1
|
Chebaibi M, Bourhia M, Amrati FEZ, Slighoua M, Mssillou I, Aboul-Soud MAM, Khalid A, Hassani R, Bousta D, Achour S, Benhida R, Daoud R. Salsoline derivatives, genistein, semisynthetic derivative of kojic acid, and naringenin as inhibitors of A42R profilin-like protein of monkeypox virus: in silico studies. Front Chem 2024; 12:1445606. [PMID: 39318419 PMCID: PMC11420140 DOI: 10.3389/fchem.2024.1445606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 08/26/2024] [Indexed: 09/26/2024] Open
Abstract
Monkeypox virus (MPV) infection has developed into a re-emerging disease, and despite the potential of tecovirimat and cidofovir drugs, there is currently no conclusive treatment. The treatment's effectiveness and cost challenges motivate us to use In Silico approaches to seek natural compounds as candidate antiviral inhibitors. Using Maestro 11.5 in Schrodinger suite 2018, available natural molecules with validated chemical structures collected from Eximed Laboratory were subjected to molecular docking and ADMET analysis against the highly conserved A42R Profilin-like Protein of Monkeypox Virus Zaire-96-I-16 (PDB: 4QWO) with resolution of 1.52 Å solved 3D structure. Compared to the FDA-approved Tecovirimat, molecular docking revealed that Salsoline derivatives, Genistein, Semisynthetic derivative of kojic acid, and Naringenin had strengthened affinity (-8.9 to -10 kcal/mol) to 4QWO, and the molecular dynamic's simulation confirmed their high binding stability. In support of these results, the hydrogen bond analysis indicated that the Salsoline derivative had the most robust interaction with the binding pockets of 4QWO among the four molecules. Moreover, the comparative free energy analyses using MM-PBSA revealed an average binding free energy of the complexes of Salsoline derivative, Genistein, Semisynthetic derivative of kojic acid, Naringenin, of -106.418, -46.808, -50.770, and -63.319 kJ/mol, respectively which are lower than -33.855 kJ/mol of the Tecovirimat complex. Interestingly, these results and the ADMET predictions suggest that the four compounds are promising inhibitors of 4QWO, which agrees with previous results showing their antiviral activities against other viruses.
Collapse
Affiliation(s)
- Mohamed Chebaibi
- Ministry of Health and Social Protection, Higher Institute of Nursing Professions and Health Techniques, Fez, Morocco
| | - Mohammed Bourhia
- Department of Chemistry and Biochemistry, Faculty of Medicine and Pharmacy, Ibn Zohr University, Laayoune, Morocco
| | - Fatima ez-zahra Amrati
- Laboratory of Biotechnology, Environment, Agri-Food, and Health (LBEAS), Faculty of Sciences, University Sidi-Mohamed-Ben-Abdellah (USMBA), Fez, Morocco
| | - Meryem Slighoua
- Laboratory of Biotechnology, Environment, Agri-Food, and Health (LBEAS), Faculty of Sciences, University Sidi-Mohamed-Ben-Abdellah (USMBA), Fez, Morocco
| | - Ibrahim Mssillou
- Laboratory of Natural Substances, Pharmacology, Environment, Modeling, Health and Quality of Life (SNAMOPEQ), Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Mourad A. M. Aboul-Soud
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Asaad Khalid
- Health Research Center, Jazan University, Jazan, Saudi Arabia
| | - Rym Hassani
- Environment and Nature Research Centre, Jazan University, Jazan, Saudi Arabia
| | - Dalila Bousta
- National Agency of Medicinal and Aromatic Plants Tounate, Taounate, Morocco
| | - Sanae Achour
- Biomedical and Translational Research Laboratory, Faculty of Medicine and Pharmacy of Fez, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Rachid Benhida
- Chemical and Biochemical Sciences-Green Processing Engineering, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Rachid Daoud
- Chemical and Biochemical Sciences-Green Processing Engineering, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| |
Collapse
|
2
|
Spanoudaki M, Stoumpou S, Papadopoulou SK, Karafyllaki D, Solovos E, Papadopoulos K, Giannakoula A, Giaginis C. Amygdalin as a Promising Anticancer Agent: Molecular Mechanisms and Future Perspectives for the Development of New Nanoformulations for Its Delivery. Int J Mol Sci 2023; 24:14270. [PMID: 37762572 PMCID: PMC10531689 DOI: 10.3390/ijms241814270] [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: 08/15/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Cancer rates are increasing, and cancer is one of the main causes of death worldwide. Amygdalin, also known as vitamin B17 (and laetrile, a synthetic compound), is a cyanogenic glycoside compound that is mainly found in the kernels and pulps of fruits. This compound has been proposed for decades as a promising naturally occurring substance which may provide anticancer effects. This is a comprehensive review which critically summarizes and scrutinizes the available studies exploring the anticancer effect of amygdalin, highlighting its potential anticancer molecular mechanisms as well as the need for a nontoxic formulation of this substance. In-depth research was performed using the most accurate scientific databases, e.g., PubMed, Cochrane, Embase, Medline, Scopus, and Web of Science, applying effective, characteristic, and relevant keywords. There are several pieces of evidence to support the idea that amygdalin can exert anticancer effects against lung, breast, prostate, colorectal, cervical, and gastrointestinal cancers. Amygdalin has been reported to induce apoptosis of cancer cells, inhibiting cancer cells' proliferation and slowing down tumor metastatic spread. However, only a few studies have been performed in in vivo animal models, while clinical studies remain even more scarce. The current evidence cannot support a recommendation of the use of nutritional supplements with amygdalin due to its cyano-moiety which exerts adverse side effects. Preliminary data have shown that the use of nanoparticles may be a promising alternative to enhance the anticancer effects of amygdalin while simultaneously reducing its adverse side effects. Amygdalin seems to be a promising naturally occurring agent against cancer disease development and progression. However, there is a strong demand for in vivo animal studies as well as human clinical studies to explore the potential prevention and/or treatment efficiency of amygdalin against cancer. Moreover, amygdalin could be used as a lead compound by effectively applying recent developments in drug discovery processes.
