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Ranteh O, Tedasen A, Rahman MA, Ibrahim MA, Sama-Ae I. Bioactive compounds from Ocimum tenuiflorum and Poria cocos: A novel natural Compound for insomnia treatment based on A computational approach. Comput Biol Med 2024; 175:108491. [PMID: 38657467 DOI: 10.1016/j.compbiomed.2024.108491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/26/2024]
Abstract
Insomnia, a widespread public health issue, is associated with substantial distress and daytime functionality impairments and can predispose to depression and cardiovascular disease. Cognitive Behavioral Anti-insomnia therapies including benzodiazepines often face limitations due to patient adherence or potential adverse effects. This study focused on identifying novel bioactive compounds from medicinal plants, aiming to discover and develop new therapeutic agents with low risk-to-benefit ratios using computational drug discovery methods. Through a systematic framework involving compound library preparation, evaluation of drug-likeness and pharmacokinetics, toxicity prediction, molecular docking, and molecular dynamic simulations, two natural compounds such as 2-(4-hydroxy-3-methoxyphenyl)-8-methoxy-6-prop-2-enyl-3,4-dihydro-2H-chromen-3-ol from Ocimum tenuiflorum and 7-(2-hydroxypropan-2-yl)-1,4a-dimethyl-9-oxo-3,4,10,10a-tetrahydro-2H-phenanthrene-1-carboxylic acid from Poria cocos exhibited high binding affinity with orexin receptor type 1 (OX1R) and type 2 (OX2R), surpassing commercial drugs used in insomnia treatment. Additionally, they showed interactions with critical amino acid residues within the receptors that play crucial roles in competitive inhibitor activity, like commercial drugs such as Suvorexant, Lemborexant, and Daridorexant. Further, molecular dynamics simulations of the protein-ligand complexes under conditions that mimic the in vivo environment revealed both compounds' sustained and robust interactions with the OX1R and OX2R, reinforcing their potential as effective therapeutic candidates. Furthermore, upon evaluating both compounds' drug-likeness, pharmacokinetics, and toxicity profiles, it was discerned that they displayed considerable drug-like properties and favorable pharmacokinetics, along with diminished toxicity. The research provides a solid foundation for further exploring and validating these compounds as potential anti-insomnia therapeutics.
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Affiliation(s)
- Onggan Ranteh
- Department of Community Public Health, School of Public Health, Walailak University, Tha Sala District, Nakhon Si Thammarat, 80160, Thailand; Excellent Centre of Dengue and Community Public Health (EC for DACH), Walailak University, Tha Sala District, Nakhon Si Thammarat, 80160, Thailand.
| | - Aman Tedasen
- Department of Medical Technology, School of Allied Health Sciences, Walailak University, Tha Sala District, Nakhon Si Thammarat, 80160, Thailand; Research Excellence Center for Innovation and Health Products, Walailak University, Tha Sala, Nakhon Si Thammarat, 80161, Thailand.
| | - Md Atiar Rahman
- Department of Medical Technology, School of Allied Health Sciences, Walailak University, Tha Sala District, Nakhon Si Thammarat, 80160, Thailand; Department of Biochemistry and Molecular Biology, University of Chittagong, Chittagong-4331, Bangladesh.
| | | | - Imran Sama-Ae
- Department of Medical Technology, School of Allied Health Sciences, Walailak University, Tha Sala District, Nakhon Si Thammarat, 80160, Thailand; Center of Excellence Research for Melioidosis and Microorganisms (CERMM), Walailak University, Tha Sala District, Nakhon Si Thammarat, 80160, Thailand.
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Rahangdale R, Ghormode P, Tender T, Balireddy S, Birangal S, Kishore R, Mohammad FS, Pasupuleti M, Chandrashekar H R. Anti-HSV activity of nectin-1-derived peptides targeting HSV gD: an in-silico and in-vitro approach. J Biomol Struct Dyn 2024:1-14. [PMID: 38720617 DOI: 10.1080/07391102.2024.2349525] [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: 11/29/2023] [Accepted: 03/24/2024] [Indexed: 05/22/2024]
Abstract
Herpes simplex virus (HSV) infections affect a wide range of the global population. The emergence of resistance to the existing anti-HSV therapy highlights the necessity for an innovative strategy. The interaction of HSV gD with its main host receptor nectin-1 is a potential target for new antiviral drugs. The aim of this study was to develop a peptide derived from nectin-1 targeting HSV gD using the in-silico method and evaluate them for anti-HSV activity. Residues 59-133 of the Nectin-1 V-domain constitute the interaction interface with HSV gD. Bioinformatic tools viz., PEP-FOLD3, ClusPro 2.0, HawkDock and Desmond were used to model the peptide and confirm its binding specificity with HSV gD protein. The peptides with potential interactions were custom synthesized and anti-HSV activity was evaluated in vitro against HSV-1 and HSV-2 by CPE inhibition assay. Five peptide sequences were identified as exhibiting good interaction with HSV-gD proteins. Among them, peptide N1 (residues 76-90) offered maximum protection against HSV-1 (66.57%) and HSV-2 (71.12%) infections. Modification of the identified peptide through peptidomimetic approaches may further enhance the activity and stability of the identified peptide.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rakesh Rahangdale
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Parnavi Ghormode
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Tenzin Tender
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Sridevi Balireddy
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Sumit Birangal
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Raj Kishore
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow, India
- Jawaharlal Nehru University, New Delhi, India
| | - Fayaz Shaik Mohammad
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
| | - Mukesh Pasupuleti
- Microbiology Division, Council of Scientific and Industrial Research, Central Drug Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Raghu Chandrashekar H
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, India
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Majrashi TA, El Hassab MA, Mahmoud SH, Mostafa A, Wahsh EA, Elkaeed EB, Hassan FE, Eldehna WM, Abdelgawad SM. In vitro biological evaluation and in silico insights into the antiviral activity of standardized olive leaves extract against SARS-CoV-2. PLoS One 2024; 19:e0301086. [PMID: 38662719 PMCID: PMC11045091 DOI: 10.1371/journal.pone.0301086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 03/08/2024] [Indexed: 04/28/2024] Open
Abstract
There is still a great global need for efficient treatments for the management of SARS-CoV-2 illness notwithstanding the availability and efficacy of COVID-19 vaccinations. Olive leaf is an herbal remedy with a potential antiviral activity that could improve the recovery of COVID-19 patients. In this work, the olive leaves major metabolites were screened in silico for their activity against SARS-CoV-2 by molecular docking on several viral targets such as methyl transferase, helicase, Plpro, Mpro, and RdRp. The results of in silico docking study showed that olive leaves phytoconstituents exhibited strong potential antiviral activity against SARS-CoV-2 selected targets. Verbacoside demonstrated a strong inhibition against methyl transferase, helicase, Plpro, Mpro, and RdRp (docking scores = -17.2, -20, -18.2, -19.8, and -21.7 kcal/mol.) respectively. Oleuropein inhibited 5rmm, Mpro, and RdRp (docking scores = -15, -16.6 and -18.6 kcal/mol., respectively) respectively. Apigenin-7-O-glucoside exhibited activity against methyl transferase and RdRp (docking score = -16.1 and -19.4 kcal/mol., respectively) while Luteolin-7-O-glucoside inhibited Plpro and RdRp (docking score = -15.2 and -20 kcal/mol., respectively). The in vitro antiviral assay was carried out on standardized olive leaf extract (SOLE) containing 20% oleuropein and IC50 was calculated. The results revealed that 20% SOLE demonstrated a moderate antiviral activity against SARS-CoV-2 with IC50 of 118.3 μg /mL. Accordingly, olive leaf could be a potential herbal therapy against SARS-CoV-2 but more in vivo and clinical investigations are recommended.
