1
|
Structural and Biochemical Analyses Reveal that Chlorogenic Acid Inhibits the Shikimate Pathway. J Bacteriol 2020; 202:JB.00248-20. [PMID: 32661075 DOI: 10.1128/jb.00248-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/01/2020] [Indexed: 11/20/2022] Open
Abstract
Chlorogenic acid (CGA) is a phenolic compound with well-known antibacterial properties against pathogens. In this study, structural and biochemical characterization was used to show the inhibitory role of CGA against the enzyme of the shikimate pathway, a well-characterized drug target in several pathogens. Here, we report the crystal structures of dehydroquinate synthase (DHQS), the second enzyme of the shikimate pathway, from Providencia alcalifaciens (PaDHQS), in binary complex with NAD and ternary complex with NAD and CGA. Structural analyses reveal that CGA occupies the substrate position in the active site of PaDHQS, which disables domain movements, leaving the enzyme in an open and catalysis-incompetent state. The binding analyses by isothermal titration calorimetry (ITC) and surface plasmon resonance (SPR) show that CGA binds to PaDHQS with KD (equilibrium dissociation constant) values of 6.3 μM and 0.5 μM, respectively. In vitro enzyme inhibition studies show that CGA inhibits PaDHQS with a Ki of 235 ± 21 μM, while it inhibits the growth of Providencia alcalifaciens, Moraxella catarrhalis, Staphylococcus aureus, and Escherichia coli with MIC values of 60 to 100 μM. In the presence of aromatic amino acids supplied externally, CGA does not show the toxic effect. These results, along with the observations of the inhibition of the 3-deoxy-d-arabino-heptulosonate-7-phosphate (DAHP) regulatory domain by CGA in our previous study, suggest that CGA binds to shikimate pathway enzymes with high affinity and inhibits their catalysis and can be further exploited for designing novel drug-like molecules.IMPORTANCE The shikimate pathway is an attractive target for the development of herbicides and antimicrobial agents, as it is essential in plants, bacteria, and apicomplexan parasites but absent in humans. The enzymes of shikimate pathway are conserved among bacteria. Thus, the inhibitors of the shikimate pathway act on wide range of pathogens. We have identified that chlorogenic acid targets the enzymes of the shikimate pathway. The crystal structure of dehydroquinate synthase, the second enzyme of the pathway, in complex with chlorogenic acid and enzymatic inhibition studies explains the mechanism of inhibition of chlorogenic acid. These results suggest that chlorogenic acid has a good chemical scaffold and have important implications for its further development as a potent inhibitor of shikimate pathway enzymes.
Collapse
|
2
|
Favela-Candia A, Téllez-Valencia A, Campos-Almazán M, Sierra-Campos E, Valdez-Solana M, Oria-Hernández J, Castillo-Villanueva A, Nájera H, Avitia-Domínguez C. Biochemical, Kinetic, and Computational Structural Characterization of Shikimate Kinase from Methicillin-Resistant Staphylococcus aureus. Mol Biotechnol 2019; 61:274-285. [PMID: 30747382 DOI: 10.1007/s12033-019-00159-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One of the most widespread pathogens worldwide is methicillin-resistant Staphylococcus aureus, a bacterium that provokes severe life-threatening illnesses both in hospitals and in the community. The principal challenge lies in the resistance of MRSA to current treatments, which encourages the study of different molecular targets that could be used to develop new drugs against this infectious agent. With this goal, a detailed characterization of shikimate kinase from this microorganism (SaSK) is described. The results showed that SaSK has a Km of 0.153 and 224 µM for shikimate and ATP, respectively, and a global reaction rate of 13.4 µmol/min/mg; it is suggested that SaSK utilizes the Bi-Bi Ping Pong reaction mechanism. Furthermore, the physicochemical data indicated that SaSK is an unstable, hydrophilic, and acidic protein. Finally, structural information showed that SaSK presented folding that is typical of its homologous counterparts and contains the typical domains of this family of proteins. Amino acids that have been shown to be important for SaSK protein function are conserved. Therefore, this study provides fundamental information that may aid in the design of inhibitors that could be used to develop new antibacterial agents.
