1
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Boswell BR, Zhao Z, Gonciarz RL, Pandya KM. Regioselective Pyridine to Benzene Edit Inspired by Water-Displacement. J Am Chem Soc 2024; 146:19660-19666. [PMID: 38996188 DOI: 10.1021/jacs.4c05999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2024]
Abstract
Late-stage derivatization of drug-like functional groups can accelerate drug discovery efforts by swiftly exchanging hydrogen-bond donors with acceptors, or by modulating key physicochemical properties like logP, solubility, or polar surface area. A proven derivatization strategy to improve ligand potency is to extend the ligand to displace water molecules that are mediating the interactions with a receptor. Inspired by this application, we developed a method to regioselectively transmute the nitrogen atom from pyridine into carbon bearing an ester, a flexible functional group handle. We applied this method to a variety of substituted pyridines, as well as late-stage transformation of FDA-approved drugs.
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Affiliation(s)
- Benjamin R Boswell
- Discovery Chemistry, Exelixis Inc., Alameda, California 94502, United States
| | - Zhensheng Zhao
- Discovery Chemistry, Exelixis Inc., Alameda, California 94502, United States
| | - Ryan L Gonciarz
- Discovery Chemistry, Exelixis Inc., Alameda, California 94502, United States
| | - Keyur M Pandya
- Pharmaceutical Operations & Supply Chain, Exelixis Inc., Alameda, California 94502, United States
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2
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Kaczor AA, Zięba A, Matosiuk D. The application of WaterMap-guided structure-based virtual screening in novel drug discovery. Expert Opin Drug Discov 2024; 19:73-83. [PMID: 37807912 DOI: 10.1080/17460441.2023.2267015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/02/2023] [Indexed: 10/10/2023]
Abstract
INTRODUCTION Nowadays, it is widely accepted that water molecules play a key role in binding a ligand to a molecular target. Neglecting water molecules in the process of molecular recognition was the result of several failures of the structure-based drug discovery campaigns. The application of WaterMap, in particular WaterMap-guided molecular docking, enables the reasonably accurate and quick description of the location and energetics of water molecules at the ligand-protein interface. AREAS COVERED In this review, the authors shortly discuss the importance of water in drug design and discovery and provide a brief overview of the computational approaches used to predict the solvent-related effects for the purposes of presenting WaterMap in the context of other available techniques and tools. A concise description of WaterMap concept is followed by the presentation of WaterMap-assisted virtual screening literature published between 2013 and 2023. EXPERT OPINION In recent years, WaterMap software has been extensively used to support structure-based drug design, in particular structure-based virtual screening. Indeed, it is a useful tool to rescore docking results considering water molecules in the binding pocket. Although WaterMap allows for the consideration of the dynamic behavior of water molecules in the binding site, for best accuracy, its application in conjunction with other techniques such as molecular mechanics-generalized Born surface area of FEP (Free Energy Perturbation) is recommended.
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Affiliation(s)
- Agnieszka A Kaczor
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Lublin, Poland
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Agata Zięba
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Lublin, Poland
| | - Dariusz Matosiuk
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Lublin, Poland
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3
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Meanwell NA. Applications of Bioisosteres in the Design of Biologically Active Compounds. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:18087-18122. [PMID: 36961953 DOI: 10.1021/acs.jafc.3c00765] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The design of bioisosteres represents a creative and productive approach to improve a molecule, including by enhancing potency, addressing pharmacokinetic challenges, reducing off-target liabilities, and productively modulating physicochemical properties. Bioisosterism is a principle exploited in the design of bioactive compounds of interest to both medicinal and agricultural chemists, and in this review, we provide a synopsis of applications where this kind of molecular editing has proved to be advantageous in molecule optimization. The examples selected for discussion focus on bioisosteres of carboxylic acids, applications of fluorine and fluorinated motifs in compound design, some applications of the sulfoximine functionality, the design of bioisosteres of drug-H2O complexes, and the design of bioisosteres of the phenyl ring.
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Affiliation(s)
- Nicholas A Meanwell
- The Baruch S. Blumberg Institute, 3805 Old Easton Rd, Doylestown, Pennsylvania 18902, United States
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4
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Yoon HR, Park GJ, Balupuri A, Kang NS. TWN-FS method: A novel fragment screening method for drug discovery. Comput Struct Biotechnol J 2023; 21:4683-4696. [PMID: 37841326 PMCID: PMC10568351 DOI: 10.1016/j.csbj.2023.09.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/17/2023] Open
Abstract
Fragment-based drug discovery (FBDD) is a well-established and effective method for generating diverse and novel hits in drug design. Kinases are suitable targets for FBDD due to their well-defined structure. Water molecules contribute to structure and function of proteins and also influence the environment within the binding pocket. Water molecules form a variety of hydrogen-bonded cyclic water-ring networks, collectively known as topological water networks (TWNs). Analyzing the TWNs in protein binding sites can provide valuable insights into potential locations and shapes for fragments within the binding site. Here, we introduce TWN-based fragment screening (TWN-FS) method, a novel screening method that suggests fragments through grouped TWN analysis within the protein binding site. We used this method to screen known CDK2, CHK1, IGF1R and ERBB4 inhibitors. Our findings suggest that TWN-FS method has the potential to effectively screen fragments. The TWN-FS method package is available on GitHub at https://github.com/pkj0421/TWN-FS.
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Affiliation(s)
- Hye Ree Yoon
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, South Korea
| | - Gyoung Jin Park
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, South Korea
| | - Anand Balupuri
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, South Korea
| | - Nam Sook Kang
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, South Korea
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5
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Zsidó BZ, Bayarsaikhan B, Börzsei R, Szél V, Mohos V, Hetényi C. The Advances and Limitations of the Determination and Applications of Water Structure in Molecular Engineering. Int J Mol Sci 2023; 24:11784. [PMID: 37511543 PMCID: PMC10381018 DOI: 10.3390/ijms241411784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Water is a key actor of various processes of nature and, therefore, molecular engineering has to take the structural and energetic consequences of hydration into account. While the present review focuses on the target-ligand interactions in drug design, with a focus on biomolecules, these methods and applications can be easily adapted to other fields of the molecular engineering of molecular complexes, including solid hydrates. The review starts with the problems and solutions of the determination of water structures. The experimental approaches and theoretical calculations are summarized, including conceptual classifications. The implementations and applications of water models are featured for the calculation of the binding thermodynamics and computational ligand docking. It is concluded that theoretical approaches not only reproduce or complete experimental water structures, but also provide key information on the contribution of individual water molecules and are indispensable tools in molecular engineering.
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Affiliation(s)
- Balázs Zoltán Zsidó
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Bayartsetseg Bayarsaikhan
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Rita Börzsei
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Viktor Szél
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Violetta Mohos
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Csaba Hetényi
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
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6
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Chen W, He H, Wang J, Wang J, Chang CEA. Uncovering water effects in protein-ligand recognition: importance in the second hydration shell and binding kinetics. Phys Chem Chem Phys 2023; 25:2098-2109. [PMID: 36562309 PMCID: PMC9970846 DOI: 10.1039/d2cp04584b] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Developing a ligand with high affinity for a specific protein target is essential for drug design, and water molecules are well known to play a key role in protein-drug recognition. However, predicting the role of particularly ordered water molecules in drug binding remains challenging. Furthermore, hydration free energy contributed from the water network, including the second shell of water molecules, is far from being well studied. In this research we focused on these aspects to accurately and efficiently evaluate water effects in protein-ligand binding affinity. We developed a new strategy using a free-energy calculation method, VM2. We successfully predicted the stable ordered water molecules in a number of protein systems: PDE 10a, HSP90, tryptophan synthase (TRPS), CDK2 and Factor Xa. In some of these, the second shell of water molecules appeared to be critical in protein-ligand binding. We also applied the strategy to largely improve binding free energy calculation using the MM/PBSA method. When applying MM/PBSA alone for two systems, CDK2 and Factor Xa, the computed binding free energy resulted in poor to moderate R2 values with experimental data. However, including water free energy correction greatly improved the free energy calculation. Furthermore, our work helped to explain how xk263 is a 1000 times faster binder to HIVp than ritonavir, a potentially useful tool for investigating binding kinetics. Our studies reveal the importance of fully considering water effects in therapeutic developments in pharmaceutical and biotechnology industries and for fundamental research in protein-ligand recognition.
