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Akash S, Hossain A, Hossain MS, Rahman MM, Ahmed MZ, Ali N, Valis M, Kuca K, Sharma R. Anti-viral drug discovery against monkeypox and smallpox infection by natural curcumin derivatives: A Computational drug design approach. Front Cell Infect Microbiol 2023; 13:1157627. [PMID: 37033493 PMCID: PMC10073709 DOI: 10.3389/fcimb.2023.1157627] [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: 02/02/2023] [Accepted: 03/02/2023] [Indexed: 04/11/2023] Open
Abstract
Background In the last couple of years, viral infections have been leading the globe, considered one of the most widespread and extremely damaging health problems and one of the leading causes of mortality in the modern period. Although several viral infections are discovered, such as SARS CoV-2, Langya Henipavirus, there have only been a limited number of discoveries of possible antiviral drug, and vaccine that have even received authorization for the protection of human health. Recently, another virial infection is infecting worldwide (Monkeypox, and Smallpox), which concerns pharmacists, biochemists, doctors, and healthcare providers about another epidemic. Also, currently no specific treatment is available against Monkeypox. This research gap encouraged us to develop a new molecule to fight against monkeypox and smallpox disease. So, firstly, fifty different curcumin derivatives were collected from natural sources, which are available in the PubChem database, to determine antiviral capabilities against Monkeypox and Smallpox. Material and method Preliminarily, the molecular docking experiment of fifty different curcumin derivatives were conducted, and the majority of the substances produced the expected binding affinities. Then, twelve curcumin derivatives were picked up for further analysis based on the maximum docking score. After that, the density functional theory (DFT) was used to determine chemical characterizations such as the highest occupied molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO), softness, and hardness, etc. Results The mentioned derivatives demonstrated docking scores greater than 6.80 kcal/mol, and the most significant binding affinity was at -8.90 kcal/mol, even though 12 molecules had higher binding scores (-8.00 kcal/mol to -8.9 kcal/mol), and better than the standard medications. The molecular dynamic simulation is described by root mean square deviation (RMSD) and root-mean-square fluctuation (RMSF), demonstrating that all the compounds might be stable in the physiological system. Conclusion In conclusion, each derivative of curcumin has outstanding absorption, distribution, metabolism, excretion, and toxicity (ADMET) characteristics. Hence, we recommended the aforementioned curcumin derivatives as potential antiviral agents for the treatment of Monkeypox and Smallpox virus, and more in vivo investigations are warranted to substantiate our findings.
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Affiliation(s)
- Shopnil Akash
- Department of Pharmacy, Faculty of Allied Health Science, Daffodil International University, Dhaka, Bangladesh
| | - Arafat Hossain
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - Md. Sarowar Hossain
- Department of Pharmacy, Faculty of Allied Health Science, Daffodil International University, Dhaka, Bangladesh
| | - Md. Mominur Rahman
- Department of Pharmacy, Faculty of Allied Health Science, Daffodil International University, Dhaka, Bangladesh
| | - Mohammad Z. Ahmed
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Nemat Ali
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Martin Valis
- Department of Neurology, Medical Faculty, Charles University and University Hospital in Hradec Králové, Hradec Králové, Czechia
| | - Kamil Kuca
- Department of Chemistry, Faculty of Science, University of Hradec Králové, Hradec Králové, Czechia
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czechia
| | - Rohit Sharma
- Department of Rasa Shastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
- *Correspondence: Rohit Sharma,
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Mirza AZ, Shamshad H, Osra FA, Habeebullah TM, Morad M. An overview of viruses discovered over the last decades and drug development for the current pandemic. Eur J Pharmacol 2021; 890:173746. [PMID: 33221318 PMCID: PMC8711773 DOI: 10.1016/j.ejphar.2020.173746] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/01/2020] [Accepted: 11/04/2020] [Indexed: 01/06/2023]
Abstract
Since the discovery of the yellow fever virus in 1901, thus far, two hundred nineteen viral species are recognized as human pathogens. Each year, the number of viruses causing infections in humans increases, triggering epidemics and pandemics, such as the current COVID-19 pandemic. Pointing to bats as the natural host, in 2019, a genome highly identical to a bat coronavirus (COVID-19) spread all over the world, and the World Health Organization (WHO) officially confirmed it as a pandemic. The virus mainly spreads through the respiratory tract, uses angiotensin-converting enzyme 2 (ACE2) as a receptor, and is characterized by symptoms of fever, cough, and fatigue. Antivirals and vaccines have provided improvements in some cases, but the discovery of a new and diverse variety of viruses with outbreaks has posed a challenge in timely treatments for medical scientists. Currently, few specific antiviral strategies are being used, and many of the effective antiviral drugs and reported active molecules are under vital exploration. In this review, with the details of viral diseases, we summarize the current attempts in drug development, epidemiology, and the latest treatments and scientific advancements to combat the COVID-19 epidemic. Moreover, we discuss ways to reduce epidemics and pandemics in the near future.
