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Szabó D, Crowe A, Mamotte C, Strappe P. Natural products as a source of Coronavirus entry inhibitors. Front Cell Infect Microbiol 2024; 14:1353971. [PMID: 38449827 PMCID: PMC10915212 DOI: 10.3389/fcimb.2024.1353971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/01/2024] [Indexed: 03/08/2024] Open
Abstract
The COVID-19 pandemic has had a significant and lasting impact on the world. Four years on, despite the existence of effective vaccines, the continuous emergence of new SARS-CoV-2 variants remains a challenge for long-term immunity. Additionally, there remain few purpose-built antivirals to protect individuals at risk of severe disease in the event of future coronavirus outbreaks. A promising mechanism of action for novel coronavirus antivirals is the inhibition of viral entry. To facilitate entry, the coronavirus spike glycoprotein interacts with angiotensin converting enzyme 2 (ACE2) on respiratory epithelial cells. Blocking this interaction and consequently viral replication may be an effective strategy for treating infection, however further research is needed to better characterize candidate molecules with antiviral activity before progressing to animal studies and clinical trials. In general, antiviral drugs are developed from purely synthetic compounds or synthetic derivatives of natural products such as plant secondary metabolites. While the former is often favored due to the higher specificity afforded by rational drug design, natural products offer several unique advantages that make them worthy of further study including diverse bioactivity and the ability to work synergistically with other drugs. Accordingly, there has recently been a renewed interest in natural product-derived antivirals in the wake of the COVID-19 pandemic. This review provides a summary of recent research into coronavirus entry inhibitors, with a focus on natural compounds derived from plants, honey, and marine sponges.
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Affiliation(s)
- Dávid Szabó
- Curtin Health Innovation Research Institute, Curtin University, Bentley, WA, Australia
- Curtin Medical School, Curtin University, Bentley, WA, Australia
| | - Andrew Crowe
- Curtin Health Innovation Research Institute, Curtin University, Bentley, WA, Australia
- Curtin Medical School, Curtin University, Bentley, WA, Australia
| | - Cyril Mamotte
- Curtin Health Innovation Research Institute, Curtin University, Bentley, WA, Australia
- Curtin Medical School, Curtin University, Bentley, WA, Australia
| | - Padraig Strappe
- Curtin Health Innovation Research Institute, Curtin University, Bentley, WA, Australia
- Curtin Medical School, Curtin University, Bentley, WA, Australia
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Ilesanmi A, Dairo G, Salimat S, Bodun DS, Awoyale B, Balogun TA. Identification of bioactive compounds from Vaccinium vitis-idaea L. (Lingonberry) as inhibitors for treating KRAS-associated cancer: a computational approach. In Silico Pharmacol 2023; 11:32. [PMID: 37915613 PMCID: PMC10616029 DOI: 10.1007/s40203-023-00165-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 10/04/2023] [Indexed: 11/03/2023] Open
Abstract
Lung cancer is the cancer of the lung's epithelial cells typically characterized by difficulty breathing, chest pain, blood-stained coughs, headache, and weight loss. If left unmanaged, lung cancer can spread to other body parts. While several treatment methods exist for managing lung cancer, exploring natural plant sources for developing therapeutics offers great potential in complementing other treatment approaches. In this study, we evaluated the bioactive compounds in Vaccinium vitis-idaea for treating KRAS-associated lung cancer types. In this study, we concentrated on inhibiting the mutated Kirsten rat sarcoma viral oncogene homolog (KRAS) by targeting an associated protein (Phosphodiesterase 6δ) to which KRAS form complexes. We evaluated bioactive compounds from Lingonberry (Vaccinium vitis-idaea L.), adopting computational approaches such as molecular docking, molecular dynamics simulation, molecular mechanics/generalized Born surface area (MM/GBSA) calculations, and pharmacokinetics analysis. A total of 26 out of 39 bioactive compounds of Vaccinium vitis-idaea L. had a higher binding affinity to the target receptor than an approved drug, Sotorasib. Also, further analyses of all lead/top compounds in this study identified (+)-Catechin (Cianidanol), Arbutin, Resveratrol, and Sinapic acid, to be potential drug candidates that could be pursued. In sum, Arbutin, (+)-Catechin, and Sinapic acid are predicted to be the top compound of Vaccinium vitis-idaea L. because of their pharmacokinetic properties and drug-likeness attributes. Also, their stability to the target receptor makes them a potential drug candidate that could be explored for treating KRAS mutation-associated lung cancer. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-023-00165-1.
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Affiliation(s)
- Ayooluwa Ilesanmi
- Department of Sciences and Mathematics, Mississippi University for Women, Columbus, USA
| | - Gbenga Dairo
- Department of Biological Sciences, Western Illinois University, Macomb, IL USA
| | - Sofela Salimat
- Department of Chemistry, University of Lagos, Lagos, Nigeria
| | - Damilola S. Bodun
- Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Nigeria
| | - Bibiire Awoyale
- Department of Chemistry, University of Ilorin, Ilorin, Nigeria
| | - Toheeb A. Balogun
- Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Nigeria
- Department of Biological Sciences, University of California, San Diego, La Jolla, USA
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Sahoo AK, Augusthian PD, Muralitharan I, Vivek-Ananth RP, Kumar K, Kumar G, Ranganathan G, Samal A. In silico identification of potential inhibitors of vital monkeypox virus proteins from FDA approved drugs. Mol Divers 2023; 27:2169-2184. [PMID: 36331784 PMCID: PMC9638297 DOI: 10.1007/s11030-022-10550-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022]
Abstract
The World Health Organization (WHO) recently declared the monkeypox outbreak 'A public health emergency of international concern'. The monkeypox virus belongs to the same Orthopoxvirus genus as smallpox. Although smallpox drugs are recommended for use against monkeypox, monkeypox-specific drugs are not yet available. Drug repurposing is a viable and efficient approach in the face of such an outbreak. Therefore, we present a computational drug repurposing study to identify the existing approved drugs which can be potential inhibitors of vital monkeypox virus proteins, thymidylate kinase and D9 decapping enzyme. The target protein structures of the monkeypox virus were modelled using the corresponding protein structures in the vaccinia virus. We identified four potential inhibitors namely, Tipranavir, Cefiderocol, Doxorubicin, and Dolutegravir as candidates for repurposing against monkeypox virus from a library of US FDA approved antiviral and antibiotic drugs using molecular docking and molecular dynamics simulations. The main goal of this in silico study is to identify potential inhibitors against monkeypox virus proteins that can be further experimentally validated for the discovery of novel therapeutic agents against monkeypox disease.
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Affiliation(s)
- Ajaya Kumar Sahoo
- The Institute of Mathematical Sciences (IMSc), Chennai, 600113, India
- Homi Bhabha National Institute (HBNI), Mumbai, 400094, India
| | | | | | - R P Vivek-Ananth
- The Institute of Mathematical Sciences (IMSc), Chennai, 600113, India
- Homi Bhabha National Institute (HBNI), Mumbai, 400094, India
| | - Kishan Kumar
- The Institute of Mathematical Sciences (IMSc), Chennai, 600113, India
| | - Gaurav Kumar
- The Institute of Mathematical Sciences (IMSc), Chennai, 600113, India
| | | | - Areejit Samal
- The Institute of Mathematical Sciences (IMSc), Chennai, 600113, India.
- Homi Bhabha National Institute (HBNI), Mumbai, 400094, India.
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Verburgh ML, van der Valk M, Rijnders BJ, Reiss P, Wit FW. No association between use of tenofovir disoproxil fumarate, etravirine, or integrase-strand transfer inhibitors and acquisition or severe outcomes of SARS-CoV-2 infection in people with HIV in the Netherlands. AIDS 2023; 37:1481-1486. [PMID: 37395254 PMCID: PMC10328501 DOI: 10.1097/qad.0000000000003577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/09/2023] [Indexed: 07/04/2023]
Abstract
In two Dutch observational cohorts of people with HIV, the use of TDF, ETR, or INSTIs was not independently associated with either the risk of incident SARS-CoV-2 infection or severe COVID-19 outcomes, as was suggested by previous observational and molecular docking studies. Our findings do not support a strategy of modifying antiretroviral therapy to include these agents to protect against SARS-CoV-2 infection and severe COVID-19 outcomes.
