1
|
Viswanathan V, Ahmad MI, Singh PK, Ahmad N, Sharma P, Sharma S, Singh TP. Structural evidence of the conversion of nitric oxide (NO) to nitrite ion (NO 2-) by lactoperoxidase (LPO): Structure of the complex of LPO with NO 2- at 1.89 Å resolution. J Inorg Biochem 2023; 247:112311. [PMID: 37421730 DOI: 10.1016/j.jinorgbio.2023.112311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/26/2023] [Accepted: 06/30/2023] [Indexed: 07/10/2023]
Abstract
Lactoperoxidase (LPO) is a heme containing mammalian enzyme which uses hydrogen peroxide (H2O2) to catalyze the conversion of substrates into oxidized products. LPO is found in body fluids and tissues such as milk, saliva, tears, mucosa and other body secretions. The previous structural studies have shown that LPO converts substrates, thiocyanate (SCN-) and iodide (I-) ions into oxidized products, hypothiocyanite (OSCN-) and hypoiodite (IO-) ions respectively. We report here a new structure of the complex of LPO with an oxidized product, nitrite (NO2-). This product was generated from NO using the two step reaction of LPO by adding hydrogen peroxide (H2O2) in the solution of LPO in 0.1 M phosphate buffer at pH 6.8 as the first step. In the second step, NO gas was added to the above mixture. This was crystallized using 20% (w/v) PEG-3350 and 0.2 M ammonium iodide at pH 6.8. The structure determination showed the presence of NO2- ion in the distal heme cavity of the substrate binding site of LPO. The structure also showed that the propionate group which is linked to pyrrole ring D of the heme moiety was disordered. Similarly, the side chain of Asp108, which is covalently linked to heme moiety, was also split into two components. As a result of these changes, the conformation of the side chain of Arg255 was altered allowing it to form new interactions with the disordered carboxylic group of propionate moiety. These structural changes are indicative of an intermediate state in the catalytic reaction pathway of LPO.
Collapse
Affiliation(s)
- V Viswanathan
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Md Irshad Ahmad
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Prashant K Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Nayeem Ahmad
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Pradeep Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Sujata Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Tej P Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
| |
Collapse
|
2
|
Barreiro DS, Oliveira RN, Pauleta SR. Bacterial peroxidases – Multivalent enzymes that enable the use of hydrogen peroxide for microaerobic and anaerobic proliferation. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2023.215114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
|
3
|
Borges EL, Goulart HA, Perin G, Schneider PH, Rieder GS, Nogara PA, da Rocha JBT. One-Pot Synthesis and in Silico Molecular Docking Studies of Arylselanyl Hydrazides as Potential Antituberculosis Agents. Chem Biodivers 2022; 19:e202100793. [PMID: 35293125 DOI: 10.1002/cbdv.202100793] [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: 10/01/2021] [Accepted: 03/14/2022] [Indexed: 11/06/2022]
Abstract
The present study reports a simple two-step method for the synthesis of arylselanyl hydrazide derivatives using hypophosphorous acid and polyethylene glycol (H3 PO2 /PEG-400) as an alternative reducing system and hydrazine hydrate (NH2 NH2 ⋅xH2 O/50-60 %). This single-vessel procedure was employed with methyl acrylate 2a and methyl bromoacetate 2b using diaryl diselenides to generate the nucleophile species to produce, respectively, 3-(arylselanyl)propane-hydrazides 4a-e and 2-(arylselanyl)acetohydrazides 5a-e with good yields by accelerating the reduction of -Se-Se- bond, when compared to available methods. The synthesized molecules are structurally similar to the isoniazid (INH). Therefore, we perform in silico molecular docking studies, using the lactoperoxidase enzyme, in order to verify whether the INH Se derivatives could interact in a similar way to INH at the active site of the mammalian enzyme. The in silico results indicated a similar type of interaction of the arylselanyl hydrazide derivatives with that of INH. In view of the similar in silico interaction of the selenium derivatives of INH, the arylselanyl hydrazide derivatives reported here should be tested against Mycobacterium tuberculosis in vitro.
Collapse
Affiliation(s)
- Elton L Borges
- Grupo de Pesquisa em Síntese Orgânica da Região Amazônica (LASORA, DAEPA), Fundação Universidade Federal de Rondônia (UNIR), Rua da Paz 4376, 76916-000, Presidente Médici, RO, Brazil
| | - Helen A Goulart
- Laboratório de Síntese Orgânica Limpa (LASOL, CCQFA), Universidade Federal de Pelotas (UFPel), PO Box 354, 96010-900, Pelotas, RS, Brazil
| | - Gelson Perin
- Laboratório de Síntese Orgânica Limpa (LASOL, CCQFA), Universidade Federal de Pelotas (UFPel), PO Box 354, 96010-900, Pelotas, RS, Brazil
| | - Paulo H Schneider
- Instituto de Química, Universidade Federal do Rio Grande do Sul (UFRGS), 91501-970, Porto Alegre, RS, Brazil
| | - Guilherme S Rieder
- Programa de Pós-graduação em Ciências Biológicas: Bioquímica Toxicológica, Universidade Federal de Santa Maria (UFSM), 97105-90, Santa Maria, RS, Brazil
| | - Pablo A Nogara
- Programa de Pós-graduação em Ciências Biológicas: Bioquímica Toxicológica, Universidade Federal de Santa Maria (UFSM), 97105-90, Santa Maria, RS, Brazil
| | - João B T da Rocha
- Programa de Pós-graduação em Ciências Biológicas: Bioquímica Toxicológica, Universidade Federal de Santa Maria (UFSM), 97105-90, Santa Maria, RS, Brazil
| |
Collapse
|
4
|
Singh PK, Ahmad N, Yamini S, Singh RP, Singh AK, Sharma P, Smith ML, Sharma S, Singh TP. Structural evidence of the oxidation of iodide ion into hyper-reactive hypoiodite ion by mammalian heme lactoperoxidase. Protein Sci 2022; 31:384-395. [PMID: 34761444 PMCID: PMC8819834 DOI: 10.1002/pro.4230] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 02/03/2023]
Abstract
Lactoperoxidase (1.11.1.7, LPO) is a mammalian heme peroxidase found in the extracellular fluids of mammals including plasma, saliva, airway epithelial lining fluids, nasal lining fluid, milk, tears, gastric juices, and intestinal mucosa. To perform its innate immune action against invading microbes, LPO utilizes hydrogen peroxide (H2 O2 ) to convert thiocyanate (SCN- ) and iodide (I- ) ions into the oxidizing compounds hypothiocyanite (OSCN- ) and hypoiodite (IO- ). Previously determined structures of the complexes of LPO with SCN- , OSCN- , and I- show that SCN- and I- occupy appropriate positions in the distal heme cavity as substrates while OSCN- binds in the distal heme cavity as a product inhibitor. We report here the structure of the complex of LPO with IO- as the first structural evidence of the conversion of iodide into hypoiodite by LPO. To obtain this complex, a solution of LPO was first incubated with H2 O2 , then mixed with ammonium iodide solution and the complex crystallized by the addition of PEG-3350, 20% (wt/vol). These crystals were used for X-ray intensity data collection and structure analysis. The structure determination revealed the presence of four hypoiodite ions in the substrate binding channel of LPO. In addition to these, six other hypoiodite ions were observed at different exterior sites. We surmise that the presence of hypoiodite ions in the distal heme cavity blocks the substrate binding site and inhibits catalysis. This was confirmed by activity experiments with the colorimetric substrate, ABTS (2,2'-azino-bis(3-ethylbenzthiazoline-sulfonic acid)), in the presence of hypoiodite and iodide ions.