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Affiliation(s)
- Taghreed A. Majrashi
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Asir, Saudi Arabia
| | - Mahmoud A. El Hassab
- Department of Medicinal Chemistry, Faculty of Pharmacy, King Salman International University (KSIU), South Sinai, Egypt
| | - Sara H. Mahmoud
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt
| | - Ahmed Mostafa
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt
| | - Engy A. Wahsh
- Clinical Pharmacy Department, Faculty of Pharmacy, October 6 University, Giza Governorate, Egypt
| | - Eslam B. Elkaeed
- Department of Pharmaceutical Sciences, College of Pharmacy, AlMaarefa University, Riyadh, Saudi Arabia
| | - Fatma E. Hassan
- Department of Physiology, General Medicine Practice Program, Batterjee Medical College, Jeddah, Saudi Arabia
- Medical Physiology Department, Kasr Alainy, Faculty of Medicine, Cairo University, Giza, Egypt
| | - Wagdy M. Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
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Filardo S, Roberto M, Di Risola D, Mosca L, Di Pietro M, Sessa R. Olea europaea L-derived secoiridoids: Beneficial health effects and potential therapeutic approaches. Pharmacol Ther 2024; 254:108595. [PMID: 38301769 DOI: 10.1016/j.pharmthera.2024.108595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/21/2023] [Accepted: 01/08/2024] [Indexed: 02/03/2024]
Abstract
Over the years, health challenges have become increasingly complex and global and, at the beginning of the 21st century, chronic diseases, including cardiovascular, neurological, and chronic respiratory diseases, as well as cancer and diabetes, have been identified by World Health Organization as one of the biggest threats to human health. Recently, antimicrobial resistance has also emerged as a growing problem of public health for the management of infectious diseases. In this scenario, the exploration of natural products as supplementation or alternative therapeutic options is acquiring great importance, and, among them, the olive tree, Olea europaea L, specifically leaves, fruits, and oil, has been increasingly investigated for its health promoting properties. Traditionally, these properties have been largely attributed to the high concentration of monounsaturated fatty acids, although, in recent years, beneficial effects have also been associated to other components, particularly polyphenols. Among them, the most interesting group is represented by Olea europaea L secoiridoids, comprising oleuropein, oleocanthal, oleacein, and ligstroside, which display anti-inflammatory, antioxidant, cardioprotective, neuroprotective and anticancer activities. This review provides an overview of the multiple health beneficial effects, the molecular mechanisms, and the potential applications of secoiridoids from Olea europaea L.
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Affiliation(s)
- Simone Filardo
- Department of Public Health and Infectious Diseases, Sapienza University, p.le Aldo Moro, 5, 00185 Rome, Italy
| | - Mattioli Roberto
- Department of Biochemical Sciences, Faculty of Pharmacy and Medicine, Sapienza University, p.le Aldo Moro, 5, 00185 Rome, Italy
| | - Daniel Di Risola
- Department of Biochemical Sciences, Faculty of Pharmacy and Medicine, Sapienza University, p.le Aldo Moro, 5, 00185 Rome, Italy
| | - Luciana Mosca
- Department of Biochemical Sciences, Faculty of Pharmacy and Medicine, Sapienza University, p.le Aldo Moro, 5, 00185 Rome, Italy
| | - Marisa Di Pietro
- Department of Public Health and Infectious Diseases, Sapienza University, p.le Aldo Moro, 5, 00185 Rome, Italy
| | - Rosa Sessa
- Department of Public Health and Infectious Diseases, Sapienza University, p.le Aldo Moro, 5, 00185 Rome, Italy.
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Shah M, Yamin R, Ahmad I, Wu G, Jahangir Z, Shamim A, Nawaz H, Nishan U, Ullah R, Ali EA, Sheheryar, Chen K. In-silico evaluation of natural alkaloids against the main protease and spike glycoprotein as potential therapeutic agents for SARS-CoV-2. PLoS One 2024; 19:e0294769. [PMID: 38175855 PMCID: PMC10766191 DOI: 10.1371/journal.pone.0294769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 11/08/2023] [Indexed: 01/06/2024] Open
Abstract
Severe Acute Respiratory Syndrome Corona Virus (SARS-CoV-2) is the causative agent of COVID-19 pandemic, which has resulted in global fatalities since late December 2019. Alkaloids play a significant role in drug design for various antiviral diseases, which makes them viable candidates for treating COVID-19. To identify potential antiviral agents, 102 known alkaloids were subjected to docking studies against the two key targets of SARS-CoV-2, namely the spike glycoprotein and main protease. The spike glycoprotein is vital for mediating viral entry into host cells, and main protease plays a crucial role in viral replication; therefore, they serve as compelling targets for therapeutic intervention in combating the disease. From the selection of alkaloids, the top 6 dual inhibitory compounds, namely liensinine, neferine, isoliensinine, fangchinoline, emetine, and acrimarine F, emerged as lead compounds with favorable docked scores. Interestingly, most of them shared the bisbenzylisoquinoline alkaloid framework and belong to Nelumbo nucifera, commonly known as the lotus plant. Docking analysis was conducted by considering the key active site residues of the selected proteins. The stability of the top three ligands with the receptor proteins was further validated through dynamic simulation analysis. The leads underwent ADMET profiling, bioactivity score analysis, and evaluation of drug-likeness and physicochemical properties. Neferine demonstrated a particularly strong affinity for binding, with a docking score of -7.5025 kcal/mol for main protease and -10.0245 kcal/mol for spike glycoprotein, and therefore a strong interaction with both target proteins. Of the lead alkaloids, emetine and fangchinoline demonstrated the lowest toxicity and high LD50 values. These top alkaloids, may support the body's defense and reduce the symptoms by their numerous biological potentials, even though some properties naturally point to their direct antiviral nature. These findings demonstrate the promising anti-COVID-19 properties of the six selected alkaloids, making them potential candidates for drug design. This study will be beneficial in effective drug discovery and design against COVID-19 with negligible side effects.