Collapse
Affiliation(s)
- Maria Spanoudaki
- Department of Nutritional Sciences and Dietetics, School of Health Sciences, International Hellenic University, 54700 Sindos, Greece; (M.S.); (S.S.); (S.K.P.); (A.G.)
- Clinical Dietetics and Nutritional Department, 424 General Military Hospital, 56429 Thessaloniki, Greece
| | - Sofia Stoumpou
- Department of Nutritional Sciences and Dietetics, School of Health Sciences, International Hellenic University, 54700 Sindos, Greece; (M.S.); (S.S.); (S.K.P.); (A.G.)
| | - Sousana K. Papadopoulou
- Department of Nutritional Sciences and Dietetics, School of Health Sciences, International Hellenic University, 54700 Sindos, Greece; (M.S.); (S.S.); (S.K.P.); (A.G.)
| | - Dimitra Karafyllaki
- Department of Nutrition and Dietetics, School of Physical Education, Sport Science and Dietetics, University of Thessaly, 42132 Trikala, Greece;
| | - Evangelos Solovos
- Orthopedic Department, 424 General Military Hospital, 56429 Thessaloniki, Greece; (E.S.); (K.P.)
| | | | - Anastasia Giannakoula
- Department of Nutritional Sciences and Dietetics, School of Health Sciences, International Hellenic University, 54700 Sindos, Greece; (M.S.); (S.S.); (S.K.P.); (A.G.)
- Laboratory of Plant Physiology and Postharvest Physiology of Fruits, Department of Agriculture, International Hellenic University, 54700 Sindos, Greece
| | - Constantinos Giaginis
- Department of Food Science and Nutrition, School of Environment, University of Aegean, 81400 Lemnos, Greece
| |
Collapse
|
3
|
Alwan AM, Rokaya D, Kathayat G, Afshari JT. Onco-immunity and therapeutic application of amygdalin: A review. J Oral Biol Craniofac Res 2023; 13:155-163. [PMID: 36618007 PMCID: PMC9816781 DOI: 10.1016/j.jobcr.2022.12.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/23/2022] [Accepted: 12/27/2022] [Indexed: 12/29/2022] Open
Abstract
Background Amygdalin is known as a chemical compound derived from various fruits. The glycosides existing in this plant have been historically utilized as an anticancer agent. This review presented an overview of amygdalin and its onco-immunity and other therapeutic medical applications. Method A literature search for studies relating to amygdalin and cancer treatment was carried out using PubMed and Google Scholar. Combinations of the following terms were used in the search strategies: "amygdalin," "rhodanese," "cyanide," "cyanogenic," "hypothiocyanite," "mandelonitrile," "glucosides," "cancer," "apoptosis," and "cytotoxicity," combined with a cancer term such as "seed," "almond," or "apricot," "cancer + cell line, antiproliferation or inhibition," "BAX From the March 3, 1981 until the April 15, 2021, all of the English-language papers were evaluated based on the inclusion criteria. Publications included reviews, chapters from books, and original research papers. Results The FDA prohibits Amygdalin from medical usage as an anticancer treatment due to a lack of proof of cure in cancer cases. When this natural-based compound is used with conditional chemotherapeutic medicines causes synergistic effects. Besides, amygdalin is used to manage asthma, improve the immune system, induce apoptosis in human renal fibroblasts, and inhibit hyperglycemia. Conclusion Various medical uses of amygdalin have been found such as managing asthma, improving the immune system, inducing apoptosis in human renal fibroblasts, and inhibiting hyperglycemia. More effective in vitro and review studies are required to elucidate the exact role of this herb in medical applications.
