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Bhargavi G, Mallakuntla MK, Kale D, Tiwari S. Rv0687 a Putative Short-Chain Dehydrogenase is indispensable for pathogenesis of Mycobacterium tuberculosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.12.571312. [PMID: 38168250 PMCID: PMC10760034 DOI: 10.1101/2023.12.12.571312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Mycobacterium tuberculosis (Mtb), a successful human pathogen, resides in host sentinel cells and combats the stressful intracellular environment induced by reactive oxygen and nitrogen species during infection. Mtb employs several evasion mechanisms in the face of the host as a survival strategy, including detoxifying enzymes as short-chain dehydrogenases/ reductases (SDRs) to withstand host-generated insults. In this study, using specialized transduction we have generated a Rv0687 deletion mutant and its complemented strain and investigated the functional role of Rv0687, a member of SDRs family genes in Mtb pathogenesis. Wildtype (WT) and mutant Mtb strain lacking Rv0687 (RvΔ0687) were tested for in-vitro stress response and in-vivo survival in macrophages and mice models of infection. The study demonstrates that Rv0687 is crucial for sustaining bacterial growth in nutrition-limited conditions. The deletion of Rv0687 elevated the sensitivity of Mtb to oxidative and nitrosative stress-inducing agents. Furthermore, the lack of Rv0687 compromised the survival of Mtb in primary bone marrow macrophages and led to an increase in the levels of the secreted proinflammatory cytokines TNF-α, and MIP-1α. Interestingly, the growth of WT and RvΔ0687 was similar in the lungs of infected immunocompromised mice however, a significant reduction in RvΔ0687 growth was observed in the spleen of immunocompromised Rag -/- mice at 4 weeks post-infection. Moreover Rag -/- mice infected with RvΔ0687 survived longer compared to WT Mtb strain. Additionally, we observed significant reduction in bacterial burden in spleens and lungs of immunocompetent C57BL/6 mice infected with RvΔ0687 compared to complemented and WT Mtb strains. Collectively, this study reveals that Rv0687 plays a role in Mtb pathogenesis.
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Qiu S, Zhang X, Xia W, Li Z, Wang L, Chen Z, Ge S. Effect of extreme pH conditions on methanogenesis: Methanogen metabolism and community structure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 877:162702. [PMID: 36898547 DOI: 10.1016/j.scitotenv.2023.162702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 03/03/2023] [Accepted: 03/03/2023] [Indexed: 05/06/2023]
Abstract
The control of pH is effective for inhibiting methanogenesis in the chain elongation fermentation (CEF) system. However, obscure conclusions exist especially with regard to the underlying mechanism. This study comprehensively explored the responses of methanogenesis in granular sludge at various pH levels, ranging from 4.0 to 10.0, from multiple aspects including methane production, methanogenesis pathway, microbial community structure, energy metabolism and electron transport. Results demonstrated that compared with that at pH 7.0, pH at 4.0, 5.5, 8.5 and 10.0 triggered a 100%, 71.7%, 23.8% and 92.1% suppression on methanogenesis by the end of 3 cycles lasting 21 days. This might be explained by the remarkably inhibited metabolic pathways and intracellular regulations. To be more specific, extreme pH conditions decreased the abundance of the acetoclastic methanogens. However, obligate hydrogenotrophic and facultative acetolactic/hydrogenotrophic methanogens were significantly enriched by 16.9%-19.5 fold. pH stress reduced the gene abundance and/or activity of most enzymes involved in methanogenesis such as acetate kinase (by 81.1%-93.1%), formylmethanofuran dehydrogenase (by 10.9%-54.0%) and tetrahydromethanopterin S-methyltransferase (by 9.3%-41.5%). Additionally, pH stress suppressed electron transport via improper electron carriers and decreased electron amount as evidenced by 46.3%-70.4% reduced coenzyme F420 content and diminished abundance of CO dehydrogenase (by 15.5%-70.5%) and NADH:ubiquinone reductase (by 20.2%-94.5%). pH stress also regulated energy metabolism with inhibited ATP synthesis (e.g., ATP citrate synthase level reduced by 20.1%-95.3%). Interestingly, the protein and carbohydrate content secreted in EPS failed to show consistent responses to acidic and alkaline conditions. Specifically, when compared with pH 7.0, the acidic condition remarkably reduced the levels of total EPS and EPS protein while both levels were enhanced in the alkaline condition. However, the EPS carbohydrate content at pH 4.0 and 10.0 both decreased. This study is expected to promote the understanding of the pH control-induced methanogenesis inhibition in the CEF system.
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Affiliation(s)
- Shuang Qiu
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, Jiangsu, China
| | - Xingchen Zhang
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, Jiangsu, China
| | - Wenhao Xia
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, Jiangsu, China
| | - Zimu Li
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, Jiangsu, China
| | - Lingfeng Wang
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, Jiangsu, China
| | - Zhipeng Chen
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, Jiangsu, China
| | - Shijian Ge
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Xiao Ling Wei 200, Nanjing 210094, Jiangsu, China.
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Kabongo AT, Acharjee R, Sakura T, Bundutidi GM, Hartuti ED, Davies C, Gundogdu O, Kita K, Shiba T, Inaoka DK. Biochemical characterization and identification of ferulenol and embelin as potent inhibitors of malate:quinone oxidoreductase from Campylobacter jejuni. Front Mol Biosci 2023; 10:1095026. [PMID: 36776743 PMCID: PMC9908594 DOI: 10.3389/fmolb.2023.1095026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/18/2023] [Indexed: 01/27/2023] Open
Abstract
Campylobacter jejuni infection poses a serious global threat to public health. The increasing incidence and antibiotic resistance of this bacterial infection have necessitated the adoption of various strategies to curb this trend, primarily through developing new drugs with new mechanisms of action. The enzyme malate:quinone oxidoreductase (MQO) has been shown to be essential for the survival of several bacteria and parasites. MQO is a peripheral membrane protein that catalyses the oxidation of malate to oxaloacetate, a crucial step in the tricarboxylic acid cycle. In addition, MQO is involved in the reduction of the quinone pool in the electron transport chain and thus contributes to cellular bioenergetics. The enzyme is an attractive drug target as it is not conserved in mammals. As a preliminary step in assessing the potential application of MQO from C. jejuni (CjMQO) as a new drug target, we purified active recombinant CjMQO and conducted, for the first time, biochemical analyses of MQO from a pathogenic bacterium. Our study showed that ferulenol, a submicromolar mitochondrial MQO inhibitor, and embelin are nanomolar inhibitors of CjMQO. We showed that both inhibitors are mixed-type inhibitors versus malate and noncompetitive versus quinone, suggesting the existence of a third binding site to accommodate these inhibitors; indeed, such a trait appears to be conserved between mitochondrial and bacterial MQOs. Interestingly, ferulenol and embelin also inhibit the in vitro growth of C. jejuni, supporting the hypothesis that MQO is essential for C. jejuni survival and is therefore an important drug target.
