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Bai L, Deng Z, Xu M, Zhang Z, Guo G, Xue X, Wang S, Yang J, Xia Z. CETSA-MS-based target profiling of anti-aging natural compound quercetin. Eur J Med Chem 2024; 267:116203. [PMID: 38342014 DOI: 10.1016/j.ejmech.2024.116203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/16/2024] [Accepted: 01/31/2024] [Indexed: 02/13/2024]
Abstract
BACKGROUND Quercetin is widely distributed in nature and abundant in the human diet, which exhibits diverse biological activities and potential medical benefits. However, there remains a lack of comprehensive understanding about its cellular targets, impeding its in-depth mechanistic studies and clinical applications. PURPOSE This study aimed to profile protein targets of quercetin at the proteome level. METHODS A label-free CETSA-MS proteomics technique was employed for target enrichment and identification. The R package Inflect was used for melting curve fitting and target selection. D3Pocket and LiBiSco tools were used for binding pocket prediction and binding pocket analysis. Western blotting, molecular docking, site-directed mutagenesis and pull-down assays were used for target verification and validation. RESULTS We curated a library of direct binding targets of quercetin in cells. This library comprises 37 proteins that show increased thermal stability upon quercetin binding and 33 proteins that display decreased thermal stability. Through Western blotting, molecular docking, site-directed mutagenesis and pull-down assays, we validated CBR1 and GSK3A from the stabilized protein group and MAPK1 from the destabilized group as direct binding targets of quercetin. Moreover, we characterized the shared chemical properties of the binding pockets of quercetin with targets. CONCLUSION Our findings deepen our understanding of the proteins pivotal to the bioactivity of quercetin and lay the groundwork for further exploration into its mechanisms of action and potential clinical applications.
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Affiliation(s)
- Lin Bai
- Clinical Systems Biology Laboratories, Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Zhifen Deng
- Clinical Systems Biology Laboratories, Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Mengfei Xu
- Clinical Systems Biology Laboratories, Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Zhehao Zhang
- Department of Biochemistry, Faculty of Life Science, Faculty of Natural Science, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Guangyu Guo
- Clinical Systems Biology Laboratories, Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China; Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China; Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xinli Xue
- Clinical Systems Biology Laboratories, Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Shaochi Wang
- Clinical Systems Biology Laboratories, Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Jinghua Yang
- Clinical Systems Biology Laboratories, Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Zongping Xia
- Clinical Systems Biology Laboratories, Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China; Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China; Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
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Khan SA, Akhtar MJ, Gogoi U, Meenakshi DU, Das A. An Overview of 1,2,3-triazole-Containing Hybrids and Their Potential Anticholinesterase Activities. Pharmaceuticals (Basel) 2023; 16:179. [PMID: 37259329 PMCID: PMC9961747 DOI: 10.3390/ph16020179] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/18/2023] [Accepted: 01/22/2023] [Indexed: 07/30/2023] Open
Abstract
Acetylcholine (ACh) neurotransmitter of the cholinergic system in the brain is involved in learning, memory, stress responses, and cognitive functioning. It is hydrolyzed into choline and acetic acid by two key cholinesterase enzymes, viz., acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE). A loss or degeneration of cholinergic neurons that leads to a reduction in ACh levels is considered a significant contributing factor in the development of neurodegenerative diseases (NDs) such as Alzheimer's disease (AD). Numerous studies have shown that cholinesterase inhibitors can raise the level of ACh and, therefore, enhance people's quality of life, and, at the very least, it can temporarily lessen the symptoms of NDs. 1,2,3-triazole, a five-membered heterocyclic ring, is a privileged moiety, that is, a central scaffold, and is capable of interacting with a variety of receptors and enzymes to exhibit a broad range of important biological activities. Recently, it has been clubbed with other pharmacophoric fragments/molecules in hope of obtaining potent and selective AChE and/or BuChE inhibitors. The present updated review succinctly summarizes the different synthetic strategies used to synthesize the 1,2,3-triazole moiety. It also highlights the anticholinesterase potential of various 1,2,3-triazole di/trihybrids reported in the past seven years (2015-2022), including a rationale for hybridization and with an emphasis on their structural features for the development and optimization of cholinesterase inhibitors to treat NDs.
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Affiliation(s)
- Shah Alam Khan
- College of Pharmacy, National University of Science and Technology, Muscat 130, Oman
| | | | - Urvashee Gogoi
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh 786004, India
| | | | - Aparoop Das
- Department of Pharmaceutical Sciences, Dibrugarh University, Dibrugarh 786004, India
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Moinul M, Khatun S, Amin SA, Jha T, Gayen S. Recent trends in fragment-based anticancer drug design strategies against different targets: A mini-review. Biochem Pharmacol 2022; 206:115301. [DOI: 10.1016/j.bcp.2022.115301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 11/02/2022]
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Discovery of novel DprE1 inhibitors via computational bioactivity fingerprints and structure-based virtual screening. Acta Pharmacol Sin 2022; 43:1605-1615. [PMID: 34667293 PMCID: PMC9160271 DOI: 10.1038/s41401-021-00779-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/16/2021] [Indexed: 02/07/2023] Open
Abstract
Decaprenylphosphoryl-β-D-ribose oxidase (DprE1) plays important roles in the biosynthesis of mycobacterium cell wall. DprE1 inhibitors have shown great potentials in the development of new regimens for tuberculosis (TB) treatment. In this study, an integrated molecular modeling strategy, which combined computational bioactivity fingerprints and structure-based virtual screening, was employed to identify potential DprE1 inhibitors. Two lead compounds (B2 and H3) that could inhibit DprE1 and thus kill Mycobacterium smegmatis in vitro were identified. Moreover, compound H3 showed potent inhibitory activity against Mycobacterium tuberculosis in vitro (MICMtb = 1.25 μM) and low cytotoxicity against mouse embryo fibroblast NIH-3T3 cells. Our research provided an effective strategy to discover novel anti-TB lead compounds.
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Yu M, Yang Y, Sykes M, Wang S. Small-Molecule Inhibitors of Tankyrases as Prospective Therapeutics for Cancer. J Med Chem 2022; 65:5244-5273. [PMID: 35306814 DOI: 10.1021/acs.jmedchem.1c02139] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Tankyrases are multifunctional poly(adenosine diphosphate-ribose) polymerases that regulate diverse biological processes including telomere maintenance and cellular signaling. These processes are often implicated in a number of human diseases, with cancer being the most prevalent example. Accordingly, tankyrase inhibitors have gained increasing attention as potential therapeutics. Since the discovery of XAV939 and IWR-1 as the first tankyrase inhibitors over two decades ago, tankyrase-targeted drug discovery has made significant progress. This review starts with an introduction of tankyrases, with emphasis placed on their cancer-related functions. Small-molecule inhibitors of tankyrases are subsequently delineated based on their distinct modes of binding to the enzymes. In addition to inhibitors that compete with oxidized nicotinamide adenine dinucleotide (NAD+) for binding to the catalytic domain of tankyrases, non-NAD+-competitive inhibitors are detailed. This is followed by a description of three clinically trialled tankyrase inhibitors. To conclude, some of challenges and prospects in developing tankyrase-targeted cancer therapies are discussed.
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Affiliation(s)
- Mingfeng Yu
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Yuchao Yang
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Matthew Sykes
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Shudong Wang
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
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Patel A, Bhatt H, Patel B. Structural insights on 2-phenylquinazolin-4-one derivatives as tankyrase inhibitors through CoMFA, CoMSIA, topomer CoMFA and HQSAR studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131636] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Glumoff T, Sowa ST, Lehtiö L. Assay technologies facilitating drug discovery for ADP-ribosyl writers, readers and erasers. Bioessays 2021; 44:e2100240. [PMID: 34816463 DOI: 10.1002/bies.202100240] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 12/14/2022]
Abstract
ADP-ribosylation is a post-translational modification catalyzed by writer enzymes - ADP-ribosyltransferases. The modification is part of many signaling events, can modulate the function and stability of target proteins, and often results in the recruitment of reader proteins that bind to the ADP-ribosyl groups. Erasers are integral actors in these signaling events and reverse the modification. ADP-ribosylation can be targeted with therapeutics and many inhibitors against writers exist, with some being in clinical use. Inhibitors against readers and erasers are sparser and development of these has gained momentum only in recent years. Drug discovery has been hampered by the lack of specific tools, however many significant advances in the methods have recently been reported. We discuss assays used in the field with a focus on methods allowing efficient identification of small molecule inhibitors and profiling against enzyme families. While human proteins are focused, the methods can be also applied to bacterial toxins and virus encoded erasers that can be targeted to treat infectious diseases in the future.
