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Wang Q, Wang X, Ding J, Huang L, Wang Z. Structural insight of cell surface sugars in viral infection and human milk glycans as natural antiviral substance. Int J Biol Macromol 2024; 277:133867. [PMID: 39009265 DOI: 10.1016/j.ijbiomac.2024.133867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/24/2024] [Accepted: 07/11/2024] [Indexed: 07/17/2024]
Abstract
Viral infections are caused by the adhesion of viruses to host cell receptors, including sialylated glycans, glycosaminoglycans, and human blood group antigens (HBGAs). Atomic-level structural information on the interactions between viral particles or proteins with glycans can be determined to provide precise targets for designing antiviral drugs. Milk glycans, existing as free oligosaccharides or glycoconjugates, have attracted increasing attention; milk glycans protect infants against infectious diseases, particularly poorly manageable viral infections. Furthermore, several glycans containing structurally distinct sialic acid/fucose/sulfate modifications in human milk acting as a "receptor decoy" and serving as the natural antiviral library, could interrupt virus-receptor interaction in the first line of defense for viral infection. This review highlights the basis of virus-glycan interactions, presents specific glycan receptor binding by gastroenterovirus viruses, including norovirus, enteroviruses, and the breakthroughs in the studies on the antiviral properties of human milk glycans, and also elucidates the role of glycans in respiratory viruses infection. In addition, recent advances in methods for performing virus/viral protein-glycan interactions were reported. Finally, we discuss the prospects and challenges of the studies on the clinical application of human milk glycan for viral interventions.
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Affiliation(s)
- Qingling Wang
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, China
| | - Xiaoqin Wang
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, China
| | - Jieqiong Ding
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, China
| | - Linjuan Huang
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, China.
| | - Zhongfu Wang
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, China.
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Garmeh Motlagh F, Azimzadeh Irani M, Masoomi Nomandan SZ, Assadizadeh M. Computational design and investigation of the monomeric spike SARS-CoV-2-ferritin nanocage vaccine stability and interactions. Front Mol Biosci 2024; 11:1403635. [PMID: 38933369 PMCID: PMC11199398 DOI: 10.3389/fmolb.2024.1403635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024] Open
Abstract
Since the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) outbreak, several solutions have been proposed to manage the disease. The most viable option for controlling this virus is to produce effective vaccines. Most of the current SARS-CoV-2 vaccines have focused on the infusion spike protein. Spike exists as a trimer and plays a vital role in infecting host cells by binding to the Angiotensin-Converting Enzyme 2 (ACE2) receptor through its Receptor Binding Domain (RBD). Ferritin protein, a naturally occurring iron-storage protein, has gained attention for vaccine production due to its self-assembling property, non-toxic nature, and biocompatibility. Ferritin nanocages have recently been employed in the development of a SARS-CoV-2 vaccination eliciting not only long-term protective memory cells but also a sustained antibody response. In this study, a combination of in silico investigations including molecular docking, molecular dynamics simulations, and immune simulations were carried out to computationally model the monomeric spike protein on the ferritin nanocage as well as to evaluate its stability and interactions for the first time. The structural dynamics of the modeled complex demonstrated noticeable stability. In particular, the Receptor Binding Domain (RBD) and ferritin within the monomeric spike-ferritin complex illustrated significant stability. The lack of alterations in the secondary structure further supported the overall steadiness of the complex. The decline in the distance between ferritin and spike suggests a strong interaction over time. The cross-correlation matrices revealed that the monomeric spike and ferritin move towards each other supporting the stable interaction between spike and ferritin. Further, the orientation of monomeric spike protein within the ferritin unit facilitated the exposure of critical epitopes, specifically upward active Receptor Binding Domain (RBD), enabling effective interactions with the ACE2 receptor. The immune simulations of the model indicated high-level stimulations of both cellular and humoral immunity in the human body. It was also found that the employed model is effective regardless of the mutated spikes in different variants. These findings shed light on the current status of the SARS-CoV-2-ferritin nanoparticle vaccines and could be used as a framework for other similar vaccine designs.
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Pashameah RA, Soltane R, Sayed AM. A novel inhibitor of SARS-CoV infection: Lactulose octasulfate interferes with ACE2-Spike protein binding. Heliyon 2024; 10:e23222. [PMID: 38163229 PMCID: PMC10754899 DOI: 10.1016/j.heliyon.2023.e23222] [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: 10/14/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 01/03/2024] Open
Abstract
The ongoing challenge of managing coronaviruses, particularly SARS-CoV-2, necessitates the development of effective antiviral agents. This study introduces Lactulose octasulfate (LOS), a sulfated disaccharide, demonstrating significant antiviral activity against key coronaviruses including SARS-CoV-2, SARS-CoV, and MERS-CoV. We hypothesize LOS operates extracellularly, targeting the ACE2-S-protein axis, due to its low cellular permeability. Our investigation combines biolayer interferometry (BLI), isothermal titration calorimetry (ITC)-based experiments with in silico studies, revealing LOS's ability to reduce SARS-CoV-2's RBD's affinity for ACE2 in a dose-dependent manner, and bind tightly to ACE2 without inhibiting its enzymatic activity. Gaussian accelerated molecular dynamics simulations (GaMD) further supported these findings, illustrating LOS's potential as a broad-spectrum antiviral agent against current and future coronavirus strains, meriting in vivo and clinical exploration.
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Affiliation(s)
- Rami Adel Pashameah
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Raya Soltane
- Department of Biology, Adham University College, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Ahmed M. Sayed
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, 62513 Beni-Suef, Egypt
- Department of Pharmacognosy, collage of Pharmacy, Almaaqal University, 61014 Basra, Iraq
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Hafezi SG, Seifi N, Bahari H, Mohammadi M, Ghasemabadi A, ferns GA, Farkhani EM, Ghayour-mobarhan M. The association between macronutrient intakes and coronavirus disease 2019 (COVID-19) in an Iranian population: applying a dynamical system model. JOURNAL OF HEALTH, POPULATION, AND NUTRITION 2023; 42:114. [PMID: 37884984 PMCID: PMC10601229 DOI: 10.1186/s41043-023-00448-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 09/22/2023] [Indexed: 10/28/2023]
Abstract
AIMS The possible role of lifestyle including diet on immunity led us to investigate the association between dietary macronutrient intake and COVID-19 in an Iranian population. METHODS Dietary intakes were recorded in the first phase of the MASHAD cohort study (started in 2007), using a 24-h dietary recall. To determine the COVID-19 incidence, data from all PCR-positive patients in Mashhad were recorded between February 2020 and June 2022. Dietary macronutrients were included in the regression model, adjusting for age and sex. System dynamical models were also applied. RESULTS The analysis included 1957 participants, including 193 COVID-19-positive patients. Dietary intakes of non-starch polysaccharides (NSP) and fiber were significantly lower in COVID-19 patients (P < 0.05). After adjusting for age and sex, starch and total sugar were significantly associated with COVID-19 infection ((OR = 1.0008, P = 0.001) and (OR = 1.0006, P = 0.026), respectively). There was also a significant association between dietary fiber intake and hospitalization (OR = 0.99, P = 0.018). In the dynamical system models, dietary intakes of cholesterol, polyunsaturated fatty acids (PUFA), and total sugar above 180.2 mg, 13.11 g, and 79.53 mg, respectively, were associated with an increased susceptibility to COVID-19 infection, while dietary fiber had a protective role. CONCLUSION Dietary intake of starch and total sugars was associated with increased odds of COVID-19, while fiber intake decreased the odds of hospitalization due to COVID-19. The dynamical system models showed that dietary intake of cholesterol, PUFAs, and total sugar was associated with an increased risk of COVID-19, while fiber had a protective role.
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Affiliation(s)
- Somayeh Ghiasi Hafezi
- International UNESCO Center for Health-Related Basic Sciences and Human Nutrition, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Najmeh Seifi
- International UNESCO Center for Health-Related Basic Sciences and Human Nutrition, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hossein Bahari
- Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Maryam Mohammadi
- International UNESCO Center for Health-Related Basic Sciences and Human Nutrition, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Gordon A. ferns
- Brighton & Sussex Medical School, Division of Medical Education, Falmer, Brighton, Sussex UK
| | | | - Majid Ghayour-mobarhan
- International UNESCO Center for Health-Related Basic Sciences and Human Nutrition, Mashhad University of Medical Sciences, Mashhad, Iran
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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Wang L, Wang Y, Zhou H. Potent antibodies against immune invasive SARS-CoV-2 Omicron subvariants. Int J Biol Macromol 2023; 249:125997. [PMID: 37499711 DOI: 10.1016/j.ijbiomac.2023.125997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/23/2023] [Accepted: 07/24/2023] [Indexed: 07/29/2023]
Abstract
The development of neutralizing antibodies (nAbs) is an important strategy to tackle the Omicron variant. Omicron N-terminal domain (NTD) mutations including A67V, G142D, and N212I alter the antigenic structure, and mutations in the spike (S) receptor binding domain (RBD), such as N501Y, R346K, and T478K enhance affinity between the RBD and angiotensin-converting enzyme 2 (ACE2), thus conferring Omicron powerful immune evasion. Most nAbs (COV2-2130, ZCB11, REGN10933) and combinations of nAbs (COV2-2196 + COV2-2130, REGN10933 + REGN10987, Brii-196 + Brii-198) have either greatly reduced or lost their neutralizing ability against Omicron, but several nAbs such as SA55, SA58, S309, LY-CoV1404 are still effective in neutralizing most Omicron subvariants. This paper focuses on Omicron subvariants mutations and mechanisms of current therapeutic antibodies that remain efficacious against Omicron subvariants, which will guide us in exploring a new generation of broad nAbs as key therapeutics to tackle SARS-CoV-2 and accelerate the exploration of novel clinical antiviral reagents.
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Affiliation(s)
- Lidong Wang
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Yang Wang
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Hao Zhou
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, Chongqing Traditional Chinese Medicine Hospital, Chongqing 400016, China.
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Yadav SK, Verma D, Yadav U, Kalkal A, Priyadarshini N, Kumar A, Mahato K. Point-of-Care Devices for Viral Detection: COVID-19 Pandemic and Beyond. MICROMACHINES 2023; 14:1744. [PMID: 37763907 PMCID: PMC10535693 DOI: 10.3390/mi14091744] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023]
Abstract
The pandemic of COVID-19 and its widespread transmission have made us realize the importance of early, quick diagnostic tests for facilitating effective cure and management. The primary obstacles encountered were accurately distinguishing COVID-19 from other illnesses including the flu, common cold, etc. While the polymerase chain reaction technique is a robust technique for the determination of SARS-CoV-2 in patients of COVID-19, there arises a high demand for affordable, quick, user-friendly, and precise point-of-care (POC) diagnostic in therapeutic settings. The necessity for available tests with rapid outcomes spurred the advancement of POC tests that are characterized by speed, automation, and high precision and accuracy. Paper-based POC devices have gained increasing interest in recent years because of rapid, low-cost detection without requiring external instruments. At present, microfluidic paper-based analysis devices have garnered public attention and accelerated the development of such POCT for efficient multistep assays. In the current review, our focus will be on the fabrication of detection modules for SARS-CoV-2. Here, we have included a discussion on various strategies for the detection of viral moieties. The compilation of these strategies would offer comprehensive insight into the detection of the causative agent preparedness for future pandemics. We also provide a descriptive outline for paper-based diagnostic platforms, involving the determination mechanisms, as well as a commercial kit for COVID-19 as well as their outlook.
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Affiliation(s)
- Sumit K. Yadav
- Department of Biotechnology, Vinoba Bhave University, Hazaribagh 825301, Jharkhand, India
| | - Damini Verma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Ujala Yadav
- Department of Life Sciences, Central University of Jharkhand, Ranchi 835205, Jharkhand, India
| | - Ashish Kalkal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Nivedita Priyadarshini
- Department of Zoology, DAV PG College Siwan, Jai Prakash University, Chhapra 841226, Bihar, India
| | - Ashutosh Kumar
- Department of Electrical Engineering, University of Notre Dame, Notre Dame, IN 46637, USA
| | - Kuldeep Mahato
- Department of Nanoengineering, University of California San Diego, 9500 Gilman Dr, La Jolla, San Diego, CA 92093, USA
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Pashameah RA, Soltane R, Sayed AM. Discovery of raffinose sulfate as a potential SARS CoV-2 inhibitor via blocking its binding with angiotensin converting enzyme 2. Int J Biol Macromol 2023; 248:125818. [PMID: 37473891 DOI: 10.1016/j.ijbiomac.2023.125818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/23/2023] [Accepted: 07/11/2023] [Indexed: 07/22/2023]
Abstract
The present study aimed to characterize the possible binding sites on the SARS CoV-2 RBD-ACE2 complex and to highlight sulfated oligosaccharides as potential anti-SARS CoV-2 via inducing RBD-ACE2 complex destabilization and dissociation. By combining pharmacophore-based and structural-based virtual screening approaches we were able to discover raffinose sulfate (RS) as a potential antiviral sulfated oligosaccharide against two SARS CoV-2 variants (i.e., wild type and Omicron) (IC50 = 4.45 ± 0.28 μM and 4.65 ± 0.32 μM, respectively). Upon MD simulation, RS was able to establish stable binding at the RBD-ACE2 interface inducing a rapid dissociation. Accordingly, and by using bio-layer interferometry (BLI) assays, RS was able to significantly weaken the affinity between RBD (of both variants) and ACE2. Additionally, we found that RS has a poor cellular permeability indicating that its interaction with the RBD-ACE2 complex may be the main mechanism by which it mediates its antiviral activity against SARS CoV-2. Despite its proposed interaction with the RBD-ACE2 complex, RS did not show any inhibitory activity against ACE2 catalytic activity. In light of these findings, the RS scaffold can be further developed into a novel anti-SARS CoV-2 drug with improved activity and tolerability in comparison with other sulfated polysaccharides e.g., heparin and heparan.