Collapse
Affiliation(s)
- Prashant K. Singh
- Department of BiophysicsAll India Institute of Medical SciencesNew DelhiIndia
| | - Nayeem Ahmad
- Department of BiophysicsAll India Institute of Medical SciencesNew DelhiIndia
| | - Shavait Yamini
- Department of BiophysicsAll India Institute of Medical SciencesNew DelhiIndia
| | - Rashmi P. Singh
- Department of BiophysicsAll India Institute of Medical SciencesNew DelhiIndia
| | - Amit K. Singh
- Department of BiophysicsAll India Institute of Medical SciencesNew DelhiIndia
| | - Pradeep Sharma
- Department of BiophysicsAll India Institute of Medical SciencesNew DelhiIndia
| | | | - Sujata Sharma
- Department of BiophysicsAll India Institute of Medical SciencesNew DelhiIndia
| | - Tej P. Singh
- Department of BiophysicsAll India Institute of Medical SciencesNew DelhiIndia
| |
Collapse
|
5
|
Dhankhar P, Dalal V, Singh V, Sharma AK, Kumar P. Structure of dye-decolorizing peroxidase from Bacillus subtilis in complex with veratryl alcohol. Int J Biol Macromol 2021; 193:601-608. [PMID: 34687768 DOI: 10.1016/j.ijbiomac.2021.10.100] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/04/2021] [Accepted: 10/14/2021] [Indexed: 11/17/2022]
Abstract
Dye-decolorizing peroxidases (DyPs) are heme-containing peroxidases, which have promising application in biodegradation of phenolic lignin compounds and in detoxification of dyes. In this study, the crystal structure of BsDyP- veratryl alcohol (VA) complex delves deep into the binding of small substrate molecules within the DyP heme cavity. The biochemical analysis shows that BsDyP oxidizes the VA with a turnover number of 0.065 s-1, followed by the oxidation of 2,6-dimethoxyphenol (DMP) and guaiacol with a comparable turnover number (kcat) of 0.07 s-1 and 0.07 s-1, respectively. Moreover, biophysical and computational studies reveal the comparable binding affinity of substrates to BsDyP and produce lower-energy stable BsDyP-ligand(s) complexes. All together with our previous findings, we are providing a complete structural description of substrate-binding sites in DyP. The structural insight of BsDyP helps to modulate its engineering to enhance the activity towards the oxidation of a wide range of substrates.
Collapse
Affiliation(s)
- Poonam Dhankhar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, 247667, India
| | - Vikram Dalal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, 247667, India
| | - Vishakha Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, 247667, India
| | - Ashwani Kumar Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, 247667, India
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, 247667, India.
| |
Collapse
|
6
|
Singh PK, Sharma P, Bhushan A, Kaur P, Sharma S, Singh TP. Structure of a ternary complex of lactoperoxidase with iodide and hydrogen peroxide at 1.77 Å resolution. J Inorg Biochem 2021; 220:111461. [PMID: 33882424 DOI: 10.1016/j.jinorgbio.2021.111461] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/05/2021] [Accepted: 04/05/2021] [Indexed: 11/16/2022]
Abstract
Lactoperoxidase (LPO) is a mammalian heme peroxidase which catalyzes the conversion of thiocyanate (SCN¯) and iodide (I-) by hydrogen peroxide (H2O2) into antimicrobial hypothiocyanite (OSCN¯) and hypoiodite (IO-). The prosthetic heme group is covalently attached to LPO through two ester linkages involving conserved glutamate and aspartate residues. On the proximal side, His351 is coordinated to heme iron while His 109 is located in the substrate binding site on the distal heme side. We report here the first structure of the ternary complex of LPO with iodide (I-) and H2O2 at 1.77 Å resolution. LPO was crystallized with ammonium iodide and the crystals were soaked in the reservoir solution containing H2O2. Structure determination showed the presence of an iodide ion and a H2O2 molecule in the substrate binding site. The iodide ion occupied the position which is stabilized by the interactions with heme moiety, His109, Arg255 and Glu258 while H2O2 was held between the heme iron and His109. The presence of I- in the distal heme cavity seems to screen the positive charge of Arg255 thus suppressing the proton transfer from H2O2 to His109. This prevents compound I formation and allows trapping of a stable enzyme-substrate (LPO-I--H2O2) ternary complex. This stable geometrical arrangement of H2O2 in the distal heme cavity of LPO is similar to that of H2O2 in the structure of the transient intermediate of the palm tree heme peroxidase. The biochemical studies showed that the catalytic activity of LPO decreased when the samples of LPO were preincubated with ammonium iodide.
Collapse
Affiliation(s)
- Prashant K Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Pradeep Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Asha Bhushan
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Sujata Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Tej P Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
| |
Collapse
|
7
|
Singh PK, Pandey S, Rani C, Ahmad N, Viswanathan V, Sharma P, Kaur P, Sharma S, Singh TP. Potassium-induced partial inhibition of lactoperoxidase: structure of the complex of lactoperoxidase with potassium ion at 2.20 Å resolution. J Biol Inorg Chem 2021; 26:149-159. [PMID: 33427997 DOI: 10.1007/s00775-020-01844-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/07/2020] [Indexed: 11/30/2022]
Abstract
Lactoperoxidase, a heme-containing glycoprotein, catalyzes the oxidation of thiocyanate by hydrogen peroxide into hypothiocyanite which acts as an antibacterial agent. The prosthetic heme moiety is attached to the protein through two ester linkages via Glu258 and Asp108. In lactoperoxidase, the substrate-binding site is formed on the distal heme side. To study the effect of physiologically important potassium ion on the structure and function of lactoperoxidase, the fresh protein samples were isolated from yak (Bos grunniens) colostrum and purified to homogeneity. The biochemical studies with potassium fluoride showed a significant reduction in the catalytic activity. Lactoperoxidase was crystallized using 200 mM ammonium nitrate and 20% PEG-3350 at pH 6.0. The crystals of LPO were soaked in the solution of potassium fluoride and used for the X-ray intensity data collection. Structure determination at 2.20 Å resolution revealed the presence of a potassium ion in the distal heme cavity. Structure determination further revealed that the propionic chain attached to pyrrole ring C of the heme moiety, was disordered into two components each having an occupancy of 0.5. One component occupied a position similar to the normally observed position of propionic chain while the second component was found in the distal heme cavity. The potassium ion in the distal heme cavity formed five coordinate bonds with two oxygen atoms of propionic moiety, Nε2 atom of His109 and two oxygen atoms of water molecules. The presence of potassium ion in the distal heme cavity hampered the catalytic activity of lactoperoxidase.