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Affiliation(s)
- Myrthe L. Verburgh
- Amsterdam UMC location University of Amsterdam
- Amsterdam Institute for Infection and Immunity, Infectious Diseases
- Amsterdam Public Health, Global Health
- Amsterdam Institute for Global Health and Development
| | - Marc van der Valk
- Amsterdam UMC location University of Amsterdam
- Amsterdam Institute for Infection and Immunity, Infectious Diseases
- HIV Monitoring Foundation, Amsterdam
| | - Bart J.A. Rijnders
- Erasmus Medical Center, Departments of Internal Medicine & Medical Microbiology, Rotterdam
| | - Peter Reiss
- Amsterdam UMC location University of Amsterdam
- Amsterdam Institute for Infection and Immunity, Infectious Diseases
- Amsterdam Institute for Global Health and Development
- Amsterdam UMC location University of Amsterdam, Global Health, Amsterdam, The Netherlands
| | - Ferdinand W.N.M. Wit
- Amsterdam UMC location University of Amsterdam
- Amsterdam Institute for Infection and Immunity, Infectious Diseases
- HIV Monitoring Foundation, Amsterdam
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Akinyele OF, Fakola EG, Adeboye OO, Chinuomah SC. Investigation of Methyl-5-(pentan-3-yloxy)-7-oxabicyclo[4.1.0]hept-3-ene-3-carboxyhydrazide Derivatives as Potential Inhibitors of COVID-19 Main Protease: DFT and Molecular Docking Study. Bioinform Biol Insights 2023; 17:11779322231182050. [PMID: 37377795 PMCID: PMC10291222 DOI: 10.1177/11779322231182050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/27/2023] [Indexed: 06/29/2023] Open
Abstract
The search for effective therapeutics to combat COVID-19 has led to the exploration of the biological activity of numerous compounds. In this study, hydrazones derived from oseltamivir intermediate, methyl 5-(pentan-3-yloxy)-7-oxabicyclo[4.1.0]hept-3-ene-3-carboxylate have been investigated for their potential as drug candidates against the COVID-19 virus using computational methods, including density functional theory (DFT) studies, molecular docking, and absorption, distribution, metabolism, excretion and toxicity (ADMET) analysis. The DFT studies provide information on the electronic properties of the compounds while the molecular docking results using AutoDock reported the binding energies between the main protease of COVID-19 and the compounds. The DFT results revealed that the energy gap of the compounds ranged from 4.32 to 5.82 eV while compound HC had the highest energy gap (5.82 eV) and chemical potential (2.90 eV). The electrophilicity index values of the 11 compounds ranged from 2.49 to 3.86, thus they were classified as strong electrophiles. The molecular electrostatic potential (MESP) revealed electron-rich and electron-deficient regions of the compounds. The docking results reveal that all the compounds had better docking scores than remdesivir and chloroquine, frontline drugs employed in combating COVID-19, with HC having the best docking score of -6.5. The results were visualized using Discovery studio, which revealed hydrogen bonding, pi-alkyl interaction, alkyl interaction, salt bridge interaction, halogen interaction as being responsible for the docking scores. The drug-likeness results showed that the compounds qualify as oral drug candidates as none of them violated Vebers and Lipinski's rule. Thus, they could serve as potential inhibitors of COVID-19.
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Mateev E, Kondeva-Burdina M, Georgieva M, Zlatkov A. Repurposing of FDA-approved drugs as dual-acting MAO-B and AChE inhibitors against Alzheimer's disease: An in silico and in vitro study. J Mol Graph Model 2023; 122:108471. [PMID: 37087882 DOI: 10.1016/j.jmgm.2023.108471] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/30/2023] [Accepted: 04/03/2023] [Indexed: 04/25/2023]
Abstract
An in silico consensus molecular docking approach and in vitro evaluations were adopted in the present study to explore a dataset of FDA-approved drugs as novel multitarget MAO-B/AChE agents in the treatment of Alzheimer's disease (AD). GOLD 5.3 and Glide were employed in the virtual assessments and consensus superimpositions of the obtained poses were applied to increase the reliability of the docking protocols. Furthermore, the top ranked molecules were subjected to binding free energy calculations using MM/GBSA, Induced fit docking (IFD) simulations, and a literature review. Consequently, the top four multitarget drugs were examined for their in vitro MAO-B and AChE inhibition effects. The consensus molecular docking identified Dolutegravir, Rebamipide, Loracarbef and Diflunisal as potential multitarget drugs. The biological data demonstrated that most of the docking scores were in good correlation with the in vitro experiments, however the theoretical simulations in the active site of MAO-B identified two false-positives - Rebamipide and Diflunisal. Dolutegravir and Loracarbef were accessed as active MAO-B inhibitors, while Dolutegravir, Rebamapide and Diflunisal as potential AChE inhibitors. The antiretroviral agent Dolutegravir exhibited the most potent multitarget activity - 41% inhibition of MAO-B (1 μM) and 68% inhibition of AChE (10 μM). Visualizations of the intermolecular interactions of Dolutegravir in the active sites of MAO-B and AChE revealed the formation of several stable hydrogen bonds. Overall, Dolutegravir was identified as a potential anti-AD drug, however further in vivo evaluations should be considered.
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Affiliation(s)
- Emilio Mateev
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Medical University, Sofia, Bulgaria.
| | - Magdalena Kondeva-Burdina
- Department of Pharmacology, Pharmacotherapy and Toxicology, Faculty of Pharmacy, Medical University, Sofia, Bulgaria
| | - Maya Georgieva
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Medical University, Sofia, Bulgaria
| | - Alexander Zlatkov
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Medical University, Sofia, Bulgaria
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Sunny Kumar, Malini Basu, Pratyasha Ghosh, Uttam Pal, Mrinal K. Ghosh. COVID-19 therapeutics: Clinical application of repurposed drugs and futuristic strategies for target-based drug discovery. Genes Dis 2023. [ DOI: 10.1016/j.gendis.2022.12.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 12/07/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes the complicated disease COVID-19. Clinicians are continuously facing huge problems in the treatment of patients, as COVID-19-specific drugs are not available hence the principle of drug repurposing serves as a one-and-only hope. Globally, the repurposing of many drugs is underway; few of them are already approved by the regulatory bodies for their clinical use and most of them are in different phases of clinical trials. Here in this review, our main aim is to discuss in detail the up-to-date information on the target-based pharmacological classification of repurposed drugs, the potential mechanism of actions, and the current clinical trial status of various drugs which are under repurposing since early 2020. At last, we briefly proposed the probable pharmacological and therapeutic drug targets that may be preferred as a futuristic drug discovery approach in the development of effective medicines.
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Oyouni AAA. Human papillomavirus in cancer: Infection, disease transmission, and progress in vaccines. J Infect Public Health 2023; 16:626-631. [PMID: 36868166 DOI: 10.1016/j.jiph.2023.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/04/2023] [Accepted: 02/15/2023] [Indexed: 02/23/2023] Open
Abstract
Human papillomaviruses (HPVs) infect epithelial cells of human beings, and their replication cycle is associated with epithelial differentiation. More than 200 genotypes of HPVs were identified, and each of these HPVs shows distinct specificity for tissues and infection. HPV infection was involved in the development of lesions on the feet, genital warts and hands. The evidence of HPV infection revealed the role of HPVs in neck and head squamous cell carcinoma, esophageal cancer, cervical cancer, head and neck cancer, brain and lung tumours. The independent traditional risk factors, various clinical outcomes, and increased prevalence among certain populations and geographical regions have led increasing interest in HPV infection. The mode of HPVs transmission remains unclear. Moreover, in recent years, vertical transmission of HPVs was reported. This review concludes present knowledge about HPV infection, virulence strains, clinical significance of HPVs, and mode of transmission, and vaccination strategies.
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Affiliation(s)
- Atif Abdulwahab A Oyouni
- Department of Biology, Faculty of Sciences, University of Tabuk, Tabuk, Kingdom of Saudi Arabia; Genome and Biotechnology Unit, Faculty of Sciences, University of Tabuk, Tabuk, Kingdom of Saudi Arabia.
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Sayyed SK, Quraishi M, Jobby R, Rameshkumar N, Kayalvizhi N, Krishnan M, Sonawane T. A computational overview of integrase strand transfer inhibitors (INSTIs) against emerging and evolving drug-resistant HIV-1 integrase mutants. Arch Microbiol 2023; 205:142. [PMID: 36966200 PMCID: PMC10039815 DOI: 10.1007/s00203-023-03461-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/26/2023] [Accepted: 03/01/2023] [Indexed: 03/27/2023]
Abstract
AIDS (Acquired immunodeficiency syndrome) is one of the chronic and potentially life-threatening epidemics across the world. Hitherto, the non-existence of definitive drugs that could completely cure the Human immunodeficiency virus (HIV) implies an urgent necessity for the discovery of novel anti-HIV agents. Since integration is the most crucial stage in retroviral replication, hindering it can inhibit overall viral transmission. The 5 FDA-approved integrase inhibitors were computationally investigated, especially owing to the rising multiple mutations against their susceptibility. This comparative study will open new possibilities to guide the rational design of novel lead compounds for antiretroviral therapies (ARTs), more specifically the structure-based design of novel Integrase strand transfer inhibitors (INSTIs) that may possess a better resistance profile than present drugs. Further, we have discussed potent anti-HIV natural compounds and their interactions as an alternative approach, recommending the urgent need to tap into the rich vein of indigenous knowledge for reverse pharmacology. Moreover, herein, we discuss existing evidence that might change in the near future.
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Affiliation(s)
- Sharif Karim Sayyed
- Amity Institute of Biotechnology, Amity University, Mumbai, Maharashtra, 410206, India
| | - Marzuqa Quraishi
- Amity Institute of Biotechnology, Amity University, Mumbai, Maharashtra, 410206, India
| | - Renitta Jobby
- Amity Institute of Biotechnology, Amity University, Mumbai, Maharashtra, 410206, India
| | | | - Nagarajan Kayalvizhi
- Regenerative Medicine Laboratory, Department of Zoology, School of Life Sciences, Periyar University, Salem, Tamil Nadu, 636011, India
| | | | - Tareeka Sonawane
- Amity Institute of Biotechnology, Amity University, Mumbai, Maharashtra, 410206, India.
