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Alhawarri MB, Dianita R, Rawa MSA, Nogawa T, Wahab HA. Potential Anti-Cholinesterase Activity of Bioactive Compounds Extracted from Cassia grandis L.f. and Cassia timoriensis DC. PLANTS (BASEL, SWITZERLAND) 2023; 12:344. [PMID: 36679057 PMCID: PMC9862305 DOI: 10.3390/plants12020344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/27/2022] [Accepted: 07/27/2022] [Indexed: 06/17/2023]
Abstract
Acetylcholinesterase (AChE) inhibitors remain the primary therapeutic drug that can alleviate Alzheimer's disease's (AD) symptoms. Several Cassia species have been shown to exert significant anti-AChE activity, which can be an alternative remedy for AD. Cassia timoriensis and Cassia grandis are potential plants with anti-AChE activity, but their phytochemical investigation is yet to be further conducted. The aims of this study were to identify the phytoconstituents of C. timoriensis and C. grandis and evaluate their inhibitory activity against AChE and butyrylcholinesterase (BChE). Two compounds were isolated for the first time from C. timoriensis: arachidyl arachidate (1) and luteolin (2). Five compounds were identified from C. grandis: β-sitosterol (3), stigmasterol (4), cinnamic acid (5), 4-hydroxycinnamic acid (6), and hydroxymethylfurfural (7). Compound 2 showed significant inhibition towards AChE (IC50: 20.47 ± 1.10 µM) and BChE (IC50: 46.15 ± 2.20 µM), followed by 5 (IC50: 40.5 ± 1.28 and 373.1 ± 16.4 µM) and 6 (IC50: 43.4 ± 0.61 and 409.17 ± 14.80 µM) against AChE and BChE, respectively. The other compounds exhibited poor to slightly moderate AChE inhibitory activity. Molecular docking revealed that 2 showed good binding affinity towards TcAChE (PDB ID: 1W6R) and HsBChE (PDB ID: 4BDS). It formed a hydrogen bond with TYR121 at the peripheral anionic site (PAS, 2.04 Å), along with hydrophobic interactions with the anionic site and PAS (TRP84 and TYR121, respectively). Additionally, 2 formed three H-bonds with the binding site residues: one bond with catalytic triad, HIS438 at distance 2.05 Å, and the other two H-bonds with GLY115 and GLU197 at distances of 2.74 Å and 2.19 Å, respectively. The evidence of molecular interactions of 2 may justify the relevance of C. timoriensis as a cholinesterase inhibitor, having more promising activity than C. grandis.
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Affiliation(s)
- Maram B. Alhawarri
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Minden 11800, Malaysia
- Faculty of Pharmacy, Jadara University, Irbid 21110, Jordan
| | - Roza Dianita
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Minden 11800, Malaysia
| | - Mira Syahfriena Amir Rawa
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Minden 11800, Malaysia
- USM-RIKEN Interdisciplinary Collaboration for Advanced Sciences (URICAS), Universiti Sains Malaysia, Gelugor 11800, Malaysia
| | - Toshihiko Nogawa
- USM-RIKEN Interdisciplinary Collaboration for Advanced Sciences (URICAS), Universiti Sains Malaysia, Gelugor 11800, Malaysia
- Molecular Structure Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Saitama 351-0198, Japan
| | - Habibah A. Wahab
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Minden 11800, Malaysia
- USM-RIKEN Interdisciplinary Collaboration for Advanced Sciences (URICAS), Universiti Sains Malaysia, Gelugor 11800, Malaysia
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2
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Kim HK, Kim M, Marquez JC, Jeong SH, Ko TH, Noh YH, Kha PT, Choi HM, Kim DH, Kim JT, Yang YI, Ko KS, Rhee BD, Shubina LK, Makarieva TN, Yashunsky DY, Gerbst AG, Nifantiev NE, Stonik VA, Han J. Novel GSK-3β Inhibitor Neopetroside A Protects Against Murine Myocardial Ischemia/Reperfusion Injury. JACC Basic Transl Sci 2022; 7:1102-1116. [PMID: 36687267 PMCID: PMC9849271 DOI: 10.1016/j.jacbts.2022.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 03/31/2022] [Accepted: 05/09/2022] [Indexed: 02/01/2023]
Abstract
Recent trends suggest novel natural compounds as promising treatments for cardiovascular disease. The authors examined how neopetroside A, a natural pyridine nucleoside containing an α-glycoside bond, regulates mitochondrial metabolism and heart function and investigated its cardioprotective role against ischemia/reperfusion injury. Neopetroside A treatment maintained cardiac hemodynamic status and mitochondrial respiration capacity and significantly prevented cardiac fibrosis in murine models. These effects can be attributed to preserved cellular and mitochondrial function caused by the inhibition of glycogen synthase kinase-3 beta, which regulates the ratio of nicotinamide adenine dinucleotide to nicotinamide adenine dinucleotide, reduced, through activation of the nuclear factor erythroid 2-related factor 2/NAD(P)H quinone oxidoreductase 1 axis in a phosphorylation-independent manner.
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Key Words
- ATP, adenosine triphosphate
- GSK-3, glycogen synthase kinase–3
- GSK-3β inhibition
- I/R, ischemia/reperfusion
- MI, myocardial infarction
- NAD+, nicotinamide adenine dinucleotide
- NADH, nicotinamide adenine dinucleotide, reduced
- NPS A
- NPS A, neopetroside A
- Nqo1, NAD(P)H:quinone oxidoreductase 1
- Nrf2, nuclear factor erythroid 2–related factor 2
- OCR, oxygen consumption rate
- ischemia/reperfusion injury
- mPTP, mitochondrial permeability transition pore
- mTOR, mammalian target of rapamycin
- marine pyridine α-nucleoside
- mitochondria
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Affiliation(s)
- Hyoung Kyu Kim
- Cardiovascular and Metabolic Disease Center, Inje University, Busan, South Korea,Department of Health Sciences and Technology, Graduate School, Inje University, Busan, South Korea
| | - Min Kim
- Cardiovascular and Metabolic Disease Center, Inje University, Busan, South Korea,Department of Physiology, BK Plus Project Team, College of Medicine, Inje University, Busan, South Korea
| | - Jubert C. Marquez
- Cardiovascular and Metabolic Disease Center, Inje University, Busan, South Korea,Department of Health Sciences and Technology, Graduate School, Inje University, Busan, South Korea
| | - Seung Hun Jeong
- Cardiovascular and Metabolic Disease Center, Inje University, Busan, South Korea,Department of Physiology, BK Plus Project Team, College of Medicine, Inje University, Busan, South Korea
| | - Tae Hee Ko
- Cardiovascular and Metabolic Disease Center, Inje University, Busan, South Korea,Department of Physiology, BK Plus Project Team, College of Medicine, Inje University, Busan, South Korea
| | - Yeon Hee Noh
- Cardiovascular and Metabolic Disease Center, Inje University, Busan, South Korea,Department of Physiology, BK Plus Project Team, College of Medicine, Inje University, Busan, South Korea
| | - Pham Trong Kha
- Cardiovascular and Metabolic Disease Center, Inje University, Busan, South Korea,Department of Physiology, BK Plus Project Team, College of Medicine, Inje University, Busan, South Korea
| | - Ha Min Choi
- Cardiovascular and Metabolic Disease Center, Inje University, Busan, South Korea,Department of Physiology, BK Plus Project Team, College of Medicine, Inje University, Busan, South Korea
| | - Dong Hyun Kim
- Department of Pharmacology and Pharmaco-Genomics Research Center, College of Medicine, Inje University, Busan, South Korea
| | - Jong Tae Kim
- Paik Institute for Clinical Research, Inje University College of Medicine, Busan, South Korea
| | - Young Il Yang
- Paik Institute for Clinical Research, Inje University College of Medicine, Busan, South Korea
| | - Kyung Soo Ko
- Cardiovascular and Metabolic Disease Center, Inje University, Busan, South Korea,Department of Health Sciences and Technology, Graduate School, Inje University, Busan, South Korea
| | - Byoung Doo Rhee
- Cardiovascular and Metabolic Disease Center, Inje University, Busan, South Korea,Department of Health Sciences and Technology, Graduate School, Inje University, Busan, South Korea
| | - Larisa K. Shubina
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Science, Vladivostok, Russia
| | - Tatyana N. Makarieva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Science, Vladivostok, Russia
| | - Dmitry Y. Yashunsky
- Laboratory of Glycoconjugate Chemistry, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexey G. Gerbst
- Laboratory of Glycoconjugate Chemistry, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Nikolay E. Nifantiev
- Laboratory of Glycoconjugate Chemistry, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Valentin A. Stonik
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Science, Vladivostok, Russia
| | - Jin Han
- Cardiovascular and Metabolic Disease Center, Inje University, Busan, South Korea,Department of Health Sciences and Technology, Graduate School, Inje University, Busan, South Korea,Department of Physiology, BK Plus Project Team, College of Medicine, Inje University, Busan, South Korea,Address for correspondence: Dr Jin Han, National Research Laboratory for Mitochondrial Signaling, Department of Physiology, College of Medicine, Cardiovascular and Metabolic Disease Center, Inje University, Busan 47393, South Korea.
