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Computational Design of Inhibitors Targeting the Catalytic β Subunit of Escherichia coli FOF1-ATP Synthase. Antibiotics (Basel) 2022; 11:antibiotics11050557. [PMID: 35625201 PMCID: PMC9138118 DOI: 10.3390/antibiotics11050557] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/22/2022] [Accepted: 03/25/2022] [Indexed: 01/27/2023] Open
Abstract
With the uncontrolled growth of multidrug-resistant bacteria, there is an urgent need to search for new therapeutic targets, to develop drugs with novel modes of bactericidal action. FoF1-ATP synthase plays a crucial role in bacterial bioenergetic processes, and it has emerged as an attractive antimicrobial target, validated by the pharmaceutical approval of an inhibitor to treat multidrug-resistant tuberculosis. In this work, we aimed to design, through two types of in silico strategies, new allosteric inhibitors of the ATP synthase, by targeting the catalytic β subunit, a centerpiece in communication between rotor subunits and catalytic sites, to drive the rotary mechanism. As a model system, we used the F1 sector of Escherichia coli, a bacterium included in the priority list of multidrug-resistant pathogens. Drug-like molecules and an IF1-derived peptide, designed through molecular dynamics simulations and sequence mining approaches, respectively, exhibited in vitro micromolar inhibitor potency against F1. An analysis of bacterial and Mammalia sequences of the key structural helix-turn-turn motif of the C-terminal domain of the β subunit revealed highly and moderately conserved positions that could be exploited for the development of new species-specific allosteric inhibitors. To our knowledge, these inhibitors are the first binders computationally designed against the catalytic subunit of FOF1-ATP synthase.
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Li Y, Ma X, Weber J. Interaction between γC87 and γR242 residues participates in energy coupling between catalysis and proton translocation in Escherichia coli ATP synthase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:679-687. [PMID: 31251901 DOI: 10.1016/j.bbabio.2019.06.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 06/19/2019] [Accepted: 06/22/2019] [Indexed: 11/25/2022]
Abstract
Functioning as a nanomotor, ATP synthase plays a vital role in the cellular energy metabolism. Interactions at the rotor and stator interface are critical to the energy transmission in ATP synthase. From mutational studies, we found that the γC87K mutation impairs energy coupling between proton translocation and nucleotide synthesis/hydrolysis. An additional glutamine mutation at γR242 (γR242Q) can restore efficient energy coupling to the γC87K mutant. Arrhenius plots and molecular dynamics simulations suggest that an extra hydrogen bond could form between the side chains of γC87K and βTPE381 in the γC87K mutant, thus impeding the free rotation of the rotor complex. In the enzyme with γC87K/γR242Q double mutations, the polar moiety of γR242Q side chain can form a hydrogen bond with γC87K, so that the amine group in the side chain of γC87K will not hydrogen-bond with βE381. As a conclusion, the intra-subunit interaction between positions γC87 and γR242 modulates the energy transmission in ATP synthase. This study should provide more information of residue interactions at the rotor and stator interface in order to further elucidate the energetic mechanism of ATP synthase.
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Affiliation(s)
- Yunxiang Li
- Department of Chemistry and Biochemistry, Texas Woman's University, Denton, TX 76204, USA; Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA.
| | - Xinyou Ma
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Joachim Weber
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA; The Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
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Xiaoyun X, Chaofei H, Weiqi Z, Chen C, Lixia L, Queping L, Cong P, Shuang Z, Juan S, Xiang C. Possible Involvement of F1F0-ATP synthase and Intracellular ATP in Keratinocyte Differentiation in normal skin and skin lesions. Sci Rep 2017; 7:42672. [PMID: 28209970 PMCID: PMC5314331 DOI: 10.1038/srep42672] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 01/11/2017] [Indexed: 12/15/2022] Open
Abstract
The F1F0-ATP synthase, an enzyme complex, is mainly located on the mitochondrial inner membrane or sometimes cytomembrane to generate or hydrolyze ATP, play a role in cell proliferation. This study focused on the role of F1F0-ATP synthase in keratinocyte differentiation, and its relationship with intracellular and extracellular ATP (InATP and ExATP). The F1F0-ATP synthase β subunit (ATP5B) expression in various skin tissues and confluence-dependent HaCaT differentiation models was detected. ATP5B expression increased with keratinocyte and HaCaT cell differentiation in normal skin, some epidermis hyper-proliferative diseases, squamous cell carcinoma, and the HaCaT cell differentiation model. The impact of InATP and ExATP content on HaCaT differentiation was reflected by the expression of the differentiation marker involucrin. Inhibition of F1F0-ATP synthase blocked HaCaT cell differentiation, which was associated with a decrease of InATP content, but not with changes of ExATP. Our results revealed that F1F0-ATP synthase expression is associated with the process of keratinocyte differentiation which may possibly be related to InATP synthesis.
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Affiliation(s)
- Xie Xiaoyun
- Department of Dermatology, XiangYa Hospital, Central South University, Changsha, China.,Department of Rheumatology and Immunology, XiangYa Hospital, Central South University, Changsha, China
| | - Han Chaofei
- Department of Plastic and Reconstructive Surgery, The Third XiangYa Hospital, Central South University, Changsha, China
| | - Zeng Weiqi
- Department of Dermatology, XiangYa Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, XiangYa Hospital, Central South University, Changsha, China
| | - Chen Chen
- Department of Dermatology, XiangYa Hospital, Central South University, Changsha, China.,Department of Nephrology, XiangYa Hospital, Central South University, Changsha, China
| | - Lu Lixia
- Department of Dermatology, XiangYa Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, XiangYa Hospital, Central South University, Changsha, China
| | - Liu Queping
- Department of Dermatology, XiangYa Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, XiangYa Hospital, Central South University, Changsha, China
| | - Peng Cong
- Department of Dermatology, XiangYa Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, XiangYa Hospital, Central South University, Changsha, China
| | - Zhao Shuang
- Department of Dermatology, XiangYa Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, XiangYa Hospital, Central South University, Changsha, China
| | - Su Juan
- Department of Dermatology, XiangYa Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, XiangYa Hospital, Central South University, Changsha, China
| | - Chen Xiang
- Department of Dermatology, XiangYa Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Skin Cancer and Psoriasis, XiangYa Hospital, Central South University, Changsha, China
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