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Affiliation(s)
- Mohibullah Shah
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Ramsha Yamin
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Iqra Ahmad
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Gang Wu
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Zainab Jahangir
- Department of Computer Science, University of Agriculture Faisalabad, Punjab, Pakistan
| | - Amen Shamim
- Department of Computer Science, University of Agriculture Faisalabad, Punjab, Pakistan
| | - Haq Nawaz
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Umar Nishan
- Department of Chemistry, Kohat University of Science & Technology, Kohat, Pakistan
| | - Riaz Ullah
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Essam A. Ali
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Sheheryar
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, Brazil
| | - Ke Chen
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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Akter T, Bulbul MRH, Sama-ae I, Azadi MA, Nira KN, Al-Araby SQ, Deen JI, Rafi MKJ, Saha S, Ezaj MMA, Rahman MA. Sour Tamarind Is More Antihypertensive than the Sweeter One, as Evidenced by In Vivo Biochemical Indexes, Ligand-Protein Interactions, Multitarget Interactions, and Molecular Dynamic Simulation. Nutrients 2023; 15:3402. [PMID: 37571339 PMCID: PMC10420995 DOI: 10.3390/nu15153402] [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: 06/11/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 08/13/2023] Open
Abstract
This research investigated the antihypertensive effects of tamarind products and compared their potentials based on an animal model's data verified by molecular docking, multitarget interactions, and dynamic simulation assays. GC-MS-characterized tamarind products were administered to cholesterol-induced hypertensive albino rat models. The two-week-intervened animals were dissected to collect their serum and organs and respectively subjected to analyses of their hypertension-linked markers and tissue architectures. The lead biometabolites of tamarinds interacted with eight target receptors in the molecular docking and dynamic simulation studies and with multitarget in the network pharmacological analyses. The results show that the serum alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP), C-reactive protein (CRP), troponin I, and lipid profiles were maximally reinstated by the phenolic-enriched ripened sour tamarind extract compared to the sweet one, but the seed extracts had a smaller influence. Among the tamarind's biometabolites, ϒ-sitosterol was found to be the best ligand to interact with the guanylate cyclase receptor, displaying the best drug-likeliness with the highest binding energy, -9.3 Kcal. A multitargeted interaction-based degree algorithm and a phylogenetic tree of pathways showed that the NR3C1, REN, PPARG, and CYP11B1 hub genes were consistently modulated by ϒ-sitosterol to reduce hypertension and related risk factors. The dynamic simulation study showed that the P-RMSD values of ϒ-sitosterol-guanylate cyclase were stable between 75.00 and 100.00 ns at the binding pocket. The findings demonstrate that ripened sour tamarind extract may be a prospective antihypertensive nutraceutical or supplement target affirmed through advanced preclinical and clinical studies.
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Affiliation(s)
- Taslima Akter
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chittagong 4331, Bangladesh; (T.A.); (K.N.N.); (S.Q.A.-A.); (J.I.D.); (M.K.J.R.); (S.S.)
| | | | - Imran Sama-ae
- School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat 80160, Thailand;
| | - M. A. Azadi
- Department of Zoology, University of Chittagong, Chittagong 4331, Bangladesh;
| | - Kamrun Nahar Nira
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chittagong 4331, Bangladesh; (T.A.); (K.N.N.); (S.Q.A.-A.); (J.I.D.); (M.K.J.R.); (S.S.)
| | - Salahuddin Quader Al-Araby
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chittagong 4331, Bangladesh; (T.A.); (K.N.N.); (S.Q.A.-A.); (J.I.D.); (M.K.J.R.); (S.S.)
| | - Jobaier Ibne Deen
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chittagong 4331, Bangladesh; (T.A.); (K.N.N.); (S.Q.A.-A.); (J.I.D.); (M.K.J.R.); (S.S.)
| | - Md. Khalid Juhani Rafi
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chittagong 4331, Bangladesh; (T.A.); (K.N.N.); (S.Q.A.-A.); (J.I.D.); (M.K.J.R.); (S.S.)
| | - Srabonti Saha
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chittagong 4331, Bangladesh; (T.A.); (K.N.N.); (S.Q.A.-A.); (J.I.D.); (M.K.J.R.); (S.S.)
| | - Md. Muzahid Ahmed Ezaj
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chittagong 4331, Bangladesh;
| | - Md. Atiar Rahman
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chittagong 4331, Bangladesh; (T.A.); (K.N.N.); (S.Q.A.-A.); (J.I.D.); (M.K.J.R.); (S.S.)
- School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat 80160, Thailand;
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Vijakumaran U, Goh NY, Razali RA, Abdullah NAH, Yazid MD, Sulaiman N. Role of Olive Bioactive Compounds in Respiratory Diseases. Antioxidants (Basel) 2023; 12:1140. [PMID: 37371870 DOI: 10.3390/antiox12061140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/16/2023] [Accepted: 05/19/2023] [Indexed: 06/29/2023] Open
Abstract
Respiratory diseases recently became the leading cause of death worldwide, due to the emergence of COVID-19. The pathogenesis of respiratory diseases is centred around inflammation and oxidative stress. Plant-based alongside synthetic drugs were considered as therapeutics due to their proven nutraceutical value. One such example is the olive, which is a traditional symbol of the MedDiet. Olive bioactive compounds are enriched with antioxidant, anti-inflammatory, anticancer and antiviral properties. However, there are few studies relating to the beneficial effect of olive bioactive compounds on respiratory diseases. A vague understanding of its molecular action, dosage and bioavailability limits its usefulness for clinical trials about respiratory infections. Hence, our review aims to explore olive bioactive compound's antioxidant, anti-inflammatory and antiviral properties in respiratory disease defence and treatment. Molecular insight into olive compounds' potential for respiratory system protection against inflammation and ensuing infection is also presented. Olive bioactive compounds mainly protect the respiratory system by subsiding proinflammatory cytokines and oxidative stress.
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Affiliation(s)
- Ubashini Vijakumaran
- Centre for Tissue Engineering & Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Cheras, Kuala Lumpur 56000, Malaysia
| | - Neng-Yao Goh
- Centre for Tissue Engineering & Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Cheras, Kuala Lumpur 56000, Malaysia
| | - Rabiatul Adawiyah Razali
- Centre for Tissue Engineering & Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Cheras, Kuala Lumpur 56000, Malaysia
| | - Nur Atiqah Haizum Abdullah
- Centre for Tissue Engineering & Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Cheras, Kuala Lumpur 56000, Malaysia
| | - Muhammad Dain Yazid
- Centre for Tissue Engineering & Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Cheras, Kuala Lumpur 56000, Malaysia
| | - Nadiah Sulaiman
- Centre for Tissue Engineering & Regenerative Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Cheras, Kuala Lumpur 56000, Malaysia
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Ragunathan V, Chithra K. Extraction and characterization of metabolites from Olea europaea pulp and their molecular docking against SARS-CoV-2 main-protease (M pro). Nat Prod Res 2023; 37:522-528. [PMID: 34581234 DOI: 10.1080/14786419.2021.1983813] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The present study is the first to extract the bioactive metabolites from Olea europaea fruit using the Soxhlet-maceration extraction method. The preliminary phytochemical; Fourier transform-infrared spectroscopy (FT-IR); gas chromatography-mass spectrometry (GC-MS) analyses, and their potential against SARS-CoV-2 Mpro through molecular docking were studied. The preliminary qualitative phytochemical analyses showed coumarin glycosides, tannins, terpenoids, cholesterol, carbohydrates, and proteins. FT-IR spectroscopy revealed C-H, C = O, O-H, C-N, C-O-C, C-O, CO-O-CO, C = C, and C-Br functional groups in the extract. GC-MS analysis was done and the compounds detected were docked against SARS-CoV-2 Mpro using AutoDock Vina.The squalene (ΔG = -6.2 kcal/mol) posed the best inhibition potential and was comparable with the control drug remdesivir. The compounds possessed excellent pharmacokinetic and toxicity properties and are safe and reliable. Thus, the present research unveiled the valuable metabolites from O. europaea and their antiviral potential against the SARS-CoV-2.
