1
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Quang De T, Nguyen CQ, Le Dang Q, Nguyen Thi NY, Trong Tuan N, Hoon Suh D, Chu J, Bepary S, Lee GH, Kang NS, Cho H, Park WK, Lim HJ. Rational design of novel diaryl ether-linked benzimidazole derivatives as potent and selective BACE1 inhibitors. Biochem Biophys Res Commun 2024; 698:149538. [PMID: 38271836 DOI: 10.1016/j.bbrc.2024.149538] [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: 01/04/2024] [Accepted: 01/14/2024] [Indexed: 01/27/2024]
Abstract
Due to the large size and high flexibility of the catalytic active site of BACE1 enzyme, the development of nonpeptide inhibitors with optimal pharmacological properties is still highly demanding. In this work, we have discovered 2-aminobenzimidazole-containg ether scaffolds having potent and selective inhibitory potentials against BACE1 enzyme. We have synthesized novel 29 compounds and optimization of aryl linker region resulted in highly potent BACE1 inhibitory activities with EC50 values of 0.05-2.71 μM. The aryloxy-phenyl analogs 20j showed the EC50 value as low as 0.07 μM in the enzyme assay, whereas, the benzyloxyphenyl dervative 24b was comparatively less effective in the enzyme assay. But interestingly the latter was more effective in the cell assay (EC50 value 1.2 μM). While comparing synthesized derivatives in the cell assay using PC12-APPSW cell, compound 27f appeared as the most potent BACE1 inhibitor having EC50 value 0.7 μM. This scaffold also showed high selectivity over BACE2 enzyme and cathepsin D. Furthermore, the research findings were bolstered through the incorporation of molecular docking, molecular dynamics, and DFT studies. We firmly believe that these discoveries will pave the way for the development of a novel class of small-molecule selective BACE1 inhibitors.
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Affiliation(s)
- Tran Quang De
- Department of Medicinal and Pharmaceutical Chemistry, University of Science and Technology, 217 Gajeong-ro Yuseong-gu, Daejeon, 305-333, South Korea
| | - Cuong Quoc Nguyen
- Department of Chemistry, College of Natural Sciences, Can Tho University, Can Tho, 94000, Viet Nam; Analytical Techniques Lab (1.16-ATL), CTU High-tech Building, Can Tho University, Can Tho, 94000, Viet Nam.
| | - Quang Le Dang
- Institute for Tropical Technology, Vietnam Academy of Science and Technology, Hanoi, 10072, Viet Nam; Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, 10072, Viet Nam
| | | | - Nguyen Trong Tuan
- Department of Chemistry, College of Natural Sciences, Can Tho University, Can Tho, 94000, Viet Nam
| | - Dong Hoon Suh
- Division of Drug Discovery Research, Korea Research Institute of Chemical Technology, P.O.Box 107, Yuseong-Gu, Daejeon, 305-600, South Korea
| | - Jeonghyun Chu
- Division of Drug Discovery Research, Korea Research Institute of Chemical Technology, P.O.Box 107, Yuseong-Gu, Daejeon, 305-600, South Korea
| | - Sukumar Bepary
- Division of Drug Discovery Research, Korea Research Institute of Chemical Technology, P.O.Box 107, Yuseong-Gu, Daejeon, 305-600, South Korea
| | - Ge Hyeong Lee
- Division of Drug Discovery Research, Korea Research Institute of Chemical Technology, P.O.Box 107, Yuseong-Gu, Daejeon, 305-600, South Korea
| | - Nam Sook Kang
- Division of Drug Discovery Research, Korea Research Institute of Chemical Technology, P.O.Box 107, Yuseong-Gu, Daejeon, 305-600, South Korea
| | - Heeyeong Cho
- Division of Drug Discovery Research, Korea Research Institute of Chemical Technology, P.O.Box 107, Yuseong-Gu, Daejeon, 305-600, South Korea
| | - Woo Kyu Park
- Division of Drug Discovery Research, Korea Research Institute of Chemical Technology, P.O.Box 107, Yuseong-Gu, Daejeon, 305-600, South Korea
| | - Hee-Jong Lim
- Division of Drug Discovery Research, Korea Research Institute of Chemical Technology, P.O.Box 107, Yuseong-Gu, Daejeon, 305-600, South Korea.
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2
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Pitman M, Hahn DF, Tresadern G, Mobley DL. To Design Scalable Free Energy Perturbation Networks, Optimal Is Not Enough. J Chem Inf Model 2023; 63:1776-1793. [PMID: 36878475 PMCID: PMC10547263 DOI: 10.1021/acs.jcim.2c01579] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Drug discovery is accelerated with computational methods such as alchemical simulations to estimate ligand affinities. In particular, relative binding free energy (RBFE) simulations are beneficial for lead optimization. To use RBFE simulations to compare prospective ligands in silico, researchers first plan the simulation experiment, using graphs where nodes represent ligands and graph edges represent alchemical transformations between ligands. Recent work demonstrated that optimizing the statistical architecture of these perturbation graphs improves the accuracy of the predicted changes in the free energy of ligand binding. Therefore, to improve the success rate of computational drug discovery, we present the open-source software package High Information Mapper (HiMap)─a new take on its predecessor, Lead Optimization Mapper (LOMAP). HiMap removes heuristics decisions from design selection and instead finds statistically optimal graphs over ligands clustered with machine learning. Beyond optimal design generation, we present theoretical insights for designing alchemical perturbation maps. Some of these results include that for n number of nodes, the precision of perturbation maps is stable at n·ln(n) edges. This result indicates that even an "optimal" graph can result in unexpectedly high errors if a plan includes too few alchemical transformations for the given number of ligands and edges. And, as a study compares more ligands, the performance of even optimal graphs will deteriorate with linear scaling of the edge count. In this sense, ensuring an A- or D-optimal topology is not enough to produce robust errors. We additionally find that optimal designs will converge more rapidly than radial and LOMAP designs. Moreover, we derive bounds for how clustering reduces cost for designs with a constant expected relative error per cluster, invariant of the size of the design. These results inform how to best design perturbation maps for computational drug discovery and have broader implications for experimental design.
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Affiliation(s)
- Mary Pitman
- Department of Pharmacy & Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA
| | - David F. Hahn
- Computational Chemistry, Janssen Research & Development, Turnhoutseweg 30, Beerse B-2340, Belgium
| | - Gary Tresadern
- Computational Chemistry, Janssen Research & Development, Turnhoutseweg 30, Beerse B-2340, Belgium
| | - David L. Mobley
- Department of Pharmacy & Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA
- Department of Chemistry, University of California, Irvine, CA 92697, USA
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3
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Guanidine-based β amyloid precursor protein cleavage enzyme 1 (BACE-1) inhibitors for the Alzheimer's disease (AD): A review. Bioorg Med Chem 2022; 74:117047. [DOI: 10.1016/j.bmc.2022.117047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/16/2022] [Accepted: 10/04/2022] [Indexed: 11/02/2022]
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4
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In silico screening of potential β-secretase (BACE1) inhibitors from VIETHERB database. J Mol Model 2022; 28:60. [DOI: 10.1007/s00894-022-05051-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/07/2022] [Indexed: 11/25/2022]
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5
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Pan L, He Q, Wu Y, Zhang N, Cai H, Yang B, Wang Y, Li Y, Wu X. Synthesis, radiolabeling, and evaluation of a potent β-site APP cleaving enzyme (BACE1) inhibitor for PET imaging of BACE1 in vivo. Bioorg Med Chem Lett 2022; 59:128543. [PMID: 35031452 DOI: 10.1016/j.bmcl.2022.128543] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/24/2021] [Accepted: 01/09/2022] [Indexed: 02/05/2023]
Abstract
The β-site APP-cleaving enzyme 1 (BACE1) plays important roles in the proteolytic processing of amyloid precursor protein, and can be regarded as an important target for the diagnosis and treatment of AD. This study aimed to report the synthesis and evaluation of an 18F-labeled 2-amino-3,4-dihydroquinazoline analog as a potential BACE1 radioligand. A fluoropropyl side chain was introduced to the phenyl of this 3,4-dihydroquinazoline scaffold to generate the radioligand. Our preliminary data indicated that although the 2-amino-3,4-dihydroquinazoline scaffold possessed favorable in-vitro properties as a PET ligand, its poor brain uptake hindered the in-vivo imaging of BACE1. Further investigation would be required to optimize the scaffold for the development of a blood-brain-barrier-permeable BACE1-targeted PET ligand.
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Affiliation(s)
- Lili Pan
- Department of Nuclear Medicine, Laboratory of Clinical Nuclear Medicine, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Qian He
- Department of Emergency, West China Hospital, Sichuan University, Chengdu 610000, Sichuan, China
| | - Yi Wu
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou 341000, China
| | - Ni Zhang
- Department of Psychiatry, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Huawei Cai
- Department of Nuclear Medicine, Laboratory of Clinical Nuclear Medicine, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Bo Yang
- Department of Pharmacy, Panzhihua Central Hospital, Panzhihua, Sichuan, 617067, China
| | - Yuxi Wang
- Department of Respiratory and Critical Care Medicine, West China Medical School/West China Hospital, Sichuan University, Chengdu 610000, China
| | - Yunchun Li
- Department of Nuclear Medicine, Laboratory of Clinical Nuclear Medicine, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China; Department of Nuclear Medicine, The Second People's Hospital of Yibin, Yibin 644000, Sichuan, China.
| | - Xiaoai Wu
- Department of Nuclear Medicine, Laboratory of Clinical Nuclear Medicine, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China.
