1
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Rafalskiy VV, Zyubin AY, Moiseeva EM, Kupriyanova GS, Mershiev IG, Kryukova NO, Kon II, Samusev IG, Belousova YD, Doktorova SA. Application of vibrational spectroscopy and nuclear magnetic resonance methods for drugs pharmacokinetics research. Drug Metab Pers Ther 2023; 38:3-13. [PMID: 36169571 DOI: 10.1515/dmpt-2022-0109] [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: 04/14/2022] [Accepted: 06/21/2022] [Indexed: 11/15/2022]
Abstract
OBJECTIVES The development of new methods for determining the concentration of drugs is an actual topic today. The article contains a detailed review on vibrational spectroscopy and nuclear magnetic resonance methods using for pharmacokinetic research. This study is devoted to the possibility of using vibrational spectroscopy and 1H nuclear magnetic resonance spectroscopy to determine the concentration of drugs and the use of these groups of techniques for therapeutic drug monitoring. CONTENT The study was conducted by using scientific libraries (Scopus, Web of Science Core Collection, Medline, GoogleScholar, eLIBRARY, PubMed) and reference literature. A search was conducted for the period from 2011 to 2021 in Russian and English, by combinations of words: 1H nuclear magnetic resonance (1H NMR), vibrational spectroscopy, Surface-Enhanced Raman spectroscopy, drug concentration, therapeutic drug monitoring. These methods have a number of advantages and are devoid of some of the disadvantages of classical therapeutic drug monitoring (TDM) methods - high performance liquid chromatography and mass spectrometry. This review considers the possibility of using the methods of surface-enhanced Raman scattering (SERS) and 1H NMR-spectroscopy to assess the concentration of drugs in various biological media (blood, urine), as well as to study intracellular metabolism and the metabolism of ophthalmic drugs. 1Н NMR-spectroscopy can be chosen as a TDM method, since it allows analyzing the structure and identifying metabolites of various drugs. 1Н NMR-based metabolomics can provide information on the side effects of drugs, predict response to treatment, and provide key information on the mechanisms of action of known and new drug compounds. SUMMARY AND OUTLOOK SERS and 1Н NMR-spectroscopy have great potential for further study and the possibility of introducing them into clinical practice, including for evaluating the efficacy and safety of drugs.
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Affiliation(s)
- Vladimir V Rafalskiy
- Department of Therapy of the Medical Institute of the IKBFU, Kaliningrad, Russia
| | - Andrey Yu Zyubin
- REC "Fundamental and Applied Photonics, Nanophotonics", IKBFU, Kaliningrad, Russia
| | | | | | | | - Nadezhda O Kryukova
- Department of Fundamental Medicine of the Medical Institute of the IKBFU, Kaliningrad, Russia
| | - Igor I Kon
- REC "Fundamental and Applied Photonics, Nanophotonics", Kaliningrad, Russia
| | - Ilya G Samusev
- REC "Fundamental and Applied Photonics, Nanophotonics", Kaliningrad, Russia
| | | | - Svetlana A Doktorova
- Medical Institute of the IKBFU, Kaliningrad, Russia
- Immanuel Kant Baltic Federal University Institute of Medicine - Clinical Trial Center of IKBFUA, Kaliningrad, Russia
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2
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Diethelm-Varela B. Using NMR Spectroscopy in the Fragment-Based Drug Discovery of Small-Molecule Anticancer Targeted Therapies. ChemMedChem 2020; 16:725-742. [PMID: 33236493 DOI: 10.1002/cmdc.202000756] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/21/2020] [Indexed: 12/19/2022]
Abstract
Against the challenge of providing personalized cancer care, the development of targeted therapies stands as a promising approach. The discovery of these agents can benefit from fragment-based drug discovery (FBDD) methods that help guide ligand design and provide key structural information on the targets of interest. In particular, nuclear magnetic resonance spectroscopy is a promising biophysical tool in fragment discovery due to its detection capabilities and versatility. This review provides an overview of FBDD, describes the basis of NMR-based fragment screening, summarizes some exciting technical advances reported over the past decades, and closes with a discussion of selected case studies where this technique has been used as part of drug discovery campaigns to produce lead compounds towards the design of anti-cancer targeted therapies.
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Affiliation(s)
- Benjamin Diethelm-Varela
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St., Baltimore, MD 21201, USA
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3
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Emwas AH, Szczepski K, Poulson BG, Chandra K, McKay RT, Dhahri M, Alahmari F, Jaremko L, Lachowicz JI, Jaremko M. NMR as a "Gold Standard" Method in Drug Design and Discovery. Molecules 2020; 25:E4597. [PMID: 33050240 PMCID: PMC7594251 DOI: 10.3390/molecules25204597] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 12/11/2022] Open
Abstract
Studying disease models at the molecular level is vital for drug development in order to improve treatment and prevent a wide range of human pathologies. Microbial infections are still a major challenge because pathogens rapidly and continually evolve developing drug resistance. Cancer cells also change genetically, and current therapeutic techniques may be (or may become) ineffective in many cases. The pathology of many neurological diseases remains an enigma, and the exact etiology and underlying mechanisms are still largely unknown. Viral infections spread and develop much more quickly than does the corresponding research needed to prevent and combat these infections; the present and most relevant outbreak of SARS-CoV-2, which originated in Wuhan, China, illustrates the critical and immediate need to improve drug design and development techniques. Modern day drug discovery is a time-consuming, expensive process. Each new drug takes in excess of 10 years to develop and costs on average more than a billion US dollars. This demonstrates the need of a complete redesign or novel strategies. Nuclear Magnetic Resonance (NMR) has played a critical role in drug discovery ever since its introduction several decades ago. In just three decades, NMR has become a "gold standard" platform technology in medical and pharmacology studies. In this review, we present the major applications of NMR spectroscopy in medical drug discovery and development. The basic concepts, theories, and applications of the most commonly used NMR techniques are presented. We also summarize the advantages and limitations of the primary NMR methods in drug development.
