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Abacı N, Senol Deniz FS, Ekhteiari Salmas R, Uysal Bayar F, Turgut K, Orhan IE. In vitro and in silico cholinesterase inhibitory and antioxidant effects of essential oils and extracts of two new Salvia fruticosa mill. cultivars (Turgut and Uysal) and GC-MS analysis of the essential oils. Int J Environ Health Res 2024; 34:674-686. [PMID: 36739545 DOI: 10.1080/09603123.2022.2163988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/27/2022] [Indexed: 06/18/2023]
Abstract
The EtOH extracts of the leaves of two new cultivars (Uysal-SFU and Turgut-SFT) of Salvia fruticosa Mill. was tested against acetylcholinesterase (IC50: 30.62 ± 3.27 and 32.97 ± 2.33 µg/mL for SFU and SFT, respectively) and butyrylcholinesterase (IC50: 69.91 ± 1.08 µg/mL and 86.55 ± 1.26 µg/mL), respectively, relevant to Alzheimer's disease. The essential oils showed a stumpy inhibition against AChE and no inhibition against BChE. DPPH radical scavenging activity of the extracts (86.70 ± 0.17% and 86.14 ± 1.13% for SFU and SFT, respectively) was stronger than that of quercetin (85.51 ± 0.17%): Their (1.24 ± 0.05 and 1.04 ± 0.16 for SFU and SFT, respectively) ferric-reducing antioxidant power were close to that of the reference (e.g. quercetin, 1.42 ± 0.14). Molecular docking simulations were performed on their major monoterpenes. Our findings revealed that the leaf EtOH extracts of two cultivars are promising inhibitors of both AChE and BChE.
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Affiliation(s)
- Nurten Abacı
- Department of Pharmacognosy, Gazi University, Faculty of Pharmacy, Ankara, Türkiye
| | - F Sezer Senol Deniz
- Department of Pharmacognosy, Gazi University, Faculty of Pharmacy, Ankara, Türkiye
| | | | - Fatma Uysal Bayar
- Department of Food Technology, Bati Akdeniz Agricultural Research Institute, Medicinal and Aromatic Plants, Antalya, Türkiye
| | - Kenan Turgut
- Department of Field Crops, Akdeniz University, Faculty of Agriculture, Antalya, Türkiye
| | - Ilkay Erdogan Orhan
- Department of Pharmacognosy, Gazi University, Faculty of Pharmacy, Ankara, Türkiye
- Principal Member of Turkish Academy of Sciences (TÜBA), Ankara, Türkiye
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Senol Deniz FS, Ekhteiari Salmas R, Emerce E, Sener B, Erdogan Orhan I. Cholinesterase Inhibitory and In Silico Toxicity Assessment of Thirty-Four Isoquinoline Alkaloids - Berberine as the Lead Compound. CNS Neurol Disord Drug Targets 2023:CNSNDDT-EPUB-130955. [PMID: 37073143 DOI: 10.2174/1871527322666230417083053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 01/21/2023] [Accepted: 01/24/2023] [Indexed: 04/20/2023]
Abstract
BACKGROUND Cholinesterase (ChE) inhibitors used currently in clinics for the treatment of Alzheimer's disease (AD) are the most prescribed drug class with nitrogen-containing chemical formula. Galanthamine, the latest generation anti-ChE drug, contains an isoquinoline structure. OBJECTIVE The aim of the current study was to investigate the inhibitory potential of thirty-four isoquinoline alkaloids, e.g. (-)-adlumidine, β-allocryptopine, berberine, (+)-bicuculline, (-)-bicuculline, (+)-bulbocapnine, (-)-canadine, (±)-chelidimerine, corydaldine, (±)-corydalidzine, (-)-corydalmine, (+)-cularicine, dehydrocavidine, (+)-fumariline, (-)-fumarophycine, (+)-α-hydrastine, (+)-isoboldine, 13-methylcolumbamine, (-)-norjuziphine, norsanguinarine, (-)-ophiocarpine, (-)-ophiocarpine-N-oxide, oxocularine, oxosarcocapnine, palmatine, (+)-parfumine, protopine, (+)-reticuline, sanguinarine, (+)-scoulerine, (±)-sibiricine, (±)-sibiricine acetate, (-)-sinactine, and (-)-stylopine isolated from several Fumaria (fumitory) and Corydalis species towards acetyl- (AChE) and butyrylcholinesterase (BChE) by microtiter plate assays. The alkaloids with strong ChE inhibition were proceeded to molecular docking simulations as well as in silico toxicity screening for their mutagenic capacity through VEGA QSAR (AMES test) consensus model and VEGA platform as statistical approaches. The inputs were evaluated in a simplified molecular input-line entry system (SMILES). RESULTS ChE inhibition assays indicated that the highest AChE inhibition was caused by berberine (IC50: 0.72 ± 0.04 µg/mL), palmatine (IC50: 6.29 ± 0.61 µg/mL), β-allocryptopine (IC50: 10.62 ± 0.45 µg/mL), (-)-sinactine (IC50: 11.94 ± 0.44 µg/mL), and dehydrocavidine (IC50: 15.01 ± 1.87 µg/mL) as compared to that of galanthamine (IC50: 0.74 ± 0.01 µg/mL), the reference drug with isoquinoline skeleton. Less number of the tested alkaloids exhibited notable BChE inhibition. Among them, berberine (IC50: 7.67 ± 0.36 µg/mL) and (-)-corydalmine (IC50: 7.78 ± 0.38 µg/mL) displayed a stronger inhibition than that of galanthamine (IC50: 12.02 ± 0.25 µg/mL). The mutagenic activity was shown for β-allocryptopine, (+)- and (-)-bicuculline, (±)-corydalidzine, (-)-corydalmine, (+)-cularicine, (-)-fumarophycine, (-)-norjuziphine, (-)-ophiocarpine-N-oxide, (+)-scoulerine, (-)-sinactine, and (-)-stylopine by means of in silico experiments. The results obtained by molecular docking simulations of berberine, palmatine, and (-)-corydalmine suggested that the estimated free ligand-binding energies of these compounds inside the binding domains of their targets are reasonable to make them capable of establishing strong polar and nonpolar bonds with the atoms of the active site amino acids. CONCLUSION Our findings revealed that berberine, palmatin, and (-)-corydalmine stand out as the most promising isoquinoline alkaloids in terms of ChE inhibition. Among them, berberine has displayed a robust dual inhibition against both ChEs and could be evaluated further as a lead compound for AD.
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Affiliation(s)
| | | | - Esra Emerce
- Gazi University Pharmaceutical Toxicology Ankara Turkey
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Erdogan Orhan I, Deniz FSS, Salmas RE, Irmak S, Acar OO, Turgut GC, Sen A, Zbancioc AM, Luca SV, Skiba A, Skalicka-Woźniak K, Tataringa G. Evaluation of Anti-Alzheimer Activity of Synthetic Coumarins by Combination of in Vitro and in Silico Approaches. Chem Biodivers 2022; 19:e202200315. [PMID: 36282001 DOI: 10.1002/cbdv.202200315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 10/19/2022] [Indexed: 12/27/2022]
Abstract
Series of synthetic coumarin derivatives (1-16) were tested against acetylcholinesterase (AChE) and butyrylcholinesterase (BChE), two enzymes linked to the pathology of Alzheimer's disease (AD). Compound 16 was the most active AChE inhibitor with IC50 32.23±2.91 μM, while the reference (galantamine) had IC50 =1.85±0.12 μM. Compounds 9 (IC50 75.14±1.82 μM), 13 (IC50 =16.14±0.43 μM), were determined to be stronger BChE inhibitors than the reference galantamine (IC50 =93.53±2.23 μM). The IC50 value of compound 16 for BChE inhibition (IC50 =126.56±11.96 μM) was slightly higher than galantamine. The atomic interactions between the ligands and the key amino acids inside the binding cavities were simulated to determine their ligand-binding positions and free energies. The three inhibitory coumarins (9, 13, 16) were next tested for their effects on the genes associated with AD using human neuroblastoma (SH-SY5Y) cell lines. Our data indicate that they could be considered for further evaluation as new anti-Alzheimer drug candidates.
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Affiliation(s)
- Ilkay Erdogan Orhan
- Department of Pharmacognosy, Faculty of Pharmacy, Gazi University, 06330, Ankara, Turkey
| | - F Sezer Senol Deniz
- Department of Pharmacognosy, Faculty of Pharmacy, Gazi University, 06330, Ankara, Turkey
| | | | - Sule Irmak
- Pamukkale University, Faculty of Arts & Sciences, Department of Biology, 20070, Denizli, Turkey
| | - Ozden Ozgun Acar
- Pamukkale University, Seed Breeding & Genetics Application Research Center, 20070, Denizli, Turkey
| | - Gurbet Celik Turgut
- Pamukkale University, Faculty of Applied Sciences, Organic Agriculture Management, Civril, 20680, Denizli, Turkey
| | - Alaattin Sen
- Pamukkale University, Faculty of Arts & Sciences, Department of Biology, 20070, Denizli, Turkey.,Abdullah Gul University, Faculty of Life and Natural Sciences, Department of Molecular Biology and Genetics, 38080, Kayseri, Turkey
| | - Ana-Maria Zbancioc
- University of Medicine and Pharmacy Grigore T. Popa Iasi, Faculty of Pharmacy, Romania
| | - Simon Vlad Luca
- Biothermodynamics, TUM School of Life Sciences, Technical University of Munich, 85354, Freising, Germany
| | - Adrianna Skiba
- Department of Natural Products Chemistry, Medical University of Lublin, 20-093, Lublin, Poland
| | | | - Gabriela Tataringa
- University of Medicine and Pharmacy Grigore T. Popa Iasi, Faculty of Pharmacy, Romania
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Salmas RE, Borysik AJ. Exploiting the Propagation of Constrained Variables for Enhanced HDX-MS Data Optimization. Anal Chem 2021; 93:16417-16424. [PMID: 34860510 DOI: 10.1021/acs.analchem.1c03082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Nonlinear programming has found useful applications in protein biophysics to help understand the microscopic exchange kinetics of data obtained using hydrogen-deuterium exchange mass spectrometry (HDX-MS). Finding a microscopic kinetic solution for HDX-MS data provides a window into local protein stability and energetics allowing them to be quantified and understood. Optimization of HDX-MS data is a significant challenge, however, due to the requirement to solve a large number of variables simultaneously with exceptionally large variable bounds. Modeled rates are frequently uncertain with an explicate dependency on the initial guess values. In order to enhance the search for a minimum solution in HDX-MS optimization, the ability of selected constrained variables to propagate throughout the data is considered. We reveal that locally bound constrained optimization induces a global effect on all variables. The global response to local constraints is large and surprisingly long-range, but the outcome is unpredictable, unexpectedly decreasing the overall accuracy of certain data sets depending on the stringency of the constraints. Utilizing previously described in-house validation criteria based on covariance matrices, a method is described that is able to accurately determine whether constraints benefit or impair the optimization of HDX-MS data. From this, we establish a new two-stage method for our online optimizer HDXmodeller that can effectively leverage locally bound variables to enhance HDX-MS data modeling.