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Hanai T. Further quantitative in silico analysis of SARS-CoV-2 S-RBD Omicron BA.4, BA.5, BA.2.75, BQ.1, and BQ.1.1 transmissibility. Talanta 2023; 254:124127. [PMID: 36462284 PMCID: PMC9682881 DOI: 10.1016/j.talanta.2022.124127] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/15/2022] [Accepted: 11/21/2022] [Indexed: 11/24/2022]
Abstract
The Covid-19 variants' transmissibility was further quantitatively analyzed in silico to study the binding strength with ACE-2 and find the binding inhibitors. The molecular interaction energy values of their optimized complex structures (MIFS) demonstrated that Omicron BA.4 and 5's MIFS value (344.6 kcal mol-1) was equivalent to wild-type MIFS (346.1 kcal mol-1), that of Omicron BQ.1 and BQ. 1.1's MIFS value (309.9 and 364.6 kcal mol-1). Furthermore, the MIFS value of Omicron BA.2.75 (515.1 kcal mol-1) was about Delta-plus (511.3 kcal mol-1). The binding strength of Omicron BA.4, BA. 5, and BQ.1.1 may be neglectable, but that of Omicron BA.2.75 was urging. Furthermore, the 79 medicine candidates were analyzed as the binding inhibitors from binding strength with ACE-2. Only carboxy compounds were repulsed from the ACE-2 binding site indicating that further modification of medical treatment candidates may produce an effective binding inhibitor.
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Mohamed EAR, Abdel-Rahman IM, Zaki MEA, Al-Khdhairawi A, Abdelhamid MM, Alqaisi AM, Rahim LBA, Abu-Hussein B, El-Sheikh AAK, Abdelwahab SF, Hassan HA. In silico prediction of potential inhibitors for SARS-CoV-2 Omicron variant using molecular docking and dynamics simulation-based drug repurposing. J Mol Model 2023; 29:70. [PMID: 36808314 PMCID: PMC9939377 DOI: 10.1007/s00894-023-05457-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 01/16/2023] [Indexed: 02/23/2023]
Abstract
BACKGROUND In November 2021, variant B.1.1.529 of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified by the World Health Organization (WHO) and designated Omicron. Omicron is characterized by a high number of mutations, thirty-two in total, making it more transmissible than the original virus. More than half of those mutations were found in the receptor-binding domain (RBD) that directly interacts with human angiotensin-converting enzyme 2 (ACE2). This study aimed to discover potent drugs against Omicron, which were previously repurposed for coronavirus disease 2019 (COVID-19). All repurposed anti-COVID-19 drugs were compiled from previous studies and tested against the RBD of SARS-CoV-2 Omicron. METHODS As a preliminary step, a molecular docking study was performed to investigate the potency of seventy-one compounds from four classes of inhibitors. The molecular characteristics of the best-performing five compounds were predicted by estimating the drug-likeness and drug score. Molecular dynamics simulations (MD) over 100 ns were performed to inspect the relative stability of the best compound within the Omicron receptor-binding site. RESULTS The current findings point out the crucial roles of Q493R, G496S, Q498R, N501Y, and Y505H in the RBD region of SARS-CoV-2 Omicron. Raltegravir, hesperidin, pyronaridine, and difloxacin achieved the highest drug scores compared with the other compounds in the four classes, with values of 81%, 57%, 18%, and 71%, respectively. The calculated results showed that raltegravir and hesperidin had high binding affinities and stabilities to Omicron with ΔGbinding of - 75.7304 ± 0.98324 and - 42.693536 ± 0.979056 kJ/mol, respectively. Further clinical studies should be performed for the two best compounds from this study.
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Affiliation(s)
- Eslam A. R. Mohamed
- Department of Chemistry, Faculty of Science, Minia University, Minia, 61511 Egypt
| | - Islam M. Abdel-Rahman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Deraya University, New-Minia, 61519 Minia Egypt
| | - Magdi E. A. Zaki
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Ahmad Al-Khdhairawi
- Department of Biological Science and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
| | - Mahmoud M. Abdelhamid
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Azhar University, Asyut, 71524 Egypt
| | - Ahmad M. Alqaisi
- Chemistry Department, University of Jordan, Amman, 11942 Jordan
- Present Address: School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287 USA
| | - Lyana binti Abd Rahim
- Department of Medicine, Hospital Tuanku Ampuan Najihah, Kuala Pilah, Negeri Sembilan Malaysia
| | - Bilal Abu-Hussein
- Albayader Specialty Hospital, Amman, Jordan
- Present Address: Department of General Surgery, Cumberland Infirmary Hospital, Carlisle, England
| | - Azza A. K. El-Sheikh
- Basic Health Sciences Department, College of Medicine, Princess Nourah bint Abdulrahman University, P.O. 13 Box 84428, Riyadh, 11671 Saudi Arabia
| | - Sayed F. Abdelwahab
- Department of Pharmaceutics and Industrial Pharmacy, College of Pharmacy, Taif University, PO Box 11099, Taif, 21944 Saudi Arabia
| | - Heba Ali Hassan
- Department of Pharmacognosy, Faculty of Pharmacy, Sohag University, Sohag, 82524 Egypt
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Novak J, Zykova AR, Potemkin VA, Sharutin VV, Sharutina OK. Platinum(IV) compounds as potential drugs: a quantitative structure-activity relationship study. Bioimpacts 2023; 13:373-382. [PMID: 37736338 PMCID: PMC10509740 DOI: 10.34172/bi.2023.24180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/09/2022] [Accepted: 05/10/2022] [Indexed: 09/23/2023]
Abstract
Introduction Machine learning methods, coupled with a tremendous increase in computer power in recent years, are promising tools in modern drug design and drug repurposing. Methods Machine learning predictive models, publicly available at chemosophia.com, were used to predict the bioactivity of recently synthesized platinum(IV) complexes against different kinds of diseases and medical conditions. Two novel QSAR models based on the BiS algorithm are developed and validated, capable to predict activities against the SARS-CoV virus and its RNA dependent RNA polymerase. Results The internal predictive power of the QSAR models was tested by 10-fold cross-validation, giving cross-R2 from 0.863 to 0.903. 38 different activities, ranging from antioxidant, antibacterial, and antiviral activities, to potential anti-inflammatory, anti-arrhythmic and anti-malarial activity were predicted for a series of eighteen platinum(IV) complexes. Conclusion Complexes 1, 3 and 13 have high generalized optimality criteria and are predicted as potential SARS-CoV RNA dependent RNA polymerase inhibitors.
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Affiliation(s)
- Jurica Novak
- Department of Biotechnology, University of Rijeka, Rijeka, Croatia
- Center for Artificial Intelligence and Cyber security, University of Rijeka, Rijeka, Croatia
| | - Alena R. Zykova
- Faculty of Chemistry, Department of Theoretical and Applied Chemistry, South Ural State University, Chelyabinsk, Russia
| | | | - Vladimir V. Sharutin
- Faculty of Chemistry, Department of Theoretical and Applied Chemistry, South Ural State University, Chelyabinsk, Russia
| | - Olga K. Sharutina
- Faculty of Chemistry, Department of Theoretical and Applied Chemistry, South Ural State University, Chelyabinsk, Russia
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Shahabadi N, Zendehcheshm S, Mahdavi M, Khademi F. Repurposing FDA-approved drugs cetilistat, abiraterone, diiodohydroxyquinoline, bexarotene, and remdesivir as potential inhibitors against RNA dependent RNA polymerase of SARS-CoV-2: A comparative in silico perspective. Inform Med Unlocked 2023; 36:101147. [PMID: 36510496 PMCID: PMC9729590 DOI: 10.1016/j.imu.2022.101147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/19/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022] Open
Abstract
Vaccines are undoubtedly the most effective means of combating viral diseases like COVID-19. However, there are risks associated with vaccination, such as incomplete viral deactivation or potential adverse effects in humans. However, designing and developing a panel of new drug molecules is always encouraged. In an emergency, drug repurposing research is one of the most potent and rapid options. RdRp (RNA-dependent RNA polymerase) has been discovered to play a pivotal role in viral replication. In this study, FDA-approved drugs bexarotene, diiodohydroxyquinoline, abiraterone, cetilistat, and remdesivir were repurposed against the RdRp by molecular modeling, docking, and dynamic simulation. Furthermore, to validate the potency of these drugs, we compared them to the antiviral remdesivir, which inhibits RdRp. Our finding indicated that the selected drugs have a high potential to be developed as RdRp inhibitors and, with further validation studies, could serve as potential drugs for the treatment of COVID-19.