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Affiliation(s)
- Tuomo Glumoff
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Sven T Sowa
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Lari Lehtiö
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
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Mamedov VA, Mamedova VL, Qu ZW, Zhu H, Galimullina VR, Korshin DE, Khikmatova GZ, Litvinov IA, Latypov SK, Sinyashin OG, Grimme S. Synthesis and Mechanistic Insights of the Formation of 3-Hydroxyquinolin-2-ones including Viridicatin from 2-Chloro- N,3-diaryloxirane-2-carboxamides under Acid-Catalyzed Rearrangements. J Org Chem 2021; 86:13514-13534. [PMID: 34505764 DOI: 10.1021/acs.joc.1c01592] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
N-Benzyl-2-chloro-N,3-diaryloxirane-2-carboxamides, easily obtained from aromatic aldehydes and anilides of dichloroacetic acid under Darzens condensation conditions, proved to be excellent starting compounds for the synthesis of 3-hydroxyindolin-2-ones, cyclohepto[b]pyrrole-2,3-diones, and 1-azaspiro[4.5]deca-3,6,9-triene-2-ones via the C(sp2)-C(sp2) bond formation in the first case and C(sp2)-C(sp3) bond formation in the second and third cases. Under optimized reaction conditions, 3-hydroxyindolin-2-ones are obtained in a one-pot process, which involves the treatment of N-benzyl-2-chloro-N,3-diaryloxirane-2-carboxamides with CF3CO2H or AcOH/H2SO4. In the case of intramolecular cyclization, the detailed reaction channels depend strongly on the substituents present in the anilide component and in the aromatic ring of the aldehyde component of N-benzyl-2-chloro-N,3-diaryloxirane-2-carboxamides, as well as the temperature and duration of the reaction. A combined experimental and DFT mechanistic study of the formation of 1-benzyl-3-hydroxy-4-arylquinolin-2(1H)-ones showed that there are three competing reaction channels: (a) ring-closure via the ipso site, (b) ring-closure via the 1,2-Cl shift, and (c) ring-closure via the ortho site. Such mechanistic insights enabled an effective one-pot gram-scale synthesis of viridicatin from benzaldehyde and 2,2-dichloro-N-(4-methoxybenzyl)-N-phenylacetamide.
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Affiliation(s)
- Vakhid A Mamedov
- A.E. Arbuzov Institute of Organic and Physical Chemistry, RFC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Street 8, 420088 Kazan, Russian Federation
| | - Vera L Mamedova
- A.E. Arbuzov Institute of Organic and Physical Chemistry, RFC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Street 8, 420088 Kazan, Russian Federation
| | - Zheng-Wang Qu
- Mulliken Center for Theoretical Chemistry University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Hui Zhu
- Mulliken Center for Theoretical Chemistry University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Venera R Galimullina
- A.E. Arbuzov Institute of Organic and Physical Chemistry, RFC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Street 8, 420088 Kazan, Russian Federation
| | - Dmitry E Korshin
- A.E. Arbuzov Institute of Organic and Physical Chemistry, RFC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Street 8, 420088 Kazan, Russian Federation
| | - Gul'naz Z Khikmatova
- A.E. Arbuzov Institute of Organic and Physical Chemistry, RFC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Street 8, 420088 Kazan, Russian Federation
| | - Igor A Litvinov
- A.E. Arbuzov Institute of Organic and Physical Chemistry, RFC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Street 8, 420088 Kazan, Russian Federation
| | - Shamil K Latypov
- A.E. Arbuzov Institute of Organic and Physical Chemistry, RFC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Street 8, 420088 Kazan, Russian Federation
| | - Oleg G Sinyashin
- A.E. Arbuzov Institute of Organic and Physical Chemistry, RFC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Street 8, 420088 Kazan, Russian Federation
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry University of Bonn, Beringstr. 4, 53115 Bonn, Germany
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Liu Z, Wang P, Wold EA, Song Q, Zhao C, Wang C, Zhou J. Small-Molecule Inhibitors Targeting the Canonical WNT Signaling Pathway for the Treatment of Cancer. J Med Chem 2021; 64:4257-4288. [PMID: 33822624 DOI: 10.1021/acs.jmedchem.0c01799] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Canonical WNT signaling is an important developmental pathway that has attracted increased attention for anticancer drug discovery. From the production and secretion of WNT ligands, their binding to membrane receptors, and the β-catenin destruction complex to the expansive β-catenin transcriptional complex, multiple components have been investigated as drug targets to modulate WNT signaling. Significant progress in developing WNT inhibitors such as porcupine inhibitors, tankyrase inhibitors, β-catenin/coactivators, protein-protein interaction inhibitors, casein kinase modulators, DVL inhibitors, and dCTPP1 inhibitors has been made, with several candidates (e.g., LGK-974, PRI-724, and ETC-159) in human clinical trials. Herein we summarize recent progress in the drug discovery and development of small-molecule inhibitors targeting the canonical WNT pathway, focusing on their specific target proteins, in vitro and in vivo activities, physicochemical properties, and therapeutic potential. The relevant opportunities and challenges toward maintaining the balance between efficacy and toxicity in effectively targeting this pathway are also highlighted.
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Affiliation(s)
- Zhiqing Liu
- Institute of Evolution and Marine Biodiversity, College of Food Science and Technology, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Pingyuan Wang
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, Texas 77555, United States
| | - Eric A Wold
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, Texas 77555, United States
| | - Qiaoling Song
- Institute of Evolution and Marine Biodiversity, College of Food Science and Technology, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Chenyang Zhao
- Institute of Evolution and Marine Biodiversity, College of Food Science and Technology, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Changyun Wang
- Institute of Evolution and Marine Biodiversity, College of Food Science and Technology, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, Texas 77555, United States
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Bioinformatic Analysis of the Nicotinamide Binding Site in Poly(ADP-Ribose) Polymerase Family Proteins. Cancers (Basel) 2021; 13:cancers13061201. [PMID: 33801950 PMCID: PMC8002165 DOI: 10.3390/cancers13061201] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/02/2021] [Accepted: 03/05/2021] [Indexed: 12/27/2022] Open
Abstract
Simple Summary The PARP family consists of 17 proteins, and some of them are responsible for cancer cells’ viability. Much attention is therefore given to the search for chemical compounds with the ability to suppress distinct PARP family members (for example, PARP-5a and 5b). Here, we present the results of a family-wide bioinformatic analysis of an important functional region in the PARP structure and describe factors that can guide the design of highly selective compounds. Abstract The PARP family consists of 17 members with diverse functions, including those related to cancer cells’ viability. Several PARP inhibitors are of great interest as innovative anticancer drugs, but they have low selectivity towards distinct PARP family members and exert serious adverse effects. We describe a family-wide study of the nicotinamide (NA) binding site, an important functional region in the PARP structure, using comparative bioinformatic analysis and molecular modeling. Mutations in the NA site and D-loop mobility around the NA site were identified as factors that can guide the design of selective PARP inhibitors. Our findings are of particular importance for the development of novel tankyrase (PARPs 5a and 5b) inhibitors for cancer therapy.
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Damale MG, Pathan SK, Shinde DB, Patil RH, Arote RB, Sangshetti JN. Insights of tankyrases: A novel target for drug discovery. Eur J Med Chem 2020; 207:112712. [PMID: 32877803 DOI: 10.1016/j.ejmech.2020.112712] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 12/24/2022]
Abstract
Tankyrases are the group of enzymes belonging to a class of Poly (ADP-ribose) polymerase (PARP) recently named ADP-ribosyltransferase (ARTD). The two isoforms of tankyrase i.e. tankyrase1 (TNKS1) and tankyrase2 (TNKS2) were abundantly expressed in various biological functions in telomere regulation, Wnt/β-catenin signaling pathway, viral replication, endogenous hormone regulation, glucose transport, cherubism disease, erectile dysfunction, and apoptosis. The structural analysis, mechanistic information, in vitro and in vivo studies led identification and development of several classes of tankyrase inhibitors under clinical phases. In the nutshell, this review will drive future research on tankyrase as it enlighten the structural and functional features of TNKS 1 and TNKS 2, different classes of inhibitors with their structure-activity relationship studies, molecular modeling studies, as well as past, current and future perspective of the different class of tankyrase inhibitors.
