51
|
Acharya A, Prajapati JD, Kleinekathöfer U. Atomistic Simulation of Molecules Interacting with Biological Nanopores: From Current Understanding to Future Directions. J Phys Chem B 2022; 126:3995-4008. [PMID: 35616602 DOI: 10.1021/acs.jpcb.2c01173] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biological nanopores have been at the focus of numerous studies due to their role in many biological processes as well as their (prospective) technological applications. Among many other topics, recent studies on nanopores have addressed two key areas: antibiotic permeation through bacterial channels and sensing of analytes. Although the two areas are quite far apart in terms of their objectives, in both cases atomistic simulations attempt to understand the solute dynamics and the solute-protein interactions within the channel lumen. While decades of studies on various channels have culminated in an improved understanding of the key molecular factors and led to practical applications in some cases, successful utilization is limited. In this Perspective we summarize recent progress in understanding key issues in molecular simulations of antibiotic translocation and in the development of nanopore sensors. Moreover, we comment on possible advancements in computational algorithms that can potentially resolve some of the issues.
Collapse
Affiliation(s)
- Abhishek Acharya
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
| | | | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
| |
Collapse
|
52
|
Leus IV, Weeks JW, Bonifay V, Shen Y, Yang L, Cooper CJ, Nash D, Duerfeldt AS, Smith JC, Parks JM, Rybenkov VV, Zgurskaya HI. Property space mapping of Pseudomonas aeruginosa permeability to small molecules. Sci Rep 2022; 12:8220. [PMID: 35581346 PMCID: PMC9114115 DOI: 10.1038/s41598-022-12376-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/10/2022] [Indexed: 02/03/2023] Open
Abstract
Two membrane cell envelopes act as selective permeability barriers in Gram-negative bacteria, protecting cells against antibiotics and other small molecules. Significant efforts are being directed toward understanding how small molecules permeate these barriers. In this study, we developed an approach to analyze the permeation of compounds into Gram-negative bacteria and applied it to Pseudomonas aeruginosa, an important human pathogen notorious for resistance to multiple antibiotics. The approach uses mass spectrometric measurements of accumulation of a library of structurally diverse compounds in four isogenic strains of P. aeruginosa with varied permeability barriers. We further developed a machine learning algorithm that generates a deterministic classification model with minimal synonymity between the descriptors. This model predicted good permeators into P. aeruginosa with an accuracy of 89% and precision above 58%. The good permeators are broadly distributed in the property space and can be mapped to six distinct regions representing diverse chemical scaffolds. We posit that this approach can be used for more detailed mapping of the property space and for rational design of compounds with high Gram-negative permeability.
Collapse
Affiliation(s)
- Inga V Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Jon W Weeks
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Vincent Bonifay
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Yue Shen
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Liang Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Connor J Cooper
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Dinesh Nash
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Adam S Duerfeldt
- Department of Medicinal Chemistry, University of Minnesota, 717 Delaware St. SE, Minneapolis, MN, 55414, USA
| | - Jeremy C Smith
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Valentin V Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA.
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA.
| |
Collapse
|
53
|
Shi H, Pan X, Wang Y, Wang H, Liu W, Wang L, Chen Z. Restricting Bond Rotations by Ring Fusion: A Novel Molecular Design Strategy to Improve Photodynamic Antibacterial Efficacy of AIE Photosensitizers. ACS APPLIED MATERIALS & INTERFACES 2022; 14:17055-17064. [PMID: 35380770 DOI: 10.1021/acsami.1c24329] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In recent years, aggregation-induced emission photosensitizers (AIE-PSs) for antibacterial photodynamic therapy (aPDT) have received increasing attention because of their ability to increase reactive oxygen species (ROS) generation in the aggregation state. However, their antibacterial effect still has great room for improvement. Herein, we propose that if the rotation of some bonds in AIE-PSs is restricted, the nonradiative decay could be further suppressed to boost the generation of fluorescence and ROS, so as to improve their antibacterial efficacy. Following this molecular design strategy, we developed a new class of carbazole group-based AIE-PSs (CPVBA, CPVBP, CPVBP2, and CPVBP3), in which the rotation of phenyl-N bonds is restricted in the carbazole ring. Compared with diphenylamine group-based AIE-PSs with free rotation of phenyl-N bonds, carbazole group-based AIE-PSs showed stronger fluorescence, ROS generation, and antibacterial abilities, demonstrating the feasibility of this new design strategy. Notably, CPVBP3 can enter the entire cell of E. coli to exert its antibacterial effect, and there are few reports of photosensitizers with similar functions. Furthermore, to the best of our knowledge, the light dose (1.2 J/cm2) we used for CPVBP2 to kill Staphylococcus aureus is much lower than that of many reported photosensitizers, indicating great prospects for AIE antimicrobial photosensitizers.
