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Diao Y, Liu D, Ge H, Zhang R, Jiang K, Bao R, Zhu X, Bi H, Liao W, Chen Z, Zhang K, Wang R, Zhu L, Zhao Z, Hu Q, Li H. Macrocyclization of linear molecules by deep learning to facilitate macrocyclic drug candidates discovery. Nat Commun 2023; 14:4552. [PMID: 37507402 PMCID: PMC10382584 DOI: 10.1038/s41467-023-40219-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Interest in macrocycles as potential therapeutic agents has increased rapidly. Macrocyclization of bioactive acyclic molecules provides a potential avenue to yield novel chemical scaffolds, which can contribute to the improvement of the biological activity and physicochemical properties of these molecules. In this study, we propose a computational macrocyclization method based on Transformer architecture (which we name Macformer). Leveraging deep learning, Macformer explores the vast chemical space of macrocyclic analogues of a given acyclic molecule by adding diverse linkers compatible with the acyclic molecule. Macformer can efficiently learn the implicit relationships between acyclic and macrocyclic structures represented as SMILES strings and generate plenty of macrocycles with chemical diversity and structural novelty. In data augmentation scenarios using both internal ChEMBL and external ZINC test datasets, Macformer display excellent performance and generalisability. We showcase the utility of Macformer when combined with molecular docking simulations and wet lab based experimental validation, by applying it to the prospective design of macrocyclic JAK2 inhibitors.
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Affiliation(s)
- Yanyan Diao
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Dandan Liu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Huan Ge
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Rongrong Zhang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Kexin Jiang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Runhui Bao
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Xiaoqian Zhu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Hongjie Bi
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Wenjie Liao
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Ziqi Chen
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Kai Zhang
- Innovation Center for AI and Drug Discovery, East China Normal University, Shanghai, 200062, China
| | - Rui Wang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Lili Zhu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Zhenjiang Zhao
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China
| | - Qiaoyu Hu
- Innovation Center for AI and Drug Discovery, East China Normal University, Shanghai, 200062, China
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China.
- Innovation Center for AI and Drug Discovery, East China Normal University, Shanghai, 200062, China.
- Lingang Laboratory, Shanghai, 200031, China.
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Bhujbal SP, Hah JM. An Intriguing Purview on the Design of Macrocyclic Inhibitors for Unexplored Protein Kinases through Their Binding Site Comparison. Pharmaceuticals (Basel) 2023; 16:1009. [PMID: 37513921 PMCID: PMC10386424 DOI: 10.3390/ph16071009] [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: 06/07/2023] [Revised: 07/02/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Kinases play an important role in regulating various intracellular signaling pathways that control cell proliferation, differentiation, survival, and other cellular processes, and their deregulation causes more than 400 diseases. Consequently, macrocyclization can be considered a noteworthy approach to developing new therapeutic agents for human diseases. Macrocyclization has emerged as an effective drug discovery strategy over the past decade to improve target selectivity and potency of small molecules. Small compounds with linear structures upon macrocyclization can lead to changes in their physicochemical and biological properties by firmly reducing conformational flexibility. A number of distinct protein kinases exhibit similar binding sites. Comparison of protein binding sites provides crucial insights for drug discovery and development. Binding site similarities are helpful in understanding polypharmacology, identifying potential off-targets, and repurposing known drugs. In this review, we focused on comparing the binding sites of those kinases for which macrocyclic inhibitors are available/studied so far. Furthermore, we calculated the volume of the binding site pocket for each targeted kinase and then compared it with the binding site pocket of the kinase for which only acyclic inhibitors were designed to date. Our review and analysis of several explored kinases might be useful in targeting new protein kinases for macrocyclic drug discovery.
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Affiliation(s)
- Swapnil P Bhujbal
- College of Pharmacy, Hanyang University, Ansan 426-791, Republic of Korea
- Institute of Pharmaceutical Science and Technology, Hanyang University, Ansan 426-791, Republic of Korea
| | - Jung-Mi Hah
- College of Pharmacy, Hanyang University, Ansan 426-791, Republic of Korea
- Institute of Pharmaceutical Science and Technology, Hanyang University, Ansan 426-791, Republic of Korea
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3
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Liang Y, Fang R, Rao Q. An Insight into the Medicinal Chemistry Perspective of Macrocyclic Derivatives with Antitumor Activity: A Systematic Review. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27092837. [PMID: 35566196 PMCID: PMC9100616 DOI: 10.3390/molecules27092837] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/24/2022] [Accepted: 04/27/2022] [Indexed: 11/16/2022]
Abstract
The profound pharmacological properties of macrocyclic compounds have led to their development as drugs. In conformationally pre-organized ring structures, the multiple functions and stereochemical complexity provided by the macrocycle result in high affinity and selectivity of protein targets while maintaining sufficient bioavailability to reach intracellular locations. Therefore, the construction of macrocycles is an ideal choice to solve the problem of “undruggable” targets. Inspection of 68 macrocyclic drugs on the market showed that 10 of them were used to treat cancer, but this structural class still has been poorly explored within drug discovery. This perspective considers the macrocyclic compounds used for anti-tumor with different targets, their advantages and disadvantages, and the various synthetic methods of them.
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Affiliation(s)
| | | | - Qiu Rao
- Correspondence: (Y.L.); (Q.R.)
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4
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Karati D, Mahadik KR, Trivedi P, Kumar D. A Molecular Insight into Pyrazole Congeners as Antimicrobial, Anticancer, and Antimalarial Agents. Med Chem 2022; 18:1044-1059. [PMID: 35240964 DOI: 10.2174/1573406418666220303150640] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/08/2021] [Accepted: 12/23/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Pyrazole is a bioactive heterocyclic congener found in a wide range of biological and pharmacological applications. Due to their multiple prospective uses, developing innovative pyrazoles and analogues, disclosing revolutionary ways for synthesizing this nucleus, investigating diverse potencies of that heterocycle, and seeking for possible applications of pyrazoles are all growing more significant Objectives: Pyrazole scaffolds have been proven to be successful as antimicrobial, anticancer, antimalarial therapeutic against multiple targets like DNA gyrase, topoisomerase IV, Hsp90, and several kinase enzymes. Its moiety has absorbed the attention of many scientists to research chemical and pharmacological profile due to this miscellany in the biotic region. RESULTS The review covers pyrazole scaffolds with a variety of biological functions, as well as attempts to connect the structure-activity relationship. Multiple pyrazole analogues have been produced as lead compounds, and their activities have been evaluated. CONCLUSION The combination of pyrazole with other pharmacophores in a molecule might lead to novel potent therapeutic medicines, which could aid in the development of potent lead compounds.
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Affiliation(s)
- Dipanjan Karati
- Poona College of Pharmacy, Department of Pharmaceutical Chemistry, Bharati Vidyapeeth (Deemed to be University), Erandwane, Pune- 411038, Maharashtra, India
| | - Kakasaheb Ramoo Mahadik
- Poona College of Pharmacy, Department of Pharmaceutical Chemistry, Bharati Vidyapeeth (Deemed to be University), Erandwane, Pune- 411038, Maharashtra, India
| | - Piyush Trivedi
- Hon. Director, Center of Innovation and Translational Research, Poona College of Pharmacy, Bhartiya Vidyapeeth, Pune 411038, India
| | - Dileep Kumar
- Poona College of Pharmacy, Department of Pharmaceutical Chemistry, Bharati Vidyapeeth (Deemed to be University), Erandwane, Pune- 411038, Maharashtra, India
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5
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Abstract
Abstract
Macrocycles represent an important class of ligands, both in natural products and designed drugs. In drug design, macrocyclizations can impart specific ligand conformations and contribute to passive permeation by encouraging intramolecular H-bonds. AutoDock-GPU and Vina can model macrocyclic ligands flexibly, without requiring the enumeration of macrocyclic conformers before docking. Here, we characterize the performance of the method for handling macrocyclic compounds, which is implemented and the default behaviour for ligand preparation with our ligand preparation pipeline, Meeko. A pseudoatom is used to encode bond geometry and produce an anisotropic closure force for macrocyclic rings. This method is evaluated on a diverse set of small molecule and peptide macrocycles, ranging from 7- to 33-membered rings, showing little accuracy loss compared to rigid redocking of the X-ray macrocycle conformers. This suggests that for conformationally flexible macrocycles with unknown binding modes, this method can be effectively used to predict the macrocycle conformation.
