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Waqas M, Ullah S, Ullah A, Halim SA, Rehman NU, Khalid A, Ali A, Khan A, Gibbons S, Csuk R, Al-Harrasi A. Disrupting protease and deubiquitinase activities of SARS-CoV-2 papain-like protease by natural and synthetic products discovered through multiple computational and biochemical approaches. Int J Biol Macromol 2024; 277:134476. [PMID: 39111477 DOI: 10.1016/j.ijbiomac.2024.134476] [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: 12/21/2023] [Revised: 07/31/2024] [Accepted: 08/02/2024] [Indexed: 08/12/2024]
Abstract
The single-stranded RNA genome of SARS-CoV-2 encodes several structural and non-structural proteins, among which the papain-like protease (PLpro) is crucial for viral replication and immune evasion and has emerged as a promising therapeutic target. The current study aims to discover new inhibitors of PLpro that can simultaneously disrupt its protease and deubiquitinase activities. Using multiple computational approaches, six compounds (CP1-CP6) were selected from our in-house compounds database, with higher docking scores (-7.97 kcal/mol to -8.14 kcal/mol) and fitted well in the active pocket of PLpro. Furthermore, utilizing microscale molecular dynamics simulations (MD), the dynamic behavior of selected compounds was studied. Those molecules strongly binds at the PLpro active site and forms stable complexes. The dynamic motions suggest that the binding of CP1-CP6 brought the protein to a closed conformational state, thereby altering its normal function. In an in vitro evaluation, CP2 showed the most significant inhibitory potential for PLpro (protease activity = 2.71 ± 0.33 μM and deubiquitinase activity = 3.11 ± 0.75 μM), followed by CP1, CP5, CP4 and CP6. Additionally, CP1-CP6 showed no cytotoxicity at a concentration of 30 μM in the human BJ cell line.
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Affiliation(s)
- Muhammad Waqas
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra 2100, Pakistan
| | - Saeed Ullah
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman
| | - Atta Ullah
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman
| | - Sobia Ahsan Halim
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman
| | - Najeeb Ur Rehman
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman
| | - Asaad Khalid
- Health Research Center, Jazan University, P.O. Box: 114, Jazan 45142, Saudi Arabia
| | - Amjad Ali
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra 2100, Pakistan.
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman.
| | - Simon Gibbons
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman
| | - Rene Csuk
- Martin-Luther-University Halle-Wittenberg, Organic Chemistry, Kurt-Mothes-Str. 2, D-06120 Halle (Saale), Germany
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman.
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2
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Al Adem K, Ferreira JC, Villanueva AJ, Fadl S, El-Sadaany F, Masmoudi I, Gidiya Y, Gurudza T, Cardoso THS, Saksena NK, Rabeh WM. 3-chymotrypsin-like protease in SARS-CoV-2. Biosci Rep 2024; 44:BSR20231395. [PMID: 39036877 DOI: 10.1042/bsr20231395] [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: 01/31/2024] [Revised: 07/16/2024] [Accepted: 07/19/2024] [Indexed: 07/23/2024] Open
Abstract
Coronaviruses constitute a significant threat to the human population. Severe acute respiratory syndrome coronavirus-2, SARS-CoV-2, is a highly pathogenic human coronavirus that has caused the coronavirus disease 2019 (COVID-19) pandemic. It has led to a global viral outbreak with an exceptional spread and a high death toll, highlighting the need for effective antiviral strategies. 3-Chymotrypsin-like protease (3CLpro), the main protease in SARS-CoV-2, plays an indispensable role in the SARS-CoV-2 viral life cycle by cleaving the viral polyprotein to produce 11 individual non-structural proteins necessary for viral replication. 3CLpro is one of two proteases that function to produce new viral particles. It is a highly conserved cysteine protease with identical structural folds in all known human coronaviruses. Inhibitors binding with high affinity to 3CLpro will prevent the cleavage of viral polyproteins, thus impeding viral replication. Multiple strategies have been implemented to screen for inhibitors against 3CLpro, including peptide-like and small molecule inhibitors that covalently and non-covalently bind the active site, respectively. In addition, allosteric sites of 3CLpro have been identified to screen for small molecules that could make non-competitive inhibitors of 3CLpro. In essence, this review serves as a comprehensive guide to understanding the structural intricacies and functional dynamics of 3CLpro, emphasizing key findings that elucidate its role as the main protease of SARS-CoV-2. Notably, the review is a critical resource in recognizing the advancements in identifying and developing 3CLpro inhibitors as effective antiviral strategies against COVID-19, some of which are already approved for clinical use in COVID-19 patients.