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Affiliation(s)
- Wei Chen
- School of Pharmacy, Fuzhou Medical College of NanChang University, Fuzhou, JiangXi 344000, P. R. China.
| | - Huan He
- School of Pharmacy, Fuzhou Medical College of NanChang University, Fuzhou, JiangXi 344000, P. R. China.
| | - Jing Wang
- School of Pharmacy, Fuzhou Medical College of NanChang University, Fuzhou, JiangXi 344000, P. R. China.
| | - Jiahui Wang
- School of Pharmacy, Fuzhou Medical College of NanChang University, Fuzhou, JiangXi 344000, P. R. China.
| | - Chia-En A Chang
- Department of Chemistry, University of California at Riverside, Riverside, CA 92521, USA.
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7
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Ghani A, Sadiq Z, Iqbal S, Yasmeen A, Shujaat S, Ali I. Screening of anti-inflammatory and antioxidant potential of functionalized tetrahydrocarbazole linked 1,2-diazoles and their docking studies. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.104195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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8
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Ring replacement recommender: Ring modifications for improving biological activity. Eur J Med Chem 2022; 238:114483. [DOI: 10.1016/j.ejmech.2022.114483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 11/19/2022]
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9
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Samways ML, Taylor RD, Bruce Macdonald HE, Essex JW. Water molecules at protein-drug interfaces: computational prediction and analysis methods. Chem Soc Rev 2021; 50:9104-9120. [PMID: 34184009 DOI: 10.1039/d0cs00151a] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The fundamental importance of water molecules at drug-protein interfaces is now widely recognised and a significant feature in structure-based drug design. Experimental methods for analysing the role of water in drug binding have many challenges, including the accurate location of bound water molecules in crystal structures, and problems in resolving specific water contributions to binding thermodynamics. Computational analyses of binding site water molecules provide an alternative, and in principle complete, structural and thermodynamic picture, and their use is now commonplace in the pharmaceutical industry. In this review, we describe the computational methodologies that are available and discuss their strengths and weaknesses. Additionally, we provide a critical analysis of the experimental data used to validate the methods, regarding the type and quality of experimental structural data. We also discuss some of the fundamental difficulties of each method and suggest directions for future study.
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Affiliation(s)
- Marley L Samways
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK.
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10
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Awasthi A, Raju MB, Rahman MA. Current Insights of Inhibitors of p38 Mitogen-Activated Protein Kinase in Inflammation. Med Chem 2021; 17:555-575. [PMID: 32106802 DOI: 10.2174/1573406416666200227122849] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 10/01/2019] [Accepted: 11/25/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND The inflammatory process is one of the mechanisms by which our body upholds us from pathogens such as parasites, bacteria, viruses, and other harmful microorganisms. Inflammatory stimuli activate many intracellular signaling pathways such as the nuclear factor-kB (NF-kB) pathway and three mitogen-activated protein kinase (MAPK) pathways, which are mediated through extracellular-signal regulated kinase (ERK), c-Jun N-terminal kinase (JNK) and p38. The p38 has evolved as an enticing target in treating many persistent inflammatory diseases. Hence, designing novel p38 inhibitors targeting MAPK pathways has acquired significance. OBJECTIVE Peruse to identify the lead target to discover novel p38MAPK inhibitors with different scaffolds having improved selectivity over the prototype drugs. METHODS Structure and the binding sites of p38MAPK were focused. Various scaffolds designed for inhibition and the molecules which have entered the clinical trials are discussed. RESULTS This review aspires to present the available information on the structure and the 3D binding sites of p38MAPK, various scaffolds designed for imidazole, urea, benzamide, azoles, quinoxaline, chromone, ketone as a potent p38MAPK inhibitors and their SAR studies and the molecules which have entered the clinical trials. CONCLUSION The development of successful selective p38MAPK inhibitors in inflammatory diseases is in progress despite all challenges. It was speculated that p38MAPK also plays an important role in treating diseases such as neuroinflammation, arterial inflammation, vascular inflammation, cancer and so on, which are posing the world with treatment challenges. In this review, clinical trials of drugs are discussed related to inflammatory and its related diseases. Research is in progress to design and develop novel p38MAPK inhibitors with minimal side effects.
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Affiliation(s)
- Archana Awasthi
- Department of Pharmaceutical Chemistry, Sri Venkateshwara College of Pharmacy, Madhapur, Hyderabad, Telangana, India
| | - Mantripragada Bhagavan Raju
- Department of Pharmaceutical Chemistry, Sri Venkateshwara College of Pharmacy, Madhapur, Hyderabad, Telangana, India
| | - Md Azizur Rahman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Integral University, Lucknow, Uttar Pradesh, India
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11
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Synthesis and cytotoxic activity of novel 4-amino-5-cyano-2-sulfonylpyrimidines. MENDELEEV COMMUNICATIONS 2020. [DOI: 10.1016/j.mencom.2020.09.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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12
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Oh Y, Lee J, Shin H, Sohn JH. Selective reductive cleavage of 2-(phenylthio)pyrimidines for efficient synthesis of 2-(H)pyrimidines. Tetrahedron Lett 2019. [DOI: 10.1016/j.tetlet.2019.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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13
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Wrobleski ST, Moslin R, Lin S, Zhang Y, Spergel S, Kempson J, Tokarski JS, Strnad J, Zupa-Fernandez A, Cheng L, Shuster D, Gillooly K, Yang X, Heimrich E, McIntyre KW, Chaudhry C, Khan J, Ruzanov M, Tredup J, Mulligan D, Xie D, Sun H, Huang C, D’Arienzo C, Aranibar N, Chiney M, Chimalakonda A, Pitts WJ, Lombardo L, Carter PH, Burke JR, Weinstein DS. Highly Selective Inhibition of Tyrosine Kinase 2 (TYK2) for the Treatment of Autoimmune Diseases: Discovery of the Allosteric Inhibitor BMS-986165. J Med Chem 2019; 62:8973-8995. [DOI: 10.1021/acs.jmedchem.9b00444] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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14
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Zhu C, Li G, Xiao K, Shao X, Cheng J, Li Z. Water bridges are essential to neonicotinoids: Insights from synthesis, bioassay and molecular modelling studies. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2018.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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15
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Abstract
In classical medicinal chemistry, nitrile groups were commonly considered as bioisosteres of carbonyl, hydroxyl and carboxyl groups, as well as halogen atoms. However, there is a lack of in-depth understanding about the structural and energetic characteristics of nitrile groups in protein–ligand interactions. Here, we have surveyed the Protein Data Bank and ChEMBL databases with the goal of characterizing such protein–ligand interactions for nitrile-containing compounds. We discuss the versatile roles of nitrile groups in improving binding affinities, and give special attention to examples of displacing and mimicking binding-site waters by nitrile groups. We expect that this review article will further inspire medicinal chemists to exploit nitrile groups rationally in structure-based drug design.
