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Salamat A, Kosar N, Mohyuddin A, Imran M, Zahid MN, Mahmood T. SAR, Molecular Docking and Molecular Dynamic Simulation of Natural Inhibitors against SARS-CoV-2 Mpro Spike Protein. Molecules 2024; 29:1144. [PMID: 38474656 DOI: 10.3390/molecules29051144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 02/22/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
The SARS-CoV-2 virus and its mutations have affected human health globally and created significant danger for the health of people all around the world. To cure this virus, the human Angiotensin Converting Enzyme-2 (ACE2) receptor, the SARS-CoV-2 main protease (Mpro), and spike proteins were found to be likely candidates for the synthesis of novel therapeutic drug. In the past, proteins were capable of engaging in interaction with a wide variety of ligands, including both manmade and plant-derived small molecules. Pyrus communis L., Ginko bibola, Carica papaya, Syrian rue, and Pimenta dioica were some of the plant species that were studied for their tendency to interact with SARS-CoV-2 main protease (Mpro) in this research project (6LU7). This scenario investigates the geometry, electronic, and thermodynamic properties computationally. Assessing the intermolecular forces of phytochemicals with the targets of the SARS-CoV-2 Mpro spike protein (SP) resulted in the recognition of a compound, kaempferol, as the most potent binding ligand, -7.7 kcal mol-1. Kaempferol interacted with ASP-187, CYS-145, SER-144, LEU 141, MET-165, and GLU-166 residues. Through additional molecular dynamic simulations, the stability of ligand-protein interactions was assessed for 100 ns. GLU-166 remained intact with 33% contact strength with phenolic OH group. We noted a change in torsional conformation, and the molecular dynamics simulation showed a potential variation in the range from 3.36 to 7.44 against a 45-50-degree angle rotation. SAR, pharmacokinetics, and drug-likeness characteristic investigations showed that kaempferol may be the suitable candidate to serve as a model for designing and developing new anti-COVID-19 medicines.
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Affiliation(s)
- Aqsa Salamat
- Department of Chemistry, University of Management and Technology (UMT), C-II, Johar Town, Lahore 54770, Pakistan
| | - Naveen Kosar
- Department of Chemistry, University of Management and Technology (UMT), C-II, Johar Town, Lahore 54770, Pakistan
| | - Ayesha Mohyuddin
- Department of Chemistry, University of Management and Technology (UMT), C-II, Johar Town, Lahore 54770, Pakistan
| | - Muhammad Imran
- Department of Chemistry, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Muhammad Nauman Zahid
- Department of Biology, College of Science, University of Bahrain, Sakhir P.O. Box 32038, Bahrain
| | - Tariq Mahmood
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
- Department of Chemistry, College of Science, University of Bahrain, Sakhir P.O. Box 32038, Bahrain
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Shokry S, Hegazy A, Abbas AM, Mostafa I, Eissa IH, Metwaly AM, Yahya G, El-Shazly AM, Aboshanab KM, Mostafa A. Phytoestrogen β-Sitosterol Exhibits Potent In Vitro Antiviral Activity against Influenza A Viruses. Vaccines (Basel) 2023; 11:228. [PMID: 36851106 PMCID: PMC9964242 DOI: 10.3390/vaccines11020228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/14/2023] [Accepted: 01/17/2023] [Indexed: 01/22/2023] Open
Abstract
Influenza is a contagious infection in humans that is caused frequently by low pathogenic seasonal influenza viruses and occasionally by pathogenic avian influenza viruses (AIV) of H5, H7, and H9 subtypes. Recently, the clinical sector in poultry and humans has been confronted with many challenges, including the limited number of antiviral drugs and the rapid evolution of drug-resistant variants. Herein, the anti-influenza activities of various plant-derived phytochemicals were investigated against highly pathogenic avian influenza A/H5N1 virus (HPAIV H5N1) and seasonal low pathogenic human influenza A/H1N1 virus (LPHIV H1N1). Out of the 22 tested phytochemicals, the steroid compounds β-sitosterol and β-sitosterol-O-glucoside have very potent activity against the predefined influenza A viruses (IAV). Both steroids could induce such activity by affecting multiple stages during IAV replication cycles, including viral adsorption and replication with a major and significant impact on the virus directly in a cell-free status "viricidal effect". On a molecular level, several molecular docking studies suggested that β-sitosterol and β-sitosterol-O-glucoside exhibited viricidal effects through blocking active binding sites of the hemagglutinin surface protein, as well as showing inhibitory effects against replication through the binding with influenza neuraminidase activity and blocking the active sites of the M2 proton channel activity. The phytoestrogen β-sitosterol has structural similarity with the active form of the female sex hormone estradiol, and this similarity is likely one of the molecular determinants that enables the phytoestrogen β-sitosterol and its derivative to control IAV infection in vitro. This promising anti-influenza activity of β-sitosterol and its O-glycoside derivative, according to both in vitro and cheminformatics studies, recommend both phytochemicals for further studies going through preclinical and clinical phases as efficient anti-influenza drug candidates.