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Affiliation(s)
- Augustin Tshibaka Kabongo
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan,Department of Molecular Infection Dynamics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan,Department of Internal Medicine, Faculty of Medicine, Pharmacy and Public Health, University of Mbujimayi, Kinshasa, Congo
| | - Rajib Acharjee
- Department of Parasitology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan,Program for Nurturing Global Leaders in Tropical and Emerging Communicable Disease, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan,Department of Zoology, University of Chittagong, Chittagong, Bangladesh
| | - Takaya Sakura
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan,Department of Molecular Infection Dynamics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Gloria Mavinga Bundutidi
- Department of Molecular Infection Dynamics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan,Department of Parasitology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan,Program for Nurturing Global Leaders in Tropical and Emerging Communicable Disease, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan,Department of Pediatrics, Kinshasa University Hospital, University of Kinshasa, Kinshasa, Congo
| | - Endah Dwi Hartuti
- Department of Parasitology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan,Program for Nurturing Global Leaders in Tropical and Emerging Communicable Disease, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan,Research Center for Genetic Engineering, National Research and Innovation Agency, West Java, Indonesia
| | - Cadi Davies
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Ozan Gundogdu
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Kiyoshi Kita
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan,Department of Host-Defense Biochemistry, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan,Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tomoo Shiba
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto, Japan,*Correspondence: Tomoo Shiba, ; Daniel Ken Inaoka,
| | - Daniel Ken Inaoka
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan,Department of Molecular Infection Dynamics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan,Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan,*Correspondence: Tomoo Shiba, ; Daniel Ken Inaoka,
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Anand P, Akhter Y. A review on enzyme complexes of electron transport chain from Mycobacterium tuberculosis as promising drug targets. Int J Biol Macromol 2022; 212:474-494. [PMID: 35613677 DOI: 10.1016/j.ijbiomac.2022.05.124] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/05/2022] [Accepted: 05/17/2022] [Indexed: 12/20/2022]
Abstract
Energy metabolism is a universal process occurring in all life forms. In Mycobacterium tuberculosis (Mtb), energy production is carried out in two possible ways, oxidative phosphorylation (OxPhos) and substrate-level phosphorylation. Mtb is an obligate aerobic bacterium, making it dependent on OxPhos for ATP synthesis and growth. Mtb inhabits varied micro-niches during the infection cycle, outside and within the host cells, which alters its primary metabolic pathways during the pathogenesis. In this review, we discuss cellular respiration in the context of the mechanism and structural importance of the proteins and enzyme complexes involved. These protein-protein complexes have been proven to be essential for Mtb virulence as they aid the bacteria's survival during aerobic and hypoxic conditions. ATP synthase, a crucial component of the electron transport chain, has been in the limelight, as a prominent drug target against tuberculosis. Likewise, in this review, we have explored other protein-protein complexes of the OxPhos pathway, their functional essentiality, and their mechanism in Mtb's diverse lifecycle. The review summarises crucial target proteins and reported inhibitors of the electron transport chain pathway of Mtb.
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Affiliation(s)
- Pragya Anand
- Department of Biotechnology, School of Life Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Lucknow, Uttar Pradesh 226025, India
| | - Yusuf Akhter
- Department of Biotechnology, School of Life Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Lucknow, Uttar Pradesh 226025, India.
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Shen GB, Xie L, Wang YX, Gong TY, Wang BY, Hu YH, Fu YH, Yan M. Quantitative Estimation of the Hydrogen-Atom-Donating Ability of 4-Substituted Hantzsch Ester Radical Cations. ACS OMEGA 2021; 6:23621-23629. [PMID: 34549160 PMCID: PMC8444320 DOI: 10.1021/acsomega.1c03872] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 08/19/2021] [Indexed: 05/22/2023]
Abstract
The purpose of this study is to investigate thermodynamic and kinetic properties on the hydrogen-atom-donating ability of 4-substituted Hantzsch ester radical cations (XRH•+), which are excellent NADH coenzyme models. Gibbs free energy changes and activation free energies of 17 XRH•+ releasing H• [denoted as ΔG HD o(XRH•+) and ΔG HD ≠(XRH•+)] were calculated using density functional theory (DFT) and compared with that of Hantzsch ester (HEH2) and NADH. ΔG HD o(XRH•+) range from 19.35 to 31.25 kcal/mol, significantly lower than that of common antioxidants (such as ascorbic acid, BHT, the NADH coenzyme, and so forth). ΔG HD ≠(XRH•+) range from 29.81 to 39.00 kcal/mol, indicating that XRH•+ spontaneously releasing H• are extremely slow unless catalysts or active intermediate radicals exist. According to the computed data, it can be inferred that the Gibbs free energies and activation free energies of the core 1,4-dihydropyridine radical cation structure (DPH•+) releasing H• [ΔG HD o(DPH•+) and ΔG HD ≠(DPH•+)] should be 19-32 kcal/mol and 29-39 kcal/mol in acetonitrile, respectively. The correlations between the thermodynamic driving force [ΔG HD o(XRH•+)] and the activation free energy [ΔG HD ≠(XRH•+)] are also explored. Gibbs free energy is the important and decisive parameter, and ΔG HD ≠(XRH•+) increases in company with the increase of ΔG HD o(XRH•+), but no simple linear correlations are found. Even though all XRH•+ are judged as excellent antioxidants from the thermodynamic view, the computed data indicate that whether XRH•+ is an excellent antioxidant in reaction is decided by the R substituents in 4-position. XRH•+ with nonaromatic substituents tend to release R• instead of H• to quench radicals. XRH•+ with aromatic substituents tend to release H• and be used as antioxidants, but not all aromatic substituted Hantzsch esters are excellent antioxidants.
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Affiliation(s)
- Guang-Bin Shen
- School of Medical Engineering, Jining Medical University, Jining, Shandong 272000, P. R. China
| | - Li Xie
- School of Medical Engineering, Jining Medical University, Jining, Shandong 272000, P. R. China
| | - Yun-Xia Wang
- School of Medical Engineering, Jining Medical University, Jining, Shandong 272000, P. R. China
| | - Teng-Yang Gong
- School of Pharmacy, Jining Medical University, Rizhao, Shandong 276800, P. R. China
| | - Bin-Yu Wang
- School of Medical Engineering, Jining Medical University, Jining, Shandong 272000, P. R. China
| | - Yu-He Hu
- School of Medical Engineering, Jining Medical University, Jining, Shandong 272000, P. R. China
| | - Yan-Hua Fu
- College of Chemistry and Environmental Engineering, Anyang Institute of Technology, Anyang, Henan 455000, P. R. China
| | - Maocai Yan
- School of Pharmacy, Jining Medical University, Rizhao, Shandong 276800, P. R. China
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Coghi PS, Zhu Y, Xie H, Hosmane NS, Zhang Y. Organoboron Compounds: Effective Antibacterial and Antiparasitic Agents. Molecules 2021; 26:3309. [PMID: 34072937 PMCID: PMC8199504 DOI: 10.3390/molecules26113309] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 05/27/2021] [Accepted: 05/27/2021] [Indexed: 11/16/2022] Open
Abstract
The unique electron deficiency and coordination property of boron led to a wide range of applications in chemistry, energy research, materials science and the life sciences. The use of boron-containing compounds as pharmaceutical agents has a long history, and recent developments have produced encouraging strides. Boron agents have been used for both radiotherapy and chemotherapy. In radiotherapy, boron neutron capture therapy (BNCT) has been investigated to treat various types of tumors, such as glioblastoma multiforme (GBM) of brain, head and neck tumors, etc. Boron agents playing essential roles in such treatments and other well-established areas have been discussed elsewhere. Organoboron compounds used to treat various diseases besides tumor treatments through BNCT technology have also marked an important milestone. Following the clinical introduction of bortezomib as an anti-cancer agent, benzoxaborole drugs, tavaborole and crisaborole, have been approved for clinical use in the treatments of onychomycosis and atopic dermatitis. Some heterocyclic organoboron compounds represent potentially promising candidates for anti-infective drugs. This review highlights the clinical applications and perspectives of organoboron compounds with the natural boron atoms in disease treatments without neutron irradiation. The main topic focuses on the therapeutic applications of organoboron compounds in the diseases of tuberculosis and antifungal activity, malaria, neglected tropical diseases and cryptosporidiosis and toxoplasmosis.