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Ghosh B, Bera S, Ghosh P, Samanta R. Rh(III)-Catalyzed mild straightforward synthesis of quinoline-braced cyclophane macrocycles via migratory insertion. Chem Commun (Camb) 2021; 57:13134-13137. [PMID: 34807203 DOI: 10.1039/d1cc04418d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An efficient Rh(III)-catalyzed straightforward strategy is developed for the synthesis of quinoline braced cyclophane macrocycles via methyl (sp3) C-H functionalization. The method is mild, simple and regioselective with various ring sizes and has good functional group tolerance. The method proceeds via C8-methyl metalation, metal-carbene formation and a subsequent migratory insertion. High dilution is not necessary for this macrocyclization and the only byproduct is nitrogen. A preliminary investigation shows that the C-H metalation step is the rate-determining step.
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Affiliation(s)
- Bidhan Ghosh
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
| | - Satabdi Bera
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
| | - Pintu Ghosh
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
| | - Rajarshi Samanta
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
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7
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Zou J, Li Z, Liu S, Peng C, Fang D, Wan X, Lin Z, Lee TS, Raleigh DP, Yang M, Simmerling C. Scaffold Hopping Transformations Using Auxiliary Restraints for Calculating Accurate Relative Binding Free Energies. J Chem Theory Comput 2021; 17:3710-3726. [PMID: 34029468 PMCID: PMC8215533 DOI: 10.1021/acs.jctc.1c00214] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In silico screening of drug-target interactions is a key part of the drug discovery process. Changes in the drug scaffold via contraction or expansion of rings, the breaking of rings, and the introduction of cyclic structures from acyclic structures are commonly applied by medicinal chemists to improve binding affinity and enhance favorable properties of candidate compounds. These processes, commonly referred to as scaffold hopping, are challenging to model computationally. Although relative binding free energy (RBFE) calculations have shown success in predicting binding affinity changes caused by perturbing R-groups attached to a common scaffold, applications of RBFE calculations to modeling scaffold hopping are relatively limited. Scaffold hopping inevitably involves breaking and forming bond interactions of quadratic functional forms, which is highly challenging. A novel method for handling ring opening/closure/contraction/expansion and linker contraction/expansion is presented here. To the best of our knowledge, RBFE calculations on linker contraction/expansion have not been previously reported. The method uses auxiliary restraints to hold the atoms at the ends of a bond in place during the breaking and forming of the bonds. The broad applicability of the method was demonstrated by examining perturbations involving small-molecule macrocycles and mutations of proline in proteins. High accuracy was obtained using the method for most of the perturbations studied. The rigor of the method was isolated from the force field by validating the method using relative and absolute hydration free energy calculations compared to standard simulation results. Unlike other methods that rely on λ-dependent functional forms for bond interactions, the method presented here can be employed using modern molecular dynamics software without modification of codes or force field functions.
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Affiliation(s)
- Junjie Zou
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Zhipeng Li
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Shuai Liu
- XtalPi Inc., 245 Main St, 11th Floor, Cambridge, MA 02142, United States
| | - Chunwang Peng
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Dong Fang
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Xiao Wan
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Zhixiong Lin
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Tai-Sung Lee
- Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research, Rutgers University, Piscataway, New Jersey, 08854-8076, United States
| | - Daniel P. Raleigh
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Mingjun Yang
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045, China
| | - Carlos Simmerling
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794-3400, United States
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Xu X, Wang J, Wang M, Yuan X, Li L, Zhang C, Huang H, Jing T, Wang C, Tong C, Zhou L, Meng Y, Xu P, Kou J, Qiu Z, Li Z, Bian J. Structure-Enabled Discovery of Novel Macrocyclic Inhibitors Targeting Glutaminase 1 Allosteric Binding Site. J Med Chem 2021; 64:4588-4611. [PMID: 33792311 DOI: 10.1021/acs.jmedchem.0c02044] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The inhibition of glutaminase 1 (GLS1) represents a potential treatment of malignant tumors. Structural analysis led to the design of a novel series of macrocyclic GLS1 allosteric inhibitors. Through extensive structure-activity relationship studies, a promising candidate molecule 13b (LL202) was identified with robust GLS1 inhibitory activity (IC50 = 6 nM) and high GLS1 binding affinity (SPR, Kd = 24 nM; ITC, Kd = 37 nM). The X-ray crystal structure of the 13b-GLS1 complex was resolved, revealing a unique binding mode and providing a novel structural scaffold for GLS1 allosteric inhibitors. Importantly, 13b clearly adjusted the cellular metabolites and induced an increase in the ROS level by blocking glutamine metabolism. Furthermore, 13b exhibited a similar in vivo antitumor activity as CB839. This study adds to the growing body of evidence that macrocyclization provides an alternative and complementary approach for the design of small-molecule inhibitors, with the potential to improve the binding affinity to the targets.
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Affiliation(s)
- Xi Xu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P. R. China
| | - Jubo Wang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P. R. China
| | - Min Wang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P. R. China
| | - Xinyu Yuan
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P. R. China
| | - Lei Li
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P. R. China
| | - Chao Zhang
- School of Pharmacy, Wannan Medical College, Wuhu 241002, P. R. China
| | - Huidan Huang
- School of Pharmacy, Wannan Medical College, Wuhu 241002, P. R. China
| | - Tian Jing
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P. R. China
| | - Chenchen Wang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P. R. China
| | - Chao Tong
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P. R. China
| | - Liwen Zhou
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P. R. China
| | - Ying Meng
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P. R. China
| | - Pengfei Xu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P. R. China
| | - Junping Kou
- State Key Laboratory of Natural Products, Jiangsu Key Laboratory of TCM Evaluation and Translational Research, Department of Pharmacology of Chinese Material Medical, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, P. R. China
| | - Zhixia Qiu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P. R. China
| | - Zhiyu Li
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P. R. China
| | - Jinlei Bian
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P. R. China
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Zhang W, Zhou ZX, Zhu XJ, Sun ZH, Dai WM, Li CC. Asymmetric Total Synthesis of the Highly Strained 4β-Acetoxyprobotryane-9β,15α-diol. J Am Chem Soc 2020; 142:19868-19873. [DOI: 10.1021/jacs.0c10116] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Wen Zhang
- Shenzhen Grubbs Institute, Department of Chemistry, Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Zi-Xiong Zhou
- Shenzhen Grubbs Institute, Department of Chemistry, Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xu-Jiang Zhu
- Shenzhen Grubbs Institute, Department of Chemistry, Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zhang-Hua Sun
- Shenzhen Grubbs Institute, Department of Chemistry, Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Wei-Min Dai
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Chuang-Chuang Li
- Shenzhen Grubbs Institute, Department of Chemistry, Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
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Singh I, Luxami V, Paul K. Synthesis and in vitro evaluation of naphthalimide-benzimidazole conjugates as potential antitumor agents. Org Biomol Chem 2019; 17:5349-5366. [PMID: 31099353 DOI: 10.1039/c8ob02973c] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of novel naphthalimide-benzimidazoles was designed and synthesized for the first time and studied for their effect on antiproliferative activity. Some of these compounds possessed good antitumor activity towards the tested cancer cell lines. Noticeably, (diethylamino)ethyl 15 and (dimethylamino)ethyl 23 derivatives displayed superior antiproliferative activity towards human cancer cell lines with MG_MID GI50 values of 1.43 and 1.83 μM, respectively. Preliminary investigation revealed that compounds 15 and 23 might bind with ct-DNA through the intercalation mode which is responsible for potent bioactivity. Moreover, transportation behaviour indicated that these molecules could efficiently bind to and be carried by bovine albumin, and the hydrogen bonding and hydrophobic interactions played important roles in interaction with serum albumin.
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Affiliation(s)
- Iqubal Singh
- School of Chemistry and Biochemistry, Thapar University, Patiala, 147 004, India.