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Affiliation(s)
- Manoj G Damale
- Department of Pharmaceutical Medicinal Chemistry, Srinath College of Pharmacy, Aurangabad, 431136, MS, India
| | - Shahebaaz K Pathan
- Y.B. Chavan College of Pharmacy, Dr. Rafiq Zakaria Campus, Rauza Baugh, Aurangabad, MS, 431001, India
| | | | - Rajendra H Patil
- Department of Biotechnology, Savitribai Phule Pune University, Pune, 411007, M.S, India
| | - Rohidas B Arote
- Department of Molecular Genetics, School of Dentistry, Seoul National University, Seoul, Republic of Korea
| | - Jaiprakash N Sangshetti
- Y.B. Chavan College of Pharmacy, Dr. Rafiq Zakaria Campus, Rauza Baugh, Aurangabad, MS, 431001, India.
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Discovery of small molecules targeting GRP78 for antiangiogenic and anticancer therapy. Eur J Med Chem 2020; 193:112228. [DOI: 10.1016/j.ejmech.2020.112228] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 03/10/2020] [Accepted: 03/10/2020] [Indexed: 12/30/2022]
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Gao K, Oerlemans R, Groves MR. Theory and applications of differential scanning fluorimetry in early-stage drug discovery. Biophys Rev 2020; 12:85-104. [PMID: 32006251 PMCID: PMC7040159 DOI: 10.1007/s12551-020-00619-2] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 01/08/2020] [Indexed: 02/06/2023] Open
Abstract
Differential scanning fluorimetry (DSF) is an accessible, rapid, and economical biophysical technique that has seen many applications over the years, ranging from protein folding state detection to the identification of ligands that bind to the target protein. In this review, we discuss the theory, applications, and limitations of DSF, including the latest applications of DSF by ourselves and other researchers. We show that DSF is a powerful high-throughput tool in early drug discovery efforts. We place DSF in the context of other biophysical methods frequently used in drug discovery and highlight their benefits and downsides. We illustrate the uses of DSF in protein buffer optimization for stability, refolding, and crystallization purposes and provide several examples of each. We also show the use of DSF in a more downstream application, where it is used as an in vivo validation tool of ligand-target interaction in cell assays. Although DSF is a potent tool in buffer optimization and large chemical library screens when it comes to ligand-binding validation and optimization, orthogonal techniques are recommended as DSF is prone to false positives and negatives.
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Affiliation(s)
- Kai Gao
- Structure Biology in Drug Design, Drug Design Group XB20, Departments of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Rick Oerlemans
- Structure Biology in Drug Design, Drug Design Group XB20, Departments of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Matthew R Groves
- Structure Biology in Drug Design, Drug Design Group XB20, Departments of Pharmacy, University of Groningen, Groningen, The Netherlands.
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Hot CoFi Blot: A High-Throughput Colony-Based Screen for Identifying More Thermally Stable Protein Variants. Methods Mol Biol 2019. [PMID: 31267459 DOI: 10.1007/978-1-4939-9624-7_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Highly soluble and stable proteins are desirable for many different applications, from basic science to reaching a cancer patient in the form of a biological drug. For X-ray crystallography-where production of a protein crystal might take weeks and even months-a stable protein sample of high purity and concentration can greatly increase the chances of producing a well-diffracting crystal. For a patient receiving a specific protein drug, its safety, efficacy, and even cost are factors affected by its solubility and stability. Increased protein expression and protein stability can be achieved by randomly altering the coding sequence. As the number of mutants generated might be overwhelming, a powerful protein expression and stability screen is required. In this chapter, we describe a colony filtration technology, which allows us to screen random mutagenesis libraries for increased thermal stability-the Hot CoFi blot. We share how to create the random mutagenesis library, how to perform the Hot CoFi blot, and how to identify more thermally stable clones. We use the Tobacco Etch Virus protease as a target to exemplify the procedure.
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Alam S, Khan F. 3D-QSAR, Docking, ADME/Tox studies on Flavone analogs reveal anticancer activity through Tankyrase inhibition. Sci Rep 2019; 9:5414. [PMID: 30932078 PMCID: PMC6443786 DOI: 10.1038/s41598-019-41984-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 03/22/2019] [Indexed: 12/28/2022] Open
Abstract
Flavones are known as an inhibitor of tankyrase, a potential drug target of cancer. We here expedited the use of different computational approaches and presented a fast, easy, cost-effective and high throughput screening method to identify flavones analogs as potential tankyrase inhibitors. For this, we developed a field point based (3D-QSAR) quantitative structure-activity relationship model. The developed model showed acceptable predictive and descriptive capability as represented by standard statistical parameters r2 (0.89) and q2 (0.67). This model may help to explain SAR data and illustrated the key descriptors which were firmly related with the anticancer activity. Using the QSAR model a dataset of 8000 flavonoids were evaluated to classify the bioactivity, which resulted in the identification of 1480 compounds with the IC50 value of less than 5 µM. Further, these compounds were scrutinized through molecular docking and ADMET risk assessment. Total of 25 compounds identified which further analyzed for drug-likeness, oral bioavailability, synthetic accessibility, lead-likeness, and alerts for PAINS & Brenk. Besides, metabolites of screened compounds were also analyzed for pharmacokinetics compliance. Finally, compounds F2, F3, F8, F11, F13, F20, F21 and F25 with predicted activity (IC50) of 1.59, 1, 0.62, 0.79, 3.98, 0.79, 0.63 and 0.64, respectively were find as top hit leads. This study is offering the first example of a computationally-driven tool for prioritization and discovery of novel flavone scaffold for tankyrase receptor affinity with high therapeutic windows.
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Affiliation(s)
- Sarfaraz Alam
- Metabolic & Structural Biology Department, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O.-CIMAP, Lucknow, 226015, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Feroz Khan
- Metabolic & Structural Biology Department, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O.-CIMAP, Lucknow, 226015, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Bai N, Roder H, Dickson A, Karanicolas J. Isothermal Analysis of ThermoFluor Data can readily provide Quantitative Binding Affinities. Sci Rep 2019; 9:2650. [PMID: 30804351 PMCID: PMC6389909 DOI: 10.1038/s41598-018-37072-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 11/30/2018] [Indexed: 01/20/2023] Open
Abstract
Differential scanning fluorimetry (DSF), also known as ThermoFluor or Thermal Shift Assay, has become a commonly-used approach for detecting protein-ligand interactions, particularly in the context of fragment screening. Upon binding to a folded protein, most ligands stabilize the protein; thus, observing an increase in the temperature at which the protein unfolds as a function of ligand concentration can serve as evidence of a direct interaction. While experimental protocols for this assay are well-developed, it is not straightforward to extract binding constants from the resulting data. Because of this, DSF is often used to probe for an interaction, but not to quantify the corresponding binding constant (Kd). Here, we propose a new approach for analyzing DSF data. Using unfolding curves at varying ligand concentrations, our "isothermal" approach collects from these the fraction of protein that is folded at a single temperature (chosen to be temperature near the unfolding transition). This greatly simplifies the subsequent analysis, because it circumvents the complicating temperature dependence of the binding constant; the resulting constant-temperature system can then be described as a pair of coupled equilibria (protein folding/unfolding and ligand binding/unbinding). The temperature at which the binding constants are determined can also be tuned, by adding chemical denaturants that shift the protein unfolding temperature. We demonstrate the application of this isothermal analysis using experimental data for maltose binding protein binding to maltose, and for two carbonic anhydrase isoforms binding to each of four inhibitors. To facilitate adoption of this new approach, we provide a free and easy-to-use Python program that analyzes thermal unfolding data and implements the isothermal approach described herein ( https://sourceforge.net/projects/dsf-fitting ).
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Affiliation(s)
- Nan Bai
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA
| | - Heinrich Roder
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Alex Dickson
- Department of Biochemistry & Molecular Biology and Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI, 48824, USA
| | - John Karanicolas
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.