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Affiliation(s)
- Paolo Saul Coghi
- School of Pharmacy Macau, University of Science and Technology, Taipa Macau 999078, China;
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa Macau 999078, China
| | - Yinghuai Zhu
- The State Key Laboratory of Anti-Infective Drug Development (NO. 2015DQ780357), Sunshine Lake Pharma Co., Ltd., Dongguan 523871, China;
| | - Hongming Xie
- The State Key Laboratory of Anti-Infective Drug Development (NO. 2015DQ780357), Sunshine Lake Pharma Co., Ltd., Dongguan 523871, China;
| | - Narayan S. Hosmane
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA
| | - Yingjun Zhang
- The State Key Laboratory of Anti-Infective Drug Development (NO. 2015DQ780357), Sunshine Lake Pharma Co., Ltd., Dongguan 523871, China;
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Boes DM, Godoy-Hernandez A, McMillan DGG. Peripheral Membrane Proteins: Promising Therapeutic Targets across Domains of Life. MEMBRANES 2021; 11:membranes11050346. [PMID: 34066904 PMCID: PMC8151925 DOI: 10.3390/membranes11050346] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/28/2021] [Accepted: 05/05/2021] [Indexed: 11/16/2022]
Abstract
Membrane proteins can be classified into two main categories—integral and peripheral membrane proteins—depending on the nature of their membrane interaction. Peripheral membrane proteins are highly unique amphipathic proteins that interact with the membrane indirectly, using electrostatic or hydrophobic interactions, or directly, using hydrophobic tails or GPI-anchors. The nature of this interaction not only influences the location of the protein in the cell, but also the function. In addition to their unique relationship with the cell membrane, peripheral membrane proteins often play a key role in the development of human diseases such as African sleeping sickness, cancer, and atherosclerosis. This review will discuss the membrane interaction and role of periplasmic nitrate reductase, CymA, cytochrome c, alkaline phosphatase, ecto-5’-nucleotidase, acetylcholinesterase, alternative oxidase, type-II NADH dehydrogenase, and dihydroorotate dehydrogenase in certain diseases. The study of these proteins will give new insights into their function and structure, and may ultimately lead to ground-breaking advances in the treatment of severe diseases.
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Affiliation(s)
- Deborah M. Boes
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, NL-2629 HZ Delft, The Netherlands; (D.M.B.); (A.G.-H.)
| | - Albert Godoy-Hernandez
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, NL-2629 HZ Delft, The Netherlands; (D.M.B.); (A.G.-H.)
| | - Duncan G. G. McMillan
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, NL-2629 HZ Delft, The Netherlands; (D.M.B.); (A.G.-H.)
- School of Fundamental Sciences, Massey University, Palmerston North, Private Bag 11 222, New Zealand
- Correspondence:
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Shahbaaz M, Potemkin V, Bisetty K, Hassan MI, Hussien MA. Classification and functional analyses of putative virulence factors of Mycobacterium tuberculosis: A combined sequence and structure based study. Comput Biol Chem 2020; 87:107270. [PMID: 32438116 DOI: 10.1016/j.compbiolchem.2020.107270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 04/16/2020] [Accepted: 04/26/2020] [Indexed: 11/17/2022]
Abstract
The emergence of the drug-resistant mechanisms in Mycobacterium tuberculosis poses the biggest challenges to the current therapeutic measures, which necessitates the identification of new drug targets. The Hypothetical Proteins (HPs), a class of functionally uncharacterized proteins, may provide a new class of undiscovered therapeutic targets. The genome of M. tuberculosis contains 1000 HPs with their sequences were analyzed using a variety of bioinformatics tools and the functional annotations were performed. The functions of 662 HPs were successfully predicted and further classified 483 HPs as enzymes, 141 HPs were predicted to be involved in the diverse cellular mechanisms and 38 HPs may function as transporters and carriers proteins. Furthermore, 28 HPs were predicted to be virulent in nature. Amongst them, the HP P95201, HP P9WM79, HP I6WZ30, HP I6 × 9T8, HP P9WKP3, and HP P9WK89 showed the highest virulence scores. Therefore, these proteins were subjected to extensive structure analyses and dynamics of their conformations were investigated using the principles of molecular dynamics simulations, each for a 150 ns time scale. This study provides a deeper understanding of the undiscovered drug targets and the generated outputs will facilitate the process of drug design and discovery against the infection of M. tuberculosis.
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Affiliation(s)
- Mohd Shahbaaz
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute (SANBI), University of the Western Cape, Private Bag X17, Bellville 7535, Cape Town, South Africa; Laboratory of Computational Modeling of Drugs, South Ural State University, 76 Lenin prospekt, 454080 Chelyabinsk, Russia
| | - Vladimir Potemkin
- Laboratory of Computational Modeling of Drugs, South Ural State University, 76 Lenin prospekt, 454080 Chelyabinsk, Russia
| | - Krishna Bisetty
- Department of Chemistry, Durban University of Technology, Durban, 4000, South Africa
| | - Md Imtaiyaz Hassan
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Mostafa A Hussien
- Department of Chemistry, Faculty of Science, King Abdulaziz University, P.O. Box 80203 Jeddah 21589, Saudi Arabia; Department of Chemistry, Faculty of Science, Port Said University, Port Said, 42521, Egypt
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9
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Wu M, Gu J, Zong S, Guo R, Liu T, Yang M. Research journey of respirasome. Protein Cell 2020; 11:318-338. [PMID: 31919741 PMCID: PMC7196574 DOI: 10.1007/s13238-019-00681-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 12/11/2019] [Indexed: 12/11/2022] Open
Abstract
Respirasome, as a vital part of the oxidative phosphorylation system, undertakes the task of transferring electrons from the electron donors to oxygen and produces a proton concentration gradient across the inner mitochondrial membrane through the coupled translocation of protons. Copious research has been carried out on this lynchpin of respiration. From the discovery of individual respiratory complexes to the report of the high-resolution structure of mammalian respiratory supercomplex I1III2IV1, scientists have gradually uncovered the mysterious veil of the electron transport chain (ETC). With the discovery of the mammalian respiratory mega complex I2III2IV2, a new perspective emerges in the research field of the ETC. Behind these advances glitters the light of the revolution in both theory and technology. Here, we give a short review about how scientists 'see' the structure and the mechanism of respirasome from the macroscopic scale to the atomic scale during the past decades.
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Affiliation(s)
- Meng Wu
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jinke Gu
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Shuai Zong
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Runyu Guo
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Tianya Liu
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Maojun Yang
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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Makarov V, Salina E, Reynolds RC, Kyaw Zin PP, Ekins S. Molecule Property Analyses of Active Compounds for Mycobacterium tuberculosis. J Med Chem 2020; 63:8917-8955. [PMID: 32259446 DOI: 10.1021/acs.jmedchem.9b02075] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Tuberculosis (TB) continues to claim the lives of around 1.7 million people per year. Most concerning are the reports of multidrug drug resistance. Paradoxically, this global health pandemic is demanding new therapies when resources and interest are waning. However, continued tuberculosis drug discovery is critical to address the global health need and burgeoning multidrug resistance. Many diverse classes of antitubercular compounds have been identified with activity in vitro and in vivo. Our analyses of over 100 active leads are representative of thousands of active compounds generated over the past decade, suggests that they come from few chemical classes or natural product sources. We are therefore repeatedly identifying compounds that are similar to those that preceded them. Our molecule-centered cheminformatics analyses point to the need to dramatically increase the diversity of chemical libraries tested and get outside of the historic Mtb property space if we are to generate novel improved antitubercular leads.