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Affiliation(s)
- Ramin Ekhteiari Salmas
- Department of Chemistry, Britannia House, King's College London, London SE1 1DB, United Kingdom
| | - Antoni James Borysik
- Department of Chemistry, Britannia House, King's College London, London SE1 1DB, United Kingdom
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Abstract
Quantification of hydrogen deuterium exchange (HDX) kinetics can provide information on the stability of individual amino acids in proteins by finding the degree to which the local backbone environment corresponds to that of a random coil. When characterized by mass spectrometry, extraction of HDX kinetics is not possible because different residue exchange rates become merged depending on the peptides that are formed during proteolytic digestion. We have recently developed an advanced programming tool called HDXmodeller, which enables the exchange rates of individual amino acids to be understood by optimization of low-resolution HDX-mass spectrometry (MS) data. HDXmodeller is also uniquely able to appraise each optimization and quantify the accuracy of modeled exchange rates ab initio using a novel autovalidation method based on a covariance matrix. Here, we address the noise-handling capabilities of HDXmodeller and demonstrate the effectiveness of the algorithm on self-inconsistent datasets. Reference intervals for experimental HDX-MS data are also derived, and this information is presented in an updated online workflow for HDXmodeller, allowing users to evaluate the consistency of their data. The development of a modified version of HDXmodeller is also discussed with enhanced noise-handling capability brought about through loss function optimization. Changes in optimizer accuracy with different loss functions are also demonstrated along with the effectiveness of HDXmodeller to select the most effective optimizer for different data using currently embedded autovalidation criteria.
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Ishaq M, Taslimi P, Shafiq Z, Khan S, Ekhteiari Salmas R, Zangeneh MM, Saeed A, Zangeneh A, Sadeghian N, Asari A, Mohamad H. Synthesis, bioactivity and binding energy calculations of novel 3-ethoxysalicylaldehyde based thiosemicarbazone derivatives. Bioorg Chem 2020; 100:103924. [PMID: 32442818 DOI: 10.1016/j.bioorg.2020.103924] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/01/2020] [Accepted: 05/07/2020] [Indexed: 01/21/2023]
Abstract
In recent decade, the entrance of α-N-heterocyclic thiosemicarbazones derivates (Triapne, COTI-2 and DpC) in clinical trials for cancer and HIV-1 has vastly increased the interests of medicinal chemists towards this class of organic compounds. In the given study, a series of eighteen new (3a-r) 3-ethoxy salicylaldehyde-based thiosemicarbazones (TSC), bearing aryl and cycloalkyl substituents, were synthesized and assayed for their pharmacological potential against carbonic anhydrases (hCA I and hCA II), cholinesterases (AChE and BChE) and α-glycosidase. The hCA I isoform was inhibited by these novel 3-ethoxysalicylaldehyde thiosemicarbazone derivatives (3a-r) in low nanomolar levels, the Ki of which differed between 144.18 ± 26.74 and 454.92 ± 48.32 nM. Against the physiologically dominant isoform hCA II, the novel compounds demonstrated Kis varying from 110.54 ± 14.05 to 444.12 ± 36.08 nM. Also, these novel derivatives (3a-r) effectively inhibited AChE, with Ki values in the range of 385.38 ± 45.03 to 983.04 ± 104.64 nM. For BChE was obtained with Ki values in the range of 400.21 ± 35.68 to 1003.02 ± 154.27 nM. For α-glycosidase the most effective Ki values of 3l, 3n, and 3q were with Ki values of 12.85 ± 1.05, 16.03 ± 2.84, and 19.16 ± 2.66 nM, respectively. Moreover, the synthesized TCSs were simulated using force field methods whereas the binding energies of the selected compounds were estimated using MM-GBSA method. The findings indicate the present novel 3-ethoxy salicylaldehyde-based thiosemicarbazones to be excellent hits for pharmaceutical applications.
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Affiliation(s)
- Muhammad Ishaq
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Parham Taslimi
- Department of Biotechnology, Faculty of Science, Bartin University, 74100 Bartin, Turkey.
| | - Zahid Shafiq
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan 60800, Pakistan.
| | - Samra Khan
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan 60800, Pakistan
| | | | - Mohammad Mahdi Zangeneh
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Razi University, Kermanshah, Iran; Biotechnology and Medicinal Plants Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Aamer Saeed
- Department of Chemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Akram Zangeneh
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Razi University, Kermanshah, Iran; Biotechnology and Medicinal Plants Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Nastaran Sadeghian
- Department of Chemistry, Faculty of Sciences, Ataturk University, 25240 Erzurum, Turkey
| | - Asnuzilawati Asari
- School of Fundamental Science, Universiti Malaysia Terengganu, 21030 Kuala Terengganu, Terengganu, Malaysia
| | - Habsah Mohamad
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
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Zengin Kurt B, Durdagi S, Celebi G, Ekhteiari Salmas R, Sonmez F. Synthesis, anticholinesterase activity and molecular modeling studies of novel carvacrol-substituted amide derivatives. J Biomol Struct Dyn 2019; 38:841-859. [PMID: 30836858 DOI: 10.1080/07391102.2019.1590243] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In the present study, 23 novel carvacrol derivatives involving the amide moiety as a linker between the alkyl chains and/or the heterocycle nucleus were synthesized and tested in vitro as acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) inhibitors. 2-(5-Isopropyl-2-methylphenoxy)-N-(quinolin-8-yl)acetamide (5v) revealed the highest inhibition properties against AChE and BuChE with the IC50 values of 1.93 and 0.05 µM, respectively. The blood-brain barrier (BBB) permeability of the potent inhibitor (5v) was also assessed by the widely used parallel artificial membrane permeability assay (PAMPA-BBB). The results showed that 5v is capable of crossing the BBB. Pharmacokinetic and toxicity profiles of the studied molecule predictions were investigated by MetaCore/MetaDrug comprehensive systems biology analysis suite. Bioactive conformations of the synthesized molecules, their predicted binding energies as well as structural and dynamical profiles of molecules at the binding pockets of AChE and BuChE targets were also investigated using different docking algorithms and molecular dynamics (MD) simulations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Belma Zengin Kurt
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Bezmialem Vakif University, Istanbul, Turkey
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Gulsen Celebi
- Department of Pharmacology, Faculty of Medicine, Kocaeli University, Kocaeli, Turkey
| | - Ramin Ekhteiari Salmas
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Fatih Sonmez
- Pamukova Vocational High School, Sakarya University of Applied Sciences, Sakarya, Turkey
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Orhan IE, Senol Deniz FS, Salmas RE, Durdagi S, Epifano F, Genovese S, Fiorito S. Combined molecular modeling and cholinesterase inhibition studies on some natural and semisynthetic O-alkylcoumarin derivatives. Bioorg Chem 2018; 84:355-362. [PMID: 30530106 DOI: 10.1016/j.bioorg.2018.11.044] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 11/21/2018] [Accepted: 11/24/2018] [Indexed: 11/27/2022]
Abstract
Coumarins of synthetic or natural origins are an important chemical class exerting diverse pharmacological activities. In the present study, 26 novel O-alkylcoumarin derivatives were synthesized and have been tested at 100 µM for their in vitro inhibitory potential against acetylcholinesterase (AChE) and butyrlcholinesterase (BChE) targets which are the key enzymes playing role in the pathogenesis of Alzheimer's disease. Among the tested coumarins, none of them could inhibit AChE, whereas 12 of them exerted a marked and selective inhibition against BChE as compared to the reference (galanthamine, IC50 = 46.58 ± 0.91 µM). In fact, 10 of the active coumarins showed higher inhibition (IC50 = 7.01 ± 0.28 µM - 43.31 ± 3.63 µM) than that of galanthamine. The most active ones were revealed to be 7-styryloxycoumarin (IC50 = 7.01 ± 0.28 µM) and 7-isopentenyloxy-4-methylcoumarin (IC50 = 8.18 ± 0.74 µM). In addition to the in vitro tests, MetaCore/MetaDrug binary QSAR models and docking simulations were applied to evaluate the active compounds by ligand-based and target-driven approaches. The predicted pharmacokinetic profiles of the compounds suggested that the compounds reveal lipophilic character and permeate blood brain barrier (BBB) and the ADME models predict higher human serum protein binding percentages (>50%) for the compounds. The calculated docking scores indicated that the coumarins showing remarkable BChE inhibition possessed favorable free binding energies in interacting with the ligand-binding domain of the target. Therefore, our results disclose that O-alkylcoumarins are promising selective inhibitors of cholinesterase enzymes, particularly BChE in our case, which definitely deserve further studies.
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Affiliation(s)
- Ilkay Erdogan Orhan
- Department of Pharmacognosy, Faculty of Pharmacy, Gazi University, 06330 Ankara, Turkey.
| | - F Sezer Senol Deniz
- Department of Pharmacognosy, Faculty of Pharmacy, Gazi University, 06330 Ankara, Turkey
| | - Ramin Ekhteiari Salmas
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, 34349 Istanbul, Turkey
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, 34349 Istanbul, Turkey
| | - Francesco Epifano
- Dipartimento di Farmacia, Università "G. d'Annunzio" Chieti-Pescara, Via dei Vestini 31, 66100 Chieti Scalo, CH, Italy.
| | - Salvatore Genovese
- Dipartimento di Farmacia, Università "G. d'Annunzio" Chieti-Pescara, Via dei Vestini 31, 66100 Chieti Scalo, CH, Italy
| | - Serena Fiorito
- Dipartimento di Farmacia, Università "G. d'Annunzio" Chieti-Pescara, Via dei Vestini 31, 66100 Chieti Scalo, CH, Italy
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Durdagi S, Tahir Ul Qamar M, Salmas RE, Tariq Q, Anwar F, Ashfaq UA. Investigating the molecular mechanism of staphylococcal DNA gyrase inhibitors: A combined ligand-based and structure-based resources pipeline. J Mol Graph Model 2018; 85:122-129. [PMID: 30176384 DOI: 10.1016/j.jmgm.2018.07.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 07/18/2018] [Accepted: 07/19/2018] [Indexed: 01/12/2023]
Abstract
Appropriate therapeutic solutions against Staphylococcal infections are currently limited. To work out the complex task of challenging drug resistance in Staphylococcus aureus, new compounds with novel modes of action are required. In this study, we performed target-driven virtual screening to filter exhaustive phytochemical libraries that can inhibit the activity of S. aureus DNA Gyrase B (Gyr B). Three top-ranked hit molecules (Mangostenone E, Candenatenin A and 2,4,4'-trihydroxydihydrochalcone) were identified from comprehensive molecular docking studies based on their strong spatial affinity with key catalytic residues of the binding pocket of DNA GyrB, especially with the well-known crucial residue Asp81. Molecular dynamics (MD) simulations were performed for these identified hit molecules for better understanding of their dynamical and structural profiles throughout the MD simulations. These compounds can be explored as future lead optimization molecules to discover a new class of antibiotics against resistant Staphylococcus aureus strains.
