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Abdel-Halim H, Hajar M, Hasouneh L, Abdelmalek SMA. Identification of Drug Combination Therapies for SARS-CoV-2: A Molecular Dynamics Simulations Approach. Drug Des Devel Ther 2022; 16:2995-3013. [PMID: 36110398 PMCID: PMC9469804 DOI: 10.2147/dddt.s366423] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 08/31/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose The development of effective treatments for coronavirus infectious disease 19 (COVID-19) caused by SARS-Coronavirus-2 was hindered by the little data available about this virus at the start of the pandemic. Drug repurposing provides a good strategy to explore approved drugs' possible SARS-CoV-2 antiviral activity. Moreover, drug synergism is essential in antiviral treatment due to improved efficacy and reduced toxicity. In this work, we studied the effect of approved and investigational drugs on one of SARS-CoV-2 essential proteins, the main protease (Mpro), in search of antiviral treatments and/or drug combinations. Methods Different possible druggable sites of Mpro were identified and screened against an in-house library of more than 4000 chemical compounds. Molecular dynamics simulations were carried out to explore conformational changes induced by different ligands' binding. Subsequently, the inhibitory effect of the identified compounds and the suggested drug combinations on the Mpro were established using a 3CL protease (SARS-CoV-2) assay kit. Results Three potential inhibitors in three different binding sites were identified; favipiravir, cefixime, and carvedilol. Molecular dynamics simulations predicted the synergistic effect of two drug combinations: favipiravir/cefixime, and favipiravir/carvedilol. The in vitro inhibitory effect of the predicted drug combinations was established on this enzyme. Conclusion In this work, we could study one of the promising SARS-CoV-2 viral protein targets in searching for treatments for COVID-19. The inhibitory effect of several drugs on Mpro was established in silico and in vitro assays. Molecular dynamics simulations showed promising results in predicting the synergistic effect of drug combinations.
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Affiliation(s)
- Heba Abdel-Halim
- Department of Medicinal Chemistry, Faculty of Pharmacy and Medical Sciences, University of Petra, Amman, Jordan
| | - Malak Hajar
- Department of Medicinal Chemistry, Faculty of Pharmacy and Medical Sciences, University of Petra, Amman, Jordan
| | - Luma Hasouneh
- Department of Medicinal Chemistry, Faculty of Pharmacy and Medical Sciences, University of Petra, Amman, Jordan
| | - Suzanne M A Abdelmalek
- Department of Pharmacology and Biomedical Sciences, Faculty of Pharmacy and Medical Sciences, University of Petra, Amman, Jordan
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Association of the Transmembrane Serine Protease-2 (TMPRSS2) Polymorphisms with COVID-19. Viruses 2022; 14:v14091976. [PMID: 36146782 PMCID: PMC9505830 DOI: 10.3390/v14091976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/29/2022] [Accepted: 09/01/2022] [Indexed: 12/23/2022] Open
Abstract
SARS-CoV-2 uses the ACE2 receptor and the cellular protease TMPRSS2 for entry into target cells. The present study aimed to establish if the TMPRSS2 polymorphisms are associated with COVID-19 disease. The study included 609 patients with COVID-19 confirmed by RT-PCR test and 291 individuals negative for the SARS-CoV-2 infection confirmed by RT-PCR test and without antibodies anti-SARS-CoV-2. Four TMPRSS2 polymorphisms (rs12329760, rs2298659, rs456298, and rs462574) were determined using the 5′exonuclease TaqMan assays. Under different inheritance models, the rs2298659 (pcodominant2 = 0.018, precessive = 0.006, padditive = 0.019), rs456298 (pcodominant1 = 0.014, pcodominant2 = 0.004; pdominant = 0.009, precessive = 0.004, padditive = 0.0009), and rs462574 (pcodominant1 = 0.017, pcodominant2 = 0.004, pdominant = 0.041, precessive = 0.002, padditive = 0.003) polymorphisms were associated with high risk of developing COVID-19. Two risks (ATGC and GAAC) and two protectives (GAGC and GAGT) haplotypes were detected. High levels of lactic acid dehydrogenase (LDH) were observed in patients with the rs462574AA and rs456298TT genotypes (p = 0.005 and p = 0.020, respectively), whereas, high heart rate was present in patients with the rs462574AA genotype (p = 0.028). Our data suggest that the rs2298659, rs456298, and rs462574 polymorphisms independently and as haplotypes are associated with the risk of COVID-19. The rs456298 and rs462574 genotypes are related to high levels of LDH and heart rate.
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Nepali K, Sharma R, Sharma S, Thakur A, Liou JP. Beyond the vaccines: a glance at the small molecule and peptide-based anti-COVID19 arsenal. J Biomed Sci 2022; 29:65. [PMID: 36064696 PMCID: PMC9444709 DOI: 10.1186/s12929-022-00847-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/16/2022] [Indexed: 02/08/2023] Open
Abstract
Unprecedented efforts of the researchers have been witnessed in the recent past towards the development of vaccine platforms for the control of the COVID-19 pandemic. Albeit, vaccination stands as a practical strategy to prevent SARS-CoV-2 infection, supplementing the anti-COVID19 arsenal with therapeutic options such as small molecules/peptides and antibodies is being conceived as a prudent strategy to tackle the emerging SARS-CoV-2 variants. Noteworthy to mention that collective efforts from numerous teams have led to the generation of a voluminous library composed of chemically and mechanistically diverse small molecules as anti-COVID19 scaffolds. This review article presents an overview of medicinal chemistry campaigns and drug repurposing programs that culminated in the identification of a plethora of small molecule-based anti-COVID19 drugs mediating their antiviral effects through inhibition of proteases, S protein, RdRp, ACE2, TMPRSS2, cathepsin and other targets. In light of the evidence ascertaining the potential of small molecule drugs to approach conserved proteins required for the viral replication of all coronaviruses, accelerated FDA approvals are anticipated for small molecules for the treatment of COVID19 shortly. Though the recent attempts invested in this direction in pursuit of enrichment of the anti-COVID-19 armoury (chemical tools) are praiseworthy, some strategies need to be implemented to extract conclusive benefits of the recently reported small molecule viz. (i) detailed preclinical investigation of the generated anti-COVID19 scaffolds (ii) in-vitro profiling of the inhibitors against the emerging SARS-CoV-2 variants (iii) development of assays enabling rapid screening of the libraries of anti-COVID19 scaffold (iv) leveraging the applications of machine learning based predictive models to expedite the anti-COVID19 drug discovery campaign (v) design of antibody-drug conjugates.
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Affiliation(s)
- Kunal Nepali
- School of Pharmacy, College of Pharmacy, Taipei Medical University, 250 Wuxing Street, Taipei, 11031, Taiwan
- TMU Research Center for Drug Discovery, Taipei Medical University, Taipei, 11031, Taiwan
| | - Ram Sharma
- School of Pharmacy, College of Pharmacy, Taipei Medical University, 250 Wuxing Street, Taipei, 11031, Taiwan
| | - Sachin Sharma
- School of Pharmacy, College of Pharmacy, Taipei Medical University, 250 Wuxing Street, Taipei, 11031, Taiwan
| | - Amandeep Thakur
- School of Pharmacy, College of Pharmacy, Taipei Medical University, 250 Wuxing Street, Taipei, 11031, Taiwan
| | - Jing-Ping Liou
- School of Pharmacy, College of Pharmacy, Taipei Medical University, 250 Wuxing Street, Taipei, 11031, Taiwan.
- TMU Research Center for Drug Discovery, Taipei Medical University, Taipei, 11031, Taiwan.
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Tirado-Kulieva VA, Hernández-Martínez E, Choque-Rivera TJ. Phenolic compounds versus SARS-CoV-2: An update on the main findings against COVID-19. Heliyon 2022; 8:e10702. [PMID: 36157310 PMCID: PMC9484857 DOI: 10.1016/j.heliyon.2022.e10702] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/04/2022] [Accepted: 09/14/2022] [Indexed: 11/25/2022] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 remains an international concern. Although there are drugs to fight it, new natural alternatives such as polyphenols are essential due to their antioxidant activity and high antiviral potential. In this context, this review reports the main findings on the effect of phenolic compounds (PCs) against SARS-CoV-2 virus. First, the proven activity of PCs against different human viruses is briefly detailed, which serves as a starting point to study their anti-COVID-19 potential. SARS-CoV-2 targets (its proteins) are defined. Findings from in silico, in vitro and in vivo studies of a wide variety of phenolic compounds are shown, emphasizing their mechanism of action, which is fundamental for drug design. Furthermore, clinical trials have demonstrated the effectiveness of PCs in the prevention and as a possible therapeutic management against COVID-19. The results were complemented with information on the influence of polyphenols in strengthening/modulating the immune system. It is recommended to investigate compounds such as vitamins, minerals, alkaloids, triterpenes and fatty acids, and their synergistic use with PCs, many of which have been successful against SARS-CoV-2. Based on findings on other viruses, synergistic evaluation of PCs with accepted drugs against COVID-19 is also suggested. Other recommendations and limitations are also shown, which is useful for professionals involved in the development of efficient, safe and low-cost therapeutic strategies based on plant matrices rich in PCs. To the authors' knowledge, this manuscript is the first to evaluate the relationship between the antiviral and immunomodulatory (including anti-inflammatory and antioxidant effects) activity of PCs and their underlying mechanisms in relation to the fight against COVID-19. It is also of interest for the general population to be informed about the importance of consuming foods rich in bioactive compounds for their health benefits.
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Shang Y, Wu J, Liu J, Long Y, Xie J, Zhang D, Hu B, Zong Y, Liao X, Shang X, Ding R, Kang K, Liu J, Pan A, Xu Y, Wang C, Xu Q, Zhang X, Zhang J, Liu L, Zhang J, Yang Y, Yu K, Guan X, Chen D. Expert consensus on the diagnosis and treatment of severe and critical coronavirus disease 2019 (COVID-19). JOURNAL OF INTENSIVE MEDICINE 2022; 2:199-222. [PMID: 36785648 PMCID: PMC9411033 DOI: 10.1016/j.jointm.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 07/24/2022] [Indexed: 12/16/2022]
Affiliation(s)
- You Shang
- Department of Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China
| | - Jianfeng Wu
- Department of Critical Care Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong 510010, China
| | - Jinglun Liu
- Department of Emergency and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yun Long
- Department of Critical Care Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Science, Beijing 100730, China
| | - Jianfeng Xie
- Department of Critical Care Medicine, Jiangsu Provincial Key Laboratory of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, China
| | - Dong Zhang
- Department of Critical Care Medicine, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Bo Hu
- Department of Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Yuan Zong
- Department of Critical Care Medicine, Shaanxi Provincial Hospital, Xi'an, Shannxi 710068, China
| | - Xuelian Liao
- Department of Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xiuling Shang
- Department of Critical Care Medicine, Fujian Provincial Hospital, Fujian Provincial Center for Critical Care Medicine, Fuzhou, Fujian 350001, China
| | - Renyu Ding
- Department of Critical Care Medicine, The First Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Kai Kang
- Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, China
| | - Jiao Liu
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Aijun Pan
- Department of Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Yonghao Xu
- Department of Critical Care Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, China
| | - Changsong Wang
- Department of Critical Care Medicine, Harbin Medical University Cancer Hospital, Harbin, Heilongjiang 150001, China
| | - Qianghong Xu
- Department of Critical Care Medicine, Zhejiang Hospital Affiliated to Medical College of Zhejiang University, Hangzhou, Zhejiang 310013, China
| | - Xijing Zhang
- Department of Critical Care Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, Shannxi 710032, China
| | - Jicheng Zhang
- Department of Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, China
| | - Ling Liu
- Department of Critical Care Medicine, Jiangsu Provincial Key Laboratory of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, China
| | - Jiancheng Zhang
- Department of Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, China
| | - Yi Yang
- Department of Critical Care Medicine, Jiangsu Provincial Key Laboratory of Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, China
| | - Kaijiang Yu
- Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, China
- Corresponding authors: Dechang Chen, Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China. Xiangdong Guan, Department of Critical Care Medicine, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510080, China. Kaijiang Yu, Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, China.
| | - Xiangdong Guan
- Department of Critical Care Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong 510010, China
- Corresponding authors: Dechang Chen, Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China. Xiangdong Guan, Department of Critical Care Medicine, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510080, China. Kaijiang Yu, Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, China.
| | - Dechang Chen
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Corresponding authors: Dechang Chen, Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China. Xiangdong Guan, Department of Critical Care Medicine, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510080, China. Kaijiang Yu, Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, China.
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Expression profiles of respiratory V-ATPase and calprotectin in SARS-CoV-2 infection. Cell Death Dis 2022; 8:362. [PMID: 35974012 PMCID: PMC9379883 DOI: 10.1038/s41420-022-01158-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/01/2022] [Accepted: 08/03/2022] [Indexed: 11/16/2022]
Abstract
Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) represents a pandemic threat that has been declared a public health emergency of international concern, whereas the effects of cellular microenvironment in the pathogenesis of SARS-CoV-2 are poorly understood. The detailed message of intracellular/lysosome pH was rarely concerned in SARS-CoV-2 infection, which was crucial for the cleavage of SARS-CoV-2 spike (S) protein. Calprotectin, an endogenous danger signal to activate inflammatory response, was vital for the proceeding of COVID-19. We found that the expressions of both vacuolar-ATPase (V-ATPase) and calprotectin (S100A8/S100A9) increased in SARS-CoV-2 infection, by analyzing single-cell RNA sequencing (bronchoalveolar lavage fluid), bulk-RNA sequencing (A549, lung tissue, NHBE), and proteomics (lung tissue), respectively. Furtherly, our wet experiments of flow cytometry and fluorescent assay identified that the intracellular and lysosome pH value was decreased after SARS-CoV-2 S plasmid transfection in A549 cells. Meanwhile, the enhancement of V-ATPase and calprotectin was verified by our real-time polymerase chain reaction and western blot experiment. Collectively, these data suggested that S protein increased V-ATPase in SARS-CoV-2 infection, which provided a microenvironment easier for the cleavage of S protein, and inflammatory cells were apt to be activated by the enhancement of calprotectin in respiratory epithelium. The comprehensive information on profiles of V-ATPase and calprotectin will make clearer about the involvement of cellular microenvironment in the pathogenesis of SARS-CoV-2, and provide a promising approach to combat COVID-19.
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Chitosan and its derivatives as polymeric anti-viral therapeutics and potential anti-SARS-CoV-2 nanomedicine. Carbohydr Polym 2022; 290:119500. [PMID: 35550778 PMCID: PMC9020865 DOI: 10.1016/j.carbpol.2022.119500] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 01/07/2023]
Abstract
The coronavirus pandemic, COVID-19 has a global impact on the lives and livelihoods of people. It is characterized by a widespread infection by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), where infected patients may develop serious medical complications or even face death. Development of therapeutic is essential to reduce the morbidity and mortality of infected patients. Chitosan is a versatile biomaterial in nanomedicine and exhibits anti-microbial, anti-cancer and immunomodulatory properties. This review highlights the progress in chitosan design and application pertaining to the anti-viral effects of chitosan and chitosan derivatives (hydroxypropyl trimethylammonium, sulfate, carboxymethyl, bromine, sialylglycopolymer, peptide and phosphonium conjugates) as a function of molecular weight, degree of deacetylation, type of substituents and their degree and site of substitution. The physicochemical attributes of these polymeric therapeutics are identified against the possibility of processing them into nanomedicine which can confer a higher level of anti-viral efficacy. The designs of chitosan for the purpose of targeting SARS-CoV-2, as well as the ever-evolving strains of viruses with a broad spectrum anti-viral activity to meet pandemic preparedness at the early stages of outbreak are discussed.
