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Gadali KE, Rafya M, El Mansouri AE, Maatallah M, Vanderlee A, Mehdi A, Neyts J, Jochmans D, De Jonghe S, Benkhalti F, Sanghvi YS, Taourirte M, Lazrek HB. Design, synthesis, and molecular modeling studies of novel 2-quinolone-1,2,3-triazole-α-aminophosphonates hybrids as dual antiviral and antibacterial agents. Eur J Med Chem 2024; 268:116235. [PMID: 38377828 DOI: 10.1016/j.ejmech.2024.116235] [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: 02/01/2024] [Accepted: 02/12/2024] [Indexed: 02/22/2024]
Abstract
With the aim to identify new antiviral agents with antibacterial properties, a series of 2-quinolone-1,2,3-triazole derivatives bearing α-aminophosphonates was synthesized and characterized by 1H NMR, 13C NMR, 31P NMR, single crystal XRD and HRMS analyses. These compounds were examined against five RNA viruses (YFV, ZIKV, CHIKV, EV71 and HRV) from three distinct families (Picornaviridae, Togaviridae and Flaviviridae) and four bacterial strains (S. aureus, E. feacalis, E. coli and P. aeruginosa). The α-aminophosphonates 4f, 4i, 4j, 4k, 4p and 4q recorded low IC50 values of 6.8-10.91 μM, along with elevated selectivity indices ranging from 2 to more than 3, particularly against YFV, CHIKV and HRV-B14. Besides, the synthesized compounds were generally more sensitive toward Gram-positive bacteria, with the majority of them displaying significant potency against E. feacalis. Specifically, an excellent anti-enterococcus activity was obtained by compound 4q with MIC and MBC values of 0.03 μmol/mL, which were 8.7 and 10 times greater than those of the reference drugs ampicillin and rifampicin, respectively. Also, compounds 4f, 4p and 4q showed potent anti-staphylococcal activity with MIC values varying between 0.11 and 0.13 μmol/mL, compared to 0.27 μmol/mL for ampicillin. The results from DFT and molecular docking simulations were in agreement with the biological assays, proving the binding capability of hybrids 4f, 4i, 4j, 4k, 4p and 4q with viral and bacterial target enzymes through hydrogen bonds and other non-covalent interactions. The in silico ADME/Tox prediction revealed that these molecules possess moderate to good drug-likeness and pharmacokinetic properties, with a minimal chance of causing liver toxicity or carcinogenic effects.
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Affiliation(s)
- Khadija El Gadali
- Laboratoire de Recherche en Développement Durable et Santé, Faculty of Sciences and Technology Gueliz (FSTG), BP549, Marrakech 40000, Morocco; Laboratory of Molecular Chemistry, Department of Chemistry, Faculty of Sciences Semlalia, Marrakech 40000, Morocco
| | - Meriem Rafya
- Laboratoire de Recherche en Développement Durable et Santé, Faculty of Sciences and Technology Gueliz (FSTG), BP549, Marrakech 40000, Morocco
| | - Az-Eddine El Mansouri
- University of the Free State Faculty of Natural and Agricultural Sciences Chemistry Department 205 Nelson Mandela, Bloemfontein, 9301, South Africa
| | - Mohamed Maatallah
- Laboratory of Molecular Chemistry, Department of Chemistry, Faculty of Sciences Semlalia, Marrakech 40000, Morocco
| | - Arie Vanderlee
- Institut Européen des Membranes, IEM, UMR 5635, Univ. Montpellier, CNRS, ENSCM, 34095 Montpellier, France
| | - Ahmad Mehdi
- ICGM, UMR5253 1919, Route de Mende 34293 Montpellier cedex 5, France
| | - Johan Neyts
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, Box 1043, B-3000 Leuven, Belgium
| | - Dirk Jochmans
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, Box 1043, B-3000 Leuven, Belgium
| | - Steven De Jonghe
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, Box 1043, B-3000 Leuven, Belgium
| | - Fatiha Benkhalti
- Laboratoire de Recherche en Développement Durable et Santé, Faculty of Sciences and Technology Gueliz (FSTG), BP549, Marrakech 40000, Morocco
| | - Yogesh S Sanghvi
- Rasayan Inc, 2802 Crystal Ridge Road, Encinitas, CA 92024-6615, USA
| | - Moha Taourirte
- Laboratoire de Recherche en Développement Durable et Santé, Faculty of Sciences and Technology Gueliz (FSTG), BP549, Marrakech 40000, Morocco.
| | - Hassan B Lazrek
- Laboratory of Molecular Chemistry, Department of Chemistry, Faculty of Sciences Semlalia, Marrakech 40000, Morocco.
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2
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Begum S, Parvej H, Dalui R, Paul S, Maity S, Sepay N, Afzal M, Chandra Halder U. Structural modulation of insulin by hydrophobic and hydrophilic molecules. RSC Adv 2023; 13:34097-34106. [PMID: 38019994 PMCID: PMC10662218 DOI: 10.1039/d3ra06647a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 11/13/2023] [Indexed: 12/01/2023] Open
Abstract
In the bloodstream, insulin interacts with various kinds of molecules, which can alter its structure and modulate its function. In this work, we have synthesized two molecules having extremely hydrophilic and hydrophobic side chains. The effects of hydrophilic and hydrophobic molecules on the binding with insulin have been investigated through a multi-spectroscopic approach. We found that hydrophilic molecules have a slightly higher binding affinity towards insulin. Insulin can bind with the hydrophilic molecules as it binds glucose. The high insulin binding affinity of a hydrophobic molecule indicates its dual nature. The hydrophobic molecule binds at the hydrophobic pocket of the insulin surface, where hydrophilic molecules interact at the polar surface of the insulin. Such binding with the hydrophobic molecule perturbs strongly the secondary structure of the insulin much more in comparison to hydrophilic molecules. Therefore, the stability of insulin decreases in the presence of hydrophobic molecules.
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Affiliation(s)
- Shahnaz Begum
- Department of Chemistry, Jadavpur University Kolkata-700032 India
| | - Hasan Parvej
- Department of Chemistry, Jadavpur University Kolkata-700032 India
| | - Ramkrishna Dalui
- Department of Chemistry, Jadavpur University Kolkata-700032 India
| | - Swarnali Paul
- Department of Chemistry, Jadavpur University Kolkata-700032 India
| | - Sanhita Maity
- Department of Chemistry, Jadavpur University Kolkata-700032 India
| | - Nayim Sepay
- Department of Chemistry, Lady Brabourne College Kolkata-700017 India
| | - Mohd Afzal
- Department of Chemistry, College of Science, King Saud University Riyadh 11451 Saudi Arabia
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Oliveira LPS, Lima LR, Silva LB, Cruz JN, Ramos RS, Lima LS, Cardoso FMN, Silva AV, Rodrigues DP, Rodrigues GS, Proietti-Junior AA, dos Santos GB, Campos JM, Santos CBR. Hierarchical Virtual Screening of Potential New Antibiotics from Polyoxygenated Dibenzofurans against Staphylococcus aureus Strains. Pharmaceuticals (Basel) 2023; 16:1430. [PMID: 37895901 PMCID: PMC10610096 DOI: 10.3390/ph16101430] [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: 08/16/2023] [Revised: 09/25/2023] [Accepted: 10/01/2023] [Indexed: 10/29/2023] Open
Abstract
Staphylococcus aureus is a microorganism with high morbidity and mortality due to antibiotic-resistant strains, making the search for new therapeutic options urgent. In this context, computational drug design can facilitate the drug discovery process, optimizing time and resources. In this work, computational methods involving ligand- and structure-based virtual screening were employed to identify potential antibacterial agents against the S. aureus MRSA and VRSA strains. To achieve this goal, tetrahydroxybenzofuran, a promising antibacterial agent according to in vitro tests described in the literature, was adopted as the pivotal molecule and derivative molecules were considered to generate a pharmacophore model, which was used to perform virtual screening on the Pharmit platform. Through this result, twenty-four molecules were selected from the MolPort® database. Using the Tanimoto Index on the BindingDB web server, it was possible to select eighteen molecules with greater structural similarity in relation to commercial antibiotics (methicillin and oxacillin). Predictions of toxicological and pharmacokinetic properties (ADME/Tox) using the eighteen most similar molecules, showed that only three exhibited desired properties (LB255, LB320 and LB415). In the molecular docking study, the promising molecules LB255, LB320 and LB415 showed significant values in both molecular targets. LB320 presented better binding affinity to MRSA (-8.18 kcal/mol) and VRSA (-8.01 kcal/mol) targets. Through PASS web server, the three molecules, specially LB320, showed potential for antibacterial activity. Synthetic accessibility (SA) analysis performed on AMBIT and SwissADME web servers showed that LB255 and LB415 can be considered difficult to synthesize and LB320 is considered easy. In conclusion, the results suggest that these ligands, particularly LB320, may bind strongly to the studied targets and may have appropriate ADME/Tox properties in experimental studies.
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Affiliation(s)
- Lana P. S. Oliveira
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá 68903-419, Brazil; (L.P.S.O.); (R.S.R.); (F.M.N.C.); (A.V.S.); (A.A.P.-J.)
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
| | - Lúcio R. Lima
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
- Graduate Program in Network in Pharmaceutical Innovation, Federal University of Amapá, Macapá 68902-280, Brazil
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Health Science Institute, Federal Univesity of Pará, Belém 66075-110, Brazil
| | - Luciane B. Silva
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Health Science Institute, Federal Univesity of Pará, Belém 66075-110, Brazil
| | - Jorddy N. Cruz
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
| | - Ryan S. Ramos
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá 68903-419, Brazil; (L.P.S.O.); (R.S.R.); (F.M.N.C.); (A.V.S.); (A.A.P.-J.)
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
| | - Luciana S. Lima
- Special Laboratory of Applied Microbiology, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil;
| | - Francy M. N. Cardoso
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá 68903-419, Brazil; (L.P.S.O.); (R.S.R.); (F.M.N.C.); (A.V.S.); (A.A.P.-J.)
