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Minadakis MP, Mavreas K, Neofytos DD, Paschou M, Kogkaki A, Athanasiou V, Mamais M, Veclani D, Iatrou H, Venturini A, Chrysina ED, Papazafiri P, Gimisis T. A glucose-based molecular rotor inhibitor of glycogen phosphorylase as a probe of cellular enzymatic function. Org Biomol Chem 2022; 20:2407-2423. [DOI: 10.1039/d1ob02211c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molecular rotors belong to a family of fluorescent compounds characterized as molecular switches, where a fluorescence on/off signal signifies a change in the molecule’s microenvironment. Herein, the successful synthesis and...
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Synthetic flavonoid derivatives targeting the glycogen phosphorylase inhibitor site: QM/MM-PBSA motivated synthesis of substituted 5,7-dihydroxyflavones, crystallography, in vitro kinetics and ex-vivo cellular experiments reveal novel potent inhibitors. Bioorg Chem 2020; 102:104003. [DOI: 10.1016/j.bioorg.2020.104003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/02/2020] [Accepted: 06/07/2020] [Indexed: 01/31/2023]
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3
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Barr D, Szennyes E, Bokor É, Al-Oanzi ZH, Moffatt C, Kun S, Docsa T, Sipos Á, Davies MP, Mathomes RT, Snape TJ, Agius L, Somsák L, Hayes JM. Identification of C-β-d-Glucopyranosyl Azole-Type Inhibitors of Glycogen Phosphorylase That Reduce Glycogenolysis in Hepatocytes: In Silico Design, Synthesis, in Vitro Kinetics, and ex Vivo Studies. ACS Chem Biol 2019; 14:1460-1470. [PMID: 31243960 DOI: 10.1021/acschembio.9b00172] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Several C-β-d-glucopyranosyl azoles have recently been uncovered as among the most potent glycogen phosphorylase (GP) catalytic site inhibitors discovered to date. Toward further exploring their translational potential, ex vivo experiments have been performed for their effectiveness in reduction of glycogenolysis in hepatocytes. New compounds for these experiments were predicted in silico where, for the first time, effective ranking of GP catalytic site inhibitor potencies using the molecular mechanics-generalized Born surface area (MM-GBSA) method has been demonstrated. For a congeneric training set of 27 ligands, excellent statistics in terms of Pearson (RP) and Spearman (RS) correlations (both 0.98), predictive index (PI = 0.99), and area under the receiver operating characteristic curve (AU-ROC = 0.99) for predicted versus experimental binding affinities were obtained, with ligand tautomeric/ionization states additionally considered using density functional theory (DFT). Seven 2-aryl-4(5)-(β-d-glucopyranosyl)-imidazoles and 2-aryl-4-(β-d-glucopyranosyl)-thiazoles were subsequently synthesized, and kinetics experiments against rabbit muscle GPb revealed new potent inhibitors with best Ki values in the low micromolar range (5c = 1.97 μM; 13b = 4.58 μM). Ten C-β-d-glucopyranosyl azoles were then tested ex vivo in mouse primary hepatocytes. Four of these (5a-c and 9d) demonstrated significant reduction of glucagon stimulated glycogenolysis (IC50 = 30-60 μM). Structural and predicted physicochemical properties associated with their effectiveness were analyzed with permeability related parameters identified as crucial factors. The most effective ligand series 5 contained an imidazole ring, and the calculated pKa (Epik: 6.2; Jaguar 5.5) for protonated imidazole suggests that cellular permeation through the neutral state is favored, while within the cell, there is predicted more favorable binding to GP in the protonated form.
