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Saritha K, Alivelu M, Mohammad M. Drug-likeness analysis, in silico ADMET profiling of compounds in Kedrostis foetidissima (Jacq.) Cogn, and antibacterial activity of the plant extract. In Silico Pharmacol 2024; 12:67. [PMID: 39050777 PMCID: PMC11264488 DOI: 10.1007/s40203-024-00240-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 07/10/2024] [Indexed: 07/27/2024] Open
Abstract
Plants are a treasure trove of bioactive compounds. Kedrostis foetidissima (Jacq.) Cogn. has many important phytoconstituents like cucurbitacins, rutin, and quercitin compounds. Among these compounds, Quercetin-3-O- Rhamnoside (1) has antioxidant, anti-inflammatory, anticancer properties. Rutin (2) has anti-inflammatory, antioxidant, anti-diabetic, anti-microbial, antiviral properties, 7, 10-Hexa decadienoic acid methyl ester (3) has anti-inflammatory, antioxidant, hypocholesterolemia and anticancer activities. Docosanoic acid (4) has antioxidant, α-Glucosidase inhibitory activity. 3,7,11,15-Tetra methyl hexa decan-1-ol (5) has antiviral properties. Cucurbitacin-B (6) has antipyretic, analgesic, anti-inflammatory, antimicrobial, and antitumor activities. Performance of experimental studies on phytochemicals become more difficult as the availability of compounds in small quantities, hence the computational methods becomes important for drug discovery. Based on their biological activity, compounds 1-6 were tested for in silico ADMET (absorption, distribution, metabolism, excretion, and toxicity) profiling and drug-likeness properties using the Swiss ADME online web server and the pkCSM server. All the studied compounds obey Lipinski's rule of five except compounds 1 and 2 with two and three violations each. The entire selected compounds have a good bioavailability score in the recommended range of 0 to 1. Compound 4 has high (0.85) and compounds 1 and 2 have low (0.17) oral bioavailability scores. All the selected compounds from Kedrostis foetidissima have strong pharmacological activities. Supporting this, the selected plant methanol extracts of leaf, stem callus, and tuber have shown well in vitro antibacterial activity against Bacillus subtilis, Escherichia coli, and Proteus vulgaris. Therefore, these compounds may be developed into drug molecules with additional clinical research.
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Affiliation(s)
- Kommidi Saritha
- Department of Botany, Pingle Govt. College for Women (A), Hanumakonda, Telangana 506370 India
| | - Munagala Alivelu
- Department of Chemistry, Pingle Govt. College for Women (A), Hanumakonda, Telangana 506370 India
| | - Mustafa Mohammad
- Department of Botany, Kakatiya University, Warangal, Telangana 506009 India
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Ali MA, Sheikh H, Yaseen M, Faruqe MO, Ullah I, Kumar N, Bhat MA, Mollah MNH. Exploring the Therapeutic Potential of Petiveria alliacea L. Phytochemicals: A Computational Study on Inhibiting SARS-CoV-2's Main Protease (Mpro). Molecules 2024; 29:2524. [PMID: 38893400 PMCID: PMC11173994 DOI: 10.3390/molecules29112524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 06/21/2024] Open
Abstract
The outbreak of SARS-CoV-2, also known as the COVID-19 pandemic, is still a critical risk factor for both human life and the global economy. Although, several promising therapies have been introduced in the literature to inhibit SARS-CoV-2, most of them are synthetic drugs that may have some adverse effects on the human body. Therefore, the main objective of this study was to carry out an in-silico investigation into the medicinal properties of Petiveria alliacea L. (P. alliacea L.)-mediated phytocompounds for the treatment of SARS-CoV-2 infections since phytochemicals have fewer adverse effects compared to synthetic drugs. To explore potential phytocompounds from P. alliacea L. as candidate drug molecules, we selected the infection-causing main protease (Mpro) of SARS-CoV-2 as the receptor protein. The molecular docking analysis of these receptor proteins with the different phytocompounds of P. alliacea L. was performed using AutoDock Vina. Then, we selected the three top-ranked phytocompounds (myricitrin, engeletin, and astilbin) as the candidate drug molecules based on their highest binding affinity scores of -8.9, -8.7 and -8.3 (Kcal/mol), respectively. Then, a 100 ns molecular dynamics (MD) simulation study was performed for their complexes with Mpro using YASARA software, computed RMSD, RMSF, PCA, DCCM, MM/PBSA, and free energy landscape (FEL), and found their almost stable binding performance. In addition, biological activity, ADME/T, DFT, and drug-likeness analyses exhibited the suitable pharmacokinetics properties of the selected phytocompounds. Therefore, the results of this study might be a useful resource for formulating a safe treatment plan for SARS-CoV-2 infections after experimental validation in wet-lab and clinical trials.
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Affiliation(s)
- Md. Ahad Ali
- Bioinformatics Laboratory, Department of Statistics, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh;
- Department of Chemistry, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Humaira Sheikh
- Department of Chemistry, Faculty of Science, Bangabandhu Sheikh Mujibur Rahman Science & Technology University, Gopalganj 8100, Bangladesh;
| | - Muhammad Yaseen
- Institute of Chemical Sciences, University of Swat, Main Campus, Charbagh 19130, Pakistan;
| | - Md Omar Faruqe
- Department of Computer Science and Engineering, Faculty of Engineering, University of Rajshahi, Rajshahi 6205, Bangladesh;
| | - Ihsan Ullah
- Institute of Chemical Sciences, University of Swat, Main Campus, Charbagh 19130, Pakistan;
| | - Neeraj Kumar
- Department of Pharmaceutical Chemistry, Bhupal Nobles’ College of Pharmacy, Udaipur 313001, Rajasthan, India;
| | - Mashooq Ahmad Bhat
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Md. Nurul Haque Mollah
- Bioinformatics Laboratory, Department of Statistics, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh;
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Dávila-Rangel IE, Charles-Rodríguez AV, López-Romero JC, Flores-López ML. Plants from Arid and Semi-Arid Zones of Mexico Used to Treat Respiratory Diseases: A Review. PLANTS (BASEL, SWITZERLAND) 2024; 13:792. [PMID: 38592789 PMCID: PMC10974781 DOI: 10.3390/plants13060792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 04/11/2024]
Abstract
Medicinal plants have been a traditional remedy for numerous ailments for centuries. However, their usage is limited due to a lack of evidence-based studies elucidating their mechanisms of action. In some countries, they are still considered the first treatment due to their low cost, accessibility, and minor adverse effects. Mexico is in second place, after China, in inventoried plants for medicinal use. It has around 4000 species of medicinal plants; however, pharmacological studies have only been carried out in 5% of its entirety. The species of the Mexican arid zones, particularly in semi-desert areas, exhibit outstanding characteristics, as their adverse growing conditions (e.g., low rainfall and high temperatures) prompt these plants to produce interesting metabolites with diverse biological activities. This review explores medicinal plants belonging to the arid and semi-arid zones of Mexico, focusing on those that have stood out for their bioactive potential, such as Jatropha dioica, Turnera diffusa, Larrea tridentata, Opuntia ficus-indica, Flourensia cernua, Fouquieria splendes, and Prosopis glandulosa. Their extraction conditions, bioactive compounds, mechanisms of action, and biological efficacy are presented, with emphasis on their role in the treatment of respiratory diseases. Additionally, current research, novel applications, and perspectives concerning medicinal plants from these zones are also discussed.
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Affiliation(s)
| | - Ana V. Charles-Rodríguez
- Departamento de Ciencia y Tecnología de Alimentos, Universidad Autónoma Agraria Antonio Narro, Saltillo 25315, Mexico
| | - Julio C. López-Romero
- Departamento de Ciencias Químico-Biológicas y Agropecuarias, Universidad de Sonora, Caborca 83600, Mexico;
| | - María L. Flores-López
- Universidad Interserrana del Estado de Puebla Ahuactlán, Ahuacatlán 73330, Mexico;
- Centro de Investigación e Innovación Científica y Tecnológica, Universidad Autónoma de Coahuila, Saltillo 25070, Mexico
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Mjokane N, Akintemi EO, Sabiu S, Gcilitshana OMN, Albertyn J, Pohl CH, Sebolai OM. Aspergillus fumigatus secretes a protease(s) that displays in silico binding affinity towards the SARS-CoV-2 spike protein and mediates SARS-CoV-2 pseudovirion entry into HEK-293T cells. Virol J 2024; 21:58. [PMID: 38448991 PMCID: PMC10919004 DOI: 10.1186/s12985-024-02331-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 02/27/2024] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND The novel coronavirus disease of 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Data from the COVID-19 clinical control case studies showed that this disease could also manifest in patients with underlying microbial infections such as aspergillosis. The current study aimed to determine if the Aspergillus (A.) fumigatus culture media (i.e., supernatant) possessed protease activity that was sufficient to activate the SARS-CoV-2 spike protein. METHODS The supernatant was first analysed for protease activity. Thereafter, it was assessed to determine if it possessed proteolytic activity to cleave a fluorogenic mimetic peptide of the SARS-CoV-2 spike protein that contained the S1/S2 site and a full-length spike protein contained in a SARS-CoV-2 pseudovirion. To complement this, a computer-based tool, HADDOCK, was used to predict if A. fumigatus alkaline protease 1 could bind to the SARS-CoV-2 spike protein. RESULTS We show that the supernatant possessed proteolytic activity, and analyses of the molecular docking parameters revealed that A. fumigatus alkaline protease 1 could bind to the spike protein. To confirm the in silico data, it was imperative to provide experimental evidence for enzymatic activity. Here, it was noted that the A. fumigatus supernatant cleaved the mimetic peptide as well as transduced the HEK-293T cells with SARS-CoV-2 pseudovirions. CONCLUSION These results suggest that A. fumigatus secretes a protease(s) that activates the SARS-CoV-2 spike protein. Importantly, should these two infectious agents co-occur, there is the potential for A. fumigatus to activate the SARS-CoV-2 spike protein, thus aggravating COVID-19 development.
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Affiliation(s)
- Nozethu Mjokane
- Department of Microbiology and Biochemistry, University of the Free State, 205 Nelson Mandela Drive, Park West, 9301, Bloemfontein, South Africa
| | - Eric O Akintemi
- Department of Microbiology and Biochemistry, University of the Free State, 205 Nelson Mandela Drive, Park West, 9301, Bloemfontein, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Faculty of Applied Science, Durban University of Technology, 4000, Durban, P.O. Box 1334, South Africa
| | - Onele M N Gcilitshana
- Department of Microbiology and Biochemistry, University of the Free State, 205 Nelson Mandela Drive, Park West, 9301, Bloemfontein, South Africa
| | - Jacobus Albertyn
- Department of Microbiology and Biochemistry, University of the Free State, 205 Nelson Mandela Drive, Park West, 9301, Bloemfontein, South Africa
| | - Carolina H Pohl
- Department of Microbiology and Biochemistry, University of the Free State, 205 Nelson Mandela Drive, Park West, 9301, Bloemfontein, South Africa
| | - Olihile M Sebolai
- Department of Microbiology and Biochemistry, University of the Free State, 205 Nelson Mandela Drive, Park West, 9301, Bloemfontein, South Africa.
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Sopjani M, Falco F, Impellitteri F, Guarrasi V, Nguyen Thi X, Dërmaku-Sopjani M, Faggio C. Flavonoids derived from medicinal plants as a COVID-19 treatment. Phytother Res 2024; 38:1589-1609. [PMID: 38284138 DOI: 10.1002/ptr.8123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/30/2023] [Accepted: 12/29/2023] [Indexed: 01/30/2024]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19 disease. Through its viral spike (S) protein, the virus enters and infects epithelial cells by utilizing angiotensin-converting enzyme 2 as a host cell's receptor protein. The COVID-19 pandemic had a profound impact on global public health and economies. Although various effective vaccinations and medications are now available to prevent and treat COVID-19, natural compounds derived from medicinal plants, particularly flavonoids, demonstrated therapeutic potential to treat COVID-19 disease. Flavonoids exhibit dual antiviral mechanisms: direct interference with viral invasion and inhibition of replication. Specifically, they target key viral molecules, particularly viral proteases, involved in infection. These compounds showcase significant immunomodulatory and anti-inflammatory properties, effectively inhibiting various inflammatory cytokines. Additionally, emerging evidence supports the potential of flavonoids to mitigate the progression of COVID-19 in individuals with obesity by positively influencing lipid metabolism. This review aims to elucidate the molecular structure of SARS-CoV-2 and the underlying mechanism of action of flavonoids on the virus. This study evaluates the potential anti-SARS-CoV-2 properties exhibited by flavonoid compounds, with a specific interest in their structure and mechanisms of action, as therapeutic applications for the prevention and treatment of COVID-19. Nevertheless, a significant portion of existing knowledge is based on theoretical frameworks and findings derived from in vitro investigations. Further research is required to better assess the effectiveness of flavonoids in combating SARS-CoV-2, with a particular emphasis on in vivo and clinical investigations.