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Al-Humaidi JY, Badrey MG, Aly AA, Nayl AA, Zayed MEM, Jefri OA, Gomha SM. Evaluation of the Binding Relationship of the RdRp Enzyme to Novel Thiazole/Acid Hydrazone Hybrids Obtainable through Green Synthetic Procedure. Polymers (Basel) 2022; 14:polym14153160. [PMID: 35956675 PMCID: PMC9371204 DOI: 10.3390/polym14153160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/17/2022] [Accepted: 07/21/2022] [Indexed: 02/01/2023] Open
Abstract
The viral RNA-dependent RNA polymerase (RdRp) complex is used by SARS-CoV-2 for genome replication and transcription, making RdRp an interesting target for developing the antiviral treatment. Hence the current work is concerned with the green synthesis, characterization and docking study with the RdRp enzyme of the series of novel and diverse hydrazones and pyrazoles. 4-Methyl-2-(2-(1-phenylethylidene)hydrazineyl)thiazole-5-carbohydrazide was prepared and then condensed with different carbonyl compounds (aldehydes and ketones either carbocyclic aromatic or heterocyclic) afforded the corresponding hydrazide-hydrazones. The combination of the acid hydrazide with bifunctional reagents such as acetylacetone, β-ketoesters (ethyl acetoacetate and ethyl benzoylacetate) resulted in the formation of pyrazole derivatives. The synthesized compounds were all obtained through grinding method using drops of AcOH. Various analytical and spectral analyses were used to determine the structures of the prepared compounds. Molecular Operating Environment (MOE®) version 2014.09 was used to estimate interactions between the prepared thiazole/hydrazone hybrids and RdRp obtained from the protein data bank (PDB: 7bv2) using enzyme-ligand docking for all synthesized derivatives and Remdesivir as a reference. Docking results with the RdRp enzyme revealed that the majority of the investigated drugs bind well to the enzyme via various types of interactions in comparison with the reference drug.
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Affiliation(s)
- Jehan Y. Al-Humaidi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, P.O. BOX 84428, Riyadh 11671, Saudi Arabia;
| | - Mohamed G. Badrey
- Chemistry Department, Faculty of Science, Fayoum University, El-Fayoum 63514, Egypt;
- Chemistry Department, Faculty of Science and Arts-Almandaq, Al-Baha University, Al-Baha 65515, Saudia Arabia
| | - Ashraf A. Aly
- Chemistry Department, Faculty of Science, Organic Division, Minia University, El-Minia 61519, Egypt;
| | - AbdElAziz A. Nayl
- Department of Chemistry, College of Science, Jouf University, Sakaka 72341, Saudi Arabia
- Correspondence: or (A.A.N.); or (S.M.G.)
| | - Mohie E. M. Zayed
- Department of Chemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (M.E.M.Z.); (O.A.J.)
| | - Ohoud A. Jefri
- Department of Chemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (M.E.M.Z.); (O.A.J.)
| | - Sobhi M. Gomha
- Department of Chemistry, Faculty of Science, Cairo University, Giza 12613, Egypt
- Department of Chemistry, Faculty of Science, Islamic University of Madinah, Madinah 42351, Saudi Arabia
- Correspondence: or (A.A.N.); or (S.M.G.)
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Ma Y, Luo M, Deng Y, Yang X, Wang X, Chen G, Qin Z, Deng Y, Nan M, Chen Y, Wang P, Wei H, Han L, Fang X, Liu Z. Antibiotic-Induced Primary Biles Inhibit SARS-CoV-2 Endoribonuclease Nsp15 Activity in Mouse Gut. Front Cell Infect Microbiol 2022; 12:896504. [PMID: 35967852 PMCID: PMC9366059 DOI: 10.3389/fcimb.2022.896504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 06/14/2022] [Indexed: 11/16/2022] Open
Abstract
The gut microbiome profile of COVID-19 patients was found to correlate with a viral load of SARS-CoV-2, COVID-19 severity, and dysfunctional immune responses, suggesting that gut microbiota may be involved in anti-infection. In order to investigate the role of gut microbiota in anti-infection against SARS-CoV-2, we established a high-throughput in vitro screening system for COVID-19 therapeutics by targeting the endoribonuclease (Nsp15). We also evaluated the activity inhibition of the target by substances of intestinal origin, using a mouse model in an attempt to explore the interactions between gut microbiota and SARS-CoV-2. The results unexpectedly revealed that antibiotic treatment induced the appearance of substances with Nsp15 activity inhibition in the intestine of mice. Comprehensive analysis based on functional profiling of the fecal metagenomes and endoribonuclease assay of antibiotic-enriched bacteria and metabolites demonstrated that the Nsp15 inhibitors were the primary bile acids that accumulated in the gut as a result of antibiotic-induced deficiency of bile acid metabolizing microbes. This study provides a new perspective on the development of COVID-19 therapeutics using primary bile acids.
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Affiliation(s)
- Yao Ma
- Department of Biotechnology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Mei Luo
- Department of Biotechnology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yusheng Deng
- Department of Scientific Research, KMHD, Shenzhen, China
| | - Xiaoman Yang
- Department of Biotechnology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xionglue Wang
- Department of Biotechnology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Guozhong Chen
- Department of Biotechnology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Zixin Qin
- Department of Biotechnology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yun Deng
- Department of Biotechnology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Meiling Nan
- Key Laboratory for Experimental Teratology of Ministry of Education and Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yang Chen
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Peihui Wang
- Key Laboratory for Experimental Teratology of Ministry of Education and Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Hong Wei
- State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Lijuan Han
- Department of Scientific Research, KMHD, Shenzhen, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- *Correspondence: Zhi Liu, ; Xiaodong Fang, ; Lijuan Han,
| | - Xiaodong Fang
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- *Correspondence: Zhi Liu, ; Xiaodong Fang, ; Lijuan Han,
| | - Zhi Liu
- Department of Biotechnology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Zhi Liu, ; Xiaodong Fang, ; Lijuan Han,
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Migliorini F, Vaishya R, Eschweiler J, Oliva F, Hildebrand F, Maffulli N. Vitamins C and D and COVID-19 Susceptibility, Severity and Progression: An Evidence Based Systematic Review. MEDICINA (KAUNAS, LITHUANIA) 2022; 58:941. [PMID: 35888660 PMCID: PMC9318801 DOI: 10.3390/medicina58070941] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 07/02/2022] [Accepted: 07/12/2022] [Indexed: 04/07/2023]
Abstract
Background and Objectives: Starting in early December 2019, the novel Coronavirus Disease (COVID-19) from infection with COVID-19 has caused a global pandemic. Many aspects of its pathogenesis and related clinical consequences are still unclear. Early diagnosis and dynamic monitoring of prognostic factors are essential to improve the ability to manage COVID-19 infection. This study aimed to provide an account of the role played by vitamins C and D on the onset, progression and severity of COVID-19. Clinical features and infection-related risk factors are also briefly discussed. Material and Methods: In March 2022, the main online databases were accessed. All the articles that investigate the possible role of vitamins C and D on COVID-19 susceptibility, severity and progression were considered. Results: The current evidence on vitamin C and D supplementation in patients with COVID-19 infection is inconsistent and controversial. In some studies, vitamins were used as coadjuvant of a formal experimental therapy, while in others as main treatment. Ethnicity and hospital setting (inpatient/outpatient) were also variable. Moreover, there was no consensus between studies in administration protocol: high heterogeneity in dosage, administration, and duration of the treatment were evident. Finally, some studies administered vitamins pre- and/or during COVID infection, in patients with different risk factors and infection severity. Conclusions: While waiting to develop a targeted, safe and effective therapy, it is important to investigate individual predisposition and proper disease management. Concluding, available data on the use of nutraceuticals in COVID-19 are inconsistent. However, there is a lack of evidence-based guidelines which recommend vitamin C and D supplementation in patients with COVID-19, and results from high quality randomised controlled trials (RCTs) are inconsistent. Current investigations so far are mostly observational, and include a relatively small sample size which can lead to biased results. Large-scale multicentre studies are therefore needed.
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Affiliation(s)
- Filippo Migliorini
- Department of Orthopaedic, Trauma and Reconstructive Surgery, RWTH Aachen University Hospital, 52074 Aachen, Germany; (J.E.); (F.H.)
| | - Raju Vaishya
- Department of Orthopaedics, Indraprastha Apollo Hospitals Institutes of Orthopaedics, New Delhi 110076, India;
| | - Jörg Eschweiler
- Department of Orthopaedic, Trauma and Reconstructive Surgery, RWTH Aachen University Hospital, 52074 Aachen, Germany; (J.E.); (F.H.)
| | - Francesco Oliva
- Department of Medicine, Surgery and Dentistry, University of Salerno, Via S. Allende, 84081 Baronissi, Italy; (F.O.); (N.M.)
| | - Frank Hildebrand
- Department of Orthopaedic, Trauma and Reconstructive Surgery, RWTH Aachen University Hospital, 52074 Aachen, Germany; (J.E.); (F.H.)
| | - Nicola Maffulli
- Department of Medicine, Surgery and Dentistry, University of Salerno, Via S. Allende, 84081 Baronissi, Italy; (F.O.); (N.M.)
- School of Pharmacy and Bioengineering, Keele University Faculty of Medicine, Thornburrow Drive, Stoke on Trent ST5 5BG, UK
- Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Centre for Sports and Exercise Medicine, Mile End Hospital, 275 Bancroft Road, London E1 4DG, UK
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61
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Elsbaey M, Ibrahim MAA, Shawky AM, Miyamoto T. Eryngium creticum L.: Chemical Characterization, SARS-CoV-2 Inhibitory Activity, and In Silico Study. ACS OMEGA 2022; 7:22725-22734. [PMID: 35811931 PMCID: PMC9260913 DOI: 10.1021/acsomega.2c02237] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 06/03/2022] [Indexed: 06/01/2023]
Abstract
Phytochemical investigation of Eryngium creticum L. has resulted in isolation of five compounds, including four compounds that are reported from the plant for the first time. Compound 1 was identified as (E)-rosmarinic acid, meanwhile, compound 2 was isolated as an (E/Z)-rosmarinic acid mixture. Interestingly, the E/Z-isomeric mixture was about 4 times as active as the single E-isomer toward the severe acute respiratory syndrome coronavirus 2 3-chymotrypsin-like protease (3CLpro), IC50 = 6.062 and 25.75 μM, respectively. Utilizing combined molecular docking and molecular dynamics (MD) techniques, the binding affinities and features of the isolated compounds were evaluated against 3CLpro. Compound 2Z demonstrated a higher binding affinity for 3CLpro than 2E , with docking scores of -8.9 and -8.5 kcal/mol and MM-GBSA/150 ns MD binding energies of -26.5 and -22.1 kcal/mol, respectively. This justifies the superior activity of the E/Z-isomeric mixture versus the single E-isomer. Structural and energetic analyses revealed the stability of 2Z and 2E compared to the reference HIV-1 protease inhibitor, lopinavir. Besides, DFT calculations demonstrated the more energetic stability of 2E compared to 2Z , which justifies the difficulty in isolating the Z-isomer in a pure form, where it readily isomerizes to the E-isomer.
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Affiliation(s)
- Marwa Elsbaey
- Department
of Pharmacognosy, Faculty of Pharmacy, Mansoura
University, Mansoura 35516, Egypt
| | - Mahmoud A. A. Ibrahim
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Ahmed M. Shawky
- Science
and Technology Unit (STU), Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Tomofumi Miyamoto
- Department
of Natural Products Chemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan
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62
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The impact of the suppression of highly connected protein interactions on the corona virus infection. Sci Rep 2022; 12:9188. [PMID: 35654986 PMCID: PMC9160517 DOI: 10.1038/s41598-022-13373-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 05/09/2022] [Indexed: 11/28/2022] Open
Abstract
Several highly effective Covid-19 vaccines are in emergency use, although more-infectious coronavirus strains, could delay the end of the pandemic even further. Because of this, it is highly desirable to develop fast antiviral drug treatments to accelerate the lasting immunity against the virus. From a theoretical perspective, computational approaches are useful tools for antiviral drug development based on the data analysis of gene expression, chemical structure, molecular pathway, and protein interaction mapping. This work studies the structural stability of virus–host interactome networks based on the graphical representation of virus–host protein interactions as vertices or nodes connected by commonly shared proteins. These graphical network visualization methods are analogous to those use in the design of artificial neural networks in neuromorphic computing. In standard protein-node-based network representation, virus–host interaction merges with virus–protein and host–protein networks, introducing redundant links associated with the internal virus and host networks. On the contrary, our approach provides a direct geometrical representation of viral infection structure and allows the effective and fast detection of the structural robustness of the virus–host network through proteins removal. This method was validated by applying it to H1N1 and HIV viruses, in which we were able to pinpoint the changes in the Interactome Network produced by known vaccines. The application of this method to the SARS-CoV-2 virus–host protein interactome implies that nonstructural proteins nsp4, nsp12, nsp16, the nuclear pore membrane glycoprotein NUP210, and ubiquitin specific peptidase USP54 play a crucial role in the viral infection, and their removal may provide an efficient therapy. This method may be extended to any new mutations or other viruses for which the Interactome Network is experimentally determined. Since time is of the essence, because of the impact of more-infectious strains on controlling the spread of the virus, this method may be a useful tool for novel antiviral therapies.
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63
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Khalatbari A, Aghazadeh Z, Ji C. Adverse Effects of Anti-Covid-19 Drug Candidates and Alcohol on Cellular Stress Responses of Hepatocytes. Hepatol Commun 2022; 6:1262-1277. [PMID: 34910385 PMCID: PMC9134820 DOI: 10.1002/hep4.1887] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 11/16/2021] [Accepted: 12/12/2021] [Indexed: 12/15/2022] Open
Abstract
During the pandemic, dexamethasone (DEX), remdesivir (RDV), hydroxychloroquine (HCQ), thapsigargin (TG), camostat mesylate (CaM), and pralatrexate were repurposed drugs for coronavirus disease 2019 (COVID-19). However, the side effects on the liver associated with the anti-COVID therapies are unknown. Cellular stresses by these drugs at 0-30 μM were studied using HepG2, Huh7, and/or primary human hepatocytes. DEX or RDV induced endoplasmic reticulum stress with increased X-box binding protein 1 and autophagic response with increased accumulation of microtubule-associated protein 1A/1B-light chain 3 (LC3-II). DEX and RDV had additive effects on the stress responses in the liver cells, which further increased expression of activating transcription factor 4 and C/EBP homology protein 1 (CHOP), and cell death. Alcohol pretreatment (50 mM) and DEX induced greater cellular stress responses than DEX and RDV. Pralatrexate induced Golgi fragmentation, cell cycle arrest at G0/G1 phase, activations of poly (ADP-ribose) polymerase-1 (PARP) and caspases, and cell death. Pralatrexate and alcohol had synergistic effects on the cell death mediators of Bim, caspase3, and PARP. The protease inhibitor CaM and TG induced autophagic response and mitochondrial stress with altered mitochondrial membrane potential, B-cell lymphoma 2, and cytochrome C. TG and HCQ induced autophagic response markers of Unc-51 like autophagy activating kinase, LC3-II, Beclin1, and Atg5, and severe ER stress marker CHOP. Conclusion: These results suggest that the anti-COVID-19 drugs, especially with drug-drug or alcohol-drug combinations, cause cellular stress responses and injuries in the liver cells.