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6
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Haghighijoo Z, Zamani L, Moosavi F, Emami S. Therapeutic potential of quinazoline derivatives for Alzheimer's disease: A comprehensive review. Eur J Med Chem 2022; 227:113949. [PMID: 34742016 DOI: 10.1016/j.ejmech.2021.113949] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 10/02/2021] [Accepted: 10/22/2021] [Indexed: 12/24/2022]
Abstract
Quinazolines are considered as a promising class of bioactive heterocyclic compounds with broad properties. Particularly, the quinazoline scaffold has an impressive role in the design and synthesis of new CNS-active drugs. The drug-like properties and pharmacological characteristics of quinazoline could lead to different drugs with various targets. Among CNS disorders, Alzheimer's disease (AD) is a progressive neurodegenerative disorder with memory loss, cognitive decline and language dysfunction. AD is a complex and multifactorial disease therefore, the need for finding multi-target drugs against this devastative disease is urgent. A literature survey revealed that quinazoline derivatives have diverse therapeutic potential for AD as modulators/inhibitors of β-amyloid, tau protein, cholinesterases, monoamine oxidases, and phosphodiesterases as well as other protective effects. Thus, we describe here the most relevant and recent studies about anti-AD agents with quinazoline structure which can further aid the development and discovery of new anti-AD agents.
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Affiliation(s)
- Zahra Haghighijoo
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, LA, 70504, USA
| | - Leila Zamani
- Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA, 01609, USA
| | - Fatemeh Moosavi
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Saeed Emami
- Department of Medicinal Chemistry and Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran.
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7
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Karimian S, Shekouhy M, Pirhadi S, Iraji A, Attarroshan M, Edraki N, Khoshneviszadeh M. Synthesis and biological evaluation of benzimidazoles/1,3,5-triazine-2,4-diamine hybrid compounds: a new class of multifunctional alzheimer targeting agents. NEW J CHEM 2022. [DOI: 10.1039/d2nj00371f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Twelve novel benzimidazole/1,3,5-triazine-2,4-diamine hybrids were synthesized and biologically studied as multifunctional Alzheimer-controlling agents.
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Affiliation(s)
- Somaye Karimian
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohsen Shekouhy
- Department of Chemistry, College of Sciences, Shiraz University, Shiraz 71454, Iran
| | - Somayeh Pirhadi
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Aida Iraji
- Stem Cells Technology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Central Research Laboratory, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mahshid Attarroshan
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Najmeh Edraki
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mehdi Khoshneviszadeh
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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8
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Zhang W, Li Y, Zhou H, Su X, Zhang X, Zhang W. One-pot, two-step synthesis of 3,4-dihydroquinazoline-2(1H)-thiones from o-azidobenzenealdehydes, aryl amines and carbon disulfide. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2021.153361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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9
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Kazemi E, Darehkordi A, Abbasi A. Friedel-Crafts synthesis of bis(trifluoromethylated)-4-aryl-3,4-dihydroquinazolines, bis(trifluoromethylated)-3,4-dihydroquinazoline-4-ols and trifluoromethyl arylketoimines using N-aryltrifluoroacetimidoyl chlorides and benzene derivatives. Mol Divers 2021; 26:815-825. [PMID: 33534024 DOI: 10.1007/s11030-021-10189-4] [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: 10/17/2020] [Accepted: 01/21/2021] [Indexed: 11/29/2022]
Abstract
A simple and straightforward approach to access biologically important N-heterocycles, namely bis(trifluoromethylated)-4-aryl-3,4-dihydroquinazolines, bis(trifluoromethylated)-3,4-dihydroquinazoline-4-ols and trifluoromethyl arylketoimines, as a group of important frameworks or initial substance from N-aryltrifluoroacetimidoyl chlorides with benzene derivatives via Friedel-Crafts reaction has been described. This novel strategy provides synthesis of trifluoromethylated dihydroquinazolines and trifluoromethyl arylketoimines in good to excellent yields.
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Affiliation(s)
- Elham Kazemi
- Department of Chemistry, Faculty of Science, Vali-e-Asr University of Rafsanja, Rafsanjan, 77176, Iran
| | - Ali Darehkordi
- Department of Chemistry, Faculty of Science, Vali-e-Asr University of Rafsanja, Rafsanjan, 77176, Iran.
| | - Alireza Abbasi
- School of Chemistry, College of Science, University of Tehran, P.O. Box 14155-6455, Tehran, Iran
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10
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Dynamic Docking Using Multicanonical Molecular Dynamics: Simulating Complex Formation at the Atomistic Level. Methods Mol Biol 2021; 2266:187-202. [PMID: 33759128 DOI: 10.1007/978-1-0716-1209-5_11] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Multicanonical molecular dynamics (McMD)-based dynamic docking has been applied to predict the native binding configurations for several protein receptors and their ligands. Due to the enhanced sampling capabilities of McMD, it can exhaustively sample bound and unbound ligand configurations, as well as receptor conformations, and thus enables efficient sampling of the conformational and configurational space, not possible using canonical MD simulations. As McMD samples a wide configurational space, extensive analysis is required to study the diverse ensemble consisting of bound and unbound structures. By projecting the reweighted ensemble onto the first two principal axes obtained via principal component analysis of the multicanonical ensemble, the free energy landscape (FEL) can be obtained. Further analysis produces representative structures positioned at the local minima of the FEL, where these structures are then ranked by their free energy. In this chapter, we describe our dynamic docking methodology, which has successfully reproduced the native binding configuration for small compounds, medium-sized compounds, and peptide molecules.
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11
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Bais J, Benedetti F, Berti F, Cerminara I, Drioli S, Funicello M, Regini G, Vidali M, Felluga F. One Pot Synthesis of Micromolar BACE-1 Inhibitors Based on the Dihydropyrimidinone Scaffold and Their Thia and Imino Analogues. Molecules 2020; 25:molecules25184152. [PMID: 32927879 PMCID: PMC7571164 DOI: 10.3390/molecules25184152] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/31/2020] [Accepted: 09/02/2020] [Indexed: 12/05/2022] Open
Abstract
A library of dihydropyrimidinones was synthesized via a “one-pot” three component Biginelli reaction using different aldehydes in combination with β-dicarbonyl compounds and urea. Selected 2-thiooxo and 2-imino analogs were also obtained with the Biginelli reaction from thiourea and guanidine hydrochloride, respectively. The products were screened in vitro for their β-secretase inhibitory activity. The majority of the compounds resulted to be active, with IC50 in the range 100 nM–50 μM.
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Affiliation(s)
- Jessica Bais
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, via Licio Giorgieri 1, 34127 Trieste, Italy; (J.B.); (F.B.); (F.B.); (S.D.); (G.R.); (M.V.)
| | - Fabio Benedetti
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, via Licio Giorgieri 1, 34127 Trieste, Italy; (J.B.); (F.B.); (F.B.); (S.D.); (G.R.); (M.V.)
| | - Federico Berti
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, via Licio Giorgieri 1, 34127 Trieste, Italy; (J.B.); (F.B.); (F.B.); (S.D.); (G.R.); (M.V.)
| | - Iole Cerminara
- Dipartimento di Scienze, Università della Basilicata, Viale dell’Ateneo Lucano 10, 85100 Potenza, Italy; (I.C.); (M.F.)
| | - Sara Drioli
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, via Licio Giorgieri 1, 34127 Trieste, Italy; (J.B.); (F.B.); (F.B.); (S.D.); (G.R.); (M.V.)
| | - Maria Funicello
- Dipartimento di Scienze, Università della Basilicata, Viale dell’Ateneo Lucano 10, 85100 Potenza, Italy; (I.C.); (M.F.)
| | - Giorgia Regini
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, via Licio Giorgieri 1, 34127 Trieste, Italy; (J.B.); (F.B.); (F.B.); (S.D.); (G.R.); (M.V.)
| | - Mattia Vidali
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, via Licio Giorgieri 1, 34127 Trieste, Italy; (J.B.); (F.B.); (F.B.); (S.D.); (G.R.); (M.V.)
| | - Fulvia Felluga
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, via Licio Giorgieri 1, 34127 Trieste, Italy; (J.B.); (F.B.); (F.B.); (S.D.); (G.R.); (M.V.)
- Correspondence:
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12
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Jagtap AD, Kondekar NB, Hung PY, Hsieh CE, Yang CR, Chen GS, Chern JW. 4-Substituted 2-amino-3,4-dihydroquinazolines with a 3-hairpin turn side chain as novel inhibitors of BACE-1. Bioorg Chem 2020; 95:103135. [PMID: 31923631 DOI: 10.1016/j.bioorg.2019.103135] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/13/2019] [Accepted: 07/19/2019] [Indexed: 11/29/2022]
Abstract
Herein, we report the identification, design, and synthesis of a series of 4-substituted 2-amino-3,4-dihydroquinazolines with hairpin turn side chains as novel inhibitors of BACE-1. The dihydroquinazoline derivatives were rationally designed by modifying the amide group and relocating the α -hydrophobic substituent on the hairpin turn side chain of lead compound 2 to the C4-position on the 3,4-dihydroquinazoline scaffold to facilitate interactions with the S1, S2 and S1' subsites of BACE-1. Among these derivatives, two compounds exhibited potent BACE-1 inhibitory activity: 4-methyl-substituted (22a, BACE-1 CFA IC50 = 0.38 μM; BACE-1 WCA IC50 = 0.14 μM) and 4-cyclohexylmethyl-substituted (22b, BACE-1 CFA IC50 = 0.49 μM; BACE-1 WCA IC50 = 0.14 μM) 2-amino-3,4-dihydroquinazoline, each bearing a side chain of N-cyclohexyl-N-((1-methyl-1H-pyrazol-4-yl)methyl amide. The results suggest that the structural modifications maintain the hairpin turn topology similar to that of compound 2 and provide an additional interaction with the S2 subsite.