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Affiliation(s)
- Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey; Neuroscience Program, Graduate School of Health Sciences, Bahcesehir University, Istanbul, Turkey.
| | | | - Ramin Ekhteiari Salmas
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Quratulain Tariq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Farooq Anwar
- Department of Chemistry, University of Sargodha, Sargodha, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan.
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Salmas RE, Seeman P, Stein M, Durdagi S. Structural Investigation of the Dopamine-2 Receptor Agonist Bromocriptine Binding to Dimeric D2 HighR and D2 LowR States. J Chem Inf Model 2018. [PMID: 29537837 DOI: 10.1021/acs.jcim.7b00722] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The active (D2HighR) and inactive (D2LowR) states of dimeric dopamine D2 receptor (D2R) models were investigated to clarify the binding mechanisms of the dopamine agonist bromocriptine, using Molecular Dynamics (MD) simulation. The aim of this comprehensive study was to investigate the critical effects of bromocriptine binding on each distinct receptor conformation. The different binding modes of the bromocriptine ligand in the active and inactive states have a significant effect on the conformational changes of the receptor. Based on the MM/GBSA approach, the calculated binding enthalpies of bromocriptine demonstrated selectivity toward the D2HighR active state. There is good agreement between the calculated and experimentally measured D2HighR selectivity. In the ligand-binding site, the key amino acids identified for D2HighR were Asp114(3.32) and Glu95(2.65), and for D2LowR, it was Ser193(5.42). Moreover, analysis of replicate MD trajectories demonstrated that the bromocriptine structure was more rigid at the D2HighR state and more flexible at the D2LowR state. However, the side chains of the ligand-receptor complex of D2HighR showed larger variations relative to the corresponding regions of D2LowR. The present study is part of an ongoing research program to study D2R conformational changes during ligand activation and to evaluate the conformational state selectivity for ligand binding.
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Affiliation(s)
- Ramin Ekhteiari Salmas
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine , Bahcesehir University , Istanbul 34349 , Turkey
| | - Philip Seeman
- Departments of Pharmacology and Psychiatry , University of Toronto , 260 Heath Street West, Unit 605 , M5P 3L6 Toronto , Ontario , Canada
| | - Matthias Stein
- Molecular Simulations and Design Group , Max Planck Institute for Dynamics of Complex Technical Systems , Sandtorstrasse 1 , 39106 Magdeburg , Germany
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine , Bahcesehir University , Istanbul 34349 , Turkey.,Neuroscience Program, Graduate School of Health Sciences , Bahcesehir University , Istanbul 34349 , Turkey
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Durdagi S, Erol I, Salmas RE, Aksoydan B, Kantarcioglu I. Oligomerization and cooperativity in GPCRs from the perspective of the angiotensin AT1 and dopamine D2 receptors. Neurosci Lett 2018; 700:30-37. [PMID: 29684528 DOI: 10.1016/j.neulet.2018.04.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 04/13/2018] [Accepted: 04/16/2018] [Indexed: 12/22/2022]
Abstract
G Protein-Coupled Receptors (GPCRs) can form homo- and heterodimers or constitute higher oligomeric clusters with other heptahelical GPCRs. In this article, multiscale molecular modeling approaches as well as experimental techniques which are used to study oligomerization of GPCRs are reviewed. In particular, the effect of dimerization/oligomerization to the ligand binding affinity of individual protomers and also on the efficacy of the oligomer are discussed by including diverse examples from the literature. In addition, possible allosteric effects that may emerge upon interaction of GPCRs with membrane components, like cholesterol, is also discussed. Investigation of these above-mentioned interactions may greatly contribute to the candidate molecule screening studies and development of novel therapeutics with fewer adverse effects.
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Affiliation(s)
- Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey; Neuroscience Program, Graduate School of Health Sciences, Bahcesehir University, Istanbul, Turkey.
| | - Ismail Erol
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey; Department of Chemistry, Gebze Technical University, Kocaeli, Turkey
| | - Ramin Ekhteiari Salmas
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey
| | - Busecan Aksoydan
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey; Neuroscience Program, Graduate School of Health Sciences, Bahcesehir University, Istanbul, Turkey
| | - Isik Kantarcioglu
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey; Bioengineering Program, Graduate School of Natural and Applied Sciences, Bahcesehir University, Istanbul, Turkey
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12
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Orhan IE, Jedrejek D, Senol FS, Salmas RE, Durdagi S, Kowalska I, Pecio L, Oleszek W. Molecular modeling and in vitro approaches towards cholinesterase inhibitory effect of some natural xanthohumol, naringenin, and acyl phloroglucinol derivatives. Phytomedicine 2018; 42:25-33. [PMID: 29655693 DOI: 10.1016/j.phymed.2018.03.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 01/07/2018] [Accepted: 03/04/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Many natural products, particularly phenolic compounds, have been reported to have a strong inhibition against acetylcholinesterase (AChE) and butyrylcholinesterase (BChE), the key enzymes in the pathology of Alzheimer's disease (AD). HYPOTHESIS Therefore, we hypothesized that some xanthahumol, naringenin, and acyl phloroglucinol derivatives (1-14) isolated from Humulus lupulus L. (hops) may have an inhibitory potential against AChE and BChE. METHODS Inhibitory potential of compounds 1-14 were tested against AChE and BChE using ELISA microtiter assay. Different molecular docking simulations, including IFD and GOLD protocols, were implemented to verify the interactions between the ligands and the active site amino acids and also their binding energies inside the catalytic crevices of AChE and BChE. ADME/Tox analysis were used to determine pharmacological activities of the compounds. RESULTS Among them, 3‑hydroxy‑xanthohumol (IC50 = 51.25 ± 0.88 µM) and xanthohumol (IC50 = 71.34 ± 2.09 µM), displayed a moderate AChE inhibition in comparison to that of the reference (galanthamine, IC50 = 2.52 ± 0.15 µM). In addition to 3‑hydroxy‑xanthohumol (IC50 = 63.07 ± 3.76 µM) and xanthohumol (IC50 = 32.67 ± 2.82 µM), 8-prenylnaringenin (IC50 = 86.58 ± 3.74 µM) also showed micromolar-range inhibition against BChE (galanthamine, IC50 = 46.58 ± 0.91 µM). Rest of the compounds were found to be either inactive or having inhibition below 50%. Prediction of pharmacokinetic studies suggested that all the ligands revealed acceptable drug-like profiles. Docking simulations demonstrate not only the prediction of ligand binding energies of the compounds inside the catalytic domains of the targets, but also highlight the critical amino acids contributing to stabilizations of the ligands. CONCLUSION Our findings revealed that xanthohumol in particular could be considered as lead molecule to explore new cholinesterase inhibitors for AD.
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Affiliation(s)
- Ilkay Erdogan Orhan
- Department of Pharmacognosy, Faculty of Pharmacy, Gazi University, Ankara 06330, Turkey.
| | - Dariusz Jedrejek
- Institute of Soil Science and Plant Cultivation, State Research Institute, Czartoryskich 8, Pulawy 24-100, Poland
| | - F Sezer Senol
- Department of Pharmacognosy, Faculty of Pharmacy, Gazi University, Ankara 06330, Turkey
| | - Ramin Ekhteiari Salmas
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul 34349, Turkey
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul 34349, Turkey
| | - Iwona Kowalska
- Institute of Soil Science and Plant Cultivation, State Research Institute, Czartoryskich 8, Pulawy 24-100, Poland
| | - Lukasz Pecio
- Institute of Soil Science and Plant Cultivation, State Research Institute, Czartoryskich 8, Pulawy 24-100, Poland
| | - Wieslaw Oleszek
- Institute of Soil Science and Plant Cultivation, State Research Institute, Czartoryskich 8, Pulawy 24-100, Poland
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13
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Mollica A, Zengin G, Durdagi S, Ekhteiari Salmas R, Macedonio G, Stefanucci A, Dimmito MP, Novellino E. Combinatorial peptide library screening for discovery of diverse α-glucosidase inhibitors using molecular dynamics simulations and binary QSAR models. J Biomol Struct Dyn 2018; 37:726-740. [DOI: 10.1080/07391102.2018.1439403] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Adriano Mollica
- Dipartimento di Farmacia, Università̀ di Chieti-Pescara “G. d’Annunzio”, Via dei Vestini 31, Chieti 66100, Italy
| | - Gokhan Zengin
- Department of Biology, Science Faculty, Selcuk University, Konya, Turkey
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul 34349, Turkey
- Neuroscience Program, Graduate School of Health Sciences, Bahcesehir University, Istanbul, Turkey
| | - Ramin Ekhteiari Salmas
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul 34349, Turkey
| | - Giorgia Macedonio
- Dipartimento di Farmacia, Università̀ di Chieti-Pescara “G. d’Annunzio”, Via dei Vestini 31, Chieti 66100, Italy
| | - Azzurra Stefanucci
- Dipartimento di Farmacia, Università̀ di Chieti-Pescara “G. d’Annunzio”, Via dei Vestini 31, Chieti 66100, Italy
| | - Marilisa Pia Dimmito
- Dipartimento di Farmacia, Università̀ di Chieti-Pescara “G. d’Annunzio”, Via dei Vestini 31, Chieti 66100, Italy
| | - Ettore Novellino
- Dipartimento di Farmacia, Università di Napoli “Federico II”, Via D. Montesano, Naples 49, 80131, Italy
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14
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Mirza SB, Lee RCH, Chu JJH, Salmas RE, Mavromoustakos T, Durdagi S. Discovery of selective dengue virus inhibitors using combination of molecular fingerprint-based virtual screening protocols, structure-based pharmacophore model development, molecular dynamics simulations and in vitro studies. J Mol Graph Model 2017; 79:88-102. [PMID: 29156382 DOI: 10.1016/j.jmgm.2017.10.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Dengue virus is a major issue of tropical and sub-tropical regions. The proliferation of virus results in immense number of deaths each year because of unavailability of on-shelf drugs. This issue necessitates the design of novel anti-Dengue drugs. The protease enzyme pathway is the critical target for drug design due to its significance in the replication, survival and other cellular activities of Dengue virus. Keeping in mind the worsening situation regarding Dengue virus, approximately eighteen million drug-like compounds from the ZINC small molecule database have been screened against Nonstructural Protein 3 (NS3) previously by our group. In this study, in order to investigate the effect of extended time of molecular dynamics (MD) simulations on structural and dynamical profiles of used complexes, simulation run time is increased from 50-ns to 100-ns for the each system. In addition, a well-known Dengue virus inhibitor (MB21) from literature is used as reference structure (positive control) to compare the proposed molecules. Post-processing MD analyses including Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) calculations were conducted to predict binding free energies of inhibitors from derived trajectory frames of MD simulations. Identified compounds are further directed to Quantum-Polarized Ligand Docking (QPLD), molecular fingerprint-based virtual screening of another small molecule database (Otava Drug Like small molecule database), and Structure-based Pharmacophore Modeling (E-Pharmacophore). Finally, cell proliferation and cytotoxicity tests as well as pre- and post-treatment on HUH7 cells infected with DENV2 NGC strain are applied for four identified hit molecules (ZINC36681949, ZINC44921800, ZINC95518765 and ZINC39500661) to check whether these drugs inhibit DENV2 from entry and/or exit pathways. Based on cell-based Dengue quantification assays, there is no effect seen on pre-treatment of cells with these compounds indicating that the early infection processes of virus is not affected. In contrast, the post-treatment of cells with these compounds after Dengue virus infection has resulted in a significant 1 log PFU/ml reduction of the virus infectious titre.