Collapse
Affiliation(s)
- Alejandro Favela-Candia
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Av. Universidad y Fanny Anitua S/N, C.P. 34000, Durango, Dgo, Mexico
| | - Alfredo Téllez-Valencia
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Av. Universidad y Fanny Anitua S/N, C.P. 34000, Durango, Dgo, Mexico
| | - Mara Campos-Almazán
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Av. Universidad y Fanny Anitua S/N, C.P. 34000, Durango, Dgo, Mexico
| | - Erick Sierra-Campos
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Av. Artículo 123 S/N Fracc. Filadelfia, Gómez Palacio, C.P. 35010, Durango, Mexico
| | - Mónica Valdez-Solana
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Av. Artículo 123 S/N Fracc. Filadelfia, Gómez Palacio, C.P. 35010, Durango, Mexico
| | - Jesús Oria-Hernández
- Laboratorio de Bioquímica Genética, Secretaría de Salud, Instituto Nacional de Pediatría, C.P. 04534, Ciudad de México, Mexico
| | - Adriana Castillo-Villanueva
- Laboratorio de Bioquímica Genética, Secretaría de Salud, Instituto Nacional de Pediatría, C.P. 04534, Ciudad de México, Mexico
| | - Hugo Nájera
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Delegación Cuajimalpa de Morelos, Av. Vasco de Quiroga 4871, Colonia Santa Fe Cuajimalpa, C.P. 05300, Ciudad de México, Mexico
| | - Claudia Avitia-Domínguez
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Av. Universidad y Fanny Anitua S/N, C.P. 34000, Durango, Dgo, Mexico.
| |
Collapse
|
3
|
IMB-T130 targets 3-dehydroquinate synthase and inhibits Mycobacterium tuberculosis. Sci Rep 2018; 8:17439. [PMID: 30487577 PMCID: PMC6262012 DOI: 10.1038/s41598-018-35701-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 11/02/2018] [Indexed: 11/08/2022] Open
Abstract
The anti-tuberculosis (TB) agent IMB-T130 was speculated to be a multi-target compound. In this research, we found that IMB-T130 inhibits the catalytic activity of Mycobacterium tuberculosis 3-dehydroquinate synthase (MtDHQS), the enzyme in the second step of the shikimate pathway. IMB-T130 was identified as a selective inhibitor of MtDHQS with an IC50 value of 0.87 μg/mL. The interaction between the compound and protein was analysed by surface plasmon resonance and circular dichroism. Based on the in silico molecular docking results, the essential amino acids in the binding pocket were then confirmed by site-directed mutagenesis. Overexpression of DHQS reduced the antibacterial activity of IMB-T130 in cells, verifying that DHQS is the target of IMB-T130. IMB-T130 inhibited standard and drug-resistant M. tuberculosis strains by targeting DHQS. Our findings improve our understanding of MtDHQS and make it to be a potential target for new anti-TB drug discovery.
Collapse
|
4
|
In silico identification of potential inhibitors against shikimate dehydrogenase through virtual screening and toxicity studies for the treatment of tuberculosis. Int Microbiol 2018; 22:7-17. [PMID: 30810932 DOI: 10.1007/s10123-018-0021-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/05/2018] [Accepted: 07/06/2018] [Indexed: 10/28/2022]
Abstract
The present study attempts to identify the novel inhibitors of shikimate dehydrogenase (SD), the enzyme that catalyzes the fourth reaction in the shikimate pathway, through virtual screening and toxicity studies. Crystal structure of SD was obtained from Protein Data Bank (PDB ID 4P4G, 1.7 Å) and subjected to energy minimization and structure optimization. A total of 13,803 compounds retrieved from two public databases and used for the virtual screening based on physicochemical properties (Lipinski rule of five) and molecular docking analyses. A total of 26 compounds with good AutoDock binding energies values ranging between - 12.03 and - 8.33 kcal/mol was selected and further filtered for absorption distribution metabolism excretion and toxicity analyses (ADMET). In this, eight compounds were selected, which satisfied all the ADME and toxicity analysis properties. Three compounds with better AutoDock binding energies values (ZINC12135132, - 12.03 kcal/mol; ZINC08951370, - 10.04 kcal/mol; and ZINC14733847, 9.82 kcal/mol) were considered for molecular dynamic (MD) simulation and molecular generalized born surface area (MM-GBSA) analyses. The results of the analyses revealed that the two ligands (ZINC12135132 and ZINC08951370) had better inhibitory activities within their complexes, after the 50-ns MD simulation, which suggested that the complexes formed stable conformation. It is noteworthy that compounds identified by docking, MD simulation, and MM-GBSA methods could be a drug for tuberculosis which required further experimental validation.
