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Ul-Haq Z, Ashraf S, Bkhaitan MM. Molecular dynamics simulations reveal structural insights into inhibitor binding modes and mechanism of casein kinase II inhibitors. J Biomol Struct Dyn 2018. [DOI: 10.1080/07391102.2018.1450166] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Sajda Ashraf
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Majdi M. Bkhaitan
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Umm Al-Qura University, Makkah, KSA, Saudi Arabia
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2
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Abstract
In silico three-dimensional (3D) molecular modeling tools based upon the receptor/enzyme-ligand docking simulation in protein crystal structures and/or homology modeling of receptors have been reliably used in pharmacological research and development for decades. Molecular docking methodologies are helpful for revealing facets of activation and inactivation, thus improving mechanistic understanding and predicting molecular ligand binding activity, and they can have a high level of accuracy, and have also been explored and applied in chemical risk assessment. This computational approach is, however, only applicable for chemical hazard identification situations where the specific target receptor for a given chemical is known and the crystal structure/homology model of the receptor is available.
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Affiliation(s)
- Stefano Moro
- Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Università Padova, via Marzolo 5, 35131, Padova, Italy.
| | - Mattia Sturlese
- Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Università Padova, via Marzolo 5, 35131, Padova, Italy
| | - Antonella Ciancetta
- Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Università Padova, via Marzolo 5, 35131, Padova, Italy
| | - Matteo Floris
- Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, v.le San Pietro 43/C, 07100, Sassari, Italy
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3
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Binding affinity models for Falcipain inhibition based on the Linear Interaction Energy method. J Mol Graph Model 2016; 70:236-245. [DOI: 10.1016/j.jmgm.2016.06.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 06/06/2016] [Accepted: 06/15/2016] [Indexed: 02/04/2023]
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4
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Kjellgren ER, Glue OES, Reinholdt P, Meyer JE, Kongsted J, Poongavanam V. A comparative study of binding affinities for 6,7-dimethoxy-4-pyrrolidylquinazolines as phosphodiesterase 10A inhibitors using the linear interaction energy method. J Mol Graph Model 2015; 61:44-52. [PMID: 26188794 DOI: 10.1016/j.jmgm.2015.06.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 06/05/2015] [Accepted: 06/20/2015] [Indexed: 01/29/2023]
Abstract
The linear interaction energy (LIE) method was used to estimate the free energies of binding for a set of 27 pyrrolidylquinazoline derivatives as phosphodiesterase 10A inhibitors. Twenty-six X-ray crystal structures of phosphodiesterase 10A and two sampling methods, minimization and Hybrid Monte Carlo, were used to assess the affinity models based on the linear interaction energies. The best model was obtained based on the parameters α=0.16 and β=0.04, which represent non-polar and polar interactions, respectively, with a root mean square error (RMSE) of 0.42kcal/mol (R(2)=0.71) and 0.52kcal/mol (R(2)=0.86) for the training and test sets, respectively. In addition, the applicability domain of the model was investigated. After validation of the models, the best model was subsequently used in a virtual screening process, which resulted in a set of optimized compounds. The models developed in this study could be useful as filter for virtual screening and lead optimization processes for phosphodiesterase 10A drug developments.
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Affiliation(s)
- Erik Rosendahl Kjellgren
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Oliver Emil Skytte Glue
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Peter Reinholdt
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Julie Egeskov Meyer
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
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5
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Lv M, Ma S, Tian Y, Zhang X, Zhai H, Lv W. Structural insights into flavones as protein kinase CK2 inhibitors derived from a combined computational study. RSC Adv 2015. [DOI: 10.1039/c4ra10381e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Binding conformation of flavone inhibitors to protein kinase CK2.
