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Somnarin T, Krawmanee P, Gleeson MP, Gleeson D. Computational investigation of the radical-mediated mechanism of formation of difluoro methyl oxindoles: Elucidation of the reaction selectivity and yields. J Comput Chem 2023; 44:670-676. [PMID: 36398747 DOI: 10.1002/jcc.27031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/17/2022] [Accepted: 10/11/2022] [Indexed: 11/19/2022]
Abstract
Oxindoles are an important class of heterocyclic alkaloids with demonstrated pharmacological activity at multiple biological targets. Preparation of new analogs through novel synthetic routes is therefore highly attractive. In this work, we report a computational study to investigate the synthesis of ethoxycarbonyldifluoromethylated oxindoles from N-arylmethacrylamides. The reaction tolerates a diverse range of acrylamides, shows yields ranging from approximately 38%-96%. We have applied density functional theory (DFT) to explore the reaction mechanism, kinetics and thermodynamics to gain further understanding. We demonstrate that a radical-based ring closure reaction is energetically more favorable than a heterolytic process, that the rate-determining step is the formation of the arylmethacrylamide radical, and that the product yields and selectivities are consistent with experiment. The results demonstrate that theoretical methods can prove useful to understand how such reaction and could be potentially employed to rapidly explore the reaction scope further.
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Affiliation(s)
- Thanachon Somnarin
- Applied Computational Chemistry Research Unit & Department of Chemistry, School of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand.,Department of Biomedical Engineering, School of Engineering, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Pacharaporn Krawmanee
- Applied Computational Chemistry Research Unit & Department of Chemistry, School of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Matthew Paul Gleeson
- Department of Biomedical Engineering, School of Engineering, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Duangkamol Gleeson
- Applied Computational Chemistry Research Unit & Department of Chemistry, School of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
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Somnarin T, Pobsuk N, Chantakul R, Panklai T, Temkitthawon P, Hannongbua S, Chootip K, Ingkaninan K, Boonyarattanakalin K, Gleeson D, Paul Gleeson M. Computational design, synthesis and biological evaluation of PDE5 inhibitors based on N 2,N 4-diaminoquinazoline and N 2,N 6-diaminopurine scaffolds. Bioorg Med Chem 2022; 76:117092. [PMID: 36450167 DOI: 10.1016/j.bmc.2022.117092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/27/2022] [Accepted: 11/02/2022] [Indexed: 11/18/2022]
Abstract
We report the synthesis, and characterization of twenty-nine new inhibitors of PDE5. Structure-based design was employed to modify to our previously reported 2,4-diaminoquinazoline series. Modification include scaffold hopping to 2,6-diaminopurine core as well as incorporation of ionizable groups to improve both activity and solubility. The prospective binding mode of the compounds was determined using 3D ligand-based similarity methods to inhibitors of known binding mode, combined with a PDE5 docking and molecular dynamics based-protocol, each of which pointed to the same binding mode. Chemical modifications were then designed to both increase potency and solubility as well as validate the binding mode prediction. Compounds containing a quinazoline core displayed IC50s ranging from 0.10 to 9.39 µM while those consisting of a purine scaffold ranging from 0.29 to 43.16 µM. We identified 25 with a PDE5 IC50 of 0.15 µM, and much improved solubility (1.77 mg/mL) over the starting lead. Furthermore, it was found that the predicted binding mode was consistent with the observed SAR validating our computationally driven approach.
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Affiliation(s)
- Thanachon Somnarin
- Department of Biomedical Engineering, School of Engineering, King Mongkut's Institute of Technology Ladkrabang, Bangkok 10520, Thailand
| | - Nattakarn Pobsuk
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Ruttanaporn Chantakul
- Center of Excellence in Cannabis Research, Faculty of Pharmaceutical Sciences & Center of Excellence in Innovation in Chemistry, Naresuan University, Phitsanulok 65000, Thailand
| | - Teerapap Panklai
- Center of Excellence in Cannabis Research, Faculty of Pharmaceutical Sciences & Center of Excellence in Innovation in Chemistry, Naresuan University, Phitsanulok 65000, Thailand
| | - Prapapan Temkitthawon
- Center of Excellence in Cannabis Research, Faculty of Pharmaceutical Sciences & Center of Excellence in Innovation in Chemistry, Naresuan University, Phitsanulok 65000, Thailand
| | - Supa Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Krongkarn Chootip
- Department of Physiology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Kornkanok Ingkaninan
- Center of Excellence in Cannabis Research, Faculty of Pharmaceutical Sciences & Center of Excellence in Innovation in Chemistry, Naresuan University, Phitsanulok 65000, Thailand.
| | - Kanokthip Boonyarattanakalin
- College of Materials Innovation and Technology, King Mongkut's Institute of Technology Ladkrabang, Bangkok 10520, Thailand
| | - Duangkamol Gleeson
- Department of Chemistry & Applied Computational Chemistry Research Unit, School of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok 10520, Thailand
| | - M Paul Gleeson
- Department of Biomedical Engineering, School of Engineering, King Mongkut's Institute of Technology Ladkrabang, Bangkok 10520, Thailand.
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