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Affiliation(s)
- Mentor Sopjani
- Faculty of Medicine, University of Prishtina, Prishtina, Kosova
| | - Francesca Falco
- Institute for Marine Biological Resources and Biotechnology (IRBIM)-CNR, Mazara del Vallo, Italy
| | | | - Valeria Guarrasi
- Institute of Biophysics, National Research Council (CNR), Palermo, Italy
| | - Xuan Nguyen Thi
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | | | - Caterina Faggio
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, Messina, Italy
- Department of Eco sustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Naples, Italy
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Elkolli M, Elkolli H, Alam M, Benguerba Y. In silico study of antibacterial tyrosyl-tRNA synthetase and toxicity of main phytoconstituents from three active essential oils. J Biomol Struct Dyn 2024; 42:1404-1416. [PMID: 37066614 DOI: 10.1080/07391102.2023.2199865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 04/01/2023] [Indexed: 04/18/2023]
Abstract
The misuse and overuse of antibiotics have resulted in antibiotic resistance. However, there are alternative approaches that could either substitute antibiotics or enhance their effectiveness without harmful side effects. One such approach is the use of terpene-rich essential oils. In this study, we aimed to demonstrate the antibacterial activity of the main components of three plant essential oils, namely Anthemis punctata, Anthemis pedunculata and Daucus crinitus. Specifically, we targeted bacterial tyrosyl-tRNA synthetase, an enzyme that plays a critical role in bacterial protein synthesis. To investigate how the phytocompounds interact with the enzyme's active sites, we employed a molecular docking study using Autodock Software Tools 1.5.7. Our findings revealed that all 28 phytocompounds bound to the enzyme's active sites with binding energies ranging from -6.96 to -4.03 kcal/mol. These results suggest that terpene-rich essential oils could be a potential source of novel antimicrobial agents.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Meriem Elkolli
- Laboratoire de Microbiologie Appliquée, Faculté des Sciences de la Nature et de la Vie, Setif, Algeria
| | - Hayet Elkolli
- Laboratoire des Matériaux Polymériques Multiphasiques, Département de Génie des Procédés, Faculté de Technologie, Sétif, Algeria
| | - Manawwer Alam
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Yacine Benguerba
- Laboratoire de Biopharmacie et Pharmacotechnie (LPBT), Ferhat Abbas Setif 1 University, Setif, Algeria
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Purnawita W, Rahayu WP, Lioe HN, Nurjanah S, Wahyudi ST. Potential molecular mechanism of reuterin on the inhibition of Aspergillus flavus conidial germination: An in silico study. J Food Sci 2024; 89:1167-1186. [PMID: 38193164 DOI: 10.1111/1750-3841.16904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/28/2023] [Accepted: 12/08/2023] [Indexed: 01/10/2024]
Abstract
Reuterin is a natural antifungal agent derived from certain strains of Limosilactobacillus reuteri. Our previous study revealed that 6 mM reuterin inhibited completely the conidial germination of aflatoxigenic Aspergillus flavus. This study investigated the potential molecular mechanism of reuterin in inhibiting A. flavus conidial germination, which was pre-assumed that it correlated to the inhibition of some essential enzyme activity involved in conidial germination, specifically 1,3-β-glucan synthase, chitin synthase, and catalases (catalase, bifunctional catalase-peroxidase, and spore-specific catalase). The complex of 1,3-β-glucan synthase and chitin synthase with reuterin had a lower binding affinity than that with the substrate. Conversely, the complex of catalases with reuterin had a higher binding affinity than that with the substrate. It was suggested that 1,3-β-glucan synthase and chitin synthase tended to bind the substrate rather than bind reuterin. In contrast, catalases tended to bind reuterin rather than bind the substrate. Therefore, reuterin could be a potential inhibitor of catalases but may not be an inhibitor of 1,3-β-glucan synthase and chitin synthase. In this in silico study, we predicted that the potential molecular mechanism of reuterin in inhibiting A. flavus conidial germination was due to the inhibition of catalases activities by competitively binding to the enzymes active sites, thus resulting in the accumulation of reactive oxygen species in cells, leading to cells damage. PRACTICAL APPLICATION: This in silico study revealed that reuterin is a potential inhibitor of catalases in A. flavus, thereby interfering with the antioxidant system during conidial germination. This finding shows that reuterin can be used as an antifungal agent in food or agricultural products, inhibiting conidial germination completely.
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Affiliation(s)
- Widiati Purnawita
- Department of Food Science and Technology, Faculty of Agricultural Engineering and Technology, IPB University (Bogor Agricultural University), Bogor, Indonesia
| | - Winiati Pudji Rahayu
- Department of Food Science and Technology, Faculty of Agricultural Engineering and Technology, IPB University (Bogor Agricultural University), Bogor, Indonesia
- Southeast Asian Food and Agricultural Science and Technology (SEAFAST) Center, IPB University (Bogor Agricultural University), Bogor, Indonesia
| | - Hanifah Nuryani Lioe
- Department of Food Science and Technology, Faculty of Agricultural Engineering and Technology, IPB University (Bogor Agricultural University), Bogor, Indonesia
- Southeast Asian Food and Agricultural Science and Technology (SEAFAST) Center, IPB University (Bogor Agricultural University), Bogor, Indonesia
| | - Siti Nurjanah
- Department of Food Science and Technology, Faculty of Agricultural Engineering and Technology, IPB University (Bogor Agricultural University), Bogor, Indonesia
- Southeast Asian Food and Agricultural Science and Technology (SEAFAST) Center, IPB University (Bogor Agricultural University), Bogor, Indonesia
| | - Setyanto Tri Wahyudi
- Southeast Asian Food and Agricultural Science and Technology (SEAFAST) Center, IPB University (Bogor Agricultural University), Bogor, Indonesia
- Tropical Biopharmaca Research Center, IPB University (Bogor Agricultural University), Bogor, Indonesia
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Hu C. Marine natural products and human immunity: novel biomedical resources for anti-infection of SARS-CoV-2 and related cardiovascular disease. NATURAL PRODUCTS AND BIOPROSPECTING 2024; 14:12. [PMID: 38282092 PMCID: PMC10822835 DOI: 10.1007/s13659-024-00432-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 01/17/2024] [Indexed: 01/30/2024]
Abstract
Marine natural products (MNPs) and marine organisms include sea urchin, sea squirts or ascidians, sea cucumbers, sea snake, sponge, soft coral, marine algae, and microalgae. As vital biomedical resources for the discovery of marine drugs, bioactive molecules, and agents, these MNPs have bioactive potentials of antioxidant, anti-infection, anti-inflammatory, anticoagulant, anti-diabetic effects, cancer treatment, and improvement of human immunity. This article reviews the role of MNPs on anti-infection of coronavirus, SARS-CoV-2 and its major variants (such as Delta and Omicron) as well as tuberculosis, H. Pylori, and HIV infection, and as promising biomedical resources for infection related cardiovascular disease (irCVD), diabetes, and cancer. The anti-inflammatory mechanisms of current MNPs against SARS-CoV-2 infection are also discussed. Since the use of other chemical agents for COVID-19 treatment are associated with some adverse effects in cardiovascular system, MNPs have more therapeutic advantages. Herein, it's time to protect this ecosystem for better sustainable development in the new era of ocean economy. As huge, novel and promising biomedical resources for anti-infection of SARS-CoV-2 and irCVD, the novel potential mechanisms of MNPs may be through multiple targets and pathways regulating human immunity and inhibiting inflammation. In conclusion, MNPs are worthy of translational research for further clinical application.
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Affiliation(s)
- Chunsong Hu
- Department of Cardiovascular Medicine, Jiangxi Academy of Medical Science, Nanchang University, Hospital of Nanchang University, No. 461 Bayi Ave, Nanchang, 330006, Jiangxi, China.
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He Z, Yuan J, Zhang Y, Li R, Mo M, Wang Y, Ti H. Recent advances towards natural plants as potential inhibitors of SARS-Cov-2 targets. PHARMACEUTICAL BIOLOGY 2023; 61:1186-1210. [PMID: 37605622 PMCID: PMC10446791 DOI: 10.1080/13880209.2023.2241518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 05/29/2023] [Accepted: 07/23/2023] [Indexed: 08/23/2023]
Abstract
CONTEXT Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is still ongoing and currently the most striking epidemic disease. With the rapid global spread of SARS-CoV-2 variants, new antivirals are urgently needed to avert a more serious crisis. Inhibitors from traditional medicines or natural plants have shown promising results to fight COVID-19 with different mechanisms of action. OBJECTIVES To provide comprehensive and promising approaches to the medical community in the fight against this epidemic by reviewing potential plant-derived anti-SARS-CoV-2 inhibitors. METHODS Structural databases such as TCMSP (http://lsp.nwu.edu.cn/tcmsp.php), TCM Database @ Taiwan (http://tcm.cmu.edu.tw/), BATMAN-TCM (http://bionet.ncpsb.org/batman-tcm/) and TCMID (http://www.megabionet.org/tcmid/), as well as PubMed, Sci Finder, Research Gate, Science Direct, CNKI, Web of Science and Google Scholar were searched for relevant articles on TCMs and natural products against SARS-CoV-2. RESULTS Seven traditional Chinese medicines formulas have unique advantages in regulating the immune system for treating COVID-19. The plant-derived natural compounds as anti-SARS-CoV-2 inhibitors were identified based on 5 SARS-CoV-2 key proteins, namely, angiotensin-converting enzyme 2 (ACE2), 3 C-like protease (3CLpro), papain-like protease (PLpro), spike (S) protein, and nucleocapsid (N) protein. CONCLUSIONS A variety of natural products, such as flavonoids, terpenoids, phenols, and alkaloids, were identified, which could be used as potential SASR-Cov-2 inhibitors. These shed new light on the efficient discovery of SASR-Cov-2 inhibitors from natural products.
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Affiliation(s)
- Zhouman He
- School of Chinese Medicinal Resource, Guangdong Pharmaceutical University, Guangzhou, P. R. China
| | - Jia Yuan
- School of Chinese Medicinal Resource, Guangdong Pharmaceutical University, Guangzhou, P. R. China
| | - Yuanwen Zhang
- School of Chinese Medicinal Resource, Guangdong Pharmaceutical University, Guangzhou, P. R. China
| | - Runfeng Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, P. R. China
| | - Meilan Mo
- School of Chinese Medicinal Resource, Guangdong Pharmaceutical University, Guangzhou, P. R. China
| | - Yutao Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, P. R. China
| | - Huihui Ti
- School of Chinese Medicinal Resource, Guangdong Pharmaceutical University, Guangzhou, P. R. China
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Mushebenge AGA, Ugbaja SC, Mbatha NA, B. Khan R, Kumalo HM. Assessing the Potential Contribution of In Silico Studies in Discovering Drug Candidates That Interact with Various SARS-CoV-2 Receptors. Int J Mol Sci 2023; 24:15518. [PMID: 37958503 PMCID: PMC10647470 DOI: 10.3390/ijms242115518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/18/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
The COVID-19 pandemic has spurred intense research efforts to identify effective treatments for SARS-CoV-2. In silico studies have emerged as a powerful tool in the drug discovery process, particularly in the search for drug candidates that interact with various SARS-CoV-2 receptors. These studies involve the use of computer simulations and computational algorithms to predict the potential interaction of drug candidates with target receptors. The primary receptors targeted by drug candidates include the RNA polymerase, main protease, spike protein, ACE2 receptor, and transmembrane protease serine 2 (TMPRSS2). In silico studies have identified several promising drug candidates, including Remdesivir, Favipiravir, Ribavirin, Ivermectin, Lopinavir/Ritonavir, and Camostat Mesylate, among others. The use of in silico studies offers several advantages, including the ability to screen a large number of drug candidates in a relatively short amount of time, thereby reducing the time and cost involved in traditional drug discovery methods. Additionally, in silico studies allow for the prediction of the binding affinity of the drug candidates to target receptors, providing insight into their potential efficacy. This study is aimed at assessing the useful contributions of the application of computational instruments in the discovery of receptors targeted in SARS-CoV-2. It further highlights some identified advantages and limitations of these studies, thereby revealing some complementary experimental validation to ensure the efficacy and safety of identified drug candidates.
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Affiliation(s)
- Aganze Gloire-Aimé Mushebenge
- Discipline of Pharmaceutical Sciences, University of KwaZulu-Natal, Westville, Durban 4000, South Africa;
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa
- Faculty of Pharmaceutical Sciences, University of Lubumbashi, Lubumbashi 1825, Democratic Republic of the Congo
| | - Samuel Chima Ugbaja
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa
- Africa Health Research Institute, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Nonkululeko Avril Mbatha
- KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Rene B. Khan
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Hezekiel M. Kumalo
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa
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El-Hosari DG, Hussein WM, Elgendy MO, Elgendy SO, Ibrahim ARN, Fahmy AM, Hassan A, Mokhtar FA, Hussein MF, Abdelrahim MEA, Haggag EG. Galangal-Cinnamon Spice Mixture Blocks the Coronavirus Infection Pathway through Inhibition of SARS-CoV-2 M Pro, Three HCoV-229E Targets; Quantum-Chemical Calculations Support In Vitro Evaluation. Pharmaceuticals (Basel) 2023; 16:1378. [PMID: 37895849 PMCID: PMC10610207 DOI: 10.3390/ph16101378] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/17/2023] [Accepted: 09/19/2023] [Indexed: 10/29/2023] Open
Abstract
Natural products such as domestic herbal drugs which are easily accessible and cost-effective can be used as a complementary treatment in mild and moderate COVID-19 cases. This study aimed to detect and describe the efficiency of phenolics detected in the galangal-cinnamon mixture in the inhibition of SARS-CoV-2's different protein targets. The potential antiviral effect of galangal-cinnamon aqueous extract (GCAE) against Low Pathogenic HCoV-229E was assessed using cytopathic effect inhibition assay and the crystal violet method. Low Pathogenic HCoV-229E was used as it is safer for in vitro laboratory experimentation and due to the conformation and the binding pockets similarity between HCoV-229E and SARS-CoV-2 MPro. The GCAE showed a significant antiviral effect against HCoV-229E (IC50 15.083 µg/mL). Twelve phenolic compounds were detected in the extract with ellagic, cinnamic, and gallic acids being the major identified phenolic acids, while rutin was the major identified flavonoid glycoside. Quantum-chemical calculations were made to find molecular properties using the DFT/B3LYP method with 6-311++G(2d,2p) basis set. Quantum-chemical values such as EHOMO, ELUMO, energy gap, ionization potential, chemical hardness, softness, and electronegativity values were calculated and discussed. Phenolic compounds detected by HPLC-DAD-UV in the GCAE were docked into the active site of 3 HCoV-229E targets (PDB IDs. 2ZU2, 6U7G, 7VN9, and 6WTT) to find the potential inhibitors that block the Coronavirus infection pathways from quantum and docking data for these compounds. There are good adaptations between the theoretical and experimental results showing that rutin has the highest activity against Low Pathogenic HCoV-229E in the GCAE extract.
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Affiliation(s)
- Doaa G. El-Hosari
- Pharmacognosy Department, Faculty of Pharmacy, Helwan University, Cairo 11795, Egypt; (W.M.H.); (E.G.H.)
| | - Wesam M. Hussein
- Pharmacognosy Department, Faculty of Pharmacy, Helwan University, Cairo 11795, Egypt; (W.M.H.); (E.G.H.)
| | - Marwa O. Elgendy
- Department of Clinical Pharmacy, Beni-Suef University Hospitals, Faculty of Medicine, Beni-Suef University, Beni-Suef 62521, Egypt
- Department of Clinical Pharmacy, Faculty of Pharmacy, Nahda University (NUB), Beni-Suef 62513, Egypt
| | - Sara O. Elgendy
- Clinical and Chemical Pathology Department, Faculty of Medicine, Beni-Suef University, Beni-Suef 62521, Egypt;
| | - Ahmed R. N. Ibrahim
- Department of Clinical Pharmacy, College of Pharmacy, King Khalid University, Abha 61421, Saudi Arabia;
| | - Alzhraa M. Fahmy
- Tropical Medicine and Infectious Diseases Department, Faculty of Medicine, Beni-Suef University, Beni-Suef 62521, Egypt;
| | - Afnan Hassan
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Cairo 12578, Egypt;
| | - Fatma Alzahraa Mokhtar
- Department of Pharmacognosy, Faculty of Pharmacy, El Saleheya El Gadida University, El Saleheya El Gadida 44813, Egypt;
| | - Modather F. Hussein
- Chemistry Department, Collage of Science, Jouf University, P.O. Box 2014, Sakaka 72388, Saudi Arabia;
- Chemistry Department, Faculty of Science, Al-Azhar University, Asyut Branch, Assiut 71524, Egypt
| | - Mohamed E. A. Abdelrahim
- Clinical Pharmacy Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62521, Egypt;
| | - Eman G. Haggag
- Pharmacognosy Department, Faculty of Pharmacy, Helwan University, Cairo 11795, Egypt; (W.M.H.); (E.G.H.)