Collapse
|
5
|
Preliminary SAR and biological evaluation of antitubercular triazolothiadiazine derivatives against drug-susceptible and drug-resistant Mtb strains. Bioorg Med Chem 2017; 25:213-220. [DOI: 10.1016/j.bmc.2016.10.027] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 10/15/2016] [Accepted: 10/20/2016] [Indexed: 11/23/2022]
|
6
|
Masoko P, Mabusa IH, Howard RL. Isolation of alpha-linolenic acid from Sutherlandia frutescens and its inhibition of Mycobacterium tuberculosis' shikimate kinase enzyme. Altern Ther Health Med 2016; 16:366. [PMID: 27639973 PMCID: PMC5027073 DOI: 10.1186/s12906-016-1344-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 09/08/2016] [Indexed: 11/10/2022]
Abstract
BACKGROUND Sutherlandia frutescens (L) R.Br. is one of traditional herbal medicines that formed the basis of primary health care systems since the earliest days and is still widely used. Sutherlandia is prescribed for people with tuberculosis (TB), but is still not known which compound(s) acts against M. tuberculosis and its mode of action. The aim of this study was to identify and isolate antimycobacterial compounds from S. frutescens extracts against shikimate kinase, a drug target for M. tuberculosis. METHODS S. frutescens were dried, ground and extracted with ethanol, dichloromethane: methanol and water. Fractionation and separation of compounds was done with column chromatography. Chromatograms were developed in butanol/acetic acid/water (BAW) [21:6:3]; chloroform/methanol/water/formic acid (CMWF1) [60:15:2:1] and (CMWF2) [21:9:1:0.3]. Separation and isolation of active compounds were done using preparative HPLC. The activity of the plant extracts were also screened against shikimate kinase enzyme (MtbSK) using the MtbSK inhibition assay. RESULTS The DCM: MeOH (1:1) extract showed a high percentage inhibition (with an IC50 of 0.1 μg/ml) of MtbSK and the purified inhibitor was an Alpha-Linolenic Acid (ALA) compound and it had a significant IC50 of 3.7 μg/ml. CONCLUSIONS This study demonstrated that ALA from S. frustescens is an inhibitor of shikimate kinase a good drug target for M. tuberculosis.