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Affiliation(s)
- Shaher Bano Mirza
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey; Research Laboratory of Electronics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Department of Biosciences, COMSATS Institute of Information Technology (CIIT), Park Road, Chak Shahzad, Islamabad, Pakistan
| | - Regina Ching Hua Lee
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
| | - Justin Jang Hann Chu
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
| | - Ramin Ekhteiari Salmas
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | | | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
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15
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Aksoydan B, Kantarcioglu I, Erol I, Salmas RE, Durdagi S. Structure-based design of hERG-neutral antihypertensive oxazalone and imidazolone derivatives. J Mol Graph Model 2017; 79:103-117. [PMID: 29156380 DOI: 10.1016/j.jmgm.2017.10.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Angiotensin II receptor type 1 (AT1) antagonists are the most recent drug class against hypertension. Recently first crystal structure of AT1 receptor is deposited to the protein data bank (PDB ID: 4YAY). In this work, several molecular screening methods such as molecular docking and de novo design studies were performed and it is found that oxazolone and imidazolone derivatives reveal similar/better interaction energy profiles compared to the FDA approved sartan molecules at the binding site of the AT1 receptor. A database consisting of 3500-fragments were used to enumerate de novo designed imidazolone and oxazolone derivatives and hereby more than 50000 novel small molecules were generated. These derivatives were then used in high throughput virtual screening simulations (Glide/HTVS) to find potent hit molecules. In addition, virtual screening of around 18 million small drug-like compounds from ZINC database were screened at the binding pocket of the AT1 receptor via Glide/HTVS method. Filtered structures were then used in more sophisticated molecular docking simulations protocols (i.e., Glide/SP; Glide/XP; Glide/IFD; Glide/QPLD, and GOLD). However, the K+ ion channel/drug interactions should also be considered in studies implemented in molecular level against their cardiovascular risks. Thus, selected compounds with high docking scores via all diverse docking algorithms are also screened at the pore domain regions of human ether-a-go-go-related gene (hERG1) K+ channel to remove the high affinity hERG1 blocking compounds. High docking scored compounds at the AT1 with low hERG1 affinity is considered for long molecular dynamics (MD) simulations. Post-processing analysis of MD simulations assisted for better understanding of molecular mechanism of studied compounds at the binding cavity of AT1 receptor. Results of this study can be useful for designing of novel and safe AT1 inhibitors.
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Affiliation(s)
- Busecan Aksoydan
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey
| | - Isik Kantarcioglu
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey
| | - Ismail Erol
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey; Department of Chemistry, Gebze Technical University, Kocaeli, Turkey
| | - Ramin Ekhteiari Salmas
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey.
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16
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Zengin Kurt B, Sonmez F, Durdagi S, Aksoydan B, Ekhteiari Salmas R, Angeli A, Kucukislamoglu M, Supuran CT. Synthesis, biological activity and multiscale molecular modeling studies for coumaryl-carboxamide derivatives as selective carbonic anhydrase IX inhibitors. J Enzyme Inhib Med Chem 2017; 32:1042-1052. [PMID: 28776440 PMCID: PMC6009903 DOI: 10.1080/14756366.2017.1354857] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
New coumaryl-carboxamide derivatives with the thiourea moiety as a linker between the alkyl chains and/or the heterocycle nucleus were synthesized and their inhibitory activity against the human carbonic anhydrase (hCA) isoforms hCA I, II, VII and IX were evaluated. While the hCA I, II and VII isoforms were not inhibited by the investigated compounds, the tumour-associated isoform hCA IX was inhibited in the high nanomolar range. 2-Oxo-N-((2-(pyrrolidin-1-yl)ethyl)carbamothioyl)-2H-chromene-3-carboxamide (e11) exhibited a selective inhibitory action against hCA IX with the Ki of 107.9 nM. In order to better understand the inhibitory profiles of studied molecules, multiscale molecular modeling approaches were used. Different molecular docking algorithms were used to investigate binding poses and predicted binding energies of studied compounds at the active sites of the CA I, II, VII and IX isoforms.
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Affiliation(s)
- Belma Zengin Kurt
- a Faculty of Pharmacy, Department of Pharmaceutical Chemistry , Bezmialem Vakıf University , Istanbul , Turkey
| | - Fatih Sonmez
- b Faculty of Arts and Science, Department of Chemistry , Sakarya University , Sakarya , Turkey
| | - Serdar Durdagi
- c Computational Biology and Molecular Simulations Laboratory, Department of Biophysics , School of Medicine, Bahcesehir University , Istanbul , Turkey
| | - Busecan Aksoydan
- c Computational Biology and Molecular Simulations Laboratory, Department of Biophysics , School of Medicine, Bahcesehir University , Istanbul , Turkey
| | - Ramin Ekhteiari Salmas
- c Computational Biology and Molecular Simulations Laboratory, Department of Biophysics , School of Medicine, Bahcesehir University , Istanbul , Turkey
| | - Andrea Angeli
- d Dipartimento Neurofarba, Sezione di ScienzeFarmaceutiche e Nutraceutiche , Università degli Studi di Firenze , Florence , Italy
| | - Mustafa Kucukislamoglu
- b Faculty of Arts and Science, Department of Chemistry , Sakarya University , Sakarya , Turkey
| | - Claudiu T Supuran
- d Dipartimento Neurofarba, Sezione di ScienzeFarmaceutiche e Nutraceutiche , Università degli Studi di Firenze , Florence , Italy
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17
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Akıncıoğlu A, Kocaman E, Akıncıoğlu H, Salmas RE, Durdagi S, Gülçin İ, Supuran CT, Göksu S. The synthesis of novel sulfamides derived from β-benzylphenethylamines as acetylcholinesterase, butyrylcholinesterase and carbonic anhydrase enzymes inhibitors. Bioorg Chem 2017; 74:238-250. [DOI: 10.1016/j.bioorg.2017.08.012] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 08/18/2017] [Accepted: 08/22/2017] [Indexed: 10/19/2022]
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18
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Ekhteiari Salmas R, Serhat Is Y, Durdagi S, Stein M, Yurtsever M. A QM protein–ligand investigation of antipsychotic drugs with the dopamine D2 Receptor (D2R). J Biomol Struct Dyn 2017; 36:2668-2677. [DOI: 10.1080/07391102.2017.1365772] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
| | - Yusuf Serhat Is
- Department of Chemistry, Istanbul Technical University, Istanbul, Turkey
- Vocational School Department of Chemistry Technology, Istanbul Gedik University, Istanbul, Turkey
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Matthias Stein
- Molecular Simulations and Design Group, Max-Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Mine Yurtsever
- Department of Chemistry, Istanbul Technical University, Istanbul, Turkey
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19
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Salmas RE, Gulhan MF, Durdagi S, Sahna E, Abdullah HI, Selamoglu Z. Effects of propolis, caffeic acid phenethyl ester, and pollen on renal injury in hypertensive rat: An experimental and theoretical approach. Cell Biochem Funct 2017; 35:304-314. [PMID: 28833317 DOI: 10.1002/cbf.3277] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 06/23/2017] [Accepted: 07/03/2017] [Indexed: 12/20/2022]
Abstract
The objective of this study was to evaluate the antioxidant effects of propolis, caffeic acid phenethyl ester (CAPE; active compound in propolis), and pollen on biochemical oxidative stress biomarkers in rat kidney tissue inhibited by Nω -nitro-L-arginine methyl ester (L-NAME). The biomarkers evaluated were paraoxonase (PON1), oxidative stress index (OSI), total antioxidant status (TAS), total oxidant status (TOS), asymmetric dimethylarginine (ADMA), and nuclear factor kappa B (NF-κB). TAS levels and PON1 activity were significantly decreased in kidney tissue samples in the L-NAME-treated group (P < 0.05). The levels of TAS and PONI were higher in the L-NAME plus propolis, CAPE, and pollen groups compared with the L-NAME-treated group. TOS, ADMA, and NF-κB levels were significantly increased in the kidney tissue samples of the L-NAME-treated group (P < 0.05). However, these parameters were significantly lower in the L-NAME plus propolis, CAPE, and pollen groups (P < 0.05) compared with rats administered L-NAME alone (P < 0.05). Furthermore, the binding energy of CAPE within catalytic domain of glutathione reductase (GR) enzyme as well as its inhibitory mechanism was determined using molecular modeling approaches. In conclusion, experimental and theoretical data suggested that oxidative alterations occurring in the kidney tissue of chronic hypertensive rats may be prevented via active compound of propolis, CAPE administration.