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Affiliation(s)
- Venkataraghavan Ragunathan
- Nanomaterials and Environmental Research Laboratory, Department of Chemical Engineering, Alagappa College of Technology, Anna University, Chennai, India
| | - K Chithra
- Nanomaterials and Environmental Research Laboratory, Department of Chemical Engineering, Alagappa College of Technology, Anna University, Chennai, India
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Comparative Study of Novel Methods for Olive Leaf Phenolic Compound Extraction Using NADES as Solvents. Molecules 2023; 28:molecules28010353. [PMID: 36615544 PMCID: PMC9823617 DOI: 10.3390/molecules28010353] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/17/2022] [Accepted: 12/21/2022] [Indexed: 01/04/2023] Open
Abstract
Natural deep eutectic solvents (NADES) composed of choline chloride with maltose (CMA), glycerol (CGL), citric (CCA) and lactic acid (CLA) combined with microwave (MAE), ultrasound (UAE), homogenate (HAE) and high hydrostatic pressure (HHPAE)-assisted extraction methods were applied to recover and compare olive leaf phenolic compounds. The resultant extracts were evaluated for their total phenol content (TPC), phenolic profile and antioxidant activity and compared with those of water and ethanol:water 70% v/v extracts. HAE was proven to be the most efficient method for the recovery of olive leaf phenolic compounds. The highest TPC (55.12 ± 1.08 mg GAE/g d.w.) was found in CCA extracts after HAE at 60 °C and 12,000 rpm, and the maximum antioxidant activity (3.32 ± 0.39 g d.w./g DPPH) was found in CGL extracts after UAE at 60 °C for 30 min. The TPCs of ethanol extracts were found to be higher than those of NADES extracts in most cases. The predominant phenolic compounds in the extracts were oleuropein, hydrohytyrosol and rutin.
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Evaluation of Susceptibility of the Human Pathogen Helicobacter pylori to the Antibiotic Capreomycin. ScientificWorldJournal 2022; 2022:8924023. [PMID: 35958801 PMCID: PMC9357814 DOI: 10.1155/2022/8924023] [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: 03/30/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 11/23/2022] Open
Abstract
Helicobacter pylori infection causes gastritis, peptic ulcer disease, mucosa-associated lymphoid tissue lymphoma, and gastric cancer and can also promote thrombosis. It is estimated that approximately 4.5 billion individuals are infected, thus rendering H. pylori the most prevalent microbial pathogen. Currently established regimes for antibiotic treatment are massively challenged by increasing drug resistance and the development of novel antimicrobial therapies is urgently required. The antibiotic capreomycin is clinically used against multiple drug-resistant strains of Mycobacterium tuberculosis. It targets the complex between TlyA, a hemolysin- and RNA-binding protein, and the bacterial rRNA. In this study we have explored the possible antibacterial effects of capreomycin against several strains of H. pylori and found only moderate activity which was comparable to metronidazole-resistant strains. Molecular docking of capreomycin to TlyA proteins from H. pylori and M. tuberculosis identified several residues within TlyA which interact with the drug; however, binding affinities of H. pylori– TlyA for capreomycin appear to be higher than those of Mycobacterium– TlyA. The data suggest that capreomycin may warrant further investigations into its potential use as antibiotic against H. pylori.
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Oleuropein as a Potent Compound against Neurological Complications Linked with COVID-19: A Computational Biology Approach. ENTROPY 2022; 24:e24070881. [PMID: 35885104 PMCID: PMC9319675 DOI: 10.3390/e24070881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/22/2022] [Accepted: 06/22/2022] [Indexed: 12/04/2022]
Abstract
The association of COVID-19 with neurological complications is a well-known fact, and researchers are endeavoring to investigate the mechanistic perspectives behind it. SARS-CoV-2 can bind to Toll-like receptor 4 (TLR-4) that would eventually lead to α-synuclein aggregation in neurons and stimulation of neurodegeneration pathways. Olive leaves have been reported as a promising phytotherapy or co-therapy against COVID-19, and oleuropein is one of the major active components of olive leaves. In the current study, oleuropein was investigated against SARS-CoV-2 target (main protease 3CLpro), TLR-4 and Prolyl Oligopeptidases (POP), to explore oleuropein potency against the neurological complications associated with COVID-19. Docking experiments, docking validation, interaction analysis, and molecular dynamic simulation analysis were performed to provide insight into the binding pattern of oleuropein with the three target proteins. Interaction analysis revealed strong bonding between oleuropein and the active site amino acid residues of the target proteins. Results were further compared with positive control lopinavir (3CLpro), resatorvid (TLR-4), and berberine (POP). Moreover, molecular dynamic simulation was performed using YASARA structure tool, and AMBER14 force field was applied to examine an 100 ns trajectory run. For each target protein-oleuropein complex, RMSD, RoG, and total potential energy were estimated, and 400 snapshots were obtained after each 250 ps. Docking analyses showed binding energy as −7.8, −8.3, and −8.5 kcal/mol for oleuropein-3CLpro, oleuropein-TLR4, and oleuropein-POP interactions, respectively. Importantly, target protein-oleuropein complexes were stable during the 100 ns simulation run. However, an experimental in vitro study of the binding of oleuropein to the purified targets would be necessary to confirm the present study outcomes.
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Abstract
Over the past few months, numerous studies harnessed in silico methods such as molecular docking to evaluate food compounds for inhibitory activity against coronavirus infection and replication. These studies capitalize on the efficiency of computational methods to quickly guide subsequent research and examine diet-disease relationships, and their sudden widespread utility may signal new opportunities for future antiviral and bioactive food research. Using Coronavirus Disease 2019 (COVID-19) research as a case study, we herein provide an overview of findings from studies using molecular docking to study food compounds as potential inhibitors of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), explore considerations for the critical interpretation of study findings, and discuss how these studies help shape larger conversations of diet and disease.