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3
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Pathak S, Gokhroo A, Kumar Dubey A, Majumdar S, Gupta S, Almeida A, Mahajan GB, Kate A, Mishra P, Sharma R, Kumar S, Vishwakarma R, Balakrishnan A, Atreya H, Nandi D. 7-Hydroxy Frullanolide, a sesquiterpene lactone, increases intracellular calcium amounts, lowers CD4 + T cell and macrophage responses, and ameliorates DSS-induced colitis. Int Immunopharmacol 2021; 97:107655. [PMID: 33901737 DOI: 10.1016/j.intimp.2021.107655] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/19/2021] [Accepted: 04/03/2021] [Indexed: 12/16/2022]
Abstract
Sesquiterpene lactones are a class of anti-inflammatory molecules obtained from plants belonging to the Asteraceae family. In this study, the effects of 7-hydroxy frullanolide (7HF), a sesquiterpene lactone, in inhibiting CD4+ T cell and peritoneal macrophage responses were investigated. 7HF, in a dose dependent manner, lowers CD69 upregulation, IL2 production and CD4+ T cell cycling upon activation with the combination of anti-CD3 and anti-CD28. Further mechanistic studies demonstrated that 7HF, at early time points, increases intracellular Ca2+ amounts, over and above the levels induced upon activation. The functional relevance of 7HF-induced Ca2+ increase was confirmed using sub-optimal amounts of BAPTA, an intracellular Ca2+ chelator, which lowers lactate and rescues CD4+ T cell cycling. In addition, 7HF lowers T cell cycling with the combination of PMA and Ionomycin. However, 7HF increases CD4+ T cell cycling with sub-optimal activating signals: only PMA or anti-CD3. Furthermore, LPS-induced nitrite and IL6 production by peritoneal macrophages is inhibited by 7HF in a Ca2+-dependent manner. Studies with Ca2+ channel inhibitors, Ruthenium Red and 2-Aminoethoxydiphenyl borate, lowers the inhibitory effects of 7HF on CD4+ T cell and macrophage responses. In silico studies demonstrated that 7HF binds to Ca2+ channels, TRPV1, IP3R and SERCA, which is mechanistically important. Finally, intraperitoneal administration of 7HF lowers serum inflammatory cytokines, IFNγ and IL6, and reduces the effects of DSS-induced colitis with respect to colon length and colon damage. Overall, this study sheds mechanistic light on the anti-inflammatory potential of 7HF, a natural plant compound, in lowering immune responses.
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Affiliation(s)
- Sanmoy Pathak
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Abhijeet Gokhroo
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Ashim Kumar Dubey
- Undergraduate Program, Indian Institute of Science, Bangalore 560012, India
| | - Shamik Majumdar
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Souradeep Gupta
- NMR Research Facility, Indian Institute of Science, Bangalore 560012, India
| | - Asha Almeida
- High Throughput Department, Piramal Research Center,1 Nirlon Complex, Off Western Express Highway, Goregaon East, Mumbai 400063, India
| | - Girish B Mahajan
- High Throughput Department, Piramal Research Center,1 Nirlon Complex, Off Western Express Highway, Goregaon East, Mumbai 400063, India
| | - Abhijeet Kate
- High Throughput Department, Piramal Research Center,1 Nirlon Complex, Off Western Express Highway, Goregaon East, Mumbai 400063, India
| | - Prabhu Mishra
- High Throughput Department, Piramal Research Center,1 Nirlon Complex, Off Western Express Highway, Goregaon East, Mumbai 400063, India
| | - Rajiv Sharma
- High Throughput Department, Piramal Research Center,1 Nirlon Complex, Off Western Express Highway, Goregaon East, Mumbai 400063, India
| | - Sanjay Kumar
- High Throughput Department, Piramal Research Center,1 Nirlon Complex, Off Western Express Highway, Goregaon East, Mumbai 400063, India
| | - Ram Vishwakarma
- High Throughput Department, Piramal Research Center,1 Nirlon Complex, Off Western Express Highway, Goregaon East, Mumbai 400063, India
| | - Arun Balakrishnan
- High Throughput Department, Piramal Research Center,1 Nirlon Complex, Off Western Express Highway, Goregaon East, Mumbai 400063, India
| | - Hanudatta Atreya
- NMR Research Facility, Indian Institute of Science, Bangalore 560012, India
| | - Dipankar Nandi
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
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4
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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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5
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Design, synthesis and evaluation of cholinesterase hybrid inhibitors using a natural steroidal alkaloid as precursor. Bioorg Chem 2021; 111:104893. [PMID: 33882364 DOI: 10.1016/j.bioorg.2021.104893] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 04/01/2021] [Accepted: 04/03/2021] [Indexed: 01/05/2023]
Abstract
To date, Alzheimer's disease is the most alarming neurodegenerative disorder worldwide. This illness is multifactorial in nature and cholinesterase inhibitors have been the ones used in clinical treatments. In this context, many of these drugs selectively inhibit the acetylcholinesterase enzyme interacting in both the active site and the peripheric anionic site. Besides, some agents have exhibited extensive benefits being able to co-inhibit butyrylcholinesterase. In this contribution, a strategy previously explored by numerous authors is reported; the synthesis of hybrid cholinesterase inhibitors. This strategy uses a molecule of recognized high inhibitory activity (tacrine) together with a steroidal alkaloid of natural origin using different connectors. The biological assays demonstrated the improvement in the inhibitory activity compared to the alkaloidal precursor, together with the reinforcement of the interactions in multiple sites of the enzymatic cavity. This strategy should be explored and exploited in this area. Docking and molecular dynamic studies were performed to explain enzyme-ligand interactions, assisting a structure-activity relationship analysis.
