1
|
Soro SD, Lattard V, Kodjo A, Benoît E, Chatron N. Structural investigation of vitamin K epoxide reductase domain-containing protein in Leptospira species: a potential target for the development of new leptospirosis treatments as an alternative to antibiotics. J Biomol Struct Dyn 2024:1-13. [PMID: 38197604 DOI: 10.1080/07391102.2024.2302925] [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: 09/28/2023] [Accepted: 12/30/2023] [Indexed: 01/11/2024]
Abstract
Leptospirosis is a worldwide zoonosis caused by the motile bacterium Leptospira. This disease can cause hemorrhagic symptoms, multi-visceral and renal failures, resulting in one million cases and approximately 60,000 deaths each year. The motility of Leptospira is highly involved in its virulence and is ensured by the presence of two flagella in the periplasm. Several proteins that require the formation of disulfide bridges are essential for flagellar function. In Leptospira, these redox reactions are catalysed by the vitamin K epoxide reductase domain-containing protein (VKORdcp). The aim of the present work was to study the conservation of VKORdcp among Leptospira species and its interactions with putative substrates and inhibitor. Our results evidenced the presence of ten amino acids specific to either pathogenic or saprophytic species. Furthermore, structural studies revealed a higher affinity of the enzyme for vitamin K1 quinone, compared to ubiquinone. Finally, characterisation of the binding of a potential inhibitor revealed the involvement of some VKORdcp amino acids that have not been present in the human enzyme, in particular the polar residue D114. Our study thus paves the way for the future development of Leptospira VKORdcp inhibitors, capable of blocking bacterial motility. Such molecules could therefore offer a promising therapeutic alternative to antibiotics, especially in the event of the emergence of antibiotic-resistant strains.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
| | - Virginie Lattard
- USC 1233-RS2GP, VetAgro Sup, INRAE, Université de Lyon, Marcy L'Etoile, France
| | - Angeli Kodjo
- USC 1233-RS2GP, VetAgro Sup, INRAE, Université de Lyon, Marcy L'Etoile, France
| | - Etienne Benoît
- USC 1233-RS2GP, VetAgro Sup, INRAE, Université de Lyon, Marcy L'Etoile, France
| | - Nolan Chatron
- USC 1233-RS2GP, VetAgro Sup, INRAE, Université de Lyon, Marcy L'Etoile, France
| |
Collapse
|
2
|
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
|
3
|
Chen Y, Wang D, Li N, Wang D, Liu XH, Song Y. Accelerated evolution of Vkorc1 in desert rodent species reveals genetic preadaptation to anticoagulant rodenticides. PEST MANAGEMENT SCIENCE 2022; 78:2704-2713. [PMID: 35394111 DOI: 10.1002/ps.6905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 03/23/2022] [Accepted: 04/08/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Some rodent species living in arid areas show elevated physiological tolerance to anti-vitamin K rodenticides (AVKs), which seems to be due to some unknown selective pressures that rodents may experience in desert habitats. Genes involved in the ϒ-carboxylation of blood coagulation, including vitamin K epoxide reductase complex, subunit 1 (Vkorc1), ϒ-glutamyl-carboxylase (Ggcx) and NAD(P)H quinone one dehydrogenase (Nqo1) are associated with anticoagulant resistance, or some levels of elevated tolerance, in rodents. To detect whether the DNA sequences of the three genes are also under natural selection in the desert rodent species, we analyzed the Vkorc1, Ggcx and Nqo1 genes of the desert rodents and compared them with other rodent species. RESULTS We found an accelerated evolutionary rate in Vkorc1 of desert rodents, especially in Mus spretus, Nannospalax galili and Psammomys obesus. By contrast, signals of positive selection were absent for Ggcx and Nqo1 in all species. Mapping the amino acid variations on the VKORC1 protein three-dimensional model suggested most interspecific amino acid variations occur on the outer surface of the VKORC1 pocket, whereas most intraspecific amino acid changes and known AVK resistance mutations occurred on the inner surface and endoplasmic reticulum luminal loop regions. Some desert-species-specific amino acid variations were found on the positions where known resistance mutations occurred, indicating these variations might be related to the elevated physical tolerance to AVKs in desert rodents. CONCLUSION The evolution of Vkorc1 has been accelerated in some desert rodent species, indicating genetic preadaptation to anticoagulant rodenticides. Positive selection and relaxed selection have been detected in Psammomys obesus and Nannospalax galili, indicating the two rodent species might also show tolerance to AVKs, which needs further verification. © 2022 Society of Chemical Industry.
