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Millán-Pacheco C, Rios-Soto L, Corral-Rodríguez N, Sierra-Campos E, Valdez-Solana M, Téllez-Valencia A, Avitia-Domínguez C. Discovery of Potential Noncovalent Inhibitors of Dehydroquinate Dehydratase from Methicillin-Resistant Staphylococcus aureus through Computational-Driven Drug Design. Pharmaceuticals (Basel) 2023; 16:1148. [PMID: 37631063 PMCID: PMC10458038 DOI: 10.3390/ph16081148] [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: 06/30/2023] [Revised: 08/10/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
Bacteria resistance to antibiotics is a concerning global health problem; in this context, methicillin-resistant Staphylococcus aureus (MRSA) is considered as a high priority by the World Health Organization. Furthermore, patients with a positive result for COVID-19 received early antibiotic treatment, a fact that potentially encourages the increase in antibiotic resistance. Therefore, there is an urgency to develop new drugs with molecular mechanisms different from those of the actual treatments. In this context, enzymes from the shikimate pathway, a route absent in humans, such as dehydroquinate dehydratase (DHQD), are considered good targets. In this work, a computer-aided drug design strategy, which involved exhaustive virtual screening and molecular dynamics simulations with MM-PBSA analysis, as well as an in silico ADMETox characterization, was performed to find potential noncovalent inhibitors of DHQD from MRSA (SaDHQD). After filtering the 997 million compounds from the ZINC database, 6700 compounds were submitted to an exhaustive virtual screening protocol. From these data, four molecules were selected and characterized (ZINC000005753647 (1), ZINC000001720488 (2), ZINC000082049768 (3), and ZINC000644149506 (4)). The results indicate that the four potential inhibitors interacted with residues important for substrate binding and catalysis, with an estimated binding free energy like that of the enzyme's substrate. Their ADMETox-predicted properties suggest that all of them support the structural characteristics to be considered good candidates. Therefore, the four compounds reported here are excellent option to be considered for future in vitro studies to design new SaDHQD noncovalent inhibitors and contribute to the search for new drugs against MRSA.
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Affiliation(s)
- César Millán-Pacheco
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos 62209, Mexico;
| | - Lluvia Rios-Soto
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Av. Universidad y Fanny Anitua S/N, Durango 34000, Mexico; (L.R.-S.); (N.C.-R.)
| | - Noé Corral-Rodríguez
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Av. Universidad y Fanny Anitua S/N, Durango 34000, Mexico; (L.R.-S.); (N.C.-R.)
| | - Erick Sierra-Campos
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango Campus Gómez Palacio, Avenida Artículo 123 S/N, Fracc. Filadelfia, Gómez Palacio 35010, Mexico; (E.S.-C.); (M.V.-S.)
| | - Mónica Valdez-Solana
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango Campus Gómez Palacio, Avenida Artículo 123 S/N, Fracc. Filadelfia, Gómez Palacio 35010, Mexico; (E.S.-C.); (M.V.-S.)
| | - Alfredo Téllez-Valencia
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Av. Universidad y Fanny Anitua S/N, Durango 34000, Mexico; (L.R.-S.); (N.C.-R.)
| | - Claudia Avitia-Domínguez
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Av. Universidad y Fanny Anitua S/N, Durango 34000, Mexico; (L.R.-S.); (N.C.-R.)
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Naveen N, Balamurugan R. Catalyst free synthesis of α-fluoro-β-hydroxy ketones/α-fluoro-ynols via electrophilic fluorination of tertiary propargyl alcohols using Selectfluor™ (F-TEDA-BF4). Org Biomol Chem 2017; 15:2063-2072. [DOI: 10.1039/c7ob00140a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A facile access to α-fluoro-β-hydroxyketones via electrophilic fluorination.
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Specific chemical modification of bacterial type I dehydroquinase – opportunities for drug discovery. Future Med Chem 2015; 7:2371-83. [DOI: 10.4155/fmc.15.145] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Type I dehydroquinase (DHQ1) is a class I aldolase enzyme that catalyzes the reversible dehydration of 3-dehydroquinic acid to form 3-dehydroshikimic acid by multistep mechanism that involves the formation of Schiff-base species. DHQ1 is present in plants and several bacterial sources but it does not have any counterpart in human cells. It has been suggested that DHQ1 may act as a virulence factor in vivo and therefore a promising target in the search for new antivirulence agents to combat widespread antibiotic resistance. This review covers recent progress in the structure-based design and chemical modifications caused by selective irreversible inhibitors. Computational studies aimed at understanding the experimentally obtained covalent modifications and inhibitory potencies of these inhibitors are also described.