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12
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Shamim A, Ansari MJ, Aodah A, Iqbal M, Aqil M, Mirza MA, Iqbal Z, Ali A. QbD-Engineered Development and Validation of a RP-HPLC Method for Simultaneous Estimation of Rutin and Ciprofloxacin HCl in Bilosomal Nanoformulation. ACS OMEGA 2023; 8:21618-21627. [PMID: 37360463 PMCID: PMC10286274 DOI: 10.1021/acsomega.3c00956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/23/2023] [Indexed: 06/28/2023]
Abstract
In the given study, a new reverse-phase high-performance liquid chromatography (RP-HPLC) method has been reported for the simultaneous estimation of ciprofloxacin hydrochloride (CPX) and rutin (RUT) using quality by design (QbD) approach. The analysis was carried out by applying the Box-Behnken design having fewer design points and less experimental runs. It relates between factors and responses and gives statistically significant values, along with enhancing the quality of the analysis. CPX and RUT were separated on the Kromasil C18 column (4.6 × 150 mm, 5 μm) using an isocratic mobile phase combination of phosphoric acid buffer (pH 3.0) and acetonitrile with the ratio of 87:13% v/v at a flow rate of 1.0 mL/min. CPX and RUT were detected at their respective wavelengths of 278 and 368 nm using a photodiode array detector. The developed method was validated according to guideline ICH Q2 R (1). The validation parameters taken were linearity, system suitability, accuracy, precision, robustness, sensitivity, and solution stability which were in the acceptable range. The findings suggest that the developed RP-HPLC method can be successfully applied to analyze novel CPX-RUT-loaded bilosomal nanoformulation prepared by thin-film hydration technique.
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Affiliation(s)
- Athar Shamim
- Department
of Pharmaceutics, School of Pharmaceutical
Education and Research, Jamia Hamdard, New Delhi 110062, India
| | - Mohammad Javed Ansari
- Department
of Pharmaceutics, College of Pharmacy, Prince
Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Alhussain Aodah
- Department
of Pharmaceutics, College of Pharmacy, Prince
Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Muzaffar Iqbal
- Department
of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451,Saudi Arabia
| | - Mohd. Aqil
- Department
of Pharmaceutics, School of Pharmaceutical
Education and Research, Jamia Hamdard, New Delhi 110062, India
| | - Mohd. Aamir Mirza
- Department
of Pharmaceutics, School of Pharmaceutical
Education and Research, Jamia Hamdard, New Delhi 110062, India
| | - Zeenat Iqbal
- Department
of Pharmaceutics, School of Pharmaceutical
Education and Research, Jamia Hamdard, New Delhi 110062, India
| | - Asgar Ali
- Department
of Pharmaceutics, School of Pharmaceutical
Education and Research, Jamia Hamdard, New Delhi 110062, India
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13
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Akter R, Rahman MR, Ahmed ZS, Afrose A. Plausibility of natural immunomodulators in the treatment of COVID-19-A comprehensive analysis and future recommendations. Heliyon 2023; 9:e17478. [PMID: 37366526 PMCID: PMC10284624 DOI: 10.1016/j.heliyon.2023.e17478] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 06/15/2023] [Accepted: 06/19/2023] [Indexed: 06/28/2023] Open
Abstract
The COVID-19 pandemic has inflicted millions of deaths worldwide. Despite the availability of several vaccines and some special drugs approved for emergency use to prevent or treat this disease still, there is a huge concern regarding their effectiveness, adverse effects, and most importantly, their efficacy against the new variants. A cascade of immune-inflammatory responses is involved with the pathogenesis and severe complications with COVID-19. People with dysfunctional and compromised immune systems display severe complications, including acute respiratory distress syndrome, sepsis, multiple organ failure etc., when they get infected with the SARS-CoV-2 virus. Plant-derived natural immune-suppressant compounds, such as resveratrol, quercetin, curcumin, berberine, luteolin, etc., have been reported to inhibit pro-inflammatory cytokines and chemokines. Therefore, natural products with immunomodulatory and anti-inflammatory potential could be plausible targets to treat this contagious disease. This review aims to delineate the clinical trials status and outcomes of natural compounds with immunomodulatory potential in COVID-19 patients along with the outcomes of their in-vivo studies. In clinical trials several natural immunomodulators resulted in significant improvement of COVID-19 patients by diminishing COVID-19 symptoms such as fever, cough, sore throat, and breathlessness. Most importantly, they reduced the duration of hospitalization and the need for supplemental oxygen therapy, improved clinical outcomes in patients with COVID-19, especially weakness, and eliminated acute lung injury and acute respiratory distress syndrome. This paper also discusses many potent natural immunomodulators yet to undergo clinical trials. In-vivo studies with natural immunomodulators demonstrated reduction of a wide range of proinflammatory cytokines. Natural immunomodulators that were found effective, safe, and well tolerated in small-scale clinical trials are warranted to undergo large-scale trials to be used as drugs to treat COVID-19 infections. Alongside, compounds yet to test clinically must undergo clinical trials to find their effectiveness and safety in the treatment of COVID-19 patients.
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Affiliation(s)
- Raushanara Akter
- School of Pharmacy, Brac University, 66 Mohakhali, Dhaka, Bangladesh
| | - Md Rashidur Rahman
- Department of Pharmacy, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Zainab Syed Ahmed
- School of Pharmacy, Brac University, 66 Mohakhali, Dhaka, Bangladesh
| | - Afrina Afrose
- School of Pharmacy, Brac University, 66 Mohakhali, Dhaka, Bangladesh
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14
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Matsumura Y, Kitabatake M, Kayano SI, Ito T. Dietary Phenolic Compounds: Their Health Benefits and Association with the Gut Microbiota. Antioxidants (Basel) 2023; 12:antiox12040880. [PMID: 37107256 PMCID: PMC10135282 DOI: 10.3390/antiox12040880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 04/08/2023] Open
Abstract
Oxidative stress causes various diseases, such as type II diabetes and dyslipidemia, while antioxidants in foods may prevent a number of diseases and delay aging by exerting their effects in vivo. Phenolic compounds are phytochemicals such as flavonoids which consist of flavonols, flavones, flavanonols, flavanones, anthocyanidins, isoflavones, lignans, stilbenoids, curcuminoids, phenolic acids, and tannins. They have phenolic hydroxyl groups in their molecular structures. These compounds are present in most plants, are abundant in nature, and contribute to the bitterness and color of various foods. Dietary phenolic compounds, such as quercetin in onions and sesamin in sesame, exhibit antioxidant activity and help prevent cell aging and diseases. In addition, other kinds of compounds, such as tannins, have larger molecular weights, and many unexplained aspects still exist. The antioxidant activities of phenolic compounds may be beneficial for human health. On the other hand, metabolism by intestinal bacteria changes the structures of these compounds with antioxidant properties, and the resulting metabolites exert their effects in vivo. In recent years, it has become possible to analyze the composition of the intestinal microbiota. The augmentation of the intestinal microbiota by the intake of phenolic compounds has been implicated in disease prevention and symptom recovery. Furthermore, the “brain–gut axis”, which is a communication system between the gut microbiome and brain, is attracting increasing attention, and research has revealed that the gut microbiota and dietary phenolic compounds affect brain homeostasis. In this review, we discuss the usefulness of dietary phenolic compounds with antioxidant activities against some diseases, their biotransformation by the gut microbiota, the augmentation of the intestinal microflora, and their effects on the brain–gut axis.
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Affiliation(s)
- Yoko Matsumura
- Department of Nutrition, Faculty of Health Sciences, Kio University, Kitakatsuragi-gun, Nara 635-0832, Japan
- Department of Immunology, Nara Medical University, Kashihara, Nara 634-8521, Japan
| | - Masahiro Kitabatake
- Department of Immunology, Nara Medical University, Kashihara, Nara 634-8521, Japan
| | - Shin-ichi Kayano
- Department of Nutrition, Faculty of Health Sciences, Kio University, Kitakatsuragi-gun, Nara 635-0832, Japan
| | - Toshihiro Ito
- Department of Immunology, Nara Medical University, Kashihara, Nara 634-8521, Japan
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15
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Study of the phytochemical profile of hydroponically cultivated buckwheat (Fagopyrum esculentum Moench) at different phenological stages. BIOCHEM SYST ECOL 2023. [DOI: 10.1016/j.bse.2023.104612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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16
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Akbarzadeh I, Rezaei N, Bazzazan S, Mezajin MN, Mansouri A, Karbalaeiheidar H, Ashkezari S, Moghaddam ZS, Lalami ZA, Mostafavi E. In silico and in vitro studies of GENT-EDTA encapsulated niosomes: A novel approach to enhance the antibacterial activity and biofilm inhibition in drug-resistant Klebsiella pneumoniae. BIOMATERIALS ADVANCES 2023; 149:213384. [PMID: 37060635 DOI: 10.1016/j.bioadv.2023.213384] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 12/06/2022] [Accepted: 03/10/2023] [Indexed: 03/17/2023]
Abstract
Klebsiella pneumoniae (Kp) is a common pathogen inducing catheter-related biofilm infections. Developing effective therapy to overcome antimicrobial resistance (AMR) in Kp is a severe therapeutic challenge that must be solved. This study aimed to prepare niosome-encapsulated GENT (Gentamicin) and EDTA (Ethylenediaminetetraacetic acid) (GENT-EDTA/Nio) to evaluate its efficacy toward Kp strains. The thin-film hydration method was used to prepare various formulations of GENT-EDTA/Nio. Formulations were characterized for their physicochemical characteristics. GENT-EDTA/Nio properties were used for optimization with Design-Expert Software. Molecular docking was utilized to determine the antibacterial activity of GENT. The niosomes displayed a controlled drug release and storage stability of at least 60 days at 4 and 25 °C. GENT-EDTA/Nio performance as antimicrobial agents has been evaluated by employing agar well diffusion method, minimum bactericidal concentration (MBC), and minimum inhibitory concentration (MIC) against the Kp bacteria strains. Biofilm formation was investigated after GENT-EDTA/Nio administration through different detection methods, which showed that this formulation reduces biofilm formation. The effect of GENT-EDTA/Nio on the expression of biofilm-related genes (mrkA, ompA, and vzm) was estimated using QRT-PCR. MTT assay was used to evaluate the toxicity effect of niosomal formulations on HFF cells. The present study results indicate that GENT-EDTA/Nio decreases Kp's resistance to antibiotics and increases its antibiotic and anti-biofilm activity and could be helpful as a new approach for drug delivery.
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17
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Sundaramahalingam MA, Amrutha C, Rajeshbanu J, Thirukumaran K, Manibalan S, Ashokkumar M, Sivashanmugam P. In silico approach for enhancing innate lipid content of Yarrowia lipolytica, by blocking the acyl-CoA oxidase-1 enzyme, using various analogous compounds of lipids. J Biomol Struct Dyn 2023; 41:511-524. [PMID: 34825634 DOI: 10.1080/07391102.2021.2008498] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Yarrowia lipolytica is used as a model in this study to screen the potential candidates for inflating the innate lipid content of the cell. This study focuses on reducing the lipid degradation that occurs by the β-oxidation process and discursively increasing the innate lipid content. Acyl-CoA oxidase-1, the primary and initial enzyme involved in the lipid degradation pathway, was selected as a target and blocked using various lipid analogous compounds. The blocking study was carried out using molecular docking and dynamic studies using computation tools. The largest active site pocket located around the Phe-394 amino acid of the target protein is taken as a site for docking. The molecular docking was performed for the selected compounds (citric acid, Finsolv, lactic acid, oxalic acid, Tween-80 and Triton X-100) and the docking results were compared with the outcome of the standard molecule (octadecatrienoic acid). Citric acid, Finsolv, Tween-80 and Triton X-100 were found to be the potential candidates for blocking the target molecule in the static condition using docking studies, revealing a minimum binding energy requirement than the standard molecule. They were further taken for a dynamics study using GROMACS software. The RMSD, RMSF, number of hydrogen bond interactions and radius of gyration of the complex molecules were studied in a dynamic approach for 100 ns. Citric acid has been found to be the potential hit compound to block acyl-CoA oxidase-1 enzyme with its maximum hydrogen interaction and minimum fluctuations. It also revealed out the minimum total energy requirement for the complex formation.
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Affiliation(s)
- M A Sundaramahalingam
- Chemical and Biochemical Process Engineering Laboratory, Department of Chemical Engineering, National Institute of Technology Tiruchirappalli, Tamilnadu, India
| | - C Amrutha
- Chemical and Biochemical Process Engineering Laboratory, Department of Chemical Engineering, National Institute of Technology Tiruchirappalli, Tamilnadu, India
| | - J Rajeshbanu
- Department of Life Sciences, Central University of Tamil Nadu, Neelakudi, Thiruvarur, Tamilnadu, India
| | - K Thirukumaran
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam, India
| | - S Manibalan
- Department of Biotechnology, Kamaraj College of Engineering and Technology, Madurai, Tamilnadu, India
| | | | - P Sivashanmugam
- Chemical and Biochemical Process Engineering Laboratory, Department of Chemical Engineering, National Institute of Technology Tiruchirappalli, Tamilnadu, India
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18
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Zhang K, Wang L, Peng J, Sangji K, Luo Y, Zeng Y, Zeweng Y, Fan G. Traditional Tibetan medicine to fight against COVID-19: Basic theory and therapeutic drugs. Front Pharmacol 2023; 14:1098253. [PMID: 36874035 PMCID: PMC9978713 DOI: 10.3389/fphar.2023.1098253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/31/2023] [Indexed: 02/18/2023] Open
Abstract
The Coronavirus Diseases 2019 (COVID-19) has been rapidly spreading globally and has caused severe harm to the health of people and a substantial social burden. In response to this situation, experts around the world have considered various treatments, including the use of traditional medicine. Traditional Tibetan medicine (TTM), one of the traditional medicines in China, has played an important role in the treatment of infectious diseases in history. It has formed a solid theoretical foundation and accumulated rich experience in the treatment of infectious diseases. In this review, we provide a comprehensive introduction to the basic theory, treatment strategies, and commonly used drugs of TTM for the treatment of COVID-19. In addition, the efficacies and potential mechanisms of these TTM drugs against COVID-19 are discussed based on available experimental data. This review may provide important information for the basic research, clinical application and drug development of traditional medicines for the treatment of COVID-19 or other infectious diseases. More pharmacological studies are needed to reveal the therapeutic mechanisms and active ingredients of TTM drugs in the treatment of COVID-19.