Collapse
Affiliation(s)
- Haixing Shi
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fujian Academy, University of Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
- Fujian Agriculture and Forestry University Fuzhou, Fujian 350002, China
| | - Xiaohong Pan
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fujian Academy, University of Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
| | - Yaqi Wang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fujian Academy, University of Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
- Fujian Agriculture and Forestry University Fuzhou, Fujian 350002, China
| | - Huanhuan Wang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fujian Academy, University of Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenzhen Liu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fujian Academy, University of Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
| | - Le Wang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fujian Academy, University of Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuo Chen
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fujian Academy, University of Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
54
|
Gurvic D, Leach AG, Zachariae U. Data-Driven Derivation of Molecular Substructures That Enhance Drug Activity in Gram-Negative Bacteria. J Med Chem 2022; 65:6088-6099. [PMID: 35427114 PMCID: PMC9059115 DOI: 10.1021/acs.jmedchem.1c01984] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The complex cell
envelope of Gram-negative bacteria creates a formidable
barrier to antibiotic influx. Reduced drug uptake impedes drug development
and contributes to a wide range of drug-resistant bacterial infections,
including those caused by extremely resistant species prioritized
by the World Health Organization. To develop new and efficient treatments,
a better understanding of the molecular features governing Gram-negative
permeability is essential. Here, we present a data-driven approach,
using matched molecular pair analysis and machine learning on minimal
inhibitory concentration data from Gram-positive and Gram-negative
bacteria to uncover chemical features that influence Gram-negative
bioactivity. We find recurring chemical moieties, of a wider range
than previously known, that consistently improve activity and suggest
that this insight can be used to optimize compounds for increased
Gram-negative uptake. Our findings may help to expand the chemical
space of broad-spectrum antibiotics and aid the search for new antibiotic
compound classes.
Collapse
Affiliation(s)
- Dominik Gurvic
- Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Andrew G. Leach
- Division of Pharmacy and Optometry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
- Medchemica Limited, Mereside, Alderley Park, Macclesfield, SK10 4TG, United Kingdom
| | - Ulrich Zachariae
- Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| |
Collapse
|
55
|
On the Hunt for Next-Generation Antimicrobial Agents: An Online Symposium Organized Jointly by the French Society for Medicinal Chemistry (Société de Chimie Thérapeutique) and the French Microbiology Society (Société Française de Microbiologie) on 9–10 December 2021. Pharmaceuticals (Basel) 2022; 15:ph15040388. [PMID: 35455385 PMCID: PMC9029193 DOI: 10.3390/ph15040388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 03/17/2022] [Indexed: 01/27/2023] Open
Abstract
The restrictions posed by the COVID-19 pandemic obliged the French Society for Medicinal Chemistry (Société de chimie thérapeutique) and the French Microbiology Society (Société Française de Microbiologie) to organize their joint autumn symposium (entitled “On the hunt for next-generation antimicrobial agents”) online on 9–10 December 2021. The meeting attracted more than 200 researchers from France and abroad with interests in drug discovery, antimicrobial resistance, medicinal chemistry, and related disciplines. This review summarizes the 13 invited keynote lectures. The symposium generated high-level scientific dialogue on the most recent advances in combating antimicrobial resistance. The University of Lille, the Institut Pasteur de Lille, the journal Pharmaceuticals, Oxeltis, and INCATE, sponsored the event.