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16
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Wahl J, Smieško M. Thermodynamic Insight into the Effects of Water Displacement and Rearrangement upon Ligand Modifications using Molecular Dynamics Simulations. ChemMedChem 2018; 13:1325-1335. [DOI: 10.1002/cmdc.201800093] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/07/2018] [Indexed: 01/11/2023]
Affiliation(s)
- Joel Wahl
- Molecular Modeling, Department of Pharmaceutical Sciences; University of Basel; Klingelbergstrasse 50 4056 Basel Switzerland
| | - Martin Smieško
- Molecular Modeling, Department of Pharmaceutical Sciences; University of Basel; Klingelbergstrasse 50 4056 Basel Switzerland
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17
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Tariq S, Alam O, Amir M. Synthesis, p38α MAP kinase inhibition, anti-inflammatory activity, and molecular docking studies of 1,2,4-triazole-based benzothiazole-2-amines. Arch Pharm (Weinheim) 2018; 351:e1700304. [PMID: 29611883 DOI: 10.1002/ardp.201700304] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 01/31/2018] [Accepted: 02/06/2018] [Indexed: 12/30/2022]
Abstract
Recent studies have demonstrated that inhibition of p38α MAP kinase could effectively inhibit pro-inflammatory cytokines including TNF-α and interleukins. Thus, inhibition of this enzyme can prove greatly beneficial in the therapy of chronic inflammatory diseases. A new series of N-[3-(substituted-4H-1,2,4-triazol-4-yl)]-benzo[d]thiazol-2-amines (4a-n) were synthesized and subjected to in vitro evaluation for anti-inflammatory activity (BSA anti-denaturation assay) and p38α MAPK inhibition. Among the compounds selected for in vivo screening of anti-inflammatory activity (4b, 4c, 4f, 4g, 4j, 4m, and 4n), compound 4f was found to be the most active with an in vivo anti-inflammatory efficacy of 85.31% when compared to diclofenac sodium (83.68%). It was also found to have a low ulcerogenic risk and a protective effect on lipid peroxidation. The p38α MAP kinase inhibition of this compound (IC50 = 0.036 ± 0.12 μM) was also found to be superior to the standard SB203580 (IC50 = 0.043 ± 0.27 μM). Furthermore, the in silico binding mode of the compound on docking against p38α MAP kinase exemplified stronger interactions than those of SB203580.
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Affiliation(s)
- Sana Tariq
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Hamdard University, New Delhi, India
| | - Ozair Alam
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Hamdard University, New Delhi, India
| | - Mohammad Amir
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Hamdard University, New Delhi, India
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18
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Rudling A, Orro A, Carlsson J. Prediction of Ordered Water Molecules in Protein Binding Sites from Molecular Dynamics Simulations: The Impact of Ligand Binding on Hydration Networks. J Chem Inf Model 2018; 58:350-361. [PMID: 29308882 PMCID: PMC6716772 DOI: 10.1021/acs.jcim.7b00520] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Water
plays a major role in ligand binding and is attracting increasing
attention in structure-based drug design. Water molecules can make
large contributions to binding affinity by bridging protein–ligand
interactions or by being displaced upon complex formation, but these
phenomena are challenging to model at the molecular level. Herein,
networks of ordered water molecules in protein binding sites were
analyzed by clustering of molecular dynamics (MD) simulation trajectories.
Locations of ordered waters (hydration sites) were first identified
from simulations of high resolution crystal structures of 13 protein–ligand
complexes. The MD-derived hydration sites reproduced 73% of the binding
site water molecules observed in the crystal structures. If the simulations
were repeated without the cocrystallized ligands, a majority (58%)
of the crystal waters in the binding sites were still predicted. In
addition, comparison of the hydration sites obtained from simulations
carried out in the absence of ligands to those identified for the
complexes revealed that the networks of ordered water molecules were
preserved to a large extent, suggesting that the locations of waters
in a protein–ligand interface are mainly dictated by the protein.
Analysis of >1000 crystal structures showed that hydration sites
bridged
protein–ligand interactions in complexes with different ligands,
and those with high MD-derived occupancies were more likely to correspond
to experimentally observed ordered water molecules. The results demonstrate
that ordered water molecules relevant for modeling of protein–ligand
complexes can be identified from MD simulations. Our findings could
contribute to development of improved methods for structure-based
virtual screening and lead optimization.
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Affiliation(s)
- Axel Rudling
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University , SE-106 91 Stockholm, Sweden
| | - Adolfo Orro
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University , SE-106 91 Stockholm, Sweden
| | - Jens Carlsson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC , Box 596, SE-751 24 Uppsala, Sweden
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Synthesis, anti-inflammatory, p38α MAP kinase inhibitory activities and molecular docking studies of quinoxaline derivatives containing triazole moiety. Bioorg Chem 2018; 76:343-358. [DOI: 10.1016/j.bioorg.2017.12.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 11/17/2017] [Accepted: 12/01/2017] [Indexed: 01/25/2023]
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20
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Cournia Z, Allen B, Sherman W. Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations. J Chem Inf Model 2017; 57:2911-2937. [PMID: 29243483 DOI: 10.1021/acs.jcim.7b00564] [Citation(s) in RCA: 401] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Accurate in silico prediction of protein-ligand binding affinities has been a primary objective of structure-based drug design for decades due to the putative value it would bring to the drug discovery process. However, computational methods have historically failed to deliver value in real-world drug discovery applications due to a variety of scientific, technical, and practical challenges. Recently, a family of approaches commonly referred to as relative binding free energy (RBFE) calculations, which rely on physics-based molecular simulations and statistical mechanics, have shown promise in reliably generating accurate predictions in the context of drug discovery projects. This advance arises from accumulating developments in the underlying scientific methods (decades of research on force fields and sampling algorithms) coupled with vast increases in computational resources (graphics processing units and cloud infrastructures). Mounting evidence from retrospective validation studies, blind challenge predictions, and prospective applications suggests that RBFE simulations can now predict the affinity differences for congeneric ligands with sufficient accuracy and throughput to deliver considerable value in hit-to-lead and lead optimization efforts. Here, we present an overview of current RBFE implementations, highlighting recent advances and remaining challenges, along with examples that emphasize practical considerations for obtaining reliable RBFE results. We focus specifically on relative binding free energies because the calculations are less computationally intensive than absolute binding free energy (ABFE) calculations and map directly onto the hit-to-lead and lead optimization processes, where the prediction of relative binding energies between a reference molecule and new ideas (virtual molecules) can be used to prioritize molecules for synthesis. We describe the critical aspects of running RBFE calculations, from both theoretical and applied perspectives, using a combination of retrospective literature examples and prospective studies from drug discovery projects. This work is intended to provide a contemporary overview of the scientific, technical, and practical issues associated with running relative binding free energy simulations, with a focus on real-world drug discovery applications. We offer guidelines for improving the accuracy of RBFE simulations, especially for challenging cases, and emphasize unresolved issues that could be improved by further research in the field.
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Affiliation(s)
- Zoe Cournia
- Biomedical Research Foundation, Academy of Athens , 4 Soranou Ephessiou, 11527 Athens, Greece
| | - Bryce Allen
- Silicon Therapeutics , 300 A Street, Boston, Massachusetts 02210, United States
| | - Woody Sherman
- Silicon Therapeutics , 300 A Street, Boston, Massachusetts 02210, United States
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21
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Meanwell NA. Drug-target interactions that involve the replacement or displacement of magnesium ions. Bioorg Med Chem Lett 2017; 27:5355-5372. [DOI: 10.1016/j.bmcl.2017.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 10/30/2017] [Accepted: 11/02/2017] [Indexed: 01/11/2023]
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Abstract
Drug discovery is a multidisciplinary and multivariate optimization endeavor. As such, in silico screening tools have gained considerable importance to archive, analyze and exploit the vast and ever-increasing amount of experimental data generated throughout the process. The current review will focus on the computer-aided prediction of the numerous properties that need to be controlled during the discovery of a preliminary hit and its promotion to a viable clinical candidate. It does not pretend to the almost impossible task of an exhaustive report but will highlight a few key points that need to be collectively addressed both by chemists and biologists to fuel the drug discovery pipeline with innovative and safe drug candidates.