Collapse
Affiliation(s)
- Prashant K Singh
- Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110 029, India
| | - Sadanand Pandey
- Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110 029, India
| | - Chitra Rani
- Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110 029, India
| | - Nayeem Ahmad
- Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110 029, India
| | - V Viswanathan
- Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110 029, India
| | - Pradeep Sharma
- Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110 029, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110 029, India
| | - Sujata Sharma
- Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110 029, India
| | - Tej P Singh
- Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110 029, India.
| |
Collapse
|
8
|
|
9
|
Kaur H, Singh L, Chibale K, Singh K. Structure elaboration of isoniazid: synthesis, in silico molecular docking and antimycobacterial activity of isoniazid–pyrimidine conjugates. Mol Divers 2019; 24:949-955. [DOI: 10.1007/s11030-019-10004-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/11/2019] [Indexed: 12/11/2022]
|
10
|
Erwin ER, Addison AP, John SF, Olaleye OA, Rosell RC. Pharmacokinetics of isoniazid: The good, the bad, and the alternatives. Tuberculosis (Edinb) 2019; 116S:S66-S70. [PMID: 31076322 DOI: 10.1016/j.tube.2019.04.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 11/19/2018] [Indexed: 01/26/2023]
Abstract
Although isoniazid (INH) has been successful in treating Tuberculosis (TB) since its introduction in 1952, there has been continual reports of drug-associated hepatotoxicity in TB patients. These toxic side effects may reveal more about the recipient of the drug, than the drug itself. A combination of pharmacogenetic and pharmacokinetic studies have identified polymorphisms within enzymes involved in INH metabolism and detoxification. These essential metabolic enzymes include N-acetyltransferase 2, Cytochrome P450 2E1, and glutathione S transferases. Different phenotypes of these enzymes can affect the rate of INH metabolism, resulting in production of hepatotoxic metabolites. This review is intended to elucidate the pharmacokinetics of INH by examining its Administration, Distribution, Metabolism, and Elimination, while suggesting potential alternatives within INH personalized treatment to help reduce hepatotoxicity.
Collapse
Affiliation(s)
- Emily R Erwin
- Biology Department, University of St. Thomas, Houston, TX 77006, USA.
| | - Angela P Addison
- Biology Department, University of St. Thomas, Houston, TX 77006, USA.
| | - Sarah Finney John
- Biology Department, University of St. Thomas, Houston, TX 77006, USA.
| | - Omonike Arike Olaleye
- College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX 77004, USA.
| | | |
Collapse
|
11
|
Al-Baarri AN, Damayanti NT, Legowo AM, Tekiner İH, Hayakawa S. Enhanced Antibacterial Activity of Lactoperoxidase-Thiocyanate-Hydrogen Peroxide System in Reduced-Lactose Milk Whey. INTERNATIONAL JOURNAL OF FOOD SCIENCE 2019; 2019:8013402. [PMID: 31179314 PMCID: PMC6507251 DOI: 10.1155/2019/8013402] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 03/03/2019] [Accepted: 04/03/2019] [Indexed: 11/17/2022]
Abstract
The product of the lactoperoxidase system (LPOS) has been developed as a preservative agent to inhibit foodborne bacteria, but its action was, heretofore, limited to several original compounds in milk. This research was conducted to analyze the application of the lactoperoxidase system against Escherichia coli in fresh bovine milk and its derivative products to determine the strength of antibacterial activity. Lactoperoxidase was purified from bovine whey using the SP Sepharose Big Beads Column. The enzymatic reaction involving lactoperoxidase, thiocyanate, and hydrogen peroxide was used to generate the antibacterial agent from LPOS. This solution was then added to milk, skimmed milk, untreated whey, reduced-LPO whey, reduced-lactose whey, and high-lactose solution containing E. coli at an initial count of 6.0 log CFU/mL. LPOS showed the greatest reduction of bacteria (1.68 ± 0.1 log CFU/mL) in the reduced-lactose whey among the products tested. This result may lead to a method for enhancement of the antimicrobial activity of LPOS in milk and derived products.
Collapse
Affiliation(s)
| | - Novia Tri Damayanti
- Animal Sciences Department, Faculty of Animal and Agricultural Sciences, Diponegoro University, Indonesia
| | - Anang Mohamad Legowo
- Animal Sciences Department, Faculty of Animal and Agricultural Sciences, Diponegoro University, Indonesia
| | - İsmail Hakkı Tekiner
- Gastronomy Department, School of Applied Sciences, Istanbul Gelişim University, Turkey
| | - Shigeru Hayakawa
- Applied Biological Sciences, Faculty of Agriculture, Kagawa University, Japan
| |
Collapse
|
12
|
Babu D, Morgan AG, Reiz B, Whittal RM, Almas S, Lacy P, Siraki AG. Eosinophil peroxidase oxidizes isoniazid to form the active metabolite against M. tuberculosis, isoniazid-NAD . Chem Biol Interact 2019; 305:48-53. [PMID: 30922765 DOI: 10.1016/j.cbi.2019.03.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/14/2019] [Accepted: 03/21/2019] [Indexed: 11/24/2022]
Abstract
The formation of isonicotinyl-nicotinamide adenine dinucleotide (INH-NAD+) by the mycobacterial catalase-peroxidase enzyme, KatG, was known to be the major component of the mode of action of isoniazid (INH), an anti-tuberculosis drug. However, there are other enzymes that may catalyze this reaction. We have previously reported that neutrophil myeloperoxidase (MPO) is capable of metabolizing INH through the formation of INH-NAD+ adduct, which could be attributed to being a possible mode of action of INH. However, eosinophilic infiltration of the lungs is more pronounced and characteristic of granulomas in Mycobacterium tuberculosis-infected patients. Thus, the aim of the present study is to investigate the role of eosinophil peroxidase (EPO), a key eosinophil enzyme, during INH metabolism and the formation of its active metabolite, INH-NAD+ using purified EPO and eosinophils isolated from asthmatic donors. UV-Vis spectroscopy revealed INH oxidation by EPO led to a new product (λmax = 326 nm) in the presence of NAD+. This adduct was confirmed to be INH-NAD+ using LC-MS analysis where the intact adduct was detected (m/z = 769). Furthermore, EPO catalyzed the oxidation of INH and formed several free radical intermediates as assessed by electron paramagnetic resonance (EPR) spin-trapping; a carbon-centred radical, which is considered to be the reactive metabolite that binds with NAD+, was found when superoxide dismutase was included in the reaction. Our findings suggest that eosinophilic EPO may also play a role in the pharmacological activity of INH through the formation of INH-NAD+ adduct, and supports further evidence that human cells and enzymes are capable of producing the active metabolite involved in tuberculosis treatment.