Collapse
Affiliation(s)
- Ahmed Mohammed Alwan
- Department of Immunology and Allergy, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Dinesh Rokaya
- Department of Clinical Dentistry, Walailak University International College of Dentistry, Walailak University, Bangkok 10400, Thailand
| | - Goma Kathayat
- Department of Biochemistry, Manipal College of Medical Sciences and Teaching Hospital, Pokhara, Nepal
| | - Jalil Tavakol Afshari
- Department of Immunology and Allergy, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| |
Collapse
|
4
|
Jose S, Devi SS, P S, Al-Khafaji K. Phytochemical constituents of Inula britannica as potential inhibitors of dihydrofolate reductase: A strategic approach against shigellosis. J Biomol Struct Dyn 2022; 40:11932-11947. [PMID: 34424817 DOI: 10.1080/07391102.2021.1966508] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Shigella dysenteriae type 1 is considered as an epidemic in different developing countries, which is responsible for the most severe form of bacterial dysentery. It habitually can develop to the most severe form of dysentery with deadly complications. Development of drugs against this disease is still ongoing. Therefore, we used in silico studies to screen the Inula britannica phytocompounds that are used in traditional Chinese and Kampo Medicines and have activities against different diseases. Spinacetin, eupatin, chrysoeriol and diosmetin were successfully passed through the docking-based screening and absorption, distribution, metabolism, excretion and toxicity (ADMET) filtration. The estimated docking affinities of eupatin, diosmetin, chrysoeriol and spinacetin with Dihydrofolate reductase type 1 (DHFR-1), were -6.5, -6.5, -6.3 and -6.1 kcal/mol, respectively. Which were selected for further investigations based on their favorable ADME/Tox characteristics. Then, the 100 ns molecular dynamics (MD) simulations of apo DHFR, spinacetin-DHFR, eupatin-DHFR, chrysoeriol-DHFR and diosmetin-DHFR complexes were carried out. The RMSD fluctuations of the spinacetin, eupatin, chrysoeriol and diosmetin inside the binding site were explored. Subsequently, the effect of binding Spinacetin, eupatin, chrysoeriol and diosmetin upon the dynamic stability of protein was assessed. Additionally, Principal Component Analysis (PCA) and Hydrogen bond analysis was performed for the apo protein and the protein ligand complexes. The results revealed that chrysoeriol and eupatin has good inhibitory effects against DHFR-1 as treatment for Shigella dysenteriae type when compared to other compounds under study. Hence this study implies that eupatin and chrysoeriol are a significantly potential drug like molecule for the treatment of Shigellosis and must undergo validation through in vivo and in vitro experiments.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Sandra Jose
- Department of Biotechnology, Vels Institute of Science, Technology and Advanced Studies, Chennai, Tamil Nadu, India
| | - Sreevidya S Devi
- School of Biosciences, Mar Athanasios College for Advanced Studies, Thiruvalla, Kerala, India
| | - Shakthi P
- Department of Biotechnology, Sri Krishna Arts and Science College, Coimbatore, Tamil Nadu, India
| | - Khattab Al-Khafaji
- Faculty of Arts and Sciences, Department of Chemistry, Gaziantep University, Gaziantep, Turkey
| |
Collapse
|
5
|
Mukerjee N, Al-Khafaji K, Maitra S, Suhail Wadi J, Sachdeva P, Ghosh A, Buchade RS, Chaudhari SY, Jadhav SB, Das P, Hasan MM, Rahman MH, Albadrani GM, Altyar AE, Kamel M, Algahtani M, Shinan K, Theyab A, Abdel-Daim MM, Ashraf GM, Rahman MM, Sharma R. Recognizing novel drugs against Keap1 in Alzheimer's disease using machine learning grounded computational studies. Front Mol Neurosci 2022; 15:1036552. [PMID: 36561895 PMCID: PMC9764216 DOI: 10.3389/fnmol.2022.1036552] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 10/21/2022] [Indexed: 12/12/2022] Open
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disorder in the world, affecting an estimated 50 million individuals. The nerve cells become impaired and die due to the formation of amyloid-beta (Aβ) plaques and neurofibrillary tangles (NFTs). Dementia is one of the most common symptoms seen in people with AD. Genes, lifestyle, mitochondrial dysfunction, oxidative stress, obesity, infections, and head injuries are some of the factors that can contribute to the development and progression of AD. There are just a few FDA-approved treatments without side effects in the market, and their efficacy is restricted due to their narrow target in the etiology of AD. Therefore, our aim is to identify a safe and potent treatment for Alzheimer's disease. We chose the ursolic acid (UA) and its similar compounds as a compounds' library. And the ChEMBL database was adopted to obtain the active and inactive chemicals against Keap1. The best Quantitative structure-activity relationship (QSAR) model was created by evaluating standard machine learning techniques, and the best model has the lowest RMSE and greatest R2 (Random Forest Regressor). We chose pIC50 of 6.5 as threshold, where the top five potent medicines (DB06841, DB04310, DB11784, DB12730, and DB12677) with the highest predicted pIC50 (7.091184, 6.900866, 6.800155, 6.768965, and 6.756439) based on QSAR analysis. Furthermore, the top five medicines utilize as ligand molecules were docked in Keap1's binding region. The structural stability of the nominated medications was then evaluated using molecular dynamics simulations, RMSD, RMSF, Rg, and hydrogen bonding. All models are stable at 20 ns during simulation, with no major fluctuations observed. Finally, the top five medications are shown as prospective inhibitors of Keap1 and are the most promising to battle AD.
