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Mazur T, Malik M, Bieńko DC. The impact of chelating compounds on Cu 2+, Fe 2+/ 3+, and Zn 2+ ions in Alzheimer's disease treatment. J Inorg Biochem 2024; 257:112601. [PMID: 38744143 DOI: 10.1016/j.jinorgbio.2024.112601] [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: 03/18/2024] [Revised: 04/22/2024] [Accepted: 05/07/2024] [Indexed: 05/16/2024]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder characterized by the accumulation of amyloid - β extracellular plaques and tau interfibrillar tangles, leading to memory loss, cognitive decline, and behavioral changes. With dementia posing a growing global health concern, there is an urgent need for comprehensive strategies to address its challenges. The economic burden of dementia is projected to rise significantly, emphasizing the necessity for collaborative efforts in research and healthcare. In the United States alone, millions are affected by AD, with prevalence increasing with age and even affecting younger individuals. The complexity of AD involves intricate biological processes, including the aggregation of amyloid beta, oxidative stress, and metal ion dysregulation. Metal ions, particularly those from copper, iron, and zinc, play pivotal roles in AD pathology, influencing Aβ deposition and tau protein accumulation. Current treatments offer symptomatic relief but do not address the underlying disease mechanisms. This paper explores the potential of various chelating compounds to target metal ions involved in AD pathology. N-acylhydrazones, morpholine, chrysin, quinoline, oxindole, cyclam, catechol-based, and quinazolinone-based derivatives show promising chelation activity and therapeutic effects. Metal chelation therapy offers a targeted approach to AD treatment by addressing the core pathology. By selectively binding to metal ions implicated in disease progression, chelators may minimize side effects associated with broad-spectrum treatments. Additionally, chelators may offer neuroprotective effects beyond metal binding, further enhancing their therapeutic potential. Overall, metal chelation therapy presents a promising strategy in combating AD, with the potential to significantly impact disease progression and improve patient outcomes.
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Affiliation(s)
- Tomasz Mazur
- Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland.
| | - Magdalena Malik
- Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Dariusz C Bieńko
- Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
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2
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Yu N, Pasha M, Chua JJE. Redox changes and cellular senescence in Alzheimer's disease. Redox Biol 2024; 70:103048. [PMID: 38277964 PMCID: PMC10840360 DOI: 10.1016/j.redox.2024.103048] [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: 11/20/2023] [Revised: 01/08/2024] [Accepted: 01/16/2024] [Indexed: 01/28/2024] Open
Abstract
The redox process and cellular senescence are involved in a range of essential physiological functions. However, they are also implicated in pathological processes underlying age-related neurodegenerative disorders, including Alzheimer's disease (AD). Elevated levels of reactive oxygen species (ROS) are generated as a result of abnormal accumulation of beta-amyloid peptide (Aβ), tau protein, and heme dyshomeostasis and is further aggravated by mitochondria dysfunction and endoplasmic reticulum (ER) stress. Excessive ROS damages vital cellular components such as proteins, DNA and lipids. Such damage eventually leads to impaired neuronal function and cell death. Heightened oxidative stress can also induce cellular senescence via activation of the senescence-associated secretory phenotype to further exacerbate inflammation and tissue dysfunction. In this review, we focus on how changes in the redox system and cellular senescence contribute to AD and how they are affected by perturbations in heme metabolism and mitochondrial function. While potential therapeutic strategies targeting such changes have received some attention, more research is necessary to bring them into clinical application.
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Affiliation(s)
- Nicole Yu
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; LSI Neurobiology Programme, National University of Singapore, Singapore; Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Mazhar Pasha
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; LSI Neurobiology Programme, National University of Singapore, Singapore; Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - John Jia En Chua
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; LSI Neurobiology Programme, National University of Singapore, Singapore; Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore.
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3
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Jevtić II, Suručić RV, Tovilović-Kovačević G, Zogović N, Kostić-Rajačić SV, Andrić DB, Penjišević JZ. Multi-target potential of newly designed tacrine-derived cholinesterase inhibitors: Synthesis, computational and pharmacological study. Bioorg Med Chem 2024; 101:117649. [PMID: 38401458 DOI: 10.1016/j.bmc.2024.117649] [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: 11/20/2023] [Revised: 01/30/2024] [Accepted: 02/16/2024] [Indexed: 02/26/2024]
Abstract
Simple and scalable synthetic approach was used for the preparation of thirteen novel tacrine derivatives consisting of tacrine and N-aryl-piperidine-4-carboxamide moiety connected by a five-methylene group linker. An anti-Alzheimer disease (AD) potential of newly designed tacrine derivatives was evaluated against two important AD targets, acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE). In vitro pharmacological evaluation showed strong ChE inhibitory activity of all compounds, with IC50 values ranging from 117.5 to 455 nM for AChE and 34 to 324 nM for BuChE. As a representative of the series with the best cytotoxicity / ChE inhibitory activity ratio, expressed as the selectivity index (SI), 2-chlorobenzoyl derivative demonstrated mixed-type inhibition on AChE and BuChE, suggesting binding to both CAS and PAS of the enzymes. It also exhibited antioxidant capacity and neuroprotective potential against amyloid-β (Aβ) toxicity in the culture of neuron-like cells. In-depth computational analysis corroborated well with in vitro ChE inhibition, illuminating that all compounds exhibit significant potential in targeting both enzymes. Molecular dynamics (MD) simulations revealed that 2-chlorobenzoyl derivative, created complexes with AChE and BuChE that demonstrated sufficient stability throughout the observed MD simulation. Computationally predicted ADME properties indicated that these compounds should have good blood-brain barrier (BBB) permeability, an important factor for CNS-targeting drugs. Overall, all tested compounds showed promising pharmacological behavior, highlighting the multi-target potential of 2-chlorobenzoyl derivative which should be further investigated as a new lead in the drug development process.
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Affiliation(s)
- Ivana I Jevtić
- University of Belgrade-Institute of Chemistry, Technology and Metallurgy, Department of Chemistry, Njegoševa 12, 11000 Belgrade, Serbia.
| | - Relja V Suručić
- University of Banja Luka, Faculty of Medicine, Save Mrkalja 14, 78000 Banja Luka, Bosnia and Herzegovina.
| | - Gordana Tovilović-Kovačević
- University of Belgrade-Institute for Biological Research "Siniša Stanković"-National Institute of the Republic of Serbia, Bulevar despota Stefana 142, 11108 Belgrade, Serbia.
| | - Nevena Zogović
- University of Belgrade-Institute for Biological Research "Siniša Stanković"-National Institute of the Republic of Serbia, Bulevar despota Stefana 142, 11108 Belgrade, Serbia.
| | - Slađana V Kostić-Rajačić
- University of Belgrade-Institute of Chemistry, Technology and Metallurgy, Department of Chemistry, Njegoševa 12, 11000 Belgrade, Serbia.
| | - Deana B Andrić
- University of Belgrade, Faculty of Chemistry, Department of Organic chemistry, Studentski trg 12-16, 11158 Belgrade, Serbia.
| | - Jelena Z Penjišević
- University of Belgrade-Institute of Chemistry, Technology and Metallurgy, Department of Chemistry, Njegoševa 12, 11000 Belgrade, Serbia.