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6
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Bhol P, Mohanty M, Mohanty PS. Polymer-matrix stabilized metal nanoparticles: Synthesis, characterizations and insight into molecular interactions between metal ions, atoms and polymer moieties. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.115135] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Pathak G, Singh S, Kumari P, Hussain Y, Raza W, Luqman S, Meena A. Cirsilineol inhibits proliferation of lung squamous cell carcinoma by inducing ROS mediated apoptosis. Food Chem Toxicol 2020; 143:111550. [DOI: 10.1016/j.fct.2020.111550] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/05/2020] [Accepted: 06/20/2020] [Indexed: 02/07/2023]
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8
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Ding F, Peng W, Peng YK, Liu BQ. Elucidating the potential neurotoxicity of chiral phenthoate: Molecular insight from experimental and computational studies. CHEMOSPHERE 2020; 255:127007. [PMID: 32416396 DOI: 10.1016/j.chemosphere.2020.127007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 06/11/2023]
Abstract
Chiral organophosphorus pollutants are existed ubiquitously in the ecological environment, but the enantioselective toxicities of these nerve agents to humans and their molecular bases have not been fully elucidated. Using experimental and computational approaches, this story was to explore the neurotoxic response process of the target acetylcholinesterase (AChE) to chiral phenthoate and further decipher the microscopic mechanism of such toxicological effect at the enantiomeric level. The results showed that the toxic reaction of AChE with chiral phenthoate exhibited significant enantioselectivity, and (R)-phenthoate (K=1.486 × 105 M-1) has a bioaffinity for the nerve enzyme nearly three times that of (S)-phenthoate (K=4.503 × 104 M-1). Dynamic research outcomes interpreted the wet experiments, and the inherent conformational flexibility of the target enzyme has a great influence on the enantioselective neurotoxicological action processes, especially reflected in the conformational changes of the three key loop regions (i.e. residues His-447, Gly-448, and Tyr-449; residues Gly-122, Phe-123, and Tyr-124; and residues Thr-75, Leu-76, and Tyr-77) around the reaction patch. This was supported by the quantitative results of conformational studies derived from circular dichroism spectroscopy (α-helix: 34.7%→30.2%/31.6%; β-sheet: 23.6%→19.5%/20.7%; turn: 19.2%→22.4%/21.9%; and random coil: 22.5%→27.9%/25.8%). Meanwhile, via analyzing the modes of toxic action and free energies, we can find that (R)-phenthoate has a strong inhibitory effect on the enzymatic activity of AChE, as compared with (S)-phenthoate, and electrostatic energy (-23.79/-17.77 kJ mol-1) played a critical role in toxicological reactions. These points were the underlying causes of chiral phenthoate displaying different degrees of enantioselective neurotoxicity.
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Affiliation(s)
- Fei Ding
- Department of Environmental Science and Engineering, School of Water and Environment, Chang'an University, Xi'an, 710054, China; Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education, Chang'an University, No. 126 Yanta Road, Yanta District, Xi'an, 710054, China
| | - Wei Peng
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Yu-Kui Peng
- Center for Food Quality Supervision, Inspection & Testing, Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, 712100, China
| | - Bing-Qi Liu
- Department of Agricultural Chemistry, Qingdao Agricultural University, Qingdao, 266109, China
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Khare N, Maheshwari SK, Jha AK. Screening and identification of secondary metabolites in the bark of Bauhinia variegata to treat Alzheimer's disease by using molecular docking and molecular dynamics simulations. J Biomol Struct Dyn 2020; 39:5988-5998. [PMID: 32720564 DOI: 10.1080/07391102.2020.1796798] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Acetylcholinesterase (AChE) and Butyrylcholinesterase (BChE) acts as a promising protein targets for which drug as an inhibitor can be designed to treat Alzheimer's Disease. Different flavonoids and alkaloids of Bauhinia variegata were used as an inhibitor to target the protein. The current in silico study was carried out to explore the binding patterns of flavanoids and alkaloids against Acetylcholinesterase (PDB ID: 4PQE) and Butyrylcholinesterase (PDB ID: 1P0I) using molecular docking and molecular dynamics simulations approach. Molecular docking result shows that Dihydroquercetin (CID:439533) binds with the active region of AChE and BChE. Using molsoft, molinspiration, and pkCSM all the properties of the candidate were analyzed. The best compound Dihydroquercetin was compared with Donepezil drug through molecular dynamic simulation studies. The analysis of Molecular Dynamics Simulations showed that AChE and AChE-Dihydroquercetin complex became stable at 3000 ps and there was little conformational change in BChE and BChE-Dihydroquercetin complex. The in silico study finally predicts that Dihydroquercetin may act as a good inhibitor for treating Alzheimer's disease and further in vitro and in vivo studies may prove its therapeutic potential.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Noopur Khare
- Institute of Technology and Management, Meerut, Uttar Pradesh, Affiliated to Dr. A.P.J. Abdul Kalam Technical University, Lucknow, India.,Shri Ramswaroop Memorial University, Barabanki, India
| | | | - Abhimanyu Kumar Jha
- Institute of Technology and Management, Meerut, Uttar Pradesh, Affiliated to Dr. A.P.J. Abdul Kalam Technical University, Lucknow, India.,Faculty of Life Sciences, Institute of Applied Medicines and Research, Ghaziabad, India
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Pathak G, Singh S, Kumari P, Raza W, Hussain Y, Meena A. Cirsimaritin, a lung squamous carcinoma cells (NCIH-520) proliferation inhibitor. J Biomol Struct Dyn 2020; 39:3312-3323. [PMID: 32362196 DOI: 10.1080/07391102.2020.1763198] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Cirsimaritin is a dimethoxy flavone, which is present in Ocimum sanctum, Microtea debilis, Artemisia judaica, Cirsium japonicum, and Lithocarpus dealbatus. Its antiproliferative potential has been explored in breast and gall bladder cancer cell lines. However, no reports are available on skin and squamous lung carcinoma. Also, the complete mode of action is unknown. Therefore, in the present study, the anticancer potential of cirsimaritin is explored in organ-specific cell lines by using MTT assay. Further, the inhibitory potential and binding interaction with the selected targets were analyzed through in vitro and in-silico analysis. Cirsimaritin showed selective anticancer activity against NCIH-520 cell-line (IC50 23.29 µM), also inhibited the proliferation of other cell-lines up to 48% at 100 µM. In NCIH-520 cell-line, cirsimaritin significantly increased the apoptosis of the cells at both the tested concentrations (10 and 100 µM), which was confirmed by Annexin-V signifying the induction of late apoptosis. Besides, an increase in the ROS levels of 1.6 fold (10 µM) and 1.8 fold (100 µM), circimaritin also inhibits the activity of ODC and CATD with the IC50 57.30 and 68.22 µM respectively. It exhibited a good binding score with the selected targets, follow Lipinski's rule of five and non-mutagenic. Hence, cirsimaritin is a potent molecule, which inhibits the proliferation of lung squamous cell lines by inducing apoptosis. It also inhibited the activity of ODC and CATD responsible for the progression phase in the cancer cells. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gauri Pathak
- Molecular Bioprospection Department, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Shilpi Singh
- Molecular Bioprospection Department, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Priyanka Kumari
- Molecular Bioprospection Department, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Waseem Raza
- Molecular Bioprospection Department, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India.,Jawaharlal Nehru University, New Delhi, India
| | - Yusuf Hussain
- Molecular Bioprospection Department, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Abha Meena
- Molecular Bioprospection Department, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Ansari F, Ghasemi JB, Niazi A. Three Dimensional Quantitative Structure Activity Relationship and Pharmacophore Modeling of Tacrine Derivatives as Acetylcholinesterase Inhibitors in Alzheimer's Treatment. Med Chem 2020; 16:155-168. [DOI: 10.2174/1573406415666190513100646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 03/23/2019] [Accepted: 05/01/2019] [Indexed: 11/22/2022]
Abstract
Background:
Three dimensional quantitative structure activity relationship and pharmacophore
modeling are studied for tacrine derivatives as acetylcholinesterase inhibitors.