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Affiliation(s)
- Atousa Khalatbari
- Department of MedicineKeck School of Medicine of USCUniversity of Southern CaliforniaLos AngelesCAUSA
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64
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Faraji SN, Raee MJ, Hashemi SMA, Daryabor G, Tabrizi R, Dashti FS, Behboudi E, Heidarnejad K, Nowrouzi-Sohrabi P, Hatam G. Human interaction targets of SARS-COV-2 spike protein: A systematic review. EUR J INFLAMM 2022. [PMCID: PMC9160582 DOI: 10.1177/1721727x221095382] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Objectives: The development of effective targeted therapy and drug-design approaches against the SARS-CoV-2 is a universal health priority. Therefore, it is important to assess possible therapeutic strategies against SARS-CoV-2 via its most interaction targets. The present study aimed to perform a systematic review on clinical and experimental investigations regarding SARS-COV-2 interaction targets for human cell entry. Methods: A systematic search using relevant MeSH terms and keywords was performed in PubMed, Scopus, Embase, and Web of Science (ISI) databases up to July 2021. Two reviewers independently assessed the eligibility of the studies, extracted the data, and evaluated the methodological quality of the included studies. Additionally, a narrative synthesis was done as a qualitative method for data gathering and synthesis of each outcome measure. Results: A total of 5610 studies were identified, and 128 articles were included in the systematic review. Based on the results, spike antigen was the only interaction protein from SARS-CoV-2. However, the interaction proteins from humans varied including different spike receptors and several cleavage enzymes. The most common interactions of the spike protein of SARS-CoV-2 for cell entry were ACE2 (entry receptor) and TMPRSS2 (for spike priming). A lot of published studies have mainly focused on the ACE2 receptor followed by the TMPRSS family and furin. Based on the results, ACE2 polymorphisms as well as spike RBD mutations affected the SARS-CoV-2 binding affinity. Conclusion: The included studies shed more light on SARS-CoV-2 cellular entry mechanisms and detailed interactions, which could enhance the understanding of SARS-CoV-2 pathogenesis and the development of new and comprehensive therapeutic approaches.
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Affiliation(s)
- Seyed Nooreddin Faraji
- School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohamad Javad Raee
- Center for Nanotechnology in Drug Delivery, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Mohamad Ali Hashemi
- Department of Bacteriology and Virology, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Microbiology, Golestan University of Medical Sciences, Gorgan, Iran
| | - Gholamreza Daryabor
- Autoimmune Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Reza Tabrizi
- Non-communicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Fateme Sadat Dashti
- Research Center for Food Hygiene and Safety, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Emad Behboudi
- Department of Microbiology, Golestan University of Medical Sciences, Gorgan, Iran
| | - Kamran Heidarnejad
- Recombinant Antibody Laboratory, Department of Immunology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Peyman Nowrouzi-Sohrabi
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Gholamreza Hatam
- Basic Sciences in Infectious Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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65
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Tekale S, Gore V, Kendrekar P, Thore S, Kótai L, Pawar R. COVID-19 Global Pandemic Fight by Drugs: A Mini-Review on Hope and Hype. MINI-REV ORG CHEM 2022. [DOI: 10.2174/1570193x18666210629103117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
:
Coronavirus disease 2019 (Covid-19), a serious disease caused by the Severe Acute Respiratory
Syndrome-Corona Virus-2 (SARS-CoV-2), was firstly identified in the city of Wuhan of
China in December 2019, which then spread and became a global issue due to its high transmission
rate. To date, the outbreak of COVID-19 has resulted in infection to 230,868,745 people and the death
of 4,732,669 patients. It has paralyzed the economy of all the countries worldwide. Considering the
possible mutations of SARS-CoV-2, the current medical emergency requires a longer time for drug
design and vaccine development. Drug repurposing is a promising option for potent therapeutics
against the pandemic. The present review encompasses various drugs or appropriate combinations of
already FDA-approved antimalarial, antiviral, anticancer, anti-inflammatory, and antibiotic therapeutic
candidates for use in the clinical trials as a ray of hope against COVID-19. It is expected to deliver
better clinical and laboratory outcomes of drugs as a prevention strategy for the eradication of the disease.
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Affiliation(s)
- Sunil Tekale
- Department of Chemistry, Deogiri College, Aurangabad-431005, Maharashtra, India
| | - Vishnu Gore
- Department of Chemistry, Deogiri College, Aurangabad-431005, Maharashtra, India
| | - Pravin Kendrekar
- Unit for Drug Discovery Research (UDDR), Department of Health and Environmental Sciences, Central University of Technology, Free State (CUT) Private Bag X20539, Bloemfontein, 9300, South Africa
| | - Shivaji Thore
- Department of Chemistry, Deogiri College, Aurangabad-431005, Maharashtra, India
| | - László Kótai
- Research Centre for Natural Sciences, ELKH, H-1117, Budapest, Hungary
| | - Rajendra Pawar
- Department of Chemistry, Shiv Chhatrapati College, Cidco, Aurangabad-431005, Maharashtra, India
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66
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SARS-CoV-2 ORF7a potently inhibits the antiviral effect of the host factor SERINC5. Nat Commun 2022; 13:2935. [PMID: 35618710 PMCID: PMC9135752 DOI: 10.1038/s41467-022-30609-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 04/22/2022] [Indexed: 01/03/2023] Open
Abstract
Serine Incorporator 5 (SERINC5), a cellular multipass transmembrane protein that is involved in sphingolipid and phosphatydilserine biogenesis, potently restricts a number of retroviruses, including Human Immunodeficiency Virus (HIV). SERINC5 is incorporated in the budding virions leading to the inhibition of virus infectivity. In turn, retroviruses, including HIV, encode factors that counteract the antiviral effect of SERINC5. While SERINC5 has been well studied in retroviruses, little is known about its role in other viral families. Due to the paucity of information regarding host factors targeting Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), we evaluated the effect of SERINC proteins on SARS-CoV-2 infection. Here, we show SERINC5 inhibits SARS-CoV-2 entry by blocking virus-cell fusion, and SARS-CoV-2 ORF7a counteracts the antiviral effect of SERINC5 by blocking the incorporation of over expressed SERINC5 in budding virions. SERINC5, is a cellular multipass transmembrane protein involved in sphingolipid and phosphatydilserine biogenesis and a known retroviral restriction factor. Here, Timilsina et al. show that SERINC5 is a host restriction factor for SARS-CoV-2 that prevents viral fusion during entry. Further they show that viral ORF7a counteracts SERINC5 anti-viral activity by blocking its incorporation into progeny virions.
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67
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Xie D, He S, Han L, Wu L, Huang H, Tao H, Zhou P, Shi X, Bai H, Bo X. Systematic optimization of host-directed therapeutic targets and preclinical validation of repositioned antiviral drugs. Brief Bioinform 2022; 23:bbac047. [PMID: 35238349 PMCID: PMC9116211 DOI: 10.1093/bib/bbac047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 11/12/2022] Open
Abstract
Inhibition of host protein functions using established drugs produces a promising antiviral effect with excellent safety profiles, decreased incidence of resistant variants and favorable balance of costs and risks. Genomic methods have produced a large number of robust host factors, providing candidates for identification of antiviral drug targets. However, there is a lack of global perspectives and systematic prioritization of known virus-targeted host proteins (VTHPs) and drug targets. There is also a need for host-directed repositioned antivirals. Here, we integrated 6140 VTHPs and grouped viral infection modes from a new perspective of enriched pathways of VTHPs. Clarifying the superiority of nonessential membrane and hub VTHPs as potential ideal targets for repositioned antivirals, we proposed 543 candidate VTHPs. We then presented a large-scale drug-virus network (DVN) based on matching these VTHPs and drug targets. We predicted possible indications for 703 approved drugs against 35 viruses and explored their potential as broad-spectrum antivirals. In vitro and in vivo tests validated the efficacy of bosutinib, maraviroc and dextromethorphan against human herpesvirus 1 (HHV-1), hepatitis B virus (HBV) and influenza A virus (IAV). Their drug synergy with clinically used antivirals was evaluated and confirmed. The results proved that low-dose dextromethorphan is better than high-dose in both single and combined treatments. This study provides a comprehensive landscape and optimization strategy for druggable VTHPs, constructing an innovative and potent pipeline to discover novel antiviral host proteins and repositioned drugs, which may facilitate their delivery to clinical application in translational medicine to combat fatal and spreading viral infections.
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Affiliation(s)
- Dafei Xie
- Beijing Institute of Radiation Medicine, Beijing, China, 100850
| | - Song He
- Beijing Institute of Radiation Medicine, Beijing, China, 100850
| | - Lu Han
- Beijing Institute of Pharmacology and Toxicology, Beijing, China, 100850
| | - Lianlian Wu
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China, 300072
| | - Hai Huang
- Department of Biological Medicines, School of Pharmacy, Fudan University, Shanghai, China, 201203
| | - Huan Tao
- Beijing Institute of Radiation Medicine, Beijing, China, 100850
| | - Pingkun Zhou
- Beijing Institute of Radiation Medicine, Beijing, China, 100850
| | - Xunlong Shi
- Department of Biological Medicines, School of Pharmacy, Fudan University, Shanghai, China, 201203
| | - Hui Bai
- BioMap (Beijing) Intelligence Technology Limited, Beijing, China, 100005
| | - Xiaochen Bo
- Beijing Institute of Radiation Medicine, Beijing, China, 100850
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68
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Naik RR, Shakya AK, Aladwan SM, El-Tanani M. Kinase Inhibitors as Potential Therapeutic Agents in the Treatment of COVID-19. Front Pharmacol 2022; 13:806568. [PMID: 35444538 PMCID: PMC9014181 DOI: 10.3389/fphar.2022.806568] [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] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/17/2022] [Indexed: 12/12/2022] Open
Abstract
Corona virus is quickly spreading around the world. The goal of viral management is to disrupt the virus’s life cycle, minimize lung damage, and alleviate severe symptoms. Numerous strategies have been used, including repurposing existing antivirals or drugs used in previous viral outbreaks. One such strategy is to repurpose FDA-approved kinase inhibitors that are potential chemotherapeutic agents and have demonstrated antiviral activity against a variety of viruses, including MERS, SARS-CoV-1, and others, by inhibiting the viral life cycle and the inflammatory response associated with COVID-19. The purpose of this article is to identify licensed kinase inhibitors that have the ability to reduce the virus’s life cycle, from entrance through viral propagation from cell to cell. Several of these inhibitors, including imatinib, ruxolitinib, silmitasertib, and tofacitinib (alone and in conjunction with hydroxychloroquine), are now undergoing clinical studies to determine their efficacy as a possible treatment drug. The FDA approved baricitinib (a Janus kinase inhibitor) in combination with remdesivir for the treatment of COVID-19 patients receiving hospital care in November 2020. While in vitro trials with gilteritinib, fedratinib, and osimertinib are encouraging, further research is necessary before these inhibitors may be used to treat COVID-19 patients.
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Affiliation(s)
- Rajashri R Naik
- Department of Biopharmaceutics and Clinical Pharmacy, Al-Ahliyya Amman University, Faculty of Pharmacy, Amman, Jordan.,Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, Amman, Jordan
| | - Ashok K Shakya
- Faculty of Pharmacy, Pharmacological and Diagnostic Research Centre, Al-Ahliyya Amman University, Amman, Jordan.,Department of Pharmaceutical Sciences, Faculty of Pharmacy, Al-Ahliyya Amman University, Amman, Jordan
| | - Safwan M Aladwan
- Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, Amman, Jordan
| | - Mohamed El-Tanani
- Department of Biopharmaceutics and Clinical Pharmacy, Al-Ahliyya Amman University, Faculty of Pharmacy, Amman, Jordan.,Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, Amman, Jordan.,Faculty of Pharmacy, Pharmacological and Diagnostic Research Centre, Al-Ahliyya Amman University, Amman, Jordan.,Department of Pharmaceutical Sciences, Faculty of Pharmacy, Al-Ahliyya Amman University, Amman, Jordan
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69
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Ghosh D, Ghosh Dastidar D, Roy K, Ghosh A, Mukhopadhyay D, Sikdar N, Biswas NK, Chakrabarti G, Das A. Computational prediction of the molecular mechanism of statin group of drugs against SARS-CoV-2 pathogenesis. Sci Rep 2022; 12:6241. [PMID: 35422113 PMCID: PMC9009757 DOI: 10.1038/s41598-022-09845-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 03/23/2022] [Indexed: 01/18/2023] Open
Abstract
Recently published clinical data from COVID-19 patients indicated that statin therapy is associated with a better clinical outcome and a significant reduction in the risk of mortality. In this study by computational analysis, we have aimed to predict the possible mechanism of the statin group of drugs by which they can inhibit SARS-CoV-2 pathogenesis. Blind docking of the critical structural and functional proteins of SARS-CoV-2 like RNA-dependent RNA polymerase, M-protease of 3-CL-Pro, Helicase, and the Spike proteins ( wild type and mutants from different VOCs) were performed using the Schrodinger docking tool. We observed that fluvastatin and pitavastatin showed fair, binding affinities to RNA polymerase and 3-CL-Pro, whereas fluvastatin showed the strongest binding affinity to the helicase. Fluvastatin also showed the highest affinity for the SpikeDelta and a fair docking score for other spike variants. Additionally, molecular dynamics simulation confirmed the formation of a stable drug-protein complex between Fluvastatin and target proteins. Thus our study shows that of all the statins, fluvastatin can bind to multiple target proteins of SARS-CoV-2, including the spike-mutant proteins. This property might contribute to the potent antiviral efficacy of this drug.
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Affiliation(s)
- Dipanjan Ghosh
- Department of Biotechnology, Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, West Bengal, 700019, India
| | - Debabrata Ghosh Dastidar
- Guru Nanak Institute of Pharmaceutical Science and Technology, 157/F Nilgunj Road, Panihati, Kolkata, West Bengal, 700114, India
| | - Kamalesh Roy
- Department of Genetics, Institute of Genetic Engineering, 30, Thakurhat Road, Badu, Madhyamgram, West Bengal, 700128, India
| | - Arnab Ghosh
- National Institute of Biomedical Genomics, PO NSS, Kalyani, West Bengal, 741251, India
| | - Debanjan Mukhopadhyay
- National Institute of Biomedical Genomics, PO NSS, Kalyani, West Bengal, 741251, India
| | - Nilabja Sikdar
- Human Genetics Unit, Kolmogorov Bhaban, Biological Sciences Division, Indian Statistical Institute, 203, BT road, Kolkata, West Bengal, 700108, India.
| | - Nidhan K Biswas
- National Institute of Biomedical Genomics, PO NSS, Kalyani, West Bengal, 741251, India
| | - Gopal Chakrabarti
- Department of Biotechnology, Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, West Bengal, 700019, India.
| | - Amlan Das
- National Institute of Biomedical Genomics, PO NSS, Kalyani, West Bengal, 741251, India.
