1
|
Seydimemet M, Yang Y, Lv Y, Liu J, Yan Z, Zhao Y, Wang X, Lu X. Design, Construction, and Screening of Diversified Pyrimidine-Focused DNA-Encoded Libraries. ACS Med Chem Lett 2023; 14:1073-1078. [PMID: 37583819 PMCID: PMC10424316 DOI: 10.1021/acsmedchemlett.3c00205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 07/24/2023] [Indexed: 08/17/2023] Open
Abstract
Pyrimidine is a ubiquitous component in natural products and approved drugs, providing an ideal modular scaffold for generating libraries with drug-like properties. DNA-encoded library technology introduces a novel library modality where each small molecule is covalently linked to a unique oligo tag. This technology offers the advantages of rapidly generating and interrogating large-scale libraries containing billions of members, substantially reducing the entry barrier to their use in both academia and the pharmaceutical industry. In this Letter, we describe the synthesis of three DNA-encoded libraries based on different functionalized pyrimidine cores featuring diversified chemoselectivity and regioselectivity. Preliminary screening of these DNA-encoded libraries against BRD4 identified compounds with nanomolar inhibition activities.
Collapse
Affiliation(s)
- Mengnisa Seydimemet
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech
Park, Pudong, Shanghai 201203, China
| | - Yixuan Yang
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech
Park, Pudong, Shanghai 201203, China
| | - Yuhan Lv
- School
of Pharmacy, Weifang Medical University, Weifang, 261053, Shandong P.R. China
| | - Jiaxiang Liu
- Alphama
Biotechnology Suzhou Co., Ltd., 108 Yuxin Road, Suzhou City, Jiangsu Province 215123, China
| | - Ziqin Yan
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech
Park, Pudong, Shanghai 201203, China
| | - Yujun Zhao
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech
Park, Pudong, Shanghai 201203, China
- University
of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Xuan Wang
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech
Park, Pudong, Shanghai 201203, China
| | - Xiaojie Lu
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
- State
Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Zhang Jiang Hi-Tech
Park, Pudong, Shanghai 201203, China
- University
of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| |
Collapse
|
2
|
Hordiyenko OV, Tkachuk VA, Shishkanu VO, Tkachuk TM, Shishkina SV. 2-Carbamimidoylbenzoic Acid as a New Effective and Available Precursor for the Synthesis of Substituted 2-(Pyrimidin-2-yl)benzoic Acids. SYNTHESIS-STUTTGART 2021. [DOI: 10.1055/s-0040-1705941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
AbstractA new approach to the synthesis of 2-(pyrimidin-2-yl)benzoic acids based on the ring contraction of the 2-carbamimidoylbenzoic acid [(2-amidinobenzoic) acid] with 1,3-dicarbonyl compounds and their synthetic equivalents has been developed. The intramolecular condensation of the obtained acids with 1,3-dielectrophiles proceeds with the formation of the 4,6-dihydropyrimido[2,1-a]isoindole-4,6-dione system, the pyrrolidone ring of which is easily opened under the action of weak nucleophiles. The reaction of 2-amidinobenzoic acid with chromones, which have an aryloxy group at 3-position does not stop at the step of pyrimidine ring formation and undergoes further spontaneous cyclization into 2-(benzo[4,5]furo[3,2-d]pyrimidin-2-yl)benzoic acids.
Collapse
|
3
|
Wu TT, Guo QQ, Chen ZL, Wang LL, Du Y, Chen R, Mao YH, Yang SG, Huang J, Wang JT, Wang L, Tang L, Zhang JQ. Design, synthesis and bioevaluation of novel substituted triazines as potential dual PI3K/mTOR inhibitors. Eur J Med Chem 2020; 204:112637. [PMID: 32717477 DOI: 10.1016/j.ejmech.2020.112637] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/29/2020] [Accepted: 07/01/2020] [Indexed: 12/16/2022]
Abstract
A series of novel substituted triazines bearing a benzimidazole scaffold were designed and synthesized based on the structures of known anti-cancer agents, namely gedatolisib and alpelisib. All the target compounds were screened for inhibitory activity against PI3Kα and mTOR kinases. Notably, most analogs exhibited IC50 in the nanomolar range. Investigation of the isozyme selectivity indicated that the compounds exhibited remarkable inhibitory activity against PI3Kδ, especially compound 19f showed an IC50 value of 2.3 nM for PI3Kδ and moderate δ-isozyme selectivity over other class I PI3K isoforms and mTOR (with IC50 values of 14.6, 34.0, 849.0 and 15.4 nM for PI3Kα, β, γ and mTOR, respectively). An in vitro MTT assay was conducted to assess the antiproliferative and cytotoxic effects of the prepared analogs. It was revealed that the compounds displayed significant inhibitory activities against the HCT116 human colon cancer cell line. Compound 19i showed 4.7-fold higher potency than the positive control gedatolisib (0.3 vs. 1.4 μM, IC50 values). Phosphoblot studies demonstrated that 19c and 19i could significantly suppress the PI3K/Akt/mTOR signaling pathway at 10 μM. Moreover, analogs 19b, 19c and 19i displayed better stability in artificial gastric fluids than gedatolisib, while 19i was indicated not very stable in rat liver microsomes, and may occur phase I metabolic transformations.