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Affiliation(s)
- Daniel Barr
- School of Physical Sciences & Computing, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Eszter Szennyes
- Department of Organic Chemistry, University of Debrecen, POB 400, H-4002 Debrecen, Hungary
| | - Éva Bokor
- Department of Organic Chemistry, University of Debrecen, POB 400, H-4002 Debrecen, Hungary
| | - Ziad H. Al-Oanzi
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Colin Moffatt
- Health & Life Sciences, De Montfort University, Gateway House, Leicester LE1 9BH, United Kingdom
| | - Sándor Kun
- Department of Organic Chemistry, University of Debrecen, POB 400, H-4002 Debrecen, Hungary
| | - Tibor Docsa
- Department of Medical Chemistry, Medical and Health Science Centre, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Ádám Sipos
- Department of Medical Chemistry, Medical and Health Science Centre, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Matthew P. Davies
- School of Physical Sciences & Computing, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Rachel T. Mathomes
- School of Pharmacy & Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Timothy J. Snape
- School of Pharmacy & Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Loranne Agius
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - László Somsák
- Department of Organic Chemistry, University of Debrecen, POB 400, H-4002 Debrecen, Hungary
| | - Joseph M. Hayes
- School of Pharmacy & Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
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Pałasz A, Cież D, Trzewik B, Miszczak K, Tynor G, Bazan B. In the Search of Glycoside-Based Molecules as Antidiabetic Agents. Top Curr Chem (Cham) 2019; 377:19. [PMID: 31165274 PMCID: PMC6548768 DOI: 10.1007/s41061-019-0243-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 05/14/2019] [Indexed: 02/06/2023]
Abstract
This review is an effort to summarize recent developments in synthesis of O-glycosides and N-, C-glycosyl molecules with promising antidiabetic potential. Articles published after 2000 are included. First, the O-glycosides used in the treatment of diabetes are presented, followed by the N-glycosides and finally the C-glycosides constituting the largest group of antidiabetic drugs are described. Within each group of glycosides, we presented how the structure of compounds representing potential drugs changes and when discussing chemical compounds of a similar structure, achievements are presented in the chronological order. C-Glycosyl compounds mimicking O-glycosides structure, exhibit the best features in terms of pharmacodynamics and pharmacokinetics. Therefore, the largest part of the article is concerned with the description of the synthesis and biological studies of various C-glycosides. Also N-glycosides such as N-(β-d-glucopyranosyl)-amides, N-(β-d-glucopyranosyl)-ureas, and 1,2,3-triazolyl derivatives belong to the most potent classes of antidiabetic agents. In order to indicate which of the compounds presented in the given sections have the best inhibitory properties, a list of the best inhibitors is presented at the end of each section. In summary, the best inhibitors were selected from each of the summarizing figures and the results of the ranking were placed. In this way, the reader can learn about the structure of the compounds having the best antidiabetic activity. The compounds, whose synthesis was described in the article but did not appear on the figures presenting the structures of the most active inhibitors, did not show proper activity as inhibitors. Thus, the article also presents studies that have not yielded the desired results and show directions of research that should not be followed. In order to show the directions of the latest research, articles from 2018 to 2019 are described in a separate Sect. 5. In Sect. 6, biological mechanisms of action of the glycosides and patents of marketed drugs are described.
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Affiliation(s)
- Aleksandra Pałasz
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Kraków, Poland.
