapeutic compounds or testing the existing ones is progressing at a slower phase. In this context, genomics and biotechnology offer various tools and strategies to manipulate plants for producing those complex biopharmaceutical products. This review enumerates the scope for research on plant-based molecules for their potential application in treating SARS-CoV-2 infection. Strategies to edit gene and genome, overexpression and silencing approaches, and molecular breeding for producing target biomolecules in the plant system are discussed in detail. Altogether, the present review provides a roadmap for expediting research on using plants as a novel source of active biomolecules having therapeutic applications.
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Affiliation(s)
- Namisha Sharma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Ashish Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
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13
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Prasad A, Prasad M. Single Virus Targeting Multiple Organs: What We Know and Where We Are Heading? Front Med (Lausanne) 2020; 7:370. [PMID: 32850890 PMCID: PMC7419463 DOI: 10.3389/fmed.2020.00370] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 06/17/2020] [Indexed: 12/14/2022] Open
Abstract
COVID-19 caused by SARS-CoV-2 has already infected more than 6. 3 million people worldwide as of 1st June 2020 and caused a global medical emergency. Healthcare professionals have been struggling to devise appropriate therapeutic strategies against the virus mainly due to the diverse range of symptoms and multiple-organ failure in infected patients. Several broad-spectrum antiviral drugs are being used for treatment; however, there is yet no specific drug or vaccine against the virus. Multiple-organ failure due to hyperactivity of the immune system resulting in cytokine storms is a major reason for death among the 5% critically ill patients. In this article, we have discussed the damage caused by COVID-19 on different organs of the human body.
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14
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Molecular docking and dynamic simulations for antiviral compounds against SARS-CoV-2: A computational study. INFORMATICS IN MEDICINE UNLOCKED 2020; 19:100345. [PMID: 32395606 PMCID: PMC7211761 DOI: 10.1016/j.imu.2020.100345] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/03/2020] [Accepted: 05/03/2020] [Indexed: 12/20/2022] Open
Abstract
The aim of this study was to develop an appropriate anti-viral drug against the SARS-CoV-2 virus. An immediately qualifying strategy would be to use existing powerful drugs from various virus treatments. The strategy in virtual screening of antiviral databases for possible therapeutic effect would be to identify promising drug molecules, as there is currently no vaccine or treatment approved against COVID-19. Targeting the main protease (pdb id: 6LU7) is gaining importance in anti-CoV drug design. In this conceptual context, an attempt has been made to suggest an in silico computational relationship between US-FDA approved drugs, plant-derived natural drugs, and Coronavirus main protease (6LU7) protein. The evaluation of results was made based on Glide (Schrödinger) dock score. Out of 62 screened compounds, the best docking scores with the targets were found for compounds: lopinavir, amodiaquine, and theaflavin digallate (TFDG). Molecular dynamic (MD) simulation study was also performed for 20 ns to confirm the stability behaviour of the main protease and inhibitor complexes. The MD simulation study validated the stability of three compounds in the protein binding pocket as potent binders.
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