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Affiliation(s)
- Ajit Dhananjay Jagtap
- School of Pharmacy, College of Medicine and Center for Innovative Therapeutics Discovery, National Taiwan University, No. 33, Lin Sen South Road, Taipei 10050, Taiwan; AnnJi Pharmaceutical Co., Ltd., 18, Siyuan Street, Taipei 10087, Taiwan
| | - Nagendra B Kondekar
- School of Pharmacy, College of Medicine and Center for Innovative Therapeutics Discovery, National Taiwan University, No. 33, Lin Sen South Road, Taipei 10050, Taiwan
| | - Pei-Yun Hung
- AnnJi Pharmaceutical Co., Ltd., 18, Siyuan Street, Taipei 10087, Taiwan
| | - Chen-En Hsieh
- Department of Applied Chemistry, Providence University, No. 200, Section 7, Taiwan Boulevard, Taichung 43301, Taiwan
| | - Chia-Ron Yang
- School of Pharmacy, College of Medicine and Center for Innovative Therapeutics Discovery, National Taiwan University, No. 33, Lin Sen South Road, Taipei 10050, Taiwan
| | - Grace Shiahuy Chen
- Department of Applied Chemistry, Providence University, No. 200, Section 7, Taiwan Boulevard, Taichung 43301, Taiwan.
| | - Ji-Wang Chern
- School of Pharmacy, College of Medicine and Center for Innovative Therapeutics Discovery, National Taiwan University, No. 33, Lin Sen South Road, Taipei 10050, Taiwan.
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13
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Magyar CL, Wall TJ, Davies SB, Campbell MV, Barna HA, Smith SR, Savich CJ, Mosey RA. Triflic anhydride mediated synthesis of 3,4-dihydroquinazolines: a three-component one-pot tandem procedure. Org Biomol Chem 2020; 17:7995-8000. [PMID: 31408069 DOI: 10.1039/c9ob01596e] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A one-pot three-component tandem reaction involving a key Pictet-Spengler-like annulation step has been developed, providing an efficient method for the synthesis of 3,4-dihydroquinazolines in moderate to good yields from amides, aldehydes, and amines. The multicomponent triflic anhydride mediated reaction tolerates the installation of numerous functional groups, affording extensive diversity about the heterocyclic scaffold.
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Affiliation(s)
- Christina L Magyar
- Department of Chemistry, Lake Superior State University, Sault Sainte Marie, MI 49783, USA.
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14
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Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset. J Comput Aided Mol Des 2019; 33:1031-1043. [PMID: 31677003 DOI: 10.1007/s10822-019-00232-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 10/09/2019] [Indexed: 12/11/2022]
Abstract
Using the D3R Grand Challenge 4 dataset containing Beta-secretase 1 (BACE) and Cathepsin S (CatS) inhibitors, we have evaluated the performance of our in-house docking workflow that involves in the first step the selection of the most suitable docking software for the system of interest based on structural and functional information available in public databases, followed by the docking of the dataset to predict the binding modes and ranking of ligands. The macrocyclic nature of the BACE ligands brought additional challenges, which were dealt with by a careful preparation of the three-dimensional input structures for ligands. This provided top-performing predictions for BACE, in contrast with CatS, where the predictions in the absence of guiding constraints provided poor results. These results highlight the importance of previous structural knowledge that is needed for correct predictions on some challenging targets. After the end of the challenge, we also carried out free energy calculations (i.e. in a non-blinded manner) for CatS using the pmx software and several force fields (AMBER, Charmm). Using knowledge-based starting pose construction allowed reaching remarkable accuracy for the CatS free energy estimates. Interestingly, we show that the use of a consensus result, by averaging the results from different force fields, increases the prediction accuracy.
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15
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Oehlrich D, Peschiulli A, Tresadern G, Van Gool M, Vega JA, De Lucas AI, Alonso de Diego SA, Prokopcova H, Austin N, Van Brandt S, Surkyn M, De Cleyn M, Vos A, Rombouts FJR, Macdonald G, Moechars D, Gijsen HJM, Trabanco AA. Evaluation of a Series of β-Secretase 1 Inhibitors Containing Novel Heteroaryl-Fused-Piperazine Amidine Warheads. ACS Med Chem Lett 2019; 10:1159-1165. [PMID: 31413800 DOI: 10.1021/acsmedchemlett.9b00181] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 07/02/2019] [Indexed: 02/08/2023] Open
Abstract
Despite several years of research, only a handful of β-secretase (BACE) 1 inhibitors have entered clinical trials as potential therapeutics against Alzheimer's disease. The intrinsic basic nature of low molecular weight, amidine-containing BACE 1 inhibitors makes them far from optimal as central nervous system drugs. Herein we present a set of novel heteroaryl-fused piperazine amidine inhibitors designed to lower the basicity of the key, enzyme binding, amidine functionality. This study resulted in the identification of highly potent (IC50 ≤ 10 nM), permeable lead compounds with a reduced propensity to suffer from P-glycoprotein-mediated efflux.
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Affiliation(s)
| | | | | | - Michiel Van Gool
- Discovery Sciences Medicinal Chemistry, Janssen Research & Development, Janssen−Cilag S.A., C/Jarama 75A, 45007 Toledo, Spain
| | - Juan Antonio Vega
- Discovery Sciences Medicinal Chemistry, Janssen Research & Development, Janssen−Cilag S.A., C/Jarama 75A, 45007 Toledo, Spain
| | - Ana Isabel De Lucas
- Discovery Sciences Medicinal Chemistry, Janssen Research & Development, Janssen−Cilag S.A., C/Jarama 75A, 45007 Toledo, Spain
| | - Sergio A. Alonso de Diego
- Discovery Sciences Medicinal Chemistry, Janssen Research & Development, Janssen−Cilag S.A., C/Jarama 75A, 45007 Toledo, Spain
| | | | | | | | | | | | | | | | | | | | | | - Andrés A. Trabanco
- Discovery Sciences Medicinal Chemistry, Janssen Research & Development, Janssen−Cilag S.A., C/Jarama 75A, 45007 Toledo, Spain
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16
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Ramesh S, Balakumar R, Rizzo JR, Zhang TY. Enantiospecific Synthesis of 2‐Substituted Piperidine‐4‐carboxylic Acids from α‐Amino Acids. ChemistrySelect 2019. [DOI: 10.1002/slct.201900620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Subbiah Ramesh
- Syngene International Ltd.Biocon Park, Plot No. 2 & 3, Bommasandra IV Phase Jigani Link Road Bangalore 560 099 India
| | - Ramadas Balakumar
- Syngene International Ltd.Biocon Park, Plot No. 2 & 3, Bommasandra IV Phase Jigani Link Road Bangalore 560 099 India
| | - John R. Rizzo
- Small Molecule Design and DevelopmentLilly Research LaboratoriesEli Lilly and Company, Indianapolis Indiana 46285 USA
| | - Tony Y. Zhang
- Small Molecule Design and DevelopmentLilly Research LaboratoriesEli Lilly and Company, Indianapolis Indiana 46285 USA
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17
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Chen L, Wei Z, Chan K, Cai S, Liu G, Lu H, Wong PC, van Zijl PCM, Li T, Xu J. Protein aggregation linked to Alzheimer's disease revealed by saturation transfer MRI. Neuroimage 2019; 188:380-390. [PMID: 30553917 PMCID: PMC6401270 DOI: 10.1016/j.neuroimage.2018.12.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 12/08/2018] [Accepted: 12/10/2018] [Indexed: 12/12/2022] Open
Abstract
The goal of this study was to develop a molecular biomarker for the detection of protein aggregation involved in Alzheimer's disease (AD) by exploiting the features of the water saturation transfer spectrum (Z-spectrum), the CEST signal of which is sensitive to the molecular configuration of proteins. A radial-sampling steady-state sequence based ultrashort echo time (UTE) readout was implemented to image the Z-spectrum in the mouse brain, especially the contributions from mobile proteins at the frequency offsets for the composite protein amide proton (+3.6 ppm) and aliphatic proton (-3.6 ppm) signals. Using a relatively weak radiofrequency (RF) saturation amplitude, contributions due to strong magnetization transfer contrast (MTC) from solid-like macromolecules and direct water saturation (DS) were minimized. For practical measure of the changes in the mobile protein configuration, we defined a saturation transfer difference (ΔST) by subtracting the Z-spectral signals at ±3.6 ppm from a control signal at 8 ppm. Phantom studies of glutamate solution, protein (egg white) and hair conditioner show the capability of the proposed scheme to minimize the contributions from amine protons, DS, and MTC, respectively. The ST signal at ±3.6 ppm of the cross-linked bovine serum albumin (BSA) solutions demonstrated that the ΔST signal can be used to monitor the aggregation process of the mobile proteins. High-resolution ΔST images of AD mouse brains at ±3.6 ppm of mouse brains showed significantly reduced ΔST (-3.6) signal compared to the age-matched wild-type (WT) mice. Thus, this signal has potential to serve as a molecular biomarker for monitoring protein aggregation in AD.