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13
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Sama-ae I, Sangkanu S, Siyadatpanah A, Norouzi R, Chuprom J, Mitsuwan W, Surinkaew S, Boonhok R, Paul AK, Mahboob T, Abtahi NS, Jimoh TO, Oliveira SM, Gupta M, Sin C, de Lourdes Pereira M, Wilairatana P, Wiart C, Rahmatullah M, Dolma KG, Nissapatorn V. Targeting Acanthamoeba proteins interaction with flavonoids of Propolis extract by in vitro and in silico studies for promising therapeutic effects. F1000Res 2022; 11:1274. [PMID: 36936052 PMCID: PMC10015121 DOI: 10.12688/f1000research.126227.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/25/2022] [Indexed: 11/09/2022] Open
Abstract
Background : Propolis is a natural resinous mixture produced by bees. It provides beneficial effects on human health in the treatment/management of many diseases. The present study was performed to demonstrate the anti- Acanthamoeba activity of ethanolic extracts of Propolis samples from Iran. The interactions of the compounds and essential proteins of Acanthamoeba were also visualized through docking simulation. Methods: The minimal inhibitory concentrations (MICs) of Propolis extract against Acanthamoeba trophozoites and cysts was determined in vitro. In addition, two-fold dilutions of each of the agents were tested for encystment, excystment and adhesion inhibitions. Three major compounds of Propolis extract such as chrysin, tectochrysin and pinocembrin have been selected in molecular docking approach to predict the compounds that might be responsible for encystment, excystment and adhesion inhibitions of A. castellanii. Furthermore, to confirm the docking results, molecular dynamics (MD) simulations were also carried out for the most promising two ligand-pocket complexes from docking studies. Results : The minimal inhibitory concentrations (MICs) 62.5 and 125 µg/mL of the most active Propolis extract were assessed in trophozoites stage of Acanthamoeba castellanii ATCC30010 and ATCC50739, respectively. At concentrations lower than their MICs values (1/16 MIC), Propolis extract revealed inhibition of encystation. However, at 1/2 MIC, it showed a potential inhibition of excystation and anti-adhesion. The molecular docking and dynamic simulation revealed the potential capability of Pinocembrin to form hydrogen bonds with A. castellanii Sir2 family protein (AcSir2), an encystation protein of high relevance for this process in Acanthamoeba. Conclusions : The results obtained provided a candidate for the development of therapeutic drugs against Acanthamoeba infection. In vivo experiments and clinical trials are necessary to support this claim.
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Affiliation(s)
- Imran Sama-ae
- Department of Medical Technology, School of Allied Health Sciences and Center of Excellence Research for Melioidosis and Microorganisms (CERMM), Walailak University, Nakhon Si Thammarat, Thailand
| | - Suthinee Sangkanu
- School of Allied Health Sciences, Southeast Asia Water Team (SEA Water Team) and World Union for Herbal Drug Discovery (WUHeDD), Walailak University, Nakhon Si Thammarat, Thailand
| | - Abolghasem Siyadatpanah
- Ferdows School of Paramedical and Health, Birjand University of Medical Sciences, Birjand, Iran
- Department of Microbiology, School of Medicine, Infectious Diseases Research Center, Gonabad University of Medical Sciences, Gonabad, Iran
| | - Roghayeh Norouzi
- Department of Pathobiology, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
| | - Julalak Chuprom
- School of Allied Health Sciences, Southeast Asia Water Team (SEA Water Team) and World Union for Herbal Drug Discovery (WUHeDD), Walailak University, Nakhon Si Thammarat, Thailand
| | - Watcharapong Mitsuwan
- Akkhraratchakumari Veterinary College and Research Center of Excellence in Innovation of Essential Oil, Walailak University, Nakhon Si Thammarat, Thailand
| | - Sirirat Surinkaew
- Department of Medical Technology, School of Allied Health Sciences and Research Excellence Center for Innovation and Health Products (RECIHP), Walailak University, Nakhon Si Thammarat, Thailand
| | - Rachasak Boonhok
- Department of Medical Technology, School of Allied Health Sciences and Research Excellence Center for Innovation and Health Products (RECIHP), Walailak University, Nakhon Si Thammarat, Thailand
| | - Alok K. Paul
- School of Pharmacy and Pharmacology, University of Tasmania, TAS, Australia
| | - Tooba Mahboob
- School of Allied Health Sciences, Southeast Asia Water Team (SEA Water Team) and World Union for Herbal Drug Discovery (WUHeDD), Walailak University, Nakhon Si Thammarat, Thailand
| | - Najme Sadat Abtahi
- Department of Clinical Biochemistry, Faculty of Medicine International Campus, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Tajudeen O. Jimoh
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Health Sciences, Islamic University in Uganda, Kampala, Uganda
| | - Sónia M.R. Oliveira
- CICECO-Aveiro Institute of Materials, University of Aveiro, Aveiro, Portugal
- Hunter Medical Research Institute, NSW, Australia
| | - Madhu Gupta
- Department of Pharmaceutics, Delhi Pharmaceutical Sciences and Research University, New Delhi, India
| | - Chea Sin
- Faculty of Pharmacy, University of Puthisastra, Phnom Penh, Cambodia
| | - Maria de Lourdes Pereira
- CICECO-Aveiro Institute of Materials, University of Aveiro, Aveiro, Portugal
- Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Polrat Wilairatana
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Christophe Wiart
- Institute for Tropical Biology & Conservation, University Malaysia Sabah, Sabah, Malaysia
| | - Mohammed Rahmatullah
- Department of Biotechnology & Genetic Engineering, University of Development Alternative, Dhaka, Bangladesh
| | - Karma G. Dolma
- Department of Microbiology, Sikkim Manipal Institute of Medical Sciences, Sikkim Manipal University, Sikkim, India
| | - Veeranoot Nissapatorn
- School of Allied Health Sciences, Southeast Asia Water Team (SEA Water Team) and World Union for Herbal Drug Discovery (WUHeDD), Walailak University, Nakhon Si Thammarat, Thailand
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Sama-ae I, Sangkanu S, Siyadatpanah A, Norouzi R, Chuprom J, Mitsuwan W, Surinkaew S, Boonhok R, Paul AK, Mahboob T, Abtahi NS, Jimoh TO, Oliveira SM, Gupta M, Sin C, de Lourdes Pereira M, Wilairatana P, Wiart C, Rahmatullah M, Dolma KG, Nissapatorn V. Targeting Acanthamoeba proteins interaction with flavonoids of Propolis extract by in vitro and in silico studies for promising therapeutic effects. F1000Res 2022; 11:1274. [PMID: 36936052 PMCID: PMC10015121.3 DOI: 10.12688/f1000research.126227.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/15/2023] [Indexed: 03/29/2023] Open
Abstract
Background : Propolis is a natural resinous mixture produced by bees. It provides beneficial effects on human health in the treatment/management of many diseases. The present study was performed to demonstrate the anti- Acanthamoeba activity of ethanolic extracts of Propolis samples from Iran. The interactions of the compounds and essential proteins of Acanthamoeba were also visualized through docking simulation. Methods: The minimal inhibitory concentrations (MICs) of Propolis extract against Acanthamoeba trophozoites and cysts was determined in vitro. In addition, two-fold dilutions of each of agents were tested for encystment, excystment and adhesion inhibitions. Three major compounds of Propolis extract such as chrysin, tectochrysin and pinocembrin have been selected in molecular docking approach to predict the compounds that might be responsible for encystment, excystment and adhesion inhibitions of A. castellanii. Furthermore, to confirm the docking results, molecular dynamics (MD) simulations were also carried out for the most promising two ligand-pocket complexes from docking studies. Results : The minimal inhibitory concentrations (MICs) 62.5 and 125 µg/mL of the most active Propolis extract were assessed in trophozoites stage of Acanthamoeba castellanii ATCC30010 and ATCC50739, respectively. At concentrations lower than their MICs values (1/16 MIC), Propolis extract revealed inhibition of encystation. However, at 1/2 MIC, it showed a potential inhibition of excystation and anti-adhesion. The molecular docking and dynamic simulation revealed the potential capability of Pinocembrin to form hydrogen bonds with A. castellanii Sir2 family protein (AcSir2), an encystation protein of high relevance for this process in Acanthamoeba. Conclusions : The results provided a candidate for the development of therapeutic drugs against Acanthamoeba infection. In vivo experiments and clinical trials are necessary to support this claim.