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
- Special Laboratory of Applied Microbiology, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil;
| | - Aderaldo V. Silva
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá 68903-419, Brazil; (L.P.S.O.); (R.S.R.); (F.M.N.C.); (A.V.S.); (A.A.P.-J.)
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
| | - Dália P. Rodrigues
- Laboratory of Bacterial Enteric Pathogens, Oswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro 21045-900, Brazil;
| | - Gabriela S. Rodrigues
- Graduate Program in Health Sciences, Institute of Collective Health, Federal University of Western Pará, Santarém 68270-000, Brazil; (G.S.R.); (G.B.d.S.)
| | - Aldo A. Proietti-Junior
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá 68903-419, Brazil; (L.P.S.O.); (R.S.R.); (F.M.N.C.); (A.V.S.); (A.A.P.-J.)
- Special Laboratory of Applied Microbiology, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil;
| | - Gabriela B. dos Santos
- Graduate Program in Health Sciences, Institute of Collective Health, Federal University of Western Pará, Santarém 68270-000, Brazil; (G.S.R.); (G.B.d.S.)
| | - Joaquín M. Campos
- Department of Pharmaceutical and Organic Chemistry, Faculty of Pharmacy, Institute of Biosanitary Research ibs. GRANADA, University of Granada, 18071 Granada, Spain;
| | - Cleydson B. R. Santos
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá 68903-419, Brazil; (L.P.S.O.); (R.S.R.); (F.M.N.C.); (A.V.S.); (A.A.P.-J.)
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
- Graduate Program in Network in Pharmaceutical Innovation, Federal University of Amapá, Macapá 68902-280, Brazil
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Shakibay Senobari Z, Masoumian Hosseini M, Teimouri MB, Rezayan AH, Samarghandian S, Hekmat A. Chromone-embedded peptidomimetics and furopyrimidines as highly potent SARS-CoV-2 infection inhibitors: docking and MD simulation study. BMC Res Notes 2023; 16:224. [PMID: 37735703 PMCID: PMC10515067 DOI: 10.1186/s13104-023-06508-7] [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: 02/06/2023] [Accepted: 09/14/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND COVID-19 is a respiratory illness caused by SARS-CoV-2. Pharmaceutical companies aim to control virus spread through effective drugs. This study investigates chromone compound derivatives' ability to inhibit viral entry and prevent replication. METHOD This study investigated the inhibitory effect of chromone-embedded peptidomimetics and furopyrimidines on 7BZ5 from Severe Acute Respiratory Syndrome CoV-2, Homo sapiens, and 6LU7 from Bat SARS-like CoV using molecular docking. The crystal structure of these proteins was obtained from the Protein Data Bank, and the inhibition site was determined using ligand binding interaction options. The 3D structure was protonated and energetically minimised using MOE software. Chromone derivatives were designed in three dimensions, and their energy was minimised using MOE 2019. The molecular drug-likeness was calculated using SwissADME, Lipinski and Benigni-Bossa's rule, and toxicity was calculated using Toxtree v3.1.0 software. Compounds with pharmacological properties were selected for molecular docking, and interactions were assessed using MOE 2019. MD simulations of Mpro-ch-p complexes were performed to evaluate root mean square fluctuations (RMSF) and measure protein stability. RESULT The pharmacokinetic tests revealed that chromone derivatives of the peptidomimetic family have acceptable pharmacokinetic activity in the human body. Some compounds, such as Ch-p1, Ch-p2, Ch-p6, Ch-p7, Ch-p12, and Ch-p13, have pronounced medicinal properties. Molecular docking revealed high affinity for binding to SARS-CoV-2 protease. Ch-p7 had the highest binding energy, likely due to its inhibitory property. A 10 ns molecular dynamics study confirmed the stability of the protein-ligand complex, resulting in minimal fluctuations in the system's backbone. The MM-GBSA analysis revealed free energies of binding of - 19.54 kcal/mol. CONCLUSIONS The study investigated the inhibition of viral replication using chromone derivatives, finding high inhibitory effects in the peptidomimetic family compared to other studies.
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Affiliation(s)
| | - Mohsen Masoumian Hosseini
- Department of Biochemistry, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Department of E-Learning in Medical Science, Tehran University of Medical Sciences, Tehran, Iran.
| | | | - Ali Hossein Rezayan
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, 1417466191, Iran
| | - Saeed Samarghandian
- Department of Basic Medical Sciences, Neyshabur University of Medical Sciences, Neyshabur, Iran
| | - Azadeh Hekmat
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
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5
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Bastos RS, de Lima LR, Neto MFA, Yousaf N, Cruz JN, Campos JM, Kimani NM, Ramos RS, Santos CBR. Design and Identification of Inhibitors for the Spike-ACE2 Target of SARS-CoV-2. Int J Mol Sci 2023; 24:ijms24108814. [PMID: 37240165 DOI: 10.3390/ijms24108814] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 05/28/2023] Open
Abstract
When an epidemic started in the Chinese city of Wuhan in December 2019, coronavirus was identified as the cause. Infection by the virus occurs through the interaction of viral S protein with the hosts' angiotensin-converting enzyme 2. By leveraging resources such as the DrugBank database and bioinformatics techniques, ligands with potential activity against the SARS-CoV-2 spike protein were designed and identified in this investigation. The FTMap server and the Molegro software were used to determine the active site of the Spike-ACE2 protein's crystal structure. Virtual screening was performed using a pharmacophore model obtained from antiparasitic drugs, obtaining 2000 molecules from molport®. The ADME/Tox profiles were used to identify the most promising compounds with desirable drug characteristics. The binding affinity investigation was then conducted with selected candidates. A molecular docking study showed five structures with better binding affinity than hydroxychloroquine. Ligand_003 showed a binding affinity of -8.645 kcal·mol-1, which was considered an optimal value for the study. The values presented by ligand_033, ligand_013, ligand_044, and ligand_080 meet the profile of novel drugs. To choose compounds with favorable potential for synthesis, synthetic accessibility studies and similarity analyses were carried out. Molecular dynamics and theoretical IC50 values (ranging from 0.459 to 2.371 µM) demonstrate that these candidates are promising for further tests. Chemical descriptors showed that the candidates had strong molecule stability. Theoretical analyses here show that these molecules have potential as SARS-CoV-2 antivirals and therefore warrant further investigation.
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Affiliation(s)
- Ruan S Bastos
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Federal University of Pará, Belem 66075-110, PA, Brazil
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapa 68903-419, AP, Brazil
| | - Lúcio R de Lima
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Federal University of Pará, Belem 66075-110, PA, Brazil
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapa 68903-419, AP, Brazil
| | - Moysés F A Neto
- Laboratory of Molecular Modeling, State University of Feira de Santana, Feira de Santana 44036-900, BA, Brazil
| | - Numan Yousaf
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad 45550, Pakistan
| | - Jorddy N Cruz
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapa 68903-419, AP, Brazil
| | - Joaquín M Campos
- Department of Pharmaceutical and Organic Chemistry, Faculty of Pharmacy, Campus of Cartuja, University of Granada, 18071 Granada, Spain
- Biosanitary Institute of Granada (ibs.GRANADA), University of Granada, 18071 Granada, Spain
| | - Njogu M Kimani
- Department of Physical Sciences, University of Embu, Embu 6-60100, Kenya
| | - Ryan S Ramos
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapa 68903-419, AP, Brazil
| | - Cleydson B R Santos
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Federal University of Pará, Belem 66075-110, PA, Brazil
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapa 68903-419, AP, Brazil
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6
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Rodrigues ET, Peretti P, Bezerra RM, Biancardi MF, Sousa FFO, Mendes EP, Dutra JBR, Silveira CCR, Castro CH, Cruz JN, Santos CBR, Santos FCA, Pinheiro MT. Pharmacological Characteristics of the Hydroethanolic Extract of Acmella oleracea (L) R. K. Jansen Flowers: ADME/Tox In Silico and In Vivo Antihypertensive and Chronic Toxicity Evaluation. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2023; 2023:1278720. [PMID: 37159592 PMCID: PMC10163967 DOI: 10.1155/2023/1278720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 05/11/2023]
Abstract
Acmella oleracea (L.) R. K. Jansen, popularly known as jambu in Northern Brazil, is widely used in folk medicine and local cuisine. Its consumption in different ways reinforces the need for safety assessments. In this study, the major compounds found in the hydroethanolic extract of A. oleracea flowers (EHFAO) were characterized by ultra-performance liquid mass spectrometry (UHPLC-ESI-QTOF-MS/MS). The effects of oral administration of 100/mg/kg of EHFAO extract over 60 days in male spontaneously hypertensive (SHR) and Wistar (WR) rats and the in silico ADME/Tox predictions, lipophilicity, and water solubility were accomplished for the compounds identified. Spilanthol was detected as the foremost major compound at a concentration of 97.7%, followed by 1.53% scopoletin and 0.77% d-limonene. The treatment with EHFAO did not alter the animals´ weight over the studied period. Moderate alterations were observed solely in the hepatic enzymes AST (WR = 97 UI/L and SHR = 150 UI/L ∗ p < 0.05) and ALT (WR = 55 UI/L and SHR = 95 UI/L ∗ p < 0.05), while no relevant histopathological alterations were found. The in-silico study confirmed the in vivo findings, as the identified compounds were considered highly bioactive orally, due to their drug similarity profiles, adequate lipid solubility, bioavailability, and pharmacokinetics. Therefore, the chronic treatment with EHFAO was found safe at the concentration of 100/mg/kg, with no interference in the blood pressure levels neither appreciable toxic effects.