| | - Dariusz Cież
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Kraków, Poland
| | - Bartosz Trzewik
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Kraków, Poland
| | - Katarzyna Miszczak
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Kraków, Poland
| | - Grzegorz Tynor
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Kraków, Poland
| | - Bartłomiej Bazan
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Kraków, Poland
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5
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Perez-Castillo Y, Helguera AM, Cordeiro MNDS, Tejera E, Paz-Y-Mino C, Sanchez-Rodriguez A, Borges F, Cruz-Monteagudo M. Fusing Docking Scoring Functions Improves the Virtual Screening Performance for Discovering Parkinson's Disease Dual Target Ligands. Curr Neuropharmacol 2018; 15:1107-1116. [PMID: 28067172 PMCID: PMC5725543 DOI: 10.2174/1570159x15666170109143757] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Revised: 01/18/2016] [Accepted: 11/03/2016] [Indexed: 11/22/2022] Open
Affiliation(s)
- Yunierkis Perez-Castillo
- Seccion Fisico Quimica y Matematicas, Departamento de Quimica, Universidad Tecnica Particular de Loja, San Cayetano Alto S/N, EC1101608 Loja, Ecuador.,Molecular Simulation and Drug Design Group, Centro de Bioactivos Quimicos (CBQ), Universidad Central "Marta Abreu" de Las Villas, Santa Clara, 54830, Cuba
| | - Aliuska Morales Helguera
- Molecular Simulation and Drug Design Group, Centro de Bioactivos Quimicos (CBQ), Universidad Central "Marta Abreu" de Las Villas, Santa Clara, 54830, Cuba
| | - M Natalia D S Cordeiro
- REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Eduardo Tejera
- Instituto de Investigaciones Biomedicas (IIB), Universidad de Las Americas, 170513 Quito, Ecuador
| | - Cesar Paz-Y-Mino
- Instituto de Investigaciones Biomedicas (IIB), Universidad de Las Americas, 170513 Quito, Ecuador
| | - Aminael Sanchez-Rodriguez
- Departamento de Ciencias Naturales, Universidad Tecnica Particular de Loja, Calle Paris S/N, EC1101608 Loja, Ecuador
| | - Fernanda Borges
- CIQUP/Departamento de Quimica e Bioquimica, Faculdade de Ciencias, Universidade do Porto, Porto 4169-007, Portugal
| | - Maykel Cruz-Monteagudo
- Instituto de Investigaciones Biomedicas (IIB), Universidad de Las Americas, 170513 Quito, Ecuador.,CIQUP/Departamento de Quimica e Bioquimica, Faculdade de Ciencias, Universidade do Porto, Porto 4169-007, Portugal
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A multidisciplinary study of 3-(β- d -glucopyranosyl)-5-substituted-1,2,4-triazole derivatives as glycogen phosphorylase inhibitors: Computation, synthesis, crystallography and kinetics reveal new potent inhibitors. Eur J Med Chem 2018; 147:266-278. [DOI: 10.1016/j.ejmech.2018.01.095] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 01/26/2018] [Accepted: 01/30/2018] [Indexed: 12/17/2022]
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Merzoug A, Chikhi A, Bensegueni A, Boucherit H, Okay S. Virtual Screening Approach of Bacterial Peptide Deformylase Inhibitors Results in New Antibiotics. Mol Inform 2017; 37. [PMID: 28991412 DOI: 10.1002/minf.201700087] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Accepted: 09/27/2017] [Indexed: 11/07/2022]
Abstract
The increasing resistance of bacteria to antibacterial therapy poses an enormous health problem, it renders the development of new antibacterial agents with novel mechanism of action an urgent need. Peptide deformylase, a metalloenzyme which catalytically removes N-formyl group from N-terminal methionine of newly synthesized polypeptides, is an important target in antibacterial drug discovery. In this study, we report the structure-based virtual screening of ZINC database in order to discover potential hits as bacterial peptide deformylase enzyme inhibitors with more affinity as compared to GSK1322322, previously known inhibitor. After virtual screening, fifteen compounds of the top hits predicted were purchased and evaluated in vitro for their antibacterial activities against one Gram positive (Staphylococcus aureus) and three Gram negative (Escherichia coli, Pseudomonas aeruginosa and Klebsiella. pneumoniae) bacteria in different concentrations by disc diffusion method. Out of these, three compounds, ZINC00039650, ZINC03872971 and ZINC00126407, exhibited significant zone of inhibition. The results obtained were confirmed using the dilution method. Thus, these proposed compounds may aid the development of more efficient antibacterial agents.