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70
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Mukherjee PK, Efferth T, Das B, Kar A, Ghosh S, Singha S, Debnath P, Sharma N, Bhardwaj PK, Haldar PK. Role of medicinal plants in inhibiting SARS-CoV-2 and in the management of post-COVID-19 complications. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 98:153930. [PMID: 35114450 PMCID: PMC8730822 DOI: 10.1016/j.phymed.2022.153930] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 12/30/2021] [Accepted: 01/03/2022] [Indexed: 05/07/2023]
Abstract
BACKGROUND The worldwide corona virus disease outbreak, generally known as COVID-19 pandemic outbreak resulted in a major health crisis globally. The morbidity and transmission modality of COVID-19 appear more severe and uncontrollable. The respiratory failure and following cardiovascular complications are the main pathophysiology of this deadly disease. Several therapeutic strategies are put forward for the development of safe and effective treatment against SARS-CoV-2 virus from the pharmacological view point but till date there are no specific treatment regimen developed for this viral infection. PURPOSE The present review emphasizes the role of herbs and herbs-derived secondary metabolites in inhibiting SARS-CoV-2 virus and also for the management of post-COVID-19 related complications. This approach will foster and ensure the safeguards of using medicinal plant resources to support the healthcare system. Plant-derived phytochemicals have already been reported to prevent the viral infection and to overcome the post-COVID complications like parkinsonism, kidney and heart failure, liver and lungs injury and mental problems. In this review, we explored mechanistic approaches of herbal medicines and their phytocomponenets as antiviral and post-COVID complications by modulating the immunological and inflammatory states. STUDY DESIGN Studies related to diagnosis and treatment guidelines issued for COVID-19 by different traditional system of medicine were included. The information was gathered from pharmacological or non-pharmacological interventions approaches. The gathered information sorted based on therapeutic application of herbs and their components against SARSCoV-2 and COVID-19 related complications. METHODS A systemic search of published literature was conducted from 2003 to 2021 using different literature database like Google Scholar, PubMed, Science Direct, Scopus and Web of Science to emphasize relevant articles on medicinal plants against SARS-CoV-2 viral infection and Post-COVID related complications. RESULTS Collected published literature from 2003 onwards yielded with total 625 articles, from more than 18 countries. Among these 625 articles, more than 95 medicinal plants and 25 active phytomolecules belong to 48 plant families. Reports on the therapeutic activity of the medicinal plants belong to the Lamiaceae family (11 reports), which was found to be maximum reported from 4 different countries including India, China, Australia, and Morocco. Other reports on the medicinal plant of Asteraceae (7 reports), Fabaceae (8 reports), Piperaceae (3 reports), Zingiberaceae (3 reports), Ranunculaceae (3 reports), Meliaceae (4 reports) were found, which can be explored for the development of safe and efficacious products targeting COVID-19. CONCLUSION Keeping in mind that the natural alternatives are in the priority for the management and prevention of the COVID-19, the present review may help to develop an alternative approach for the management of COVID-19 viral infection and post-COVID complications from a mechanistic point of view.
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Affiliation(s)
- Pulok K Mukherjee
- Institute of Bioresources and Sustainable Development, Imphal-795001, India; School of Natural Product Studies, Department of Pharmaceutical Technology, Jadavpur University, Kolkata -700 032, India.
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Mainz, Germany
| | - Bhaskar Das
- School of Natural Product Studies, Department of Pharmaceutical Technology, Jadavpur University, Kolkata -700 032, India
| | - Amit Kar
- Institute of Bioresources and Sustainable Development, Imphal-795001, India
| | - Suparna Ghosh
- School of Natural Product Studies, Department of Pharmaceutical Technology, Jadavpur University, Kolkata -700 032, India
| | - Seha Singha
- School of Natural Product Studies, Department of Pharmaceutical Technology, Jadavpur University, Kolkata -700 032, India
| | - Pradip Debnath
- School of Natural Product Studies, Department of Pharmaceutical Technology, Jadavpur University, Kolkata -700 032, India
| | - Nanaocha Sharma
- Institute of Bioresources and Sustainable Development, Imphal-795001, India
| | | | - Pallab Kanti Haldar
- School of Natural Product Studies, Department of Pharmaceutical Technology, Jadavpur University, Kolkata -700 032, India
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71
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Ahmad S, Bhanu P, Kumar J, Pathak RK, Mallick D, Uttarkar A, Niranjan V, Mishra V. Molecular dynamics simulation and docking analysis of NF-κB protein binding with sulindac acid. Bioinformation 2022; 18:170-179. [PMID: 36518123 PMCID: PMC9722428 DOI: 10.6026/97320630018170] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/24/2022] [Accepted: 03/31/2022] [Indexed: 08/22/2023] Open
Abstract
It is of interest to document the Molecular Dynamics Simulation and docking analysis of NF-κB target with sulindac sodium in combating COVID-19 for further consideration. Sulindac is a nonsteroidal anti-inflammatory drug (NSAID) of the arylalkanoic acid class that is marketed by Merck under the brand name Clinoril. We show the binding features of sulindac sodium with NF-κB that can be useful in drug repurposing in COVID-19 therapy.
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Affiliation(s)
- Shaban Ahmad
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
- Department of Computer Science, Jamia Milia Islamia, New Delhi 110025, India
| | - Piyush Bhanu
- Xome Life Sciences, Bangalore Bioinnovation Centre, Helix Biotech Park, Bengaluru 560100, Karnataka, India
| | - Jitendra Kumar
- Bangalore Bioinnovation Centre (BBC), Helix Biotech Park, Electronics City Phase 1, Bengaluru 560100, Karnataka, India
| | - Ravi Kant Pathak
- School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar-Delhi Grand Trunk Rd, Phagwara 144001, Punjab, India
| | - Dharmendra Mallick
- Department of Botany, Deshbandhu College, University of Delhi, Delhi 110019, India
| | - Akshay Uttarkar
- Department of Biotechnology, RV College of Engineering, RV Vidyanikethan Post, Mysuru Road, Bengaluru 560059, India
| | - Vidya Niranjan
- Department of Biotechnology, RV College of Engineering, RV Vidyanikethan Post, Mysuru Road, Bengaluru 560059, India
| | - Vachaspati Mishra
- Department of Botany, Hindu College, University of Delhi, Delhi 110007, India
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Frausto-Parada F, Várgas-Rodríguez I, Mercado-Sánchez I, Bazán-Jiménez A, Díaz-Cervantes E, Sotelo-Figueroa MA, García-Revilla MA. Grammatical evolution-based design of SARS-CoV-2 main protease inhibitors. Phys Chem Chem Phys 2022; 24:5233-5245. [PMID: 35167639 DOI: 10.1039/d1cp04159b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A series of SARS-CoV-2 main protease (SARS-CoV-2-Mpro) inhibitors were modeled using evolutive grammar algorithms. We have generated an automated program that finds the best candidate to inhibit the main protease, Mpro, of SARS-CoV-2. The candidates were constructed based on a pharmacophore model of the above-mentioned target; relevant moieties of such molecules were modified using data-basis sets with similar chemical behavior to the reference moieties. Additionally, we used the SMILES language to translate 3D chemical structures to 1D words; then, an evolutive grammar algorithm was used to explore the chemical space and obtain new candidates, which were evaluated via the binding energy of molecular coupling assays as an evaluation function. Finally, sixteen molecules were obtained in 3 runs of our program, three of which show promising binding properties as SARS-CoV-2-Mpro inhibitors. One of them, TTO, maintained its relevant binding properties during 100 ns molecular dynamics experiments. For this reason, TTO is the best candidate to inhibit SARS-CoV-2-Mpro. The software we developed for this contribution is available at the following URL: https://github.com/masotelof/GEMolecularDesign.
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Affiliation(s)
- Francisco Frausto-Parada
- Department of Chemistry, Natural and Exact Sciences Division, University of Guanajuato, Noria Alta S/N, Guanajuato-36050, Mexico.
| | - Ismael Várgas-Rodríguez
- Department of Chemistry, Natural and Exact Sciences Division, University of Guanajuato, Noria Alta S/N, Guanajuato-36050, Mexico.
| | - Itzel Mercado-Sánchez
- Department of Chemistry, Natural and Exact Sciences Division, University of Guanajuato, Noria Alta S/N, Guanajuato-36050, Mexico.
| | - Adán Bazán-Jiménez
- Department of Chemistry, Natural and Exact Sciences Division, University of Guanajuato, Noria Alta S/N, Guanajuato-36050, Mexico.
| | - Erik Díaz-Cervantes
- Departamento de Alimentos, Centro Interdisciplinario del Noreste de la Universidad de Guanajuato, Tierra Blanca, Guanajuato-37975, Mexico
| | - Marco A Sotelo-Figueroa
- 3Department of Organizational Studies, Economical and Administrative Sciences Division, University of Guanajuato, Guanajuato-36000, Mexico.
| | - Marco A García-Revilla
- Department of Chemistry, Natural and Exact Sciences Division, University of Guanajuato, Noria Alta S/N, Guanajuato-36050, Mexico.
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Bakour M, Laaroussi H, Ousaaid D, El Ghouizi A, Es-safi I, Mechchate H, Lyoussi B. New Insights into Potential Beneficial Effects of Bioactive Compounds of Bee Products in Boosting Immunity to Fight COVID-19 Pandemic: Focus on Zinc and Polyphenols. Nutrients 2022; 14:nu14050942. [PMID: 35267917 PMCID: PMC8912813 DOI: 10.3390/nu14050942] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/16/2022] [Accepted: 02/20/2022] [Indexed: 02/01/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) is an epidemic caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). Populations at risk as well as those who can develop serious complications are people with chronic diseases such as diabetes, hypertension, and the elderly. Severe symptoms of SARS-CoV-2 infection are associated with immune failure and dysfunction. The approach of strengthening immunity may be the right choice in order to save lives. This review aimed to provide an overview of current information revealing the importance of bee products in strengthening the immune system against COVID-19. We highlighted the immunomodulatory and the antiviral effects of zinc and polyphenols, which may actively contribute to improving symptoms and preventing complications caused by COVID-19 and can counteract viral infections. Thus, this review will pave the way for conducting advanced experimental research to evaluate zinc and polyphenols-rich bee products to prevent and reduce the severity of COVID-19 symptoms.
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Affiliation(s)
- Meryem Bakour
- Laboratory of Natural Substances, Pharmacology, Environment, Modeling, Health, and Quality of Life (SNAMOPEQ), Faculty of Sciences Dhar El Mahraz, University Sidi Mohamed Ben Abdellah, Fez 30000, Morocco; (M.B.); (H.L.); (D.O.); (A.E.G.); (B.L.)
| | - Hassan Laaroussi
- Laboratory of Natural Substances, Pharmacology, Environment, Modeling, Health, and Quality of Life (SNAMOPEQ), Faculty of Sciences Dhar El Mahraz, University Sidi Mohamed Ben Abdellah, Fez 30000, Morocco; (M.B.); (H.L.); (D.O.); (A.E.G.); (B.L.)
| | - Driss Ousaaid
- Laboratory of Natural Substances, Pharmacology, Environment, Modeling, Health, and Quality of Life (SNAMOPEQ), Faculty of Sciences Dhar El Mahraz, University Sidi Mohamed Ben Abdellah, Fez 30000, Morocco; (M.B.); (H.L.); (D.O.); (A.E.G.); (B.L.)
| | - Asmae El Ghouizi
- Laboratory of Natural Substances, Pharmacology, Environment, Modeling, Health, and Quality of Life (SNAMOPEQ), Faculty of Sciences Dhar El Mahraz, University Sidi Mohamed Ben Abdellah, Fez 30000, Morocco; (M.B.); (H.L.); (D.O.); (A.E.G.); (B.L.)
| | - Imane Es-safi
- Laboratory of Inorganic Chemistry, Department of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland;
| | - Hamza Mechchate
- Laboratory of Inorganic Chemistry, Department of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland;
- Correspondence:
| | - Badiaa Lyoussi
- Laboratory of Natural Substances, Pharmacology, Environment, Modeling, Health, and Quality of Life (SNAMOPEQ), Faculty of Sciences Dhar El Mahraz, University Sidi Mohamed Ben Abdellah, Fez 30000, Morocco; (M.B.); (H.L.); (D.O.); (A.E.G.); (B.L.)
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Li X, Zhang Y, He L, Si J, Qiu S, He Y, Wei J, Wang Z, Xie L, Li Y, Teng T. Immune response and potential therapeutic strategies for the SARS-CoV-2 associated with the COVID-19 pandemic. Int J Biol Sci 2022; 18:1865-1877. [PMID: 35342348 PMCID: PMC8935217 DOI: 10.7150/ijbs.66369] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 01/28/2022] [Indexed: 02/07/2023] Open
Abstract
Following onset of the first recorded case of Coronavirus disease 2019 (COVID-19) in December 2019, more than 269 million cases and over 5.3 million deaths have been confirmed worldwide. COVID-19 is a highly infectious pneumonia, caused by a novel virus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Currently, it poses a severe threat to human health across the globe, a trend that is likely to persist in the foreseeable future. This paper reviews SARS-CoV-2 immunity, the latest development of anti-SARS-CoV-2 drugs as well as exploring in detail, immune escape induced by SARS-CoV-2. We expect that the findings will provide a basis for COVID-19 prevention and treatment.