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18
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Malinowski Z, Fornal E, Warpas A, Nowak M. Synthesis of benzoquinoline derivatives from formyl naphthylamines via Friedländer annulation under metal-free conditions. MONATSHEFTE FUR CHEMIE 2018. [DOI: 10.1007/s00706-018-2268-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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19
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Conventional and microwave prompted synthesis, antioxidant, anticholinesterase activity screening and molecular docking studies of new quinolone-triazole hybrids. Bioorg Chem 2018; 78:236-248. [DOI: 10.1016/j.bioorg.2018.03.017] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 03/09/2018] [Accepted: 03/18/2018] [Indexed: 11/22/2022]
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20
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Youssef KM, Fawzy IM, El-Subbagh HI. N -substituted-piperidines as Novel Anti-alzheimer Agents: Synthesis, antioxidant activity, and molecular docking study. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2018. [DOI: 10.1016/j.fjps.2017.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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21
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Toxoplasma Calcium-Dependent Protein Kinase 1 Inhibitors: Probing Activity and Resistance Using Cellular Thermal Shift Assays. Antimicrob Agents Chemother 2018; 62:AAC.00051-18. [PMID: 29555627 DOI: 10.1128/aac.00051-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 03/12/2018] [Indexed: 11/20/2022] Open
Abstract
In Toxoplasma gondii, calcium-dependent protein kinase 1 (CDPK1) is an essential protein kinase required for invasion of host cells. We have developed several hundred CDPK1 inhibitors, many of which block invasion. Inhibitors with similar 50% inhibitory concentrations (IC50s) were tested in thermal shift assays for their ability to stabilize CDPK1 in cell lysates, in intact cells, or in purified form. Compounds that inhibited parasite growth stabilized CDPK1 in all assays. In contrast, two compounds that showed poor growth inhibition stabilized CDPK1 in lysates but not in cells. Thus, cellular exclusion could explain exceptions in the correlation between the action on the target and cellular activity. We used thermal shift assays to examine CDPK1 in two clones that were independently selected by growth in the CDPK1 inhibitor RM-1-132 and that had increased 50% effective concentrations (EC50s) for the compound. The A and C clones had distinct point mutations in the CDPK1 kinase domain, H201Q and L96P, respectively, residues that lie near one another in the inactive isoform. Purified mutant proteins showed RM-1-132 IC50s and thermal shifts similar to those shown by wild-type CDPK1. Reduced inhibitor stabilization (and a presumed reduced interaction) was observed only in cellular thermal shift assays. This highlights the utility of cellular thermal shift assays in demonstrating that resistance involves reduced on-target engagement (even if biochemical assays suggest otherwise). Indeed, similar EC50s were observed upon overexpression of the mutant proteins, as in the corresponding drug-selected parasites, although high levels of CDPK1(H201Q) only modestly increased resistance compared to that achieved with high levels of wild-type enzyme.
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22
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Yu ZJ, Liu S, Zhou S, Li H, Yang F, Yang LL, Wu Y, Guo L, Li GB. Virtual target screening reveals rosmarinic acid and salvianolic acid A inhibiting metallo- and serine-β-lactamases. Bioorg Med Chem Lett 2018; 28:1037-1042. [PMID: 29477271 DOI: 10.1016/j.bmcl.2018.02.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 01/31/2018] [Accepted: 02/13/2018] [Indexed: 01/08/2023]
Abstract
Rosmarinic acid (RA), a polyphenolic phytochemical, has broad-spectrum biological and pharmacological activity. A virtual target screening method termed IFPTarget combined with enzyme inhibition assays led to the identification of the clinically relevant metallo-β-lactamase (MBL) VIM-2 as one of unexploited targets of RA. The enzyme kinetic studies indicated that RA is a fully reversible, substrate-competitive VIM-2 inhibitor. The isothermal titration calorimetry (ITC) analyses revealed that the initial binding of RA to VIM-2 is mainly due to enthalpy contribution. Further inhibition assays with RA related compounds revealed that salvianolic acid A, a derivative of RA, manifests potent inhibition to VIM-2, more interestingly, which shows inhibitory activity against the NDM-1, another clinically relevant MBL subtype, and the serine-β-lactamase TEM-1 that is structurally and mechanistically distinct from the VIM-2 and NDM-1.
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Affiliation(s)
- Zhu-Jun Yu
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Sha Liu
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Shu Zhou
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Hui Li
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Fan Yang
- College of Food and Bioengineering, Xihua University, Sichuan 610039, China
| | - Ling-Ling Yang
- College of Food and Bioengineering, Xihua University, Sichuan 610039, China
| | - Yong Wu
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Li Guo
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Sichuan 610041, China
| | - Guo-Bo Li
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Sichuan 610041, China.
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23
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Mariotti L, Pollock K, Guettler S. Regulation of Wnt/β-catenin signalling by tankyrase-dependent poly(ADP-ribosyl)ation and scaffolding. Br J Pharmacol 2017; 174:4611-4636. [PMID: 28910490 PMCID: PMC5727255 DOI: 10.1111/bph.14038] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 07/28/2017] [Accepted: 08/07/2017] [Indexed: 12/24/2022] Open
Abstract
The Wnt/β-catenin signalling pathway is pivotal for stem cell function and the control of cellular differentiation, both during embryonic development and tissue homeostasis in adults. Its activity is carefully controlled through the concerted interactions of concentration-limited pathway components and a wide range of post-translational modifications, including phosphorylation, ubiquitylation, sumoylation, poly(ADP-ribosyl)ation (PARylation) and acetylation. Regulation of Wnt/β-catenin signalling by PARylation was discovered relatively recently. The PARP tankyrase PARylates AXIN1/2, an essential central scaffolding protein in the β-catenin destruction complex, and targets it for degradation, thereby fine-tuning the responsiveness of cells to the Wnt signal. The past few years have not only seen much progress in our understanding of the molecular mechanisms by which PARylation controls the pathway but also witnessed the successful development of tankyrase inhibitors as tool compounds and promising agents for the therapy of Wnt-dependent dysfunctions, including colorectal cancer. Recent work has hinted at more complex roles of tankyrase in Wnt/β-catenin signalling as well as challenges and opportunities in the development of tankyrase inhibitors. Here we review some of the latest advances in our understanding of tankyrase function in the pathway and efforts to modulate tankyrase activity to re-tune Wnt/β-catenin signalling in colorectal cancer cells. LINKED ARTICLES This article is part of a themed section on WNT Signalling: Mechanisms and Therapeutic Opportunities. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v174.24/issuetoc.
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Affiliation(s)
- Laura Mariotti
- Division of Structural BiologyThe Institute of Cancer ResearchLondonUK
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
| | - Katie Pollock
- Division of Structural BiologyThe Institute of Cancer ResearchLondonUK
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
- Division of Cancer TherapeuticsThe Institute of Cancer ResearchLondonUK
| | - Sebastian Guettler
- Division of Structural BiologyThe Institute of Cancer ResearchLondonUK
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
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24
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Ferri M, Liscio P, Carotti A, Asciutti S, Sardella R, Macchiarulo A, Camaioni E. Targeting Wnt-driven cancers: Discovery of novel tankyrase inhibitors. Eur J Med Chem 2017; 142:506-522. [PMID: 29107427 DOI: 10.1016/j.ejmech.2017.09.030] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 09/15/2017] [Accepted: 09/16/2017] [Indexed: 01/11/2023]
Abstract
Recent years have seen substantially heightened interest in the discovery of tankyrase inhibitors (TNKSi) as new promising anticancer agents. In this framework, the aim of this review article is focused on the description of potent TNKSi also endowed with disruptor activity toward the Wnt/β-catenin signaling pathway. Beginning with an overview of the most characterized TNKSi deriving from several drug design approaches and classifying them on the basis of the molecular interactions with the target, we discuss only those ones acting against Wnt cancer cell lines. In addition, comprehensive structure property relationships (SPR) emerging from the hit evolution processes and preclinical results are provided. We then review the most promising TNKSi hitherto reported in literature, acting in vivo models of Wnt-driven cancers. Some outlooks on current issues and future directions in this field are also discussed.
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Affiliation(s)
- Martina Ferri
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Paride Liscio
- TES Pharma, Via P. Togliatti 22bis, 06073 Terrioli, Corciano, Italy
| | - Andrea Carotti
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Stefania Asciutti
- Icahn School of Medicine at Mount Sinai, Department of Oncological Sciences, 1425 Madison Ave, New York, NY 10029 USA
| | - Roccaldo Sardella
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Antonio Macchiarulo
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Emidio Camaioni
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy.
