1
|
Yang S, Yan B, Zhong L, Jia C, Yao D, Yang C, Sun K, Li G. AIBN for Ru-catalyzed meta-C Ar–H alkylation. Org Chem Front 2020. [DOI: 10.1039/d0qo00703j] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The meta-CAr–H alkylation of arenes with radicals produced from AIBN in the presence of a RuCl3 catalyst is presented.
Collapse
Affiliation(s)
- Suling Yang
- College of Chemistry and Chemical Engineering
- Henan Province Key Laboratory of New Optoelectronic Functional Materials
- Anyang Normal University
- Anyang 455002
- PR China
| | - Bingxu Yan
- College of Chemistry and Chemical Engineering
- Henan Province Key Laboratory of New Optoelectronic Functional Materials
- Anyang Normal University
- Anyang 455002
- PR China
| | - Lei Zhong
- College of Chemistry and Chemical Engineering
- Henan Province Key Laboratory of New Optoelectronic Functional Materials
- Anyang Normal University
- Anyang 455002
- PR China
| | - Chunqi Jia
- Engineering Research Center of Molecular Medicine of Ministry of Education
- Key Laboratory of Fujian Molecular Medicine
- Key Laboratory of Xiamen Marine and Gene Drugs
- School of Biomedical Sciences
- Huaqiao University
| | - Dan Yao
- College of Chemistry and Chemical Engineering
- Henan Province Key Laboratory of New Optoelectronic Functional Materials
- Anyang Normal University
- Anyang 455002
- PR China
| | - Chunli Yang
- College of Chemistry and Chemical Engineering
- Henan Province Key Laboratory of New Optoelectronic Functional Materials
- Anyang Normal University
- Anyang 455002
- PR China
| | - Kai Sun
- College of Chemistry and Chemical Engineering
- Henan Province Key Laboratory of New Optoelectronic Functional Materials
- Anyang Normal University
- Anyang 455002
- PR China
| | - Gang Li
- College of Chemistry and Chemical Engineering
- Henan Province Key Laboratory of New Optoelectronic Functional Materials
- Anyang Normal University
- Anyang 455002
- PR China
| |
Collapse
|
2
|
Singh P, Mishra M, Agarwal S, Sau S, Iyer AK, Kashaw SK. Exploring the Role of Water Molecules in the Ligand Binding Domain of PDE4B and PDE4D: Virtual Screening Based Molecular Docking of Some Active Scaffolds. Curr Comput Aided Drug Des 2018; 15:334-366. [PMID: 30394213 DOI: 10.2174/1573409914666181105153543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 11/01/2018] [Accepted: 11/01/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND The phosphodiesterase (PDE) is a superfamily represented by four genes: PDE4A, B,C, and D which cause the hydrolysis of phosphodiester bond of cAMP to yield inactive AMP. c-AMP catalyzing enzyme is predominant in inflammatory and immunomodulatory cells. Therapy to treat Chronic Obstructive Pulmonary Disease (COPD) with the use of PDE4 inhibitors is highly envisaged. OBJECTIVE A molecular docking experiment with large dataset of diverse scaffolds has been performed on PDE4 inhibitors to analyze the role of amino acid responsible for binding and activation of the secondary transmitters. Apart from the general docking experiment, the main focus was to discover the role of water molecules present in the ligand-binding domain. METHODS All the compounds were docked in the PDE4B and PDE4D active cavity to produce the free binding energy scores and spatial disposition/orientation of chemical groups of inhibitors around the cavity. Under uniform condition, the experiments were carried out with and without water molecules in the LBD. The exhaustive study was carried out on the Autodock 4.2 software and explored the role of water molecules present in the binding domain. RESULTS In presence of water molecule, Roflumilast has more binding affinity (-8.48 Kcal/mol with PDE4B enzyme and -8.91 Kcal/mol with PDE4D enzyme) and forms two hydrogen bonds with Gln443 and Glu369 and amino acid with PDE4B and PDE4D enzymes respectively. While in absence of water molecule its binding affinity has decreased (-7.3 Kcal/mol with PDE4B enzyme and -5.17 Kcal/mol with PDE4D enzyme) as well as no H-bond interactions were observed. Similar observation was made with clinically tested molecules. CONCLUSION In protein-ligand binding interactions, appropriate selection of water molecules facilitated the ligand binding, which eventually enhances the efficiency as well as the efficacy of ligand binding.