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Affiliation(s)
- Kun Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Lijie Wang
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jiayan Peng
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Kangzhuo Sangji
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yuting Luo
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yujiao Zeng
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yongzhong Zeweng
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Gang Fan
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China.,School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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19
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Lopes SM, de Medeiros HIR, Scotti MT, Scotti L. Natural Products Against COVID-19 Inflammation: A Mini-Review. Comb Chem High Throughput Screen 2022; 25:2358-2369. [PMID: 35088662 DOI: 10.2174/1386207325666220128114547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/03/2021] [Accepted: 11/18/2021] [Indexed: 01/27/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) is a virus whose genetic material is positive single-stranded RNA, being responsible for coronavirus disease 2019 (COVID- 19), an infection that compromises the lungs and consequently the respiratory capacity of the infected individual, according to the WHO in November 2021, 249,743,428 cases were confirmed, of which 5,047,652 individuals died due to complications resulting from the infection caused by SARSCOV- 2. As the infection progresses, the individual may experience loss of smell and taste, as well as breathing difficulties, severe respiratory failure, multiple organ failure, and death. Due to this new epidemiological agent in March 2020 it was announced by the director general of the World Health Organization (WHO) a pandemic status, and with that, many research groups are looking for new therapeutic alternatives through synthetic and natural bioactives. This research is a literature review of some in silico studies involving natural products against COVID-19 inflammation published in 2020 and 2021. Work like this presents relevant information to the scientific community, boosting future research and encouraging the use of natural products for the search for new antivirals against COVID-19.
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Affiliation(s)
- Simone Mendes Lopes
- Postgraduate Program in Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraíba, João Pessoa Pb, Brazil
| | - Herbert Igor Rodrigues de Medeiros
- Postgraduate Program in Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraíba, João Pessoa Pb, Brazil
| | - Marcus Tullius Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraíba, João Pessoa Pb, Brazil
| | - Luciana Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products (PgPNSB), Health Sciences Center, Federal University of Paraíba, João Pessoa Pb, Brazil.,Lauro Wanderley University Hospital (HULW), Health Sciences Center, Federal University of Paraíba, João Pessoa Pb, Brazil
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20
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Salehpour P, Abri A. Preparation and characterization of Rutin loaded on magnetic graphene quantum dot nano career with metals (Ag, Zn, Mg, Co, and Fe) and study of antioxidant and electrochemical properties. Colloids Surf B Biointerfaces 2022; 220:112903. [DOI: 10.1016/j.colsurfb.2022.112903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/29/2022] [Accepted: 10/02/2022] [Indexed: 11/07/2022]
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21
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Alqathama AA, Ahmad R, Alsaedi RB, Alghamdi RA, Abkar EH, Alrehaly RH, Abdalla AN. The vital role of animal, marine, and microbial natural products against COVID-19. PHARMACEUTICAL BIOLOGY 2022; 60:509-524. [PMID: 35234563 PMCID: PMC8896193 DOI: 10.1080/13880209.2022.2039215] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 01/21/2022] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
CONTEXT Since the outbreak of SARS-CoV-2, researchers have been working on finding ways to prevent viral entry and pathogenesis. Drug development from naturally-sourced pharmacological constituents may be a fruitful approach to COVID-19 therapy. OBJECTIVE Most of the published literature has focussed on medicinal plants, while less attention has been given to biodiverse sources such as animal, marine, and microbial products. This review focuses on highlighting natural products and their derivatives that have been evaluated for antiviral, anti-inflammatory, and immunomodulatory properties. METHODS We searched electronic databases such as PubMed, Scopus, Science Direct and Springer Link to gather raw data from publications up to March 2021, using terms such as 'natural products', marine, micro-organism, and animal, COVID-19. We extracted a number of documented clinical trials of products that were tested in silico, in vitro, and in vivo which paid specific attention to chemical profiles and mechanisms of action. RESULTS Various classes of flavonoids, 2 polyphenols, peptides and tannins were found, which exhibit inhibitory properties against viral and host proteins, including 3CLpro, PLpro, S, hACE2, and NF-κB, many of which are in different phases of clinical trials. DISCUSSION AND CONCLUSIONS The synergistic effects of logical combinations with different mechanisms of action emphasizes their value in COVID19 management, such as iota carrageenan nasal spray, ermectin oral drops, omega-3 supplementation, and a quadruple treatment of zinc, quercetin, bromelain, and vitamin C. Though in vivo efficacy of these compounds has yet to be established, these bioproducts are potentially useful in counteracting the effects of SARS-CoV-2.
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Affiliation(s)
- Aljawharah A. Alqathama
- Department of Pharmacognosy, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Rizwan Ahmad
- Department of Natural Products and Alternative Medicines, College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Ruba B. Alsaedi
- Department of Pharmacognosy, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Raghad A. Alghamdi
- Department of Pharmacognosy, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Ekram H. Abkar
- Department of Pharmacognosy, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Rola H. Alrehaly
- Department of Pharmacognosy, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Ashraf N. Abdalla
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
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22
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Alavi M, Mozafari MR, Ghaemi S, Ashengroph M, Hasanzadeh Davarani F, Mohammadabadi M. Interaction of Epigallocatechin Gallate and Quercetin with Spike Glycoprotein (S-Glycoprotein) of SARS-CoV-2: In Silico Study. Biomedicines 2022; 10:biomedicines10123074. [PMID: 36551830 PMCID: PMC9775955 DOI: 10.3390/biomedicines10123074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/14/2022] [Accepted: 11/19/2022] [Indexed: 12/03/2022] Open
Abstract
Severe acute respiratory syndrome (SARS)-CoV-2 from the family Coronaviridae is the cause of the outbreak of severe pneumonia, known as coronavirus disease 2019 (COVID-19), which was first recognized in 2019. Various potential antiviral drugs have been presented to hinder SARS-CoV-2 or treat COVID-19 disease. Side effects of these drugs are among the main complicated issues for patients. Natural compounds, specifically primary and secondary herbal metabolites, may be considered as alternative options to provide therapeutic activity and reduce cytotoxicity. Phenolic materials such as epigallocatechin gallate (EGCG, polyphenol) and quercetin have shown antibacterial, antifungal, antiviral, anticancer, and anti-inflammatory effects in vitro and in vivo. Therefore, in this study, molecular docking was applied to measure the docking property of epigallocatechin gallate and quercetin towards the transmembrane spike (S) glycoprotein of SARS-CoV-2. Results of the present study showed Vina scores of -9.9 and -8.3 obtained for EGCG and quercetin by CB-Dock. In the case of EGCG, four hydrogen bonds of OG1, OD2, O3, and O13 atoms interacted with the Threonine (THR778) and Aspartic acid (ASP867) amino acids of the spike glycoprotein (6VSB). According to these results, epigallocatechin gallate and quercetin can be considered potent therapeutic compounds for addressing viral diseases.
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Affiliation(s)
- Mehran Alavi
- Department of Biological Science, Faculty of Science, University of Kurdistan, Kurdistan 6617715175, Iran
- Nanobiotechnology Department, Faculty of Innovative Science and Technology, Razi University, Kermanshah 6714414971, Iran
- Correspondence: (M.A.); (M.R.M.)
| | - M. R. Mozafari
- Australasian Nanoscience and Nanotechnology Initiative (ANNI), Monash University LPO, Clayton, VIC 3168, Australia
- Correspondence: (M.A.); (M.R.M.)
| | - Saba Ghaemi
- Research Committee of Medical School, Alborz University of Medical Science, Karaj 3149779453, Iran
| | - Morahem Ashengroph
- Department of Biological Science, Faculty of Science, University of Kurdistan, Kurdistan 6617715175, Iran
| | | | - Mohammadreza Mohammadabadi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman 7616913439, Iran
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23
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Yang X, Xing X, Liu Y, Zheng Y. Screening of potential inhibitors targeting the main protease structure of SARS-CoV-2 via molecular docking. Front Pharmacol 2022; 13:962863. [PMID: 36278156 PMCID: PMC9579442 DOI: 10.3389/fphar.2022.962863] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/12/2022] [Indexed: 11/25/2022] Open
Abstract
The novel coronavirus disease (COVID-19) caused by SARS-CoV-2 virus spreads rapidly to become a global pandemic. Researchers have been working to develop specific drugs to treat COVID-19. The main protease (Mpro) of SARS-CoV-2 virus plays a pivotal role in mediating viral replication and transcription, which makes it a potential therapeutic drug target against COVID-19. In this study, a virtual drug screening method based on the Mpro structure (Protein Data Bank ID: 6LU7) was proposed, and 8,820 compounds collected from the DrugBank database were used for molecular docking and virtual screening. A data set containing 1,545 drug molecules, derived from compounds with a low binding free energy score in the docking experiment, was established. N-1H-Indazol-5-yl-2-(6-methylpyridin-2-yl)quinazolin-4-amine, ergotamine, antrafenine, dihydroergotamine, and phthalocyanine outperformed the other compounds in binding conformation and binding free energy over the N3 inhibitor in the crystal structure. The bioactivity and ADMET properties of these five compounds were further investigated. These experimental results for five compounds suggested that they were potential therapeutics to be developed for clinical trials. To further verify the results of molecular docking, we also carried out molecular dynamics (MD) simulations on the complexes formed by the five compounds and Mpro. The five complexes showed stable affinity in terms of root mean square distance (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), and hydrogen bond. It was further confirmed that the five compounds had potential inhibitory effects on SARS-CoV-2 Mpro.
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Affiliation(s)
- Xinbo Yang
- School of Information Science and Engineering, Shandong Normal University, Jinan, China
- *Correspondence: Xinbo Yang, ; Yuanjie Zheng,
| | - Xianrong Xing
- Department of Pharmacy, Shandong Medical College, Jinan, China
| | - Yirui Liu
- School of Clinical Medicine, Harbin Medical University, Daqing, China
| | - Yuanjie Zheng
- School of Information Science and Engineering, Shandong Normal University, Jinan, China
- *Correspondence: Xinbo Yang, ; Yuanjie Zheng,
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24
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Rieder AS, Deniz BF, Netto CA, Wyse ATS. A Review of In Silico Research, SARS-CoV-2, and Neurodegeneration: Focus on Papain-Like Protease. Neurotox Res 2022; 40:1553-1569. [PMID: 35917086 PMCID: PMC9343570 DOI: 10.1007/s12640-022-00542-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/17/2022] [Accepted: 06/30/2022] [Indexed: 01/18/2023]
Abstract
Since the appearance of SARS-CoV-2 and the COVID-19 pandemic, the search for new approaches to treat this disease took place in the scientific community. The in silico approach has gained importance at this moment, once the methodologies used in this kind of study allow for the identification of specific protein-ligand interactions, which may serve as a filter step for molecules that can act as specific inhibitors. In addition, it is a low-cost and high-speed technology. Molecular docking has been widely used to find potential viral protein inhibitors for structural and non-structural proteins of the SARS-CoV-2, aiming to block the infection and the virus multiplication. The papain-like protease (PLpro) participates in the proteolytic processing of SARS-CoV-2 and composes one of the main targets studied for pharmacological intervention by in silico methodologies. Based on that, we performed a systematic review about PLpro inhibitors from the perspective of in silico research, including possible therapeutic molecules in relation to this viral protein. The neurological problems triggered by COVID-19 were also briefly discussed, especially relative to the similarities of neuroinflammation present in Alzheimer's disease. In this context, we focused on two molecules, curcumin and glycyrrhizinic acid, given their PLpro inhibitory actions and neuroprotective properties and potential therapeutic effects on COVID-19.
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Affiliation(s)
- Alessandra S Rieder
- Laboratory of Neuroprotection and Neurometabolic Diseases, Wyse's Lab, Department of Biochemistry, ICBS, Universidade Federal Do Rio Grande Do Sul (UFRGS), Rua Ramiro Barcelos, 2600-Anexo, Porto Alegre, RS, 90035-003, Brazil
| | - Bruna F Deniz
- Laboratory of Neuroprotection and Neurometabolic Diseases, Wyse's Lab, Department of Biochemistry, ICBS, Universidade Federal Do Rio Grande Do Sul (UFRGS), Rua Ramiro Barcelos, 2600-Anexo, Porto Alegre, RS, 90035-003, Brazil
| | - Carlos Alexandre Netto
- Laboratory of Neuroprotection and Neurometabolic Diseases, Wyse's Lab, Department of Biochemistry, ICBS, Universidade Federal Do Rio Grande Do Sul (UFRGS), Rua Ramiro Barcelos, 2600-Anexo, Porto Alegre, RS, 90035-003, Brazil
| | - Angela T S Wyse
- Laboratory of Neuroprotection and Neurometabolic Diseases, Wyse's Lab, Department of Biochemistry, ICBS, Universidade Federal Do Rio Grande Do Sul (UFRGS), Rua Ramiro Barcelos, 2600-Anexo, Porto Alegre, RS, 90035-003, Brazil.
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25
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Novel Drug Design for Treatment of COVID-19: A Systematic Review of Preclinical Studies. CANADIAN JOURNAL OF INFECTIOUS DISEASES AND MEDICAL MICROBIOLOGY 2022; 2022:2044282. [PMID: 36199815 PMCID: PMC9527439 DOI: 10.1155/2022/2044282] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 05/23/2022] [Accepted: 08/03/2022] [Indexed: 11/27/2022]
Abstract
Background Since the beginning of the novel coronavirus (SARS-CoV-2) disease outbreak, there has been an increasing interest in discovering potential therapeutic agents for this disease. In this regard, we conducted a systematic review through an overview of drug development (in silico, in vitro, and in vivo) for treating COVID-19. Methods A systematic search was carried out in major databases including PubMed, Web of Science, Scopus, EMBASE, and Google Scholar from December 2019 to March 2021. A combination of the following terms was used: coronavirus, COVID-19, SARS-CoV-2, drug design, drug development, In silico, In vitro, and In vivo. A narrative synthesis was performed as a qualitative method for the data synthesis of each outcome measure. Results A total of 2168 articles were identified through searching databases. Finally, 315 studies (266 in silico, 34 in vitro, and 15 in vivo) were included. In studies with in silico approach, 98 article study repurposed drug and 91 studies evaluated herbal medicine on COVID-19. Among 260 drugs repurposed by the computational method, the best results were observed with saquinavir (n = 9), ritonavir (n = 8), and lopinavir (n = 6). Main protease (n = 154) following spike glycoprotein (n = 62) and other nonstructural protein of virus (n = 45) was among the most studied targets. Doxycycline, chlorpromazine, azithromycin, heparin, bepridil, and glycyrrhizic acid showed both in silico and in vitro inhibitory effects against SARS-CoV-2. Conclusion The preclinical studies of novel drug design for COVID-19 focused on main protease and spike glycoprotein as targets for antiviral development. From evaluated structures, saquinavir, ritonavir, eucalyptus, Tinospora cordifolia, aloe, green tea, curcumin, pyrazole, and triazole derivatives in in silico studies and doxycycline, chlorpromazine, and heparin from in vitro and human monoclonal antibodies from in vivo studies showed promised results regarding efficacy. It seems that due to the nature of COVID-19 disease, finding some drugs with multitarget antiviral actions and anti-inflammatory potential is valuable and some herbal medicines have this potential.