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Affiliation(s)
- Kenana Al Adem
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Juliana C Ferreira
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Adrian J Villanueva
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Samar Fadl
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Farah El-Sadaany
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Imen Masmoudi
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Yugmee Gidiya
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Tariro Gurudza
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Thyago H S Cardoso
- OMICS Centre of Excellence, G42 Healthcare, Masdar City, Abu Dhabi, United Arab Emirates
| | - Nitin K Saksena
- Victoria University, Footscray Campus, Melbourne, VIC. Australia
| | - Wael M Rabeh
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
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3
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Lima Bezerra JJ, Lucena RB. Poisonings in ruminants by Cenostigma pyramidale (Tul.) Gagnon & G.P.Lewis (Fabaceae): A mini-review of teratogenic potential and phytochemical evidence. Toxicon 2024; 246:107794. [PMID: 38851021 DOI: 10.1016/j.toxicon.2024.107794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 05/29/2024] [Accepted: 06/03/2024] [Indexed: 06/10/2024]
Abstract
Teratogenic plants can be found in pastures in different parts of the world and represent a threat to the reproduction of ruminants. In the northeast region of Brazil, several studies have indicated that Cenostigma pyramidale (Tul.) Gagnon & G.P.Lewis is one of the main poisonous plants that causes reproductive problems in sheep and goats. In this context, the present study reviewed spontaneous and experimental poisonings reports by C. pyramidale in sheep and goats, as well as analyzing the phytochemical evidence related to this species. The scientific documents were retrieved from different databases and, after applying the selection criteria, a total of 16 articles published between 2000 and 2024 were included in this review. Cenostigma pyramidale causes embryonic loss, abortion, and congenital malformations in pregnant sheep and goats in the Brazilian semi-arid region. The main malformations observed in newborn animals are arthrogryposis, scoliosis, micrognathia, multiple skull deformities, cleft palate, and brachygnathism. Many secondary metabolites have already been isolated from C. pyramidale, however, to date, no evidence has been found regarding the possible teratogenic compounds that occur in this plant. From this perspective, new phytochemical studies are necessary to help unravel the mechanisms of action of embryotoxic agents from C. pyramidale.
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Affiliation(s)
- José Jailson Lima Bezerra
- Universidade Federal de Pernambuco, Departamento de Botânica, Av. da Engenharia, s/n, Cidade Universitária, 50670-420, Recife, PE, Brazil
| | - Ricardo Barbosa Lucena
- Universidade Federal da Paraíba, Centro de Ciências Agrárias, Rodovia PB 079 - Km 12, 58397-000, Areia, PB, Brazil.
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4
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Moreira Costa MA, de Sousa NF, Mansur Pontes CL, Scotti MT, de Assis FF, Braga AL, Sandjo LP. Inhibitory effects against SARSCoV-2 main protease (M pro) of biflavonoids and benzophenones from the fruit of Platonia insignis. Fitoterapia 2024; 173:105784. [PMID: 38128621 DOI: 10.1016/j.fitote.2023.105784] [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: 10/05/2023] [Revised: 12/07/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023]
Abstract
The SARS-CoV-2 mutation and the limitation of the approved drug against COVID-19 are still a challenge in many country healthcare systems and need to be affronted despite the set of vaccines to prevent this viral infection. To contribute to the identification of new antiviral agents, the present study focused on natural products from an edible fruit with potential inhibitory effects against the SARS-CoV-2 main protease (Mpro). First, LC-ESIMS analysis of Platonia insignis fruits was performed and showed the presence of biflavonoids and benzophenones in the seed and pulp, respectively. Then, maceration and chromatographic purification led to the identification of two triglycerides (1 and 2) alongside chamaejasmine (3) and volkensiflavone (4) from the seed and isogarcinol (5) and cycloxanthochymol (6), from the pulp. Compounds 1-6 after evaluating their inhibitory against Mpro, displayed from no to significant activity. Compound 5 was the most potent with an IC50 value of 0.72 μM and was more active than the positive control, Ebselen (IC50 of 3.4 μM). It displayed weak and no cytotoxicity against THP-1 (CC50 of 116.2 μM) and Vero cell lines, respectively. Other active compounds showed no cytotoxicity against THP-1. and Vero cell lines. Molecular docking studies revealed interactions in the catalytic pocket between compound 5 and amino acid residues that composed the catalytic dyads (His 41 and Cyst 145).
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Affiliation(s)
- Monalisa A Moreira Costa
- Department of Chemistry, CFM, Universidade Federal de Santa Catarina, Campus Universitário-Trindade, Florianópolis 88040-900, SC, Brazil
| | - Natália F de Sousa
- Department of Chemistry, Center for Exact and Natural Sciences, Universidade Federal de Paraíba, Campus I, João Pessoa, PB, Brazil
| | - Carime L Mansur Pontes
- Department of Chemistry, CFM, Universidade Federal de Santa Catarina, Campus Universitário-Trindade, Florianópolis 88040-900, SC, Brazil
| | - Marcus T Scotti
- Department of Chemistry, Center for Exact and Natural Sciences, Universidade Federal de Paraíba, Campus I, João Pessoa, PB, Brazil
| | - Francisco F de Assis
- Department of Chemistry, CFM, Universidade Federal de Santa Catarina, Campus Universitário-Trindade, Florianópolis 88040-900, SC, Brazil
| | - Antonio L Braga
- Department of Chemistry, CFM, Universidade Federal de Santa Catarina, Campus Universitário-Trindade, Florianópolis 88040-900, SC, Brazil
| | - Louis P Sandjo
- Department of Chemistry, CFM, Universidade Federal de Santa Catarina, Campus Universitário-Trindade, Florianópolis 88040-900, SC, Brazil.