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Affiliation(s)
- Amina Merzoug
- Laboratory of Applied Biochemistry, Department of Biochemistry and Cellular and Molecular Biology, Faculty of Natural and Life Sciences, Mentouri Brothers University, Constantine 1 -, Algeria.,Abdelhafid.Boussouf University Center, Mila, Algeria
| | - Abdelouahab Chikhi
- Laboratory of Applied Biochemistry, Department of Biochemistry and Cellular and Molecular Biology, Faculty of Natural and Life Sciences, Mentouri Brothers University, Constantine 1 -, Algeria
| | - Abderrahmane Bensegueni
- Laboratory of Applied Biochemistry, Department of Biochemistry and Cellular and Molecular Biology, Faculty of Natural and Life Sciences, Mentouri Brothers University, Constantine 1 -, Algeria
| | - Hanane Boucherit
- Laboratory of Applied Biochemistry, Department of Biochemistry and Cellular and Molecular Biology, Faculty of Natural and Life Sciences, Mentouri Brothers University, Constantine 1 -, Algeria.,Abdelhafid.Boussouf University Center, Mila, Algeria
| | - Sezer Okay
- Department of Biology, Faculty of Sciences, Cankiri Karatekin University, Turk
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8
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Spasov AA, Chepljaeva NI, Vorob’ev ES. Glycogen phosphorylase inhibitors in the regulation of carbohydrate metabolism in type 2 diabetes. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2016. [DOI: 10.1134/s1068162016020138] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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9
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Abstract
It is now plausible to dock libraries of 10 million molecules against targets over several days or weeks. When the molecules screened are commercially available, they may be rapidly tested to find new leads. Although docking retains important liabilities (it cannot calculate affinities accurately nor even reliably rank order high-scoring molecules), it can often can distinguish likely from unlikely ligands, often with hit rates above 10%. Here we summarize the improvements in libraries, target quality, and methods that have supported these advances, and the open access resources that make docking accessible. Recent docking screens for new ligands are sketched, as are the binding, crystallographic, and in vivo assays that support them. Like any technique, controls are crucial, and key experimental ones are reviewed. With such controls, docking campaigns can find ligands with new chemotypes, often revealing the new biology that may be docking's greatest impact over the next few years.
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Affiliation(s)
- John J Irwin
- Department of Pharmaceutical Chemistry and QB3 Institute, University of California-San Francisco , San Francisco, California 94158, United States
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry and QB3 Institute, University of California-San Francisco , San Francisco, California 94158, United States
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Parmenopoulou V, Manta S, Dimopoulou A, Kollatos N, Schols D, Komiotis D. Synthesis of novel N-acyl- β-d-glucopyranosylamines and ureas as potential lead cytostatic agents. Med Chem Res 2016; 25:932-940. [PMID: 32214768 PMCID: PMC7079967 DOI: 10.1007/s00044-016-1539-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 02/16/2016] [Indexed: 10/29/2022]
Abstract
Novel classes of acetylated and fully deprotected N-acyl-β-d-glucopyranosylamines and ureas have been synthesized and biologically evaluated. Acylation of the per-O-acetylated β-d-glucopyranosylurea (5), easily prepared via its corresponding phosphinimine derivative, by zinc chloride catalyzed reaction of the corresponding acyl chlorides RCOCl (a-f) gave the protected N-acyl-β-d-glucopyranosylureas (6a-f), in acceptable-to-moderate yields. Subsequent deacetylation of analogues 6a-f under Zemplén conditions afforded the fully deprotected derivatives 7a,b,d,e,f, while the desired urea 7c was formed after treatment of 6c with dibutyltin oxide. All protected and unprotected compounds were examined for their cytotoxic activity in different L1210, CEM and HeLa tumor cell lines and were also evaluated against a broad panel of DΝΑ and RNA viruses. Derivative 7c exhibited cytostatic activity against the three evaluated tumor cell lines (IC50 9-24 μΜ) and might be the basis for the synthesis of structure-related derivatives with improved cytostatic potential. Only analogue 6f weakly but significantly inhibited the replication of parainfluenza-3 virus, Sindbis virus and Coxsackie virus B4 in cell cultures at concentrations of 45-58 μM.