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Affiliation(s)
- Lin Chen
- F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Research Institute, Baltimore, MD, USA
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zhiliang Wei
- F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Research Institute, Baltimore, MD, USA
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kannie Chan
- F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Research Institute, Baltimore, MD, USA
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, China
| | - Shuhui Cai
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Xiamen University, Xiamen, China
| | - Guanshu Liu
- F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Research Institute, Baltimore, MD, USA
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hanzhang Lu
- F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Research Institute, Baltimore, MD, USA
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Philip C. Wong
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Peter C. M. van Zijl
- F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Research Institute, Baltimore, MD, USA
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tong Li
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jiadi Xu
- F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Research Institute, Baltimore, MD, USA
- Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
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18
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Bekker GJ, Araki M, Oshima K, Okuno Y, Kamiya N. Dynamic Docking of a Medium-Sized Molecule to Its Receptor by Multicanonical MD Simulations. J Phys Chem B 2019; 123:2479-2490. [DOI: 10.1021/acs.jpcb.8b12419] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Gert-Jan Bekker
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Mitsugu Araki
- Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Kanji Oshima
- Biotechnology Research Laboratories, Kaneka Corporation, 1-8 Miyamae-cho, Takasago-cho, Takasago, Hyogo 676-8688, Japan
| | - Yasushi Okuno
- Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Narutoshi Kamiya
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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19
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Gutiérrez M, Vallejos GA, Cortés MP, Bustos C. Bennett acceptance ratio method to calculate the binding free energy of BACE1 inhibitors: Theoretical model and design of new ligands of the enzyme. Chem Biol Drug Des 2019; 93:1117-1128. [PMID: 30693676 DOI: 10.1111/cbdd.13456] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 11/02/2018] [Accepted: 11/24/2018] [Indexed: 11/29/2022]
Abstract
In recent years, the design, development, and evaluation of several inhibitors of the BACE1 enzyme, as part of Alzheimer's treatment, have gathered the scientific community's interest. Here, a linear regression model was built using binding free energy calculations through the Bennett acceptance ratio method for 20 known inhibitors of the BACE1 enzyme, with a Pearson coefficient of R = 0.88 and R2 = 0.78. The validation of this model was verified employing eight additional random inhibitors, which also gave a linear correlation with R = 0.97 and R2 = 0.93. Furthermore, this linear regression model was also used for proposing the structure of four potential BACE1 inhibitors, and the most active of them gave a theoretical Kd = 10 nM. However, these molecules have not been synthesized yet. Our team used a total time of more than 800 ns for the Molecular Dynamics to carry out this study, and all the software used were freely available.
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Affiliation(s)
- Margarita Gutiérrez
- Laboratorio de Síntesis Orgánica y Actividades Biológicas (LSO-Act-Bio), Instituto de Química de los Recursos Naturales, Universidad de Talca, Talca, Chile
| | - Gabriel A Vallejos
- Facultad de Ciencias, Instituto de Ciencias Químicas, Universidad Austral de Chile, Valdivia, Chile
| | - Magdalena P Cortés
- Escuela de Química y Farmacia, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso, Chile
| | - Carlos Bustos
- Facultad de Ciencias, Instituto de Ciencias Químicas, Universidad Austral de Chile, Valdivia, Chile
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20
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Gruber N, Díaz JE, Orelli LR. Synthesis of dihydroquinazolines from 2-aminobenzylamine: N 3 -aryl derivatives with electron-withdrawing groups. Beilstein J Org Chem 2018; 14:2510-2519. [PMID: 30344774 PMCID: PMC6178284 DOI: 10.3762/bjoc.14.227] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Accepted: 08/31/2018] [Indexed: 11/23/2022] Open
Abstract
The sequential N-functionalization of 2-aminobenzylamine (2-ABA) followed by cyclodehydration allowed for a straightforward and efficient synthesis of 3,4-dihydroquinazolines with N-aryl substituents bearing electron-withdrawing groups. The sequence involves an initial SNAr displacement, N-acylation and MW-assisted ring closure. Remarkably, the uncatalyzed N-arylation of 2-ABA led to the monosubstitution product using equimolar amounts of both reagents. The individual steps were optimized achieving good to excellent overall yields of the desired heterocycles, avoiding additional protection and deprotection steps. A mechanistic interpretation for the cyclodehydration reaction promoted by trimethylsilyl polyphosphate (PPSE) is also proposed on the basis of literature data and our experimental observations.
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Affiliation(s)
- Nadia Gruber
- Universidad de Buenos Aires, CONICET, Departamento de Química Orgánica, Facultad de Farmacia y Bioquímica, Junín 956, (1113) Buenos Aires, Argentina
| | - Jimena E Díaz
- Universidad de Buenos Aires, CONICET, Departamento de Química Orgánica, Facultad de Farmacia y Bioquímica, Junín 956, (1113) Buenos Aires, Argentina
| | - Liliana R Orelli
- Universidad de Buenos Aires, CONICET, Departamento de Química Orgánica, Facultad de Farmacia y Bioquímica, Junín 956, (1113) Buenos Aires, Argentina
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21
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Scholz D, Chernyshova Y, Ückert AK, Leist M. Reduced Aβ secretion by human neurons under conditions of strongly increased BACE activity. J Neurochem 2018; 147:256-274. [PMID: 29804308 DOI: 10.1111/jnc.14467] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 05/06/2018] [Accepted: 05/23/2018] [Indexed: 12/20/2022]
Abstract
The initial step in the amyloidogenic cascade of amyloid precursor protein (APP) processing is catalyzed by beta-site APP-cleaving enzyme (BACE), and this protease has increased activities in affected areas of Alzheimer's disease brains. We hypothesized that altered APP processing, because of augmented BACE activity, would affect the actions of direct and indirect BACE inhibitors. We therefore compared post-mitotic human neurons (LUHMES) with their BACE-overexpressing counterparts (BLUHMES). Although β-cleavage of APP was strongly increased in BLUHMES, they produced less full-length and truncated amyloid beta (Aβ) than LUHMES. Moreover, low concentrations of BACE inhibitors decreased cellular BACE activity as expected, but increased Aβ1-40 levels. Several other approaches to modulate BACE activity led to a similar, apparently paradoxical, behavior. For instance, reduction in intracellular acidification by bepridil increased Aβ production in parallel with decreased BACE activity. In contrast to BLUHMES, the respective control cells (LUHMES or BLUHMES with catalytically inactive BACE) showed conventional pharmacological responses. Other non-canonical neurochemical responses (so-called 'rebound effects') are well-documented for the Aβ pathway, especially for γ-secretase: a partial block of its activity leads to an increased Aβ secretion by some cell types. We therefore compared LUHMES and BLUHMES regarding rebound effects of γ-secretase inhibitors and found an Aβ rise in LUHMES but not in BLUHMES. Thus, different cellular factors are responsible for the γ-secretase- versus BACE-related Aβ rebound. We conclude that increased BACE activity, possibly accompanied by an altered cellular localization pattern, can dramatically influence Aβ generation in human neurons and affect pharmacological responses to secretase inhibitors. OPEN PRACTICES: Open Science: This manuscript was awarded with the Open Materials Badge. For more information see: https://cos.io/our-services/open-science-badges/.
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Affiliation(s)
- Diana Scholz
- Chair for in vitro Toxicology and Biomedicine, University of Konstanz, Konstanz, Germany
| | - Yana Chernyshova
- Chair for in vitro Toxicology and Biomedicine, University of Konstanz, Konstanz, Germany
| | - Anna-Katharina Ückert
- Chair for in vitro Toxicology and Biomedicine, University of Konstanz, Konstanz, Germany
| | - Marcel Leist
- Chair for in vitro Toxicology and Biomedicine, University of Konstanz, Konstanz, Germany
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22
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Gold‐Catalyzed Intermolecular [4+2] Annulation of 2‐Ethynylanilines with Ynamides: An Access to Substituted 2‐Aminoquinolines. Adv Synth Catal 2018. [DOI: 10.1002/adsc.201800341] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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23
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Hernández-Vázquez E, Chávez-Riveros A, Romo-Pérez A, Ramírez-Apán MT, Chávez-Blanco AD, Morales-Bárcenas R, Dueñas-González A, Miranda LD. Cytotoxic Activity and Structure-Activity Relationship of Triazole-Containing Bis(Aryl Ether) Macrocycles. ChemMedChem 2018; 13:1193-1209. [DOI: 10.1002/cmdc.201800075] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 03/12/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Eduardo Hernández-Vázquez
- Department of Organic Chemistry; Instituto de Química; UNAM, Circuito Exterior S.N.; Ciudad Universitaria; Coyoacán México, DF 04510 México
| | - Alejandra Chávez-Riveros
- Department of Organic Chemistry; Instituto de Química; UNAM, Circuito Exterior S.N.; Ciudad Universitaria; Coyoacán México, DF 04510 México
| | - Adriana Romo-Pérez
- Department of Organic Chemistry; Instituto de Química; UNAM, Circuito Exterior S.N.; Ciudad Universitaria; Coyoacán México, DF 04510 México
| | - María Teresa Ramírez-Apán
- Department of Organic Chemistry; Instituto de Química; UNAM, Circuito Exterior S.N.; Ciudad Universitaria; Coyoacán México, DF 04510 México
| | | | | | - Alfonso Dueñas-González
- Instituto de Investigaciones Biomédicas / Instituto Nacional de Cancerología, Tlalpan; Ciudad de México, CP 14080 Mexico
| | - Luis D. Miranda
- Department of Organic Chemistry; Instituto de Química; UNAM, Circuito Exterior S.N.; Ciudad Universitaria; Coyoacán México, DF 04510 México
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24
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Sindhikara D, Borrelli K. High throughput evaluation of macrocyclization strategies for conformer stabilization. Sci Rep 2018; 8:6585. [PMID: 29700331 PMCID: PMC5920116 DOI: 10.1038/s41598-018-24766-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 04/03/2018] [Indexed: 01/12/2023] Open
Abstract
While macrocyclization of a linear compound to stabilize a known bioactive conformation can be a useful strategy to increase binding potency, the difficulty of macrocycle synthesis can limit the throughput of such strategies. Thus computational techniques may offer the higher throughput required to screen large numbers of compounds. Here we introduce a method for evaluating the propensity of a macrocyclic compound to adopt a conformation similar that of a known active linear compound in the binding site. This method can be used as a fast screening tool for prioritizing macrocycles by leveraging the assumption that the propensity for the known bioactive substructural conformation relates to the affinity. While this method cannot to identify new interactions not present in the known linear compound, it could quickly differentiate compounds where the three dimensional geometries imposed by the macrocyclization prevent adoption of conformations with the same contacts as the linear compound in their conserved region. Here we report the implementation of this method using an RMSD-based structural descriptor and a Boltzmann-weighted propensity calculation and apply it retrospectively to three macrocycle linker optimization design projects. We found the method performs well in terms of prioritizing more potent compounds.
