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Pereira D, Palmeira A, Lima É, Vasconcelos V, Pinto M, Correia-da-Silva M, Almeida JR, Cidade H. Chalcone derivatives as promising antifoulants: Molecular optimization, bioactivity evaluation and performance in coatings. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 280:116560. [PMID: 38865941 DOI: 10.1016/j.ecoenv.2024.116560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 06/14/2024]
Abstract
Marine biofouling remains a huge concern for maritime industries and for environmental health. Although the current biocide-based antifouling coatings can prevent marine biofouling, their use has been associated with toxicity for the marine environment, being urgent to find sustainable alternatives. Previously, our research group has identified a prenylated chalcone (1) with promising antifouling activity against the settlement of larvae of the macrofouling species Mytilus galloprovincialis (EC50 = 16.48 µM and LC50 > 200 µM) and lower ecotoxicity when compared to Econea®, a commercial antifouling agent in use. Herein, a series of chalcone 1 analogues were designed and synthesized in order to obtain optimized antifouling compounds with improved potency while maintaining low ecotoxicity. Compounds 8, 15, 24, and 27 showed promising antifouling activity against the settlement of M. galloprovincialis larvae, being dihydrochalcone 27 the most potent. The effect of compound 24 was associated with the inhibition of acetylcholinesterase activity. Among the synthesized compounds, compound 24 also showed potent complementary activity against Navicula sp. (EC50 = 4.86 µM), similarly to the lead chalcone 1 (EC50 = 6.75 µM). Regarding the structure-activity relationship, the overall results demonstrate that the substitution of the chalcone of the lead compound 1 by a dihydrochalcone scaffold resulted in an optimized potency against the settlement of mussel larvae. Marine polyurethane (PU)-based coatings containing the best performed compound concerning anti-settlement activity (dihydrochalcone 27) were prepared, and mussel larvae adherence was reduced compared to control PU coatings.
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Affiliation(s)
- Daniela Pereira
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira 228, Porto 4050-313, Portugal; Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Edifício do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, Matosinhos 4450-208, Portugal
| | - Andreia Palmeira
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira 228, Porto 4050-313, Portugal; Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Edifício do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, Matosinhos 4450-208, Portugal
| | - Érica Lima
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Edifício do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, Matosinhos 4450-208, Portugal
| | - Vitor Vasconcelos
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Edifício do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, Matosinhos 4450-208, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, Porto 4069-007, Portugal
| | - Madalena Pinto
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira 228, Porto 4050-313, Portugal; Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Edifício do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, Matosinhos 4450-208, Portugal
| | - Marta Correia-da-Silva
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira 228, Porto 4050-313, Portugal; Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Edifício do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, Matosinhos 4450-208, Portugal
| | - Joana R Almeida
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Edifício do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, Matosinhos 4450-208, Portugal.
| | - Honorina Cidade
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira 228, Porto 4050-313, Portugal; Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Edifício do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, Matosinhos 4450-208, Portugal.
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Bandiwadekar A, Jose J, Gopan G, Augustin V, Ashtekar H, Khot KB. Transdermal delivery of resveratrol loaded solid lipid nanoparticle as a microneedle patch: a novel approach for the treatment of Parkinson's disease. Drug Deliv Transl Res 2024:10.1007/s13346-024-01656-0. [PMID: 38949746 DOI: 10.1007/s13346-024-01656-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2024] [Indexed: 07/02/2024]
Abstract
Parkinson's disease (PD), affecting millions of people worldwide and expected to impact 10 million by 2030, manifests a spectrum of motor and non-motor symptoms linked to the decline of dopaminergic neurons. Current therapies manage PD symptoms but lack efficacy in slowing disease progression, emphasizing the urgency for more effective treatments. Resveratrol (RSV), recognized for its neuroprotective and antioxidative properties, encounters challenges in clinical use for PD due to limited bioavailability. Researchers have investigated lipid-based nanoformulations, specifically solid lipid nanoparticles (SLNs), to enhance RSV stability. Oral drug delivery via SLNs faces obstacles, prompting exploration into transdermal delivery using SLNs integrated with microneedles (MNs) for improved patient compliance. In this study, an RSV-loaded SLNs (RSV -SLNs) incorporated into the MN patch was developed for transdermal RSV delivery to improve its stability and patient compliance. Characterization studies demonstrated favorable physical properties of SLNs with a sustained drug release profile of 78.36 ± 0.74%. The developed MNs exhibited mechanical robustness and skin penetration capabilities. Ex vivo permeation studies displayed substantial drug permeation of 68.39 ± 1.4% through the skin. In an in vivo pharmacokinetic study, the RSV-SLNs delivered through MNs exhibited a significant increase in Cmax, Tmax, and AUC0 - t values, alongside a reduced elimination rate in blood plasma in contrast to the administration of pure RSV via MNs. Moreover, an in vivo study showcased enhanced behavioral functioning and increased brain antioxidant levels in the treated animals. In-vivo skin irritation study revealed no signs of irritation till 24 h which permits long-term MNs application. Histopathological analysis showed notable changes in the brain regions of the rat, specifically the striatum and substantia nigra, after the completion of the treatment. Based on these findings, the development of an RSV-SLN loaded MNs (RSVSNLMP) patch presents a novel approach, with the potential to enhance the drug's efficiency, patient compliance, and therapeutic outcomes for PD, offering a promising avenue for advanced PD therapy.
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Affiliation(s)
- Akshay Bandiwadekar
- NGSM Institute of Pharmaceutical Sciences, Department of Pharmaceutics,, NITTE Deemed-to-be University, Mangalore, 575018, India
| | - Jobin Jose
- NGSM Institute of Pharmaceutical Sciences, Department of Pharmaceutics,, NITTE Deemed-to-be University, Mangalore, 575018, India.
| | - Gopika Gopan
- NGSM Institute of Pharmaceutical Sciences, Department of Pharmaceutics,, NITTE Deemed-to-be University, Mangalore, 575018, India
| | - Varsha Augustin
- NGSM Institute of Pharmaceutical Sciences, NITTE Deemed-to-be University, Department of NITTE University Center for Animal Research & Experimentation (NUCARE), Mangalore, 575018, India
| | - Harsha Ashtekar
- NGSM Institute of Pharmaceutical Sciences, Department of Pharmacology, NITTE Deemed-to-be University, Mangalore, 575018, India
| | - Kartik Bhairu Khot
- NGSM Institute of Pharmaceutical Sciences, Department of Pharmaceutics,, NITTE Deemed-to-be University, Mangalore, 575018, India
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He J, Tam KY. Dual-target inhibitors of cholinesterase and GSK-3β to modulate Alzheimer's disease. Drug Discov Today 2024; 29:103914. [PMID: 38340951 DOI: 10.1016/j.drudis.2024.103914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/24/2024] [Accepted: 02/05/2024] [Indexed: 02/12/2024]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease that affects over 55 million patients worldwide. Most of the approved small-molecule drugs for AD have been designed to tackle a single pathological hallmark, such as cholinergic dysfunction or amyloid toxicity, and thus may not fully address the multifactorial nature of the disease. Inhibition of both cholinesterase and glycogen synthase kinase-3β (GSK-3β) has emerged as a promising strategy to modulate AD. However, the dual inhibition of these two targets posts challenges in molecular design: issues related to target engagements and biopharmaceutical properties in particular must be overcome. In this review, we discuss the physiopathological roles and structures of cholinesterase and GSK-3β as well as recently reported dual-target inhibitors. We critically evaluate the current status of the discovery of dual-target inhibitors of cholinesterase and GSK-3β, and highlight further perspectives.
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Affiliation(s)
- Junqiu He
- Faculty of Health Sciences, University of Macau SAR, Avenida de Universidade, Taipa, Macau SAR, China
| | - Kin Yip Tam
- Faculty of Health Sciences, University of Macau SAR, Avenida de Universidade, Taipa, Macau SAR, China.
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Jain U, Johari S, Srivastava P. Current Insights of Nanocarrier-Mediated Gene Therapeutics to Treat Potential Impairment of Amyloid Beta Protein and Tau Protein in Alzheimer's Disease. Mol Neurobiol 2024; 61:1969-1989. [PMID: 37831361 DOI: 10.1007/s12035-023-03671-7] [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: 07/19/2023] [Accepted: 09/20/2023] [Indexed: 10/14/2023]
Abstract
Alzheimer's disease (AD), is the major type of dementia and most progressive, irreversible widespread neurodegenerative disorder affecting the elderly worldwide. The prime hallmarks of Alzheimer's disease (AD) are beta-amyloid plaques (Aβ) and neurofibrillary tangles (NFT). In spite of recent advances and developments in targeting the hallmarks of AD, symptomatic medications that promise neuroprotective activity against AD are currently unable to treat degenerating brain clinically or therapeutically and show little efficacy. The extensive progress of AD therapies over time has resulted in the advent of disease-modifying medications with the potential to alleviate AD. However, due to the presence of a defensive connection between the vascular system and the neural tissues known as the blood-brain barrier (BBB), directing these medications to the site of action in the degenerating brain is the key problem. BBB acts as a highly selective semipermeable membrane that prevents any type of foreign substance from entering the microenvironment of neurons. To overcome this limitation, the revolutionary approach of nanoparticle(NP)/nanocarrier-mediated drug delivery system has marked the era with its unique property to cross, avoid, or disrupt the defensive BBB efficiently and release the modified drug at the target site of action. After comprehensive data mining, this review focuses on the detailed understanding of different types of nanoparticle(NP)/nanocarrier-mediated drug delivery system like liposomes, micelles, gold nanoparticles(NP), polymeric NPs, etc. which have promising potential in carrying the desired drug(cargo) to the location in the degenerated brain thus mitigating the Alzheimer's disease.
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Affiliation(s)
- Unnati Jain
- School of Biosciences, Institute of Management Studies Ghaziabad (University Courses Campus), Adhyatmik Nagar, NH09, Ghaziabad, Uttar Pradesh, India
| | - Surabhi Johari
- School of Biosciences, Institute of Management Studies Ghaziabad (University Courses Campus), Adhyatmik Nagar, NH09, Ghaziabad, Uttar Pradesh, India.
| | - Priyanka Srivastava
- School of Biosciences, Institute of Management Studies Ghaziabad (University Courses Campus), Adhyatmik Nagar, NH09, Ghaziabad, Uttar Pradesh, India.