Collapse
Affiliation(s)
- Dinesh Babu
- Faculty of Pharmacy and Pharmaceutical Sciences, Katz Group Centre for Pharmacy & Health Research, University of Alberta, Edmonton, AB, Canada
| | - Andrew G Morgan
- Faculty of Pharmacy and Pharmaceutical Sciences, Katz Group Centre for Pharmacy & Health Research, University of Alberta, Edmonton, AB, Canada
| | - Béla Reiz
- Department of Chemistry, Faculty of Sciences, University of Alberta, Edmonton, AB, Canada
| | - Randy M Whittal
- Department of Chemistry, Faculty of Sciences, University of Alberta, Edmonton, AB, Canada
| | - Sarah Almas
- Pulmonary Research Group, Department of Medicine, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Paige Lacy
- Pulmonary Research Group, Department of Medicine, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Arno G Siraki
- Faculty of Pharmacy and Pharmaceutical Sciences, Katz Group Centre for Pharmacy & Health Research, University of Alberta, Edmonton, AB, Canada.
| |
Collapse
|
13
|
Structural basis of activation of mammalian heme peroxidases. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 133:49-55. [DOI: 10.1016/j.pbiomolbio.2017.11.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/14/2017] [Accepted: 11/15/2017] [Indexed: 12/27/2022]
|
14
|
Sirohi HV, Singh PK, Iqbal N, Sharma P, Singh AK, Kaur P, Sharma S, Singh TP. Design of anti-thyroid drugs: Binding studies and structure determination of the complex of lactoperoxidase with 2-mercaptoimidazole at 2.30 Å resolution. Proteins 2017; 85:1882-1890. [PMID: 28653416 DOI: 10.1002/prot.25342] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 06/08/2017] [Accepted: 06/21/2017] [Indexed: 11/08/2022]
Abstract
Lactoperoxidase (LPO) belongs to mammalian heme peroxidase superfamily, which also includes myeloperoxidase (MPO), eosinophil peroxidase (EPO), and thyroid peroxidase (TPO). LPO catalyzes the oxidation of a number of substrates including thiocyanate while TPO catalyzes the biosynthesis of thyroid hormones. LPO is also been shown to catalyze the biosynthesis of thyroid hormones indicating similar functional and structural properties. The binding studies showed that 2-mercaptoimidazole (MZY) bound to LPO with a dissociation constant of 0.63 µM. The inhibition studies showed that the value of IC50 was 17 µM. The crystal structure of the complex of LPO with MZY showed that MZY bound to LPO in the substrate-binding site on the distal heme side. MZY was oriented in the substrate-binding site in such a way that the sulfur atom is at a distance of 2.58 Å from the heme iron. Previously, a similar compound, 3-amino-1,2,4-triazole (amitrole) was also shown to bind to LPO in the substrate-binding site on the distal heme side. The amino nitrogen atom of amitrole occupied the same position as that of sulfur atom in the present structure indicating a similar mode of binding. Recently, the structure of the complex of LPO with a potent antithyroid drug, 1-methylimidazole-2-thiol (methimazole, MMZ) was also determined. It showed that MMZ bound to LPO in the substrate-binding site on the distal heme side with 2 orientations. The position of methyl group was same in the 2 orientations while the positions of sulfur atom differed indicating a higher preference for a methyl group.
Collapse
Affiliation(s)
- Harsh V Sirohi
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi
| | - Prashant K Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi
| | - Naseer Iqbal
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi
| | - Pradeep Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi
| | - Amit K Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi
| | - Sujata Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi
| | - Tej P Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi
| |
Collapse
|
15
|
Singh PK, Sirohi HV, Iqbal N, Tiwari P, Kaur P, Sharma S, Singh TP. Structure of bovine lactoperoxidase with a partially linked heme moiety at 1.98Å resolution. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:329-335. [DOI: 10.1016/j.bbapap.2016.12.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 12/05/2016] [Accepted: 12/10/2016] [Indexed: 11/26/2022]
|
16
|
Brossier F, Boudinet M, Jarlier V, Petrella S, Sougakoff W. Comparative study of enzymatic activities of new KatG mutants from low- and high-level isoniazid-resistant clinical isolates of Mycobacterium tuberculosis. Tuberculosis (Edinb) 2016; 100:15-24. [DOI: 10.1016/j.tube.2016.06.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 05/08/2016] [Accepted: 06/05/2016] [Indexed: 11/29/2022]
|
17
|
Singh RP, Singh A, Sirohi HV, Singh AK, Kaur P, Sharma S, Singh TP. Dual binding mode of antithyroid drug methimazole to mammalian heme peroxidases - structural determination of the lactoperoxidase-methimazole complex at 1.97 Å resolution. FEBS Open Bio 2016; 6:640-50. [PMID: 27398304 PMCID: PMC4932444 DOI: 10.1002/2211-5463.12051] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/27/2016] [Accepted: 02/29/2016] [Indexed: 11/09/2022] Open
Abstract
Lactoperoxidase (LPO, EC 1.11.1.7) is a member of the mammalian heme peroxidase family which also includes thyroid peroxidase (TPO). These two enzymes have a sequence homology of 76%. The structure of LPO is known but not that of TPO. In order to determine the mode of binding of antithyroid drugs to thyroid peroxidase, we have determined the crystal structure of LPO complexed with an antithyroid drug, methimazole (MMZ) at 1.97 Å resolution. LPO was isolated from caprine colostrum, purified to homogeneity and crystallized with 20% poly(ethylene glycol)‐3350. Crystals of LPO were soaked in a reservoir solution containing MMZ. The structure determination showed the presence of two crystallographically independent molecules in the asymmetric unit. Both molecules contained one molecule of MMZ, but with different orientations. MMZ was held tightly between the heme moiety on one side and the hydrophobic parts of the side chains of Arg255, Glu258, and Leu262 on the opposite side. The back of the cleft contained the side chains of Gln105 and His109 which also interacted with MMZ. In both orientations, MMZ had identical buried areas and formed a similar number of interactions. It appears that the molecules of MMZ can enter the substrate‐binding channel of LPO in two opposite orientations. But once they reach the distal heme pocket, their orientations are frozen due to equally tight packing of MMZ in both orientations. This is a novel example of an inhibitor binding to an enzyme with two orientations at the same site with nearly equal occupancies.