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11
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Shi L, He Y, Gong J, Yang Z. Concise gram-scale synthesis of Euphorikanin A skeleton through a domino ring-closing metathesis strategy. Chem Commun (Camb) 2019; 56:531-534. [PMID: 31829345 DOI: 10.1039/c9cc08830j] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Euphorikanin A is a diterpenoid possessing a highly congested and unprecedented 5/6/7/3-fused tetracyclic ring skeleton. To access the challenging chemical structure of Euphorikanins, an efficient total synthetic approach is described. The stereoselective synthesis of the core structure of Euphorikanin A has been achieved from a simple dienyne building block, and a domino ring-closing metathesis (RCM) strategy was used for the gram-scale synthesis of the highly strained Euphorikanin A core. This paves the way for the synthesis of structurally diverse Euphorikanins.
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Affiliation(s)
- Linlin Shi
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
| | - Yingdong He
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
| | - Jianxian Gong
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
| | - Zhen Yang
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055, China. and Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education and Beijing National Laboratory for Molecular Science (BNLMS), College of Chemistry, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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12
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Roos K, Wu C, Damm W, Reboul M, Stevenson JM, Lu C, Dahlgren MK, Mondal S, Chen W, Wang L, Abel R, Friesner RA, Harder ED. OPLS3e: Extending Force Field Coverage for Drug-Like Small Molecules. J Chem Theory Comput 2019; 15:1863-1874. [PMID: 30768902 DOI: 10.1021/acs.jctc.8b01026] [Citation(s) in RCA: 645] [Impact Index Per Article: 129.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Katarina Roos
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, United States
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24 Uppsala, Sweden
| | - Chuanjie Wu
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Wolfgang Damm
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Mark Reboul
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - James M. Stevenson
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Chao Lu
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Markus K. Dahlgren
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Sayan Mondal
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Wei Chen
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Lingle Wang
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Robert Abel
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Richard A. Friesner
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, United States
| | - Edward D. Harder
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
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13
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Kalinowska-Tłuścik J, Staroń J, Krawczuk A, Mordalski S, Warszycki D, Satała G, Hogendorf AS, Bojarski AJ. The effect of the intramolecular C–H⋯O interactions on the conformational preferences of bis-arylsulfones – 5-HT6 receptor antagonists and beyond. RSC Adv 2018; 8:18672-18681. [PMID: 35541096 PMCID: PMC9080534 DOI: 10.1039/c8ra03107j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 05/15/2018] [Indexed: 11/21/2022] Open
Abstract
The development of compounds with enhanced activity and selectivity by a conserved spatial orientation of the pharmacophore elements has a long history in medicinal chemistry. Rigidified compounds are an example of this concept. However, the intramolecular interactions were seldom used as a basis for conformational restraints. Here, we show the weak intramolecular interactions that contribute to the relatively well-conserved geometry of N1-arylsulfonyl indole derivatives. The structure analysis along with quantum mechanics calculations revealed a crucial impact of the sulfonyl group on the compound geometry. The weak intramolecular C–H⋯O interaction stabilizes the mutual "facing" orientation of two aromatic fragments. These findings extend the pharmacological interpretation of the sulfonyl group role from the double hydrogen bond acceptor to the conformational scaffold based on intramolecular forces. This feature has, to date, been omitted in in silico drug discovery. Our results should increase the awareness of researchers to consider the conformational preference when designing new compounds or improving computational methods. The impact of weak intramolecular C–H⋯O interactions on the conformational stability of bis-arylsulfones is discussed, suggesting different role of sulfonyl group in the ligand – 5HT6 receptor interaction.![]()
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Affiliation(s)
- Justyna Kalinowska-Tłuścik
- Department of Crystal Chemistry and Crystal Physic
- Faculty of Chemistry
- Jagiellonian University
- 30-387 Kraków
- Poland
| | - Jakub Staroń
- Department of Medicinal Chemistry
- Institute of Pharmacology Polish Academy of Sciences
- 31-343 Kraków
- Poland
| | - Anna Krawczuk
- Department of Crystal Chemistry and Crystal Physic
- Faculty of Chemistry
- Jagiellonian University
- 30-387 Kraków
- Poland
| | - Stefan Mordalski
- Department of Medicinal Chemistry
- Institute of Pharmacology Polish Academy of Sciences
- 31-343 Kraków
- Poland
| | - Dawid Warszycki
- Department of Medicinal Chemistry
- Institute of Pharmacology Polish Academy of Sciences
- 31-343 Kraków
- Poland
| | - Grzegorz Satała
- Department of Medicinal Chemistry
- Institute of Pharmacology Polish Academy of Sciences
- 31-343 Kraków
- Poland
| | - Adam S. Hogendorf
- Department of Crystal Chemistry and Crystal Physic
- Faculty of Chemistry
- Jagiellonian University
- 30-387 Kraków
- Poland
| | - Andrzej J. Bojarski
- Department of Medicinal Chemistry
- Institute of Pharmacology Polish Academy of Sciences
- 31-343 Kraków
- Poland
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14
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Malvacio I, Cuzzolin A, Sturlese M, Vera DMA, Moyano EL, Moro S. Synthesis and preliminary structure-activity relationship study of 2-aryl-2H-pyrazolo[4,3-c]quinolin-3-ones as potential checkpoint kinase 1 (Chk1) inhibitors. J Enzyme Inhib Med Chem 2017; 33:171-183. [PMID: 29210298 PMCID: PMC6010083 DOI: 10.1080/14756366.2017.1404592] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The serine-threonine checkpoint kinase 1 (Chk1) plays a critical role in the cell cycle arrest in response to DNA damage. In the last decade, Chk1 inhibitors have emerged as a novel therapeutic strategy to potentiate the anti-tumour efficacy of cytotoxic chemotherapeutic agents. In the search for new Chk1 inhibitors, a congeneric series of 2-aryl-2 H-pyrazolo[4,3-c]quinolin-3-one (PQ) was evaluated by in-vitro and in-silico approaches for the first time. A total of 30 PQ structures were synthesised in good to excellent yields using conventional or microwave heating, highlighting that 14 of them are new chemical entities. Noteworthy, in this preliminary study two compounds 4e2 and 4h2 have shown a modest but significant reduction in the basal activity of the Chk1 kinase. Starting from these preliminary results, we have designed the second generation of analogous in this class and further studies are in progress in our laboratories.
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Affiliation(s)
- Ivana Malvacio
- a Department of Organic Chemistry, INFIQC, School of Chemical Sciences , National University of Cordoba , Cordoba , Argentina.,b Molecular Modeling Section (MMS), Dipartimento di Scienze Farmaceutiche , Università degli Studi di Padova , via Marzolo, Padova , Italy
| | - Alberto Cuzzolin
- b Molecular Modeling Section (MMS), Dipartimento di Scienze Farmaceutiche , Università degli Studi di Padova , via Marzolo, Padova , Italy
| | - Mattia Sturlese
- b Molecular Modeling Section (MMS), Dipartimento di Scienze Farmaceutiche , Università degli Studi di Padova , via Marzolo, Padova , Italy
| | - D Mariano A Vera
- c Department of Chemistry, QUIAMM-INBIOTEC, School of Exact and Natural Sciences , National University of Mar del Plata , Mar del Plata , Buenos Aires , Argentina
| | - E Laura Moyano
- a Department of Organic Chemistry, INFIQC, School of Chemical Sciences , National University of Cordoba , Cordoba , Argentina
| | - Stefano Moro
- b Molecular Modeling Section (MMS), Dipartimento di Scienze Farmaceutiche , Università degli Studi di Padova , via Marzolo, Padova , Italy
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15
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Yu HS, Deng Y, Wu Y, Sindhikara D, Rask AR, Kimura T, Abel R, Wang L. Accurate and Reliable Prediction of the Binding Affinities of Macrocycles to Their Protein Targets. J Chem Theory Comput 2017; 13:6290-6300. [PMID: 29120625 DOI: 10.1021/acs.jctc.7b00885] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Macrocycles have been emerging as a very important drug class in the past few decades largely due to their expanded chemical diversity benefiting from advances in synthetic methods. Macrocyclization has been recognized as an effective way to restrict the conformational space of acyclic small molecule inhibitors with the hope of improving potency, selectivity, and metabolic stability. Because of their relatively larger size as compared to typical small molecule drugs and the complexity of the structures, efficient sampling of the accessible macrocycle conformational space and accurate prediction of their binding affinities to their target protein receptors poses a great challenge of central importance in computational macrocycle drug design. In this article, we present a novel method for relative binding free energy calculations between macrocycles with different ring sizes and between the macrocycles and their corresponding acyclic counterparts. We have applied the method to seven pharmaceutically interesting data sets taken from recent drug discovery projects including 33 macrocyclic ligands covering a diverse chemical space. The predicted binding free energies are in good agreement with experimental data with an overall root-mean-square error (RMSE) of 0.94 kcal/mol. This is to our knowledge the first time where the free energy of the macrocyclization of linear molecules has been directly calculated with rigorous physics-based free energy calculation methods, and we anticipate the outstanding accuracy demonstrated here across a broad range of target classes may have significant implications for macrocycle drug discovery.