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Swain S, Sen A, Metya AK. Rational design for novel heterocyclic based Donepezil analogs for Alzheimer's disease: an in silico approach. J Biomol Struct Dyn 2024:1-12. [PMID: 38260972 DOI: 10.1080/07391102.2024.2306200] [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: 06/09/2023] [Accepted: 01/10/2024] [Indexed: 01/24/2024]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disease and has devastating impacts on the elderly population. During the last two decades, there has been a significant focus on developing effective and safe treatments for AD. Acetylcholinesterase (AChE) has been identified as one of the primary therapeutic targets for developing drug candidates for AD. However, there is still a need for more efficient therapies. In this study, our aim is to design a new series of heterocyclic-based AChE inhibitors inspired by a standard drug. Here, we carried out molecular docking, drug-likeliness characteristics, and molecular dynamics (MD) to predict important pharmacophore features and understand the inhibitory mechanism of the designed inhibitors towards the AChE. We have designed 112 new derivatives by replacing the piperidine moiety of Donepezil with the different five and six-membered heterocyclic rings and selected 15 compounds that show higher or comparable docking scores as compared to standard Donepezil and pose no risk for carcinogenicity. Furthermore, MD results imply the structural stability of the selected docked complexes and seven exhibit a stronger binding affinity towards the AChE than Donepezil. Thus, heterocyclic-based derivatives based on oxazole, pyrazole, and tetrahydropyran may be potential therapeutic candidates for AD. Our structure-based drug design approach allows us to identify and gain insight into the structural stability of the inhibitor-protein complex and the inhibition mechanism of the newly designed inhibitors. The present finding might be an initial selection for developing a new inhibitor for AD and provide a direction for further experiments on its biological activities.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sunandini Swain
- Department of Chemical and Biochemical Engineering, Indian Institute of Technology Patna, Patna, India
| | - Anik Sen
- Department of Chemistry (CMDD Lab), GSS, GITAM (Deemed to Be University), Visakhapatnam, AP, India
| | - Atanu K Metya
- Department of Chemical and Biochemical Engineering, Indian Institute of Technology Patna, Patna, India
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Singh YP, Kumar N, Chauhan BS, Garg P. Carbamate as a potential anti-Alzheimer's pharmacophore: A review. Drug Dev Res 2023; 84:1624-1651. [PMID: 37694498 DOI: 10.1002/ddr.22113] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/20/2023] [Accepted: 08/30/2023] [Indexed: 09/12/2023]
Abstract
Alzheimer's disease (AD) is a progressive age-related neurodegenerative brain disorder, which leads to loss of memory and other cognitive dysfunction. The underlying mechanisms of AD pathogenesis are very complex and still not fully explored. Cholinergic neuronal loss, accumulation of amyloid plaque, metal ions dyshomeostasis, tau hyperphosphorylation, oxidative stress, neuroinflammation, and mitochondrial dysfunction are major hallmarks of AD. The current treatment options for AD are acetylcholinesterase inhibitors (donepezil, rivastigmine, and galantamine) and NMDA receptor antagonists (memantine). These FDA-approved drugs mainly provide symptomatic relief without addressing the pathological aspects of disease progression. So, there is an urgent need for novel drug development that not only addresses the basic mechanisms of the disease but also shows the neuroprotective property. Various research groups across the globe are working on the development of multifunctional agents for AD amelioration using different core scaffolds for their design, and carbamate is among them. Rivastigmine was the first carbamate drug investigated for AD management. The carbamate fragment, a core scaffold of rivastigmine, act as a potential inhibitor of acetylcholinesterase. In this review, we summarize the last 10 years of research conducted on the modification of carbamate with different substituents which primarily target ChE inhibition, reduce oxidative stress, and modulate Aβ aggregation.
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Affiliation(s)
- Yash Pal Singh
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Navneet Kumar
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Punjab, India
| | | | - Prabha Garg
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Punjab, India
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Bappi MH, Prottay AAS, Kamli H, Sonia FA, Mia MN, Akbor MS, Hossen MM, Awadallah S, Mubarak MS, Islam MT. Quercetin Antagonizes the Sedative Effects of Linalool, Possibly through the GABAergic Interaction Pathway. Molecules 2023; 28:5616. [PMID: 37513487 PMCID: PMC10384931 DOI: 10.3390/molecules28145616] [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: 06/09/2023] [Revised: 07/15/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Sedatives promote calmness or sleepiness during surgery or severely stressful events. In addition, depression is a mental health issue that negatively affects emotional well-being. A group of drugs called anti-depressants is used to treat major depressive illnesses. The aim of the present work was to evaluate the effects of quercetin (QUR) and linalool (LIN) on thiopental sodium (TS)-induced sleeping mice and to investigate the combined effects of these compounds using a conventional co-treatment strategy and in silico studies. For this, the TS-induced sleeping mice were monitored to compare the occurrence, latency, and duration of the sleep-in response to QUR (10, 25, 50 mg/kg), LIN (10, 25, 50 mg/kg), and diazepam (DZP, 3 mg/kg, i.p.). Moreover, an in silico investigation was undertaken to assess this study's putative modulatory sedation mechanism. For this, we observed the ability of test and standard medications to interact with various gamma-aminobutyric acid A receptor (GABAA) subunits. Results revealed that QUR and LIN cause dose-dependent antidepressant-like and sedative-like effects in animals, respectively. In addition, QUR-50 mg/kg and LIN-50 mg/kg and/or DZP-3 mg/kg combined were associated with an increased latency period and reduced sleeping times in animals. Results of the in silico studies demonstrated that QUR has better binding interaction with GABAA α3, β1, and γ2 subunits when compared with DZP, whereas LIN showed moderate affinity with the GABAA receptor. Taken together, the sleep duration of LIN and DZP is opposed by QUR in TS-induced sleeping mice, suggesting that QUR may be responsible for providing sedation-antagonizing effects through the GABAergic interaction pathway.