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Affiliation(s)
- Nahid Shahabadi
- Inorganic Chemistry Department, Faculty of Chemistry, Razi University, Kermanshah, Iran,Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran,Corresponding author. Faculty of Chemistry, Razi University, Kermanshah, Iran
| | - Saba Zendehcheshm
- Inorganic Chemistry Department, Faculty of Chemistry, Razi University, Kermanshah, Iran,Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mohammad Mahdavi
- Inorganic Chemistry Department, Faculty of Chemistry, Razi University, Kermanshah, Iran
| | - Fatemeh Khademi
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
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14
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Zapata-Cardona MI, Florez-Alvarez L, Guerra-Sandoval AL, Chvatal-Medina M, Guerra-Almonacid CM, Hincapie-Garcia J, Hernandez JC, Rugeles MT, Zapata-Builes W. In vitro and in silico evaluation of antiretrovirals against SARS-CoV-2: A drug repurposing approach. AIMS Microbiol 2023; 9:20-40. [PMID: 36891537 PMCID: PMC9988408 DOI: 10.3934/microbiol.2023002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 11/26/2022] [Accepted: 12/13/2022] [Indexed: 01/18/2023] Open
Abstract
Background Drug repurposing is a valuable strategy for rapidly developing drugs for treating COVID-19. This study aimed to evaluate the antiviral effect of six antiretrovirals against SARS-CoV-2 in vitro and in silico. Methods The cytotoxicity of lamivudine, emtricitabine, tenofovir, abacavir, efavirenz and raltegravir on Vero E6 was evaluated by MTT assay. The antiviral activity of each of these compounds was evaluated via a pre-post treatment strategy. The reduction in the viral titer was assessed by plaque assay. In addition, the affinities of the antiretroviral interaction with viral targets RdRp (RNA-dependent RNA polymerase), ExoN-NSP10 (exoribonuclease and its cofactor, the non-structural protein 10) complex and 3CLpro (3-chymotrypsin-like cysteine protease) were evaluated by molecular docking. Results Lamivudine exhibited antiviral activity against SARS-CoV-2 at 200 µM (58.3%) and 100 µM (66.7%), while emtricitabine showed anti-SARS-CoV-2 activity at 100 µM (59.6%), 50 µM (43.4%) and 25 µM (33.3%). Raltegravir inhibited SARS-CoV-2 at 25, 12.5 and 6.3 µM (43.3%, 39.9% and 38.2%, respectively). The interaction between the antiretrovirals and SARS-CoV-2 RdRp, ExoN-NSP10 and 3CLpro yielded favorable binding energies (from -4.9 kcal/mol to -7.7 kcal/mol) using bioinformatics methods. Conclusion Lamivudine, emtricitabine and raltegravir showed in vitro antiviral effects against the D614G strain of SARS-CoV-2. Raltegravir was the compound with the greatest in vitro antiviral potential at low concentrations, and it showed the highest binding affinities with crucial SARS-CoV-2 proteins during the viral replication cycle. However, further studies on the therapeutic utility of raltegravir in patients with COVID-19 are required.
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Affiliation(s)
- Maria I Zapata-Cardona
- Grupo Inmunovirologia, Facultad de Medicina, Universidad de Antioquia UdeA, Medellin, Colombia
| | - Lizdany Florez-Alvarez
- Grupo Inmunovirologia, Facultad de Medicina, Universidad de Antioquia UdeA, Medellin, Colombia.,Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | | | - Mateo Chvatal-Medina
- Grupo Inmunovirologia, Facultad de Medicina, Universidad de Antioquia UdeA, Medellin, Colombia
| | | | - Jaime Hincapie-Garcia
- Grupo de investigacion, Promocion y prevencion farmaceutica, Facultad de ciencias farmaceuticas yalimentarias, Universidad de Antioquia UdeA, Medellin, Colombia
| | - Juan C Hernandez
- Grupo Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia, Medellin, Colombia
| | - Maria T Rugeles
- Grupo Inmunovirologia, Facultad de Medicina, Universidad de Antioquia UdeA, Medellin, Colombia
| | - Wildeman Zapata-Builes
- Grupo Inmunovirologia, Facultad de Medicina, Universidad de Antioquia UdeA, Medellin, Colombia.,Grupo Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia, Medellin, Colombia
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15
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Abstract
The renin protein is an upstream enzymatic regulator of the renin-aldosterone-angiotensin system (RAAS) essential for the maintenance of blood pressure. The angiotensin-converting enzyme-2 (ACE2) is a major component of the RAAS and a cell surface receptor exploited by the SARS-CoV-2 virus to enter host cells. A recent molecular modeling study has revealed that the direct renin peptide inhibitor remikiren can bind to the catalytic site of SARS-CoV-2 main protease (Mpro). By analogy, we postulated that the non-peptidic drug aliskiren, a more potent renin inhibitor than remikiren and a drug routinely used to treat hypertension, may also be able to interact with Mpro. An in silico comparison of the binding of the two compounds to Mpro indicates that aliskiren (ΔE = -75.9 kcal/mol) can form stable complexes with the main viral protease, binding to the active site, as remikiren (ΔE = -83.2 kcal/mol). The comparison with a panoply of 30 references compounds (mainly antiviral drugs) indicated that remikiren is a potent Mpro binder comparable to drugs like glecaprevir and pibrentasvir (ΔE = -96.5 kcal/mol). The energy of interaction (ΔE) of aliskiren with Mpro is about 10% lower than with remikiren, comparable to that calculated with drugs like velpatasvir and sofosbuvir. A model is proposed to define the drug binding site, with the best binders (including remikiren) penetrating deeply into the site, whereas the less potent binders (including aliskiren) interact more superficially with the protein.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gérard Vergoten
- Inserm, INFINITE - U1286, Institut de Chimie Pharmaceutique Albert Lespagnol (ICPAL), Faculté de Pharmacie, University of Lille, Lille, France
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16
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Lei S, Chen X, Wu J, Duan X, Men K. Small molecules in the treatment of COVID-19. Signal Transduct Target Ther 2022; 7:387. [PMID: 36464706 PMCID: PMC9719906 DOI: 10.1038/s41392-022-01249-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 12/11/2022] Open
Abstract
The outbreak of COVID-19 has become a global crisis, and brought severe disruptions to societies and economies. Until now, effective therapeutics against COVID-19 are in high demand. Along with our improved understanding of the structure, function, and pathogenic process of SARS-CoV-2, many small molecules with potential anti-COVID-19 effects have been developed. So far, several antiviral strategies were explored. Besides directly inhibition of viral proteins such as RdRp and Mpro, interference of host enzymes including ACE2 and proteases, and blocking relevant immunoregulatory pathways represented by JAK/STAT, BTK, NF-κB, and NLRP3 pathways, are regarded feasible in drug development. The development of small molecules to treat COVID-19 has been achieved by several strategies, including computer-aided lead compound design and screening, natural product discovery, drug repurposing, and combination therapy. Several small molecules representative by remdesivir and paxlovid have been proved or authorized emergency use in many countries. And many candidates have entered clinical-trial stage. Nevertheless, due to the epidemiological features and variability issues of SARS-CoV-2, it is necessary to continue exploring novel strategies against COVID-19. This review discusses the current findings in the development of small molecules for COVID-19 treatment. Moreover, their detailed mechanism of action, chemical structures, and preclinical and clinical efficacies are discussed.
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Affiliation(s)
- Sibei Lei
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041 People’s Republic of China
| | - Xiaohua Chen
- grid.54549.390000 0004 0369 4060Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072 China
| | - Jieping Wu
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041 People’s Republic of China
| | - Xingmei Duan
- grid.54549.390000 0004 0369 4060Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072 China
| | - Ke Men
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041 People’s Republic of China
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17
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Brunt D, Lakernick PM, Wu C. Discovering new potential inhibitors to SARS-CoV-2 RNA dependent RNA polymerase (RdRp) using high throughput virtual screening and molecular dynamics simulations. Sci Rep 2022; 12:19986. [PMID: 36411383 DOI: 10.1038/s41598-022-24695-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 03/14/2022] [Indexed: 11/23/2022] Open
Abstract
RNA dependent RNA polymerase (RdRp), is an essential in the RNA replication within the life cycle of the severely acute respiratory coronavirus-2 (SARS-CoV-2), causing the deadly respiratory induced sickness COVID-19. Remdesivir is a prodrug that has seen some success in inhibiting this enzyme, however there is still the pressing need for effective alternatives. In this study, we present the discovery of four non-nucleoside small molecules that bind favorably to SARS-CoV-2 RdRp over the active form of the popular drug remdesivir (RTP) and adenosine triphosphate (ATP) by utilizing high-throughput virtual screening (HTVS) against the vast ZINC compound database coupled with extensive molecular dynamics (MD) simulations. After post-trajectory analysis, we found that the simulations of complexes containing both ATP and RTP remained stable for the duration of their trajectories. Additionally, it was revealed that the phosphate tail of RTP was stabilized by both the positive amino acid pocket and magnesium ions near the entry channel of RdRp which includes residues K551, R553, R555 and K621. It was also found that residues D623, D760, and N691 further stabilized the ribose portion of RTP with U10 on the template RNA strand forming hydrogen pairs with the adenosine motif. Using these models of RdRp, we employed them to screen the ZINC database of ~ 17 million molecules. Using docking and drug properties scoring, we narrowed down our selection to fourteen candidates. These were subjected to 200 ns simulations each underwent free energy calculations. We identified four hit compounds from the ZINC database that have similar binding poses to RTP while possessing lower overall binding free energies, with ZINC097971592 having a binding free energy two times lower than RTP.