Methods:
The three dimensional quantitative structure–activity relationship and pharmacophore
methods were used to model the 68 derivatives of tacrine as human acetylcholinesterase inhibitors.
The effect of the docked conformer of each molecule in the enzyme cavity was investigated on the
predictive ability and statistical quality of the produced models.
Results:
The whole data set was divided into two training and test sets using hierarchical clustering
method. 3D-QSAR model, based on the comparative molecular field analysis has good statistical
parameters as indicated by q2 =0.613, r2 =0.876, and r2pred =0.75. In the case of comparative
molecular similarity index analysis, q2, r2 and r2pred values were 0.807, 0.96, and 0.865 respectively.
The statistical parameters of the models proved that the inhibition data are well fitted and
they have satisfactory predictive abilities.
Conclusion :
The results from this study illustrate the reliability of using techniques in exploring
the likely bonded conformations of the ligands in the active site of the protein target and improve
the understanding over the structural and chemical features of AChE.
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Affiliation(s)
- Fatemeh Ansari
- Department of Chemistry, Arak Branch, Islamic Azad University, Arak, Iran
| | - Jahan B. Ghasemi
- Drug Design in Silico Lab, School of Sciences, Chemistry Faculty, University of Tehran, Tehran, Iran
| | - Ali Niazi
- Department of Chemistry, Central Tehran Branch, Islamic Azad University, Tehran, Iran
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12
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Hartman Z, Geldenhuys WJ, Agazie YM. A specific amino acid context in EGFR and HER2 phosphorylation sites enables selective binding to the active site of Src homology phosphatase 2 (SHP2). J Biol Chem 2020; 295:3563-3575. [PMID: 32024694 DOI: 10.1074/jbc.ra119.011422] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 01/22/2020] [Indexed: 11/06/2022] Open
Abstract
The Src homology phosphatase 2 (SHP2) is a cytoplasmic enzyme that mediates signaling induced by multiple receptor tyrosine kinases, including signaling by the epidermal growth factor receptor (EGFR) family (EGFR1-4 or the human homologs HER1-4). In EGFR (HER1) and EGFR2 (HER2) signaling, SHP2 increases the half-life of activated Ras by blocking recruitment of Ras GTPase-activating protein (RasGAP) to the plasma membrane through dephosphorylation of docking sites on the receptors. However, it is unclear how SHP2 selectively recognizes RasGAP-binding sites on EGFR and HER2. In this report, we show that SHP2-targeted pTyr residues exist in a specific amino acid context that allows selective binding. More specifically, we show that acidic residues N-terminal to the substrate pTyr in EGFR and HER2 mediate specific binding by the SHP2 active site, leading to blockade of RasGAP binding and optimal signaling by the two receptors. Molecular modeling studies revealed that a peptide derived from the region of pTyr992-EGFR packs well and makes stronger interactions with the SHP2 active site than with the SHP1 active site, suggesting a built-in mechanism that enables selective substrate recognition by SHP2. A phosphorylated form of this peptide inhibits SHP2 activity in vitro and EGFR and HER2 signaling in cells, suggesting inhibition of SHP2 protein tyrosine phosphatase activity by this peptide. Although we do not expect this peptide to be a strong inhibitor by itself, we foresee that the insights into SHP2 selectivity described here will be useful in future development of active-site small molecule-based inhibitors.
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Affiliation(s)
- Zachary Hartman
- Department of Biochemistry, School of Medicine West Virginia University, Morgantown, West Virginia 26506
| | - Werner J Geldenhuys
- Department of Basic Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia 26506
| | - Yehenew M Agazie
- Department of Biochemistry, School of Medicine West Virginia University, Morgantown, West Virginia 26506; WVU Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia 26506.
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13
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Bahrami H, Salehabadi H, Nazari Z, Amanlou M. Combined Virtual Screening, DFT Calculations and Molecular Dynamics Simulations to Discovery of Potent MMP-9 Inhibitors. LETT DRUG DES DISCOV 2019. [DOI: 10.2174/1570180815666181008095950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background:
Matrix metalloproteinase-9 (MMP-9) plays a crucial role in the development
and progression of cancer. Therefore, identifying its inhibitors has enjoyed numerous
attentions. In this report, a hybrid approach, including pharmacophore-based virtual screening,
docking studies, and density functional theory (DFT) binding energy calculations followed by
molecular dynamics simulations, was used to identify potential MMP-9 inhibitors.
Methods:
Pharmacophore modeling based on ARP101, as a known MMP-9 inhibitor, was performed
and followed by virtual screening of ZINC database and docking studies to introduce a set
of new ligands as candidates for potent inhibitors of MMP-9. The binding energies of MMP-9
and the selected ligands as well as ARP101, were estimated via the DFT energy calculations.
Subsequently, molecular dynamics simulations were applied to evaluate and compare the behavior
of ARP101 and the selected ligand in a dynamic environment.
Results:
(S,Z)-6-(((2,3-dihydro-1H-benzo[d]imidazol-2-yl)thio)methylene)-2-((4,6,7- trimethylquinazolin-
2-yl)amino)-1,4,5,6-tetrahydropyrimidin-4-ol, ZINC63611396, with the largest
DFT binding energy, was selected as a proper potent MMP-9 inhibitor. Molecular dynamics simulations
indicated that the new ligand was stable in the active site.
Conclusion:
The results of this study revealed that compared to the binding energies achieved
from the docking studies, the binding energies obtained from the DFT calculations were more
consistent with the intermolecular interactions. Also, the interaction between the Zinc ion and
ligand, in particular the Zn2+-ligand distance, played a profound role in the quantity of DFT
binding energies.
