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Ward K, Williams APL, Blair CA, Chatterjee AM, Karthikeyan A, Roper AS, Kellogg CN, Steed PR, Wolfe AL. Amine Basicity of Quinoline ATP Synthase Inhibitors Drives Antibacterial Activity against Pseudomonas aeruginosa. ACS Med Chem Lett 2024; 15:149-155. [PMID: 38229742 PMCID: PMC10789121 DOI: 10.1021/acsmedchemlett.3c00480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 01/18/2024] Open
Abstract
Pseudomonas aeruginosa (PA), a Gram-negative pathogen, is a common cause of nosocomial infections, especially in immunocompromised and cystic fibrosis patients. PA is intrinsically resistant to many currently prescribed antibiotics due to its tightly packed, anionic lipopolysaccharide outer membrane, efflux pumps, and ability to form biofilms. PA can acquire additional resistance through mutation and horizontal gene transfer. PA ATP synthase is an attractive target for antibiotic development because it is essential for cell survival even under fermentation conditions. Previously, we developed two lead quinoline compounds that were capable of selectively inhibiting PA ATP synthase and acting as antibacterial agents against multidrug-resistant PA. Herein we conduct a structure-activity relationship analysis of the lead compounds through the synthesis and evaluation of 18 quinoline derivatives. These compounds function as new antibacterial agents while providing insight into the balance of physical properties needed to promote cellular entry while maintaining PA ATP synthase inhibition.
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Affiliation(s)
- Katie
T. Ward
- Department of Chemistry and
Biochemistry, University of North Carolina
Asheville, One University Heights, Asheville, North Carolina 28804, United States
| | | | | | | | | | | | | | - P. Ryan Steed
- Department of Chemistry and
Biochemistry, University of North Carolina
Asheville, One University Heights, Asheville, North Carolina 28804, United States
| | - Amanda L. Wolfe
- Department of Chemistry and
Biochemistry, University of North Carolina
Asheville, One University Heights, Asheville, North Carolina 28804, United States
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2
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Fraunfelter V, Pugh BA, Williams APL, Ward KT, Jackson DO, Austin M, Ciprich JF, Dippy L, Dunford J, Edwards GN, Glass E, Handy KM, Kellogg CN, Llewellyn K, Nyberg KQ, Shepard SJ, Thomas C, Wolfe AL, Steed PR. Quinoline Compounds Targeting the c-Ring of ATP Synthase Inhibit Drug-Resistant Pseudomonas aeruginosa. ACS Infect Dis 2023; 9:2448-2456. [PMID: 37922420 PMCID: PMC10714390 DOI: 10.1021/acsinfecdis.3c00317] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 11/05/2023]
Abstract
Pseudomonas aeruginosa (PA) is a Gram-negative, biofilm-forming bacterium and an opportunistic pathogen. The growing drug resistance of PA is a serious threat that necessitates the discovery of novel antibiotics, ideally with previously underexplored mechanisms of action. Due to their central role in cell metabolism, bacterial bioenergetic processes are of increasing interest as drug targets, especially with the success of the ATP synthase inhibitor bedaquiline to treat drug-resistant tuberculosis. Like Mycobacterium tuberculosis, PA requires F1Fo ATP synthase for growth, even under anaerobic conditions, making the PA ATP synthase an ideal drug target for the treatment of drug-resistant infection. In previous work, we conducted an initial screen for quinoline compounds that inhibit ATP synthesis activity in PA. In the present study, we report additional quinoline derivatives, including one with increased potency against PA ATP synthase in vitro and antibacterial activity against drug-resistant PA. Moreover, by expressing the PA ATP synthase in Escherichia coli, we show that mutations in the H+ binding site on the membrane-embedded rotor ring alter inhibition by the reported quinoline compounds. Identification of a potent inhibitor and its probable binding site on ATP synthase enables further development of promising quinoline derivatives into a viable treatment for drug-resistant PA infection.
