1
|
Chatron N, Boulven M, Montagut-Romans A, Ponsot F, Jacolot M, Caruel H, Benoît E, Popowycz F, Lattard V. Design of a structure-activity relationship model of vitamin K epoxide reductase (VKORC1) inhibitors combining chemical synthesis of new compounds, enzymatic assays and molecular modelling. Bioorg Med Chem 2023; 94:117453. [PMID: 37741121 DOI: 10.1016/j.bmc.2023.117453] [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: 05/05/2023] [Revised: 08/13/2023] [Accepted: 08/21/2023] [Indexed: 09/25/2023]
Abstract
Vitamin K antagonists (VKAs) anticoagulants have been used since the 1950s as medicines and rodenticides. These molecules are mainly 4-hydroxycoumarin derivatives and act by inhibiting the vitamin K epoxide reductase (VKORC1), an endoplasmic reticulum membrane resident enzyme. However, many VKORC1 mutations have been reported over the last decade, inducing VKAs resistances and thus treatments failures. Although studies have reported experimental and computational investigations of VKAs based on VKORC1 structural homology models, the development of new effective anticoagulants has been quite complex due to the lack of structural data and reliable structure-activity relationships. However, the recent publication of VKORC1 crystal structure provides new information for further studies. Based on these findings, we combined chemical synthesis, enzymatic assays and molecular modelling methods to design a structure-activity relationship (SAR) model. Our results proved that the lipophilicity, the membrane permeability of inhibitors and their affinity towards human VKORC1 enzyme are the main characteristics for potent anticoagulants. Our SAR model managed to rank compounds according to their ability to inhibit the human VKORC1. Such a tool might constitute an alternative to evaluate new molecules potency before their chemical synthesis and biological assessment and might assist the development of new VKAs.
Collapse
Affiliation(s)
- Nolan Chatron
- USC 1233 RS2GP, VetAgro Sup, INRAE, University of Lyon, 69280 Marcy L'Etoile, France.
| | - Manon Boulven
- Univ Lyon, INSA Lyon, Université Lyon 1, CNRS, CPE Lyon, UMR 5246, ICBMS, 1 rue Victor Grignard, 69621 Villeurbanne Cedex, France; Liphatech, Bonnel, 47480 Pont-du-Casse, France
| | - Adrien Montagut-Romans
- Univ Lyon, INSA Lyon, Université Lyon 1, CNRS, CPE Lyon, UMR 5246, ICBMS, 1 rue Victor Grignard, 69621 Villeurbanne Cedex, France; Liphatech, Bonnel, 47480 Pont-du-Casse, France
| | - Flavien Ponsot
- Univ Lyon, INSA Lyon, Université Lyon 1, CNRS, CPE Lyon, UMR 5246, ICBMS, 1 rue Victor Grignard, 69621 Villeurbanne Cedex, France
| | - Maïwenn Jacolot
- Univ Lyon, INSA Lyon, Université Lyon 1, CNRS, CPE Lyon, UMR 5246, ICBMS, 1 rue Victor Grignard, 69621 Villeurbanne Cedex, France
| | | | - Etienne Benoît
- USC 1233 RS2GP, VetAgro Sup, INRAE, University of Lyon, 69280 Marcy L'Etoile, France
| | - Florence Popowycz
- Univ Lyon, INSA Lyon, Université Lyon 1, CNRS, CPE Lyon, UMR 5246, ICBMS, 1 rue Victor Grignard, 69621 Villeurbanne Cedex, France
| | - Virginie Lattard
- USC 1233 RS2GP, VetAgro Sup, INRAE, University of Lyon, 69280 Marcy L'Etoile, France
| |
Collapse
|
2
|
Annunziata F, Pinna C, Dallavalle S, Tamborini L, Pinto A. An Overview of Coumarin as a Versatile and Readily Accessible Scaffold with Broad-Ranging Biological Activities. Int J Mol Sci 2020; 21:E4618. [PMID: 32610556 PMCID: PMC7370201 DOI: 10.3390/ijms21134618] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/22/2020] [Accepted: 06/28/2020] [Indexed: 12/19/2022] Open
Abstract
Privileged structures have been widely used as an effective template for the research and discovery of high value chemicals. Coumarin is a simple scaffold widespread in Nature and it can be found in a considerable number of plants as well as in some fungi and bacteria. In the last years, these natural compounds have been gaining an increasing attention from the scientific community for their wide range of biological activities, mainly due to their ability to interact with diverse enzymes and receptors in living organisms. In addition, coumarin nucleus has proved to be easily synthetized and decorated, giving the possibility of designing new coumarin-based compounds and investigating their potential in the treatment of various diseases. The versatility of coumarin scaffold finds applications not only in medicinal chemistry but also in the agrochemical field as well as in the cosmetic and fragrances industry. This review is intended to be a critical overview on coumarins, comprehensive of natural sources, metabolites, biological evaluations and synthetic approaches.