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Affiliation(s)
- Abdul-Hamid Emwas
- Core Labs, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Kacper Szczepski
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
| | - Benjamin Gabriel Poulson
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
| | - Kousik Chandra
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
| | - Ryan T. McKay
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2W2, Canada;
| | - Manel Dhahri
- Biology Department, Faculty of Science, Taibah University, Yanbu El-Bahr 46423, Saudi Arabia;
| | - Fatimah Alahmari
- Nanomedicine Department, Institute for Research and Medical, Consultations (IRMC), Imam Abdulrahman Bin Faisal University (IAU), Dammam 31441, Saudi Arabia;
| | - Lukasz Jaremko
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
| | - Joanna Izabela Lachowicz
- Department of Medical Sciences and Public Health, Università di Cagliari, Cittadella Universitaria, 09042 Monserrato, Italy
| | - Mariusz Jaremko
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (K.S.); (B.G.P.); (K.C.); (L.J.)
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4
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Li Q. Application of Fragment-Based Drug Discovery to Versatile Targets. Front Mol Biosci 2020; 7:180. [PMID: 32850968 PMCID: PMC7419598 DOI: 10.3389/fmolb.2020.00180] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/10/2020] [Indexed: 12/14/2022] Open
Abstract
Fragment-based drug discovery (FBDD) is a powerful method to develop potent small-molecule compounds starting from fragments binding weakly to targets. As FBDD exhibits several advantages over high-throughput screening campaigns, it becomes an attractive strategy in target-based drug discovery. Many potent compounds/inhibitors of diverse targets have been developed using this approach. Methods used in fragment screening and understanding fragment-binding modes are critical in FBDD. This review elucidates fragment libraries, methods utilized in fragment identification/confirmation, strategies applied in growing the identified fragments into drug-like lead compounds, and applications of FBDD to different targets. As FBDD can be readily carried out through different biophysical and computer-based methods, it will play more important roles in drug discovery.
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Affiliation(s)
- Qingxin Li
- Guangdong Provincial Engineering Laboratory of Biomass High Value Utilization, Guangdong Provincial Bioengineering Institute, Guangzhou Sugarcane Industry Research Institute, Guangdong Academy of Sciences, Guangzhou, China
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5
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Xia D, Liu B, Xu X, Ding Y, Zheng Q. Drug target discovery by magnetic nanoparticles coupled mass spectrometry. J Pharm Anal 2020; 11:122-127. [PMID: 33717618 PMCID: PMC7930636 DOI: 10.1016/j.jpha.2020.02.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 12/24/2019] [Accepted: 02/04/2020] [Indexed: 11/25/2022] Open
Abstract
Drug target discovery is the basis of drug screening. It elucidates the cause of disease and the mechanism of drug action, which is the essential of drug innovation. Target discovery performed in biological systems is complicated as proteins are in low abundance and endogenous compounds may interfere with drug binding. Therefore, methods to track drug-target interactions in biological matrices are urgently required. In this work, a Fe3O4 nanoparticle-based approach was developed for drug-target screening in biofluids. A known ligand-protein complex was selected as a principle-to-proof example to validate the feasibility. After incubation in cell lysates, ligand-modified Fe3O4 nanoparticles bound to the target protein and formed complexes that were separated from the lysates by a magnet for further analysis. The large surface-to-volume ratio of the nanoparticles provides more active sites for the modification of chemical drugs. It enhances the opportunity for ligand-protein interactions, which is beneficial for capturing target proteins, especially for those with low abundance. Additionally, a one-step magnetic separation simplifies the pre-processing of ligand-protein complexes, so it effectively reduces the endogenous interference. Therefore, the present nanoparticle-based approach has the potential to be used for drug target screening in biological systems. Fe3O4 NPs were made hydrophilic to adequately disperse in the cell lysate and fully contact with target proteins. The magnetic property of the NPs allowed one-step isolation while maintaining ligand-protein non-covalent bindings. It enabled the capture of low abundant targets in biological matrices while eliminated the endogenous interference.