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Affiliation(s)
- Mehedi Hasan Bappi
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
| | - Abdullah Al Shamsh Prottay
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
| | - Hossam Kamli
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha 61421, Saudi Arabia
| | - Fatema Akter Sonia
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
| | - Md Nayem Mia
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
| | - Md Showkoth Akbor
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
| | - Md Munnaf Hossen
- School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC 3083, Australia
| | - Samir Awadallah
- Department of Medical Lab Sciences, Faculty of Allied Medical Sciences, Zarqa University, Zarqa 13110, Jordan
| | | | - Muhammad Torequl Islam
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
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Gade AC, Murahari M, Pavadai P, Kumar MS. Virtual Screening of a Marine Natural Product Database for In Silico Identification of a Potential Acetylcholinesterase Inhibitor. Life (Basel) 2023; 13:1298. [PMID: 37374081 DOI: 10.3390/life13061298] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/27/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Alzheimer's disease is characterized by amyloid-beta aggregation and neurofibrillary tangles. Acetylcholinesterase (AChE) hydrolyses acetylcholine and induces amyloid-beta aggregation. Acetylcholinesterase inhibitors (AChEI) inhibit this aggregation by binding to AChE, making it a potential target for the treatment of AD. In this study, we have focused on the identification of potent and safe AChEI from the Comprehensive Marine Natural Product Database (CMNPD) using computational tools. For the screening of CMNPD, a structure-based pharmacophore model was generated using a structure of AChE complexed with the co-crystallized ligand galantamine (PDB ID: 4EY6). The 330 molecules that passed through the pharmacophore filter were retrieved, their drug-likeness was determined, and they were then subjected to molecular docking studies. The top ten molecules were selected depending upon their docking score and were submitted for toxicity profiling. Based on these studies, molecule 64 (CMNPD8714) was found to be the safest and was subjected to molecular dynamics simulations and density functional theory calculations. This molecule showed stable hydrogen bonding and stacked interactions with TYR341, mediated through a water bridge. In silico results can be correlated with in vitro studies for checking its activity and safety in the future.
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Affiliation(s)
| | - Manikanta Murahari
- Department of Pharmacy, Koneru Lakshmaiah Education Foundation, Vaddeswaram 522302, India
| | - Parasuraman Pavadai
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bengaluru 560054, India
| | - Maushmi Shailesh Kumar
- Somaiya Institute of Research and Consultancy, Somaiya Vidyavihar University, Mumbai 400077, India
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Molecular docking and biological studies of the Cu(II) and Ni(II) macroacyclic complexes with 1,4-bis(o-aminobenzyl)-1,4-diazacycloheptane, a ligand containing the homopiperazine moiety. INORG CHEM COMMUN 2023. [DOI: 10.1016/j.inoche.2023.110392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Akash S, Hossain A, Mukerjee N, Sarker MMR, Khan MF, Hossain MJ, Rashid MA, Kumer A, Ghosh A, León-Figueroa DA, Barboza JJ, Padhi BK, Sah R. Modified coptisine derivatives as an inhibitor against pathogenic Rhizomucor miehei, Mycolicibacterium smegmatis (Black Fungus), Monkeypox, and Marburg virus by molecular docking and molecular dynamics simulation-based drug design approach. Front Pharmacol 2023; 14:1140494. [PMID: 37153804 PMCID: PMC10154673 DOI: 10.3389/fphar.2023.1140494] [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: 01/09/2023] [Accepted: 03/29/2023] [Indexed: 05/10/2023] Open
Abstract
During the second phase of SARS-CoV-2, an unknown fungal infection, identified as black fungus, was transmitted to numerous people among the hospitalized COVID-19 patients and increased the death rate. The black fungus is associated with the Mycolicibacterium smegmatis, Mucor lusitanicus, and Rhizomucor miehei microorganisms. At the same time, other pathogenic diseases, such as the Monkeypox virus and Marburg virus, impacted global health. Policymakers are concerned about these pathogens due to their severe pathogenic capabilities and rapid spread. However, no standard therapies are available to manage and treat those conditions. Since the coptisine has significant antimicrobial, antiviral, and antifungal properties; therefore, the current investigation has been designed by modifying coptisine to identify an effective drug molecule against Black fungus, Monkeypox, and Marburg virus. After designing the derivatives of coptisine, they have been optimized to get a stable molecular structure. These ligands were then subjected to molecular docking study against two vital proteins obtained from black fungal pathogens: Rhizomucor miehei (PDB ID: 4WTP) and Mycolicibacterium smegmatis (PDB ID 7D6X), and proteins found in Monkeypox virus (PDB ID: 4QWO) and Marburg virus (PDB ID 4OR8). Following molecular docking, other computational investigations, such as ADMET, QSAR, drug-likeness, quantum calculation and molecular dynamics, were also performed to determine their potentiality as antifungal and antiviral inhibitors. The docking score reported that they have strong affinities against Black fungus, Monkeypox virus, and Marburg virus. Then, the molecular dynamic simulation was conducted to determine their stability and durability in the physiological system with water at 100 ns, which documented that the mentioned drugs were stable over the simulated time. Thus, our in silico investigation provides a preliminary report that coptisine derivatives are safe and potentially effective against Black fungus, Monkeypox virus, and Marburg virus. Hence, coptisine derivatives may be a prospective candidate for developing drugs against Black fungus, Monkeypox and Marburg viruses.
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Affiliation(s)
- Shopnil Akash
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Arafat Hossain
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - Nobendu Mukerjee
- Department of Microbiology, West Bengal State University, Kolkata, West Bengal, India
- Department of Health Sciences, Novel Global Community Educational Foundation, Hebersham, NSW, Australia
| | - Md. Moklesur Rahman Sarker
- Health Med. Science Research Network, Dhaka, Bangladesh
- Department of Pharmacy, State University of Bangladesh, Dhaka, Bangladesh
| | | | - Md. Jamal Hossain
- Department of Pharmacy, State University of Bangladesh, Dhaka, Bangladesh
| | - Mohammad A. Rashid
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Dhaka, Dhaka, Bangladesh
| | - Ajoy Kumer
- Laboratory of Computational Research for Drug Design and Material Science, Department of Chemistry, European University of Bangladesh, Dhaka, Bangladesh
| | - Arabinda Ghosh
- Microbiology Division, Department of Botany, Gauhati University, Guwahati, Assam, India
| | | | - Joshuan J. Barboza
- Escuela de Medicina, Universidad Cesar Vallejo, Trujillo, Peru
- *Correspondence: Joshuan J. Barboza, ; Ranjit Sah,
| | - Bijaya Kumar Padhi
- Department of Community Medicine, School of Public Health, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Ranjit Sah
- Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
- Dr. D.Y Patil Medical College, Hospital and Research Centre, Pune, Maharashtra, India
- Green City Hospital, Tokha, Nepal
- *Correspondence: Joshuan J. Barboza, ; Ranjit Sah,
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Isolation and In Silico Prediction of Potential Drug-like Compounds with a New Dimeric Prenylated Quinolone Alkaloid from Zanthoxylum rhetsa (Roxb.) Root Extracts Targeted against SARS-CoV-2 (Mpro). Molecules 2022; 27:molecules27238191. [PMID: 36500282 PMCID: PMC9737416 DOI: 10.3390/molecules27238191] [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: 10/15/2022] [Revised: 11/06/2022] [Accepted: 11/09/2022] [Indexed: 11/27/2022] Open
Abstract
A new dimeric prenylated quinolone alkaloid, named 2,11-didemethoxy-vepridimerine A, was isolated from the root bark of Zanthoxylum rhetsa, together with twelve known compounds. The structure of the new compound was elucidated on the basis of spectroscopic investigations (NMR and Mass). The interaction of the isolated compounds with the main protease of SARS-CoV-2 (Mpro) was evaluated using molecular docking followed by MD simulations. The result suggests that 2,11-didemethoxy-vepridimerine A, the new compound, has the highest negative binding affinity against the Mpro with a free energy of binding of -8.5 Kcal/mol, indicating interaction with the Mpro. This interaction was further validated by 100 ns MD simulation. This implies that the isolated new compound, which can be employed as a lead compound for an Mpro-targeting drug discovery program, may be able to block the action of Mpro.