Collapse
|
56
|
Richter R, Kamal MAM, Koch M, Niebuur B, Huber A, Goes A, Volz C, Vergalli J, Kraus T, Müller R, Schneider‐Daum N, Fuhrmann G, Pagès J, Lehr C. An Outer Membrane Vesicle-Based Permeation Assay (OMPA) for Assessing Bacterial Bioavailability. Adv Healthc Mater 2022; 11:e2101180. [PMID: 34614289 DOI: 10.1002/adhm.202101180] [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: 06/15/2021] [Revised: 09/14/2021] [Indexed: 11/11/2022]
Abstract
When searching for new antibiotics against Gram-negative bacterial infections, a better understanding of the permeability across the cell envelope and tools to discriminate high from low bacterial bioavailability compounds are urgently needed. Inspired by the phospholipid vesicle-based permeation assay (PVPA), which is designed to predict non-facilitated permeation across phospholipid membranes, outer membrane vesicles (OMVs) of Escherichia coli either enriched or deficient of porins are employed to coat filter supports for predicting drug uptake across the complex cell envelope. OMVs and the obtained in vitro model are structurally and functionally characterized using cryo-TEM, SEM, CLSM, SAXS, and light scattering techniques. In vitro permeability, obtained from the membrane model for a set of nine antibiotics, correlates with reported in bacterio accumulation data and allows to discriminate high from low accumulating antibiotics. In contrast, the correlation of the same data set generated by liposome-based comparator membranes is poor. This better correlation of the OMV-derived membranes points to the importance of hydrophilic membrane components, such as lipopolysaccharides and porins, since those features are lacking in liposomal comparator membranes. This approach can offer in the future a high throughput screening tool with high predictive capacity or can help to identify compound- and bacteria-specific passive uptake pathways.
Collapse
Affiliation(s)
- Robert Richter
- Helmholtz Centre for Infection Research Helmholtz Institute for Pharmaceutical Research Saarland Campus E8.1 Saarbrücken 66123 Germany
| | - Mohamed A. M. Kamal
- Helmholtz Centre for Infection Research Helmholtz Institute for Pharmaceutical Research Saarland Campus E8.1 Saarbrücken 66123 Germany
- Saarland University Department of Pharmacy Campus E8.1 Saarbrücken 66123 Germany
| | - Marcus Koch
- INM – Leibniz Institute for New Materials Campus D2.2 Saarbrücken 66123 Germany
| | - Bart‐Jan Niebuur
- INM – Leibniz Institute for New Materials Campus D2.2 Saarbrücken 66123 Germany
| | - Anna‐Lena Huber
- Helmholtz Centre for Infection Research Helmholtz Institute for Pharmaceutical Research Saarland Campus E8.1 Saarbrücken 66123 Germany
- Saarland University Department of Pharmacy Campus E8.1 Saarbrücken 66123 Germany
| | - Adriely Goes
- Helmholtz Centre for Infection Research Helmholtz Institute for Pharmaceutical Research Saarland Campus E8.1 Saarbrücken 66123 Germany
- Saarland University Department of Pharmacy Campus E8.1 Saarbrücken 66123 Germany
| | - Carsten Volz
- Helmholtz Centre for Infection Research Helmholtz Institute for Pharmaceutical Research Saarland Campus E8.1 Saarbrücken 66123 Germany
| | - Julia Vergalli
- UMR_MD1 U‐1261 Aix‐Marseille Université INSERM IRBA MCT Faculté de Pharmacie 27 Boulevard Jean Moulin Marseille 13005 France
| | - Tobias Kraus
- INM – Leibniz Institute for New Materials Campus D2.2 Saarbrücken 66123 Germany
- Colloid and Interface Chemistry Saarland University Campus D2.2 Saarbrücken 66123 Germany
| | - Rolf Müller
- Helmholtz Centre for Infection Research Helmholtz Institute for Pharmaceutical Research Saarland Campus E8.1 Saarbrücken 66123 Germany
- Saarland University Department of Pharmacy Campus E8.1 Saarbrücken 66123 Germany
| | - Nicole Schneider‐Daum
- Helmholtz Centre for Infection Research Helmholtz Institute for Pharmaceutical Research Saarland Campus E8.1 Saarbrücken 66123 Germany
| | - Gregor Fuhrmann
- Helmholtz Centre for Infection Research Helmholtz Institute for Pharmaceutical Research Saarland Campus E8.1 Saarbrücken 66123 Germany