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Affiliation(s)
- Emanuelle T. Rodrigues
- Laboratory of Biotechnology in Natural Products, Faculty of Pharmacy, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
- Graduate Program in Health Sciences, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
| | - Paulo Peretti
- Laboratory of Biotechnology in Natural Products, Faculty of Pharmacy, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
- Graduate Program in Health Sciences, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
| | - Roberto M. Bezerra
- Graduate Program in Health Sciences, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
- Laboratory of Atomic Absorption and Bioprospecting, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
| | - Manoel F. Biancardi
- Department of Histology, Embryology and Cell Biology, Laboratory of Microscopy Applied to Reproduction, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Francisco F. O. Sousa
- Laboratory of Quality Control and Bromatology, Faculty of Pharmacy, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
| | - Elizabeth P. Mendes
- Department of Physiological Sciences, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - João B. R. Dutra
- Department of Physiological Sciences, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
- Integrated Laboratory of Cardiovascular and Neurological Pathophysiology, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Carla C. R. Silveira
- Department of Physiological Sciences, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
- Integrated Laboratory of Cardiovascular and Neurological Pathophysiology, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Carlos H. Castro
- Department of Physiological Sciences, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
- Integrated Laboratory of Cardiovascular and Neurological Pathophysiology, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Jorddy N. Cruz
- Laboratory of Biotechnology in Natural Products, Faculty of Pharmacy, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
| | - Cleydson B. R. Santos
- Laboratory of Biotechnology in Natural Products, Faculty of Pharmacy, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
| | - Fernanda C. A. Santos
- Laboratory of Atomic Absorption and Bioprospecting, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
| | - Mayara T. Pinheiro
- Laboratory of Biotechnology in Natural Products, Faculty of Pharmacy, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
- Graduate Program in Health Sciences, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
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Şahin İ, Çeşme M, Yüce N, Tümer F. Discovery of new 1,4-disubstituted 1,2,3-triazoles: in silico ADME profiling, molecular docking and biological evaluation studies. J Biomol Struct Dyn 2023; 41:1988-2001. [PMID: 35057704 DOI: 10.1080/07391102.2022.2025905] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In this work, eight new 1,2,3-triazoles (6a-h) were synthesized from acetylenes' "click" reaction with p-substituted azide derivatives. The structures of the compounds were characterized using standard analytical and spectroscopic methods (elemental analysis, FT-IR, 1H(13C)NMR). The anticancer, antioxidant, α-amylase, ADME, molecular docking studies of synthesized triazoles were investigated. According to α -amylase enzyme inhibition results, all compounds except 6c (IC50: 2299 μg/mL) were found to have a higher IC50 value than the standard drug acarbose (IC50: 891 μg/mL). Compound 6g (IC50: 68 μg/mL) exhibited 13 times higher activity than standard acarbose. All compounds, except 6e, have been shown to have greater DPPH radical scavenging capabilities than BHT and β-carotene standards. According to ABTS radical scavenging studies, all compounds showed higher scavenging activity than ascorbic acid and Trolox. To determine the anticancer activity of the synthesized compounds, they were screened against the Hela cell line, and the results were compared with standard cisplatin (IC50: 16.30 μg/mL). Compound 6a (IC50: 49.03 μg/mL) was determined to have moderate activity relative to cisplatin. The compounds were examined comprehensively for ADME characteristics and did not violate any drug-likeness rule. ADME data showed that all physicochemical and pharmacological parameters of the compounds remained within defined limits as specified in Lipinski's rules (RO5) and put forth a high bioavailability profile. The molecular docking findings show that all molecules have a high affinity by exhibiting polar and apolar contact with essential residues in the binding pocket of α-amylase.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- İrfan Şahin
- Department of Chemistry, Faculty of Art and Sciences, Kahramanmaras Sutcu Imam University, Kahramanmaras, Turkey
| | - Mustafa Çeşme
- Department of Chemistry, Faculty of Art and Sciences, Kahramanmaras Sutcu Imam University, Kahramanmaras, Turkey
| | - Neslihan Yüce
- Department of Medical Biochemistry, Faculty of Medicine, Ataturk University, Erzurum, Turkey
| | - Ferhan Tümer
- Department of Chemistry, Faculty of Art and Sciences, Kahramanmaras Sutcu Imam University, Kahramanmaras, Turkey
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8
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Kılıçaslan D, Kurt AH, Köse M, Çeşme M, Güngör Ö, Oztabag CK, Doganer A. A Novel Donepezil–Caffeic Acid Hybrid: Synthesis, Biological Evaluation, and Molecular Docking Studies. BIOCHEMISTRY (MOSCOW) 2023; 88:50-63. [PMID: 37068881 DOI: 10.1134/s0006297923010054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
A novel donepezil-caffeic acid (DP-CA) hybrid molecule was designed, synthesis, and investigated by molecular modeling. Its biological activity and protective effect were investigated by the IR spectroscopy, 1H and 13C NMR spectroscopy, and mass spectrometry. DP-CA was highly active against acetylcholine esterase and inhibited it at the micromolar concentrations. Fluorescence and UV-Vis spectroscopy studies showed strong binding of DP-CA to DNA. Moreover, DP-CA exhibited protective effects against H2O2-induced toxicity in U-118 MG glioblastoma cells. Finally, molecular docking showed a high affinity of DP-CA in all concentrations, and the active 4EY7 site exhibited essential residues with polar and apolar contacts. Taken together, these findings indicate that DP-CA could be a prospective multifunctional agent for the treatment of neurodegenerative diseases.
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Affiliation(s)
- Derya Kılıçaslan
- Afsin Vocational School, Department of Chemistry and Chemical Processing Technologies, Kahramanmaras Sutcu Imam University, Kahramanmaras, Turkey.
| | - Akif Hakan Kurt
- Department of Pharmacology, Faculty of Medicine, Bolu Abant Izzet Baysal University, Bolu, Turkey
| | - Muhammet Köse
- Department of Chemistry, Faculty of Art and Sciences, Kahramanmaras Sutcu Imam University, Kahramanmaras, Turkey
| | - Mustafa Çeşme
- Department of Chemistry, Faculty of Art and Sciences, Kahramanmaras Sutcu Imam University, Kahramanmaras, Turkey
| | - Özge Güngör
- Department of Chemistry, Faculty of Art and Sciences, Kahramanmaras Sutcu Imam University, Kahramanmaras, Turkey
| | - Cansu Kara Oztabag
- Department of Interdisciplinary Neuroscience, Bolu Abant Izzet Baysal University, Institute of Health Sciences, Bolu, Turkey
| | - Adem Doganer
- Department Biostatistics and Medical Informatics, Faculty of Medicine, Kahramanmaras Sutcu Imam University, Kahramanmaras, Turkey
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9
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Rudrapal M, Issahaku AR, Agoni C, Bendale AR, Nagar A, Soliman MES, Lokwani D. In silico screening of phytopolyphenolics for the identification of bioactive compounds as novel protease inhibitors effective against SARS-CoV-2. J Biomol Struct Dyn 2022; 40:10437-10453. [PMID: 34182889 DOI: 10.1080/07391102.2021.1944909] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Due to the unavailability specific drugs or vaccines (FDA approved) that can cure COVID-19, the development of potent antiviral drug candidates/therapeutic molecules against COVID-19 is urgently required. This study was aimed at in silico screening and study of polyphenolic phytochemical compounds in a rational way by virtual screening, molecular docking and molecular dynamics studies against SARS-CoV-2 main protease (Mpro) and papain-like protease (PLpro) enzymes. The objective of the study was to identify plant-derived polyphenolic compounds and/or flavonoid molecules as possible antiviral agents with protease inhibitory potential against SARS-CoV-2. In this study, we report plant-derived polyphenolic compounds (including flavonoids) as novel protease inhibitors against SARS-CoV-2. From virtual docking and molecular docking study, 31 polyphenolic compounds were identified as active antiviral molecules possessing well-defined binding affinity with acceptable ADMET, toxicity and lead-like or drug-like properties. Six polyphenolic compounds, namely, enterodiol, taxifolin, eriodictyol, leucopelargonidin, morin and myricetin were found to exhibit remarkable binding affinities against the proteases with taxifolin and morin exhibiting the highest binding affinity toward Mpro and PLpro respectively. Molecular dynamics simulation studies of these compounds in complex with the proteases showed that the binding of the compounds is characterized by structural perturbations of the proteases suggesting their antiviral activities. These compounds can therefore be investigated further by in vivo and in vitro techniques to assess their potential efficacy against SARS-CoV-2 and thus serve as the starting point for the development of potent antiviral agents against the deadly COVID-19.
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Affiliation(s)
- Mithun Rudrapal
- Rasiklal M. Dhariwal Institute of Pharmaceutical Education and Research, Pune, Maharashtra, India
| | - Abdul Rashid Issahaku
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Clement Agoni
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Atul R Bendale
- Sandip Institute of Pharmaceutical Sciences, Nashik, Maharashtra, India
| | - Akhil Nagar
- R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| | - Mahmoud E S Soliman
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Deepak Lokwani
- R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
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10
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Mousavi S, Zare S, Mirzaei M, Feizi A. Novel Drug Design for Treatment of COVID-19: A Systematic Review of Preclinical Studies. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 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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Affiliation(s)
- Sarah Mousavi
- Department of Clinical Pharmacy and Pharmacy Practice, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Shima Zare
- School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mahmoud Mirzaei
- Child Growth and Development Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Awat Feizi
- Department of Epidemiology and Biostatistics, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran
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11
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Çeşme M. 2-Aminophenol-based ligands and Cu(II) complexes: synthesis, characterization, X-ray structure, thermal and electrochemical properties, and in vitro biological evaluation, ADMET study and molecular docking simulation. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Plant Metabolites as SARS-CoV-2 Inhibitors Candidates: In Silico and In Vitro Studies. Pharmaceuticals (Basel) 2022; 15:ph15091045. [PMID: 36145266 PMCID: PMC9501068 DOI: 10.3390/ph15091045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/22/2022] [Accepted: 08/22/2022] [Indexed: 01/08/2023] Open
Abstract
Since it acquired pandemic status, SARS-CoV-2 has been causing all kinds of damage all over the world. More than 6.3 million people have died, and many cases of sequelae are in survivors. Currently, the only products available to most of the world’s population to fight the pandemic are vaccines, which still need improvement since the number of new cases, admissions into intensive care units, and deaths are again reaching worrying rates, which makes it essential to compounds that can be used during infection, reducing the impacts of the disease. Plant metabolites are recognized sources of diverse biological activities and are the safest way to research anti-SARS-CoV-2 compounds. The present study computationally evaluated 55 plant compounds in five SARS-CoV-2 targets such Main Protease (Mpro or 3CL or MainPro), RNA-dependent RNA polymerase (RdRp), Papain-Like Protease (PLpro), NSP15 Endoribonuclease, Spike Protein (Protein S or Spro) and human Angiotensin-converting enzyme 2 (ACE-2) followed by in vitro evaluation of their potential for the inhibition of the interaction of the SARS-CoV-2 Spro with human ACE-2. The in silico results indicated that, in general, amentoflavone, 7-O-galloylquercetin, kaempferitrin, and gallagic acid were the compounds with the strongest electronic interaction parameters with the selected targets. Through the data obtained, we can demonstrate that although the indication of individual interaction of plant metabolites with both Spro and ACE-2, the metabolites evaluated were not able to inhibit the interaction between these two structures in the in vitro test. Despite this, these molecules still must be considered in the research of therapeutic agents for treatment of patients affected by COVID-19 since the activity on other targets and influence on the dynamics of viral infection during the interaction Spro x ACE-2 should be investigated.