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Affiliation(s)
- Agha Zeeshan Mirza
- Chemistry Department, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia.
| | - Hina Shamshad
- Research Institute of Pharmaceutical Sciences, Faculty of Pharmacy, University of Karachi, Karachi, 75270, Pakistan
| | | | - Turki M Habeebullah
- Department of Environment and Health Research, Custodian of Two Holy Mosques Institute for Hajj and Umrah Research, Umm-Al-Qura University, Makkah, Saudi Arabia
| | - Moataz Morad
- Chemistry Department, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
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Ali S, Alamzeb M, Rashid MU, Setzer WN. Effect of Temperature on 1H NMR Spectra, Antitrypanosomal Activity, Conformational Analysis, and Molecular Docking of Curine Derivatives from Berberis brevissima. JOURNAL OF NATURAL PRODUCTS 2020; 83:1383-1393. [PMID: 32364734 DOI: 10.1021/acs.jnatprod.9b00397] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The ethanolic root extract of Berberis brevissima afforded a new bisbenzylisoquinoline alkaloid, 13-nitrochondrofoline (2), and two known bisbenzylisoquinoline alkaloids, chondrofoline (1) and curine (4). The acetylation of chondrofoline (1) gave O-acetylchondrofoline (3). The dimeric structures of 1 and 2 were studied through variable-temperature 1H NMR spectroscopy at 25, 40, 60, and 80 °C and conformational analysis, using density functional theory employing the M06-2X functional and the 6-31G* basis set. The in vitro antitrypanosomal activity of compounds 1, 2, 3, and 4 against Trypanosoma brucei showed significant potential with MIC values of 2.6, 2.2, 2.3, and 3.8 μM, respectively. Molecular docking evaluation of alkaloids 1, 2, 3, and 4 against known T. brucei protein targets revealed T. brucei phosphodiesterase B1 to be the preferred target. The docking energies of the alkaloids with Tb6PGL (PDB 3EB9) ranged from -88.8 to -106.0 kJ/mol and was comparable to the cocrystallized ligand, citrate (Edock = -78.3 kJ/mol). It seems reasonable that the curine alkaloids may compete with the natural substrates for these protein targets and serve as leads in designing and developing more potent and selective drugs against T. brucei.
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Affiliation(s)
- Saqib Ali
- Department of Chemistry, Faculty of Sciences, University of Kotli, Azad Jammu and Kashmir, Kotli 11100, Pakistan
| | - Muhammad Alamzeb
- Department of Chemistry, Faculty of Sciences, University of Kotli, Azad Jammu and Kashmir, Kotli 11100, Pakistan
| | - Mamoon Ur Rashid
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City 729000, Vietnam
| | - William N Setzer
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, Alabama 35899, United States
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Beig M, Oellien F, Garoff L, Noack S, Krauth-Siegel RL, Selzer PM. Trypanothione reductase: a target protein for a combined in vitro and in silico screening approach. PLoS Negl Trop Dis 2015; 9:e0003773. [PMID: 26042772 PMCID: PMC4456413 DOI: 10.1371/journal.pntd.0003773] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 04/21/2015] [Indexed: 12/04/2022] Open
Abstract
With the goal to identify novel trypanothione reductase (TR) inhibitors, we performed a combination of in vitro and in silico screening approaches. Starting from a highly diverse compound set of 2,816 compounds, 21 novel TR inhibiting compounds could be identified in the initial in vitro screening campaign against T. cruzi TR. All 21 in vitro hits were used in a subsequent similarity search-based in silico screening on a database containing 200,000 physically available compounds. The similarity search resulted in a data set containing 1,204 potential TR inhibitors, which was subjected to a second in vitro screening campaign leading to 61 additional active compounds. This corresponds to an approximately 10-fold enrichment compared to the initial pure in vitro screening. In total, 82 novel TR inhibitors with activities down to the nM range could be identified proving the validity of our combined in vitro/in silico approach. Moreover, the four most active compounds, showing IC50 values of <1 μM, were selected for determining the inhibitor constant. In first on parasites assays, three compounds inhibited the proliferation of bloodstream T. brucei cell line 449 with EC50 values down to 2 μM.