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18
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Nepali K, Sharma R, Sharma S, Thakur A, Liou JP. Beyond the vaccines: a glance at the small molecule and peptide-based anti-COVID19 arsenal. J Biomed Sci 2022; 29:65. [PMID: 36064696 PMCID: PMC9444709 DOI: 10.1186/s12929-022-00847-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/16/2022] [Indexed: 02/08/2023] Open
Abstract
Unprecedented efforts of the researchers have been witnessed in the recent past towards the development of vaccine platforms for the control of the COVID-19 pandemic. Albeit, vaccination stands as a practical strategy to prevent SARS-CoV-2 infection, supplementing the anti-COVID19 arsenal with therapeutic options such as small molecules/peptides and antibodies is being conceived as a prudent strategy to tackle the emerging SARS-CoV-2 variants. Noteworthy to mention that collective efforts from numerous teams have led to the generation of a voluminous library composed of chemically and mechanistically diverse small molecules as anti-COVID19 scaffolds. This review article presents an overview of medicinal chemistry campaigns and drug repurposing programs that culminated in the identification of a plethora of small molecule-based anti-COVID19 drugs mediating their antiviral effects through inhibition of proteases, S protein, RdRp, ACE2, TMPRSS2, cathepsin and other targets. In light of the evidence ascertaining the potential of small molecule drugs to approach conserved proteins required for the viral replication of all coronaviruses, accelerated FDA approvals are anticipated for small molecules for the treatment of COVID19 shortly. Though the recent attempts invested in this direction in pursuit of enrichment of the anti-COVID-19 armoury (chemical tools) are praiseworthy, some strategies need to be implemented to extract conclusive benefits of the recently reported small molecule viz. (i) detailed preclinical investigation of the generated anti-COVID19 scaffolds (ii) in-vitro profiling of the inhibitors against the emerging SARS-CoV-2 variants (iii) development of assays enabling rapid screening of the libraries of anti-COVID19 scaffold (iv) leveraging the applications of machine learning based predictive models to expedite the anti-COVID19 drug discovery campaign (v) design of antibody-drug conjugates.
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Affiliation(s)
- Kunal Nepali
- School of Pharmacy, College of Pharmacy, Taipei Medical University, 250 Wuxing Street, Taipei, 11031, Taiwan
- TMU Research Center for Drug Discovery, Taipei Medical University, Taipei, 11031, Taiwan
| | - Ram Sharma
- School of Pharmacy, College of Pharmacy, Taipei Medical University, 250 Wuxing Street, Taipei, 11031, Taiwan
| | - Sachin Sharma
- School of Pharmacy, College of Pharmacy, Taipei Medical University, 250 Wuxing Street, Taipei, 11031, Taiwan
| | - Amandeep Thakur
- School of Pharmacy, College of Pharmacy, Taipei Medical University, 250 Wuxing Street, Taipei, 11031, Taiwan
| | - Jing-Ping Liou
- School of Pharmacy, College of Pharmacy, Taipei Medical University, 250 Wuxing Street, Taipei, 11031, Taiwan.
- TMU Research Center for Drug Discovery, Taipei Medical University, Taipei, 11031, Taiwan.
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19
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Negru PA, Miculas DC, Behl T, Bungau AF, Marin RC, Bungau SG. Virtual screening of substances used in the treatment of SARS-CoV-2 infection and analysis of compounds with known action on structurally similar proteins from other viruses. Biomed Pharmacother 2022; 153:113432. [PMID: 36076487 PMCID: PMC9289048 DOI: 10.1016/j.biopha.2022.113432] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/07/2022] [Accepted: 07/15/2022] [Indexed: 12/12/2022] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is considered the etiological agent of the disease that caused the COVID-19 pandemic, and for which there is currently no effective treatment. This pandemic has shown that the rapid identification of therapeutic compounds is critical (when a new virus with high transmissibility occurs) to prevent or reduce as much as possible the loss of human lives. To meet the urgent need for drugs, many strategies were applied for the discovery, respectively the identification of potential therapies / drugs for SARS-CoV-2. Molecular docking and virtual screening are two of the in silico tools/techniques that provided the identification of few SARS-CoV-2 inhibitors, removing ineffective or less effective drugs and thus preventing the loss of resources such as time and additional costs. The main target of this review is to provide a comprehensive overview of how in-silico tools have been used in the crisis management of anti-SARS-CoV-2 drugs, especially in virtual screening of substances used in the treatment of SARS-CoV-2 infection and analysis of compounds with known action on structurally similar proteins from other viruses; also, completions were added to the way in which these methods came to meet the requirements of biomedical research in the field. Moreover, the importance and impact of the topic approached for researchers was highlighted by conducting an extensive bibliometric analysis.
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20
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Piplani S, Singh P, Winkler DA, Petrovsky N. Potential COVID-19 Therapies from Computational Repurposing of Drugs and Natural Products against the SARS-CoV-2 Helicase. Int J Mol Sci 2022; 23:7704. [PMID: 35887049 PMCID: PMC9322913 DOI: 10.3390/ijms23147704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 02/05/2023] Open
Abstract
Repurposing of existing drugs is a rapid way to find potential new treatments for SARS-CoV-2. Here, we applied a virtual screening approach using Autodock Vina and molecular dynamic simulation in tandem to screen and calculate binding energies of repurposed drugs against the SARS-CoV-2 helicase protein (non-structural protein nsp13). Amongst the top hits from our study were antivirals, antihistamines, and antipsychotics, plus a range of other drugs. Approximately 30% of our top 87 hits had published evidence indicating in vivo or in vitro SARS-CoV-2 activity. Top hits not previously reported to have SARS-CoV-2 activity included the antiviral agents, cabotegravir and RSV-604; the NK1 antagonist, aprepitant; the trypanocidal drug, aminoquinuride; the analgesic, antrafenine; the anticancer intercalator, epirubicin; the antihistamine, fexofenadine; and the anticoagulant, dicoumarol. These hits from our in silico SARS-CoV-2 helicase screen warrant further testing as potential COVID-19 treatments.
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Affiliation(s)
- Sakshi Piplani
- Vaxine Pty Ltd., 11 Walkley Avenue, Adelaide 5046, Australia; (S.P.); (P.S.)
| | - Puneet Singh
- Vaxine Pty Ltd., 11 Walkley Avenue, Adelaide 5046, Australia; (S.P.); (P.S.)
| | - David A. Winkler
- Biochemistry and Chemistry Department, La Trobe University, Kingsbury Drive, Melbourne 3086, Australia;
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Australia
- School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
| | - Nikolai Petrovsky
- Vaxine Pty Ltd., 11 Walkley Avenue, Adelaide 5046, Australia; (S.P.); (P.S.)
- Department of Diabetes and Endocrinology, Flinders Medical Centre, Flinders University, 1 Flinders Drive, Adelaide 5042, Australia
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21
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Hua Y, Dai X, Xu Y, Xing G, Liu H, Lu T, Chen Y, Zhang Y. Drug repositioning: Progress and challenges in drug discovery for various diseases. Eur J Med Chem 2022; 234:114239. [PMID: 35290843 PMCID: PMC8883737 DOI: 10.1016/j.ejmech.2022.114239] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 02/20/2022] [Accepted: 02/24/2022] [Indexed: 12/17/2022]
Abstract
Compared with traditional de novo drug discovery, drug repurposing has become an attractive drug discovery strategy due to its low-cost and high efficiency. Through a comprehensive analysis of the candidates that have been identified with drug repositioning potentials, it is found that although some drugs do not show obvious advantages in the original indications, they may exert more obvious effects in other diseases. In addition, some drugs have a synergistic effect to exert better clinical efficacy if used in combination. Particularly, it has been confirmed that drug repositioning has benefits and values on the current public health emergency such as the COVID-19 pandemic, which proved the great potential of drug repositioning. In this review, we systematically reviewed a series of representative drugs that have been repositioned for different diseases and illustrated successful cases in each disease. Especially, the mechanism of action for the representative drugs in new indications were explicitly explored for each disease, we hope this review can provide important insights for follow-up research.
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Affiliation(s)
- Yi Hua
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Xiaowen Dai
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Yuan Xu
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Guomeng Xing
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Haichun Liu
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Tao Lu
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, China
| | - Yadong Chen
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China.
| | - Yanmin Zhang
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China.
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22
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Lee RKL, Li TN, Chang SY, Chao TL, Kuo CH, Pan MYC, Chiou YT, Liao KJ, Yang Y, Wu YH, Huang CH, Juan HF, Hsieh HP, Wang LHC. Identification of Entry Inhibitors against Delta and Omicron Variants of SARS-CoV-2. Int J Mol Sci 2022; 23:ijms23074050. [PMID: 35409412 PMCID: PMC8999638 DOI: 10.3390/ijms23074050] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 03/30/2022] [Accepted: 04/01/2022] [Indexed: 12/15/2022] Open
Abstract
Entry inhibitors against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are urgently needed to control the outbreak of coronavirus disease 2019 (COVID-19). This study developed a robust and straightforward assay that detected the molecular interaction between the receptor-binding domain (RBD) of viral spike protein and the angiotensin-converting enzyme 2 (ACE2) receptor in just 10 min. A drug library of 1068 approved compounds was used to screen for SARS-CoV2 entry inhibition, and 9 active drugs were identified as specific pseudovirus entry inhibitors. A plaque reduction neutralization test using authentic SARS-CoV-2 virus in Vero E6 cells confirmed that 2 of these drugs (Etravirine and Dolutegravir) significantly inhibited the infection of SARS-CoV-2. With molecular docking, we showed that both Etravirine and Dolutegravir are preferentially bound to primary ACE2-interacting residues on the RBD domain, implying that these two drug blocks may prohibit the viral attachment of SARS-CoV-2. We compared the neutralizing activities of these entry inhibitors against different pseudoviruses carrying spike proteins from alpha, beta, gamma, and delta variants. Both Etravirine and Dolutegravir showed similar neutralizing activities against different variants, with EC50 values between 4.5 to 5.8 nM for Etravirine and 10.2 to 22.9 nM for Dolutegravir. These data implied that Etravirine and Dolutegravir may serve as general spike inhibitors against dominant viral variants of SARS-CoV-2.
