1
|
Zhao F, Moriwaki Y, Noguchi T, Shimizu K, Kuzuyama T, Terada T. QM/MM Study of the Catalytic Mechanism and Substrate Specificity of the Aromatic Substrate C-Methyltransferase Fur6. Biochemistry 2024; 63:806-814. [PMID: 38422553 DOI: 10.1021/acs.biochem.3c00556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
In the field of medical chemistry and other organic chemistry, introducing a methyl group into a designed position has been difficult to achieve. However, owing to the vigorous developments in the field of enzymology, methyltransferases are considered potential tools for addressing this problem. Within the methyltransferase family, Fur6 catalyzes the methylation of C3 of 1,2,4,5,7-pentahydroxynaphthalene (PHN) using S-adenosyl-l-methionine (SAM) as the methyl donor. Here, we report the catalytic mechanism and substrate specificity of Fur6 based on computational studies. Our molecular dynamics (MD) simulation studies reveal the reactive form of PHN and its interactions with the enzyme. Our hybrid quantum mechanics/molecular mechanics (QM/MM) calculations suggest the reaction pathway of the methyl transfer step in which the energy barrier is 8.6 kcal mol-1. Our free-energy calculations with a polarizable continuum model (PCM) indicate that the final deprotonation step of the methylated intermediate occurs after it is ejected into the water solvent from the active center pocket of Fur6. Additionally, our studies on the protonation states, the highest occupied molecular orbital (HOMOs), and the energy barriers of the methylation reaction for the analogs of PHN demonstrate the mechanism of the specificity to PHN. Our study provides valuable insights into Fur6 chemistry, contributing to a deeper understanding of molecular mechanisms and offering an opportunity to engineer the enzyme to achieve high yields of the desired product(s).
Collapse
Affiliation(s)
- Fan Zhao
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yoshitaka Moriwaki
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
- Graduate School of Agricultural and Life Sciences and Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tomohiro Noguchi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kentaro Shimizu
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tomohisa Kuzuyama
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
- Graduate School of Agricultural and Life Sciences and Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tohru Terada
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
- Graduate School of Agricultural and Life Sciences and Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| |
Collapse
|
2
|
Yang QL, Liu Y, Liang L, Li ZH, Qu GR, Guo HM. Facilitating Rh-Catalyzed C-H Alkylation of (Hetero)arenes and 6-Arylpurine Nucleosides (Nucleotides) with Electrochemistry. J Org Chem 2022; 87:6161-6178. [PMID: 35438486 DOI: 10.1021/acs.joc.2c00391] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An electrochemical approach to promote the ortho-C-H alkylation of (hetero)arenes via rhodium catalysis under mild conditions is described. This approach features mild conditions with high levels of regio- and monoselectivity that tolerate a variety of aromatic and heteroaromatic groups and offers a widely applicable method for late-stage diversification of complex molecular architectures including tryptophan, estrone, diazepam, nucleosides, and nucleotides. Alkyl boronic acids and esters and alkyl trifluoroborates are demonstrated as suitable coupling partners. The isolation of key rhodium intermediates and mechanistic studies provided strong support for a rhodium(III/IV or V) regime.
Collapse
Affiliation(s)
- Qi-Liang Yang
- NMPA Key Laboratory for Research and Evaluation of Innovative Drug, Henan Key Laboratory of Organic Functional Molecules and Drug Innovation, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, China
| | - Ying Liu
- NMPA Key Laboratory for Research and Evaluation of Innovative Drug, Henan Key Laboratory of Organic Functional Molecules and Drug Innovation, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, China
| | - Lei Liang
- School of Chemistry and Chemical Engineering, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Zhi-Hao Li
- NMPA Key Laboratory for Research and Evaluation of Innovative Drug, Henan Key Laboratory of Organic Functional Molecules and Drug Innovation, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, China
| | - Gui-Rong Qu
- NMPA Key Laboratory for Research and Evaluation of Innovative Drug, Henan Key Laboratory of Organic Functional Molecules and Drug Innovation, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, China
| | - Hai-Ming Guo
- NMPA Key Laboratory for Research and Evaluation of Innovative Drug, Henan Key Laboratory of Organic Functional Molecules and Drug Innovation, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, China
| |
Collapse
|
3
|
Kolupaeva EV, Ozeryanskii VA. Dialkylamino and trialkylammonium groups in close proximity: intra- and intermolecular ways of formation, structural consequences, and properties. A case of metal-free directed ortho alkylation. NEW J CHEM 2022. [DOI: 10.1039/d2nj02653h] [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
All principal approaches to get to quaternised 1,8-bis(dialkylamino)naphthalenes along with their unusual properties are reported for the first time.