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Boulaamane Y, Kandpal P, Chandra A, Britel MR, Maurady A. Chemical library design, QSAR modeling and molecular dynamics simulations of naturally occurring coumarins as dual inhibitors of MAO-B and AChE. J Biomol Struct Dyn 2024; 42:1629-1646. [PMID: 37199265 DOI: 10.1080/07391102.2023.2209650] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 04/05/2023] [Indexed: 05/19/2023]
Abstract
Coumarins are a highly privileged scaffold in medicinal chemistry. It is present in many natural products and is reported to display various pharmacological properties. A large plethora of compounds based on the coumarin ring system have been synthesized and were found to possess biological activities such as anticonvulsant, antiviral, anti-inflammatory, antibacterial, antioxidant as well as neuroprotective properties. Despite the wide activity spectrum of coumarins, its naturally occurring derivatives are yet to be investigated in detail. In the current study, a chemical library was created to assemble all chemical information related to naturally occurring coumarins from the literature. Additionally, a multi-stage virtual screening combining QSAR modeling, molecular docking, and ADMET prediction was conducted against monoamine oxidase B and acetylcholinesterase, two relevant targets known for their neuroprotective properties and 'disease-modifying' potential in Parkinson's and Alzheimer's disease. Our findings revealed ten coumarin derivatives that may act as dual-target drugs against MAO-B and AChE. Two coumarin candidates were selected from the molecular docking study: CDB0738 and CDB0046 displayed favorable interactions for both proteins as well as suitable ADMET profiles. The stability of the selected coumarins was assessed through 100 ns molecular dynamics simulations which revealed promising stability through key molecular interactions for CDB0738 to act as dual inhibitor of MAO-B and AChE. However, experimental studies are necessary to evaluate the bioactivity of the proposed candidate. The current results may generate an increasing interest in bioprospecting naturally occurring coumarins as potential candidates against relevant macromolecular targets by encouraging virtual screening studies against our chemical library.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yassir Boulaamane
- Laboratory of Innovative Technologies, National School of Applied Sciences of Tangier, Abdelmalek Essaadi University, Tetouan, Morocco
| | | | | | - Mohammed Reda Britel
- Laboratory of Innovative Technologies, National School of Applied Sciences of Tangier, Abdelmalek Essaadi University, Tetouan, Morocco
| | - Amal Maurady
- Laboratory of Innovative Technologies, National School of Applied Sciences of Tangier, Abdelmalek Essaadi University, Tetouan, Morocco
- Faculty of Sciences and Techniques of Tangier, Abdelmalek Essaadi University, Tetouan, Morocco
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6
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Veras JPC, França VLB, Carvalho HF, Freire VN. Noncovalent binding of carbofuran to acetylcholinesterase from Homo sapiens, Danio rerio, Apis mellifera and Caenorhabditis elegans: Homology modelling, molecular docking and dynamics, and quantum biochemistry description. Chem Biol Interact 2024; 388:110826. [PMID: 38101596 DOI: 10.1016/j.cbi.2023.110826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/16/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023]
Abstract
Although various regulatory agencies have banned or severely restricted the use of carbofuran (CAR), recent reports indicate the presence of CAR residues in both cultivated and wild areas. This pesticide is a potent inhibitor of acetylcholinesterase (AChE), which acts by preventing the hydrolysis of acetylcholine (ACh). Given the critical role of AChE::ACh in the proper functioning of the nervous system, we thought it appropriate to investigate the binding of CAR to AChEs from Homo sapiens, Danio rerio, Apis mellifera, and Caenorhabditis elegans using homology modelling, molecular docking, molecular dynamics, and quantum biochemistry. Molecular docking and dynamics results indicated peculiar structural behavior in each AChE::CAR system. Quantum biochemistry results showed similar affinities for all complexes, confirming the description of carbofuran as a broad-spectrum pesticide, and have a limited correlation with IC50 values. We found the following decreasing affinity order of AChE species: H. sapiens > A. mellifera > C. elegans > D. rerio. The computational results suggest that CAR occupies different pockets in the AChEs studied. In addition, our results showed that CAR binds to hsAChE and ceAChE in a very similar manner: it has high affinities for the same subsites in both species and forms hydrogen bonds with residues (hsTYR124 and ceTRP107) occupying homologous positions in the peripheral site. This suggests that this nematode is a potential model to evaluate the toxicity of carbamates, even though the sequence identity between them is only 41 %. Interestingly, we also observed that the catalytic histidines of drAChE and amAChE exhibited favorable contacts with carbofuran, suggesting that the non-covalent binding of carbofuran to these proteins may promote faster carbamylation rates than the binding modes to human and worm acetylcholinesterases. Our computational results provide a better understanding of the binding mechanisms in these complexes, as well as new insights into the mechanism of carbamylation.
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Affiliation(s)
- João P C Veras
- Department of Physics, Federal University of Ceará, Campus of Pici, 60440-554, Fortaleza, Ceará, Brazil
| | - Victor L B França
- Department of Physics, Federal University of Ceará, Campus of Pici, 60440-554, Fortaleza, Ceará, Brazil; Department of Physiology and Pharmacology, Federal University of Ceará, Fortaleza, 60430-275, Brazil.
| | - Hernandes F Carvalho
- Department of Structural and Functional Biology, Institute of Biology, State University of Campinas, 13083-864, Campinas, São Paulo, Brazil
| | - Valder N Freire
- Department of Physics, Federal University of Ceará, Campus of Pici, 60440-554, Fortaleza, Ceará, Brazil
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Mu X, Yuan S, Zhang D, Lai R, Liao C, Li G. Selective modulation of alkali metal ions on acetylcholinesterase. Phys Chem Chem Phys 2023; 25:30308-30318. [PMID: 37934509 DOI: 10.1039/d3cp02887a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Acetylcholinesterase (AChE) is an important hydrolase in cholinergic synapses and a candidate target in the treatment of Alzheimer's disease. The lithium treatment widely used in neurological disorders can alter the AChE activity, yet the underlying mechanism of how the ion species regulate the enzymatic activity remains unclear. In this work, we performed combined quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics (MD) simulations and well-tempered metadynamics to understand the modulation of human AChE (hAChE) activity using three alkali metal ions (Li+, Na+, and K+) in different concentrations. Our simulations show that the binding affinity and catalytic activity are affected by different ion species through allosteric ion coordination geometries on the hAChE complex and distant electrostatic screening effect. A Li+ cluster involving D330, E393, and D397 residues and three Li+ ions was found to be highly conserved and can be critical to the enzyme activity. Binding energy calculations indicate that the electrostatic screening from allosterically bound cations can affect the key residues at the catalytic site and active-site gorge, including E199. Furthermore, an increase in ion concentration can lead to lower reactivity, especially for Li+ ions, which exhibit more cation-hAChE contacts than Na+ and K+. The selective ion binding and their preferred modulation on hAChE are highly related to ion species. This work provides a molecular perspective on selective modulation by different ion species of the enzyme catalytic processes.
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Affiliation(s)
- Xia Mu
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
| | - Shengwei Yuan
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
- University of Chinese Academy of Sciences, Beijing, China
| | - Dinglin Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
| | - Rui Lai
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
| | - Chenyi Liao
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
| | - Guohui Li
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
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Aljabri M, Alharbi K, Alonazi M. In vitro and in silico analysis of Solanum torvum fruit and methyl caffeate interaction with cholinesterases. Saudi J Biol Sci 2023; 30:103815. [PMID: 37811479 PMCID: PMC10558794 DOI: 10.1016/j.sjbs.2023.103815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 08/26/2023] [Accepted: 09/15/2023] [Indexed: 10/10/2023] Open
Abstract
Oxidative stress along with dysfunction in cholinergic neurotransmission primarily underlies cognitive impairment. A significant approach to mitigate cognitive dysfunction involves the inhibition of cholinesterases, namely acetylcholinesterase (AChE) and butyrylcholinesterase (BChE). Exploring the potential antioxidant and anticholinesterase effects of edible plants holds promise for their utilization as botanicals to enhance cognition. Solanum torvum fruit with vast biological properties are used as food. In the present study, butanolic extract of S. torvum fruits (BESTF) was prepared. Additionally, the study investigated into the properties of methyl caffeate (MC), a compound present in S. torvum, obtained in its pure form. In vitro antioxidant and anticholinesterases activity of BESTF and MC were determined. BESTF and MC showed potent antioxidant property. BESTF and MC dose-dependently inhibited AChE (IC50 values: 166.6 µg/ml and 680.6 µM, respectively) and BChE (IC50 values: 161.55 µg/ml and 413 µM, respectively). BESTF and MC inhibited AChE and BChE in competitive mode. Active site gorge of AChE/BChE was occupied by MC which formed interaction with amino acids present in catalytic site and PAS in in silico. Further, molecular dynamics simulations followed by free energy calculation, principal component analysis and dynamic cross-correlation matrix provided the compelling evidence that that MC maintained stable interactions during MD simulation with AChE and BChE. Collectively, the results from the present study underlines the cognitive-enhancing effect of BESTF and MC.
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Affiliation(s)
- Maha Aljabri
- Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Khadiga Alharbi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Mona Alonazi
- Biochemistry Department, College of Science, King Saud University, Riyadh 11495, Saudi Arabia
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Pharmacotherapy Evolution in Alzheimer's Disease: Current Framework and Relevant Directions. Cells 2022; 12:cells12010131. [PMID: 36611925 PMCID: PMC9818415 DOI: 10.3390/cells12010131] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 12/24/2022] [Accepted: 12/25/2022] [Indexed: 12/30/2022] Open
Abstract
Alzheimer's disease (AD), once considered a rare disease, is now the most common form of dementia in the elderly population. Current drugs (cholinesterase inhibitors and glutamate antagonists) are safe but of limited benefit to most patients, offering symptomatic relief without successful cure of the disease. Since the last several decades, there has been a great need for the development of a treatment that might cure the underlying causes of AD and thereby slow its progression in vulnerable individuals. That is why phase I, II, and III studies that act on several fronts, such as cognitive improvement, symptom reduction, and enhancing the basic biology of AD, are imperative to stop the disease. This review discusses current treatment strategies, summarizing the clinical features and pharmacological properties, along with molecular docking analyses of the existing medications.
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Zhang Y, Luo M, Wu P, Wu S, Lee TY, Bai C. Application of Computational Biology and Artificial Intelligence in Drug Design. Int J Mol Sci 2022; 23:13568. [PMID: 36362355 PMCID: PMC9658956 DOI: 10.3390/ijms232113568] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 10/29/2022] [Accepted: 11/03/2022] [Indexed: 08/24/2023] Open
Abstract
Traditional drug design requires a great amount of research time and developmental expense. Booming computational approaches, including computational biology, computer-aided drug design, and artificial intelligence, have the potential to expedite the efficiency of drug discovery by minimizing the time and financial cost. In recent years, computational approaches are being widely used to improve the efficacy and effectiveness of drug discovery and pipeline, leading to the approval of plenty of new drugs for marketing. The present review emphasizes on the applications of these indispensable computational approaches in aiding target identification, lead discovery, and lead optimization. Some challenges of using these approaches for drug design are also discussed. Moreover, we propose a methodology for integrating various computational techniques into new drug discovery and design.