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Affiliation(s)
- Xianghui Li
- Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China.,Henan International Joint Laboratory of Nuclear Protein Regulation, School of Basic Medical Science, Henan University, Kaifeng, Henan 475004, China
| | - Yabo Zhang
- Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China.,Henan International Joint Laboratory of Nuclear Protein Regulation, School of Basic Medical Science, Henan University, Kaifeng, Henan 475004, China
| | - Libing He
- Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China.,Henan International Joint Laboratory of Nuclear Protein Regulation, School of Basic Medical Science, Henan University, Kaifeng, Henan 475004, China
| | - Jiangzhe Si
- Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China.,Henan International Joint Laboratory of Nuclear Protein Regulation, School of Basic Medical Science, Henan University, Kaifeng, Henan 475004, China
| | - Shuai Qiu
- Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China.,Henan International Joint Laboratory of Nuclear Protein Regulation, School of Basic Medical Science, Henan University, Kaifeng, Henan 475004, China
| | - Yuhua He
- Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China.,Henan International Joint Laboratory of Nuclear Protein Regulation, School of Basic Medical Science, Henan University, Kaifeng, Henan 475004, China
| | - Jiacun Wei
- Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China.,Henan International Joint Laboratory of Nuclear Protein Regulation, School of Basic Medical Science, Henan University, Kaifeng, Henan 475004, China
| | - Zhili Wang
- Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China.,Henan International Joint Laboratory of Nuclear Protein Regulation, School of Basic Medical Science, Henan University, Kaifeng, Henan 475004, China
| | - Longxiang Xie
- Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China.,Henan International Joint Laboratory of Nuclear Protein Regulation, School of Basic Medical Science, Henan University, Kaifeng, Henan 475004, China.,✉ Corresponding authors: E-mail: ; Tel.: +86-0371-22892865
| | - Yanzhang Li
- Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China.,Henan International Joint Laboratory of Nuclear Protein Regulation, School of Basic Medical Science, Henan University, Kaifeng, Henan 475004, China.,✉ Corresponding authors: E-mail: ; Tel.: +86-0371-22892865
| | - Tieshan Teng
- Institute of Biomedical Informatics, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China.,Henan International Joint Laboratory of Nuclear Protein Regulation, School of Basic Medical Science, Henan University, Kaifeng, Henan 475004, China.,✉ Corresponding authors: E-mail: ; Tel.: +86-0371-22892865
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75
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Alzain AA, Elbadwi FA, Alsamani FO. Discovery of novel TMPRSS2 inhibitors for COVID-19 using in silico fragment-based drug design, molecular docking, molecular dynamics, and quantum mechanics studies. INFORMATICS IN MEDICINE UNLOCKED 2022; 29:100870. [PMID: 35128036 PMCID: PMC8806845 DOI: 10.1016/j.imu.2022.100870] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/29/2022] [Accepted: 01/29/2022] [Indexed: 01/18/2023] Open
Abstract
The global expansion of COVID-19 and the mutations of severe acute respiratory syndrome coronavirus necessitate quick development of treatment and vaccination. Because the androgen-responsive serine protease TMPRSS2 is involved in cleaving the SARS-CoV-2 spike protein allowing the virus to enter the cell, therefore, direct TMPRSS2 inhibition will inhibit virus activation and disease progression which make it an important target for drug discovery. In this study, a homology model of TMPRSS2 protein was initially developed. Then, we used the fragment-based drug design (FBDD) technique to develop effective TMPRSS2 inhibitors. Over a half-million fragments from the enamine database were screened for their binding ability to target protein, and then best-scoring fragments were linked to building new molecules with a good binding affinity. XP docking and MM-GBSA studies revealed 10 new formed molecules with docking score ≤ -14.982 kcal/mol compared to ambroxol (control) with a docking score of -6.464 kcal/mol. Finally, molecular dynamics (MD) and density functional theory (DFT) were calculated for the top 3 molecules.
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Affiliation(s)
- Abdulrahim A Alzain
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Fatima A Elbadwi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Fatima O Alsamani
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
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76
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Yin J, Li C, Ye C, Ruan Z, Liang Y, Li Y, Wu J, Luo Z. Advances in the development of therapeutic strategies against COVID-19 and perspectives in the drug design for emerging SARS-CoV-2 variants. Comput Struct Biotechnol J 2022; 20:824-837. [PMID: 35126885 PMCID: PMC8802458 DOI: 10.1016/j.csbj.2022.01.026] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/18/2022] [Accepted: 01/27/2022] [Indexed: 12/15/2022] Open
Abstract
Since Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was identified in late 2019, the coronavirus disease 2019 (COVID-19) pandemic has challenged public health around the world. Currently, there is an urgent need to explore antiviral therapeutic targets and effective clinical drugs. In this study, we systematically summarized two main therapeutic strategies against COVID-19, namely drugs targeting the SARS-CoV-2 life cycle and SARS-CoV-2-induced inflammation in host cells. The development of above two strategies is implemented by repurposing drugs and exploring potential targets. A comprehensive summary of promising drugs, especially cytokine inhibitors, and traditional Chinese medicine (TCM), provides recommendations for clinicians as evidence-based medicine in the actual clinical COVID-19 treatment. Considering the emerging SARS-CoV-2 variants greatly impact the effectiveness of drugs and vaccines, we reviewed the appearance and details of SARS-CoV-2 variants for further perspectives in drug design, which brings updating clues to develop therapeutical agents against the variants. Based on this, the development of broadly antiviral drugs, combined with immunomodulatory, or holistic therapy in the host, is prior to being considered for therapeutic interventions on mutant strains of SARS-CoV-2. Therefore, it is highly acclaimed the requirements of the concerted efforts from multi-disciplinary basic studies and clinical trials, which improves the accurate treatment of COVID-19 and optimizes the contingency measures to emerging SARS-CoV-2 variants.
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Key Words
- ACE2, Angiotensin-converting enzyme 2
- ARDS, acute respiratory distress syndrome
- CEP, Cepharanthine
- COVID-19 pandemic
- COVID-19, coronavirus disease 2019
- CRS, cytokine release syndrome
- CTD, C-terminal domain
- Drug target
- EMA, European Medicines Agency
- ERGIC, endoplasmic reticulum-Golgi intermediate compartment
- FDA, U.S. Food and Drug Administration
- JAK, Janus kinase
- MODS, multiple organ dysfunction syndrome
- NMPA, National Medical Products Administration
- NTD, N-terminal domain
- Nbs, nanobodies
- RBD, receptor-binding domain
- RdRp, RNA dependent RNA polymerase
- SARS-CoV-2
- SARS-CoV-2 variants
- SARS-CoV-2, Severe Acute Respiratory Syndrome Coronavirus 2
- STAT, Signal Transducer and Activator of Transcription
- TCM, traditional Chinese medicine
- TCZ, Tocilizumab
- Therapeutic strategies
- VOC, variants of concern
- VOI, variants of interest
- VUM, variants under monitoring
- mAb, monoclonal antibody
- α1AT, alpha-1 antitrypsin
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Affiliation(s)
- Jialing Yin
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou 510632, PR China
| | - Chengcheng Li
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou 510632, PR China
| | - Chunhong Ye
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou 510632, PR China
| | - Zhihui Ruan
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou 510632, PR China
- Foshan Institute of Medical Microbiology, Foshan 528315, PR China
| | - Yicong Liang
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou 510632, PR China
| | - Yongkui Li
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou 510632, PR China
| | - Jianguo Wu
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou 510632, PR China
- Foshan Institute of Medical Microbiology, Foshan 528315, PR China
| | - Zhen Luo
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou 510632, PR China
- Foshan Institute of Medical Microbiology, Foshan 528315, PR China
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77
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Sanchez-Burgos L, Gómez-López G, Al-Shahrour F, Fernandez-Capetillo O. An in silico analysis identifies drugs potentially modulating the cytokine storm triggered by SARS-CoV-2 infection. Sci Rep 2022; 12:1626. [PMID: 35102208 PMCID: PMC8803893 DOI: 10.1038/s41598-022-05597-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 01/11/2022] [Indexed: 12/12/2022] Open
Abstract
The ongoing COVID-19 pandemic is one of the biggest health challenges of recent decades. Among the causes of mortality triggered by SARS-CoV-2 infection, the development of an inflammatory "cytokine storm" (CS) plays a determinant role. Here, we used transcriptomic data from the bronchoalveolar lavage fluid (BALF) of COVID-19 patients undergoing a CS to obtain gene-signatures associated to this pathology. Using these signatures, we interrogated the Connectivity Map (CMap) dataset that contains the effects of over 5000 small molecules on the transcriptome of human cell lines, and looked for molecules which effects on transcription mimic or oppose those of the CS. As expected, molecules that potentiate immune responses such as PKC activators are predicted to worsen the CS. In addition, we identified the negative regulation of female hormones among pathways potentially aggravating the CS, which helps to understand the gender-related differences in COVID-19 mortality. Regarding drugs potentially counteracting the CS, we identified glucocorticoids as a top hit, which validates our approach as this is the primary treatment for this pathology. Interestingly, our analysis also reveals a potential effect of MEK inhibitors in reverting the COVID-19 CS, which is supported by in vitro data that confirms the anti-inflammatory properties of these compounds.
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Affiliation(s)
- Laura Sanchez-Burgos
- Genomic Instability Group, Spanish National Cancer Research Centre, 28029, Madrid, Spain
| | - Gonzalo Gómez-López
- Bioinformatics Unit, Spanish National Cancer Research Centre, 28029, Madrid, Spain
| | - Fátima Al-Shahrour
- Bioinformatics Unit, Spanish National Cancer Research Centre, 28029, Madrid, Spain
| | - Oscar Fernandez-Capetillo
- Genomic Instability Group, Spanish National Cancer Research Centre, 28029, Madrid, Spain.
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 21, Stockholm, Sweden.
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78
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Sen D, Debnath B, Debnath P, Debnath S, Zaki MEA, Masand VH. Identification of potential edible mushroom as SARS-CoV-2 main protease inhibitor using rational drug designing approach. Sci Rep 2022; 12:1503. [PMID: 35087077 PMCID: PMC8795408 DOI: 10.1038/s41598-022-05349-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 01/03/2022] [Indexed: 12/13/2022] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is highly pathogenic to humans and has created health care threats worldwide. This urgent situation has focused the researchers worldwide towards the development of novel vaccine or small molecule therapeutics for SARS-CoV-2. Although several vaccines have already been discovered and are in use for the masses, no therapeutic medication has yet been approved by FDA for the treatment of COVID-19. Keeping this in view, in the present study, we have identified promising hits against the main protease (Mpro) of SARS-CoV-2 from edible mushrooms. Structure-based virtual screening (VS) of 2433 compounds derived from mushrooms was performed with Mpro protein (6LU7). Four promising hits, namely, Kynapcin-12 (M_78), Kynapcin-28 (M_82), Kynapcin-24 (M_83), and Neonambiterphenyls-A (M_366) were identified based on the result of docking, Lipinski's rule, 100 ns molecular dynamics (MD) simulation and MM/PBSA binding free energy calculations. Finally, the inhibitory properties of these hits were compared with three known inhibitors, baicalein (1), baicalin (2), and biflavonoid (3). Data indicated that M_78, M_82 and M_83 compounds present in edible mushroom Polyozellus multiplex were potent inhibitors of Mproprotein (6LU7). It could be concluded that edible mushroom Polyozellus multiplex has potential activity against SARS-CoV-2 infection and identified molecules could be further explored as therapeutic inhibitors against SARS-CoV-2.
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Affiliation(s)
- Debanjan Sen
- BCDA College of Pharmacy & Technology, Jessore Road South, Hridaypur, Kolkata, West Bengal, 700127, India
| | - Bimal Debnath
- Department of Forestry and Biodiversity, Tripura University, Suryamaninagar, Tripura, 799022, India
| | - Pradip Debnath
- Department of Chemistry, Majaraja Bir Bikram College, Agartala, Tripura, 799004, India
| | - Sudhan Debnath
- Department of Chemistry, Netaji Subhash Mahavidyalaya, Udaipur, Tripura, 799114, India.
| | - Magdi E A Zaki
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, 13318, Saudi Arabia.
| | - Vijay H Masand
- Department of Chemistry, Vidya Bharati Mahavidyalaya, Amravati, Maharashtra, 444 602, India
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Abstract
The global coronavirus disease-19 (COVID-19) has affected more than 140 million and killed more than 3 million people worldwide as of April 20, 2021. The novel human severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been identified as an etiological agent for COVID-19. Several kinases have been proposed as possible mediators of multiple viral infections, including life-threatening coronaviruses like SARS-CoV-1, Middle East syndrome coronavirus (MERS-CoV), and SARS-CoV-2. Viral infections hijack abundant cell signaling pathways, resulting in drastic phosphorylation rewiring in the host and viral proteins. Some kinases play a significant role throughout the viral infection cycle (entry, replication, assembly, and egress), and several of them are involved in the virus-induced hyperinflammatory response that leads to cytokine storm, acute respiratory distress syndrome (ARDS), organ injury, and death. Here, we highlight kinases that are associated with coronavirus infections and their inhibitors with antiviral and potentially anti-inflammatory, cytokine-suppressive, or antifibrotic activity.
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Affiliation(s)
- Thanigaimalai Pillaiyar
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry
and Tuebingen Center for Academic Drug Discovery, Eberhard Karls University
Tübingen, Auf der Morgenstelle 8, 72076 Tübingen,
Germany
| | - Stefan Laufer
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry
and Tuebingen Center for Academic Drug Discovery, Eberhard Karls University
Tübingen, Auf der Morgenstelle 8, 72076 Tübingen,
Germany
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80
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Karthic A, Kesarwani V, Singh RK, Yadav PK, Chaturvedi N, Chauhan P, Yadav BS, Kushwaha SK. Computational Analysis Reveals Monomethylated Triazolopyrimidine as a Novel Inhibitor of SARS-CoV-2 RNA-Dependent RNA Polymerase (RdRp). Molecules 2022; 27:801. [PMID: 35164069 PMCID: PMC8840377 DOI: 10.3390/molecules27030801] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 01/03/2022] [Accepted: 01/07/2022] [Indexed: 01/18/2023] Open
Abstract
The human population is still facing appalling conditions due to several outbreaks of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) virus. The absence of specific drugs, appropriate vaccines for mutants, and knowledge of potential therapeutic agents makes this situation more difficult. Several 1, 2, 4-triazolo [1, 5-a] pyrimidine (TP)-derivative compounds were comprehensively studied for antiviral activities against RNA polymerase of HIV, HCV, and influenza viruses, and showed immense pharmacological interest. Therefore, TP-derivative compounds can be repurposed against the RNA-dependent RNA polymerase (RdRp) protein of SARS-CoV-2. In this study, a meta-analysis was performed to ensure the genomic variability and stability of the SARS-CoV-2 RdRp protein. The molecular docking of natural and synthetic TP compounds to RdRp and molecular dynamic (MD) simulations were performed to analyse the dynamic behaviour of TP compounds at the active site of the RdRp protein. TP compounds were also docked against other non-structural proteins (NSP1, NSP2, NSP3, NSP5, NSP8, NSP13, and NSP15) of SARS-CoV-2. Furthermore, the inhibition potential of TP compounds was compared with Remdesivir and Favipiravir drugs as a positive control. Additionally, TP compounds were analysed for inhibitory activity against SARS-CoV RdRp protein. This study demonstrates that TP analogues (monomethylated triazolopyrimidine and essramycin) represent potential lead molecules for designing an effective inhibitor to control viral replication. Furthermore, in vitro and in vivo studies will strengthen the use of these inhibitors as suitable drug candidates against SARS-CoV-2.
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Affiliation(s)
- Anandakrishnan Karthic
- Bioinformatics, DBT-National Institute of Animal Biotechnology (NIAB), Hyderabad 500032, India; (A.K.); (V.K.)
- Amity Institute of Biotechnology, Amity University Mumbai, Navi Mumbai 410206, India
| | - Veerbhan Kesarwani
- Bioinformatics, DBT-National Institute of Animal Biotechnology (NIAB), Hyderabad 500032, India; (A.K.); (V.K.)