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Sepay N, Chakrabarti S, Afzal M, Alarifi A, Mal D. Identification of 4-acrylamido- N-(pyridazin-3-yl)benzamide as anti-COVID-19 compound: a DFTB, molecular docking, and molecular dynamics study. RSC Adv 2022; 12:24178-24186. [PMID: 36128538 PMCID: PMC9403657 DOI: 10.1039/d2ra04333e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/16/2022] [Indexed: 11/21/2022] Open
Abstract
Omicron is one of the variants of COVID-19 and continuing member of a pandemic. There are several types of vaccines that were developed around the globe to fight against the virus. However, the world is suffering to find suitable drug candidates for the virus. The main protease (Mpro) enzyme of the virus is the best target for finding drug molecules because of its involvement in viral infection and protein synthesis. ZINC-15 is a database of 750 million commercially available compounds. We find 125 compounds having two aromatic rings and amide groups for non-covalent interactions with active site amino acids and functional groups with the capability to bind -SH group of C145 of Mpro through covalent bonding by a nucleophilic addition reaction. The lead compound (Z144) was identified using molecular docking. The non-covalent interactions (NCI) calculations show the interactions between amino acids present in the active site of the protein and the lead molecules are attractive in nature. The density functional-based tight-binding (DFTB) study of the lead compound with amino acids in the active site indicates that Q190 and Q193 play a very critical role in stabilization. The Michael addition of the acrylamide group of the lead molecule at β-position is facile because the low energy lowest unoccupied molecular orbital (LUMO) is concentrated on the group. From molecular dynamics during 100 ns, it has come to light that strong non-covalent interactions are key for the stability of the lead inside the protein and such binding can fold the protein. The free energy for this interaction is -42.72 kcal mol-1 which was obtained from MM-GB/SA calculations.
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Affiliation(s)
- Nayim Sepay
- Department of Chemistry, Lady Brabourne College Kolkata 700017 India
| | | | - Mohd Afzal
- Department of Chemistry, College of Science, King Saud University Riyadh 11451 Saudi Arabia
| | - Abdullah Alarifi
- Department of Chemistry, College of Science, King Saud University Riyadh 11451 Saudi Arabia
| | - Dasarath Mal
- Department of Chemistry, Vijaygarh Jyotish Ray College Kolkata 700032 India
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dos Santos IV, Borges RS, Silva GM, de Lima LR, Bastos RS, Ramos RS, Silva LB, da Silva CHTP, dos Santos CBR. Hierarchical Virtual Screening Based on Rocaglamide Derivatives to Discover New Potential Anti-Skin Cancer Agents. Front Mol Biosci 2022; 9:836572. [PMID: 35720115 PMCID: PMC9201829 DOI: 10.3389/fmolb.2022.836572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/26/2022] [Indexed: 12/04/2022] Open
Abstract
Skin Cancer (SC) is among the most common type of cancers worldwide. The search for SC therapeutics using molecular modeling strategies as well as considering natural plant-derived products seems to be a promising strategy. The phytochemical Rocaglamide A (Roc-A) and its derivatives rise as an interesting set of reference compounds due to their in vitro cytotoxic activity with SC cell lines. In view of this, we performed a hierarchical virtual screening study considering Roc-A and its derivatives, with the aim to find new chemical entities with potential activity against SC. For this, we selected 15 molecules (Roc-A and 14 derivatives) and initially used them in docking studies to predict their interactions with Checkpoint kinase 1 (Chk1) as a target for SC. This allowed us to compile and use them as a training set to build robust pharmacophore models, validated by Pearson’s correlation (p) values and hierarchical cluster analysis (HCA), subsequentially submitted to prospective virtual screening using the Molport® database. Outputted compounds were then selected considering their similarities to Roc-A, followed by analyses of predicted toxicity and pharmacokinetic properties as well as of consensus molecular docking using three software. 10 promising compounds were selected and analyzed in terms of their properties and structural features and, also, considering their previous reports in literature. In this way, the 10 promising virtual hits found in this work may represent potential anti-SC agents and further investigations concerning their biological tests shall be conducted.
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Affiliation(s)
- Igor V.F. dos Santos
- Modeling and Computational Chemistry Laboratory, Federal University of Amapá, Macapá, Brazil
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá, Brazil
| | - Rosivaldo S. Borges
- Modeling and Computational Chemistry Laboratory, Federal University of Amapá, Macapá, Brazil
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Federal University of Pará, Belém, Brazil
| | - Guilherme M. Silva
- Computational Laboratory of Pharmaceutical Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto - Universidade de São Paulo, Ribeirão Preto, Brazil
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto - Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Lúcio R. de Lima
- Modeling and Computational Chemistry Laboratory, Federal University of Amapá, Macapá, Brazil
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Federal University of Pará, Belém, Brazil
| | - Ruan S. Bastos
- Modeling and Computational Chemistry Laboratory, Federal University of Amapá, Macapá, Brazil
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Federal University of Pará, Belém, Brazil
| | - Ryan S. Ramos
- Modeling and Computational Chemistry Laboratory, Federal University of Amapá, Macapá, Brazil
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá, Brazil
| | - Luciane B. Silva
- Modeling and Computational Chemistry Laboratory, Federal University of Amapá, Macapá, Brazil
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Federal University of Pará, Belém, Brazil
| | - Carlos H. T. P. da Silva
- Computational Laboratory of Pharmaceutical Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto - Universidade de São Paulo, Ribeirão Preto, Brazil
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto - Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Cleydson B. R. dos Santos
- Modeling and Computational Chemistry Laboratory, Federal University of Amapá, Macapá, Brazil
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá, Brazil
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Federal University of Pará, Belém, Brazil
- *Correspondence: Cleydson B. R. dos Santos,
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15
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Bibi S, Khan MS, El-Kafrawy SA, Alandijany TA, El-Daly MM, Yousafi Q, Fatima D, Faizo AA, Bajrai LH, Azhar EI. Virtual screening and molecular dynamics simulation analysis of Forsythoside A as a plant-derived inhibitor of SARS-CoV-2 3CLpro. Saudi Pharm J 2022; 30:979-1002. [PMID: 35637849 PMCID: PMC9132386 DOI: 10.1016/j.jsps.2022.05.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 05/20/2022] [Indexed: 12/24/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a more severe strain of coronavirus (CoV) that was first emerged in China in 2019. Available antiviral drugs could be repurposed and natural compounds with antiviral activity could be safer and cheaper source of medicine for SARS-CoV-2. 78 natural antiviral compounds database was identified from literature and virtual screening technique was applied to identify potential 3-chymotrypsin-like protease (3CLpro) inhibitors. Molecular docking studies were conducted to analyze the main protease (3CLpro) and inhibitors interactions with key residues of active site of target protein (PDB ID: 6LU7), active site constitute the part of active domain I and II of 3CLpro. 10 compounds with highest dock score were subjected to calculate ADMET parameters to figure out drug-likeness. Molecular dynamic (MD) simulation of the selected lead was performed by Amber simulation package to understand the conformational changes in docked complex. MD simulations analysis (RMSD, RMSF, Rg, BF, HBs, and SASA plots) of lead bounded with 3CLpro, hence revealed the important structural turns and twists during MD simulations from 0 to 100 ns. MM-PBSA/GBSA methods has also been applied for the estimation binding free energy (BFE) of the selected lead-complex. The present study has identified lead compound “Forsythoside A” an active extract of Forsythia suspense as SARS-CoV-2 3CLpro inhibitor that can block the viral replication and translation. Structural analysis of target protein and lead compound performed in this study could contribute to the development of potential drug against SARS-CoV-2 infection.
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Affiliation(s)
- Shabana Bibi
- Department of Biosciences, Shifa-Tameer-e-Milat University, Islamabad, Pakistan
- Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, Yunnan, China
- Corresponding authors at: Department of Biosciences, Shifa-Tameer-e-Milat University, Islamabad, Pakistan. Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, Yunnan, China (S. Bibi). Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia (E.I. Azhar).
| | - Muhammad Saad Khan
- Department of Biosciences, COMSATS University Islamabad, Sahiwal, Pakistan
| | - Sherif A. El-Kafrawy
- Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Thamir A. Alandijany
- Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mai M. El-Daly
- Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Qudsia Yousafi
- Department of Biosciences, COMSATS University Islamabad, Sahiwal, Pakistan
| | - Dua Fatima
- Department of Biosciences, COMSATS University Islamabad, Sahiwal, Pakistan
| | - Arwa A. Faizo
- Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Leena H. Bajrai
- Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
- Biochemistry Department, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Esam I. Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Corresponding authors at: Department of Biosciences, Shifa-Tameer-e-Milat University, Islamabad, Pakistan. Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, Yunnan, China (S. Bibi). Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia (E.I. Azhar).