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Affiliation(s)
- Haoyu S Yu
- Schrodinger, Inc. , 120 West 45th Street, New York, New York 10036, United States
| | - Yuqing Deng
- Schrodinger, Inc. , 120 West 45th Street, New York, New York 10036, United States
| | - Yujie Wu
- Schrodinger, Inc. , 120 West 45th Street, New York, New York 10036, United States
| | - Dan Sindhikara
- Schrodinger, Inc. , 120 West 45th Street, New York, New York 10036, United States
| | - Amy R Rask
- Schrodinger, Inc. , 120 West 45th Street, New York, New York 10036, United States
| | - Takayuki Kimura
- Schrodinger, Inc. , 120 West 45th Street, New York, New York 10036, United States
| | - Robert Abel
- Schrodinger, Inc. , 120 West 45th Street, New York, New York 10036, United States
| | - Lingle Wang
- Schrodinger, Inc. , 120 West 45th Street, New York, New York 10036, United States
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16
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Dow M, Marchetti F, Abrahams KA, Vaz L, Besra GS, Warriner S, Nelson A. Modular Synthesis of Diverse Natural Product-Like Macrocycles: Discovery of Hits with Antimycobacterial Activity. Chemistry 2017; 23:7207-7211. [PMID: 28374952 PMCID: PMC5488202 DOI: 10.1002/chem.201701150] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Indexed: 12/24/2022]
Abstract
A modular synthetic approach was developed in which variation of the triplets of building blocks used enabled systematic variation of the macrocyclic scaffolds prepared. The approach was demonstrated in the synthesis of 17 diverse natural product-like macrocyclic scaffolds of varied (12-20-membered) ring size. The biological relevance of the chemical space explored was demonstrated through the discovery of a series of macrocycles with significant antimycobacterial activity.
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Affiliation(s)
- Mark Dow
- School of ChemistryUniversity of LeedsLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Francesco Marchetti
- School of ChemistryUniversity of LeedsLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | | | - Luis Vaz
- AstraZenecaCharter WayMacclesfieldSK10 2NAUK
| | - Gurdyal S. Besra
- School of BiosiencesUniversity of BirminghamEdgbaston, BirminghamB15 2TTUK
| | - Stuart Warriner
- School of ChemistryUniversity of LeedsLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Adam Nelson
- School of ChemistryUniversity of LeedsLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsLS2 9JTUK
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17
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Zhang Z, Li Y, Zhao D, He Y, Gong J, Yang Z. A Concise Synthesis of Presilphiperfolane Core through a Tandem TMTU-Co-Catalyzed Pauson-Khand Reaction and a 6π Electrocyclization Reaction (TMTU=Tetramethyl Thiourea). Chemistry 2017; 23:1258-1262. [DOI: 10.1002/chem.201605438] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Zichun Zhang
- Laboratory of Chemical Genomics; School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Yuanhe Li
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Beijing National Laboratory for Molecular Science (BNLMS); College of Chemistry and Molecular Engineering
- Peking-Tsinghua Center for Life Sciences; Peking University; Beijing 100871 China
| | - Dandan Zhao
- Laboratory of Chemical Genomics; School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Yingdong He
- Laboratory of Chemical Genomics; School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Jianxian Gong
- Laboratory of Chemical Genomics; School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Zhen Yang
- Laboratory of Chemical Genomics; School of Chemical Biology and Biotechnology; Peking University Shenzhen Graduate School; Shenzhen 518055 China
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education; Beijing National Laboratory for Molecular Science (BNLMS); College of Chemistry and Molecular Engineering
- Peking-Tsinghua Center for Life Sciences; Peking University; Beijing 100871 China
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18
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Krieger JP, Ricci G, Lesuisse D, Meyer C, Cossy J. Harnessing C−H Activation of Benzhydroxamates as a Macrocyclization Strategy: Synthesis of Structurally Diverse Macrocyclic Isoquinolones. Chemistry 2016; 22:13469-73. [DOI: 10.1002/chem.201602332] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Jean-Philippe Krieger
- Laboratory of Organic Chemistry; Institute of Chemistry, Biology and Innovation (CBI); ESPCI Paris, CNRS (UMR8231), PSL Research University; 10 rue Vauquelin 75231 Paris Cedex 05 France
| | - Gino Ricci
- Sanofi Process Development; 45 chemin de Mételine BP15 04210 Sisteron Cedex France
| | - Dominique Lesuisse
- R&D Sanofi; 1 avenue Pierre Brossolette 91385 Chilly-Mazarin Cedex France
| | - Christophe Meyer
- Laboratory of Organic Chemistry; Institute of Chemistry, Biology and Innovation (CBI); ESPCI Paris, CNRS (UMR8231), PSL Research University; 10 rue Vauquelin 75231 Paris Cedex 05 France
| | - Janine Cossy
- Laboratory of Organic Chemistry; Institute of Chemistry, Biology and Innovation (CBI); ESPCI Paris, CNRS (UMR8231), PSL Research University; 10 rue Vauquelin 75231 Paris Cedex 05 France
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19
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Osborne JD, Matthews TP, McHardy T, Proisy N, Cheung KMJ, Lainchbury M, Brown N, Walton MI, Eve PD, Boxall KJ, Hayes A, Henley AT, Valenti MR, De Haven Brandon AK, Box G, Jamin Y, Robinson SP, Westwood IM, van Montfort RLM, Leonard PM, Lamers MBAC, Reader JC, Aherne GW, Raynaud FI, Eccles SA, Garrett MD, Collins I. Multiparameter Lead Optimization to Give an Oral Checkpoint Kinase 1 (CHK1) Inhibitor Clinical Candidate: (R)-5-((4-((Morpholin-2-ylmethyl)amino)-5-(trifluoromethyl)pyridin-2-yl)amino)pyrazine-2-carbonitrile (CCT245737). J Med Chem 2016; 59:5221-37. [PMID: 27167172 DOI: 10.1021/acs.jmedchem.5b01938] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Multiparameter optimization of a series of 5-((4-aminopyridin-2-yl)amino)pyrazine-2-carbonitriles resulted in the identification of a potent and selective oral CHK1 preclinical development candidate with in vivo efficacy as a potentiator of deoxyribonucleic acid (DNA) damaging chemotherapy and as a single agent. Cellular mechanism of action assays were used to give an integrated assessment of compound selectivity during optimization resulting in a highly CHK1 selective adenosine triphosphate (ATP) competitive inhibitor. A single substituent vector directed away from the CHK1 kinase active site was unexpectedly found to drive the selective cellular efficacy of the compounds. Both CHK1 potency and off-target human ether-a-go-go-related gene (hERG) ion channel inhibition were dependent on lipophilicity and basicity in this series. Optimization of CHK1 cellular potency and in vivo pharmacokinetic-pharmacodynamic (PK-PD) properties gave a compound with low predicted doses and exposures in humans which mitigated the residual weak in vitro hERG inhibition.