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Affiliation(s)
- Dandan Xia
- Department of Pharmaceutical Analysis, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Baoling Liu
- Department of Pharmaceutical Analysis, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Xiaowei Xu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China.,Key Laboratory of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, 210009, China
| | - Ya Ding
- Department of Pharmaceutical Analysis, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Qiuling Zheng
- Department of Pharmaceutical Analysis, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
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6
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Xu X, Lü P, Wang J, Xu F, Liang L, Wang C, Niu Y, Xu P. Design, synthesis, and biological evaluation of 4‐aminopyrimidine or 4,6‐diaminopyrimidine derivatives as beta amyloid cleaving enzyme‐1 inhibitors. Chem Biol Drug Des 2019; 93:926-933. [DOI: 10.1111/cbdd.13489] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 12/14/2018] [Accepted: 01/09/2019] [Indexed: 02/02/2023]
Affiliation(s)
- Xiufeng Xu
- Department of Medicinal ChemistrySchool of Pharmaceutical SciencesPeking University Health Science Center Beijing China
| | - Peng Lü
- Department of Medicinal ChemistrySchool of Pharmaceutical SciencesPeking University Health Science Center Beijing China
| | - Junjie Wang
- Department of Medicinal ChemistrySchool of Pharmaceutical SciencesPeking University Health Science Center Beijing China
| | - Fengrong Xu
- Department of Medicinal ChemistrySchool of Pharmaceutical SciencesPeking University Health Science Center Beijing China
| | - Lei Liang
- Department of Medicinal ChemistrySchool of Pharmaceutical SciencesPeking University Health Science Center Beijing China
| | - Chao Wang
- Department of Medicinal ChemistrySchool of Pharmaceutical SciencesPeking University Health Science Center Beijing China
| | - Yan Niu
- Department of Medicinal ChemistrySchool of Pharmaceutical SciencesPeking University Health Science Center Beijing China
| | - Ping Xu
- Department of Medicinal ChemistrySchool of Pharmaceutical SciencesPeking University Health Science Center Beijing China
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7
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Yamaotsu N, Hirono S. In silico fragment-mapping method: a new tool for fragment-based/structure-based drug discovery. J Comput Aided Mol Des 2018; 32:1229-1245. [PMID: 30196523 DOI: 10.1007/s10822-018-0160-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 09/04/2018] [Indexed: 01/09/2023]
Abstract
Here, we propose an in silico fragment-mapping method as a potential tool for fragment-based/structure-based drug discovery (FBDD/SBDD). For this method, we created a database named Canonical Subsite-Fragment DataBase (CSFDB) and developed a knowledge-based fragment-mapping program, Fsubsite. CSFDB consists of various pairs of subsite-fragments derived from X-ray crystal structures of known protein-ligand complexes. Using three-dimensional similarity-matching between subsites on one protein and another, Fsubsite compares the surface of a target protein with all subsites in CSFDB. When a local topography similar to the subsite is found on the surface, Fsubsite places a fragment combined with the subsite in CSFDB on the target protein. For validation purposes, we applied the method to the apo-structure of cyclin-dependent kinase 2 (CDK2) and identified four compounds containing three mapped fragments that existed in the list of known inhibitors of CDK2. Next, the utility of our fragment-mapping method for fragment-growing was examined on the complex structure of tRNA-guanine transglycosylase with a small ligand. Fsubsite mapped appropriate fragments on the same position as the binding ligand or in the vicinity of the ligand. Finally, a 3D-pharmacophore model was constructed from the fragments mapped on the apo-structure of heat shock protein 90-α (HSP90α). Then, 3D pharmacophore-based virtual screening was carried out using a commercially available compound database. The resultant hit compounds were very similar to a known ligand of HSP90α. As a result of these findings, this in silico fragment-mapping method seems to be a useful tool for computational FBDD and SBDD.
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Affiliation(s)
- Noriyuki Yamaotsu
- Department of Pharmaceutical Sciences, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan.
| | - Shuichi Hirono
- Department of Pharmaceutical Sciences, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan.
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8
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Wang L, Yan J, Yan J, Xu H, Zhang D, Wang X, Sheng J. Expression and purification of the human epidermal growth factor receptor extracellular domain. Protein Expr Purif 2018; 144:33-38. [DOI: 10.1016/j.pep.2017.11.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 11/17/2017] [Accepted: 11/29/2017] [Indexed: 01/22/2023]
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9
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Baggio C, Cerofolini L, Fragai M, Luchinat C, Pellecchia M. HTS by NMR for the Identification of Potent and Selective Inhibitors of Metalloenzymes. ACS Med Chem Lett 2018; 9:137-142. [PMID: 29456802 DOI: 10.1021/acsmedchemlett.7b00483] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 01/17/2018] [Indexed: 11/28/2022] Open
Abstract
We have recently proposed a novel drug discovery approach based on biophysical screening of focused positional scanning libraries in which each element of the library contained a common binding moiety for the given target or class of targets. In this Letter, we report on the implementation of this approach to target metal containing proteins. In our implementation, we first derived a focused positional scanning combinatorial library of peptide mimetics (of approximately 100,000 compounds) in which each element of the library contained the metal-chelating moiety hydroxamic acid at the C-terminal. Screening of this library by nuclear magnetic resonance spectroscopy in solution allowed the identification of a novel and selective compound series targeting MMP-12. The data supported that our general approach, perhaps applied using other metal chelating agents or other initial binding fragments, may result very effective in deriving novel and selective agents against metalloenzyme.
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Affiliation(s)
- Carlo Baggio
- Division of Biomedical
Sciences, School of Medicine, University of California—Riverside, Riverside, California 92521, United States
| | - Linda Cerofolini
- Magnetic
Resonance Center (CERM), University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Via L. Sacconi
6, 50019 Sesto Fiorentino, Italy
| | - Marco Fragai
- Magnetic
Resonance Center (CERM), University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Via L. Sacconi
6, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic
Resonance Center (CERM), University of Florence and Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Via L. Sacconi
6, 50019 Sesto Fiorentino, Italy
| | - Maurizio Pellecchia
- Division of Biomedical
Sciences, School of Medicine, University of California—Riverside, Riverside, California 92521, United States
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10
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Manoharan P, Ghoshal N. Fragment-based virtual screening approach and molecular dynamics simulation studies for identification of BACE1 inhibitor leads. J Biomol Struct Dyn 2017; 36:1878-1892. [PMID: 28617091 DOI: 10.1080/07391102.2017.1337590] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Traditional structure-based virtual screening method to identify drug-like small molecules for BACE1 is so far unsuccessful. Location of BACE1, poor Blood Brain Barrier permeability and P-glycoprotein (Pgp) susceptibility of the inhibitors make it even more difficult. Fragment-based drug design method is suitable for efficient optimization of initial hit molecules for target like BACE1. We have developed a fragment-based virtual screening approach to identify/optimize the fragment molecules as a starting point. This method combines the shape, electrostatic, and pharmacophoric features of known fragment molecules, bound to protein conjugate crystal structure, and aims to identify both chemically and energetically feasible small fragment ligands that bind to BACE1 active site. The two top-ranked fragment hits were subjected for a 53 ns MD simulation. Principle component analysis and free energy landscape analysis reveal that the new ligands show the characteristic features of established BACE1 inhibitors. The potent method employed in this study may serve for the development of potential lead molecules for BACE1-directed Alzheimer's disease therapeutics.