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Affiliation(s)
- Vanessa Parmenopoulou
- 1Laboratory of Bioorganic Chemistry, Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Str., 41 221 Larissa, Greece
| | - Stella Manta
- 1Laboratory of Bioorganic Chemistry, Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Str., 41 221 Larissa, Greece
| | - Athina Dimopoulou
- 1Laboratory of Bioorganic Chemistry, Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Str., 41 221 Larissa, Greece
| | - Nikolaos Kollatos
- 1Laboratory of Bioorganic Chemistry, Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Str., 41 221 Larissa, Greece
| | - Dominique Schols
- 2Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, Louvain, Belgium
| | - Dimitri Komiotis
- 1Laboratory of Bioorganic Chemistry, Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Str., 41 221 Larissa, Greece
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11
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Role of glycogen phosphorylase in liver glycogen metabolism. Mol Aspects Med 2015; 46:34-45. [PMID: 26519772 DOI: 10.1016/j.mam.2015.09.002] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 09/11/2015] [Indexed: 02/05/2023]
Abstract
Liver glycogen is synthesized after a meal in response to an increase in blood glucose concentration in the portal vein and endocrine and neuroendocrine signals, and is degraded to glucose between meals to maintain blood glucose homeostasis. Glycogen degradation and synthesis during the diurnal cycle are mediated by changes in the activities of phosphorylase and glycogen synthase. Phosphorylase is regulated by phosphorylation of serine-14. Only the phosphorylated form of liver phosphorylase (GPa) is catalytically active. Interconversion between GPa and GPb (unphosphorylated) is dependent on the activities of phosphorylase kinase and of phosphorylase phosphatase. The latter comprises protein phosphatase-1 in conjunction with a glycogen-targeting protein (G-subunit) of the PPP1R3 family. At least two of six G-subunits (GL and PTG) expressed in liver are involved in GPa dephosphorylation. GPa to GPb interconversion is dependent on the conformational state of phosphorylase which can be relaxed (R) or tense (T) depending on the concentrations of allosteric effectors such as glucose, glucose 6-phosphate and adenine nucleotides and on the acetylation state of lysine residues. The G-subunit, GL, encoded by PPP1R3B gene is expressed at high levels in liver and can function as a phosphorylase phosphatase and a synthase phosphatase and has an allosteric binding site for GPa at the C-terminus which inhibits synthase phosphatase activity. GPa to GPb conversion is a major upstream event in the regulation of glycogen synthesis by glucose, its downstream metabolites and extracellular signals such as insulin and neurotransmitters.
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Begum J, Skamnaki VT, Moffatt C, Bischler N, Sarrou J, Skaltsounis AL, Leonidas DD, Oikonomakos NG, Hayes JM. An evaluation of indirubin analogues as phosphorylase kinase inhibitors. J Mol Graph Model 2015; 61:231-42. [PMID: 26364215 DOI: 10.1016/j.jmgm.2015.07.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Revised: 07/24/2015] [Accepted: 07/27/2015] [Indexed: 11/24/2022]
Abstract
Phosphorylase kinase (PhK) has been linked with a number of conditions such as glycogen storage diseases, psoriasis, type 2 diabetes and more recently, cancer (Camus et al., 2012 [6]). However, with few reported structural studies on PhK inhibitors, this hinders a structure based drug design approach. In this study, the inhibitory potential of 38 indirubin analogues have been investigated. 11 of these ligands had IC50 values in the range 0.170-0.360μM, with indirubin-3'-acetoxime (1c) the most potent. 7-Bromoindirubin-3'-oxime (13b), an antitumor compound which induces caspase-independent cell-death (Ribas et al., 2006 [20]) is revealed as a specific inhibitor of PhK (IC50=1.8μM). Binding assay experiments performed using both PhK-holo and PhK-γtrnc confirmed the inhibitory effects to arise from binding at the kinase domain (γ subunit). High level computations using QM/MM-PBSA binding free energy calculations were in good agreement with experimental binding data, as determined using statistical analysis, and support binding at the ATP-binding site. The value of a QM description for the binding of halogenated ligands exhibiting σ-hole effects is highlighted. A new statistical metric, the 'sum of the modified logarithm of ranks' (SMLR), has been defined which measures performance of a model for both the "early recognition" (ranking earlier/higher) of active compounds and their relative ordering by potency. Through a detailed structure activity relationship analysis considering other kinases (CDK2, CDK5 and GSK-3α/β), 6'(Z) and 7(L) indirubin substitutions have been identified to achieve selective PhK inhibition. The key PhK binding site residues involved can also be targeted using other ligand scaffolds in future work.