Collapse
Affiliation(s)
- Priya Singh
- Department of Pharmaceutical Sciences, Dr. Harisingh Gour University (A Central University), Sagar, MP, India
| | - Mitali Mishra
- Department of Pharmaceutical Sciences, Dr. Harisingh Gour University (A Central University), Sagar, MP, India
| | - Shivangi Agarwal
- Department of Pharmaceutical Sciences, Dr. Harisingh Gour University (A Central University), Sagar, MP, India
| | - Samaresh Sau
- Use-inspired Biomaterials & Integrated Nano Delivery (U-BiND) Systems Laboratory, Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan, MI, United States
| | - Arun K Iyer
- Use-inspired Biomaterials & Integrated Nano Delivery (U-BiND) Systems Laboratory, Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan, MI, United States.,Molecular Therapeutics Program, Karmanos Cancer Institute, Detroit, Michigan, MI, United States
| | - Sushil K Kashaw
- Department of Pharmaceutical Sciences, Dr. Harisingh Gour University (A Central University), Sagar, MP, India.,Use-inspired Biomaterials & Integrated Nano Delivery (U-BiND) Systems Laboratory, Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan, MI, United States
| |
Collapse
|
3
|
Niu M, Dong F, Tang S, Fida G, Qin J, Qiu J, Liu K, Gao W, Gu Y. Pharmacophore modeling and virtual screening for the discovery of new type 4 cAMP phosphodiesterase (PDE4) inhibitors. PLoS One 2013; 8:e82360. [PMID: 24340020 PMCID: PMC3858292 DOI: 10.1371/journal.pone.0082360] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 10/23/2013] [Indexed: 11/19/2022] Open
Abstract
Type 4 cAMP phosphodiesterase (PDE4) inhibitors show a broad spectrum of anti-inflammatory effects in almost all kinds of inflamed cells, by an increase in cAMP levels which is a pivotal second messenger responsible for various biological processes. These inhibitors are now considered as the potential drugs for treatment of chronic inflammatory diseases. However, some recently marketed inhibitors e.g., roflumilast, have shown adverse effects such as nausea and emesis, thus restricting its use. In order to identify novel PDE4 inhibitors with improved therapeutic indexes, a highly correlating (r = 0.963930) pharmacophore model (Hypo1) was established on the basis of known PDE4 inhibitors. Validated Hypo1 was used in database screening to identify chemical with required pharmacophoric features. These compounds are further screened by using the rule of five, ADMET and molecular docking. Finally, twelve hits which showed good results with respect to following properties such as estimated activity, calculated drug-like properties and scores were proposed as potential leads to inhibit the PDE4 activity. Therefore, this study will not only assist in the development of new potent hits for PDE4 inhibitors, but also give a better understanding of their interaction with PDE4. On a wider scope, this will be helpful for the rational design of novel potent enzyme inhibitors.
Collapse
Affiliation(s)
- Miaomiao Niu
- Department of Biomedical Engineering, School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Fenggong Dong
- Department of Biomedical Engineering, School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Shi Tang
- Department of Biomedical Engineering, School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Guissi Fida
- Department of Biomedical Engineering, School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Jingyi Qin
- Department of Biomedical Engineering, School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Jiadan Qiu
- Department of Biomedical Engineering, School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Kangbo Liu
- Department of Biomedical Engineering, School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Weidong Gao
- Department of Biomedical Engineering, School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Yueqing Gu
- Department of Biomedical Engineering, School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
- * E-mail:
| |
Collapse
|
4
|
Predictive QSAR modeling of phosphodiesterase 4 inhibitors. J Mol Graph Model 2012; 32:32-8. [DOI: 10.1016/j.jmgm.2011.10.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Revised: 10/04/2011] [Accepted: 10/05/2011] [Indexed: 11/20/2022]
|
5
|
Zheng S, Kaur G, Wang H, Li M, Macnaughtan M, Yang X, Reid S, Prestegard J, Wang B, Ke H. Design, synthesis, and structure-activity relationship, molecular modeling, and NMR studies of a series of phenyl alkyl ketones as highly potent and selective phosphodiesterase-4 inhibitors. J Med Chem 2009; 51:7673-88. [PMID: 19049349 DOI: 10.1021/jm701635j] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Phosphodiesterase 4 catalyzes the hydrolysis of cyclic AMP and is a target for the development of anti-inflammatory agents. We have designed and synthesized a series of phenyl alkyl ketones as PDE4 inhibitors. Among them, 13 compounds were identified as having submicromolar IC(50) values. The most potent compounds have IC(50) values of in the mid- to low-nanomolar range. Compound 5v also showed preference for PDE4 with selectivity of >2000-fold over PDE7, PDE9, PDE2, and PDE5. Docking of 5v, 5zf, and 5za into the binding pocket of the PDE4 catalytic domain revealed a similar binding profile to PDE4 with rolipram except that the fluorine atoms of the difluoromethyl groups of 5v, 5za, and 5zf are within a reasonable range for hydrogen bond formation with the amide hydrogen of Thr 333 and the long alkyl chain bears additional van der Waals interactions with His 160, Asp 318, and Tyr 159.