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Affiliation(s)
- Yue Zhang
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
- Warshel Institute for Computational Biology, Shenzhen 518172, China
| | - Mengqi Luo
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- South China Hospital, Health Science Center, Shenzhen University, Shenzhen 518116, China
| | - Peng Wu
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518055, China
| | - Song Wu
- South China Hospital, Health Science Center, Shenzhen University, Shenzhen 518116, China
| | - Tzong-Yi Lee
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- Warshel Institute for Computational Biology, Shenzhen 518172, China
| | - Chen Bai
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- Warshel Institute for Computational Biology, Shenzhen 518172, China
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11
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Inhibition of Cholinesterases by Benzothiazolone Derivatives. Processes (Basel) 2022. [DOI: 10.3390/pr10091872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Thirteen benzothiazolone derivatives (M1–M13) were synthesized and evaluated for their inhibitory activity against cholinesterases (ChEs) and monoamine oxidases (MAOs). All the compounds inhibited ChEs more effectively than MAOs. In addition, most of the compounds showed higher inhibitory activities against butyrylcholinesterase (BChE) than acetylcholinesterase (AChE). Compound M13 most potently inhibited BChE with an IC50 value of 1.21 μM, followed by M2 (IC50 = 1.38 μM). Compound M2 had a higher selectivity index (SI) value for BChE over AChE (28.99) than M13 (4.16). The 6-methoxy indole group of M13 was expected to have a greater effect on BChE inhibitory activity than the other groups. Kinetics and reversibility tests showed that M13 was a reversible noncompetitive BChE inhibitor with a Ki value of 1.14 ± 0.21 μM. In a docking simulation, M13 is predicted to form a hydrogen bond with the backbone carbonyl group of Ser287 of BChE through its methoxy indole moiety and π−π interactions between its benzothiazolone group and the side chain of Trp82 with the five-membered pyrrole ring and with the six-membered benzene ring. From these results, it is suggested that M13 is a BChE inhibitor and a potential candidate agent for the treatment of Alzheimer’s disease.
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Jamal QMS, Alharbi AH. Molecular docking and dynamics studies of cigarette smoke carcinogens interacting with acetylcholinesterase and butyrylcholinesterase enzymes of the central nervous system. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:61972-61992. [PMID: 34382170 DOI: 10.1007/s11356-021-15269-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 06/28/2021] [Indexed: 06/13/2023]
Abstract
The free radicals produced by cigarette smoking are responsible for tissue damage, heart and lung diseases, and carcinogenesis. The effect of tobacco on the central nervous system (CNS) has received increased attention nowadays in research. Therefore, to explore the molecular interaction of cigarette smoke carcinogens (CSC) 4-(methylnitrosamine)-1-(3-pyridyl)-1-butanol (NNAL), 4-(methylnitrosamine)-1-(3-pyridyl)-1-butanone (NNK), and N'-nitrosonornicotine (NNN) with well-known targets of CNS-related disorders, acetylcholinesterase (AChE), and butyrylcholinesterase (BuChE) enzymes, a cascade of the computational study was conducted including molecular docking and molecular dynamics simulations (MDS). The investigated results of NNAL+AChEcomplex, NNK+AChEcomplex, and NNK+BuChEcomplex based on intermolecular energies (∆G) were found to -8.57 kcal/mol, -8.21 kcal/mol, and -8.08 kcal/mol, respectively. MDS deviation and fluctuation plots of the NNAL and NNK interaction with AChE and BuChE have shown significant results. Further, Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) results shown the best total binding energy (Binding∆G) -87.381 (+/-13.119) kJ/mol during NNK interaction with AChE. Our study suggests that CSC is well capable of altering the normal biomolecular mechanism of CNS; thus, obtained data could be useful to design extensive wet laboratory experimentation to know the effects of CSC on human CNS.
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Affiliation(s)
- Qazi Mohammad Sajid Jamal
- Department of Health Informatics, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah, Saudi Arabia.
| | - Ali H Alharbi
- Department of Health Informatics, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah, Saudi Arabia
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Hormozi Jangi SR, Akhond M. Introducing a covalent thiol-based protected immobilized acetylcholinesterase with enhanced enzymatic performances for biosynthesis of esters. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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Nakata H, Filatov Gulak M, Choi CH. Accelerated Deep Learning Dynamics for Atomic Layer Deposition of Al(Me) 3 and Water on OH/Si(111). ACS APPLIED MATERIALS & INTERFACES 2022; 14:26116-26127. [PMID: 35608478 DOI: 10.1021/acsami.2c01768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Knowledge of the detailed mechanism behind the atomic layer deposition (ALD) can greatly facilitate the optimization of the manufacturing process. Computational modeling can potentially foster the understanding; however, the presently available capabilities of the accurate ab initio computational techniques preclude their application to modeling surface processes occurring on a long time scale, such as ALD. Although the situation can be greatly improved using machine learning (ML), this technique requires an enormous amount of data for training datasets. Here, we propose an iterative protocol for optimizing ML training datasets and apply ML-assisted ab initio calculations to model surface reactions occurring during the Al(Me)3/H2O ALD process on the OH-terminated Si (111) surface. The protocol uses a recently developed low-dimensional projection technique (TDUS), greatly reducing the amount of information required to achieve high accuracy (ca. 1 kcal/mol or less) of the developed ML models. The resulting free energy landscapes reveal fine details of various aspects of the target ALD process, such as the surface proton transfer, zwitterionic surface configurations, elimination-addition/addition-elimination, and SN2 reactions as well as the role of the surface entropic and temperature effects. Simulations of adsorption dynamics predict that the maximum physisorption rate of ca. 70% is achieved at the incidence velocity urms of the reactants in the range of 15-20 Å/ps. Hence, the proposed protocol furnishes a very effective tool to study complex chemical reaction dynamics at a much reduced computational cost.
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Affiliation(s)
- Hiroya Nakata
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
| | | | - Cheol Ho Choi
- Department of Chemistry, Kyungpook National University, Daegu 41566, South Korea
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15
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Rudzki S, Praet S. Five-Year PTSD Symptom Remission in Two Patients Following Treatment With Rivastigmine. Mil Med 2022; 188:usac094. [PMID: 35446431 DOI: 10.1093/milmed/usac094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/24/2022] [Indexed: 11/14/2022] Open
Abstract
INTRODUCTION The beneficial effect of rivastigmine, an acetylcholinesterase inhibitor (AChEi), which increases levels of acetylcholine (ACh), was first reported in 2013. This paper replicates those findings and reports sustained symptom remission. METHODS AND MATERIALS The high-frequency (HF) component of heart rate variability (HRV) is a measure of cholinergic withdrawal and was measured using a Zephyr Bioharness HR monitor, pre- and post-commencement of treatment. Data analysis was performed using Kubios HRV software. PTSD symptom severity was assessed using the Post-Traumatic Checklist-Civilian (PCL-C). RESULTS Low HF HRV was observed in both patients before rivastigmine treatment and reductions in PCL-C scores paralleled increases in HF HRV values. Follow-up revealed low HF HRV values in both patients despite PCL-C scores indicating remission. Sympathetic nervous system hyperactivity was observed in one patient, just before a suicide attempt. Following rivastigmine treatment, the patient had no further suicidal ideation or attempts. Another patient reported worsening of her PTSD symptoms in the peri-menstrual period, which was abolished by rivastigmine. She also experienced symptom relapse following prolonged infections. CONCLUSION Low HF HRV has been reported in PTSD patients, but findings have been inconsistent. Cholinergic withdrawal could explain the disturbances in sleep, learning, and memory seen in PTSD patients. The relapse of symptoms following prolonged infection implicates the immune system as a possible initiator of the disorder. ACh and estrogen have anti-inflammatory properties, supporting a possible role of inflammation in initiating PTSD. The effect of rivastigmine treatment should be tested in properly controlled clinical trials.
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Affiliation(s)
| | - Stephan Praet
- Ochre Health Medical Centre, University of Canberra, Bruce, ACT 2617, Australia
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16
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Taheri M, Aslani S, Ghafouri H, Mohammadi A, Akbary Moghaddam V, Moradi N, Naeimi H. Synthesis, in vitro biological evaluation and molecular modelling of new 2-chloro-3-hydrazinopyrazine derivatives as potent acetylcholinesterase inhibitors on PC12 cells. BMC Chem 2022; 16:7. [PMID: 35193649 PMCID: PMC8864858 DOI: 10.1186/s13065-022-00799-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 02/14/2022] [Indexed: 11/30/2022] Open
Abstract
Background The loss of cholinergic neurotransmission in Alzheimer's disease (AD) patients' brain is accompanied by a reduced concentration of Acetylcholine (ACh) within synaptic clefts. Thus, the use of acetylcholinesterase inhibitors (AChEIs) to block the cholinergic degradation of ACh is a promising approach for AD treatment. In the present study, a series of 2-chloro-3-hydrazinopyrazine derivatives (CHP1-5) were designed, synthesized, and biologically evaluated as potential multifunctional anti-AD agents. Methods In addition, the chemical structures and purity of the synthesized compounds were elucidated through using IR, 1H and 13C NMR, and elemental analyses. Further, the intended compounds were assessed in vitro for their AChE inhibitory and neuroprotective effects. Furthermore, DPPH, FRAP and ABTS assays were utilized to determine their antioxidant activity. The statistical analysis was performed using one-way ANOVA. Results Based on the results, CHP4 and CHP5 exhibited strong AChE inhibitory effects with the IC50 values of 3.76 and 4.2 µM compared to the donepezil (0.53 µM), respectively. The study examined the effect and molecular mechanism of CHP4 on the Ab1–42-induced cytotoxicity in differentiated PC12 cells. At concentrations of 0–100 μM, CHP4 was non-toxic in PC12. Additionally, Ab1–42 significantly stimulated tau hyperphosphorylation and induced differentiated PC12 cell death. Further, CHP4 resulted in diminishing the Ab1–42-induced toxicity in PC12 cell significantly. CHP4 at 30 μM concentration significantly increased the Ab1–42-induced HSP70 expression and decreased tau hyperphosphorylation. Conclusions According to the results of our studies CHP4 can be considered as safe and efficient AChEI and employed as a potential multifunctional anti-AD agent. Supplementary Information The online version contains supplementary material available at 10.1186/s13065-022-00799-w.
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Affiliation(s)
- Maryam Taheri
- Department of Biology, Faculty of Basic Sciences, University of Guilan, Rasht, Iran
| | - Samira Aslani
- Department of Biology, Faculty of Basic Sciences, University of Guilan, Rasht, Iran
| | - Hossein Ghafouri
- Department of Biology, Faculty of Basic Sciences, University of Guilan, Rasht, Iran. .,Department of Marine Sciences, The Caspian Sea Basin Research Center, University of Guilan, Rasht, Iran.
| | - Asadollah Mohammadi
- Department of Chemistry, Faculty of Sciences, University of Guilan, Rasht, Iran
| | | | - Nastarn Moradi
- Department of Biology, Faculty of Basic Sciences, University of Guilan, Rasht, Iran
| | - Hananeh Naeimi
- Department of Biology, Faculty of Basic Sciences, University of Guilan, Rasht, Iran
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17
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Zheng C, Schneider M, Marion A, Antes I. The Q41R mutation in the HCV-protease enhances the reactivity towards MAVS by suppressing non-reactive pathways. Phys Chem Chem Phys 2022; 24:2126-2138. [PMID: 35029245 DOI: 10.1039/d1cp05002h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recent experimental findings pointed out a new mutation in the HCV protease, Q41R, responsible for a significant enhancement of the enzyme's reactivity towards the mitochondrial antiviral-signaling protein (MAVS). The Q41R mutation is located rather far from the active site, and its involvement in the overall reaction mechanism is thus unclear. We used classical molecular dynamics and QM/MM to study the acylation reaction of HCV NS3/4A protease variants bound to MAVS and the NS4A/4B substrate and uncovered the indirect mechanism by which the Q41R mutation plays a critical role in the efficient cleavage of the substrate. Our simulations reveal that there are two major conformations of the MAVS H1'(p) residue for the wild type protease and only one conformation for the Q41R mutant. The conformational space of H1'(p) is restricted by the Q41R mutation due to a π-π stacking between H1'(p) and R41 as well as a strong hydrogen bond between the backbone of H57 and the side chain of R41. Further QM/MM calculations indicate that the complex with the conformation ruled out by the Q41R substitution is a non-reactive species due to its higher free energy barrier for the acylation reaction. Based on our calculations, we propose a kinetic mechanism that explains experimental data showing an increase of apparent rate constants for MAVS cleavage in Q41R mutants. Our model predicts that the non-reactive conformation of the enzyme-substrate complex modulates reaction kinetics like an uncompetitive inhibitor.