- Hap Biosolutions, Pvt. Ltd., Bhopal 462042, India
| | - Rahul Kunwar Singh
- Cyano Biotech Lab, Department of Microbiology, School of Life Sciences, Hemvati Nandan Bahuguna Garhwal University, Srinagar (Garhwal) 246174, India;
| | - Pavan Kumar Yadav
- Department of Veterinary Physiology and Biochemistry, Faculty of Veterinary and Animal Sciences, Banaras Hindu University, Mirzapur 231001, India;
| | - Navaneet Chaturvedi
- Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester LE1 7RH, UK;
| | | | - Brijesh Singh Yadav
- Faculty of Biosciences and Aquaculture, Nord University, N-8049 Bodø, Norway
| | - Sandeep Kumar Kushwaha
- Bioinformatics, DBT-National Institute of Animal Biotechnology (NIAB), Hyderabad 500032, India; (A.K.); (V.K.)
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81
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Ruiz-Fresneda MA, Jiménez-Contreras E, Ruiz-Fresneda C, Ruiz-Pérez R. Bibliometric Analysis of International Scientific Production on Pharmacologic Treatments for SARS-CoV-2/COVID-19 During 2020. Front Public Health 2022; 9:778203. [PMID: 35127621 PMCID: PMC8811030 DOI: 10.3389/fpubh.2021.778203] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 12/03/2021] [Indexed: 01/04/2023] Open
Abstract
Background COVID-19 is causing a grave global health and economic crisis and the fight against the pandemic has led to unprecedented scientific activity. Bibliometrics could be a useful tool for guiding future researches lines and promoting international collaboration for an effective treatment. For this purpose, we have conducted a bibliometric analysis of scientific publications on drugs and therapies used to treat COVID-19 during 2020. Methods Data source: Web of Science. We gathered data on scientific production relating to drugs used to treat COVID-19. We calculated impact factors and analyzed production by institution, country, and journal, visualizing our results in bibliometric networks. Results In 1 year, production relating to COVID-19 exceeded 100 000 publications, with over 6,500 on Drugs and COVID-19. Research into hydroxychloroquine and chloroquine, remdesivir, lopinavir and ritonavir, tocilizumab and convalescent plasma is particularly noteworthy. Mean citations/study range from 11.9 to 15.4. Producer institutions fall into three groups: one in the US and centered on Harvard Medical School; another in Europe led by INSERS; and another in China led by Huazhong University of Science and Technology. Production by journal is widespread but the Journal of Medical Virology, International Journal of Antimicrobial Agents, and American Journal of Transplantation are noteworthy. Conclusions The volume of research that is currently under way is comparable to the magnitude of the pandemic itself. Such a high volume of studies is infrequent and the impact they have achieved has no known precedent. The producing countries are those with highest incidence of the pandemic and greatest scientific potential; moreover, inter-agency and international collaboration has reached extraordinarily high levels.
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Affiliation(s)
- Miguel A. Ruiz-Fresneda
- Department of Crystallography and Structural Biology, Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Madrid, Spain
- *Correspondence: Miguel A. Ruiz-Fresneda
| | - Evaristo Jiménez-Contreras
- EC3 Research Group, Department of Information and Communication Sciences, University of Granada, Granada, Spain
| | - Carlos Ruiz-Fresneda
- EC3 Research Group, Department of Information and Communication Sciences, University of Granada, Granada, Spain
- EC3metrics Spin-Off, University of Granada, Granada, Spain
| | - Rafael Ruiz-Pérez
- EC3 Research Group, Department of Information and Communication Sciences, University of Granada, Granada, Spain
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82
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Jha P, Singh P, Arora S, Sultan A, Nayek A, Ponnusamy K, Syed MA, Dohare R, Chopra M. Integrative multiomics and in silico analysis revealed the role of ARHGEF1 and its screened antagonist in mild and severe COVID-19 patients. J Cell Biochem 2022; 123:673-690. [PMID: 35037717 PMCID: PMC9015317 DOI: 10.1002/jcb.30213] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/21/2021] [Accepted: 12/30/2021] [Indexed: 12/22/2022]
Abstract
COVID‐19 is a sneaking deadly disease caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). The rapid increase in the number of infected patients worldwide enhances the exigency for medicines. However, precise therapeutic drugs are not available for COVID‐19; thus, exhaustive research is critically required to unscramble the pathogenic tools and probable therapeutic targets for the development of effective therapy. This study utilizes a chemogenomics strategy, including computational tools for the identification of viral‐associated differentially expressed genes (DEGs), and molecular docking of potential chemical compounds available in antiviral, anticancer, and natural product‐based libraries against these DEGs. We scrutinized the messenger RNA expression profile of SARS‐CoV‐2 patients, publicly available on the National Center for Biotechnology Information–Gene Expression Omnibus database, stratified them into different groups based on the severity of infection, superseded by identification of overlapping mild and severe infectious (MSI)‐DEGs. The profoundly expressed MSI‐DEGs were then subjected to trait‐linked weighted co‐expression network construction and hub module detection. The hub module MSI‐DEGs were then exposed to enrichment (gene ontology + pathway) and protein–protein interaction network analyses where Rho guanine nucleotide exchange factor 1 (ARHGEF1) gene conjectured in all groups and could be a probable target of therapy. Finally, we used the molecular docking and molecular dynamics method to identify inherent hits against the ARHGEF1 gene from antiviral, anticancer, and natural product‐based libraries. Although the study has an identified significant association of the ARHGEF1 gene in COVID19; and probable compounds targeting it, using in silico methods, these targets need to be validated by both in vitro and in vivo methods to effectively determine their therapeutic efficacy against the devastating virus.
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Affiliation(s)
- Prakash Jha
- Laboratory of Molecular Modeling and Anticancer Drug Development, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, New Delhi, India
| | - Prithvi Singh
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Shweta Arora
- Department of Biotechnology, Translational Research Lab, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India
| | - Armiya Sultan
- Department of Biosciences, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India
| | - Arnab Nayek
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Kalaiarasan Ponnusamy
- Synthetic Biology Lab, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Mansoor Ali Syed
- Department of Biotechnology, Translational Research Lab, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India
| | - Ravins Dohare
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Madhu Chopra
- Laboratory of Molecular Modeling and Anticancer Drug Development, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, New Delhi, India
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83
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Asadirad A, Nashibi R, Khodadadi A, Ghadiri AA, Sadeghi M, Aminian A, Dehnavi S. Antiinflammatory potential of nano-curcumin as an alternative therapeutic agent for the treatment of mild-to-moderate hospitalized COVID-19 patients in a placebo-controlled clinical trial. Phytother Res 2022; 36:1023-1031. [PMID: 35040210 DOI: 10.1002/ptr.7375] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 12/11/2021] [Accepted: 12/22/2021] [Indexed: 12/18/2022]
Abstract
The present study conducted a placebo-controlled clinical trial to evaluate the impact of nano-curcumin on the inflammatory cytokines in mild-to-moderate hospitalized COVID-19 patients. A total of 60 COVID-19 patients were randomly divided into nano-curcumin and control groups, and then they received 240 mg/day nano-curcumin for 7 days. The clinical manifestation and laboratory parameters in patients were recorded on days 0 and seven. Also, SYBR Green real-time PCR and ELISA techniques were implicated in assessing the mRNA expression of IFN-γ, IL-1β, IL-6, MCP-1, and TNF-α and the serum levels of IL-1β, IL-6, and TNF-α inflammatory mediators, respectively. Although the clinical manifestations and laboratory parameters improved via the nano-curcumin treatment, the mRNA expression of IFN-γ (p = 0.006) and TNF-α (p = 0.04) were significantly reduced. Besides, a considerable difference was observed between the nano-curcumin and control groups in the expression of IFN-γ (p = 0.001), IL-1β (p = 0.0002), and IL-6 (p = 0.008). In addition, there was a significant difference between the nano-curcumin and control groups in the serum levels of IL-1β (p = 0.042). The evidence demonstrated that nano-curcumin could be implicated as a complementary medication to act as an antiinflammatory agent and inhibit inflammatory complications.
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Affiliation(s)
- Ali Asadirad
- Department of Immunology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Cancer, Petroleum and Environmental Pollutants Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Roohangiz Nashibi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ali Khodadadi
- Department of Immunology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Cancer, Petroleum and Environmental Pollutants Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ata A Ghadiri
- Department of Immunology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mahvash Sadeghi
- Department of Immunology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Student Research Committee, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Azam Aminian
- Cancer, Petroleum and Environmental Pollutants Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Nursing, School of Nursing and Midwifery, Ilam University of Medical Sciences, Ilam, Iran
| | - Sajad Dehnavi
- Department of Immunology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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84
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Ahmad W, Shabbiri K. Two years of SARS-CoV-2 infection (2019-2021): structural biology, vaccination, and current global situation. THE EGYPTIAN JOURNAL OF INTERNAL MEDICINE 2022; 34:5. [PMID: 35043040 PMCID: PMC8759062 DOI: 10.1186/s43162-021-00092-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 12/03/2021] [Indexed: 11/10/2022] Open
Abstract
The deadly SARS-CoV-2 virus has infected more than 259,502,031 confirmed cases with 5,183,003 deaths in 223 countries during the last 22 months (Dec 2019-Nov 2021), whereas approximately 7,702,859,718, vaccine doses have been administered (WHO: https://covid19.who.int/) as of the 24th of Nov 2021. Recent announcements of test trial completion of several new vaccines resulted in the launching of immunization for the common person around the globe highlighting a ray of hope to cope with this infection. Meanwhile, genetic variations in SARS-CoV-2 and third layer of infection spread in numerous countries emerged as a stronger prototype than the parental. New and parental SARS-CoV-2 strains appeared as a risk factor for other pre-existing diseases like cancer, diabetes, neurological disorders, kidney, liver, heart, and eye injury. This situation requires more attention and re-structuring of the currently developed vaccines and/or drugs against SARS-CoV-2 infection. Although a decline in COVID-19 infection has been reported globally, an increase in COVID-19 cases in the subcontinent and east Mediterranean area could be alarming. In this review, we have summarized the current information about the SARS-CoV-2 biology, its interaction and possible infection pathways within the host, epidemiology, risk factors, economic collapse, and possible vaccine and drug development.
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Affiliation(s)
- Waqar Ahmad
- Department of Biochemistry, College of Medicine and Health Sciences, UAE University, Al Ain, United Arab Emirates
- The University of Queensland, Brisbane, Australia
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85
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Hornick MG, Olson ME, Jadhav AL. SARS-CoV-2 Psychiatric Sequelae: A Review of Neuroendocrine Mechanisms and Therapeutic Strategies. Int J Neuropsychopharmacol 2022; 25:1-12. [PMID: 34648616 PMCID: PMC8524640 DOI: 10.1093/ijnp/pyab069] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/07/2021] [Accepted: 10/12/2021] [Indexed: 12/15/2022] Open
Abstract
From the earliest days of the coronavirus disease 2019 (COVID-19) pandemic, there have been reports of significant neurological and psychological symptoms following Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection. This narrative review is designed to examine the potential psychoneuroendocrine pathogenic mechanisms by which SARS-CoV-2 elicits psychiatric sequelae as well as to posit potential pharmacologic strategies to address and reverse these pathologies. Following a brief overview of neurological and psychological sequelae from previous viral pandemics, we address mechanisms by which SARS-CoV-2 could enter or otherwise elicit changes in the CNS. We then examine the hypothesis that COVID-19-induced psychiatric disorders result from challenges to the neuroendocrine system, in particular the hypothalamic-pituitary-adrenal stress axis and monoamine synthesis, physiological mechanisms that are only further enhanced by the pandemic-induced social environment of fear, isolation, and socioeconomic pressure. Finally, we evaluate several FDA-approved therapeutics in the context of COVID-19-induced psychoneuroendocrine disorders.
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Affiliation(s)
- Mary G Hornick
- Roosevelt University, College of Science, Health and Pharmacy, Schaumburg, Illinois, USA
| | - Margaret E Olson
- Roosevelt University, College of Science, Health and Pharmacy, Schaumburg, Illinois, USA
| | - Arun L Jadhav
- Roosevelt University, College of Science, Health and Pharmacy, Schaumburg, Illinois, USA
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86
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Yao Y, Ma D, Xu Y, Yuan XL, Liang JJ, Chen SL, Jhanji V, Ng TK. Hydroxychloroquine treatment on SARS-CoV-2 receptor ACE2, TMPRSS2 and NRP1 expression in human primary pterygium and conjunctival cells. Exp Eye Res 2022; 214:108864. [PMID: 34826419 PMCID: PMC8610570 DOI: 10.1016/j.exer.2021.108864] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/17/2021] [Accepted: 11/22/2021] [Indexed: 02/05/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the pathogen for coronavirus disease 2019 (COVID-19) pandemic. Its infection depends on the binding of spike protein to the host cell receptor angiotensin-converting enzyme 2 (ACE2), type II transmembrane serine protease (TMPRSS2) and neuropilin-1 (NRP1). Hydroxychloroquine has been applied as one of the COVID-19 treatment strategies. Here we aimed to evaluate hydroxychloroquine treatment on SARS-CoV-2 receptor expression in human primary pterygium and conjunctival cells and its potential influences. Expression of ACE2, TMPRSS2 and NRP1 proteins were found in the epithelial layer of both primary pterygium and conjunctiva tissues as well as in their isolated fibroblasts. High concentration of hydroxychloroquine treatment significantly reduced the viability of both primary pterygium and conjunctival cells. ACE2 protein expression was significantly decreased in both pterygium and conjunctival cells after hydroxychloroquine treatment. Hydroxychloroquine also reduced NRP1 protein expression in conjunctival cells. In contrast, TMPRSS2 protein expression showed slightly increased in conjunctival cells. Notably, ROS production and SOD2 expression was significantly elevated in both pterygium and conjunctival cells after hydroxychloroquine treatment. In summary, this study revealed the reduction of ACE2 and NRP1 expression by hydroxychloroquine in human primary pterygium and conjunctival fibroblasts; yet with the increase in TMPRSS2 expression and oxidative stress and decrease in cell viability. Implementation of hydroxychloroquine for COVID-19 treatment should be carefully considered with its potential side effects and in combination with TMPRSS2 inhibitor.
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Affiliation(s)
- Yao Yao
- Joint Shantou International Eye Center of Shantou University and the Chinese University of Hong Kong, Shantou, Guangdong, China
- Shantou University Medical College, Shantou, Guangdong, China
| | - Di Ma
- Joint Shantou International Eye Center of Shantou University and the Chinese University of Hong Kong, Shantou, Guangdong, China
| | - Yanxuan Xu
- Joint Shantou International Eye Center of Shantou University and the Chinese University of Hong Kong, Shantou, Guangdong, China
| | - Xiang-Ling Yuan
- Joint Shantou International Eye Center of Shantou University and the Chinese University of Hong Kong, Shantou, Guangdong, China
- Shantou University Medical College, Shantou, Guangdong, China
| | - Jia-Jian Liang
- Joint Shantou International Eye Center of Shantou University and the Chinese University of Hong Kong, Shantou, Guangdong, China
| | - Shao-Lang Chen
- Joint Shantou International Eye Center of Shantou University and the Chinese University of Hong Kong, Shantou, Guangdong, China
| | - Vishal Jhanji
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong
- Department of Ophthalmology, UPMC Eye Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Tsz Kin Ng
- Joint Shantou International Eye Center of Shantou University and the Chinese University of Hong Kong, Shantou, Guangdong, China
Shantou University Medical College, Shantou, Guangdong, China
Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong
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87
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Jeffreys LN, Pennington SH, Duggan J, Caygill CH, Lopeman RC, Breen AF, Jinks JB, Ardrey A, Donnellan S, Patterson EI, Hughes GL, Hong DW, O'Neill PM, Aljayyoussi G, Owen A, Ward SA, Biagini GA. Remdesivir-ivermectin combination displays synergistic interaction with improved in vitro activity against SARS-CoV-2. Int J Antimicrob Agents 2022; 59:106542. [PMID: 35093538 PMCID: PMC8801767 DOI: 10.1016/j.ijantimicag.2022.106542] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 11/05/2022]
Abstract
A key element for the prevention and management of coronavirus disease 2019 is the development of effective therapeutics. Drug combination strategies offer several advantages over monotherapies. They have the potential to achieve greater efficacy, to increase the therapeutic index of drugs and to reduce the emergence of drug resistance. We assessed the in vitro synergistic interaction between remdesivir and ivermectin, both approved by the US Food and Drug Administration, and demonstrated enhanced antiviral activity against severe acute respiratory syndrome coronavirus-2. Whilst the in vitro synergistic activity reported here does not support the clinical application of this combination treatment strategy due to insufficient exposure of ivermectin in vivo, the data do warrant further investigation. Efforts to define the mechanisms underpinning the observed synergistic action could lead to the development of novel treatment strategies.