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Affiliation(s)
- Rami Adel Pashameah
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah 21955, Saudi Arabia.
| | - Raya Soltane
- Department of Basic Sciences, Adham University College, Umm Al-Qura University, Makkah 21955, Saudi Arabia.
| | - Ahmed M Sayed
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, 62513 Beni-Suef, Egypt.
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8
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Godoy AS, Nakamura AM, Douangamath A, Song Y, Noske GD, Gawriljuk VO, Fernandes RS, Pereira H, Oliveira K, Fearon D, Dias A, Krojer T, Fairhead M, Powell A, Dunnet L, Brandao-Neto J, Skyner R, Chalk R, Bajusz D, Bege M, Borbás A, Keserű GM, von Delft F, Oliva G. Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease. Nucleic Acids Res 2023; 51:5255-5270. [PMID: 37115000 PMCID: PMC10250223 DOI: 10.1093/nar/gkad314] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). The NSP15 endoribonuclease enzyme, known as NendoU, is highly conserved and plays a critical role in the ability of the virus to evade the immune system. NendoU is a promising target for the development of new antiviral drugs. However, the complexity of the enzyme's structure and kinetics, along with the broad range of recognition sequences and lack of structural complexes, hampers the development of inhibitors. Here, we performed enzymatic characterization of NendoU in its monomeric and hexameric form, showing that hexamers are allosteric enzymes with a positive cooperative index, and with no influence of manganese on enzymatic activity. Through combining cryo-electron microscopy at different pHs, X-ray crystallography and biochemical and structural analysis, we showed that NendoU can shift between open and closed forms, which probably correspond to active and inactive states, respectively. We also explored the possibility of NendoU assembling into larger supramolecular structures and proposed a mechanism for allosteric regulation. In addition, we conducted a large fragment screening campaign against NendoU and identified several new allosteric sites that could be targeted for the development of new inhibitors. Overall, our findings provide insights into the complex structure and function of NendoU and offer new opportunities for the development of inhibitors.
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Affiliation(s)
- Andre Schutzer Godoy
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil
| | - Aline Minalli Nakamura
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil
| | - Alice Douangamath
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Yun Song
- Electron Bio-imaging Centre, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0QX, UK
| | - Gabriela Dias Noske
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil
| | - Victor Oliveira Gawriljuk
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil
| | - Rafaela Sachetto Fernandes
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil
| | - Humberto D Muniz Pereira
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil
| | - Ketllyn Irene Zagato Oliveira
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil
| | - Daren Fearon
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Alexandre Dias
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Tobias Krojer
- BioMAX, MAX IV Laboratory, Fotongatan 2, Lund 224 84, Sweden
| | - Michael Fairhead
- Centre for Medicines Discovery, Oxford University, Oxford OX1 3QU, UK
| | - Alisa Powell
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Louise Dunnet
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Jose Brandao-Neto
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Rachael Skyner
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Rod Chalk
- Centre for Medicines Discovery, Oxford University, Oxford OX1 3QU, UK
| | - Dávid Bajusz
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117 Budapest, Hungary
| | - Miklós Bege
- Department of Pharmaceutical Chemistry, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
- MTA-DE Molecular Recognition and Interaction Research Group, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Anikó Borbás
- Department of Pharmaceutical Chemistry, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
- National Laboratory of Virology, University of Pécs, Ifjúság útja 20, H-7624 Pécs, Hungary
| | - György Miklós Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117 Budapest, Hungary
| | - Frank von Delft
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
- Centre for Medicines Discovery, Oxford University, Oxford OX1 3QU, UK
- Department of Biochemistry, University of Johannesburg, PO Box 524, Auckland Park 2006, South Africa
| | - Glaucius Oliva
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil
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9
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Raghav PK, Mann Z, Ahluwalia SK, Rajalingam R. Potential treatments of COVID-19: Drug repurposing and therapeutic interventions. J Pharmacol Sci 2023; 152:1-21. [PMID: 37059487 PMCID: PMC9930377 DOI: 10.1016/j.jphs.2023.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 01/31/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The infection is caused when Spike-protein (S-protein) present on the surface of SARS-CoV-2 interacts with human cell surface receptor, Angiotensin-converting enzyme 2 (ACE2). This binding facilitates SARS-CoV-2 genome entry into the human cells, which in turn causes infection. Since the beginning of the pandemic, many different therapies have been developed to combat COVID-19, including treatment and prevention. This review is focused on the currently adapted and certain other potential therapies for COVID-19 treatment, which include drug repurposing, vaccines and drug-free therapies. The efficacy of various treatment options is constantly being tested through clinical trials and in vivo studies before they are made medically available to the public.
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Affiliation(s)
- Pawan Kumar Raghav
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA.
| | | | - Simran Kaur Ahluwalia
- Amity Institute of Biotechnology, Amity University, Sector-125, Noida, Uttar Pradesh, India
| | - Raja Rajalingam
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, USA
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10
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Sayed AM, Ibrahim AH, Tajuddeen N, Seibel J, Bodem J, Geiger N, Striffler K, Bringmann G, Abdelmohsen UR. Korupensamine A, but not its atropisomer, korupensamine B, inhibits SARS-CoV-2 in vitro by targeting its main protease (M pro). Eur J Med Chem 2023; 251:115226. [PMID: 36893625 PMCID: PMC9972725 DOI: 10.1016/j.ejmech.2023.115226] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/07/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023]
Abstract
By combining docking and molecular dynamics simulations, we explored a library of 65 mostly axially chiral naphthylisoquinoline alkaloids and their analogues, with most different molecular architectures and structural analogues, for their activity against SARS-CoV-2. Although natural biaryls are often regarded without consideration of their axial chirality, they can bind to protein targets in an atroposelective manner. By combining docking results with steered molecular dynamics simulations, we identified one alkaloid, korupensamine A, that atropisomer-specifically inhibited the main protease (Mpro) activity of SARS-CoV-2 significantly in comparison to the reference covalent inhibitor GC376 (IC50 = 2.52 ± 0.14 and 0.88 ± 0.15 μM, respectively) and reduced viral growth by five orders of magnitude in vitro (EC50 = 4.23 ± 1.31 μM). To investigate the binding pathway and mode of interaction of korupensamine A within the active site of the protease, we utilized Gaussian accelerated molecular dynamics simulations, which reproduced the docking pose of korupensamine A inside the active site of the enzyme. The study presents naphthylisoquinoline alkaloids as a new class of potential anti-COVID-19 agents.
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Affiliation(s)
- Ahmed M Sayed
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, Beni-Suef, 62513, Egypt
| | - Alyaa Hatem Ibrahim
- Department of Pharmacognosy, Faculty of Pharmacy, Sohag University, Sohag, 82524, Egypt
| | - Nasir Tajuddeen
- Department of Chemistry, Ahmadu Bello University, 15 Sokoto Road Samaru, Zaria, 810107, Nigeria
| | - Jürgen Seibel
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Jochen Bodem
- Institute of Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, 97078, Würzburg, Germany
| | - Nina Geiger
- Institute of Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, 97078, Würzburg, Germany
| | - Kathrin Striffler
- Institute of Virology and Immunobiology, University of Würzburg, Versbacher Str. 7, 97078, Würzburg, Germany
| | - Gerhard Bringmann
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074, Würzburg, Germany.
| | - Usama Ramadan Abdelmohsen
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia, 61519, Egypt; Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, Universities Zone, New Minia City, 61111, Egypt.
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11
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Chen J, Li Y, Liu Z. Functional nucleic acids as potent therapeutics against SARS-CoV-2 infection. CELL REPORTS. PHYSICAL SCIENCE 2023; 4:101249. [PMID: 36714073 PMCID: PMC9869493 DOI: 10.1016/j.xcrp.2023.101249] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The COVID-19 pandemic has posed a severe threat to human life and the global economy. Although conventional treatments, including vaccines, antibodies, and small-molecule inhibitors, have been broadly developed, they usually fall behind the constant mutation of SARS-CoV-2, due to the long screening process and high production cost. Functional nucleic acid (FNA)-based therapeutics are a newly emerging promising means against COVID-19, considering their timely adaption to different mutants and easy design for broad-spectrum virus inhibition. In this review, we survey typical FNA-related therapeutics against SARS-CoV-2 infection, including aptamers, aptamer-integrated DNA frameworks, functional RNA, and CRISPR-Cas technology. We first introduce the pathogenesis, transmission, and evolution of SARS-CoV-2, then analyze the existing therapeutic and prophylactic strategies, including their pros and cons. Subsequently, the FNAs are recommended as potent alternative therapeutics from their screening process and controllable engineering to effective neutralization. Finally, we put forward the remaining challenges of the existing field and sketch out the future development directions.
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Affiliation(s)
- Jingran Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Ying Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Zhen Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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12
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Shamkh IM, Elkazzaz M, Radwan ES, Najeeb J, Rehman MT, AlAjmi MF, Shahwan M, Sufyan M, Alaqeel NK, Ibrahim IA, Jabbar B, Khan MS, Karpiński TM, Haikal A, Aljowaie RM, Almutairi SM, Ahmed A. AI-driven Discovery of Celecoxib and Dexamethasone for Exploring their Mode of Action as Human Interleukin (IL-6) Inhibitors to Treat COVID-19-induced Cytokine Storm in Humans. Curr Pharm Des 2023; 29:2752-2762. [PMID: 37921134 DOI: 10.2174/0113816128260449231017091824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/31/2023] [Accepted: 08/25/2023] [Indexed: 11/04/2023]
Abstract
BACKGROUND In the case of COVID-19 patients, it has been observed that the immune system of the infected person exhibits an extreme inflammatory response known as cytokine release syndrome (CRS) where the inflammatory cytokines are swiftly produced in quite large amounts in response to infective stimuli. Numerous case studies of COVID-19 patients with severe symptoms have documented the presence of higher plasma concentrations of human interleukin-6 (IL-6), which suggests that IL-6 is a crucial factor in the pathophysiology of the disease. In order to prevent CRS in COVID-19 patients, the drugs that can exhibit binding interactions with IL-6 and block the signaling pathways to decrease the IL-6 activity may be repurposed. METHODS This research work focused on molecular docking-based screening of the drugs celecoxib (CXB) and dexamethasone (DME) to explore their potential to interact with the binding sites of IL-6 protein and reduce the hyper-activation of IL-6 in the infected personnel. RESULTS Both of the drugs were observed to bind with the IL-6 (IL-6 receptor alpha chain) and IL-6Rα receptor with the respective affinities of -7.3 kcal/mol and -6.3 kcal/mol, respectively, for CXB and DME. Moreover, various types of binding interactions of the drugs with the target proteins were also observed in the docking studies. The dynamic behaviors of IL-6/IL-6Rα in complex with the drugs were also explored through molecular dynamics simulation analysis. The results indicated significant stabilities of the acquired drug-protein complexes up to 100 ns. CONCLUSION The findings of this study have suggested the potential of the drugs studied to be utilized as antagonists for countering CRS in COVID-19 ailment. This study presents the studied drugs as promising candidates both for the clinical and pre-clinical treatment of COVID-19.
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Affiliation(s)
- Israa M Shamkh
- Chemo and Bioinformatics Lab, Bio Search Research Institution BSRI, Giza 12613, Egypt
| | - Mahmoud Elkazzaz
- Department of Chemistry and Biochemistry, Faculty of Science, Damietta University, Damietta 7952567, Egypt
| | - Enas S Radwan
- Faculty of Science, Zarqa University, Zarqa 13132, Jordan
| | - Jawayria Najeeb
- Department of Chemistry, University of Gujrat, Gujrat 50700, Pakistan
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
- Center for Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
| | - Mohamed F AlAjmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Moayad Shahwan
- Center for Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
- Department of Clinical Sciences, College of Pharmacy and Health Sciences, Ajman University, Ajman, United Arab Emirates
| | - Muhammad Sufyan
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Nouf Khalifa Alaqeel
- Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
| | - Ibrahim A Ibrahim
- Botany and Microbiology Department (Biotechnology Program), Faculty of Science, Damietta University, Damietta, Egypt
| | - Basit Jabbar
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Mohammad Shahbaz Khan
- Children's National Hospital, George Washington University, Washington, DC 20010, USA
| | - Tomasz M Karpiński
- Chair and Department of Medical Microbiology, Poznań University of Medical Sciences, Wieniawskiego 3, Poznań 61-712, Poland
| | - Abdullah Haikal
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Reem M Aljowaie
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. 2455, Riyadh 11451, Saudi Arabia
| | - Saeedah Musaed Almutairi
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. 2455, Riyadh 11451, Saudi Arabia
| | - Amr Ahmed
- Director of Tuberculosis Ghubera Mobile Team, Public Health Department, First Health Cluster, Ministry of Health, Riyadh 966-11, Saudi Arabia
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13
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Barrera Saldaña HA, Rivera Santiago C, Rodríguez Palacios R. SARS-CoV-2: Challenges in Reconverting Diagnostic Laboratories to Combat the Pandemic. Microbiol Spectr 2022; 10:e0147722. [PMID: 36314981 PMCID: PMC9769709 DOI: 10.1128/spectrum.01477-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 10/05/2022] [Indexed: 11/05/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) was first detected in Mexico in February 2020. Even though health authorities did not perceive then the value of viral detection tests, we anticipated the demand for them. We set up to develop an expeditious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) molecular diagnostic service through the implementation of standardized protocols for biospecimen sampling, transportation, biobanking, preanalytical validation, and nucleic acids (NA) testing (NAT). Nasopharyngeal and oropharyngeal swabs collected in a special transportation medium were the biospecimens from which NAs were purified either manually or automatically. Viral RNA genome presence was determined using commercial SARS-CoV-2 detection kits (based on reverse transcription coupled with real-time PCR [RT-PCR]). Improvements in laboratory processing speed and reliability resulted from semi-automatizing laboratory processes and adopting a quality control/quality assurance system (QC/QA), respectively. NAs that were purified, either manually or automatically, were validated by preanalytical spectrophotometric characterization. Automated purification was less prone to contamination and reduced the processing time. The following six RT-PCR kits were evaluated for their convenience, specificity, sensitivity, time consumption, and required materials (in order, starting with the kit with the best results): RIDA gene and Viasure (tied), Vircell, LightMix, 1copy, and Logix Smart. Redesigning the laboratories' working areas, equipment, fluxes of personnel and material, and personnel skills, and overemphasizing biosafety safeguards were major challenges encountered in the middle of the sanitary crisis. Adopting a QC/QA system, utilizing automatization processes, and working closely with health authorities were key factors in our success. IMPORTANCE Rearranging our diagnostic laboratories to improve the fight against a new unexpected, unpredictable, and sudden public health threat demanded that we move quickly to redesign not only the laboratory processes but also the distribution of space, personnel activities, and fluxes of material coming in and out. We also had to work closely with governmental health authorities to gain their trust in our technical competence. Gaining the confidence of the clients, i.e., mainly individuals, the human resource departments of factories and corporations sending employees for testing, and medical institutions, and implementing as much automatization as possible of processes, in which only officially approved reagents (for extraction and analysis of NA) were used to generate opportune trustable testing results, were key factors. Our laboratories have gathered a considerable amount of experience and significant number of solutions, considering our geographic contexts alongside this continuously morphing pandemic, validating many techniques that might help other laboratories find a better and more precise workflow.
