1
|
Lin H, Wang L, Jiang X, Wang J. Glutathione dynamics in subcellular compartments and implications for drug development. Curr Opin Chem Biol 2024; 81:102505. [PMID: 39053236 DOI: 10.1016/j.cbpa.2024.102505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/30/2024] [Accepted: 07/08/2024] [Indexed: 07/27/2024]
Abstract
Glutathione (GSH) is a pivotal tripeptide antioxidant essential for maintaining cellular redox homeostasis and regulating diverse cellular processes. Subcellular compartmentalization of GSH underscores its multifaceted roles across various organelles including the cytosol, mitochondria, endoplasmic reticulum, and nucleus, each exhibiting distinct regulatory mechanisms. Perturbations in GSH dynamics contribute to pathophysiological conditions, emphasizing the clinical significance of understanding its intricate regulation. This review consolidates current knowledge on subcellular GSH dynamics, highlighting its implications in drug development, particularly in covalent drug design and antitumor strategies targeting intracellular GSH levels. Challenges and future directions in deciphering subcellular GSH dynamics are discussed, advocating for innovative methodologies to advance our comprehension and facilitate the development of precise therapeutic interventions based on GSH modulation.
Collapse
Affiliation(s)
- Hanfeng Lin
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA; Center for NextGen Therapeutics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lingfei Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xiqian Jiang
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Jin Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA; Center for NextGen Therapeutics, Baylor College of Medicine, Houston, TX 77030, USA.
| |
Collapse
|
2
|
Ngo HX, Wen YW, Pisupati S, Huang W, Mandlekar S. A Comparative Clinical Pharmacology Analysis of FDA-Approved Targeted Covalent Inhibitors vs. Reversible Inhibitors in Oncology. Clin Pharmacol Ther 2024. [PMID: 39072721 DOI: 10.1002/cpt.3390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 06/28/2024] [Indexed: 07/30/2024]
Abstract
Targeted covalent inhibitors (TCIs) are an emerging class of anticancer therapeutics. TCIs are designed to selectively engage their targeted proteins via covalent warheads. From the drug development standpoint, the covalent inhibition mechanism is anticipated to elicit the following theoretical benefits: (i) an extended duration of therapeutic action that is determined by the target protein turnover rate and not necessarily by drug half-life, (ii) a lower therapeutic dose owing to greater pharmacological potency, (iii) lower risk of off-target binding and associated adverse events, and (iv) reduced drug-drug interaction (DDI) liability due to high selectivity and low dose. Elucidating the clinical relevance of these expected benefits requires an integrated assessment of pharmacokinetics (PK), efficacy, safety, and DDI data. In this review, we compared the clinical pharmacology attributes of FDA-approved oncology TCIs within the last 10 years against their reversible inhibitor (RI) counterparts. Our findings indicated that (i) PK half-lives of TCIs were typically shorter and (ii) at their respective recommended clinical doses per drug label, the molar unbound steady state areas under the concentration-time curve (AUCss) of TCIs were lower than those of RIs, but with longer clinically observed durations of response. However, (iii) there was no conclusive evidence supporting improved clinical safety profiles for TCIs, and (iv) DDI perpetrator profiles appeared to be similar between TCIs and RIs. The overall clinical pharmacology comparison of TCI vs. RI surveyed in this paper suggested that at least two of the four forecasted clinical benefits were achieved by TCIs.
Collapse
Affiliation(s)
- Huy X Ngo
- Clinical Pharmacology, Genentech, Inc., South San Francisco, California, USA
| | - Yue Winnie Wen
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington, USA
| | - Swathi Pisupati
- Clinical Pharmacology, Genentech, Inc., South San Francisco, California, USA
| | - Weize Huang
- Clinical Pharmacology, Genentech, Inc., South San Francisco, California, USA
| | - Sandhya Mandlekar
- Clinical Pharmacology, Genentech, Inc., South San Francisco, California, USA
| |
Collapse
|
3
|
Himmelbauer M, Bajrami B, Basile R, Capacci A, Chen T, Choi CK, Gilfillan R, Gonzalez-Lopez de Turiso F, Gu C, Hoemberger M, Johnson DS, Jones JH, Kadakia E, Kirkland M, Lin EY, Liu Y, Ma B, Magee T, Mantena S, Marx IE, Metrick CM, Mingueneau M, Murugan P, Muste CA, Nadella P, Nevalainen M, Parker Harp CR, Pattaropong V, Pietrasiewicz A, Prince RJ, Purgett TJ, Santoro JC, Schulz J, Sciabola S, Tang H, Vandeveer HG, Wang T, Yousaf Z, Helal CJ, Hopkins BT. Discovery and Preclinical Characterization of BIIB129, a Covalent, Selective, and Brain-Penetrant BTK Inhibitor for the Treatment of Multiple Sclerosis. J Med Chem 2024; 67:8122-8140. [PMID: 38712838 PMCID: PMC11129193 DOI: 10.1021/acs.jmedchem.4c00220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/03/2024] [Accepted: 04/10/2024] [Indexed: 05/08/2024]
Abstract
Multiple sclerosis (MS) is a chronic disease with an underlying pathology characterized by inflammation-driven neuronal loss, axonal injury, and demyelination. Bruton's tyrosine kinase (BTK), a nonreceptor tyrosine kinase and member of the TEC family of kinases, is involved in the regulation, migration, and functional activation of B cells and myeloid cells in the periphery and the central nervous system (CNS), cell types which are deemed central to the pathology contributing to disease progression in MS patients. Herein, we describe the discovery of BIIB129 (25), a structurally distinct and brain-penetrant targeted covalent inhibitor (TCI) of BTK with an unprecedented binding mode responsible for its high kinome selectivity. BIIB129 (25) demonstrated efficacy in disease-relevant preclinical in vivo models of B cell proliferation in the CNS, exhibits a favorable safety profile suitable for clinical development as an immunomodulating therapy for MS, and has a low projected total human daily dose.
Collapse
Affiliation(s)
- Martin
K. Himmelbauer
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Bekim Bajrami
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Rebecca Basile
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Andrew Capacci
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - TeYu Chen
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Colin K. Choi
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Rab Gilfillan
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | | | - Chungang Gu
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Marc Hoemberger
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Douglas S. Johnson
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - J. Howard Jones
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Ekta Kadakia
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Melissa Kirkland
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Edward Y. Lin
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Ying Liu
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Bin Ma
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Tom Magee
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Srinivasa Mantena
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Isaac E. Marx
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Claire M. Metrick
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Michael Mingueneau
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Paramasivam Murugan
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Cathy A. Muste
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Prasad Nadella
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Marta Nevalainen
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Chelsea R. Parker Harp
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Vatee Pattaropong
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Alicia Pietrasiewicz
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Robin J. Prince
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Thomas J. Purgett
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Joseph C. Santoro
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Jurgen Schulz
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Simone Sciabola
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Hao Tang
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - H. George Vandeveer
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Ti Wang
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Zain Yousaf
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Christopher J. Helal
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Brian T. Hopkins
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| |
Collapse
|
4
|
Kim KY, Jeong YJ, Park SY, Park EJ, Jeon JH, Song IS, Liu KH. Evaluation of the Drug-Induced Liver Injury Potential of Saxagliptin through Reactive Metabolite Identification in Rats. Pharmaceutics 2024; 16:106. [PMID: 38258116 PMCID: PMC10819019 DOI: 10.3390/pharmaceutics16010106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
A liver injury was recently reported for saxagliptin, which is a dipeptidyl peptidase-4 (DPP-4) inhibitor. However, the underlying mechanisms of saxagliptin-induced liver injury remain unknown. This study aimed to evaluate whether saxagliptin, a potent and selective DPP-4 inhibitor that is globally used for treating type 2 diabetes mellitus, binds to the nucleophiles in vitro. Four DPP-4 inhibitors, including vildagliptin, were evaluated for comparison. Only saxagliptin and vildagliptin, which both contain a cyanopyrrolidine group, quickly reacted with L-cysteine to enzyme-independently produce thiazolinic acid metabolites. This saxagliptin-cysteine adduct was also found in saxagliptin-administered male Sprague-Dawley rats. In addition, this study newly identified cysteinyl glycine conjugates of saxagliptin and 5-hydroxysaxagliptin. The observed metabolic pathways were hydroxylation and conjugation with cysteine, glutathione, sulfate, and glucuronide. In summary, we determined four new thiazoline-containing thiol metabolites (cysteine and cysteinylglycine conjugates of saxagliptin and 5-hydroxysaxagliptin) in saxagliptin-administered male rats. Our results reveal that saxagliptin can covalently bind to the thiol groups of cysteine residues of endogenous proteins in vivo, indicating the potential for saxagliptin to cause drug-induced liver injury.
Collapse
Affiliation(s)
- Ki-Young Kim
- BK21 FOUR KNU Community-Based Intelligent Novel Drug Discovery Education Unit, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, Daegu 41566, Republic of Korea; (K.-Y.K.); (Y.-J.J.); (S.-Y.P.); (E.-J.P.); (J.-H.J.)
| | - Yeo-Jin Jeong
- BK21 FOUR KNU Community-Based Intelligent Novel Drug Discovery Education Unit, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, Daegu 41566, Republic of Korea; (K.-Y.K.); (Y.-J.J.); (S.-Y.P.); (E.-J.P.); (J.-H.J.)
| | - So-Young Park
- BK21 FOUR KNU Community-Based Intelligent Novel Drug Discovery Education Unit, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, Daegu 41566, Republic of Korea; (K.-Y.K.); (Y.-J.J.); (S.-Y.P.); (E.-J.P.); (J.-H.J.)
- Mass Spectrometry Based Convergence Research Institute, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Eun-Ji Park
- BK21 FOUR KNU Community-Based Intelligent Novel Drug Discovery Education Unit, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, Daegu 41566, Republic of Korea; (K.-Y.K.); (Y.-J.J.); (S.-Y.P.); (E.-J.P.); (J.-H.J.)
| | - Ji-Hyeon Jeon
- BK21 FOUR KNU Community-Based Intelligent Novel Drug Discovery Education Unit, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, Daegu 41566, Republic of Korea; (K.-Y.K.); (Y.-J.J.); (S.-Y.P.); (E.-J.P.); (J.-H.J.)
| | - Im-Sook Song
- BK21 FOUR KNU Community-Based Intelligent Novel Drug Discovery Education Unit, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, Daegu 41566, Republic of Korea; (K.-Y.K.); (Y.-J.J.); (S.-Y.P.); (E.-J.P.); (J.-H.J.)
| | - Kwang-Hyeon Liu
- BK21 FOUR KNU Community-Based Intelligent Novel Drug Discovery Education Unit, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, Daegu 41566, Republic of Korea; (K.-Y.K.); (Y.-J.J.); (S.-Y.P.); (E.-J.P.); (J.-H.J.)