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Affiliation(s)
- Vadim Makarov
- FRC Fundamentals of Biotechnology, Russian Academy of Science, Moscow 119071, Russia
| | - Elena Salina
- FRC Fundamentals of Biotechnology, Russian Academy of Science, Moscow 119071, Russia
| | - Robert C Reynolds
- Department of Medicine, Division of Hematology and Oncology, University of Alabama at Birmingham, NP 2540 J, 1720 Second Avenue South, Birmingham, Alabama 35294-3300, United States
| | - Phyo Phyo Kyaw Zin
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States.,Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Sean Ekins
- Collaborations Pharmaceuticals, Inc., 840 Main Campus Drive, Lab 3510 Raleigh, North Carolina 27606, United States
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Nakatani Y, Shimaki Y, Dutta D, Muench SP, Ireton K, Cook GM, Jeuken LJC. Unprecedented Properties of Phenothiazines Unraveled by a NDH-2 Bioelectrochemical Assay Platform. J Am Chem Soc 2020; 142:1311-1320. [PMID: 31880924 DOI: 10.1021/jacs.9b10254] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Type II NADH:quinone oxidoreductase (NDH-2) plays a crucial role in the respiratory chains of many organisms. Its absence in mammalian cells makes NDH-2 an attractive new target for developing antimicrobials and antiprotozoal agents. We established a novel bioelectrochemical platform to characterize the catalytic behavior of NDH-2 from Caldalkalibacillus thermarum and Listeria monocytogenes strain EGD-e while bound to native-like lipid membranes. Catalysis of both NADH oxidation and lipophilic quinone reduction by membrane-bound NDH-2 followed the Michaelis-Menten model; however, the maximum turnover was only achieved when a high concentration of quinone (>3 mM) was present in the membrane, suggesting that quinone availability regulates NADH-coupled respiration activity. The quinone analogue 2-heptyl-4-hydroxyquinoline-N-oxide inhibited C. thermarum NDH-2 activity, and its potency is higher in a membrane environment compared to assays performed with water-soluble quinone analogues, demonstrating the importance of testing compounds under physiologically relevant conditions. Furthermore, when phenothiazines, one of the most commonly identified NDH-2 inhibitors, were tested, they did not inhibit membrane-bound NDH-2. Instead, our assay platform unexpectedly suggests a novel mode of phenothiazine action where chlorpromazine, a promising antitubercular agent and key medicine used to treat psychotic disorders, is able to disrupt pH gradients across bacterial membranes.
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Affiliation(s)
- Yoshio Nakatani
- Department of Microbiology and Immunology , University of Otago , Dunedin 9054 , New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery , The University of Auckland , Private Bag 92019, Auckland 1042 , New Zealand
| | - Yosuke Shimaki
- Department of Microbiology and Immunology , University of Otago , Dunedin 9054 , New Zealand
| | - Debajyoti Dutta
- School of Biomedical Sciences and the Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Stephen P Muench
- School of Biomedical Sciences and the Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Keith Ireton
- Department of Microbiology and Immunology , University of Otago , Dunedin 9054 , New Zealand
| | - Gregory M Cook
- Department of Microbiology and Immunology , University of Otago , Dunedin 9054 , New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery , The University of Auckland , Private Bag 92019, Auckland 1042 , New Zealand
| | - Lars J C Jeuken
- School of Biomedical Sciences and the Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , United Kingdom
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12
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The synthesis and evaluation of quinolinequinones as anti-mycobacterial agents. Bioorg Med Chem 2019; 27:3532-3545. [DOI: 10.1016/j.bmc.2019.06.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 05/30/2019] [Accepted: 06/01/2019] [Indexed: 12/30/2022]
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13
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Murugesan D, Ray PC, Bayliss T, Prosser GA, Harrison JR, Green K, Soares de Melo C, Feng TS, Street LJ, Chibale K, Warner DF, Mizrahi V, Epemolu O, Scullion P, Ellis L, Riley J, Shishikura Y, Ferguson L, Osuna-Cabello M, Read KD, Green SR, Lamprecht DA, Finin PM, Steyn AJC, Ioerger TR, Sacchettini J, Rhee KY, Arora K, Barry CE, Wyatt PG, Boshoff HIM. 2-Mercapto-Quinazolinones as Inhibitors of Type II NADH Dehydrogenase and Mycobacterium tuberculosis: Structure-Activity Relationships, Mechanism of Action and Absorption, Distribution, Metabolism, and Excretion Characterization. ACS Infect Dis 2018. [PMID: 29522317 PMCID: PMC5996347 DOI: 10.1021/acsinfecdis.7b00275] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Mycobacterium tuberculosis (MTb) possesses
two nonproton pumping type II NADH dehydrogenase (NDH-2)
enzymes which are predicted to be jointly essential for respiratory
metabolism. Furthermore, the structure of a closely related bacterial
NDH-2 has been reported recently, allowing for the structure-based
design of small-molecule inhibitors. Herein, we disclose MTb whole-cell structure–activity relationships (SARs) for a series of 2-mercapto-quinazolinones which target the ndh encoded NDH-2 with nanomolar potencies. The compounds were inactivated by glutathione-dependent adduct formation as well as quinazolinone oxidation in microsomes. Pharmacokinetic studies demonstrated modest bioavailability and compound exposures. Resistance to the compounds in MTb was conferred by promoter mutations in the alternative nonessential NDH-2 encoded by ndhA in MTb. Bioenergetic analyses revealed a decrease in oxygen consumption rates in response to inhibitor in cells in which membrane potential was uncoupled from ATP production, while inverted membrane vesicles showed mercapto-quinazolinone-dependent inhibition of ATP production when NADH was the electron donor to the respiratory chain. Enzyme kinetic studies further demonstrated noncompetitive inhibition, suggesting binding of this scaffold to an allosteric site. In summary, while the initial MTb SAR showed limited improvement in potency, these results, combined with structural information on the bacterial protein, will aid in the future discovery of new and improved NDH-2 inhibitors.