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16
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Rudrapal M, Gogoi N, Chetia D, Khan J, Banwas S, Alshehri B, Alaidarous MA, Laddha UD, Khairnar SJ, Walode SG. Repurposing of phytomedicine-derived bioactive compounds with promising anti-SARS-CoV-2 potential: Molecular docking, MD simulation and drug-likeness/ADMET studies. Saudi J Biol Sci 2022; 29:2432-2446. [PMID: 34924801 PMCID: PMC8667520 DOI: 10.1016/j.sjbs.2021.12.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 11/28/2021] [Accepted: 12/08/2021] [Indexed: 12/14/2022] Open
Abstract
In view of the potential of traditional plant-based remedies (or phytomedicines) in the management of COVID-19, the present investigation was aimed at finding novel anti-SARS-CoV-2 molecules by in silico screening of bioactive phytochemicals (database) using computational methods and drug repurposing approach. A total of 160 compounds belonging to various phytochemical classes (flavonoids, limonoids, saponins, triterpenoids, steroids etc.) were selected (as initial hits) and screened against three specific therapeutic targets (Mpro/3CLpro, PLpro and RdRp) of SARS-CoV-2 by docking, molecular dynamics simulation and drug-likeness/ADMET studies. From our studies, six phytochemicals were identified as notable ant-SARS-CoV-2 agents (best hit molecules) with promising inhibitory effects effective against protease (Mpro and PLpro) and polymerase (RdRp) enzymes. These compounds are namely, ginsenoside Rg2, saikosaponin A, somniferine, betulinic acid, soyasapogenol C and azadirachtin A. On the basis of binding modes and dynamics studies of protein-ligand intercations, ginsenoside Rg2, saikosaponin A, somniferine were found to be the most potent (in silico) inhibitors potentially active against Mpro, PLpro and RdRp, respectively. The present investigation can be directed towards further experimental studies in order to confirm the anti-SARS-CoV-2 efficacy along with toxicities of identified phytomolecules.
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Affiliation(s)
- Mithun Rudrapal
- Department of Pharmaceutical Chemistry, Rasiklal M. Dhariwal Institute of Pharmaceutical Education and Research, Chinchwad, Pune 411019, Maharashtra, India
| | - Neelutpal Gogoi
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh 786004, Assam, India
| | - Dipak Chetia
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh 786004, Assam, India
| | - Johra Khan
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia
- Health and Basic Sciences Research Center, Majmaah University, Al Majmaah 11952, Saudi Arabia
| | - Saeed Banwas
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia
- Health and Basic Sciences Research Center, Majmaah University, Al Majmaah 11952, Saudi Arabia
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Bader Alshehri
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia
- Health and Basic Sciences Research Center, Majmaah University, Al Majmaah 11952, Saudi Arabia
| | - Mohammed A. Alaidarous
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia
- Health and Basic Sciences Research Center, Majmaah University, Al Majmaah 11952, Saudi Arabia
| | - Umesh D. Laddha
- MET Institute of Pharmacy, Bhujbal Knowledge City, Adgaon, Nasik 422003, Maharashtra, India
| | - Shubham J. Khairnar
- MET Institute of Pharmacy, Bhujbal Knowledge City, Adgaon, Nasik 422003, Maharashtra, India
| | - Sanjay G. Walode
- Department of Pharmaceutical Chemistry, Rasiklal M. Dhariwal Institute of Pharmaceutical Education and Research, Chinchwad, Pune 411019, Maharashtra, India
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17
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Gorai S, Junghare V, Kundu K, Gharui S, Kumar M, Patro BS, Nayak SK, Hazra S, Mula S. Synthesis of Dihydrobenzofuro[3,2-b]chromenes as a potential 3CLpro inhibitors of SARS-CoV-2: A molecular docking and dynamics simulation study. ChemMedChem 2022; 17:e202100782. [PMID: 35112482 PMCID: PMC9015348 DOI: 10.1002/cmdc.202100782] [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: 01/03/2022] [Indexed: 11/29/2022]
Abstract
The recent emergence of pandemic of coronavirus (COVID‐19) caused by SARS‐CoV‐2 has raised significant global health concerns. More importantly, there is no specific therapeutics currently available to combat against this deadly infection. The enzyme 3‐chymotrypsin‐like cysteine protease (3CLpro) is known to be essential for viral life cycle as it controls the coronavirus replication. 3CLpro could be a potential drug target as established before in the case of severe acute respiratory syndrome coronavirus (SARS‐CoV) and Middle East respiratory syndrome coronavirus (MERS‐CoV). In the current study, we wanted to explore the potential of fused flavonoids as 3CLpro inhibitors. Fused flavonoids (5a,10a‐dihydro‐11H‐benzofuro[3,2‐b]chromene) are unexplored for their potential bioactivities due to their low natural occurrences. Their synthetic congeners are also rare due to unavailability of general synthetic methodology. Here we designed a simple strategy to synthesize 5a,10a‐dihydro‐11H‐benzofuro[3,2‐b]chromene skeleton and it's four novel derivatives. Our structural bioinformatics study clearly shows excellent potential of the synthesized compounds in comparison to experimentally validated inhibitor N3. Moreover, in‐silico ADMET study displays excellent druggability and extremely low level of toxicity of the synthesized molecules. Further, for better understanding, the molecular dynamic approach was implemented to study the change in dynamicity after the compounds bind to the protein. A detailed investigation through clustering analysis and distance calculation gave us sound comprehensive data about their molecular interaction. In summary, we anticipate that the currently synthesized molecules could not only be a potential set of inhibitors against 3CLpro but also the insights acquired from the current study would be instrumental in further developing novel natural flavonoid based anti‐COVID therapeutic spectrums.
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Affiliation(s)
- Sudip Gorai
- Bhabha Atomic Research Centre, Department of Atomic Energy, INDIA
| | - Vivek Junghare
- IIT Roorkee: Indian Institute of Technology Roorkee, Biotechnology, INDIA
| | - Kshama Kundu
- Bhabha Atomic Research Centre, Department of Atomic Energy, INDIA
| | | | - Mukesh Kumar
- Bhabha Atomic Research Centre, Department of Atomic Energy, INDIA
| | | | - Sandip K Nayak
- Bhabha Atomic Research Centre, Department of Atomic Energy, INDIA
| | - Saugata Hazra
- IIT Roorkee: Indian Institute of Technology Roorkee, Biotechnology, INDIA
| | - Soumyaditya Mula
- Bhabha Atomic Research Centre, Bio-Organic Division, 1-28H, Modular Laboratory, 400085, Mumbai, INDIA
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18
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Sepay N, Mondal R, Al-Muhanna MK, Saha D. Identification of natural flavonoids as novel EGFR inhibitors using DFT, molecular docking, and molecular dynamics. NEW J CHEM 2022. [DOI: 10.1039/d2nj00389a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The quantum mechanical descriptors from DFT, molecular docking, molecular dynamics, and NCIplot methodology have been utilized to find a potential anti-EGFR flavonoid.
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Affiliation(s)
- Nayim Sepay
- Department of Chemistry, Lady Brabourne College, Kolkata, 700017, India
| | - Rina Mondal
- Department of Chemistry, Uluberia College, Howrah, West Bengal, 711 315, India
| | - Muhanna K. Al-Muhanna
- Material Science Research Institute, King Abdulaziz City for Science and Technology (KACST), Riyadh, 11442, Saudi Arabia
| | - Debajyoti Saha
- Department of Chemistry, Krishnagar Govt College, Krishnagar, West Bengal, 74110, India
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19
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Şahin İ, Çeşme M, Özgeriş FB, Güngör Ö, Tümer F. Design and synthesis of 1,4-disubstituted 1,2,3-triazoles: Biological evaluation, in silico molecular docking and ADME screening. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131344] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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20
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Lochab A, Thareja R, Gadre SD, Saxena R. Potential Protein and Enzyme Targets for In‐silico Development and Repurposing of Drug Against Coronaviruses. ChemistrySelect 2021. [DOI: 10.1002/slct.202103350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Amit Lochab
- Department of Chemistry Kirori Mal College University of Delhi Delhi India
| | - Rakhi Thareja
- Department of Chemistry St. Stephens College University of Delhi Delhi India
| | - Sangeeta D. Gadre
- Department of Physics Kirori Mal College University of Delhi Delhi India
| | - Reena Saxena
- Department of Chemistry Kirori Mal College University of Delhi Delhi India
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21
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Afzal M, Alarifi A, Hasnain MS, Muddassir M. Elucidation of DNA binding interaction of new Cu(II)/Zn(II) complexes derived from Schiff base and L-tryptophan amino acid: a multispectroscopic and molecular docking approach. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:44039-44050. [PMID: 33846920 DOI: 10.1007/s11356-021-13826-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 04/05/2021] [Indexed: 06/12/2023]
Abstract
Herein, we describe the synthesis, structural elucidation, and DNA interaction of newly synthesized Cu(II) and Zn(II) complexes, i.e., [Cu(SB)(L-trp)(H2O)2]NO3 (1) and [Zn(SB)(L-trp)(H2O)2]NO3 (2) (SB = Schiff base obtained from the reaction between o-vanillin and 2-amino-2-methylpropane-1,3-diol; L-trp = L-tryptophan). From the analysis, a six-coordinated environment around the Cu(II) or Zn(II) center is proposed. The ability of the complexes to bind with calf thymus DNA was examined by optical spectroscopy (UV-vis titrations and steady-state fluorescence emission) and viscosity measurements. The vivid experimental results revealed that complexes 1 and 2 avidly bind to DNA through surface and groove binding modes, albeit with dissimilar intrinsic binding constants (1.54 × 104 and 1.36 × 104 M-1 for 1 and 2, respectively). Both complexes can displace ethidium bromide (EB) to some extent from the intercalated EB-DNA system, resulting in fluorescence quenching. Additional experiments such as [Fe(CN)6]4--induced quenching and thermal melting confirmed the electrostatic and groove binding mode. Furthermore, molecular docking studies verified that both complexes locate in the DNA minor groove by surface binding and were stabilized through weak intermolecular forces. The binding affinity of the lowest energy docked pose was found to be -5.37 kcal/mol for complex 1 and - 5.18 kcal/mol for complex 2. The present work is expected to pave the way for the synthesis of DNA-targeting Cu(II)/Zn(II) metal complexes for the development of chemotherapeutic agents.