Collapse
|
7
|
Mehra R, Rajput VS, Gupta M, Chib R, Kumar A, Wazir P, Khan IA, Nargotra A. Benzothiazole Derivative as a Novel Mycobacterium tuberculosis Shikimate Kinase Inhibitor: Identification and Elucidation of Its Allosteric Mode of Inhibition. J Chem Inf Model 2016; 56:930-40. [PMID: 27149193 DOI: 10.1021/acs.jcim.6b00056] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mycobacterium tuberculosis shikimate kinase (Mtb-SK) is a key enzyme involved in the biosynthesis of aromatic amino acids through the shikimate pathway. Since it is proven to be essential for the survival of the microbe and is absent from mammals, it is a promising target for anti-TB drug discovery. In this study, a combined approach of in silico similarity search and pharmacophore building using already reported inhibitors was used to screen a procured library of 20,000 compounds of the commercially available ChemBridge database. From the in silico screening, 15 hits were identified, and these hits were evaluated in vitro for Mtb-SK enzyme inhibition. Two compounds presented significant enzyme inhibition with IC50 values of 10.69 ± 0.9 and 46.22 ± 1.2 μM. The best hit was then evaluated for the in vitro mode of inhibition where it came out to be an uncompetitive and noncompetitive inhibitor with respect to shikimate (SKM) and ATP, respectively, suggesting its binding at an allosteric site. Potential binding sites of Mtb-SK were identified which confirmed the presence of an allosteric binding pocket apart from the ATP and SKM binding sites. The docking simulations were performed at this pocket in order to find the mode of binding of the best hit in the presence of substrates and the products of the enzymatic reaction. Molecular dynamics (MD) simulations elucidated the probability of inhibitor binding at the allosteric site in the presence of ADP and shikimate-3-phosphate (S-3-P), that is, after the formation of products of the reaction. The inhibitor binding may prevent the release of the product from Mtb-SK, thereby inhibiting its activity. The binding stability and the key residue interactions of the inhibitor to this product complex were also revealed by the MD simulations. Residues ARG43, ILE45, and PHE57 were identified as crucial that were involved in interactions with the best hit. This is the first report of an allosteric binding site of Mtb-SK, which could largely address the selectivity issue associated with kinase inhibitors.
Collapse
Affiliation(s)
- Rukmankesh Mehra
- Discovery Informatics Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India
| | - Vikrant Singh Rajput
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India.,Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India
| | - Monika Gupta
- Discovery Informatics Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India
| | - Reena Chib
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India
| | - Amit Kumar
- Discovery Informatics Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India
| | - Priya Wazir
- Instrumentation Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India
| | - Inshad Ali Khan
- Clinical Microbiology Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India.,Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India
| | - Amit Nargotra
- Discovery Informatics Division, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India.,Academy of Scientific and Innovative Research, CSIR-Indian Institute of Integrative Medicine , Canal Road, Jammu 180001, India
| |
Collapse
|
8
|
Screening of antitubercular compound library identifies novel shikimate kinase inhibitors of Mycobacterium tuberculosis. Appl Microbiol Biotechnol 2016; 100:5415-26. [DOI: 10.1007/s00253-015-7268-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Revised: 11/26/2015] [Accepted: 12/22/2015] [Indexed: 10/22/2022]
|
9
|
Li Z, Liu Y, Bai X, Deng Q, Wang J, Zhang G, Xiao C, Mei Y, Wang Y. SAR studies on 1,2,4-triazolo[3,4-b][1,3,4]thiadiazoles as inhibitors of Mtb shikimate dehydrogenase for the development of novel antitubercular agents. RSC Adv 2015. [DOI: 10.1039/c5ra19334f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Triazolothiadiazoles are potent antitubercular agents with modest inhibitory for Mt SD and without appreciable cytotoxicity.
Collapse
Affiliation(s)
- Ziqiang Li
- Institute of Medicinal Biotechnology
- Chinese Academy of Medical Science
- Peking Union Medical College
- Beijing 100050
- China
| | - Yishuang Liu
- Institute of Medicinal Biotechnology
- Chinese Academy of Medical Science
- Peking Union Medical College
- Beijing 100050
- China
| | - Xiaoguang Bai
- Institute of Medicinal Biotechnology
- Chinese Academy of Medical Science
- Peking Union Medical College
- Beijing 100050
- China
| | - Qi Deng