- Saarland University Department of Pharmacy Campus E8.1 Saarbrücken 66123 Germany
| | - Jean‐Marie Pagès
- UMR_MD1 U‐1261 Aix‐Marseille Université INSERM IRBA MCT Faculté de Pharmacie 27 Boulevard Jean Moulin Marseille 13005 France
| | - Claus‐Michael Lehr
- Helmholtz Centre for Infection Research Helmholtz Institute for Pharmaceutical Research Saarland Campus E8.1 Saarbrücken 66123 Germany
- Saarland University Department of Pharmacy Campus E8.1 Saarbrücken 66123 Germany
| |
Collapse
|
57
|
Kaya C, Konstantinović J, Kany AM, Andreas A, Kramer JS, Brunst S, Weizel L, Rotter MJ, Frank D, Yahiaoui S, Müller R, Hartmann RW, Haupenthal J, Proschak E, Wichelhaus TA, Hirsch AKH. N-Aryl Mercaptopropionamides as Broad-Spectrum Inhibitors of Metallo-β-Lactamases. J Med Chem 2022; 65:3913-3922. [PMID: 35188771 DOI: 10.1021/acs.jmedchem.1c01755] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Drug-resistant pathogens pose a global challenge to public health as they cause diseases that are extremely difficult to cure. Metallo-β-lactamases (MBLs) are a diverse set of zinc-containing enzymes that catalyze the hydrolysis of β-lactam drugs, including carbapenems, which are considered as the last resort to fight severe infections. To restore the activity of current β-lactam antibiotics and to offer an orthogonal strategy to the discovery of new antibiotics, we have identified a series of polar N-aryl mercaptopropionamide derivatives as potent inhibitors of several class B1 MBLs. We have identified a hit structure with high selectivity restoring the effect of imipenem and reducing minimum inhibitory concentration (MIC) values up to 256-fold in resistant isolates from Escherichia coli. Furthermore, the combination of imipenem with our inhibitor showed in vivo efficacy in a Galleria mellonella model, increasing the survival rate of infected larvae by up to 31%.
Collapse
Affiliation(s)
- Cansu Kaya
- Helmholtz Institute for Pharmaceutical Research Saarland, (HIPS)─Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Jelena Konstantinović
- Helmholtz Institute for Pharmaceutical Research Saarland, (HIPS)─Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
| | - Andreas M Kany
- Helmholtz Institute for Pharmaceutical Research Saarland, (HIPS)─Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
| | - Anastasia Andreas
- Helmholtz Institute for Pharmaceutical Research Saarland, (HIPS)─Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Jan S Kramer
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
| | - Steffen Brunst
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
| | - Lilia Weizel
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
| | - Marco J Rotter
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
| | - Denia Frank
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Paul-Ehrlich-Straße 40, 60596 Frankfurt, Germany
| | - Samir Yahiaoui
- Helmholtz Institute for Pharmaceutical Research Saarland, (HIPS)─Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland, (HIPS)─Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.,Helmholtz International Lab for Anti-infectives, Campus E8.1, 66123 Saarbrücken, Germany
| | - Rolf W Hartmann
- Helmholtz Institute for Pharmaceutical Research Saarland, (HIPS)─Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Jörg Haupenthal
- Helmholtz Institute for Pharmaceutical Research Saarland, (HIPS)─Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
| | - Ewgenij Proschak
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
| | - Thomas A Wichelhaus
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Paul-Ehrlich-Straße 40, 60596 Frankfurt, Germany
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland, (HIPS)─Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.,Helmholtz International Lab for Anti-infectives, Campus E8.1, 66123 Saarbrücken, Germany
| |
Collapse
|
58
|
Woods A, Parker D, Glick MM, Peng Y, Lenoir F, Mulligan E, Yu V, Piizzi G, Lister T, Lilly MD, Dzink-Fox J, Jansen JM, Ryder NS, Dean CR, Smith TM. High-Throughput Screen for Inhibitors of Klebsiella pneumoniae Virulence Using a Tetrahymena pyriformis Co-Culture Surrogate Host Model. ACS OMEGA 2022; 7:5401-5414. [PMID: 35187355 PMCID: PMC8851646 DOI: 10.1021/acsomega.1c06633] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 12/08/2021] [Indexed: 05/31/2023]