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Affiliation(s)
- Chen Zheng
- Technische Universität München (TUM), TUM School of Life Sciences, Freising 85354, Germany. .,Technische Universität München (TUM), TUM Center for Functional Protein Assemblies, Garching 85747, Germany
| | - Markus Schneider
- Technische Universität München (TUM), TUM School of Life Sciences, Freising 85354, Germany. .,Technische Universität München (TUM), TUM Center for Functional Protein Assemblies, Garching 85747, Germany
| | - Antoine Marion
- Technische Universität München (TUM), TUM School of Life Sciences, Freising 85354, Germany. .,Middle East Technical University, Department of Chemistry, Ankara 06800, Turkey.
| | - Iris Antes
- Technische Universität München (TUM), TUM School of Life Sciences, Freising 85354, Germany. .,Technische Universität München (TUM), TUM Center for Functional Protein Assemblies, Garching 85747, Germany
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18
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Adeowo FY, Oyetunji TP, Ejalonibu MA, Ndagi U, Kumalo HM, Lawal MM. Tailored Modeling of Rivastigmine Derivatives as Dual Acetylcholinesterase and Butyrylcholinesterase Inhibitors for Alzheimer's Disease Treatment. Chem Biodivers 2021; 18:e2100361. [PMID: 34547176 DOI: 10.1002/cbdv.202100361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 09/21/2021] [Indexed: 12/13/2022]
Abstract
Rational modification of known drug candidates to design more potent ones using computational methods has found application in drug design, development, and discovery. Herein, we integrate computational and theoretical methodologies to unveil rivastigmine derivatives as dual inhibitors of acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) for Alzheimer's disease (AD) management. The investigation entails pharmacokinetics screening, density functional theory (DFT) mechanistic study, molecular docking, and molecular dynamics (MD) simulation. We designed over 20 rivastigmine substituents, subject them to some analyses, and identified RL2 with an appreciable blood-brain barrier score and no permeability glycoprotein binding. The compound shows higher acylation energy and a favored binding affinity to the cholinesterase enzymes. RL2 interacts with the AChE and BuChE active sites showing values of -41.1/-39.5 kcal mol-1 while rivastigmine binds with -32.7/-30.7 kcal mol-1 for these enzymes. The study revealed RL2 (4-fluorophenyl rivastigmine) as a potential dual inhibitor for AChE and BuChE towards Alzheimer's disorder management.
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Affiliation(s)
- Fatima Y Adeowo
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, 4001, South Africa
| | | | - Murtala A Ejalonibu
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Umar Ndagi
- Center for Trans-Sahara Disease, Vaccine and Drug Research, IBB University Lapai, Niger State, Minna, Nigeria
| | - Hezekiel M Kumalo
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Monsurat M Lawal
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, 4001, South Africa
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Ganeshpurkar A, Singh R, Shivhare S, Divya, Kumar D, Gutti G, Singh R, Kumar A, Singh SK. Improved machine learning scoring functions for identification of Electrophorus electricus's acetylcholinesterase inhibitors. Mol Divers 2021; 26:1455-1479. [PMID: 34328603 DOI: 10.1007/s11030-021-10280-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 07/17/2021] [Indexed: 10/20/2022]
Abstract
Structure-based drug design (SBDD) is an important in silico technique, used for the identification of enzyme inhibitors. Acetylcholinesterase (AChE), obtained from Electrophorus electricus (ee), is widely used for the screening of AChE inhibitors. It shares structural homology with the AChE of human and other organisms. Till date, the three-dimensional crystal structure of enzyme from ee is not available that makes it challenging to use the SBDD approach for the identification of inhibitors. A homology model was developed for eeAChE in the present study, followed by its structural refinement through energy minimisation. The docking protocol was developed using a grid dimension of 84 × 66 × 72 and grid point spacing of 0.375 Å for eeAChE. The protocol was validated by redocking a set of co-crystallised inhibitors obtained from mouse AChE, and their interaction profiles were compared. The results indicated a poor performance of the Autodock scoring function. Hence, a batch of machine learning-based scoring functions were developed. The validation results displayed an accuracy of 81.68 ± 1.73% and 82.92 ± 3.05% for binary and multiclass classification scoring function, respectively. The regression-based scoring function produced [Formula: see text] and [Formula: see text] values of 0.94, 0.635 and 0.634, respectively.
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Affiliation(s)
- Ankit Ganeshpurkar
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India
| | - Ravi Singh
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India
| | - Shalini Shivhare
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India
| | - Divya
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India
| | - Devendra Kumar
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India
| | - Gopichand Gutti
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India
| | | | - Ashok Kumar
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India
| | - Sushil Kumar Singh
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India.
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20
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Bagri K, Kumar A, Manisha, Kumar P. Computational Studies on Acetylcholinesterase Inhibitors: From Biochemistry to Chemistry. Mini Rev Med Chem 2021; 20:1403-1435. [PMID: 31884928 DOI: 10.2174/1389557520666191224144346] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/23/2019] [Accepted: 10/28/2019] [Indexed: 11/22/2022]
Abstract
Acetylcholinesterase inhibitors are the most promising therapeutics for Alzheimer's disease treatment as these prevent the loss of acetylcholine and slows the progression of the disease. The drugs approved for the management of Alzheimer's disease by the FDA are acetylcholinesterase inhibitors but are associated with side effects. Consistent and stringent efforts by the researchers with the help of computational methods opened new ways of developing novel molecules with good acetylcholinesterase inhibitory activity. In this manuscript, we reviewed the studies that identified the essential structural features of acetylcholinesterase inhibitors at the molecular level as well as the techniques like molecular docking, molecular dynamics, quantitative structure-activity relationship, virtual screening, and pharmacophore modelling that were used in designing these inhibitors.
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Affiliation(s)
- Kiran Bagri
- Department of Pharmaceutical Sciences, Guru Jambheshwar University of Science & Technology, Hisar 125001, India
| | - Ashwani Kumar
- Department of Pharmaceutical Sciences, Guru Jambheshwar University of Science & Technology, Hisar 125001, India
| | - Manisha
- Department of Pharmaceutical Sciences, Guru Jambheshwar University of Science & Technology, Hisar 125001, India
| | - Parvin Kumar
- Department of Chemistry, Kurukshetra University, Kurukshetra, India
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21
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Anticholinesterase Activity of Eight Medicinal Plant Species: In Vitro and In Silico Studies in the Search for Therapeutic Agents against Alzheimer's Disease. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2021; 2021:9995614. [PMID: 34257698 PMCID: PMC8260289 DOI: 10.1155/2021/9995614] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/29/2021] [Accepted: 06/08/2021] [Indexed: 01/28/2023]
Abstract
Many Bangladeshi medicinal plants have been used to treat Alzheimer's disease and other neurodegenerative diseases. In the present study, the anticholinesterase effects of eight selected Bangladeshi medicinal plant species were investigated. Species were selected based on the traditional uses against CNS-related diseases. Extracts were prepared using a gentle cold extraction method. In vitro cholinesterase inhibitory effects were measured by Ellman's method in 96-well microplates. Blumea lacera (Compositae) and Cyclea barbata (Menispermaceae) were found to have the highest acetylcholinesterase inhibitory (IC50, 150 ± 11 and 176 ± 14 µg/mL, respectively) and butyrylcholinesterase inhibitory effect (IC50, 297 ± 13 and 124 ± 2 µg/mL, respectively). Cyclea barbata demonstrated competitive inhibition, where Blumea lacera showed an uncompetitive inhibition mode for acetylcholinesterase. Smilax guianensis (Smilacaceae) and Byttneria pilosa (Malvaceae) were also found to show moderate AChE inhibition (IC50, 205 ± 31 and 221 ± 2 µg/mL, respectively), although no significant BChE inhibitory effect was observed for extracts from these plant species. Among others, Thunbergia grandiflora (Acanthaceae) and Mikania micrantha (Compositae) were found to display noticeable AChE (IC50, 252 ± 22 µg/mL) and BChE (IC50, 314 ± 15 µg/mL) inhibitory effects, respectively. Molecular docking experiment suggested that compounds 5-hydroxy-3,6,7,3′,4′-pentamethoxyflavone (BL4) and kaempferol-3-O-α-L-rhamnopyranosyl-(1⟶6)-β-D-glucopyranoside (BL5) from Blumea lacera bound stably to the binding groove of the AChE and BChE by hydrogen-bond interactions, respectively. Therefore, these compounds could be candidates for cholinesterase inhibitors. The present findings demonstrated that Blumea lacera and Cyclea barbata are interesting objects for further studies aiming at future therapeutics for Alzheimer's disease.
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De Boer D, Nguyen N, Mao J, Moore J, Sorin EJ. A Comprehensive Review of Cholinesterase Modeling and Simulation. Biomolecules 2021; 11:580. [PMID: 33920972 PMCID: PMC8071298 DOI: 10.3390/biom11040580] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/08/2021] [Accepted: 04/11/2021] [Indexed: 01/18/2023] Open
Abstract
The present article reviews published efforts to study acetylcholinesterase and butyrylcholinesterase structure and function using computer-based modeling and simulation techniques. Structures and models of both enzymes from various organisms, including rays, mice, and humans, are discussed to highlight key structural similarities in the active site gorges of the two enzymes, such as flexibility, binding site location, and function, as well as differences, such as gorge volume and binding site residue composition. Catalytic studies are also described, with an emphasis on the mechanism of acetylcholine hydrolysis by each enzyme and novel mutants that increase catalytic efficiency. The inhibitory activities of myriad compounds have been computationally assessed, primarily through Monte Carlo-based docking calculations and molecular dynamics simulations. Pharmaceutical compounds examined herein include FDA-approved therapeutics and their derivatives, as well as several other prescription drug derivatives. Cholinesterase interactions with both narcotics and organophosphate compounds are discussed, with the latter focusing primarily on molecular recognition studies of potential therapeutic value and on improving our understanding of the reactivation of cholinesterases that are bound to toxins. This review also explores the inhibitory properties of several other organic and biological moieties, as well as advancements in virtual screening methodologies with respect to these enzymes.