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Affiliation(s)
- Mathias Beig
- MSD Animal Health Innovation GmbH, Zur Propstei, Schwabenheim, Germany
| | - Frank Oellien
- MSD Animal Health Innovation GmbH, Zur Propstei, Schwabenheim, Germany
| | - Linnéa Garoff
- Universität Heidelberg, Biochemie-Zentrum (BZH), Heidelberg, Germany
| | - Sandra Noack
- MSD Animal Health Innovation GmbH, Zur Propstei, Schwabenheim, Germany
| | | | - Paul M. Selzer
- MSD Animal Health Innovation GmbH, Zur Propstei, Schwabenheim, Germany
- Universität Tübingen, Interfakultäres Institut für Biochemie, Tübingen, Germany
- Wellcome Trust Centre for Molecular Parasitology, Division of Infection, Immunity and Inflammation, Faculty of Biomedical & Life Sciences, University of Glasgow, Glasgow, United Kingdom
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Meng F, Dai E, Yu X, Zhang Y, Chen X, Liu X, Wang S, Wang L, Jiang W. Constructing and characterizing a bioactive small molecule and microRNA association network for Alzheimer's disease. J R Soc Interface 2013; 11:20131057. [PMID: 24352679 DOI: 10.1098/rsif.2013.1057] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Alzheimer's disease (AD) is an incurable neurodegenerative disorder. Much effort has been devoted to developing effective therapeutic agents. Recently, targeting microRNAs (miRNAs) with small molecules has become a novel therapy for human diseases. In this study, we present a systematic computational approach to construct a bioactive Small molecule and miRNA association Network in AD (SmiRN-AD), which is based on the gene expression signatures of bioactive small molecule perturbation and AD-related miRNA regulation. We also performed topological and functional analysis of the SmiRN-AD from multiple perspectives. At the significance level of p ≤ 0.01, 496 small molecule-miRNA associations, including 25 AD-related miRNAs and 275 small molecules, were recognized and used to construct the SmiRN-AD. The drugs that were connected with the same miRNA tended to share common drug targets (p = 1.72 × 10(-4)) and belong to the same therapeutic category (p = 4.22 × 10(-8)). The miRNAs that were linked to the same small molecule regulated more common miRNA targets (p = 6.07 × 10(-3)). Further analysis of the positive connections (quinostatin and miR-148b, amantadine and miR-15a) and the negative connections (melatonin and miR-30e-5p) indicated that our large-scale predictions afforded specific biological insights into AD pathogenesis and therapy. This study proposes a holistic strategy for deciphering the associations between small molecules and miRNAs in AD, which may be helpful for developing a novel effective miRNA-associated therapeutic strategy for AD. A comprehensive database for the SmiRN-AD and the differential expression patterns of the miRNA targets in AD is freely available at http://bioinfo.hrbmu.edu.cn/SmiRN-AD/.
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Affiliation(s)
- Fanlin Meng
- College of Bioinformatics Science and Technology, Harbin Medical University, , 194 Xuefu Road, Harbin 150081, People's Republic of China
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Koch O, Jäger T, Heller K, Khandavalli PC, Pretzel J, Becker K, Flohé L, Selzer PM. Identification of M. tuberculosis Thioredoxin Reductase Inhibitors Based on High-Throughput Docking Using Constraints. J Med Chem 2013; 56:4849-59. [DOI: 10.1021/jm3015734] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Oliver Koch
- MSD Animal Health Innovation GmbH, Schwabenheim, Germany
- MOLISA GmbH, Magdeburg,
Germany
| | - Timo Jäger
- MOLISA GmbH, Magdeburg,
Germany
- Helmholtz Zentrum für Infektionsforschung, Braunschweig, Germany
| | | | | | - Jette Pretzel
- Biochemie und Molekularbiologie, Justus-Liebig-Universität, Giessen, Germany
| | - Katja Becker
- Biochemie und Molekularbiologie, Justus-Liebig-Universität, Giessen, Germany
| | | | - Paul M. Selzer
- MSD Animal Health Innovation GmbH, Schwabenheim, Germany
- Interfakultäres
Institut für
Biochemie, Universität Tübingen, Tübingen, Germany
- Wellcome Trust Centre for Molecular
Parasitology and Division of Infection and Immunity, University of Glasgow, Glasgow, U.K
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