Abstract
The continuing emergence of antibacterial resistance reduces the effectiveness of antibiotics and drives an ongoing search for effective replacements. Screening compound libraries for antibacterial activity in standard growth media has been extensively explored and may be showing diminishing returns. Inhibition of bacterial targets that are selectively important under in vivo (infection) conditions and, therefore, would be missed by conventional in vitro screens might be an alternative. Surrogate host models of infection, however, are often not suitable for high-throughput screens. Here, we adapted a medium-throughput Tetrahymena pyriformis surrogate host model that was successfully used to identify inhibitors of a hyperviscous Klebsiella pneumoniae strain to a high-throughput format and screened circa 1.2 million compounds. The screen was robust and identified confirmed hits from different chemical classes with potent inhibition of K. pneumoniae growth in the presence of T. pyriformis that lacked any appreciable direct antibacterial activity. Several of these appeared to inhibit capsule/mucoidy, which are key virulence factors in hypervirulent K. pneumoniae. A weakly antibacterial inhibitor of LpxC (essential for the synthesis of the lipid A moiety of lipopolysaccharides) also appeared to be more active in the presence of T. pyriformis, which is consistent with the role of LPS in virulence as well as viability in K. pneumoniae.
Collapse
Affiliation(s)
- Angela
L. Woods
- Infectious
Diseases, Novartis Institutes for Biomedical
Research Inc, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - David Parker
- Global
Discovery Chemistry, Novartis Institutes
for Biomedical Research Inc, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Meir M. Glick
- Chemical
Biology and Therapeutics, Novartis Institutes
for Biomedical Research Inc, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Yunshan Peng
- Global
Discovery Chemistry, Novartis Institutes
for Biomedical Research Inc, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Francois Lenoir
- Global
Discovery Chemistry, Novartis Institutes
for Biomedical Research Inc, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Evan Mulligan
- Chemical
Biology and Therapeutics, Novartis Institutes
for Biomedical Research Inc, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Vincent Yu
- Chemical
Biology and Therapeutics, Novartis Institutes
for Biomedical Research Inc, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Grazia Piizzi
- Global
Discovery Chemistry, Novartis Institutes
for Biomedical Research Inc, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Troy Lister
- Global
Discovery Chemistry, Novartis Institutes
for Biomedical Research Inc, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Maria-Dawn Lilly
- Infectious
Diseases, Novartis Institutes for Biomedical
Research Inc, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - JoAnn Dzink-Fox
- Infectious
Diseases, Novartis Institutes for Biomedical
Research Inc, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Johanna M. Jansen
- Global
Discovery Chemistry, Novartis Institutes
for Biomedical Research Inc, Emeryville California 94608-2916, United States
| | - Neil S. Ryder
- Infectious
Diseases, Novartis Institutes for Biomedical
Research Inc, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Charles R. Dean
- Infectious
Diseases, Novartis Institutes for Biomedical
Research Inc, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Thomas M. Smith
- Chemical
Biology and Therapeutics, Novartis Institutes
for Biomedical Research Inc, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
59
|
Koteva K, Sychantha D, Rotondo CM, Hobson C, Britten JF, Wright GD. Three-Dimensional Structure and Optimization of the Metallo-β-Lactamase Inhibitor Aspergillomarasmine A. ACS OMEGA 2022; 7:4170-4184. [PMID: 35155911 PMCID: PMC8829947 DOI: 10.1021/acsomega.1c05757] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