- Mass Spectrometry Based Convergence Research Institute, Kyungpook National University, Daegu 41566, Republic of Korea
| |
Collapse
|
5
|
Wang S, Ballard TE, Christopher LJ, Foti RS, Gu C, Khojasteh SC, Liu J, Ma S, Ma B, Obach RS, Schadt S, Zhang Z, Zhang D. The Importance of Tracking "Missing" Metabolites: How and Why? J Med Chem 2023; 66:15586-15612. [PMID: 37769129 DOI: 10.1021/acs.jmedchem.3c01293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
Technologies currently employed to find and identify drug metabolites in complex biological matrices generally yield results that offer a comprehensive picture of the drug metabolite profile. However, drug metabolites can be missed or are captured only late in the drug development process. This could be due to a variety of factors, such as metabolism that results in partial loss of the molecule, covalent bonding to macromolecules, the drug being metabolized in specific human tissues, or poor ionization in a mass spectrometer. These scenarios often draw a great deal of attention from chemistry, safety assessment, and pharmacology. This review will summarize scenarios of missing metabolites, why they are missing, and associated uncovering strategies from deeper investigations. Uncovering previously missed metabolites can have ramifications in drug development with toxicological and pharmacological consequences, and knowledge of these can help in the design of new drugs.
Collapse
Affiliation(s)
- Shuai Wang
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - T Eric Ballard
- Takeda Development Center Americas, Inc., 35 Landsdowne St, Cambridge, Massachusetts 02139, United States
| | - Lisa J Christopher
- Department of Clinical Pharmacology, Pharmacometrics, Disposition & Bioanalysis, Bristol-Myers Squibb, Route 206 & Province Line Road, Princeton, New Jersey 08543, United States
| | - Robert S Foti
- Preclinical Development, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Chungang Gu
- Drug Metabolism and Pharmacokinetics, Biogen Inc., 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - S Cyrus Khojasteh
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Joyce Liu
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Shuguang Ma
- Drug Metabolism and Pharmacokinetics, Pliant Therapeutics, 260 Littlefield Avenue, South San Francisco, California 94080, United States
| | - Bin Ma
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - R Scott Obach
- Pharmacokinetics, Dynamics, and Metabolism, Pfizer, Inc., Eastern Point Road, Groton, Connecticut 06340, United States
| | - Simone Schadt
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacher Strasse 124, 4070 Basel, Switzerland
| | - Zhoupeng Zhang
- DMPK Oncology R&D, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Donglu Zhang
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| |
Collapse
|
6
|
Yamane D, Tetsukawa R, Zenmyo N, Tabata K, Yoshida Y, Matsunaga N, Shindo N, Ojida A. Expanding the Chemistry of Dihaloacetamides as Tunable Electrophiles for Reversible Covalent Targeting of Cysteines. J Med Chem 2023. [PMID: 37393576 DOI: 10.1021/acs.jmedchem.3c00737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The choice of an appropriate electrophile is crucial in the design of targeted covalent inhibitors (TCIs). In this report, we systematically investigated the glutathione (GSH) reactivity of various haloacetamides and the aqueous stability of their thiol adducts. Our findings revealed that dihaloacetamides cover a broad range of GSH reactivity depending on the combination of the halogen atoms and the structure of the amine scaffold. Among the dihaloacetamides, dichloroacetamide (DCA) exhibited slightly lower GSH reactivity than chlorofluoroacetamide (CFA). The DCA-thiol adduct is readily hydrolyzed under aqueous conditions, but it can stably exist in the solvent-sequestered binding pocket of the protein. These reactivity profiles of DCA were successfully exploited in the design of TCIs targeting noncatalytic cysteines of KRASG12C and EGFRL858R/T790M. These inhibitors exhibited strong antiproliferative activities against cancer cells. Our findings provide valuable insights for designing dihaloacetamide-based reversible covalent inhibitors.
Collapse
Affiliation(s)
- Daiki Yamane
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Ryo Tetsukawa
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Naoki Zenmyo
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kaori Tabata
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yuya Yoshida
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Naoya Matsunaga
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Naoya Shindo
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Akio Ojida
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| |
Collapse
|
7
|
Lu G, Ou K, Zhang Y, Zhang H, Feng S, Yang Z, Sun G, Liu J, Wei S, Pan S, Chen Z. Structural Analysis, Multi-Conformation Virtual Screening and Molecular Simulation to Identify Potential Inhibitors Targeting pS273R Proteases of African Swine Fever Virus. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28020570. [PMID: 36677630 PMCID: PMC9866604 DOI: 10.3390/molecules28020570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/26/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023]
Abstract
The African Swine Fever virus (ASFV) causes an infectious viral disease in pigs of all ages. The development of antiviral drugs primarily aimed at inhibition of proteases required for the proteolysis of viral polyproteins. In this study, the conformation of the pS273R protease in physiological states were investigated, virtually screened the multi-protein conformation of pS273R target proteins, combined various molecular docking scoring functions, and identified five potential drugs from the Food and Drug Administration drug library that may inhibit pS273R. Subsequent validation of the dynamic interactions of pS273R with the five putative inhibitors was achieved using molecular dynamics simulations and binding free energy calculations using the molecular mechanics/Poison-Boltzmann (Generalized Born) (MM/PB(GB)SA) surface area. These findings demonstrate that the arm domain and Thr159-Lys167 loop region of pS273R are significantly more flexible compared to the core structural domain, and the Thr159-Lys167 loop region can serve as a "gatekeeper" in the substrate channel. Leucovorin, Carboprost, Protirelin, Flavin Mononucleotide, and Lovastatin Acid all have Gibbs binding free energies with pS273R that were less than -20 Kcal/mol according to the MM/PBSA analyses. In contrast to pS273R in the free energy landscape, the inhibitor and drug complexes of pS273R showed distinct structural group distributions. These five drugs may be used as potential inhibitors of pS273R and may serve as future drug candidates for treating ASFV.
Collapse
Affiliation(s)
- Gen Lu
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, No. 120, Dongling Road, Shenhe District, Shenyang 110866, China
| | - Kang Ou
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, No. 120, Dongling Road, Shenhe District, Shenyang 110866, China
| | - Yihan Zhang
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, No. 120, Dongling Road, Shenhe District, Shenyang 110866, China
| | - Huan Zhang
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, No. 120, Dongling Road, Shenhe District, Shenyang 110866, China
| | - Shouhua Feng
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, No. 120, Dongling Road, Shenhe District, Shenyang 110866, China
| | - Zuofeng Yang
- The Preventive and Control Center of Animal Disease of Liaoning Province, Liaoning Agricultural Development Service Center, No. 95, Renhe Road, Shenbei District, Shenyang 110164, China
| | - Guo Sun
- Qianyuanhao Biological Co., Ltd., Building 20, District 11, No. 188 South Fourth Ring West Road, Fengtai District, Beijing 100070, China
| | - Jinling Liu
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, No. 120, Dongling Road, Shenhe District, Shenyang 110866, China
- Correspondence: (J.L.); (S.W.); (S.P.); (Z.C.); Tel.: +86-13022453165 (J.L.); Fax: +86-24-88487156 (J.L.)
| | - Shu Wei
- The Preventive and Control Center of Animal Disease of Liaoning Province, Liaoning Agricultural Development Service Center, No. 95, Renhe Road, Shenbei District, Shenyang 110164, China
- Correspondence: (J.L.); (S.W.); (S.P.); (Z.C.); Tel.: +86-13022453165 (J.L.); Fax: +86-24-88487156 (J.L.)
| | - Shude Pan
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, No. 120, Dongling Road, Shenhe District, Shenyang 110866, China
- Correspondence: (J.L.); (S.W.); (S.P.); (Z.C.); Tel.: +86-13022453165 (J.L.); Fax: +86-24-88487156 (J.L.)
| | - Zeliang Chen
- Key Laboratory of Livestock Infectious Diseases, Ministry of Education, Shenyang Agricultural University, No. 120, Dongling Road, Shenhe District, Shenyang 110866, China
- Correspondence: (J.L.); (S.W.); (S.P.); (Z.C.); Tel.: +86-13022453165 (J.L.); Fax: +86-24-88487156 (J.L.)
| |
Collapse
|
8
|
Teslenko I, Watson CJW, Chen G, Lazarus P. Inhibition of the aromatase enzyme by exemestane cysteine conjugates. Mol Pharmacol 2022; 102:MOLPHARM-AR-2022-000545. [PMID: 35953090 PMCID: PMC9595203 DOI: 10.1124/molpharm.122.000545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 08/02/2022] [Accepted: 08/05/2022] [Indexed: 11/25/2022] Open
Abstract
Exemestane (EXE) is an aromatase inhibitor used to treat hormone-dependent breast cancer. EXE is extensively metabolized, with unchanged EXE and its active metabolite 17-dihydroexemestane (17-DHE) accounting for 17 and 12%, respectively, of total plasma EXE in vivo The major circulating EXE metabolites are the cysteine conjugates of EXE and 17-DHE, and the 17-DHE glucuronide, which together account for 70% of total plasma EXE in vivo The goal of the present study was to examine the inhibition potential of major metabolites of EXE through inhibition assays using aromatase-overexpressing cells and pooled ovarian tissues. Estrone formation was used as a measure of aromatase activity and was detected and quantified using UPLC-MS. EXE-cys, 17β-DHE, and 17β-DHE-cys all exhibited inhibition of estrone formation at both 1 µM and 10 µM concentrations, with 17β-DHE and EXE-cys showing significant inhibition of estrone formation (63% each) at 10 µM. In contrast, 17β-DHE-Gluc displayed minimal inhibition (5-8%) at both concentrations. In ovarian tissue, EXE-cys and 17β-DHE showed similar patterns of inhibition, with 49% and 47% inhibition, respectively, at 10 µM. The IC50 value for EXE-cys (16 {plus minus} 10 µM) was similar to 17β-DHE (9.2 {plus minus} 2.7 µM) and higher than EXE (1.3 {plus minus} 0.28 µM), and all three compounds showed time-dependent inhibition with IC50 shifts of 13 {plus minus} 10, 5.0 {plus minus} 2.5 and 36 {plus minus} 12-fold, respectively. Given its high circulating levels in patients taking EXE, these results suggest that EXE-cys may contribute to the pharmacologic effect of EXE in vivo Significance Statement The current study is the first to examine the major phase II metabolites of EXE (EXE-cys, 17β-DHE-cys, and 17β-DHE-Gluc) for inhibition potential against the target enzyme, aromatase (CYP19A1). EXE-cys was found to significantly inhibit aromatase in a time dependent manner. Given its high circulating levels in patients taking EXE, this phase II metabolite may play an important role in reducing circulating estrogen levels in vivo.