Collapse
Affiliation(s)
- Rashmi Prabha Singh
- Department of Biophysics All India Institute of Medical Sciences New Delhi India
| | - Avinash Singh
- Department of Biophysics All India Institute of Medical Sciences New Delhi India
| | - Harsh Vardhan Sirohi
- Department of Biophysics All India Institute of Medical Sciences New Delhi India
| | - Amit Kumar Singh
- Department of Biophysics All India Institute of Medical Sciences New Delhi India
| | - Punit Kaur
- Department of Biophysics All India Institute of Medical Sciences New Delhi India
| | - Sujata Sharma
- Department of Biophysics All India Institute of Medical Sciences New Delhi India
| | - Tej P Singh
- Department of Biophysics All India Institute of Medical Sciences New Delhi India
| |
Collapse
|
18
|
Flemmig J, Gau J, Schlorke D, Arnhold J. Lactoperoxidase as a potential drug target. Expert Opin Ther Targets 2015; 20:447-61. [DOI: 10.1517/14728222.2016.1112378] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jörg Flemmig
- Institute for Medical Physics and Biophysics, Medical Faculty, University of Leipzig, Härtelstraße 16 – 18, 04107 Leipzig, Germany
- Translational Centre for Regenerative Medicine (TRM) Leipzig, University of Leipzig, Leipzig, Germany
| | - Jana Gau
- Institute for Medical Physics and Biophysics, Medical Faculty, University of Leipzig, Härtelstraße 16 – 18, 04107 Leipzig, Germany
| | - Denise Schlorke
- Institute for Medical Physics and Biophysics, Medical Faculty, University of Leipzig, Härtelstraße 16 – 18, 04107 Leipzig, Germany
- Translational Centre for Regenerative Medicine (TRM) Leipzig, University of Leipzig, Leipzig, Germany
| | - Jürgen Arnhold
- Institute for Medical Physics and Biophysics, Medical Faculty, University of Leipzig, Härtelstraße 16 – 18, 04107 Leipzig, Germany
- Translational Centre for Regenerative Medicine (TRM) Leipzig, University of Leipzig, Leipzig, Germany
| |
Collapse
|
19
|
Pang AH, Garneau-Tsodikova S, Tsodikov OV. Crystal structure of halogenase PltA from the pyoluteorin biosynthetic pathway. J Struct Biol 2015; 192:349-357. [PMID: 26416533 DOI: 10.1016/j.jsb.2015.09.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 09/24/2015] [Accepted: 09/25/2015] [Indexed: 10/23/2022]
Abstract
Pyoluteorin is an antifungal agent composed of a 4,5-dichlorinated pyrrole group linked to a resorcinol moiety. The pyoluteorin biosynthetic gene cluster in Pseudomonas fluorescens Pf-5 encodes the halogenase PltA, which has been previously demonstrated to perform both chlorinations in vitro. PltA selectively accepts as a substrate a pyrrole moiety covalently tethered to a nonribosomal peptide thiolation domain PltL (pyrrolyl-S-PltL) for FAD-dependent di-chlorination, yielding 4,5-dichloropyrrolyl-S-PltL. We report a 2.75 Å-resolution crystal structure of PltA in complex with FAD and chloride. PltA is a dimeric enzyme, containing a flavin-binding fold conserved in flavin-dependent halogenases and monooxygenases, and an additional unique helical region at the C-terminus. This C-terminal region blocks a putative substrate-binding cleft, suggesting that a conformational change involving repositioning of this region is necessary to allow binding of the pyrrolyl-S-PltL substrate for its dichlorination by PltA.
Collapse
Affiliation(s)
- Allan H Pang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536-0596, USA
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536-0596, USA
| | - Oleg V Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536-0596, USA.
| |
Collapse
|
20
|
Singh RP, Singh A, Kushwaha GS, Singh AK, Kaur P, Sharma S, Singh TP. Mode of binding of the antithyroid drug propylthiouracil to mammalian haem peroxidases. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2015; 71:304-10. [PMID: 25760705 DOI: 10.1107/s2053230x15001806] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 01/27/2015] [Indexed: 11/10/2022]
Abstract
The mammalian haem peroxidase superfamily consists of myeloperoxidase (MPO), lactoperoxidase (LPO), eosinophil peroxidase (EPO) and thyroid peroxidase (TPO). These enzymes catalyze a number of oxidative reactions of inorganic substrates such as Cl(-), Br(-), I(-) and SCN(-) as well as of various organic aromatic compounds. To date, only structures of MPO and LPO are known. The substrate-binding sites in these enzymes are located on the distal haem side. Propylthiouracil (PTU) is a potent antithyroid drug that acts by inhibiting the function of TPO. It has also been shown to inhibit the action of LPO. However, its mode of binding to mammalian haem peroxidases is not yet known. In order to determine the mode of its binding to peroxidases, the structure of the complex of LPO with PTU has been determined. It showed that PTU binds to LPO in the substrate-binding site on the distal haem side. The IC50 values for the inhibition of LPO and TPO by PTU are 47 and 30 µM, respectively. A comparision of the residues surrounding the substrate-binding site on the distal haem side in LPO with those in TPO showed that all of the residues were identical except for Ala114 (LPO numbering scheme), which is replaced by Thr205 (TPO numbering scheme) in TPO. A threonine residue in place of alanine in the substrate-binding site may affect the affinity of PTU for peroxidases.
Collapse
Affiliation(s)
- R P Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - A Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - G S Kushwaha
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - A K Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - P Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - S Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - T P Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| |
Collapse
|
21
|
Rapid in vivo detection of isoniazid-sensitive Mycobacterium tuberculosis by breath test. Nat Commun 2014; 5:4989. [PMID: 25247851 PMCID: PMC4182730 DOI: 10.1038/ncomms5989] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 08/14/2014] [Indexed: 11/28/2022] Open
Abstract
There is urgent need for rapid, point of care diagnostic tools for tuberculosis (TB) and drug sensitivity. Current methods based on in vitro growth take weeks, while DNA amplification can neither differentiate live from dead organisms nor determine phenotypic drug resistance. Here we show the development and evaluation of a rapid breath test for isoniazid (INH)-sensitive TB based on detection of labeled N2 gas formed specifically from labeled INH by mycobacterial KatG enzyme. In vitro data shows the assay is specific, dependent on mycobacterial abundance, and discriminates between INH-sensitive and resistant (S315T mutant KatG) TB. In vivo, the assay is rapid with maximal detection of 15N2 in exhaled breath of infected rabbits within five to ten minutes. No increase in 15N2 is detected in un-infected animals, and the increases in 15N2 are dependent on infection dose. This test may allow rapid detection of INH-sensitive TB.