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20
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Dube D, Tiwari P, Kaur P. The hunt for antimitotic agents: an overview of structure-based design strategies. Expert Opin Drug Discov 2016; 11:579-97. [PMID: 27077683 DOI: 10.1080/17460441.2016.1174689] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Structure-based drug discovery offers a rational approach for the design and development of novel anti-mitotic agents which target specific proteins involved in mitosis. This strategy has paved the way for development of a new generation of chemotypes which selectively interfere with the target proteins. The interference of these anti-mitotic targets implicated in diverse stages of mitotic cell cycle progression culminates in cancer cell apoptosis. AREAS COVERED This review covers the various mitotic inhibitors developed against validated mitotic checkpoint protein targets using structure-based design and optimization strategies. The protein-ligand interactions and the insights gained from these studies, culminating in the development of more potent and selective inhibitors, have been presented. EXPERT OPINION The advent of structure-based drug design coupled with advances in X-ray crystallography has revolutionized the discovery of candidate lead molecules. The structural insights gleaned from the co-complex protein-drug interactions have provided a new dimension in the design of anti-mitotic molecules to develop drugs with a higher selectivity and specificity profile. Targeting non-catalytic domains has provided an alternate approach to address cross-reactivity and broad selectivity among kinase inhibitors. The elucidation of structures of emerging mitotic drug targets has opened avenues for the design of inhibitors that target cancer.
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Affiliation(s)
- D Dube
- a Department of Biophysics , All India Institute of Medical Sciences , New Delhi , India
| | - P Tiwari
- a Department of Biophysics , All India Institute of Medical Sciences , New Delhi , India
| | - P Kaur
- a Department of Biophysics , All India Institute of Medical Sciences , New Delhi , India
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21
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Bodireddy MR, Mahla RS, Khaja Mohinuddin PM, Reddy GT, Raghava Prasad DV, Kumar H, Reddy NCG. Discovery of a new class of 16-membered (2Z,11Z)-3,11-di(aryl/naphthyl)-1,13-dioxa-5,9-dithia-2,12-diazacyclohexadeca-2,11-dienes as anti-tumor agents. RSC Adv 2016. [DOI: 10.1039/c6ra15140j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
A series of new 16-membered macrocyclic compounds were synthesized and evaluation of in vitro anti-tumor activities on MDAMB-231 cell lines reveal that the macrocycles, 1a, 1f, 1g, 1i and 1k are promising anti-tumor agents.
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Affiliation(s)
- Mohan Reddy Bodireddy
- Department of Chemistry
- School of Physical Sciences
- Yogi Vemana University
- Kadapa-516 003
- India
| | - Ranjeet Singh Mahla
- Department of Biological Sciences
- Indian Institute of Science Education and Research (IISER)
- Bhopal-462023
- India
| | | | - G. Trivikram Reddy
- Department of Chemistry
- School of Physical Sciences
- Yogi Vemana University
- Kadapa-516 003
- India
| | | | - Himanshu Kumar
- Department of Biological Sciences
- Indian Institute of Science Education and Research (IISER)
- Bhopal-462023
- India
- Laboratory of Host Defense
| | - N. C. Gangi Reddy
- Department of Chemistry
- School of Physical Sciences
- Yogi Vemana University
- Kadapa-516 003
- India
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22
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Knight JL, Krilov G, Borrelli KW, Williams J, Gunn JR, Clowes A, Cheng L, Friesner RA, Abel R. Leveraging Data Fusion Strategies in Multireceptor Lead Optimization MM/GBSA End-Point Methods. J Chem Theory Comput 2015; 10:3207-20. [PMID: 26588291 DOI: 10.1021/ct500189s] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Accurate and efficient affinity calculations are critical to enhancing the contribution of in silico modeling during the lead optimization phase of a drug discovery campaign. Here, we present a large-scale study of the efficacy of data fusion strategies to leverage results from end-point MM/GBSA calculations in multiple receptors to identify potent inhibitors among an ensemble of congeneric ligands. The retrospective analysis of 13 congeneric ligand series curated from publicly available data across seven biological targets demonstrates that in 90% of the individual receptor structures MM/GBSA scores successfully identify subsets of inhibitors that are more potent than a random selection, and data fusion strategies that combine MM/GBSA scores from each of the receptors significantly increase the robustness of the predictions. Among nine different data fusion metrics based on consensus scores or receptor rankings, the SumZScore (i.e., converting MM/GBSA scores into standardized Z-Scores within a receptor and computing the sum of the Z-Scores for a given ligand across the ensemble of receptors) is found to be a robust and physically meaningful metric for combining results across multiple receptors. Perhaps most surprisingly, even with relatively low to modest overall correlations between SumZScore and experimental binding affinities, SumZScore tends to reliably prioritize subsets of inhibitors that are at least as potent as those that are prioritized from a "best" single receptor identified from known compounds within the congeneric series.
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Affiliation(s)
- Jennifer L Knight
- Schrödinger, 120 West 45th Street, 17th Floor, Tower 45, New York, New York 10036-4041, United States
| | - Goran Krilov
- Schrödinger, 120 West 45th Street, 17th Floor, Tower 45, New York, New York 10036-4041, United States
| | - Kenneth W Borrelli
- Schrödinger, 120 West 45th Street, 17th Floor, Tower 45, New York, New York 10036-4041, United States
| | - Joshua Williams
- Schrödinger, 120 West 45th Street, 17th Floor, Tower 45, New York, New York 10036-4041, United States
| | - John R Gunn
- Schrödinger, 120 West 45th Street, 17th Floor, Tower 45, New York, New York 10036-4041, United States
| | - Alec Clowes
- Schrödinger, 120 West 45th Street, 17th Floor, Tower 45, New York, New York 10036-4041, United States
| | - Luciano Cheng
- Schrödinger, 120 West 45th Street, 17th Floor, Tower 45, New York, New York 10036-4041, United States
| | - Richard A Friesner
- Columbia University , Department of Chemistry, 3000 Broadway, MC 3110, New York, New York 10027, United States
| | - Robert Abel
- Schrödinger, 120 West 45th Street, 17th Floor, Tower 45, New York, New York 10036-4041, United States
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23
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Harder E, Damm W, Maple J, Wu C, Reboul M, Xiang JY, Wang L, Lupyan D, Dahlgren MK, Knight JL, Kaus JW, Cerutti DS, Krilov G, Jorgensen WL, Abel R, Friesner RA. OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins. J Chem Theory Comput 2015; 12:281-96. [PMID: 26584231 DOI: 10.1021/acs.jctc.5b00864] [Citation(s) in RCA: 2075] [Impact Index Per Article: 230.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The parametrization and validation of the OPLS3 force field for small molecules and proteins are reported. Enhancements with respect to the previous version (OPLS2.1) include the addition of off-atom charge sites to represent halogen bonding and aryl nitrogen lone pairs as well as a complete refit of peptide dihedral parameters to better model the native structure of proteins. To adequately cover medicinal chemical space, OPLS3 employs over an order of magnitude more reference data and associated parameter types relative to other commonly used small molecule force fields (e.g., MMFF and OPLS_2005). As a consequence, OPLS3 achieves a high level of accuracy across performance benchmarks that assess small molecule conformational propensities and solvation. The newly fitted peptide dihedrals lead to significant improvements in the representation of secondary structure elements in simulated peptides and native structure stability over a number of proteins. Together, the improvements made to both the small molecule and protein force field lead to a high level of accuracy in predicting protein-ligand binding measured over a wide range of targets and ligands (less than 1 kcal/mol RMS error) representing a 30% improvement over earlier variants of the OPLS force field.