Collapse
Affiliation(s)
- Yan Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dawei Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ning Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Deng Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Xiao-Hui Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ying Song
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
4
|
Holcomb D, Alexaki A, Hernandez N, Hunt R, Laurie K, Kames J, Hamasaki-Katagiri N, Komar AA, DiCuccio M, Kimchi-Sarfaty C. Gene variants of coagulation related proteins that interact with SARS-CoV-2. PLoS Comput Biol 2021; 17:e1008805. [PMID: 33730015 PMCID: PMC8007013 DOI: 10.1371/journal.pcbi.1008805] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 03/29/2021] [Accepted: 02/15/2021] [Indexed: 12/30/2022] Open
Abstract
Thrombosis is a recognized complication of Coronavirus disease of 2019 (COVID-19) and is often associated with poor prognosis. There is a well-recognized link between coagulation and inflammation, however, the extent of thrombotic events associated with COVID-19 warrants further investigation. Poly(A) Binding Protein Cytoplasmic 4 (PABPC4), Serine/Cysteine Proteinase Inhibitor Clade G Member 1 (SERPING1) and Vitamin K epOxide Reductase Complex subunit 1 (VKORC1), which are all proteins linked to coagulation, have been shown to interact with SARS proteins. We computationally examined the interaction of these with SARS-CoV-2 proteins and, in the case of VKORC1, we describe its binding to ORF7a in detail. We examined the occurrence of variants of each of these proteins across populations and interrogated their potential contribution to COVID-19 severity. Potential mechanisms, by which some of these variants may contribute to disease, are proposed. Some of these variants are prevalent in minority groups that are disproportionally affected by severe COVID-19. Therefore, we are proposing that further investigation around these variants may lead to better understanding of disease pathogenesis in minority groups and more informed therapeutic approaches.
Collapse
Affiliation(s)
- David Holcomb
- Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Aikaterini Alexaki
- Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Nancy Hernandez
- Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Ryan Hunt
- Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Kyle Laurie
- Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Jacob Kames
- Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Nobuko Hamasaki-Katagiri
- Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Anton A. Komar
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio, United States of America
| | - Michael DiCuccio
- National Center of Biotechnology Information, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (MD); (CKS)
| | - Chava Kimchi-Sarfaty
- Center for Biologics Evaluation and Research, Office of Tissues and Advanced Therapies, Division of Plasma Protein Therapeutics, Food and Drug Administration, Silver Spring, Maryland, United States of America
- * E-mail: (MD); (CKS)
| |
Collapse
|
5
|
Holcomb D, Alexaki A, Hernandez N, Laurie K, Kames J, Hamasaki-Katagiri N, Komar AA, DiCuccio M, Kimchi-Sarfaty C. Potential impact on coagulopathy of gene variants of coagulation related proteins that interact with SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32935103 DOI: 10.1101/2020.09.08.272328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Thrombosis has been one of the complications of the Coronavirus disease of 2019 (COVID-19), often associated with poor prognosis. There is a well-recognized link between coagulation and inflammation, however, the extent of thrombotic events associated with COVID-19 warrants further investigation. Poly(A) Binding Protein Cytoplasmic 4 (PABPC4), Serine/Cysteine Proteinase Inhibitor Clade G Member 1 (SERPING1) and Vitamin K epOxide Reductase Complex subunit 1 (VKORC1), which are all proteins linked to coagulation, have been shown to interact with SARS proteins. We computationally examined the interaction of these with SARS-CoV-2 proteins and, in the case of VKORC1, we describe its binding to ORF7a in detail. We examined the occurrence of variants of each of these proteins across populations and interrogated their potential contribution to COVID-19 severity. Potential mechanisms by which some of these variants may contribute to disease are proposed. Some of these variants are prevalent in minority groups that are disproportionally affected by severe COVID-19. Therefore, we are proposing that further investigation around these variants may lead to better understanding of disease pathogenesis in minority groups and more informed therapeutic approaches. Author summary Increased blood clotting, especially in the lungs, is a common complication of COVID-19. Infectious diseases cause inflammation which in turn can contribute to increased blood clotting. However, the extent of clot formation that is seen in the lungs of COVID-19 patients suggests that there may be a more direct link. We identified three human proteins that are involved indirectly in the blood clotting cascade and have been shown to interact with proteins of SARS virus, which is closely related to the novel coronavirus. We examined computationally the interaction of these human proteins with the viral proteins. We looked for genetic variants of these proteins and examined how these variants are distributed across populations. We investigated whether variants of these genes could impact severity of COVID-19. Further investigation around these variants may provide clues for the pathogenesis of COVID-19 particularly in minority groups.
Collapse
|