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5
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Dos Santos BL, Dos Santos CC, da Silva KC, Nonaka CKV, Souza BSDF, David JM, de Oliveira JVR, Costa MDFD, Butt AM, da Silva VDA, Costa SL. The Phytochemical Agathisflavone Modulates miR146a and miR155 in Activated Microglia Involving STAT3 Signaling. Int J Mol Sci 2024; 25:2547. [PMID: 38473794 DOI: 10.3390/ijms25052547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/23/2024] [Accepted: 02/06/2024] [Indexed: 03/14/2024] Open
Abstract
MicroRNAs (miRs) act as important post-transcriptional regulators of gene expression in glial cells and have been shown to be involved in the pathogenesis of neurodegenerative diseases, including Alzheimer's disease (AD). Here, we investigated the effects of agathisflavone, a biflavonoid purified from the leaves of Cenostigma pyramidale (Tul.), on modulating the expression of miRs and inflammatory mediators in activated microglia. C20 human microglia were exposed to oligomers of the β-amyloid peptide (Aβ, 500 nM) for 4 h or to lipopolysaccharide (LPS, 1 µg/mL) for 24 h and then treated or not with agathisflavone (1 µM) for 24 h. We observed that β-amyloid and LPS activated microglia to an inflammatory state, with increased expression of miR-146a, miR-155, IL1-β, IL-6, and NOS2. Treatment with agathisflavone resulted in a significant reduction in miR146a and miR-155 induced by LPS or Aβ, as well as inflammatory cytokines IL1-β, IL-6, and NOS2. In cells stimulated with Aβ, there was an increase in p-STAT3 expression that was reduced by agathisflavone treatment. These data identify a role for miRs in the anti-inflammatory effect of agathisflavone on microglia in models of neuroinflammation and AD.
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Affiliation(s)
- Balbino Lino Dos Santos
- Laboratory of Neurochemistry and Cellular Biology, Institute of Health Sciences, Federal University of Bahia, Av. Reitor Miguel Calmon S/N, Salvador 40231-300, BA, Brazil
- College of Nursing, Federal University of Vale do São Francisco, Av. José de Sá Maniçoba, S/N, Petrolina 56304-917, PE, Brazil
| | - Cleonice Creusa Dos Santos
- Laboratory of Neurochemistry and Cellular Biology, Institute of Health Sciences, Federal University of Bahia, Av. Reitor Miguel Calmon S/N, Salvador 40231-300, BA, Brazil
| | - Karina Costa da Silva
- Laboratory of Neurochemistry and Cellular Biology, Institute of Health Sciences, Federal University of Bahia, Av. Reitor Miguel Calmon S/N, Salvador 40231-300, BA, Brazil
| | - Carolina Kymie Vasques Nonaka
- Center of Biotechnology and Cell Therapy, São Rafael Hospital, D'Or Institute for Research and Teaching (IDOR), Salvador 41253-190, BA, Brazil
| | - Bruno Solano de Freitas Souza
- Center of Biotechnology and Cell Therapy, São Rafael Hospital, D'Or Institute for Research and Teaching (IDOR), Salvador 41253-190, BA, Brazil
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz (FIOCRUZ), Salvador 40296-710, BA, Brazil
| | - Jorge Mauricio David
- Department of General and Inorganic Chemistry, Institute of Chemistry, Federal University of Bahia, Salvador 40231-300, BA, Brazil
| | - Juciele Valéria Ribeiro de Oliveira
- Laboratory of Neurochemistry and Cellular Biology, Institute of Health Sciences, Federal University of Bahia, Av. Reitor Miguel Calmon S/N, Salvador 40231-300, BA, Brazil
| | - Maria de Fátima Dias Costa
- Laboratory of Neurochemistry and Cellular Biology, Institute of Health Sciences, Federal University of Bahia, Av. Reitor Miguel Calmon S/N, Salvador 40231-300, BA, Brazil
- National Institute of Translational Neuroscience (INNT), Rio de Janeiro 21941-971, RJ, Brazil
| | - Arthur Morgan Butt
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DT, UK
| | - Victor Diogenes Amaral da Silva
- Laboratory of Neurochemistry and Cellular Biology, Institute of Health Sciences, Federal University of Bahia, Av. Reitor Miguel Calmon S/N, Salvador 40231-300, BA, Brazil
| | - Silvia Lima Costa
- Laboratory of Neurochemistry and Cellular Biology, Institute of Health Sciences, Federal University of Bahia, Av. Reitor Miguel Calmon S/N, Salvador 40231-300, BA, Brazil
- National Institute of Translational Neuroscience (INNT), Rio de Janeiro 21941-971, RJ, Brazil
- Instituto de Ciências da Saúde, Av. Reitor Miguel Calmon S/N Vale do Canela, Salvador 40110-902, BA, Brazil
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6
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Waqas M, Ullah S, Halim SA, Rehman NU, Ali A, Jan A, Muhsinah AB, Khan A, Al-Harrasi A. Targeting papain-like protease by natural products as novel therapeutic potential SARS-CoV-2. Int J Biol Macromol 2024; 258:128812. [PMID: 38114011 DOI: 10.1016/j.ijbiomac.2023.128812] [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: 10/31/2023] [Revised: 11/27/2023] [Accepted: 12/12/2023] [Indexed: 12/21/2023]
Abstract
The highly infectious respiratory illness 'COVID-19' was caused by SARS-CoV-2 and is responsible for millions of deaths. SARS-single-stranded viral RNA genome encodes several structural and nonstructural proteins, including papain-like protease (PLpro), which is essential for viral replication and immune evasion and serve as a potential therapeutic target. Multiple computational techniques were used to search the natural compounds that may block the protease and deubiquitinase activities of PLpro. Five compounds showed strong interactions and binding energy (ranges between -8.18 to -8.69 Kcal/mol) in our in-silico studies. Interestingly, those molecules strongly bind in the PLpro active site and form a stable complex, as shown by microscale molecular dynamic simulations (MD). The dynamic movements indicate that PLpro acquires closed conformation by the attachment of these molecules, thereby changing its normal function. In the in-vitro evaluation, compound COMP4 showed the most potent inhibitory potential for PLpro (protease activity: 2.24 ± 0.17 μM and deubiquitinase activity: 1.43 ± 0.14 μM), followed by COMP1, 2, 3, and 5. Furthermore, the cytotoxic effect of COMP1-COMP5 on a human BJ cell line revealed that these compounds demonstrate negligible cytotoxicity at a dosage of 30 μM. The results suggest that these entities bear therapeutic efficacy for SARS-CoV-2 PLpro.