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Affiliation(s)
- Prabu Manoharan
- a Structural Biology and Bioinformatics Division , CSIR-Indian Institute of Chemical Biology , Kolkata 700032 , India.,b Centre of Excellence in Bioinformatics , School of Biotechnology, Madurai Kamaraj University , Madurai 625021 , India
| | - Nanda Ghoshal
- a Structural Biology and Bioinformatics Division , CSIR-Indian Institute of Chemical Biology , Kolkata 700032 , India
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11
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Hernández-Rodríguez M, Correa-Basurto J, Gutiérrez A, Vitorica J, Rosales-Hernández MC. Asp32 and Asp228 determine the selective inhibition of BACE1 as shown by docking and molecular dynamics simulations. Eur J Med Chem 2016; 124:1142-1154. [DOI: 10.1016/j.ejmech.2016.08.028] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 08/10/2016] [Accepted: 08/13/2016] [Indexed: 11/28/2022]
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12
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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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13
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Jordan JB, Whittington DA, Bartberger MD, Sickmier EA, Chen K, Cheng Y, Judd T. Fragment-Linking Approach Using 19F NMR Spectroscopy To Obtain Highly Potent and Selective Inhibitors of β-Secretase. J Med Chem 2016; 59:3732-49. [DOI: 10.1021/acs.jmedchem.5b01917] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- John B. Jordan
- Therapeutic Discovery, Amgen, Inc. One Amgen Center Drive, Thousand
Oaks, California 91320, United States
| | - Douglas A. Whittington
- Therapeutic Discovery, Amgen, Inc. One Amgen Center Drive, Thousand
Oaks, California 91320, United States
| | - Michael D. Bartberger
- Therapeutic Discovery, Amgen, Inc. One Amgen Center Drive, Thousand
Oaks, California 91320, United States
| | - E. Allen Sickmier
- Therapeutic Discovery, Amgen, Inc. One Amgen Center Drive, Thousand
Oaks, California 91320, United States
| | - Kui Chen
- Therapeutic Discovery, Amgen, Inc. One Amgen Center Drive, Thousand
Oaks, California 91320, United States
| | - Yuan Cheng
- Therapeutic Discovery, Amgen, Inc. One Amgen Center Drive, Thousand
Oaks, California 91320, United States
| | - Ted Judd
- Therapeutic Discovery, Amgen, Inc. One Amgen Center Drive, Thousand
Oaks, California 91320, United States
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14
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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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15
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Bottini A, Wu B, Barile E, De SK, Leone M, Pellecchia M. High-Throughput Screening (HTS) by NMR Guided Identification of Novel Agents Targeting the Protein Docking Domain of YopH. ChemMedChem 2015; 11:919-27. [PMID: 26592695 DOI: 10.1002/cmdc.201500441] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Indexed: 11/08/2022]
Abstract
Recently we described a novel approach, named high-throughput screening (HTS) by NMR that allows the identification, from large combinatorial peptide libraries, of potent and selective peptide mimetics against a given target. Here, we deployed the "HTS by NMR" approach for the design of novel peptoid sequences targeting the N-terminal domain of Yersinia outer protein H (YopH-NT), a bacterial toxin essential for the virulence of Yersinia pestis. We aimed at disrupting the protein-protein interactions between YopH-NT and its cellular substrates, with the goal of inhibiting indirectly YopH enzymatic function. These studies resulted in a novel agent of sequence Ac-F-pY-cPG-d-P-NH2 (pY=phosphotyrosine; cPG=cyclopentyl glycine) with a Kd value against YopH-NT of 310 nm. We demonstrated that such a pharmacological inhibitor of YopH-NT results in the inhibition of the dephosphorylation by full-length YopH of a cellular substrate. Hence, potentially this agent represents a valuable stepping stone for the development of novel therapeutics against Yersinia infections. The data reported further demonstrate the utility of the HTS by NMR approach in deriving novel peptide mimetics targeting protein-protein interactions.
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Affiliation(s)
- Angel Bottini
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA.,Sanford Burnham Prebys Graduate School of Biomedical Sciences, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Bainan Wu
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Elisa Barile
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA.,Division of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Surya K De
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA.,Division of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Marilisa Leone
- Institute of Biostructures & Bioimaging, National Research Council (IBB-CNR), Via De Amicis 95, Naples, 80145, Italy
| | - Maurizio Pellecchia
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA. .,Division of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, CA, 92521, USA.