Collapse
|
22
|
|
23
|
Sharma S, Singh AK, Kaushik S, Sinha M, Singh RP, Sharma P, Sirohi H, Kaur P, Singh TP. Lactoperoxidase: structural insights into the function,ligand binding and inhibition. INTERNATIONAL JOURNAL OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2013; 4:108-128. [PMID: 24049667 PMCID: PMC3776144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 08/21/2013] [Indexed: 06/02/2023]
Abstract
Lactoperoxidase (LPO) is a member of a large group of mammalian heme peroxidases that include myeloperoxidase (MPO), eosinophil peroxidase (EPO) and thyroid peroxidase (TPO). The LPO is found in exocrine secretions including milk. It is responsible for the inactivation of a wide range of micro-organisms and hence, is an important component of defense mechanism in the body. With the help of hydrogen peroxide, it catalyzes the oxidation of halides, pseudohalides and organic aromatic molecules. Historically, LPO was isolated in 1943, nearly seventy years ago but its three-dimensional crystal structure has been elucidated only recently. This review provides various details of this protein from its discovery to understanding its structure, function and applications. In order to highlight species dependent variations in the structure and function of LPO, a detailed comparison of sequence, structure and function of LPO from various species have been made. The structural basis of ligand binding and distinctions in the modes of binding of substrates and inhibitors have been analyzed extensively.
Collapse
Affiliation(s)
- Sujata Sharma
- Department of Biophysics, All India Institute of Medical Sciences New Delhi - 110029, India
| | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Ascenzi P, Coletta A, Cao Y, Trezza V, Leboffe L, Fanali G, Fasano M, Pesce A, Ciaccio C, Marini S, Coletta M. Isoniazid inhibits the heme-based reactivity of Mycobacterium tuberculosis truncated hemoglobin N. PLoS One 2013; 8:e69762. [PMID: 23936350 PMCID: PMC3731299 DOI: 10.1371/journal.pone.0069762] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Accepted: 06/12/2013] [Indexed: 11/19/2022] Open
Abstract
Isoniazid represents a first-line anti-tuberculosis medication in prevention and treatment. This prodrug is activated by a mycobacterial catalase-peroxidase enzyme called KatG in Mycobacterium tuberculosis), thereby inhibiting the synthesis of mycolic acid, required for the mycobacterial cell wall. Moreover, isoniazid activation by KatG produces some radical species (e.g., nitrogen monoxide), that display anti-mycobacterial activity. Remarkably, the ability of mycobacteria to persist in vivo in the presence of reactive nitrogen and oxygen species implies the presence in these bacteria of (pseudo-)enzymatic detoxification systems, including truncated hemoglobins (trHbs). Here, we report that isoniazid binds reversibly to ferric and ferrous M. tuberculosis trHb type N (or group I; Mt-trHbN(III) and Mt-trHbN(II), respectively) with a simple bimolecular process, which perturbs the heme-based spectroscopic properties. Values of thermodynamic and kinetic parameters for isoniazid binding to Mt-trHbN(III) and Mt-trHbN(II) are K = (1.1±0.1)×10−4 M, kon = (5.3±0.6)×103 M−1 s−1 and koff = (4.6±0.5)×10−1 s−1; and D = (1.2±0.2)×10−3 M, don = (1.3±0.4)×103 M−1 s−1, and doff = 1.5±0.4 s−1, respectively, at pH 7.0 and 20.0°C. Accordingly, isoniazid inhibits competitively azide binding to Mt-trHbN(III) and Mt-trHbN(III)-catalyzed peroxynitrite isomerization. Moreover, isoniazid inhibits Mt-trHbN(II) oxygenation and carbonylation. Although the structure of the Mt-trHbN-isoniazid complex is not available, here we show by docking simulation that isoniazid binding to the heme-Fe atom indeed may take place. These data suggest a direct role of isoniazid to impair fundamental functions of mycobacteria, e.g. scavenging of reactive nitrogen and oxygen species, and metabolism.
Collapse
Affiliation(s)
- Paolo Ascenzi
- Interdepartmental Laboratory of Electron Microscopy, University Roma Tre, Roma, Italy.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Chim N, Owens CP, Contreras H, Goulding CW. Withdrawn. Infect Disord Drug Targets 2012:CDTID-EPUB-20121116-2. [PMID: 23167715 PMCID: PMC3695056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Withdrawn by the publisher.
Collapse
Affiliation(s)
- Nicholas Chim
- Department of Molecular Biology and Biochemistry, University of California, Irvine CA 92697, USA
| | - Cedric P. Owens
- Department of Molecular Biology and Biochemistry, University of California, Irvine CA 92697, USA
| | - Heidi Contreras
- Department of Molecular Biology and Biochemistry, University of California, Irvine CA 92697, USA
| | - Celia W. Goulding
- Department of Molecular Biology and Biochemistry, University of California, Irvine CA 92697, USA
- Department of Pharmaceutical Sciences, University of California, Irvine CA 92697, USA
| |
Collapse
|
26
|
Forbes LV, Furtmüller PG, Khalilova I, Turner R, Obinger C, Kettle AJ. Isoniazid as a substrate and inhibitor of myeloperoxidase: Identification of amine adducts and the influence of superoxide dismutase on their formation. Biochem Pharmacol 2012; 84:949-60. [DOI: 10.1016/j.bcp.2012.07.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 07/17/2012] [Accepted: 07/18/2012] [Indexed: 12/01/2022]
|
27
|
Banerjee D, Bhattacharyya R. Isoniazid and thioacetazone may exhibit antitubercular activity by binding directly with the active site of mycolic acid cyclopropane synthase: Hypothesis based on computational analysis. Bioinformation 2012; 8:787-9. [PMID: 23055630 PMCID: PMC3449388 DOI: 10.6026/97320630008787] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 08/20/2012] [Indexed: 11/23/2022] Open
Abstract
Isoniazid and thioacetazone are the two important antitubercular drugs. In case of thioacetazone it is established that it inhibits mycolic acid cyclopropane synthase but the exact binding site accounting for such inhibition is presently unknown. In case of isoniazid its action on the said enzyme is unexplored. In this work we have analyzed the binding of isoniazid and thioacetazone with mycolic acid cyclopropane synthase (CmaA1 and CmaA2) using tools of computational biology. We have observed that thioacetazone fits well at the active site of CmaA1 and CmaA2 while isoniazid binds at the active site of CmaA1 only. We have recommended experimental validation of such results. If such results are proved to be fact it will explore the exact binding site of thioacetazone and discover a new mechanism of anti-tubercular action of isoniazid.
Collapse
Affiliation(s)
- Dibyajyoti Banerjee
- Department of Experimental Medicine and Biotechnology, Postgraduate Institute of Medical Education and Research, (PGIMER) Chandigarh-160012
| | - Rajasri Bhattacharyya
- Department of Experimental Medicine and Biotechnology, Postgraduate Institute of Medical Education and Research, (PGIMER) Chandigarh-160012
| |
Collapse
|
28
|
Bovine Carbonyl Lactoperoxidase Structure at 2.0Å Resolution and Infrared Spectra as a Function of pH. Protein J 2012; 31:598-608. [DOI: 10.1007/s10930-012-9436-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
29
|
Murphy EJ, Metcalfe CL, Nnamchi C, Moody PCE, Raven EL. Crystal structure of guaiacol and phenol bound to a heme peroxidase. FEBS J 2011; 279:1632-9. [PMID: 22093282 DOI: 10.1111/j.1742-4658.2011.08425.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Guaiacol is a universal substrate for all peroxidases, and its use in a simple colorimetric assay has wide applications. However, its exact binding location has never been defined. Here we report the crystal structures of guaiacol bound to cytochrome c peroxidase (CcP). A related structure with phenol bound is also presented. The CcP-guaiacol and CcP-phenol crystal structures show that both guaiacol and phenol bind at sites distinct from the cytochrome c binding site and from the δ-heme edge, which is known to be the binding site for other substrates. Although neither guaiacol nor phenol is seen bound at the δ-heme edge in the crystal structures, inhibition data and mutagenesis strongly suggest that the catalytic binding site for aromatic compounds is the δ-heme edge in CcP. The functional implications of these observations are discussed in terms of our existing understanding of substrate binding in peroxidases [Gumiero A et al. (2010) Arch Biochem Biophys 500, 13-20].