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Affiliation(s)
- Hamed Bahrami
- Department of Chemistry, University of Zanjan, P.O. Box 45371-38791 Zanjan, Iran
| | - Hafezeh Salehabadi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, 14176-53955, Iran
| | - Zahra Nazari
- Department of Chemistry, University of Zanjan, P.O. Box 45371-38791 Zanjan, Iran
| | - Massoud Amanlou
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, 14176-53955, Iran
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14
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Bathula R, Lanka G, Muddagoni N, Dasari M, Nakkala S, Bhargavi M, Somadi G, Sivan SK, Rajender Potlapally S. Identification of potential Aurora kinase-C protein inhibitors: an amalgamation of energy minimization, virtual screening, prime MMGBSA and AutoDock. J Biomol Struct Dyn 2019; 38:2314-2325. [DOI: 10.1080/07391102.2019.1630318] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Revanth Bathula
- Molecular Modeling Laboratory, Department of Chemistry, Nizam College, Osmania University, Hyderabad, India
| | - Goverdhan Lanka
- Molecular Modeling Laboratory, Department of Chemistry, Nizam College, Osmania University, Hyderabad, India
| | - Narasimha Muddagoni
- Molecular Modeling Laboratory, Department of Chemistry, Nizam College, Osmania University, Hyderabad, India
| | - Mahendar Dasari
- Molecular Modeling Laboratory, Department of Chemistry, Nizam College, Osmania University, Hyderabad, India
| | - Sravanthi Nakkala
- Molecular Modeling Laboratory, Department of Chemistry, Nizam College, Osmania University, Hyderabad, India
| | - Manan Bhargavi
- Molecular Modeling Laboratory, Department of Chemistry, Nizam College, Osmania University, Hyderabad, India
| | - Gururaj Somadi
- Molecular Modeling Laboratory, Department of Chemistry, Nizam College, Osmania University, Hyderabad, India
| | - Sree Kanth Sivan
- Molecular Modeling Laboratory, Department of Chemistry, Nizam College, Osmania University, Hyderabad, India
| | - Sarita Rajender Potlapally
- Molecular Modeling Laboratory, Department of Chemistry, Nizam College, Osmania University, Hyderabad, India
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15
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Agatonovic-Kustrin S, Kettle C, Morton DW. A molecular approach in drug development for Alzheimer's disease. Biomed Pharmacother 2018; 106:553-565. [PMID: 29990843 DOI: 10.1016/j.biopha.2018.06.147] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 06/20/2018] [Accepted: 06/27/2018] [Indexed: 01/08/2023] Open
Abstract
An increase in dementia numbers and global trends in population aging across the world prompts the need for new medications to treat the complex biological dysfunctions, such as neurodegeneration associated with dementia. Alzheimer's disease (AD) is the most common form of dementia. Cholinergic signaling, which is important in cognition, is slowly lost in AD, so the first line therapy is to treat symptoms with acetylcholinesterase inhibitors to increase levels of acetylcholine. Out of five available FDA-approved AD medications, donepezil, galantamine and rivastigmine are cholinesterase inhibitors while memantine, a N-methyl d-aspartate (NMDA) receptor antagonist, blocks the effects of high glutamate levels. The fifth medication consists of a combination of donepezil and memantine. Although these medications can reduce and temporarily slow down the symptoms of AD, they cannot stop the damage to the brain from progressing. For a superior therapeutic effect, multi-target drugs are required. Thus, a Multi-Target-Directed Ligand (MTDL) strategy has received more attention by scientists who are attempting to develop hybrid molecules that simultaneously modulate multiple biological targets. This review highlights recent examples of the MTDL approach and fragment based strategy in the rational design of new potential AD medications.
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Affiliation(s)
- Snezana Agatonovic-Kustrin
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500, Selangor Darul Ehsan, Malaysia; School of Pharmacy and Applied Science, La Trobe Institute for Molecular Sciences, La Trobe University, Edwards Rd., Bendigo, 3550, Australia.
| | - Christine Kettle
- School of Pharmacy and Applied Science, La Trobe Institute for Molecular Sciences, La Trobe University, Edwards Rd., Bendigo, 3550, Australia
| | - David W Morton
- School of Pharmacy and Applied Science, La Trobe Institute for Molecular Sciences, La Trobe University, Edwards Rd., Bendigo, 3550, Australia
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16
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Hassan M, Shahzadi S, Seo SY, Alashwal H, Zaki N, Moustafa AA. Molecular Docking and Dynamic Simulation of AZD3293 and Solanezumab Effects Against BACE1 to Treat Alzheimer's Disease. Front Comput Neurosci 2018; 12:34. [PMID: 29910719 PMCID: PMC5992503 DOI: 10.3389/fncom.2018.00034] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 05/11/2018] [Indexed: 12/21/2022] Open
Abstract
The design of novel inhibitors to target BACE1 with reduced cytotoxicity effects is a promising approach to treat Alzheimer's disease (AD). Multiple clinical drugs and antibodies such as AZD3293 and Solanezumab are being tested to investigate their therapeutical potential against AD. The current study explores the binding pattern of AZD3293 and Solanezumab against their target proteins such as β-secretase (BACE1) and mid-region amyloid-beta (Aβ) (PDBIDs: 2ZHV & 4XXD), respectively using molecular docking and dynamic simulation (MD) approaches. The molecular docking results show that AZD3293 binds within the active region of BACE1 by forming hydrogen bonds against Asp32 and Lys107 with distances 2.95 and 2.68 Å, respectively. However, the heavy chain of Solanezumab interacts with Lys16 and Asp23 of amyloid beta having bond length 2.82, 2.78, and 3.00 Å, respectively. The dynamic cross correlations and normal mode analyses show that BACE1 depicted good residual correlated motions and fluctuations, as compared to Solanezumab. Using MD, the Root Mean Square Deviation and Fluctuation (RMSD/F) graphs show that AZD3293 residual fluctuations and RMSD value (0.2 nm) was much better compared to Solanezumab (0.7 nm). Moreover, the radius of gyration (Rg) results also depicts the significance of AZD3293 docked complex compared to Solanezumab through residual compactness. Our comparative results show that AZD3293 is a better therapeutic agent for treating AD than Solanezumab.
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Affiliation(s)
- Mubashir Hassan
- College of Natural Science, Department of Biological Sciences, Kongju National University, Gongju, South Korea
| | - Saba Shahzadi
- Institute of Molecular Science and Bioinformatics, Lahore, Pakistan.,Department of Bioinformatics, Virtual University Davis Road, Lahore, Pakistan
| | - Sung Y Seo
- College of Natural Science, Department of Biological Sciences, Kongju National University, Gongju, South Korea
| | - Hany Alashwal
- College of Information Technology, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Nazar Zaki
- College of Information Technology, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Ahmed A Moustafa
- School of Social Sciences and Psychology, MARCS Institute for Brain and Behaviour, Western Sydney University, Sydney, NSW, Australia
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17
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Shi H, Cui Y, Qin Y. Discovery and characterization of a novel tryptophan hydroxylase 1 inhibitor as a prodrug. Chem Biol Drug Des 2017; 91:202-212. [DOI: 10.1111/cbdd.13071] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Revised: 05/31/2017] [Accepted: 06/24/2017] [Indexed: 01/05/2023]
Affiliation(s)
- Hailong Shi
- Laboratory for Functional Glycomics; College of Life Sciences; Northwest University; Xi'an City Shaanxi Province China
- College of Basic Medicine; Shaanxi University of Chinese Medicine; Xi'an-Xianyang New Economic Zone; Xianyang City Shaanxi Province China
| | - Yaya Cui
- College of Basic Medicine; Shaanxi University of Chinese Medicine; Xi'an-Xianyang New Economic Zone; Xianyang City Shaanxi Province China
| | - Yifei Qin
- The Second Clinical Medical College; Shaanxi University of Chinese Medicine; Xi'an-Xianyang New Economic Zone; Xianyang City Shaanxi Province China
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18
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Saeed A, Rehman SU, Channar PA, Larik FA, Abbas Q, Hassan M, Raza H, Flörke U, Seo SY. Long chain 1-acyl-3-arylthioureas as jack bean urease inhibitors, synthesis, kinetic mechanism and molecular docking studies. J Taiwan Inst Chem Eng 2017. [DOI: 10.1016/j.jtice.2017.04.044] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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19
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Meghani NM, Amin HH, Lee BJ. Mechanistic applications of click chemistry for pharmaceutical drug discovery and drug delivery. Drug Discov Today 2017; 22:1604-1619. [PMID: 28754291 DOI: 10.1016/j.drudis.2017.07.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 06/18/2017] [Accepted: 07/17/2017] [Indexed: 01/30/2023]
Abstract
The concept of click chemistry (CC), first introduced by K.B. Sharpless, has been widely adopted for use in drug discovery, novel drug delivery systems (DDS), polymer chemistry, and material sciences. In this review, we outline novel aspects of CC related to drug discovery and drug delivery, with a brief overview of molecular mechanisms underlying each click reaction commonly used by researchers, and the main patents that paved the way for further diverse medicinal applications. We also describe recent progress in drug discovery and polymeric and carbon material-based drug delivery for potential pharmaceutical applications and advancements based on the CC approach, and discuss some intrinsic limitations of this popular conjugation reaction. The use of CC is likely to significantly advance drug discovery and bioconjugation development.