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Affiliation(s)
- Hugo Alberto Barrera Saldaña
- Columbia Comercial, SA de CV, División Columbia Biotec, Tlalpan, Mexico City, México
- Vitagénesis, SA de CV, and Innbiogem SC at LANSEIDI-CONACyT, Monterrey, Nuevo León, México
- Universidad Autónoma de Nuevo León, School of Medicine, San Nicolás de los Garza, Nuevo León, México
- Universidad Autónoma de Nuevo León, School of Biological Sciences, San Nicolás de los Garza, Nuevo León, México
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14
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Sharun K, Tiwari R, Yatoo MI, Natesan S, Megawati D, Singh KP, Michalak I, Dhama K. A comprehensive review on pharmacologic agents, immunotherapies and supportive therapeutics for COVID-19. NARRA J 2022; 2:e92. [PMID: 38449903 PMCID: PMC10914132 DOI: 10.52225/narra.v2i3.92] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/06/2022] [Indexed: 03/08/2024]
Abstract
The emergence of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has affected many countries throughout the world. As urgency is a necessity, most efforts have focused on identifying small molecule drugs that can be repurposed for use as anti-SARS-CoV-2 agents. Although several drug candidates have been identified using in silico method and in vitro studies, most of these drugs require the support of in vivo data before they can be considered for clinical trials. Several drugs are considered promising therapeutic agents for COVID-19. In addition to the direct-acting antiviral drugs, supportive therapies including traditional Chinese medicine, immunotherapies, immunomodulators, and nutritional therapy could contribute a major role in treating COVID-19 patients. Some of these drugs have already been included in the treatment guidelines, recommendations, and standard operating procedures. In this article, we comprehensively review the approved and potential therapeutic drugs, immune cells-based therapies, immunomodulatory agents/drugs, herbs and plant metabolites, nutritional and dietary for COVID-19.
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Affiliation(s)
- Khan Sharun
- Division of Surgery, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, UP Pandit Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan (DUVASU), Mathura, India
| | - Mohd I. Yatoo
- Division of Veterinary Clinical Complex, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, Alusteng Srinagar, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Jammu and Kashmir, India
| | - Senthilkumar Natesan
- Department of Infectious Diseases, Indian Institute of Public Health Gandhinagar, Opp to Airforce station HQ, Gandhinagar, India
| | - Dewi Megawati
- Department of Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Warmadewa University, Denpasar, Indonesia
- Department of Medical Microbiology and Immunology, University of California, Davis, California, USA
| | - Karam P. Singh
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Izabela Michalak
- Faculty of Chemistry, Department of Advanced Material Technologies, Wrocław University of Science and Technology, Wrocław, Poland
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, India
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15
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Masoomi Nomandan SZ, Azimzadeh Irani M, Hosseini SM. In silico design of refined ferritin-SARS-CoV-2 glyco-RBD nanoparticle vaccine. Front Mol Biosci 2022; 9:976490. [PMID: 36148012 PMCID: PMC9486171 DOI: 10.3389/fmolb.2022.976490] [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] [Accepted: 08/11/2022] [Indexed: 12/04/2022] Open
Abstract
With the onset of Coronavirus disease 2019 (COVID-19) pandemic, all attention was drawn to finding solutions to cure the coronavirus disease. Among all vaccination strategies, the nanoparticle vaccine has been shown to stimulate the immune system and provide optimal immunity to the virus in a single dose. Ferritin is a reliable self-assembled nanoparticle platform for vaccine production that has already been used in experimental studies. Furthermore, glycosylation plays a crucial role in the design of antibodies and vaccines and is an essential element in developing effective subunit vaccines. In this computational study, ferritin nanoparticles and glycosylation, which are two unique facets of vaccine design, were used to model improved nanoparticle vaccines for the first time. In this regard, molecular modeling and molecular dynamics simulation were carried out to construct three atomistic models of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) receptor binding domain (RBD)-ferritin nanoparticle vaccine, including unglycosylated, glycosylated, and modified with additional O-glycans at the ferritin–RBD interface. It was shown that the ferritin–RBD complex becomes more stable when glycans are added to the ferritin–RBD interface and optimal performance of this nanoparticle can be achieved. If validated experimentally, these findings could improve the design of nanoparticles against all microbial infections.
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16
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Fernandes RS, de Oliveira Silva J, Gomes KB, Azevedo RB, Townsend DM, de Paula Sabino A, Branco de Barros AL. Recent advances in point of care testing for COVID-19 detection. Biomed Pharmacother 2022; 153:113538. [PMID: 36076617 PMCID: PMC9371983 DOI: 10.1016/j.biopha.2022.113538] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/03/2022] [Accepted: 08/04/2022] [Indexed: 12/23/2022] Open
Abstract
The World Health Organizations declaration of the COVID-19 pandemic was a milestone for the scientific community. The high transmission rate and the huge number of deaths, along with the lack of knowledge about the virus and the evolution of the disease, stimulated a relentless search for diagnostic tests, treatments, and vaccines. The main challenges were the differential diagnosis of COVID-19 and the development of specific, rapid, and sensitive tests that could reach all people. RT-PCR remains the gold standard for diagnosing COVID-19. However, new methods, such as other molecular techniques and immunoassays emerged. Also, the need for accessible tests with quick results boosted the development of point of care tests (POCT) that are fast, and automated, with high precision and accuracy. This assay reduces the dependence on laboratory conditions and mass testing of the population, dispersing the pressure regarding screening and detection. This review summarizes the advances in the diagnostic field since the pandemic started, emphasizing various laboratory techniques for detecting COVID-19. We reviewed the main existing diagnostic methods, as well as POCT under development, starting with RT-PCR detection, but also exploring other nucleic acid techniques, such as digital PCR, loop-mediated isothermal amplification-based assay (RT-LAMP), clustered regularly interspaced short palindromic repeats (CRISPR), and next-generation sequencing (NGS), and immunoassay tests, and nanoparticle-based biosensors, developed as portable instruments for the rapid standard diagnosis of COVID-19.
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17
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Goldenbogen B, Adler SO, Bodeit O, Wodke JAH, Escalera‐Fanjul X, Korman A, Krantz M, Bonn L, Morán‐Torres R, Haffner JEL, Karnetzki M, Maintz I, Mallis L, Prawitz H, Segelitz PS, Seeger M, Linding R, Klipp E. Control of COVID-19 Outbreaks under Stochastic Community Dynamics, Bimodality, or Limited Vaccination. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2200088. [PMID: 35607290 PMCID: PMC9348421 DOI: 10.1002/advs.202200088] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/24/2022] [Indexed: 06/15/2023]
Abstract
Reaching population immunity against COVID-19 is proving difficult even in countries with high vaccination levels. Thus, it is critical to identify limits of control and effective measures against future outbreaks. The effects of nonpharmaceutical interventions (NPIs) and vaccination strategies are analyzed with a detailed community-specific agent-based model (ABM). The authors demonstrate that the threshold for population immunity is not a unique number, but depends on the vaccination strategy. Prioritizing highly interactive people diminishes the risk for an infection wave, while prioritizing the elderly minimizes fatalities when vaccinations are low. Control over COVID-19 outbreaks requires adaptive combination of NPIs and targeted vaccination, exemplified for Germany for January-September 2021. Bimodality emerges from the heterogeneity and stochasticity of community-specific human-human interactions and infection networks, which can render the effects of limited NPIs uncertain. The authors' simulation platform can process and analyze dynamic COVID-19 epidemiological situations in diverse communities worldwide to predict pathways to population immunity even with limited vaccination.
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Affiliation(s)
- Björn Goldenbogen
- Theoretical BiophysicsHumboldt‐Universität zu BerlinInvalidenstr. 42Berlin10115Germany
| | - Stephan O. Adler
- Theoretical BiophysicsHumboldt‐Universität zu BerlinInvalidenstr. 42Berlin10115Germany
| | - Oliver Bodeit
- Theoretical BiophysicsHumboldt‐Universität zu BerlinInvalidenstr. 42Berlin10115Germany
- Institute of BiochemistryCharité – Universitätsmedizin BerlinVirchowweg 6Berlin10117Germany
- Institute of Quantitative and Theoretical BiologyHeinrich‐Heine‐UniversitätUniversitätsstraße 1Düsseldorf40225Germany
| | - Judith A. H. Wodke
- Theoretical BiophysicsHumboldt‐Universität zu BerlinInvalidenstr. 42Berlin10115Germany
| | | | - Aviv Korman
- Theoretical BiophysicsHumboldt‐Universität zu BerlinInvalidenstr. 42Berlin10115Germany
| | - Maria Krantz
- Theoretical BiophysicsHumboldt‐Universität zu BerlinInvalidenstr. 42Berlin10115Germany
| | - Lasse Bonn
- Theoretical BiophysicsHumboldt‐Universität zu BerlinInvalidenstr. 42Berlin10115Germany
| | - Rafael Morán‐Torres
- Theoretical BiophysicsHumboldt‐Universität zu BerlinInvalidenstr. 42Berlin10115Germany
| | - Johanna E. L. Haffner
- Theoretical BiophysicsHumboldt‐Universität zu BerlinInvalidenstr. 42Berlin10115Germany
| | - Maxim Karnetzki
- Theoretical BiophysicsHumboldt‐Universität zu BerlinInvalidenstr. 42Berlin10115Germany
| | - Ivo Maintz
- Theoretical BiophysicsHumboldt‐Universität zu BerlinInvalidenstr. 42Berlin10115Germany
| | - Lisa Mallis
- Theoretical BiophysicsHumboldt‐Universität zu BerlinInvalidenstr. 42Berlin10115Germany
| | - Hannah Prawitz
- Theoretical BiophysicsHumboldt‐Universität zu BerlinInvalidenstr. 42Berlin10115Germany
| | - Patrick S. Segelitz
- Theoretical BiophysicsHumboldt‐Universität zu BerlinInvalidenstr. 42Berlin10115Germany
| | - Martin Seeger
- Theoretical BiophysicsHumboldt‐Universität zu BerlinInvalidenstr. 42Berlin10115Germany
- Rewire TxHumboldt‐Universität zu BerlinInvalidenstr. 42Berlin10115Germany
| | - Rune Linding
- Theoretical BiophysicsHumboldt‐Universität zu BerlinInvalidenstr. 42Berlin10115Germany
- Rewire TxHumboldt‐Universität zu BerlinInvalidenstr. 42Berlin10115Germany
| | - Edda Klipp
- Theoretical BiophysicsHumboldt‐Universität zu BerlinInvalidenstr. 42Berlin10115Germany
- Rewire TxHumboldt‐Universität zu BerlinInvalidenstr. 42Berlin10115Germany
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Kabi AK, Pal M, Gujjarappa R, Malakar CC, Roy M. Overview of Hydroxychloroquine and Remdesivir on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). J Heterocycl Chem 2022; 60:JHET4541. [PMID: 35942205 PMCID: PMC9349740 DOI: 10.1002/jhet.4541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 11/08/2022]
Abstract
The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the ongoing pandemic named COVID-19 which causes a serious emergency on public health hazards of international concern. In the face of a critical medical emergency, repositioning of drugs is one of the most authentic options to design an adequate treatment for infected patients immediately. In this strategy, Remdesivir (Veklury), Hydroxychloroquine appears to be the drug of choice and garnered unprecedented attention as potential therapeutic agents against the pandemic realized worldwide due to SARS-CoV-2 infection. These are the breathtaking instances of possible repositioning of drugs, whose pharmacokinetics and optimal dosage are familiar. In this review, we provide an overview of these medications, their synthesis, and the possible mechanism of action against SARS-CoV-2.
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Affiliation(s)
- Arup K. Kabi
- Department of ChemistryNational Institute of Technology ManipurImphalManipurIndia
| | - Maynak Pal
- Department of ChemistryNational Institute of Technology ManipurImphalManipurIndia
| | - Raghuram Gujjarappa
- Department of ChemistryNational Institute of Technology ManipurImphalManipurIndia
| | - Chandi C. Malakar
- Department of ChemistryNational Institute of Technology ManipurImphalManipurIndia
| | - Mithun Roy
- Department of ChemistryNational Institute of Technology ManipurImphalManipurIndia
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Celecoxib Microparticles for Inhalation in COVID-19-Related Acute Respiratory Distress Syndrome. Pharmaceutics 2022; 14:pharmaceutics14071392. [PMID: 35890288 PMCID: PMC9320401 DOI: 10.3390/pharmaceutics14071392] [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: 06/06/2022] [Revised: 06/23/2022] [Accepted: 06/28/2022] [Indexed: 11/17/2022] Open
Abstract
Inhalation therapy is gaining increasing attention for the delivery of drugs destined to treat respiratory disorders associated with cytokine storms, such as COVID-19. The pathogenesis of COVID-19 includes an inflammatory storm with the release of cytokines from macrophages, which may be treated with anti-inflammatory drugs as celecoxib (CXB). For this, CXB-loaded PLGA microparticles (MPs) for inhaled therapy and that are able to be internalized by alveolar macrophages, were developed. MPs were prepared with 5% and 10% initial percentages of CXB (MP-C1 and MP-C2). For both systems, the mean particle size was around 5 µm, which was adequate for macrophage uptake, and the mean encapsulation efficiency was >89%. The in vitro release of CXB was prolonged for more than 40 and 70 days, respectively. The uptake of fluorescein-loaded PLGA MPs by the RAW 264.7 macrophage cell line was evidenced by flow cytometry, fluorescence microscopy and confocal microscopy. CXB-loaded PLGA MPs did not produce cytotoxicity at the concentrations assayed. The anti-inflammatory activity of CXB (encapsulated and in solution) was evaluated by determining the IL-1, IL-6 and TNF-α levels at 24 h and 72 h in RAW 264.7 macrophages, resulting in a higher degree of reduction in the expression of inflammatory mediators for CXB in solution. A potent degree of gene expression reduction was obtained with the developed CXB-loaded MPs.