- Institute of Medicinal Biotechnology
- Chinese Academy of Medical Science
- Peking Union Medical College
- Beijing 100050
- China
| | - Juxian Wang
- Institute of Medicinal Biotechnology
- Chinese Academy of Medical Science
- Peking Union Medical College
- Beijing 100050
- China
| | - Guoning Zhang
- Institute of Medicinal Biotechnology
- Chinese Academy of Medical Science
- Peking Union Medical College
- Beijing 100050
- China
| | - Chunling Xiao
- Institute of Medicinal Biotechnology
- Chinese Academy of Medical Science
- Peking Union Medical College
- Beijing 100050
- China
| | - Yaning Mei
- Department of Laboratory Medicine
- The First Affiliated Hospital of Nanjing Medical University
- Nanjing 210029
- China
| | - Yucheng Wang
- Institute of Medicinal Biotechnology
- Chinese Academy of Medical Science
- Peking Union Medical College
- Beijing 100050
- China
| |
Collapse
|
10
|
Inhibition and biochemical characterization of methicillin-resistant Staphylococcus aureus shikimate dehydrogenase: an in silico and kinetic study. Molecules 2014; 19:4491-509. [PMID: 24727420 PMCID: PMC6270726 DOI: 10.3390/molecules19044491] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 04/03/2014] [Accepted: 04/04/2014] [Indexed: 12/19/2022] Open
Abstract
Methicillin-resistant Staphylococcus auerus (MRSA) strains are having a major impact worldwide, and due to their resistance to all β-lactams, an urgent need for new drugs is emerging. In this regard, the shikimate pathway is considered to be one of the metabolic features of bacteria and is absent in humans. Therefore enzymes involved in this route, such as shikimate dehydrogenase (SDH), are considered excellent targets for discovery of novel antibacterial drugs. In this study, the SDH from MRSA (SaSDH) was characterized. The results showed that the enzyme is a monomer with a molecular weight of 29 kDa, an optimum temperature of 65 °C, and a maximal pH range of 9–11 for its activity. Kinetic studies revealed that SDH showed Michaelis-Menten kinetics toward both substrates (shikimate and NADP+). Initial velocity analysis suggested that SaSDH catalysis followed a sequential random mechanism. Additionally, a tridimensional model of SaSDH was obtained by homology modeling and validated. Through virtual screening three inhibitors of SaSDH were found (compounds 238, 766 and 894) and their inhibition constants and mechanism were obtained. Flexible docking studies revealed that these molecules make interactions with catalytic residues. The data of this study could serve as starting point in the search of new chemotherapeutic agents against MRSA.
Collapse
|
11
|
Negron L, Patchett ML, Parker EJ. Expression, Purification, and Characterisation of Dehydroquinate Synthase from Pyrococcus furiosus. Enzyme Res 2011; 2011:134893. [PMID: 21603259 PMCID: PMC3092513 DOI: 10.4061/2011/134893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 01/28/2011] [Accepted: 02/08/2011] [Indexed: 11/30/2022] Open
Abstract
Dehydroquinate synthase (DHQS) catalyses the second step of the shikimate pathway to aromatic compounds. DHQS from the archaeal hyperthermophile Pyrococcus furiosus was insoluble when expressed in Escherichia coli but was partially solubilised when KCl was included in the cell lysis buffer. A purification procedure was developed, involving lysis by sonication at 30°C followed by a heat treatment at 70°C and anion exchange chromatography. Purified recombinant P. furiosus DHQS is a dimer with a subunit Mr of 37,397 (determined by electrospray ionisation mass spectrometry) and is active over broad pH and temperature ranges. The kinetic parameters are KM (3-deoxy-D-arabino-heptulosonate 7-phosphate) 3.7 μM and kcat 3.0 sec−1 at 60°C and pH 6.8. EDTA inactivates the enzyme, and enzyme activity is restored by several divalent metal ions including (in order of decreasing effectiveness) Cd2+, Co2+, Zn2+, and Mn2+. High activity of a DHQS in the presence of Cd2+ has not been reported for enzymes from other sources, and may be related to the bioavailability of Cd2+ for P. furiosus. This study is the first biochemical characterisation of a DHQS from a thermophilic source. Furthermore, the characterisation of this hyperthermophilic enzyme was carried out at elevated temperatures using an enzyme-coupled assay.
Collapse
Affiliation(s)
- Leonardo Negron
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | | | | |
Collapse
|
12
|
Tapas S, Kumar Patel G, Dhindwal S, Tomar S. In Silico sequence analysis and molecular modeling of the three-dimensional structure of DAHP synthase from Pseudomonas fragi. J Mol Model 2010; 17:621-31. [DOI: 10.1007/s00894-010-0764-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2010] [Accepted: 05/18/2010] [Indexed: 11/30/2022]
|