Collapse
Affiliation(s)
- Ting-Ting Wu
- State Key Laboratory of Functions and Applications of Medicinal Plants, College of Pharmacy, Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, Guiyang, 550004, China
| | - Qing-Qing Guo
- Joint International Research Laboratory of Synthetic Biology and Medicine, Ministry of Education, Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Zi-Li Chen
- The Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Li-Li Wang
- State Key Laboratory of Functions and Applications of Medicinal Plants, College of Pharmacy, Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, Guiyang, 550004, China
| | - Yao Du
- State Key Laboratory of Functions and Applications of Medicinal Plants, College of Pharmacy, Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, Guiyang, 550004, China
| | - Rui Chen
- State Key Laboratory of Functions and Applications of Medicinal Plants, College of Pharmacy, Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, Guiyang, 550004, China
| | - Yuan-Hu Mao
- State Key Laboratory of Functions and Applications of Medicinal Plants, College of Pharmacy, Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, Guiyang, 550004, China
| | - Sheng-Gang Yang
- State Key Laboratory of Functions and Applications of Medicinal Plants, College of Pharmacy, Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, Guiyang, 550004, China
| | - Jing Huang
- State Key Laboratory of Functions and Applications of Medicinal Plants, College of Pharmacy, Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, Guiyang, 550004, China
| | - Jian-Ta Wang
- State Key Laboratory of Functions and Applications of Medicinal Plants, College of Pharmacy, Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, Guiyang, 550004, China
| | - Ling Wang
- Joint International Research Laboratory of Synthetic Biology and Medicine, Ministry of Education, Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China.
| | - Lei Tang
- State Key Laboratory of Functions and Applications of Medicinal Plants, College of Pharmacy, Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, Guiyang, 550004, China
| | - Ji-Quan Zhang
- State Key Laboratory of Functions and Applications of Medicinal Plants, College of Pharmacy, Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, Guiyang, 550004, China.
| |
Collapse
|
4
|
Wu G, Wang H, Zhou W, Zeng B, Mo W, Zhu K, Liu R, Zhou J, Chen C, Chen H. Synthesis and structure–activity relationship studies of MI-2 analogues as MALT1 inhibitors. Bioorg Med Chem 2018; 26:3321-3344. [DOI: 10.1016/j.bmc.2018.04.059] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/25/2018] [Accepted: 04/30/2018] [Indexed: 12/13/2022]
|
5
|
Heterogeneous gold(I)-catalyzed [2 + 2 + 2] annulation between ynamides and nitriles: Straightforward synthesis of tetrasubstituted pyrimidines. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
6
|
Andrs M, Korabecny J, Jun D, Hodny Z, Bartek J, Kuca K. Phosphatidylinositol 3-Kinase (PI3K) and phosphatidylinositol 3-kinase-related kinase (PIKK) inhibitors: importance of the morpholine ring. J Med Chem 2014; 58:41-71. [PMID: 25387153 DOI: 10.1021/jm501026z] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Phosphatidylinositol 3-kinases (PI3Ks) and phosphatidylinositol 3-kinase-related protein kinases (PIKKs) are two related families of kinases that play key roles in regulation of cell proliferation, metabolism, migration, survival, and responses to diverse stresses including DNA damage. To design novel efficient strategies for treatment of cancer and other diseases, these kinases have been extensively studied. Despite their different nature, these two kinase families have related origin and share very similar kinase domains. Therefore, chemical inhibitors of these kinases usually carry analogous structural motifs. The most common feature of these inhibitors is a critical hydrogen bond to morpholine oxygen, initially present in the early nonspecific PI3K and PIKK inhibitor 3 (LY294002), which served as a valuable chemical tool for development of many additional PI3K and PIKK inhibitors. While several PI3K pathway inhibitors have recently shown promising clinical responses, inhibitors of the DNA damage-related PIKKs remain thus far largely in preclinical development.