Collapse
Affiliation(s)
- Irina Teslenko
- Pharmaceutical Sciences, Washington State University, United States
| | | | - Gang Chen
- Pharmaceutical Sciences, WSU College of Pharmacy, United States
| | - Philip Lazarus
- Pharmaceutical Sciences, Washington State University College of Pharmacy, United States
| |
Collapse
|
9
|
Wang Z, Chan ECY. Inhibition of cytochrome P450 2J2-mediated metabolism of rivaroxaban and arachidonic acid by ibrutinib and osimertinib. Drug Metab Dispos 2022; 50:1332-1341. [PMID: 35817438 DOI: 10.1124/dmd.122.000928] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 06/29/2022] [Indexed: 11/22/2022] Open
Abstract
Covalent tyrosine kinase inhibitors (TKIs) ibrutinib and osimertinib are associated with cardiac arrhythmia. The interactions between these TKIs with cytochrome P450 2J2 (CYP2J2) that is highly expressed in human heart are unknown. In vitro metabolism experiments were performed to characterize CYP2J2-mediated metabolism of ibrutinib and osimertinib. Unbound distribution coefficient (Kpuu) for both TKIs was determined in AC16 cardiomyocytes. In vitroreversible and time-dependent CYP2J2 inhibition experiments were conducted with exogenous and endogenous substrates, namely rivaroxaban and arachidonic acid (AA), respectively, where kinetic parameters were estimated via one-site and multisite kinetic modeling. Ibrutinib was efficiently metabolized by CYP2J2 to a hydroxylated metabolite, M35, following substrate inhibition kinetics. Osimertinib is not a substrate of CYP2J2. Both TKIs depicted Kpuu values above 1 and equipotently inhibited CYP2J2-mediated hydroxylation of rivaroxaban in a concentration-dependent manner without time-dependency. The mode of reversible inhibition of CYP2J2-mediated metabolism of rivaroxaban and AA by osimertinib was described by Michaelis-Menten kinetics, while a two-site kinetic model recapitulated the atypical inhibitory kinetics of ibrutinib assuming multiple substrate-binding domains within the CYP2J2 active site. The inhibition of ibrutinib and osimertinib on cardiac AA metabolism could be clinically significant considering the preferable distribution of both TKIs to cardiomyocytes with R cut-off values of 1.160 and 1.026, respectively. The dysregulation of CYP2J2-mediated metabolism of AA to cardioprotective epoxyeicosatrienoic acids by ibrutinib and osimertinib serves as a novel mechanism for TKI-induced cardiac arrhythmia. Mechanistic characterization of CYP2J2-mediated typical and atypical enzyme kinetics further illuminates the unique catalytic properties of CYP2J2. Significance Statement We reported for the first time that ibrutinib is efficiently metabolized by cytochrome P450 2J2 (CYP2J2). By using rivaroxaban and arachidonic acid (AA) as substrates, we characterized the typical and atypical inhibition kinetics of CYP2J2 by ibrutinib and osimertinib. The inhibition of both drugs on cardiac AA metabolism could be clinically significant considering their preferable distribution to cardiomyocytes. Our findings serve as a novel mechanism for drug-induced cardiac arrhythmia and shed insights into the multisite interactions between CYP2J2 and ligands.
Collapse
|
10
|
Yamane D, Onitsuka S, Re S, Isogai H, Hamada R, Hiramoto T, Kawanishi E, Mizuguchi K, Shindo N, Ojida A. Selective covalent targeting of SARS-CoV-2 main protease by enantiopure chlorofluoroacetamide. Chem Sci 2022; 13:3027-3034. [PMID: 35432850 PMCID: PMC8905997 DOI: 10.1039/d1sc06596c] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 02/15/2022] [Indexed: 12/12/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has necessitated the development of antiviral agents against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The main protease (Mpro) is a promising target for COVID-19 treatment. Here, we report an irreversible SARS-CoV-2 Mpro inhibitor possessing chlorofluoroacetamide (CFA) as a warhead for the covalent modification of Mpro. Ugi multicomponent reaction using chlorofluoroacetic acid enabled the rapid synthesis of dipeptidic CFA derivatives that identified 18 as a potent inhibitor of SARS-CoV-2 Mpro. Among the four stereoisomers, (R,R)-18 exhibited a markedly higher inhibitory activity against Mpro than the other isomers. Reaction kinetics and computational docking studies suggest that the R configuration of the CFA warhead is crucial for the rapid covalent inhibition of Mpro. Our findings highlight the prominent influence of the CFA chirality on the covalent modification of proteinous cysteines and provide the basis for improving the potency and selectivity of CFA-based covalent inhibitors.
Collapse
Affiliation(s)
- Daiki Yamane
- Graduate School of Pharmaceutical Sciences, Kyushu University 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| | - Satsuki Onitsuka
- Graduate School of Pharmaceutical Sciences, Kyushu University 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| | - Suyong Re
- Artificial Intelligence Center for Health and Biomedical Research, National Institute of Biomedical Innovation, Health and Nutrition 7-6-8 Saito-Asagi, Ibaraki Osaka 567-0085 Japan
| | - Hikaru Isogai
- Graduate School of Pharmaceutical Sciences, Kyushu University 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| | - Rui Hamada
- Graduate School of Pharmaceutical Sciences, Kyushu University 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| | - Tadanari Hiramoto
- Graduate School of Pharmaceutical Sciences, Kyushu University 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| | - Eiji Kawanishi
- Graduate School of Pharmaceutical Sciences, Kyushu University 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| | - Kenji Mizuguchi
- Artificial Intelligence Center for Health and Biomedical Research, National Institute of Biomedical Innovation, Health and Nutrition 7-6-8 Saito-Asagi, Ibaraki Osaka 567-0085 Japan
- Institute for Protein Research, Osaka University 3-2 Yamadaoka, Suita Osaka 565-0871 Japan
| | - Naoya Shindo
- Graduate School of Pharmaceutical Sciences, Kyushu University 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| | - Akio Ojida
- Graduate School of Pharmaceutical Sciences, Kyushu University 3-1-1 Maidashi, Higashi-ku Fukuoka 812-8582 Japan
| |
Collapse
|
11
|
Guengerich FP. Roles of cytochrome P450 enzymes in pharmacology and toxicology: Past, present, and future. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2022; 95:1-47. [PMID: 35953152 PMCID: PMC9869358 DOI: 10.1016/bs.apha.2021.12.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The development of the cytochrome P450 (P450) field has been remarkable in the areas of pharmacology and toxicology, particularly in drug development. Today it is possible to use the knowledge base and relatively straightforward assays to make intelligent predictions about drug disposition prior to human dosing. Much is known about the structures, regulation, chemistry of catalysis, and the substrate and inhibitor specificity of human P450s. Many aspects of drug-drug interactions and side effects can be understood in terms of P450s. This knowledge has also been useful in pharmacy practice, as well as in the pharmaceutical industry and medical practice. However, there are still basic and practical questions to address regarding P450s and their roles in pharmacology and toxicology. Another aspect is the discovery of drugs that inhibit P450 to treat diseases.
Collapse
|
12
|
Shindo N, Ojida A. Recent progress in covalent warheads for in vivo targeting of endogenous proteins. Bioorg Med Chem 2021; 47:116386. [PMID: 34509863 DOI: 10.1016/j.bmc.2021.116386] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 01/21/2023]
Abstract
Covalent drugs exert potent and durable activity by chemical modification of the endogenous target protein in vivo. To maximize the pharmacological efficacy while alleviating the risk of toxicity due to nonspecific off-target reactions, current covalent drug discovery focuses on the development of targeted covalent inhibitors (TCIs), wherein a reactive group (warhead) is strategically incorporated onto a reversible ligand of the target protein to facilitate specific covalent engagement. Various aspects of warheads, such as intrinsic reactivity, chemoselectivity, mode of reaction, and reversibility of the covalent engagement, would affect the target selectivity of TCIs. Although TCIs clinically approved to date largely rely on Michael acceptor-type electrophiles for cysteine targeting, a wide array of novel warheads have been devised and tested in TCI development in recent years. In this short review, we provide an overview of recent progress in chemistry for selective covalent targeting of proteins and their applications in TCI designs.
Collapse
Affiliation(s)
- Naoya Shindo
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku Fukuoka, Japan
| | - Akio Ojida
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku Fukuoka, Japan.
| |
Collapse
|
13
|
Sabat M, Dougan DR, Knight B, Lawson JD, Scorah N, Smith CR, Taylor ER, Vu P, Wyrick C, Wang H, Balakrishna D, Hixon M, Madakamutil L, McConn D. Discovery of the Bruton's Tyrosine Kinase Inhibitor Clinical Candidate TAK-020 ( S)-5-(1-((1-Acryloylpyrrolidin-3-yl)oxy)isoquinolin-3-yl)-2,4-dihydro-3 H-1,2,4-triazol-3-one, by Fragment-Based Drug Design. J Med Chem 2021; 64:12893-12902. [PMID: 34448571 DOI: 10.1021/acs.jmedchem.1c01026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
This publication details the successful use of FBDD (fragment-based drug discovery) principles in the invention of a novel covalent Bruton's tyrosine kinase inhibitor, which ultimately became the Takeda Pharmaceuticals clinical candidate TAK-020. Described herein are the discovery of the fragment 5-phenyl-2,4-dihydro-3H-1,2,4-triazol-3-one, the subsequent optimization of this hit molecule to the candidate, and synthesis and performance in pharmacodynamic and efficacy models along with direct biophysical comparison of TAK-020 with other clinical-level assets and the marketed drug Ibrutinib.
Collapse
Affiliation(s)
- Mark Sabat
- Takeda California, 9625 Towne Centre Dr., San Diego, California 92121, United States
| | - Douglas R Dougan
- Takeda California, 9625 Towne Centre Dr., San Diego, California 92121, United States
| | - Beverly Knight
- Pfizer, 10777 Science Center Dr., San Diego, California 92121, United States
| | - J David Lawson
- Mirati Therapeutics, Inc., 9393 Towne Centre Dr. #200, San Diego, California 92121, United States
| | - Nicholas Scorah
- Takeda California, 9625 Towne Centre Dr., San Diego, California 92121, United States
| | - Christopher R Smith
- Mirati Therapeutics, Inc., 9393 Towne Centre Dr. #200, San Diego, California 92121, United States
| | - Ewan R Taylor
- Takeda California, 9625 Towne Centre Dr., San Diego, California 92121, United States
| | - Phong Vu
- Takeda California, 9625 Towne Centre Dr., San Diego, California 92121, United States
| | - Corey Wyrick
- Takeda California, 9625 Towne Centre Dr., San Diego, California 92121, United States
| | - Haixia Wang
- Takeda California, 9625 Towne Centre Dr., San Diego, California 92121, United States
| | - Deepika Balakrishna
- Takeda California, 9625 Towne Centre Dr., San Diego, California 92121, United States
| | - Mark Hixon
- VeriSIM Life, 1 Sansome Street Suite 3500, San Francisco, California 94104, United States
| | - Loui Madakamutil
- Invivoscribe Therapeutics, Inc., 10222 Barnes Canyon Rd., Bldg. 1, San Diego, California 92121, United States
| | - Donavon McConn
- Takeda California, 9625 Towne Centre Dr., San Diego, California 92121, United States
| |
Collapse
|
14
|
Yuan M, Chu Y, Duan Y. Reversible Covalent PROTACs: Novel and Efficient Targeted Degradation Strategy. Front Chem 2021; 9:691093. [PMID: 34291036 PMCID: PMC8287302 DOI: 10.3389/fchem.2021.691093] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/07/2021] [Indexed: 11/13/2022] Open
Abstract
The proteolysis targeting chimeras (PROTACs), which are composed of a target protein binding moiety, a linker, and an E3 ubiquitin ligase binder, have been a promising strategy for drug design and discovery. Given the advantages of potency, selectivity, and drug resistance over inhibitors, several PROTACs have been reported in literature, which mostly focus on noncovalent or irreversible covalent binding to the target proteins. However, it must be noted that noncovalent or irreversible PROTACs have several drawbacks such as weak binding affinity and unpredictable off-target effects. Reversible covalent PROTACs, with properties of enhanced potency, selectivity, and long duration of action, have attracted an increasing amount of attention. Here, we propose a comparison between these three patterns and highlight that reversible covalent PROTACs could pave the way for a wide variety of challenging target degradations.