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Affiliation(s)
- Vesper
M. Fraunfelter
- Department of Chemistry and
Biochemistry, University of North Carolina
Asheville, One University Heights, Asheville, North Carolina 28804, United States
| | - Bryce A. Pugh
- Department of Chemistry and
Biochemistry, University of North Carolina
Asheville, One University Heights, Asheville, North Carolina 28804, United States
| | - Alexander P. L. Williams
- Department of Chemistry and
Biochemistry, University of North Carolina
Asheville, One University Heights, Asheville, North Carolina 28804, United States
| | - Katie T. Ward
- Department of Chemistry and
Biochemistry, University of North Carolina
Asheville, One University Heights, Asheville, North Carolina 28804, United States
| | - Dietrich O. Jackson
- Department of Chemistry and
Biochemistry, University of North Carolina
Asheville, One University Heights, Asheville, North Carolina 28804, United States
| | - Molly Austin
- Department of Chemistry and
Biochemistry, University of North Carolina
Asheville, One University Heights, Asheville, North Carolina 28804, United States
| | - John F. Ciprich
- Department of Chemistry and
Biochemistry, University of North Carolina
Asheville, One University Heights, Asheville, North Carolina 28804, United States
| | - Lorelei Dippy
- Department of Chemistry and
Biochemistry, University of North Carolina
Asheville, One University Heights, Asheville, North Carolina 28804, United States
| | - Jason Dunford
- Department of Chemistry and
Biochemistry, University of North Carolina
Asheville, One University Heights, Asheville, North Carolina 28804, United States
| | - G. Nathaniel Edwards
- Department of Chemistry and
Biochemistry, University of North Carolina
Asheville, One University Heights, Asheville, North Carolina 28804, United States
| | - Evan Glass
- Department of Chemistry and
Biochemistry, University of North Carolina
Asheville, One University Heights, Asheville, North Carolina 28804, United States
| | - Kyle M. Handy
- Department of Chemistry and
Biochemistry, University of North Carolina
Asheville, One University Heights, Asheville, North Carolina 28804, United States
| | - Casey N. Kellogg
- Department of Chemistry and
Biochemistry, University of North Carolina
Asheville, One University Heights, Asheville, North Carolina 28804, United States
| | - Kaitlyn Llewellyn
- Department of Chemistry and
Biochemistry, University of North Carolina
Asheville, One University Heights, Asheville, North Carolina 28804, United States
| | - K. Quinn Nyberg
- Department of Chemistry and
Biochemistry, University of North Carolina
Asheville, One University Heights, Asheville, North Carolina 28804, United States
| | - Sam J. Shepard
- Department of Chemistry and
Biochemistry, University of North Carolina
Asheville, One University Heights, Asheville, North Carolina 28804, United States
| | - Casey Thomas
- Department of Chemistry and
Biochemistry, University of North Carolina
Asheville, One University Heights, Asheville, North Carolina 28804, United States
| | - Amanda L. Wolfe
- Department of Chemistry and
Biochemistry, University of North Carolina
Asheville, One University Heights, Asheville, North Carolina 28804, United States
| | - P. Ryan Steed
- Department of Chemistry and
Biochemistry, University of North Carolina
Asheville, One University Heights, Asheville, North Carolina 28804, United States
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Wolfe AL, Steed PR. Generating Publishable Data from Course-Based Undergraduate Research Experiences in Chemistry. JOURNAL OF CHEMICAL EDUCATION 2023; 100:3419-3424. [PMID: 37720522 PMCID: PMC10501119 DOI: 10.1021/acs.jchemed.3c00354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/21/2023] [Indexed: 09/19/2023]
Abstract
Embedding Course-based Undergraduate Research Experiences (CUREs) into chemistry curricula has become a best practice due to the overwhelming evidence that these experiences deepen students' content comprehension, improve students' problem-solving skills, and increase retention within the major. For these reasons, faculty are often encouraged to develop CUREs for their courses, which typically take a substantial amount of effort and administrative/financial support. To justify these efforts, one of the most cited benefits of CURE development for faculty specifically is that they can pilot research projects and publish data produced during CUREs in scientific publications. However, there is less evidence in the literature that these benefits commonly occur. Based on direct upper-level, interdisciplinary CURE development experience and a national survey of faculty across institution types, it is clear that translating CURE data into publishable science is quite challenging due to several common barriers. Barriers identified include the need for follow up data that must be generated by either the faculty or a research student, the lack of reproducibility of data generated by novice students, and the lack of faculty time to write the manuscripts. Additionally, institution type (private vs public non-PhD granting; non-PhD granting vs PhD granting), faculty rank, and CURE level (lower vs upper-level courses), among other factors, impacted the likelihood of publication of CURE data. Based on these results and experiences, best practices for maximizing positive outcomes for both students and faculty with regard to CURE design and implementation have been developed.
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Affiliation(s)
- Amanda L. Wolfe
- Department of Chemistry and
Biochemistry, University of North Carolina
Asheville, Asheville, North Carolina 28804, United States
| | - P. Ryan Steed
- Department of Chemistry and
Biochemistry, University of North Carolina
Asheville, Asheville, North Carolina 28804, United States
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Mohammed A, Aabed K, Benabdelkamel H, Shami A, Alotaibi MO, Alanazi M, Alfadda AA, Rahman I. Proteomic Profiling Reveals Cytotoxic Mechanisms of Action and Adaptive Mechanisms of Resistance in Porphyromonas gingivalis: Treatment with Juglans regia and Melaleuca alternifolia. ACS OMEGA 2023; 8:12980-12991. [PMID: 37065043 PMCID: PMC10099446 DOI: 10.1021/acsomega.3c00168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/08/2023] [Indexed: 06/19/2023]
Abstract
The increasing trend in the rise of antibiotic-resistant bacteria pushes research to discover new efficacious antibacterial agents from natural and synthetic sources. Porphyromonas gingivalis is a well-known bacterium commonly known for causing periodontal disease, and it is associated with the pathogenesis of life-changing systemic conditions such as Alzheimer's. Proteomic research can be utilized to test new antibacterial drugs and understand the adaptive resistive mechanisms of bacteria; hence, it is important in the drug discovery process. The current study focuses on identifying the antibacterial effects of Juglans regia (JR) and Melaleuca alternifolia (MA) on P. gingivalis and uses proteomics to identify modes of action while exploring its adaptive mechanisms. JR and MA extracts were tested for antibacterial efficacy using the agar well diffusion assay. A proteomic study was conducted identifying upregulated and downregulated proteins compared to control by 2D-DIGE analysis, and proteins were identified using MADLI-TOF/MS. The bacterial inhibition for JR was 20.14 ± 0.2, and that for MA was 19.72 ± 0.5 mm. Out of 88 differentially expressed proteins, there were 17 common differentially expressed proteins: 10 were upregulated and 7 were downregulated in both treatments. Among the upregulated proteins were Arginine-tRNA ligase, ATP-dependent Clp protease proteolytic, and flavodoxins. In contrast, down-regulated proteins were ATP synthase subunit alpha and quinone, among others, which are known antibacterial targets. STRING analysis indicated a strong network of interactions between differentially expressed proteins, mainly involved in protein translation, post-translational modification, energy production, metabolic pathways, and protein repair and degradation. Both extracts were equi-efficacious at inhibiting P. gingivalis and displayed some overlapping proteomic profiles. However, the MR extract had a greater fold change in its profile than the JA extract. Downregulated proteins indicated similarity in the mode of action, and upregulated proteins appear to be related to adaptive mechanisms important in promoting repair, growth, survival, virulence, and resistance. Hence, both extracts may be useful in preventing P. gingivalis-associated conditions. Furthermore, our results may be helpful to researchers in identifying new antibiotics which may offset these mechanisms of resistance.