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Affiliation(s)
- Edward Harder
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Wolfgang Damm
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Jon Maple
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Chuanjie Wu
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Mark Reboul
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Jin Yu Xiang
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Lingle Wang
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Dmitry Lupyan
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Markus K Dahlgren
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Jennifer L Knight
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Joseph W Kaus
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - David S Cerutti
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Goran Krilov
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - William L Jorgensen
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States
| | - Robert Abel
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Richard A Friesner
- Department of Chemistry, Columbia University , 3000 Broadway, New York, New York 10027, United States
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24
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Combining docking-based comparative intermolecular contacts analysis and k-nearest neighbor correlation for the discovery of new check point kinase 1 inhibitors. J Comput Aided Mol Des 2015; 29:561-81. [PMID: 25956379 DOI: 10.1007/s10822-015-9848-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Accepted: 05/03/2015] [Indexed: 01/15/2023]
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25
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Fabbro D, Cowan-Jacob SW, Moebitz H. Ten things you should know about protein kinases: IUPHAR Review 14. Br J Pharmacol 2015; 172:2675-700. [PMID: 25630872 DOI: 10.1111/bph.13096] [Citation(s) in RCA: 233] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Revised: 12/31/2014] [Accepted: 01/20/2015] [Indexed: 12/12/2022] Open
Abstract
Many human malignancies are associated with aberrant regulation of protein or lipid kinases due to mutations, chromosomal rearrangements and/or gene amplification. Protein and lipid kinases represent an important target class for treating human disorders. This review focus on 'the 10 things you should know about protein kinases and their inhibitors', including a short introduction on the history of protein kinases and their inhibitors and ending with a perspective on kinase drug discovery. Although the '10 things' have been, to a certain extent, chosen arbitrarily, they cover in a comprehensive way the past and present efforts in kinase drug discovery and summarize the status quo of the current kinase inhibitors as well as knowledge about kinase structure and binding modes. Besides describing the potentials of protein kinase inhibitors as drugs, this review also focus on their limitations, particularly on how to circumvent emerging resistance against kinase inhibitors in oncological indications.
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Affiliation(s)
| | | | - Henrik Moebitz
- Novartis Institutes of Biomedical Research, Basel, Switzerland
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26
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Fabbro D. 25 Years of Small Molecular Weight Kinase Inhibitors: Potentials and Limitations. Mol Pharmacol 2014; 87:766-75. [DOI: 10.1124/mol.114.095489] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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27
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Novel approaches for targeting kinases: allosteric inhibition, allosteric activation and pseudokinases. Future Med Chem 2014; 6:541-61. [PMID: 24649957 DOI: 10.4155/fmc.13.216] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Protein kinases are involved in many essential cellular processes and their deregulation can lead to a variety of diseases, including cancer. The pharmaceutical industry has invested heavily in the identification of kinase inhibitors to modulate these disease-promoting pathways, resulting in several successful drugs. However, the field is challenging as it is difficult to identify novel selective inhibitors with good pharmacokinetic/pharmacodynamic properties. In addition, resistance to kinase inhibitor treatment frequently arises. The identification of non-ATP site targeting ('allosteric') inhibitors, the identification of kinase activators and the expansion of kinase target space to include the less studied members of the family, including atypical- and pseudo-kinases, are potential avenues to overcome these challenges. In this perspective, the opportunities and challenges of following these approaches and others will be discussed.
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Wink C, Andernach L, Opatz T, Waldvogel SR. Total Synthesis of (±)-Oxalicumone C and Chiral Resolution and Elucidation of Its Absolute Configuration. European J Org Chem 2014. [DOI: 10.1002/ejoc.201403189] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Poulsen A, William AD, Dymock BW. Designed Macrocyclic Kinase Inhibitors. MACROCYCLES IN DRUG DISCOVERY 2014. [DOI: 10.1039/9781782623113-00141] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Cancer continues to present as an increasing and serious global unmet medical need in today's aging population.1 Macrocyclic kinase inhibitors have reached advanced clinical testing and are making an impact in oncologic conditions including myelofibrosis, lymphomas and leukemias. Rheumatoid arthritis (RA) is also beginning to be impacted with the first macrocycle having entered Phase I clinical evaluation in healthy volunteers. Increasing reports of innovative macrocycles in preclinical research are appearing in the literature. Desirable, selective, multi-kinase inhibitory profiles against specific kinases known to be abrogated in cancer, RA, and other diseases have been achieved in a first generation series of clinical stage compact small molecule macrocyclic kinase inhibitors. Herein we discuss their design, synthesis, structure activity relationships and assessment of the latest clinical data in a range of oncologic conditions. Macrocyclic kinase inhibitors have the potential to offer new hope to patients and their families.
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Affiliation(s)
- Anders Poulsen
- Experimental Therapeutics Centre, A*STAR 11 Biopolis Way, #03-10/11 The Helios 138667 Singapore
| | - Anthony D. William
- Institute of Chemical and Engineering Sciences, A*STAR 11 Biopolis Way, The Helios #03-08 138667 Singapore
| | - Brian W. Dymock
- Department of Pharmacy, National University of Singapore 18 Science Drive 4 117543 Singapore
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Identification of novel inhibitors of human Chk1 using pharmacophore-based virtual screening and their evaluation as potential anti-cancer agents. J Comput Aided Mol Des 2014; 28:1247-56. [DOI: 10.1007/s10822-014-9800-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 10/03/2014] [Indexed: 12/22/2022]
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31
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Balupuri A, Balasubramanian PK, Gadhe CG, Cho SJ. Docking-based 3D-QSAR study of pyridyl aminothiazole derivatives as checkpoint kinase 1 inhibitors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2014; 25:651-671. [PMID: 24911214 DOI: 10.1080/1062936x.2014.923040] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Checkpoint kinase 1 (Chk1) is a promising target for the design of novel anticancer agents. In the present work, molecular docking simulations and three-dimensional quantitative structure-activity relationship (3D-QSAR) studies were performed on pyridyl aminothiazole derivatives as Chk1 inhibitors. AutoDock was used to determine the probable binding conformations of all the compounds inside the active site of Chk1. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) models were developed based on the docking conformations and alignments. The CoMFA model produced statistically significant results with a cross-validated correlation coefficient (q2) of 0.608 and a coefficient of determination (r2) of 0.972. The reliable CoMSIA model with q2 of 0.662 and r2 of 0.970 was obtained from the combination of steric, electrostatic and hydrogen bond acceptor fields. The predictive power of the models were assessed using an external test set of 14 compounds and showed reasonable external predictabilities (r(2)pred) of 0.668 and 0.641 for CoMFA and CoMSIA models, respectively. The models were further evaluated by leave-ten-out cross-validation, bootstrapping and progressive scrambling analyses. The study provides valuable information about the key structural elements that are required in the rational design of potential drug candidates of this class of Chk1 inhibitors.
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Affiliation(s)
- A Balupuri
- a Department of Bio-New Drug Development, College of Medicine , Chosun University , Gwangju 501-759 , Republic of Korea
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32
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Xiao Y, Ramiscal J, Kowanetz K, Del Nagro C, Malek S, Evangelista M, Blackwood E, Jackson PK, O'Brien T. Identification of preferred chemotherapeutics for combining with a CHK1 inhibitor. Mol Cancer Ther 2013; 12:2285-95. [PMID: 24038068 DOI: 10.1158/1535-7163.mct-13-0404] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Here we report that GNE-783, a novel checkpoint kinase-1 (CHK1) inhibitor, enhances the activity of gemcitabine by disabling the S- and G2 cell-cycle checkpoints following DNA damage. Using a focused library of 51 DNA-damaging agents, we undertook a systematic screen using three different cell lines to determine which chemotherapeutics have their activity enhanced when combined with GNE-783. We found that GNE-783 was most effective at enhancing activity of antimetabolite-based DNA-damaging agents; however, there was a surprisingly wide range of activity within each class of agents. We, next, selected six different therapeutic agents and screened these in combination with GNE-783 across a panel of cell lines. This revealed a preference for enhanced chemopotentiation of select agents within tumor types, as, for instance, GNE-783 preferentially enhanced the activity of temozolomide only in melanoma cell lines. Additionally, although p53 mutant status was important for the overall response to combinations with some agents; our data indicate that this alone was insufficient to predict synergy. We finally compared the ability of a structurally related CHK1 inhibitor, GNE-900, to enhance the in vivo activity of gemcitabine, CPT-11, and temozolomide in xenograft models. GNE-900 significantly enhanced activity of only gemcitabine in vivo, suggesting that strong chemopotentiation in vitro can translate into chemopotentiation in vivo. In conclusion, our results show that selection of an appropriate agent to combine with a CHK1 inhibitor needs to be carefully evaluated in the context of the genetic background and tumor type in which it will be used.
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Affiliation(s)
- Yang Xiao
- Corresponding Author: Thomas O'Brien, Department of Translational Oncology, Genentech, 1 DNA Way, South San Francisco, CA 94080.