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Affiliation(s)
- Didier Rognan
- Laboratoire d'Innovation Thérapeutique, UMR 7200 CNRS-Université de Strasbourg, 74 route du Rhin, 67400 Illkirch, France.
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Ross GA, Bodnarchuk MS, Essex JW. Water Sites, Networks, And Free Energies with Grand Canonical Monte Carlo. J Am Chem Soc 2015; 137:14930-43. [PMID: 26509924 DOI: 10.1021/jacs.5b07940] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Water molecules play integral roles in the formation of many protein-ligand complexes, and recent computational efforts have been focused on predicting the thermodynamic properties of individual waters and how they may be exploited in rational drug design. However, when water molecules form highly coupled hydrogen-bonding networks, there is, as yet, no method that can rigorously calculate the free energy to bind the entire network or assess the degree of cooperativity between waters. In this work, we report theoretical and methodological developments to the grand canonical Monte Carlo simulation technique. Central to our results is a rigorous equation that can be used to calculate efficiently the binding free energies of water networks of arbitrary size and complexity. Using a single set of simulations, our methods can locate waters, estimate their binding affinities, capture the cooperativity of the water network, and evaluate the hydration free energy of entire protein binding sites. Our techniques have been applied to multiple test systems and compare favorably to thermodynamic integration simulations and experimental data. The implications of these methods in drug design are discussed.
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Affiliation(s)
- Gregory A Ross
- School of Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, United Kingdom
| | - Michael S Bodnarchuk
- School of Mechanical Engineering, Imperial College London , Exhibition Road, London, SW1 2AZ, United Kingdom
| | - Jonathan W Essex
- School of Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, United Kingdom
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24
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Spyrakis F, Cavasotto CN. Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description. Arch Biochem Biophys 2015; 583:105-19. [DOI: 10.1016/j.abb.2015.08.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 08/03/2015] [Accepted: 08/03/2015] [Indexed: 01/05/2023]
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25
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Gerogiokas G, Southey MWY, Mazanetz MP, Hefeitz A, Bodkin M, Law RJ, Michel J. Evaluation of water displacement energetics in protein binding sites with grid cell theory. Phys Chem Chem Phys 2015; 17:8416-26. [DOI: 10.1039/c4cp05572a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The grid cell theory method was used to elucidate perturbations in water network energetics in a range of protein–ligand complexes.
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Affiliation(s)
| | | | | | | | | | | | - J. Michel
- EaStCHEM School of Chemistry
- Edinburgh
- UK
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26
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Wang M, Gao M, Zheng QH. Synthesis of carbon-11-labeled 4-(phenylamino)-pyrrolo[2,1-f][1,2,4]triazine derivatives as new potential PET tracers for imaging of p38α mitogen-activated protein kinase. Bioorg Med Chem Lett 2014; 24:3700-5. [PMID: 25065491 DOI: 10.1016/j.bmcl.2014.07.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 07/04/2014] [Accepted: 07/07/2014] [Indexed: 12/30/2022]
Abstract
The reference standards methyl 4-(2-methyl-5-(methoxycarbamoyl)phenylamino)-5-methylpyrrolo[2,1-f][1,2,4]triazine-6-carboxylate (10a), methyl 4-(2-methyl-5-(ethoxycarbamoyl)phenylamino)-5-methylpyrrolo[2,1-f][1,2,4]triazine-6-carboxylate (10b) and corresponding precursors 4-(2-methyl-5-(methoxycarbamoyl)phenylamino)-5-methylpyrrolo[2,1-f][1,2,4]triazine-6-carboxylic acid (11a), methyl 4-(2-methyl-5-(ethoxycarbamoyl)phenylamino)-5-methylpyrrolo[2,1-f][1,2,4]triazine-6-carboxylic acid (11b) were synthesized from methyl crotonate and 3-amino-4-methylbenzoic acid in multiple steps with moderate to excellent yields. The target tracer [(11)C]methyl 4-(2-methyl-5-(methoxycarbamoyl)phenylamino)-5-methylpyrrolo[2,1-f][1,2,4]triazine-6-carboxylate ([(11)C]10a) and [(11)C]methyl 4-(2-methyl-5-(ethoxycarbamoyl)phenylamino)-5-methylpyrrolo[2,1-f][1,2,4]triazine-6-carboxylate ([(11)C]10b) were prepared from their corresponding precursors with [(11)C]CH3OTf under basic condition through O-[(11)C]methylation and isolated by a simplified solid-phase extraction (SPE) method in 50-60% radiochemical yields at end of bombardment (EOB) with 185-555 GBq/μmol specific activity at end of synthesis (EOS).
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Affiliation(s)
- Min Wang
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, 1345 West 16th Street, Room 202, Indianapolis, IN 46202, USA
| | - Mingzhang Gao
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, 1345 West 16th Street, Room 202, Indianapolis, IN 46202, USA
| | - Qi-Huang Zheng
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, 1345 West 16th Street, Room 202, Indianapolis, IN 46202, USA.
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27
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Meanwell NA. The Influence of Bioisosteres in Drug Design: Tactical Applications to Address Developability Problems. TACTICS IN CONTEMPORARY DRUG DESIGN 2014; 9. [PMCID: PMC7416817 DOI: 10.1007/7355_2013_29] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The application of bioisosteres in drug discovery is a well-established design concept that has demonstrated utility as an approach to solving a range of problems that affect candidate optimization, progression, and durability. In this chapter, the application of isosteric substitution is explored in a fashion that focuses on the development of practical solutions to problems that are encountered in typical optimization campaigns. The role of bioisosteres to affect intrinsic potency and selectivity, influence conformation, solve problems associated with drug developability, including P-glycoprotein recognition, modulating basicity, solubility, and lipophilicity, and to address issues associated with metabolism and toxicity is used as the underlying theme to capture a spectrum of creative applications of structural emulation in the design of drug candidates.