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Cabral MB, Dela Cruz CJ, Sato Y, Oyong G, Rempillo O, Galvez MC, Vallar E. In Silico Approach in the Evaluation of Pro-Inflammatory Potential of Polycyclic Aromatic Hydrocarbons and Volatile Organic Compounds through Binding Affinity to the Human Toll-Like Receptor 4. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19148360. [PMID: 35886213 PMCID: PMC9318662 DOI: 10.3390/ijerph19148360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 06/30/2022] [Accepted: 07/06/2022] [Indexed: 12/04/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) and volatile organic compounds (VOCs) are widespread across the globe, existing in the environment in complex mixtures potentially capable of initiating respiratory illnesses. Here, we use an in silico approach to evaluate the potential pro-inflammatory effects of various carcinogenic PAHs and VOCs through their binding affinity towards the human toll-like receptor 4 (TLR4). For receptors and ligands, RCSB Protein Data Bank and PubChem were used in obtaining their 3D structures, respectively. Autodock Vina was utilized to obtain the best docking poses and binding affinities of each PAH and VOC. Out of the 14 PAHs included in this study, indeno(1,2,3-cd)pyrene, benzo(ghi)perylene, and benzo[a]pyrene had the highest binding affinity values of −10, −9, and −8.9 kcal/mol, respectively. For the VOCs, out of the 10 compounds studied, benzene, 1,4-dichlorobenzene, and styrene had the highest binding affinity values of −3.6, −3.9, and −4.6 kcal/mol, respectively. Compounds with higher affinity than LPS (−4.1 kcal/com) could potentially induce inflammation, while compounds with lower affinity would be less likely to induce an inflammatory response. Meanwhile, molecular dynamics simulation and RMSF statistical analysis proved that the protein, TLR4, stably preserve its conformation despite ligand interactions. Overall, the structure of the TLR4 was considered inflexible.
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Affiliation(s)
- Marie Beatriz Cabral
- Environment and RemoTe Sensing Research (EARTH) Laboratory, Department of Physics, College of Science, De La Salle University Manila, 2401 Taft Avenue, Manila 0922, Philippines; (M.B.C.); (C.J.D.C.); (Y.S.); (O.R.); (M.C.G.)
| | - Celine Joy Dela Cruz
- Environment and RemoTe Sensing Research (EARTH) Laboratory, Department of Physics, College of Science, De La Salle University Manila, 2401 Taft Avenue, Manila 0922, Philippines; (M.B.C.); (C.J.D.C.); (Y.S.); (O.R.); (M.C.G.)
| | - Yumika Sato
- Environment and RemoTe Sensing Research (EARTH) Laboratory, Department of Physics, College of Science, De La Salle University Manila, 2401 Taft Avenue, Manila 0922, Philippines; (M.B.C.); (C.J.D.C.); (Y.S.); (O.R.); (M.C.G.)
| | - Glenn Oyong
- Molecular Science Unit Laboratory, Center for Natural Sciences and Ecological Research, De La Salle University, 2401 Taft Avenue, Manila 0922, Philippines;
| | - Ofelia Rempillo
- Environment and RemoTe Sensing Research (EARTH) Laboratory, Department of Physics, College of Science, De La Salle University Manila, 2401 Taft Avenue, Manila 0922, Philippines; (M.B.C.); (C.J.D.C.); (Y.S.); (O.R.); (M.C.G.)
| | - Maria Cecilia Galvez
- Environment and RemoTe Sensing Research (EARTH) Laboratory, Department of Physics, College of Science, De La Salle University Manila, 2401 Taft Avenue, Manila 0922, Philippines; (M.B.C.); (C.J.D.C.); (Y.S.); (O.R.); (M.C.G.)
| | - Edgar Vallar
- Environment and RemoTe Sensing Research (EARTH) Laboratory, Department of Physics, College of Science, De La Salle University Manila, 2401 Taft Avenue, Manila 0922, Philippines; (M.B.C.); (C.J.D.C.); (Y.S.); (O.R.); (M.C.G.)