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Affiliation(s)
- Muhammad Waqas
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Mansehra 2100, Pakistan
| | - Saeed Ullah
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman
| | - Sobia Ahsan Halim
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman
| | - Najeeb Ur Rehman
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman
| | - Amjad Ali
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Mansehra 2100, Pakistan.
| | - Afnan Jan
- Department of Biochemistry, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Abdullatif Bin Muhsinah
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Abha 62529, Saudi Arabia
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman.
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa 616, Sultanate of Oman.
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7
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Tucci AR, da Rosa RM, Rosa AS, Augusto Chaves O, Ferreira VNS, Oliveira TKF, Coutinho Souza DD, Borba NRR, Dornelles L, Rocha NS, Mayer JCP, da Rocha JBT, Rodrigues OED, Miranda MD. Antiviral Effect of 5'-Arylchalcogeno-3-aminothymidine Derivatives in SARS-CoV-2 Infection. Molecules 2023; 28:6696. [PMID: 37764472 PMCID: PMC10537738 DOI: 10.3390/molecules28186696] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/04/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
The understanding that zidovudine (ZDV or azidothymidine, AZT) inhibits the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 and that chalcogen atoms can increase the bioactivity and reduce the toxicity of AZT has directed our search for the discovery of novel potential anti-coronavirus compounds. Here, the antiviral activity of selenium and tellurium containing AZT derivatives in human type II pneumocytes cell model (Calu-3) and monkey kidney cells (Vero E6) infected with SARS-CoV-2, and their toxic effects on these cells, was evaluated. Cell viability analysis revealed that organoselenium (R3a-R3e) showed lower cytotoxicity than organotellurium (R3f, R3n-R3q), with CC50 ≥ 100 µM. The R3b and R3e were particularly noteworthy for inhibiting viral replication in both cell models and showed better selectivity index. In Vero E6, the EC50 values for R3b and R3e were 2.97 ± 0.62 µM and 1.99 ± 0.42 µM, respectively, while in Calu-3, concentrations of 3.82 ± 1.42 µM and 1.92 ± 0.43 µM (24 h treatment) and 1.33 ± 0.35 µM and 2.31 ± 0.54 µM (48 h) were observed, respectively. The molecular docking calculations were carried out to main protease (Mpro), papain-like protease (PLpro), and RdRp following non-competitive, competitive, and allosteric inhibitory approaches. The in silico results suggested that the organoselenium is a potential non-competitive inhibitor of RdRp, interacting in the allosteric cavity located in the palm region. Overall, the cell-based results indicated that the chalcogen-zidovudine derivatives were more potent than AZT in inhibiting SARS-CoV-2 replication and that the compounds R3b and R3e play an important inhibitory role, expanding the knowledge about the promising therapeutic capacity of organoselenium against COVID-19.
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Affiliation(s)
- Amanda Resende Tucci
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (A.S.R.); (V.N.S.F.); (T.K.F.O.); (D.D.C.S.); (N.R.R.B.)
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
| | - Raquel Mello da Rosa
- LabSelen-NanoBio—Departamento de Química, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil; (R.M.d.R.); (L.D.); (N.S.R.); (J.C.P.M.)
| | - Alice Santos Rosa
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (A.S.R.); (V.N.S.F.); (T.K.F.O.); (D.D.C.S.); (N.R.R.B.)
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
| | - Otávio Augusto Chaves
- CQC-IMS, Departamento de Química, Universidade de Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
- Laboratório de Imunofarmacologia, Centro de Pesquisa, Inovação e Vigilância em COVID-19 e Emergências Sanitárias (CPIV), Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-900, RJ, Brazil
| | - Vivian Neuza Santos Ferreira
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (A.S.R.); (V.N.S.F.); (T.K.F.O.); (D.D.C.S.); (N.R.R.B.)
| | - Thamara Kelcya Fonseca Oliveira
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (A.S.R.); (V.N.S.F.); (T.K.F.O.); (D.D.C.S.); (N.R.R.B.)