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Affiliation(s)
- Dan Sindhikara
- Schrodinger, Inc. Department of Life Sciences, New York, NY, 10036, USA.
| | - Ken Borrelli
- Schrodinger, Inc. Department of Life Sciences, New York, NY, 10036, USA
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25
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Li L, Tan TD, Zhang YQ, Liu X, Ye LW. Recent advances in transition-metal-catalyzed reactions of alkynes with isoxazoles. Org Biomol Chem 2018; 15:8483-8492. [PMID: 28875211 DOI: 10.1039/c7ob01895a] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Isoxazoles, as masked 1,3-dicarbonyl equivalents, have proven to be versatile building blocks and pivotal intermediates for the construction of a variety of useful azacycles with molecular complexity. As a result, a range of new reactions have been discovered based on isoxazoles in the past decade. However, the relevant reactions of isoxazoles with alkynes have seldom been explored. In this review, we will focus on the recent progress in the transition-metal-catalyzed formal annulations for the efficient synthesis of N-heterocycles between alkynes and isoxazoles by highlighting their specificity and applicability, and the mechanistic rationale is presented where possible.
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Affiliation(s)
- Long Li
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
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26
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Wu C, Wang J, Zhang XY, Jia GK, Cao Z, Tang Z, Yu X, Xu X, He WM. Palladium-catalyzed selective synthesis of 3,4-dihydroquinazolines from electron-rich arylamines, electron-poor arylamines and glyoxalates. Org Biomol Chem 2018; 16:5050-5054. [DOI: 10.1039/c8ob01005f] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Palladium-catalyzed selective synthesis of various 3,4-dihydroquinazolines from electron-rich arylamines, electron-poor arylamines and glyoxalates was developed.
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Affiliation(s)
- Chao Wu
- Department of Chemistry
- Hunan University of Science and Engineering
- Yongzhou 425100
- China
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation
| | - Jie Wang
- Department of Chemistry
- Hunan University of Science and Engineering
- Yongzhou 425100
- China
| | - Xing-Yu Zhang
- Department of Chemistry
- Hunan University of Science and Engineering
- Yongzhou 425100
- China
| | - Guo-Kai Jia
- Department of Chemistry
- Hunan University of Science and Engineering
- Yongzhou 425100
- China
| | - Zhong Cao
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation
- Changsha University of Science and Technology
- Changsha
- China
| | - Zilong Tang
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecule of Ministry of Education
- Hunan University of Science and Technology
- Xiangtan 411201
- China
| | - Xianyong Yu
- Key Laboratory of Theoretical Organic Chemistry and Functional Molecule of Ministry of Education
- Hunan University of Science and Technology
- Xiangtan 411201
- China
| | - Xinhua Xu
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- Hunan University
- Changsha
- China
| | - Wei-Min He
- Department of Chemistry
- Hunan University of Science and Engineering
- Yongzhou 425100
- China
- State Key Laboratory of Chemo/Biosensing and Chemometrics
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27
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Yu HS, Deng Y, Wu Y, Sindhikara D, Rask AR, Kimura T, Abel R, Wang L. Accurate and Reliable Prediction of the Binding Affinities of Macrocycles to Their Protein Targets. J Chem Theory Comput 2017; 13:6290-6300. [PMID: 29120625 DOI: 10.1021/acs.jctc.7b00885] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Macrocycles have been emerging as a very important drug class in the past few decades largely due to their expanded chemical diversity benefiting from advances in synthetic methods. Macrocyclization has been recognized as an effective way to restrict the conformational space of acyclic small molecule inhibitors with the hope of improving potency, selectivity, and metabolic stability. Because of their relatively larger size as compared to typical small molecule drugs and the complexity of the structures, efficient sampling of the accessible macrocycle conformational space and accurate prediction of their binding affinities to their target protein receptors poses a great challenge of central importance in computational macrocycle drug design. In this article, we present a novel method for relative binding free energy calculations between macrocycles with different ring sizes and between the macrocycles and their corresponding acyclic counterparts. We have applied the method to seven pharmaceutically interesting data sets taken from recent drug discovery projects including 33 macrocyclic ligands covering a diverse chemical space. The predicted binding free energies are in good agreement with experimental data with an overall root-mean-square error (RMSE) of 0.94 kcal/mol. This is to our knowledge the first time where the free energy of the macrocyclization of linear molecules has been directly calculated with rigorous physics-based free energy calculation methods, and we anticipate the outstanding accuracy demonstrated here across a broad range of target classes may have significant implications for macrocycle drug discovery.
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Affiliation(s)
- Haoyu S Yu
- Schrodinger, Inc. , 120 West 45th Street, New York, New York 10036, United States
| | - Yuqing Deng
- Schrodinger, Inc. , 120 West 45th Street, New York, New York 10036, United States
| | - Yujie Wu
- Schrodinger, Inc. , 120 West 45th Street, New York, New York 10036, United States
| | - Dan Sindhikara
- Schrodinger, Inc. , 120 West 45th Street, New York, New York 10036, United States
| | - Amy R Rask
- Schrodinger, Inc. , 120 West 45th Street, New York, New York 10036, United States
| | - Takayuki Kimura
- Schrodinger, Inc. , 120 West 45th Street, New York, New York 10036, United States
| | - Robert Abel
- Schrodinger, Inc. , 120 West 45th Street, New York, New York 10036, United States
| | - Lingle Wang
- Schrodinger, Inc. , 120 West 45th Street, New York, New York 10036, United States
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28
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Martín-Maestro P, Gargini R, A Sproul A, García E, Antón LC, Noggle S, Arancio O, Avila J, García-Escudero V. Mitophagy Failure in Fibroblasts and iPSC-Derived Neurons of Alzheimer's Disease-Associated Presenilin 1 Mutation. Front Mol Neurosci 2017; 10:291. [PMID: 28959184 PMCID: PMC5603661 DOI: 10.3389/fnmol.2017.00291] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 08/28/2017] [Indexed: 12/21/2022] Open
Abstract
Familial Alzheimer’s disease (FAD) is clearly related with the accumulation of amyloid-beta (Aβ) and its deleterious effect on mitochondrial function is well established. Anomalies in autophagy have also been described in these patients. In the present work, functional analyses have been performed to study mitochondrial recycling process in patient-derived fibroblasts and neurons from induced pluripotent stem cells harboring the presenilin 1 mutation A246E. Mitophagy impairment was observed due to a diminished autophagy degradation phase associated with lysosomal anomalies, thus causing the accumulation of dysfunctional mitochondria labeled by Parkin RBR E3 ubiquitin protein ligase (PARK2). The failure of mitochondrial recycling by autophagy was enhanced in the patient-derived neuronal model. Our previous studies have demonstrated similar mitophagy impairment in sporadic Alzheimer’s disease (AD); therefore, our data indicate that mitophagy deficiency should be considered a common nexus between familial and sporadic cases of the disease.
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Affiliation(s)
- Patricia Martín-Maestro
- Departamento de Neurobiología, Centro de Biología Molecular "Severo Ochoa" (UAM-CSIC)Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED)Madrid, Spain.,Brain and Mind Research Institute, Weill Cornell Medical College, Cornell UniversityNew York, NY, United States
| | - Ricardo Gargini
- Departamento de Neurobiología, Centro de Biología Molecular "Severo Ochoa" (UAM-CSIC)Madrid, Spain
| | - Andrew A Sproul
- Department of Pathology & Cell Biology and the Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia UniversityNew York, NY, United States
| | - Esther García
- Departamento de Neurobiología, Centro de Biología Molecular "Severo Ochoa" (UAM-CSIC)Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED)Madrid, Spain
| | - Luis C Antón
- Departamento de Neurobiología, Centro de Biología Molecular "Severo Ochoa" (UAM-CSIC)Madrid, Spain
| | - Scott Noggle
- The New York Stem Cell FoundationNew York, NY, United States
| | - Ottavio Arancio
- Department of Pathology & Cell Biology and the Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia UniversityNew York, NY, United States
| | - Jesús Avila
- Departamento de Neurobiología, Centro de Biología Molecular "Severo Ochoa" (UAM-CSIC)Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED)Madrid, Spain
| | - Vega García-Escudero
- Departamento de Neurobiología, Centro de Biología Molecular "Severo Ochoa" (UAM-CSIC)Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED)Madrid, Spain.,Departamento de Anatomía, Histología y Neurociencia, Facultad de Medicina, Universidad Autónoma de MadridMadrid, Spain
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29
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Sonochemical synthesis of 2,3-dihydro-4(1H)-quinazolinones and 1-amidoalkyl-2-naphthols using magnetic nanoparticle-supported ionic liquid as a heterogeneous catalyst. RESEARCH ON CHEMICAL INTERMEDIATES 2017. [DOI: 10.1007/s11164-017-3093-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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30
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Díaz JE, Ranieri S, Gruber N, Orelli LR. Syntheses of 3,4- and 1,4-dihydroquinazolines from 2-aminobenzylamine. Beilstein J Org Chem 2017; 13:1470-1477. [PMID: 28845190 PMCID: PMC5550820 DOI: 10.3762/bjoc.13.145] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 06/30/2017] [Indexed: 11/23/2022] Open
Abstract
A straightforward strategy for the synthesis of dihydroquinazolines is presented, which allows for the preparation of 3,4- and 1,4-dihydroquinazolines with different substitution patterns from 2-aminobenzylamine (2-ABA) as common precursor. The required functionalization of both amino groups present in 2-ABA was achieved by different routes involving selective N-acylation and cesium carbonate-mediated N-alkylation reactions, avoiding protection/deprotection steps. The heterocycles were efficiently synthesized in short reaction times by microwave-assisted ring closure of the corresponding aminoamides promoted by ethyl polyphosphate (PPE).