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Affiliation(s)
- Ramin Ekhteiari Salmas
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Mehmet Fuat Gulhan
- Department of Medicinal and Aromatic Plants, Vocational School of Technical Sciences, Aksaray, Turkey
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Engin Sahna
- Department of Pharmacology, Faculty of Medicine, Firat University, Elazig, Turkey
| | - Huda I Abdullah
- Department of Medical Biology, Faculty of Medicine, Omer Halisdemir University, Nigde, Turkey
| | - Zeliha Selamoglu
- Department of Medical Biology, Faculty of Medicine, Omer Halisdemir University, Nigde, Turkey
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20
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Mirza SB, Lee RCH, Chu JJH, Salmas RE, Mavromoustakos T, Durdagi S. Discovery of selective dengue virus inhibitors using combination of molecular fingerprint-based virtual screening protocols, structure-based pharmacophore model development, molecular dynamics simulations and in vitro studies. J Mol Graph Model 2017; 77:338. [PMID: 28957754 DOI: 10.1016/j.jmgm.2017.08.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 07/20/2017] [Accepted: 08/07/2017] [Indexed: 12/29/2022]
Abstract
Dengue virus is a major issue of tropical and sub-tropical regions. The proliferation of virus results in immense number of deaths each year because of unavailability of on-shelf drugs. This issue necessitates the design of novel anti-Dengue drugs. The protease enzyme pathway is the critical target for drug design due to its significance in the replication, survival and other cellular activities of Dengue virus. Keeping in mind the worsening situation regarding Dengue virus, approximately eighteen million drug-like compounds from the ZINC small molecule database have been screened against Nonstructural Protein 3 (NS3) previously by our group. In this study, in order to investigate the effect of extended time of molecular dynamics (MD) simulations on structural and dynamical profiles of used complexes, simulation run time is increased from 50-ns to 100-ns for the each system. In addition, a well-known Dengue virus inhibitor (MB21) from literature is used as reference structure (positive control) to compare the proposed molecules. Post-processing MD analyses including Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) calculations were conducted to predict binding free energies of inhibitors from derived trajectory frames of MD simulations. Identified compounds are further directed to Quantum-Polarized Ligand Docking (QPLD), molecular fingerprint-based virtual screening of another small molecule database (Otava Drug Like small molecule database), and Structure-based Pharmacophore Modeling (E-Pharmacophore). Finally, cell proliferation and cytotoxicity tests as well as pre- and post-treatment on HUH7 cells infected with DENV2 NGC strain are applied for four identified hit molecules (ZINC36681949, ZINC44921800, ZINC95518765 and ZINC39500661) to check whether these drugs inhibit DENV2 from entry and/or exit pathways. Based on cell-based Dengue quantification assays, there is no effect seen on pre-treatment of cells with these compounds indicating that the early infection processes of virus is not affected. In contrast, the post-treatment of cells with these compounds after Dengue virus infection has resulted in a significant 1logPFU/ml reduction of the virus infectious titre.
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Affiliation(s)
- Shaher Bano Mirza
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey; Research Laboratory of Electronics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Department of Biosciences, COMSATS Institute of Information Technology (CIIT), Park Road, Chak Shahzad, Islamabad, Pakistan
| | - Regina Ching Hua Lee
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
| | - Justin Jang Hann Chu
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
| | - Ramin Ekhteiari Salmas
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | | | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey.
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Salmas RE, Seeman P, Aksoydan B, Erol I, Kantarcioglu I, Stein M, Yurtsever M, Durdagi S. Analysis of the Glutamate Agonist LY404,039 Binding to Nonstatic Dopamine Receptor D2 Dimer Structures and Consensus Docking. ACS Chem Neurosci 2017; 8:1404-1415. [PMID: 28272861 DOI: 10.1021/acschemneuro.7b00070] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Dopamine receptor D2 (D2R) plays an important role in the human central nervous system and is a focal target of antipsychotic agents. The D2HighR and D2LowR dimeric models previously developed by our group are used to investigate the prediction of binding affinity of the LY404,039 ligand and its binding mechanism within the catalytic domain. The computational data obtained using molecular dynamics simulations fit well with the experimental results. The calculated binding affinities of LY404,039 using MM/PBSA for the D2HighR and D2LowR targets were -12.04 and -9.11 kcal/mol, respectively. The experimental results suggest that LY404,039 binds to D2HighR and D2LowR with binding affinities (Ki) of 8.2 and 1640 nM, respectively. The high binding affinity of LY404,039 in terms of binding to [3H]domperidone was inhibited by the presence of a guanine nucleotide, indicating an agonist action of the drug at D2HighR. The interaction analysis demonstrated that while Asp114 was among the most critical amino acids for D2HighR binding, residues Ser193 and Ser197 were significantly more important within the binding cavity of D2LowR. Molecular modeling analyses are extended to ensemble docking as well as structure-based pharmacophore model (E-pharmacophore) development using the bioactive conformation of LY404,039 at the binding pocket as a template and screening of small-molecule databases with derived pharmacophore models.
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Affiliation(s)
- Ramin Ekhteiari Salmas
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahcesehir University, 34349 Istanbul, Turkey
| | - Philip Seeman
- Departments
of Pharmacology and Psychiatry, University of Toronto, 260 Heath
Street West, Unit 605, Toronto, Ontario M5P 3L6, Canada
| | - Busecan Aksoydan
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahcesehir University, 34349 Istanbul, Turkey
| | - Ismail Erol
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahcesehir University, 34349 Istanbul, Turkey
- Department
of Chemistry, Gebze Technical University, 41400, Kocaeli, Turkey
| | - Isik Kantarcioglu
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahcesehir University, 34349 Istanbul, Turkey
| | - Matthias Stein
- Max-Planck Institute for Dynamics of Complex Technical Systems, Molecular Simulations and Design Group, Sandtorstrasse 1, 39106 Magdeburg, Germany
| | - Mine Yurtsever
- Department
of Chemistry, Istanbul Technical University, 34469 Istanbul, Turkey
| | - Serdar Durdagi
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahcesehir University, 34349 Istanbul, Turkey
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Ekhteiari Salmas R, Seeman P, Aksoydan B, Stein M, Yurtsever M, Durdagi S. Biological Insights of the Dopaminergic Stabilizer ACR16 at the Binding Pocket of Dopamine D2 Receptor. ACS Chem Neurosci 2017; 8:826-836. [PMID: 28001043 DOI: 10.1021/acschemneuro.6b00396] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The dopamine D2 receptor (D2R) plays an important part in the human central nervous system and it is considered to be a focal target of antipsychotic agents. It is structurally modeled in active and inactive states, in which homodimerization reaction of the D2R monomers is also applied. The ASP2314 (also known as ACR16) ligand, a D2R stabilizer, is used in tests to evaluate how dimerization and conformational changes may alter the ligand binding space and to provide information on alterations in inhibitory mechanisms upon activation. The administration of the D2R agonist ligand ACR16 [3H](+)-4-propyl-3,4,4a,5,6,10b-hexahydro-2H-naphtho[1,2-b][1,4]oxazin-9-ol ((+)PHNO) revealed Ki values of 32 nM for the D2highR and 52 μM for the D2lowR. The calculated binding affinities of ACR16 with post processing molecular dynamics (MD) simulations analyses using MM/PBSA for the monomeric and homodimeric forms of the D2highR were -9.46 and -8.39 kcal/mol, respectively. The data suggests that the dimerization of the D2R leads negative cooperativity for ACR16 binding. The dimerization reaction of the D2highR is energetically favorable by -22.95 kcal/mol. The dimerization reaction structurally and thermodynamically stabilizes the D2highR conformation, which may be due to the intermolecular forces formed between the TM4 of each monomer, and the result strongly demonstrates dimerization essential for activation of the D2R.
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Affiliation(s)
- Ramin Ekhteiari Salmas
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Philip Seeman
- Departments
of Pharmacology and Psychiatry, University of Toronto, 260 Heath
Street West, Unit 605, M5P 3L6 Toronto, Ontario Canada
| | - Busecan Aksoydan
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Matthias Stein
- Max-Planck
Institute
for Dynamics of Complex Technical Systems, Molecular Simulations and
Design Group, Sandtorstrasse 1, 39106 Magdeburg, Germany
| | - Mine Yurtsever
- Department
of Chemistry, Istanbul Technical University, 34467 Istanbul, Turkey
| | - Serdar Durdagi
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahcesehir University, Istanbul, Turkey
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Erdemli ME, Ekhteiari Salmas R, Durdagi S, Akgul H, Demirkol M, Aksungur Z, Selamoglu Z. Biochemical changes induced by grape seed extract and low level laser therapy administration during intraoral wound healing in rat liver: an experimental and in silico study. J Biomol Struct Dyn 2017; 36:993-1008. [PMID: 28279122 DOI: 10.1080/07391102.2017.1305297] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In the present study, the changes that occur in rat liver tissue as a result of the use of grape seed extract (GSE) and low level laser therapy (LLLT) in intraoral wound (IW) healing are analyzed using biochemical parameters. Diode laser application groups received 8 J/cm2 dose LLLT once a day for 4 days (810 nm wavelength, continuous mode, 0.25 W, 9 s). As a result of the biological parameter analysis, it was determined that the oxidative damage caused by the IWs and recovery period on 7th and 14th days could be substantially removed with GSE applications that have antioxidant capacity especially in rat liver tissue. In addition, the active compound of grape seed, catechin is studied in the active site of glycogen synthase kinase 3 (GSK3) target using molecular modeling approaches. Post-processing molecular dynamics (MD) results for catechin is compared with a standard GSK3 inhibitor. MD simulations assisted for better understanding of inhibition mechanism and the crucial amino acids contributing in the ligand binding. These results along with a through free energy analysis of ligands using sophisticated simulations methods are quite striking and it suggests a greater future role for simulation in deciphering complex patterns of molecular mechanism in combination with methods for understanding drug-receptor interactions.