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Affiliation(s)
- Danna De Boer
- Department of Chemistry & Biochemistry, California State University, Long Beach, CA 90840, USA;
| | - Nguyet Nguyen
- Department of Chemical Engineering, California State University, Long Beach, CA 90840, USA; (N.N.); (J.M.)
| | - Jia Mao
- Department of Chemical Engineering, California State University, Long Beach, CA 90840, USA; (N.N.); (J.M.)
| | - Jessica Moore
- Department of Biomedical Engineering, California State University, Long Beach, CA 90840, USA;
| | - Eric J. Sorin
- Department of Chemistry & Biochemistry, California State University, Long Beach, CA 90840, USA;
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Berselli A, Ramos MJ, Menziani MC. Novel Pet-Degrading Enzymes: Structure-Function from a Computational Perspective. Chembiochem 2021; 22:2032-2050. [PMID: 33470503 DOI: 10.1002/cbic.202000841] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/19/2021] [Indexed: 12/12/2022]
Abstract
The bacterium strain Ideonella sakaiensis 201-F6 is able to hydrolyze low-crystallinity PET films at 30 °C due to two enzymes named PETase and MHETase. Since its discovery, many efforts have been dedicated to elucidating the structure and features of those two enzymes, and various authors have highlighted the necessity to optimize both the substrate binding site and the global structure in order to enhance the stability and catalytic activity of these PET biocatalysts so as to make them more suitable for industrial applications. In this review, the strategies adopted by different research groups to investigate the structure and functionality of both PETase and MHETase in depth are described, emphasizing the advantages provided by the use of computational methods to complement and drive experiments. Subsequently, the modifications implemented with protein engineering are discussed. The versatility of the enzymes secreted by I. sakaiensis enables the prediction that they will find several applications in the disposal of PET debris, encouraging a prioritization of efforts in this prolific research field.
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Affiliation(s)
- Alessandro Berselli
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy
| | - Maria J Ramos
- LAQV/REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Maria Cristina Menziani
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy
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López AFF, Martínez OMM, Hernández HFC. Evaluation of Amaryllidaceae alkaloids as inhibitors of human acetylcholinesterase by QSAR analysis and molecular docking. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129142] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Ghosh S, Jana K, Wakchaure PD, Ganguly B. Revealing the cholinergic inhibition mechanism of Alzheimer's by galantamine: a metadynamics simulation study. J Biomol Struct Dyn 2020; 40:5100-5111. [PMID: 33382027 DOI: 10.1080/07391102.2020.1867644] [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: 10/22/2022]
Abstract
Galantamine is one of the approved drugs based on the cholinergic hypothesis for the symptomatic treatment of mild to moderate Alzheimer's disease (AD). The etiology of AD is not fully known; however, the reported cholinergic hypothesis suggests the inadequate synthesis of the neurotransmitter acetylcholine (ACh) is responsible for this disease. The crystal structure of galantamine bound human acetylcholinesterase (hAChE) has been reported; however, the inhibition mechanism of hAChE by galantamine is not well understood. A Well-tempered metadynamics (WTMtD) simulation study has been performed with the crystal structure of galantamine bound hAChE. The reported mechanism for the degradation of ACh is suggested through a proton transfer process from a carboxylic group of Glu334 to the hydroxyl group of Ser203, which attacks ACh for the degradation to acetic acid and choline. Such proton transfer process is lowered in the presence of galantamine due to the separation of catalytic triad inside the gorge of AChE as observed with WTMtD. A docking study has been performed to examine the ACh's binding with the catalytic triad of galantamine bound hAChE. The docking results reveal that the approach of ACh to the catalytic triad is interrupted due to the galantamine's presence in the gorge of the enzyme.
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Affiliation(s)
- Shibaji Ghosh
- Computation and Simulation Unit (Analytical and Environmental Science Division and Centralized Instrument Facility), CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Kalyanashis Jana
- Computation and Simulation Unit (Analytical and Environmental Science Division and Centralized Instrument Facility), CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Padmaja D Wakchaure
- Computation and Simulation Unit (Analytical and Environmental Science Division and Centralized Instrument Facility), CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Bishwajit Ganguly
- Computation and Simulation Unit (Analytical and Environmental Science Division and Centralized Instrument Facility), CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
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Ionophoric polyphenols are permeable to the blood–brain barrier, interact with human serum albumin and Calf Thymus DNA, and inhibit AChE enzymatic activity. Med Chem Res 2020. [DOI: 10.1007/s00044-020-02615-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Characterization and engineering of a two-enzyme system for plastics depolymerization. Proc Natl Acad Sci U S A 2020; 117:25476-25485. [PMID: 32989159 PMCID: PMC7568301 DOI: 10.1073/pnas.2006753117] [Citation(s) in RCA: 198] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Deconstruction of recalcitrant polymers, such as cellulose or chitin, is accomplished in nature by synergistic enzyme cocktails that evolved over millions of years. In these systems, soluble dimeric or oligomeric intermediates are typically released via interfacial biocatalysis, and additional enzymes often process the soluble intermediates into monomers for microbial uptake. The recent discovery of a two-enzyme system for polyethylene terephthalate (PET) deconstruction, which employs one enzyme to convert the polymer into soluble intermediates and another enzyme to produce the constituent PET monomers (MHETase), suggests that nature may be evolving similar deconstruction strategies for synthetic plastics. This study on the characterization of the MHETase enzyme and synergy of the two-enzyme PET depolymerization system may inform enzyme cocktail-based strategies for plastics upcycling. Plastics pollution represents a global environmental crisis. In response, microbes are evolving the capacity to utilize synthetic polymers as carbon and energy sources. Recently, Ideonella sakaiensis was reported to secrete a two-enzyme system to deconstruct polyethylene terephthalate (PET) to its constituent monomers. Specifically, the I. sakaiensis PETase depolymerizes PET, liberating soluble products, including mono(2-hydroxyethyl) terephthalate (MHET), which is cleaved to terephthalic acid and ethylene glycol by MHETase. Here, we report a 1.6 Å resolution MHETase structure, illustrating that the MHETase core domain is similar to PETase, capped by a lid domain. Simulations of the catalytic itinerary predict that MHETase follows the canonical two-step serine hydrolase mechanism. Bioinformatics analysis suggests that MHETase evolved from ferulic acid esterases, and two homologous enzymes are shown to exhibit MHET turnover. Analysis of the two homologous enzymes and the MHETase S131G mutant demonstrates the importance of this residue for accommodation of MHET in the active site. We also demonstrate that the MHETase lid is crucial for hydrolysis of MHET and, furthermore, that MHETase does not turnover mono(2-hydroxyethyl)-furanoate or mono(2-hydroxyethyl)-isophthalate. A highly synergistic relationship between PETase and MHETase was observed for the conversion of amorphous PET film to monomers across all nonzero MHETase concentrations tested. Finally, we compare the performance of MHETase:PETase chimeric proteins of varying linker lengths, which all exhibit improved PET and MHET turnover relative to the free enzymes. Together, these results offer insights into the two-enzyme PET depolymerization system and will inform future efforts in the biological deconstruction and upcycling of mixed plastics.
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Hassanzadeh P. Towards the quantum-enabled technologies for development of drugs or delivery systems. J Control Release 2020; 324:260-279. [DOI: 10.1016/j.jconrel.2020.04.050] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 12/20/2022]
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Pham VD, To TA, Gagné-Thivierge C, Couture M, Lagüe P, Yao D, Picard MÈ, Lortie LA, Attéré SA, Zhu X, Levesque RC, Charette SJ, Shi R. Structural insights into the putative bacterial acetylcholinesterase ChoE and its substrate inhibition mechanism. J Biol Chem 2020; 295:8708-8724. [PMID: 32371400 PMCID: PMC7324521 DOI: 10.1074/jbc.ra119.011809] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 05/04/2020] [Indexed: 01/01/2023] Open
Abstract
Mammalian acetylcholinesterase (AChE) is well-studied, being important in both cholinergic brain synapses and the peripheral nervous systems and also a key drug target for many diseases. In contrast, little is known about the structures and molecular mechanism of prokaryotic acetylcholinesterases. We report here the structural and biochemical characterization of ChoE, a putative bacterial acetylcholinesterase from Pseudomonas aeruginosa Analysis of WT and mutant strains indicated that ChoE is indispensable for P. aeruginosa growth with acetylcholine as the sole carbon and nitrogen source. The crystal structure of ChoE at 1.35 Å resolution revealed that this enzyme adopts a typical fold of the SGNH hydrolase family. Although ChoE and eukaryotic AChEs catalyze the same reaction, their overall structures bear no similarities constituting an interesting example of convergent evolution. Among Ser-38, Asp-285, and His-288 of the catalytic triad residues, only Asp-285 was not essential for ChoE activity. Combined with kinetic analyses of WT and mutant proteins, multiple crystal structures of ChoE complexed with substrates, products, or reaction intermediate revealed the structural determinants for substrate recognition, snapshots of the various catalytic steps, and the molecular basis of substrate inhibition at high substrate concentrations. Our results indicate that substrate inhibition in ChoE is due to acetate release being blocked by the binding of a substrate molecule in a nonproductive mode. Because of the distinct overall folds and significant differences of the active site between ChoE and eukaryotic AChEs, these structures will serve as a prototype for other prokaryotic acetylcholinesterases.
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Affiliation(s)
- Van Dung Pham
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada; PROTEO, the Québec Network for Research on Protein Function, Engineering, and Applications, Québec, Canada
| | - Tuan Anh To
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada; PROTEO, the Québec Network for Research on Protein Function, Engineering, and Applications, Québec, Canada
| | - Cynthia Gagné-Thivierge
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada; Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Hôpital Laval, Québec, Canada
| | - Manon Couture
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada; PROTEO, the Québec Network for Research on Protein Function, Engineering, and Applications, Québec, Canada
| | - Patrick Lagüe
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada; PROTEO, the Québec Network for Research on Protein Function, Engineering, and Applications, Québec, Canada
| | - Deqiang Yao
- iHuman Institute, ShanghaiTech University, Shanghai, P.R. China
| | - Marie-Ève Picard
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada; PROTEO, the Québec Network for Research on Protein Function, Engineering, and Applications, Québec, Canada
| | - Louis-André Lortie
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, Canada
| | - Sabrina A Attéré
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada; Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Hôpital Laval, Québec, Canada
| | - Xiaojun Zhu
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada; PROTEO, the Québec Network for Research on Protein Function, Engineering, and Applications, Québec, Canada
| | - Roger C Levesque
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - Steve J Charette
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada; Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Hôpital Laval, Québec, Canada
| | - Rong Shi
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, Canada; Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada; PROTEO, the Québec Network for Research on Protein Function, Engineering, and Applications, Québec, Canada.