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Houchi S, Messasma Z. Exploring the inhibitory potential of Saussurea costus and Saussurea involucrata phytoconstituents against the Spike glycoprotein receptor binding domain of SARS-CoV-2 Delta (B.1.617.2) variant and the main protease (M pro) as therapeutic candidates, using Molecular docking, DFT, and ADME/Tox studies. J Mol Struct 2022; 1263:133032. [PMID: 35431327 PMCID: PMC8993769 DOI: 10.1016/j.molstruc.2022.133032] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/20/2022] [Accepted: 04/07/2022] [Indexed: 02/06/2023]
Abstract
The B.1.617.2 Delta variant is considered to be the most infectious of all SARS-CoV2 variants. Here, an attempt has been made through in-silico screening of 55 bioactive compounds from two selected plants, Saussurea costus and Saussurea involucrata as potential inhibitors of two viral proteases, main protease Mpro (PDB ID:6LU7) and the RBD of SGP of Sars-CoV-2 B1.617.2 Delta variant (PDB ID:7ORB) where the binding energy, molecular interactions, ADMET/Tox, chemical descriptors and Quantum-Chemical Calculations were explored. Molecular docking results demonstrated that the three top docked compounds formed relatively stable complexes within the active site and displayed remarkable binding energy in the order of Tangshenoside III, Rutin and Hesperidin (-9.35, -9.14 and -8.57 kcal/mol, respectively) with Mpro and Rutin, Tangshenoside III and Hesperidin (-9.07, -7.71 and -7.57 kcal/mol) with RBD of SGP. These compounds are non-Mutagen and non-carcinogen. Therefore, according to the Lipinski's Rule of Five they exhibited three violations concerning hydrogen acceptor, donor and molecular weight. However, based on the Quantum-Chemical Calculations results the selected ligands have effective reactivity, as they showed lower band gaps. The difference of the ELUMO and EHOMO was low, ranging from 0.0639 to 0.0978 a.u, implying the strong affinity of these inhibitors towards the target proteins. Among the three inhibitors, Rutin exhibited higher reactivity against two viral proteases, main protease (Mpro) and the Sars-CoV-2 B1.617.2, as the band energy gap was lowest among all the three phytochemicals, 0.0639 a.u This could indicate that Rutincan be potential anti-viral drug candidates against the existing SARS-CoV-2, the B.1.617.2 Delta variant.
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Affiliation(s)
- Selma Houchi
- Department of Biochemistry, Laboratory of Applied Biochemistry, Faculty of Life and Nature Sciences, University of Ferhat Abbas Setif-1, Algeria
| | - Zakia Messasma
- Department of Process Engineering, Laboratory of Electrochemistry, Molecular Engineering and Redox Catalysis, Faculty of Technology, University of Ferhat Abbas Setif-1, 19000, Algeria
- Department of Chemistry, Faculty of Sciences, University of Ferhat Abbas Setif-1, 19000, Algeria
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27
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Yusuf AP, Zhang JY, Li JQ, Muhammad A, Abubakar MB. Herbal medications and natural products for patients with covid-19 and diabetes mellitus: Potentials and challenges. PHYTOMEDICINE PLUS : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 2:100280. [PMID: 35463625 PMCID: PMC9014648 DOI: 10.1016/j.phyplu.2022.100280] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 03/25/2022] [Accepted: 04/12/2022] [Indexed: 04/21/2023]
Abstract
BACKGROUND The presence of diabetes mellitus (DM) among COVID-19 patients is associated with increased hospitalization, morbidity, and mortality. Evidence has shown that hyperglycemia potentiates SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) infection and plays a central role in severe COVID-19 and diabetes comorbidity. In this review, we explore the therapeutic potentials of herbal medications and natural products in the management of COVID-19 and DM comorbidity and the challenges associated with the preexisting or concurrent use of these substances. METHODS Research papers that were published from January 2016 to December 2021 were retrieved from PubMed, ScienceDirect, and Google Scholar databases. Papers reporting clinical evidence of antidiabetic activities and any available evidence of the anti-COVID-19 potential of ten selected natural products were retrieved and analyzed for discussion in this review. RESULTS A total of 548 papers (73 clinical trials on the antidiabetic activities of the selected natural products and 475 research and review articles on their anti-COVID-19 potential) were retrieved from the literature search for further analysis. A total of 517 articles (reviews and less relevant research papers) were excluded. A cumulative sum of thirty-one (31) research papers (20 clinical trials and 10 others) met the criteria and have been discussed in this review. CONCLUSION The findings of this review suggest that phenolic compounds are the most promising phytochemicals in the management of COVID-19 and DM comorbidity. Curcumin and propolis have shown substantial evidence against COVID-19 and DM in humans and are thus, considered the best potential therapeutic options.
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Key Words
- 8-OHDG, 8-hydroxy-2’-deoxyguanosine
- ACE2
- ACE2, Angiotensin-converting enzyme 2
- ADMA, asymmetric de-methyl-arginine
- ARDS, acute respiratory distress syndrome
- COVID-19
- Comorbidity
- DM, diabetes mellitus
- Diabetes
- FBS, fasting blood sugar
- GLUT-4, glucose transporter-4
- GSK-3β, glycogen synthase kinase-3β
- HDL, high-density lipoprotein
- HOMA, homeostasis model assessment
- Herbal medication
- IAPP, islet amyloid polypeptide
- IFN, interferon
- IFNAR2, interferon-alpha receptor 2
- IL-6, interleukin-6
- LDL, low-density lipoprotein
- MDA, malondialdehyde
- Mpro, main protease
- Natural products
- PLpro, papain-like protease
- PON1, paraoxonase-1
- RBD, receptor-binding domain
- RCT, randomized control trial
- RdRp, RNA-dependent RNA polymerase
- SARS-CoV-2, severe acute respiratory syndrome coronavirus-2
- SFJDC, Shufeng Jiedu Capsule
- T1D, type 1 diabetes
- T2D, type 2 diabetes
- TAC, total antioxidant capacity
- TMPRSS2, transmembrane protease serine 2
- hs-CRP, high-sensitivity C-reactive protein
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Affiliation(s)
- Abdurrahman Pharmacy Yusuf
- Department of Biochemistry, School of Life Sciences, Federal University of Technology, P.M.B 65, Minna, Niger State, Nigeria
| | - Jian-Ye Zhang
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, P.R. China
| | - Jing-Quan Li
- The first Affiliated Hospital, Hainan Medical University, Haikou, P.R. China
| | - Aliyu Muhammad
- Department of Biochemistry, Faculty of Life Sciences, Ahmadu Bello University Zaria, 810107, Kaduna State, Nigeria
| | - Murtala Bello Abubakar
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, Sokoto, Nigeria
- Department of Physiology, Faculty of Basic Medical Sciences, College of Health Sciences, Usmanu Danfodiyo University, P.M.B. 2254, Sokoto, Nigeria
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28
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Gao K, Wang R, Chen J, Cheng L, Frishcosy J, Huzumi Y, Qiu Y, Schluckbier T, Wei X, Wei GW. Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. Chem Rev 2022; 122:11287-11368. [PMID: 35594413 PMCID: PMC9159519 DOI: 10.1021/acs.chemrev.1c00965] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein-protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.
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Affiliation(s)
- Kaifu Gao
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Rui Wang
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiahui Chen
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Limei Cheng
- Clinical
Pharmacology and Pharmacometrics, Bristol
Myers Squibb, Princeton, New Jersey 08536, United States
| | - Jaclyn Frishcosy
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuta Huzumi
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuchi Qiu
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tom Schluckbier
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Xiaoqi Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Guo-Wei Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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29
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Chen X, Song X, Li L, Chen Y, Jia R, Zou Y, Wan H, Zhao L, Tang H, Lv C, Zhao X, Yin Z. Resveratrol Inhibits Pseudorabies Virus Replication by Targeting IE180 Protein. Front Microbiol 2022; 13:891978. [PMID: 35722304 PMCID: PMC9203040 DOI: 10.3389/fmicb.2022.891978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/12/2022] [Indexed: 11/13/2022] Open
Abstract
Resveratrol is a natural polyphenolic product in red wine and peanuts and has many pharmacological activities in humans. Our previous studies showed that resveratrol has good antiviral activity against the pseudorabies virus (PRV). However, little is known about the antiviral mechanism of resveratrol against PRV. In this study, we found that resveratrol inhibited the nuclear localization of IE180 protein, which is an important step for activating early/late genes transcription. Interestingly, the results show that resveratrol inhibited the activity of IE180 protein by dual-luciferase assay. Furthermore, molecular docking analysis shows that resveratrol could bind to the Thr601, Ser603, and Pro606 of IE180 protein. Point mutation assay confirmed that resveratrol lost its inhibition activity against the mutant IE180 protein. The results demonstrate that resveratrol exerts its antiviral activity against PRV by targeting the Thr601/Ser603/Pro606 sites of IE180 protein and inhibiting the transcriptional activation activity of IE180 protein. This study provides a novel insight into the antiviral mechanism of resveratrol against herpes viruses.
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Affiliation(s)
- Xiangxiu Chen
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xu Song
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Lixia Li
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yaqin Chen
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Renyong Jia
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yuanfeng Zou
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Hongping Wan
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ling Zhao
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Huaqiao Tang
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Cheng Lv
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xinghong Zhao
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Zhongqiong Yin
- Natural Medicine Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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30
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Al-Rajhi AMH, Yahya R, Abdelghany TM, Fareid MA, Mohamed AM, Amin BH, Masrahi AS. Anticancer, Anticoagulant, Antioxidant and Antimicrobial Activities of Thevetia peruviana Latex with Molecular Docking of Antimicrobial and Anticancer Activities. Molecules 2022; 27:molecules27103165. [PMID: 35630642 PMCID: PMC9145871 DOI: 10.3390/molecules27103165] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/07/2022] [Accepted: 05/09/2022] [Indexed: 12/13/2022] Open
Abstract
Natural origin molecules represent reliable and excellent sources to overcome some medicinal problems. The study of anticancer, anticoagulant, and antimicrobial activities of Thevetia peruviana latex were the aim of the current research. An investigation using high-performance liquid chromatography (HPLC) revealed that the major content of the flavonoids are rutin (11.45 µg/mL), quersestin (7.15 µg/mL), naringin (5.25 µg/mL), and hisperdin (6.07 µg/mL), while phenolic had chlorogenic (12.39 µg/mL), syringenic (7.45 µg/mL), and ferulic (5.07 µg/mL) acids in latex of T. peruviana. Via 1,1-diphenyl-2- picrylhydrazyl (DPPH) radical scavenging, the experiment demonstrated that latex had a potent antioxidant activity with the IC50 43.9 µg/mL for scavenging DPPH. Hemolysis inhibition was 58.5% at 1000 µg/mL of latex compared with 91.0% at 200 µg/mL of indomethacin as positive control. Negligible anticoagulant properties of latex were reported where the recorded time was 11.9 s of prothrombin time (PT) and 29.2 s of the activated partial thromboplastin time (APTT) at 25 µg/mL, compared with the same concentration of heparin (PT 94.6 s and APPT 117.7 s). The anticancer potential of latex was recorded against PC-3 (97.11% toxicity) and MCF-7 (96.23% toxicity) at 1000 μg/mL with IC50 48.26 μg/mL and 40.31 µg/mL, respectively. Disc diffusion assessment for antimicrobial activity recorded that the most sensitive tested microorganisms to latex were Bacillus subtilis followed by Escherichia coli, with an inhibition zone (IZ) of 31 mm with minimum inhibitory concentration (MIC) (10.2 μg/mL) and 30 mm (MIC, 12.51 μg/mL), respectively. Moreover, Candida albicans was sensitive (IZ, 28 mm) to latex, unlike black fungus (Mucor circinelloides). TEM examination exhibited ultrastructure changes in cell walls and cell membranes of Staphylococcus aureus and Pseudomonas aeruginosa treated with latex. Energy scores of the molecular docking of chlorogenic acid with E. coli DNA (7C7N), and Rutin with human prostate-specific antigen (3QUM) and breast cancer-associated protein (1JNX), result in excellent harmony with the experimental results. The outcome of research recommended that the latex is rich in constituents and considered a promising source that contributes to fighting cancer and pathogenic microorganisms.
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Affiliation(s)
- Aisha M. H. Al-Rajhi
- Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia;
| | - Reham Yahya
- Medical Microbiology, College of Science and Health Professions, King Saud Bin Abdulaziz University for Health Sciences, Riyadh 11426, Saudi Arabia;
- King Abduallah International Medical Research Center, Riyadh 11671, Saudi Arabia
| | - Tarek M. Abdelghany
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Cairo 11751, Egypt;
- Correspondence:
| | - Mohamed A. Fareid
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Cairo 11751, Egypt;
- Basic Science Department, Prep Year Deanship, University of Ha’il, Ha’il 2440, Saudi Arabia
| | - Alawlaqi M. Mohamed
- Biology Department, Faculty of Science, Jazan University, Jazan 45142, Saudi Arabia; (A.M.M.); (A.S.M.)
| | - Basma H. Amin
- The Regional Centre for Mycology and Biotechnology (RCMB), Al-Azhar University, Cairo 11751, Egypt;
| | - Abdurrahman S. Masrahi
- Biology Department, Faculty of Science, Jazan University, Jazan 45142, Saudi Arabia; (A.M.M.); (A.S.M.)
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31
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Kreft I, Germ M, Golob A, Vombergar B, Bonafaccia F, Luthar Z. Impact of Rutin and Other Phenolic Substances on the Digestibility of Buckwheat Grain Metabolites. Int J Mol Sci 2022; 23:3923. [PMID: 35409281 PMCID: PMC8999605 DOI: 10.3390/ijms23073923] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 02/01/2023] Open
Abstract
Tartary buckwheat (Fagopyrum tataricum Gaertn.) is grown in eastern and central Asia (the Himalayan regions of China, Nepal, Bhutan and India) and in central and eastern Europe (Luxemburg, Germany, Slovenia and Bosnia and Herzegovina). It is known for its high concentration of rutin and other phenolic metabolites. Besides the grain, the other aboveground parts of Tartary buckwheat contain rutin as well. After the mixing of the milled buckwheat products with water, the flavonoid quercetin is obtained in the flour-water mixture, a result of rutin degradation by rutinosidase. Heating by hot water or steam inactivates the rutin-degrading enzymes in buckwheat flour and dough. The low buckwheat protein digestibility is due to the high content of phenolic substances. Phenolic compounds have low absorption after food intake, so, after ingestion, they remain for some time in the gastrointestinal tract. They can act in an inhibitory manner on enzymes, degrading proteins and other food constituents. In common and Tartary buckwheat, the rutin and quercetin complexation with protein and starch molecules has an impact on the in vitro digestibility and the appearance of resistant starch and slowly digestible proteins. Slowly digestible starch and proteins are important for the functional and health-promoting properties of buckwheat products.