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Affiliation(s)
- Mohd Afzal
- Department of Chemistry, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia.
| | - Abdullah Alarifi
- Department of Chemistry, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Md Saquib Hasnain
- Department of Pharmacy, Palamau Institute of Pharmacy, Chianki, Daltonganj, Jharkhand, 822102, India
| | - Mohd Muddassir
- Department of Chemistry, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia.
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22
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Singh R, Singh PK, Kumar R, Kabir MT, Kamal MA, Rauf A, Albadrani GM, Sayed AA, Mousa SA, Abdel-Daim MM, Uddin MS. Multi-Omics Approach in the Identification of Potential Therapeutic Biomolecule for COVID-19. Front Pharmacol 2021; 12:652335. [PMID: 34054532 PMCID: PMC8149611 DOI: 10.3389/fphar.2021.652335] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 04/21/2021] [Indexed: 02/05/2023] Open
Abstract
COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It has a disastrous effect on mankind due to the contagious and rapid nature of its spread. Although vaccines for SARS-CoV-2 have been successfully developed, the proven, effective, and specific therapeutic molecules are yet to be identified for the treatment. The repurposing of existing drugs and recognition of new medicines are continuously in progress. Efforts are being made to single out plant-based novel therapeutic compounds. As a result, some of these biomolecules are in their testing phase. During these efforts, the whole-genome sequencing of SARS-CoV-2 has given the direction to explore the omics systems and approaches to overcome this unprecedented health challenge globally. Genome, proteome, and metagenome sequence analyses have helped identify virus nature, thereby assisting in understanding the molecular mechanism, structural understanding, and disease propagation. The multi-omics approaches offer various tools and strategies for identifying potential therapeutic biomolecules for COVID-19 and exploring the plants producing biomolecules that can be used as biopharmaceutical products. This review explores the available multi-omics approaches and their scope to investigate the therapeutic promises of plant-based biomolecules in treating SARS-CoV-2 infection.
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Affiliation(s)
- Rachana Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, India
| | - Pradhyumna Kumar Singh
- Plant Molecular Biology and Biotechnology Division, Council of Scientific and Industrial Research- National Botanical Research Institute (CSIR-NBRI), Lucknow, India
| | - Rajnish Kumar
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, India
| | | | - Mohammad Amjad Kamal
- West China School of Nursing/Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Enzymoics, Novel Global Community Educational Foundation, Hebersham, NSW, Australia
| | - Abdur Rauf
- Department of Chemistry, University of Swabi, Khyber Pakhtunkhwa, Pakistan
| | - Ghadeer M. Albadrani
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Amany A. Sayed
- Zoology Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Shaker A. Mousa
- Pharmaceutical Research Institute, Albany College of Pharmacy and Health Sciences, Rensselaer, NY, United States
| | - Mohamed M. Abdel-Daim
- Pharmacology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Md. Sahab Uddin
- Department of Pharmacy, Southeast University, Dhaka, Bangladesh
- Pharmakon Neuroscience Research Network, Dhaka, Bangladesh
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23
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Ojo OA, Ojo AB, Maimako RF, Rotimi D, Iyobhebhe M, Alejolowo OO, Nwonuma CO, Elebiyo TC. Exploring the potentials of some compounds from Garcinia kola seeds towards identification of novel PDE-5 inhibitors in erectile dysfunction therapy. Andrologia 2021; 53:e14092. [PMID: 33945159 DOI: 10.1111/and.14092] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 11/28/2022] Open
Abstract
Erectile dysfunction (ED) is one of the main challenges occurring among men worldwide, and is characterised by trouble getting or keeping steady erection during sexual intercourse. Various drugs like sildenafil, a phosphodiesterase-5 inhibitor (PDE-5) are freely available in the pharmacies, though normally associated with several adverse. This study was designed to assess the molecular relations obtainable between catechin, garcinal, garcinoic acid and d-tocotrienol compounds isolated from Garcinia kola and targeted receptor linked to ED. These processes include the molecular docking of catechin, garcinal, garcinoic acid, d-tocotrienol, and sildenafil to receptor: PDE-5 via AutoDock Vina. Following the docking of catechin, garcinal, garcinoic acid and d-tocotrienol with the PDE-5-receptor protein, we observed that all are protein inhibitors with garcinoic acid showing better binding affinity -10.0 kcal/mol with PDE-5 receptor relevant to ED. Hence, the results provided insights into the development of garcinoic acid as a replacement for present ED management, with further analysis worth considering.
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Affiliation(s)
- Oluwafemi Adeleke Ojo
- Phytomedicine, Natural Products, Drug and Biochemical Toxicology Group, Department of Biochemistry, Landmark University, Omu Aran, Nigeria
| | - Adebola Busola Ojo
- Department of Biochemistry, Faculty of Sciences, Ekiti State University, Ado-Ekiti, Nigeria
| | - Rotdelmwa Filibus Maimako
- Phytomedicine, Natural Products, Drug and Biochemical Toxicology Group, Department of Biochemistry, Landmark University, Omu Aran, Nigeria
| | - Damilare Rotimi
- Phytomedicine, Natural Products, Drug and Biochemical Toxicology Group, Department of Biochemistry, Landmark University, Omu Aran, Nigeria
| | - Matthew Iyobhebhe
- Phytomedicine, Natural Products, Drug and Biochemical Toxicology Group, Department of Biochemistry, Landmark University, Omu Aran, Nigeria
| | - Omokolade Oluwaseyi Alejolowo
- Phytomedicine, Natural Products, Drug and Biochemical Toxicology Group, Department of Biochemistry, Landmark University, Omu Aran, Nigeria
| | - Charles Obiora Nwonuma
- Phytomedicine, Natural Products, Drug and Biochemical Toxicology Group, Department of Biochemistry, Landmark University, Omu Aran, Nigeria
| | - Tobiloba Christaina Elebiyo
- Phytomedicine, Natural Products, Drug and Biochemical Toxicology Group, Department of Biochemistry, Landmark University, Omu Aran, Nigeria
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24
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Ojo OA, Ojo AB, Okolie C, Nwakama MAC, Iyobhebhe M, Evbuomwan IO, Nwonuma CO, Maimako RF, Adegboyega AE, Taiwo OA, Alsharif KF, Batiha GES. Deciphering the Interactions of Bioactive Compounds in Selected Traditional Medicinal Plants against Alzheimer's Diseases via Pharmacophore Modeling, Auto-QSAR, and Molecular Docking Approaches. Molecules 2021; 26:molecules26071996. [PMID: 33915968 PMCID: PMC8037217 DOI: 10.3390/molecules26071996] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/22/2021] [Accepted: 03/29/2021] [Indexed: 02/06/2023] Open
Abstract
Neurodegenerative diseases, for example Alzheimer’s, are perceived as driven by hereditary, cellular, and multifaceted biochemical actions. Numerous plant products, for example flavonoids, are documented in studies for having the ability to pass the blood-brain barrier and moderate the development of such illnesses. Computer-aided drug design (CADD) has achieved importance in the drug discovery world; innovative developments in the aspects of structure identification and characterization, bio-computational science, and molecular biology have added to the preparation of new medications towards these ailments. In this study we evaluated nine flavonoid compounds identified from three medicinal plants, namely T. diversifolia, B. sapida, and I. gabonensis for their inhibitory role on acetylcholinesterase (AChE), butyrylcholinesterase (BChE) and monoamine oxidase (MAO) activity, using pharmacophore modeling, auto-QSAR prediction, and molecular studies, in comparison with standard drugs. The results indicated that the pharmacophore models produced from structures of AChE, BChE and MAO could identify the active compounds, with a recuperation rate of the actives found near 100% in the complete ranked decoy database. Moreso, the robustness of the virtual screening method was accessed by well-established methods including enrichment factor (EF), receiver operating characteristic curve (ROC), Boltzmann-enhanced discrimination of receiver operating characteristic (BEDROC), and area under accumulation curve (AUAC). Most notably, the compounds’ pIC50 values were predicted by a machine learning-based model generated by the AutoQSAR algorithm. The generated model was validated to affirm its predictive model. The best models achieved for AChE, BChE and MAO were models kpls_radial_17 (R2 = 0.86 and Q2 = 0.73), pls_38 (R2 = 0.77 and Q2 = 0.72), kpls_desc_44 (R2 = 0.81 and Q2 = 0.81) and these externally validated models were utilized to predict the bioactivities of the lead compounds. The binding affinity results of the ligands against the three selected targets revealed that luteolin displayed the highest affinity score of −9.60 kcal/mol, closely followed by apigenin and ellagic acid with docking scores of −9.60 and −9.53 kcal/mol, respectively. The least binding affinity was attained by gallic acid (−6.30 kcal/mol). The docking scores of our standards were −10.40 and −7.93 kcal/mol for donepezil and galanthamine, respectively. The toxicity prediction revealed that none of the flavonoids presented toxicity and they all had good absorption parameters for the analyzed targets. Hence, these compounds can be considered as likely leads for drug improvement against the same.
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Affiliation(s)
- Oluwafemi Adeleke Ojo
- Medicinal Biochemistry and Biochemical Toxicology Group, Department of Biochemistry, Landmark University, Omu-Aran PMB 1001, Nigeria; (M.-A.C.N.); (M.I.); (C.O.N.); (R.F.M.)