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28
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Yan S, Niu Y, Chen X, Liu Y, Lin J. Microwave-Assisted Solvent-Free Synthesis of Highly Functionalized Pyrimidine Derivatives. J Heterocycl Chem 2012. [DOI: 10.1002/jhet.891] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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29
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Basarab GS, Hill P, Eyermann CJ, Gowravaram M, Käck H, Osimoni E. Design of inhibitors of Helicobacter pylori glutamate racemase as selective antibacterial agents: Incorporation of imidazoles onto a core pyrazolopyrimidinedione scaffold to improve bioavailabilty. Bioorg Med Chem Lett 2012; 22:5600-7. [DOI: 10.1016/j.bmcl.2012.07.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 06/28/2012] [Accepted: 07/02/2012] [Indexed: 12/21/2022]
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30
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Fischer S, Koeberle SC, Laufer SA. p38α mitogen-activated protein kinase inhibitors, a patent review (2005 – 2011). Expert Opin Ther Pat 2011; 21:1843-66. [DOI: 10.1517/13543776.2011.636737] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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31
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Kinoshita T, Sekiguchi Y, Fukada H, Nakaniwa T, Tada T, Nakamura S, Kitaura K, Ohno H, Suzuki Y, Hirasawa A, Nakanishi I, Tsujimoto G. A detailed thermodynamic profile of cyclopentyl and isopropyl derivatives binding to CK2 kinase. Mol Cell Biochem 2011; 356:97-105. [PMID: 21735094 DOI: 10.1007/s11010-011-0960-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2011] [Accepted: 06/24/2011] [Indexed: 12/12/2022]
Abstract
The detailed understanding of the molecular features of a ligand binding to a target protein, facilitates the successful design of potent and selective inhibitors. We present a case study of ATP-competitive kinase inhibitors that include a pyradine moiety. These compounds have similar chemical structure, except for distinct terminal hydrophobic cyclopentyl or isopropyl groups, and block kinase activity of casein kinase 2 subunit α (CK2α), which is a target for several diseases, such as cancer and glomerulonephritis. Although these compounds display similar inhibitory potency against CK2α, the crystal structures reveal that the cyclopentyl derivative gains more favorable interactions compared with the isopropyl derivative, because of the additional ethylene moiety. The structural observations and biological data are consistent with the thermodynamic profiles of these inhibitors in binding to CK2α, revealing that the enthalpic advantage of the cyclopentyl derivative is accompanied with a lower entropic loss. Computational analyses indicated that the relative enthalpic gain of the cyclopentyl derivative arises from an enhancement of a wide range of van der Waals interactions from the whole complex. Conversely, the relative entropy loss of the cyclopentyl derivative arises from a decrease in the molecular fluctuation and higher conformational restriction in the active site of CK2α. These structural insights, in combination with thermodynamic and computational observations, should be helpful in developing potent and selective CK2α inhibitors.
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Affiliation(s)
- Takayoshi Kinoshita
- Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan.
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32
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Discovery of pyrrolo[2,1-f][1,2,4]triazine C6-ketones as potent, orally active p38α MAP kinase inhibitors. Bioorg Med Chem Lett 2011; 21:4633-7. [PMID: 21705217 DOI: 10.1016/j.bmcl.2011.05.091] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 05/20/2011] [Accepted: 05/23/2011] [Indexed: 11/23/2022]
Abstract
Pyrrolo[2,1-f][1,2,4]triazine based inhibitors of p38α have been prepared exploring functional group modifications at the C6 position. Incorporation of aryl and heteroaryl ketones at this position led to potent inhibitors with efficacy in in vivo models of acute and chronic inflammation.
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33
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Lu SY, Jiang YJ, Lv J, Zou JW, Wu TX. Role of bridging water molecules in GSK3β-inhibitor complexes: insights from QM/MM, MD, and molecular docking studies. J Comput Chem 2011; 32:1907-18. [PMID: 21469159 DOI: 10.1002/jcc.21775] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2010] [Revised: 01/02/2011] [Accepted: 01/21/2011] [Indexed: 02/01/2023]
Abstract
The role of water molecules is increasingly gaining interest in drug design, and several studies have highlighted their paramount contributions to the specificity and the affinity of ligand binding. In this study, we employ the two-layer ONIOM-based quantum mechanics/molecular mechanics (QM/MM) calculations, molecular dynamics (MD) simulations, and molecular docking studies to investigate the effect of bridging water molecules at the GSK3β-inhibitors interfaces. The results obtained from the ONIOM geometry optimization and AIM analysis corroborated the presence of bridging water molecules that form hydrogen bonds with protein side chain of Thr138 and/or backbone of Gln185, and mediate interactions with inhibitors in the 10 selected GSK3β-inhibitor complexes. Subsequently, MD simulations carried out on a representative system of 1R0E demonstrated that the bridging water molecule is stable at the GSK3β-inhibitor interface and appears to contribute to the stability of the protein-inhibitor interactions. Furthermore, molecular docking studies of GSK3β-inhibitor complexes indicated that the inhibitors can increase binding affinities and the better docked conformation of inhibitors can be obtained by inclusion of the bridging water molecules, especially for the flexible inhibitors, in docking experiments into individual protein conformations. Our results elucidate the importance of bridging water molecules at the GSK3β-inhibitor interfaces and suggest that they might prove useful in rational drug design.
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Affiliation(s)
- Shao-Yong Lu
- Key Laboratory for Molecular Design and Nutrition Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315104, China
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34
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Meanwell NA. Synopsis of Some Recent Tactical Application of Bioisosteres in Drug Design. J Med Chem 2011; 54:2529-91. [DOI: 10.1021/jm1013693] [Citation(s) in RCA: 1876] [Impact Index Per Article: 144.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Nicholas A. Meanwell
- Department of Medicinal Chemistry, Bristol-Myers Squibb Pharmaceutical Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
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35
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Waszkowycz B, Clark DE, Gancia E. Outstanding challenges in protein–ligand docking and structure‐based virtual screening. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.18] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
| | - David E. Clark
- Argenta, 8/9 Spire Green Centre, Flex Meadow, Harlow CM19 5TR, UK
| | - Emanuela Gancia
- Argenta, 8/9 Spire Green Centre, Flex Meadow, Harlow CM19 5TR, UK
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36
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Abstract
IMPORTANCE OF THE FIELD Water molecules often appear around ligands in protein crystal structures. Reliable prediction of the effects of water on ligand binding remains a challenge. Solvation effects are crucial for lead optimization where a 100-fold difference in binding affinity is significant but correspond to only ∼3 kcal/mol in binding free energy. Well-known examples, such as nonpeptidic urea inhibitors of HIV protease, prove that careful examination of water molecules and their energetics can contribute significantly to a successful drug design campaign. AREAS COVERED IN THIS REVIEW In this review, we examine methods to account for the effect of water in ligand binding at two stages of drug discovery: lead identification via docking calculations and lead optimization. We provide a survey of the models and techniques available to account for water in drug design. WHAT THE READER WILL GAIN The reader will become aware of common practices and pitfalls in dealing with water molecules in structure-based drug design. TAKE HOME MESSAGE Although solvation effects are not fully understood, some pragmatic recommendations at the end of the article provide guidance for modelers in this area as well as new practitioners.
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Affiliation(s)
- Sergio E Wong
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, CA 94550, USA.
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37
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Liu C, Lin J, Wrobleski ST, Lin S, Hynes J, Wu H, Dyckman AJ, Li T, Wityak J, Gillooly KM, Pitt S, Shen DR, Zhang RF, McIntyre KW, Salter-Cid L, Shuster DJ, Zhang H, Marathe PH, Doweyko AM, Sack JS, Kiefer SE, Kish KF, Newitt JA, McKinnon M, Dodd JH, Barrish JC, Schieven GL, Leftheris K. Discovery of 4-(5-(cyclopropylcarbamoyl)-2-methylphenylamino)-5-methyl-N-propylpyrrolo[1,2-f][1,2,4]triazine-6-carboxamide (BMS-582949), a clinical p38α MAP kinase inhibitor for the treatment of inflammatory diseases. J Med Chem 2010; 53:6629-39. [PMID: 20804198 DOI: 10.1021/jm100540x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The discovery and characterization of 7k (BMS-582949), a highly selective p38α MAP kinase inhibitor that is currently in phase II clinical trials for the treatment of rheumatoid arthritis, is described. A key to the discovery was the rational substitution of N-cyclopropyl for N-methoxy in 1a, a previously reported clinical candidate p38α inhibitor. Unlike alkyl and other cycloalkyls, the sp(2) character of the cyclopropyl group can confer improved H-bonding characteristics to the directly substituted amide NH. Inhibitor 7k is slightly less active than 1a in the p38α enzymatic assay but displays a superior pharmacokinetic profile and, as such, was more effective in both the acute murine model of inflammation and pseudoestablished rat AA model. The binding mode of 7k with p38α was confirmed by X-ray crystallographic analysis.