Collapse
Affiliation(s)
- Minghua Yuan
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China.,School of Pharmaceutical Science, Zhengzhou University, Zhengzhou, China
| | - Yanan Chu
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China.,School of Pharmaceutical Science, Zhengzhou University, Zhengzhou, China
| | - Yongtao Duan
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
| |
Collapse
|
15
|
Grand DL, Gosling M, Baettig U, Bahra P, Bala K, Brocklehurst C, Budd E, Butler R, Cheung AK, Choudhury H, Collingwood SP, Cox B, Danahay H, Edwards L, Everatt B, Glaenzel U, Glotin AL, Groot-Kormelink P, Hall E, Hatto J, Howsham C, Hughes G, King A, Koehler J, Kulkarni S, Lightfoot M, Nicholls I, Page C, Pergl-Wilson G, Popa MO, Robinson R, Rowlands D, Sharp T, Spendiff M, Stanley E, Steward O, Taylor RJ, Tranter P, Wagner T, Watson H, Williams G, Wright P, Young A, Sandham DA. Discovery of Icenticaftor (QBW251), a Cystic Fibrosis Transmembrane Conductance Regulator Potentiator with Clinical Efficacy in Cystic Fibrosis and Chronic Obstructive Pulmonary Disease. J Med Chem 2021; 64:7241-7260. [PMID: 34028270 DOI: 10.1021/acs.jmedchem.1c00343] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) ion channel are established as the primary causative factor in the devastating lung disease cystic fibrosis (CF). More recently, cigarette smoke exposure has been shown to be associated with dysfunctional airway epithelial ion transport, suggesting a role for CFTR in the pathogenesis of chronic obstructive pulmonary disease (COPD). Here, the identification and characterization of a high throughput screening hit 6 as a potentiator of mutant human F508del and wild-type CFTR channels is reported. The design, synthesis, and biological evaluation of compounds 7-33 to establish structure-activity relationships of the scaffold are described, leading to the identification of clinical development compound icenticaftor (QBW251) 33, which has subsequently progressed to deliver two positive clinical proofs of concept in patients with CF and COPD and is now being further developed as a novel therapeutic approach for COPD patients.
Collapse
Affiliation(s)
- Darren Le Grand
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Martin Gosling
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Urs Baettig
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Parmjit Bahra
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Kamlesh Bala
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Cara Brocklehurst
- Novartis Institutes for Biomedical Research, Novartis Campus, Basel, CH 4002, Switzerland
| | - Emma Budd
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Rebecca Butler
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Atwood K Cheung
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Hedaythul Choudhury
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Stephen P Collingwood
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Brian Cox
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Henry Danahay
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Lee Edwards
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Brian Everatt
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Ulrike Glaenzel
- Novartis Institutes for Biomedical Research, Novartis Campus, Basel, CH 4002, Switzerland
| | - Anne-Lise Glotin
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Paul Groot-Kormelink
- Novartis Institutes for Biomedical Research, Novartis Campus, Basel, CH 4002, Switzerland
| | - Edward Hall
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Julia Hatto
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Catherine Howsham
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Glyn Hughes
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Anna King
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Julia Koehler
- Novartis Institutes for Biomedical Research, Novartis Campus, Basel, CH 4002, Switzerland
| | - Swarupa Kulkarni
- Novartis Institutes for Biomedical Research, East Hanover, New Jersey 07936, United States
| | - Megan Lightfoot
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Ian Nicholls
- Novartis Institutes for Biomedical Research, Novartis Campus, Basel, CH 4002, Switzerland
| | - Christopher Page
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Giles Pergl-Wilson
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Mariana Oana Popa
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Richard Robinson
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - David Rowlands
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Tom Sharp
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Matthew Spendiff
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Emily Stanley
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Oliver Steward
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Roger J Taylor
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Pamela Tranter
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Trixie Wagner
- Novartis Institutes for Biomedical Research, Novartis Campus, Basel, CH 4002, Switzerland
| | - Hazel Watson
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Gareth Williams
- Novartis Institutes for Biomedical Research, Novartis Campus, Basel, CH 4002, Switzerland
| | - Penny Wright
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - Alice Young
- Novartis Institutes for Biomedical Research, Horsham Research Center, Wimblehurst Road, Horsham RH12 5AB, U.K
| | - David A Sandham
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
16
|
Yang Z. Achieving a low human dose for targeted covalent drugs: Pharmacokinetic and pharmacodynamic considerations on target characteristics and drug attributes. Biopharm Drug Dispos 2021; 42:150-159. [PMID: 33547681 DOI: 10.1002/bdd.2263] [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: 10/18/2020] [Revised: 12/30/2020] [Accepted: 01/06/2021] [Indexed: 11/08/2022]
Abstract
Covalent modifications of off-target biomolecules remain to be a concern for targeted covalent drugs. To guide the design of targeted covalent drugs in achieving a low human daily dose, a pharmacokinetic/pharmacodynamic (PK/PD) model was established to quantitatively evaluate target characteristics and drug properties that affect the human dose. Target characteristics, such as expression levels, turnover, and degree of inhibition relevant to efficacy, were evaluated systematically using the model. The drug properties including inactivation potency and drug clearance were also examined. Model simulations revealed that the interplay of target characteristics and drug properties governed the human dose. Particularly, the extent and the duration of target inactivation meaningful to efficacy, as well as the target resynthesis rate measured as the target turnover half-life, needed to be determined. The target information then served as a basis to inform desired drug inactivation potency and PK properties. The model-based approach provided a theoretical framework in achieving a low human dose of targeted covalent drugs, and the resultant strategy was successfully applied in the early stage of a Bruton's tyrosine kinase covalent inhibitor project that discovered low-dose branebrutinib. The PK/PD considerations described are also applicable to the drug design for protein degraders that share the same endpoint as targeted covalent drugs in reducing target levels.
Collapse
Affiliation(s)
- Zheng Yang
- Department of Metabolism and Pharmacokinetics, Pharmaceutical Candidate Optimization, Bristol Myers Squibb, Princeton, New Jersey, USA
| |
Collapse
|
17
|
Miura C, Shindo N, Okamoto K, Kuwata K, Ojida A. Fragment-Based Discovery of Irreversible Covalent Inhibitors of Cysteine Proteases Using Chlorofluoroacetamide Library. Chem Pharm Bull (Tokyo) 2020; 68:1074-1081. [PMID: 33132374 DOI: 10.1248/cpb.c20-00547] [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] [Indexed: 11/22/2022]
Abstract
Fragment-based approach combined with electrophilic reactive compounds is a powerful strategy to discover novel covalent ligands for protein target. However, the promiscuous reactivity often interferes with identification of the fragments possessing specific binding affinity to the targeted protein. In our study, we report the fragment-based covalent drug discovery using the chemically tuned weak reactivity of chlorofluoroacetamide (CFA). We constructed a small fragment library composed of 30 CFA-appended compounds and applied it to the covalent ligand screening for cysteine protease papain as a model protein target. Using the fluorescence enzymatic assay, we identified CFA-benzothiazole 30 as a papain inhibitor, which was found to irreversibly inactivate papain upon enzyme kinetic analysis. The formation of the covalent papain-30 adduct was confirmed using electrospray ionization mass spectrometry analysis. The activity-based protein profiling (ABPP) experiment using an alkynylated analog of 30 (i.e., 30-yne) revealed that 30-yne covalently labeled papain with high selectivity. These data demonstrate potential utility of the CFA-fragment library for de novo discovery of target selective covalent inhibitors.
Collapse
Affiliation(s)
- Chizuru Miura
- Graduate School of Pharmaceutical Sciences, Kyushu University
| | - Naoya Shindo
- Graduate School of Pharmaceutical Sciences, Kyushu University
| | - Kei Okamoto
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University
| | - Keiko Kuwata
- Graduate School of Pharmaceutical Sciences, Kyushu University
| | - Akio Ojida
- Graduate School of Pharmaceutical Sciences, Kyushu University
| |
Collapse
|
18
|
Baillie TA. Approaches to mitigate the risk of serious adverse reactions in covalent drug design. Expert Opin Drug Discov 2020; 16:275-287. [PMID: 33006907 DOI: 10.1080/17460441.2021.1832079] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Covalent inhibition of target proteins using high affinity ligands bearing weakly electrophilic warheads is being adopted increasingly as design strategy in the discovery of novel therapeutics, and several covalent drugs have now received regulatory approval for indications in oncology. Experience to date with targeted covalent inhibitors has led to a number of design principles that underlie the safety and efficacy of this increasingly important class of molecules. AREAS COVERED A review is provided of the current status of the covalent drug approach, emphasizing the unique benefits and attendant risks associated with reversible and irreversible binders. Areas of application beyond inhibition of tyrosine kinases are presented, and design considerations to de-risk covalent inhibitors with respect to undesirable off-target effects are discussed. EXPERT OPINION High selectivity for the intended protein target has emerged as a key consideration in mitigating safety risks associated with widespread proteome reactivity. Powerful chemical proteomics-based techniques are now available to assess selectivity in a drug discovery setting. Optimizing pharmacokinetics to capitalize on the intrinsically high potency of covalent drugs should lead to low daily doses and greater safety margins, while minimizing susceptibility to metabolic activation likewise will attenuate the risk of covalent drug toxicity.