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Affiliation(s)
- Richard Kuan-Lin Lee
- Institute of Molecular and Cellular Biology, College of Life Science, National Tsing Hua University, Hsinchu 300013, Taiwan; (R.K.-L.L.); (T.-N.L.); (M.Y.-C.P.); (Y.-T.C.); (Y.Y.); (Y.-H.W.)
- SMOBIO Technology, Inc., Hsinchu 300096, Taiwan;
| | - Tian-Neng Li
- Institute of Molecular and Cellular Biology, College of Life Science, National Tsing Hua University, Hsinchu 300013, Taiwan; (R.K.-L.L.); (T.-N.L.); (M.Y.-C.P.); (Y.-T.C.); (Y.Y.); (Y.-H.W.)
| | - Sui-Yuan Chang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei 100225, Taiwan; (S.-Y.C.); (T.-L.C.)
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei 100225, Taiwan
| | - Tai-Ling Chao
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei 100225, Taiwan; (S.-Y.C.); (T.-L.C.)
| | | | - Max Yu-Chen Pan
- Institute of Molecular and Cellular Biology, College of Life Science, National Tsing Hua University, Hsinchu 300013, Taiwan; (R.K.-L.L.); (T.-N.L.); (M.Y.-C.P.); (Y.-T.C.); (Y.Y.); (Y.-H.W.)
| | - Yu-Ting Chiou
- Institute of Molecular and Cellular Biology, College of Life Science, National Tsing Hua University, Hsinchu 300013, Taiwan; (R.K.-L.L.); (T.-N.L.); (M.Y.-C.P.); (Y.-T.C.); (Y.Y.); (Y.-H.W.)
| | - Kuan-Ju Liao
- Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, Hsinchu 300013, Taiwan;
| | - Yi Yang
- Institute of Molecular and Cellular Biology, College of Life Science, National Tsing Hua University, Hsinchu 300013, Taiwan; (R.K.-L.L.); (T.-N.L.); (M.Y.-C.P.); (Y.-T.C.); (Y.Y.); (Y.-H.W.)
| | - Yi-Hsuan Wu
- Institute of Molecular and Cellular Biology, College of Life Science, National Tsing Hua University, Hsinchu 300013, Taiwan; (R.K.-L.L.); (T.-N.L.); (M.Y.-C.P.); (Y.-T.C.); (Y.Y.); (Y.-H.W.)
| | - Chen-Hao Huang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 106319, Taiwan; (C.-H.H.); (H.-F.J.)
| | - Hsueh-Fen Juan
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 106319, Taiwan; (C.-H.H.); (H.-F.J.)
- Department of Life Science, National Taiwan University, Taipei 106319, Taiwan
| | - Hsing-Pang Hsieh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli 350401, Taiwan;
- Department of Chemistry, National Tsing Hua University, Hsinchu 300013, Taiwan
- Biomedical Translation Research Center, Academia Sinica, Taipei 115202, Taiwan
| | - Lily Hui-Ching Wang
- Institute of Molecular and Cellular Biology, College of Life Science, National Tsing Hua University, Hsinchu 300013, Taiwan; (R.K.-L.L.); (T.-N.L.); (M.Y.-C.P.); (Y.-T.C.); (Y.Y.); (Y.-H.W.)
- Department of Medical Science, National Tsing Hua University, Hsinchu 300013, Taiwan
- Correspondence:
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Omer SE, Ibrahim TM, Krar OA, Ali AM, Makki AA, Ibraheem W, Alzain AA. Drug repurposing for SARS-CoV-2 main protease: Molecular docking and molecular dynamics investigations. Biochem Biophys Rep 2022; 29:101225. [PMID: 35128086 PMCID: PMC8801302 DOI: 10.1016/j.bbrep.2022.101225] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 01/18/2022] [Accepted: 01/27/2022] [Indexed: 12/23/2022] Open
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Kumar S, Kovalenko S, Bhardwaj S, Sethi A, Yu. Gorobets N, Desenko SM, Poonam, Rathi B. Drug repurposing against SARS-CoV-2 using computational approaches. Drug Discov Today 2022; 27:2015-2027. [PMID: 35151891 PMCID: PMC8830191 DOI: 10.1016/j.drudis.2022.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/05/2022] [Accepted: 02/04/2022] [Indexed: 12/11/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has generated a critical need for treatments to reduce morbidity and mortality associated with this disease. However, traditional drug development takes many years, which is not practical solution given the current pandemic. Therefore, a viable option is to repurpose existing drugs. The structural data of several proteins vital for the virus became available shortly after the start of the pandemic. In this review, we discuss the importance of these targets and their available potential inhibitors predicted by the computational approaches. Among the hits identified by computational approaches, 35 candidates were suggested for further evaluation, among which ten drugs are in clinical trials (Phase III and IV) for treating Coronavirus 2019 (COVID-19).
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Wang H, Zhang J, Lu Z, Dai W, Ma C, Xiang Y, Zhang Y. Identification of potential therapeutic targets and mechanisms of COVID-19 through network analysis and screening of chemicals and herbal ingredients. Brief Bioinform 2022; 23:bbab373. [PMID: 34505138 PMCID: PMC8499921 DOI: 10.1093/bib/bbab373] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/06/2021] [Accepted: 08/23/2021] [Indexed: 12/12/2022] Open
Abstract
After experiencing the COVID-19 pandemic, it is widely acknowledged that a rapid drug repurposing method is highly needed. A series of useful drug repurposing tools have been developed based on data-driven modeling and network pharmacology. Based on the disease module, we identified several hub proteins that play important roles in the onset and development of the COVID-19, which are potential targets for repositioning approved drugs. Moreover, different network distance metrics were applied to quantify the relationship between drug targets and COVID-19 disease targets in the protein-protein-interaction (PPI) network and predict COVID-19 therapeutic effects of bioactive herbal ingredients and chemicals. Furthermore, the tentative mechanisms of candidates were illustrated through molecular docking and gene enrichment analysis. We obtained 15 chemical and 15 herbal ingredient candidates and found that different drugs may play different roles in the process of virus invasion and the onset and development of the COVID-19 disease. Given pandemic outbreaks, our method has an undeniable immense advantage in the feasibility analysis of drug repurposing or drug screening, especially in the analysis of herbal ingredients.
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Affiliation(s)
- Hong Wang
- Chongqing Key Research Laboratory for Drug Metabolism, College of Pharmacy, Chongqing Medical University, Chongqing, 400016, China
- Medical Data Science Academy, Chongqing Medical University, Chongqing, 400016, China
- Chongqing Engineering Research Center for Clinical Big-data and Drug Evaluation, Chongqing Medical University, Chongqing, 401331, China
| | - Jingqing Zhang
- Chongqing Key Research Laboratory for Drug Metabolism, College of Pharmacy, Chongqing Medical University, Chongqing, 400016, China
| | - Zhigang Lu
- Department of Neurology, The First People's Hospital of Jingmen affiliated to Hubei Minzu University, Jingmen, 448000, China
| | - Weina Dai
- Chongqing Key Research Laboratory for Drug Metabolism, College of Pharmacy, Chongqing Medical University, Chongqing, 400016, China
| | - Chuanjiang Ma
- Chongqing Key Research Laboratory for Drug Metabolism, College of Pharmacy, Chongqing Medical University, Chongqing, 400016, China
| | - Yun Xiang
- Gynaecology and Obstetrics, Guangzhou Women and Children's Medical Center, Guangzhou, 510623, China
| | - Yonghong Zhang
- Chongqing Key Research Laboratory for Drug Metabolism, College of Pharmacy, Chongqing Medical University, Chongqing, 400016, China
- Medical Data Science Academy, Chongqing Medical University, Chongqing, 400016, China
- Chongqing Engineering Research Center for Clinical Big-data and Drug Evaluation, Chongqing Medical University, Chongqing, 401331, China
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Novak J, Potemkin VA. A new glimpse on the active site of SARS-CoV-2 3CLpro, coupled with drug repurposing study. Mol Divers 2022; 26:2631-2645. [PMID: 35001230 PMCID: PMC8743077 DOI: 10.1007/s11030-021-10355-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/21/2021] [Indexed: 11/03/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is caused by novel severe acute respiratory syndrome coronavirus (SARS-CoV-2). Its main protease, 3C-like protease (3CLpro), is an attractive target for drug design, due to its importance in virus replication. The analysis of the radial distribution function of 159 3CLpro structures reveals a high similarity index. A study of the catalytic pocket of 3CLpro with bound inhibitors reveals that the influence of the inhibitors is local, perturbing dominantly only residues in the active pocket. A machine learning based model with high predictive ability against SARS-CoV-2 3CLpro is designed and validated. The model is used to perform a drug-repurposing study, with the main aim to identify existing drugs with the highest 3CLpro inhibition power. Among antiviral agents, lopinavir, idoxuridine, paritaprevir, and favipiravir showed the highest inhibition potential. Enzyme - ligand interactions as a key ingredient for successful drug design.