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Affiliation(s)
- Afrah
E. Mohammed
- Department
of Biology, College of Science, Princess
Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Kawther Aabed
- Department
of Biology, College of Science, Princess
Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Hicham Benabdelkamel
- Proteomics
Resource Unit, Obesity Research Center, College of Medicine, King Saud University, P.O. Box 2925 (98), Riyadh 11461, Saudi Arabia
| | - Ashwag Shami
- Department
of Biology, College of Science, Princess
Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Modhi O. Alotaibi
- Department
of Biology, College of Science, Princess
Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Mona Alanazi
- Department
of Biology, College of Science, Princess
Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Assim A. Alfadda
- Proteomics
Resource Unit, Obesity Research Center, College of Medicine, King Saud University, P.O. Box 2925 (98), Riyadh 11461, Saudi Arabia
- Department
of Medicine, College of Medicine and King Saud Medical City, King Saud University,
P.O. Box 2925 (98), Riyadh 11461, Saudi Arabia
| | - Ishrat Rahman
- Department
of Basic Dental Sciences, College of Dentistry, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
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5
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Shrestha RK, Founds MW, Shepard SJ, Rothrock MM, Defnet AE, Steed PR. Mutational analysis of a conserved positive charge in the c-ring of E. coli ATP synthase. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148962. [PMID: 36822493 PMCID: PMC9998364 DOI: 10.1016/j.bbabio.2023.148962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 01/25/2023] [Accepted: 02/13/2023] [Indexed: 02/25/2023]
Abstract
F1Fo ATP synthase is a ubiquitous molecular motor that utilizes a rotary mechanism to synthesize adenosine triphosphate (ATP), the fundamental energy currency of life. The membrane-embedded Fo motor converts the electrochemical gradient of protons into rotation, which is then used to drive the conformational changes in the soluble F1 motor that catalyze ATP synthesis. In E. coli, the Fo motor is composed of a c10 ring (rotor) alongside subunit a (stator), which together provide two aqueous half channels that facilitate proton translocation. Previous work has suggested that Arg50 and Thr51 on the cytoplasmic side of each subunit c are involved in the proton translocation process, and positive charge is conserved in this region of subunit c. To further investigate the role of these residues and the chemical requirements for activity at these positions, we generated 13 substitution mutants and assayed their in vitro ATP synthesis, H+ pumping, and passive H+ permeability activities, as well as the ability of mutants to carry out oxidative phosphorylation in vivo. While polar and hydrophobic mutations were generally tolerated in either position, introduction of negative charge or removal of polarity caused a substantial defect. We discuss the possible effects of altered electrostatics on the interaction between the rotor and stator, water structure in the aqueous channel, and interaction of the rotor with cardiolipin.
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Affiliation(s)
- Rashmi K Shrestha
- Department of Chemistry & Biochemistry, University of North Carolina Asheville, One University Heights, Asheville, NC 28804, United States of America
| | - Michael W Founds
- Department of Chemistry & Biochemistry, University of North Carolina Asheville, One University Heights, Asheville, NC 28804, United States of America
| | - Sam J Shepard
- Department of Chemistry & Biochemistry, University of North Carolina Asheville, One University Heights, Asheville, NC 28804, United States of America
| | - Mallory M Rothrock
- Department of Chemistry & Biochemistry, University of North Carolina Asheville, One University Heights, Asheville, NC 28804, United States of America
| | - Amy E Defnet
- Department of Chemistry & Biochemistry, University of North Carolina Asheville, One University Heights, Asheville, NC 28804, United States of America
| | - P Ryan Steed
- Department of Chemistry & Biochemistry, University of North Carolina Asheville, One University Heights, Asheville, NC 28804, United States of America.
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