The aminopolycarboxylic acid aspergillomarasmine A (AMA) is a natural Zn2+ metallophore and inhibitor of metallo-β-lactamases (MBLs) which reverses β-lactam resistance. The first crystal structure of an AMA coordination complex is reported and reveals a pentadentate ligand with distorted octahedral geometry. We report the solid-phase synthesis of 23 novel analogs of AMA involving structural diversification of each subunit (l-Asp, l-APA1, and l-APA2). Inhibitory activity was evaluated in vitro using five strains of Escherichia coli producing globally prevalent MBLs. Further in vitro assessment was performed with purified recombinant enzymes and intracellular accumulation studies. Highly constrained structure-activity relationships were demonstrated, but three analogs revealed favorable characteristics where either Zn2+ affinity or the binding mode to MBLs were improved. This study identifies compounds that can further be developed to produce more potent and broader-spectrum MBL inhibitors with improved pharmacodynamic/pharmacokinetic properties.
Collapse
Affiliation(s)
- Kalinka Koteva
- David
Braley Centre for Antibiotic Discovery, M.G. DeGroote Institute for
Infectious Disease Research, Department of Biochemistry and Biomedical
Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - David Sychantha
- David
Braley Centre for Antibiotic Discovery, M.G. DeGroote Institute for
Infectious Disease Research, Department of Biochemistry and Biomedical
Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Caitlyn M. Rotondo
- David
Braley Centre for Antibiotic Discovery, M.G. DeGroote Institute for
Infectious Disease Research, Department of Biochemistry and Biomedical
Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Christian Hobson
- David
Braley Centre for Antibiotic Discovery, M.G. DeGroote Institute for
Infectious Disease Research, Department of Biochemistry and Biomedical
Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
- Willow
Biosciences, 2250 Boundary
Rd, Burnaby, BC V5M 3Z3, Canada
| | - James F. Britten
- McMaster
Analytical X-ray Diffraction Facility (MAX), McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Gerard D. Wright
- David
Braley Centre for Antibiotic Discovery, M.G. DeGroote Institute for
Infectious Disease Research, Department of Biochemistry and Biomedical
Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| |
Collapse
|
60
|
Enzyme Inhibitors: The Best Strategy to Tackle Superbug NDM-1 and Its Variants. Int J Mol Sci 2021; 23:ijms23010197. [PMID: 35008622 PMCID: PMC8745225 DOI: 10.3390/ijms23010197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 12/20/2021] [Accepted: 12/23/2021] [Indexed: 01/06/2023] Open
Abstract
Multidrug bacterial resistance endangers clinically effective antimicrobial therapy and continues to cause major public health problems, which have been upgraded to unprecedented levels in recent years, worldwide. β-Lactam antibiotics have become an important weapon to fight against pathogen infections due to their broad spectrum. Unfortunately, the emergence of antibiotic resistance genes (ARGs) has severely astricted the application of β-lactam antibiotics. Of these, New Delhi metallo-β-lactamase-1 (NDM-1) represents the most disturbing development due to its substrate promiscuity, the appearance of variants, and transferability. Given the clinical correlation of β-lactam antibiotics and NDM-1-mediated resistance, the discovery, and development of combination drugs, including NDM-1 inhibitors, for NDM-1 bacterial infections, seems particularly attractive and urgent. This review summarizes the research related to the development and optimization of effective NDM-1 inhibitors. The detailed generalization of crystal structure, enzyme activity center and catalytic mechanism, variants and global distribution, mechanism of action of existing inhibitors, and the development of scaffolds provides a reference for finding potential clinically effective NDM-1 inhibitors against drug-resistant bacteria.