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Affiliation(s)
- Jurica Novak
- Higher Medical and Biological School, Laboratory of Computational Modeling of Drugs, South Ural State University, Tchaikovsky Str. 20-A, Chelyabinsk, 454080, Russia.
| | - Vladimir A Potemkin
- Higher Medical and Biological School, Laboratory of Computational Modeling of Drugs, South Ural State University, Tchaikovsky Str. 20-A, Chelyabinsk, 454080, Russia
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Subhaswaraj P, Siddhardha B. Molecular docking and molecular dynamic simulation approaches for drug development and repurposing of drugs for severe acute respiratory syndrome-Coronavirus-2. Computational Approaches for Novel Therapeutic and Diagnostic Designing to Mitigate SARS-CoV-2 Infection 2022. [DOI: 10.1016/b978-0-323-91172-6.00007-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Zhang G, Li M, Zheng M, Cai X, Yang J, Zhang S, Yilifate A, Zheng Y, Lin Q, Liang J, Guo L, Ou H. Effect of Surgical Masks on Cardiopulmonary Function in Healthy Young Subjects: A Crossover Study. Front Physiol 2021; 12:710573. [PMID: 34566679 PMCID: PMC8461071 DOI: 10.3389/fphys.2021.710573] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 07/26/2021] [Indexed: 12/21/2022] Open
Abstract
Objective: Mask plays an important role in preventing infectious respiratory diseases. The influence of wearing masks in physical exercise on the human body needs to be studied. The purpose of this study is to explore the influence of wearing surgical masks on the cardiopulmonary function of healthy people during exercise. Methods: The physiological responses of 71 healthy subjects (35 men and 36 women, age 27.77 ± 7.76 years) to exercises with and without surgical masks (mask-on and mask-off) were analyzed. Cardiopulmonary function and metabolic reaction were measured by the cardiopulmonary exercise test (CPET). All tests were carried out in random sequence and should be completed in 1 week. Results: The CPETs with the mask-on condition were performed undesirably (p < 0.05), and the Borg scale was higher than the mask-off (p < 0.001). Rest oxygen uptake ( V . O 2 ) and carbon dioxide production ( V . CO2) with the mask-on condition were lower than mask-off (p < 0.01), which were more obvious at peak exercise ( V . O2 peak : 1454.8 ± 418.9 vs. 1628.6 ± 447.2 ml/min, p < 0.001; V . CO2 peak : 1873.0 ± 578.7 vs. 2169.9 ± 627.8 ml/min, p = 0.005), and the anaerobic threshold (AT) brought forward (p < 0.001). At different stages of CPET with the mask-on condition, inspiratory and expiratory time (Te) was longer (p < 0.05), and respiratory frequency (Rf) and minute ventilation ( V . E ) were shorter than mask-off, especially at peak exercise (Rf peak : 33.8 ± 7.98 vs. 37.91 ± 6.72 b/min, p < 0.001; V . Epeak : 55.07 ± 17.28 vs. 66.46 ± 17.93 l/min, p < 0.001). V T was significantly lower than mask-off just at peak exercise (1.66 ± 0.45 vs. 1.79 ± 0.5 l, p < 0.001). End-tidal oxygen partial pressure (PetO2), end-tidal carbon dioxide partial pressure (PetCO2), oxygen ventilation equivalent ( V . E / V . O2), and carbon dioxide ventilation equivalent ( V . E / V . CO2) with mask-on, which reflected pulmonary ventilation efficiency, were significantly different from mask-off at different stages of CPET (p < 0.05), but no significant difference in percutaneous oxygen saturation (SpO2) was found. Differences in oxygen pulse ( V . O2/HR), oxygen uptake efficiency slope (OUES), work efficiency (△ V . O2/△W), peak heart rate (HR), and peak systolic blood pressure (BP) existed between two conditions (p < 0.05). Conclusion: Wearing surgical masks during aerobic exercise showed certain negative impacts on cardiopulmonary function, especially during high-intensity exercise in healthy young subjects. These results provide an important recommendation for wearing a mask at a pandemic during exercises of varying intensity. Future research should focus on the response of wearing masks in patients with related cardiopulmonary diseases.
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Affiliation(s)
- Guolin Zhang
- Department of Cardiac Rehabilitation, Guangdong Provincial People's Hospital, Guangzhou, China
| | - Mei Li
- Department of Rehabilitation Medicine, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Rehabilitation Medicine, Guangzhou Medical University, Guangzhou, China
| | - Meifeng Zheng
- Department of Rehabilitation Medicine, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Rehabilitation Medicine, Guangzhou Medical University, Guangzhou, China
| | - Xiaoqing Cai
- Department of Rehabilitation Medicine, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Rehabilitation Medicine, Guangzhou Medical University, Guangzhou, China
| | - Jinyu Yang
- Department of Rehabilitation Medicine, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shengqing Zhang
- Department of Cardiac Rehabilitation, Guangdong Provincial People's Hospital, Guangzhou, China
| | - Anniwaer Yilifate
- Department of Rehabilitation Medicine, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yuxin Zheng
- Department of Rehabilitation Medicine, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qiang Lin
- Department of Rehabilitation Medicine, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Guangzhou Key Laboratory of Enhanced Recovery After Abdominal Surgery, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Junjie Liang
- Department of Rehabilitation Medicine, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Lan Guo
- Department of Cardiac Rehabilitation, Guangdong Provincial People's Hospital, Guangzhou, China
| | - Haining Ou
- Department of Rehabilitation Medicine, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Guangzhou Key Laboratory of Enhanced Recovery After Abdominal Surgery, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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Nižić Nodilo L, Ugrina I, Špoljarić D, Amidžić Klarić D, Jakobušić Brala C, Perkušić M, Pepić I, Lovrić J, Saršon V, Safundžić Kučuk M, Zadravec D, Kalogjera L, Hafner A. A Dry Powder Platform for Nose-to-Brain Delivery of Dexamethasone: Formulation Development and Nasal Deposition Studies. Pharmaceutics 2021; 13:795. [PMID: 34073500 DOI: 10.3390/pharmaceutics13060795] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/11/2021] [Accepted: 05/20/2021] [Indexed: 12/26/2022] Open
Abstract
Nasal route of administration offers a unique opportunity of brain targeted drug delivery via olfactory and trigeminal pathway, providing effective CNS concentrations at lower doses and lower risk for adverse reactions compared to systemic drug administration. Therefore, it has been recently proposed as a route of choice for glucocorticoids to control neuroinflammation processes in patients with severe Covid-19. However, appropriate delivery systems tailored to enhance their efficacy yet need to emerge. In this work we present the development of sprayable brain targeting powder delivery platform of dexamethasone sodium phosphate (DSP). DSP-loaded microspheres, optimised employing Quality-by-Design approach, were blended with soluble inert carriers (mannitol or lactose monohydrate). Powder blends were characterized in terms of homogeneity, flow properties, sprayability, in vitro biocompatibility, permeability and mucoadhesion. Nasal deposition studies were performed using 3D printed nasal cavity model. Mannitol provided better powder blend flow properties compared to lactose. Microspheres blended with mannitol retained or enlarged their mucoadhesive properties and enhanced DSP permeability across epithelial model barrier. DSP dose fraction deposited in the olfactory region reached 17.0% revealing the potential of developed powder platform for targeted olfactory delivery. The observed impact of nasal cavity asymmetry highlighted the importance of individual approach when aiming olfactory region.
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Sharma SK, Bangia A, Alshehri M, Bhardwaj R. Nonlinear dynamics for the spread of pathogenesis of COVID-19 pandemic. J Infect Public Health 2021; 14:817-831. [PMID: 34118731 PMCID: PMC8056826 DOI: 10.1016/j.jiph.2021.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 03/23/2021] [Accepted: 04/06/2021] [Indexed: 01/29/2023] Open
Abstract
Coronaviruses did not invite attention at a global level and responsiveness until the series of 2003-SARS contagion followed by year-2012 MERS plus, most recently, 2019-nCoV eruptions. SARS-CoV & MERS-CoV are painstaking, extremely pathogenic. Also, very evidently, both have been communicated from bats to palm-civets & dromedary camels and further transferred ultimately to humans. No country has been deprived of this viral genomic contamination wherever populaces reside and are interconnected. This study aimed to develop a mathematical model for calculating the transmissibility of this viral genome. The analysis aids the study of the outbreak of this Virus towards the other parts of the continent and the world. The parameters such as population mobility, natural history, epidemiological characteristics, and the transmission mechanism towards viral spread when considered into crowd dynamism result in improved estimation. This article studies the impact of time on the amount of susceptible, exposed, the infected person taking into account asymptomatic and symptomatic ones; recovered i.e., removed from this model and the virus particles existing in the open surfaces. The transition from stable phase to attractor phase happens after 13 days i.e.; it takes nearly a fortnight for the spread to randomize among people. Further, the pandemic transmission remains in the attractor phase for a very long time if no control measures are taken up. The attractor-source phase continues up to 385 days i.e., more than a year, and perhaps stabilizes on 386th day as per the Lyapunov exponent's analysis. The time series helps to know the period of the Virus's survival in the open sources i.e. markets, open spaces and various other carriers of the Virus if not quarantined or sanitized. The Virus cease to exist in around 60 days if it does not find any carrier or infect more places, people etc. The changes in LCEs of all variables as time progresses for around 400 days have been forecasted. It can be observed that phase trajectories indicate how the two variables interact with each other and affect the overall system's dynamics. It has been observed that for exposed and asymptomatically infected (y–z), as exposed ones (y) change from 0 to 100 the value of asymptomatically infected (z) increased upto around 58, at exposed ones (y) = 100, asymptomatically infected (z) has two values as 58 and 10 i.e. follows bifurcation and as exposed ones (y) changes values upto 180, the value of asymptomatically infected (z) decreases to 25 so for exposed ones (y) from 100 to 180, asymptomatically infected (z) varies from 58 to 25 to 10 follows bifurcation. Also, phase structures of exposed-symptomatically infected (y–u), exposed-removed (y–v), exposed-virus in the reservoir (y–w), asymptomatically infected-removed (z–v), symptomatically infected-removed (u–v) specifically depict bifurcations in various forms at different points. In case of asymptomatically infected-virus in the reservoir (z–w), at asymptomatically infected (z) = 10, the value of viruses in the reservoir (w) = 50, then as asymptomatically infected (z) increases to upto around 60. At this point, removed ones (v) increase from 50 to 70 and asymptomatically infected (z) decrease to 20 i.e., crosses the same value twice, which shows its limiting is known as limit cycle behavior and both the values tend to decrease towards zero. It shows a closed-loop limit cycle. Today, there has been no scientific revolution in the development of vaccination, nor has any antiviral treatment been successful, resulting in lack of its medication. Based on the phases, time series, and complexity analysis of the model's various parameters, it is studied to understand the variation in this pandemic's scenario.