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Affiliation(s)
- Mehmet Erman Erdemli
- a Faculty of Medicine, Department of Medical Biochemistry , Omer Halisdemir University , Nigde , Turkey
| | - Ramin Ekhteiari Salmas
- b Computational Biology and Molecular Simulations Laboratory, Department of Biophysics , School of Medicine, Bahcesehir University , Istanbul , Turkey
| | - Serdar Durdagi
- b Computational Biology and Molecular Simulations Laboratory, Department of Biophysics , School of Medicine, Bahcesehir University , Istanbul , Turkey
| | - Hasan Akgul
- c Faculty of Arts and Science, Department of Biology , Akdeniz University , Antalya , Turkey
| | - Mehmet Demirkol
- d Faculty of Dentistry, Department of Oral and Maxillofacial Surgery , Gaziantep University , Gaziantep , Turkey
| | - Zeynep Aksungur
- e Faculty of Medicine, Department of Medical Biochemistry , Inonu University , Malatya , Turkey
| | - Zeliha Selamoglu
- f Faculty of Arts and Science, Department of Biotechnology , Omer Halisdemir University , Nigde , Turkey
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Durdagi S, Erol I, Salmas RE, Patterson M, Noskov SY. First universal pharmacophore model for hERG1 K + channel activators: acthER. J Mol Graph Model 2017; 74:153-170. [PMID: 28499268 DOI: 10.1016/j.jmgm.2017.03.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 03/28/2017] [Accepted: 03/29/2017] [Indexed: 01/31/2023]
Abstract
The intra-cavitary drug blockade of hERG1 channel has been extensively studied, both experimentally and theoretically. Structurally diverse ligands inadvertently block the hERG1 K+ channel currents lead to drug induced Long QT Syndrome (LQTS). Accordingly, designing either hERG1 channel openers or current activators, with the potential to target other binding pockets of the channel, has been introduced as a viable approach in modern anti-arrhythmia drug development. However, reports and investigations on the molecular mechanisms underlying activators binding to the hERG1 channel remain sparse and the overall molecular design principles are largely unknown. Most of the hERG1 activators were discovered during mandatory screening for hERG1 blockade. To fill this apparent deficit, the first universal pharmacophore model for hERG1 K+ channel activators was developed using PHASE. 3D structures of 18 hERG1 K+ channel activators and their corresponding measured binding affinity values were used in the development of pharmacophore models. These compounds spanned a range of structurally different chemotypes with moderate variation in binding affinity. A five sites AAHRR (A, hydrogen-bond accepting, H, hydrophobic, R, aromatic) pharmacophore model has shown reasonable high statistical results compared to the other developed more than 1000 hypotheses. This model was used to construct steric and electrostatic contour maps. The predictive power of the model was tested with 3 external test set compounds as true unknowns. Finally, the pharmacophore model was combined with the previously developed receptor-based model of hERG1 K+ channel to develop and screen novel activators. The results are quite striking and it suggests a greater future role for pharmacophore modeling and virtual drug screening simulations in deciphering complex patterns of molecular mechanisms of hERG1 channel openers at the target sites. The developed model is available upon request and it may serve as basis for the synthesis of novel therapeutic hERG1 activators.
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Affiliation(s)
- Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey.
| | - Ismail Erol
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey; Department of Chemistry, Gebze Technical University, Kocaeli, Turkey
| | - Ramin Ekhteiari Salmas
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Matthew Patterson
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Sergei Y Noskov
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.
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Shityakov S, Salmas RE, Durdagi S, Roewer N, Förster C, Broscheit J. Solubility profiles, hydration and desolvation of curcumin complexed with γ-cyclodextrin and hydroxypropyl-γ-cyclodextrin. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.12.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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26
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Ekhteiari Salmas R, Durdagi S, Gulhan MF, Duruyurek M, Abdullah HI, Selamoglu Z. The effects of pollen, propolis, and caffeic acid phenethyl ester on tyrosine hydroxylase activity and total RNA levels in hypertensive rats caused by nitric oxide synthase inhibition: experimental, docking and molecular dynamic studies. J Biomol Struct Dyn 2017; 36:609-620. [DOI: 10.1080/07391102.2017.1288660] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Ramin Ekhteiari Salmas
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Mehmet Fuat Gulhan
- Department of Medicinal and Aromatic Plants, Vocational School of Technical Sciences, Aksaray, Turkey
| | - Merve Duruyurek
- Faculty of Arts and Science, Department of Biotechnology, Omer Halisdemir University, Nigde 51240, Turkey
| | - Huda I. Abdullah
- Department of Pharmacology, New York Medical College, Valhalla 10595, NY, USA
| | - Zeliha Selamoglu
- Faculty of Arts and Science, Department of Biotechnology, Omer Halisdemir University, Nigde 51240, Turkey
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Shityakov S, Salmas RE, Salvador E, Roewer N, Broscheit J, Förster C. Evaluation of the potential toxicity of unmodified and modified cyclodextrins on murine blood-brain barrier endothelial cells. J Toxicol Sci 2016; 41:175-84. [PMID: 26961601 DOI: 10.2131/jts.41.175] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
In this study, we investigated the cytotoxic effects of unmodified α-cyclodextrin (α-CD) and modified cyclodextrins, including trimethyl-β-cyclodextrin (TRIMEB) and hydroxypropyl-β-cyclodextrin (HPβCD), on immortalized murine microvascular endothelial (cEND) cells of the blood-brain barrier (BBB). A CellTiter-Glo viability test, performed on the cEND cells showed significant differences among the different cyclodextrins. After 24 hr of incubation, TRIMEB was the most cytotoxic, and HPβCD was non-toxic. α-CD and TRIMEB exhibited greater cytotoxicity in the Dulbecco's modified Eagle's medium than in heat-inactivated human serum indicating protective properties of the human serum. The predicted dynamic toxicity profiles (Td) for α-CD and TRIMEB indicated higher cytotoxicity for these cyclodextrins compared to the reference compound (dimethylsulfoxide). Molecular dynamics simulation of cholesterol binding to the CDs suggested that not just cholesterol but phospholipids extraction might be involved in the cytotoxicity. Overall, the results demonstrate that HPβCD has the potential to be used as a candidate for drug delivery vector development and signify a correlation between the in vitro cytotoxic effect and cholesterol binding of cyclodextrins.
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Affiliation(s)
- Sergey Shityakov
- Department of Anesthesia and Critical Care, University of Würzburg, Germany
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28
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Mirza SB, Ekhteiari Salmas R, Fatmi MQ, Durdagi S. Discovery of Klotho peptide antagonists against Wnt3 and Wnt3a target proteins using combination of protein engineering, protein-protein docking, peptide docking and molecular dynamics simulations. J Enzyme Inhib Med Chem 2016; 32:84-98. [PMID: 27766889 PMCID: PMC6009926 DOI: 10.1080/14756366.2016.1235569] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The Klotho is known as lifespan enhancing protein involved in antagonizing the effect of Wnt proteins. Wnt proteins are stem cell regulators, and uninterrupted exposure of Wnt proteins to the cell can cause stem and progenitor cell senescence, which may lead to aging. Keeping in mind the importance of Klotho in Wnt signaling, in silico approaches have been applied to study the important interactions between Klotho and Wnt3 and Wnt3a (wingless-type mouse mammary tumor virus (MMTV) integration site family members 3 and 3a). The main aim of the study is to identify important residues of the Klotho that help in designing peptides which can act as Wnt antagonists. For this aim, a protein engineering study is performed for Klotho, Wnt3 and Wnt3a. During the theoretical analysis of homology models, unexpected role of number of disulfide bonds and secondary structure elements has been witnessed in case of Wnt3 and Wnt3a proteins. Different in silico experiments were carried out to observe the effect of correct number of disulfide bonds on 3D protein models. For this aim, total of 10 molecular dynamics (MD) simulations were carried out for each system. Based on the protein–protein docking simulations of selected protein models of Klotho with Wnt3 and Wnt3a, different peptides derived from Klotho have been designed. Wnt3 and Wnt3a proteins have three important domains: Index finger, N-terminal domain and a patch of ∼10 residues on the solvent exposed surface of palm domain. Protein–peptide docking of designed peptides of Klotho against three important domains of palmitoylated Wnt3 and Wnt3a yields encouraging results and leads better understanding of the Wnt protein inhibition by proposed Klotho peptides. Further in vitro studies can be carried out to verify effects of novel designed peptides as Wnt antagonists.
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Affiliation(s)
- Shaher Bano Mirza
- a Department of Biophysics, School of Medicine , Bahcesehir University (BAU) , Istanbul , Turkey.,b Department of Biosciences , COMSATS Institute of Information Technology (CIIT) , Islamabad , Pakistan
| | - Ramin Ekhteiari Salmas
- a Department of Biophysics, School of Medicine , Bahcesehir University (BAU) , Istanbul , Turkey
| | - M Qaiser Fatmi
- b Department of Biosciences , COMSATS Institute of Information Technology (CIIT) , Islamabad , Pakistan
| | - Serdar Durdagi
- a Department of Biophysics, School of Medicine , Bahcesehir University (BAU) , Istanbul , Turkey
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29
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Shityakov S, Salmas RE, Durdagi S, Salvador E, Pápai K, Yáñez-Gascón MJ, Pérez-Sánchez H, Puskás I, Roewer N, Förster C, Broscheit JA. Characterization, in Vivo Evaluation, and Molecular Modeling of Different Propofol-Cyclodextrin Complexes To Assess Their Drug Delivery Potential at the Blood-Brain Barrier Level. J Chem Inf Model 2016; 56:1914-1922. [PMID: 27589557 DOI: 10.1021/acs.jcim.6b00215] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, we investigated the ability of the general anesthetic propofol (PR) to form inclusion complexes with modified β-cyclodextrins, including sulfobutylether-β-cyclodextrin (SBEβCD) and hydroxypropyl-β-cyclodextrin (HPβCD). The PR/SBEβCD and PR/HPβCD complexes were prepared and characterized, and the blood-brain barrier (BBB) permeation potential of the formulated PR was examined in vivo for the purpose of controlled drug delivery. The PR/SBEβCD complex was found to be more stable in solution with a minimal degradation constant of 0.25 h-1, a t1/2 of 2.82 h, and a Kc of 5.19 × 103 M-1 and revealed higher BBB permeability rates compared with the reference substance (PR-LIPURO) considering the calculated brain-to-blood concentration ratio (logBB) values. Additionally, the diminished PR binding affinity to SBEβCD was confirmed in molecular dynamics simulations by a maximal Gibbs free energy of binding (ΔGbind = -18.44 kcal·mol-1), indicating the more rapid PR/SBEβCD dissociation. Overall, the results demonstrated that SBEβCD has the potential to be used as a prospective candidate for drug delivery vector development to improve the pharmacokinetic and pharmacodynamic properties of general anesthetic agents at the BBB level.