Collapse
Affiliation(s)
- Nobendu Mukerjee
- Department of Microbiology, West Bengal State University, Kolkata, India,Department of Health Sciences, Novel Global Community Educational Foundation, Hebersham, NSW, Australia
| | | | - Swastika Maitra
- Department of Microbiology, Adamas University, Kolkata, India
| | | | - Punya Sachdeva
- Amity Institute of Neuropsychology and Neurosciences, Amity University, Noida, India
| | - Arabinda Ghosh
- Microbiology Division, Department of Botany, Gauhati University, Guwahati, India
| | - Rahul Subhash Buchade
- Department of Pharmaceutical Chemistry, SCES’s Indira College of Pharmacy “Niramay”, Pune, India
| | - Somdatta Yashwant Chaudhari
- Department of Pharmaceutical Chemistry, Progressive Education Society’s Modern College of Pharmacy, Pune, India
| | - Shailaja B. Jadhav
- Department of Pharmaceutical Chemistry, Progressive Education Society’s Modern College of Pharmacy, Pune, India
| | - Padmashree Das
- Center for Biotechnology and Bioinformatics, Dibrugarh University, Dibrugarh, India
| | - Mohammad Mehedi Hasan
- Department of Biochemistry and Molecular Biology, Faculty of Life Science, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | - Md. Habibur Rahman
- Department of Global Medical Science, Wonju College of Medicine, Yonsei University, Wonju-si, South Korea
| | - Ghadeer M. Albadrani
- Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Ahmed E. Altyar
- Department of Pharmacy Practice, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohamed Kamel
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Mohammad Algahtani
- Department of Laboratory and Blood Bank, Security Forces Hospital, Mecca, Saudi Arabia
| | - Khlood Shinan
- Department of Computer Science, College Computer Science in Al-Leith, Umm Al-Qura University, Mecca, Saudi Arabia
| | - Abdulrahman Theyab
- Department of Laboratory and Blood Bank, Security Forces Hospital, Mecca, Saudi Arabia,College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Mohamed M. Abdel-Daim
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, Jeddah, Saudi Arabia,Department of Pharmacology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt,*Correspondence: Mohamed M. Abdel-Daim,
| | - Ghulam Md. Ashraf
- Department of Medical Laboratory Sciences, College of Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Md. Mominur Rahman
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Rohit Sharma
- Department of Rasa Shastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India,Rohit Sharma,
| |
Collapse
|
6
|
New N-Alkylated Heterocyclic Compounds as Prospective NDM1 Inhibitors: Investigation of In Vitro and In Silico Properties. Pharmaceuticals (Basel) 2022; 15:ph15070803. [PMID: 35890102 PMCID: PMC9322059 DOI: 10.3390/ph15070803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/21/2022] [Accepted: 06/21/2022] [Indexed: 02/06/2023] Open
Abstract
A new family of pyrazole-based compounds (1–15) was synthesized and characterized using different physicochemical analyses, such as FTIR, UV-Visible, 1H, 13C NMR, and ESI/LC-MS. The compounds were evaluated for their in vitro antifungal and antibacterial activities against several fungal and bacterial strains. The results indicate that some compounds showed excellent antibacterial activity against E. coli, S. aureus, C. freundii, and L. monocytogenes strains. In contrast, none of the compounds had antifungal activity. Molecular electrostatic potential (MEP) map analyses and inductive and mesomeric effect studies were performed to study the relationship between the chemical structure of our compounds and the biological activity. In addition, molecular docking and virtual screening studies were carried out to rationalize the antibacterial findings to characterize the modes of binding of the most active compounds to the active pockets of NDM1 proteins.