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Khan S, Fakhar Z, Hussain A, Ahmad A, Jairajpuri DS, Alajmi MF, Hassan MI. Structure-based identification of potential SARS-CoV-2 main protease inhibitors. J Biomol Struct Dyn 2022; 40:3595-3608. [PMID: 33210561 PMCID: PMC7682383 DOI: 10.1080/07391102.2020.1848634] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 11/04/2020] [Indexed: 01/09/2023]
Abstract
To address coronavirus disease (COVID-19), currently, no effective drug or vaccine is available. In this regard, molecular modeling approaches are highly useful to discover potential inhibitors of the main protease (Mpro) enzyme of SARS-CoV-2. Since, the Mpro enzyme plays key roles in mediating viral replication and transcription; therefore, it is considered as an attractive drug target to control SARS-CoV-2 infection. By using structure-based drug design, pharmacophore modeling, and virtual high throughput drug screening combined with docking and all-atom molecular dynamics simulation approach, we have identified five potential inhibitors of SARS-CoV-2 Mpro. MD simulation studies revealed that compound 54035018 binds to the Mpro with high affinity (ΔGbind -37.40 kcal/mol), and the complex is more stable in comparison with other protein-ligand complexes. We have identified promising leads to fight COVID-19 infection as these compounds fulfill all drug-likeness properties. However, experimental and clinical validations are required for COVID-19 therapy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shama Khan
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Zeynab Fakhar
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg, South Africa
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Aijaz Ahmad
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- National Health Laboratory Service, Infection Control, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Deeba Shamim Jairajpuri
- Department of Medical Biochemistry, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Bahrain
| | - Mohamed F. Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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Calcuttawala F. Nutrition as a key to boost immunity against COVID-19. Clin Nutr ESPEN 2022; 49:17-23. [PMID: 35623808 PMCID: PMC9012504 DOI: 10.1016/j.clnesp.2022.04.007] [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: 10/20/2021] [Revised: 03/20/2022] [Accepted: 04/08/2022] [Indexed: 11/16/2022]
Abstract
The Coronavirus-disease 2019 (COVID-19) was declared as a global pandemic on March 11, 2020 by the World Health Organization. Since then, the scientific community has been actively engaged in developing a vaccine against the dreaded disease. Considerable research has also been performed for drugs that can directly interfere with the viral replication pathway. However, the production of these vaccines and drugs demands a lot of time and effort which is undesirable considering the pace at which the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is spreading across the continents. For this reason, the possible role of dietary nutrients in reducing the risk of SARS-CoV-2 infection as well as mitigating the symptoms, may be explored. These natural substances are readily available, have negligible side effects and confer several benefits to the immune system. Macronutrients like proteins are vital for antibody production. Dietary constituents such as omega-3-fatty acids, vitamin C, vitamin E, phytochemicals such as carotenoids and polyphenols exhibit anti-inflammatory and antioxidant properties. This review highlights the significance of relevant nutrients in boosting the immune system.
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Jung BK, An YH, Jang JJ, Jeon JH, Jang SH, Jang H. The human ACE-2 receptor binding domain of SARS-CoV-2 express on the viral surface of the Newcastle disease virus as a non-replicating viral vector vaccine candidate. PLoS One 2022; 17:e0263684. [PMID: 35134091 PMCID: PMC8824364 DOI: 10.1371/journal.pone.0263684] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 01/24/2022] [Indexed: 12/24/2022] Open
Abstract
Since the SARS-CoV-2 infection was identified in December 2019, SARS-CoV-2 infection has rapidly spread worldwide and has become a significant pandemic disease. In addition, human death and serious health problem caused by SARS-CoV-2 infection, the socio-economic impact has been very serious. Here, we describe the development of the viral vector vaccine, which is the receptor-binding domain (RBD) of SARS-CoV-2 expressed on the surface of Newcastle disease virus (LVP-K1-RBD19). The RBD protein concentrations on the viral surface were measured by the sandwich ELISA method. 106.7 TCID50/ml of LVP-K1-RBD19 has a 0.17 μg of RBD protein. Optical density (OD) values of mouse sera inoculated with 10 μg of RBD protein expressed on the surface of LVP-K1-RBD19 generated 1.78-fold higher RBD-specific antibody titers than mice inoculated with 10 μg RBD protein with alum at 28 dpi. Moreover, mice inoculated with 10 μg of RBD protein expressed on the surface of LVP-K1-RBD19 virus showed more than 80% neutralization at 1:256 against the SARS-CoV-2 pseudovirus. These results demonstrated that inactivated LVP-K1-RBD19 virus produces neutralizing antibodies against SARS-CoV-2 in a short period and could be elect protective immunity in humans and LVP-K1-RBD19 will be a good candidate for the COVID-19 vaccine.
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Affiliation(s)
| | - Yong Hee An
- Libentech Co. LTD, Daejeon, Republic of Korea
| | - Jin-Ju Jang
- Libentech Co. LTD, Daejeon, Republic of Korea
| | | | - Sung Hoon Jang
- Department of Biological Sciences, College of Natural Sciences, Inha University, Incheon, Republic of Korea
| | - Hyun Jang
- Libentech Co. LTD, Daejeon, Republic of Korea
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Cao J, Liu Y, Zhou M, Dong S, Hou Y, Jia X, Lan X, Zhang Y, Guo J, Xiao G, Wang W. Screening of Botanical Drugs against SARS-CoV-2 Entry Reveals Novel Therapeutic Agents to Treat COVID-19. Viruses 2022; 14:v14020353. [PMID: 35215943 PMCID: PMC8877376 DOI: 10.3390/v14020353] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/02/2022] [Accepted: 02/05/2022] [Indexed: 01/27/2023] Open
Abstract
An escalating pandemic caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has severely impacted global health. There is a severe lack of specific treatment options for diseases caused by SARS-CoV-2. In this study, we used a pseudotype virus (pv) containing the SARS-CoV-2 S glycoprotein to screen a botanical drug library containing 1037 botanical drugs to identify agents that prevent SARS-CoV-2 entry into the cell. Our study identified four hits, including angeloylgomisin O, schisandrin B, procyanidin, and oleanonic acid, as effective SARS-CoV-2 S pv entry inhibitors in the micromolar range. A mechanistic study revealed that these four agents inhibited SARS-CoV-2 S pv entry by blocking spike (S) protein-mediated membrane fusion. Furthermore, angeloylgomisin O and schisandrin B inhibited authentic SARS-CoV-2 with a high selective index (SI; 50% cytotoxic concentration/50% inhibition concentration). Our drug combination studies performed in cellular antiviral assays revealed that angeloylgomisin O has synergistic effects in combination with remdesivir, a drug widely used to treat SARS-CoV-2-mediated infections. We also showed that two hits could inhibit the newly emerged alpha (B.1.1.7) and beta (B.1.351) variants. Our findings collectively indicate that angeloylgomisin O and schisandrin B could inhibit SARS-CoV-2 efficiently, thereby making them potential therapeutic agents to treat the coronavirus disease of 2019.
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Affiliation(s)
- Junyuan Cao
- State Key Laboratory of Virology, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (J.C.); (Y.L.); (M.Z.); (S.D.); (Y.H.); (X.J.); (X.L.); (Y.Z.); (J.G.); (G.X.)
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Liu
- State Key Laboratory of Virology, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (J.C.); (Y.L.); (M.Z.); (S.D.); (Y.H.); (X.J.); (X.L.); (Y.Z.); (J.G.); (G.X.)
| | - Minmin Zhou
- State Key Laboratory of Virology, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (J.C.); (Y.L.); (M.Z.); (S.D.); (Y.H.); (X.J.); (X.L.); (Y.Z.); (J.G.); (G.X.)
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Siqi Dong
- State Key Laboratory of Virology, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (J.C.); (Y.L.); (M.Z.); (S.D.); (Y.H.); (X.J.); (X.L.); (Y.Z.); (J.G.); (G.X.)
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yuxia Hou
- State Key Laboratory of Virology, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (J.C.); (Y.L.); (M.Z.); (S.D.); (Y.H.); (X.J.); (X.L.); (Y.Z.); (J.G.); (G.X.)
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoying Jia
- State Key Laboratory of Virology, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (J.C.); (Y.L.); (M.Z.); (S.D.); (Y.H.); (X.J.); (X.L.); (Y.Z.); (J.G.); (G.X.)
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaohao Lan
- State Key Laboratory of Virology, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (J.C.); (Y.L.); (M.Z.); (S.D.); (Y.H.); (X.J.); (X.L.); (Y.Z.); (J.G.); (G.X.)
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin 300071, China
| | - Yueli Zhang
- State Key Laboratory of Virology, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (J.C.); (Y.L.); (M.Z.); (S.D.); (Y.H.); (X.J.); (X.L.); (Y.Z.); (J.G.); (G.X.)
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin 300071, China
| | - Jiao Guo
- State Key Laboratory of Virology, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (J.C.); (Y.L.); (M.Z.); (S.D.); (Y.H.); (X.J.); (X.L.); (Y.Z.); (J.G.); (G.X.)
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Gengfu Xiao
- State Key Laboratory of Virology, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (J.C.); (Y.L.); (M.Z.); (S.D.); (Y.H.); (X.J.); (X.L.); (Y.Z.); (J.G.); (G.X.)
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Wang
- State Key Laboratory of Virology, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (J.C.); (Y.L.); (M.Z.); (S.D.); (Y.H.); (X.J.); (X.L.); (Y.Z.); (J.G.); (G.X.)
- University of the Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: ; Tel.: +86-87198232
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25
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Agoston DV. COVID-19 and Traumatic Brain Injury (TBI); What We Can Learn From the Viral Pandemic to Better Understand the Biology of TBI, Improve Diagnostics and Develop Evidence-Based Treatments. Front Neurol 2021; 12:752937. [PMID: 34987462 PMCID: PMC8720751 DOI: 10.3389/fneur.2021.752937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 12/01/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Denes V. Agoston
- Department of Anatomy, Physiology and Genetics, Uniformed Services University, Bethesda, MD, United States
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Khanali J, Azangou-Khyavy M, Asaadi Y, Jamalkhah M, Kiani J. Nucleic Acid-Based Treatments Against COVID-19: Potential Efficacy of Aptamers and siRNAs. Front Microbiol 2021; 12:758948. [PMID: 34858370 PMCID: PMC8630580 DOI: 10.3389/fmicb.2021.758948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 10/19/2021] [Indexed: 01/10/2023] Open
Abstract
Despite significant efforts, there are currently no approved treatments for COVID-19. However, biotechnological approaches appear to be promising in the treatment of the disease. Accordingly, nucleic acid-based treatments including aptamers and siRNAs are candidates that might be effective in COVID-19 treatment. Aptamers can hamper entry and replication stages of the SARS-CoV-2 infection, while siRNAs can cleave the viral genomic and subgenomic RNAs to inhibit the viral life cycle and reduce viral loads. As a conjugated molecule, aptamer–siRNA chimeras have proven to be dual-functioning antiviral therapy, acting both as virus-neutralizing and replication-interfering agents as well as being a siRNA targeted delivery approach. Previous successful applications of these compounds against various stages of the pathogenesis of diseases and viral infections, besides their advantages over other alternatives, might provide sufficient rationale for the application of these nucleic acid-based drugs against the SARS-CoV-2. However, none of them are devoid of limitations. Here, the literature was reviewed to assess the plausibility of using aptamers, siRNAs, and aptamer–siRNA chimeras against the SARS-CoV-2 based on their previously established effectiveness, and discussing challenges lie in applying these molecules.
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Affiliation(s)
- Javad Khanali
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Yasaman Asaadi
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Monire Jamalkhah
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Jafar Kiani
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
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SARS-CoV-2, Zika viruses and mycoplasma: Structure, pathogenesis and some treatment options in these emerging viral and bacterial infectious diseases. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166264. [PMID: 34481867 PMCID: PMC8413106 DOI: 10.1016/j.bbadis.2021.166264] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 07/22/2021] [Accepted: 08/30/2021] [Indexed: 01/28/2023]
Abstract
The molecular evolution of life on earth along with changing environmental, conditions has rendered mankind susceptible to endemic and pandemic emerging infectious diseases. The effects of certain systemic viral and bacterial infections on morbidity and mortality are considered as examples of recent emerging infections. Here we will focus on three examples of infections that are important in pregnancy and early childhood: SARS-CoV-2 virus, Zika virus, and Mycoplasma species. The basic structural characteristics of these infectious agents will be examined, along with their general pathogenic mechanisms. Coronavirus infections, such as caused by the SARS-CoV-2 virus, likely evolved from zoonotic bat viruses to infect humans and cause a pandemic that has been the biggest challenge for humanity since the Spanish Flu pandemic of the early 20th century. In contrast, Zika Virus infections represent an expanding infectious threat in the context of global climate change. The relationship of these infections to pregnancy, the vertical transmission and neurological sequels make these viruses highly relevant to the topics of this special issue. Finally, mycoplasmal infections have been present before mankind evolved, but they were rarely identified as human pathogens until recently, and they are now recognized as important coinfections that are able to modify the course and prognosis of various infectious diseases and other chronic illnesses. The infectious processes caused by these intracellular microorganisms are examined as well as some general aspects of their pathogeneses, clinical presentations, and diagnoses. We will finally consider examples of treatments that have been used to reduce morbidity and mortality of these infections and discuss briefly the current status of vaccines, in particular, against the SARS-CoV-2 virus. It is important to understand some of the basic features of these emerging infectious diseases and the pathogens involved in order to better appreciate the contributions of this special issue on how infectious diseases can affect human pregnancy, fetuses and neonates.