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An Y, Sherman W, Dixon SL. Kernel-Based Partial Least Squares: Application to Fingerprint-Based QSAR with Model Visualization. J Chem Inf Model 2013; 53:2312-21. [PMID: 23901898 DOI: 10.1021/ci400250c] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuling An
- Schrödinger, Inc., 120
West 45th Street, New York, New York 10036, United States
| | - Woody Sherman
- Schrödinger, Inc., 120
West 45th Street, New York, New York 10036, United States
| | - Steven L. Dixon
- Schrödinger, Inc., 120
West 45th Street, New York, New York 10036, United States
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34
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Naphthalimides exhibit in vitro antiproliferative and antiangiogenic activities by inhibiting both topoisomerase II (topo II) and receptor tyrosine kinases (RTKs). Eur J Med Chem 2013; 65:477-86. [DOI: 10.1016/j.ejmech.2013.05.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 04/30/2013] [Accepted: 05/03/2013] [Indexed: 11/22/2022]
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Matthews TP, Jones AM, Collins I. Structure-based design, discovery and development of checkpoint kinase inhibitors as potential anticancer therapies. Expert Opin Drug Discov 2013; 8:621-40. [PMID: 23594139 DOI: 10.1517/17460441.2013.788496] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
INTRODUCTION Checkpoint kinase (CHK) inhibitors offer the promise of enhancing the effectiveness of widely prescribed cancer chemotherapies and radiotherapy by inhibiting the DNA damage response, as well as the potential for single agent efficacy. AREAS COVERED This article surveys structural insights into the checkpoint kinases CHK1 and CHK2 that have been exploited to enhance the selectivity and potency of small molecule inhibitors. Furthermore, the authors review the use of mechanistic cellular assays to guide the optimisation of inhibitors. Finally, the authors discuss the status of the current clinical candidates and emerging new clinical contexts for CHK1 and CHK2 inhibitors, including the prospects for single agent efficacy. EXPERT OPINION Protein-bound water molecules play key roles in structural features that can be targeted to gain high selectivity for either enzyme. The results of early phase clinical trials of checkpoint inhibitors have been mixed, but significant progress has been made in testing the combination of CHK1 inhibitors with genotoxic chemotherapy. Second-generation CHK1 inhibitors are likely to benefit from increased selectivity and oral bioavailability. While the optimum therapeutic context for CHK2 inhibition remains unclear, the emergence of single agent preclinical efficacy for CHK1 inhibitors in specific tumour types exhibiting constitutive replication stress represents exciting progress in exploring the therapeutic potential of these agents.
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Affiliation(s)
- Thomas P Matthews
- Institute of Cancer Research, Cancer Research UK Cancer Therapeutics Unit, London SM2 5NG, UK
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37
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An efficient synthesis of 3-aryl-2,3-dihydrothiophene-2-carboxamide derivatives by one-pot, four-component reaction. RESEARCH ON CHEMICAL INTERMEDIATES 2013. [DOI: 10.1007/s11164-012-0579-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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38
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Lainchbury M, Matthews TP, McHardy T, Boxall KJ, Walton MI, Eve PD, Hayes A, Valenti MR, de Haven Brandon AK, Box G, Aherne GW, Reader JC, Raynaud FI, Eccles SA, Garrett MD, Collins I. Discovery of 3-alkoxyamino-5-(pyridin-2-ylamino)pyrazine-2-carbonitriles as selective, orally bioavailable CHK1 inhibitors. J Med Chem 2012; 55:10229-40. [PMID: 23082860 PMCID: PMC3506129 DOI: 10.1021/jm3012933] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
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Inhibitors of checkpoint kinase 1 (CHK1) are of current
interest
as potential antitumor agents, but the most advanced inhibitor series
reported to date are not orally bioavailable. A novel series of potent
and orally bioavailable 3-alkoxyamino-5-(pyridin-2-ylamino)pyrazine-2-carbonitrile
CHK1 inhibitors was generated by hybridization of two lead scaffolds
derived from fragment-based drug design and optimized for CHK1 potency
and high selectivity using a cell-based assay cascade. Efficient in
vivo pharmacokinetic assessment was used to identify compounds with
prolonged exposure following oral dosing. The optimized compound (CCT244747)
was a potent and highly selective CHK1 inhibitor, which modulated
the DNA damage response pathway in human tumor xenografts and showed
antitumor activity in combination with genotoxic chemotherapies and
as a single agent.
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Affiliation(s)
- Michael Lainchbury
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, 15 Cotswold Road, Sutton, SM2 5NG U. K
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Abstract
The use of drug-like macrocycles is emerging as an exciting area of medicinal chemistry, with several recent examples highlighting the favorable changes in biological and physicochemical properties that macrocyclization can afford. Natural product macrocycles and their synthetic derivatives have long been clinically useful and attention is now being focused on the wider use of macrocyclic scaffolds in medicinal chemistry in the search for new drugs for increasingly challenging targets. With the increasing awareness of concepts of drug-likeness and the dangers of ‘molecular obesity’, functionalized macrocyclic scaffolds could provide a way to generate ligand-efficient molecules with enhanced properties. In this review we will separately discuss the effects of macrocyclization upon potency, selectivity and physicochemical properties, concentrating on recent case histories in oncology drug discovery. Additionally, we will highlight selected advances in the synthesis of macrocycles and provide an outlook on the future use of macrocyclic scaffolds in medicinal chemistry.
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40
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Zhao L, Liu Y, Hu S, Zhang H. 3D-QSAR study of Chk1 kinase inhibitors based on docking. J Mol Model 2012; 18:3669-94. [DOI: 10.1007/s00894-012-1363-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Accepted: 01/17/2012] [Indexed: 11/24/2022]
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Bogdan AR, Jerome SV, Houk KN, James K. Strained cyclophane macrocycles: impact of progressive ring size reduction on synthesis and structure. J Am Chem Soc 2012; 134:2127-38. [PMID: 22133103 DOI: 10.1021/ja208503y] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The synthesis, X-ray crystal structures, and calculated strain energies are reported for a homologous series of 11- to 14-membered drug-like cyclophane macrocycles, representing an unusual region of chemical space that can be difficult to access synthetically. The ratio of macrocycle to dimer, generated via a copper catalyzed azide-alkyne cycloaddition macrocyclization in flow at elevated temperature, could be rationalized in terms of the strain energy in the macrocyclic product. The progressive increase in strain resulting from reduction in macrocycle ring size, or the introduction of additional conformational constraints, results in marked deviations from typical geometries. These strained cyclophane macrocyclic systems provide access to spatial orientations of functionality that would not be readily available in unstrained or acyclic analogs. The most strained system prepared represents the first report of an 11-membered cyclophane containing a 1,4-disubstituted 1,2,3-triazole ring and establishes a limit to the ring strain that can be generated using this macrocycle synthesis methodology.
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Affiliation(s)
- Andrew R Bogdan
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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42
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Collins JC, James K. Emac – a comparative index for the assessment of macrocyclization efficiency. MEDCHEMCOMM 2012. [DOI: 10.1039/c2md20176c] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Based upon a critical analysis of macrocyclization reactions published over the last three years, a macrocyclization efficiency index, Emac, is proposed, which takes into account both yield and concentration, as a means of determining the true efficiency of a macrocyclization reaction.