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Affiliation(s)
- Ivan Kreft
- Nutrition Institute, Tržaška 40, SI-1000 Ljubljana, Slovenia
- Biotechnical Faculty, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (M.G.); (A.G.); (F.B.)
| | - Mateja Germ
- Biotechnical Faculty, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (M.G.); (A.G.); (F.B.)
| | - Aleksandra Golob
- Biotechnical Faculty, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (M.G.); (A.G.); (F.B.)
| | - Blanka Vombergar
- The Education Centre Piramida Maribor, SI-2000 Maribor, Slovenia;
| | - Francesco Bonafaccia
- Biotechnical Faculty, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (M.G.); (A.G.); (F.B.)
| | - Zlata Luthar
- Biotechnical Faculty, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (M.G.); (A.G.); (F.B.)
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Rahman F, Ali R, Tabrez S, Mobeen A, Akand SK, Arish M, AlAsmari AF, Ali N, Rub A. Exploration of potential inhibitors for autophagy-related protein 8 as antileishmanial agents. Chem Biol Drug Des 2022; 99:816-827. [PMID: 35147279 DOI: 10.1111/cbdd.14029] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/25/2021] [Accepted: 01/29/2022] [Indexed: 11/27/2022]
Abstract
Leishmaniasis is considered a tropical neglected disease, which is caused by an intra-macrophagicparasite, Leishmania. It is endemic in 89 different countries. Autophagy-related protein 8 (Ldatg8) is responsible for the transformation of parasites from promastigote to amastigote differentiation. Ldatg8 is one of the key drug targets of Leishmania donovani (L. donovani) responsible for the defense of parasites during stress conditions. Virtual screening of natural ligands library hadbeen performed against Ldatg8 to identify novel and potent inhibitors. Molecular-docking and molecular dynamics simulation studies showed that urolithin A stably blocked Ldatg8. Urolithins are combinations of coumarin and isocoumarin. Further, we evaluated the antileishmanial effects of urolithin A by antileishmanial assays. Urolithin A inhibited the growth and proliferation of L. donovani promastigotes with an IC50 value of 90.3 ± 6.014 μM. It also inhibited the intra-macrophagic parasite significantly with an IC50 value of 78.67±4.62 μM. It showed limited cytotoxicity to the human THP-1 differentiated macrophages with a CC50 value of 190.80 ± 16.89 μM. Further, we assayed reactive oxygen species (ROS) generation and annexin V/PI staining upon Urolithin A treatment of parasites to have an insight into the mechanism of its action. It induced ROS significantly in a dose-dependent manner which caused apoptosis partially in parasites. The potential inhibitors for Ldatg8, identified in this study would provide the platform for the development of an effective and affordable antileishmanial drug.
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Affiliation(s)
- Fazlur Rahman
- Infection and Immunity Lab (414), Department of Biotechnology, Jamia Millia Islamia (A Central University), New Delhi, India, 110025
| | - Rahat Ali
- Infection and Immunity Lab (414), Department of Biotechnology, Jamia Millia Islamia (A Central University), New Delhi, India, 110025
| | - Shams Tabrez
- Infection and Immunity Lab (414), Department of Biotechnology, Jamia Millia Islamia (A Central University), New Delhi, India, 110025
| | - Ahmed Mobeen
- Institute of Genomics and Integrative Biology, New Delhi, India
| | - Sajjadul Kadir Akand
- Infection and Immunity Lab (414), Department of Biotechnology, Jamia Millia Islamia (A Central University), New Delhi, India, 110025
| | - Mohd Arish
- Department of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Abdullah F AlAsmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box55760, 11451, Saudi Arabia
| | - Nemat Ali
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box55760, 11451, Saudi Arabia
| | - Abdur Rub
- Infection and Immunity Lab (414), Department of Biotechnology, Jamia Millia Islamia (A Central University), New Delhi, India, 110025
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Abstract
COVID-19, the infectious disease caused by the beta-corona virus SARS-CoV2, has posed a global health threat causing more than five million of deaths in the last two years in the world. Although the disease often presents with mild cold-like symptoms, it may have lethal consequences following thromboembolisms, hyperinflammation and cytokine storm eventually leading to pulmonary fibrosis and multiple organ failure. Despite the progress made in the understanding of the SARS-CoV2 pathology and the clinical management of COVID-19, the viral illness is still a health concern since outbreaks continue to resurge due to the emergence of mutant variants of the virus that resist the vaccines. Therefore, there is an urgent need for therapeutics that can block SARS-CoV2 viral transmission and the progression from infection to severe symptomatic illness. Natural products could be a valuable source of drugs for the management of COVID-19 disease, particularly because they can act on multitargets and through different mechanisms including inhibition of biochemical pathways, epigenetic regulation of gene expression, modulation of immune response, regulation of pathophysiological stress response. Here we present an overview of the natural products that possess SARS-CoV2 antiviral activity and the potential to benefit the management of COVID-19.
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Affiliation(s)
- Ciro Isidoro
- Corresponding author. Dipartimento di Scienze della Salute, Università del Piemonte Orientale “A. Avogadro”, Via P. Solaroli 17, 28100, Novara, Italy
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Uthra C, Reshi MS, Jaswal A, Yadav D, Shrivastava S, Sinha N, Shukla S. Protective efficacy of rutin against acrylamide-induced oxidative stress, biochemical alterations and histopathological lesions in rats. Toxicol Res (Camb) 2022; 11:215-225. [PMID: 35237426 PMCID: PMC8882811 DOI: 10.1093/toxres/tfab125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/11/2021] [Accepted: 12/12/2021] [Indexed: 01/28/2023] Open
Abstract
Acrylamide is a well-known neurotoxicant and carcinogen. Apart from industrial exposure, acrylamide is also found in different food products. The present study deals with in vivo experiment to test the protective effect of rutin against acrylamide induced toxicity in rats. The study was carried out on female rats with exposure of acrylamide at the dose of 38.27 mg/kg body weight, orally for 10 days followed by the therapy of rutin (05, 10, 20 and 40 mg/kg orally), for three consecutive days. All animals were sacrificed after 24 h of last treatment and various biochemical parameters in blood and tissue were investigated. Histopathology of liver, kidney and brain was also done. On administration of acrylamide for 10 days, neurotoxicity was observed in terms of decreased acetylcholinesterase activity and oxidative stress was observed in terms of increased lipid peroxidation, declined level of reduced glutathione, antioxidant enzymes (superoxide dismutase and catalase) in liver, kidney and brain. Acrylamide exposure increased the activities of serum transaminases, lipid profile, bilirubin, urea, uric acid and creatinine in serum indicating damage. Our experimental results conclude that rutin showed remarkable protection against oxidative DNA damage induced by acrylamide, which may be due to its antioxidant potential.
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Affiliation(s)
- Chhavi Uthra
- Correspondence address. Reproductive Biology and Toxicology Laboratory, UNESCO-Trace Element Satellite Centre, School of Studies in Zoology, Jiwaji University, Gwalior, Madhya Pradesh, 474011, India. Tel: 9755952336 (M); E-mail:
| | - Mohd Salim Reshi
- Toxicology and Pharmacology Lab, Department of Zoology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, Jammu & Kashmir, 185234, India
| | - Amita Jaswal
- Reproductive Biology and Toxicology Laboratory, UNESCO-Trace Element Satellite Centre, School of Studies in Zoology, Jiwaji University, Gwalior, Madhya Pradesh, 474011, India
| | - Deepa Yadav
- Reproductive Biology and Toxicology Laboratory, UNESCO-Trace Element Satellite Centre, School of Studies in Zoology, Jiwaji University, Gwalior, Madhya Pradesh, 474011, India
| | - Sadhana Shrivastava
- Reproductive Biology and Toxicology Laboratory, UNESCO-Trace Element Satellite Centre, School of Studies in Zoology, Jiwaji University, Gwalior, Madhya Pradesh, 474011, India
| | - Neelu Sinha
- Reproductive Biology and Toxicology Laboratory, UNESCO-Trace Element Satellite Centre, School of Studies in Zoology, Jiwaji University, Gwalior, Madhya Pradesh, 474011, India
| | - Sangeeta Shukla
- Reproductive Biology and Toxicology Laboratory, UNESCO-Trace Element Satellite Centre, School of Studies in Zoology, Jiwaji University, Gwalior, Madhya Pradesh, 474011, India
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Singh R, Bhardwaj VK, Sharma J, Purohit R, Kumar S. In-silico evaluation of bioactive compounds from tea as potential SARS-CoV-2 nonstructural protein 16 inhibitors. J Tradit Complement Med 2022; 12:35-43. [PMID: 34099976 PMCID: PMC8172245 DOI: 10.1016/j.jtcme.2021.05.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/29/2021] [Accepted: 05/29/2021] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND AND AIM A novel coronavirus, called the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been found to cause COVID-19 in humans and some other mammals. The nonstructural protein 16 (NSP16) of SARS-CoV-2 plays a significant part in the replication of viruses and suppresses the ability of innate immune system to detect the virus. Therefore, inhibiting NSP16 can be a secure path towards identifying a potent medication against SARS-CoV-2. Tea (Camellia sinensis) polyphenols have been reported to exhibit potential treatment options against various viral diseases. METHODS We conducted molecular docking and structural dynamics studies with a set of 65 Tea bioactive compounds to illustrate their ability to inhibit NSP16 of SARS-CoV-2. Moreover, post-simulations end state thermodynamic free energy calculations were estimated to strengthen our results. RESULTS AND CONCLUSION Six bioactive tea molecules showed better docking scores than the standard molecule sinefungin. These results were further validated by MD simulations, where Theaflavin compound demonstrated lower binding free energy in comparison to the standard molecule sinefungin. The compound theaflavin could be considered as a novel lead compound for further evaluation by in-vitro and in-vivo studies.
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Affiliation(s)
- Rahul Singh
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India
- Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India
| | - Vijay Kumar Bhardwaj
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India
- Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Jatin Sharma
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India
- Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India
| | - Rituraj Purohit
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India
- Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sanjay Kumar
- Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India
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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. [PMCID: PMC9300476 DOI: 10.1016/b978-0-323-91172-6.00007-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Zaki AA, Ashour A, Elhady SS, Darwish KM, Al-Karmalawy AA. Calendulaglycoside A showing potential activity against SARS-CoV-2 main protease: Molecular docking, molecular dynamics, and SAR studies. J Tradit Complement Med 2022; 12:16-34. [PMID: 34026584 PMCID: PMC8126476 DOI: 10.1016/j.jtcme.2021.05.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/09/2021] [Accepted: 05/11/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND AND AIM The discovery of drugs capable of inhibiting SARS-CoV-2 is a priority for human beings due to the severity of the global health pandemic caused by COVID-19. To this end, natural products can provide therapeutic alternatives that could be employed as an effective safe treatment for COVID-19. EXPERIMENTAL PROCEDURE Twelve compounds were isolated from the aerial parts of C. officinalis L. and investigated for their inhibitory activities against SARS-CoV-2 Mpro compared to its co-crystallized N3 inhibitor using molecular docking studies. Furthermore, a 100 ns MD simulation was performed for the most active two promising compounds, Calendulaglycoside A (SAP5) and Osteosaponin-I (SAP8). RESULTS AND CONCLUSION At first, molecular docking studies showed interesting binding scores as compared to the N3 inhibitor. Calendulaglycoside A (SAP5) achieved a superior binding than the co-crystallized inhibitor indicating promising affinity and intrinsic activity towards the Mpro of SARS-CoV-2 as well. Moreover, findings illustrated preferential stability for SAP5 within the Mpro pocket over that of N3 beyond the 40 ns MD simulation course. Structural preferentiality for triterpene-Mpro binding highlights the significant role of 17β-glucosyl and carboxylic 3α-galactosyl I moieties through high electrostatic interactions across the MD simulation trajectories. Furthermore, this study clarified a promising SAR responsible for the antiviral activity against the SARS-CoV-2 Mpro and the design of new drug candidates targeting it as well. The above findings could be promising for fast examining the previously isolated triterpenes both pre-clinically and clinically for the treatment of COVID-19.
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Affiliation(s)
- Ahmed A. Zaki
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
- Department of Pharmacognosy, Faculty of Pharmacy, Horus University-Egypt, New Damietta, 34518, Egypt
| | - Ahmed Ashour
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
- Department of Pharmacognosy, Faculty of Pharmacy, Horus University-Egypt, New Damietta, 34518, Egypt
| | - Sameh S. Elhady
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Khaled M. Darwish
- Department of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University, Ismailia, 41522, Egypt
| | - Ahmed A. Al-Karmalawy
- Department of Pharmaceutical Medicinal Chemistry, Faculty of Pharmacy, Horus University-Egypt, New Damietta, 34518, Egypt
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Alanazi KM, Farah MA, Hor YY. Multi-Targeted Approaches and Drug Repurposing Reveal Possible SARS-CoV-2 Inhibitors. Vaccines (Basel) 2021; 10:vaccines10010024. [PMID: 35062685 PMCID: PMC8781363 DOI: 10.3390/vaccines10010024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 12/03/2021] [Accepted: 12/16/2021] [Indexed: 01/09/2023] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 is unprecedented in recent memory owing to the non-stop escalation in number of infections and deaths in almost every country of the world. The lack of treatment options further worsens the scenario, thereby necessitating the exploration of already existing US FDA-approved drugs for their effectiveness against COVID-19. In the present study, we have performed virtual screening of nutraceuticals available from DrugBank against 14 SARS-CoV-2 proteins. Molecular docking identified several inhibitors, two of which, rutin and NADH, displayed strong binding affinities and inhibitory potential against SARS-CoV-2 proteins. Further normal model-based simulations were performed to gain insights into the conformational transitions in proteins induced by the drugs. The computational analysis in the present study paves the way for experimental validation and development of multi-target guided inhibitors to fight COVID-19.
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Affiliation(s)
- Khalid Mashay Alanazi
- Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; (K.M.A.); (M.A.F.)
| | - Mohammad Abul Farah
- Department of Zoology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; (K.M.A.); (M.A.F.)
| | - Yan-Yan Hor
- Department of Biotechnology, Yeungnam University, 280 Daehak-ro, Gyeongsan 38541, Gyeongbuk-do, Korea
- Correspondence:
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Nanotechnology Applications of Flavonoids for Viral Diseases. Pharmaceutics 2021; 13:pharmaceutics13111895. [PMID: 34834309 PMCID: PMC8625292 DOI: 10.3390/pharmaceutics13111895] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/14/2021] [Accepted: 11/01/2021] [Indexed: 12/14/2022] Open
Abstract
Recent years have witnessed the emergence of several viral diseases, including various zoonotic diseases such as the current pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Other viruses, which possess pandemic-causing potential include avian flu, Ebola, dengue, Zika, and Nipah virus, as well as the re-emergence of SARS (Severe Acute Respiratory Syndrome) and MERS (Middle East Respiratory Syndrome) coronaviruses. Notably, effective drugs or vaccines against these viruses are still to be discovered. All the newly approved vaccines against the SARS-CoV-2-induced disease COVID-19 possess real-time possibility of becoming obsolete because of the development of ‘variants of concern’. Flavonoids are being increasingly recognized as prophylactic and therapeutic agents against emerging and old viral diseases. Around 10,000 natural flavonoid compounds have been identified, being phytochemicals, all plant-based. Flavonoids have been reported to have lesser side effects than conventional anti-viral agents and are effective against more viral diseases than currently used anti-virals. Despite their abundance in plants, which are a part of human diet, flavonoids have the problem of low bioavailability. Various attempts are in progress to increase the bioavailability of flavonoids, one of the promising fields being nanotechnology. This review is a narrative of some anti-viral dietary flavonoids, their bioavailability, and various means with an emphasis on the nanotechnology system(s) being experimented with to deliver anti-viral flavonoids, whose systems show potential in the efficient delivery of flavonoids, resulting in increased bioavailability.