Collapse
|
7
|
Rafi MO, Al-Khafaji K, Sarker MT, Taskin-Tok T, Rana AS, Rahman MS. Design of a multi-epitope vaccine against SARS-CoV-2: immunoinformatic and computational methods. RSC Adv 2022; 12:4288-4310. [PMID: 35425433 PMCID: PMC8981096 DOI: 10.1039/d1ra06532g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 01/23/2022] [Indexed: 12/17/2022] Open
Abstract
A novel infectious agent, SARS-CoV-2, is responsible for causing the severe respiratory disease COVID-19 and death in humans. Spike glycoprotein plays a key role in viral particles entering host cells, mediating receptor recognition and membrane fusion, and are considered useful targets for antiviral vaccine candidates. Therefore, computational techniques can be used to design a safe, antigenic, immunogenic, and stable vaccine against this pathogen. Drawing upon the structure of the S glycoprotein, we are trying to develop a potent multi-epitope subunit vaccine against SARS-CoV-2. The vaccine was designed based on cytotoxic T-lymphocyte and helper T-lymphocyte epitopes with an N-terminal adjuvant via conducting immune filters and an extensive immunoinformatic investigation. The safety and immunogenicity of the designed vaccine were further evaluated via using various physicochemical, allergenic, and antigenic characteristics. Vaccine-target (toll-like receptors: TLR2 and TLR4) interactions, binding affinities, and dynamical stabilities were inspected through molecular docking and molecular dynamic (MD) simulation methods. Moreover, MD simulations for dimeric TLRs/vaccine in the membrane-aqueous environment were performed to understand the differential domain organization of TLRs/vaccine. Further, dynamical behaviors of vaccine/TLR systems were inspected via identifying the key residues (named HUB nodes) that control interaction stability and provide a clear molecular mechanism. The obtained results from molecular docking and MD simulation revealed a strong and stable interaction between vaccine and TLRs. The vaccine's ability to stimulate the immune response was assessed by using computational immune simulation. This predicted a significant level of cytotoxic T cell and helper T cell activation, as well as IgG, interleukin 2, and interferon-gamma production. This study shows that the designed vaccine is structurally and dynamically stable and can trigger an effective immune response against viral infections.
Collapse
Affiliation(s)
- Md Oliullah Rafi
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology Jashore 7408 Bangladesh
- Bioinformatics and Microbial Biotechnology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology Jashore 7408 Bangladesh
| | - Khattab Al-Khafaji
- Department of Medical Laboratory Technology, AL-Nisour University College Baghdad Iraq
| | - Md Takim Sarker
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology Jashore 7408 Bangladesh
| | - Tugba Taskin-Tok
- Department of Bioinformatics and Computational Biology, Institute of Health Sciences, Gaziantep University Gaziantep 27310 Turkey
- Faculty of Arts and Sciences, Department of Chemistry, Gaziantep University Gaziantep Turkey
| | - Abdus Samad Rana
- School of Biotechnology, Jiangnan University Wuxi 214122 PR China
| | - Md Shahedur Rahman
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology Jashore 7408 Bangladesh
- Bioinformatics and Microbial Biotechnology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology Jashore 7408 Bangladesh
| |
Collapse
|
8
|
El-Mageed HRA, Abdelrheem DA, Rafi MO, Sarker MT, Al-Khafaji K, Hossain MJ, Capasso R, Emran TB. In Silico Evaluation of Different Flavonoids from Medicinal Plants for Their Potency against SARS-CoV-2. BIOLOGICS 2021; 1:416-434. [DOI: 10.3390/biologics1030024] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
The ongoing pandemic situation of COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a global threat to both the world economy and public health. Therefore, there is an urgent need to discover effective vaccines or drugs to fight against this virus. The flavonoids and their medicinal plant sources have already exhibited various biological effects, including antiviral, anti-inflammatory, antioxidant, etc. This study was designed to evaluate different flavonoids from medicinal plants as potential inhibitors against the spike protein (Sp) and main protease (Mpro) of SARS-CoV-2 using various computational approaches such as molecular docking, molecular dynamics. The binding affinity and inhibitory effects of all studied flavonoids were discussed and compared with some antiviral drugs that are currently being used in COVID-19 treatment namely favipiravir, lopinavir, and hydroxychloroquine, respectively. Among all studies flavonoids and proposed antiviral drugs, luteolin and mundulinol exhibited the highest binding affinity toward Mpro and Sp. Drug-likeness and ADMET studies revealed that the chosen flavonoids are safe and non-toxic. One hundred ns-MD simulations were implemented for luteolin-Mpro, mundulinol-Mpro, luteolin-Sp, and mundulinol-Sp complexes and the results revealed strong stability of these flavonoid-protein complexes. Furthermore, MM/PBSA confirms the stability of luteolin and mundulinol interactions within the active sites of this protein. In conclusion, our findings reveal that the promising activity of luteolin and mundulinol as inhibitors against COVID-19 via inhibiting the spike protein and major protease of SARS CoV-2, and we urge further research to achieve the clinical significance of our proposed molecular-based efficacy.