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Affiliation(s)
- Min Lv
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
- People's Republic of China
| | - Shuying Ma
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
- People's Republic of China
| | - Yueli Tian
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
- People's Republic of China
| | - Xiaoyun Zhang
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
- People's Republic of China
| | - Honglin Zhai
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
- People's Republic of China
| | - Wenjuan Lv
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
- People's Republic of China
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6
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Bereau T, Kramer C, Meuwly M. Leveraging Symmetries of Static Atomic Multipole Electrostatics in Molecular Dynamics Simulations. J Chem Theory Comput 2013; 9:5450-9. [DOI: 10.1021/ct400803f] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Tristan Bereau
- Department
of Chemistry, University of Basel, 4056 Basel, Switzerland
| | - Christian Kramer
- Institute
of General, Inorganic and Theoretical Chemistry, and Center for Molecular
Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
| | - Markus Meuwly
- Department
of Chemistry, University of Basel, 4056 Basel, Switzerland
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7
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Perdih A, Wolber G, Solmajer T. Molecular dynamics simulation and linear interaction energy study of d-Glu-based inhibitors of the MurD ligase. J Comput Aided Mol Des 2013; 27:723-38. [DOI: 10.1007/s10822-013-9673-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 08/06/2013] [Indexed: 12/31/2022]
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8
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Bortolato A, Tehan BG, Bodnarchuk MS, Essex JW, Mason JS. Water Network Perturbation in Ligand Binding: Adenosine A2A Antagonists as a Case Study. J Chem Inf Model 2013; 53:1700-13. [DOI: 10.1021/ci4001458] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrea Bortolato
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Herts,
AL7 3AX, U.K
| | - Ben G. Tehan
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Herts,
AL7 3AX, U.K
| | - Michael S. Bodnarchuk
- School of
Chemistry, University of Southampton, Highfield,
Southampton,
Hampshire, SO17 1BJ, U.K
| | - Jonathan W. Essex
- School of
Chemistry, University of Southampton, Highfield,
Southampton,
Hampshire, SO17 1BJ, U.K
| | - Jonathan S. Mason
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Herts,
AL7 3AX, U.K
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9
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Abstract
BACKGROUND Drug approval applications to the FDA have shown a remarkably small increment compared with what was expected. In the last few years several efforts have been made to improve the results of rational drug design approaches and in particular to predict inhibitor-target structure and to evaluate the free energy of binding. Virtual database screening, combined with other computational methods, is one of the most promising methods to overcome this key issue. OBJECTIVE It is possible to understand how computational medicinal chemistry is changing, improving from its errors and moving towards becoming a more important tool for drug development. METHODS Some of the most recent modeling techniques have been presented and in particular the benefits of combining these techniques are highlighted. RESULTS/CONCLUSION At present computational chemists can understand the peculiar problems associated with the study of biological systems and on this basis they can choose the right collection of complementary in silico approaches to solve the medicinal chemistry problem in a better manner.
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Affiliation(s)
- Andrea Bortolato
- University of Padova, Molecular Modeling Section, Department of Pharmaceutical Sciences, Via Marzolo 5, 35131 Padova, Italy +39 049 8275704 ; +39 049 827 5366 ;
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10
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Park K, Sung NK, Cho AE. Importance of Accurate Charges in Binding Affinity Calculations: A Case of Neuraminidase Series. B KOREAN CHEM SOC 2013. [DOI: 10.5012/bkcs.2013.34.2.545] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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11
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Abstract
Molecular docking represents an important technology for structure-based drug design. Docking is a computational technique aimed at the prediction of the most favorable ligand-target spatial configuration and an estimate of the corresponding complex free energy, although as stated at the beginning accurate scoring methods remain still elusive. In this chapter, the state of art of molecular docking methodologies and their applications in drug discovery is summarized.