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Jiang YL, Xu ZJ, Cao YF, Wang F, Chu C, Zhang C, Tao Y, Wang P. HPLC fingerprinting-based multivariate analysis of chemical components in Tetrastigma Hemsleyanum Diels et Gilg: Correlation to their antioxidant and neuraminidase inhibition activities. J Pharm Biomed Anal 2021; 205:114314. [PMID: 34416550 DOI: 10.1016/j.jpba.2021.114314] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/28/2021] [Accepted: 08/04/2021] [Indexed: 10/20/2022]
Abstract
Tetrastigma Hemsleyanum Diels & Gilg (TDG) has attracted growing attention in China; however, there were few studies on its bioactive components. Herein, the characteristic chemical components and dual antioxidant and neuraminidase inhibitory activities of fifteen batches of TDG from different places of origin and their relevance were investigated. The HPLC fingerprint was first established and the marker components were identified by using UPLC-Q-TOF-MS/MS. Catechin-5-O-β-d-glucopyranoside, tartaric acid, (1R, 2R, 4S)-2-hydroxy-1, 8-cineole-β-d-glucopyranoside, and phlorizin were identified for the first time. The result of multivariate statistical analysis indicated that multiple components have a significant contribution to the classification of TDG, such as chlorogenic acid, saccharumoside C/D, robinin, procyanidin B2, rutin, isoquercitrin, etc. Then, the antioxidant and neuraminidase inhibitory activities of fifteen batches of TDG were measured. The result of grey relationship analysis showed that the contents of rutin, isoquercitrin, kaempferol-3-rutinoside, and astragalin were positively correlated with these two activities with correlation coefficients more than 0.8. The quantitative analysis of these four bioactive compounds was performed by using HPLC-DAD. The recovery rate of the method varied from 98.02% to 100.21%, the RSD values of precision, stability and repeatability were between 1.32-3.15 %, and the R value of the linear equation was above 0.9990. To sum up, this study is valuable in the quality control of TDG.
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Affiliation(s)
- Yu-Li Jiang
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Zi-Jin Xu
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yi-Feng Cao
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Fang Wang
- Department of Pharmacy, Jiangxi Medical College, Shangrao, 334000, China
| | - Chu Chu
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Cheng Zhang
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yi Tao
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China.
| | - Ping Wang
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China.
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Xue X, Zhao A, Wang Y, Ren H, Du J, Li D, Li Y. Composition and content of phenolic acids and flavonoids among the different varieties, development stages, and tissues of Chinese Jujube (Ziziphus jujuba Mill.). PLoS One 2021; 16:e0254058. [PMID: 34648512 PMCID: PMC8516285 DOI: 10.1371/journal.pone.0254058] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/20/2021] [Indexed: 12/03/2022] Open
Abstract
The composition and content of phenolic acids and flavonoids among the different varieties, development stages, and tissues of Chinese jujube (Ziziphus jujuba Mill.) were systematically examined using ultra-high-performance liquid chromatography to provide a reference for the evaluation and selection of high-value resources. Five key results were identified: (1) Overall, 13 different phenolic acids and flavonoids were detected from among the 20 excellent jujube varieties tested, of which 12 were from the fruits, 11 from the leaves, and 10 from the stems. Seven phenolic acids and flavonoids, including (+)-catechin, rutin, quercetin, luteolin, spinosin, gallic acid, and chlorogenic acid, were detected in all tissues. (2) The total and individual phenolic acids and flavonoids contents significantly decreased during fruit development in Ziziphus jujuba cv.Hupingzao. (3) The total phenolic acids and flavonoids content was the highest in the leaves of Ziziphus jujuba cv.Hupingzao, followed by the stems and fruits with significant differences among the content of these tissues. The main composition of the tissues also differed, with quercetin and rutin present in the leaves; (+)-catechin and rutin in the stems; and (+)-catechin, epicatechin, and rutin in the fruits. (4) The total content of phenolic acid and flavonoid ranged from 359.38 to 1041.33 μg/g FW across all examined varieties, with Ziziphus jujuba cv.Jishanbanzao having the highest content, and (+)-catechin as the main composition in all 20 varieties, followed by epicatechin, rutin, and quercetin. (5) Principal component analysis showed that (+)-catechin, epicatechin, gallic acid, and rutin contributed to the first two principal components for each variety. Together, these findings will assist with varietal selection when developing phenolic acids and f lavonoids functional products.
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Affiliation(s)
- Xiaofang Xue
- College of Horticulture, Shanxi Agricultural University, Taigu, Shanxi, People’s Republic of China
- Research Institute of Pomology, Shanxi Agricultural University, Shanxi Key Laboratory of Germplasm Improvement and Utilization in Pomology, Taiyuan, Shanxi, People’s Republic of China
| | - Ailing Zhao
- Research Institute of Pomology, Shanxi Agricultural University, Shanxi Key Laboratory of Germplasm Improvement and Utilization in Pomology, Taiyuan, Shanxi, People’s Republic of China
| | - Yongkang Wang
- Research Institute of Pomology, Shanxi Agricultural University, Shanxi Key Laboratory of Germplasm Improvement and Utilization in Pomology, Taiyuan, Shanxi, People’s Republic of China
| | - Haiyan Ren
- Research Institute of Pomology, Shanxi Agricultural University, Shanxi Key Laboratory of Germplasm Improvement and Utilization in Pomology, Taiyuan, Shanxi, People’s Republic of China
| | - Junjie Du
- College of Horticulture, Shanxi Agricultural University, Taigu, Shanxi, People’s Republic of China
- * E-mail: (JD); (DL)
| | - Dengke Li
- Research Institute of Pomology, Shanxi Agricultural University, Shanxi Key Laboratory of Germplasm Improvement and Utilization in Pomology, Taiyuan, Shanxi, People’s Republic of China
- * E-mail: (JD); (DL)
| | - Yi Li
- Research Institute of Pomology, Shanxi Agricultural University, Shanxi Key Laboratory of Germplasm Improvement and Utilization in Pomology, Taiyuan, Shanxi, People’s Republic of China
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l-Arginine Improves Solubility and ANTI SARS-CoV-2 Mpro Activity of Rutin but Not the Antiviral Activity in Cells. Molecules 2021; 26:molecules26196062. [PMID: 34641606 PMCID: PMC8512140 DOI: 10.3390/molecules26196062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 11/28/2022] Open
Abstract
The COVID-19 pandemic outbreak prompts an urgent need for efficient therapeutics, and repurposing of known drugs has been extensively used in an attempt to get to anti-SARS-CoV-2 agents in the shortest possible time. The glycoside rutin shows manifold pharmacological activities and, despite its use being limited by its poor solubility in water, it is the active principle of many pharmaceutical preparations. We herein report our in silico and experimental investigations of rutin as a SARS-CoV-2 Mpro inhibitor and of its water solubility improvement obtained by mixing it with l-arginine. Tests of the rutin/l-arginine mixture in a cellular model of SARS-CoV-2 infection highlighted that the mixture still suffers from unfavorable pharmacokinetic properties, but nonetheless, the results of this study suggest that rutin might be a good starting point for hit optimization.
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Research Progression of the Genus Merremia: A Comprehensive Review on the Nutritional Value, Ethnomedicinal Uses, Phytochemistry, Pharmacology, and Toxicity. PLANTS 2021; 10:plants10102070. [PMID: 34685875 PMCID: PMC8537340 DOI: 10.3390/plants10102070] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 12/22/2022]
Abstract
The genus Merremia Dennst. ex Endl. (Convolvulaceae) is a rich source of structurally diverse phytochemicals with therapeutic relevance. This review presents the first comprehensive, up-to-date information and research progression on the nutritional value, ethnomedicinal uses, phytochemistry, pharmacological activities, and toxicity of the genus Merremia. Using the key search term “Merremia”, relevant documents and information were retrieved from electronic databases. Relevant documents were uploaded in RStudio with installed bibliometric software packages and used for data retrieval, tabulation, and network visualization. Bibliometric analysis revealed that ca. 55% of the studies related to Merremia were published in the last decade, which can be grouped into four thematic areas: (i) drug formulation, (ii) taxonomy, (iii) chemical analysis, and (iv) treatment of diseases. Ethnomedicinal uses, phytochemistry, and biological activities studies showed that species in the genus are promising medicinal plants with various pharmaceutical potentials. However, clinical studies to validate the efficacy of the reported bioactivities and the mechanisms underlying the various activities are lacking and should constitute a future research focus. Additionally, reports on the nutritional and antinutritional constituents of Merremia species revealed that the species meet high nutritional quality criteria for animals and are therefore suitable for inclusion in livestock diets. The few available investigations on toxicity indicated that most Merremia species are safe for human and animal use but not with prolonged chronic administration.
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Mousavi SS, Karami A, Haghighi TM, Tumilaar SG, Fatimawali, Idroes R, Mahmud S, Celik I, Ağagündüz D, Tallei TE, Emran TB, Capasso R. In Silico Evaluation of Iranian Medicinal Plant Phytoconstituents as Inhibitors against Main Protease and the Receptor-Binding Domain of SARS-CoV-2. Molecules 2021; 26:5724. [PMID: 34577194 PMCID: PMC8470205 DOI: 10.3390/molecules26185724] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 08/22/2021] [Accepted: 09/01/2021] [Indexed: 12/22/2022] Open
Abstract
The novel coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which initially appeared in Wuhan, China, in December 2019. Elderly individuals and those with comorbid conditions may be more vulnerable to this disease. Consequently, several research laboratories continue to focus on developing drugs to treat this infection because this disease has developed into a global pandemic with an extremely limited number of specific treatments available. Natural herbal remedies have long been used to treat illnesses in a variety of cultures. Modern medicine has achieved success due to the effectiveness of traditional medicines, which are derived from medicinal plants. The objective of this study was to determine whether components of natural origin from Iranian medicinal plants have an antiviral effect that can prevent humans from this coronavirus infection using the most reliable molecular docking method; in our case, we focused on the main protease (Mpro) and a receptor-binding domain (RBD). The results of molecular docking showed that among 169 molecules of natural origin from common Iranian medicinal plants, 20 molecules (chelidimerine, rutin, fumariline, catechin gallate, adlumidine, astragalin, somniferine, etc.) can be proposed as inhibitors against this coronavirus based on the binding free energy and type of interactions between these molecules and the studied proteins. Moreover, a molecular dynamics simulation study revealed that the chelidimerine-Mpro and somniferine-RBD complexes were stable for up to 50 ns below 0.5 nm. Our results provide valuable insights into this mechanism, which sheds light on future structure-based designs of high-potency inhibitors for SARS-CoV-2.
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Affiliation(s)
- Seyyed Sasan Mousavi
- Department of Horticultural Science, School of Agriculture, Shiraz University, Shiraz 71441, Iran; (S.S.M.); (A.K.); (T.M.H.)
| | - Akbar Karami
- Department of Horticultural Science, School of Agriculture, Shiraz University, Shiraz 71441, Iran; (S.S.M.); (A.K.); (T.M.H.)
| | - Tahereh Movahhed Haghighi
- Department of Horticultural Science, School of Agriculture, Shiraz University, Shiraz 71441, Iran; (S.S.M.); (A.K.); (T.M.H.)
| | - Sefren Geiner Tumilaar
- Pharmacy Study Program, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, Indonesia; (S.G.T.); (F.)
| | - Fatimawali
- Pharmacy Study Program, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, Indonesia; (S.G.T.); (F.)
- The University Center of Excellence for Biotechnology and Conservation of Wallacea, Sam Ratulangi University, Manado 95115, Indonesia
| | - Rinaldi Idroes
- Department of Pharmacy, Faculty of Mathematics and Natural Sciences, Universitas Syiah Kuala, Kopelma Darussalam, Banda Aceh 23111, Indonesia;
| | - Shafi Mahmud
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh;
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri 38039, Turkey;
| | - Duygu Ağagündüz
- Department of Nutrition and Dietetics, Faculty of Health Sciences, Gazi University, Emek, Ankara 06490, Turkey;
| | - Trina Ekawati Tallei
- The University Center of Excellence for Biotechnology and Conservation of Wallacea, Sam Ratulangi University, Manado 95115, Indonesia
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, Indonesia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
| | - Raffaele Capasso
- Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055 Naples, Italy
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Gour A, Manhas D, Bag S, Gorain B, Nandi U. Flavonoids as potential phytotherapeutics to combat cytokine storm in SARS-CoV-2. Phytother Res 2021; 35:4258-4283. [PMID: 33786876 PMCID: PMC8250405 DOI: 10.1002/ptr.7092] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/22/2021] [Accepted: 03/12/2021] [Indexed: 01/08/2023]
Abstract
Emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection, COVID-19, has become the global panic since December 2019, which urges the global healthcare professionals to identify novel therapeutics to counteract this pandemic. So far, there is no approved treatment available to control this public health issue; however, a few antiviral agents and repurposed drugs support the patients under medical supervision by compromising their adverse effects, especially in emergency conditions. Only a few vaccines have been approved to date. In this context, several plant natural products-based research studies are evidenced to play a crucial role in immunomodulation that can prevent the chances of infection as well as combat the cytokine release storm (CRS) generated during COVID-19 infection. In this present review, we have focused on flavonoids, especially epicatechin, epigallocatechin gallate, hesperidin, naringenin, quercetin, rutin, luteolin, baicalin, diosmin, ge nistein, biochanin A, and silymarin, which can counteract the virus-mediated elevated levels of inflammatory cytokines leading to multiple organ failure. In addition, a comprehensive discussion on available in silico, in vitro, and in vivo findings with critical analysis has also been evaluated, which might pave the way for further development of phytotherapeutics to identify the potential lead candidatetoward effective and safe management of the SARS-CoV-2 disease.