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
| | - Daniel Dias Coutinho Souza
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (A.S.R.); (V.N.S.F.); (T.K.F.O.); (D.D.C.S.); (N.R.R.B.)
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
| | - Nathalia Roberto Resende Borba
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (A.S.R.); (V.N.S.F.); (T.K.F.O.); (D.D.C.S.); (N.R.R.B.)
| | - Luciano Dornelles
- LabSelen-NanoBio—Departamento de Química, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil; (R.M.d.R.); (L.D.); (N.S.R.); (J.C.P.M.)
| | - Nayra Salazar Rocha
- LabSelen-NanoBio—Departamento de Química, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil; (R.M.d.R.); (L.D.); (N.S.R.); (J.C.P.M.)
| | - João Candido Pilar Mayer
- LabSelen-NanoBio—Departamento de Química, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil; (R.M.d.R.); (L.D.); (N.S.R.); (J.C.P.M.)
| | - João B. Teixeira da Rocha
- Programa de Pós-Graduação em Bioquímica Toxicológica, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil;
| | - Oscar Endrigo D. Rodrigues
- LabSelen-NanoBio—Departamento de Química, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil; (R.M.d.R.); (L.D.); (N.S.R.); (J.C.P.M.)
| | - Milene Dias Miranda
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (A.S.R.); (V.N.S.F.); (T.K.F.O.); (D.D.C.S.); (N.R.R.B.)
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
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Mohammad A, Alshawaf E, Arefanian H, Marafie SK, Khan A, Wei DQ, Al-Mulla F, Abubaker J. Targeting SARS-CoV-2 Macrodomain-1 to Restore the Innate Immune Response Using In Silico Screening of Medicinal Compounds and Free Energy Calculation Approaches. Viruses 2023; 15:1907. [PMID: 37766313 PMCID: PMC10538035 DOI: 10.3390/v15091907] [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: 07/17/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Among the different drug targets of SARS-CoV-2, a multi-domain protein known as NSP3 is a critical element of the translational and replication machinery. The macrodomain-I, in particular, has been reported to have an essential role in the viral attack on the innate immune response. In this study, we explore natural medicinal compounds and identify potential inhibitors to target the SARS-CoV-2-NSP3 macrodomain-I. Computational modeling and simulation tools were utilized to investigate the structural-dynamic properties using triplicates of 100 ns MD simulations. In addition, the MM/GBSA method was used to calculate the total binding free energy of each inhibitor bound to macrodomain-I. Two significant hits were identified: 3,5,7,4'-tetrahydroxyflavanone 3'-(4-hydroxybenzoic acid) and 2-hydroxy-3-O-beta-glucopyranosyl-benzoic acid. The structural-dynamic investigation of both compounds with macrodomain-I revealed stable dynamics and compact behavior. In addition, the total binding free energy for each complex demonstrated a robust binding affinity, of ΔG -61.98 ± 0.9 kcal/mol for Compound A, while for Compound B, the ΔG was -45.125 ± 2.8 kcal/mol, indicating the inhibitory potential of these compounds. In silico bioactivity and dissociation constant (KD) determination for both complexes further validated the inhibitory potency of each compound. In conclusion, the aforementioned natural products have the potential to inhibit NSP3, to directly rescue the host immune response. The current study provides the basis for novel drug development against SARS-CoV-2 and its variants.
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Affiliation(s)
- Anwar Mohammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman 15462, Kuwait; (E.A.); (S.K.M.); (J.A.)
| | - Eman Alshawaf
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman 15462, Kuwait; (E.A.); (S.K.M.); (J.A.)
| | - Hossein Arefanian
- Department of Immunology and Microbiology, Dasman Diabetes Institute, Dasman 15462, Kuwait;
| | - Sulaiman K. Marafie
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman 15462, Kuwait; (E.A.); (S.K.M.); (J.A.)
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (A.K.); (D.-Q.W.)
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (A.K.); (D.-Q.W.)
| | - Fahd Al-Mulla
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman 15462, Kuwait;
- Translational Research Department, Dasman Diabetes Institute, Dasman 15462, Kuwait
| | - Jehad Abubaker
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman 15462, Kuwait; (E.A.); (S.K.M.); (J.A.)