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12
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Linder M, Ranganathan A, Brinck T. “Adapted Linear Interaction Energy”: A Structure-Based LIE Parametrization for Fast Prediction of Protein–Ligand Affinities. J Chem Theory Comput 2012; 9:1230-9. [DOI: 10.1021/ct300783e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mats Linder
- Applied Physical
Chemistry, KTH Royal Institute of
Technology, Teknikringen 30, S-100 44 Stockholm, Sweden
| | - Anirudh Ranganathan
- Applied Physical
Chemistry, KTH Royal Institute of
Technology, Teknikringen 30, S-100 44 Stockholm, Sweden
| | - Tore Brinck
- Applied Physical
Chemistry, KTH Royal Institute of
Technology, Teknikringen 30, S-100 44 Stockholm, Sweden
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13
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Liu S, Fu R, Zhou LH, Chen SP. Application of consensus scoring and principal component analysis for virtual screening against β-secretase (BACE-1). PLoS One 2012; 7:e38086. [PMID: 22701601 PMCID: PMC3372491 DOI: 10.1371/journal.pone.0038086] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2011] [Accepted: 05/03/2012] [Indexed: 01/19/2023] Open
Abstract
Background In order to identify novel chemical classes of β-secretase (BACE-1) inhibitors, an alternative scoring protocol, Principal Component Analysis (PCA), was proposed to summarize most of the information from the original scoring functions and re-rank the results from the virtual screening against BACE-1. Method Given a training set (50 BACE-1 inhibitors and 9950 inactive diverse compounds), three rank-based virtual screening methods, individual scoring, conventional consensus scoring and PCA, were judged by the hit number in the top 1% of the ranked list. The docking poses were generated by Surflex, five scoring functions (Surflex_Score, D_Score, G_Score, ChemScore, and PMF_Score) were used for pose extraction. For each pose group, twelve scoring functions (Surflex_Score, D_Score, G_Score, ChemScore, PMF_Score, LigScore1, LigScore2, PLP1, PLP2, jain, Ludi_1, and Ludi_2) were used for the pose rank. For a test set, 113,228 chemical compounds (Sigma-Aldrich® corporate chemical directory) were docked by Surflex, then ranked by the same three ranking methods motioned above to select the potential active compounds for experimental test. Results For the training set, the PCA approach yielded consistently superior rankings compared to conventional consensus scoring and single scoring. For the test set, the top 20 compounds according to conventional consensus scoring were experimentally tested, no inhibitor was found. Then, we relied on PCA scoring protocol to test another different top 20 compounds and two low micromolar inhibitors (S450588 and 276065) were emerged through the BACE-1 fluorescence resonance energy transfer (FRET) assay. Conclusion The PCA method extends the conventional consensus scoring in a quantitative statistical manner and would appear to have considerable potential for chemical screening applications.
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Affiliation(s)
- Shu Liu
- Department of Anatomy, Zhong Shan School of Medicine, Sun Yat-Sen University, Guangzhou, People’s Republic of China
- * E-mail: (S-PC); (SL)
| | - Rao Fu
- Department of Anatomy, Zhong Shan School of Medicine, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Li-Hua Zhou
- Department of Anatomy, Zhong Shan School of Medicine, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Sheng-Ping Chen
- Guangdong Province Key Laboratory of Functional Molecules in Oceanic Microorganism, Zhong Shan School of Medicine, Sun Yat-Sen University, Guangzhou, People’s Republic of China
- * E-mail: (S-PC); (SL)
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14
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Sotriffer C, Matter H. The Challenge of Affinity Prediction: Scoring Functions for Structure-Based Virtual Screening. METHODS AND PRINCIPLES IN MEDICINAL CHEMISTRY 2011. [DOI: 10.1002/9783527633326.ch7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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15
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Lannutti F, Marrone A, Re N. Prediction of the PPARα agonism of fibrates by combined MM–docking approaches. J Mol Graph Model 2011; 29:865-75. [DOI: 10.1016/j.jmgm.2011.02.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Revised: 02/11/2011] [Accepted: 02/16/2011] [Indexed: 11/30/2022]
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Abstract
CK2 is a pleiotropic, ubiquitous, and constitutively active protein kinase (PK), with both cytosolic and nuclear localization in most mammalian cells. The holoenzyme is generally composed of two catalytic (alpha and/or alpha') and two regulatory (beta) subunits, but the free alpha/alpha' subunits are catalytically active by themselves and can be present in cells under some circumstances. CK2 catalyzes the phosphorylation of more than 300 substrates characterized by multiple acidic residues surrounding the phosphor-acceptor amino acid, and, consequently, it plays a key role in several physiological and pathological processes. But how can one kinase orchestrate all these tasks faithfully? How is it possible that one kinase can, despite all pleiotropic characteristics of PKs in general, be involved in so many different biochemical events? Is CK2 a druggable target? Several questions are still to be clearly answered, and this review is an occasion for a fruitful discussion.