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Affiliation(s)
- Jimena E Díaz
- Universidad de Buenos Aires. CONICET. Departamento de Química Orgánica. Facultad de Farmacia y Bioquímica. Junín 956, (1113) Buenos Aires, Argentina
| | - Silvia Ranieri
- Universidad de Buenos Aires. CONICET. Departamento de Química Orgánica. Facultad de Farmacia y Bioquímica. Junín 956, (1113) Buenos Aires, Argentina
- Department of Industrial Chemistry “Toso Montanari”, University of Bologna, Viale Risorgimento 4, 40136 Bologna, Italy
| | - Nadia Gruber
- Universidad de Buenos Aires. CONICET. Departamento de Química Orgánica. Facultad de Farmacia y Bioquímica. Junín 956, (1113) Buenos Aires, Argentina
| | - Liliana R Orelli
- Universidad de Buenos Aires. CONICET. Departamento de Química Orgánica. Facultad de Farmacia y Bioquímica. Junín 956, (1113) Buenos Aires, Argentina
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31
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Kumar A, Srivastava G, Srivastava S, Verma S, Negi AS, Sharma A. Investigation of naphthofuran moiety as potential dual inhibitor against BACE-1 and GSK-3β: molecular dynamics simulations, binding energy, and network analysis to identify first-in-class dual inhibitors against Alzheimer's disease. J Mol Model 2017; 23:239. [PMID: 28741112 DOI: 10.1007/s00894-017-3396-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 06/25/2017] [Indexed: 12/11/2022]
Abstract
BACE-1 and GSK-3β are potential therapeutic drug targets for Alzheimer's disease. Recently, both the targets received attention for designing dual inhibitors for Alzheimer's disease. Until now, only two-scaffold triazinone and curcumin have been reported as BACE-1 and GSK-3β dual inhibitors. Docking, molecular dynamics, clustering, binding energy, and network analysis of triazinone derivatives with BACE-1 and GSK-3β was performed to get molecular insight into the first reported dual inhibitor. Further, we designed and evaluated a naphthofuran series for its ability to inhibit BACE-1 and GSK-3β with the computational approaches. Docking study of naphthofuran series showed a good binding affinity towards both the targets. Molecular dynamics, binding energy, and network analysis were performed to compare their binding with the targets and amino acids responsible for binding. Naphthofuran series derivatives showed good interaction within the active site residues of both of the targets. Hydrogen bond occupancy and binding energy suggested strong binding with the targets. Dual-inhibitor binding was mostly governed by the hydrophobic interactions for both of the targets. Per residue energy decomposition and network analysis identified the key residues involved in the binding and inhibiting BACE-1 and GSK-3β. The results indicated that naphthofuran series derivative 11 may be a promising first-in-class dual inhibitor against BACE-1 and GSK-3β. This naphthofuran series may be further explored to design better dual inhibitors. Graphical abstract Naphthofuran derivative as a dual inhibitor for BACE-1 and GSK-3β.
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Affiliation(s)
- Akhil Kumar
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, UP, 226015, India
| | - Gaurava Srivastava
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, UP, 226015, India
| | - Swati Srivastava
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, UP, 226015, India
| | - Seema Verma
- Chemical Sciences Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, UP, 226015, India
| | - Arvind S Negi
- Chemical Sciences Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, UP, 226015, India
| | - Ashok Sharma
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, UP, 226015, India.
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32
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Azimi S, Zonouzi A, Firuzi O, Iraji A, Saeedi M, Mahdavi M, Edraki N. Discovery of imidazopyridines containing isoindoline-1,3-dione framework as a new class of BACE1 inhibitors: Design, synthesis and SAR analysis. Eur J Med Chem 2017; 138:729-737. [PMID: 28728105 DOI: 10.1016/j.ejmech.2017.06.040] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 05/31/2017] [Accepted: 06/22/2017] [Indexed: 10/19/2022]
Abstract
Alzheimer's disease is characterized by chronic neurodegeneration leading to dementia. The main cause of neurodegeneration is considered to be the accumulation of amyloid-β. Inhibiting BACE1 is a well-studied approach to lower the burden of amyloid-β aggregates. We designed a series of imidazopyridines-based compounds bearing phthalimide moieties as inhibitors of BACE1. The compounds 8a-o were synthesized by the Groebke-Blackburn-Bienaymé three-component reaction of heteroaromatic amidines, aldehydes and isocyanides. Evaluating the BACE1 inhibitory effects of the synthesized compounds revealed that introducing an aminocyclohexyl moiety in the imidazopyridine core resulted in a significant improvement in its BACE1 inhibitory potential. In this regard, compound 8e was the most potent against BACE1 with an IC50 value of 2.84 (±0.95) μM. Molecular docking revealed that the nitrogen atom of imidazopyridines and the oxygen atom of the phenoxypropyl linker were involved in hydrogen bound interactions with Asp228 and Asp32 of BACE1 active site, respectively. The phthalimide moiety oriented toward the flap pocket and interacted with phe108, lle110, Trp115, Ile118 through van der Waal's and hydrophobic interactions. These findings demonstrate that imidazopyridines-based compounds bearing phthalimide moiety have the potential to decrease amyloid-β levels and ameliorate the symptoms of Alzheimer's disease.
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Affiliation(s)
- Sara Azimi
- School of Chemistry, College of Science, University of Tehran, PO Box 14155-6455, Tehran, Iran
| | - Afsaneh Zonouzi
- School of Chemistry, College of Science, University of Tehran, PO Box 14155-6455, Tehran, Iran
| | - Omidreza Firuzi
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Aida Iraji
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mina Saeedi
- Medicinal Plants Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran; Persian Medicine and Pharmacy Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Mahdavi
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
| | - Najmeh Edraki
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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33
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Chéron N, Shakhnovich EI. Effect of sampling on BACE-1 ligands binding free energy predictions via MM-PBSA calculations. J Comput Chem 2017; 38:1941-1951. [PMID: 28568844 DOI: 10.1002/jcc.24839] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 05/02/2017] [Accepted: 05/04/2017] [Indexed: 01/04/2023]
Abstract
The BACE-1 enzyme is a prime target to find a cure to Alzheimer's disease. In this article, we used the MM-PBSA approach to compute the binding free energies of 46 reported ligands to this enzyme. After showing that the most probable protonation state of the catalytic dyad is mono-protonated (on ASP32), we performed a thorough analysis of the parameters influencing the sampling of the conformational space (in total, more than 35 μs of simulations were performed). We show that ten simulations of 2 ns gives better results than one of 50 ns. We also investigated the influence of the protein force field, the water model, the periodic boundary conditions artifacts (box size), as well as the ionic strength. Amber03 with TIP3P, a minimal distance of 1.0 nm between the protein and the box edges and a ionic strength of I = 0.2 M provides the optimal correlation with experiments. Overall, when using these parameters, a Pearson correlation coefficient of R = 0.84 (R2 = 0.71) is obtained for the 46 ligands, spanning eight orders of magnitude of Kd (from 0.017 nm to 2000 μM, i.e., from -14.7 to -3.7 kcal/mol), with a ligand size from 22 to 136 atoms (from 138 to 937 g/mol). After a two-parameter fit of the binding affinities for 12 of the ligands, an error of RMSD = 1.7 kcal/mol was obtained for the remaining ligands. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Nicolas Chéron
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, 02138.,Département de Chimie, UMR 8640 PASTEUR, Ecole Normale Supérieure, PSL Research University, UPMC Univ. Paris 06, CNRS, 24 rue Lhomond, Paris, 75005, France
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, 02138
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34
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Remennikov GY. Synthesis of Condensed Heterocycles, Containing Partially Saturated Pyrimidine Nuclei, from Aromatic Pyrimidine Derivatives. J Heterocycl Chem 2017. [DOI: 10.1002/jhet.2864] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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35
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Iron-catalyzed C sp3 C sp3 bond formation via dehydrative cross coupling reaction: Facile access to new hybrid dihydroquinazolines having quinoline, isoquinoline, quinoxaline and azoles. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.03.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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36
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Hamada Y, Kiso Y. New directions for protease inhibitors directed drug discovery. Biopolymers 2016; 106:563-79. [PMID: 26584340 PMCID: PMC7161749 DOI: 10.1002/bip.22780] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 10/25/2015] [Accepted: 11/02/2015] [Indexed: 12/29/2022]
Abstract
Proteases play crucial roles in various biological processes, and their activities are essential for all living organisms-from viruses to humans. Since their functions are closely associated with many pathogenic mechanisms, their inhibitors or activators are important molecular targets for developing treatments for various diseases. Here, we describe drugs/drug candidates that target proteases, such as malarial plasmepsins, β-secretase, virus proteases, and dipeptidyl peptidase-4. Previously, we reported inhibitors of aspartic proteases, such as renin, human immunodeficiency virus type 1 protease, human T-lymphotropic virus type I protease, plasmepsins, and β-secretase, as drug candidates for hypertension, adult T-cell leukaemia, human T-lymphotropic virus type I-associated myelopathy, malaria, and Alzheimer's disease. Our inhibitors are also described in this review article as examples of drugs that target proteases. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 563-579, 2016.