Collapse
Affiliation(s)
- Thomas A Baillie
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington Seattle, Seattle, WA, USA
| |
Collapse
|
19
|
Tokunaga K, Sato M, Kuwata K, Miura C, Fuchida H, Matsunaga N, Koyanagi S, Ohdo S, Shindo N, Ojida A. Bicyclobutane Carboxylic Amide as a Cysteine-Directed Strained Electrophile for Selective Targeting of Proteins. J Am Chem Soc 2020; 142:18522-18531. [PMID: 33047956 DOI: 10.1021/jacs.0c07490] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Expanding the repertoire of electrophiles with unique reactivity features would facilitate the development of covalent inhibitors with desirable reactivity profiles. We herein introduce bicyclo[1.1.0]butane (BCB) carboxylic amide as a new class of thiol-reactive electrophiles for selective and irreversible inhibition of targeted proteins. We first streamlined the synthetic routes to generate a variety of BCB amides. The strain-driven nucleophilic addition to BCB amides proceeded chemoselectively with cysteine thiols under neutral aqueous conditions, the rate of which was significantly slower than that of acrylamide. This reactivity profile of BCB amide was successfully exploited to develop covalent ligands targeting Bruton's tyrosine kinase (BTK). By tuning BCB amide reactivity and optimizing its disposition on the ligand, we obtained a selective covalent inhibitor of BTK. The in-gel activity-based protein profiling and mass spectrometry-based chemical proteomics revealed that the selected BCB amide had a higher target selectivity for BTK in human cells than did a Michael acceptor probe. Further chemical proteomic study revealed that BTK probes bearing different classes of electrophiles exhibited distinct off-target profiles. This result suggests that incorporation of BCB amide as a cysteine-directed electrophile could expand the capability to develop covalent inhibitors with the desired proteome reactivity profile.
Collapse
Affiliation(s)
- Keisuke Tokunaga
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Mami Sato
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Furocho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Chizuru Miura
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Hirokazu Fuchida
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Naoya Matsunaga
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Satoru Koyanagi
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Shigehiro Ohdo
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Naoya Shindo
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Akio Ojida
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| |
Collapse
|
20
|
Kakutani N, Iwai T, Ohno Y, Kobayashi S, Nomura Y. Evaluation of covalent binding of flutamide and its risk assessment using 19F-NMR. Xenobiotica 2020; 51:88-94. [PMID: 32876521 DOI: 10.1080/00498254.2020.1817626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The formation of reactive metabolites (RMs) is a problem in drug development that sometimes results in severe hepatotoxicity. As detecting RMs themselves is difficult, a covalent binding assay using expensive radiolabelled tracers is usually performed for candidate selection. This study aimed to provide a practical approach toward the risk assessment of hepatotoxicity induced by covalent binding before candidate selection. We focused on flutamide because it contains a trifluoromethyl group that shows a strong singlet peak by 19F nuclear magnetic resonance (NMR) spectrometry. The covalent binding of flutamide was evaluated using quantitative NMR and its risk for hepatotoxicity was assessed by estimating the RM burden, an index that reflects the body burden associated with RM exposure by determining the extent of covalent binding, clinical dose and in vivo clearance. The extent of covalent binding and RM burden was 296 pmol/mg/h and 37.9 mg/day, respectively. Flutamide was categorised as high risk with an RM burden >10 mg/day consistent with its clinical hepatotoxicity. These results indicate that a combination of covalent binding assay using 19F-NMR and RM burden is useful for the risk assessment of RMs without using radiolabelled compounds.
Collapse
Affiliation(s)
- Nobuyuki Kakutani
- Drug Metabolism and Pharmacokinetics Research Laboratories, Japan Tobacco Inc, Takatsuki, Japan
| | - Takahiro Iwai
- Product Development Laboratories, Japan Tobacco Inc, Takatsuki, Japan
| | - Yasushi Ohno
- Product Development Laboratories, Japan Tobacco Inc, Takatsuki, Japan
| | - Satoru Kobayashi
- Drug Metabolism and Pharmacokinetics Research Laboratories, Japan Tobacco Inc, Takatsuki, Japan
| | - Yukihiro Nomura
- Drug Metabolism and Pharmacokinetics Research Laboratories, Japan Tobacco Inc, Takatsuki, Japan
| |
Collapse
|
21
|
Sato M, Fuchida H, Shindo N, Kuwata K, Tokunaga K, Xiao-Lin G, Inamori R, Hosokawa K, Watari K, Shibata T, Matsunaga N, Koyanagi S, Ohdo S, Ono M, Ojida A. Selective Covalent Targeting of Mutated EGFR(T790M) with Chlorofluoroacetamide-Pyrimidines. ACS Med Chem Lett 2020; 11:1137-1144. [PMID: 32550993 DOI: 10.1021/acsmedchemlett.9b00574] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 04/08/2020] [Indexed: 12/14/2022] Open
Abstract
Covalent modification of disease-associated proteins with small molecules is a powerful approach for achieving an increased and sustained pharmacological effect. To reduce the potential risk of nonselective covalent modification, molecular design of covalent inhibitors is critically important. We report herein the development of a targeted covalent inhibitor for mutated epidermal growth factor receptor (EGFR) (L858R/T790M) using α-chlorofluoroacetamide (CFA) as the reactive group. The chemically tuned weak reactivity of CFA was suitable for the design of third-generation EGFR inhibitors that possess the pyrimidine scaffold. The structure-activity relationship study revealed that CFA inhibitor 18 (NSP-037) possessed higher inhibition selectivity to the mutated EGFR over wild-type EGFR when compared to clinically approved osimertinib. Mass-based chemical proteomics analyses further revealed that 18 displayed high covalent modification selectivity for the mutated EGFR in living cells. These findings highlight the utility of CFA as a warhead of targeted covalent inhibitors and the potential application of the CFA-pyrimidines for treatment of non-small-cell lung cancer.
Collapse
Affiliation(s)
- Mami Sato
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Hirokazu Fuchida
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Naoya Shindo
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa, Nagoya 464-8601, Japan
| | - Keisuke Tokunaga
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Guo Xiao-Lin
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Ryo Inamori
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Keitaro Hosokawa
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kosuke Watari
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Tomohiro Shibata
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Naoya Matsunaga
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Satoru Koyanagi
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Shigehiro Ohdo
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Mayumi Ono
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Akio Ojida
- Graduate School of Pharmaceutical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| |
Collapse
|
22
|
Khojasteh SC, Bumpus NN, Driscoll JP, Miller GP, Mitra K, Rietjens IMCM, Zhang D. Biotransformation and bioactivation reactions - 2018 literature highlights. Drug Metab Rev 2019; 51:121-161. [PMID: 31170851 DOI: 10.1080/03602532.2019.1615937] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In the past three decades, ADME sciences have become an integral component of the drug discovery and development process. At the same time, the field has continued to evolve, thus, requiring ADME scientists to be knowledgeable of and engage with diverse aspects of drug assessment: from pharmacology to toxicology, and from in silico modeling to in vitro models and finally in vivo models. Progress in this field requires deliberate exposure to different aspects of ADME; however, this task can seem daunting in the current age of mass information. We hope this review provides a focused and brief summary of a wide array of critical advances over the past year and explains the relevance of this research ( Table 1 ). We divided the articles into categories of (1) drug optimization, (2) metabolites and drug metabolizing enzymes, and (3) bioactivation. This annual review is the fourth of its kind (Baillie et al. 2016 ; Khojasteh et al. 2017 , 2018 ). We have followed the same format we used in previous years in terms of the selection of articles and the authoring of each section. This effort in itself also continues to evolve. I am pleased that Rietjens, Miller, and Mitra have again contributed to this annual review. We would like to welcome Namandjé N. Bumpus, James P. Driscoll, and Donglu Zhang as authors for this year's issue. We strive to maintain a balance of authors from academic and industry settings. We would be pleased to hear your opinions of our commentary, and we extend an invitation to anyone who would like to contribute to a future edition of this review. Cyrus Khojasteh, on behalf of the authors.
Collapse
Affiliation(s)
- S Cyrus Khojasteh
- Department of Drug Metabolism and Pharmacokinetics, Genentech Inc , South San Francisco , CA , USA
| | - Namandjé N Bumpus
- Department of Medicine - Division of Clinical Pharmacology, The Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | - James P Driscoll
- Department of Drug Metabolism and Pharmacokinetics, MyoKardia Inc. , South San Francisco , CA , USA
| | - Grover P Miller
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences , Little Rock , AR , USA
| | - Kaushik Mitra
- Department of Safety Assessment and Laboratory Animal Resources, Merck Research Laboratories (MRL), Merck & Co., Inc , West Point , PA , USA
| | | | - Donglu Zhang
- Department of Drug Metabolism and Pharmacokinetics, Genentech Inc , South San Francisco , CA , USA
| |
Collapse
|
23
|
Resnick E, Bradley A, Gan J, Douangamath A, Krojer T, Sethi R, Geurink PP, Aimon A, Amitai G, Bellini D, Bennett J, Fairhead M, Fedorov O, Gabizon R, Gan J, Guo J, Plotnikov A, Reznik N, Ruda GF, Díaz-Sáez L, Straub VM, Szommer T, Velupillai S, Zaidman D, Zhang Y, Coker AR, Dowson CG, Barr HM, Wang C, Huber KVM, Brennan PE, Ovaa H, von Delft F, London N. Rapid Covalent-Probe Discovery by Electrophile-Fragment Screening. J Am Chem Soc 2019; 141:8951-8968. [PMID: 31060360 PMCID: PMC6556873 DOI: 10.1021/jacs.9b02822] [Citation(s) in RCA: 182] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Covalent probes can display unmatched potency, selectivity, and duration of action; however, their discovery is challenging. In principle, fragments that can irreversibly bind their target can overcome the low affinity that limits reversible fragment screening, but such electrophilic fragments were considered nonselective and were rarely screened. We hypothesized that mild electrophiles might overcome the selectivity challenge and constructed a library of 993 mildly electrophilic fragments. We characterized this library by a new high-throughput thiol-reactivity assay and screened them against 10 cysteine-containing proteins. Highly reactive and promiscuous fragments were rare and could be easily eliminated. In contrast, we found hits for most targets. Combining our approach with high-throughput crystallography allowed rapid progression to potent and selective probes for two enzymes, the deubiquitinase OTUB2 and the pyrophosphatase NUDT7. No inhibitors were previously known for either. This study highlights the potential of electrophile-fragment screening as a practical and efficient tool for covalent-ligand discovery.