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25
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Thomson DW, Wagner AJ, Bantscheff M, Benson RE, Dittus L, Duempelfeld B, Drewes G, Krause J, Moore JT, Mueller K, Poeckel D, Rau C, Salzer E, Shewchuk L, Hopf C, Emery JG, Muelbaier M. Discovery of a Highly Selective Tankyrase Inhibitor Displaying Growth Inhibition Effects against a Diverse Range of Tumor Derived Cell Lines. J Med Chem 2017; 60:5455-5471. [DOI: 10.1021/acs.jmedchem.7b00137] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Douglas W. Thomson
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Anne J. Wagner
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Marcus Bantscheff
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - R. Edward Benson
- GlaxoSmithKline, Research Triangle Park, 5 Moore Drive, North Carolina 27709, United States
| | - Lars Dittus
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Birgit Duempelfeld
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Gerard Drewes
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Jana Krause
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - John T. Moore
- GlaxoSmithKline, Research Triangle Park, 5 Moore Drive, North Carolina 27709, United States
| | - Katrin Mueller
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Daniel Poeckel
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Christina Rau
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Elsa Salzer
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Lisa Shewchuk
- Protein, Cellular & Structural Sciences, GlaxoSmithKline, 1250 South Collegeville Road, Upper Providence, Pennsylvania 19426, United States
| | - Carsten Hopf
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - John G. Emery
- Virtual
Proof of Concept DPU, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Marcel Muelbaier
- Cellzome GmbH, A GlaxoSmithKline Company, Meyerhofstraße 1, 69117 Heidelberg, Germany
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26
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Discovery of a B-Cell Lymphoma 6 Protein-Protein Interaction Inhibitor by a Biophysics-Driven Fragment-Based Approach. J Med Chem 2017; 60:4358-4368. [PMID: 28471657 DOI: 10.1021/acs.jmedchem.7b00313] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
B-cell lymphoma 6 (BCL6) is a transcriptional factor that expresses in lymphocytes and regulates the differentiation and proliferation of lymphocytes. Therefore, BCL6 is a therapeutic target for autoimmune diseases and cancer treatment. This report presents the discovery of BCL6-corepressor interaction inhibitors by using a biophysics-driven fragment-based approach. Using the surface plasmon resonance (SPR)-based fragment screening, we successfully identified fragment 1 (SPR KD = 1200 μM, ligand efficiency (LE) = 0.28), a competitive binder to the natural ligand BCoR peptide. Moreover, we elaborated 1 into the more potent compound 7 (SPR KD = 0.078 μM, LE = 0.37, cell-free protein-protein interaction (PPI) IC50 = 0.48 μM (ELISA), cellular PPI IC50 = 8.6 μM (M2H)) by a structure-based design and structural integration with a second high-throughput screening hit.
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27
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Chan CK, Tsai YL, Chan YL, Chang MY. Synthesis of Substituted 2,3-Benzodiazepines. J Org Chem 2016; 81:9836-9847. [DOI: 10.1021/acs.joc.6b01935] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Chieh-Kai Chan
- Department of Medicinal and Applied Chemistry and General Research Centers of R&D Office, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Yu-Lin Tsai
- Department of Medicinal and Applied Chemistry and General Research Centers of R&D Office, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Yi-Ling Chan
- Department of Medicinal and Applied Chemistry and General Research Centers of R&D Office, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Meng-Yang Chang
- Department of Medicinal and Applied Chemistry and General Research Centers of R&D Office, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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28
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Scott DE, Spry C, Abell C. Differential Scanning Fluorimetry as Part of a Biophysical Screening Cascade. FRAGMENT-BASED DRUG DISCOVERY LESSONS AND OUTLOOK 2016. [DOI: 10.1002/9783527683604.ch07] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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29
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Martinez Molina D, Nordlund P. The Cellular Thermal Shift Assay: A Novel Biophysical Assay for In Situ Drug Target Engagement and Mechanistic Biomarker Studies. Annu Rev Pharmacol Toxicol 2016; 56:141-61. [DOI: 10.1146/annurev-pharmtox-010715-103715] [Citation(s) in RCA: 166] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Daniel Martinez Molina
- Division of Biophysics, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden;
- Pelago Bioscience AB, 171 65 Stockholm, Sweden
| | - Pär Nordlund
- Division of Biophysics, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden;
- School of Biological Sciences, Nanyang Technological University, Singapore 138673
- Institute of Cellular and Molecular Biology, Agency for Science, Technology and Research, Singapore 138673
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30
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Haikarainen T, Waaler J, Ignatev A, Nkizinkiko Y, Venkannagari H, Obaji E, Krauss S, Lehtiö L. Development and structural analysis of adenosine site binding tankyrase inhibitors. Bioorg Med Chem Lett 2016; 26:328-333. [DOI: 10.1016/j.bmcl.2015.12.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 12/01/2015] [Accepted: 12/07/2015] [Indexed: 01/08/2023]
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31
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Small-molecule inhibitors of Wnt signaling pathway: towards novel anticancer therapeutics. Future Med Chem 2015; 7:2485-505. [PMID: 26670195 DOI: 10.4155/fmc.15.159] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The Wnt signaling pathway involves secreted glycoproteins that bind to the Frizzled family receptors to activate intracellular signal transduction events that regulate cell proliferation, apoptosis, cell migration and many critical aspects of developmental biology. DISCUSSION Aberrant Wnt signaling underlies a wide range of pathologies in humans including tumor initiation, tumor growth, cell senescence, cell death, differentiation and metastasis. The inhibition of Wnt signaling offers a novel approach for anticancer therapeutics. CONCLUSION Focusing on recent developments, we reviewed the small-molecule inhibitors targeting various components of Wnt signaling pathways and the progress from the discovery of lead compounds to highly potent inhibitors with significant therapeutic potential.
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32
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Passeri D, Camaioni E, Liscio P, Sabbatini P, Ferri M, Carotti A, Giacchè N, Pellicciari R, Gioiello A, Macchiarulo A. Concepts and Molecular Aspects in the Polypharmacology of PARP-1 Inhibitors. ChemMedChem 2015; 11:1219-26. [PMID: 26424664 DOI: 10.1002/cmdc.201500391] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Indexed: 11/08/2022]
Abstract
Recent years have witnessed a renewed interest in PARP-1 inhibitors as promising anticancer agents with multifaceted functions. Particularly exciting developments include the approval of olaparib (Lynparza) for the treatment of refractory ovarian cancer in patients with BRCA1/2 mutations, and the increasing understanding of the polypharmacology of PARP-1 inhibitors. The aim of this review article is to provide the reader with a comprehensive overview of the distinct levels of the polypharmacology of PARP-1 inhibitors, including 1) inter-family polypharmacology, 2) intra-family polypharmacology, and 3) multi-signaling polypharmacology. Progress made in gaining insight into the molecular basis of these multiple target-independent and target-dependent activities of PARP-1 inhibitors are discussed, with an outlook on the potential impact that a better understanding of polypharmacology may have in aiding the explanation as to why some drug candidates work better than others in clinical settings, albeit acting on the same target with similar inhibitory potency.
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Affiliation(s)
- Daniela Passeri
- TES Pharma S.r.l., via Palmiro Togliatti 20, 06073 Corciano, Perugia, Italy
| | - Emidio Camaioni
- Dipartimento di Scienze Farmaceutiche, University of Perugia, Via del Liceo 1, 06123, Perugia, Italy
| | - Paride Liscio
- TES Pharma S.r.l., via Palmiro Togliatti 20, 06073 Corciano, Perugia, Italy
| | - Paola Sabbatini
- TES Pharma S.r.l., via Palmiro Togliatti 20, 06073 Corciano, Perugia, Italy
| | - Martina Ferri
- Dipartimento di Scienze Farmaceutiche, University of Perugia, Via del Liceo 1, 06123, Perugia, Italy
| | - Andrea Carotti
- Dipartimento di Scienze Farmaceutiche, University of Perugia, Via del Liceo 1, 06123, Perugia, Italy
| | - Nicola Giacchè
- TES Pharma S.r.l., via Palmiro Togliatti 20, 06073 Corciano, Perugia, Italy
| | | | - Antimo Gioiello
- Dipartimento di Scienze Farmaceutiche, University of Perugia, Via del Liceo 1, 06123, Perugia, Italy
| | - Antonio Macchiarulo
- Dipartimento di Scienze Farmaceutiche, University of Perugia, Via del Liceo 1, 06123, Perugia, Italy.
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33
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de Vicente J, Tivitmahaisoon P, Berry P, Bolin DR, Carvajal D, He W, Huang KS, Janson C, Liang L, Lukacs C, Petersen A, Qian H, Yi L, Zhuang Y, Hermann JC. Fragment-Based Drug Design of Novel Pyranopyridones as Cell Active and Orally Bioavailable Tankyrase Inhibitors. ACS Med Chem Lett 2015; 6:1019-24. [PMID: 26396691 DOI: 10.1021/acsmedchemlett.5b00251] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 08/04/2015] [Indexed: 11/29/2022] Open
Abstract
Tankyrase activity has been linked to the regulation of intracellular axin levels, which have been shown to be crucial for the Wnt pathway. Deregulated Wnt signaling is important for the genesis of many diseases including cancer. We describe herein the discovery and development of a new series of tankyrase inhibitors. These pyranopyridones are highly active in various cell-based assays. A fragment/structure based optimization strategy led to a compound with good pharmacokinetic properties that is suitable for in vivo studies and further development.