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88
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Ergül E, Yılmaz AS, Öğütveren MM, Emlek N, Kostakoğlu U, Çetin M. COVID 19 disease independently predicted endothelial dysfunction measured by flow-mediated dilatation. Int J Cardiovasc Imaging 2022; 38:25-32. [PMID: 34286447 PMCID: PMC8294249 DOI: 10.1007/s10554-021-02356-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 07/16/2021] [Indexed: 11/28/2022]
Abstract
The systemic effects of COVID-19 disease are still largely uncertain and needs to be scrutinized with further trials. Endothelial dysfunction (ED) is responsible for the majority of adverse cardiovascular events. Flow-mediated dilation (FMD) is easily obtainable method to assess ED accurately. It is aimed to evaluate ED by measuring FMD following COVID-19 disease. Patients diagnosed with COVID-19 disease were recruited to the hospital two month after the discharge. Sex and age-matched healthy subjects were determined as the control group. Blood samples and FMD measurements were obtained from each participant. All subjects were divided into two groups according to the presence of ED determined by FMD measurements. These two groups were compared in terms of demographic features and the presence of recovered COVID-19 disease. A total of 92 subjects consisting of 59 without ED and 33 with ED were included in the study. ED (+) group was older (p = 0.015) and more likely to have hypertension (p = 0.044) and COVID-19 rate was higher in ED (+) group (p = 0.009). While neutrophil count (p = 0.047) and CRP (p = 0.036) were higher, eGFR (p = 0.044) was lower in ED (+) group. In the backward multivariable regression analysis, COVID-19 disease [OR = 3.611, 95% CI 1.069-12.198, p = 0.039] and BMI [OR = 1.122, 95% CI 1.023-1.231, p = 0.015] were independent predictors of ED. COVID-19 disease may cause ED which is the major underlying factor of cardiovascular diseases. Furthermore, COVID-19 disease may deteriorate the existing cardiovascular disease course. Detecting ED in the early phase or preventing by new treatment modalities may improve short and long-term outcome.
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Affiliation(s)
- Elif Ergül
- Department of Cardiology, Faculty of Medicine, Recep Tayyip Erdogan University, 53020, Rize, Turkey
| | - Ahmet Seyda Yılmaz
- Department of Cardiology, Faculty of Medicine, Recep Tayyip Erdogan University, 53020, Rize, Turkey.
| | | | - Nadir Emlek
- Department of Cardiology, Faculty of Medicine, Recep Tayyip Erdogan University, 53020, Rize, Turkey
| | - Uğur Kostakoğlu
- Department of Infectious Disease, Faculty of Medicine, Recep Tayyip Erdogan University, Rize, Turkey
| | - Mustafa Çetin
- Department of Cardiology, Faculty of Medicine, Recep Tayyip Erdogan University, 53020, Rize, Turkey
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89
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Gwenzi W, Selvasembian R, Offiong NAO, Mahmoud AED, Sanganyado E, Mal J. COVID-19 drugs in aquatic systems: a review. ENVIRONMENTAL CHEMISTRY LETTERS 2022; 20:1275-1294. [PMID: 35069060 PMCID: PMC8760103 DOI: 10.1007/s10311-021-01356-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 11/02/2021] [Indexed: 05/14/2023]
Abstract
The outbreak of the human coronavirus disease 2019 (COVID-19) has induced an unprecedented increase in the use of several old and repurposed therapeutic drugs such as veterinary medicines, e.g. ivermectin, nonsteroidal anti-inflammatory drugs, protein and peptide therapeutics, disease-modifying anti-rheumatic drugs and antimalarial drugs, antiretrovirals, analgesics, and supporting agents, e.g. azithromycin and corticosteroids. Excretion of drugs and their metabolites in stools and urine release these drugs into wastewater, and ultimately into surface waters and groundwater systems. Here, we review the sources, behaviour, environmental fate, risks, and remediation of those drugs. We discuss drug transformation in aquatic environments and in wastewater treatment systems. Degradation mechanisms and metabolite toxicity are poorly known. Potential risks include endocrine disruption, acute and chronic toxicity, disruption of ecosystem functions and trophic interactions in aquatic organisms, and the emergence of antimicrobial resistance.
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Affiliation(s)
- Willis Gwenzi
- Biosystems and Environmental Engineering Research Group, Department of Agricultural and Biosystems Engineering, Faculty of Agriculture, Environment and Food Systems, University of Zimbabwe, P.O. Box MP 167, Mount Pleasant, Harare, Zimbabwe
| | - Rangabhashiyam Selvasembian
- Department of Biotechnology, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamilnadu 613401 India
| | - Nnanake-Abasi O. Offiong
- International Centre for Energy and Environmental Sustainability Research (ICEESR), University of Uyo, Uyo, Nigeria
- Department of Chemical Sciences, Faculty of Computing and Applied Sciences, Topfaith University, Mkpatak, Nigeria
| | - Alaa El Din Mahmoud
- Environmental Sciences Department, Faculty of Science, Alexandria University, Alexandria, 21511 Egypt
- Green Technology Group, Faculty of Science, Alexandria University, Alexandria, 21511 Egypt
| | - Edmond Sanganyado
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou, 515063 China
| | - Joyabrata Mal
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj, Uttar Pradesh India
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90
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Docking study of transmembrane serine protease type 2 inhibitors for the treatment of COVID-19. DATA SCIENCE FOR COVID-19 2022. [PMCID: PMC8988994 DOI: 10.1016/b978-0-323-90769-9.00029-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The recent pandemic development of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its quick national and international spread present a global health emergency. Entry of coronaviruses into the cell depends on binding of the viral spike (S) proteins to host cells receptors, which rely on cell proteases for activation. One of the proteases, transmembrane serine protease type 2 (TMPRSS2) was proven to be crucial for S protein priming. Our research emphasizes on identifying presupposing drug candidates for the TMPRSS2 inhibitors to combat coronavirus disease 2019 (COVID-19). TMPRSS2 homology model is generated by utilizing Modeller9.22, whereas we perform molecular docking with AutoDock Vina. Docking of peptidomimetic inhibitors (inhibitor “92” and inhibitor “50”) and allosteric inhibitors (nafamostat and camostat mesilate) in this study is carried out at the active site of the TMPRSS2 homology model. Known active ligands have low docking score energies varying from −7.6 to −8.7 kcal/mol. The docking study has confirmed peptidomimetic inhibitors bind with the catalytic triad HIS 41 and ASP 90 by strong hydrogen bonding. Allosteric inhibitors block access to the catalytic triad (HIS 41, ASP 90, and SER 186) by forming hydrogen bonds with ASP 180, GLN 183, and GLY 209 in the S1 pocket. This investigation gives an insight into the design and identification of drug repurposing candidates for the management of COVID-19.
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91
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Mou Q, Yang YW, Chen L, Fang T, Yao YC, Du ZQ, Yang CX. Melatonin mitigates Chloroquine-induced defects in porcine immature Sertoli cells. Theriogenology 2022; 177:1-10. [PMID: 34653791 DOI: 10.1016/j.theriogenology.2021.10.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/27/2021] [Accepted: 10/07/2021] [Indexed: 12/13/2022]
Abstract
Chloroquine (CQ) could function as a lysosomotropic agent to inhibit the endolysosomal trafficking in the autophagy pathway, and is widely used on malarial, tumor and recently COVID-19. However, the effect of CQ treatment on porcine immature Sertoli cells (iSCs) remains unclear. Here we showed that CQ could reduce iSC viability in a dose-dependent manner. CQ treatment (20 μM) on iSCs for 36h could elevate oxidative stress, damage mitochondrial function and promote apoptosis, which could be partially rescued by melatonin (MT) (10 nM). Transcriptome profiling identified 1611 differentially expressed genes (DEGs) (776 up- and 835 down-regulated) (20 μM CQ vs. DMSO), mainly involved in MAPK cascade, cell proliferation/apoptosis, HIF-1, PI3K-Akt and lysosome signaling pathways. In contrast, only 467 (224 up- and 243 down-regulated) DEGs (CQ + MT vs. DMSO) could be found after MT (10 nM) addition, enriched in cell cycle, regulation of apoptotic process, lysosome and reproduction pathways. Therefore, the partial rescue effects of MT on CQ treatment were confirmed by multiple assays (cell viability, ROS level, mitochondrial function, apoptosis, and mRNA levels of selected genes). Collectively, CQ treatment could impair porcine iSC viability by deranging the signaling pathways related to apoptosis and autophagy, which could be partially rescued by MT supplementation.
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Affiliation(s)
- Qiao Mou
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China
| | - Yu-Wei Yang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China
| | - Lu Chen
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China
| | - Ting Fang
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Yu-Chang Yao
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China
| | - Zhi-Qiang Du
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China.
| | - Cai-Xia Yang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China; College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China.
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92
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COVID-19: Origin, epidemiology, virology, pathogenesis, and treatment. LESSONS FROM COVID-19 2022. [PMCID: PMC9347366 DOI: 10.1016/b978-0-323-99878-9.00012-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
COVID-19 (or Coronavirus Disease) originated in China (Hubei provenance, Wuhan city). The first recorded illness occurred in December 2019. It has affected all parts of the world, and the WHO designated the COVID-19 disease, caused by the new Coronavirus SARS-CoV-2, a pandemic on March 11, 2020. Some debatable speculations indicate that it is a man-made virus, intentionally synthesized in the laboratory but was unintentionally emancipated from a laboratory of Wuhan, China. The primitive theory suggested the spread from the Hunan seafood market of China probably from an animal source. However, this theory is not fully supported. COVID-19 infection has a varying range of signs and symptoms from low fever, dry cough to lower respiratory tract infection, breathing difficulties, pulmonary edema, acute respiratory distress syndrome (ARDS), metabolic acidosis, sepsis, coagulation, lymphopenia, hypoxemia, multiorgan failure, and eventually, mortality. In patients with comorbidity such as diabetes, cardiovascular disease, high blood pressure, stroke, and kidney disease, fatality rate is higher. Young and elderly people are more likely to experience unfavorable outcomes due to poor immunity. There have been several treatment methods explored to tackle the COVID-19 pandemic, including medications, interferon, vaccines, oligonucleotides, peptides, and monoclonal and immunomodulatory antibodies, among other things. The World Health Organization has recommended preventive measures like washing hands, using face masks, sanitizers, and maintaining a safe distance to prevent the spread of the pandemic. One of the promising alternatives is the vaccine. One must take all preventive measures in the pandemic until it becomes feeble.
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93
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KÜÇÜK BEYZANUR, ŞİMŞEK RAHİME, ERDEMLİ KÖSE SELİNAYBAŞAK, YİRÜN ANIL, Erkekoglu P. Adverse Effects of COVID-19 Treatments: A Special Focus on Susceptible Populations. J Environ Pathol Toxicol Oncol 2022; 41:45-64. [DOI: 10.1615/jenvironpatholtoxicoloncol.2022039271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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94
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Therapeutic options in coronavirus treatment. CORONAVIRUS DRUG DISCOVERY 2022. [PMCID: PMC9217689 DOI: 10.1016/b978-0-323-85156-5.00021-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This chapter details the various therapeutic options available for the treatment of the novel coronavirus, SARS-CoV-2, that has brought the world to a standstill. As at 3.53 CEST, June 28, 2020, WHO reported 9,843,073 confirmed cases of COVID-19, with a death toll of 495,760. The rate of the spread of this disease is alarming posing serious threat to the world healthcare system. Clinical investigations and research are on the way for the development of vaccines or antiviral drugs. Despite this effort, no medication has been found to be very effective for its treatment. In this chapter, emphasis was laid on the need for repurposing of antiviral drugs to combat COVID-19 along with other alternatives such as convalescent plasma therapy and exploitation of drugs from medicinal plants and other natural resources.
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95
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Liu L, Qin JF, Zuo MZ, Zhou Q. Multi-omics of the expression and clinical outcomes of TMPRSS2 in human various cancers: A potential therapeutic target for COVID-19. J Cell Mol Med 2021; 26:709-724. [PMID: 34951103 PMCID: PMC8817140 DOI: 10.1111/jcmm.17090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 11/07/2021] [Accepted: 11/18/2021] [Indexed: 12/12/2022] Open
Abstract
Growing evidence has shown that Transmembrane Serine Protease 2 (TMPRSS2) not only contributes to the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection, but is also closely associated with the incidence and progression of tumours. However, the correlation of coronavirus disease (COVID‐19) and cancers, and the prognostic value and molecular function of TMPRSS2 in various cancers have not been fully understood. In this study, the expression, genetic variations, correlated genes, immune infiltration and prognostic value of TMPRSS2 were analysed in many cancers using different bioinformatics platforms. The observed findings revealed that the expression of TMPRSS2 was considerably decreased in many tumour tissues. In the prognostic analysis, the expression of TMPRSS2 was considerably linked with the clinical consequences of the brain, blood, colorectal, breast, ovarian, lung and soft tissue cancer. In protein network analysis, we determined 27 proteins as protein partners of TMPRSS2, which can regulate the progression and prognosis of cancer mediated by TMPRSS2. Besides, a high level of TMPRSS2 was linked with immune cell infiltration in various cancers. Furthermore, according to the pathway analysis of differently expressed genes (DEGs) with TMPRSS2 in lung, breast, ovarian and colorectal cancer, 160 DEGs genes were found and were significantly enriched in respiratory system infection and tumour progression pathways. In conclusion, the findings of this study demonstrate that TMPRSS2 may be an effective biomarker and therapeutic target in various cancers in humans, and may also provide new directions for specific tumour patients to prevent SARS‐CoV‐2 infection during the COVID‐19 outbreak.