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9
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Posinasetty B, Chikatipalli R, Chenchula S, Kuttiappan A, G S, G.N.A. L, Audinarayana N. Anti-arthritic efficacy of Bombax ceiba ethanolic extract in a murine model for rheumatoid arthritis using in vivo, in vitro and radiological analysis. Bioinformation 2023; 19:833-839. [PMID: 37908617 PMCID: PMC10613814 DOI: 10.6026/97320630019833] [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: 08/01/2023] [Revised: 08/31/2023] [Accepted: 08/31/2023] [Indexed: 11/02/2023] Open
Abstract
Rheumatoid arthritis (RA) is a multisystem autoimmune disease that causes discomfort, synovial membrane inflammation, peripheral joint inflammation, morning stiffness, articular tissue loss, and restricted joint movement. In the present study, we aim to explore the anti-arthritic efficacy of Bombax ceiba ethanolic extract in a Freund's Complete Adjuvant-induced arthritis, in murine model. The hot soxhlet method was used to extract dried aerial components of Bombax ceiba using an ethyl alcohol: water (70:30) ratio. Bombax ceiba ethanolic extract at two doses of 200 and 400 mg/kg was investigated in Wistar rats against Freund's full adjuvant-induced chronic immunological arthritis. Anti-arthritis efficacy was studied utilising morphological research (paw volume, paw diameter, and body weight). On the 28th day, the animals were sacrificed, and haematological parameters, pro-inflammatory cytokines (TNF-alpha, IL-6), cell culture, histological and radiological analysis were performed. BCEE inhibited paw oedema significantly (P 0.05) at a dose of 40mg/Kg, which was corroborated by paw volume and diameter, as well as haematological parameters, in Freund's complete adjuvant-induced arthritis model. The BCEE also significantly reduced pro-inflammatory cytokine levels and the histopathological changes caused by Freund's full adjuvant model. BCEE preserves synovial membranes by enhancing health and has shown a significant anti-arthritic activity. Thus, data confirms the traditional usage of Bombax ceiba for arthritis.
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Affiliation(s)
- Bhargavi Posinasetty
- />Department of Clinical Data Management, Prometrika LLC, Cambridge - MA 02140, United States
| | - Radhika Chikatipalli
- />Department of Pharmacology, Sri Venkateswara College of Pharmacy, Chittoor - 517127, A.P., India
| | - Santenna Chenchula
- />Department of clinical pharmacology, All India Institute of Medical Sciences, Bhopal, India, 462020
| | - Anitha Kuttiappan
- />Amity Institute of Pharmacy, Amity University Madhya Pradesh (AUMP), Gwalior - 474005, Madhya Pradesh, India
| | - Swapna G
- />Amity Institute of Pharmacy, Amity University Madhya Pradesh (AUMP), Gwalior - 474005, Madhya Pradesh, India
| | - Lakshmi G.N.A.
- />Amity Institute of Pharmacy, Amity University Madhya Pradesh (AUMP), Gwalior - 474005, Madhya Pradesh, India
| | - Nelavala Audinarayana
- />Amity Institute of Pharmacy, Amity University Madhya Pradesh (AUMP), Gwalior - 474005, Madhya Pradesh, India
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10
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Wang Z, Yang L. The Therapeutic Potential of Natural Dietary Flavonoids against SARS-CoV-2 Infection. Nutrients 2023; 15:3443. [PMID: 37571380 PMCID: PMC10421531 DOI: 10.3390/nu15153443] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 07/28/2023] [Accepted: 08/02/2023] [Indexed: 08/13/2023] Open
Abstract
The exploration of non-toxic and cost-effective dietary components, such as epigallocatechin 3-gallate and myricetin, for health improvement and disease treatment has recently attracted substantial research attention. The recent COVID-19 pandemic has provided a unique opportunity for the investigation and identification of dietary components capable of treating viral infections, as well as gathering the evidence needed to address the major challenges presented by public health emergencies. Dietary components hold great potential as a starting point for further drug development for the treatment and prevention of SARS-CoV-2 infection owing to their good safety, broad-spectrum antiviral activities, and multi-organ protective capacity. Here, we review current knowledge of the characteristics-chemical composition, bioactive properties, and putative mechanisms of action-of natural bioactive dietary flavonoids with the potential for targeting SARS-CoV-2 and its variants. Notably, we present promising strategies (combination therapy, lead optimization, and drug delivery) to overcome the inherent deficiencies of natural dietary flavonoids, such as limited bioavailability and poor stability.
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Affiliation(s)
- Zhonglei Wang
- Key Laboratory of Green Natural Products and Pharmaceutical Intermediates in Colleges and Universities of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, China
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorus, Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Liyan Yang
- School of Physics and Physical Engineering, Qufu Normal University, Qufu 273165, China
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
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11
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Li Z, Yan X, Wei J, Pu L, Zhu G, Cao Y, Liu Z, Liu Y, Li Y, Li L, Li X, Wu Z. A novel colchicine-myricetin heterozygous molecule: design, synthesis, and effective evaluations on the pathological models of acute lung injury in vitro and in vivo. Front Pharmacol 2023; 14:1224906. [PMID: 37456754 PMCID: PMC10340118 DOI: 10.3389/fphar.2023.1224906] [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: 05/18/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023] Open
Abstract
Acute lung injury (ALI) is an inflammatory condition and there are no effective treatments. A novel new compound----colchicine-myricetin hybrid (CMyrH) was herein designed and synthesized. To evaluate the activity of CMyrH in ALI, we used a bleomycin (BLM) induced BEAS-2B injury model in vitro and established a well-recognized rat model of BLM-induced lung injury in vivo. The results demonstrated that colchicine-myricetin hybrid protected BEAS-2B cells against BLM-induced cell injury in an increased dose manner, and reduced wet/dry weight ratio, histological scoring, and inflammation cytokines IL-1β, IL-6, IL-18, and TNF-α levels of lung tissue of the rats. Furthermore, we found colchicine-myricetin hybrid inhibited caspase-1, ASC, GSDMD, and NLRP-3 expression in vivo. Meanwhile, we used molecular docking to analyze the binding mode of colchicine-myricetin hybrid and human neutrophil elastase (HNE), it revealed that colchicine-myricetin hybrid showed strong binding affinity toward human neutrophil elastase when compared to its parent molecules. In conclusion, It is suggested that colchicine-myricetin hybrid antagonized acute lung injury by focusing on multi-targets via multi-mechanisms, and might be served as a potential therapeutic agent for acute lung injury.