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Affiliation(s)
- Dinakaran Murugesan
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Sir James Black Centre, Dundee, DD1 5EH, United Kingdom
| | - Peter C. Ray
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Sir James Black Centre, Dundee, DD1 5EH, United Kingdom
| | - Tracy Bayliss
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Sir James Black Centre, Dundee, DD1 5EH, United Kingdom
| | - Gareth A. Prosser
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Justin R. Harrison
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Sir James Black Centre, Dundee, DD1 5EH, United Kingdom
| | - Kirsteen Green
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Sir James Black Centre, Dundee, DD1 5EH, United Kingdom
| | - Candice Soares de Melo
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, 7701, South Africa
| | - Tzu-Shean Feng
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, 7701, South Africa
| | - Leslie J. Street
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, 7701, South Africa
| | - Kelly Chibale
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, 7701, South Africa
- Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, 7701, South Africa
- South African Medical Research Council Drug Discovery and Development Research Unit, Department of Chemistry, University of Cape Town, Rondebosch, 7701, South Africa
| | - Digby F. Warner
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, 7701, South Africa
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Rondebosch, 7701, South Africa
| | - Valerie Mizrahi
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, 7701, South Africa
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence for Biomedical TB Research, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Rondebosch, 7701, South Africa
| | - Ola Epemolu
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Sir James Black Centre, Dundee, DD1 5EH, United Kingdom
| | - Paul Scullion
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Sir James Black Centre, Dundee, DD1 5EH, United Kingdom
| | - Lucy Ellis
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Sir James Black Centre, Dundee, DD1 5EH, United Kingdom
| | - Jennifer Riley
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Sir James Black Centre, Dundee, DD1 5EH, United Kingdom
| | - Yoko Shishikura
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Sir James Black Centre, Dundee, DD1 5EH, United Kingdom
| | - Liam Ferguson
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Sir James Black Centre, Dundee, DD1 5EH, United Kingdom
| | - Maria Osuna-Cabello
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Sir James Black Centre, Dundee, DD1 5EH, United Kingdom
| | - Kevin D. Read
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Sir James Black Centre, Dundee, DD1 5EH, United Kingdom
| | - Simon R. Green
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Sir James Black Centre, Dundee, DD1 5EH, United Kingdom
| | - Dirk A. Lamprecht
- Africa Health Research Institute (AHRI), K-RITH Tower Building Level 3, 719 Umbilo Road, Durban, 4001, South Africa
| | - Peter M. Finin
- Africa Health Research Institute (AHRI), K-RITH Tower Building Level 3, 719 Umbilo Road, Durban, 4001, South Africa
| | - Adrie J. C. Steyn
- Africa Health Research Institute (AHRI), K-RITH Tower Building Level 3, 719 Umbilo Road, Durban, 4001, South Africa
- Department of Microbiology, University of Alabama at Birmingham, 1720 Second Avenue South, Birmingham, Alabama 35294-2170, United States
| | - Thomas R. Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Jim Sacchettini
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Kyu Y. Rhee
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medical College, New York, New York 10065, United States
| | - Kriti Arora
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
| | - Clifton E. Barry
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, 7701, South Africa
| | - Paul G. Wyatt
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Sir James Black Centre, Dundee, DD1 5EH, United Kingdom
| | - Helena I. M. Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, United States
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14
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In Silico Discovery of a Substituted 6-Methoxy-quinalidine with Leishmanicidal Activity in Leishmania infantum. Molecules 2018; 23:molecules23040772. [PMID: 29584709 PMCID: PMC6017605 DOI: 10.3390/molecules23040772] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 03/21/2018] [Accepted: 03/26/2018] [Indexed: 11/29/2022] Open
Abstract
There is an urgent need for the discovery of new antileishmanial drugs with a new mechanism of action. Type 2 NADH dehydrogenase from Leishmania infantum (LiNDH2) is an enzyme of the parasite’s respiratory system, which catalyzes the electron transfer from NADH to ubiquinone without coupled proton pumping. In previous studies of the related NADH: ubiquinone oxidoreductase crystal structure from Saccharomyces cerevisiae, two ubiquinone-binding sites (UQI and UQII) were identified and shown to play an important role in the NDH-2-catalyzed oxidoreduction reaction. Based on the available structural data, we developed a three-dimensional structural model of LiNDH2 using homology detection methods and performed an in silico virtual screening campaign to search for potential inhibitors targeting the LiNDH2 ubiquinone-binding site 1–UQI. Selected compounds displaying favorable properties in the computational screening experiments were assayed for inhibitory activity in the structurally similar recombinant NDH-2 from S. aureus and leishmanicidal activity was determined in the wild-type axenic amastigotes and promastigotes of L. infantum. The identified compound, a substituted 6-methoxy-quinalidine, showed promising nanomolar leishmanicidal activity on wild-type axenic promastigotes and amastigotes of L. infantum and the potential for further development.
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15
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Harbut MB, Yang B, Liu R, Yano T, Vilchèze C, Cheng B, Lockner J, Guo H, Yu C, Franzblau SG, Petrassi HM, Jacobs WR, Rubin H, Chatterjee AK, Wang F. Small Molecules Targeting Mycobacterium tuberculosis Type II NADH Dehydrogenase Exhibit Antimycobacterial Activity. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201800260] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | - Baiyuan Yang
- California Institute for Biomedical Research; La Jolla CA 92037 USA
| | - Renhe Liu
- California Institute for Biomedical Research; La Jolla CA 92037 USA
| | - Takahiro Yano
- Department of Medicine; University of Pennsylvania; Philadelphia PA 19104 USA
| | - Catherine Vilchèze
- Howard Hughes Medical Institute; Department of Microbiology and Immunology; Albert Einstein College of Medicine; Bronx NY 10461 USA
| | - Bo Cheng
- California Institute for Biomedical Research; La Jolla CA 92037 USA
| | - Jonathan Lockner
- California Institute for Biomedical Research; La Jolla CA 92037 USA
| | - Hui Guo
- Institute of Biophysics; Chinese Academy of Sciences; Beijing 100101 China
| | - Chenguang Yu
- California Institute for Biomedical Research; La Jolla CA 92037 USA
| | - Scott G Franzblau
- Institute for Tuberculosis Research; University of Illinois at Chicago; Chicago IL 60612 USA
| | - H. Mike Petrassi
- California Institute for Biomedical Research; La Jolla CA 92037 USA
| | - William R. Jacobs
- Howard Hughes Medical Institute; Department of Microbiology and Immunology; Albert Einstein College of Medicine; Bronx NY 10461 USA
| | - Harvey Rubin
- Department of Medicine; University of Pennsylvania; Philadelphia PA 19104 USA
| | | | - Feng Wang
- Institute of Biophysics; Chinese Academy of Sciences; Beijing 100101 China
- California Institute for Biomedical Research; La Jolla CA 92037 USA
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16
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Harbut MB, Yang B, Liu R, Yano T, Vilchèze C, Cheng B, Lockner J, Guo H, Yu C, Franzblau SG, Petrassi HM, Jacobs WR, Rubin H, Chatterjee AK, Wang F. Small Molecules Targeting Mycobacterium tuberculosis Type II NADH Dehydrogenase Exhibit Antimycobacterial Activity. Angew Chem Int Ed Engl 2018; 57:3478-3482. [PMID: 29388301 DOI: 10.1002/anie.201800260] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 01/30/2018] [Indexed: 01/15/2023]
Abstract
The generation of ATP through oxidative phosphorylation is an essential metabolic function for Mycobaterium tuberculosis (Mtb), regardless of the growth environment. The type II NADH dehydrogenase (Ndh-2) is the conduit for electrons into the pathway, and is absent in the mammalian genome, thus making it a potential drug target. Herein, we report the identification of two types of small molecules as selective inhibitors for Ndh-2 through a multicomponent high-throughput screen. Both compounds block ATP synthesis, lead to effects consistent with loss of NADH turnover, and importantly, exert bactericidal activity against Mtb. Extensive medicinal chemistry optimization afforded the best analogue with an MIC of 90 nm against Mtb. Moreover, the two scaffolds have differential inhibitory activities against the two homologous Ndh-2 enzymes in Mtb, which will allow precise control over Ndh-2 function in Mtb to facilitate the assessment of this anti-TB drug target.