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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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Novel Insights into the Thioesterolytic Activity of N-Substituted Pyridinium-4-oximes. Molecules 2020; 25:molecules25102385. [PMID: 32455554 PMCID: PMC7287890 DOI: 10.3390/molecules25102385] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/15/2020] [Accepted: 05/19/2020] [Indexed: 12/21/2022] Open
Abstract
The pyridinium oximes are known esterolytic agents, usually classified in the literature as catalysts, which mimic the catalytic mode of hydrolases. Herein, we combined kinetic and computational studies of the pyridinium-4-oxime-mediated acetylthiocholine (AcSCh+) hydrolysis to provide novel insights into their potential catalytic activity. The N-methyl- and N-benzylpyridinium-4-oximes have been tested as oximolytic agents toward the AcSCh+, while the newly synthesized O-acetyl-N-methylpyridinium-4-oxime iodide was employed for studying the consecutive hydrolytic reaction. The relevance of the AcSCh+ hydrolysis as a competitive reaction to AcSCh+ oximolysis was also investigated. The reactions were independently studied spectrophotometrically and rate constants, koxime, kw and kOH, were evaluated over a convenient pH-range at I = 0.1 M and 25 °C. The catalytic action of pyridinium-4-oximes comprises two successive stages, acetylation (oximolysis) and deacetylation stage (pyridinium-4-oxime-ester hydrolysis), the latter being crucial for understanding the whole catalytic cycle. The complete mechanism is presented by the free energy reaction profiles obtained with (CPCM)/M06–2X/6–311++G(2df,2pd)//(CPCM)/M06–2X/6–31+G(d) computational model. The comparison of the observed rates of AcSCh+ oximolytic cleavage and both competitive AcSCh+ and consecutive pyridinium-4-oxime-ester hydrolytic cleavage revealed that the pyridinium-4-oximes cannot be classified as non-enzyme catalyst of the AcSCh+ hydrolysis but as the very effective esterolytic agents.
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32
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de Oliveira VM, Estácio SP, da Silva Mendes FR, Campos OS, Marinho MM, Marinho ES. Characterization of rotenoid stemonal by semiempirical methods and molecular docking. SN APPLIED SCIENCES 2020. [DOI: 10.1007/s42452-020-2346-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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Özçelik AB, Özdemir Z, Sari S, Utku S, Uysal M. A new series of pyridazinone derivatives as cholinesterases inhibitors: Synthesis, in vitro activity and molecular modeling studies. Pharmacol Rep 2019; 71:1253-1263. [DOI: 10.1016/j.pharep.2019.07.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 07/08/2019] [Accepted: 07/19/2019] [Indexed: 11/26/2022]
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Parvaz S, Taheri-Ledari R, Esmaeili MS, Rabbani M, Maleki A. A brief survey on the advanced brain drug administration by nanoscale carriers: With a particular focus on AChE reactivators. Life Sci 2019; 240:117099. [PMID: 31760098 DOI: 10.1016/j.lfs.2019.117099] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/16/2019] [Accepted: 11/19/2019] [Indexed: 10/25/2022]
Abstract
Obviously, delivery of the medications to the brain is more difficult than other tissues due to the existence of a strong obstacle, which is called blood-brain barrier (BBB). Because of the lipophilic nature of this barrier, it would be a complex (and in many cases impossible) process to cross the medications with hydrophilic behavior from BBB and deliver them to the brain. Thus, novel intricate drug-carriers in nano scales have been recently developed and suitably applied for this purpose. One of the most important categories of these hydrophilic medications, are reactivators for acetyl cholinesterase (AChE) enzyme that facilitates the breakdown of acetylcholine (as a neurotransmitter). The AChE function is inhibited by organophosphorus (OP) nerve agents that are extremely used in military conflicts. In this review, the abilities of the nanosized drug delivery systems to perform as suitable vehicles for AChE reactivators are comprehensively discussed.
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Affiliation(s)
- Sina Parvaz
- Department of Chemistry, Iran University of Science and Technology, Tehran 16846-13114, Iran
| | - Reza Taheri-Ledari
- Department of Chemistry, Iran University of Science and Technology, Tehran 16846-13114, Iran
| | - Mir Saeed Esmaeili
- Department of Chemistry, Iran University of Science and Technology, Tehran 16846-13114, Iran
| | - Mahboubeh Rabbani
- Department of Chemistry, Iran University of Science and Technology, Tehran 16846-13114, Iran
| | - Ali Maleki
- Department of Chemistry, Iran University of Science and Technology, Tehran 16846-13114, Iran.
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Enzymatic reactions in the production of biomethane from organic waste. Enzyme Microb Technol 2019; 132:109410. [PMID: 31731967 DOI: 10.1016/j.enzmictec.2019.109410] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 07/06/2019] [Accepted: 08/15/2019] [Indexed: 11/23/2022]
Abstract
Enzymatic reactions refer to organic reactions catalyzed by enzymes. This review aims to enrich the documentation relative to enzymatic reactions occurring during the anaerobic degradation of residual organic substances with emphasis on the structures of organic compounds and reaction mechanisms. This allows to understand the displacement of electrons between electron-rich and electron-poor entities to form new bonds in products. The detailed mechanisms of enzymatic reactions relative to the production of biomethane have not yet been reviewed in the scientific literature. Hence, this review is novel and timely since it discusses the chemical behavior or reactivity of different functional groups, thereby allowing to better understand the enzymatic catalysis in the transformations of residual proteins, carbohydrates, and lipids into biomethane and fertilizers. Such understanding allows to improve the overall biomethanation efficiency in industrial applications.
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Yan M, Zhang Z, Liu Z, Zhang C, Zhang J, Fan S, Yang Z. Catalytic Hydrolysis Mechanism of Cocaine by Human Carboxylesterase 1: An Orthoester Intermediate Slows Down the Reaction. Molecules 2019; 24:molecules24224057. [PMID: 31717501 PMCID: PMC6891567 DOI: 10.3390/molecules24224057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 11/05/2019] [Accepted: 11/07/2019] [Indexed: 11/18/2022] Open
Abstract
Human carboxylesterase 1 (hCES1) is a major carboxylesterase in the human body and plays important roles in the metabolism of a wide variety of substances, including lipids and drugs, and therefore is attracting more and more attention from areas including lipid metabolism, pharmacokinetics, drug–drug interactions, and prodrug activation. In this work, we studied the catalytic hydrolysis mechanism of hCES1 by the quantum mechanics computation method, using cocaine as a model substrate. Our results support the four-step theory of the esterase catalytic hydrolysis mechanism, in which both the acylation stage and the deacylation stage include two transition states and a tetrahedral intermediate. The roles and cooperation of the catalytic triad, S221, H468, and E354, were also analyzed in this study. Moreover, orthoester intermediates were found in hCES1-catalyzed cocaine hydrolysis reaction, which significantly elevate the free energy barrier and slow down the reaction. Based on this finding, we propose that hCES1 substrates with β-aminocarboxylester structure might form orthoester intermediates in hCES1-catalyzed hydrolysis, and therefore prolong their in vivo half-life. Thus, this study helps to clarify the catalytic mechanism of hCES1 and elucidates important details of its catalytic process, and furthermore, provides important insights into the metabolism of hCES1 substrates and drug designing.
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Affiliation(s)
- Maocai Yan
- School of Pharmacy, Jining Medical University, Rizhao 276800, China
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- Correspondence: (M.Y.); (Z.Y.); Tel.: +86-(633)-2983781 (M.Y.); +86-(10)-63165283 (Z.Y.)
| | - Zhen Zhang
- School of Pharmacy, Jining Medical University, Rizhao 276800, China
| | - Zhaoming Liu
- School of Pharmacy, Jining Medical University, Rizhao 276800, China
| | - Chunyan Zhang
- School of Pharmacy, Jining Medical University, Rizhao 276800, China
| | - Jingchang Zhang
- School of Pharmacy, Jining Medical University, Rizhao 276800, China
| | - Shuai Fan
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Zhaoyong Yang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- Correspondence: (M.Y.); (Z.Y.); Tel.: +86-(633)-2983781 (M.Y.); +86-(10)-63165283 (Z.Y.)
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Bozbey İ, Özdemir Z, Uslu H, Özçelik AB, Şenol FS, Orhan İE, Uysal M. A Series of New Hydrazone Derivatives: Synthesis, Molecular Docking and Anticholinesterase Activity Studies. Mini Rev Med Chem 2019; 20:1042-1060. [PMID: 31660824 DOI: 10.2174/1389557519666191010154444] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 11/01/2018] [Accepted: 09/12/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND Acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) are known to be serine hydrolase enzymes responsible for the hydrolysis of acetylcholine (ACh), which is a significant neurotransmitter for regulation of cognition in animals. Inhibition of cholinesterases is an effective method to curb Alzheimer's disease, a progressive and fatal neurological disorder. OBJECTIVE In this study, 30 new hydrazone derivatives were synthesized. Then we evaluated their anticholinesterase activity of compounds. We also tried to get insights into binding interactions of the synthesized compounds in the active site of both enzymes by using molecular docking approach. METHODS The compounds were synthesized by the reaction of various substituted/nonsubstituted benzaldehydes with 6-(substitute/nonsubstituephenyl)-3(2H)-pyridazinone-2-yl propiyohydrazide. Anticholinesterase activity of the compounds was determined using Ellman's method. Molecular docking studies were done by using the ADT package version 1.5.6rc3 and showed by Maestro. RMSD values were obtained using Lamarckian Genetic Algorithm and scoring function of AutoDock 4.2 release 4.2.5.1 software. RESULTS The activities of the compounds were compared with galantamine as cholinesterase enzyme inhibitor, where some of the compounds showed higher BChE inhibitory activity than galantamine. Compound F111 was shown to be the best BChE inhibitor effective in 50 μM dose, providing 89.43% inhibition of BChE (IC50=4.27±0.36 μM). CONCLUSION This study supports that novel hydrazone derivates may be used for the development of new BChE inhibitory agents.
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Affiliation(s)
- İrem Bozbey
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erzincan Binali Yıldırım University, Erzincan 24100, Turkey
| | - Zeynep Özdemir
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Inonu University, Malatya 44280, Turkey
| | - Harun Uslu
- Department of Medical Services and Techniques, Vocational School of Health Services, Firat University, Elazıg 23040, Turkey
| | - Azime Berna Özçelik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, Ankara 06100, Turkey
| | - Fatma Sezer Şenol
- Department of Pharmacognosy, Faculty of Pharmacy, Gazi University, Ankara 06100, Turkey
| | - İlkay Erdoğan Orhan
- Department of Pharmacognosy, Faculty of Pharmacy, Gazi University, Ankara 06100, Turkey
| | - Mehtap Uysal
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erzincan Binali Yıldırım University, Erzincan 24100, Turkey.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, Ankara 06100, Turkey
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Hoffmann M, Stiller C, Endres E, Scheiner M, Gunesch S, Sotriffer C, Maurice T, Decker M. Highly Selective Butyrylcholinesterase Inhibitors with Tunable Duration of Action by Chemical Modification of Transferable Carbamate Units Exhibit Pronounced Neuroprotective Effect in an Alzheimer's Disease Mouse Model. J Med Chem 2019; 62:9116-9140. [PMID: 31609115 DOI: 10.1021/acs.jmedchem.9b01012] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this study, the carbamate structure of pseudo-irreversible butyrylcholinesterase (BChE) inhibitors was optimized with regard to a longer binding to the enzyme. A set of compounds bearing different heterocycles (e.g., morpholine, tetrahydroisoquinoline, benzimidazole, piperidine) and alkylene spacers (2 to 10 methylene groups between carbamate and heterocycle) in the carbamate residue was synthesized and characterized in vitro for their binding affinity, binding kinetics, and carbamate hydrolysis. These novel BChE inhibitors are highly selective for hBChE over human acetycholinesterase (hAChE), yielding short-, medium-, and long-acting nanomolar hBChE inhibitors (with a half-life of the carbamoylated enzyme ranging from 1 to 28 h). The inhibitors show neuroprotective properties in a murine hippocampal cell line and a pharmacological mouse model of Alzheimer's disease (AD), suggesting a significant benefit of BChE inhibition for a disease-modifying treatment of AD.