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Affiliation(s)
- Sara Shokry
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Abbassia, Cairo 11566, Egypt
| | - Akram Hegazy
- Department of Agricultural Microbiology, Faculty of Agriculture, Cairo University, Giza District, Giza 12613, Egypt
| | - Ahmad M. Abbas
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Abbassia, Cairo 11566, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, King Salman International University (KSIU), Sinai 46612, Egypt
| | - Islam Mostafa
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Ibrahim H. Eissa
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
| | - Ahmed M. Metwaly
- Pharmacognosy and Medicinal Plants Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
- Biopharmaceutical Products Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications (SRTA-City), Alexandria 21934, Egypt
| | - Galal Yahya
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Assem M. El-Shazly
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
- Faculty of Pharmacy, El Saleheya El Gadida University, El Saleheya El Gadida 44813, Sharkia, Egypt
| | - Khaled M. Aboshanab
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Abbassia, Cairo 11566, Egypt
| | - Ahmed Mostafa
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt
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Zia Q, Rehman MT, Hashmi MA, Siddiqui S, Bin Dukhyil A, Ahmed MZ, Jamal A, Banawas S, Almalki SG, Owais M, Aldhafeeri HQ, Ibrahim IM, Alturaiki W, AlAjmi MF, Alsieni M, Alqurashi YE. Effect of Date Palm ( Phoenix dactylifera) Phytochemicals on Aβ 1-40 Amyloid Formation: An in-silico Analysis. Front Neurosci 2022; 16:915122. [PMID: 35958986 PMCID: PMC9359633 DOI: 10.3389/fnins.2022.915122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/23/2022] [Indexed: 11/13/2022] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease and the most prevalent form of dementia. The generation of oxygen free radicals and oxidative damage is believed to be involved in the pathogenesis of AD. It has been suggested that date palm, a plant rich in phenolic compounds and flavonoids, can provide an alternative treatment to fight memory loss and cognitive dysfunction due to its potent antioxidant activity. Thus, we studied the effect of flavonoids present in date palm on Aβ1-40 amyloid formation using molecular docking and molecular dynamics simulation. AutoDock. Myricetin was used as a positive control drug. The flavonoids Diosmetin, Luteolin, and Rutin were found to be potent inhibitors of aggregation (docking energies ≤ -8.05 kcal mol-1) targeting Aβ1-40 fibrils (both 2LMO and 6TI5), simultaneously. Further screening by physicochemical properties and drug-likeness analysis suggested that all flavonoids except Rutin followed Lipinski's rule of five. Rutin was, thus, taken as a negative control (due to its violation of Lipinski's rule) to compare its dynamics with Diosmetin. Diosmetin exhibited the highest positive scores for drug likeness. Since Luteolin exhibited moderate drug-likeness and better absorption properties, it was also included in molecular dynamics simulation. Molecular dynamics of shortlisted compounds (Rutin, Diosmetin, and Luteolin) were performed for 200 ns, and the results were analyzed by monitoring root mean square deviations (RMSD), root mean square fluctuation (RMSF) analysis, the radius of gyration (Rg), and solvent accessible surface area (SASA). The results proved the formation of a stable protein-compound complex. Based on binding energies and non-bonded interactions, Rutin and Luteolin emerged as better lead molecules than Diosmetin. However, high MW (610.5), lowest absorption rate (16.04%), and more than one violation of Lipinski's rule make Rutin a less likely candidate as an anti-amyloidogenic agent. Moreover, among non-violators of Lipinski's rule, Diosmetin exhibited a greater absorption rate than Luteolin as well as the highest positive scores for drug-likeness. Thus, we can conclude that Diosmetin and Luteolin may serve as a scaffold for the design of better inhibitors with higher affinities toward the target proteins. However, these results warrant in-vitro and in-vivo validation before practical use.