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Affiliation(s)
- Giorgio Cozza
- Molecular Modeling Section, Dipartimento di Scienze Farmaceutiche, Università di Padova, via Marzolo 5, Padova, Italy
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17
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Perdih A, Bren U, Solmajer T. Binding free energy calculations of N-sulphonyl-glutamic acid inhibitors of MurD ligase. J Mol Model 2009; 15:983-96. [PMID: 19198900 DOI: 10.1007/s00894-009-0455-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2008] [Accepted: 01/06/2009] [Indexed: 10/21/2022]
Abstract
The increasing incidence of bacterial resistance to most available antibiotics has underlined the urgent need for the discovery of novel efficacious antibacterial agents. The biosynthesis of bacterial peptidoglycan, where the MurD enzyme is involved in the intracellular phase of UDP-MurNAc-pentapeptide formation, represents a collection of highly selective targets for novel antibacterial drug design. Structural studies of N-sulfonyl-glutamic acid inhibitors of MurD have made possible the examination of binding modes of this class of compounds, providing valuable information for the lead optimization phase of the drug discovery cycle. Binding free energies were calculated for a series of MurD N-sulphonyl-Glu inhibitors using the linear interaction energy (LIE) method. Analysis of interaction energy during the 20-ns MD trajectories revealed non-polar van der Waals interactions as the main driving force for the binding of these inhibitors, and excellent agreement with the experimental free energies was obtained. Calculations of binding free energies for selected moieties of compounds in this structural class substantiated even deeper insight into the source of inhibitory activity. These results constitute new valuable information to further assist the lead optimization process.
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Affiliation(s)
- Andrej Perdih
- Laboratory for Molecular Modeling and NMR Spectroscopy, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia
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18
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Wallin G, Nervall M, Carlsson J, Åqvist J. Charges for Large Scale Binding Free Energy Calculations with the Linear Interaction Energy Method. J Chem Theory Comput 2009; 5:380-95. [DOI: 10.1021/ct800404f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Göran Wallin
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Martin Nervall
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Jens Carlsson
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Johan Åqvist
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
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19
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Murata K, Fedorov DG, Nakanishi I, Kitaura K. Cluster Hydration Model for Binding Energy Calculations of Protein−Ligand Complexes. J Phys Chem B 2008; 113:809-17. [DOI: 10.1021/jp805007f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Katsumi Murata
- Department of Theoretical Drug Design, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8501 Japan, and National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8568 Japan
| | - Dmitri G. Fedorov
- Department of Theoretical Drug Design, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8501 Japan, and National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8568 Japan
| | - Isao Nakanishi
- Department of Theoretical Drug Design, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8501 Japan, and National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8568 Japan
| | - Kazuo Kitaura
- Department of Theoretical Drug Design, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8501 Japan, and National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8568 Japan
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20
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Mor M, Lodola A, Rivara S, Vacondio F, Duranti A, Tontini A, Sanchini S, Piersanti G, Clapper JR, King AR, Tarzia G, Piomelli D. Synthesis and quantitative structure-activity relationship of fatty acid amide hydrolase inhibitors: modulation at the N-portion of biphenyl-3-yl alkylcarbamates. J Med Chem 2008; 51:3487-98. [PMID: 18507372 DOI: 10.1021/jm701631z] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Alkylcarbamic acid biphenyl-3-yl esters are a class of fatty acid amide hydrolase (FAAH) inhibitors that comprises cyclohexylcarbamic acid 3'-carbamoylbiphenyl-3-yl ester (URB597), a compound with analgesic, anxiolytic-like and antidepressant-like properties in rat and mouse models. Here, we extended the structure-activity relationships (SARs) for this class of compounds by replacing the cyclohexyl ring of the parent compound cyclohexylcarbamic acid biphenyl-3-yl ester (URB524) (FAAH IC50 = 63 nM) with a selected set of substituents of different size, shape, flexibility, and lipophilicity. Docking experiments and linear interaction energy (LIE) calculations indicated that the N-terminal group of O-arylcarbamates fits within the lipophilic region of the substrate-binding site, mimicking the arachidonoyl chain of anandamide. Significant potency improvements were observed for the beta-naphthylmethyl derivative 4q (IC50 = 5.3 nM) and its 3'-carbamoylbiphenyl-3-yl ester 4z (URB880, IC50 = 0.63 nM), indicating that shape complementarity and hydrogen bonds are crucial to obtain highly potent inhibitors.