Collapse
|
9
|
Khan RA, Hossain R, Siyadatpanah A, Al-Khafaji K, Khalipha ABR, Dey D, Asha UH, Biswas P, Saikat ASM, Chenari HA, Wilairatana P, Islam MT. Diterpenes/Diterpenoids and Their Derivatives as Potential Bioactive Leads against Dengue Virus: A Computational and Network Pharmacology Study. Molecules 2021; 26:6821. [PMID: 34833913 PMCID: PMC8623982 DOI: 10.3390/molecules26226821] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/06/2021] [Accepted: 11/08/2021] [Indexed: 12/22/2022] Open
Abstract
Dengue fever is a dangerous infectious endemic disease that affects over 100 nations worldwide, from Africa to the Western Pacific, and is caused by the dengue virus, which is transmitted to humans by an insect bite of Aedes aegypti. Millions of citizens have died as a result of dengue fever and dengue hemorrhagic fever across the globe. Envelope (E), serine protease (NS3), RNA-directed RNA polymerase (NS5), and non-structural protein 1 (NS1) are mostly required for cell proliferation and survival. Some of the diterpenoids and their derivatives produced by nature possess anti-dengue viral properties. The goal of the computational study was to scrutinize the effectiveness of diterpenoids and their derivatives against dengue viral proteins through in silico study. Methods: molecular docking was performed to analyze the binding affinity of compounds against four viral proteins: the envelope (E) protein, the NS1 protein, the NS3 protein, and the NS5 protein. Results: among the selected drug candidates, triptolide, stevioside, alepterolic acid, sphaeropsidin A, methyl dodovisate A, andrographolide, caesalacetal, and pyrimethamine have demonstrated moderate to good binding affinities (-8.0 to -9.4 kcal/mol) toward the selected proteins: E protein, NS3, NS5, and NS1 whereas pyrimethamine exerts -7.5, -6.3, -7.8, and -6.6 kcal/mol with viral proteins, respectively. Interestingly, the binding affinities of these lead compounds were better than those of an FDA-approved anti-viral medication (pyrimethamine), which is underused in dengue fever. Conclusion: we can conclude that diterpenoids can be considered as a possible anti-dengue medication option. However, in vivo investigation is recommended to back up the conclusions of this study.
Collapse
Affiliation(s)
- Rasel Ahmed Khan
- Pharmacy Discipline, Life Science School, Khulna University, Khulna 9280, Bangladesh;
| | - Rajib Hossain
- Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Dhaka 8100, Bangladesh; (A.B.R.K.); (U.H.A.)
| | - Abolghasem Siyadatpanah
- Ferdows School of Paramedical and Health, Birjand University of Medical Sciences, Birjand 9717853577, Iran; (A.S.); (H.A.C.)
| | - Khattab Al-Khafaji
- Department of Medical Laboratory Technology, Al-Nisour University College, Baghdad 10001, Iraq;
| | - Abul Bashar Ripon Khalipha
- Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Dhaka 8100, Bangladesh; (A.B.R.K.); (U.H.A.)
| | - Dipta Dey
- Department of Biochemistry and Molecular Biology, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Dhaka 8100, Bangladesh; (D.D.); (A.S.M.S.)
| | - Umma Hafsa Asha
- Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Dhaka 8100, Bangladesh; (A.B.R.K.); (U.H.A.)
| | - Partha Biswas
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology (JUST), Jashore 7408, Bangladesh;
| | - Abu Saim Mohammad Saikat
- Department of Biochemistry and Molecular Biology, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Dhaka 8100, Bangladesh; (D.D.); (A.S.M.S.)
| | - Hadi Ahmadi Chenari
- Ferdows School of Paramedical and Health, Birjand University of Medical Sciences, Birjand 9717853577, Iran; (A.S.); (H.A.C.)
| | - Polrat Wilairatana
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Muhammad Torequl Islam
- Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Dhaka 8100, Bangladesh; (A.B.R.K.); (U.H.A.)