- Correspondence:
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12
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Mahtarin R, Islam S, Islam MJ, Ullah MO, Ali MA, Halim MA. Structure and dynamics of membrane protein in SARS-CoV-2. J Biomol Struct Dyn 2022; 40:4725-4738. [PMID: 33353499 PMCID: PMC7784837 DOI: 10.1080/07391102.2020.1861983] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/05/2020] [Indexed: 12/15/2022]
Abstract
SARS-CoV-2 membrane (M) protein performs a variety of critical functions in virus infection cycle. However, the expression and purification of membrane protein structure is difficult despite tremendous progress. In this study, the 3 D structure is modeled followed by intensive validation and molecular dynamics simulation. The lack of suitable homologous templates (>30% sequence identities) leads us to construct the membrane protein models using template-free modeling (de novo or ab initio) approach with Robetta and trRosetta servers. Comparing with other model structures, it is evident that trRosetta (TM-score: 0.64; TM region RMSD: 2 Å) can provide the best model than Robetta (TM-score: 0.61; TM region RMSD: 3.3 Å) and I-TASSER (TM-score: 0.45; TM region RMSD: 6.5 Å). 100 ns molecular dynamics simulations are performed on the model structures by incorporating membrane environment. Moreover, secondary structure elements and principal component analysis (PCA) have also been performed on MD simulation data. Finally, trRosetta model is utilized for interpretation and visualization of interacting residues during protein-protein interactions. The common interacting residues including Phe103, Arg107, Met109, Trp110, Arg131, and Glu135 in the C-terminal domain of M protein are identified in membrane-spike and membrane-nucleocapsid protein complexes. The active site residues are also predicted for potential drug and peptide binding. Overall, this study might be helpful to design drugs and peptides against the modeled membrane protein of SARS-CoV-2 to accelerate further investigation. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rumana Mahtarin
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Shafiqul Islam
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Md. Jahirul Islam
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - M Obayed Ullah
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Md Ackas Ali
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Mohammad A. Halim
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
- Department of Physical Sciences, University of Arkansas - Fort Smith, Fort Smith, AR, USA
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13
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Ahmed AF, Wen ZH, Bakheit AH, Basudan OA, Ghabbour HA, Al-Ahmari A, Feng CW. A Major Diplotaxis harra-Derived Bioflavonoid Glycoside as a Protective Agent against Chemically Induced Neurotoxicity and Parkinson's Models; In Silico Target Prediction; and Biphasic HPTLC-Based Quantification. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11050648. [PMID: 35270118 PMCID: PMC8912516 DOI: 10.3390/plants11050648] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 05/15/2023]
Abstract
Oxidative stress and chronic inflammation have a role in developing neurodegenerative diseases such as Parkinson’s disease (PD) and inflammatory movement disorders such as rheumatoid arthritis that affect millions of populations. In searching for antioxidant and anti-inflammatory molecules from natural sources that can counteract neurodegenerative diseases and arthritis, the flavonoid-rich extract of Diplotaxis harra (DHE) was selected based on its in vitro antioxidant and anti-inflammatory activities. DHE could inhibit the inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2) expressions in the lipopolysaccharide (LPS)-stimulated RAW 264.7 macrophages from 100% to the level of 28.51 ± 18.67 and 30.19 ± 5.00% at 20 μg/mL, respectively. A TLC bioautography of DHE fractions using 1,1-diphenyl-2-picryl-hydrazyl radical (DPPH) led to the isolation of a major antioxidant compound which was identified by X-ray diffraction analysis as isorhamnetin-3-O-β-D-glucoside (IR3G). IR3G also exhibited a potent anti-inflammatory activity, particularly by suppressing the upregulation of iNOS expression, similar to that of dexamethasone (DEX) at 10 μM to the level of 35.96 ± 7.80 and 29.34 ± 6.34%, respectively. Moreover, IR3G displayed a strong neuroprotectivity (>60% at 1.0−4−1.0−3 μM) against 6-hydroxydopamine (6-OHDA)-challenged SHSY5Y neuroblastoma, an in vitro model of dopaminergic neurons for Parkinson’s disease (PD) research. Accordingly, the in vivo anti-Parkinson potentiality was evaluated, where it was found that IR3G successfully reversed the 6-OHDA-induced locomotor deficit in a zebrafish model. A study of molecular docking and molecular dynamic (MD) simulation of IR3G and its aglycone isorhamnetin (IR) against human acetylcholine esterase (AChE), monoamine oxidase B (MAO-B), and Polo-like kinase-2 (PLK2) was performed and further outlined a putative mechanism in modulating neurodegenerative diseases such as PD. The free radical scavenging, anti-inflammatory through anti-iNOS and anti-COX-2 expression, and neuroprotective activities assessed in this study would present partial evidence for the potentiality of D. harra-derived IR3G as a promising natural therapeutic agent against neurodegenerative diseases and inflammatory arthritis. Finally, a biphasic HPTLC method was developed to estimate the biomarker IR3G in D. harra quantitatively.
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Affiliation(s)
- Atallah F. Ahmed
- Department of Pharmacognosy, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia; (O.A.B.); (A.A.-A.)
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, El-Mansoura 35516, Egypt
- Correspondence:
| | - Zhi-Hong Wen
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung 804, Taiwan;
| | - Ahmed H. Bakheit
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia;
| | - Omer A. Basudan
- Department of Pharmacognosy, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia; (O.A.B.); (A.A.-A.)
| | - Hazem A. Ghabbour
- Department of Medicinal Chemistry, Faculty of Pharmacy, University of Mansoura, Mansoura 35516, Egypt;
| | - Abdullah Al-Ahmari
- Department of Pharmacognosy, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia; (O.A.B.); (A.A.-A.)
| | - Chien-Wei Feng
- Department of Obstetrics and Gynecology, Kaohsiung Medical University Hospital, Kaohsiung 807377, Taiwan;
- Center for Cancer Research, Kaohsiung Medical University, Kaohsiung 807377, Taiwan
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14
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Karunakaran KB, Thiyagaraj A, Santhakumar K. Novel insights on acetylcholinesterase inhibition by Convolvulus pluricaulis, scopolamine and their combination in zebrafish. NATURAL PRODUCTS AND BIOPROSPECTING 2022; 12:6. [PMID: 35212831 PMCID: PMC8881542 DOI: 10.1007/s13659-022-00332-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Acetylcholinesterase (AChE) inhibitors increase the retention of acetylcholine (ACh) in synapses. Although they alleviate cognitive deficits in Alzheimer's disease, their limited benefits warrant investigations of plant extracts with similar properties. We studied the anti-AChE activity of Convolvulus pluricaulis (CP) in a zebrafish model of cognitive impairment induced by scopolamine (SCOP). CP is a perennial herb with anti-amnesiac and anxiolytic properties. It contains alkaloid, anthocyanin, coumarin, flavonoid, phytosterol and triterpenoid components. Isoxazole (ISOX) was used as a positive control for AChE inhibition. CP-treated 168 hpf larvae showed a similar pattern of AChE inhibition (in the myelencephalon and somites) as that of ISOX-treated larvae. CP was superior to ISOX as evidenced by the retention of avoidance response behavior in adult zebrafish. Molecular docking studies indicated that ISOX binds Ser203 of the catalytic triad on the human AChE. The active components of CP-scopoletin and kaempferol-were bound by His447 of the catalytic triad, the anionic subsite of the catalytic center, and the peripheral anionic site. This suggested the ability of CP to mediate both competitive and non-competitive modes of inhibition. Surprisingly, SCOP showed AChE inhibition in larvae, possibly mediated via the choline-binding sites. CP + SCOP induced a concentration-dependent increase in AChE inhibition and ACh depletion. Abnormal motor responses were observed with ISOX, CP, ISOX + SCOP, and CP + SCOP, indicative of undesirable effects on the peripheral cholinergic system. Our study proposes the examination of CP, SCOP, and CP + SCOP as potential AChE inhibitors for their ability to modulate cognitive deficits.
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Affiliation(s)
| | - Anand Thiyagaraj
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, 603 203, India
| | - Kirankumar Santhakumar
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, 603 203, India.
- Zebrafish Genetics Laboratory, Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, 603 203, India.