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Gül Ş. In silico drug repositioning against human NRP1 to block SARS-CoV-2 host entry. Turk J Biol 2021; 45:442-458. [PMID: 34803446 PMCID: PMC8573850 DOI: 10.3906/biy-2012-52] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 05/08/2021] [Indexed: 12/21/2022] Open
Abstract
Despite COVID-19 turned into a pandemic, no approved drug for the treatment or globally available vaccine is out yet. In such a global emergency, drug repurposing approach that bypasses a costly and long-time demanding drug discovery process is an effective way in search of finding drugs for the COVID-19 treatment. Recent studies showed that SARS-CoV-2 uses neuropilin-1 (NRP1) for host entry. Here we took advantage of structural information of the NRP1 in complex with C-terminal of spike (S) protein of SARS-CoV-2 to identify drugs that may inhibit NRP1 and S protein interaction. U.S. Food and Drug Administration (FDA) approved drugs were screened using docking simulations. Among top drugs, well-tolerated drugs were selected for further analysis. Molecular dynamics (MD) simulations of drugs-NRP1 complexes were run for 100 ns to assess the persistency of binding. MM/GBSA calculations from MD simulations showed that eltrombopag, glimepiride, sitagliptin, dutasteride, and ergotamine stably and strongly bind to NRP1. In silico Alanine scanning analysis revealed that Tyr297, Trp301, and Tyr353 amino acids of NRP1 are critical for drug binding. Validating the effect of drugs analyzed in this paper by experimental studies and clinical trials will expedite the drug discovery process for COVID-19.
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Affiliation(s)
- Şeref Gül
- Department of Chemical and Biological Engineering, Koç University, İstanbul Turkey.,Biotechnology Division, Department of Biology, Faculty of Science, İstanbul University, İstanbul Turkey
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Feng F, Chen J, Zhao J, Li Y, Li M, Sun C. Killing Two Birds with One Stone by Administration of Soluble ACE2: A Promising Strategy to Treat Both Cardiovascular Diseases and SARS-CoV-2 Infection. Viruses 2021; 13:2243. [PMID: 34835049 PMCID: PMC8622942 DOI: 10.3390/v13112243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 10/31/2021] [Accepted: 11/02/2021] [Indexed: 12/19/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters host cells mainly by the angiotensin converting enzyme 2 (ACE2) receptor, which can recognize the spike (S) protein by its extracellular domain. Previously, recombinant soluble ACE2 (sACE2) has been clinically used as a therapeutic treatment for cardiovascular diseases. Recent data demonstrated that sACE2 can also be exploited as a decoy to effectively inhibit the cell entry of SARS-CoV-2, through blocking SARS-CoV-2 binding to membrane-anchored ACE2. In this study, we summarized the current findings on the optimized sACE2-based strategies as a therapeutic agent, including Fc fusion to prolong the half-life of sACE2, deep mutagenesis to create high-affinity decoys for SARS-CoV-2, or designing the truncated functional fragments to enhance its safety, among others. Considering that COVID-19 patients are often accompanied by manifestations of cardiovascular complications, we think that administration of sACE2 in COVID-19 patients may be a promising therapeutic strategy to simultaneously treat both cardiovascular diseases and SARS-CoV-2 infection. This review would provide insights for the development of novel therapeutic agents against the COVID-19 pandemic.
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Affiliation(s)
- Fengling Feng
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (F.F.); (J.C.); (J.Z.); (Y.L.); (M.L.)
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou 510080, China
| | - Jiaoshan Chen
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (F.F.); (J.C.); (J.Z.); (Y.L.); (M.L.)
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou 510080, China
| | - Jin Zhao
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (F.F.); (J.C.); (J.Z.); (Y.L.); (M.L.)
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou 510080, China
| | - Yanjun Li
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (F.F.); (J.C.); (J.Z.); (Y.L.); (M.L.)
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou 510080, China
| | - Minchao Li
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (F.F.); (J.C.); (J.Z.); (Y.L.); (M.L.)
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou 510080, China
| | - Caijun Sun
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (F.F.); (J.C.); (J.Z.); (Y.L.); (M.L.)
- Key Laboratory of Tropical Disease Control, Sun Yat-sen University, Ministry of Education, Guangzhou 510080, China
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Yoo JH. Antivirals for Coexistence with COVID-19: Brief Review for General Physicians. J Korean Med Sci 2021; 36:e298. [PMID: 34725982 PMCID: PMC8560319 DOI: 10.3346/jkms.2021.36.e298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 11/20/2022] Open
Abstract
In order to end the coronavirus disease 2019 (COVID-19) pandemic that has lasted for nearly two years, it is most necessary to introduce antiviral drugs specific to COVID-19 along with the establishment of herd immunity by vaccination. Candidates currently being studied include nucleoside analogues that inhibit replication, protease inhibitors, and entry blockers. Not only the virus itself, but also the host protein that the virus uses in its pathogenesis is the target of treatment. Although the severe acute respiratory syndrome coronavirus 2 will not be completely eradicated, if the use of antiviral drugs is established, the COVID-19 pandemic will end through coexistence with the virus.
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Affiliation(s)
- Jin-Hong Yoo
- Division of Infectious Diseases, Department of Internal Medicine, Bucheon St. Mary's Hospital, Bucheon, Korea
- Division of Infectious Diseases, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.
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Daverey A, Dutta K, Joshi S, Daverey A. Sophorolipid: A glycolipid biosurfactant as a potential therapeutic agent against COVID-19. Bioengineered 2021; 12:9550-9560. [PMID: 34709115 PMCID: PMC8810061 DOI: 10.1080/21655979.2021.1997261] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Biosurfactants are natural surfactants produced by a variety of microorganisms. In recent years, biosurfactants have garnered a lot of interest due to their biomedical and pharmaceutical applications. Sophorolipids are glycolipids types of biosurfactants produced by selected non-pathogenic yeasts. In addition to the detergent activity (reduction in surface and interfacial tension), which is commonly utilized by biomedical applications, sophorolipids have shown some unique properties such as, antiviral activity against enveloped viruses, immunomodulation, and anticancer activity. Considering their antiviral activity, the potential of sophorolipids as an antiviral therapy for the treatment of COVID-19 is discussed in this review. Being a surfactant molecule, sophorolipid could solubilize the lipid envelope of SARS-CoV-2 and inactivate it. As an immunomodulator, sophorolipid could attenuate the cytokine storm caused by the SARS-CoV-2 upon infection, and inhibit the progression of COVID-19 in patients. Sophorolipids could also be used as an effective treatment strategy for COVID-19 patients suffering from cancer. However, there is limited research on the use of sophorolipid as a therapeutic agent for the treatment of cancer and viral diseases, and to modulate the immune response. Nevertheless, the multitasking capabilities of sophorolipids make them potential therapeutic candidates for the bench-to-bedside research for the treatment of COVID-19.
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Affiliation(s)
- Amita Daverey
- Department of Neurosurgery, University of Nebraska Medical Center, Omaha, Nebraska - NE 68198-7690, USA
| | - Kasturi Dutta
- Department of Biotechnology and Medical Engineering, National Institute of Technology, Rourkela, Odisha - 769008, India
| | - Sanket Joshi
- Oil & Gas Research Center, Central Analytical and Applied Research Unit, Sultan Qaboos University, Muscat, Oman
| | - Achlesh Daverey
- School of Environment and Natural Resources, Doon University, Dehradun, Uttarakhand, 248012, India.,School of Biological Sciences, Doon University, Dehradun, Uttarakhand, 248012, India
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YILMAZ ZK, ŞENCAN N. An Examination of the Factors Affecting Community Pharmacists' Knowledge, Attitudes, and Impressions About the COVID-19 Pandemic. Turk J Pharm Sci 2021; 18:530-540. [PMID: 34708643 PMCID: PMC8562124 DOI: 10.4274/tjps.galenos.2020.01212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 12/07/2020] [Indexed: 12/01/2022]
Abstract
Objectives Coronavirus disease-2019 (COVID-19)-related cases and deaths are ongoing throughout the world, but there is still no effective drug in its treatment, and the vaccine supply is not adequate for the global population. It is important that pharmacists have sufficient knowledge and awareness to prevent and control the disease. COVID-19 has been widely covered in the media, which has been a source widely used by healthcare professionals. This study aimed to assess the knowledge, attitudes, and impressions of community pharmacists about COVID-19 and the factors affecting them. Materials and Methods The questions in this survey were formed using the guideline created by the World Health Organization, a guide composed by the Turkish COVID-19 Scholarly Commission, and data disclosed to the public on the website of the Ministry of Health. The questionnaire was designed with Google forms and then applied to community pharmacists all over Turkey by sharing the survey link. Results Analyses of 393 questionnaires showed that Ministry of Health/government statements, the internet (scientific sources), and the media were the preferred sources of information (96.7%, 89.6%, and 84%, respectively). “Ways to avoid COVID-19” was the most searched title (96.9%). It was determined that the names of the two drugs most frequently mentioned by the participants to be used in the treatment of COVID-19 in Turkey were hydroxychloroquine and azithromycin (57.5%; 50.1%, respectively). Participants who received information from the media gave less education to patients/customers on personal protection measures against COVID-19 (83.3%) and symptoms of COVID-19 (78.8%); however, their behavior regarding the training of pharmacy personnel was found to be the opposite. It has been determined that about half of the participants (46.6%) mostly trust the Ministry of Health regarding the COVID-19 pandemic. Conclusion Media and other sources influence the knowledge, behavior and impressions of pharmacists’. Having a high level of knowledge positively affects people’s behavior. It is important for pharmacists to have accurate information about COVID-19 and to transfer their knowledge to the community to provide patient education and to prevent/control the spread of COVID-19.
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Affiliation(s)
- Zekiye Kübra YILMAZ
- Acıbadem Mehmet Ali Aydınlar University Faculty of Pharmacy, Department of Clinical Pharmacy, İstanbul, Turkey
| | - Nazlı ŞENCAN
- Acıbadem Mehmet Ali Aydınlar University Faculty of Pharmacy, Department of Pharmacy Management, İstanbul, Turkey
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Kleandrova VV, Scotti MT, Speck-Planche A. Indirect-Acting Pan-Antivirals vs. Respiratory Viruses: A Fresh Perspective on Computational Multi-Target Drug Discovery. Curr Top Med Chem 2021; 21:2687-2693. [PMID: 34636311 DOI: 10.2174/1568026621666211012110819] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/23/2021] [Accepted: 09/23/2021] [Indexed: 12/22/2022]
Abstract
Respiratory viruses continue to afflict mankind. Among them, pathogens such as coronaviruses [including the current pandemic agent known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)] and the one causing influenza A (IAV) are highly contagious and deadly. These can evade the immune system defenses while causing a hyperinflammatory response that can damage different tissues/organs. Simultaneously targeting immunomodulatory proteins is a plausible antiviral strategy since it could lead to the discovery of indirect-acting pan-antiviral (IAPA) agents for the treatment of diseases caused by respiratory viruses. In this context, computational approaches, which are an essential part of the modern drug discovery campaigns, could accelerate the identification of multi-target immunomodulators. This perspective discusses the usefulness of computational multi-target drug discovery for the virtual screening (drug repurposing) of IAPA agents capable of boosting the immune system through the activation of the toll-like receptor 7 (TLR7) and/or the stimulator of interferon genes (STING) while inhibiting key pro-inflammatory proteins, such as caspase-1 and tumor necrosis factor-alpha (TNF-α).
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Affiliation(s)
- Valeria V Kleandrova
- Laboratory of Fundamental and Applied Research of Quality and Technology of Food Production, Moscow State University of Food Production, Volokolamskoe shosse 11, 125080, Moscow. Russian Federation
| | - Marcus T Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, 58051-900, João Pessoa. Brazil
| | - Alejandro Speck-Planche
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, 58051-900, João Pessoa. Brazil
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Algethami FK, Cherif M, Jlizi S, Ben Hamadi N, Romdhane A, Elamin MR, Alghamdi MA, Ben Jannet H. Design, Microwave-Assisted Synthesis and In Silico Prediction Study of Novel Isoxazole Linked Pyranopyrimidinone Conjugates as New Targets for Searching Potential Anti-SARS-CoV-2 Agents. Molecules 2021; 26:molecules26206103. [PMID: 34684683 PMCID: PMC8537412 DOI: 10.3390/molecules26206103] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/27/2021] [Accepted: 10/06/2021] [Indexed: 11/25/2022] Open
Abstract
A series of novel naphthopyrano[2,3-d]pyrimidin-11(12H)-one containing isoxazole nucleus 4 was synthesized under microwave irradiation and classical conditions in moderate to excellent yields upon 1,3-dipolar cycloaddition reaction using various arylnitrile oxides under copper(I) catalyst. A one-pot, three-component reaction, N-propargylation and Dimroth rearrangement were used as the key steps for the preparation of the dipolarophiles3. The structures of the synthesized compounds were established by 1H NMR, 13C NMR and HRMS-ES means. The present study aims to also predict the theoretical assembly of the COVID-19 protease (SARS-CoV-2 Mpro) and to discover in advance whether this protein can be targeted by the compounds 4a–1 and thus be synthesized. The docking scores of these compounds were compared to those of the co-crystallized native ligand inhibitor (N3) which was used as a reference standard. The results showed that all the synthesized compounds (4a–l) gave interesting binding scores compared to those of N3 inhibitor. It was found that compounds 4a, 4e and 4i achieved greatly similar binding scores and modes of interaction than N3, indicating promising affinity towards SARS-CoV-2 Mpro. On the other hand, the derivatives 4k, 4h and 4j showed binding energy scores (−8.9, −8.5 and −8.4 kcal/mol, respectively) higher than the Mpro N3 inhibitor (−7.0 kcal/mol), revealing, in their turn, a strong interaction with the target protease, although their interactions were not entirely comparable to that of the reference N3.