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Affiliation(s)
- Zhiyue Li
- Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
- Wu Zhengzhi Academician Workstation, Ningbo College of Health Sciences, Ningbo, China
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xueqin Yan
- Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
- Wu Zhengzhi Academician Workstation, Ningbo College of Health Sciences, Ningbo, China
| | - Jiangchun Wei
- Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
- Wu Zhengzhi Academician Workstation, Ningbo College of Health Sciences, Ningbo, China
| | - Liuyang Pu
- Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Guanbao Zhu
- Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
- Graduate School, Guangxi University of Chinese Medicine, Nanning, China
| | - Yongkai Cao
- Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Zhanyan Liu
- Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Yaqian Liu
- Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Yan Li
- Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Limin Li
- Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Xinping Li
- Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Zhengzhi Wu
- Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
- Wu Zhengzhi Academician Workstation, Ningbo College of Health Sciences, Ningbo, China
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12
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Halma MTJ, Plothe C, Marik P, Lawrie TA. Strategies for the Management of Spike Protein-Related Pathology. Microorganisms 2023; 11:1308. [PMID: 37317282 PMCID: PMC10222799 DOI: 10.3390/microorganisms11051308] [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: 03/16/2023] [Revised: 05/04/2023] [Accepted: 05/10/2023] [Indexed: 06/16/2023] Open
Abstract
In the wake of the COVID-19 crisis, a need has arisen to prevent and treat two related conditions, COVID-19 vaccine injury and long COVID-19, both of which can trace at least part of their aetiology to the spike protein, which can cause harm through several mechanisms. One significant mechanism of harm is vascular, and it is mediated by the spike protein, a common element of the COVID-19 illness, and it is related to receiving a COVID-19 vaccine. Given the significant number of people experiencing these two related conditions, it is imperative to develop treatment protocols, as well as to consider the diversity of people experiencing long COVID-19 and vaccine injury. This review summarizes the known treatment options for long COVID-19 and vaccine injury, their mechanisms, and their evidentiary basis.
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Affiliation(s)
| | - Christof Plothe
- Center for Biophysical Osteopathy, Am Wegweiser 27, 55232 Alzey, Germany
| | - Paul Marik
- Front Line COVID-19 Critical Care Alliance (FLCCC), 2001 L St. NW Suite 500, Washington, DC 20036, USA;
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13
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Guimarães Santana BC, de Almeida Marques DP, Dos Santos Freitas A, Ferreira MM, de Sousa Lopes D, Bagno FF, Guimarães da Fonseca F, Dos Reis JGAC, Oliveira Mendes TAD, Santos JLD, Pirovani CP. Protease inhibitors from Theobroma cacao impair SARS-CoV-2 replication in vitro. Heliyon 2023; 9:e15860. [PMID: 37153407 PMCID: PMC10155420 DOI: 10.1016/j.heliyon.2023.e15860] [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: 10/14/2022] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 05/09/2023] Open
Abstract
SARS-CoV-2 is a newly emerging virus from the Coronaviridae family that has already infected over 700 million people worldwide and killed over 6 million. This virus uses protease molecules to replicate and infect the host, which makes these molecules targets for therapeutic substances to eliminate the virus and treat infected people. Through the protein-protein molecular docking approach, we detected two cystatins from Theobroma cacao, TcCYS3 and TcCYS4, described as papain-like protease inhibitors. These inhibitors decreased SARS-CoV-2 genomic copies without toxicity to Vero cells. There is a need to perform comprehensive studies in relevant animal models and to investigate the action mechanisms of protease inhibitors from Theobroma cacao that control the replication of SARS-CoV-2 in human cells.