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16
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Per-Residue Energy Footprints-Based Pharmacophore Modeling as an Enhanced In Silico Approach in Drug Discovery: A Case Study on the Identification of Novel β-Secretase1 (BACE1) Inhibitors as Anti-Alzheimer Agents. Cell Mol Bioeng 2015. [DOI: 10.1007/s12195-015-0421-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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17
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Swedish mutant APP-based BACE1 binding site peptide reduces APP β-cleavage and cerebral Aβ levels in Alzheimer's mice. Sci Rep 2015; 5:11322. [PMID: 26091071 PMCID: PMC4473678 DOI: 10.1038/srep11322] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 05/14/2015] [Indexed: 11/08/2022] Open
Abstract
BACE1 initiates amyloid-β (Aβ) generation and the resultant cerebral amyloidosis, as a characteristic of Alzheimer's disease (AD). Thus, inhibition of BACE1 has been the focus of a large body of research. The most recent clinical trials highlight the difficulty involved in this type of anti-AD therapy as evidenced by side effects likely due to the ubiquitous nature of BACE1, which cleaves multiple substrates. The human Swedish mutant form of amyloid protein precursor (APPswe) has been shown to possess a higher affinity for BACE1 compared to wild-type APP (APPwt). We pursued a new approach wherein harnessing this greater affinity to modulate BACE1 APP processing activity. We found that one peptide derived from APPswe, containing the β-cleavage site, strongly inhibits BACE1 activity and thereby reduces Aβ production. This peptide, termed APPswe BACE1 binding site peptide (APPsweBBP), was further conjugated to the fusion domain of the HIV-1 Tat protein (TAT) at the C-terminus to facilitate its biomembrane-penetrating activity. APPwt and APPswe over-expressing CHO cells treated with this TAT-conjugated peptide resulted in a marked reduction of Aβ and a significant increase of soluble APPα. Intraperitoneal administration of this peptide to 5XFAD mice markedly reduced β-amyloid deposits as well as improved hippocampal-dependent learning and memory.
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18
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Abstract
Fragment-based drug design (FBDD) comprises both fragment-based screening (FBS) to find hits and elaboration of these hits to lead compounds. Typical fragment hits have lower molecular weight (<300-350 Da) and lower initial potency but higher ligand efficiency when compared to those from high-throughput screening. NMR spectroscopy has been widely used for FBDD since it identifies and localizes the binding site of weakly interacting hits on the target protein. Here we describe ligand-based NMR methods for hit identification from fragment libraries and for functional cross-validation of primary hits.
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19
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Barile E, Pellecchia M. NMR-based approaches for the identification and optimization of inhibitors of protein-protein interactions. Chem Rev 2014; 114:4749-63. [PMID: 24712885 PMCID: PMC4027952 DOI: 10.1021/cr500043b] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Indexed: 02/07/2023]
Affiliation(s)
- Elisa Barile
- Sanford-Burnham Medical
Research Institute, 10901
North Torrey Pines Road, La Jolla, California 92037, United States
| | - Maurizio Pellecchia
- Sanford-Burnham Medical
Research Institute, 10901
North Torrey Pines Road, La Jolla, California 92037, United States
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20
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Halogen-enriched fragment libraries as chemical probes for harnessing halogen bonding in fragment-based lead discovery. Future Med Chem 2014; 6:617-39. [DOI: 10.4155/fmc.14.20] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Halogen bonding has recently experienced a renaissance, gaining increased recognition as a useful molecular interaction in the life sciences. Halogen bonds are favorable, fairly directional interactions between an electropositive region on the halogen (the σ-hole) and a number of different nucleophilic interaction partners. Some aspects of halogen bonding are not yet understood well enough to take full advantage of its potential in drug discovery. We describe and present the concept of halogen-enriched fragment libraries. These libraries consist of unique chemical probes, facilitating the identification of favorable halogen bonds by sharing the advantages of classical fragment-based screening. Besides providing insights into the nature and applicability of halogen bonding, halogen-enriched fragment libraries provide smart starting points for hit-to-lead evolution.
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21
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Evin G, Barakat A. Critical analysis of the use of β-site amyloid precursor protein-cleaving enzyme 1 inhibitors in the treatment of Alzheimer's disease. Degener Neurol Neuromuscul Dis 2014; 4:1-19. [PMID: 32669897 PMCID: PMC7337240 DOI: 10.2147/dnnd.s41056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 03/06/2014] [Indexed: 01/18/2023] Open
Abstract
Alzheimer’s disease (AD) is the major cause of dementia in the elderly and an unmet clinical challenge. A variety of therapies that are currently under development are directed to the amyloid cascade. Indeed, the accumulation and toxicity of amyloid-β (Aβ) is believed to play a central role in the etiology of the disease, and thus rational interventions are aimed at reducing the levels of Aβ in the brain. Targeting β-site amyloid precursor protein-cleaving enzyme (BACE)-1 represents an attractive strategy, as this enzyme catalyzes the initial and rate-limiting step in Aβ production. Observation of increased levels of BACE1 and enzymatic activity in the brain, cerebrospinal fluid, and platelets of patients with AD and mild cognitive impairment supports the potential benefits of BACE1 inhibition. Numerous potent inhibitors have been generated, and many of these have been proved to lower Aβ levels in the brain of animal models. Over 10 years of intensive research on BACE1 inhibitors has now culminated in advancing half a dozen of these drugs into human trials, yet translating the in vitro and cellular efficacy of BACE1 inhibitors into preclinical and clinical trials represents a challenge. This review addresses the promises and also the potential problems associated with BACE1 inhibitors for AD therapy, as the complex biological function of BACE1 in the brain is becoming unraveled.
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Affiliation(s)
- Genevieve Evin
- Oxidation Biology Laboratory, Mental Health Research Institute, Florey Institute of Neuroscience and Mental Health, University of Melbourne.,Department of Pathology, University of Melbourne, Parkville, VIC, Australia
| | - Adel Barakat
- Department of Pathology, University of Melbourne, Parkville, VIC, Australia
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22
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Dessolin J. N-(3-(2-amino-6,6-difluoro-4,4a,5,6,7,7a-hexahydro-cyclopenta[e][1,3]oxazin-4-yl)-phenyl)-amides as BACE1 inhibitors: a patent evaluation of WO2013041499. Expert Opin Ther Pat 2013; 24:239-42. [PMID: 24219148 DOI: 10.1517/13543776.2014.859246] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
A new series of oxazin amides have been synthesized from isoxazoles using a reaction to increase the heterocyclic ring size and were evaluated as BACE1 inhibitors. The innovative compounds were able to diminish amyloid-β peptide concentration in cell and proved to be selective toward peptidases from the same family. Further studies on the toxicity of this series showed that these new molecules were not recognized by P-glycoprotein and that they were unsusceptible to rapid metabolization by cytochrome P450 or glutathione conjugation. These results indicate that such compounds could be useful in developing drugs to fight Alzheimer's disease and that this novel oxazin scaffold should be considered as a starting point to tackle this pathology.