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Affiliation(s)
- Nilesh M Meghani
- College of Pharmacy, Ajou University, Suwon 16499, Republic of Korea
| | - Hardik H Amin
- College of Pharmacy, Ajou University, Suwon 16499, Republic of Korea
| | - Beom-Jin Lee
- College of Pharmacy, Ajou University, Suwon 16499, Republic of Korea; Institute of Pharmaceutical Science and Technology, Ajou University, Suwon 16499, Republic of Korea.
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20
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Hamzeh-Mivehroud M, Sokouti B, Dastmalchi S. Molecular Docking at a Glance. Oncology 2017. [DOI: 10.4018/978-1-5225-0549-5.ch030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The current chapter introduces different aspects of molecular docking technique in order to give an overview to the readers about the topics which will be dealt with throughout this volume. Like many other fields of science, molecular docking studies has experienced a lagging period of slow and steady increase in terms of acquiring attention of scientific community as well as its frequency of application, followed by a pronounced era of exponential expansion in theory, methodology, areas of application and performance due to developments in related technologies such as computational resources and theoretical as well as experimental biophysical methods. In the following sections the evolution of molecular docking will be reviewed and its different components including methods, search algorithms, scoring functions, validation of the methods, and area of applications plus few case studies will be touched briefly.
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Affiliation(s)
| | | | - Siavoush Dastmalchi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Iran & School of Pharmacy, Tabriz University of Medical Sciences, Iran
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21
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Seol JH, Song TY, Oh SE, Jo C, Choi A, Kim B, Park J, Hong S, Song I, Jung KY, Yang JH, Park H, Ahn JH, Han JW, Cho EJ. Identification of small molecules that inhibit the histone chaperone Asf1 and its chromatin function. BMB Rep 2016; 48:685-90. [PMID: 26058396 PMCID: PMC4791324 DOI: 10.5483/bmbrep.2015.48.12.063] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Indexed: 12/01/2022] Open
Abstract
The eukaryotic genome is packed into chromatin, which is important for the genomic integrity and gene regulation. Chromatin structures are maintained through assembly and disassembly of nucleosomes catalyzed by histone chaperones. Asf1 (anti-silencing function 1) is a highly conserved histone chaperone that mediates histone transfer on/off DNA and promotes histone H3 lysine 56 acetylation at globular core domain of histone H3. To elucidate the role of Asf1 in the modulation of chromatin structure, we screened and identified small molecules that inhibit Asf1 and H3K56 acetylation without affecting other histone modifications. These pyrimidine-2,4,6-trione derivative molecules inhibited the nucleosome assembly mediated by Asf1 in vitro, and reduced the H3K56 acetylation in HeLa cells. Furthermore, production of HSV viral particles was reduced by these compounds. As Asf1 is implicated in genome integrity, cell proliferation, and cancer, current Asf1 inhibitor molecules may offer an opportunity for the therapeutic development for treatment of diseases. [BMB Reports 2015; 48(12): 685-690]
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Affiliation(s)
- Ja-Hwan Seol
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Tae-Yang Song
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Se Eun Oh
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 16419, Korea
| | - Chanhee Jo
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Ahreum Choi
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Byungho Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Jinyoung Park
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Suji Hong
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Ilrang Song
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Kwan Young Jung
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Jae-Hyun Yang
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Hwangseo Park
- Department of Bioscience and Biotechnology, Sejong University, Seoul 05006, Korea
| | - Jin-Hyun Ahn
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 16419, Korea
| | - Jeung-Whan Han
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Eun-Jung Cho
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
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22
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Ortiz JE, Pigni NB, Andujar SA, Roitman G, Suvire FD, Enriz RD, Tapia A, Bastida J, Feresin GE. Alkaloids from Hippeastrum argentinum and Their Cholinesterase-Inhibitory Activities: An in Vitro and in Silico Study. JOURNAL OF NATURAL PRODUCTS 2016; 79:1241-8. [PMID: 27096334 DOI: 10.1021/acs.jnatprod.5b00785] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Two new alkaloids, 4-O-methylnangustine (1) and 7-hydroxyclivonine (2) (montanine and homolycorine types, respectively), and four known alkaloids were isolated from the bulbs of Hippeastrum argentinum, and their cholinesterase-inhibitory activities were evaluated. These compounds were identified using GC-MS, and their structures were defined by physical data analysis. Compound 2 showed weak butyrylcholinesterase (BuChE)-inhibitory activity, with a half-maximal inhibitory concentration (IC50) value of 67.3 ± 0.09 μM. To better understand the experimental results, a molecular modeling study was also performed. The combination of a docking study, molecular dynamics simulations, and quantum theory of atoms in molecules calculations provides new insight into the molecular interactions of compound 2 with BuChE, which were compared to those of galantamine.