Collapse
Affiliation(s)
- Francesca Annunziata
- Department of Pharmaceutical Science, University of Milan, via Mangiagalli 25, 20133 Milan, Italy; (F.A.); (C.P.)
| | - Cecilia Pinna
- Department of Pharmaceutical Science, University of Milan, via Mangiagalli 25, 20133 Milan, Italy; (F.A.); (C.P.)
| | - Sabrina Dallavalle
- Department of Food, Environmental and Nutritional Sciences, University of Milan, via Celoria 2, 20133 Milan, Italy; (S.D.); (A.P.)
| | - Lucia Tamborini
- Department of Pharmaceutical Science, University of Milan, via Mangiagalli 25, 20133 Milan, Italy; (F.A.); (C.P.)
| | - Andrea Pinto
- Department of Food, Environmental and Nutritional Sciences, University of Milan, via Celoria 2, 20133 Milan, Italy; (S.D.); (A.P.)
| |
Collapse
|
3
|
Govindaiah P, Dumala N, Mattan I, Grover P, Jaya Prakash M. Design, synthesis, biological and in silico evaluation of coumarin-hydrazone derivatives as tubulin targeted antiproliferative agents. Bioorg Chem 2019; 91:103143. [DOI: 10.1016/j.bioorg.2019.103143] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 07/18/2019] [Accepted: 07/19/2019] [Indexed: 10/26/2022]
|
4
|
Gomes LR, Low JN, van Mourik T, da Silveira Pinto LS, de Souza MV, Wardell JL. Crystal structures, Hirsfeld surface analysis and a computational study of four ethyl 2-oxo-2 H-chromene-3-carboxylate derivatives: a survey of organyl 2-oxo-2 H-chromene-3-carboxylate structures. Z KRIST-CRYST MATER 2019. [DOI: 10.1515/zkri-2018-2117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Crystal structures, Hirshfeld surface analysis and a computational study have been carried out on 2-oxo-2H-chromene-3-carboxylates. Crystal structures are reported for ethyl R-2-oxo-2H-chromene-3-carboxylate derivatives, 2a: R=6-Me, 2b: 7-Me, 2c: 7-Me, 2d: R=7-MeO. In contrast to 2-oxo-2H-chromene-3-carboxamides, 1, in which classical intramolecular N–H···O hydrogen bonds stabilize planar structures and hinder rotation of the amido group out of the coumarin plane in 2, without an equivalent hydrogen bond, there is a greater rotational freedom of the carboxylate group. The interplanar angles between the coumarin core and its attached –C(O)–R substituent in crystalline 2a, 2b, 2c and 2d are 10.41(6), 36.65(6), 10.4(2) and 5.64(6)°, respectively, with distances between the carbonyl oxygen atoms of 2.8255(16), 2.9278(16), 4.226(2) and 2.8328(14) Å, respectively. A theoretical study of molecular conformations was carried out at the M06-2X density level with the 6-31+G(d) and aug-cc-pVTZ basis sets, in methanol solution modeled by PCM, indicated that the most stable conformations had the carbonyl group of the ester in the plane of the coumarin core: the s-cis arrangement of the ester carbonyl and the 2-oxo moieties being the slightly more stable than the s-trans form by less than 0.5 kcal/mol. The experimental conformations of 2a and 2d match well the low energy s-cis arrangement, and 2c matches the slightly lesser stable s-trans arrangement found in the theoretical study. A survey of the molecular conformations of more than 50 2H-chromene-3-carboxylates derivatives in the CCDC data base indicated two distinct groupings of conformations, s-cis and s-trans, each with interplanar angles <30°.
Collapse
Affiliation(s)
- Ligia R. Gomes
- FP-ENAS-Faculdade de Ciências de Saúde, Escola Superior de Saúde da UFP, Universidade Fernando Pessoa , Rua Carlos da Maia, 296 , P-4200-150 Porto , Portugal
- REQUIMTE, Departamento de Química e Bioquímica , Faculdade de Ciências da Universidade do Porto , Rua do Campo Alegre, 687 , P-4169-007, Porto , Portugal
| | - John N. Low
- Department of Chemistry , University of Aberdeen , Meston Walk, Old Aberdeen, AB24 3UE , Scotland , UK
| | - Tanja van Mourik
- School of Chemistry, University of St. Andrews , North Haugh, St. Andrews, Fife KY16 9ST , Scotland , UK
| | - Ligia S. da Silveira Pinto
- Universidade Federal do Rio de Janeiro, Instituto de Química , Departamento de Química Orgânica , CP 68563, 21945-970 , Rio de Janeiro , Brazil
- Instituto de Tecnologia em Fármacos e Farmanguinhos, Fundação Oswaldo Cruz , 21041-250 Rio de Janeiro, RJ , Brazil
| | - Marcus V.N. de Souza
- Instituto de Tecnologia em Fármacos e Farmanguinhos, Fundação Oswaldo Cruz , 21041-250 Rio de Janeiro, RJ , Brazil
| | - Jámes L. Wardell
- Department of Chemistry , University of Aberdeen , Meston Walk, Old Aberdeen, AB24 3UE , Scotland , UK
- Instituto de Tecnologia em Fármacos e Farmanguinhos, Fundação Oswaldo Cruz , 21041-250 Rio de Janeiro, RJ , Brazil
| |
Collapse
|