Collapse
Affiliation(s)
- Emma J Murphy
- Department of Chemistry, University of Leicester, Leicester, UK
| | | | | | | | | |
Collapse
|
30
|
Brossier F. Mécanismes d’action et de résistance de l’isoniazide, un antituberculeux de première ligne. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/j.antinf.2011.10.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
31
|
Singh AK, Pandey N, Sinha M, Kaur P, Sharma S, Singh TP. Structural evidence for the order of preference of inorganic substrates in mammalian heme peroxidases: crystal structure of the complex of lactoperoxidase with four inorganic substrates, SCN, I, Br and Cl. INTERNATIONAL JOURNAL OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2011; 2:328-339. [PMID: 22187667 PMCID: PMC3242431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Accepted: 11/12/2011] [Indexed: 05/31/2023]
Abstract
Lactoperoxidase (LPO) is a member of the family of mammalian heme peroxidases. It catalyzes the oxidation of halides and pseudohalides in presence of hydrogen peroxide. LPO has been co-crystallized with inorganic substrates, SCN(-), I(-), Br(-) and Cl(-). The structure determination of the complex of LPO with above four substrates showed that all of them occupied distinct positions in the substrate binding site on the distal heme side. The bound substrate ions were separated from each other by one or more water molecules. The heme iron is coordinated to His-351 N(ϵ2) on the proximal side while it is coordinated to conserved water molecule W-1 on the distal heme side. W-1 is hydrogen bonded to Br(-) ion which is followed by Cl(-) ion with a hydrogen bonded water molecule W-5' between them. Next to Cl(-) ion is a hydrogen bonded water molecule W-7' which in turn is hydrogen bonded to W-8' and N atom of SCN(-). W-80 is hydrogen bonded to W-9' which is hydrogen bonded to I(-). SCN(-) ion also interacts directly with Asn-230 and through water molecules with Ser-235 and Phe-254. Therefore, according to the locations of four substrate anions, the order of preference for binding to lactoperoxidase is observed as Br(-) > Cl(-) > SCN(-) > I(-). The positions of anions are further defined in terms of subsites where Br(-) is located in subsite 1, Cl(-) in subsite 2, SCN(-) in subsite 3 and I(-) in subsite 4.
Collapse
Affiliation(s)
- Amit K Singh
- Department of Biophysics, All India Institute of Medical Sciences New Delhi India
| | | | | | | | | | | |
Collapse
|
32
|
Reduction of the lipocalin type heme containing protein nitrophorin — Sensitivity of the fold-stabilizing cysteine disulfides toward routine heme-iron reduction. J Inorg Biochem 2011; 105:1405-12. [DOI: 10.1016/j.jinorgbio.2011.07.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Revised: 07/19/2011] [Accepted: 07/20/2011] [Indexed: 11/23/2022]
|
33
|
A novel metabolite of antituberculosis therapy demonstrates host activation of isoniazid and formation of the isoniazid-NAD+ adduct. Antimicrob Agents Chemother 2011; 56:28-35. [PMID: 22037847 DOI: 10.1128/aac.05486-11] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
One of the most effective and widely used antituberculosis (anti-TB) drugs is isoniazid (INH), a prodrug activated via oxidation that forms an adduct with NAD(+) to inhibit NADH-dependent targets of Mycobacterium tuberculosis, such as enoyl-acyl carrier protein reductase (InhA). The metabolic by-products and potentially toxic intermediates resulting from INH therapy have been identified through a large body of work. However, an INH-NAD adduct or structures related to this adduct have not been identified in specimens from human TB patients or animal models of TB. Analyses by mass spectrometry of urine collected from TB patients in a study conducted by the NIAID-funded Tuberculosis Research Unit identified 4-isonicotinoylnicotinamide (C(12)H(9)N(3)O(2)) as a novel metabolite of INH therapy. This compound was formed by M. tuberculosis strains in a KatG-dependent manner but could also be produced by mice treated with INH independent of an M. tuberculosis infection. Thus, the 4-isonicotinoylnicotinamide observed in human urine samples is likely derived from the degradation of oxidized INH-NAD adducts and provides direct evidence of host INH activation.
Collapse
|
34
|
Al-Baarri AN, Hayashi M, Ogawa M, Hayakawa S. Effects of mono- and disaccharides on the antimicrobial activity of bovine lactoperoxidase system. J Food Prot 2011; 74:134-9. [PMID: 21219776 DOI: 10.4315/0362-028x.jfp-10-184] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The effects of mono- and disaccharides on the antimicrobial activity of the lactoperoxidase (LPO) system against Salmonella Enteritidis were investigated. The results clearly reveal that most of the sugars inhibit the antimicrobial activity of the LPO system. The inhibitory potency varies depending on the structure of sugar. L-Fructose and D-allose were strongly inhibitive to the action of the LPO system, while sucrose was the weakest inhibitor. The decreased antimicrobial activity is due to the reduction of LPO catalytic activity by sugar. An inhibitory kinetic study showed the noncompetitive inhibitor. D-Allose and L-fructose yielded strikingly low K(i) values of 0.36 and 0.42 mM, respectively, while the K(i) values of the other sugars ranged from 1.37 to 3.60 mM. Since LPO activity is inhibited by the saccharides, the sugar content in food should be considered when the LPO system is applied to the preservation of food.