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Affiliation(s)
- Qamar Zia
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah, Saudi Arabia
- Health and Basic Sciences Research Center, Majmaah University, Al Majmaah, Saudi Arabia
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Md Amiruddin Hashmi
- Interdisciplinary Biotechnology Unit, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Sahabjada Siddiqui
- Department of Biotechnology, Era's Lucknow Medical College and Hospital, Era University, Lucknow, India
| | - Abdulaziz Bin Dukhyil
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah, Saudi Arabia
| | - Mohammad Z. Ahmed
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Azfar Jamal
- Health and Basic Sciences Research Center, Majmaah University, Al Majmaah, Saudi Arabia
- Department of Biology, College of Science Al-Zulfi, Majmaah University, Majmaah, Saudi Arabia
| | - Saeed Banawas
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah, Saudi Arabia
- Health and Basic Sciences Research Center, Majmaah University, Al Majmaah, Saudi Arabia
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR, United States
| | - Sami G. Almalki
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah, Saudi Arabia
| | - Mohammad Owais
- Interdisciplinary Biotechnology Unit, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Hamad Qasem Aldhafeeri
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah, Saudi Arabia
| | - Ibrahim M. Ibrahim
- Department of Pharmacology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Wael Alturaiki
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah, Saudi Arabia
| | - Mohamed F. AlAjmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed Alsieni
- Department of Pharmacology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Yaser E. Alqurashi
- Department of Biology, College of Science Al-Zulfi, Majmaah University, Majmaah, Saudi Arabia
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Taherkhani N, Hekmat A, Piri H, Haghbeen K. Structural and inhibitory effects of fulvic and humic acids against tyrosinase. J Food Biochem 2022; 46:e14279. [PMID: 35727699 DOI: 10.1111/jfbc.14279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/25/2022] [Accepted: 05/17/2022] [Indexed: 12/01/2022]
Abstract
Inhibition of tyrosinase activity can control fruit browning and preserve the flavor and nutritional value of food. The impacts of fulvic acid (FA) and humic acid (HA) on tyrosinase activity were investigated utilizing circular dichroism (CD) and fluorescence spectroscopy, molecular docking (MD), and molecular dynamics simulations. HA and FA demonstrated a mixed type of inhibition with Ki 2.02 and 5.2 μM, respectively. The thermodynamic parameters displayed that the hydrogen bond and hydrophobic force play a major role in the FA-tyrosinase and HA-tyrosinase interaction, respectively. Fluorescence experiments demonstrated changes in tyrosinase tertiary structures. HA could not destroy the tyrosinase secondary structure significantly, however, FA has a significant influence on the tyrosinase secondary structure. The molecular dynamics findings demonstrated the minimal fluctuations and the lowest flexibility in the complex amino acids in the HA-tyrosinase and FA-tyrosinase interaction. Altogether, HA and FA could be utilized in food industries as an accessible natural source for tyrosinase inhibition. PRACTICAL APPLICATIONS: Recently, the investigation of tyrosinase inhibitors from the biosphere for hindrance of undesired browning in the food industry has increased considerably. Mushroom tyrosinase is a suitable model for kinetic research owing to its availability as well as close conformational similarity to tyrosinase in a mammal. Natural sources and their effective compounds could have wonderful potential on tyrosinase activity and structure, thus, in this study, the interactions between tyrosinase and fulvic acid (FA) and Humic acid (HA) were investigated. Previously, it has been shown that HA and FA have antioxidant properties and they can improve the quality of food via retarding lipid oxidation. Altogether, further investigations are warranted to draw firm conclusions, HA and FA could be utilized in food industries not only as antioxidant agents but also as an accessible natural source for tyrosinase inhibition.
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Affiliation(s)
- Negar Taherkhani
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Azadeh Hekmat
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Hossein Piri
- Cellular and Molecular Research Center, Research Institute for Prevention of Non-Communicable Disease, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Kamahldin Haghbeen
- Biochemistry and Biophysics Department, National Institute for Genetic Engineering and Biotechnology, Tehran, Iran
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