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Affiliation(s)
- Chunjian Liu
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, USA.
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38
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Affiliation(s)
- Caterina Bissantz
- Discovery Chemistry, F. Hoffmann-La Roche AG, CH-4070 Basel, Switzerland
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39
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Wu B, Wang HL, Pettus L, Wurz RP, Doherty EM, Henkle B, McBride HJ, Saris CJM, Wong LM, Plant MH, Sherman L, Lee MR, Hsieh F, Tasker AS. Discovery of Pyridazinopyridinones as Potent and Selective p38 Mitogen-Activated Protein Kinase Inhibitors. J Med Chem 2010; 53:6398-411. [DOI: 10.1021/jm100567y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bin Wu
- Department of Chemistry Research and Discovery
| | | | | | | | | | | | | | | | | | | | | | | | - Faye Hsieh
- Pharmacokinetics and Drug Metabolism, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320
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40
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Michel J, Tirado-Rives J, Jorgensen WL. Energetics of displacing water molecules from protein binding sites: consequences for ligand optimization. J Am Chem Soc 2009; 131:15403-11. [PMID: 19778066 PMCID: PMC2783447 DOI: 10.1021/ja906058w] [Citation(s) in RCA: 195] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A strategy in drug design is to consider enhancing the affinity of lead molecules with structural modifications that displace water molecules from a protein binding site. Because success of the approach is uncertain, clarification of the associated energetics was sought in cases where similar structural modifications yield qualitatively different outcomes. Specifically, free-energy perturbation calculations were carried out in the context of Monte Carlo statistical mechanics simulations to investigate ligand series that feature displacement of ordered water molecules in the binding sites of scytalone dehydratase, p38-alphaMAP kinase, and EGFR kinase. The change in affinity for a ligand modification is found to correlate with the ease of displacement of the ordered water molecule. However, as in the EGFR example, the binding affinity may diminish if the free-energy increase due to the removal of the bound water molecule is not more than compensated by the additional interactions of the water-displacing moiety. For accurate computation of the effects of ligand modifications, a complete thermodynamic analysis is shown to be needed. It requires identification of the location of water molecules in the protein-ligand interface and evaluation of the free-energy changes associated with their removal and with the introduction of the ligand modification. Direct modification of the ligand in free-energy calculations is likely to trap the ordered molecule and provide misleading guidance for lead optimization.
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Affiliation(s)
- Julien Michel
- Department of Chemistry, Yale University, New Haven CT-06520, USA
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41
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Wurz RP, Pettus LH, Xu S, Henkle B, Sherman L, Plant M, Miner K, McBride H, Wong LM, Saris CJ, Lee MR, Chmait S, Mohr C, Hsieh F, Tasker AS. Part 1: Structure–Activity Relationship (SAR) investigations of fused pyrazoles as potent, selective and orally available inhibitors of p38α mitogen-activated protein kinase. Bioorg Med Chem Lett 2009; 19:4724-8. [DOI: 10.1016/j.bmcl.2009.06.058] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Revised: 06/11/2009] [Accepted: 06/15/2009] [Indexed: 10/20/2022]
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Doláková P, Dracínský M, Masojídková M, Solínová V, Kasicka V, Holý A. Acyclic nucleoside bisphosphonates: synthesis and properties of chiral 2-amino-4,6-bis[(phosphonomethoxy)alkoxy]pyrimidines. Eur J Med Chem 2009; 44:2408-24. [PMID: 18992968 PMCID: PMC2706328 DOI: 10.1016/j.ejmech.2008.09.031] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2008] [Revised: 09/15/2008] [Accepted: 09/18/2008] [Indexed: 11/26/2022]
Abstract
2-Amino-4,6-bis[(phosphonomethoxy)alkoxy]pyrimidines bearing two equal or different achiral or chiral phosphonoalkoxy chains have been prepared either by aromatic nucleophilic substitution of 2-amino-4,6-dichloropyrimidine or by alkylation of 4,6-dihydroxy-2-(methylsulfanyl)pyrimidine with appropriate phosphonate-bearing building block. Alkylation of 4,6-dihydroxy-2-(methylsulfanyl)pyrimidine proved to be the method of choice for efficient preparation of variety of bisphosphonates. The enantiomeric purity of selected compounds was determined by capillary electrophoresis. Antiviral activity of bisphosphonates is discussed.
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Affiliation(s)
- Petra Doláková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i. Flemingovo nám. 2, CZ-166 10 Prague 6, Czech Republic.
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43
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Seco J, Luque FJ, Barril X. Binding site detection and druggability index from first principles. J Med Chem 2009; 52:2363-71. [PMID: 19296650 DOI: 10.1021/jm801385d] [Citation(s) in RCA: 174] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In drug discovery, it is essential to identify binding sites on protein surfaces that drug-like molecules could exploit to exert a biological effect. Both X-ray crystallography and NMR experiments have demonstrated that organic solvents bind precisely at these locations. We show that this effect is reproduced using molecular dynamics with a binary solvent. Furthermore, analysis of the simulations give direct access to interaction free energies between the protein and small organic molecules, which can be used to detect binding sites and to predict the maximal affinity that a drug-like molecule could attain for them. On a set of pharmacologically relevant proteins, we obtain good predictions for druggable sites as well as for protein-protein and low affinity binding sites. This is the first druggability index not based on surface descriptors and, being independent of a training set, is particularly indicated to study unconventional targets such as protein-protein interactions or allosteric binding sites.
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Affiliation(s)
- Jesus Seco
- Institucio Catalana de Recerca i Estudis Avancats (ICREA), Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain
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44
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Das J, Moquin RV, Pitt S, Zhang R, Shen DR, McIntyre KW, Gillooly K, Doweyko AM, Sack JS, Zhang H, Kiefer SE, Kish K, McKinnon M, Barrish JC, Dodd JH, Schieven GL, Leftheris K. Pyrazolo-pyrimidines: a novel heterocyclic scaffold for potent and selective p38 alpha inhibitors. Bioorg Med Chem Lett 2008; 18:2652-7. [PMID: 18359226 DOI: 10.1016/j.bmcl.2008.03.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2008] [Revised: 03/05/2008] [Accepted: 03/06/2008] [Indexed: 11/15/2022]
Abstract
The synthesis and structure-activity relationships (SAR) of p38 alpha MAP kinase inhibitors based on a pyrazolo-pyrimidine scaffold are described. These studies led to the identification of compound 2x as a potent and selective inhibitor of p38 alpha MAP kinase with excellent cellular potency toward the inhibition of TNFalpha production. Compound 2x was highly efficacious in vivo in inhibiting TNFalpha production in an acute murine model of TNFalpha production. X-ray co-crystallography of a pyrazolo-pyrimidine analog 2b bound to unphosphorylated p38 alpha is also disclosed.
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Affiliation(s)
- Jagabandhu Das
- Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543-4000, USA.