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Affiliation(s)
- Javier E Ortiz
- Instituto de Biotecnología, Facultad de Ingeniería, Universidad Nacional de San Juan , Avenida Libertador General San Martín 1109 (O), 5400 San Juan, Argentina
| | - Natalia B Pigni
- Departament de Productes Naturals, Biologia Vegetal i Edafologia, Facultat de Farmàcia, Universitat de Barcelona , Avenida Joan XXIII s/n, 08028 Barcelona, Spain
- ICYTAC-CONICET, Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba , 5000 Córdoba, Argentina
| | - Sebastián A Andujar
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis , Chacabuco 915, 5700 San Luis, Argentina
| | - German Roitman
- Cátedra de Jardinería, Facultad de Agronomía, Universidad de Buenos Aires , Avenida San Martín 4453, 1417 Buenos Aires, Argentina
| | - Fernando D Suvire
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis , Chacabuco 915, 5700 San Luis, Argentina
| | - Ricardo D Enriz
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis , Chacabuco 915, 5700 San Luis, Argentina
| | - Alejandro Tapia
- Instituto de Biotecnología, Facultad de Ingeniería, Universidad Nacional de San Juan , Avenida Libertador General San Martín 1109 (O), 5400 San Juan, Argentina
| | - Jaume Bastida
- Departament de Productes Naturals, Biologia Vegetal i Edafologia, Facultat de Farmàcia, Universitat de Barcelona , Avenida Joan XXIII s/n, 08028 Barcelona, Spain
| | - Gabriela E Feresin
- Instituto de Biotecnología, Facultad de Ingeniería, Universidad Nacional de San Juan , Avenida Libertador General San Martín 1109 (O), 5400 San Juan, Argentina
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23
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Bourne Y, Sharpless KB, Taylor P, Marchot P. Steric and Dynamic Parameters Influencing In Situ Cycloadditions to Form Triazole Inhibitors with Crystalline Acetylcholinesterase. J Am Chem Soc 2016; 138:1611-21. [PMID: 26731630 DOI: 10.1021/jacs.5b11384] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ligand binding sites on acetylcholinesterase (AChE) comprise an active center, at the base of a deep and narrow gorge lined by aromatic residues, and a peripheral site at the gorge entry. These features launched AChE as a reaction vessel for in situ click-chemistry synthesis of high-affinity TZ2PA6 and TZ2PA5 inhibitors, forming a syn-triazole upon cycloaddition within the gorge from alkyne and azide reactants bound at the two sites, respectively. Subsequent crystallographic analyses of AChE complexes with the TZ2PA6 regioisomers demonstrated that syn product association is accompanied by side chain reorganization within the gorge, freezing-in-frame a conformation distinct from an unbound state or anti complex. To correlate inhibitor dimensions with reactivity and explore whether in situ cycloaddition could be accelerated in a concentrated, crystalline template, we developed crystal-soaking procedures and solved structures of AChE complexes with the TZ2PA5 regioisomers and their TZ2/PA5 precursors (2.1-2.7 Å resolution). The structures reveal motions of residue His447 in the active site and, unprecedentedly, residue Tyr341 at the gorge mouth, associated with TZ2 binding and coordinated with other side chain motions in the gorge that may guide AChE toward a transient state favoring syn-triazole formation. Despite precursor binding to crystalline AChE, coupling of rapid electric field fluctuations in the gorge with proper alignments of the azide and alkyne reactants to form the triazole remains a likely limiting step. These observations point to a prime requirement for AChE to interconvert dynamically between sequential conformations to promote favorable electrostatic factors enabling a productive apposition of the reactants for reactivity.
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Affiliation(s)
- Yves Bourne
- Aix-Marseille Université, laboratory Architecture et Fonction des Macromolécules Biologiques, Faculté des Sciences de Luminy , 13288 Marseille cedex 09, France.,Centre National de la Recherche Scientifique, laboratory Architecture et Fonction des Macromolécules Biologiques, Faculté des Sciences de Luminy , 13288 Marseille cedex 09, France
| | - K Barry Sharpless
- Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Palmer Taylor
- Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego , La Jolla, California 92093-0650, United States
| | - Pascale Marchot
- Aix-Marseille Université, laboratory Architecture et Fonction des Macromolécules Biologiques, Faculté des Sciences de Luminy , 13288 Marseille cedex 09, France.,Centre National de la Recherche Scientifique, laboratory Architecture et Fonction des Macromolécules Biologiques, Faculté des Sciences de Luminy , 13288 Marseille cedex 09, France
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24
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Chiem K, Jani S, Fuentes B, Lin DL, Rasche ME, Tolmasky ME. Identification of an Inhibitor of the Aminoglycoside 6'- N-Acetyltransferase type Ib [AAC(6')-Ib] by Glide Molecular Docking. MEDCHEMCOMM 2016; 7:184-189. [PMID: 26973774 PMCID: PMC4784703 DOI: 10.1039/c5md00316d] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The aminoglycoside 6'-N-acetyltransferase type Ib, AAC(6')-Ib, confers resistance to clinically relevant aminoglycosides and is the most widely distributed enzyme among AAC(6')-I-producing Gram-negative pathogens. An alternative to counter the action of this enzyme is the development of inhibitors. Glide is a computational strategy for rapidly docking ligands to protein sites and estimating their binding affinities. We docked a collection of 280,000 compounds from 7 sub-libraries of the Chembridge library as ligands to the aminoglycoside binding site of AAC(6')-Ib. We identified a compound, 1-[3-(2-aminoethyl)benzyl]-3-(piperidin-1-ylmethyl)pyrrolidin-3-ol (compound 1), that inhibited the acetylation of aminoglycosides in vitro with IC50 values of 39.7 and 34.9 µM when the aminoglycoside substrates assayed were kanamycin A or amikacin, respectively. The growth of an amikacin-resistant Acinetobacter baumannii clinical strain was inhibited in the presence of a combination of amikacin and compound 1.
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Affiliation(s)
- Kevin Chiem
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92834-6850, United States
| | - Saumya Jani
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92834-6850, United States
| | - Brooke Fuentes
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92834-6850, United States
| | - David L. Lin
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92834-6850, United States
| | - Madeline E. Rasche
- Center for Applied Biotechnology Studies, Department of Chemistry and Biochemistry, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92834-6850, United States
| | - Marcelo E. Tolmasky
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA 92834-6850, United States
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25
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Antunes DA, Devaurs D, Kavraki LE. Understanding the challenges of protein flexibility in drug design. Expert Opin Drug Discov 2015; 10:1301-13. [DOI: 10.1517/17460441.2015.1094458] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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26
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Yuriev E, Holien J, Ramsland PA. Improvements, trends, and new ideas in molecular docking: 2012-2013 in review. J Mol Recognit 2015; 28:581-604. [PMID: 25808539 DOI: 10.1002/jmr.2471] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Revised: 01/16/2015] [Accepted: 02/05/2015] [Indexed: 12/11/2022]
Abstract
Molecular docking is a computational method for predicting the placement of ligands in the binding sites of their receptor(s). In this review, we discuss the methodological developments that occurred in the docking field in 2012 and 2013, with a particular focus on the more difficult aspects of this computational discipline. The main challenges and therefore focal points for developments in docking, covered in this review, are receptor flexibility, solvation, scoring, and virtual screening. We specifically deal with such aspects of molecular docking and its applications as selection criteria for constructing receptor ensembles, target dependence of scoring functions, integration of higher-level theory into scoring, implicit and explicit handling of solvation in the binding process, and comparison and evaluation of docking and scoring methods.