Collapse
Affiliation(s)
- Martin Andrs
- Biomedical Research Center, University Hospital Hradec Kralove , Sokolska 81, 500 05 Hradec Kralove, Czech Republic
| | | | | | | | | | | |
Collapse
|
7
|
Design, synthesis and SAR study of novel trisubstituted pyrimidine amide derivatives as CCR4 antagonists. Molecules 2014; 19:3539-51. [PMID: 24662072 PMCID: PMC6271259 DOI: 10.3390/molecules19033539] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Revised: 03/17/2014] [Accepted: 03/18/2014] [Indexed: 01/07/2023] Open
Abstract
The design, synthesis and structure-activity relationship studies of some novel trisubstituted pyrimidine amide derivatives prepared as CCR4 antagonists are described. The activities of these compounds were evaluated by the CCR4-MDC chemotaxis inhibition assay. Compound 1, which we have previously reported as a potent antagonist of CCR4, was employed as the positive control. The results indicated that most of the synthesized compounds exhibited some chemotaxis inhibition activity against CCR4. Of these new compounds, compounds 6c, 12a and 12b, with IC50 values of 0.064, 0.077 and 0.069 μM, respectively, showed higher or similar activity compared with compound 1 (IC50 of 0.078 μM). These compounds provide a basis for further structural modifications. The systematic structure-activity relationship of these trisubstituted pyrimidine amide derivatives was discussed based on the obtained experimental data. The results from the SAR study may be useful for identifying more potent CCR4 antagonists.
Collapse
|
8
|
Chadha N, Jasuja H, Kaur M, Singh Bahia M, Silakari O. Imidazo[1,2-a]pyrazine inhibitors of phosphoinositide 3-kinase alpha (PI3Kα): 3D-QSAR analysis utilizing the Hybrid Monte Carlo algorithm to refine receptor-ligand complexes for molecular alignment. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2014; 25:221-247. [PMID: 24601789 DOI: 10.1080/1062936x.2014.883428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Phosphoinositide 3-kinase alpha (PI3Kα) is a lipid kinase involved in several cellular functions such as cell growth, proliferation, differentiation and survival, and its anomalous regulation leads to cancerous conditions. PI3Kα inhibition completely blocks the cancer signalling pathway, hence it can be explored as an important therapeutic target for cancer treatment. In the present study, docking analysis of 49 selective imidazo[1,2-a]pyrazine inhibitors of PI3Kα was carried out using the QM-Polarized ligand docking (QPLD) program of the Schrödinger software, followed by the refinement of receptor-ligand conformations using the Hybrid Monte Carlo algorithm in the Liaison program, and alignment of refined conformations of inhibitors was utilized for the development of an atom-based 3D-QSAR model in the PHASE program. Among the five generated models, the best model was selected corresponding to PLS factor 2, displaying the highest value of Q(2)test (0.650). The selected model also displayed high values of r(2)train (0.917), F-value (166.5) and Pearson-r (0.877) and a low value of SD (0.265). The contour plots generated for the selected 3D-QSAR model were correlated with the results of docking simulations. Finally, this combined information generated from 3D-QSAR and docking analysis was used to design new congeners.
Collapse
Affiliation(s)
- N Chadha
- a Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research , Punjabi University , Patiala , Punjab , India
| | | | | | | | | |
Collapse
|
9
|
Yang W, Shu M, Wang Y, Wang R, Hu Y, Meng L, Lin Z. 3D-QSAR and docking studies of 3-Pyridine heterocyclic derivatives as potent PI3K/mTOR inhibitors. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.09.049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
|
10
|
You X, Yu S, Liu Y. Reactions of Zirconocene Butadiyne or Monoyne Complexes with Nitriles: Straightfoward Synthesis of Functionalized Pyrimidines. Organometallics 2013. [DOI: 10.1021/om400880r] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Xu You
- State
Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Lu, Shanghai 200032, People’s Republic of China
| | - Shasha Yu
- State
Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Lu, Shanghai 200032, People’s Republic of China
| | - Yuanhong Liu
- State
Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Lu, Shanghai 200032, People’s Republic of China
| |
Collapse
|
11
|
Welker ME, Kulik G. Recent syntheses of PI3K/Akt/mTOR signaling pathway inhibitors. Bioorg Med Chem 2013; 21:4063-91. [PMID: 23735831 PMCID: PMC3711139 DOI: 10.1016/j.bmc.2013.04.083] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 04/30/2013] [Indexed: 12/20/2022]
Abstract
This review focuses on the syntheses of PI3K/Akt/mTOR inhibitors that have been reported outside of the patent literature in the last 5years but is largely centered on synthetic work reported in 2011 and 2012. While focused on syntheses of inhibitors, some information on in vitro and in vivo testing of compounds is also included. Many of these reported compounds are reversible, competitive adenosine triphosphate (ATP) binding inhibitors, so given the structural similarities of many of these compounds to the adenine core, this review presents recent work on inhibitors based on where the synthetic chemistry was started, that is, inhibitor syntheses which started with purines/pyrimidines are followed by inhibitor syntheses which began with pyridines, pyrazines, azoles, and triazines then moves to inhibitors which bear no structural resemblance to adenine: liphagal, wortmannin and quercetin analogs. The review then finishes with a short section on recent syntheses of phosphotidyl inositol (PI) analogs since competitive PI binding inhibitors represent an alternative to the competitive ATP binding inhibitors which have received the most attention.