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Affiliation(s)
- Yoshio Hamada
- Medicinal Chemistry LaboratoryKobe Pharmaceutical University, MotoyamakitaHigashinada‐kuKobe658‐8558Japan
| | - Yoshiaki Kiso
- Laboratory of Peptide Science, Nagahama Institute of Bio‐Science and TechnologyTamura‐choNagahama526‐0829Japan
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37
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Radeva N, Schiebel J, Wang X, Krimmer SG, Fu K, Stieler M, Ehrmann FR, Metz A, Rickmeyer T, Betz M, Winquist J, Park AY, Huschmann FU, Weiss MS, Mueller U, Heine A, Klebe G. Active Site Mapping of an Aspartic Protease by Multiple Fragment Crystal Structures: Versatile Warheads To Address a Catalytic Dyad. J Med Chem 2016; 59:9743-9759. [PMID: 27726357 DOI: 10.1021/acs.jmedchem.6b01195] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Crystallography is frequently used as follow-up method to validate hits identified by biophysical screening cascades. The capacity of crystallography to directly screen fragment libraries is often underestimated, due to its supposed low-throughput and need for high-quality crystals. We applied crystallographic fragment screening to map the protein-binding site of the aspartic protease endothiapepsin by individual soaking experiments. Here, we report on 41 fragments binding to the catalytic dyad and adjacent specificity pockets. The analysis identifies already known warheads but also reveals hydrazide, pyrazole, or carboxylic acid fragments as novel functional groups binding to the dyad. A remarkable swapping of the S1 and S1' pocket between structurally related fragments is explained by either steric demand, required displacement of a well-bound water molecule, or changes of trigonal-planar to tetrahedral geometry of an oxygen functional group in a side chain. Some warheads simultaneously occupying both S1 and S1' are promising starting points for fragment-growing strategies.
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Affiliation(s)
- Nedyalka Radeva
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Johannes Schiebel
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Xiaojie Wang
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Stefan G Krimmer
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Kan Fu
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Martin Stieler
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Frederik R Ehrmann
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Alexander Metz
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Thomas Rickmeyer
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Michael Betz
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Johan Winquist
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Ah Young Park
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Franziska U Huschmann
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany.,Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography (HZB-MX), Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Manfred S Weiss
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography (HZB-MX), Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Uwe Mueller
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography (HZB-MX), Albert-Einstein-Strasse 15, 12489 Berlin, Germany.,MAX IV Laboratory, Lund University , Fotongatan 2, 225 94 Lund, Sweden
| | - Andreas Heine
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
| | - Gerhard Klebe
- Department of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, 35032 Marburg, Germany
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38
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Jin H, Tian B, Song X, Xie J, Rudolph M, Rominger F, Hashmi ASK. Gold-katalysierte Synthese von Chinolinen aus Propargylsilylethern und Anthranilen über die Umpolung eines Goldcarben-Kohlenstoffatoms. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606043] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Hongming Jin
- Organisch-Chemisches Institut; Universität Heidelberg; Im Neuenheimer Feld 270, 6 9120 Heidelberg Deutschland
| | - Bin Tian
- Organisch-Chemisches Institut; Universität Heidelberg; Im Neuenheimer Feld 270, 6 9120 Heidelberg Deutschland
| | - Xinlong Song
- Organisch-Chemisches Institut; Universität Heidelberg; Im Neuenheimer Feld 270, 6 9120 Heidelberg Deutschland
| | - Jin Xie
- Organisch-Chemisches Institut; Universität Heidelberg; Im Neuenheimer Feld 270, 6 9120 Heidelberg Deutschland
| | - Matthias Rudolph
- Organisch-Chemisches Institut; Universität Heidelberg; Im Neuenheimer Feld 270, 6 9120 Heidelberg Deutschland
| | - Frank Rominger
- Organisch-Chemisches Institut; Universität Heidelberg; Im Neuenheimer Feld 270, 6 9120 Heidelberg Deutschland
| | - A. Stephen K. Hashmi
- Organisch-Chemisches Institut; Universität Heidelberg; Im Neuenheimer Feld 270, 6 9120 Heidelberg Deutschland
- Chemistry Department, Faculty of Science; King Abdulaziz University (KAU); 21589 Jeddah Saudi-Arabien
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39
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Jin H, Tian B, Song X, Xie J, Rudolph M, Rominger F, Hashmi ASK. Gold-Catalyzed Synthesis of Quinolines from Propargyl Silyl Ethers and Anthranils through the Umpolung of a Gold Carbene Carbon. Angew Chem Int Ed Engl 2016; 55:12688-92. [DOI: 10.1002/anie.201606043] [Citation(s) in RCA: 170] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Hongming Jin
- Organisch-Chemisches Institut; Universität Heidelberg; Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - Bin Tian
- Organisch-Chemisches Institut; Universität Heidelberg; Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - Xinlong Song
- Organisch-Chemisches Institut; Universität Heidelberg; Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - Jin Xie
- Organisch-Chemisches Institut; Universität Heidelberg; Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - Matthias Rudolph
- Organisch-Chemisches Institut; Universität Heidelberg; Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - Frank Rominger
- Organisch-Chemisches Institut; Universität Heidelberg; Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - A. Stephen K. Hashmi
- Organisch-Chemisches Institut; Universität Heidelberg; Im Neuenheimer Feld 270 69120 Heidelberg Germany
- Chemistry Department, Faculty of Science; King Abdulaziz University (KAU); 21589 Jeddah Saudi Arabia
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40
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Ciordia M, Pérez-Benito L, Delgado F, Trabanco AA, Tresadern G. Application of Free Energy Perturbation for the Design of BACE1 Inhibitors. J Chem Inf Model 2016; 56:1856-71. [PMID: 27500414 DOI: 10.1021/acs.jcim.6b00220] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Novel spiroaminodihydropyrroles probing for optimized interactions at the P3 pocket of β-secretase 1 (BACE1) were designed with the use of free energy perturbation (FEP) calculations. The resulting molecules showed pIC50 potencies in enzymatic BACE1 inhibition assays ranging from approximately 5 to 7. Good correlation was observed between the predicted activity from the FEP calculations and experimental activity. Simulations run with a default 5 ns approach delivered a mean unsigned error (MUE) between prediction and experiment of 0.58 and 0.91 kcal/mol for retrospective and prospective applications, respectively. With longer simulations of 10 and 20 ns, the MUE was in both cases 0.57 kcal/mol for the retrospective application, and 0.69 and 0.59 kcal/mol for the prospective application. Other considerations that impact the quality of the calculations are discussed. This work provides an example of the value of FEP as a computational tool for drug discovery.
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Affiliation(s)
- Myriam Ciordia
- Janssen Research and Development , c/Jarama 75A, 45007 Toledo, Spain.,Departamento de Química y Bioquímica, Facultad de Farmacia, Universidad CEU San Pablo , Urbanización Montepríncipe Ctra., Boadilla del Monte Km 5.3, 28668 Madrid, Spain
| | - Laura Pérez-Benito
- Janssen Research and Development , c/Jarama 75A, 45007 Toledo, Spain.,Laboratori de Medicina Computacional Unitat de Bioestadistica, Facultat de Medicina, Universitat Autonoma de Barcelona , 08193 Bellaterra, Spain
| | - Francisca Delgado
- Janssen Research and Development , c/Jarama 75A, 45007 Toledo, Spain
| | - Andrés A Trabanco
- Janssen Research and Development , c/Jarama 75A, 45007 Toledo, Spain
| | - Gary Tresadern
- Janssen Research and Development , c/Jarama 75A, 45007 Toledo, Spain
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41
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Mandal M, Wu Y, Misiaszek J, Li G, Buevich A, Caldwell JP, Liu X, Mazzola RD, Orth P, Strickland C, Voigt J, Wang H, Zhu Z, Chen X, Grzelak M, Hyde LA, Kuvelkar R, Leach PT, Terracina G, Zhang L, Zhang Q, Michener MS, Smith B, Cox K, Grotz D, Favreau L, Mitra K, Kazakevich I, McKittrick BA, Greenlee W, Kennedy ME, Parker EM, Cumming JN, Stamford AW. Structure-Based Design of an Iminoheterocyclic β-Site Amyloid Precursor Protein Cleaving Enzyme (BACE) Inhibitor that Lowers Central Aβ in Nonhuman Primates. J Med Chem 2016; 59:3231-48. [DOI: 10.1021/acs.jmedchem.5b01995] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Mihirbaran Mandal
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Yusheng Wu
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Jeffrey Misiaszek
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Guoqing Li
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Alexei Buevich
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - John P. Caldwell
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Xiaoxiang Liu
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Robert D. Mazzola
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Peter Orth
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Corey Strickland
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Johannes Voigt
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Hongwu Wang
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Zhaoning Zhu
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Xia Chen
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Michael Grzelak
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Lynn A. Hyde
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Reshma Kuvelkar
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Prescott T. Leach
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Giuseppe Terracina
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Lili Zhang
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Qi Zhang
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Maria S. Michener
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Brad Smith
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Kathleen Cox
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Diane Grotz
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Leonard Favreau
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Kaushik Mitra
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Irina Kazakevich
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Brian A. McKittrick
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - William Greenlee
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Matthew E. Kennedy
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Eric M. Parker
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Jared N. Cumming
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Andrew W. Stamford
- Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and
Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of
Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
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Arun Kumar R, Srinivasulu A, Saidulu G, Santhosh Kumar P, Sridhar B, Rajender Reddy K. Iron-catalyzed C–C bond formation via cross dehydrative coupling reaction of N-heterocyclic aminols with electron rich arenes: facile access to C4-aryl-dihydroquinazolines. Tetrahedron 2016. [DOI: 10.1016/j.tet.2015.12.040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Wyss DF, Cumming JN, Strickland CO, Stamford AW. BACE Inhibitors. FRAGMENT-BASED DRUG DISCOVERY LESSONS AND OUTLOOK 2016. [DOI: 10.1002/9783527683604.ch14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Ghosh AK, Cárdenas EL, Osswald HL. The Design, Development, and Evaluation of BACE1 Inhibitors for the Treatment of Alzheimer’s Disease. TOPICS IN MEDICINAL CHEMISTRY 2016. [DOI: 10.1007/7355_2016_16] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Rasina D, Otikovs M, Leitans J, Recacha R, Borysov OV, Kanepe-Lapsa I, Domraceva I, Pantelejevs T, Tars K, Blackman MJ, Jaudzems K, Jirgensons A. Fragment-Based Discovery of 2-Aminoquinazolin-4(3H)-ones As Novel Class Nonpeptidomimetic Inhibitors of the Plasmepsins I, II, and IV. J Med Chem 2015; 59:374-87. [PMID: 26670264 DOI: 10.1021/acs.jmedchem.5b01558] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
2-Aminoquinazolin-4(3H)-ones were identified as a novel class of malaria digestive vacuole plasmepsin inhibitors by using NMR-based fragment screening against Plm II. Initial fragment hit optimization led to a submicromolar inhibitor, which was cocrystallized with Plm II to produce an X-ray structure of the complex. The structure showed that 2-aminoquinazolin-4(3H)-ones bind to the open flap conformation of the enzyme and provided clues to target the flap pocket. Further improvement in potency was achieved via introduction of hydrophobic substituents occupying the flap pocket. Most of the 2-aminoquinazolin-4(3H)-one based inhibitors show a similar activity against digestive Plms I, II, and IV and >10-fold selectivity versus CatD, although varying the flap pocket substituent led to one Plm IV selective inhibitor. In cell-based assays, the compounds show growth inhibition of Plasmodium falciparum 3D7 with IC50 ∼ 1 μM. Together, these results suggest 2-aminoquinazolin-4(3H)-ones as perspective leads for future development of an antimalarial agent.