Collapse
Affiliation(s)
- Ekaterina V. Kolupaeva
- Department of Organic Chemistry, Southern Federal University, Zorge str. 7, 344090 Rostov-on-Don, Russian Federation
| | - Valery A. Ozeryanskii
- Department of Organic Chemistry, Southern Federal University, Zorge str. 7, 344090 Rostov-on-Don, Russian Federation
| |
Collapse
|
4
|
Yang X, Wang G, Ye ZS. Palladium-catalyzed nucleomethylation of alkynes for synthesis of methylated heteroaromatic compounds. Chem Sci 2022; 13:10095-10102. [PMID: 36128232 PMCID: PMC9430495 DOI: 10.1039/d2sc03294e] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/09/2022] [Indexed: 11/29/2022] Open
Abstract
Herein, we disclosed a novel and efficient palladium-catalyzed nucleomethylation of alkynes for the simultaneous construction of the heteroaromatic ring and methyl group. The 3-methylindoles, 3-methylbenzofurans and 4-methylisoquinolines were obtained in moderate to excellent yields. Notably, this methodology was employed as a key step for synthesis of a pregnane X receptor antagonist, zindoxifene, bazedoxifene and AFN-1252. The kinetic studies revealed that reductive elimination might be the rate-determining step. A novel palladium-catalyzed nucleomethylation of alkynes is developed, affording 3-methylindoles, 3-methylbenzofurans and 4-methylisoquinolines in moderate to excellent yields.![]()
Collapse
Affiliation(s)
- Xi Yang
- Zhang Dayu School of Chemistry, Dalian University of Technology, Dalian 116024, P. R. China
| | - Gang Wang
- Zhang Dayu School of Chemistry, Dalian University of Technology, Dalian 116024, P. R. China
| | - Zhi-Shi Ye
- Zhang Dayu School of Chemistry, Dalian University of Technology, Dalian 116024, P. R. China
| |
Collapse
|
5
|
Subbaiah MAM, Meanwell NA. Bioisosteres of the Phenyl Ring: Recent Strategic Applications in Lead Optimization and Drug Design. J Med Chem 2021; 64:14046-14128. [PMID: 34591488 DOI: 10.1021/acs.jmedchem.1c01215] [Citation(s) in RCA: 165] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The benzene moiety is the most prevalent ring system in marketed drugs, underscoring its historic popularity in drug design either as a pharmacophore or as a scaffold that projects pharmacophoric elements. However, introspective analyses of medicinal chemistry practices at the beginning of the 21st century highlighted the indiscriminate deployment of phenyl rings as an important contributor to the poor physicochemical properties of advanced molecules, which limited their prospects of being developed into effective drugs. This Perspective deliberates on the design and applications of bioisosteric replacements for a phenyl ring that have provided practical solutions to a range of developability problems frequently encountered in lead optimization campaigns. While the effect of phenyl ring replacements on compound properties is contextual in nature, bioisosteric substitution can lead to enhanced potency, solubility, and metabolic stability while reducing lipophilicity, plasma protein binding, phospholipidosis potential, and inhibition of cytochrome P450 enzymes and the hERG channel.
Collapse
Affiliation(s)
- Murugaiah A M Subbaiah
- Department of Medicinal Chemistry, Biocon-Bristol Myers Squibb Research and Development Centre, Biocon Park, Bommasandra IV Phase, Jigani Link Road, Bangalore, Karnataka 560099, India
| | - Nicholas A Meanwell
- Department of Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| |
Collapse
|