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Affiliation(s)
- Faisal K. Algethami
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11432, Saudi Arabia; (N.B.H.); (M.R.E.); (M.A.A.)
- Correspondence: (F.K.A.); (H.B.J.)
| | - Maher Cherif
- Laboratory of Heterocyclic Chemistry, Natural Products and Reactivity (LR11ES39), Medicinal Chemistry and Natural Products Team, Faculty of Science of Monastir, University of Monastir, Avenue of Environment, Monastir 5019, Tunisia; (M.C.); (S.J.); (A.R.)
| | - Salma Jlizi
- Laboratory of Heterocyclic Chemistry, Natural Products and Reactivity (LR11ES39), Medicinal Chemistry and Natural Products Team, Faculty of Science of Monastir, University of Monastir, Avenue of Environment, Monastir 5019, Tunisia; (M.C.); (S.J.); (A.R.)
| | - Naoufel Ben Hamadi
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11432, Saudi Arabia; (N.B.H.); (M.R.E.); (M.A.A.)
- Laboratory of Heterocyclic Chemistry, Natural Products and Reactivity (LR11ES39), Medicinal Chemistry and Natural Products Team, Faculty of Science of Monastir, University of Monastir, Avenue of Environment, Monastir 5019, Tunisia; (M.C.); (S.J.); (A.R.)
| | - Anis Romdhane
- Laboratory of Heterocyclic Chemistry, Natural Products and Reactivity (LR11ES39), Medicinal Chemistry and Natural Products Team, Faculty of Science of Monastir, University of Monastir, Avenue of Environment, Monastir 5019, Tunisia; (M.C.); (S.J.); (A.R.)
| | - Mohamed R. Elamin
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11432, Saudi Arabia; (N.B.H.); (M.R.E.); (M.A.A.)
| | - Mashael A. Alghamdi
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11432, Saudi Arabia; (N.B.H.); (M.R.E.); (M.A.A.)
| | - Hichem Ben Jannet
- Laboratory of Heterocyclic Chemistry, Natural Products and Reactivity (LR11ES39), Medicinal Chemistry and Natural Products Team, Faculty of Science of Monastir, University of Monastir, Avenue of Environment, Monastir 5019, Tunisia; (M.C.); (S.J.); (A.R.)
- Correspondence: (F.K.A.); (H.B.J.)
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Gul S, Ozcan O, Asar S, Okyar A, Barıs I, Kavakli IH. In silico identification of widely used and well-tolerated drugs as potential SARS-CoV-2 3C-like protease and viral RNA-dependent RNA polymerase inhibitors for direct use in clinical trials. J Biomol Struct Dyn 2021; 39:6772-6791. [PMID: 32752938 PMCID: PMC7484590 DOI: 10.1080/07391102.2020.1802346] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/22/2020] [Indexed: 12/14/2022]
Abstract
Despite strict measures taken by many countries, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to be an issue of global concern. Currently, there are no clinically proven pharmacotherapies for coronavirus disease 2019, despite promising initial results obtained from drugs such as azithromycin and hydroxychloroquine. Therefore, the repurposing of clinically approved drugs for use against SARS-CoV-2 has become a viable strategy. Here, we searched for drugs that target SARS-CoV-2 3C-like protease (3CLpro) and viral RNA-dependent RNA polymerase (RdRp) by in silico screening of the U.S. Food and Drug Administration approved drug library. Well-tolerated and widely used drugs were selected for molecular dynamics (MD) simulations to evaluate drug-protein interactions and their persistence under physiological conditions. Tetracycline, dihydroergotamine, ergotamine, dutasteride, nelfinavir, and paliperidone formed stable interactions with 3CLpro based on MD simulation results. Similar analysis with RdRp showed that eltrombopag, tipranavir, ergotamine, and conivaptan bound to the enzyme with high binding free energies. Docking results suggest that ergotamine, dihydroergotamine, bromocriptine, dutasteride, conivaptan, paliperidone, and tipranavir can bind to both enzymes with high affinity. As these drugs are well tolerated, cost-effective, and widely used, our study suggests that they could potentially to be used in clinical trials for the treatment of SARS-CoV-2-infected patients.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Seref Gul
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
| | - Onur Ozcan
- Department of Molecular Biology and Genetics, Koc University, Istanbul, Turkey
| | - Sinan Asar
- Department of Anesthesiology and Reanimation, Bakırköy Dr. Sadi Konuk Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Alper Okyar
- Department of Pharmacology, Istanbul University Faculty of Pharmacy, Istanbul, Turkey
| | - Ibrahim Barıs
- Department of Molecular Biology and Genetics, Koc University, Istanbul, Turkey
| | - Ibrahim Halil Kavakli
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
- Department of Molecular Biology and Genetics, Koc University, Istanbul, Turkey
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Batista CM, Foti L. Anti-SARS-CoV-2 and anti-cytokine storm neutralizing antibody therapies against COVID-19: Update, challenges, and perspectives. Int Immunopharmacol 2021; 99:108036. [PMID: 34371330 PMCID: PMC8330556 DOI: 10.1016/j.intimp.2021.108036] [Citation(s) in RCA: 6] [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: 06/24/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 12/15/2022]
Abstract
Coronavirus disease 2019 (COVID-19) has been declared by the World Health Organization (WHO) as a pandemic since March 2020. This disease is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The only available tools to avoid contamination and transmission of this virus are physical distancing, the use of N95 and surgical masks, and hand hygiene. Vaccines are another essential tool to reduce the impact of the pandemic, though these present challenges in terms of production and logistics, particularly in underdeveloped and developing countries. One of the critical early research findings is the interaction of the spike virus protein with the angiotensin-converting enzyme 2 (ACE2) human receptor. Developing strategies to block this interaction has therefore been identified as a way to treat this infection. Neutralizing antibodies (nAbs) have emerged as a therapeutic approach since the pandemic started. Infected patients may be asymptomatic or present with mild symptoms, and others may evolve to moderate or severe disease, leading to death. An immunological phenomenon known as cytokine storm has been observed in patients with severe disease characterized by a proinflammatory cytokine cascade response that leads to lung injury. Thus, some treatment strategies focus on anti-cytokine storm nAbs. This review summarizes the latest advances in research and clinical trials, challenges, and perspectives on antibody-based treatments (ABT) as therapies against COVID-19.
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Affiliation(s)
| | - Leonardo Foti
- Laboratory of Trypanosomatids Molecular and Systemic Biology, Brazil.
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Guo L, Yao Z, Yang L, Zhang H, Qi Y, Gou L, Xi W, Liu D, Zhang L, Cheng Y, Wang X, Rong M, Chen H, Kong MG. Plasma-activated water: An alternative disinfectant for S protein inactivation to prevent SARS-CoV-2 infection. CHEMICAL ENGINEERING JOURNAL (LAUSANNE, SWITZERLAND : 1996) 2021; 421:127742. [PMID: 33235538 PMCID: PMC7677677 DOI: 10.1016/j.cej.2020.127742] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/24/2020] [Accepted: 11/04/2020] [Indexed: 05/03/2023]
Abstract
SARS-CoV-2 is a highly contagious virus and is causing a global pandemic. SARS-CoV-2 infection depends on the recognition of and binding to the cellular receptor human angiotensin-converting enzyme 2 (hACE2) through the receptor-binding domain (RBD) of the spike protein, and disruption of this process can effectively inhibit SARS-CoV-2 invasion. Plasma-activated water efficiently inactivates bacteria and bacteriophages by causing damage to biological macromolecules, but its effect on coronavirus has not been reported. In this study, pseudoviruses with the SARS-CoV-2 S protein were used as a model, and plasma-activated water (PAW) effectively inhibited pseudovirus infection through S protein inactivation. The RBD was used to study the molecular details, and the RBD binding activity was inactivated by plasma-activated water through the RBD modification. The short-lived reactive species in the PAW, such as ONOO-, played crucial roles in this inactivation. Plasma-activated water after room-temperature storage of 30 days remained capable of significantly reducing the RBD binding with hACE2. Together, our findings provide evidence of a potent disinfection strategy to combat the epidemic caused by SARS-CoV-2.
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Affiliation(s)
- Li Guo
- State Key Laboratory of Electrical Insulation and Power Equipment, Center for Plasma Biomedicine, Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Zhiqian Yao
- State Key Laboratory of Electrical Insulation and Power Equipment, Center for Plasma Biomedicine, Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Lu Yang
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Hao Zhang
- State Key Laboratory of Electrical Insulation and Power Equipment, Center for Plasma Biomedicine, Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Yu Qi
- State Key Laboratory of Electrical Insulation and Power Equipment, Center for Plasma Biomedicine, Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Lu Gou
- School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Wang Xi
- State Key Laboratory of Electrical Insulation and Power Equipment, Center for Plasma Biomedicine, Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Dingxin Liu
- State Key Laboratory of Electrical Insulation and Power Equipment, Center for Plasma Biomedicine, Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Lei Zhang
- School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Yilong Cheng
- School of Chemistry, Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Xiaohua Wang
- State Key Laboratory of Electrical Insulation and Power Equipment, Center for Plasma Biomedicine, Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Mingzhe Rong
- State Key Laboratory of Electrical Insulation and Power Equipment, Center for Plasma Biomedicine, Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Hailan Chen
- Frank Reidy Center for Bioelectrics, Old Dominion University, Norfolk, VA 23508, USA
| | - Michael G Kong
- Frank Reidy Center for Bioelectrics, Old Dominion University, Norfolk, VA 23508, USA
- Department of Electrical and Computer Engineering, Old Dominion University, Norfolk, VA 23529, USA
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Le Corre P, Loas G. Repurposing functional inhibitors of acid sphingomyelinase (fiasmas): an opportunity against SARS-CoV-2 infection? J Clin Pharm Ther 2021; 46:1213-1219. [PMID: 33645763 PMCID: PMC8014536 DOI: 10.1111/jcpt.13390] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 01/09/2021] [Accepted: 02/09/2021] [Indexed: 12/31/2022]
Abstract
WHAT IS KNOWN AND OBJECTIVE Infection by SARS-CoV-2, the virus responsible of COVID-19, is associated with limited treatment options. The purpose of this study was to evaluate the rationale for repurposing functional inhibitors of acid sphingomyelinase (FIASMAs), several of which are approved medicines, for the treatment of SAR-CoV-2 infections. COMMENT We propose and discuss the FIASMAs' lysosomotropism as a possible explanation for their observed in vitro activities against viruses, and more specifically against infections caused by coronaviruses such as SARS-CoV-2. Successful in vitro-to-in vivo translation of FIASMAs requires that their pharmacokinetics (dosing regimen and drug-drug interactions) are matched with viral kinetics. WHAT IS NEW AND CONCLUSION Drug repurposing to ensure rapid patient access to effective treatment has garnered much attention in this era of the COVID-19 pandemic. The observed lysosomotropic activity of small-molecule FIASMA compounds suggests that their repurposing as potential drugs against SARS-CoV-2 is promising.
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Affiliation(s)
- Pascal Le Corre
- Pôle PharmacieService Hospitalo‐Universitaire de PharmacieCHU de RennesRennesFrance
- Univ RennesCHU RennesInsermEHESP, Irset (Institut de recherche en santé environnement et travail) ‐ UMR_S 1085RennesFrance
- Laboratoire de Biopharmacie et Pharmacie CliniqueFaculté de PharmacieUniversité de Rennes 1RennesFrance
| | - Gwenolé Loas
- Department of PsychiatryHôpital ErasmeUniversité libre de Bruxelles (ULB)BrusselsBelgium
- Research Unit (ULB 266)Hôpital ErasmeUniversité libre de Bruxelles (ULB)BrusselsBelgium
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Mirza AZ. Multiplex NanoSPR Molecular Biosensor for Blood Cytokine Monitoring. Adv Pharm Bull 2021; 12:419-422. [PMID: 35935058 PMCID: PMC9348532 DOI: 10.34172/apb.2022.046] [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: 11/09/2020] [Revised: 04/01/2021] [Accepted: 09/27/2021] [Indexed: 11/09/2022] Open
Abstract
Cytokines, as protein biomarkers, have essential functions in the diagnosis, identification, and healing of a broad range of syndromes. For the specific and accurate monitoring of immune conditions, which change rapidly throughout the duration of disease, sophisticated sensors for detecting cytokines are essential and will assist in clinical testing and studies of various diseases. The present manuscript briefly discusses fundamental principles applied to the development of tools for cytokine detection and new biomarker development. The latest developments in the technologies for highly sensitive and multiplexed cytokine quantification, with current detection capabilities across a broad, vibrant array, are also discussed. Finally, nanomaterial-based cytokine sensors, currently considered new approaches, are presented from the perspective of optimizing the sensitivity and multiplexity of cytokine detection.
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Affiliation(s)
- Agha Zeeshan Mirza
- Chemistry Department, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
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Further validation of the efficacy of mesenchymal stem cell infusions for reducing mortality in COVID-19 patients with ARDS. NPJ Regen Med 2021; 6:53. [PMID: 34504110 PMCID: PMC8429629 DOI: 10.1038/s41536-021-00161-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 08/12/2021] [Indexed: 02/07/2023] Open
Abstract
Recent double-blind, randomized, controlled trials reported that human umbilical cord-derived mesenchymal stem cell (MSC) infusions in COVID-19 patients with acute respiratory distress syndrome (ARDS) could diminish cytokine storm and lung damage. While these outcomes are significant, additional phase II/III trials are required to validate the efficacy of MSCs to improve the survival of COVID-19 patients with ARDS. Future studies also need to assess the efficacy of MSCs to prevent long COVID.