Collapse
Affiliation(s)
| | - Anthony Bradley
- Department of Chemistry , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , U.K.,Diamond Light Source Ltd., Harwell Science and Innovation Campus , Didcot OX11 0QX , U.K
| | | | - Alice Douangamath
- Diamond Light Source Ltd., Harwell Science and Innovation Campus , Didcot OX11 0QX , U.K
| | | | - Ritika Sethi
- Structural Biology Research Center , VIB , Brussels , Belgium.,Structural Biology Brussels , Vrije Universiteit Brussel , Brussels , Belgium
| | - Paul P Geurink
- Oncode Institute and Department of Cell and Chemical Biology , Leiden University Medical Center , Einthovenweg 20 , 2333 ZC Leiden , The Netherlands
| | - Anthony Aimon
- Department of Chemistry , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , U.K.,Diamond Light Source Ltd., Harwell Science and Innovation Campus , Didcot OX11 0QX , U.K
| | | | - Dom Bellini
- School of Life Sciences , University of Warwick , Coventry , U.K
| | | | | | | | | | - Jin Gan
- Oncode Institute and Department of Cell and Chemical Biology , Leiden University Medical Center , Einthovenweg 20 , 2333 ZC Leiden , The Netherlands
| | - Jingxu Guo
- Division of Medicine , University College London , Gower Street , London WC1E 6BT , U.K
| | | | | | | | | | | | | | | | | | | | - Alun R Coker
- Division of Medicine , University College London , Gower Street , London WC1E 6BT , U.K
| | | | | | | | | | - Paul E Brennan
- School of Life Sciences , University of Warwick , Coventry , U.K.,Alzheimer's Research UK Oxford Drug Discovery Institute , University of Oxford , NDMRB, Roosevelt Drive , Oxford OX3 7FZ , U.K
| | - Huib Ovaa
- Oncode Institute and Department of Cell and Chemical Biology , Leiden University Medical Center , Einthovenweg 20 , 2333 ZC Leiden , The Netherlands
| | - Frank von Delft
- Diamond Light Source Ltd., Harwell Science and Innovation Campus , Didcot OX11 0QX , U.K.,Department of Biochemistry , University of Johannesburg , Auckland Park 2006 , South Africa
| | | |
Collapse
|
24
|
Mizuno K, Takeuchi K, Umehara K, Nakajima M. Identification of Novel Metabolites of Vildagliptin in Rats: Thiazoline-Containing Thiol Adducts Formed via Cysteine or Glutathione Conjugation. Drug Metab Dispos 2019; 47:809-817. [PMID: 31097424 DOI: 10.1124/dmd.119.086546] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/14/2019] [Indexed: 01/18/2023] Open
Abstract
Vildagliptin (VG), a dipeptidyl peptidase-4 inhibitor, is used for treating type 2 diabetes. On rare occasions, VG causes liver injury as an adverse reaction. One case report suggested the involvement of immune responses in the hepatotoxicity, but the underlying mechanisms are unknown. We recently reported that VG binds covalently in vitro to l-cysteine to produce a thiazoline acid metabolite, M407, implying that the covalent binding may trigger the immune-mediated hepatotoxicity. There was no evidence, however, that such a thiazoline acid metabolite was formed in vivo. In the present study, we administered a single oral dose of VG to male Sprague-Dawley rats, and detected M407 in plasma. The sum of urinary and fecal excretions of M407 reached approximately 2% of the dose 48 hours postdosing. Using bile duct-cannulated rats, we demonstrated that M407 was secreted into bile as a glucuronide, designated as M583. Another newly identified thiazoline metabolite of VG, the cysteinylglycine conjugate M464, was detected in urine, feces, and bile. The formation of M464 was confirmed by in vitro incubation of VG with glutathione even in the absence of metabolic enzymes. A glutathione adduct against the nitrile moiety M611 was also detected in vitro but not in vivo. In summary, we found three new thiazoline-containing thiol adduct metabolites in VG-administered rats. Nonenzymatic covalent binding of VG would likely occur in humans, and it may be relevant to predicting adverse reactions.
Collapse
Affiliation(s)
- Katsuhiko Mizuno
- Department of Drug Metabolism and Pharmacokinetics, Nonclinical Research Center, Tokushima Research Institute, Otsuka Pharmaceutical Co., Ltd., Kawauchi-cho, Tokushima, Japan (K.M., K.T.); Nonclinical Research Center, Tokushima Research Institute, Otsuka Pharmaceutical Co., Ltd., Kawauchi-cho, Tokushima, Japan (K.U.); Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa Japan (K.M., M.N.); and WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Japan (M.N.)
| | - Kenji Takeuchi
- Department of Drug Metabolism and Pharmacokinetics, Nonclinical Research Center, Tokushima Research Institute, Otsuka Pharmaceutical Co., Ltd., Kawauchi-cho, Tokushima, Japan (K.M., K.T.); Nonclinical Research Center, Tokushima Research Institute, Otsuka Pharmaceutical Co., Ltd., Kawauchi-cho, Tokushima, Japan (K.U.); Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa Japan (K.M., M.N.); and WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Japan (M.N.)
| | - Ken Umehara
- Department of Drug Metabolism and Pharmacokinetics, Nonclinical Research Center, Tokushima Research Institute, Otsuka Pharmaceutical Co., Ltd., Kawauchi-cho, Tokushima, Japan (K.M., K.T.); Nonclinical Research Center, Tokushima Research Institute, Otsuka Pharmaceutical Co., Ltd., Kawauchi-cho, Tokushima, Japan (K.U.); Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa Japan (K.M., M.N.); and WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Japan (M.N.)
| | - Miki Nakajima
- Department of Drug Metabolism and Pharmacokinetics, Nonclinical Research Center, Tokushima Research Institute, Otsuka Pharmaceutical Co., Ltd., Kawauchi-cho, Tokushima, Japan (K.M., K.T.); Nonclinical Research Center, Tokushima Research Institute, Otsuka Pharmaceutical Co., Ltd., Kawauchi-cho, Tokushima, Japan (K.U.); Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa Japan (K.M., M.N.); and WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Japan (M.N.)
| |
Collapse
|
25
|
Watterson SH, Liu Q, Beaudoin Bertrand M, Batt DG, Li L, Pattoli MA, Skala S, Cheng L, Obermeier MT, Moore R, Yang Z, Vickery R, Elzinga PA, Discenza L, D’Arienzo C, Gillooly KM, Taylor TL, Pulicicchio C, Zhang Y, Heimrich E, McIntyre KW, Ruan Q, Westhouse RA, Catlett IM, Zheng N, Chaudhry C, Dai J, Galella MA, Tebben AJ, Pokross M, Li J, Zhao R, Smith D, Rampulla R, Allentoff A, Wallace MA, Mathur A, Salter-Cid L, Macor JE, Carter PH, Fura A, Burke JR, Tino JA. Discovery of Branebrutinib (BMS-986195): A Strategy for Identifying a Highly Potent and Selective Covalent Inhibitor Providing Rapid in Vivo Inactivation of Bruton’s Tyrosine Kinase (BTK). J Med Chem 2019; 62:3228-3250. [DOI: 10.1021/acs.jmedchem.9b00167] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Scott H. Watterson
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Qingjie Liu
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Myra Beaudoin Bertrand
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Douglas G. Batt
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Ling Li
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Mark A. Pattoli
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Stacey Skala
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Lihong Cheng
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Mary T. Obermeier
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Robin Moore
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Zheng Yang
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Rodney Vickery
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Paul A. Elzinga
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Lorell Discenza
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Celia D’Arienzo
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Kathleen M. Gillooly
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Tracy L. Taylor
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Claudine Pulicicchio
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Yifan Zhang
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Elizabeth Heimrich
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Kim W. McIntyre
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Qian Ruan
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Richard A. Westhouse
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Ian M. Catlett
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Naiyu Zheng
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Charu Chaudhry
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Jun Dai
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Michael A. Galella
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Andrew J. Tebben
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Matt Pokross
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Jianqing Li
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Rulin Zhao
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Daniel Smith
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Richard Rampulla
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Alban Allentoff
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Michael A. Wallace
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Arvind Mathur
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Luisa Salter-Cid
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - John E. Macor
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Percy H. Carter
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Aberra Fura
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - James R. Burke
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Joseph A. Tino
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| |
Collapse
|
26
|
Wang Z, Xu M, Bai J, Ge G, Guo X, Yu B, Xiao L, Geng D, Hao Y. Vildagliptin reduced extracellular matrix degradation in human primary chondrocytes. Eur J Pharmacol 2019; 844:49-55. [DOI: 10.1016/j.ejphar.2018.11.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 11/12/2018] [Accepted: 11/14/2018] [Indexed: 01/06/2023]
|
27
|
Shindo N, Fuchida H, Sato M, Watari K, Shibata T, Kuwata K, Miura C, Okamoto K, Hatsuyama Y, Tokunaga K, Sakamoto S, Morimoto S, Abe Y, Shiroishi M, Caaveiro JMM, Ueda T, Tamura T, Matsunaga N, Nakao T, Koyanagi S, Ohdo S, Yamaguchi Y, Hamachi I, Ono M, Ojida A. Selective and reversible modification of kinase cysteines with chlorofluoroacetamides. Nat Chem Biol 2019; 15:250-258. [PMID: 30643284 DOI: 10.1038/s41589-018-0204-3] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 11/16/2018] [Indexed: 01/27/2023]
Abstract
Irreversible inhibition of disease-associated proteins with small molecules is a powerful approach for achieving increased and sustained pharmacological potency. Here, we introduce α-chlorofluoroacetamide (CFA) as a novel warhead of targeted covalent inhibitor (TCI). Despite weak intrinsic reactivity, CFA-appended quinazoline showed high reactivity toward Cys797 of epidermal growth factor receptor (EGFR). In cells, CFA-quinazoline showed higher target specificity for EGFR than the corresponding Michael acceptors in a wide concentration range (0.1-10 μM). The cysteine adduct of the CFA derivative was susceptible to hydrolysis and reversibly yielded intact thiol but was stable in solvent-sequestered ATP-binding pocket of EGFR. This environment-dependent hydrolysis can potentially reduce off-target protein modification by CFA-based drugs. Oral administration of CFA quinazoline NS-062 significantly suppressed tumor growth in a mouse xenograft model. Further, CFA-appended pyrazolopyrimidine irreversibly inhibited Bruton's tyrosine kinase with higher target specificity. These results demonstrate the utility of CFA as a new class warheads for TCI.
Collapse
Affiliation(s)
- Naoya Shindo
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Hirokazu Fuchida
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Mami Sato
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Kosuke Watari
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Tomohiro Shibata
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
| | - Chizuru Miura
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Kei Okamoto
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Yuji Hatsuyama
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Keisuke Tokunaga
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Seiichi Sakamoto
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Satoshi Morimoto
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshito Abe
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Mitsunori Shiroishi
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Jose M M Caaveiro
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Tadashi Ueda
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Tomonori Tamura
- Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Naoya Matsunaga
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Takaharu Nakao
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Satoru Koyanagi
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Shigehiro Ohdo
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Yasuchika Yamaguchi
- Faculty of Pharmaceutical Sciences, Nagasaki International University, Sasebo, Japan
| | - Itaru Hamachi
- Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Mayumi Ono
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Akio Ojida
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan.
| |
Collapse
|
28
|
Determining molecular properties with differential mobility spectrometry and machine learning. Nat Commun 2018; 9:5096. [PMID: 30504922 PMCID: PMC6269546 DOI: 10.1038/s41467-018-07616-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 11/06/2018] [Indexed: 01/30/2023] Open
Abstract
The fast and accurate determination of molecular properties is highly desirable for many facets of chemical research, particularly in drug discovery where pre-clinical assays play an important role in paring down large sets of drug candidates. Here, we present the use of supervised machine learning to treat differential mobility spectrometry - mass spectrometry data for ten topological classes of drug candidates. We demonstrate that the gas-phase clustering behavior probed in our experiments can be used to predict the candidates' condensed phase molecular properties, such as cell permeability, solubility, polar surface area, and water/octanol distribution coefficient. All of these measurements are performed in minutes and require mere nanograms of each drug examined. Moreover, by tuning gas temperature within the differential mobility spectrometer, one can fine tune the extent of ion-solvent clustering to separate subtly different molecular geometries and to discriminate molecules of very similar physicochemical properties.