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15
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Uelisson da Silva T, Tomaz da Silva E, de Carvalho Pougy K, Henrique da Silva Lima C, de Paula Machado S. Molecular modeling of indazole-3-carboxylic acid and its metal complexes (Zn, Ni, Co, Fe and Mn) as NO synthase inhibitors: DFT calculations, docking studies and molecular dynamics simulations. INORG CHEM COMMUN 2022. [DOI: 10.1016/j.inoche.2021.109120] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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16
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Rahman MM, Junaid M, Hosen SMZ, Mostafa M, Liu L, Benkendorff K. Mollusc-Derived Brominated Indoles for the Selective Inhibition of Cyclooxygenase: A Computational Expedition. Molecules 2021; 26:molecules26216538. [PMID: 34770946 PMCID: PMC8587571 DOI: 10.3390/molecules26216538] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/25/2021] [Accepted: 10/25/2021] [Indexed: 11/16/2022] Open
Abstract
Inflammation plays an important role in different chronic diseases. Brominated indoles derived from the Australian marine mollusk Dicathais orbita (D. orbita) are of interest for their anti-inflammatory properties. This study evaluates the binding mechanism and potentiality of several brominated indoles (tyrindoxyl sulfate, tyrindoleninone, 6-bromoisatin, and 6,6′-dibromoindirubin) against inflammatory mediators cyclooxygenases-1/2 (COX-1/2) using molecular docking, followed by molecular dynamics simulation, along with physicochemical, drug-likeness, pharmacokinetic (pk), and toxicokinetic (tk) properties. Molecular docking identified that these indole compounds are anchored, with the main amino acid residues, positioned in the binding pocket of the COX-1/2, required for selective inhibition. Moreover, the molecular dynamics simulation based on root mean square deviation (RMSD), radius of gyration (Rg), solvent accessible surface area (SASA), and root mean square fluctuation (RMSF) analyses showed that these natural brominated molecules transit rapidly to a progressive constant configuration during binding with COX-1/2 and seem to accomplish a consistent dynamic behavior by maintaining conformational stability and compactness. The results were comparable to the Food and Drug Administration (FDA)-approved selective COX inhibitor, aspirin. Furthermore, the free energy of binding for the compounds assessed by molecular mechanics–Poisson–Boltzmann surface area (MM–PBSA) confirmed the binding capacity of indoles towards COX-1/2, with suitable binding energy values except for the polar precursor tyrindoxyl sulfate (with COX-1). The physicochemical and drug-likeness analysis showed zero violations of Lipinski’s rule, and the compounds are predicted to have excellent pharmacokinetic profiles. These indoles are projected to be non-mutagenic and free from hepatotoxicity, with no inhibition of human ether-a-go–go gene (hERG) I inhibitors, and the oral acute toxicity LD50 in rats is predicted to be similar or lower than aspirin. Overall, this work has identified a plausible mechanism for selective COX inhibition by natural marine indoles as potential therapeutic candidates for the mitigation of inflammation.
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Affiliation(s)
- Md. Mominur Rahman
- Marine Ecology Research Centre, Faculty of Science and Engineering, Southern Cross University, Lismore, NSW 2480, Australia;
| | - Md. Junaid
- Molecular Modeling Drug-design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories Chattogram, Bangladesh Council of Scientific and Industrial Research, Chattogram 4217, Bangladesh; (M.J.); (S.M.Z.H.); (M.M.)
| | - S. M. Zahid Hosen
- Molecular Modeling Drug-design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories Chattogram, Bangladesh Council of Scientific and Industrial Research, Chattogram 4217, Bangladesh; (M.J.); (S.M.Z.H.); (M.M.)
- Pancreatic Research Group, South Western Sydney Clinical School, and Ingham Institute for AppliedMedical Research, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Mohammad Mostafa
- Molecular Modeling Drug-design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories Chattogram, Bangladesh Council of Scientific and Industrial Research, Chattogram 4217, Bangladesh; (M.J.); (S.M.Z.H.); (M.M.)
| | - Lei Liu
- Southern Cross Plant Science, Faculty of Science and Engineering, Southern Cross University, Lismore, NSW 2480, Australia;
| | - Kirsten Benkendorff
- Marine Ecology Research Centre, Faculty of Science and Engineering, Southern Cross University, Lismore, NSW 2480, Australia;
- National Marine Science Centre, Faculty of Science and Engineering, Southern Cross University, Coffs Harbour, NSW 2450, Australia
- Correspondence:
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17
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Ahmed S, Mahtarin R, Ahmed SS, Akter S, Islam MS, Mamun AA, Islam R, Hossain MN, Ali MA, Sultana MUC, Parves MDR, Ullah MO, Halim MA. Investigating the binding affinity, interaction, and structure-activity-relationship of 76 prescription antiviral drugs targeting RdRp and Mpro of SARS-CoV-2. J Biomol Struct Dyn 2021; 39:6290-6305. [PMID: 32720571 PMCID: PMC7441766 DOI: 10.1080/07391102.2020.1796804] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 07/13/2020] [Indexed: 12/23/2022]
Abstract
SARS-CoV-2 virus outbreak poses a major threat to humans worldwide due to its highly contagious nature. In this study, molecular docking, molecular dynamics, and structure-activity relationship are employed to assess the binding affinity and interaction of 76 prescription drugs against RNA dependent RNA polymerase (RdRp) and Main Protease (Mpro) of SARS-CoV-2. The RNA-dependent RNA polymerase is a vital enzyme of coronavirus replication/transcription complex whereas the main protease acts on the proteolysis of replicase polyproteins. Among 76 prescription antiviral drugs, four drugs (Raltegravir, Simeprevir, Cobicistat, and Daclatasvir) that are previously used for human immunodeficiency virus (HIV), hepatitis C virus (HCV), Ebola, and Marburg virus show higher binding energy and strong interaction with active sites of the receptor proteins. To explore the dynamic nature of the interaction, 100 ns molecular dynamics (MD) simulation is performed on the selected protein-drug complexes and apo-protein. Binding free energy of the selected drugs is performed by MM/PBSA. Besides docking and dynamics, partial least square (PLS) regression method is applied for the quantitative structure activity relationship to generate and predict the binding energy for drugs. PLS regression satisfactorily predicts the binding energy of the effective antiviral drugs compared to binding energy achieved from molecular docking with a precision of 85%. This study highly recommends researchers to screen these potential drugs in vitro and in vivo against SARS-CoV-2 for further validation of utility.