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Affiliation(s)
- Jaida Begum
- School of Physical Sciences & Computing, Division of Chemistry, University of Central Lancashire, Preston PR1 2HE, United Kingdom; School of Forensic & Investigative Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Vassiliki T Skamnaki
- Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Str., 41221 Larissa, Greece
| | - Colin Moffatt
- School of Forensic & Investigative Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Nicolas Bischler
- Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vas. Constantinou Ave., 116 35 Athens, Greece
| | - Josephine Sarrou
- Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vas. Constantinou Ave., 116 35 Athens, Greece
| | - Alexios-Leandros Skaltsounis
- Division of Pharmacognosy, Department of Pharmacy, University of Athens, Panepistimiopolis-Zografou, Athens 15771, Greece
| | - Demetres D Leonidas
- Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos Str., 41221 Larissa, Greece
| | - Nikos G Oikonomakos
- Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation, 48 Vas. Constantinou Ave., 116 35 Athens, Greece
| | - Joseph M Hayes
- School of Physical Sciences & Computing, Division of Chemistry, University of Central Lancashire, Preston PR1 2HE, United Kingdom; School of Forensic & Investigative Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom.
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13
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Lucas X, Grüning BA, Bleher S, Günther S. The purchasable chemical space: a detailed picture. J Chem Inf Model 2015; 55:915-24. [PMID: 25894297 DOI: 10.1021/acs.jcim.5b00116] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The screening of a reduced yet diverse and synthesizable region of the chemical space is a critical step in drug discovery. The ZINC database is nowadays routinely used to freely access and screen millions of commercially available compounds. We collected ∼125 million compounds from chemical catalogs and the ZINC database, yielding more than 68 million unique molecules, including a large portion of described natural products (NPs) and drugs. The data set was filtered using advanced medicinal chemistry rules to remove potentially toxic, promiscuous, metabolically labile, or reactive compounds. We studied the physicochemical properties of this compilation and identified millions of NP-like, fragment-like, inhibitors of protein-protein interactions (i-PPIs) like, and drug-like compounds. The related focused libraries were subjected to a detailed scaffold diversity analysis and compared to reference NPs and marketed drugs. This study revealed thousands of diverse chemotypes with distinct representations of building block combinations among the data sets. An analysis of the stereogenic and shape complexity properties of the libraries also showed that they present well-defined levels of complexity, following the tendency: i-PPIs-like < drug-like < fragment-like < NP-like. As the collected compounds have huge interest in drug discovery and particularly virtual screening and library design, we offer a freely available collection comprising over 37 million molecules under: http://pbox.pharmaceutical-bioinformatics.org , as well as the filtering rules used to build the focused libraries described herein.
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Affiliation(s)
- Xavier Lucas
- Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, Hermann-Herder-Str. 9, D-79104 Freiburg, Germany
| | - Björn A Grüning
- Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, Hermann-Herder-Str. 9, D-79104 Freiburg, Germany
| | - Stefan Bleher
- Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, Hermann-Herder-Str. 9, D-79104 Freiburg, Germany
| | - Stefan Günther
- Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, Albert-Ludwigs-University, Hermann-Herder-Str. 9, D-79104 Freiburg, Germany
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