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Affiliation(s)
- Javier de Vicente
- Discovery Chemistry, ‡Non-clinical Safety,§Discovery Technologies, and ∥Discovery Oncology, Small Molecule Research, Pharma Research & Early Development, Hoffmann-La Roche Inc., pRED, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Parcharee Tivitmahaisoon
- Discovery Chemistry, ‡Non-clinical Safety,§Discovery Technologies, and ∥Discovery Oncology, Small Molecule Research, Pharma Research & Early Development, Hoffmann-La Roche Inc., pRED, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Pamela Berry
- Discovery Chemistry, ‡Non-clinical Safety,§Discovery Technologies, and ∥Discovery Oncology, Small Molecule Research, Pharma Research & Early Development, Hoffmann-La Roche Inc., pRED, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - David R. Bolin
- Discovery Chemistry, ‡Non-clinical Safety,§Discovery Technologies, and ∥Discovery Oncology, Small Molecule Research, Pharma Research & Early Development, Hoffmann-La Roche Inc., pRED, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Daisy Carvajal
- Discovery Chemistry, ‡Non-clinical Safety,§Discovery Technologies, and ∥Discovery Oncology, Small Molecule Research, Pharma Research & Early Development, Hoffmann-La Roche Inc., pRED, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Wei He
- Discovery Chemistry, ‡Non-clinical Safety,§Discovery Technologies, and ∥Discovery Oncology, Small Molecule Research, Pharma Research & Early Development, Hoffmann-La Roche Inc., pRED, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Kuo-Sen Huang
- Discovery Chemistry, ‡Non-clinical Safety,§Discovery Technologies, and ∥Discovery Oncology, Small Molecule Research, Pharma Research & Early Development, Hoffmann-La Roche Inc., pRED, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Cheryl Janson
- Discovery Chemistry, ‡Non-clinical Safety,§Discovery Technologies, and ∥Discovery Oncology, Small Molecule Research, Pharma Research & Early Development, Hoffmann-La Roche Inc., pRED, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Lena Liang
- Discovery Chemistry, ‡Non-clinical Safety,§Discovery Technologies, and ∥Discovery Oncology, Small Molecule Research, Pharma Research & Early Development, Hoffmann-La Roche Inc., pRED, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Christine Lukacs
- Discovery Chemistry, ‡Non-clinical Safety,§Discovery Technologies, and ∥Discovery Oncology, Small Molecule Research, Pharma Research & Early Development, Hoffmann-La Roche Inc., pRED, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Ann Petersen
- Discovery Chemistry, ‡Non-clinical Safety,§Discovery Technologies, and ∥Discovery Oncology, Small Molecule Research, Pharma Research & Early Development, Hoffmann-La Roche Inc., pRED, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Hong Qian
- Discovery Chemistry, ‡Non-clinical Safety,§Discovery Technologies, and ∥Discovery Oncology, Small Molecule Research, Pharma Research & Early Development, Hoffmann-La Roche Inc., pRED, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Lin Yi
- Discovery Chemistry, ‡Non-clinical Safety,§Discovery Technologies, and ∥Discovery Oncology, Small Molecule Research, Pharma Research & Early Development, Hoffmann-La Roche Inc., pRED, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Yong Zhuang
- Discovery Chemistry, ‡Non-clinical Safety,§Discovery Technologies, and ∥Discovery Oncology, Small Molecule Research, Pharma Research & Early Development, Hoffmann-La Roche Inc., pRED, 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Johannes C. Hermann
- Discovery Chemistry, ‡Non-clinical Safety,§Discovery Technologies, and ∥Discovery Oncology, Small Molecule Research, Pharma Research & Early Development, Hoffmann-La Roche Inc., pRED, 340 Kingsland Street, Nutley, New Jersey 07110, United States
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34
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Wang H, Yu S. Synthesis of Isoquinolones Using Visible-Light-Promoted Denitrogenative Alkyne Insertion of 1,2,3-Benzotriazinones. Org Lett 2015; 17:4272-5. [DOI: 10.1021/acs.orglett.5b01960] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hao Wang
- State Key
Laboratory of Analytical
Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Shouyun Yu
- State Key
Laboratory of Analytical
Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
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35
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Nkizinkiko Y, Suneel Kumar BVS, Jeankumar VU, Haikarainen T, Koivunen J, Madhuri C, Yogeeswari P, Venkannagari H, Obaji E, Pihlajaniemi T, Sriram D, Lehtiö L. Discovery of potent and selective nonplanar tankyrase inhibiting nicotinamide mimics. Bioorg Med Chem 2015; 23:4139-4149. [PMID: 26183543 DOI: 10.1016/j.bmc.2015.06.063] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 06/22/2015] [Accepted: 06/24/2015] [Indexed: 11/18/2022]
Abstract
Diphtheria toxin-like ADP-ribosyltransferases catalyse a posttranslational modification, ADP-ribosylation and form a protein family of 17 members in humans. Two of the family members, tankyrases 1 and 2, are involved in several cellular processes including mitosis and Wnt/β-catenin signalling pathway. They are often over-expressed in cancer cells and have been linked with the survival of cancer cells making them potential therapeutic targets. In this study, we identified nine tankyrase inhibitors through virtual and in vitro screening. Crystal structures of tankyrase 2 with the compounds showed that they bind to the nicotinamide binding site of the catalytic domain. Based on the co-crystal structures we designed and synthesized a series of tetrahydroquinazolin-4-one and pyridopyrimidin-4-one analogs and were subsequently able to improve the potency of a hit compound almost 100-fold (from 11 μM to 150 nM). The most potent compounds were selective towards tankyrases over a panel of other human ARTD enzymes. They also inhibited Wnt/β-catenin pathway in a cell-based reporter assay demonstrating the potential usefulness of the identified new scaffolds for further development.
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Affiliation(s)
- Yves Nkizinkiko
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, PO Box 5400, FIN-90014 Oulu, Finland
| | - B V S Suneel Kumar
- Department of Pharmacy at Birla Institute of Technology and Science-Pilani, Hyderabad campus, Hyderabad 500078, India
| | - Variam Ullas Jeankumar
- Department of Pharmacy at Birla Institute of Technology and Science-Pilani, Hyderabad campus, Hyderabad 500078, India
| | - Teemu Haikarainen
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, PO Box 5400, FIN-90014 Oulu, Finland
| | - Jarkko Koivunen
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, PO Box 5400, FIN-90014 Oulu, Finland
| | - Chanduri Madhuri
- Department of Pharmacy at Birla Institute of Technology and Science-Pilani, Hyderabad campus, Hyderabad 500078, India
| | - Perumal Yogeeswari
- Department of Pharmacy at Birla Institute of Technology and Science-Pilani, Hyderabad campus, Hyderabad 500078, India
| | - Harikanth Venkannagari
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, PO Box 5400, FIN-90014 Oulu, Finland
| | - Ezeogo Obaji
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, PO Box 5400, FIN-90014 Oulu, Finland
| | - Taina Pihlajaniemi
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, PO Box 5400, FIN-90014 Oulu, Finland
| | - Dharmarajan Sriram
- Department of Pharmacy at Birla Institute of Technology and Science-Pilani, Hyderabad campus, Hyderabad 500078, India.
| | - Lari Lehtiö
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, PO Box 5400, FIN-90014 Oulu, Finland.
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36
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Zhan P, Song Y, Itoh Y, Suzuki T, Liu X. Recent advances in the structure-based rational design of TNKSIs. MOLECULAR BIOSYSTEMS 2015; 10:2783-99. [PMID: 25211064 DOI: 10.1039/c4mb00385c] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Human tankyrases 1 and 2 (TNKS1/2) are attractive pharmacological biotargets, especially for the treatment of specific types of cancer. This article provides a fairly comprehensive overview of the structural biology of the TNKS-inhibitor complex and the current medicinal chemistry strategies being used in the structure-based rational design of tankyrase-specific inhibitors.
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Affiliation(s)
- Peng Zhan
- Department of Medicinal Chemistry, Key laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44, West Culture Road, 250012, Jinan, Shandong, P. R. China.