Collapse
|
29
|
Covalent simulations of covalent/irreversible enzyme inhibition in drug discovery: a reliable technical protocol. Future Med Chem 2018; 10:2265-2275. [DOI: 10.4155/fmc-2017-0304] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Aim: Irreversible covalent inhibition of biological targets in disease pathogenesis is an emerging field in drug design. Computational techniques have assumed a critical role in understanding covalent enzyme inhibition. However, a gap currently exists with regards to the reliability and reproducibility of currently available protocols available in literature and open scientific forums. Methodology/results: Appropriate ligand and protein target are selected, docked covalently or noncovalently using respective docking tools. Both components are subjected to premolecular dynamic preparations. This was followed by parameterization of the ligand, protein and covalent complex, respectively. The production runs were initiated and the resulting trajectories are saved and analyzed. Conclusion: This protocol is reliable and reproducible, hence would advance the development of irreversible covalent inhibitors toward disease treatment.
Collapse
|
30
|
Identification of a novel metabolite of vildagliptin in humans: Cysteine targets the nitrile moiety to form a thiazoline ring. Biochem Pharmacol 2018; 156:312-321. [PMID: 30172711 DOI: 10.1016/j.bcp.2018.08.043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 08/29/2018] [Indexed: 01/01/2023]
Abstract
The dipeptidyl peptidase-4 (DPP-4) inhibitor vildagliptin (VG) is used to treat type 2 diabetes. In rare cases, VG-induced liver injury has been reported. One case report suggested that immune responses were involved in the hepatotoxicity. However, the underlying mechanisms of VG-induced hepatotoxicity are uncertain. In the present study, we investigated whether VG has the potential to covalently bind to macromolecules in cells, a process that could initiate immune-mediated hepatotoxicity. For comparison, M20.7, a major metabolite of VG, and other DPP-4 inhibitors were also evaluated. We found that VG and anagliptin (ANG), which both contain a cyanopyrrolidine moiety, rapidly reacted in non-enzymatic manners on co-incubation with l-cysteine. Both VG and ANG had half-lives of 20-30 min. In contrast, incubation with GSH, rather than l-cysteine, failed to decrease the concentrations of VG or ANG. M20.7, sitagliptin, linagliptin, and alogliptin, having no cyanopyrrolidine moiety, were stable on incubation with l-cysteine or GSH. Structural analysis of the VG- and ANG-cysteine adducts, designated M407 and M487, respectively, revealed that the nitrile moieties of VG and ANG were irreversibly converted to a thiazoline acid. In conclusion, we found that VG and ANG have the potential to covalently bind to a thiol residue of l-cysteine in proteins. Such binding may lead to unpredictable immune responses in humans. l-Cysteine, rather than GSH, would likely be useful to detect the potential for covalent binding that could initiate immune-mediated hepatotoxicity.
Collapse
|
31
|
McAllister LA, Butler CR, Mente S, O’Neil SV, Fonseca KR, Piro JR, Cianfrogna JA, Foley TL, Gilbert AM, Harris AR, Helal CJ, Johnson DS, Montgomery JI, Nason DM, Noell S, Pandit J, Rogers BN, Samad TA, Shaffer CL, da Silva RG, Uccello DP, Webb D, Brodney MA. Discovery of Trifluoromethyl Glycol Carbamates as Potent and Selective Covalent Monoacylglycerol Lipase (MAGL) Inhibitors for Treatment of Neuroinflammation. J Med Chem 2018; 61:3008-3026. [DOI: 10.1021/acs.jmedchem.8b00070] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Laura A. McAllister
- Pfizer Worldwide Research and Development, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Christopher R. Butler
- Pfizer Worldwide Research and Development, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Scot Mente
- Pfizer Worldwide Research and Development, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Steven V. O’Neil
- Pfizer Worldwide Research and Development, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Kari R. Fonseca
- Pfizer Worldwide Research and Development, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Justin R. Piro
- Pfizer Worldwide Research and Development, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Julie A. Cianfrogna
- Pfizer Worldwide Research and Development, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Timothy L. Foley
- Pfizer Worldwide Research and Development, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Adam M. Gilbert
- Pfizer Worldwide Research and Development, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Anthony R. Harris
- Pfizer Worldwide Research and Development, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Christopher J. Helal
- Pfizer Worldwide Research and Development, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Douglas S. Johnson
- Pfizer Worldwide Research and Development, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Justin I. Montgomery
- Pfizer Worldwide Research and Development, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Deane M. Nason
- Pfizer Worldwide Research and Development, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Stephen Noell
- Pfizer Worldwide Research and Development, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Jayvardhan Pandit
- Pfizer Worldwide Research and Development, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Bruce N. Rogers
- Pfizer Worldwide Research and Development, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Tarek A. Samad
- Pfizer Worldwide Research and Development, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Christopher L. Shaffer
- Pfizer Worldwide Research and Development, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Rafael G. da Silva
- Pfizer Worldwide Research and Development, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Daniel P. Uccello
- Pfizer Worldwide Research and Development, 445 Eastern Point Road, Groton, Connecticut 06340, United States
| | - Damien Webb
- Pfizer Worldwide Research and Development, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Michael A. Brodney
- Pfizer Worldwide Research and Development, 610 Main Street, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
32
|
Rowe C, Shaeri M, Large E, Cornforth T, Robinson A, Kostrzewski T, Sison-Young R, Goldring C, Park K, Hughes D. Perfused human hepatocyte microtissues identify reactive metabolite-forming and mitochondria-perturbing hepatotoxins. Toxicol In Vitro 2017; 46:29-38. [PMID: 28919358 DOI: 10.1016/j.tiv.2017.09.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 09/03/2017] [Accepted: 09/13/2017] [Indexed: 12/17/2022]
Abstract
Hepatotoxins cause liver damage via many mechanisms but the formation of reactive metabolites and/or damage to liver mitochondria are commonly implicated. We assess 3D human primary hepatocyte microtissues as a platform for hepatotoxicity studies with reactive metabolite-forming and mitochondria-perturbing compounds. We show that microtissues formed from cryopreserved human hepatocytes had bile canaliculi, transcribed mRNA from genes associated with xenobiotic metabolism and expressed functional cytochrome P450 enzymes. Hierarchical clustering was used to distinguish dose-dependent hepatotoxicity elicited by clozapine, fialuridine and acetaminophen (APAP) from control cultures and less liver-damaging compounds, olanzapine and entecavir. The regio-isomer of acetaminophen, N-acetyl-meta-aminophenol (AMAP) clustered with the hepatotoxic compounds. The principal metabolites of APAP were formed and dose-dependent changes in metabolite profile similar to those seen in patient overdose was observed. The toxicological profile of APAP was indistinguishable from that of AMAP, confirming AMAP as a human hepatotoxin. Tissue oxygen consumption rate was significantly decreased within 2h of exposure to APAP or AMAP, concomitant with glutathione depletion. These data highlight the potential utility of perfused metabolically functional human liver microtissues in drug development and mechanistic toxicology.
Collapse
Affiliation(s)
- Cliff Rowe
- CN Bio Innovations Limited, BioPark, Broadwater Road, Welwyn Garden City AL7 3AX, UK
| | - Mohsen Shaeri
- CN Bio Innovations Limited, BioPark, Broadwater Road, Welwyn Garden City AL7 3AX, UK
| | - Emma Large
- CN Bio Innovations Limited, BioPark, Broadwater Road, Welwyn Garden City AL7 3AX, UK
| | - Terri Cornforth
- CN Bio Innovations Limited, BioPark, Broadwater Road, Welwyn Garden City AL7 3AX, UK
| | - Angela Robinson
- CN Bio Innovations Limited, BioPark, Broadwater Road, Welwyn Garden City AL7 3AX, UK
| | - Tomasz Kostrzewski
- CN Bio Innovations Limited, BioPark, Broadwater Road, Welwyn Garden City AL7 3AX, UK
| | - Rowena Sison-Young
- MRC Centre for Drug Safety Science, University of Liverpool, Ashton Street, Liverpool L69 3GE, UK
| | - Christopher Goldring
- MRC Centre for Drug Safety Science, University of Liverpool, Ashton Street, Liverpool L69 3GE, UK
| | - Kevin Park
- MRC Centre for Drug Safety Science, University of Liverpool, Ashton Street, Liverpool L69 3GE, UK
| | - David Hughes
- CN Bio Innovations Limited, BioPark, Broadwater Road, Welwyn Garden City AL7 3AX, UK.
| |
Collapse
|
33
|
Discovery and optimization of selective FGFR4 inhibitors via scaffold hopping. Bioorg Med Chem Lett 2017; 27:2420-2423. [PMID: 28433531 DOI: 10.1016/j.bmcl.2017.04.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 03/16/2017] [Accepted: 04/04/2017] [Indexed: 12/19/2022]
Abstract
Introduction of a Michael acceptor on a flexible scaffold derived from pan-FGFR inhibitors has successfully yielded a novel series of highly potent FGFR4 inhibitors with selectivity over FGFR1. Due to reduced lipophilicity and aromatic ring count, this series demonstrated improved solubility and permeability. However, plasma instability and fast metabolism limited its potential for in vivo studies. Efforts have been made to address these problems, which led to the discovery of compound (-)-11 with improved stability, CYP inhibition, and good activity/selectivity for further optimization.
Collapse
|
34
|
Plettenburg O. Was genau machen reaktive Fragmente eigentlich in Zellen? Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201607914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Oliver Plettenburg
- Helmholtz-Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt GmbH; Institut für Medizinalchemie; Ingolstädter Landstraße 1 85764 Neuherberg Deutschland
- Leibniz Universität Hannover; Schneiderberg 1B 30167 Hannover Deutschland
| |
Collapse
|
35
|
Plettenburg O. What Do Reactive Fragments Actually Do in Cells? Angew Chem Int Ed Engl 2016; 56:446-448. [PMID: 27936285 DOI: 10.1002/anie.201607914] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Indexed: 12/31/2022]
Abstract
Covalently binding molecules are frequently regarded as being generally promiscuous. In a recent study, binding selectivities and cellular target proteins of a wide variety of reactive fragments are examined in a proteome-wide context.