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45
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DiMauro EF, Newcomb J, Nunes JJ, Bemis JE, Boucher C, Chai L, Chaffee SC, Deak HL, Epstein LF, Faust T, Gallant P, Gore A, Gu Y, Henkle B, Hsieh F, Huang X, Kim JL, Lee JH, Martin MW, McGowan DC, Metz D, Mohn D, Morgenstern KA, Oliveira-dos-Santos A, Patel VF, Powers D, Rose PE, Schneider S, Tomlinson SA, Tudor YY, Turci SM, Welcher AA, Zhao H, Zhu L, Zhu X. Structure-Guided Design of Aminopyrimidine Amides as Potent, Selective Inhibitors of Lymphocyte Specific Kinase: Synthesis, Structure–Activity Relationships, and Inhibition of in Vivo T Cell Activation. J Med Chem 2008; 51:1681-94. [DOI: 10.1021/jm7010996] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Erin F. DiMauro
- Department of Medicinal Chemistry, Department of Molecular Structure, and Department of HTS and Molecular Pharmacology, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139, and Department of HTS and Molecular Pharmacology, Department of Inflammation, Department of Pharmaceutics, and Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799
| | - John Newcomb
- Department of Medicinal Chemistry, Department of Molecular Structure, and Department of HTS and Molecular Pharmacology, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139, and Department of HTS and Molecular Pharmacology, Department of Inflammation, Department of Pharmaceutics, and Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799
| | - Joseph J. Nunes
- Department of Medicinal Chemistry, Department of Molecular Structure, and Department of HTS and Molecular Pharmacology, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139, and Department of HTS and Molecular Pharmacology, Department of Inflammation, Department of Pharmaceutics, and Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799
| | - Jean E. Bemis
- Department of Medicinal Chemistry, Department of Molecular Structure, and Department of HTS and Molecular Pharmacology, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139, and Department of HTS and Molecular Pharmacology, Department of Inflammation, Department of Pharmaceutics, and Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799
| | - Christina Boucher
- Department of Medicinal Chemistry, Department of Molecular Structure, and Department of HTS and Molecular Pharmacology, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139, and Department of HTS and Molecular Pharmacology, Department of Inflammation, Department of Pharmaceutics, and Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799
| | - Lilly Chai
- Department of Medicinal Chemistry, Department of Molecular Structure, and Department of HTS and Molecular Pharmacology, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139, and Department of HTS and Molecular Pharmacology, Department of Inflammation, Department of Pharmaceutics, and Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799
| | - Stuart C. Chaffee
- Department of Medicinal Chemistry, Department of Molecular Structure, and Department of HTS and Molecular Pharmacology, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139, and Department of HTS and Molecular Pharmacology, Department of Inflammation, Department of Pharmaceutics, and Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799
| | - Holly L. Deak
- Department of Medicinal Chemistry, Department of Molecular Structure, and Department of HTS and Molecular Pharmacology, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139, and Department of HTS and Molecular Pharmacology, Department of Inflammation, Department of Pharmaceutics, and Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799
| | - Linda F. Epstein
- Department of Medicinal Chemistry, Department of Molecular Structure, and Department of HTS and Molecular Pharmacology, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139, and Department of HTS and Molecular Pharmacology, Department of Inflammation, Department of Pharmaceutics, and Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799
| | - Ted Faust
- Department of Medicinal Chemistry, Department of Molecular Structure, and Department of HTS and Molecular Pharmacology, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139, and Department of HTS and Molecular Pharmacology, Department of Inflammation, Department of Pharmaceutics, and Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799
| | - Paul Gallant
- Department of Medicinal Chemistry, Department of Molecular Structure, and Department of HTS and Molecular Pharmacology, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139, and Department of HTS and Molecular Pharmacology, Department of Inflammation, Department of Pharmaceutics, and Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799
| | - Anu Gore
- Department of Medicinal Chemistry, Department of Molecular Structure, and Department of HTS and Molecular Pharmacology, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139, and Department of HTS and Molecular Pharmacology, Department of Inflammation, Department of Pharmaceutics, and Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799
| | - Yan Gu
- Department of Medicinal Chemistry, Department of Molecular Structure, and Department of HTS and Molecular Pharmacology, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139, and Department of HTS and Molecular Pharmacology, Department of Inflammation, Department of Pharmaceutics, and Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799
| | - Brad Henkle
- Department of Medicinal Chemistry, Department of Molecular Structure, and Department of HTS and Molecular Pharmacology, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139, and Department of HTS and Molecular Pharmacology, Department of Inflammation, Department of Pharmaceutics, and Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799
| | - Faye Hsieh
- Department of Medicinal Chemistry, Department of Molecular Structure, and Department of HTS and Molecular Pharmacology, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139, and Department of HTS and Molecular Pharmacology, Department of Inflammation, Department of Pharmaceutics, and Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799
| | - Xin Huang
- Department of Medicinal Chemistry, Department of Molecular Structure, and Department of HTS and Molecular Pharmacology, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139, and Department of HTS and Molecular Pharmacology, Department of Inflammation, Department of Pharmaceutics, and Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799
| | - Joseph L. Kim
- Department of Medicinal Chemistry, Department of Molecular Structure, and Department of HTS and Molecular Pharmacology, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139, and Department of HTS and Molecular Pharmacology, Department of Inflammation, Department of Pharmaceutics, and Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799
| | - Josie H. Lee
- Department of Medicinal Chemistry, Department of Molecular Structure, and Department of HTS and Molecular Pharmacology, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139, and Department of HTS and Molecular Pharmacology, Department of Inflammation, Department of Pharmaceutics, and Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799
| | - Matthew W. Martin
- Department of Medicinal Chemistry, Department of Molecular Structure, and Department of HTS and Molecular Pharmacology, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139, and Department of HTS and Molecular Pharmacology, Department of Inflammation, Department of Pharmaceutics, and Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799
| | - David C. McGowan
- Department of Medicinal Chemistry, Department of Molecular Structure, and Department of HTS and Molecular Pharmacology, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139, and Department of HTS and Molecular Pharmacology, Department of Inflammation, Department of Pharmaceutics, and Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799
| | - Daniela Metz
- Department of Medicinal Chemistry, Department of Molecular Structure, and Department of HTS and Molecular Pharmacology, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139, and Department of HTS and Molecular Pharmacology, Department of Inflammation, Department of Pharmaceutics, and Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799
| | - Deanna Mohn
- Department of Medicinal Chemistry, Department of Molecular Structure, and Department of HTS and Molecular Pharmacology, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139, and Department of HTS and Molecular Pharmacology, Department of Inflammation, Department of Pharmaceutics, and Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799
| | - Kurt A. Morgenstern
- Department of Medicinal Chemistry, Department of Molecular Structure, and Department of HTS and Molecular Pharmacology, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139, and Department of HTS and Molecular Pharmacology, Department of Inflammation, Department of Pharmaceutics, and Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799
| | - Antonio Oliveira-dos-Santos
- Department of Medicinal Chemistry, Department of Molecular Structure, and Department of HTS and Molecular Pharmacology, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139, and Department of HTS and Molecular Pharmacology, Department of Inflammation, Department of Pharmaceutics, and Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799
| | - Vinod F. Patel
- Department of Medicinal Chemistry, Department of Molecular Structure, and Department of HTS and Molecular Pharmacology, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139, and Department of HTS and Molecular Pharmacology, Department of Inflammation, Department of Pharmaceutics, and Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799