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37
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Haikarainen T, Krauss S, Lehtio L. Tankyrases: structure, function and therapeutic implications in cancer. Curr Pharm Des 2015; 20:6472-88. [PMID: 24975604 PMCID: PMC4262938 DOI: 10.2174/1381612820666140630101525] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 06/26/2014] [Indexed: 12/22/2022]
Abstract
Several cellular signaling pathways are regulated by ADP-ribosylation, a posttranslational modification catalyzed by members of the ARTD superfamily. Tankyrases are distinguishable from the rest of this family by their unique domain organization, notably the sterile alpha motif responsible for oligomerization and ankyrin repeats mediating protein-protein interactions. Tankyrases are involved in various cellular functions, such as telomere homeostasis, Wnt/β-catenin signaling, glucose metabolism, and cell cycle progression. In these processes, Tankyrases regulate the interactions and stability of target proteins by poly (ADP-ribosyl)ation. Modified proteins are subsequently recognized by the E3 ubiquitin ligase RNF146, poly-ubiquitinated and predominantly guided to 26S proteasomal degradation. Several small molecule inhibitors have been described for Tankyrases; they compete with the co-substrate NAD+ for binding to the ARTD catalytic domain. The recent, highly potent and selective inhibitors possess several properties of lead compounds and can be used for proof-of-concept studies in cancer and other Tankyrase linked diseases.
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Affiliation(s)
| | | | - Lari Lehtio
- SFI-CAST Biomedical Innovation Center, Unit for Cell Signaling, Oslo University Hospital, Forskningsparken, Gaustadalleen 21, 0349, Oslo, Norway.
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38
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Tashima T. The structural use of carbostyril in physiologically active substances. Bioorg Med Chem Lett 2015; 25:3415-9. [PMID: 26112444 DOI: 10.1016/j.bmcl.2015.06.027] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 06/04/2015] [Accepted: 06/06/2015] [Indexed: 11/16/2022]
Abstract
Carbostyril (2-quinolinone, 2-quinolone) is an important structural component frequently used in natural products and in physiologically active substances including drugs. It is a 2-ring condensed heterocyclic compound containing several positions that can be replaced by arbitrary substituent groups and is used as a chemical building block, scaffold, fragment, and pharmacophore in drug design or discovery. Since the number of compounds that can be designed using carbostyril is exceedingly large, the steric structures of carbostyril derivatives can be adjusted to the unique, spatially oriented shape of, for example, the active sites of pharmaceutical target molecules. Moreover, the internal amide of the carbostyril unit exhibits distinctive features because of the fixed cis form of the lactam amide group. Because carbostyril has been used as a component in drugs and other bioactive compounds over time, carbostyril derivatives may improve absorption, distribution, metabolism, excretion, and toxicity (ADMET). Therefore, carbostyril derivatives have enormous potential. In this review, the potential and advantages of the use of carbostyril and its related molecular skeletons, such as 3,4-dihydrocarbostyril, are discussed by focusing on the physiologically active substances in which they are incorporated.
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Affiliation(s)
- Toshihiko Tashima
- Nippon Pharmaceutical Chemicals Co., Ltd, 2-8-18 Chodo, Higashi-Osaka, Osaka 577-0056, Japan.
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39
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Samain F, Ekblad T, Mikutis G, Zhong N, Zimmermann M, Nauer A, Bajic D, Decurtins W, Scheuermann J, Brown PJ, Hall J, Gräslund S, Schüler H, Neri D, Franzini RM. Tankyrase 1 Inhibitors with Drug-like Properties Identified by Screening a DNA-Encoded Chemical Library. J Med Chem 2015; 58:5143-9. [DOI: 10.1021/acs.jmedchem.5b00432] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Florent Samain
- Philochem AG, Libernstrasse 3, 8112 Otelfingen, Switzerland
| | - Torun Ekblad
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 2, 17177 Stockholm, Sweden
| | | | - Nan Zhong
- Structural
Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Mauro Zimmermann
- Institute
of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093 Zürich, Switzerland
| | - Angela Nauer
- Institute
of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093 Zürich, Switzerland
- Philochem AG, Libernstrasse 3, 8112 Otelfingen, Switzerland
| | - Davor Bajic
- Institute
of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093 Zürich, Switzerland
| | - Willy Decurtins
- Institute
of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093 Zürich, Switzerland
| | - Jörg Scheuermann
- Institute
of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093 Zürich, Switzerland
| | - Peter J. Brown
- Structural
Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Jonathan Hall
- Institute
of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093 Zürich, Switzerland
| | - Susanne Gräslund
- Structural
Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Herwig Schüler
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 2, 17177 Stockholm, Sweden
| | - Dario Neri
- Institute
of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093 Zürich, Switzerland
| | - Raphael M. Franzini
- Institute
of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093 Zürich, Switzerland
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40
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Kancherla R, Naveen T, Maiti D. Palladium-Catalyzed [3+3] Annulation between Diarylamines and α,β-Unsaturated Acids through CH Activation: Direct Access to 4-Substituted 2-Quinolinones. Chemistry 2015; 21:8360-4. [DOI: 10.1002/chem.201500774] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Indexed: 11/07/2022]
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41
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Kaur T, Wadhwa P, Sharma A. Arylsulfonylmethyl isocyanides: a novel paradigm in organic synthesis. RSC Adv 2015. [DOI: 10.1039/c5ra07876h] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
p-Tosylmethyl isocyanide (TosMIC), an α-acidic isocyanide has emerged as a privileged reagent to access biologically relevant fused heterocycles and some natural products like (−)-ushikulide A, variolin B, porphobilinogen and mansouramycin B.
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Affiliation(s)
- Tanpreet Kaur
- Department of Chemistry
- Indian Institute of Technology Roorkee
- Roorkee-247667
- India
| | - Preeti Wadhwa
- Department of Chemistry
- Indian Institute of Technology Roorkee
- Roorkee-247667
- India
| | - Anuj Sharma
- Department of Chemistry
- Indian Institute of Technology Roorkee
- Roorkee-247667
- India
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42
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Liscio P, Carotti A, Asciutti S, Ferri M, Pires MM, Valloscuro S, Ziff J, Clark NR, Macchiarulo A, Aaronson SA, Pellicciari R, Camaioni E. Scaffold hopping approach on the route to selective tankyrase inhibitors. Eur J Med Chem 2014; 87:611-23. [PMID: 25299683 DOI: 10.1016/j.ejmech.2014.10.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 09/30/2014] [Accepted: 10/02/2014] [Indexed: 11/15/2022]
Abstract
A virtual screening procedure was applied to identify new tankyrase inhibitors. Through pharmacophore screening of a compounds collection from the SPECS database, the methoxy[l]benzothieno[2,3-c]quinolin-6(5H)-one scaffold was identified as nicotinamide mimetic able to inhibit tankyrase activity at low micromolar concentration. In order to improve potency and selectivity, tandem structure-based and scaffold hopping approaches were carried out over the new scaffold leading to the discovery of the 2-(phenyl)-3H-benzo[4,5]thieno[3,2-d]pyrimidin-4-one as powerful chemotype suitable for tankyrase inhibition. The best compound 2-(4-tert-butyl-phenyl)-3H-benzo[4,5]thieno[3,2-d]pyrimidin-4-one (23) displayed nanomolar potencies (IC50s TNKS-1 = 21 nM and TNKS-2 = 29 nM) and high selectivity when profiled against several other PARPs. Furthermore, a striking Wnt signaling, as well as cell growth inhibition, was observed assaying 23 in DLD-1 cancer cells.
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Affiliation(s)
- Paride Liscio
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy; TES Pharma, Via P. Togliatti 22bis, 06073 Terrioli, Corciano, Italy
| | - Andrea Carotti
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Stefania Asciutti
- Icahn School of Medicine at Mount Sinai, Department of Oncological Sciences, 1425 Madison Ave, New York, NY 10029, USA
| | - Martina Ferri
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Maira M Pires
- Icahn School of Medicine at Mount Sinai, Department of Oncological Sciences, 1425 Madison Ave, New York, NY 10029, USA
| | - Sara Valloscuro
- Icahn School of Medicine at Mount Sinai, Department of Oncological Sciences, 1425 Madison Ave, New York, NY 10029, USA
| | - Jacob Ziff
- Icahn School of Medicine at Mount Sinai, Department of Oncological Sciences, 1425 Madison Ave, New York, NY 10029, USA
| | - Neil R Clark
- Icahn School of Medicine at Mount Sinai, Department of Pharmacology and Systems Therapeutics, 1425 Madison Ave, New York, NY 10029, USA
| | - Antonio Macchiarulo
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Stuart A Aaronson
- Icahn School of Medicine at Mount Sinai, Department of Oncological Sciences, 1425 Madison Ave, New York, NY 10029, USA
| | - Roberto Pellicciari
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy; TES Pharma, Via P. Togliatti 22bis, 06073 Terrioli, Corciano, Italy
| | - Emidio Camaioni
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy.