Collapse
Affiliation(s)
- Mark E Welker
- Department of Chemistry, Wake Forest University, PO Box 7486, Winston-Salem, NC 27109, USA.
| | | |
Collapse
|
12
|
5-Benzothiazole substituted pyrimidine derivatives as HCV replication (replicase) inhibitors. Bioorg Med Chem Lett 2012; 22:3229-34. [PMID: 22472692 DOI: 10.1016/j.bmcl.2012.03.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Accepted: 03/07/2012] [Indexed: 11/20/2022]
Abstract
Based on a previously identified HCV replication (replicase) inhibitor 1, SAR efforts were conducted around the pyrimidine core to improve the potency and pharmacokinetic profile of the inhibitors. A benzothiazole moiety was found to be the optimal substituent at the pyrimidine 5-position. Due to potential reactivity concern, the 4-chloro residue was replaced by a methyl group with some loss in potency and enhanced rat in vivo profile. Extensive investigations at the C-2 position resulted in identification of compound 16 that demonstrated very good replicon potency, selectivity and rodent plasma/target organ concentration. Inhibitor 16 also demonstrated good plasma levels and oral bioavailability in dogs, while monkey exposure was rather low. Chemistry optimization towards a practical route to install the benzothiazole moiety resulted in an efficient direct C-H arylation protocol.
Collapse
|
13
|
Taher AT, Helwa AA. Novel Pyrimidinone Derivatives: Synthesis, Antitumor and Antimicrobial Evaluation. Chem Pharm Bull (Tokyo) 2012; 60:521-30. [DOI: 10.1248/cpb.60.521] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Azza Taher Taher
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Cairo University
| | - Amira Atef Helwa
- Department of Organic Chemistry, Faculty of Pharmacy, Misr University for Science and Technology
| |
Collapse
|
14
|
Sasada T, Aoki Y, Ikeda R, Sakai N, Konakahara T. Synthesis of Tri- or Tetrasubstituted Pyrimidine Derivatives through the [5+1] Annulation of Enamidines with either N,N-Dimethylformamide Dialkyl Acetals or Orthoesters and Their Application in a Ring Transformation of Pyrimidines to Pyrido[2,3-d]pyrimidi. Chemistry 2011; 17:9385-94. [DOI: 10.1002/chem.201100040] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Indexed: 11/11/2022]
|
15
|
Shuttleworth SJ, Silva FA, Cecil ARL, Tomassi CD, Hill TJ, Raynaud FI, Clarke PA, Workman P. Progress in the preclinical discovery and clinical development of class I and dual class I/IV phosphoinositide 3-kinase (PI3K) inhibitors. Curr Med Chem 2011; 18:2686-714. [PMID: 21649578 PMCID: PMC3228236 DOI: 10.2174/092986711796011229] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Revised: 05/13/2011] [Accepted: 05/15/2011] [Indexed: 01/01/2023]
Abstract
The phosphoinositide 3-kinases (PI3Ks) constitute an important family of lipid kinase enzymes that control a range of cellular processes through their regulation of a network of signal transduction pathways, and have emerged as important therapeutic targets in the context of cancer, inflammation and cardiovascular diseases. Since the mid-late 1990s, considerable progress has been made in the discovery and development of small molecule ATP-competitive PI3K inhibitors, a number of which have entered early phase human trials over recent years from which key clinical results are now being disclosed. This review summarizes progress made to date, primarily on the discovery and characterization of class I and dual class I/IV subtype inhibitors, together with advances that have been made in translational and clinical research, notably in cancer.
Collapse
Affiliation(s)
- S J Shuttleworth
- Karus Therapeutics Ltd., Southampton Science Park, Southampton, SO16 7NP, UK.
| | | | | | | | | | | | | | | |
Collapse
|