| | - David Powers
- Department of Medicinal Chemistry, Department of Molecular Structure, and Department of HTS and Molecular Pharmacology, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139, and Department of HTS and Molecular Pharmacology, Department of Inflammation, Department of Pharmaceutics, and Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799
| | - Paul E. Rose
- Department of Medicinal Chemistry, Department of Molecular Structure, and Department of HTS and Molecular Pharmacology, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139, and Department of HTS and Molecular Pharmacology, Department of Inflammation, Department of Pharmaceutics, and Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799
| | - Stephen Schneider
- Department of Medicinal Chemistry, Department of Molecular Structure, and Department of HTS and Molecular Pharmacology, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139, and Department of HTS and Molecular Pharmacology, Department of Inflammation, Department of Pharmaceutics, and Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799
| | - Susan A. Tomlinson
- Department of Medicinal Chemistry, Department of Molecular Structure, and Department of HTS and Molecular Pharmacology, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139, and Department of HTS and Molecular Pharmacology, Department of Inflammation, Department of Pharmaceutics, and Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799
| | - Yan-Yan Tudor
- Department of Medicinal Chemistry, Department of Molecular Structure, and Department of HTS and Molecular Pharmacology, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139, and Department of HTS and Molecular Pharmacology, Department of Inflammation, Department of Pharmaceutics, and Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799
| | - Susan M. Turci
- Department of Medicinal Chemistry, Department of Molecular Structure, and Department of HTS and Molecular Pharmacology, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139, and Department of HTS and Molecular Pharmacology, Department of Inflammation, Department of Pharmaceutics, and Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799
| | - Andrew A. Welcher
- Department of Medicinal Chemistry, Department of Molecular Structure, and Department of HTS and Molecular Pharmacology, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139, and Department of HTS and Molecular Pharmacology, Department of Inflammation, Department of Pharmaceutics, and Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799
| | - Huilin Zhao
- Department of Medicinal Chemistry, Department of Molecular Structure, and Department of HTS and Molecular Pharmacology, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139, and Department of HTS and Molecular Pharmacology, Department of Inflammation, Department of Pharmaceutics, and Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799
| | - Li Zhu
- Department of Medicinal Chemistry, Department of Molecular Structure, and Department of HTS and Molecular Pharmacology, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139, and Department of HTS and Molecular Pharmacology, Department of Inflammation, Department of Pharmaceutics, and Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799
| | - Xiaotian Zhu
- Department of Medicinal Chemistry, Department of Molecular Structure, and Department of HTS and Molecular Pharmacology, Amgen Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139, and Department of HTS and Molecular Pharmacology, Department of Inflammation, Department of Pharmaceutics, and Department of Pharmacokinetics and Drug Metabolism, Amgen, Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799
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46
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Wrobleski ST, Lin S, Hynes J, Wu H, Pitt S, Shen DR, Zhang R, Gillooly KM, Shuster DJ, McIntyre KW, Doweyko AM, Kish KF, Tredup JA, Duke GJ, Sack JS, McKinnon M, Dodd J, Barrish JC, Schieven GL, Leftheris K. Synthesis and SAR of new pyrrolo[2,1-f][1,2,4]triazines as potent p38 alpha MAP kinase inhibitors. Bioorg Med Chem Lett 2008; 18:2739-44. [PMID: 18364256 DOI: 10.1016/j.bmcl.2008.02.067] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2007] [Revised: 02/22/2008] [Accepted: 02/27/2008] [Indexed: 10/22/2022]
Abstract
A novel series of compounds based on the pyrrolo[2,1-f][1,2,4]triazine ring system have been identified as potent p38 alpha MAP kinase inhibitors. The synthesis, structure-activity relationships (SAR), and in vivo activity of selected analogs from this class of inhibitors are reported. Additional studies based on X-ray co-crystallography have revealed that one of the potent inhibitors from this series binds to the DFG-out conformation of the p38 alpha enzyme.
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Affiliation(s)
- Stephen T Wrobleski
- Department of Immunology Chemistry, Bristol-Myers Squibb, Princeton, NJ 08543-4000, USA.
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47
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Montalban AG, Boman E, Chang CD, Ceide SC, Dahl R, Dalesandro D, Delaet NGJ, Erb E, Ernst JT, Gibbs A, Kahl J, Kessler L, Lundström J, Miller S, Nakanishi H, Roberts E, Saiah E, Sullivan R, Wang Z, Larson CJ. The design and synthesis of novel alpha-ketoamide-based p38 MAP kinase inhibitors. Bioorg Med Chem Lett 2008; 18:1772-7. [PMID: 18325768 DOI: 10.1016/j.bmcl.2008.02.033] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2007] [Revised: 02/09/2008] [Accepted: 02/13/2008] [Indexed: 11/25/2022]
Abstract
We have identified a novel series of potent p38 MAP kinase inhibitors through structure-based design which due to their extended molecular architecture bind, in addition to the ATP site, to an allosteric pocket. In vitro ADME and in vivo PK studies show these compounds to have drug-like characteristics which could result in the development of an oral treatment for inflammatory conditions.
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48
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Benzothiazole based inhibitors of p38alpha MAP kinase. Bioorg Med Chem Lett 2008; 18:1874-9. [PMID: 18296051 DOI: 10.1016/j.bmcl.2008.02.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2007] [Revised: 02/04/2008] [Accepted: 02/07/2008] [Indexed: 11/20/2022]
Abstract
Rational design, synthesis, and SAR studies of a novel class of benzothiazole based inhibitors of p38alpha MAP kinase are described. The issue of metabolic instability associated with vicinal phenyl, benzo[d]thiazol-6-yl oxazoles/imidazoles was addressed by the replacement of the central oxazole or imidazole ring with an aminopyrazole system. The proposed binding mode of this new class of p38alpha inhibitors was confirmed by X-ray crystallographic studies of a representative inhibitor (6a) bound to the p38alpha enzyme.
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49
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Murali Dhar TG, Wrobleski ST, Lin S, Furch JA, Nirschl DS, Fan Y, Todderud G, Pitt S, Doweyko AM, Sack JS, Mathur A, McKinnon M, Barrish JC, Dodd JH, Schieven GL, Leftheris K. Synthesis and SAR of p38α MAP kinase inhibitors based on heterobicyclic scaffolds. Bioorg Med Chem Lett 2007; 17:5019-24. [PMID: 17664068 DOI: 10.1016/j.bmcl.2007.07.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2007] [Revised: 07/09/2007] [Accepted: 07/09/2007] [Indexed: 10/23/2022]
Abstract
The synthesis and structure-activity relationships (SAR) of p38alpha MAP kinase inhibitors based on heterobicyclic scaffolds are described. This effort led to the identification of compound (21) as a potent inhibitor of p38alpha MAP kinase with good cellular potency toward the inhibition of TNF-alpha production. X-ray co-crystallography of an oxalamide analog (24) bound to unphosphorylated p38alpha is also disclosed.
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Affiliation(s)
- T G Murali Dhar
- Bristol-Myers Squibb Pharmaceutical Research Institute, Princeton, NJ 08543-4000, USA.
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50
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Sakya SM, Hou X, Minich ML, Rast B, Shavnya A, DeMello KML, Cheng H, Li J, Jaynes BH, Mann DW, Petras CF, Seibel SB, Haven ML. 5-Heteroatom substituted pyrazoles as canine COX-2 inhibitors. Part III: Molecular modeling studies on binding contribution of 1-(5-methylsulfonyl)pyrid-2-yl and 4-nitrile. Bioorg Med Chem Lett 2007; 17:1067-72. [PMID: 17126015 DOI: 10.1016/j.bmcl.2006.11.026] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2006] [Revised: 11/07/2006] [Accepted: 11/08/2006] [Indexed: 11/24/2022]
Abstract
The structure-activity relationship toward canine COX-1 and COX-2 in vitro whole blood activity of 4-hydrogen versus 4-cyano substituted 5-aryl or 5-heteroatom substituted N-phenyl versus N-2-pyridyl sulfone pyrazoles is discussed. The differences between the pairs of compounds with the 4-nitrile pyrazole derivatives having substantially improved in vitro activity are highlighted for both COX-2 and COX-1. This difference in activity may be due to the contribution of the hydrogen bond of the 4-cyano group with Ser 530 as shown by our molecular modeling studies. In addition, our model suggests a potential contribution from hydrogen bonding of the pyridyl nitrogen to Tyr 355 for the increased activity over the phenyl sulfone analogs.
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Affiliation(s)
- Subas M Sakya
- Veterinary Medicine Research and Development, Pfizer Inc., Groton, CT 06340, USA.
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