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Affiliation(s)
- Marco Mor
- Dipartimento Farmaceutico, Università degli Studi di Parma, Viale G P Usberti 27/A Campus Universitario, I-43100 Parma, Italy
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Waszkowycz B. Towards improving compound selection in structure-based virtual screening. Drug Discov Today 2008; 13:219-26. [PMID: 18342797 DOI: 10.1016/j.drudis.2007.12.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2007] [Revised: 12/06/2007] [Accepted: 12/15/2007] [Indexed: 10/22/2022]
Abstract
Structure-based virtual screening is now an established technology for supporting hit finding and lead optimisation in drug discovery. Recent validation studies have highlighted the poor performance of currently used scoring functions in estimating binding affinity and hence in ranking large datasets of docked ligands. Progress in the analysis of large datasets can be made through the use of appropriate data mining techniques and the derivation of a broader range of descriptors relevant to receptor-ligand binding. In addition, simple scoring functions can be supplemented by simulation-based scoring protocols. Developments in workflow design allow the automation of repetitive tasks, and also encourage the routine use of simulation-based methods and the rapid prototyping of novel modelling and analysis procedures.
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Affiliation(s)
- Bohdan Waszkowycz
- Argenta Discovery Ltd., 8/9 Spire Green Centre, Flex Meadow, Harlow, Essex CM19 5TR, UK.
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Chilin A, Battistutta R, Bortolato A, Cozza G, Zanatta S, Poletto G, Mazzorana M, Zagotto G, Uriarte E, Guiotto A, Pinna LA, Meggio F, Moro S. Coumarin as Attractive Casein Kinase 2 (CK2) Inhibitor Scaffold: An Integrate Approach To Elucidate the Putative Binding Motif and Explain Structure–Activity Relationships. J Med Chem 2008; 51:752-9. [DOI: 10.1021/jm070909t] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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Battistutta R, Mazzorana M, Cendron L, Bortolato A, Sarno S, Kazimierczuk Z, Zanotti G, Moro S, Pinna LA. The ATP-binding site of protein kinase CK2 holds a positive electrostatic area and conserved water molecules. Chembiochem 2008; 8:1804-9. [PMID: 17768728 DOI: 10.1002/cbic.200700307] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
CK2 is a highly pleiotropic Ser/Thr protein kinase that is able to promote cell survival and enhance the tumour phenotype under specific circumstances. We have determined the crystal structure of three new complexes with tetrabromobenzimidazole derivatives that display K(i) values between 0.15 and 0.30 microM. A comparative analysis of these data with those of four other inhibitors of the same family revealed the presence of some highly conserved water molecules in the ATP-binding site. These waters reside near Lys68, in an area with a positive electrostatic potential that is able to attract and orient negatively charged ligands. The presence of this positive region and two unique bulky residues that are typical of CK2, Ile66 and Ile174, play a critical role in determining the ligand orientation and binding selectivity.
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Affiliation(s)
- Roberto Battistutta
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy. roberto.
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