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Affiliation(s)
- Imran Sama-ae
- Department of Medical Technology, School of Allied Health Sciences and Center of Excellence Research for Melioidosis and Microorganisms (CERMM), Walailak University, Nakhon Si Thammarat, Thailand
| | - Suthinee Sangkanu
- School of Allied Health Sciences, Southeast Asia Water Team (SEA Water Team) and World Union for Herbal Drug Discovery (WUHeDD), Walailak University, Nakhon Si Thammarat, Thailand
| | - Abolghasem Siyadatpanah
- Department of Microbiology, School of Medicine, Infectious Diseases Research Center, Gonabad University of Medical Sciences, Gonabad, Iran
- Ferdows School of Paramedical and Health, Birjand University of Medical Sciences, Birjand, Iran
| | - Roghayeh Norouzi
- Department of Pathobiology, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
| | - Julalak Chuprom
- School of Allied Health Sciences, Southeast Asia Water Team (SEA Water Team) and World Union for Herbal Drug Discovery (WUHeDD), Walailak University, Nakhon Si Thammarat, Thailand
| | - Watcharapong Mitsuwan
- Akkhraratchakumari Veterinary College and Research Center of Excellence in Innovation of Essential Oil, Walailak University, Nakhon Si Thammarat, Thailand
| | - Sirirat Surinkaew
- Department of Medical Technology, School of Allied Health Sciences and Research Excellence Center for Innovation and Health Products (RECIHP), Walailak University, Nakhon Si Thammarat, Thailand
| | - Rachasak Boonhok
- Department of Medical Technology, School of Allied Health Sciences and Research Excellence Center for Innovation and Health Products (RECIHP), Walailak University, Nakhon Si Thammarat, Thailand
| | - Alok K. Paul
- School of Pharmacy and Pharmacology, University of Tasmania, TAS, Australia
| | - Tooba Mahboob
- School of Allied Health Sciences, Southeast Asia Water Team (SEA Water Team) and World Union for Herbal Drug Discovery (WUHeDD), Walailak University, Nakhon Si Thammarat, Thailand
| | - Najme Sadat Abtahi
- Department of Clinical Biochemistry, Faculty of Medicine International Campus, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Tajudeen O. Jimoh
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Health Sciences, Islamic University in Uganda, Kampala, Uganda
| | - Sónia M.R. Oliveira
- CICECO-Aveiro Institute of Materials, University of Aveiro, Aveiro, Portugal
- Hunter Medical Research Institute, NSW, Australia
| | - Madhu Gupta
- Department of Pharmaceutics, Delhi Pharmaceutical Sciences and Research University, New Delhi, India
| | - Chea Sin
- Faculty of Pharmacy, University of Puthisastra, Phnom Penh, Cambodia
| | - Maria de Lourdes Pereira
- CICECO-Aveiro Institute of Materials, University of Aveiro, Aveiro, Portugal
- Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Polrat Wilairatana
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Christophe Wiart
- Institute for Tropical Biology & Conservation, University Malaysia Sabah, Sabah, Malaysia
| | - Mohammed Rahmatullah
- Department of Biotechnology & Genetic Engineering, University of Development Alternative, Dhaka, Bangladesh
| | - Karma G. Dolma
- Department of Microbiology, Sikkim Manipal Institute of Medical Sciences, Sikkim Manipal University, Sikkim, India
| | - Veeranoot Nissapatorn
- School of Allied Health Sciences, Southeast Asia Water Team (SEA Water Team) and World Union for Herbal Drug Discovery (WUHeDD), Walailak University, Nakhon Si Thammarat, Thailand
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15
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Sama-ae I, Sangkanu S, Siyadatpanah A, Norouzi R, Chuprom J, Mitsuwan W, Surinkaew S, Boonhok R, Paul AK, Mahboob T, Abtahi NS, Jimoh TO, Oliveira SM, Gupta M, Sin C, de Lourdes Pereira M, Wilairatana P, Wiart C, Rahmatullah M, Dolma KG, Nissapatorn V. Targeting Acanthamoeba proteins interaction with flavonoids of Propolis extract by in vitro and in silico studies for promising therapeutic effects. F1000Res 2022; 11:1274. [PMID: 36936052 PMCID: PMC10015121 DOI: 10.12688/f1000research.126227.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/31/2023] [Indexed: 02/10/2023] Open
Abstract
Background : Propolis is a natural resinous mixture produced by bees. It provides beneficial effects on human health in the treatment/management of many diseases. The present study was performed to demonstrate the anti- Acanthamoeba activity of ethanolic extracts of Propolis samples from Iran. The interactions of the compounds and essential proteins of Acanthamoeba were also visualized through docking simulation. Methods: The minimal inhibitory concentrations (MICs) of Propolis extract against Acanthamoeba trophozoites and cysts was determined in vitro. In addition, two-fold dilutions of each of agents were tested for encystment, excystment and adhesion inhibitions. Three major compounds of Propolis extract such as chrysin, tectochrysin and pinocembrin have been selected in molecular docking approach to predict the compounds that might be responsible for encystment, excystment and adhesion inhibitions of A. castellanii. Furthermore, to confirm the docking results, molecular dynamics (MD) simulations were also carried out for the most promising two ligand-pocket complexes from docking studies. Results : The minimal inhibitory concentrations (MICs) 62.5 and 125 µg/mL of the most active Propolis extract were assessed in trophozoites stage of Acanthamoeba castellanii ATCC30010 and ATCC50739, respectively. At concentrations lower than their MICs values (1/16 MIC), Propolis extract revealed inhibition of encystation. However, at 1/2 MIC, it showed a potential inhibition of excystation and anti-adhesion. The molecular docking and dynamic simulation revealed the potential capability of Pinocembrin to form hydrogen bonds with A. castellanii Sir2 family protein (AcSir2), an encystation protein of high relevance for this process in Acanthamoeba. Conclusions : The results provided a candidate for the development of therapeutic drugs against Acanthamoeba infection. In vivo experiments and clinical trials are necessary to support this claim.