- Correspondence: ; Tel.: +234-703-782-4647
| | - Adebola Busola Ojo
- Department of Biochemistry, Faculty of Sciences, Ekiti State University, Ado-Ekiti PMB 5363, Nigeria;
| | - Charles Okolie
- Department of Microbiology, Landmark University, Omu-Aran PMB 1001, Nigeria; (C.O.); (I.O.E.)
| | - Mary-Ann Chinyere Nwakama
- Medicinal Biochemistry and Biochemical Toxicology Group, Department of Biochemistry, Landmark University, Omu-Aran PMB 1001, Nigeria; (M.-A.C.N.); (M.I.); (C.O.N.); (R.F.M.)
| | - Matthew Iyobhebhe
- Medicinal Biochemistry and Biochemical Toxicology Group, Department of Biochemistry, Landmark University, Omu-Aran PMB 1001, Nigeria; (M.-A.C.N.); (M.I.); (C.O.N.); (R.F.M.)
| | | | - Charles Obiora Nwonuma
- Medicinal Biochemistry and Biochemical Toxicology Group, Department of Biochemistry, Landmark University, Omu-Aran PMB 1001, Nigeria; (M.-A.C.N.); (M.I.); (C.O.N.); (R.F.M.)
| | - Rotdelmwa Filibus Maimako
- Medicinal Biochemistry and Biochemical Toxicology Group, Department of Biochemistry, Landmark University, Omu-Aran PMB 1001, Nigeria; (M.-A.C.N.); (M.I.); (C.O.N.); (R.F.M.)
| | | | | | - Khalaf F. Alsharif
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, AlBeheira 22511, Egypt;
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25
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Teimouri MB, Mokhtare Z, Khavasi HR. Uncatalyzed diastereoselective synthesis of alkyliminofurochromone-derived benzylmalononitriles via a three-component cascade reaction: competition between Diels-Alder cycloaddition and Michael addition. Org Biomol Chem 2021; 19:2517-2525. [PMID: 33665651 DOI: 10.1039/d0ob02540b] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Diastereoselective Michael addition reactions of 3-(alkylamino)-9H-furo[3,4-b]chromen-9-one intermediate, produced from the [1 + 4] cycloaddition/tautomerization reaction between 3-formylchromones and alkyl isocyanide in dry CH2Cl2, with arylidene malononitrile were developed to afford a wide range of functionalized 2-((S)-((R,Z)-3-(alkylimino)-9-oxo-3,9-dihydro-1H-furo[3,4-b]chromen-1-yl)(aryl)methyl)malononitrile derivatives in good yields and excellent diastereoselectivities under mild conditions. Excellent diastereoselectivity has been achieved to yield products containing two stereogenic carbons and one stereogenic imine group. Two C-C and one C-O bonds were selectively formed to provide new alkylated iminofurochromones in good yields.
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26
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Tinkov OV, Grigorev VY, Grigoreva LD. Virtual Screening and Molecular Design of Potential SARS-COV-2 Inhibitors. MOSCOW UNIVERSITY CHEMISTRY BULLETIN 2021. [PMCID: PMC8207500 DOI: 10.3103/s0027131421020127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
According to recent studies, the main Mpro protease of the SARS-CoV-2 virus, which is the most important target in the development of promising drugs for the treatment of COVID-19, is evolutionarily conservative and has not undergone significant changes compared with the main Mpro protease of the SARS-CoV virus. Many researchers note the similarity between the binding sites of the main Mpro protease of SARS-CoV and SARS-CoV-2 viruses; thus, with the spreading epidemic, further studies on inhibitors of the main Mpro protease of the SARS-CoV virus to fight COVID-19 seems logical. In the course of the study, satisfactory QSAR models are built using simplex, fractal, and HYBOT descriptors; the Partial Least Squares (PLS), Random Forest (RF), Support Vectors, Gradient Boosting (GBM) methods; and the OCHEM Internet platform (https://ochem.eu), in which different types of molecular descriptors and machine learning methods are implemented. The structural interpretation, which allowed us to identify molecular fragments that increase and decrease the activity of SARS-CoV inhibitors, is performed for the obtained models. The results of the structural interpretation are used for the rational molecular design of potential SARS-CoV-2 inhibitors. The resulting QSAR models are used for the virtual screening of 2087 FDA-approved drugs.
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27
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Murillo J, Villegas LM, Ulloa-Murillo LM, Rodríguez AR. Recent trends on omics and bioinformatics approaches to study SARS-CoV-2: A bibliometric analysis and mini-review. Comput Biol Med 2021; 128:104162. [PMID: 33310371 PMCID: PMC7710474 DOI: 10.1016/j.compbiomed.2020.104162] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND The successful sequencing of SARS-CoV-2 cleared the way for the use of omics technologies and integrative biology research for combating the COVID-19 pandemic. Currently, many research groups have slowed down their respective projects to concentrate efforts in the study of the biology of SARS-CoV-2. In this bibliometric analysis and mini-review, we aimed to describe how computational methods or omics approaches were used during the first months of the COVID-19 pandemic. METHODS We analyzed bibliometric data from Scopus, BioRxiv, and MedRxiv (dated June 19th, 2020) using quantitative and knowledge mapping approaches. We complemented our analysis with a manual process of carefully reading the selected articles to identify either the omics or bioinformatic tools used and their purpose. RESULTS From a total of 184 articles, we found that metagenomics and transcriptomics were the main sources of data to perform phylogenetic analysis aimed at corroborating zoonotic transmission, identifying the animal origin and taxonomic allocation of SARS-CoV-2. Protein sequence analysis, immunoinformatics and molecular docking were used to give insights about SARS-CoV-2 targets for drug and vaccine development. Most of the publications were from China and USA. However, China, Italy and India covered the top 10 most cited papers on this topic. CONCLUSION We found an abundance of publications using omics and bioinformatics approaches to establish the taxonomy and animal origin of SARS-CoV-2. We encourage the growing community of researchers to explore other lesser-known aspects of COVID-19 such as virus-host interactions and host response.
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Affiliation(s)
- Julieth Murillo
- Faculty of Engineering, Pontificia Universidad Javeriana-Cali, Cali, Colombia.
| | | | - Leidy Marcela Ulloa-Murillo
- Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Czech Republic.
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28
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Singh R, Singh PK, Kumar R, Kabir MT, Kamal MA, Rauf A, Albadrani GM, Sayed AA, Mousa SA, Abdel-Daim MM, Uddin MS. Multi-Omics Approach in the Identification of Potential Therapeutic Biomolecule for COVID-19. Front Pharmacol 2021. [PMID: 34054532 DOI: 10.3389/fphar2021652335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023] Open
Abstract
COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It has a disastrous effect on mankind due to the contagious and rapid nature of its spread. Although vaccines for SARS-CoV-2 have been successfully developed, the proven, effective, and specific therapeutic molecules are yet to be identified for the treatment. The repurposing of existing drugs and recognition of new medicines are continuously in progress. Efforts are being made to single out plant-based novel therapeutic compounds. As a result, some of these biomolecules are in their testing phase. During these efforts, the whole-genome sequencing of SARS-CoV-2 has given the direction to explore the omics systems and approaches to overcome this unprecedented health challenge globally. Genome, proteome, and metagenome sequence analyses have helped identify virus nature, thereby assisting in understanding the molecular mechanism, structural understanding, and disease propagation. The multi-omics approaches offer various tools and strategies for identifying potential therapeutic biomolecules for COVID-19 and exploring the plants producing biomolecules that can be used as biopharmaceutical products. This review explores the available multi-omics approaches and their scope to investigate the therapeutic promises of plant-based biomolecules in treating SARS-CoV-2 infection.
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Affiliation(s)
- Rachana Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, India
| | - Pradhyumna Kumar Singh
- Plant Molecular Biology and Biotechnology Division, Council of Scientific and Industrial Research- National Botanical Research Institute (CSIR-NBRI), Lucknow, India
| | - Rajnish Kumar
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, India
| | | | - Mohammad Amjad Kamal
- West China School of Nursing/Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Enzymoics, Novel Global Community Educational Foundation, Hebersham, NSW, Australia
| | - Abdur Rauf
- Department of Chemistry, University of Swabi, Khyber Pakhtunkhwa, Pakistan
| | - Ghadeer M Albadrani
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Amany A Sayed
- Zoology Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Shaker A Mousa
- Pharmaceutical Research Institute, Albany College of Pharmacy and Health Sciences, Rensselaer, NY, United States
| | - Mohamed M Abdel-Daim
- Pharmacology Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Md Sahab Uddin
- Department of Pharmacy, Southeast University, Dhaka, Bangladesh
- Pharmakon Neuroscience Research Network, Dhaka, Bangladesh
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29
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Batool F, Mughal EU, Zia K, Sadiq A, Naeem N, Javid A, Ul-Haq Z, Saeed M. Synthetic flavonoids as potential antiviral agents against SARS-CoV-2 main protease. J Biomol Struct Dyn 2020; 40:3777-3788. [PMID: 33251983 PMCID: PMC7754928 DOI: 10.1080/07391102.2020.1850359] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The COVID-19 pandemic has claimed more than a million lives worldwide within a short time span. Due to the unavailability of specific antiviral drugs or vaccine, the infections are causing panic both in general public and among healthcare providers. Therefore, an urgent discovery and development of effective antiviral drug for the treatment of COVID-19 is highly desired. Targeting the main protease (Mpro) of the causative agent, SARS-CoV-2 has great potential for drug discovery and drug repurposing efforts. Published crystal structures of SARS-CoV-2 Mpro further facilitated in silico investigations for discovering new inhibitors against Mpro. The present study aimed to screen several libraries of synthetic flavonoids and benzisothiazolinones as potential SARS-CoV-2 Mpro inhibitors using in silico methods. The short-listed compounds after virtual screening were filtered through SwissADME modeling tool to remove molecules with unfavorable pharmacokinetics and medicinal properties. The drug-like molecules were further subjected to iterative docking for the identification of top binders of SARS-CoV-2 Mpro. Finally, molecular dynamic (MD) simulations and binding free energy calculations were performed for the evaluation of the dynamic behavior, stability of protein–ligand complex, and binding affinity, resulting in the identification of thioflavonol, TF-9 as a potential inhibitor of Mpro. The computational studies further revealed the binding of TF-9 close to catalytic dyad and interactions with conserved residues in the S1 subsite of the substrate binding site. Our in-silico study demonstrated that synthetic analogs of flavonoids, particularly thioflavonols, have a strong tendency to inhibit the main protease Mpro, and thereby inhibit the reproduction of SARS-CoV-2. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Farwa Batool
- Department of Chemistry and Chemical Engineering, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | | | - Komal Zia
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Amina Sadiq
- Department of Chemistry, Govt. College Women University, Sialkot, Pakistan
| | - Nafeesa Naeem
- Department of Chemistry, University of Gujrat, Gujrat, Pakistan
| | - Asif Javid
- Department of Chemistry, University of Gujrat, Gujrat, Pakistan
| | - Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Muhammad Saeed
- Department of Chemistry and Chemical Engineering, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
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Adhikari N, Amin SA, Jha T. Dissecting the Drug Development Strategies Against SARS-CoV-2 Through Diverse Computational Modeling Techniques. ACTA ACUST UNITED AC 2020. [DOI: 10.1007/7653_2020_46] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Afrin LB, Weinstock LB, Molderings GJ. Covid-19 hyperinflammation and post-Covid-19 illness may be rooted in mast cell activation syndrome. Int J Infect Dis 2020; 100:327-332. [PMID: 32920235 PMCID: PMC7529115 DOI: 10.1016/j.ijid.2020.09.016] [Citation(s) in RCA: 178] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 08/28/2020] [Accepted: 09/07/2020] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVES One-fifth of Covid-19 patients suffer a severe course of Covid-19 infection; however, the specific causes remain unclear. Mast cells (MCs) are activated by SARS-CoV-2. Although only recently recognized, MC activation syndrome (MCAS), usually due to acquired MC clonality, is a chronic multisystem disorder with inflammatory and allergic themes, and an estimated prevalence of 17%. This paper describes a novel conjecture explaining how MCAS might cause a propensity for severe acute Covid-19 infection and chronic post-Covid-19 illnesses. METHODS Observations of Covid-19 illness in patients with/without MCAS were compared with extensive clinical experience with MCAS. RESULTS The prevalence of MCAS is similar to that of severe cases within the Covid-19-infected population. Much of Covid-19's hyperinflammation is concordant with manners of inflammation which MC activation can drive. Drugs with activity against MCs or their mediators have preliminarily been observed to be helpful in Covid-19 patients. None of the authors' treated MCAS patients with Covid-19 suffered severe infection, let alone mortality. CONCLUSIONS Hyperinflammatory cytokine storms in many severely symptomatic Covid-19 patients may be rooted in an atypical response to SARS-CoV-2 by the dysfunctional MCs of MCAS rather than a normal response by normal MCs. If proven, this theory has significant therapeutic and prognostic implications.