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Affiliation(s)
| | - Daisymara Priscila de Almeida Marques
- Laboratório de Virologia Básica e Aplicada, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Andria Dos Santos Freitas
- Laboratório de Proteômica, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brazil
| | - Monaliza Macêdo Ferreira
- Laboratório de Proteômica, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brazil
| | - Danielle de Sousa Lopes
- Laboratório de Imunobiologia, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brazil
| | - Flávia Fonseca Bagno
- Centro de Tecnologia de Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Jordana Grazziela Alves Coelho Dos Reis
- Laboratório de Virologia Básica e Aplicada, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Jane Lima Dos Santos
- Laboratório de Imunobiologia, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brazil
| | - Carlos Priminho Pirovani
- Laboratório de Proteômica, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brazil
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14
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Campos MF, Mendonça SC, Peñaloza EMC, de Oliveira BAC, Rosa AS, Leitão GG, Tucci AR, Ferreira VNS, Oliveira TKF, Miranda MD, Allonso D, Leitão SG. Anti-SARS-CoV-2 Activity of Ampelozizyphus amazonicus (Saracura-Mirá): Focus on the Modulation of the Spike-ACE2 Interaction by Chemically Characterized Bark Extracts by LC-DAD-APCI-MS/MS. Molecules 2023; 28:molecules28073159. [PMID: 37049921 PMCID: PMC10095690 DOI: 10.3390/molecules28073159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/22/2023] [Accepted: 03/29/2023] [Indexed: 04/05/2023] Open
Abstract
Traditional medicine shows several treatment protocols for COVID-19 based on natural products, revealing its potential as a possible source of anti-SARS-CoV-2 agents. Ampelozizyphus amazonicus is popularly used in the Brazilian Amazon as a fortifier and tonic, and recently, it has been reported to relieve COVID-19 symptoms. This work aimed to investigate the antiviral potential of A. amazonicus, focusing on the inhibition of spike and ACE2 receptor interaction, a key step in successful infection. Although saponins are the major compounds of this plant and often reported as its active principles, a polyphenol-rich extract was the best inhibitor of the spike and ACE2 interaction. Chemical characterization of A. amazonicus bark extracts by LC-DAD-APCI-MS/MS before and after clean-up steps for polyphenol removal showed that the latter play an essential role in maintaining this activity. The effects of the extracts on viral replication were also assessed, and all samples (aqueous and ethanol extracts) demonstrated in vitro activity, inhibiting viral titers in the supernatant of Calu-3 cells after 24 hpi. By acting both in the SARS-CoV-2 cell entry process and its replication, A. amazonicus bark extracts stand out as a multitarget agent, highlighting the species as a promising candidate in the development of anti-SARS-CoV-2 drugs.
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Affiliation(s)
- Mariana Freire Campos
- Programa de Pós-Graduação em Biotecnologia Vegetal e Bioprocessos, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21.941-902, RJ, Brazil
- Departamento de Produtos Naturais e Alimentos, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Ilha do Fundão, Centro de Ciências da Saúde, Rio de Janeiro 21.941-902, RJ, Brazil
| | - Simony Carvalho Mendonça
- Departamento de Produtos Naturais e Alimentos, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Ilha do Fundão, Centro de Ciências da Saúde, Rio de Janeiro 21.941-902, RJ, Brazil
| | - Evelyn Maribel Condori Peñaloza
- Departamento de Produtos Naturais e Alimentos, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Ilha do Fundão, Centro de Ciências da Saúde, Rio de Janeiro 21.941-902, RJ, Brazil
| | - Beatriz A. C. de Oliveira
- Departamento de Produtos Naturais e Alimentos, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Ilha do Fundão, Centro de Ciências da Saúde, Rio de Janeiro 21.941-902, RJ, Brazil
| | - Alice S. Rosa
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21.941-902, RJ, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, IOC-Fiocruz, Rio de Janeiro 21.941-902, RJ, Brazil
| | - Gilda Guimarães Leitão
- Instituto de Pesquisas de Produtos Naturais, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21.941-902, RJ, Brazil
| | - Amanda R. Tucci
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21.941-902, RJ, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, IOC-Fiocruz, Rio de Janeiro 21.941-902, RJ, Brazil
| | - Vivian Neuza S. Ferreira
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21.941-902, RJ, Brazil
| | - Thamara Kelcya F. Oliveira
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21.941-902, RJ, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, IOC-Fiocruz, Rio de Janeiro 21.941-902, RJ, Brazil
| | - Milene Dias Miranda
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21.941-902, RJ, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular, IOC-Fiocruz, Rio de Janeiro 21.941-902, RJ, Brazil
| | - Diego Allonso
- Departamento de Biotecnologia Farmacêutica, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21.941-902, RJ, Brazil
| | - Suzana Guimarães Leitão
- Departamento de Produtos Naturais e Alimentos, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Ilha do Fundão, Centro de Ciências da Saúde, Rio de Janeiro 21.941-902, RJ, Brazil
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15
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Zhang H, Liang B, Sang X, An J, Huang Z. Discovery of Potential Inhibitors of SARS-CoV-2 Main Protease by a Transfer Learning Method. Viruses 2023; 15:v15040891. [PMID: 37112871 PMCID: PMC10143255 DOI: 10.3390/v15040891] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 remains a global public health threat and has prompted the development of antiviral therapies. Artificial intelligence may be one of the strategies to facilitate drug development for emerging and re-emerging diseases. The main protease (Mpro) of SARS-CoV-2 is an attractive drug target due to its essential role in the virus life cycle and high conservation among SARS-CoVs. In this study, we used a data augmentation method to boost transfer learning model performance in screening for potential inhibitors of SARS-CoV-2 Mpro. This method appeared to outperform graph convolution neural network, random forest and Chemprop on an external test set. The fine-tuned model was used to screen for a natural compound library and a de novo generated compound library. By combination with other in silico analysis methods, a total of 27 compounds were selected for experimental validation of anti-Mpro activities. Among all the selected hits, two compounds (gyssypol acetic acid and hyperoside) displayed inhibitory effects against Mpro with IC50 values of 67.6 μM and 235.8 μM, respectively. The results obtained in this study may suggest an effective strategy of discovering potential therapeutic leads for SARS-CoV-2 and other coronaviruses.
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