Collapse
Affiliation(s)
- Shilong Zheng
- Department of Chemistry and Center for Biotechnology and Drug Discovery, Georgia State University, Atlanta, Georgia 30302-4098, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Jang MY, De Jonghe S, Gao LJ, Rozenski J, Herdewijn P. Development of Synthetic Strategies for the Construction of Pyrido[4,3-d]pyrimidine Libraries – the Discovery of a New Class of PDE-4 Inhibitors. European J Org Chem 2006. [DOI: 10.1002/ejoc.200600339] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
7
|
Boto A, Hernández R, de León Y, Murguía JR, Rodriguez-Afonso A. Synthesis of Functionalized Nitrogen Heterocycles by Radical Decarboxylation of β- and γ-Amino Acids. European J Org Chem 2005. [DOI: 10.1002/ejoc.200400698] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
8
|
Ochiai H, Odagaki Y, Ohtani T, Ishida A, Kusumi K, Kishikawa K, Yamamoto S, Takeda H, Obata T, Kobayashi K, Nakai H, Toda M. Design, synthesis, and biological evaluation of new phosphodiesterase type 4 inhibitors. Bioorg Med Chem 2004; 12:5063-78. [PMID: 15351390 DOI: 10.1016/j.bmc.2004.07.040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2004] [Revised: 07/16/2004] [Accepted: 07/16/2004] [Indexed: 10/26/2022]
Abstract
The design, synthesis, and biological evaluation of new phosphodiesterase type 4 inhibitors, which possess new templates instead of a cyclohexane ring, are described. The mode of interaction with the enzyme is discussed based on the structure-activity relationship (SAR) data obtained for the synthesized inhibitors. Furthermore, the roles of three pharmacophores, a catechol moiety, a nitrile moiety, and acidic moieties, are discussed using in silico docking studies. More detailed biological evaluations of selected compounds are also presented.
Collapse
Affiliation(s)
- Hiroshi Ochiai
- Minase Research Institute, Ono Pharmaceutical Co., Ltd, 3-1-1 Sakurai, Shimamoto, Mishima, Osaka 618-8585, Japan
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Boto A, Hernández R, de León Y, Murguı́a JR, Rodrı́guez-Afonso A. Synthesis of functionalized nitrogen heterocycles from β- and γ-amino acids by radical decarboxylation. Tetrahedron Lett 2004. [DOI: 10.1016/j.tetlet.2004.07.111] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
10
|
Ochiai H, Ishida A, Ohtani T, Kusumi K, Kishikawa K, Yamamoto S, Takeda H, Obata T, Nakai H, Toda M. Discovery of New Orally Active Phosphodiesterase (PDE4) Inhibitors. Chem Pharm Bull (Tokyo) 2004; 52:1098-104. [PMID: 15340197 DOI: 10.1248/cpb.52.1098] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A series of 4-anilinopyrazolopyridine derivatives were synthesized and biologically evaluated as inhibitors of phosphodiesterase (PDE4). Chemical modification of 3, a structurally new chemical lead that was found in our in-house library, was focused on 1- and 3-substituents. Full details of the discovery of a new orally active chemical lead 5 are presented. Structure-activity relationship data, pharmacological evaluation, and the subtype selectivity study are also presented.
Collapse
Affiliation(s)
- Hiroshi Ochiai
- Minase Research Institute, Ono Pharmaceutical Co., Ltd., Mishima, Osaka 618-8585, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|