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Affiliation(s)
- Sunil Kumar Sharma
- Department of Information Technology, College of Computer and Information Sciences, Majmaah University, Majmaah, Saudi Arabia.
| | - Aashima Bangia
- University School of Basic & Applied Sciences, GGS Indraprastha University, New Delhi, India.
| | - Mohammed Alshehri
- Department of Information Technology, College of Computer and Information Sciences, Majmaah University, Majmaah, Saudi Arabia.
| | - Rashmi Bhardwaj
- University School of Basic & Applied Sciences (USBAS), Head, Non-Linear Dynamics-Research-Lab, GGS Indraprastha University, New Delhi, India.
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Jo S, Kim S, Yoo J, Kim MS, Shin DH. A Study of 3CLpros as Promising Targets against SARS-CoV and SARS-CoV-2. Microorganisms 2021; 9:756. [PMID: 33916747 DOI: 10.3390/microorganisms9040756] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 12/14/2022] Open
Abstract
The outbreak of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), results in serious chaos all over the world. In addition to the available vaccines, the development of treatments to cure COVID-19 should be done quickly. One of the fastest strategies is to use a drug-repurposing approach. To provide COVID-19 patients with useful information about medicines currently being used in clinical trials, twenty-four compounds, including antiviral agents, were selected and assayed. These compounds were applied to verify the inhibitory activity for the protein function of 3CLpros (main proteases) of SARS-CoV and SARS-CoV-2. Among them, viral reverse-transcriptase inhibitors abacavir and tenofovir revealed a good inhibitory effect on both 3CLpros. Intriguingly, sildenafil, a cGMP-specific phosphodiesterase type 5 inhibitor also showed significant inhibitory function against them. The in silico docking study suggests that the active-site residues located in the S1 and S2 sites play key roles in the interactions with the inhibitors. The result indicates that 3CLpros are promising targets to cope with SAR-CoV-2 and its variants. The information can be helpful to design treatments to cure patients with COVID-19.
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Zhang Y, Greer RA, Song Y, Praveen H, Song Y. In silico identification of available drugs targeting cell surface BiP to disrupt SARS-CoV-2 binding and replication: Drug repurposing approach. Eur J Pharm Sci 2021; 160:105771. [PMID: 33617948 PMCID: PMC7894100 DOI: 10.1016/j.ejps.2021.105771] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/03/2021] [Accepted: 02/15/2021] [Indexed: 12/16/2022]
Abstract
Aims Cell surface binding immunoglobin protein (csBiP) is predicted to be susceptible to SARS-CoV-2 binding. With a substrate-binding domain (SBD) that binds to polypeptides and a nucleotide-binding domain (NBD) that can initiate extrinsic caspase-dependent apoptosis, csBiP may be a promising therapeutic target for COVID-19. This study aims to identify FDA-approved drugs that can neutralize viral binding and prevent viral replication by targeting the functional domains of csBiP. Methods In silico screening of 1999 FDA-approved drugs against the functional domains of BiP were performed using three molecular docking programs to avoid bias from individual docking programs. Top ligands were selected by averaging the ligand rankings from three programs. Interactions between top ligands and functional domains of BiP were analyzed. Key findings The top 10 SBD-binding candidates are velpatasvir, irinotecan, netupitant, lapatinib, doramectin, conivaptan, fenoverine, duvelisib, irbesartan, and pazopanib. The top 10 NBD-binding candidates are nilotinib, eltrombopag, grapiprant, topotecan, acetohexamide, vemurafenib, paritaprevir, pixantrone, azosemide, and piperaquine-phosphate. Among them, Velpatasvir and paritaprevir are antiviral agents that target the protease of hepatitis C virus. Netupitant is an anti-inflammatory drug that inhibits neurokinin-1 receptor, which contributes to acute inflammation. Grapiprant is an anti-inflammatory drug that inhibits the prostaglandin E2 receptor protein subtype 4, which is expressed on immune cells and triggers inflammation. These predicted SBD-binding drugs could disrupt SARS-CoV-2 binding to csBiP, and NBD-binding drugs may falter viral attachment and replication by locking the SBD in closed conformation and triggering apoptosis in infected cells. Significance csBiP appears to be a novel therapeutic target against COVID-19 by preventing viral attachment and replication. These identified drugs could be repurposed to treat COVID-19 patients.
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Affiliation(s)
- Yiming Zhang
- Department of Biomedical Engineering, The University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35294, United States
| | - Rory A Greer
- Department of Biomedical Engineering, The University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35294, United States
| | - Yuwei Song
- Department of Dermatology, The University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35294, United States
| | - Hrithik Praveen
- Department of Biomedical Engineering, The University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35294, United States
| | - Yuhua Song
- Department of Biomedical Engineering, The University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35294, United States.
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Panikar S, Shoba G, Arun M, Sahayarayan JJ, Usha Raja Nanthini A, Chinnathambi A, Alharbi SA, Nasif O, Kim HJ. Essential oils as an effective alternative for the treatment of COVID-19: Molecular interaction analysis of protease (M pro) with pharmacokinetics and toxicological properties. J Infect Public Health 2021; 14:601-610. [PMID: 33848890 PMCID: PMC7874929 DOI: 10.1016/j.jiph.2020.12.037] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/12/2020] [Accepted: 12/19/2020] [Indexed: 12/28/2022] Open
Abstract
Background The current health concern to the entire world is the chronic respiratory disease caused by coronavirus 2 (COVID-19). A specific treatment or proper therapy is still lacking, and the investigations from across the world for proper drug/vaccine development towards disease control are in progress. The Coronavirus replication takes place by the conversion of the polypeptide into functional protein and this occurs due to the key enzyme Main protease (Mpro). Therefore, identification of natural and effective Mpro inhibitors could be a safe and promising approach for COVID-19 control. Methods The present in silico study evaluates the effect of bioactive compounds found in Eucalyptus and Corymbia species essential oil on Mpro by docking. Molecular docking of the major seven compounds of essential oil (citronellol, alpha-terpineol, eucalyptol, d-limonene, 3-carene, o-cymene, and alpha-pinene) with Mpro was studied by AutoDock 4.2, and the properties were analysed by PreADMET and Biovia Discovery Studio visualizer. Results The calculated parameters such as binding energy, hydrophobic interactions, and hydrogen bond interactions of 6LU7 (Mpro) with Eucalyptus and Corymbia volatile secondary metabolites represented its scope as an effective therapy option against covid-19. Among the docked compounds, eucalyptol shows the least binding energy without toxicity. Conclusions The outcome of this study reported that the essential oil of Eucalyptus and Corymbia species, mainly eucalyptol can be utilized as a potential inhibitor against COVID-19 and also it can be used in its treatment. Hence, further analysis was required to explore its potential application in medicine.
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Affiliation(s)
- Sukanya Panikar
- Department of Biotechnology, Mother Teresa Women's University, Kodaikanal, Tamil Nadu, India
| | - Gunasekaran Shoba
- Department of Biotechnology, Mother Teresa Women's University, Kodaikanal, Tamil Nadu, India; Department of Biotechnology, Dwaraka Doss Goverdhan Doss Vaishnav College, Chennai, Tamil Nadu, India
| | - Muthukrishnan Arun
- Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India
| | | | - A Usha Raja Nanthini
- Department of Biotechnology, Mother Teresa Women's University, Kodaikanal, Tamil Nadu, India.
| | - Arunachalam Chinnathambi
- Department of Botany and Microbiology, College of Science, King Saud University, PO Box-2455, Riyadh 11451, Saudi Arabia
| | - Sulaiman A Alharbi
- Department of Botany and Microbiology, College of Science, King Saud University, PO Box-2455, Riyadh 11451, Saudi Arabia
| | - Omaima Nasif
- Department of Physiology, College of Medicine, King Saud University, [Medical City], King Khalid University Hospital, PO Box-2925, Riyadh 11461, Saudi Arabia
| | - Hak-Jae Kim
- Department of Clinical Pharmacology, College of Medicine, Soonchunhyang University, Cheonan, Republic of Korea.
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