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Affiliation(s)
- Imran Sama-ae
- Department of Medical Technology, School of Allied Health Sciences and Center of Excellence Research for Melioidosis and Microorganisms (CERMM), Walailak University, Nakhon Si Thammarat, Thailand
| | - Suthinee Sangkanu
- School of Allied Health Sciences, Southeast Asia Water Team (SEA Water Team) and World Union for Herbal Drug Discovery (WUHeDD), Walailak University, Nakhon Si Thammarat, Thailand
| | - Abolghasem Siyadatpanah
- Ferdows School of Paramedical and Health, Birjand University of Medical Sciences, Birjand, Iran
- Department of Microbiology, School of Medicine, Infectious Diseases Research Center, Gonabad University of Medical Sciences, Gonabad, Iran
| | - Roghayeh Norouzi
- Department of Pathobiology, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
| | - Julalak Chuprom
- School of Allied Health Sciences, Southeast Asia Water Team (SEA Water Team) and World Union for Herbal Drug Discovery (WUHeDD), Walailak University, Nakhon Si Thammarat, Thailand
| | - Watcharapong Mitsuwan
- Akkhraratchakumari Veterinary College and Research Center of Excellence in Innovation of Essential Oil, Walailak University, Nakhon Si Thammarat, Thailand
| | - Sirirat Surinkaew
- Department of Medical Technology, School of Allied Health Sciences and Research Excellence Center for Innovation and Health Products (RECIHP), Walailak University, Nakhon Si Thammarat, Thailand
| | - Rachasak Boonhok
- Department of Medical Technology, School of Allied Health Sciences and Research Excellence Center for Innovation and Health Products (RECIHP), Walailak University, Nakhon Si Thammarat, Thailand
| | - Alok K. Paul
- School of Pharmacy and Pharmacology, University of Tasmania, TAS, Australia
| | - Tooba Mahboob
- School of Allied Health Sciences, Southeast Asia Water Team (SEA Water Team) and World Union for Herbal Drug Discovery (WUHeDD), Walailak University, Nakhon Si Thammarat, Thailand
| | - Najme Sadat Abtahi
- Department of Clinical Biochemistry, Faculty of Medicine International Campus, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Tajudeen O. Jimoh
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Health Sciences, Islamic University in Uganda, Kampala, Uganda
| | - Sónia M.R. Oliveira
- CICECO-Aveiro Institute of Materials, University of Aveiro, Aveiro, Portugal
- Hunter Medical Research Institute, NSW, Australia
| | - Madhu Gupta
- Department of Pharmaceutics, Delhi Pharmaceutical Sciences and Research University, New Delhi, India
| | - Chea Sin
- Faculty of Pharmacy, University of Puthisastra, Phnom Penh, Cambodia
| | - Maria de Lourdes Pereira
- CICECO-Aveiro Institute of Materials, University of Aveiro, Aveiro, Portugal
- Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Polrat Wilairatana
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Christophe Wiart
- Institute for Tropical Biology & Conservation, University Malaysia Sabah, Sabah, Malaysia
| | - Mohammed Rahmatullah
- Department of Biotechnology & Genetic Engineering, University of Development Alternative, Dhaka, Bangladesh
| | - Karma G. Dolma
- Department of Microbiology, Sikkim Manipal Institute of Medical Sciences, Sikkim Manipal University, Sikkim, India
| | - Veeranoot Nissapatorn
- School of Allied Health Sciences, Southeast Asia Water Team (SEA Water Team) and World Union for Herbal Drug Discovery (WUHeDD), Walailak University, Nakhon Si Thammarat, Thailand
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Power H, Wu J, Turville S, Aggarwal A, Valtchev P, Schindeler A, Dehghani F. Virtual screening and in vitro validation of natural compound inhibitors against SARS-CoV-2 spike protein. Bioorg Chem 2021; 119:105574. [PMID: 34971947 PMCID: PMC8693770 DOI: 10.1016/j.bioorg.2021.105574] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 11/24/2021] [Accepted: 12/16/2021] [Indexed: 12/16/2022]
Abstract
The COVID-19 pandemic caused by the SARS-CoV-2 virus has led to a major public health burden and has resulted in millions of deaths worldwide. As effective treatments are limited, there is a significant requirement for high-throughput, low resource methods for the discovery of novel antivirals. The SARS-CoV-2 spike protein plays a key role in viral entry and has been identified as a therapeutic target. Using the available spike crystal structure, we performed a virtual screen with a library of 527 209 natural compounds against the receptor binding domain of this protein. Top hits from this screen were subjected to a second, more comprehensive molecular docking experiment and filtered for favourable ADMET properties. The in vitro activity of 10 highly ranked compounds was assessed using a virus neutralisation assay designed to facilitate viral entry in a physiologically relevant manner via the plasma membrane route. Subsequently, four compounds ZINC02111387, ZINC02122196, SN00074072 and ZINC04090608 were identified to possess antiviral activity in the µM range. These findings validate the virtual screening method as a tool for identifying novel antivirals and provide a basis for future drug development against SARS-CoV-2.
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Affiliation(s)
- Helen Power
- School of Chemical and Biomolecular Engineering, Faculty of Engineering, The University of Sydney, Sydney, NSW 2006, Australia,Centre for Advanced Food Engineering, The University of Sydney, Sydney, NSW, 2006, Australia,Bioengineering and Molecular Medicine Laboratory, The Children’s Hospital at Westmead and Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
| | - Jiadai Wu
- School of Chemical and Biomolecular Engineering, Faculty of Engineering, The University of Sydney, Sydney, NSW 2006, Australia,Centre for Advanced Food Engineering, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Stuart Turville
- The Kirby Institute, University of NSW, Kensington, NSW 2052, Australia
| | - Anupriya Aggarwal
- The Kirby Institute, University of NSW, Kensington, NSW 2052, Australia
| | - Peter Valtchev
- School of Chemical and Biomolecular Engineering, Faculty of Engineering, The University of Sydney, Sydney, NSW 2006, Australia,Centre for Advanced Food Engineering, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Aaron Schindeler
- School of Chemical and Biomolecular Engineering, Faculty of Engineering, The University of Sydney, Sydney, NSW 2006, Australia,Centre for Advanced Food Engineering, The University of Sydney, Sydney, NSW, 2006, Australia,Bioengineering and Molecular Medicine Laboratory, The Children’s Hospital at Westmead and Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
| | - Fariba Dehghani
- School of Chemical and Biomolecular Engineering, Faculty of Engineering, The University of Sydney, Sydney, NSW 2006, Australia,Centre for Advanced Food Engineering, The University of Sydney, Sydney, NSW, 2006, Australia,Corresponding author
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Zhang Y, Chen H, Zou M, Oerlemans R, Shao C, Ren Y, Zhang R, Huang X, Li G, Cong Y. Hypericin Inhibit Alpha-Coronavirus Replication by Targeting 3CL Protease. Viruses 2021; 13:v13091825. [PMID: 34578406 PMCID: PMC8473218 DOI: 10.3390/v13091825] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/05/2021] [Accepted: 09/06/2021] [Indexed: 12/13/2022] Open
Abstract
The porcine epidemic diarrhea virus (PEDV) is an Alphacoronavirus (α-CoV) that causes high mortality in infected piglets, resulting in serious economic losses in the farming industry. Hypericin is a dianthrone compound that has been shown as an antiviral activity on several viruses. Here, we first evaluated the antiviral effect of hypericin in PEDV and found the viral replication and egression were significantly reduced with hypericin post-treatment. As hypericin has been shown in SARS-CoV-2 that it is bound to viral 3CLpro, we thus established a molecular docking between hypericin and PEDV 3CLpro using different software and found hypericin bound to 3CLpro through two pockets. These binding pockets were further verified by another docking between hypericin and PEDV 3CLpro pocket mutants, and the fluorescence resonance energy transfer (FRET) assay confirmed that hypericin inhibits the PEDV 3CLpro activity. Moreover, the alignments of α-CoV 3CLpro sequences or crystal structure revealed that the pockets mediating hypericin and PEDV 3CLpro binding were highly conserved, especially in transmissible gastroenteritis virus (TGEV). We then validated the anti-TGEV effect of hypericin through viral replication and egression. Overall, our results push forward that hypericin was for the first time shown to have an inhibitory effect on PEDV and TGEV by targeting 3CLpro, and it deserves further attention as not only a pan-anti-α-CoV compound but potentially also as a compound of other coronaviral infections.