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Muralidar S, Gopal G, Visaga Ambi S. Targeting the viral-entry facilitators of SARS-CoV-2 as a therapeutic strategy in COVID-19. J Med Virol 2021; 93:5260-5276. [PMID: 33851732 PMCID: PMC8251167 DOI: 10.1002/jmv.27019] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/27/2021] [Accepted: 04/12/2021] [Indexed: 12/13/2022]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19) infection, which has emerged as a global pandemic causing serious concerns. Lack of specific and effective therapeutics for the treatment of COVID-19 is a major concern and the development of vaccines is another important aspect in managing the infection effectively. The first step in the SARS-CoV-2 pathogenesis is the viral entry and it is mediated by its densely glycosylated spike protein (S-protein). Similar to the SARS-CoV, SARS-CoV-2 also engages angiotensin-converting enzyme 2 (ACE2) as the host cell entry receptor. In addition to ACE2, several recent studies have implicated the crucial role of cell surface heparan sulfate (HS) as a necessary assisting cofactor for ACE2-mediated SARS-CoV-2 entry. Furthermore, SARS-CoV-2 was also identified to use both endosomal cysteine proteases cathepsin B and L (CatB/L) and the transmembrane serine protease 2 (TMPRSS2) for the pivotal role of S-protein priming mediating viral entry. As the entry of SARS-CoV-2 into host cells is mandatory for viral infection, it becomes an extremely attractive therapeutic intervention point. In this regard, this review will focus on the therapeutic targeting of the crucial steps of SARS-CoV-2 viral entry like S-protein/ACE2 interaction and S-protein priming by host cell proteases. In addition, this review will also give insights to the readers on several therapeutic opportunities, pharmacological targeting of the viral-entry facilitators like S-Protein, ACE2, cell surface HS, TMPRSS2, and CatB/L and evidence for those drugs currently ongoing clinical studies.
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Affiliation(s)
- Shibi Muralidar
- Biopharmaceutical Research Lab, Anusandhan Kendra‐1SASTRA Deemed‐to‐be‐UniversityThanjavurTamil NaduIndia
- School of Chemical and BiotechnologySASTRA Deemed‐to‐be‐UniversityThanjavurTamil NaduIndia
| | - Gayathri Gopal
- Biopharmaceutical Research Lab, Anusandhan Kendra‐1SASTRA Deemed‐to‐be‐UniversityThanjavurTamil NaduIndia
- School of Chemical and BiotechnologySASTRA Deemed‐to‐be‐UniversityThanjavurTamil NaduIndia
| | - Senthil Visaga Ambi
- Biopharmaceutical Research Lab, Anusandhan Kendra‐1SASTRA Deemed‐to‐be‐UniversityThanjavurTamil NaduIndia
- School of Chemical and BiotechnologySASTRA Deemed‐to‐be‐UniversityThanjavurTamil NaduIndia
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Ayele AG, Enyew EF, Kifle ZD. Roles of existing drug and drug targets for COVID-19 management. Metabol Open 2021; 11:100103. [PMID: 34222852 PMCID: PMC8239316 DOI: 10.1016/j.metop.2021.100103] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 06/27/2021] [Indexed: 02/07/2023] Open
Abstract
In December 2019, a highly transmissible, pneumonia epidemic caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), erupted in China and other countries, resulting in devastation and health crisis worldwide currently. The search and using existing drugs support to curb the current highly contagious viral infection is spirally increasing since the pandemic began. This is based on these drugs had against other related RNA-viruses such as MERS-Cov, and SARS-Cov. Moreover, researchers are scrambling to identify novel drug targets and discover novel therapeutic options to vanquish the current pandemic. Since there is no definitive treatment to control Covid-19 vaccines are remain to be a lifeline. Currently, many vaccine candidates are being developed with most of them are reported to have positive results. Therapeutic targets such as helicases, transmembrane serine protease 2, cathepsin L, cyclin G-associated kinase, adaptor-associated kinase 1, two-pore channel, viral virulence factors, 3-chymotrypsin-like protease, suppression of excessive inflammatory response, inhibition of viral membrane, nucleocapsid, envelope, and accessory proteins, and inhibition of endocytosis were identified as a potential target against COVID-19 infection. This review also summarizes plant-based medicines for the treatment of COVID-19 such as saposhnikoviae divaricata, lonicerae japonicae flos, scutellaria baicalensis, lonicera japonicae, and some others. Thus, this review aimed to focus on the most promising therapeutic targets being repurposed against COVID-19 and viral elements that are used in COVID-19 vaccine candidates.
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Key Words
- 3CLpro, 3-chymotrypsin-like protease
- AAK1, adaptor-associated kinase 1
- ACE-2, Angiotensin-Converting Enzyme-2
- CEF, Cepharanthine
- COVID-19
- COVID-19, coronavirus disease-2019
- Existing drug
- GAK, cyclin G-associated kinase
- MERS-CoV, Middle East respiratory syndrome coronavirus
- Management
- Nsp, non-structure protein
- ORF, open reading frame
- PLpro, papain-like protease
- RdRp, RNA-dependence RNA-polymerase
- SARS-COV-2, severe acute respiratory syndrome coronavirus-2
- TMPRSS2, transmembrane Serine Protease 2
- TPC2, two-pore channel 2
- Therapeutic target
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Affiliation(s)
- Akeberegn Gorems Ayele
- Department of Pharmacology and Clinical Pharmacy, School of Pharmacy, College of Health Science, Addis Ababa University, Addis Ababa, Ethiopia
| | - Engidaw Fentahun Enyew
- Department of Human Anatomy, School of Medicine, College of Medicine and Health Sciences, Gondar, Ethiopia
| | - Zemene Demelash Kifle
- Department of Pharmacology, School of Pharmacy, College of Medicine and Health Science, University of Gondar, Gondar, Ethiopia
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Değirmenci MFK, Yalçındağ FN, Tugal-Tutkun İ. COVID-19 and the Use of Immunomodulatory Agents in Ophthalmology. Turk J Ophthalmol 2021; 51:231-242. [PMID: 34461710 PMCID: PMC8411289 DOI: 10.4274/tjo.galenos.2021.68252] [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] [Indexed: 12/01/2022] Open
Abstract
Immunomodulatory agents are often used in the systemic treatment of non-infectious uveitis. These drugs consist of corticosteroids, conventional immunosuppressives, and biological agents. As it is known that they suppress the immune system, the most important concern associated with immunomodulatory therapy (IMT) is the increased risk of infection. The World Health Organization declared COVID-19 a pandemic on 11 March 2020. Although severe acute respiratory distress syndrome secondary to SARS-CoV-2 infection may develop in all people, patients who receive IMT may be at higher risk in terms of both the transmission of the infection and more severe disease course. Therefore, guidelines on the management of patients receiving IMT due to uveitis during the pandemic are needed. In this review, we examined the immunomodulatory drugs used in the treatment of uveitis in terms of infectious complications and the data of patients who received IMT during the COVID-19 pandemic and discussed recommendations for the use of these drugs. According to the latest information, patients who receive IMT may continue their treatment as long as there are no disruptions in regular complete blood count (especially white blood cell count >4,000/μL) and liver and kidney function tests. Patients diagnosed with COVID-19 should be managed with a multidisciplinary approach.
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Affiliation(s)
| | - F Nilüfer Yalçındağ
- Ankara University Faculty of Medicine, Department of Ophthalmology, Ankara, Turkey
| | - İlknur Tugal-Tutkun
- İstanbul University, İstanbul Faculty of Medicine, Department of Ophthalmology, İstanbul, Turkey
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Naidoo D, Kar P, Roy A, Mutanda T, Bwapwa J, Sen A, Anandraj A. Structural Insight into the Binding of Cyanovirin-N with the Spike Glycoprotein, M pro and PL pro of SARS-CoV-2: Protein-Protein Interactions, Dynamics Simulations and Free Energy Calculations. Molecules 2021; 26:molecules26175114. [PMID: 34500548 PMCID: PMC8434238 DOI: 10.3390/molecules26175114] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/15/2021] [Accepted: 07/26/2021] [Indexed: 02/06/2023] Open
Abstract
The emergence of COVID-19 continues to pose severe threats to global public health. The pandemic has infected over 171 million people and claimed more than 3.5 million lives to date. We investigated the binding potential of antiviral cyanobacterial proteins including cyanovirin-N, scytovirin and phycocyanin with fundamental proteins involved in attachment and replication of SARS-CoV-2. Cyanovirin-N displayed the highest binding energy scores (−16.8 ± 0.02 kcal/mol, −12.3 ± 0.03 kcal/mol and −13.4 ± 0.02 kcal/mol, respectively) with the spike protein, the main protease (Mpro) and the papainlike protease (PLpro) of SARS-CoV-2. Cyanovirin-N was observed to interact with the crucial residues involved in the attachment of the human ACE2 receptor. Analysis of the binding affinities calculated employing the molecular mechanics-Poisson–Boltzmann surface area (MM-PBSA) approach revealed that all forms of energy, except the polar solvation energy, favourably contributed to the interactions of cyanovirin-N with the viral proteins. With particular emphasis on cyanovirin-N, the current work presents evidence for the potential inhibition of SARS-CoV-2 by cyanobacterial proteins, and offers the opportunity for in vitro and in vivo experiments to deploy the cyanobacterial proteins as valuable therapeutics against COVID-19.
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Affiliation(s)
- Devashan Naidoo
- Centre for Algal Biotechnology, Mangosuthu University of Technology, P.O. Box 12363, Durban 4026, South Africa; (T.M.); (J.B.); (A.A.)
- Correspondence: (D.N.); (A.R.)
| | - Pallab Kar
- Bioinformatics Facility, Department of Botany, University of North Bengal, Siliguri 734013, India; (P.K.); (A.S.)
| | - Ayan Roy
- Department of Biotechnology, Lovely Professional University, Phagwara 144411, India
- Correspondence: (D.N.); (A.R.)
| | - Taurai Mutanda
- Centre for Algal Biotechnology, Mangosuthu University of Technology, P.O. Box 12363, Durban 4026, South Africa; (T.M.); (J.B.); (A.A.)
| | - Joseph Bwapwa
- Centre for Algal Biotechnology, Mangosuthu University of Technology, P.O. Box 12363, Durban 4026, South Africa; (T.M.); (J.B.); (A.A.)
| | - Arnab Sen
- Bioinformatics Facility, Department of Botany, University of North Bengal, Siliguri 734013, India; (P.K.); (A.S.)
| | - Akash Anandraj
- Centre for Algal Biotechnology, Mangosuthu University of Technology, P.O. Box 12363, Durban 4026, South Africa; (T.M.); (J.B.); (A.A.)
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45
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Ramakrishnan SG, Robert B, Salim A, Ananthan P, Sivaramakrishnan M, Subramaniam S, Natesan S, Suresh R, Rajeshkumar G, Maran JP, Al-Dhabi NA, Karuppiah P, Valan Arasu M. Nanotechnology based solutions to combat zoonotic viruses with special attention to SARS, MERS, and COVID 19: Detection, protection and medication. Microb Pathog 2021; 159:105133. [PMID: 34390768 PMCID: PMC8358084 DOI: 10.1016/j.micpath.2021.105133] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 04/01/2021] [Accepted: 08/09/2021] [Indexed: 12/23/2022]
Abstract
Zoonotic viruses originate from birds or animal sources and responsible for disease transmission from animals to people through zoonotic spill over and presents a significant global health concern due to lack of rapid diagnostics and therapeutics. The Corona viruses (CoV) were known to be transmitted in mammals. Early this year, SARS-CoV-2, a novel strain of corona virus, was identified as the causative pathogen of an outbreak of viral pneumonia in Wuhan, China. The disease later named corona virus disease 2019 (COVID-19), subsequently spread across the globe rapidly. Nano-particles and viruses are comparable in size, which serves to be a major advantage of using nano-material in clinical strategy to combat viruses. Nanotechnology provides novel solutions against zoonotic viruses by providing cheap and efficient detection methods, novel, and new effective rapid diagnostics and therapeutics. The prospective of nanotechnology in COVID 19 is exceptionally high due to their small size, large surface-to-volume ratio, susceptibility to modification, intrinsic viricidal activity. The nano-based strategies address the COVID 19 by extending their role in i) designing nano-materials for drug/vaccine delivery, ii) developing nano-based diagnostic approaches like nano-sensors iii) novel nano-based personal protection equipment to be used in prevention strategies.This review aims to bring attention to the significant contribution of nanotechnology to mitigate against zoonotic viral pandemics by prevention, faster diagnosis and medication point of view.
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Affiliation(s)
- Sankar Ganesh Ramakrishnan
- Bioprocess and Biomaterials laboratory, Department of Microbial Biotechnology, Bharathiar University, Coimbatore, India
| | - Becky Robert
- Bioprocess and Biomaterials laboratory, Department of Microbial Biotechnology, Bharathiar University, Coimbatore, India
| | - Anisha Salim
- Bioprocess and Biomaterials laboratory, Department of Microbial Biotechnology, Bharathiar University, Coimbatore, India
| | - Padma Ananthan
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | | | - Sadhasivam Subramaniam
- Bioprocess and Biomaterials laboratory, Department of Microbial Biotechnology, Bharathiar University, Coimbatore, India; Department of Extension and Career Guidance, Bharathiar University, Coimbatore, India.
| | - Sivarajasekar Natesan
- Unit Operations laboratory, Department of Biotechnology, Kumaraguru College of Technology, Coimbatore, India
| | - Rahul Suresh
- Department of Physics, Bharathiar University, Coimbatore, India
| | - G Rajeshkumar
- Department of Mechanical Engineering, PSG Institute of Technology and Applied Research, Coimbatore, Tamilnadu, India
| | - J Prakash Maran
- Department of Food Science and Nutrition, Periyar University, Salem, Tamilnadu, India.
| | - Naif Abdullah Al-Dhabi
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Ponmurugan Karuppiah
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia.
| | - Mariadhas Valan Arasu
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
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46
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Pratas D, Silva JM. Persistent minimal sequences of SARS-CoV-2. Bioinformatics 2021; 36:5129-5132. [PMID: 32730589 PMCID: PMC7559010 DOI: 10.1093/bioinformatics/btaa686] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 07/14/2020] [Accepted: 07/22/2020] [Indexed: 12/22/2022] Open
Abstract
Motivation Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused more than 14
million cases and more than half million deaths. Given the absence of implemented
therapies, new analysis, diagnosis, and therapeutics are of great importance. Results Analysis of SARS-CoV-2 genomes from the current outbreak reveals the presence of short
persistent DNA/RNA sequences that are absent from the human genome and transcriptome
(PmRAWs). For the PmRAWs with length 12, only four exist at the same location in all
SARS-CoV-2. At the gene level, we found one PmRAW of size 13 at the Spike glycoprotein
coding sequence. This protein is fundamental for binding in human ACE2 and further use
as an entry receptor to invade target cells. Applying protein structural prediction, we
localized this PmRAW at the surface of the Spike protein, providing a potential targeted
vector for diagnostics and therapeutics. Additionally, we show a new pattern of relative
absent words (RAWs), characterized by the progressive increase of GC content (Guanine
and Cytosine) according to the decrease of RAWs length, contrarily to the virus and host
genome distributions. New analysis shows the same property during the Ebola virus
outbreak. At a computational level, we improved the alignment-free method to identify
pathogen-specific signatures in balance with GC measures and removed previous size
limitations. Availability and Implementation https://github.com/cobilab/eagle. Supplementary information Supplementary data are
available at Bioinformatics online.