| |
Collapse
|
10
|
Hossain R, Al-Khafaji K, Khan RA, Sarkar C, Islam MS, Dey D, Jain D, Faria F, Akbor R, Atolani O, Oliveira SMR, Siyadatpanah A, Pereira MDL, Islam MT. Quercetin and/or Ascorbic Acid Modulatory Effect on Phenobarbital-Induced Sleeping Mice Possibly through GABA A and GABA B Receptor Interaction Pathway. Pharmaceuticals (Basel) 2021; 14:ph14080721. [PMID: 34451819 PMCID: PMC8398796 DOI: 10.3390/ph14080721] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 12/28/2022] Open
Abstract
Depressive disorder is a recurrent illness that affects large numbers of the general population worldwide. In recent years, the goal of depression treatment has moved from symptomatic response to that of full remission. However, treatment-resistant depression is a major challenge in the treatment of depression or depression-related disorders. Consensus opinion, therefore, suggests that effective combined aggressive initial treatment is the most appropriate strategy. This study aimed to evaluate the effects of quercetin (QUR) and/or ascorbic acid (AA) on Phenobarbital-induced sleeping mice. QUR (50 mg/kg) and/or AA (25 mg/kg) with or without intraperitoneally pre-treated with GABA receptor agonist (diazepam: 2 mg/kg, i.p.) or antagonist (Flumazenil: 2.5 mg/kg, i.p.) to underscore the effects, as well as the possible involvement of the GABA receptor in the modulatory action of QUR and AA in sleeping mice. Additionally, an in silico study was undertaken to predict the involvement of GABA receptors in the sleep mechanism. Findings suggest that the pretreatment of QUR and AA modulated the onset and duration of action of the standard drugs in experimental animals. The acute administration of QUR and/or AA significantly (p < 0.05) reversed the DZP-mediated onset of action and slightly reversed the duration of sleep time in comparison to the vehicle (control) group. A further combination of QUR or AA with the FLU resulted in an enhancement of the onset of action while reducing the duration of action, suggesting a FLU-like effect on the test animals. In in silico studies, AA and QUR showed good to moderate binding affinities with GABAA and GABAB receptors. Both QUR and AA produced a stimulatory-like effect on mice, possibly through the GABAA and GABAB receptor interaction pathways. Further studies are necessary to verify this activity and clarify the exact mechanism of action(s) involved.
Collapse
Affiliation(s)
- Rajib Hossain
- Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh; (R.H.); (C.S.); (M.S.I.); (F.F.); (R.A.)
| | - Khattab Al-Khafaji
- Department of Chemistry, Faculty of Arts and Sciences, Gaziantep University, 27310 Gaziantep, Turkey;
| | - Rasel Ahmed Khan
- Pharmacy Discipline, Life Science School, Khulna University, Khulna 9280, Bangladesh;
| | - Chandan Sarkar
- Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh; (R.H.); (C.S.); (M.S.I.); (F.F.); (R.A.)
| | - Md. Shahazul Islam
- Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh; (R.H.); (C.S.); (M.S.I.); (F.F.); (R.A.)
| | - Dipta Dey
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalgonj 8100, Bangladesh;
| | - Divya Jain
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Vanasthali 304022, Rajasthan, India;
| | - Farhana Faria
- Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh; (R.H.); (C.S.); (M.S.I.); (F.F.); (R.A.)
| | - Rukaya Akbor
- Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh; (R.H.); (C.S.); (M.S.I.); (F.F.); (R.A.)
| | - Olubunmi Atolani
- Department of Chemistry, University of Ilorin, Ilorin P.M.B. 1515, Nigeria;
| | - Sónia M. R. Oliveira
- CICECO-Aveiro Institute of Materials & Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal;
- Hunter Medical Research Institute, New Lambton, NSW 2305, Australia
| | - Abolghasem Siyadatpanah
- Ferdows School of Paramedical and Health, Birjand University of Medical Sciences, Birjand 9717853577, Iran;
| | - Maria de Lourdes Pereira
- CICECO-Aveiro Institute of Materials & Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal;
- Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal
- Correspondence: (M.d.L.P.); (M.T.I.)
| | - Muhammad Torequl Islam
- Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh; (R.H.); (C.S.); (M.S.I.); (F.F.); (R.A.)
- Correspondence: (M.d.L.P.); (M.T.I.)
| |
Collapse
|
11
|
Muhtar E, Wang M, Zhu H. In silico discovery of SARS-CoV-2 main protease inhibitors from the carboline and quinoline database. Future Virol 2021. [PMID: 34306166 PMCID: PMC8293686 DOI: 10.2217/fvl-2021-0099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 07/05/2021] [Indexed: 02/07/2023]
Abstract
Aim: SARS-CoV-2 caused more than 3.8 million deaths according to the WHO. In this urgent circumstance, we aimed at screening out potential inhibitors targeting the main protease of SARS-CoV-2. Materials & methods: An in-house carboline and quinoline database including carboline, quinoline and their derivatives was established. A virtual screening in carboline and quinoline database, 50 ns molecular dynamics simulations and molecular mechanics Poisson−Boltzmann surface area calculations were carried out. Results: The top 12 molecules were screened out preliminarily. The molecular mechanics Poisson−Boltzmann surface area ranking showed that p59_7m, p12_7e, p59_7k stood out with the lowest binding energies of -24.20, -17.98, -17.67 kcal/mol, respectively. Conclusion: The study provides powerful in silico results that indicate the selected molecules are valuable for further evaluation as SARS-CoV-2 main protease inhibitors.