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Affiliation(s)
- Lawrence B Afrin
- Department of Mast Cell Studies, AIM Center for Personalized Medicine, Purchase, New York, USA.
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Sepay N, Sekar A, Halder UC, Alarifi A, Afzal M. Anti-COVID-19 terpenoid from marine sources: A docking, admet and molecular dynamics study. J Mol Struct 2020; 1228:129433. [PMID: 33071352 PMCID: PMC7547581 DOI: 10.1016/j.molstruc.2020.129433] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 01/14/2023]
Abstract
Traditional medicines contain natural products (NPs) as main ingredient which always give new direction and paths to develop new advanced medicines. In the COVID-19 pandemic, NPs can be used or can help to find new compound against it. The SARS coronavirus-2 main protease (SARS CoV-2 Mpro) enzyme, arbitrate viral replication and transcription, is target here. The study show that, from the electronic features and binding affinity of all the NPs with the enzyme, the compounds with higher hydrophobicity and lower flexibility can be more favorable inhibitor. More than fifty NPs were screened for the target and one terpenoid (T3) from marine sponge Cacospongia mycofijiensis shows excellent SARS CoV-2 Mpro inhibitory activity in comparison with known peptide based inhibitors. The molecular dynamics simulation studies of the terpenoids with the protein indicates that the complex is stable and hydrogen bonds are involved during the complexation. Considering binding affinity, bioavailability, pharmacokinetics and toxicity of the compounds, it is proposed that the NP T3 can act as a potential drug candidate against COVID-19 virus.
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Key Words
- ADME
- ATAD5, ATPase family AAA domain-containing protein 5
- Ahr, aryl hydrocarbon receptor
- Ar, androgen receptor
- Ar-lbd, androgen receptor ligand binding domain
- Cyto, cytotoxicity
- Dili, hepatotoxicity carcino carcinogenicity
- Docking
- Er, estrogen receptor alpha
- Er-lbd, estrogen receptor ligand binding domain
- HSE, Heat shock factor response element
- MMP, Mitochondrial Membrane Potential
- Molecular dynamics
- Mutagen, mutagenicity
- Natural products
- PPAR-Gamma, Peroxisome Proliferator Activated Receptor Gamma
- Sars cov-2 mpro
- Toxicity
- nrf2/ARE, Nuclear factor (erythroid-derived 2)-like 2/antioxidant responsive element
- sars, severe acute respiratory syndrome
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Affiliation(s)
- Nayim Sepay
- Department of Chemistry, Jadavpur University, Kolkata-70032, India
| | - Aishwarya Sekar
- Department of Bioinformatics, Stella Maris College (Autonomous), Chennai, Tamilnadu-600 086, India
| | - Umesh C Halder
- Department of Chemistry, Jadavpur University, Kolkata-70032, India
| | - Abdullah Alarifi
- Catalytic Chemistry Research Chair, Department of Chemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohd Afzal
- Catalytic Chemistry Research Chair, Department of Chemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
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Rudrapal M, Khairnar SJ, Borse LB, Jadhav AG. Coronavirus Disease-2019 (COVID-19): An Updated Review. Drug Res (Stuttg) 2020; 70:389-400. [PMID: 32746481 PMCID: PMC7516369 DOI: 10.1055/a-1217-2397] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 07/08/2020] [Indexed: 12/26/2022]
Abstract
The current outbreak of novel Coronavirus Disease-2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a major pandemic situation and a catastrophe for humans. COVID-19 is a severe infectious disease particularly of the respiratory system characterized by fatal complications such as severe acute respiratory distress syndrome (SARS), pneumonia, cardiac arrhythmia, kidney failure/ multiple organ failure and even death. Since its discovery, the SARS-CoV-2 has spread across 213 countries or territories, causing more than 8.5 million people with a rising death toll over 5.5 million people (as of June 2020, WHO). In fact, the current looming crisis of COVID-19 has become an increasingly serious concern to public health. It has affected lives of millions of people with severe impact on health systems and economies globally. Since there are no specific drugs and/or vaccines available so far, combating COVID-19 remains to be a major challenging task. Therefore, development of potential and effective treatment regimens (prophylactic/therapeutic) is urgently required which could resolve the issue. In this review, we summarize the current knowledge about the coronavirus, disease epidemiology, clinical manifestations and risk factors, replication of the virus, pathophysiology and host immune responses of SARS-CoV-2 infection. The therapeutic interventions and prophylactic measures along with precautionary measures are the frontline approaches that could be undertaken in order to control and prevent the spread of the deadly and highly contagious COVID-19 are also detailed herein.
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Affiliation(s)
- Mithun Rudrapal
- Sandip Institute of Pharmaceutical Sciences, Sandip Foundation, Nashik,
Maharashtra, India
| | - Shubham J. Khairnar
- Sandip Institute of Pharmaceutical Sciences, Sandip Foundation, Nashik,
Maharashtra, India
| | - Laxmikant B. Borse
- Sandip Institute of Pharmaceutical Sciences, Sandip Foundation, Nashik,
Maharashtra, India
| | - Anil G. Jadhav
- Sandip Institute of Pharmaceutical Sciences, Sandip Foundation, Nashik,
Maharashtra, India
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Bhuiyan FR, Howlader S, Raihan T, Hasan M. Plants Metabolites: Possibility of Natural Therapeutics Against the COVID-19 Pandemic. Front Med (Lausanne) 2020; 7:444. [PMID: 32850918 PMCID: PMC7427128 DOI: 10.3389/fmed.2020.00444] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/06/2020] [Indexed: 12/16/2022] Open
Abstract
COVID-19, a disease induced by SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2), has been the cause of a worldwide pandemic. Though extensive research works have been reported in recent days on the development of effective therapeutics against this global health crisis, there is still no approved therapy against SARS-CoV-2. In the present study, plant-synthesized secondary metabolites (PSMs) have been prioritized to make a review focusing on the efficacy of plant-originated therapeutics for the treatment of COVID-19. Plant metabolites are a source of countless medicinal compounds, while the diversity of multidimensional chemical structures has made them superior to treat serious diseases. Some have already been reported as promising alternative medicines and lead compounds for drug repurposing and discovery. The versatility of secondary metabolites may provide novel antibiotics to tackle MDR (Multi-Drug Resistant) microbes too. This review attempted to find out plant metabolites that have the therapeutic potential to treat a wide range of viral pathogens. The study includes the search of remedies belonging to plant families, susceptible viral candidates, antiviral assays, and the mode of therapeutic action; this attempt resulted in the collection of an enormous number of natural therapeutics that might be suggested for the treatment of COVID-19. About 219 plants from 83 families were found to have antiviral activity. Among them, 149 plants from 71 families were screened for the identification of the major plant secondary metabolites (PSMs) that might be effective for this pandemic. Our investigation revealed that the proposed plant metabolites can serve as potential anti- SARS-CoV-2 lead molecules for further optimization and drug development processes to combat COVID-19 and future pandemics caused by viruses. This review will stimulate further analysis by the scientific community and boost antiviral plant-based research followed by novel drug designing.
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Affiliation(s)
- Farhana Rumzum Bhuiyan
- Department of Botany, University of Chittagong, Chittagong, Bangladesh
- Laboratory of Biotechnology and Molecular Biology, Department of Botany, University of Chittagong, Chittagong, Bangladesh
| | - Sabbir Howlader
- Department of Applied Chemistry and Chemical Engineering, University of Chittagong, Chittagong, Bangladesh
| | - Topu Raihan
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Mahmudul Hasan
- Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet, Bangladesh
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