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Affiliation(s)
- Diogo Pratas
- Institute of Electronics and Informatics Engineering of Aveiro, 3810-193 Aveiro, Portugal.,Department of Electronics, Telecommunications and Informatics, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.,Department of Virology, University of Helsinki, 00014 Helsinki, Finland
| | - Jorge M Silva
- Institute of Electronics and Informatics Engineering of Aveiro, 3810-193 Aveiro, Portugal.,Department of Electronics, Telecommunications and Informatics, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
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47
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Li L, Gao M, Li J, Zu S, Wang Y, Chen C, Wan D, Duan J, Aliyari R, Wang J, Zhang J, Jin Y, Huang W, Jin X, Shi M, Wang Y, Qin C, Yang H, Cheng G. Methods to Identify Immunogenic Peptides in SARS-CoV-2 Spike and Protective Monoclonal Antibodies in COVID-19 Patients. SMALL METHODS 2021; 5:2100058. [PMID: 34514088 PMCID: PMC8420616 DOI: 10.1002/smtd.202100058] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 05/19/2021] [Indexed: 05/28/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and the associated COVID-19 diseases are an emerging threat to global public health. Although considerable scientific research on the immune, especially antibody, responses to SARS-CoV-2 infection have been conducted, additional dominant epitopes and protective antibodies are needed for diagnosis and treatment of COVID-19 patients. Here, two different phage libraries are used to identify immunogenic epitopes across the spike protein and monoclonal antibodies from COVID-19 patients. Three peptides are further characterized in the receptor-binding motif (RBM) and measured their antibody levels in COVID-19 patients, from which one identifies one most immunodominant epitope with the highest antibody response in COVID-19 patients and in immunized mice. More importantly, monoclonal antibodies specifically binding to this peptide isolated from COVID-19 patients have therapeutic potential to neutralize SARS-CoV-2 infection. Thus, the approaches to systemically identify immunogenic peptides and directly identify human monoclonal antibodies from patients will provide useful diagnostic and therapeutic tools for COVID-19 and other emerging infectious diseases.
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Affiliation(s)
- Lili Li
- Center for Systems MedicineInstitute of Basic Medical SciencesChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijing100005China
- Suzhou Institute of Systems MedicineSuzhouJiangsu215123China
| | - Meiling Gao
- Center for Systems MedicineInstitute of Basic Medical SciencesChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijing100005China
- Suzhou Institute of Systems MedicineSuzhouJiangsu215123China
| | - Jie Li
- Department of Laboratory MedicineTaiHe HospitalHubei University of MedicineShiyanHubei442000China
| | - Shulong Zu
- Center for Systems MedicineInstitute of Basic Medical SciencesChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijing100005China
- Suzhou Institute of Systems MedicineSuzhouJiangsu215123China
| | - Yanan Wang
- Suzhou Func Biotech Inc.SuzhouJiangsu215123China
| | | | - Dingyi Wan
- AtaGenix Laboratories (Wuhan) Co., Ltd.WuhanHubei430075China
| | - Jing Duan
- AtaGenix Laboratories (Wuhan) Co., Ltd.WuhanHubei430075China
| | - Roghiyh Aliyari
- Department of MicrobiologyImmunology & Molecular GeneticsUniversity of CaliforniaLos AngelesLos AngelesCA90095USA
| | - Jingfeng Wang
- Center for Systems MedicineInstitute of Basic Medical SciencesChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijing100005China
- Suzhou Institute of Systems MedicineSuzhouJiangsu215123China
- Department of MicrobiologyImmunology & Molecular GeneticsUniversity of CaliforniaLos AngelesLos AngelesCA90095USA
| | - Jicai Zhang
- Department of Laboratory MedicineTaiHe HospitalHubei University of MedicineShiyanHubei442000China
| | - Yujie Jin
- Department of Laboratory MedicineTaiHe HospitalHubei University of MedicineShiyanHubei442000China
| | - Weijin Huang
- Division of HIV/AIDS and Sex‐Transmitted Virus VaccinesInstitute for Biological Product ControlNational Institutes for Food and Drug Control (NIFDC)Beijing102629China
| | - Xiaoxia Jin
- Affiliated Tumour Hospital of Nantong UniversityNantong226000China
| | - Minxin Shi
- Affiliated Tumour Hospital of Nantong UniversityNantong226000China
| | - Youchun Wang
- Division of HIV/AIDS and Sex‐Transmitted Virus VaccinesInstitute for Biological Product ControlNational Institutes for Food and Drug Control (NIFDC)Beijing102629China
| | - Cheng‐Feng Qin
- Department of VirologyState Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyAMMSBeijing100071China
| | - Heng Yang
- Center for Systems MedicineInstitute of Basic Medical SciencesChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijing100005China
- Suzhou Institute of Systems MedicineSuzhouJiangsu215123China
| | - Genhong Cheng
- Department of MicrobiologyImmunology & Molecular GeneticsUniversity of CaliforniaLos AngelesLos AngelesCA90095USA
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48
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Magdy Beshbishy A, Oti VB, Hussein DE, Rehan IF, Adeyemi OS, Rivero-Perez N, Zaragoza-Bastida A, Shah MA, Abouelezz K, Hetta HF, Cruz-Martins N, Batiha GES. Factors Behind the Higher COVID-19 Risk in Diabetes: A Critical Review. Front Public Health 2021; 9:591982. [PMID: 34307267 PMCID: PMC8292635 DOI: 10.3389/fpubh.2021.591982] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 04/29/2021] [Indexed: 01/08/2023] Open
Abstract
Diabetes mellitus (DM) and coronavirus disease 2019 (COVID-19) are public health issues worldwide, and their comorbidities trigger the progress to severe disease and even death in such patients. Globally, DM has affected an estimated 9.3% adults, and as of April 18, 2021, the World Health Organization (WHO) has confirmed 141,727,940 COVID-19 confirmed cases. The virus is spread via droplets, aerosols, and direct touch with others. Numerous predictive factors have been linked to COVID-19 severity, including impaired immune response and increased inflammatory response, among others. Angiotensin receptor blockers and angiotensin converting enzyme 2 have also been identified as playing a boosting role in both susceptibility and severity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Specifically, in DM patients, both their control and management during this pandemic is herculean as the restriction periods have markedly hampered the maintenance of means to control glycemia, hypertension, and neuroendocrine and kidney diseases. In addition, as a result of the underlyin cardio-metabolic and immunological disorders, DM patients are at a higher risk of developing the severe form of COVID-19 despite other comorbidities, such as hypertension, also potentially boosting the development of higher COVID-19 severity. However, even in non-DM patients, SARS-CoV-2 may also cause transient hyperglycemia through induction of insulin resistance and/or pancreatic β-cell injury. Therefore, a strict glucose monitoring of DM patients with COVID-19 is mandatory to prevent life-threatening complications.
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Affiliation(s)
- Amany Magdy Beshbishy
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
| | - Victor B. Oti
- Department of Microbiology, Nasarawa State University, Keffi, Nigeria
| | - Diaa E. Hussein
- Researcher, Department of Food Hygiene, Agricultural Research Center, Animal Health Research Institute, Port of Alexandria, Egypt
| | - Ibrahim F. Rehan
- Department of Husbandry and Development of Animal Wealth, Faculty of Veterinary Medicine, Menofa University, Shebin Alkom, Egypt
| | - Oluyomi S. Adeyemi
- Medicinal Biochemistry, Infectious Diseases, Nanomedicine & Toxicology Laboratory, Department of Biochemistry, Landmark University, Omu-Aran, Nigeria
| | - Nallely Rivero-Perez
- Área Académica de Medicina Veterinaria y Zootecnia, Instituto de Ciencias Agropecuaria, Universidad Autónoma del Estado de Hidalgo, Tulancingo, Mexico
| | - Adrian Zaragoza-Bastida
- Área Académica de Medicina Veterinaria y Zootecnia, Instituto de Ciencias Agropecuaria, Universidad Autónoma del Estado de Hidalgo, Tulancingo, Mexico
| | - Muhammad Ajmal Shah
- Department of Pharmacognosy, Faculty of Pharmaceutical Sciences, Government College University, Faisalabad, Pakistan
| | - Khaled Abouelezz
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Helal F. Hetta
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Natália Cruz-Martins
- Faculty of Medicine, University of Porto, Porto, Portugal
- Institute for Research and Innovation in Health (i3S), University of Porto, Porto, Portugal
- Laboratory of Neuropsychophysiology, Faculty of Psychology and Education Sciences, University of Porto, Porto, Portugal
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, Egypt
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49
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Relative synonymous codon usage of ORF1ab in SARS-CoV-2 and SARS-CoV. Genes Genomics 2021; 43:1351-1359. [PMID: 34228320 PMCID: PMC8258482 DOI: 10.1007/s13258-021-01136-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 06/29/2021] [Indexed: 01/08/2023]
Abstract
Background COVID-19, as a novel coronavirus disease caused by new coronavirus SARS-CoV-2, spreads all over the world, and brings harm to human in many countries. Humans suffered a lot from both SARS-CoV-2 now and by SARS-CoV in the year 2003. It is important to understand the differences and the relationships between these two types of viruses. Objective To compare relative synonymous codon usage of ORF1ab gene in SARS-CoV-2 and SARS-CoV, relative synonymous codon usage of their genomes are studied in this paper from the bioinformatics perspective. Methods The ORF1ab gene, which is an important non-structural polyprotein coding gene and now used for nucleic acid detection markers in many measurement method, in both SARS-CoV-2 (30 strains) and SARS-CoV (20 strains) are considered to be the research object in the present paper. The relative synonymous codon usage values of the ORF1ab gene are calculated to characterize the differences and the evolutionary characteristics among 50 strains. Results There is a significant difference between SARS-CoV and SARS-CoV-2 when the relative synonymous codon usage value of ORF1ab genes is concerned. The results suggest that codon usage pattern of SARS-CoV is more similar to human than that of the SARS-CoV-2, and that the inner difference in SARS-CoV-2 strains is larger than that of SARS-CoV, which denote the larger diversity exits in the SARS-CoV-2 virus. Conclusion These results show that the relative synonymous codon usage values in the coronavirus could be used for further research on their evolutionary phenomenon.
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50
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Liang X, Zhou R, Li Y, Yang L, Su M, Lai KP. Clinical characterization and therapeutic targets of vitamin A in patients with hepatocholangiocarcinoma and coronavirus disease. Aging (Albany NY) 2021; 13:15785-15800. [PMID: 34176789 PMCID: PMC8266307 DOI: 10.18632/aging.203220] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/04/2021] [Indexed: 02/07/2023]
Abstract
Recent reports indicate that patients with hepatocholangiocarcinoma (CHOL) have a higher morbidity and mortality rate for coronavirus disease (COVID-19). Anti-CHOL/COVID-19 medicines are inexistent. Vitamin A (VA) refers to a potent nutrient with anti-cytotoxic and anti-inflammatory actions. Therefore, this study aimed to determine the potential functions and molecular mechanisms of VA as a potential treatment for patients with both CHOL and COVID-19 (CHOL/COVID-19). The transcriptome data of CHOL patients were obtained from the Cancer Genome Analysis database. Furthermore, the network pharmacology approach and bioinformatics analysis were used to identify and reveal the molecular functions, therapeutic biotargets, and signaling of VA against CHOL/COVID-19. First, clinical findings identified the medical characteristics of CHOL patients with COVID-19, such as susceptibility gene, prognosis, recurrence, and survival rate. Anti-viral and anti-inflammatory pathways, and immunopotentiation were found as potential targets of VA against CHOL/COVID-19. These findings illustrated that VA may contribute to the clinical management of CHOL/COVID-19 achieved by induction of cell repair, suppression of oxidative stress and inflammatory reaction, and amelioration of immunity. Nine vital therapeutic targets (BRD2, NOS2, GPT, MAPK1, CXCR3, ICAM1, CDK4, CAT, and TMPRSS13) of VA against CHOL/COVID-19 were identified. For the first time, the potential pharmacological biotargets, function, and mechanism of action of VA in CHOL/COVID-19 were elucidated.
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Affiliation(s)
- Xiao Liang
- Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Guilin, Guangxi, China.,Guangxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin, Guangxi, China
| | - Rui Zhou
- Department of Hepatobiliary Surgery, Guigang City People's Hospital, The Eighth Affiliated Hospital of Guangxi Medical University, Guigang, Guangxi, China
| | - Yu Li
- Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Guilin, Guangxi, China.,Guangxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin, Guangxi, China
| | - Lu Yang
- Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Guilin, Guangxi, China.,Guangxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin, Guangxi, China
| | - Min Su
- Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Guilin, Guangxi, China.,Guangxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin, Guangxi, China
| | - Keng Po Lai
- Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Guilin, Guangxi, China.,Guangxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin, Guangxi, China
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