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43
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Design, synthesis and biological evaluation of thienopyridinones as Chk1 inhibitors. Bioorg Med Chem 2014; 22:4882-92. [DOI: 10.1016/j.bmc.2014.06.044] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 06/21/2014] [Accepted: 06/22/2014] [Indexed: 01/10/2023]
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44
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Pudlo M, Luzet V, Ismaïli L, Tomassoli I, Iutzeler A, Refouvelet B. Quinolone–benzylpiperidine derivatives as novel acetylcholinesterase inhibitor and antioxidant hybrids for Alzheimer Disease. Bioorg Med Chem 2014; 22:2496-507. [DOI: 10.1016/j.bmc.2014.02.046] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 02/20/2014] [Accepted: 02/24/2014] [Indexed: 10/25/2022]
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45
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Liscio P, Carotti A, Asciutti S, Karlberg T, Bellocchi D, Llacuna L, Macchiarulo A, Aaronson SA, Schüler H, Pellicciari R, Camaioni E. Design, synthesis, crystallographic studies, and preliminary biological appraisal of new substituted triazolo[4,3-b]pyridazin-8-amine derivatives as tankyrase inhibitors. J Med Chem 2014; 57:2807-12. [PMID: 24527792 DOI: 10.1021/jm401356t] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Searching for selective tankyrases (TNKSs) inhibitors, a new small series of 6,8-disubstituted triazolo[4,3-b]piridazines has been synthesized and characterized biologically. Structure-based optimization of the starting hit compound NNL (3) prompted us to the discovery of 4-(2-(6-methyl-[1,2,4]triazolo[4,3-b]pyridazin-8-ylamino)ethyl)phenol (12), a low nanomolar selective TNKSs inhibitor working as NAD isostere as ascertained by crystallographic analysis. Preliminary biological data candidate this new class of derivatives as a powerful pharmacological tools in the unraveling of TNKS implications in physiopathological conditions.
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Affiliation(s)
- Paride Liscio
- Dipartimento di Chimica e Tecnologia del Farmaco, Università degli Studi di Perugia , Via del Liceo 1, 06123 Perugia, Italy
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46
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Zhou SL, Guo LN, Wang S, Duan XH. Copper-catalyzed tandem oxidative cyclization of cinnamamides with benzyl hydrocarbons through cross-dehydrogenative coupling. Chem Commun (Camb) 2014; 50:3589-91. [DOI: 10.1039/c4cc00637b] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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47
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Steffen JD, Brody JR, Armen RS, Pascal JM. Structural Implications for Selective Targeting of PARPs. Front Oncol 2013; 3:301. [PMID: 24392349 PMCID: PMC3868897 DOI: 10.3389/fonc.2013.00301] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 11/26/2013] [Indexed: 12/22/2022] Open
Abstract
Poly(ADP-ribose) polymerases (PARPs) are a family of enzymes that use NAD(+) as a substrate to synthesize polymers of ADP-ribose (PAR) as post-translational modifications of proteins. PARPs have important cellular roles that include preserving genomic integrity, telomere maintenance, transcriptional regulation, and cell fate determination. The diverse biological roles of PARPs have made them attractive therapeutic targets, which have fueled the pursuit of small molecule PARP inhibitors. The design of PARP inhibitors has matured over the past several years resulting in several lead candidates in clinical trials. PARP inhibitors are mainly used in clinical trials to treat cancer, particularly as sensitizing agents in combination with traditional chemotherapy to reduce side effects. An exciting aspect of PARP inhibitors is that they are also used to selectivity kill tumors with deficiencies in DNA repair proteins (e.g., BRCA1/2) through an approach termed "synthetic lethality." In the midst of the tremendous efforts that have brought PARP inhibitors to the forefront of modern chemotherapy, most clinically used PARP inhibitors bind to conserved regions that permits cross-selectivity with other PARPs containing homologous catalytic domains. Thus, the differences between therapeutic effects and adverse effects stemming from pan-PARP inhibition compared to selective inhibition are not well understood. In this review, we discuss current literature that has found ways to gain selectivity for one PARP over another. We furthermore provide insights into targeting other domains that make up PARPs, and how new classes of drugs that target these domains could provide a high degree of selectivity by affecting specific cellular functions. A clear understanding of the inhibition profiles of PARP inhibitors will not only enhance our understanding of the biology of individual PARPs, but may provide improved therapeutic options for patients.
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Affiliation(s)
- Jamin D Steffen
- Department of Biochemistry and Molecular Biology, Kimmel Cancer Center, Thomas Jefferson University , Philadelphia, PA , USA
| | - Jonathan R Brody
- Department of Surgery, Division of Surgical Research, Jefferson Pancreas, Biliary, and Related Cancer Center, Kimmel Cancer Center, Thomas Jefferson University , Philadelphia, PA , USA
| | - Roger S Armen
- Department of Pharmaceutical Sciences, Kimmel Cancer Center, Thomas Jefferson University , Philadelphia, PA , USA
| | - John M Pascal
- Department of Biochemistry and Molecular Biology, Kimmel Cancer Center, Thomas Jefferson University , Philadelphia, PA , USA
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48
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Hua Z, Bregman H, Buchanan JL, Chakka N, Guzman-Perez A, Gunaydin H, Huang X, Gu Y, Berry V, Liu J, Teffera Y, Huang L, Egge B, Emkey R, Mullady EL, Schneider S, Andrews PS, Acquaviva L, Dovey J, Mishra A, Newcomb J, Saffran D, Serafino R, Strathdee CA, Turci SM, Stanton M, Wilson C, Dimauro EF. Development of novel dual binders as potent, selective, and orally bioavailable tankyrase inhibitors. J Med Chem 2013; 56:10003-15. [PMID: 24294969 DOI: 10.1021/jm401317z] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Tankyrases (TNKS1 and TNKS2) are proteins in the poly ADP-ribose polymerase (PARP) family. They have been shown to directly bind to axin proteins, which negatively regulate the Wnt pathway by promoting β-catenin degradation. Inhibition of tankyrases may offer a novel approach to the treatment of APC-mutant colorectal cancer. Hit compound 8 was identified as an inhibitor of tankyrases through a combination of substructure searching of the Amgen compound collection based on a minimal binding pharmacophore hypothesis and high-throughput screening. Herein we report the structure- and property-based optimization of compound 8 leading to the identification of more potent and selective tankyrase inhibitors 22 and 49 with improved pharmacokinetic properties in rodents, which are well suited as tool compounds for further in vivo validation studies.
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Affiliation(s)
- Zihao Hua
- Department of Chemistry Research and Discovery, ‡Department of Pharmacokinetics and Drug Metabolism, §Oncology Research, ∥Department of Molecular Structure, ⊥Bioassay and Profiling, and #Pharmaceutics, Amgen Inc. , 360 Binney Street, Cambridge, Massachusetts 02142, United States
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49
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Yuan H, Tai W, Hu S, Liu H, Zhang Y, Yao S, Ran T, Lu S, Ke Z, Xiong X, Xu J, Chen Y, Lu T. Fragment-based strategy for structural optimization in combination with 3D-QSAR. J Comput Aided Mol Des 2013; 27:897-915. [DOI: 10.1007/s10822-013-9687-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 10/24/2013] [Indexed: 12/14/2022]
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50
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Roussaki M, Hall B, Lima SC, da Silva AC, Wilkinson S, Detsi A. Synthesis and anti-parasitic activity of a novel quinolinone-chalcone series. Bioorg Med Chem Lett 2013; 23:6436-41. [PMID: 24119553 DOI: 10.1016/j.bmcl.2013.09.047] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 09/13/2013] [Accepted: 09/16/2013] [Indexed: 01/03/2023]
Abstract
A series of novel quinolinone-chalcone hybrids and analogues were designed, synthesized and their biological activity against the mammalian stages of Trypanosoma brucei and Leishmania infantum evaluated. Promising molecular scaffolds with significant microbicidal activity and low cytotoxicity were identified. Quinolinone-chalcone 10 exhibited anti-parasitic properties against both organisms, being the most potent anti-L. infantum agent of the entire series (IC50 value of 1.3±0.1 μM). Compounds 4 and 11 showed potency toward the intracellular, amastigote stage of L. infantum (IC50 values of 2.1±0.6 and 3.1±1.05 μM, respectively). Promising trypanocidal compounds include 5 and 10 (IC50 values of 2.6±0.1 and 3.3±0.1 μM, respectively) as well as 6 and 9 (both having IC50 values of <5 μM). Chemical modifications on the quinolinone-chalcone scaffold were performed on selected compounds in order to investigate the influence of these structural features on antiparasitic activity.
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Affiliation(s)
- Marina Roussaki
- Laboratory of Organic Chemistry, School of Chemical Engineering, National Technical University of Athens, Zografou Campus, 15780 Athens, Greece
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