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Affiliation(s)
- Matthias Hoffmann
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy and Food Chemistry , Julius Maximilian University Würzburg , Am Hubland, D-97074 Würzburg , Germany
| | - Carina Stiller
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy and Food Chemistry , Julius Maximilian University Würzburg , Am Hubland, D-97074 Würzburg , Germany
| | - Erik Endres
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy and Food Chemistry , Julius Maximilian University Würzburg , Am Hubland, D-97074 Würzburg , Germany
| | - Matthias Scheiner
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy and Food Chemistry , Julius Maximilian University Würzburg , Am Hubland, D-97074 Würzburg , Germany
| | - Sandra Gunesch
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy and Food Chemistry , Julius Maximilian University Würzburg , Am Hubland, D-97074 Würzburg , Germany
| | - Christoph Sotriffer
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy and Food Chemistry , Julius Maximilian University Würzburg , Am Hubland, D-97074 Würzburg , Germany
| | - Tangui Maurice
- INSERM UMR-S1198 , University of Montpellier , Place Eugène Bataillon , Montpellier F-34095 , France
| | - Michael Decker
- Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy and Food Chemistry , Julius Maximilian University Würzburg , Am Hubland, D-97074 Würzburg , Germany
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Gómez-Betancur I, Zhao J, Tan L, Chen C, Yu G, Rey-Suárez P, Preciado L. Bioactive Compounds Isolated from Marine Bacterium Vibrio neocaledonicus and Their Enzyme Inhibitory Activities. Mar Drugs 2019; 17:E401. [PMID: 31288374 PMCID: PMC6669558 DOI: 10.3390/md17070401] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 06/27/2019] [Accepted: 07/02/2019] [Indexed: 01/26/2023] Open
Abstract
Marine organisms are recognized as a source of compounds with interesting biological activities. Vibrio neocaledonicus has been reported on for its high effectiveness against corrosion in metals but it has been little studied for its chemical and biological activities. In this study, four compounds were isolated from V. neocaledonicus: indole (1); 1H-indole-3-carboxaldehyde (2); 4-hydroxybenzaldehyde (3) and Cyclo (-Pro-Tyr) (4); using a bioassay-guided method, since in a previous study it was found that the ethyl acetate extract was active on the enzymes acetylcholinesterase (AChE), alpha-glucosidase (AG) and xanthine oxidase (XO). The inhibitory activities of the three compounds against AChE, AG and XO was also evaluated. In addition, the enzymatic inhibitory activity of indole to the toxins from the venom of Bothrops asper was tested. Results showed that indole exhibited strong inhibitory activity to AG (IC50 = 18.65 ± 1.1 μM), to AChE, and XO (51.3% and 44.3% at 50 μg/mL, respectively). 1H-indole-3-carboxaldehyde displayed strong activity to XO (IC50 = 13.36 ± 0.39 μM). 4-hydroxybenzaldehyde showed moderate activity to XO (50.75% at 50 μg/mL) and weak activity to AChE (25.7% at 50 μg/mL). Furthermore, indole showed a significant in vitro inhibition to the coagulant effect induced by 1.0 μg of venom. The findings were supported by molecular docking. This is the first comprehensive report on the chemistry of V. neocaledonicus and the bioactivity of its metabolites.
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Affiliation(s)
- Isabel Gómez-Betancur
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
- Programa Ofidismo-Escorpionismo, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia, Medellín 1226, Colombia
| | - Jianping Zhao
- National Center for National Products Research, School of Pharmacy, University of Mississippi, MS 38677, USA
| | - Lin Tan
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China.
| | - Chang Chen
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Ge Yu
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, China
| | - Paola Rey-Suárez
- Programa Ofidismo-Escorpionismo, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia, Medellín 1226, Colombia
| | - Lina Preciado
- Programa Ofidismo-Escorpionismo, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia, Medellín 1226, Colombia
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Ghosh S, Jana K, Ganguly B. Revealing the mechanistic pathway of cholinergic inhibition of Alzheimer's disease by donepezil: a metadynamics simulation study. Phys Chem Chem Phys 2019; 21:13578-13589. [PMID: 31173012 DOI: 10.1039/c9cp02613d] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Donepezil, an acetylcholinesterase inhibitor, is an approved drug for the symptomatic treatment of Alzheimer's disease (AD). The mechanistic pathway for the inhibition mechanism of acetylcholinesterase (AChE) by donepezil is not well explored. We report for the first time, the inhibition mechanism of AChE by the donepezil drug molecule for the hydrolysis of acetylcholine (ACh) with docking and well-tempered metadynamics (WTMtD) simulations with a human acetylcholinesterase (hAChE) crystal structure (). This study explored the orientation of the donepezil drug molecule inside the gorge of AChE. The 1D free energy surface obtained from WTMtD simulation studies reveals that the orientation of donepezil in the crystal donepezil (-87.25 kJ mol-1) is energetically more favored than the other orientation of donepezil (-74.74 kJ mol-1) for inhibition of AChE. The free energy landscape computation for the two sets of CVs further corroborates the 1D free energy surface. The WTMtD simulation performed with the crystal structure of donepezil bound hAChE gives the conformation of donepezil at Basin-I as similar to the conformation of donepezil observed in the crystal structure (). The WTMtD simulations further reveal that the bridged water molecules are more ordered near the catalytic triad of AChE to deter the nucleophilicity of Ser203 through intermolecular hydrogen bonding when donepezil approaches near to the active site gorge of AChE. The presence of donepezil near the active site of AChE can inhibit its approach for ACh hydrolysis; this is revealed through the docking study, where the drug molecule inside the active gorge of hAChE restricts the approach of ACh to Ser203 for the hydrolysis process.
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Affiliation(s)
- Shibaji Ghosh
- Computation and Simulation Unit (Analytical and Environmental Science Division and Centralized Instrument Facility), CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat 364 002, India. and Academy of Scientific and Innovative Research, CSIR-CSMCRI, Bhavnagar, Gujarat 364 002, India
| | - Kalyanashis Jana
- Computation and Simulation Unit (Analytical and Environmental Science Division and Centralized Instrument Facility), CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat 364 002, India. and Academy of Scientific and Innovative Research, CSIR-CSMCRI, Bhavnagar, Gujarat 364 002, India
| | - Bishwajit Ganguly
- Computation and Simulation Unit (Analytical and Environmental Science Division and Centralized Instrument Facility), CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat 364 002, India. and Academy of Scientific and Innovative Research, CSIR-CSMCRI, Bhavnagar, Gujarat 364 002, India
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Şenocak A, Köksoy B, Akyüz D, Koca A, Klyamer D, Basova T, Demirbaş E, Durmuş M. Highly selective and ultra-sensitive electrochemical sensor behavior of 3D SWCNT-BODIPY hybrid material for eserine detection. Biosens Bioelectron 2019; 128:144-150. [DOI: 10.1016/j.bios.2018.12.052] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 12/15/2018] [Accepted: 12/28/2018] [Indexed: 10/27/2022]
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Köksal Z, Alım Z, Bayrak S, Gülçin İ, Özdemir H. Investigation of the effects of some sulfonamides on acetylcholinesterase and carbonic anhydrase enzymes. J Biochem Mol Toxicol 2019; 33:e22300. [DOI: 10.1002/jbt.22300] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/15/2019] [Accepted: 01/29/2019] [Indexed: 01/02/2023]
Affiliation(s)
- Zeynep Köksal
- Department of ChemistryFaculty of Sciences, Istanbul Medeniyet UniversityIstanbul Turkey
| | - Zuhal Alım
- Department of ChemistryFaculty of Science and Arts, Kırşehir Ahi Evran UniversityKırsehir Turkey
| | - Songül Bayrak
- Department of ChemistryFaculty of Sciences, Atatürk UniversityErzurum Turkey
| | - İlhami Gülçin
- Department of ChemistryFaculty of Sciences, Atatürk UniversityErzurum Turkey
| | - Hasan Özdemir
- Department of ChemistryFaculty of Sciences, Atatürk UniversityErzurum Turkey
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Wan Y, Guan S, Qian M, Huang H, Han F, Wang S, Zhang H. Structural basis of fullerene derivatives as novel potent inhibitors of protein acetylcholinesterase without catalytic active site interaction: insight into the inhibitory mechanism through molecular modeling studies. J Biomol Struct Dyn 2019; 38:410-425. [DOI: 10.1080/07391102.2019.1576543] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yongfeng Wan
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, People’s Republic of China
| | - Shanshan Guan
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, People’s Republic of China
- College of Biology and Food Engineering, Jilin Engineering Normal University, Changchun, Jilin, China
| | - Mengdan Qian
- State Key Laboratory on Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, Changchun, China
| | - Houhou Huang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, People’s Republic of China
| | - Fei Han
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, People’s Republic of China
| | - Song Wang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, People’s Republic of China
| | - Hao Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, People’s Republic of China
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Wang YH, Zhang F, Diao H, Wu R. Covalent Inhibition Mechanism of Antidiabetic Drugs—Vildagliptin vs Saxagliptin. ACS Catal 2019. [DOI: 10.1021/acscatal.8b05051] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yong-Heng Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Jinan University, Guangzhou 510632, P. R. China
| | - Fan Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China
| | - Hongjuan Diao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China
| | - Ruibo Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China
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Abreu PA, Carvalho KDL, Rabelo VWH, Castro HC. Computational strategy for visualizing structures and teaching biochemistry. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2019; 47:76-84. [PMID: 30578716 DOI: 10.1002/bmb.21199] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 11/08/2018] [Accepted: 12/02/2018] [Indexed: 06/09/2023]
Abstract
Computational techniques have great potential to improve the teaching-learning. In this work, we used a computational strategy to visualize three-dimensional (3D) structures of proteins and DNA and help the student to comprehend biochemistry concepts such as protein structure and function, substrate, and inhibitors as well as DNA structural features. The practical classes included tutorials to be done in the computer using structures from Protein Data Bank and a free 3D structure visualization software, Swiss PDB Viewer. The activity was done with 76 students from biology and pharmacy undergraduate courses. Questionnaires were administered to evaluate the knowledge regarding specific biochemistry contents before and after the activity and the opinion of the students. An overall increased percentage of correct answers post-classes (75.91%) were observed in comparison to pre-classes (35.53%). All the students indicated that it could contribute to the learning of DNA and protein structure contents; approximately 90% stated that it enables structures visualization or makes the learning and understanding easier. Therefore, the strategy has shown to be effective, allowing the contextualization of biochemistry themes and may complement theoretical classes. © 2018 International Union of Biochemistry and Molecular Biology, 47(1):76-84, 2018.