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Affiliation(s)
- Dace Rasina
- Latvian Institute of Organic Synthesis , Aizkraukles 21, Riga LV-1006, Latvia
| | - Martins Otikovs
- Latvian Institute of Organic Synthesis , Aizkraukles 21, Riga LV-1006, Latvia
| | - Janis Leitans
- Biomedical Research and Study Centre , Ratsupites 1, Riga LV-1067, Latvia
| | - Rosario Recacha
- Latvian Institute of Organic Synthesis , Aizkraukles 21, Riga LV-1006, Latvia
| | - Oleksandr V Borysov
- Latvian Institute of Organic Synthesis , Aizkraukles 21, Riga LV-1006, Latvia
| | - Iveta Kanepe-Lapsa
- Latvian Institute of Organic Synthesis , Aizkraukles 21, Riga LV-1006, Latvia
| | - Ilona Domraceva
- Latvian Institute of Organic Synthesis , Aizkraukles 21, Riga LV-1006, Latvia
| | - Teodors Pantelejevs
- Latvian Institute of Organic Synthesis , Aizkraukles 21, Riga LV-1006, Latvia
| | - Kaspars Tars
- Biomedical Research and Study Centre , Ratsupites 1, Riga LV-1067, Latvia
| | - Michael J Blackman
- The Francis Crick Institute, Mill Hill Laboratory , The Ridgeway, Mill Hill, London NW7 1AA, U.K
| | - Kristaps Jaudzems
- Latvian Institute of Organic Synthesis , Aizkraukles 21, Riga LV-1006, Latvia
| | - Aigars Jirgensons
- Latvian Institute of Organic Synthesis , Aizkraukles 21, Riga LV-1006, Latvia
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46
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Boy KM, Guernon JM, Wu YJ, Zhang Y, Shi J, Zhai W, Zhu S, Gerritz SW, Toyn JH, Meredith JE, Barten DM, Burton CR, Albright CF, Good AC, Grace JE, Lentz KA, Olson RE, Macor JE, Thompson LA. Macrocyclic prolinyl acyl guanidines as inhibitors of β-secretase (BACE). Bioorg Med Chem Lett 2015; 25:5040-7. [DOI: 10.1016/j.bmcl.2015.10.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/08/2015] [Accepted: 10/12/2015] [Indexed: 02/02/2023]
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47
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Rombouts FJR, Tresadern G, Delgado O, Martínez-Lamenca C, Van Gool M, García-Molina A, Alonso de Diego SA, Oehlrich D, Prokopcova H, Alonso JM, Austin N, Borghys H, Van Brandt S, Surkyn M, De Cleyn M, Vos A, Alexander R, Macdonald G, Moechars D, Gijsen H, Trabanco AA. 1,4-Oxazine β-Secretase 1 (BACE1) Inhibitors: From Hit Generation to Orally Bioavailable Brain Penetrant Leads. J Med Chem 2015; 58:8216-35. [DOI: 10.1021/acs.jmedchem.5b01101] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Frederik J. R. Rombouts
- Neuroscience Medicinal Chemistry, Janssen Research & Development, Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Gary Tresadern
- Discovery Sciences, Janssen Research & Development, Janssen−Cilag SA, C/Jarama 75A, 45007 Toledo, Spain
| | - Oscar Delgado
- Neuroscience Medicinal Chemistry, Janssen Research & Development, Janssen−Cilag SA, C/Jarama 75A, 45007 Toledo, Spain
| | - Carolina Martínez-Lamenca
- Neuroscience Medicinal Chemistry, Janssen Research & Development, Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Michiel Van Gool
- Neuroscience Medicinal Chemistry, Janssen Research & Development, Janssen−Cilag SA, C/Jarama 75A, 45007 Toledo, Spain
| | - Aránzazu García-Molina
- Neuroscience Medicinal Chemistry, Janssen Research & Development, Janssen−Cilag SA, C/Jarama 75A, 45007 Toledo, Spain
| | - Sergio A. Alonso de Diego
- Neuroscience Medicinal Chemistry, Janssen Research & Development, Janssen−Cilag SA, C/Jarama 75A, 45007 Toledo, Spain
| | - Daniel Oehlrich
- Neuroscience Medicinal Chemistry, Janssen Research & Development, Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Hana Prokopcova
- Neuroscience Medicinal Chemistry, Janssen Research & Development, Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - José Manuel Alonso
- Discovery Sciences, Janssen Research & Development, Janssen−Cilag SA, C/Jarama 75A, 45007 Toledo, Spain
| | - Nigel Austin
- Discovery Sciences, Janssen Research & Development, Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Herman Borghys
- Discovery Sciences, Janssen Research & Development, Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Sven Van Brandt
- Neuroscience Medicinal Chemistry, Janssen Research & Development, Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Michel Surkyn
- Neuroscience Medicinal Chemistry, Janssen Research & Development, Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Michel De Cleyn
- Neuroscience Medicinal Chemistry, Janssen Research & Development, Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Ann Vos
- Discovery Sciences, Janssen Research & Development, Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Richard Alexander
- Biologics Research, Janssen Research & Development, 1400 McKean Road, Spring House, Pennsylvania 19477, United States
| | - Gregor Macdonald
- Neuroscience Medicinal Chemistry, Janssen Research & Development, Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Dieder Moechars
- Neuroscience Biology, Janssen Research & Development, Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Harrie Gijsen
- Neuroscience Medicinal Chemistry, Janssen Research & Development, Janssen Pharmaceutica NV, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Andrés A. Trabanco
- Neuroscience Medicinal Chemistry, Janssen Research & Development, Janssen−Cilag SA, C/Jarama 75A, 45007 Toledo, Spain
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Mateu N, Ciordia M, Delgado O, Sánchez-Roselló M, Trabanco AA, Van Gool M, Tresadern G, Pérez-Benito L, Fustero S. A Versatile Approach to CF3-Containing 2-Pyrrolidones by Tandem Michael Addition-Cyclization: Exemplification in the Synthesis of Amidine Class BACE1 Inhibitors. Chemistry 2015; 21:11719-26. [DOI: 10.1002/chem.201501662] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Indexed: 12/19/2022]
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49
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Ghosh AK, Osswald HL. BACE1 (β-secretase) inhibitors for the treatment of Alzheimer's disease. Chem Soc Rev 2015; 43:6765-813. [PMID: 24691405 DOI: 10.1039/c3cs60460h] [Citation(s) in RCA: 233] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
BACE1 (β-secretase, memapsin 2, Asp2) has emerged as a promising target for the treatment of Alzheimer's disease. BACE1 is an aspartic protease which functions in the first step of the pathway leading to the production and deposition of amyloid-β peptide (Aβ). Its gene deletion showed only mild phenotypes. BACE1 inhibition has direct implications in the Alzheimer's disease pathology without largely affecting viability. However, inhibiting BACE1 selectively in vivo has presented many challenges to medicinal chemists. Since its identification in 2000, inhibitors covering many different structural classes have been designed and developed. These inhibitors can be largely classified as either peptidomimetic or non-peptidic inhibitors. Progress in these fields resulted in inhibitors that contain many targeted drug-like characteristics. In this review, we describe structure-based design strategies and evolution of a wide range of BACE1 inhibitors including compounds that have been shown to reduce brain Aβ, rescue the cognitive decline in transgenic AD mice and inhibitor drug candidates that are currently in clinical trials.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
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Kumar A, Roy S, Tripathi S, Sharma A. Molecular docking based virtual screening of natural compounds as potential BACE1 inhibitors: 3D QSAR pharmacophore mapping and molecular dynamics analysis. J Biomol Struct Dyn 2015; 34:239-49. [DOI: 10.1080/07391102.2015.1022603] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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