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Affiliation(s)
- Sergey Shityakov
- Department of Anesthesia and Critical Care, University of Würzburg , 97080 Würzburg, Germany
| | - Ramin Ekhteiari Salmas
- Department of Biophysics, School of Medicine, Bahcesehir University , 34349 Istanbul, Turkey
| | - Serdar Durdagi
- Department of Biophysics, School of Medicine, Bahcesehir University , 34349 Istanbul, Turkey
| | - Ellaine Salvador
- Department of Anesthesia and Critical Care, University of Würzburg , 97080 Würzburg, Germany
| | | | | | | | - István Puskás
- CycloLab Cyclodextrin Research & Development Laboratory Ltd. , H-1097 Budapest, Hungary
| | - Norbert Roewer
- Department of Anesthesia and Critical Care, University of Würzburg , 97080 Würzburg, Germany.,Sapiotec Ltd. , 97078 Würzburg, Germany
| | - Carola Förster
- Department of Anesthesia and Critical Care, University of Würzburg , 97080 Würzburg, Germany
| | - Jens-Albert Broscheit
- Department of Anesthesia and Critical Care, University of Würzburg , 97080 Würzburg, Germany.,Sapiotec Ltd. , 97078 Würzburg, Germany
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Salmas RE, Stein M, Yurtsever M, Seeman P, Erol I, Mestanoglu M, Durdagi S. The signaling pathway of dopamine D2 receptor (D2R) activation using normal mode analysis (NMA) and the construction of pharmacophore models for D2R ligands. J Biomol Struct Dyn 2016; 35:2040-2048. [PMID: 27367058 DOI: 10.1080/07391102.2016.1206487] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
G-protein-coupled receptors (GPCRs) are targets of more than 30% of marketed drugs. Investigation on the GPCRs may shed light on upcoming drug design studies. In the present study, we performed a combination of receptor- and ligand-based analysis targeting the dopamine D2 receptor (D2R). The signaling pathway of D2R activation and the construction of universal pharmacophore models for D2R ligands were also studied. The key amino acids, which contributed to the regular activation of the D2R, were in detail investigated by means of normal mode analysis (NMA). A derived cross-correlation matrix provided us an understanding of the degree of pair residue correlations. Although negative correlations were not observed in the case of the inactive D2R state, a high degree of correlation appeared between the residues in the active state. NMA results showed that the cytoplasmic side of the TM5 plays a significant role in promoting of residue-residue correlations in the active state of D2R. Tracing motions of the amino acids Arg219, Arg220, Val223, Asn224, Lys226, and Ser228 in the position of the TM5 are found to be critical in signal transduction. Complementing the receptor-based modeling, ligand-based modeling was also performed using known D2R ligands. The top-scored pharmacophore models were found as 5-sited (AADPR.671, AADRR.1398, AAPRR.3900, and ADHRR.2864) hypotheses from PHASE modeling from a pool consisting of more than 100 initial candidates. The constructed models using 38 D2R ligands (in the training set) were validated with 15 additional test set compounds. The resulting model correctly predicted the pIC50 values of an additional test set compounds as true unknowns.
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Affiliation(s)
- Ramin Ekhteiari Salmas
- a Department of Biophysics , School of Medicine, Bahcesehir University , Istanbul , Turkey
| | - Matthias Stein
- b Molecular Simulations and Design Group , Max Planck Institute for Dynamics of Complex Technical System , Sandtorstrasse 1, 39106 Magdeburg , Germany
| | - Mine Yurtsever
- c Department of Chemistry , Istanbul Technical University , Istanbul , Turkey
| | - Philip Seeman
- d Department of Pharmacology and Psychiatry , University of Toronto , 260 Heath Street West, Unit 605, M5P 3L6 Toronto , Ontario , Canada
| | - Ismail Erol
- a Department of Biophysics , School of Medicine, Bahcesehir University , Istanbul , Turkey.,e Department of Chemistry , Gebze Technical University , Gebze , Turkey
| | - Mert Mestanoglu
- a Department of Biophysics , School of Medicine, Bahcesehir University , Istanbul , Turkey
| | - Serdar Durdagi
- a Department of Biophysics , School of Medicine, Bahcesehir University , Istanbul , Turkey
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31
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Ekhteiari Salmas R, Unlu A, Bektaş M, Yurtsever M, Mestanoglu M, Durdagi S. Virtual screening of small molecules databases for discovery of novel PARP-1 inhibitors: combination of in silico and in vitro studies. J Biomol Struct Dyn 2016; 35:1899-1915. [DOI: 10.1080/07391102.2016.1199328] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
| | - Ayhan Unlu
- Faculty of Medicine, Department of Biophysics, Trakya University, Edirne, Turkey
| | - Muhammet Bektaş
- Istanbul Faculty of Medicine, Department of Biophysics, Istanbul University, Istanbul, Turkey
| | - Mine Yurtsever
- Department of Chemistry, Istanbul Technical University, Istanbul, Turkey
| | | | - Serdar Durdagi
- Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
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32
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Özgeriş B, Göksu S, Polat Köse L, Gülçin İ, Salmas RE, Durdagi S, Tümer F, Supuran CT. Acetylcholinesterase and carbonic anhydrase inhibitory properties of novel urea and sulfamide derivatives incorporating dopaminergic 2-aminotetralin scaffolds. Bioorg Med Chem 2016; 24:2318-29. [DOI: 10.1016/j.bmc.2016.04.002] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Revised: 03/30/2016] [Accepted: 04/01/2016] [Indexed: 12/20/2022]
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Salmas RE, Yurtsever M, Durdagi S. Atomistic molecular dynamics simulations of typical and atypical antipsychotic drugs at the dopamine D2 receptor (D2R) elucidates their inhibition mechanism. J Biomol Struct Dyn 2016; 35:738-754. [DOI: 10.1080/07391102.2016.1159986] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
| | - Mine Yurtsever
- Department of Chemistry, Istanbul Technical University, Istanbul, Turkey
| | - Serdar Durdagi
- Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
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Mirza SB, Salmas RE, Fatmi MQ, Durdagi S. Virtual screening of eighteen million compounds against dengue virus: Combined molecular docking and molecular dynamics simulations study. J Mol Graph Model 2016; 66:99-107. [PMID: 27054972 DOI: 10.1016/j.jmgm.2016.03.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Revised: 02/08/2016] [Accepted: 03/24/2016] [Indexed: 01/01/2023]
Abstract
Dengue virus is a major issue of tropical and sub-tropical regions. Dengue virus has been the cause behind the major alarming epidemics in the history with mass causalities from the decades. Unavailability of on-shelf drugs for the prevention of further proliferation of virus inside the human body results in immense number of deaths each year. This issue necessitates the design of novel anti-dengue drug. The protease enzyme pathway is the critical target for drug design due to its significance in the replication, survival and other cellular activities of dengue virus. Therefore, approximately eighteen million compounds from the ZINC database have been virtually screened against nonstructural protein 3 (NS3). The incremental construction algorithm of Glide docking program has been used with its features high throughput virtual screening (HTVS), standard precision (SP), extra precision (XP) and in combination of Prime module, induced fit docking (IFD) approach has also been applied. Five top-ranked compounds were then selected from the IFD results with better predicted binding energies with the catalytic triad residues (His51, Asp75, and Ser135) that may act as potential inhibitors for the underlying target protease enzyme. The top-ranked compounds ZINC95518765, ZINC44921800, ZINC71917414, ZINC39500661, ZINC36681949 have shown the predicted binding energies of -7.55, -7.36, -8.04, -8.41, -9.18kcal/mol, respectively, forming binding interactions with three catalytically important amino acids. Top-docking poses of compounds are then used in molecular dynamics (MD) simulations. In computational studies, our proposed compounds confirm promising results against all the four serotypes of dengue virus, strengthening the opportunity of these compounds to work as potential on-shelf drugs against dengue virus. Further experimentation on the proposed compounds can result in development of strong inhibitors.
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Affiliation(s)
- Shaher Bano Mirza
- Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey; Department of Biosciences, COMSATS Institute of Information Technology (CIIT), Park Road, Chak Shahzad, Islamabad, Pakistan
| | - Ramin Ekhteiari Salmas
- Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey
| | - M Qaiser Fatmi
- Department of Biosciences, COMSATS Institute of Information Technology (CIIT), Park Road, Chak Shahzad, Islamabad, Pakistan.
| | - Serdar Durdagi
- Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey.
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35
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Durdagi S, Salmas RE, Stein M, Yurtsever M, Seeman P. Binding Interactions of Dopamine and Apomorphine in D2High and D2Low States of Human Dopamine D2 Receptor Using Computational and Experimental Techniques. ACS Chem Neurosci 2016; 7:185-95. [PMID: 26645629 DOI: 10.1021/acschemneuro.5b00271] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
We have recently reported G-protein coupled receptor (GPCR) model structures for the active and inactive states of the human dopamine D2 receptor (D2R) using adrenergic crystal structures as templates. Since the therapeutic concentrations of dopamine agonists that suppress the release of prolactin are the same as those that act at the high-affinity state of the D2 receptor (D2High), D2High in the anterior pituitary gland is considered to be the functional state of the receptor. In addition, the therapeutic concentrations of anti-Parkinson drugs are also related to the dissociation constants in the D2High form of the receptor. The discrimination between the high- and low-affinity (D2Low) components of the D2R is not obvious and requires advanced computer-assisted structural biology investigations. Therefore, in this work, the derived D2High and D2Low receptor models (GPCR monomer and dimer three-dimensional structures) are used as drug-binding targets to investigate binding interactions of dopamine and apomorphine. The study reveals a match between the experimental dissociation constants of dopamine and apomorphine at their high- and low-affinity sites of the D2 receptor in monomer and dimer and their calculated dissociation constants. The allosteric receptor-receptor interaction for dopamine D2R dimer is associated with the accessibility of adjacent residues of transmembrane region 4. The measured negative cooperativity between agonist ligand at dopamine D2 receptor is also correctly predicted using the D2R homodimerization model.