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Affiliation(s)
- Paula Alvarez Abreu
- Laboratório de Modelagem molecular e Pesquisa em Ciências Farmacêuticas (LAMCIFAR), NUPEM, Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
| | - Karina de Lima Carvalho
- Laboratório de Antibióticos, Bioquímica, Ensino e Modelagem Molecular (LabiEMol), Instituto de Biologia, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil
| | - Vitor Won-Held Rabelo
- Programa de Pós-graduação em Ciências e Biotecnologia, Instituto de Biologia, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil
| | - Helena Carla Castro
- Laboratório de Antibióticos, Bioquímica, Ensino e Modelagem Molecular (LabiEMol), Instituto de Biologia, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil
- Programa de Pós-graduação em Ciências e Biotecnologia, Instituto de Biologia, Universidade Federal Fluminense, Niterói, Rio de Janeiro, Brazil
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Sharma P, Srivastava P, Seth A, Tripathi PN, Banerjee AG, Shrivastava SK. Comprehensive review of mechanisms of pathogenesis involved in Alzheimer's disease and potential therapeutic strategies. Prog Neurobiol 2018; 174:53-89. [PMID: 30599179 DOI: 10.1016/j.pneurobio.2018.12.006] [Citation(s) in RCA: 207] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 12/04/2018] [Accepted: 12/28/2018] [Indexed: 12/14/2022]
Abstract
AD is a progressive neurodegenerative disorder and a leading cause of dementia in an aging population worldwide. The enormous challenge which AD possesses to global healthcare makes it as urgent as ever for the researchers to develop innovative treatment strategies to fight this disease. An in-depth analysis of the extensive available data associated with the AD is needed for a more comprehensive understanding of underlying molecular mechanisms and pathophysiological pathways associated with the onset and progression of the AD. The currently understood pathological and biochemical manifestations include cholinergic, Aβ, tau, excitotoxicity, oxidative stress, ApoE, CREB signaling pathways, insulin resistance, etc. However, these hypotheses have been criticized with several conflicting reports for their involvement in the disease progression. Several issues need to be addressed such as benefits to cost ratio with cholinesterase therapy, the dilemma of AChE selectivity over BChE, BBB permeability of peptidic BACE-1 inhibitors, hurdles related to the implementation of vaccination and immunization therapy, and clinical failure of candidates related to newly available targets. The present review provides an insight to the different molecular mechanisms involved in the development and progression of the AD and potential therapeutic strategies, enlightening perceptions into structural information of conventional and novel targets along with the successful applications of computational approaches for the design of target-specific inhibitors.
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Affiliation(s)
- Piyoosh Sharma
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Pavan Srivastava
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Ankit Seth
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Prabhash Nath Tripathi
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Anupam G Banerjee
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Sushant K Shrivastava
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India.
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The exploration of novel Alzheimer's therapeutic agents from the pool of FDA approved medicines using drug repositioning, enzyme inhibition and kinetic mechanism approaches. Biomed Pharmacother 2018; 109:2513-2526. [PMID: 30551512 DOI: 10.1016/j.biopha.2018.11.115] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/19/2018] [Accepted: 11/25/2018] [Indexed: 12/11/2022] Open
Abstract
Novel drug development is onerous, time consuming and overpriced process with particularly low success and relatively high enfeebling rates. To overcome this burden, drug repositioning approach is being used to predict the possible therapeutic effects of FDA approved drugs in different diseases. Herein, we designed a computational and enzyme inhibitory mechanistic approach to fetch the promising drugs from the pool of FDA approved drugs against AD. The binding interaction patterns and conformations of screened drugs within active region of AChE were confirmed through molecular docking profiles. The possible associations of selected drugs with AD genes were predicted by pharmacogenomics analysis and confirmed through data mining. The stability behaviour of docked complexes (Drugs-AChE) were checked by MD simulations. The possible therapeutic potential of repositioned drugs against AChE were checked by in vitro analysis. Taken together, Cinitapride displayed a comparable results with standard and can be used as possible therapeutic agent in the treatment of AD.
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Mladenović M, Arsić BB, Stanković N, Mihović N, Ragno R, Regan A, Milićević JS, Trtić-Petrović TM, Micić R. The Targeted Pesticides as Acetylcholinesterase Inhibitors: Comprehensive Cross-Organism Molecular Modelling Studies Performed to Anticipate the Pharmacology of Harmfulness to Humans In Vitro. Molecules 2018; 23:molecules23092192. [PMID: 30200244 PMCID: PMC6225315 DOI: 10.3390/molecules23092192] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 08/24/2018] [Accepted: 08/24/2018] [Indexed: 12/26/2022] Open
Abstract
Commercially available pesticides were examined as Mus musculus and Homo sapiens acetylcholinesterase (mAChE and hAChE) inhibitors by means of ligand-based (LB) and structure-based (SB) in silico approaches. Initially, the crystal structures of simazine, monocrotophos, dimethoate, and acetamiprid were reproduced using various force fields. Subsequently, LB alignment rules were assessed and applied to determine the inter synaptic conformations of atrazine, propazine, carbofuran, carbaryl, tebufenozide, imidacloprid, diuron, monuron, and linuron. Afterwards, molecular docking and dynamics SB studies were performed on either mAChE or hAChE, to predict the listed pesticides' binding modes. Calculated energies of global minima (Eglob_min) and free energies of binding (∆Gbinding) were correlated with the pesticides' acute toxicities (i.e., the LD50 values) against mice, as well to generate the model that could predict the LD50s against humans. Although for most of the pesticides the low Eglob_min correlates with the high acute toxicity, it is the ∆Gbinding that conditions the LD50 values for all the evaluated pesticides. Derived pLD50 = f(∆Gbinding) mAChE model may predict the pLD50 against hAChE, too. The hAChE inhibition by atrazine, propazine, and simazine (the most toxic pesticides) was elucidated by SB quantum mechanics (QM) DFT mechanistic and concentration-dependent kinetic studies, enriching the knowledge for design of less toxic pesticides.
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Affiliation(s)
- Milan Mladenović
- Kragujevac Center for Computational Biochemistry, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, P.O. Box 60, 34000 Kragujevac, Serbia.
| | - Biljana B Arsić
- Department of Mathematics, Faculty of Sciences and Mathematics, University of Niš, Višegradska 33, 18000 Niš, Serbia.
- Division of Pharmacy and Optometry, University of Manchester, Oxford Road, Manchester M13 9PT, UK.
| | - Nevena Stanković
- Kragujevac Center for Computational Biochemistry, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, P.O. Box 60, 34000 Kragujevac, Serbia.
| | - Nezrina Mihović
- Kragujevac Center for Computational Biochemistry, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, P.O. Box 60, 34000 Kragujevac, Serbia.
| | - Rino Ragno
- Rome Center for Molecular Design, Department of Drug Chemistry and Technologies, Faculty of Pharmacy and Medicine, Sapienza Rome University, P.le A. Moro 5, 00185 Rome, Italy.
- Alchemical Dynamics srl, 00125 Rome, Italy.
| | - Andrew Regan
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, UK.
| | - Jelena S Milićević
- Vinča Institute of Nuclear Sciences, University of Belgrade, P.O. Box 522, 11001 Belgrade, Serbia.
| | - Tatjana M Trtić-Petrović
- Vinča Institute of Nuclear Sciences, University of Belgrade, P.O. Box 522, 11001 Belgrade, Serbia.
| | - Ružica Micić
- Faculty of Sciences and Mathematics, University of Priština, Lole Ribara 29, 38220 Kosovska Mitrovica, Serbia.
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Costanzi S, Machado JH, Mitchell M. Nerve Agents: What They Are, How They Work, How to Counter Them. ACS Chem Neurosci 2018; 9:873-885. [PMID: 29664277 DOI: 10.1021/acschemneuro.8b00148] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Nerve agents are organophosphorus chemical warfare agents that exert their action through the irreversible inhibition of acetylcholinesterase, with a consequent overstimulation of cholinergic transmission followed by its shutdown. Beyond warfare, they have notoriously been employed in acts of terrorism as well as high profile assassinations. After a brief historical introduction on the development and deployment of nerve agents, this review provides a survey of their chemistry, the way they affect cholinergic transmission, the available treatment options, and the current directions for their improvement. As the review illustrates, despite their merits, the currently available treatment options present several shortcomings. Current research directions involve the search for improved antidotes, antagonists of the nicotinic receptors, small-molecule pretreatment options, as well as bioscavengers as macromolecular pretreatment options. These efforts are making good progress in many different directions and, hopefully, will lead to a lower target susceptibility, thus reducing the appeal of nerve agents as chemical weapons.
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Affiliation(s)
| | - John-Hanson Machado
- Department of Chemistry, The George Washington University, 800 22nd Street NW, Washington, DC 20052, United States
- Computational Biology Institute, The George Washington University, 45085 University Drive Suite 305, Ashburn, Virginia 20147, United States
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Acetylcholinesterase Inhibition and Antioxidant Activity of N- trans-Caffeoyldopamine and N- trans-Feruloyldopamine. Sci Pharm 2018; 86:scipharm86020011. [PMID: 29617286 PMCID: PMC6027674 DOI: 10.3390/scipharm86020011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 03/07/2018] [Accepted: 03/24/2018] [Indexed: 11/16/2022] Open
Abstract
Phenolic acids and their derivatives found in nature are well-known for their potential biological activity. In this study, two amides derived from trans-caffeic/ferulic acid and dopamine were synthesized and characterized by Fourier-transform infrared spectroscopy (FTIR), mass spectrometry, proton and carbon-13 nuclear magnetic resonance spectroscopy. The compounds were tested for the inhibition of acetylcholinesterase (AChE) from Electrophorus electricus and for antioxidant activity by scavenging 2,2-diphenyl-1-pycrylhydrazyl free radical (DPPH•) and 2,2′-azinobis(3-ethylbenzothiazoline-6-sulphonic acid) radical cation (ABTS•+), reducing ferric ions, and ferrous ions chelation. N-trans-Feruloyldopamine displayed the highest inhibitory effect on AChE with half-maximal inhibitory concentration (IC50) values of 8.52 μM. In addition, an in silico study was done to determine the most favorable AChE cluster with the synthesized compounds. Further, these clusters were investigated for binding positions at the lowest free binding energy. Both synthesized hydroxycinnamates were found to be better antioxidants than the parent acids in in vitro tests applied. N-trans-Caffeoyldopamine showed the best antioxidant activity in the three tested methods—against non-biological stable free radicals IC50 5.95 μM for DPPH•, 0.24 μM for the ABTS•+ method, and for reducing power (ascorbic acid equivalent (AAE) 822.45 μmol/mmol)—while for chelation activity against Fe2+ ions N-trans-feruloyldopamine had slightly better antioxidant activity (IC50 3.17 mM).
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