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Affiliation(s)
- Michael B Harbut
- California Institute for Biomedical Research, La Jolla, CA, 92037, USA
| | - Baiyuan Yang
- California Institute for Biomedical Research, La Jolla, CA, 92037, USA
| | - Renhe Liu
- California Institute for Biomedical Research, La Jolla, CA, 92037, USA
| | - Takahiro Yano
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Catherine Vilchèze
- Howard Hughes Medical Institute, Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Bo Cheng
- California Institute for Biomedical Research, La Jolla, CA, 92037, USA
| | - Jonathan Lockner
- California Institute for Biomedical Research, La Jolla, CA, 92037, USA
| | - Hui Guo
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chenguang Yu
- California Institute for Biomedical Research, La Jolla, CA, 92037, USA
| | - Scott G Franzblau
- Institute for Tuberculosis Research, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - H Mike Petrassi
- California Institute for Biomedical Research, La Jolla, CA, 92037, USA
| | - William R Jacobs
- Howard Hughes Medical Institute, Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Harvey Rubin
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | | | - Feng Wang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,California Institute for Biomedical Research, La Jolla, CA, 92037, USA
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17
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Yamashita T, Inaoka DK, Shiba T, Oohashi T, Iwata S, Yagi T, Kosaka H, Miyoshi H, Harada S, Kita K, Hirano K. Ubiquinone binding site of yeast NADH dehydrogenase revealed by structures binding novel competitive- and mixed-type inhibitors. Sci Rep 2018; 8:2427. [PMID: 29402945 PMCID: PMC5799168 DOI: 10.1038/s41598-018-20775-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 01/24/2018] [Indexed: 12/20/2022] Open
Abstract
Yeast Ndi1 is a monotopic alternative NADH dehydrogenase. Its crystal structure in complex with the electron acceptor, ubiquinone, has been determined. However, there has been controversy regarding the ubiquinone binding site. To address these points, we identified the first competitive inhibitor of Ndi1, stigmatellin, along with new mixed-type inhibitors, AC0-12 and myxothiazol, and thereby determined the crystal structures of Ndi1 in complexes with the inhibitors. Two separate binding sites of stigmatellin, STG-1 and STG-2, were observed. The electron density at STG-1, located at the vicinity of the FAD cofactor, further demonstrated two binding modes: STG-1a and STG-1b. AC0-12 and myxothiazol are also located at the vicinity of FAD. The comparison of the binding modes among stigmatellin at STG-1, AC0-12, and myxothiazol revealed a unique position for the aliphatic tail of stigmatellin at STG-1a. Mutations of amino acid residues that interact with this aliphatic tail at STG-1a reduced the affinity of Ndi1 for ubiquinone. In conclusion, the position of the aliphatic tail of stigmatellin at STG-1a provides a structural basis for its competitive inhibition of Ndi1. The inherent binding site of ubiquinone is suggested to overlap with STG-1a that is distinct from the binding site for NADH.
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Affiliation(s)
- Tetsuo Yamashita
- Department of Cardiovascular Physiology, Faculty of Medicine, Kagawa University, Kita-gun, Kagawa, 761-0793, Japan.
| | - Daniel Ken Inaoka
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
- School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4, Sakamoto, Nagasaki, 852-8523, Japan
| | - Tomoo Shiba
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto, 606-8585, Japan
| | - Takumi Oohashi
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - So Iwata
- Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College, London, SW7 2AZ, UK
- Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Didcot, Oxfordshire, OX11 0DE, UK
- Japan Science and Technology Agency, Exploratory Research for Advanced Technology, Human Receptor Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-Ku, Kyoto, 606-8501, Japan
- Systems and Structural Biology Centre, RIKEN, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Takao Yagi
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Hiroaki Kosaka
- Department of Cardiovascular Physiology, Faculty of Medicine, Kagawa University, Kita-gun, Kagawa, 761-0793, Japan
- Osaka Jikei College, 1-2-8 Miyahara, Yodogawa-Ku, Osaka, 532-0003, Japan
| | - Hideto Miyoshi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Shigeharu Harada
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto, 606-8585, Japan.
| | - Kiyoshi Kita
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
- School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4, Sakamoto, Nagasaki, 852-8523, Japan
| | - Katsuya Hirano
- Department of Cardiovascular Physiology, Faculty of Medicine, Kagawa University, Kita-gun, Kagawa, 761-0793, Japan
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18
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Koehn J, Magallanes ES, Peters BJ, Beuning CN, Haase AA, Zhu MJ, Rithner CD, Crick DC, Crans DC. A Synthetic Isoprenoid Lipoquinone, Menaquinone-2, Adopts a Folded Conformation in Solution and at a Model Membrane Interface. J Org Chem 2018; 83:275-288. [PMID: 29168636 PMCID: PMC5759649 DOI: 10.1021/acs.joc.7b02649] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Indexed: 11/29/2022]
Abstract
Menaquinones (naphthoquinones, MK) are isoprenoids that play key roles in the respiratory electron transport system of some prokaryotes by shuttling electrons between membrane-bound protein complexes acting as electron acceptors and donors. Menaquinone-2 (MK-2), a truncated MK, was synthesized, and the studies presented herein characterize the conformational and chemical properties of the hydrophobic MK-2 molecule. Using 2D NMR spectroscopy, we established for the first time that MK-2 has a folded conformation defined by the isoprenyl side-chain folding back over the napthoquinone in a U-shape, which depends on the specific environmental conditions found in different solvents. We used molecular mechanics to illustrate conformations found by the NMR experiments. The measured redox potentials of MK-2 differed in three organic solvents, where MK-2 was most easily reduced in DMSO, which may suggest a combination of solvent effect (presumably in part because of differences in dielectric constants) and/or conformational differences of MK-2 in different organic solvents. Furthermore, MK-2 was found to associate with the interface of model membranes represented by Langmuir phospholipid monolayers and Aerosol-OT (AOT) reverse micelles. MK-2 adopts a slightly different U-shaped conformation within reverse micelles compared to within solution, which is in sharp contrast to the extended conformations illustrated in literature for MKs.
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Affiliation(s)
- Jordan
T. Koehn
- Chemistry
Department, Cell and Molecular Biology Program,
and Microbiology, Immunology,
and Pathology Department, Colorado State
University, Fort Collins, Colorado 80523, United States
| | - Estela S. Magallanes
- Chemistry
Department, Cell and Molecular Biology Program,
and Microbiology, Immunology,
and Pathology Department, Colorado State
University, Fort Collins, Colorado 80523, United States
| | - Benjamin J. Peters
- Chemistry
Department, Cell and Molecular Biology Program,
and Microbiology, Immunology,
and Pathology Department, Colorado State
University, Fort Collins, Colorado 80523, United States
| | - Cheryle N. Beuning
- Chemistry
Department, Cell and Molecular Biology Program,
and Microbiology, Immunology,
and Pathology Department, Colorado State
University, Fort Collins, Colorado 80523, United States
| | - Allison A. Haase
- Chemistry
Department, Cell and Molecular Biology Program,
and Microbiology, Immunology,
and Pathology Department, Colorado State
University, Fort Collins, Colorado 80523, United States
| | - Michelle J. Zhu
- Chemistry
Department, Cell and Molecular Biology Program,
and Microbiology, Immunology,
and Pathology Department, Colorado State
University, Fort Collins, Colorado 80523, United States
| | - Christopher D. Rithner
- Chemistry
Department, Cell and Molecular Biology Program,
and Microbiology, Immunology,
and Pathology Department, Colorado State
University, Fort Collins, Colorado 80523, United States
| | - Dean C. Crick
- Chemistry
Department, Cell and Molecular Biology Program,
and Microbiology, Immunology,
and Pathology Department, Colorado State
University, Fort Collins, Colorado 80523, United States
| | - Debbie C. Crans
- Chemistry
Department, Cell and Molecular Biology Program,
and Microbiology, Immunology,
and Pathology Department, Colorado State
University, Fort Collins, Colorado 80523, United States
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19
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Oxidative Phosphorylation as a Target Space for Tuberculosis: Success, Caution, and Future Directions. Microbiol Spectr 2017; 5. [PMID: 28597820 DOI: 10.1128/microbiolspec.tbtb2-0014-2016] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The emergence and spread of drug-resistant pathogens, and our inability to develop new antimicrobials to combat resistance, have inspired scientists to seek out new targets for drug development. The Mycobacterium tuberculosis complex is a group of obligately aerobic bacteria that have specialized for inhabiting a wide range of intracellular and extracellular environments. Two fundamental features in this adaptation are the flexible utilization of energy sources and continued metabolism in the absence of growth. M. tuberculosis is an obligately aerobic heterotroph that depends on oxidative phosphorylation for growth and survival. However, several studies are redefining the metabolic breadth of the genus. Alternative electron donors and acceptors may provide the maintenance energy for the pathogen to maintain viability in hypoxic, nonreplicating states relevant to latent infection. This hidden metabolic flexibility may ultimately decrease the efficacy of drugs targeted against primary dehydrogenases and terminal oxidases. However, it may also open up opportunities to develop novel antimycobacterials targeting persister cells. In this review, we discuss the progress in understanding the role of energetic targets in mycobacterial physiology and pathogenesis and the opportunities for drug discovery.