Collapse
Affiliation(s)
- Ahmad Nimatullah Al-Baarri
- Department of Applied Biological Sciences, Kagawa University, 2393, Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0795, Japan
| | | | | | | |
Collapse
|
35
|
Banerjee S, Furtmüller PG, Obinger C. Bovine lactoperoxidase - a versatile one- and two-electron catalyst of high structural and thermal stability. Biotechnol J 2010; 6:231-43. [PMID: 21298808 DOI: 10.1002/biot.201000375] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 11/09/2010] [Accepted: 11/11/2010] [Indexed: 11/07/2022]
Abstract
Lactoperoxidase (LPO), a member of the peroxidase-cyclooxygenase superfamily, is found in multiple human exocrine secretions and acts as a first line of defense against invading microorganisms by production of antimicrobial oxidants. Because of its ability to efficiently catalyze one- and two-electron oxidation reactions of inorganic and organic compounds, the heme peroxidase is widely used in food biotechnology, cosmetic industry, and diagnostic kits. In order to probe its structural integrity, conformational, and thermal stability, we have undertaken a comprehensive investigation by using complementary biophysical techniques including UV-Vis, circular dichroism and fluorescence spectroscopy as well as differential scanning calorimetry (DSC). The oxidoreductase exhibits a high chemical and thermal stability under oxidizing conditions but is significantly destabilized by addition of DTT. Due to its unique ester bonds between the prosthetic group and the protein as well as six intra-chain disulfides, unfolding of the central compact (-helical core occurs concomitantly with denaturation of the heme cavity. The corresponding enthalpic and entropic contributions to the free enthalpy of unfolding are presented. Together with spectroscopic data they will be discussed with respect to the known structure of bovine LPO and homologous myeloperoxidase as well as to its practical application.
Collapse
Affiliation(s)
- Srijib Banerjee
- Division of Biochemistry, Department of Chemistry, BOKU, University of Natural Resources and Life Sciences, Vienna, Austria
| | | | | |
Collapse
|
36
|
Unprecedented Peroxidase-like Activity of Rhodnius prolixus Nitrophorin 2: Identification of the [FeIV═O Por•]+ and [FeIV═O Por](Tyr38•) Intermediates and Their Role(s) in Substrate Oxidation. Biochemistry 2010; 49:8857-72. [DOI: 10.1021/bi100499a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
37
|
Wiseman B, Carpena X, Feliz M, Donald LJ, Pons M, Fita I, Loewen PC. Isonicotinic acid hydrazide conversion to Isonicotinyl-NAD by catalase-peroxidases. J Biol Chem 2010; 285:26662-73. [PMID: 20554537 PMCID: PMC2924108 DOI: 10.1074/jbc.m110.139428] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Revised: 05/28/2010] [Indexed: 11/06/2022] Open
Abstract
Activation of the pro-drug isoniazid (INH) as an anti-tubercular drug in Mycobacterium tuberculosis involves its conversion to isonicotinyl-NAD, a reaction that requires the catalase-peroxidase KatG. This report shows that the reaction proceeds in the absence of KatG at a slow rate in a mixture of INH, NAD(+), Mn(2+), and O(2), and that the inclusion of KatG increases the rate by >7 times. Superoxide, generated by either Mn(2+)- or KatG-catalyzed reduction of O(2), is an essential intermediate in the reaction. Elimination of the peroxidatic process by mutation slows the rate of reaction by 60% revealing that the peroxidatic process enhances, but is not essential for isonicotinyl-NAD formation. The isonicotinyl-NAD(*+) radical is identified as a reaction intermediate, and its reduction by superoxide is proposed. Binding sites for INH and its co-substrate, NAD(+), are identified for the first time in crystal complexes of Burkholderia pseudomallei catalase-peroxidase with INH and NAD(+) grown by co-crystallization. The best defined INH binding sites were identified, one in each subunit, on the opposite side of the protein from the entrance to the heme cavity in a funnel-shaped channel. The NAD(+) binding site is approximately 20 A from the entrance to the heme cavity and involves interactions primarily with the AMP portion of the molecule in agreement with the NMR saturation transfer difference results.
Collapse
Affiliation(s)
| | - Xavi Carpena
- the Institute for Research in Biomedicine and
- Institut de Biologia Molecular, Parc Científic, Baldiri Reixac 10, 08028 Barcelona, Spain, and
| | - Miguel Feliz
- the Department of Organic Chemistry, University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | | | - Miquel Pons
- the Institute for Research in Biomedicine and
- the Department of Organic Chemistry, University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Ignacio Fita
- the Institute for Research in Biomedicine and
- Institut de Biologia Molecular, Parc Científic, Baldiri Reixac 10, 08028 Barcelona, Spain, and
| | | |
Collapse
|
38
|
Gumiero A, Murphy EJ, Metcalfe CL, Moody PC, Raven EL. An analysis of substrate binding interactions in the heme peroxidase enzymes: A structural perspective. Arch Biochem Biophys 2010; 500:13-20. [DOI: 10.1016/j.abb.2010.02.015] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Revised: 02/23/2010] [Accepted: 02/27/2010] [Indexed: 11/29/2022]
|
39
|
Relationship between mutation of serine residue at 315th position in M. tuberculosis catalase-peroxidase enzyme and Isoniazid susceptibility: An in silico analysis. J Mol Model 2010; 17:869-77. [DOI: 10.1007/s00894-010-0785-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Accepted: 06/15/2010] [Indexed: 10/19/2022]
|
40
|
First structural evidence for the mode of diffusion of aromatic ligands and ligand-induced closure of the hydrophobic channel in heme peroxidases. J Biol Inorg Chem 2010; 15:1099-107. [DOI: 10.1007/s00775-010-0669-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Accepted: 04/27/2010] [Indexed: 11/26/2022]
|
41
|
Murphy EJ, Maréchal A, Segal AW, Rich PR. CO binding and ligand discrimination in human myeloperoxidase. Biochemistry 2010; 49:2150-8. [PMID: 20146436 DOI: 10.1021/bi9021507] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Despite the fact that ferrous myeloperoxidase (MPO) can bind both O(2) and NO, its ability to bind CO has been questioned. UV/visible spectroscopy was used to confirm that CO induces small spectral shifts in ferrous MPO, and Fourier transform infrared difference spectroscopy showed definitively that these arose from formation of a heme ferrous-CO compound. Recombination rates after CO photolysis were monitored at 618 and 645 nm as a function of CO concentration and pH. At pH 6.3, k(on) and k(off) were 0.14 mM(-1) x s(-1) and 0.23 s(-1), respectively, yielding an unusually high K(D) of 1.6 mM. This affinity of MPO for CO is 10 times weaker than its affinity for O(2). The observed rate constant for CO binding increased with increasing pH and was governed by a single protonatable group with a pK(a) of 7.8. Fourier transform infrared spectroscopy revealed two different conformations of bound CO with frequencies at 1927 and 1942 cm(-1). Their recombination rate constants were identical, indicative of two forms of bound CO that are in rapid thermal equilibrium rather than two distinct protein populations with different binding sites. The ratio of bound states was pH-dependent (pK(a) approximately 7.4) with the 1927 cm(-1) form favored at high pH. Structural factors that account for the ligand-binding properties of MPO are identified by comparisons with published data on a range of other ligand-binding heme proteins, and support is given to the recent suggestion that the proximal His336 in MPO is in a true imidazolate state.
Collapse
Affiliation(s)
- Emma J Murphy
- Centre for Molecular Medicine, Division of Medicine, University College London, 5 University Street, London WC1E 6JJ, UK
| | | | | | | |
Collapse
|