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Affiliation(s)
- Jean Dessolin
- Institut Européen de Chimie et Biologie (IECB), CNRS UMR 5248 Chimie et Biologie des Membranes et des Nano-objets (CBMN) CBMN-IECB , 2 rue Robert Escarpit, 33607 Pessac Cedex , France
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23
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Nilar SH, Ma NL, Keller TH. The importance of molecular complexity in the design of screening libraries. J Comput Aided Mol Des 2013; 27:783-92. [DOI: 10.1007/s10822-013-9683-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Accepted: 10/07/2013] [Indexed: 01/20/2023]
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24
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Honarparvar B, Govender T, Maguire GEM, Soliman MES, Kruger HG. Integrated Approach to Structure-Based Enzymatic Drug Design: Molecular Modeling, Spectroscopy, and Experimental Bioactivity. Chem Rev 2013; 114:493-537. [DOI: 10.1021/cr300314q] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Bahareh Honarparvar
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Thavendran Govender
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Glenn E. M. Maguire
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Mahmoud E. S. Soliman
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Hendrik G. Kruger
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
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25
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Li X, Hong L, Coughlan K, Wang L, Cao L, Tang J. Structure-activity relationship of memapsin 2: implications on physiological functions and Alzheimer's disease. Acta Biochim Biophys Sin (Shanghai) 2013; 45:613-21. [PMID: 23676825 DOI: 10.1093/abbs/gmt050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Memapsin 2 (BACE1, β-secretase), a membrane aspartic protease, functions in the cleavage of the type I transmembrane protein, β-amyloid precursor protein (APP), leading to the production of amyloid β (Aβ) in the brain. Since Aβ is closely associated with the pathogenesis of Alzheimer's disease, understanding the biological function, particularly the catalytic activities of memapsin 2, would assist in a better understanding of the disease and the development of its inhibitors. The transmembrane and cytosolic domains of memapsin 2 function in cellular transport and localization, which are important regulatory mechanisms for its activity. The catalytic ectodomain contains a long substrate cleft that is responsible for substrate recognition, specificity, and peptide bond hydrolysis. The substrate cleft accommodates 11 residues of the substrate in separate binding subsites. Besides APP, a number of membrane proteins have been reported to be substrates of memapsin 2. The elucidation for the specificity of these subsites and the amino acid sequences surrounding the memapsin 2 cleavage site in these proteins has led to the establishment of a predictive model that can quantitatively estimate the efficiency of cleavage for any potential substrates. Such tools may be employed for future studies of memapsin 2 about its biological function. Herein, we review the current knowledge on the structure-function relationship of memapsin 2 and its relationship in the biological function.
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Affiliation(s)
- Xiaoman Li
- Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110001, China
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26
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Yuan J, Venkatraman S, Zheng Y, McKeever BM, Dillard LW, Singh SB. Structure-based design of β-site APP cleaving enzyme 1 (BACE1) inhibitors for the treatment of Alzheimer's disease. J Med Chem 2013; 56:4156-80. [PMID: 23509904 DOI: 10.1021/jm301659n] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The amyloid hypothesis asserts that excess production or reduced clearance of the amyloid-β (Aβ) peptides in the brain initiates a sequence of events that ultimately lead to Alzheimer's disease and dementia. The Aβ hypothesis has identified BACE1 as a therapeutic target to treat Alzheimer's and led to medicinal chemistry efforts to design its inhibitors both in the pharmaceutical industry and in academia. This review summarizes two distinct categories of inhibitors designed based on conformational states of "closed" and "open" forms of the enzyme. In each category the inhibitors are classified based on the core catalytic interaction group or the aspartyl binding motif (ABM). This review covers the description of inhibitors in each ABM class with X-ray crystal structures of key compounds, their binding modes, related structure-activity data highlighting potency advances, and additional properties such as selectivity profile, P-gp efflux, pharmacokinetic, and pharmacodynamic data.
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Affiliation(s)
- Jing Yuan
- Vitae Pharmaceuticals, 502 W. Office Center Drive, Fort Washington, Pennsylvania 19034, USA
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27
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Ren Z, Tam D, Xu YZ, Wone D, Yuan S, Sham HL, Cheung H, Regnstrom K, Chen X, Rudolph D, Jobling MF, Artis DR, Bova MP. Development of a Novel β-Secretase Binding Assay Using the AlphaScreen Platform. ACTA ACUST UNITED AC 2013; 18:695-704. [DOI: 10.1177/1087057113482138] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Alzheimer’s disease (AD) is a devastating neurodegenerative disease affecting millions of people. β-secretase-1 (BACE1), an enzyme involved in the processing of the amyloid precursor protein (APP) to form Aβ is a validated target for AD. Herein, the authors develop and validate a novel binding assay for BACE1 using the AlphaScreen platform that is amenable for high-throughput screening (HTS). Small-molecule BACE1 inhibitors of the hydroxyethylamine, hydantoin, and sulfamide classes were functionalized by biotin PEG linkers of varying lengths forming probes that were bound to streptavidin donor beads. BACE1 was coupled to nickel-chelate acceptor beads. Upon mixing, probes designed from all three classes registered high signal-to-background values in the AlphaScreen binding assay, where the interaction between probe and BACE1 was completely blocked by free parent compound. A probe from the hydantoin class was chosen for further optimization, where the final assay conditions of 50 nM BACE and 250 nM probe were used and Z′ values >0.75 were commonly observed. IC50 values determined by the AlphaScreen assay format exhibited ~10-fold greater sensitivity when compared with a fluorescence polarization–based activity assay. The assay was miniaturized to a 1536-well format for HTS, in which 525 000 compounds were screened.