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20
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Korkegian A, O'Malley T, Xia Y, Zhou Y, Carter DS, Sunde B, Flint L, Thompson D, Ioerger TR, Sacchettini J, Alley MRK, Parish T. The 7-phenyl benzoxaborole series is active against Mycobacterium tuberculosis. Tuberculosis (Edinb) 2017. [PMID: 29523334 PMCID: PMC5854369 DOI: 10.1016/j.tube.2017.11.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We identified a series of novel 7-phenyl benzoxaborole compounds with activity against Mycobacterium tuberculosis. Compounds had a range of activity with inhibitory concentrations (IC90) as low as 5.1 μM and no cytotoxicity against eukaryotic cells (IC50 > 50 μM). Compounds were active against intracellular mycobacteria cultured in THP-1 macrophages. We isolated and characterized resistant mutants with mutations in NADH dehydrogenase (Ndh) or the regulatory protein Mce3R. Mutations suggest that Ndh may be the target of this series.
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Affiliation(s)
- Aaron Korkegian
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA
| | - Theresa O'Malley
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA
| | - Yi Xia
- Anacor Pharmaceuticals, Palo Alto, CA, USA
| | | | | | - Bjorn Sunde
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA
| | - Lindsay Flint
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA
| | - Dean Thompson
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA
| | | | | | | | - Tanya Parish
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA.
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21
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Sellamuthu S, Singh M, Kumar A, Singh SK. Type-II NADH Dehydrogenase (NDH-2): a promising therapeutic target for antitubercular and antibacterial drug discovery. Expert Opin Ther Targets 2017; 21:559-570. [PMID: 28472892 DOI: 10.1080/14728222.2017.1327577] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Tuberculosis (TB) is highly dangerous due to the development of resistance to first-line drugs. Moreover, Mycobacterium tuberculosis (Mtb) has also developed resistance to newly approved antitubercular drug bedaquiline. This necessitates the search for drugs acting on newer molecular targets. The energy metabolism of mycobacteria is the prime focus for the discovery of novel antitubercular drugs. Targeting type-2 NADH dehydrogenase (NDH-2) involved in the production of respiratory ATP could, therefore, be effective in treating the disease. Areas covered: This review describes the energetics of mycobacteria and the role of NDH-2 in ATP synthesis. Special attention has been given for genetic and chemical validations of NDH-2 as a molecular target. The reported kinetics and crystal structures of NDH-2 have been given in detail for better understanding of the enzyme. Expert opinion: NDH-2 is an essential enzyme for ATP synthesis and has a potential role in dormancy and persistence of Mtb. The human counterpart lacks this enzyme and hence NDH-2 inhibitors could have more clinical importance. Phenothiazines are potent inhibitor of NDH-2 and are effective against both drug-susceptible and drug-resistant Mtb. Thus, it is highly desirable to optimize phenothiazine class of compounds for the development of next generation anti-TB drugs.
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Affiliation(s)
- Satheeshkumar Sellamuthu
- a Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutics , Indian Institute of Technology (Banaras Hindu University) , Varanasi , India
| | - Meenakshi Singh
- a Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutics , Indian Institute of Technology (Banaras Hindu University) , Varanasi , India
| | - Ashok Kumar
- a Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutics , Indian Institute of Technology (Banaras Hindu University) , Varanasi , India
| | - Sushil Kumar Singh
- a Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutics , Indian Institute of Technology (Banaras Hindu University) , Varanasi , India
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22
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Yang Y, Yu Y, Li X, Li J, Wu Y, Yu J, Ge J, Huang Z, Jiang L, Rao Y, Yang M. Target Elucidation by Cocrystal Structures of NADH-Ubiquinone Oxidoreductase of Plasmodium falciparum (PfNDH2) with Small Molecule To Eliminate Drug-Resistant Malaria. J Med Chem 2017; 60:1994-2005. [DOI: 10.1021/acs.jmedchem.6b01733] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Yiqing Yang
- MOE
Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
- MOE
Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life
Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - You Yu
- MOE
Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life
Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaolu Li
- Department
of Biochemistry and Molecular Biology, State Key Laboratory of Medical
Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
| | - Jing Li
- MOE
Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life
Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yue Wu
- MOE
Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Jie Yu
- MOE
Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life
Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jingpeng Ge
- MOE
Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life
Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhenghui Huang
- Institut Pasteur of Shanghai, CAS Key Laboratory of Molecular Virology and Immunology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lubin Jiang
- Institut Pasteur of Shanghai, CAS Key Laboratory of Molecular Virology and Immunology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yu Rao
- MOE
Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Maojun Yang
- MOE
Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life
Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
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23
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The mechanism of catalysis by type-II NADH:quinone oxidoreductases. Sci Rep 2017; 7:40165. [PMID: 28067272 PMCID: PMC5220320 DOI: 10.1038/srep40165] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 12/01/2016] [Indexed: 11/08/2022] Open
Abstract
Type II NADH:quinone oxidoreductase (NDH-2) is central to the respiratory chains of many organisms. It is not present in mammals so may be exploited as an antimicrobial drug target or used as a substitute for dysfunctional respiratory complex I in neuromuscular disorders. NDH-2 is a single-subunit monotopic membrane protein with just a flavin cofactor, yet no consensus exists on its mechanism. Here, we use steady-state and pre-steady-state kinetics combined with mutagenesis and structural studies to determine the mechanism of NDH-2 from Caldalkalibacillus thermarum. We show that the two substrate reactions occur independently, at different sites, and regardless of the occupancy of the partner site. We conclude that the reaction pathway is determined stochastically, by the substrate/product concentrations and dissociation constants, and can follow either a ping-pong or ternary mechanism. This mechanistic versatility provides a unified explanation for all extant data and a new foundation for the development of therapeutic strategies.
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24
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Marreiros BC, Sena FV, Sousa FM, Batista AP, Pereira MM. Type II NADH:quinone oxidoreductase family: phylogenetic distribution, structural diversity and evolutionary divergences. Environ Microbiol 2016; 18:4697-4709. [PMID: 27105286 DOI: 10.1111/1462-2920.13352] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2016] [Indexed: 12/17/2022]
Abstract
Type II NADH:quinone oxidoreductases (NDH-2s) are membrane proteins, crucial for the catabolic metabolism, because they contribute to the maintenance of the NADH/NAD+ balance. In several pathogenic bacteria and protists, NDH-2s are the only enzymes performing respiratory NADH:quinone oxidoreductase activity. For this reason and for being considered absent in mammals, NDH-2s were proposed as suitable targets for novel antimicrobial therapies. We selected all sequences of genes encoding NDH-2s from fully sequenced genomes present in the KEGG database. These genes were present in 61% of the 1805 species belonging to Eukarya (83%), Bacteria (60%) and Archaea (32%). Notably sequences from mammal species including humans were retrieved in our selection as NDH-2s. The data obtained and the already available information allowed systematizing several properties of NDH-2s: (i) the existence of additional sequence motifs with putative regulatory functions, (ii) specificity towards NADH or NADPH and (iii) the type of quinone binding motif. We observed that NDH-2 family distribution is not congruent with the taxonomic tree, suggesting different origins for the eukaryotic sequences and possible lateral gene transfer among prokaryotes. We note the absence of genes coding for NDH-2 in anaerobic phyla and the presence of multiple copies in several genomes, specifically in cyanobacteria. These observations inspired us to propose a metabolic hypothesis for the appearance of NDH-2s.