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Affiliation(s)
- Li Liu
- Department of Pediatrics, The First College of Clinical Medical Science, China Three Gorges University and Yichang Central People's Hospital, Yichang, China
| | - Ju-Fang Qin
- Department of Gynecology and Obstetrics, The People's Hospital, China Three Gorges University/the First People's Hospital of Yichang, Yichang, China
| | - Man-Zhen Zuo
- Department of Gynecology and Obstetrics, The People's Hospital, China Three Gorges University/the First People's Hospital of Yichang, Yichang, China
| | - Quan Zhou
- Department of Gynecology and Obstetrics, The People's Hospital, China Three Gorges University/the First People's Hospital of Yichang, Yichang, China
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96
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Al-Shuhaib MBS, Hashim HO, Al-Shuhaib JMB. Epicatechin is a promising novel inhibitor of SARS-CoV-2 entry by disrupting interactions between angiotensin-converting enzyme type 2 and the viral receptor binding domain: A computational/simulation study. Comput Biol Med 2021; 141:105155. [PMID: 34942397 PMCID: PMC8679518 DOI: 10.1016/j.compbiomed.2021.105155] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/15/2021] [Accepted: 12/15/2021] [Indexed: 01/02/2023]
Abstract
Angiotensin-converting enzyme 2 (ACE2) is the first target of SARS-CoV-2 and a key functional host receptor through which this virus hooks into and infects human cells. The necessity to block this receptor is one of the essential means to prevent the outbreak of COVID-19. This study was conducted to determine the most eligible natural compound to suppress ACE2 to counterfeit its interaction with the viral infection. To do this, the most known compounds of sixty-six Iraqi medicinal plants were generated and retrieved from PubChem database. After preparing a library for Iraqi medicinal plants, 3663 unique ligands’ conformers were docked to ACE2 using the GLIDE tool. Results found that twenty-three compounds exhibited the highest binding affinity with ACE2. The druglikeness and toxicity potentials of these compounds were evaluated using SwissADME and Protox servers respectively. Out of these virtually screened twenty-three compounds, epicatechin and kempferol were predicted to exert the highest druglikeness and lowest toxicity potentials. Extended Molecular dynamics (MD) simulations showed that ACE2-epicatechin complex exhibited a slightly higher binding stability than ACE2-kempferol complex. In addition to the well-known ACE2 inhibitors that were identified in previous studies, this study revealed for the first time that epicatechin from Hypericum perforatum provided a better static and dynamic inhibition for ACE2 with highly favourable pharmacokinetic properties than the other known ACE2 inhibiting compounds. This study entailed the ability of epicatechin to be used as a potent natural inhibitor that can be used to block or at least weaken the SARS-CoV-2 entry and its subsequent invasion. In vitro experiments are required to validate epicatechin effectiveness against the activity of the human ACE2 receptor.
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Affiliation(s)
- Mohammed Baqur S Al-Shuhaib
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, 51013, Babil, Iraq.
| | - Hayder O Hashim
- Department of Clinical Laboratory Sciences, College of Pharmacy, University of Babylon, Babil, 51001, Iraq.
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97
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Lu C, Zheng J, Ding Y, Meng Y, Tan F, Gong W, Chu X, Kong X, Gao C. Cepharanthine loaded nanoparticles coated with macrophage membranes for lung inflammation therapy. Drug Deliv 2021; 28:2582-2593. [PMID: 34866533 PMCID: PMC8654408 DOI: 10.1080/10717544.2021.2009936] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Acute lung injury (ALI) is a disease associated with suffering and high lethality, but to date without any effective pharmacological management in the clinic. In the pathological mechanisms of ALI, a strong inflammatory response plays an important role. Herein, based on macrophage 'homing' into inflammation sites and cell membrane coating nanotechnology, we developed a biomimetic anti-inflammation nanosystem (MM-CEP/NLCs) for the treatment of ALI. MM-CEP/NLCs were made with nanostructured lipid carriers (NLCs) coated with natural macrophage membranes (MMs) to achieve effective accumulation of cepharanthine (CEP) in lung inflammation to achieve the effect of treating ALI. With the advantage of suitable physicochemical properties of NLCs and unique biological functions of the macrophage membrane, MM-CEP/NLCs were stabilized and enabled sustained drug release, providing improved biocompatibility and long-term circulation. In vivo, the macrophage membranes enabled NLCs to be targeted and accumulated in the inflammation sites. Further, MM-CEP/NLCs significantly attenuated the severity of ALI, including lung water content, histopathology, bronchioalveolar lavage cellularity, protein concentration, and inflammation cytokines. Our results provide a bionic strategy via the biological properties of macrophages, which may have greater value and application prospects in the treatment of inflammation.
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Affiliation(s)
- Caihong Lu
- School of Pharmacy, Guangxi Medical University, Nanning, P. R. China.,State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, P. R. China
| | - Jinpeng Zheng
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, P. R. China
| | - Yaning Ding
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, P. R. China
| | - Yuanyuan Meng
- School of Pharmacy, Guangxi Medical University, Nanning, P. R. China
| | - Fangyun Tan
- School of Pharmacy, Guangxi Medical University, Nanning, P. R. China
| | - Wei Gong
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, P. R. China
| | - Xiaoyang Chu
- Department of Stomatology, The Fifth Medical Center of PLA General Hospital, Beijing, P. R. China
| | - Xiaolong Kong
- School of Pharmacy, Guangxi Medical University, Nanning, P. R. China
| | - Chunsheng Gao
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, P. R. China
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98
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Verma D, Mitra D, Paul M, Chaudhary P, Kamboj A, Thatoi H, Janmeda P, Jain D, Panneerselvam P, Shrivastav R, Pant K, Das Mohapatra PK. Potential inhibitors of SARS-CoV-2 (COVID 19) proteases PL pro and M pro/ 3CL pro: molecular docking and simulation studies of three pertinent medicinal plant natural components. CURRENT RESEARCH IN PHARMACOLOGY AND DRUG DISCOVERY 2021; 2:100038. [PMID: 34870149 PMCID: PMC8178537 DOI: 10.1016/j.crphar.2021.100038] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 12/23/2022] Open
Abstract
The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) - coronavirus disease 2019 (COVID-19) has raised a severe global public health issue and creates a pandemic situation. The present work aims to study the molecular -docking and dynamic of three pertinent medicinal plants i.e. Eurycoma harmandiana, Sophora flavescens and Andrographis paniculata phyto-compounds against SARS-COV-2 papain-like protease (PLpro) and main protease (Mpro)/3-chymotrypsin-like protease (3CLpro). The interaction of protein targets and ligands was performed through AutoDock-Vina visualized using PyMOL and BIOVIA-Discovery Studio 2020. Molecular docking with canthin-6-one 9-O-beta-glucopyranoside showed highest binding affinity and less binding energy with both PLpro and Mpro/3CLpro proteases and was subjected to molecular dynamic (MD) simulations for a period of 100ns. Stability of the protein-ligand complexes was evaluated by different analyses. The binding free energy calculated using MM-PBSA and the results showed that the molecule must have stable interactions with the protein binding site. ADMET analysis of the compounds suggested that it is having drug-like properties like high gastrointestinal (GI) absorption, no blood-brain barrier permeability and high lipophilicity. The outcome revealed that canthin-6-one 9-O-beta-glucopyranoside can be used as a potential natural drug against COVID-19 protease.
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Affiliation(s)
- Devvret Verma
- Department of Biotechnology, Graphic Era (Deemed to be University), Dehradun, 248 002, Uttarakhand, India
| | - Debasis Mitra
- Department of Microbiology, Raiganj University, Raiganj, 733 134, Uttar Dinajpur, West Bengal, India
| | - Manish Paul
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Baripada, 757003, Odisha, India
| | - Priya Chaudhary
- Department of Bioscience and Biotechnology, Banasthali University, Vanasthali, 304022, Rajasthan, India
| | - Anshul Kamboj
- Department of Biotechnology, Graphic Era (Deemed to be University), Dehradun, 248 002, Uttarakhand, India
| | - Hrudayanath Thatoi
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Baripada, 757003, Odisha, India
| | - Pracheta Janmeda
- Department of Bioscience and Biotechnology, Banasthali University, Vanasthali, 304022, Rajasthan, India
| | - Divya Jain
- Department of Bioscience and Biotechnology, Banasthali University, Vanasthali, 304022, Rajasthan, India
| | - Periyasamy Panneerselvam
- Microbiology, Crop Production Division, ICAR- National Rice Research Institute, Cuttack, 753 006, Odisha, India
| | - Rakesh Shrivastav
- Department of Applied Sciences, NGF College of Engineering and Technology, Palwal, Haryana, India
| | - Kumud Pant
- Department of Biotechnology, Graphic Era (Deemed to be University), Dehradun, 248 002, Uttarakhand, India
| | - Pradeep K Das Mohapatra
- Department of Microbiology, Raiganj University, Raiganj, 733 134, Uttar Dinajpur, West Bengal, India.,PAKB Environment Conservation Centre, Raiganj University, Raiganj, 733 134, Uttar Dinajpur, West Bengal, India
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99
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Hebbani AV, Pulakuntla S, Pannuru P, Aramgam S, Badri KR, Reddy VD. COVID-19: comprehensive review on mutations and current vaccines. Arch Microbiol 2021; 204:8. [PMID: 34873656 PMCID: PMC8647783 DOI: 10.1007/s00203-021-02606-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/09/2021] [Accepted: 11/22/2021] [Indexed: 12/15/2022]
Abstract
Viral outbreaks had been a threat for the human race for a long time. Several epidemics and pandemics have been reported in the past with serious consequences on human health and subsequent social and economic aspects. According to WHO, viral infections continue to be a major health concern globally. Novel coronavirus, SARS-CoV-2 (Severe acute respiratory syndrome coronavirus-2) causes the most recent infectious pandemic disease, COVID-19 (Coronavirus disease-19). As of now, there were 249 million infections of COVID-19 worldwide with a high mortality of more than 5 million deaths reported; and the number of new additional cases is drastically increasing. Development of therapies to treat the infected cases and prophylactic agents including vaccines that are effective towards different variants are crucial to curtail the COVID-19 pandemic. Owing to the fact that there is a high mortality and morbidity rate along with the risk of virus causing further epidemic outbursts, development of additional effective therapeutic and preventive strategies are highly warranted. Prevention, early detection and treatment will reduce the spread of COVID-19 pandemic. The present review highlights the novel mutations and therapeutic updates associated with coronaviruses along with the clinical manifestations-diagnosis, clinical management and, prophylactic and therapeutic strategies of COVID-19 infection.
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Affiliation(s)
| | - Swetha Pulakuntla
- Department of Biochemistry, REVA University, Bengaluru, 560064, India
| | - Padmavathi Pannuru
- DR Biosciences, Research and Development Institute, Bettahalasur, Bengaluru, 562157, India
| | - Sreelatha Aramgam
- Department of Biochemistry, REVA University, Bengaluru, 560064, India
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Kameswara Rao Badri
- Department of Pharmacology and Toxicology, Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, GA, 30310, USA.
- Clinical Analytical Chemistry Laboratory, Clinical Research Center, Morehouse School of Medicine, Atlanta, GA, 30310, USA.
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100
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Siminea N, Popescu V, Sanchez Martin JA, Florea D, Gavril G, Gheorghe AM, Iţcuş C, Kanhaiya K, Pacioglu O, Popa IL, Trandafir R, Tusa MI, Sidoroff M, Păun M, Czeizler E, Păun A, Petre I. Network analytics for drug repurposing in COVID-19. Brief Bioinform 2021; 23:6447433. [PMID: 34864885 PMCID: PMC8690228 DOI: 10.1093/bib/bbab490] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 10/06/2021] [Accepted: 10/25/2021] [Indexed: 01/08/2023] Open
Abstract
To better understand the potential of drug repurposing in COVID-19, we analyzed control strategies over essential host factors for SARS-CoV-2 infection. We constructed comprehensive directed protein–protein interaction (PPI) networks integrating the top-ranked host factors, the drug target proteins and directed PPI data. We analyzed the networks to identify drug targets and combinations thereof that offer efficient control over the host factors. We validated our findings against clinical studies data and bioinformatics studies. Our method offers a new insight into the molecular details of the disease and into potentially new therapy targets for it. Our approach for drug repurposing is significant beyond COVID-19 and may be applied also to other diseases.
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Affiliation(s)
- Nicoleta Siminea
- Bioinformatics, National Institute of Research and Development for Biological Sciences, 296 Splaiul Independenţei, 060031, Romania.,Faculty of Mathematics and Computer Science, University of Bucharest, 14 Academiei, 010014, Romania
| | - Victor Popescu
- Department of Information Technologies, Åbo Akademi University, 3 Tuomiokirkontori, 20500, Finland
| | - Jose Angel Sanchez Martin
- Department of Computer Science, Technical University of Madrid, 7 Calle Ramiro de Maeztu, 28040, Spain
| | - Daniela Florea
- Bioinformatics, National Institute of Research and Development for Biological Sciences, 296 Splaiul Independenţei, 060031, Romania
| | - Georgiana Gavril
- Bioinformatics, National Institute of Research and Development for Biological Sciences, 296 Splaiul Independenţei, 060031, Romania
| | - Ana-Maria Gheorghe
- Bioinformatics, National Institute of Research and Development for Biological Sciences, 296 Splaiul Independenţei, 060031, Romania
| | - Corina Iţcuş
- Bioinformatics, National Institute of Research and Development for Biological Sciences, 296 Splaiul Independenţei, 060031, Romania
| | - Krishna Kanhaiya
- Department of Information Technologies, Åbo Akademi University, 3 Tuomiokirkontori, 20500, Finland
| | - Octavian Pacioglu
- Bioinformatics, National Institute of Research and Development for Biological Sciences, 296 Splaiul Independenţei, 060031, Romania
| | - Ioana Laura Popa
- Bioinformatics, National Institute of Research and Development for Biological Sciences, 296 Splaiul Independenţei, 060031, Romania
| | - Romica Trandafir
- Bioinformatics, National Institute of Research and Development for Biological Sciences, 296 Splaiul Independenţei, 060031, Romania
| | - Maria Iris Tusa
- Bioinformatics, National Institute of Research and Development for Biological Sciences, 296 Splaiul Independenţei, 060031, Romania
| | - Manuela Sidoroff
- Bioinformatics, National Institute of Research and Development for Biological Sciences, 296 Splaiul Independenţei, 060031, Romania
| | - Mihaela Păun
- Bioinformatics, National Institute of Research and Development for Biological Sciences, 296 Splaiul Independenţei, 060031, Romania.,Faculty of Administration and Business, University of Bucharest, 4-12 Regina Elisabeta Boulevard, 030018, Romania
| | - Eugen Czeizler
- Department of Information Technologies, Åbo Akademi University, 3 Tuomiokirkontori, 20500, Finland.,Bioinformatics, National Institute of Research and Development for Biological Sciences, 296 Splaiul Independenţei, 060031, Romania
| | - Andrei Păun
- Bioinformatics, National Institute of Research and Development for Biological Sciences, 296 Splaiul Independenţei, 060031, Romania.,Faculty of Mathematics and Computer Science, University of Bucharest, 14 Academiei, 010014, Romania
| | - Ion Petre
- Department of Mathematics and Statistics, University of Turku, 5 Vesilinnantie, 20014, Finland.,Bioinformatics, National Institute of Research and Development for Biological Sciences, 296 Splaiul Independenţei, 060031, Romania
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