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Affiliation(s)
- Yue Zhang
- Veterinary Pathology Laboratory, College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin 150030, China; (Y.Z.); (H.C.); (M.Z.); (C.S.); (R.Z.); (X.H.)
| | - Huijie Chen
- Veterinary Pathology Laboratory, College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin 150030, China; (Y.Z.); (H.C.); (M.Z.); (C.S.); (R.Z.); (X.H.)
- College of Pharmaceutical Engineering, Jilin Agriculture Science and Technology University, Jilin 132101, China
| | - Mengmeng Zou
- Veterinary Pathology Laboratory, College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin 150030, China; (Y.Z.); (H.C.); (M.Z.); (C.S.); (R.Z.); (X.H.)
| | - Rick Oerlemans
- Department of Drug Design, University of Groningen, 9713 AV Groningen, The Netherlands;
| | - Changhao Shao
- Veterinary Pathology Laboratory, College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin 150030, China; (Y.Z.); (H.C.); (M.Z.); (C.S.); (R.Z.); (X.H.)
| | - Yudong Ren
- Department of Computer Science and Technology, College of Electrical and Information Technology, Northeast Agricultural University, Harbin 150030, China;
| | - Ruili Zhang
- Veterinary Pathology Laboratory, College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin 150030, China; (Y.Z.); (H.C.); (M.Z.); (C.S.); (R.Z.); (X.H.)
| | - Xiaodan Huang
- Veterinary Pathology Laboratory, College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin 150030, China; (Y.Z.); (H.C.); (M.Z.); (C.S.); (R.Z.); (X.H.)
| | - Guangxing Li
- Veterinary Pathology Laboratory, College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin 150030, China; (Y.Z.); (H.C.); (M.Z.); (C.S.); (R.Z.); (X.H.)
- Correspondence: (G.L.); (Y.C.)
| | - Yingying Cong
- Veterinary Pathology Laboratory, College of Veterinary Medicine, Heilongjiang Key Laboratory for Animal and Comparative Medicine, Northeast Agricultural University, Harbin 150030, China; (Y.Z.); (H.C.); (M.Z.); (C.S.); (R.Z.); (X.H.)
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
- Correspondence: (G.L.); (Y.C.)
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Ünlü AE. Green and Non-conventional Extraction of Bioactive Compounds from Olive Leaves: Screening of Novel Natural Deep Eutectic Solvents and Investigation of Process Parameters. WASTE AND BIOMASS VALORIZATION 2021; 12:5329-5346. [PMID: 33727990 PMCID: PMC7953197 DOI: 10.1007/s12649-021-01411-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 02/21/2021] [Indexed: 06/12/2023]
Abstract
ABSTRACT Olive leaf as an agricultural waste contains valuable bioactive compounds that are mainly used for pharmaceutical and cosmetic industries. Lately the major component, oleuropein, has gained extra attention due to the anti-viral activity against SARS-CoV-2 that causes Coronavirus disease (Covid-19). In this study, extraction of the bioactive compounds from olive leaves was conducted using a non-conventional and green method. New generation green solvents, natural deep eutectic solvents (NADES) were used in combination with ultrasound assisted extraction. Screening of NADES type, temperature, and particle size were investigated using one-pot-at-a-time method while, NADES amount and liquid-to-solid ratio were optimized using experimental design. The results were evaluated in terms of total polyphenol yield (YTP), total flavonoid yield (YTF) and antiradical activity (AAR). At the optimized conditions, the highest total polyphenol yield and the highest total flavonoid yield were achieved with choline chloride-fructose-water (CFW) (5:2:5) as 187.31 ± 10.3 mg gallic acid equivalent g-1 dw and 12.75 ± 0.6 mg apigenin equivalent g-1 dw, respectively. The extracts were also analyzed for oleuropein, caffeic acid and luteolin contents. The highest amount of oleuropein and caffeic acid were extracted by glucose-fructose-water (GFW) (1:1:11) as 1630.80 mg kg-1 dw and 112.77 mg kg-1 dw, respectively. SUPPLEMENTARY INFORMATION The online version of this article (10.1007/s12649-021-01411-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ayşe Ezgi Ünlü
- Faculty of Engineering, Department of Chemical Engineering, Ankara University, 06100 Ankara, Turkey
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Chandra A, Chaudhary M, Qamar I, Singh N, Nain V. In silico identification and validation of natural antiviral compounds as potential inhibitors of SARS-CoV-2 methyltransferase. J Biomol Struct Dyn 2021; 40:6534-6544. [PMID: 33583328 PMCID: PMC7885726 DOI: 10.1080/07391102.2021.1886174] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The novel Coronavirus disease 2019 (COVID-19) is potentially fatal and caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Due to the unavailability of any proven treatment or vaccination, the outbreak of COVID-19 is wreaking havoc worldwide. Hence, there is an urgent need for therapeutics targeting SARS-CoV-2. Since, botanicals are an important resource for several efficacious antiviral agents, natural compounds gaining significant attention for COVID-19 treatment. In the present study, methyltranferase (MTase) of the SARS-CoV-2 is targeted using computational approach. The compounds were identified using molecular docking, virtual screening and molecular dynamics simulation studies. The binding mechanism of each compound was analyzed considering the stability and energetic parameter using in silico methods. We have found four natural antiviral compounds Amentoflavone, Baicalin, Daidzin and Luteoloside as strong inhibitors of methyltranferase of SARS-CoV-2. ADMET prediction and target analysis of the selected compounds showed favorable results. MD simulation was performed for four top-scored molecules to analyze the stability, binding mechanism and energy requirements. MD simulation studies indicated energetically favorable complex formation between MTase and the selected antiviral compounds. Furthermore, the structural effects on these substitutions were analyzed using the principles of each trajectories, which validated the interaction studies. Our analysis suggests that there is a very high probability that these compounds may have a good potential to inhibit Methyltransferase (MTase) of SARS-CoV-2 and to be used in the treatment of COVID-19. Further studies on these natural compounds may offer a quick therapeutic choice to treat COVID-19. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Anshuman Chandra
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
| | - Meenakshi Chaudhary
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, India
| | - Imteyaz Qamar
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
| | - Nagendra Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
| | - Vikrant Nain
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
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