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Affiliation(s)
- Bruno C Marreiros
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Filipa V Sena
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Filipe M Sousa
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Ana P Batista
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
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25
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Salewski J, Batista AP, Sena FV, Millo D, Zebger I, Pereira MM, Hildebrandt P. Substrate-Protein Interactions of Type II NADH:Quinone Oxidoreductase from Escherichia coli. Biochemistry 2016; 55:2722-34. [PMID: 27109164 DOI: 10.1021/acs.biochem.6b00070] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Type II NADH:quinone oxidoreductases (NDH-2s) are membrane proteins involved in respiratory chains and responsible for the maintenance of NADH/NAD(+) balance in cells. NDH-2s are the only enzymes with NADH dehydrogenase activity present in the respiratory chain of many pathogens, and thus, they were proposed as suitable targets for antimicrobial therapies. In addition, NDH-2s were also considered key players for the treatment of complex I-related neurodegenerative disorders. In this work, we explored substrate-protein interaction in NDH-2 from Escherichia coli (EcNDH-2) combining surface-enhanced infrared absorption spectroscopic studies with electrochemical experiments, fluorescence spectroscopy assays, and quantum chemical calculations. Because of the specific stabilization of substrate complexes of EcNDH-2 immobilized on electrodes, it was possible to demonstrate the presence of two distinct substrate binding sites for NADH and the quinone and to identify a bound semiprotonated quinol as a catalytic intermediate.
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Affiliation(s)
- Johannes Salewski
- Technische Universität Berlin , Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Ana P Batista
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa , Av. da República EAN, P-2780-157 Oeiras, Portugal
| | - Filipa V Sena
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa , Av. da República EAN, P-2780-157 Oeiras, Portugal
| | - Diego Millo
- Biomolecular Spectroscopy/LaserLaB Amsterdam, Vrije Universiteit Amsterdam , De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Ingo Zebger
- Technische Universität Berlin , Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa , Av. da República EAN, P-2780-157 Oeiras, Portugal
| | - Peter Hildebrandt
- Technische Universität Berlin , Institut für Chemie, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
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26
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Sena FV, Batista AP, Catarino T, Brito JA, Archer M, Viertler M, Madl T, Cabrita EJ, Pereira MM. Type-II NADH:quinone oxidoreductase from Staphylococcus aureus has two distinct binding sites and is rate limited by quinone reduction. Mol Microbiol 2015; 98:272-88. [PMID: 26172206 DOI: 10.1111/mmi.13120] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2015] [Indexed: 01/02/2023]
Abstract
A prerequisite for any rational drug design strategy is understanding the mode of protein-ligand interaction. This motivated us to explore protein-substrate interaction in Type-II NADH:quinone oxidoreductase (NDH-2) from Staphylococcus aureus, a worldwide problem in clinical medicine due to its multiple drug resistant forms. NDHs-2 are involved in respiratory chains and recognized as suitable targets for novel antimicrobial therapies, as these are the only enzymes with NADH:quinone oxidoreductase activity expressed in many pathogenic organisms. We obtained crystal and solution structures of NDH-2 from S. aureus, showing that it is a dimer in solution. We report fast kinetic analyses of the protein and detected a charge-transfer complex formed between NAD(+) and the reduced flavin, which is dissociated by the quinone. We observed that the quinone reduction is the rate limiting step and also the only half-reaction affected by the presence of HQNO, an inhibitor. We analyzed protein-substrate interactions by fluorescence and STD-NMR spectroscopies, which indicate that NADH and the quinone bind to different sites. In summary, our combined results show the presence of distinct binding sites for the two substrates, identified quinone reduction as the rate limiting step and indicate the establishment of a NAD(+)-protein complex, which is released by the quinone.
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Affiliation(s)
- Filipa V Sena
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Ana P Batista
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Teresa Catarino
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal.,Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - José A Brito
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Margarida Archer
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
| | - Martin Viertler
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry Technische Universität München, Lichtenbergstr.4, 85747, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München Neuherberg and Biomolecular NMR- Spectroscopy, Medical University of Graz, 8010, Graz, Austria.,Institute of Molecular Biology & Biochemistry, Center of Molecular Medicine, Medical University of Graz, 8010, Graz, Austria
| | - Tobias Madl
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry Technische Universität München, Lichtenbergstr.4, 85747, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München Neuherberg and Biomolecular NMR- Spectroscopy, Medical University of Graz, 8010, Graz, Austria.,Institute of Molecular Biology & Biochemistry, Center of Molecular Medicine, Medical University of Graz, 8010, Graz, Austria
| | - Eurico J Cabrita
- REQUIMTE, UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Manuela M Pereira
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Av. da República EAN, 2780-157, Oeiras, Portugal
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27
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Dunn EA, Roxburgh M, Larsen L, Smith RAJ, McLellan AD, Heikal A, Murphy MP, Cook GM. Incorporation of triphenylphosphonium functionality improves the inhibitory properties of phenothiazine derivatives in Mycobacterium tuberculosis. Bioorg Med Chem 2014; 22:5320-8. [PMID: 25150092 DOI: 10.1016/j.bmc.2014.07.050] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 07/21/2014] [Accepted: 07/30/2014] [Indexed: 10/24/2022]
Abstract
Tuberculosis (TB) is a difficult to treat disease caused by the bacterium Mycobacterium tuberculosis. The need for improved therapies is required to kill different M. tuberculosis populations present during infection and to kill drug resistant strains. Protein complexes associated with energy generation, required for the survival of all M. tuberculosis populations, have shown promise as targets for novel therapies (e.g., phenothiazines that target type II NADH dehydrogenase (NDH-2) in the electron transport chain). However, the low efficacy of these compounds and their off-target effects has made the development of phenothiazines as a therapeutic agent for TB limited. This study reports that a series of alkyltriphenylphosphonium (alkylTPP) cations, a known intracellular delivery functionality, improves the localization and effective concentration of phenothiazines at the mycobacterial membrane. AlkylTPP cations were shown to accumulate at biological membranes in a range of bacteria and lipophilicity was revealed as an important feature of the structure-function relationship. Incorporation of the alkylTPP cationic function significantly increased the concentration and potency of a series of phenothiazine derivatives at the mycobacterial membrane (the site of NDH-2), where the lead compound 3a showed inhibition of M. tuberculosis growth at 0.5μg/mL. Compound 3a was shown to act in a similar manner to that previously published for other active phenothiazines by targeting energetic processes (i.e., NADH oxidation and oxygen consumption), occurring in the mycobacterial membrane. This shows the enormous potential of alkylTPP cations to improve the delivery and therefore efficacy of bioactive agents targeting oxidative phosphorylation in the mycobacterial membrane.
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Affiliation(s)
- Elyse A Dunn
- Department of Microbiology & Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Marina Roxburgh
- Department of Chemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Lesley Larsen
- Department of Chemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Robin A J Smith
- Department of Chemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Alexander D McLellan
- Department of Microbiology & Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Adam Heikal
- Department of Microbiology & Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Michael P Murphy
- MRC Mitochondrial Biology Unit, Hills Road, Cambridge CB2 0XY, UK
| | - Gregory M Cook
- Department of Microbiology & Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
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