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Affiliation(s)
- Zhao Ren
- Elan Pharmaceuticals, South San Francisco, CA, USA
| | - Danny Tam
- Elan Pharmaceuticals, South San Francisco, CA, USA
| | - Ying-Zi Xu
- Elan Pharmaceuticals, South San Francisco, CA, USA
| | - David Wone
- Elan Pharmaceuticals, South San Francisco, CA, USA
| | | | - Hing L. Sham
- Elan Pharmaceuticals, South San Francisco, CA, USA
| | - Harry Cheung
- Elan Pharmaceuticals, South San Francisco, CA, USA
| | | | - Xiaohua Chen
- Elan Pharmaceuticals, South San Francisco, CA, USA
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28
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Friberg A, Vigil D, Zhao B, Daniels RN, Burke JP, Garcia-Barrantes PM, Camper D, Chauder BA, Lee T, Olejniczak ET, Fesik SW. Discovery of potent myeloid cell leukemia 1 (Mcl-1) inhibitors using fragment-based methods and structure-based design. J Med Chem 2013; 56:15-30. [PMID: 23244564 PMCID: PMC3646517 DOI: 10.1021/jm301448p] [Citation(s) in RCA: 219] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Myeloid cell leukemia 1 (Mcl-1), a member of the Bcl-2 family of proteins, is overexpressed and amplified in various cancers and promotes the aberrant survival of tumor cells that otherwise would undergo apoptosis. Here we describe the discovery of potent and selective Mcl-1 inhibitors using fragment-based methods and structure-based design. NMR-based screening of a large fragment library identified two chemically distinct hit series that bind to different sites on Mcl-1. Members of the two fragment classes were merged together to produce lead compounds that bind to Mcl-1 with a dissociation constant of <100 nM with selectivity for Mcl-1 over Bcl-xL and Bcl-2. Structures of merged compounds when complexed to Mcl-1 were obtained by X-ray crystallography and provide detailed information about the molecular recognition of small-molecule ligands binding Mcl-1. The compounds represent starting points for the discovery of clinically useful Mcl-1 inhibitors for the treatment of a wide variety of cancers.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Stephen W. Fesik
- Corresponding author; Phone, +1 (615) 322 6303; Fax, +1 (615) 875 3236
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29
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Ismail MAH, Abouzid KAM, Mohamed NS, Dokla EME. Ligand design, synthesis and biological anti-HCV evaluations for genotypes 1b and 4a of certain 4-(3- & 4-[3-(3,5-dibromo-4-hydroxyphenyl)-propylamino]phenyl) butyric acids and 3-(3,5-dibromo-4-hydroxyphenyl)-propylamino-acetamidobenzoic acid esters. J Enzyme Inhib Med Chem 2013; 28:1274-90. [PMID: 23294107 DOI: 10.3109/14756366.2012.733384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
4-(4-[N-1-carboxy-3-(3,5-dibromo-4-hydroxyphenyl)-3-oxo-propylamino]phenyl)-4-oxo-butyric acid (V), 4-(3- & 4-[N-1-carboxy-3-(3,5-dibromo-4-hydroxyphenyl)-3-oxo-propylaminophenyl]-2-aryl-4-oxo-butyric acids (Xa-e) and 4-(2-alkyl-2-[N-3-(3,5-dibromo-4-hydroxyphenyl)-1-carboxy-3-oxo-propylamino]acetamido) benzoate esters (XVa-e) were designed, synthesized and biologically evaluated as anti-HCV for genotypes 1b and 4a. The design was based on their docking scores with HCV NS3/4A protease-binding site of the genotype 1b (1W3C), which is conserved in the genotype 4a structure. The docking scores predicted that most of these molecules have higher affinity to the HCV NS3/4A enzyme more than Indoline lead. These compounds were synthesized and evaluated for their cytopathic inhibitory activity against RAW HCV cell cultures of genotype 4a and also examined against Huh 5-2 HCV cell culture of genotype 1b, utilizing Luciferase and MTS assays. Compounds Xa and Xb have 95 and 80% of the activity of Ribavirin against genotype 4a and compounds XVa, XVb and XVd exerted high percentage inhibitory activity against genotype 1b equal 87.7, 84.3 and 82.8%, respectively, with low EC50 doses.
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Affiliation(s)
- Mohamed Abdel Hamid Ismail
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University , 11655 El khalifa El Mamoon Street, Abbassia, Cairo , Egypt
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30
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Abstract
Fragment-Based Drug Discovery (FBDD) is here to stay. Validated as a technology with the delivery of Zelboraf (Vemurafenib) for the treatment of mutant B-RafV600E melanoma, it has become embedded within the pharmaceutical and biotechnology industries. FBDD has delivered clinical development candidates for a broad range of targets including some of the most challenging cases such as β-secretase (BACE1) and protein–protein interactions. But the best is surely still to come.