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González-Bello C, Tizón L, Lence E, Otero JM, van Raaij MJ, Martinez-Guitian M, Beceiro A, Thompson P, Hawkins AR. Chemical Modification of a Dehydratase Enzyme Involved in Bacterial Virulence by an Ammonium Derivative: Evidence of its Active Site Covalent Adduct. J Am Chem Soc 2015; 137:9333-43. [DOI: 10.1021/jacs.5b04080] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | | | - Mark J. van Raaij
- Departamento
de Estructura de Macromoléculas, Centro Nacional de Biotecnología (CSIC), Campus Cantoblanco, 28049 Madrid, Spain
| | - Marta Martinez-Guitian
- Servicio
de Microbiología-INIBIC, Complejo Hospitalario Universitario A Coruña (CHUAC), 15006 A Coruña, Spain
| | - Alejandro Beceiro
- Servicio
de Microbiología-INIBIC, Complejo Hospitalario Universitario A Coruña (CHUAC), 15006 A Coruña, Spain
| | - Paul Thompson
- Institute
of Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Alastair R. Hawkins
- Institute
of Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, United Kingdom
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Tizón L, Maneiro M, Peón A, Otero JM, Lence E, Poza S, van Raaij MJ, Thompson P, Hawkins AR, González-Bello C. Irreversible covalent modification of type I dehydroquinase with a stable Schiff base. Org Biomol Chem 2015; 13:706-16. [DOI: 10.1039/c4ob01782j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Structural and computational studies carried out with two epoxides provide insight into the irreversible inhibition of type I dehydroquinase.
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Affiliation(s)
- Lorena Tizón
- Centro Singular de Investigación en Química Biológica y Materiales Moleculares (CIQUS)
- Universidad de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - María Maneiro
- Centro Singular de Investigación en Química Biológica y Materiales Moleculares (CIQUS)
- Universidad de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Antonio Peón
- Centro Singular de Investigación en Química Biológica y Materiales Moleculares (CIQUS)
- Universidad de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - José M. Otero
- Departamento de Bioquímica y Biología Molecular and CIQUS
- Universidad de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Emilio Lence
- Centro Singular de Investigación en Química Biológica y Materiales Moleculares (CIQUS)
- Universidad de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Sergio Poza
- Centro Singular de Investigación en Química Biológica y Materiales Moleculares (CIQUS)
- Universidad de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Mark J. van Raaij
- Departamento de Estructura de Macromoléculas
- Centro Nacional de Biotecnología (CSIC)
- 28049 Madrid
- Spain
| | - Paul Thompson
- Institute of Cell and Molecular Biosciences
- Medical School
- University of Newcastle upon Tyne
- Newcastle upon Tyne NE2 4HH
- UK
| | - Alastair R. Hawkins
- Institute of Cell and Molecular Biosciences
- Medical School
- University of Newcastle upon Tyne
- Newcastle upon Tyne NE2 4HH
- UK
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biológica y Materiales Moleculares (CIQUS)
- Universidad de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
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Insights into substrate binding and catalysis in bacterial type I dehydroquinase. Biochem J 2014; 462:415-24. [DOI: 10.1042/bj20140614] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The crystal structure of S. typhi type I dehydroquinase in complex with (2R)-3-methyl-3-dehydroquinic acid is described. A previously unknown key role of several conserved residues and a detailed knowledge of the substrate binding process is detailed.
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González-Bello C, Castedo L. Progress in type II dehydroquinase inhibitors: From concept to practice. Med Res Rev 2007; 27:177-208. [PMID: 17004270 DOI: 10.1002/med.20076] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Scientists are concerned by an ever-increasing rise in bacterial resistance to antibiotics, particularly in diseases such as malaria, toxoplasmosis, tuberculosis, and pneumonia, where the currently used therapies become progressively less efficient. It is therefore necessary to develop new, safe, and more efficient antibiotics. Recently, the existence of the shikimic acid pathway has been demonstrated in certain parasites such as the malaria parasite. These types of parasites cause more than a million casualties per year, and their effects are particularly strong in people with a compromised immune system such as HIV patients. In such cases it is possible that inhibitors of this pathway could be active against a large variety of microorganisms responsible for the more opportunistic infections in HIV patients. Interest in this pathway has resulted in the development of a wide variety of inhibitors for the enzymes involved. This review covers recent progress made in the development of inhibitors of the third enzyme of this pathway, i.e., the type II dehydroquinase. The X-ray crystal structures of several dehydroquinases (Streptomyces coelicolor, Mycobacterium tuberculosis, etc.) with an inhibitor bound in the active site have recently been solved. These complexes identified a number of key interactions involved in inhibitor binding and have shed light on several aspects of the catalytic mechanism. These crystal structures have also proven to be a useful tool for the design of potent and selective enzyme inhibitors, a feature that will also be discussed.