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Affiliation(s)
- Serdar Durdagi
- Department
of Biophysics, School of Medicine, Bahcesehir University, 34349 Istanbul, Turkey
| | - Ramin Ekhteiari Salmas
- Department
of Biophysics, School of Medicine, Bahcesehir University, 34349 Istanbul, Turkey
- Department
of Chemistry, Istanbul Technical University, 34469 Istanbul, Turkey
| | - Matthias Stein
- Molecular
Simulations and Design Group, Max-Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106, Magdeburg, Germany
| | - Mine Yurtsever
- Department
of Chemistry, Istanbul Technical University, 34469 Istanbul, Turkey
| | - Philip Seeman
- Departments
of Pharmacology and Psychiatry, University of Toronto, 260 Heath
Street West, Unit 605, M5P 3L6, Toronto, Ontario Canada
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Salmas RE, Mestanoglu M, Unlu A, Yurtsever M, Durdagi S. Mutated form (G52E) of inactive diphtheria toxin CRM197: molecular simulations clearly display effect of the mutation to NAD binding. J Biomol Struct Dyn 2016; 34:2462-8. [PMID: 26836774 DOI: 10.1080/07391102.2015.1119060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Mutated form (G52E) of diphtheria toxin (DT) CRM197 is an inactive and nontoxic enzyme. Here, we provided a molecular insight using comparative molecular dynamics (MD) simulations to clarify the influence of a single point mutation on overall protein and active-site loop. Post-processing MD analysis (i.e. stability, principal component analysis, hydrogen-bond occupancy, etc.) is carried out on both wild and mutated targets to investigate and to better understand the mechanistic differences of structural and dynamical properties on an atomic scale especially at nicotinamide adenine dinucleotide (NAD) binding site when a single mutation (G52E) happens at the DT. In addition, a docking simulation is performed for wild and mutated forms. The docking scoring analysis and docking poses results revealed that mutant form is not able to properly accommodate the NAD molecule.
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Affiliation(s)
- Ramin Ekhteiari Salmas
- a Department of Chemistry , Istanbul Technical University , Istanbul , Turkey.,b Department of Biophysics , School of Medicine, Bahcesehir University , Istanbul , Turkey
| | - Mert Mestanoglu
- c School of Medicine , Bahcesehir University , Istanbul , Turkey
| | - Ayhan Unlu
- d Faculty of Medicine, Department of Biophysics , Trakya University , Edirne , Turkey
| | - Mine Yurtsever
- a Department of Chemistry , Istanbul Technical University , Istanbul , Turkey
| | - Serdar Durdagi
- b Department of Biophysics , School of Medicine, Bahcesehir University , Istanbul , Turkey
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Strom TA, Durdagi S, Ersoz SS, Salmas RE, Supuran CT, Barron AR. Fullerene-based inhibitors of HIV-1 protease. J Pept Sci 2015; 21:862-70. [DOI: 10.1002/psc.2828] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 09/07/2015] [Accepted: 09/14/2015] [Indexed: 11/08/2022]
Affiliation(s)
- T. Amanda Strom
- Department of Chemistry; Rice University; Houston TX 77005 USA
| | - Serdar Durdagi
- Department of Biophysics, School of Medicine; Bahcesehir University; Istanbul Turkey
- Department of Biological Sciences, Institute for Biocomplexity and Informatics; University of Calgary; Calgary Alberta Canada
| | | | | | - Claudiu T. Supuran
- Laboratorio di Chimica Bioinorganica; Università degli Studi di Firenze; Rm. 188, Via della Lastruccia 3 I-50019 Sesto Fiorentino (Firenze) Italy
| | - Andrew R. Barron
- Department of Chemistry; Rice University; Houston TX 77005 USA
- Department of Materials Science and Nanoengineering; Rice University; Houston TX 77005 USA
- Institute of Life Sciences; Swansea University; Singleton Park Swansea SA2 8PP Wales UK
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Salmas RE, Yurtsever M, Durdagi S. Investigation of Inhibition Mechanism of Chemokine Receptor CCR5 by Micro-second Molecular Dynamics Simulations. Sci Rep 2015; 5:13180. [PMID: 26299310 PMCID: PMC4547396 DOI: 10.1038/srep13180] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 07/15/2015] [Indexed: 12/20/2022] Open
Abstract
Chemokine receptor 5 (CCR5) belongs to G protein coupled receptors (GPCRs) and plays an important role in treatment of human immunodeficiency virus (HIV) infection since HIV uses CCR5 protein as a co-receptor. Recently, the crystal structure of CCR5-bound complex with an approved anti-retroviral drug (maroviroc) was resolved. During the crystallization procedure, amino acid residues (i.e., Cys224, Arg225, Asn226 and Glu227) at the third intra-cellular loop were replaced by the rubredoxin for stability reasons. In the current study, we aimed to understand the impact of the incorporated rubredoxin on the conformations of TM domains of the target protein. For this reason, rubredoxin was deleted from the crystal structure and the missing amino acids were engineered. The resultant structure was subjected to long (μs) molecular dynamics (MD) simulations to shed light into the inhibitory mechanism. The derived model structure displayed a significant deviation in the cytoplasmic domain of TM5 and IC3 in the absence of rubredoxin. The principal component analyses (PCA) and MD trajectory analyses revealed important structural and dynamical differences at apo and holo forms of the CCR5.
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Affiliation(s)
| | - Mine Yurtsever
- Department of Chemistry, Istanbul Technical University, Istanbul, Turkey
| | - Serdar Durdagi
- Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
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Salmas RE, Unlu A, Yurtsever M, Noskov SY, Durdagi S. In silicoinvestigation of PARP-1 catalytic domains inholoandapostates for the design of high-affinity PARP-1 inhibitors. J Enzyme Inhib Med Chem 2015; 31:112-20. [DOI: 10.3109/14756366.2015.1005011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Salmas RE, Senturk M, Yurtsever M, Durdagi S. Discovering novel carbonic anhydrase type IX (CA IX) inhibitors from seven million compounds using virtual screening and in vitro analysis. J Enzyme Inhib Med Chem 2015; 31:425-33. [PMID: 25950196 DOI: 10.3109/14756366.2015.1036049] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Carbonic anhydrase type IX (CA IX) enzyme is mostly over expressed in different cancer cell lines and tumor tissues. Potent CA IX inhibitors can be effective for adjusting the pH imbalance in tumor cells. In the present work, we represented the successful application of high throughput virtual screening (HTVS) of large dataset from ZINC database included of ∼7 million compounds to discover novel inhibitors of CA IX. HTVS and molecular docking were performed using consequence Glide/standard precision (SP), extra precision (XP) and induced fit docking (IFD) molecular docking protocols. For each compound, docking code calculates a set of low-energy poses and then exhaustively scans the binding pocket of the target with small compounds. Novel CA IX inhibitor candidates were suggested based on molecular modeling studies and a few of them were tested using in vitro analysis. These compounds were determined as good inhibitors against human CA IX target with Ki in the range of 0.85-1.58 μM. In order to predict the pharmaceutical properties of the selected compounds, ADME (absorption, distribution, metabolism and excretion) analysis was also carried out.
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Affiliation(s)
| | - Murat Senturk
- b Department of Chemistry , Ağrı Ibrahim Çeçen University , Ağrı , Turkey , and
| | - Mine Yurtsever
- a Department of Chemistry , İstanbul Technical University , İstanbul , Turkey
| | - Serdar Durdagi
- c Department of Biophysics , School of Medicine, Bahçeşehir University , Istanbul , Turkey
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Ekhteiari Salmas R, Mestanoglu M, Durdagi S, Sentürk M, Kaya AA, Kaya EÇ. Kinetic and in silico studies of hydroxy-based inhibitors of carbonic anhydrase isoforms I and II. J Enzyme Inhib Med Chem 2015; 31:31-7. [PMID: 25676327 DOI: 10.3109/14756366.2014.1003216] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A series of hydroxy and phenolic compounds have been assayed for the inhibition of two physiologically relevant carbonic anhydrase (CA, EC 4.2.1.1) isozymes, the cytosolic human isozymes I and II. The investigated molecules showed inhibition constants in the range of 1.07-4003 and 0.09-31.5 μM at the hCA I and hCA II enzymes, respectively. In order to investigate the binding mechanisms of these inhibitors, in silico studies were also applied. Molecular docking scores of the studied compounds are compared using three different scoring algorithms, namely Glide/SP, Glide/XP and Glide/IFD. In addition, different ADME (absorption, distribution, metabolism and excretion) analysis was performed. All the examined compounds were found within the acceptable range of pharmacokinetic profiles.
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Affiliation(s)
| | - Mert Mestanoglu
- b School of Medicine, Bahcesehir University , Istanbul , Turkey
| | - Serdar Durdagi
- c Department of Biophysics , School of Medicine, Bahcesehir University , Istanbul , Turkey
| | - Murat Sentürk
- d Department of Chemistry, Art and Science Faculty , Agri Ibrahim Cecen University , Agri , Turkey , and
| | - A Afşin Kaya
- e School of Health, Gumushane University , Gumushane , Turkey
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Salmas RE, Yurtsever M, Stein M, Durdagi S. Modeling and protein engineering studies of active and inactive states of human dopamine D2 receptor (D2R) and investigation of drug/receptor interactions. Mol Divers 2015; 19:321-32. [DOI: 10.1007/s11030-015-9569-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Accepted: 01/11/2015] [Indexed: 01/11/2023]
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Göksu S, Naderi A, Akbaba Y, Kalın P, Akıncıoğlu A, Gülçin İ, Durdagi S, Salmas RE. Carbonic anhydrase inhibitory properties of novel benzylsulfamides using molecular modeling and experimental studies. Bioorg Chem 2014; 56:75-82. [DOI: 10.1016/j.bioorg.2014.07.009] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 07/19/2014] [Accepted: 07/23/2014] [Indexed: 12/15/2022]
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Leonis G, Avramopoulos A, Salmas RE, Durdagi S, Yurtsever M, Papadopoulos MG. Elucidation of Conformational States, Dynamics, and Mechanism of Binding in Human κ-Opioid Receptor Complexes. J Chem Inf Model 2014; 54:2294-308. [DOI: 10.1021/ci5002873] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Georgios Leonis
- Institute
of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens, Attiki 11635, Greece
| | - Aggelos Avramopoulos
- Institute
of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens, Attiki 11635, Greece
| | - Ramin Ekhteiari Salmas
- Department
of Chemistry, Istanbul Technical University, Istanbul, Istanbul 34469, Turkey
| | - Serdar Durdagi
- Department
of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Istanbul 34349, Turkey
| | - Mine Yurtsever
- Department
of Chemistry, Istanbul Technical University, Istanbul, Istanbul 34469, Turkey
| | - Manthos G. Papadopoulos
- Institute
of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens, Attiki 11635, Greece
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