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Affiliation(s)
- Elizabeth Yuriev
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Jessica Holien
- ACRF Rational Drug Discovery Centre and Structural Biology Laboratory, St. Vincent's Institute of Medical Research, Fitzroy, Victoria, 3065, Australia
| | - Paul A Ramsland
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, 3004, Australia.,Department of Surgery Austin Health, University of Melbourne, Melbourne, Victoria, 3084, Australia.,Department of Immunology, Monash University, Alfred Medical Research and Education Precinct, Melbourne, Victoria, 3004, Australia.,School of Biomedical Sciences, CHIRI Biosciences, Curtin University, Perth, Western Australia, 6845, Australia
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27
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Acevedo-Sáenz L, Ochoa R, Rugeles MT, Olaya-García P, Velilla-Hernández PA, Diaz FJ. Selection pressure in CD8⁺ T-cell epitopes in the pol gene of HIV-1 infected individuals in Colombia. A bioinformatic approach. Viruses 2015; 7:1313-31. [PMID: 25803098 PMCID: PMC4379572 DOI: 10.3390/v7031313] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 02/23/2015] [Accepted: 02/24/2015] [Indexed: 01/24/2023] Open
Abstract
One of the main characteristics of the human immunodeficiency virus is its genetic variability and rapid adaptation to changing environmental conditions. This variability, resulting from the lack of proofreading activity of the viral reverse transcriptase, generates mutations that could be fixed either by random genetic drift or by positive selection. Among the forces driving positive selection are antiretroviral therapy and CD8+ T-cells, the most important immune mechanism involved in viral control. Here, we describe mutations induced by these selective forces acting on the pol gene of HIV in a group of infected individuals. We used Maximum Likelihood analyses of the ratio of non-synonymous to synonymous mutations per site (dN/dS) to study the extent of positive selection in the protease and the reverse transcriptase, using 614 viral sequences from Colombian patients. We also performed computational approaches, docking and algorithmic analyses, to assess whether the positively selected mutations affected binding to the HLA molecules. We found 19 positively-selected codons in drug resistance-associated sites and 22 located within CD8+ T-cell epitopes. A high percentage of mutations in these epitopes has not been previously reported. According to the docking analyses only one of those mutations affected HLA binding. However, algorithmic methods predicted a decrease in the affinity for the HLA molecule in seven mutated peptides. The bioinformatics strategies described here are useful to identify putative positively selected mutations associated with immune escape but should be complemented with an experimental approach to define the impact of these mutations on the functional profile of the CD8+ T-cells.
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Affiliation(s)
- Liliana Acevedo-Sáenz
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, 050010, Colombia.
| | - Rodrigo Ochoa
- Programa de Estudio y Control de Enfermedades Tropicales-PECET, Universidad de Antioquia, Medellín, 050010, Colombia.
| | - Maria Teresa Rugeles
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, 050010, Colombia.
| | | | - Paula Andrea Velilla-Hernández
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, 050010, Colombia.
| | - Francisco J Diaz
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, 050010, Colombia.
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28
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Murakawa T, Matsushita Y, Suzuki T, Khan MTH, Kurita N. Ab initio molecular simulations for proposing potent inhibitors to butyrylcholinesterases. J Mol Graph Model 2014; 54:54-61. [DOI: 10.1016/j.jmgm.2014.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Revised: 09/03/2014] [Accepted: 09/04/2014] [Indexed: 12/01/2022]
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29
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Berardi AS, Pannuzzo G, Graziano A, Costantino-Ceccarini E, Piomboni P, Luddi A. Pharmacological chaperones increase residual β-galactocerebrosidase activity in fibroblasts from Krabbe patients. Mol Genet Metab 2014; 112:294-301. [PMID: 24913062 DOI: 10.1016/j.ymgme.2014.05.009] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 05/15/2014] [Accepted: 05/15/2014] [Indexed: 11/25/2022]
Abstract
Krabbe disease or globoid cell leukodystrophy is a degenerative, lysosomal storage disease resulting from the deficiency of β-galactocerebrosidase activity. This enzyme catalyzes the lysosomal hydrolysis of galactocerebroside and psychosine. Krabbe disease is inherited as an autosomal recessive trait, and many of the 70 disease-causing mutations identified in the GALC gene are associated with protein misfolding. Recent studies have shown that enzyme inhibitors can sometimes translocate misfolded polypeptides to their appropriate target organelle bypassing the normal cellular quality control machinery and resulting in enhanced activity. In search for pharmacological chaperones that could rescue the β-galactocerebrosidase activity, we investigated the effect of α-Lobeline or 3',4',7-trihydroxyisoflavone on several patient-derived fibroblast cell lines carrying missense mutations, rather than on transduced cell lines. Incubation of these cell lines with α-lobeline or 3',4',7-trihydroxyisoflavone leads to an increase of β-galacocerebrosidase activity in p.G553R + p.G553R, in p.E130K + p.N295T and in p.G57S + p.G57S mutant forms over the critical threshold. The low but sustained expression of β-galactocerebrosidase induced by these compounds is a promising result; in fact, it is known that residual enzyme activity of only 15-20% is sufficient for clinical efficacy. The molecular interaction of the two chaperones with β-galactocerebrosidase is also supported by in silico analysis. Collectively, our combined in silico-in vitro approach indicate α-lobeline and 3',4',7-trihydroxyisoflavone as two potential pharmacological chaperones for the treatment or improvement of quality of life in selected Krabbe disease patients.
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Affiliation(s)
- Anna Sara Berardi
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Giovanna Pannuzzo
- Department of Bio-Medical Sciences, Section of Physiology, University of Catania, Catania, Italy
| | - Adriana Graziano
- Department of Bio-Medical Sciences, Section of Physiology, University of Catania, Catania, Italy
| | | | - Paola Piomboni
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Alice Luddi
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy.
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30
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Singh G, Mangat SS, Sharma H, Singh J, Arora A, Singh Pannu AP, Singh N. Design and syntheses of novel fluorescent organosilicon-based chemosensors through click silylation: detection of biogenic amines. RSC Adv 2014. [DOI: 10.1039/c4ra02270j] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
First report on the use of organosilicon-based chemosensors for the recognition of biogenic amines.
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Affiliation(s)
- Gurjaspreet Singh
- Department of Chemistry and Centre of Advanced in Chemistry
- Panjab University
- Chandigarh, India
| | | | - Hemant Sharma
- Department of Chemistry
- Indian Institute of Technology
- Ropar, India
| | - Jandeep Singh
- Department of Chemistry and Centre of Advanced in Chemistry
- Panjab University
- Chandigarh, India
| | - Aanchal Arora
- Department of Chemistry and Centre of Advanced in Chemistry
- Panjab University
- Chandigarh, India
| | | | - Narinder Singh
- Department of Chemistry
- Indian Institute of Technology
- Ropar, India
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31
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Lin DL, Tran T, Adams C, Alam JY, Herron SR, Tolmasky ME. Inhibitors of the aminoglycoside 6'-N-acetyltransferase type Ib [AAC(6')-Ib] identified by in silico molecular docking. Bioorg Med Chem Lett 2013; 23:5694-8. [PMID: 24011645 DOI: 10.1016/j.bmcl.2013.08.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 07/24/2013] [Accepted: 08/05/2013] [Indexed: 10/26/2022]
Abstract
AAC(6')-Ib is an important aminoglycoside resistance enzyme to target with enzymatic inhibitors. An in silico screening approach was used to identify potential inhibitors from the ChemBridge library. Several compounds were identified, of which two of them, 4-[(2-{[1-(3-methylphenyl)-4,6-dioxo-2-thioxotetrahydro-5(2H)-pyrimidinylidene]methyl}phenoxy)methyl]benzoic acid and 2-{5-[(4,6-dioxo-1,3-diphenyl-2-thioxotetrahydro-5(2H)-pyrimidinylidene)methyl]-2-furyl}benzoic acid, showed micromolar activity in inhibiting acetylation of kanamycin A. These compounds are predicted to bind the aminoglycoside binding site of AAC(6')-Ib and exhibited competitive inhibition against kanamycin A.
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Affiliation(s)
- David L Lin
- Center for Applied Biotechnology Studies, Department of Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, 800 N State College Boulevard, Fullerton, CA 92834-6850, United States.
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