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Affiliation(s)
- Sinthyia Ahmed
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Rumana Mahtarin
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Sayeda Samina Ahmed
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Shaila Akter
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Md. Shamiul Islam
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Abdulla Al Mamun
- Key Laboratory of Soft Chemistry and Functional Materials of MOE, School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Rajib Islam
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Md Nayeem Hossain
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Md Ackas Ali
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Mossammad U. C. Sultana
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - MD. Rimon Parves
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - M. Obayed Ullah
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Mohammad A. Halim
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
- Department of Physical Sciences, University of Arkansas - Fort Smith, Fort Smith, Arkansas, USA
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18
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Ezaj MMA, Junaid M, Akter Y, Nahrin A, Siddika A, Afrose SS, Nayeem SMA, Haque MS, Moni MA, Hosen SMZ. Whole proteome screening and identification of potential epitopes of SARS-CoV-2 for vaccine design-an immunoinformatic, molecular docking and molecular dynamics simulation accelerated robust strategy. J Biomol Struct Dyn 2021; 40:6477-6502. [PMID: 33586620 DOI: 10.1080/07391102.2021.1886171] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the most cryptic pandemic outbreak of the 21st century, has gripped more than 1.8 million people to death and infected almost eighty six million. As it is a new variant of SARS, there is no approved drug or vaccine available against this virus. This study aims to predict some promising cytotoxic T lymphocyte epitopes in the SARS-CoV-2 proteome utilizing immunoinformatic approaches. Firstly, we identified 21 epitopes from 7 different proteins of SARS-CoV-2 inducing immune response and checked for allergenicity and conservancy. Based on these factors, we selected the top three epitopes, namely KAYNVTQAF, ATSRTLSYY, and LTALRLCAY showing functional interactions with the maximum number of MHC alleles and no allergenicity. Secondly, the 3D model of selected epitopes and HLA-A*29:02 were built and Molecular Docking simulation was performed. Most interestingly, the best two epitopes predicted by docking are part of two different structural proteins of SARS-CoV-2, namely Membrane Glycoprotein (ATSRTLSYY) and Nucleocapsid Phosphoprotein (KAYNVTQAF), which are generally target of choice for vaccine designing. Upon Molecular Docking, interactions between selected epitopes and HLA-A*29:02 were further validated by 50 ns Molecular Dynamics (MD) simulation. Analysis of RMSD, Rg, SASA, number of hydrogen bonds, RMSF, MM-PBSA, PCA, and DCCM from MD suggested that ATSRTLSYY is the most stable and promising epitope than KAYNVTQAF epitope. Moreover, we also identified B-cell epitopes for each of the antigenic proteins of SARS CoV-2. Findings of our work will be a good resource for wet lab experiments and will lessen the timeline for vaccine construction.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Md Muzahid Ahmed Ezaj
- Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh.,Reverse Vaccinology Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory, Chattogram, Bangladesh
| | - Md Junaid
- Reverse Vaccinology Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory, Chattogram, Bangladesh.,Molecular Modeling Drug-design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories Chattogram, Bangladesh Council of Scientific and Industrial Research, Chattogram, Bangladesh
| | - Yeasmin Akter
- Reverse Vaccinology Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory, Chattogram, Bangladesh.,Department of Biotechnology & Genetic Engineering, Noakhali Science & Technology University, Noakhali, Bangladesh
| | - Afsana Nahrin
- Department of Pharmacy, University of Science and Technology Chittagong, Chattogram, Bangladesh
| | - Aysha Siddika
- Reverse Vaccinology Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory, Chattogram, Bangladesh.,Department of Chemistry, University of Chittagong, Chattogram, Bangladesh
| | - Syeda Samira Afrose
- Reverse Vaccinology Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory, Chattogram, Bangladesh.,Department of Chemistry, University of Chittagong, Chattogram, Bangladesh
| | - S M Abdul Nayeem
- Reverse Vaccinology Research Division, Advanced Bioinformatics, Computational Biology and Data Science Laboratory, Chattogram, Bangladesh.,Department of Chemistry, University of Chittagong, Chattogram, Bangladesh
| | - Md Sajedul Haque
- Department of Chemistry, University of Chittagong, Chattogram, Bangladesh
| | - Mohammad Ali Moni
- WHO Collaborating Centre on eHealth, UNSW Digital Health, School of Public Health and Community Medicine, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - S M Zahid Hosen
- Molecular Modeling Drug-design and Discovery Laboratory, Pharmacology Research Division, BCSIR Laboratories Chattogram, Bangladesh Council of Scientific and Industrial Research, Chattogram, Bangladesh.,Pancreatic Research Group, South Western Sydney Clinical School, and Ingham Institute for Applied Medical Research, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
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19
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Kumar N, Gahlawat A, Kumar RN, Singh YP, Modi G, Garg P. Drug repurposing for Alzheimer’s disease: in silico and in vitro investigation of FDA-approved drugs as acetylcholinesterase inhibitors. J Biomol Struct Dyn 2020; 40:2878-2892. [DOI: 10.1080/07391102.2020.1844054] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Navneet Kumar
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Mohali, Punjab, India
| | - Anuj Gahlawat
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Mohali, Punjab, India
| | - Rajaram Naresh Kumar
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Mohali, Punjab, India
| | - Yash Pal Singh
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, Uttar Pradesh, India
| | - Gyan Modi
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, Uttar Pradesh, India
| | - Prabha Garg
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), S.A.S. Nagar, Mohali, Punjab, India
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20
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Hossain MJ, Rashid MA, Sultan MZ. Transition Metal Chelation Augments the Half-life of Secnidazole: Molecular Docking and Fluorescence Spectroscopic Approaches. Drug Res (Stuttg) 2020; 70:583-592. [PMID: 33098081 DOI: 10.1055/a-1252-2322] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
This current research aimed to establish the most required pharmacodynamics parameters of two transition metal complexes of an antimicrobial drug secnidazole. The spectroscopic fluorescence quenching strategy was outlined to evaluate the binding mechanism and binding affinity of nickel (II) and chromium (III) complexes of secnidazole with bovine serum albumin (BSA). The conformational modifications and the interacting patterns of the protein due to the interaction of the parent compound of the metal complexes have been investigated by molecular docking approach. The ligand-protein interactions were confirmed by the spectral quelling of the serum protein's intensity in the presence of metal chelate of secnidazole. The quenching mechanism was an endothermic dynamic process. The calculated thermodynamic factors delineated van der Waals interactions mainly influenced the spontaneous process. The UV-fluorescence curves were studied to establish the energy transformation profile according to the Förster resonance energy transfer (FRET) theory. The double-logarithm plot exhibited the binding number that ensured the drug-protein interaction was at a 1:1 ratio. The compared binding constants dictated that both metal chelates gained higher binding affinity, longer half-life, and achieved the capacity to show the pharmacological effects by a lower dose than the parent molecule.