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Affiliation(s)
- Abhishek Gour
- PK‐PD, Toxicology and Formulation DivisionCSIR‐Indian Institute of Integrative MedicineJammuIndia
- Academy of Scientific and Innovative Research (AcSIR)GhaziabadUttar PradeshIndia
| | - Diksha Manhas
- PK‐PD, Toxicology and Formulation DivisionCSIR‐Indian Institute of Integrative MedicineJammuIndia
- Academy of Scientific and Innovative Research (AcSIR)GhaziabadUttar PradeshIndia
| | - Swarnendu Bag
- Proteomics DivisionCSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
| | - Bapi Gorain
- School of Pharmacy, Faculty of Health and Medical SciencesTaylor's UniversitySubang JayaMalaysia
| | - Utpal Nandi
- PK‐PD, Toxicology and Formulation DivisionCSIR‐Indian Institute of Integrative MedicineJammuIndia
- Academy of Scientific and Innovative Research (AcSIR)GhaziabadUttar PradeshIndia
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Cárdenas-Rodríguez N, Bandala C, Vanoye-Carlo A, Ignacio-Mejía I, Gómez-Manzo S, Hernández-Cruz EY, Pedraza-Chaverri J, Carmona-Aparicio L, Hernández-Ochoa B. Use of Antioxidants for the Neuro-Therapeutic Management of COVID-19. Antioxidants (Basel) 2021; 10:971. [PMID: 34204362 PMCID: PMC8235474 DOI: 10.3390/antiox10060971] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/07/2021] [Accepted: 06/15/2021] [Indexed: 02/07/2023] Open
Abstract
Coronavirus Disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is an emergent infectious disease that has caused millions of deaths throughout the world. COVID-19 infection's main symptoms are fever, cough, fatigue, and neurological manifestations such as headache, myalgias, anosmia, ageusia, impaired consciousness, seizures, and even neuromuscular junctions' disorders. In addition, it is known that this disease causes a series of systemic complications such as adverse respiratory distress syndrome, cardiac injury, acute kidney injury, and liver dysfunction. Due to the neurological symptoms associated with COVID-19, damage in the central nervous system has been suggested as well as the neuroinvasive potential of SARS-CoV-2. It is known that CoV infections are associated with an inflammation process related to the imbalance of the antioxidant system; cellular changes caused by oxidative stress contribute to brain tissue damage. Although anti-COVID-19 vaccines are under development, there is no specific treatment for COVID-19 and its clinical manifestations and complications; only supportive treatments with immunomodulators, anti-vascular endothelial growth factors, modulating drugs, statins, or nutritional supplements have been used. In the present work, we analyzed the potential of antioxidants as adjuvants for the treatment of COVID-19 and specifically their possible role in preventing or decreasing the neurological manifestations and neurological complications present in the disease.
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Affiliation(s)
- Noemí Cárdenas-Rodríguez
- Laboratorio de Neurociencias, Instituto Nacional de Pediatría, Secreatría de Salud, Ciudad de México 04530, Mexico; (A.V.-C.); (L.C.-A.)
| | - Cindy Bandala
- Division de Neurociencias, Instituto Nacional de Rehabilitación, Secretaría de Salud, Ciudad de México 14389, Mexico;
- Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico
| | - América Vanoye-Carlo
- Laboratorio de Neurociencias, Instituto Nacional de Pediatría, Secreatría de Salud, Ciudad de México 04530, Mexico; (A.V.-C.); (L.C.-A.)
| | - Iván Ignacio-Mejía
- Laboratorio de Medicina Traslacional, Escuela Militar de Graduados de Sanidad, SEDENA, Ciudad de México 11200, Mexico;
| | - Saúl Gómez-Manzo
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, Mexico;
| | | | - José Pedraza-Chaverri
- Departamento de Biología, Facultad de Química, UNAM, Ciudad de México 04150, Mexico; (E.Y.H.-C.); (J.P.-C.)
| | - Liliana Carmona-Aparicio
- Laboratorio de Neurociencias, Instituto Nacional de Pediatría, Secreatría de Salud, Ciudad de México 04530, Mexico; (A.V.-C.); (L.C.-A.)
| | - Beatriz Hernández-Ochoa
- Laboratorio de Inmunoquímica, Hospital Infantil de México Federico Gómez, Secretaría de Salud, Ciudad de México 06720, Mexico;
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Deetanya P, Hengphasatporn K, Wilasluck P, Shigeta Y, Rungrotmongkol T, Wangkanont K. Interaction of 8-anilinonaphthalene-1-sulfonate with SARS-CoV-2 main protease and its application as a fluorescent probe for inhibitor identification. Comput Struct Biotechnol J 2021; 19:3364-3371. [PMID: 34109016 PMCID: PMC8178945 DOI: 10.1016/j.csbj.2021.05.053] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/29/2021] [Accepted: 05/30/2021] [Indexed: 01/22/2023] Open
Abstract
The 3C-like main protease of SARS-CoV-2 (3CLPro) is responsible for the cleavage of the viral polyprotein. This process is essential for the viral life cycle. Therefore, 3CLPro is a promising target to develop antiviral drugs for COVID-19 prevention and treatment. Traditional enzymatic assays for the identification of 3CLPro inhibitors rely on peptide-based colorimetric or fluorogenic substrates. However, the COVID-19 pandemic has limit or delay access to these substrates, especially for researchers in developing countries attempting to screen natural product libraries. We explored the use of the fluorescent probe 8-anilinonaphthalene-1-sulfonate (ANS) as an alternative assay for inhibitor identification. Fluorescence enhancement upon binding of ANS to 3CLPro was observed, and this interaction was competitive with a peptide substrate. The utility of ANS-based competitive binding assay to identify 3CLPro inhibitors was demonstrated with the flavonoid natural products baicalein and rutin. The molecular nature of ANS and rutin interaction with 3CLPro was explored with molecular modeling. Our results suggested that ANS could be employed in a competitive binding assay to facilitate the identification of novel SARS-CoV-2 antiviral compounds.
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Affiliation(s)
- Peerapon Deetanya
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Molecular Crop Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kowit Hengphasatporn
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Patcharin Wilasluck
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Molecular Crop Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Thanyada Rungrotmongkol
- Program in Bioinformatics and Computational Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kittikhun Wangkanont
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Molecular Crop Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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48
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Yañez O, Osorio MI, Areche C, Vasquez-Espinal A, Bravo J, Sandoval-Aldana A, Pérez-Donoso JM, González-Nilo F, Matos MJ, Osorio E, García-Beltrán O, Tiznado W. Theobroma cacao L. compounds: Theoretical study and molecular modeling as inhibitors of main SARS-CoV-2 protease. Biomed Pharmacother 2021; 140:111764. [PMID: 34051617 PMCID: PMC8141698 DOI: 10.1016/j.biopha.2021.111764] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/07/2021] [Accepted: 05/20/2021] [Indexed: 11/23/2022] Open
Abstract
Cocoa beans contain antioxidant molecules with the potential to inhibit type 2 coronavirus (SARS-CoV-2), which causes a severe acute respiratory syndrome (COVID-19). In particular, protease. Therefore, using in silico tests, 30 molecules obtained from cocoa were evaluated. Using molecular docking and quantum mechanics calculations, the chemical properties and binding efficiency of each ligand was evaluated, which allowed the selection of 5 compounds of this series. The ability of amentoflavone, isorhoifolin, nicotiflorin, naringin and rutin to bind to the main viral protease was studied by means of free energy calculations and structural analysis performed from molecular dynamics simulations of the enzyme/inhibitor complex. Isorhoifolin and rutin stand out, presenting a more negative binding ΔG than the reference inhibitor N-[(5-methylisoxazol-3-yl)carbonyl]alanyl-l-valyl-N~1~-((1R,2Z)−4-(benzyloxy)−4-oxo-1-{[(3R)−2-oxopyrrolidin-3-yl]methyl}but-2-enyl)-L-leucinamide (N3). These results are consistent with high affinities of these molecules for the major SARS-CoV-2. The results presented in this paper are a solid starting point for future in vitro and in vivo experiments aiming to validate these molecules and /or test similar substances as inhibitors of SARS-CoV-2 protease.
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Affiliation(s)
- Osvaldo Yañez
- Computational and Theoretical Chemistry Group, Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, República 498, Santiago, Chile; Center of New Drugs for Hypertension (CENDHY), Santiago, Chile; Department of Pharmaceutical Science and Technology, School of Chemical and Pharmaceutical Sciences, Universidad de Chile, Santiago, Chile
| | - Manuel Isaías Osorio
- Facultad de Medicina, Centro de Investigación Biomédica, Universidad Diego Portales, Ejército 141, Santiago 837007, Chile; Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias de la Vida, Universidad Andres Bello, Av. República 330, Santiago 8370146, Chile
| | - Carlos Areche
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Nuñoa, Santiago 7800024, Chile
| | - Alejandro Vasquez-Espinal
- Computational and Theoretical Chemistry Group, Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, República 498, Santiago, Chile
| | - Jessica Bravo
- Facultad de Medicina, Centro de Investigación Biomédica, Universidad Diego Portales, Ejército 141, Santiago 837007, Chile
| | - Angélica Sandoval-Aldana
- Grupo Interdisciplinario de Investigación en Fruticultura Tropical, Facultad de Ingeniería Agronómica, Universidad del Tolima, Ibagué 730006, Colombia
| | - José M Pérez-Donoso
- Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias de la Vida, Universidad Andres Bello, Av. República 330, Santiago 8370146, Chile
| | - Fernando González-Nilo
- Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias de la Vida, Universidad Andres Bello, Av. República 330, Santiago 8370146, Chile
| | - Maria João Matos
- CIQUP/Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Edison Osorio
- Facultad de Ciencias Naturales y Matemáticas, Universidad de Ibagué, Carrera 22 calle 67, Ibagué 730002, Colombia
| | - Olimpo García-Beltrán
- Facultad de Ciencias Naturales y Matemáticas, Universidad de Ibagué, Carrera 22 calle 67, Ibagué 730002, Colombia; Universidad Bernardo O'Higgins, Centro Integrativo de Biología y Química Aplicada (CIBQA), General Gana 1702, Santiago, Chile, 8370854.
| | - William Tiznado
- Computational and Theoretical Chemistry Group, Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, República 498, Santiago, Chile.
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Rahman F, Tabrez S, Ali R, Akand SK, Zahid M, Alaidarous MA, Alsaweed M, Alshehri BM, Banawas S, Bin Dukhyil AA, Rub A. Virtual screening of natural compounds for potential inhibitors of Sterol C-24 methyltransferase of Leishmania donovani to overcome leishmaniasis. J Cell Biochem 2021; 122:1216-1228. [PMID: 33955051 DOI: 10.1002/jcb.29944] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/05/2021] [Accepted: 04/12/2021] [Indexed: 12/23/2022]
Abstract
Leishmaniasis is a neglected tropical disease caused by trypanosomatid parasite belonging to the genera Leishmania. Leishmaniasis is transmitted from one human to other through the bite of sandflies. It is endemic in around 98 countries including tropical and subtropical regions of Asia, Africa, Southern America, and the Mediterranean region. Sterol C-24 methyltransferase (LdSMT) of Leishmania donovani (L. donovani) mediates the transfer of CH3-group from S-adenosyl methionine to C-24 position of sterol side chain which makes the ergosterol different from cholesterol. Absence of ortholog in human made it potential druggable target. Here, we performed virtual screening of library of natural compounds against LdSMT to identify the potential inhibitor for it and to fight leishmaniasis. Gigantol, flavan-3-ol, and parthenolide showed the best binding affinity towards LdSMT. Further, based on absorption, distribution, metabolism, and excretion properties and biological activity prediction, gigantol showed the best lead-likeness and drug-likeness properties. Therefore, we further elucidated its antileishmanial properties. We found that gigantol inhibited the growth and proliferation of promastigotes as well as intra-macrophagic amastigotes. Gigantol exerted its antileishmanial action through the induction of reactive oxygen species in dose-dependent manner. Our study, suggested the possible use of gigantol as antileishmanial drug after further validations to overcome leishmaniasis.
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Affiliation(s)
- Fazlur Rahman
- Department of Biotechnology, Infection and Immunity Lab (414), Jamia Millia Islamia (A Central University), New Delhi, India
| | - Shams Tabrez
- Department of Biotechnology, Infection and Immunity Lab (414), Jamia Millia Islamia (A Central University), New Delhi, India
| | - Rahat Ali
- Department of Biotechnology, Infection and Immunity Lab (414), Jamia Millia Islamia (A Central University), New Delhi, India
| | - Sajjadul Kadir Akand
- Department of Biotechnology, Infection and Immunity Lab (414), Jamia Millia Islamia (A Central University), New Delhi, India
| | - Mariya Zahid
- Department of Biotechnology, Infection and Immunity Lab (414), Jamia Millia Islamia (A Central University), New Delhi, India
| | - Mohammed A Alaidarous
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah, Saudi Arabia
- Department of Vice Rector for Graduate Studies and Scientific Research, Health and Basic Sciences Research Center, Majmaah University, Al Majmaah, Saudi Arabia
| | - Mohammed Alsaweed
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah, Saudi Arabia
| | - Bader Mohammed Alshehri
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah, Saudi Arabia
| | - Saeed Banawas
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah, Saudi Arabia
- Department of Vice Rector for Graduate Studies and Scientific Research, Health and Basic Sciences Research Center, Majmaah University, Al Majmaah, Saudi Arabia
| | - Abdul Aziz Bin Dukhyil
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah, Saudi Arabia
| | - Abdur Rub
- Department of Biotechnology, Infection and Immunity Lab (414), Jamia Millia Islamia (A Central University), New Delhi, India
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50
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Grabowski M, Macnar JM, Cymborowski M, Cooper DR, Shabalin IG, Gilski M, Brzezinski D, Kowiel M, Dauter Z, Rupp B, Wlodawer A, Jaskolski M, Minor W. Rapid response to emerging biomedical challenges and threats. IUCRJ 2021; 8:395-407. [PMID: 33953926 PMCID: PMC8086160 DOI: 10.1107/s2052252521003018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 03/22/2021] [Indexed: 05/13/2023]
Abstract
As part of the global mobilization to combat the present pandemic, almost 100 000 COVID-19-related papers have been published and nearly a thousand models of macromolecules encoded by SARS-CoV-2 have been deposited in the Protein Data Bank within less than a year. The avalanche of new structural data has given rise to multiple resources dedicated to assessing the correctness and quality of structural data and models. Here, an approach to evaluate the massive amounts of such data using the resource https://covid19.bioreproducibility.org is described, which offers a template that could be used in large-scale initiatives undertaken in response to future biomedical crises. Broader use of the described methodology could considerably curtail information noise and significantly improve the reproducibility of biomedical research.
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Affiliation(s)
- Marek Grabowski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Joanna M. Macnar
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Warsaw, Poland
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Warsaw, Poland
| | - Marcin Cymborowski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - David R. Cooper
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Ivan G. Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Miroslaw Gilski
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Dariusz Brzezinski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, Poznan, Poland
| | - Marcin Kowiel
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Zbigniew Dauter
- Center for Structural Biology, National Cancer Institute, Frederick, Maryland, USA
| | - Bernhard Rupp
- k.-k Hofkristallamt, San Diego, California, USA
- Institute of Genetic Epidemiology, Medical University Innsbruck, Innsbruck, Austria
| | - Alexander Wlodawer
- Center for Structural Biology, National Cancer Institute, Frederick, Maryland, USA
| | - Mariusz Jaskolski
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
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