Collapse
Affiliation(s)
- Eldar Muhtar
- Beijing Area Major Laboratory of Peptide & Small Molecular Drugs, Engineering Research Center of Endogenous Prophylactic of Ministry of Education of China, Beijing Laboratory of Biomedical Materials, College of Pharmaceutical Sciences of Capital Medical University, Beijing, 100069, China
| | - Mengyang Wang
- Beijing Area Major Laboratory of Peptide & Small Molecular Drugs, Engineering Research Center of Endogenous Prophylactic of Ministry of Education of China, Beijing Laboratory of Biomedical Materials, College of Pharmaceutical Sciences of Capital Medical University, Beijing, 100069, China
| | - Haimei Zhu
- Beijing Area Major Laboratory of Peptide & Small Molecular Drugs, Engineering Research Center of Endogenous Prophylactic of Ministry of Education of China, Beijing Laboratory of Biomedical Materials, College of Pharmaceutical Sciences of Capital Medical University, Beijing, 100069, China
| |
Collapse
|
12
|
Aldahham BJM, Al-Khafaji K, Saleh MY, Abdelhakem AM, Alanazi AM, Islam MA. Identification of naphthyridine and quinoline derivatives as potential Nsp16-Nsp10 inhibitors: a pharmacoinformatics study. J Biomol Struct Dyn 2020; 40:3899-3906. [PMID: 33252031 DOI: 10.1080/07391102.2020.1851305] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This research is a recent effort to explore some new heterocyclic compounds as novel and potential nonstructural protein-16-nonstructural protein-10 (Nsp16-Nsp10) inhibitors for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) inhibition. The SARS-CoV-2 is causative agent of coronavirus disease 2019 (COVID-19) pandemic. A set of 58 molecules belongs to the naphthyridine and quinoline derivatives have been recently synthesized and considered for structure-based virtual screening against Nsp16-Nsp10. Molecular docking was virtually performed to screen for anti-SARS-CoV-2 activity against Nsp16-Nsp10. Fourteen out of fifty-eight compounds were exhibited binding affinity higher than co-crystal bound ligand s-adenosylmethionine (SAM) toward Nsp16-Nsp10. Further, the in silico pharmacokinetics assessment was carried out and it was found that two molecules possess the acceptable pharmacokinetic profile, hence considered promising Nsp16-Nsp10 inhibitors. The binding interaction analysis was revealed some crucial binding interactions between the final selected two molecules and ligand-binding amino acid residues of Nsp16-Nsp10 protein. In order to explore the characteristics of the protein-ligand complex and how selected small molecules retained inside the receptor cavity in dynamic states, all-atoms conventional molecular dynamics (MD) simulation was performed. Several factors were obtained from the MD simulation trajectory evidently suggested the potentiality of the molecules and stability of the protein-ligand complex. Finally, the binding affinity of both molecules and SAM was explored through the MM-GBSA approach which explained that both molecules possess strong affection towards the Nsp16-Nsp10. Hence, from the pharmacoinformatics assessment, it can be concluded that both heterocyclic compounds might be crucial for SARS-CoV-2 inhibition, subjected to experimental validation.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Bilal J M Aldahham
- Department of Chemistry, College of Applied Sciences-Hit, University Of Anbar, Anbar, Hit, Iraq
| | - Khattab Al-Khafaji
- Department of Chemistry, College of Arts and Sciences, Gaziantep University, Gaziantep, Turkey
| | - Mohanad Yakdhan Saleh
- Department of Chemistry, College of Education for Pure Science, University of Mosul, Ninawa, Iraq
| | | | - Amer M Alanazi
- Pharmaceutical Chemistry Department, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Md Ataul Islam
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom.,School of Health Sciences, University of Kwazulu-Natal, Durban, South Africa.,Department of Chemical Pathology, Faculty of Health Sciences, University of Pretoria and National Health Laboratory Service Tshwane Academic Division, Pretoria, South Africa
| |
Collapse
|
13
|
Al-Khafaji K, Taskin Tok T. Amygdalin as multi-target anticancer drug against targets of cell division cycle: double docking and molecular dynamics simulation. J Biomol Struct Dyn 2020; 39:1965-1974. [DOI: 10.1080/07391102.2020.1742792] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Khattab Al-Khafaji
- Faculty of Arts and Sciences, Department of Chemistry, Gaziantep University, Gaziantep, Turkey
| | - Tugba Taskin Tok
- Faculty of Arts and Sciences, Department of Chemistry, Gaziantep University, Gaziantep, Turkey
- Institute of Health Sciences, Department of Bioinformatics and Computational Biology, Gaziantep University, Gaziantep, Turkey
| |
Collapse
|