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Affiliation(s)
| | - Keith James
- Department of Chemistry
- The Scripps Research Institute
- USA
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43
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Reader JC, Matthews TP, Klair S, Cheung KMJ, Scanlon J, Proisy N, Addison G, Ellard J, Piton N, Taylor S, Cherry M, Fisher M, Boxall K, Burns S, Walton MI, Westwood IM, Hayes A, Eve P, Valenti M, de Haven Brandon A, Box G, van Montfort RLM, Williams DH, Aherne GW, Raynaud FI, Eccles SA, Garrett MD, Collins I. Structure-guided evolution of potent and selective CHK1 inhibitors through scaffold morphing. J Med Chem 2011; 54:8328-42. [PMID: 22111927 PMCID: PMC3241339 DOI: 10.1021/jm2007326] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
![]()
Pyrazolopyridine inhibitors with low micromolar potency
for CHK1
and good selectivity against CHK2 were previously identified by fragment-based
screening. The optimization of the pyrazolopyridines to a series of
potent and CHK1-selective isoquinolines demonstrates how fragment-growing
and scaffold morphing strategies arising from a structure-based understanding
of CHK1 inhibitor binding can be combined to successfully progress
fragment-derived hit matter to compounds with activity in vivo. The
challenges of improving CHK1 potency and selectivity, addressing synthetic
tractability, and achieving novelty in the crowded kinase inhibitor
chemical space were tackled by multiple scaffold morphing steps, which
progressed through tricyclic pyrimido[2,3-b]azaindoles
to N-(pyrazin-2-yl)pyrimidin-4-amines and ultimately
to imidazo[4,5-c]pyridines and isoquinolines. A potent
and highly selective isoquinoline CHK1 inhibitor (SAR-020106) was
identified, which potentiated the efficacies of irinotecan and gemcitabine
in SW620 human colon carcinoma xenografts in nude mice.
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Affiliation(s)
- John C Reader
- Cancer Research UK Cancer Therapeutics Unit and Division of Structural Biology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
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Denoyelle S, Chen T, Chen L, Wang Y, Klosi E, Halperin JA, Aktas BH, Chorev M. In vitro inhibition of translation initiation by N,N'-diarylureas--potential anti-cancer agents. Bioorg Med Chem Lett 2011; 22:402-9. [PMID: 22153346 DOI: 10.1016/j.bmcl.2011.10.126] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 10/27/2011] [Accepted: 10/31/2011] [Indexed: 10/15/2022]
Abstract
Symmetrical N,N'-diarylureas: 1,3-bis(3,4-dichlorophenyl)-, 1,3-bis[4-chloro-3-(trifluoromethyl)phenyl]- and 1,3-bis[3,5-bis(trifluoromethyl)phenyl]urea, were identified as potent activators of the eIF2α kinase heme regulated inhibitor. They reduce the abundance of the eIF2·GTP·tRNA(i)(Met) ternary complex and inhibit cancer cell proliferation. An optimization process was undertaken to improve their solubility while preserving their biological activity. Non-symmetrical hybrid ureas were generated by combining one of the hydrophobic phenyl moieties present in the symmetrical ureas with the polar 3-hydroxy-tolyl moiety. O-alkylation of the later added potentially solubilizing charge bearing groups. The new non-symmetrical N,N'-diarylureas were characterized by ternary complex reporter gene and cell proliferation assays, demonstrating good bioactivities. A representative sample of these compounds potently induced phosphorylation of eIF2α and expression of CHOP at the protein and mRNA levels. These inhibitors of translation initiation may become leads for the development of potent, non-toxic, and target specific anti-cancer agents.
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Affiliation(s)
- Séverine Denoyelle
- Laboratory for Translational Research, Harvard Medical School, One Kendall Square, Building 600, 3rd Floor, Cambridge, MA 02139, USA
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Zhang L, Darko AK, Johns JI, McElwee-White L. Catalytic Oxidative Carbonylation of Arylamines to Ureas with W(CO)6/I2 as Catalyst. European J Org Chem 2011. [DOI: 10.1002/ejoc.201100657] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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46
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Lainchbury M, Collins I. Checkpoint kinase inhibitors: a patent review (2009 - 2010). Expert Opin Ther Pat 2011; 21:1191-210. [PMID: 21599421 DOI: 10.1517/13543776.2011.586632] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Cells that suffer DNA damage activate the checkpoint kinases CHK1 and CHK2, which signal to initiate repair processes, limit cell-cycle progression and prevent cell replication, until the damaged DNA is repaired. Due to their potential application as novel anticancer therapies, inhibitors of CHK1 and CHK2 have become the focus of numerous drug discovery projects. AREAS COVERED This patent review examines the chemical structures and biological activities of recently reported CHK1 and CHK2 inhibitors. The chemical abstract and patent databases SciFinder and esp@cenet were used to locate patent applications that were published between September 2008 and December 2010, claiming chemical structures for use as CHK1 or CHK2 inhibitors. EXPERT OPINION This is an exciting time for checkpoint kinase inhibitors, with several currently in Phase I or II clinical trials. Many of the CHK1 inhibitors contained within this patent review have shown preclinical efficacy in combination with DNA-damaging chemotherapies. CHK1 inhibitors have recently been demonstrated to be efficacious as single agents in preclinical models of tumors with constitutive activation of CHK1 or high intrinsic DNA damage due to replication stress. The level of newly published patent applications covering CHK1 and CHK2 inhibitors remains high and a diverse range of scaffolds has been claimed.
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Affiliation(s)
- Michael Lainchbury
- The Institute of Cancer Research, Cancer Research UK Cancer Therapeutics Unit, Haddow Laboratories, Sutton, Surrey, UK.
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47
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Abstract
PGVL Hub is a Pfizer internal desktop tool for chemical library and singleton design. In this chapter, we give a short introduction to PGVL Hub, the core workflow it supports, and the rich design capabilities it provides. By re-creating two legacy targeted libraries against the human checkpoint kinase 1 (Chk1) as a showcase, we illustrate how PGVL Hub could be used to help library designers carry out the steps in library design and realize design objectives such as SAR expansion and improvement in both kinase selectivity and compound aqueous solubility. Finally we share several tips about library design and usage of PGVL Hub.
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Affiliation(s)
- Zhengwei Peng
- Pfizer Global Research and Development, La Jolla Laboratories, San Diego, CA, USA.
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48
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Zhao L, Zhang Y, Dai C, Guzi T, Wiswell D, Seghezzi W, Parry D, Fischmann T, Siddiqui MA. Design, synthesis and SAR of thienopyridines as potent CHK1 inhibitors. Bioorg Med Chem Lett 2010; 20:7216-21. [PMID: 21074424 DOI: 10.1016/j.bmcl.2010.10.105] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Revised: 10/20/2010] [Accepted: 10/21/2010] [Indexed: 01/04/2023]
Abstract
A novel series of CHK1 inhibitors based on thienopyridine template has been designed and synthesized. These inhibitors maintain critical hydrogen bonding with the hinge and conserved water in the ATP binding site. Several compounds show single digit nanomolar CHK1 activities. Compound 70 shows excellent enzymatic activity of 1 nM.
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Affiliation(s)
- Lianyun Zhao
- Department of Chemistry, Merck Research Laboratories, Cambridge, MA 02141, USA.
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49
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Chen Z, Liang X, Zhang H, Xie H, Liu J, Xu Y, Zhu W, Wang Y, Wang X, Tan S, Kuang D, Qian X. A new class of naphthalimide-based antitumor agents that inhibit topoisomerase II and induce lysosomal membrane permeabilization and apoptosis. J Med Chem 2010; 53:2589-600. [PMID: 20170164 DOI: 10.1021/jm100025u] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Based on the advantages of multitarget drugs for cancer treatment, a new class of naphthalimides was designed, synthesized, and proved to inhibit topoisomerase II (topo II), induced lysosomal membrane permeabilization (LMP), and ultimately caused apoptosis and cell death. The majority of compounds 7a-d and 8a-d potently inhibited the growth of the five tested cancer cell lines with IC(50) values ranging from 2 to 10 microM and are more active than amonafide, a naphthalimide that was in phase III clinical trials. These compounds were tested for their interactions with DNA and their cell-free topo II inhibition activities, which demonstrated these compounds were weak DNA binders but modest topo II inhibitors. Furthermore, compounds 7b-d were found to notably induce LMP and exhibited better antiproliferative activity compared with their single-target analogues. All of the newly synthesized compounds were demonstrated to efficiently induce apoptosis via a mitochondrial pathway. Accordingly, a new paradigm was suggested for the design of novel multitarget anticancer drugs.
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Affiliation(s)
- Zhuo Chen
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
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50
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Wang RW, Zhou L, Zuo Z, Ma X, Yang M. 3D-QSAR studies of checkpoint kinase 1 inhibitors based on molecular docking and CoMFA. MOLECULAR SIMULATION 2010. [DOI: 10.1080/08927020903115260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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