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Affiliation(s)
- Md Jamal Hossain
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Dhaka, Dhaka-1000, Bangladesh.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Dhaka, Dhaka-1000, Bangladesh
| | - Mohammad A Rashid
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Dhaka, Dhaka-1000, Bangladesh
| | - Md Zakir Sultan
- Centre for Advanced Research in Sciences (CARS), University of Dhaka, Dhaka-1000, Bangladesh
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21
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Paul AS, Islam R, Parves MR, Mamun AA, Shahriar I, Hossain MI, Hossain MN, Ali MA, Halim MA. Cysteine focused covalent inhibitors against the main protease of SARS-CoV-2. J Biomol Struct Dyn 2020; 40:1639-1658. [PMID: 33047658 DOI: 10.1080/07391102.2020.1831610] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In viral replication and transcription, the main protease (Mpro) of SARS-CoV-2 plays an important role and appears to be a vital target for drug design. In Mpro, there is a Cys-His catalytic dyad, and ligands that interact with the Cys145 assumed to be an effective approach to inhibit the Mpro. In this study, approximately 1400 cysteine-focused ligands were screened to identify the best candidates that can act as potent inhibitors against Mpro. Our results show that the selected ligands strongly interact with the key Cys145 and His41 residues. Covalent docking was performed for the selected candidates containing the acrylonitrile group, which can form a covalent bond with Cys145. All atoms molecular dynamics (MD) simulation was performed on the selected four inhibitors including L1, L2, L3 and L4 to validate the docking interactions. Our results were also compared with a control ligand, α-ketoamide (11r). Principal component analysis on structural and energy data obtained from the MD trajectories shows that L1, L3, L4 and α-ketoamide (11r) have structural similarity with the apo-form of the Mpro. Quantitative structure-activity relationship method was employed for pattern recognition of the best ligands, which discloses that ligands containing acrylonitrile and amide warheads can show better performance. ADMET analysis displays that our selected candidates appear to be safer inhibitors. Our combined studies suggest that the best cysteine focused ligands can help to design an effective lead drug for COVID-19 treatment. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Archi Sundar Paul
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Rajib Islam
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Md Rimon Parves
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Abdulla Al Mamun
- Key Laboratory of Soft Chemistry and Functional Materials of MOE, School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Imrul Shahriar
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Md Imran Hossain
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Md Nayeem Hossain
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Md Ackas Ali
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Mohammad A Halim
- Division of Infectious Diseases and Division of Computer Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh.,Department of Physical Sciences, University of Arkansas-Fort Smith, Fort Smith, AR, USA
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22
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New coumarin-benzotriazole based hybrid molecules as inhibitors of acetylcholinesterase and amyloid aggregation. Bioorg Med Chem Lett 2020; 30:127477. [DOI: 10.1016/j.bmcl.2020.127477] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 08/01/2020] [Accepted: 08/05/2020] [Indexed: 11/21/2022]
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23
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Probing ferrocene-based thiosemicarbazones and their transition metal complexes as cholinesterase inhibitors. Inorganica Chim Acta 2020. [DOI: 10.1016/j.ica.2020.119658] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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24
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The inefficacy of donepezil on glycated-AChE inhibition: Binding affinity, complex stability and mechanism. Int J Biol Macromol 2020; 160:35-46. [PMID: 32454110 DOI: 10.1016/j.ijbiomac.2020.05.177] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/17/2020] [Accepted: 05/21/2020] [Indexed: 12/14/2022]
Abstract
Donepezil (DPZ) is a well-known drug for Alzheimer's disease that inhibits acetylcholinesterase activity (AChE). In the present study, the inhibitory effect of DPZ on non-enzymatic glycated-AChE (GLY-AChE) was studied by different experimental and simulation techniques. The initial investigation revealed that glycation process could reduce AChE activity approximately 60% in the pure enzyme and 38% in the extracted crude AChE from neural cells cultured in the presence of high glucose (HG) concentration. It is suggested that glycation of lysine residues on the structure of AChE could change the conformation of the active site (Trp-86 and His-447) in a way that the orientation of acetylcholine interrupted. The further studies indicated that DPZ is although a strong inhibitor for the native enzyme, it is not able to affect the GLY-AChE activity. The KD values of AChE-DPZ and GLY-AChE-DPZ complexes were estimated to be 1.88 × 10-9 and 2.10 × 10-6, respectively. The stability assessment showed that AChE-DPZ complex is more stable than the glycated complex. Our results indicate that, glycation process could impact on the conformation of the residues involved in the DPZ binding cavity on α-helix domain. Therefore, DPZ is not able to bind its specific cavity to induce its inhibitory effects on GLY-AChE.
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25
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Poeschl A, Mountford DM, Hider RC, Cilibrizzi A. Synthetic Approaches for Piperidone-Based Templates as Scaffolds to Access Chirally Enriched Donepezil Analogues. ACS OMEGA 2020; 5:2378-2396. [PMID: 32064399 PMCID: PMC7017409 DOI: 10.1021/acsomega.9b03808] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 12/31/2019] [Indexed: 06/10/2023]
Abstract
A concise and high-yielding double aza-Michael reaction is presented as an atom-efficient method to access chiral 2-substituted 4-piperidone building blocks from divinyl ketones. The piperidones were further converted into analogues of donepezil, an acetylcholinesterase inhibiting drug used in the treatment of Alzheimer's disease. The donepezil analogues were obtained as inseparable diastereomeric mixtures with resolved stereochemistry in position 2 of the piperidine ring. Biological evaluation of the acetylcholinesterase inhibition by these analogues provides a new insight into structure-activity relationship studies with regard to donepezil's piperidine moiety toward stereochemical enhancement.
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26
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Uddin N, Ahmed S, Khan AM, Mazharol Hoque M, Halim MA. Halogenated derivatives of methotrexate as human dihydrofolate reductase inhibitors in cancer chemotherapy. J Biomol Struct Dyn 2019; 38:901-917. [PMID: 30938661 DOI: 10.1080/07391102.2019.1591302] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Methotrexate is a widely used anti-metabolite in cancer chemotherapy. A series of halogenated drugs is designed from Methotrexate to assess their interactions with human dihydrofolate reductase. The aim of this study is to evaluate the performance of the modified drugs compared to the parent Methotrexate. Density Functional Theory is employed to optimize these drugs. Molecular docking calculation of these optimized drugs against dihydrofolate reductase is performed to find out binding affinity. In addition, molecular dynamics simulation is considered for the complexes of best two modified drugs with their receptors. Modifications by the halogens show significant changes in the charge distribution, dipole moment, thermodynamic stability, enthalpy and free energy. The highest binding affinity value (-36.401 KJ/mol) was obtained for M14. Hybrid quantum mechanics/molecular mechanics calculation shows a binding energy of -255.140 KJ/mol. Modified drugs have significant hydrogen and non-covalent bonding interactions with amino acids of the receptor. Molecular dynamics simulation disclosed that the root-mean-square-deviation of the alpha carbon associated with M6-1KMV and M14-1KMV complexes is 2.367 Å and 2.622 Å, respectively. Moreover, the interactions between modified drugs and receptor are mostly persevered in 25 nanosecond molecular dynamics simulation. Ensemble-based docking also confirmed that modified drugs show strong non-bonding interactions with different crystallographic and molecular dynamics based conformers. The best scored drugs show considerable pharmacokinetic properties. Modified derivatives M5, M6, M8, M10, M13 and M14 show the better binding affinity and a good number of hydrogen and other non-bonding interactions with the target protein which are similar to other anticancer drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nizam Uddin
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh.,Department of Pharmacy, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Sinthyia Ahmed
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Akib Mahmud Khan
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Mohammad Mazharol Hoque
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Mohammad A Halim
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
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