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Affiliation(s)
- Concepción González-Bello
- Departamento de Química Orgánica, Facultad de Química, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
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Singh SA, Christendat D. Structure ofArabidopsisDehydroquinate Dehydratase-Shikimate Dehydrogenase and Implications for Metabolic Channeling in the Shikimate Pathway†,‡. Biochemistry 2006; 45:7787-96. [PMID: 16784230 DOI: 10.1021/bi060366+] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The bifunctional enzyme dehydroquinate dehydratase-shikimate dehydrogenase (DHQ-SDH) catalyzes the dehydration of dehydroquinate to dehydroshikimate and the reduction of dehydroshikimate to shikimate in the shikimate pathway. We report the first crystal structure of Arabidopsis DHQ-SDH with shikimate bound at the SDH site and tartrate at the DHQ site. The interactions observed in the DHQ-tartrate complex reveal a conserved mode for substrate binding between the plant and microbial DHQ dehydratase family of enzymes. The SDH-shikimate complex provides the first direct evidence of the role of active site residues in the catalytic mechanism. Site-directed mutagenesis and mechanistic analysis revealed that Asp 423 and Lys 385 are key catalytic groups and Ser 336 is a key binding group. The arrangement of the two functional domains reveals that the control of metabolic flux through the shikimate pathway is achieved by increasing the effective concentration of dehydroshikimate through the proximity of the two sites.
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Affiliation(s)
- Sasha Anna Singh
- Department of Botany, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
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Sánchez-Sixto C, Prazeres VFV, Castedo L, Lamb H, Hawkins AR, González-Bello C. Structure-Based Design, Synthesis, and Biological Evaluation of Inhibitors ofMycobacteriumtuberculosisType II Dehydroquinase. J Med Chem 2005; 48:4871-81. [PMID: 16033267 DOI: 10.1021/jm0501836] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The syntheses by Suzuki cross-coupling of 12 5-aryl analogues of the known inhibitor (1R,3R,4R)-1,3,4-trihydroxycyclohex-5-en-1-carboxylic acid are reported. These compounds were found to be reversible competitive inhibitors against Mycobacterium tuberculosis type II dehydroquinase, the third enzyme of the shikimic acid pathway. The most potent inhibitor, the 3-nitrophenyl derivative, has a K(i) of 54 nM, over 180 times more potent than the reported inhibitor (1R,3R,4R)-5-fluoro-1,3,4-trihydroxycyclohex-5-en-1-carboxylic acid and more than 700 times lower than the K(M) of the substrate, making it the most potent known inhibitor against any type II dehydroquinase. Docking studies using GOLD (version 2.2) indicated a key electrostatic binding interaction between the aromatic rings and Arg19, a residue that has been identified as essential for enzyme activity.
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Affiliation(s)
- Cristina Sánchez-Sixto
- Departamento de Química Orgánica y Unidad Asociada al C.S.I.C., Facultad de Química, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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González-Bello C, Lence E, Toscano MD, Castedo L, Coggins JR, Abell C. Parallel Solid-Phase Synthesis and Evaluation of Inhibitors of Streptomyces coelicolor Type II Dehydroquinase. J Med Chem 2003; 46:5735-44. [PMID: 14667226 DOI: 10.1021/jm030987q] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of 1-substituted and 4-substituted benzyl analogues of the known inhibitor (1S,3R,4R)-1,3,4-trihydroxy-5-cyclohexene-1-carboxylic acid has been synthesized and tested as inhibitors of Streptomyces coelicolor type II dehydroquinase. The solid-phase syntheses of 18 new analogues are reported. The most potent inhibitor, 2-nitrobenzyloxy analogue 5i, has K(i) of 8 microM, more than 30 times lower than the K(M) of the substrate and approximately 4 times more potent than the original inhibitor. The binding modes of the synthesized analogues in the active site were studied by molecular docking with GOLD 2.0.
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Affiliation(s)
- Concepción González-Bello
- Departamento de Química Orgánica y Unidad Asociada al C.S.I.C., Facultad de Química, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
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Toscano MD, Frederickson M, Evans DP, Coggins JR, Abell C, González-Bello C. Design, synthesis and evaluation of bifunctional inhibitors of type II dehydroquinase. Org Biomol Chem 2003; 1:2075-83. [PMID: 12945898 DOI: 10.1039/b301731a] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Inhibitors of type II dehydroquinase were designed to straddle the two distinct binding sites identified for the inhibitor (1S,3R,4R)-1,3,4-trihydroxy-5-cyclohexene-1-carboxylic acid and a glycerol molecule in a crystallographic study of the Streptomyces coelicolor enzyme. A number of compounds were designed to incorporate characteristics of both ligands. These analogues were synthesized from quinic acid, and were assayed against type I (Salmonella typhi) and type II (S. coelicolor) dehydroquinases. None of the analogues showed inhibition for type I dehydroquinase. Six of the analogues were shown to have inhibition constants in the micromolar to low millimolar range against the S. coelicolor type II dehydroquinase, while two showed no inhibition. The binding modes of the analogues in the active site of the S. coelicolor enzyme were studied by molecular docking with GOLD1.2. These studies suggest a binding mode where the ring is in a similar position to (1S,3R,4R)-1,3,4-trihydroxy-5-cyclohexene-1-carboxylic acid in the crystal structure and the side-chain occupies part of the glycerol binding-pocket.
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Affiliation(s)
- Miguel D Toscano
- University Chemical Laboratory, Lensfield Road, Cambridge, UK CB2 1EW
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