Collapse
Affiliation(s)
- Oliver Plettenburg
- Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt GmbH, Institute of Medicinal Chemistry, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany.,Leibniz Universität Hannover, Schneiderberg 1B, 30167, Hannover, Germany
| |
Collapse
|
36
|
Leung L, Yang X, Strelevitz TJ, Montgomery J, Brown MF, Zientek MA, Banfield C, Gilbert AM, Thorarensen A, Dowty ME. Clearance Prediction of Targeted Covalent Inhibitors by In Vitro-In Vivo Extrapolation of Hepatic and Extrahepatic Clearance Mechanisms. Drug Metab Dispos 2016; 45:1-7. [DOI: 10.1124/dmd.116.072983] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 10/25/2016] [Indexed: 12/22/2022] Open
|
37
|
An integrated approach for profiling oxidative metabolites and glutathione adducts using liquid chromatography coupled with ultraviolet detection and triple quadrupole-linear ion trap mass spectrometry. J Pharm Biomed Anal 2016; 129:482-491. [DOI: 10.1016/j.jpba.2016.07.048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 07/28/2016] [Accepted: 07/29/2016] [Indexed: 11/18/2022]
|
38
|
Baillie TA. Targeted Covalent Inhibitors for Drug Design. Angew Chem Int Ed Engl 2016; 55:13408-13421. [DOI: 10.1002/anie.201601091] [Citation(s) in RCA: 292] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Thomas A. Baillie
- Department of Medicinal Chemistry, School of Pharmacy; University of Washington; Box 357610 Seattle WA 98195-7610 USA
| |
Collapse
|
39
|
Affiliation(s)
- Thomas A. Baillie
- Department of Medicinal Chemistry, School of Pharmacy; University of Washington; Box 357610 Seattle WA 98195-7610 USA
| |
Collapse
|
40
|
Chen L, Zhang YH, Zou Q, Chu C, Ji Z. Analysis of the chemical toxicity effects using the enrichment of Gene Ontology terms and KEGG pathways. Biochim Biophys Acta Gen Subj 2016; 1860:2619-26. [PMID: 27208425 DOI: 10.1016/j.bbagen.2016.05.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 04/25/2016] [Accepted: 05/13/2016] [Indexed: 02/06/2023]
Abstract
BACKGROUND Chemical toxicity is one of the major barriers for designing and detecting new chemical entities during drug discovery. Unexpected toxicity of an approved drug may lead to withdrawal from the market and significant loss of the associated costs. Better understanding of the mechanisms underlying various toxicity effects can help eliminate unqualified candidate drugs in early stages, allowing researchers to focus their attention on other more viable candidates. METHODS In this study, we aimed to understand the mechanisms underlying several toxicity effects using Gene Ontology (GO) terms and KEGG pathways. GO term and KEGG pathway enrichment theories were adopted to encode each chemical, and the minimum redundancy maximum relevance (mRMR) was used to analyze the GO terms and the KEGG pathways. Based on the feature list obtained by the mRMR method, the most related GO terms and KEGG pathways were extracted. RESULTS Some important GO terms and KEGG pathways were uncovered, which were concluded to be significant for determining chemical toxicity effects. CONCLUSIONS Several GO terms and KEGG pathways are highly related to all investigated toxicity effects, while some are specific to a certain toxicity effect. GENERAL SIGNIFICANCE The findings in this study have the potential to further our understanding of different chemical toxicity mechanisms and to assist scientists in developing new chemical toxicity prediction algorithms. This article is part of a Special Issue entitled "System Genetics" Guest Editor: Dr. Yudong Cai and Dr. Tao Huang.
Collapse
Affiliation(s)
- Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai 201306, People's Republic of China.
| | - Yu-Hang Zhang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, People's Republic of China.
| | - Quan Zou
- School of Computer Science and Technology, Tianjin University, Tianjin 300072, People's Republic of China.
| | - Chen Chu
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, People's Republic of China.
| | - Zhiliang Ji
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, People's Republic of China.
| |
Collapse
|
41
|
Ballard TE, Dahal UP, Bessire AJ, Schneider RP, Geoghegan KF, Vaz ADN. A tag-free collisionally induced fragmentation approach to detect drug-adducted proteins by mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:2175-2183. [PMID: 26467230 DOI: 10.1002/rcm.7375] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 08/10/2015] [Accepted: 08/25/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE The covalent modification of proteins by toxicants, new chemical entities or drug molecules, either by metabolic activation or the presence of inherently reactive functional groups, is commonly implicated in organ toxicity and idiosyncratic reactions. In efforts to better prosecute protein modifications, we investigated a tag-free technique capable of detecting protein-small molecule adducts based solely on the collision-induced dissociation (CID) of the protein-small molecule complex. Detection of proteins using unique CID small molecule (SM) product ions would mitigate common issues associated with tagging technologies (e.g., altered reactivity/affinity of the protein-SM complex). METHODS A Waters SYNAPT G2 mass spectrometer (MS) was operated in MS(e) mode with appropriate collision energy conditions during the MS(2) acquisition for fragmentation of protein-small molecule adducts to generate characteristic small molecule product ions. RESULTS Ibrutinib, an acrylamide-containing small molecule drug, was shown to form adducts with rat serum albumin in ex vivo experiments and these adducts were detected by relying solely on the CID product ions generated from ibrutinib. Additionally, ibrutinib produced three CID product ions, one of which was a selective protein-ibrutinib fragment ion not produced by the compound alone. CONCLUSIONS Herein we describe a tag-free mass spectral detection technique for protein-small molecule conjugates that relies on the unique product ion fragmentation profile of the small molecule. This technique allows the detection of macromolecular ions containing the adducted small molecule from complex protein matrices through mass range selection for the unique product ions in the CID spectra.
Collapse
Affiliation(s)
- T Eric Ballard
- Pharmacokinetics, Dynamics and Metabolism, Pfizer, Inc., Groton, CT, 06340, USA
| | - Upendra P Dahal
- Pharmacokinetics, Dynamics and Metabolism, Pfizer, Inc., Groton, CT, 06340, USA
| | - Andrew J Bessire
- Pharmacokinetics, Dynamics and Metabolism, Pfizer, Inc., Groton, CT, 06340, USA
| | - Richard P Schneider
- Pharmacokinetics, Dynamics and Metabolism, Pfizer, Inc., Groton, CT, 06340, USA
| | | | - Alfin D N Vaz
- Pharmacokinetics, Dynamics and Metabolism, Pfizer, Inc., Groton, CT, 06340, USA
| |
Collapse
|
42
|
Theory and applications of covalent docking in drug discovery: merits and pitfalls. Molecules 2015; 20:1984-2000. [PMID: 25633330 PMCID: PMC6272664 DOI: 10.3390/molecules20021984] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 12/19/2014] [Accepted: 01/12/2015] [Indexed: 11/17/2022] Open
Abstract
The present art of drug discovery and design of new drugs is based on suicidal irreversible inhibitors. Covalent inhibition is the strategy that is used to achieve irreversible inhibition. Irreversible inhibitors interact with their targets in a time-dependent fashion, and the reaction proceeds to completion rather than to equilibrium. Covalent inhibitors possessed some significant advantages over non-covalent inhibitors such as covalent warheads can target rare, non-conserved residue of a particular target protein and thus led to development of highly selective inhibitors, covalent inhibitors can be effective in targeting proteins with shallow binding cleavage which will led to development of novel inhibitors with increased potency than non-covalent inhibitors. Several computational approaches have been developed to simulate covalent interactions; however, this is still a challenging area to explore. Covalent molecular docking has been recently implemented in the computer-aided drug design workflows to describe covalent interactions between inhibitors and biological targets. In this review we highlight: (i) covalent interactions in biomolecular systems; (ii) the mathematical framework of covalent molecular docking; (iii) implementation of covalent docking protocol in drug design workflows; (iv) applications covalent docking: case studies and (v) shortcomings and future perspectives of covalent docking. To the best of our knowledge; this review is the first account that highlights different aspects of covalent docking with its merits and pitfalls. We believe that the method and applications highlighted in this study will help future efforts towards the design of irreversible inhibitors.
Collapse
|
43
|
Flanagan ME, Abramite JA, Anderson DP, Aulabaugh A, Dahal UP, Gilbert AM, Li C, Montgomery J, Oppenheimer SR, Ryder T, Schuff BP, Uccello DP, Walker GS, Wu Y, Brown MF, Chen JM, Hayward MM, Noe MC, Obach RS, Philippe L, Shanmugasundaram V, Shapiro MJ, Starr J, Stroh J, Che Y. Chemical and computational methods for the characterization of covalent reactive groups for the prospective design of irreversible inhibitors. J Med Chem 2014; 57:10072-9. [PMID: 25375838 DOI: 10.1021/jm501412a] [Citation(s) in RCA: 213] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Interest in drugs that covalently modify their target is driven by the desire for enhanced efficacy that can result from the silencing of enzymatic activity until protein resynthesis can occur, along with the potential for increased selectivity by targeting uniquely positioned nucleophilic residues in the protein. However, covalent approaches carry additional risk for toxicities or hypersensitivity reactions that can result from covalent modification of unintended targets. Here we describe methods for measuring the reactivity of covalent reactive groups (CRGs) with a biologically relevant nucleophile, glutathione (GSH), along with kinetic data for a broad array of electrophiles. We also describe a computational method for predicting electrophilic reactivity, which taken together can be applied to the prospective design of thiol-reactive covalent inhibitors.
Collapse
Affiliation(s)
- Mark E Flanagan
- Center of Chemistry Innovation and Excellence, and ‡Department of Pharmacokinetics, Dynamics and Metabolism, Pfizer, Inc. , Eastern Point Road, Groton, Connecticut 06340, United States
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Weston JK, Uetrecht J. Activation of Inflammasomes by Agents Causing Idiosyncratic Skin Reactions: A Possible Biomarker. Chem Res Toxicol 2014; 27:949-51. [DOI: 10.1021/tx5001333] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- J. Kyle Weston
- Department of Pharmaceutical Sciences, Faculty of
Pharmacy, and ‡Department of
Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Jack Uetrecht
- Department of Pharmaceutical Sciences, Faculty of
Pharmacy, and ‡Department of
Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| |
Collapse
|
45
|
In situ selectivity profiling and crystal structure of SML-8-73-1, an active site inhibitor of oncogenic K-Ras G12C. Proc Natl Acad Sci U S A 2014; 111:8895-900. [PMID: 24889603 DOI: 10.1073/pnas.1404639111] [Citation(s) in RCA: 159] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Directly targeting oncogenic V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (K-Ras) with small-molecule inhibitors has historically been considered prohibitively challenging. Recent reports of compounds that bind directly to the K-Ras G12C mutant suggest avenues to overcome key obstacles that stand in the way of developing such compounds. We aim to target the guanine nucleotide (GN)-binding pocket because the natural contents of this pocket dictate the signaling state of K-Ras. Here, we characterize the irreversible inhibitor SML-8-73-1 (SML), which targets the GN-binding pocket of K-Ras G12C. We report a high-resolution X-ray crystal structure of G12C K-Ras bound to SML, revealing that the compound binds in a manner similar to GDP, forming a covalent linkage with Cys-12. The resulting conformation renders K-Ras in the open, inactive conformation, which is not predicted to associate productively with or activate downstream effectors. Conservation analysis of the Ras family GN-binding pocket reveals variability in the side chains surrounding the active site and adjacent regions, especially in the switch I region. This variability may enable building specificity into new iterations of Ras and other GTPase inhibitors. High-resolution in situ chemical proteomic profiling of SML confirms that SML effectively discriminates between K-Ras G12C and other cellular GTP-binding proteins. A biochemical assay provides additional evidence that SML is able to compete with millimolar concentrations of GTP and GDP for the GN-binding site.
Collapse
|