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31
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Chen D, Errey JC, Heitman LH, Marshall FH, IJzerman AP, Siegal G. Fragment screening of GPCRs using biophysical methods: identification of ligands of the adenosine A(2A) receptor with novel biological activity. ACS Chem Biol 2012; 7:2064-73. [PMID: 23013674 DOI: 10.1021/cb300436c] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Fragment-based drug discovery (FBDD) has proven a powerful method to develop novel drugs with excellent oral bioavailability against challenging pharmaceutical targets such as protein-protein interaction targets. Very recently the underlying biophysical techniques have begun to be successfully applied to membrane proteins. Here we show that novel, ligand efficient small molecules with a variety of biological activities can be found by screening a small fragment library using thermostabilized (StaR) G protein-coupled receptors (GPCRs) and target immobilized NMR screening (TINS). Detergent-solubilized StaR adenosine A(2A) receptor was immobilized with retention of functionality, and a screen of 531 fragments was performed. Hits from the screen were thoroughly characterized for biochemical activity using the wild-type receptor. Both orthosteric and allosteric modulatory activity has been demonstrated in biochemical validation assays. Allosteric activity was confirmed in cell-based functional assays. The validated fragment hits make excellent starting points for a subsequent hit-to-lead elaboration program.
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Affiliation(s)
- Dan Chen
- ZoBio BV, Leiden 2300RA, The Netherlands
| | - James C. Errey
- Heptares Therapeutics Limited, BioPark, Broadwater Road, Welwyn Garden City,
Hertfordshire AL7 3AX, U.K
| | | | - Fiona H. Marshall
- Heptares Therapeutics Limited, BioPark, Broadwater Road, Welwyn Garden City,
Hertfordshire AL7 3AX, U.K
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32
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Abstract
Fragment-based drug discovery (FBDD) concerns the screening of low-molecular weight compounds against macromolecular targets of clinical relevance. These compounds act as starting points for the development of drugs. FBDD has evolved and grown in popularity over the past 15 years. In this paper, the rationale and technology behind the use of X-ray crystallography in fragment based screening (FBS) will be described, including fragment library design and use of synchrotron radiation and robotics for high-throughput X-ray data collection. Some recent uses of crystallography in FBS will be described in detail, including interrogation of the drug targets β-secretase, phenylethanolamine N-methyltransferase, phosphodiesterase 4A and Hsp90. These examples provide illustrations of projects where crystallography is straightforward or difficult, and where other screening methods can help overcome the limitations of crystallography necessitated by diffraction quality.
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Affiliation(s)
- Zorik Chilingaryan
- School of Chemistry, University of Wollongong, Northfields Ave, Wollongong 2522, NSW, Australia.
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33
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Saric A, Brügge LZ, Müller-Pompalla D, Rysiok T, Ousson S, Permanne B, Quattropani A, Busch M, Beher D, Hussain I. Development and characterization of a novel membrane assay for full-length BACE-1 at pH 6.0. ACTA ACUST UNITED AC 2012; 18:277-85. [PMID: 23023105 DOI: 10.1177/1087057112462237] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
β-Site amyloid precursor protein cleaving enzyme-1 (BACE-1) is a transmembrane aspartic protease that mediates the initial cleavage of the amyloid precursor protein (APP), leading to the generation of amyloid-β (Aβ) peptides that are thought to be causative of Alzheimer's disease (AD). Consequently, inhibition of BACE-1 is an attractive therapeutic approach for the treatment of AD. In general, in vitro biochemical assays to monitor BACE-1 activity have used the extracellular domain of the protein that contains the catalytic active site. This form of BACE-1 is catalytically active at acidic pH and cleaves APP-based peptide substrates at the β-site. However, this form of BACE-1 does not mimic the natural physiology of BACE-1 and shows minimal activity at pH 6.0, which is more representative of the pH within the intracellular compartments where BACE-1 resides. Moreover, high-throughput screens with recombinant BACE-1 at pH 4.5 have failed to identify tractable leads for drug discovery, and hence, BACE-1 inhibitor development has adopted a rational drug design approach. Here we describe the development and validation of a novel membrane assay comprising full-length BACE-1 with measurable activity at pH 6.0, which could be used for the identification of novel inhibitors of BACE-1.
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Affiliation(s)
- Arman Saric
- Global Research & Early Development, Merck Serono S.A., Geneva, Switzerland
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34
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Moumné R, Catala M, Larue V, Micouin L, Tisné C. Fragment-based design of small RNA binders: Promising developments and contribution of NMR. Biochimie 2012; 94:1607-19. [DOI: 10.1016/j.biochi.2012.02.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 02/01/2012] [Indexed: 02/06/2023]
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35
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Targeting Protein–Protein Interactions and Fragment-Based Drug Discovery. Top Curr Chem (Cham) 2011; 317:145-79. [DOI: 10.1007/128_2011_265] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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36
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Abstract
Fragment-based drug discovery (FBDD) has emerged in the past decade as a powerful tool for discovering drug leads. The approach first identifies starting points: very small molecules (fragments) that are about half the size of typical drugs. These fragments are then expanded or linked together to generate drug leads. Although the origins of the technique date back some 30 years, it was only in the mid-1990s that experimental techniques became sufficiently sensitive and rapid for the concept to be become practical. Since that time, the field has exploded: FBDD has played a role in discovery of at least 18 drugs that have entered the clinic, and practitioners of FBDD can be found throughout the world in both academia and industry. Literally dozens of reviews have been published on various aspects of FBDD or on the field as a whole, as have three books (Jahnke and Erlanson, Fragment-based approaches in drug discovery, 2006; Zartler and Shapiro, Fragment-based drug discovery: a practical approach, 2008; Kuo, Fragment based drug design: tools, practical approaches, and examples, 2011). However, this chapter will assume that the reader is approaching the field with little prior knowledge. It will introduce some of the key concepts, set the stage for the chapters to follow, and demonstrate how X-ray crystallography plays a central role in fragment identification and advancement.
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