Collapse
|
61
|
Abutaleb NS, Elhassanny AEM, Nocentini A, Hewitt CS, Elkashif A, Cooper BR, Supuran CT, Seleem MN, Flaherty DP. Repurposing FDA-approved sulphonamide carbonic anhydrase inhibitors for treatment of Neisseria gonorrhoeae. J Enzyme Inhib Med Chem 2021; 37:51-61. [PMID: 34894972 PMCID: PMC8667909 DOI: 10.1080/14756366.2021.1991336] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Neisseria gonorrhoeae is a high-priority pathogen of concern due to the growing prevalence of resistance development against approved antibiotics. Herein, we report the anti-gonococcal activity of ethoxzolamide, the FDA-approved human carbonic anhydrase inhibitor. Ethoxzolamide displayed an MIC50, against a panel of N. gonorrhoeae isolates, of 0.125 µg/mL, 16-fold more potent than acetazolamide, although both molecules exhibited almost similar potency against the gonococcal carbonic anhydrase enzyme (NgCA) in vitro. Acetazolamide displayed an inhibition constant (Ki) versus NgCA of 74 nM, while Ethoxzolamide’s Ki was estimated to 94 nM. Therefore, the increased anti-gonococcal potency of ethoxzolamide was attributed to its increased permeability in N. gonorrhoeae as compared to that of acetazolamide. Both drugs demonstrated bacteriostatic activity against N. gonorrhoeae, exhibited post-antibiotic effects up to 10 hours, and resistance was not observed against both. Taken together, these results indicate that acetazolamide and ethoxzolamide warrant further investigation for translation into effective anti-N. gonorrhoeae agents.
Collapse
Affiliation(s)
- Nader S Abutaleb
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VI, USA
| | - Ahmed E M Elhassanny
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VI, USA
| | - Alessio Nocentini
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Polo Scientifico, Firenze, Italy
| | - Chad S Hewitt
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN, USA
| | - Ahmed Elkashif
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA
| | - Bruce R Cooper
- Metabolite Profiling Facility, Bindley Bioscience Center, Purdue University, West Lafayette, Indiana, United States
| | - Claudiu T Supuran
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Polo Scientifico, Firenze, Italy
| | - Mohamed N Seleem
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VI, USA.,Center for Emerging, Zoonotic and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VI, USA
| | - Daniel P Flaherty
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN, USA.,Purdue Institute for Drug Discovery, West Lafayette, IN, USA.,Purdue Institute of Inflammation, Immunology and Infectious Disease, West Lafayette, IN, USA
| |
Collapse
|
62
|
Haloi N, Vasan AK, Geddes EJ, Prasanna A, Wen PC, Metcalf WW, Hergenrother PJ, Tajkhorshid E. Rationalizing the generation of broad spectrum antibiotics with the addition of a positive charge. Chem Sci 2021; 12:15028-15044. [PMID: 34909143 PMCID: PMC8612397 DOI: 10.1039/d1sc04445a] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/13/2021] [Indexed: 11/28/2022] Open
Abstract
Antibiotic resistance of Gram-negative bacteria is largely attributed to the low permeability of their outer membrane (OM). Recently, we disclosed the eNTRy rules, a key lesson of which is that the introduction of a primary amine enhances OM permeation in certain contexts. To understand the molecular basis for this finding, we perform an extensive set of molecular dynamics (MD) simulations and free energy calculations comparing the permeation of aminated and amine-free antibiotic derivatives through the most abundant OM porin of E. coli, OmpF. To improve sampling of conformationally flexible drugs in MD simulations, we developed a novel, Monte Carlo and graph theory based algorithm to probe more efficiently the rotational and translational degrees of freedom visited during the permeation of the antibiotic molecule through OmpF. The resulting pathways were then used for free-energy calculations, revealing a lower barrier against the permeation of the aminated compound, substantiating its greater OM permeability. Further analysis revealed that the amine facilitates permeation by enabling the antibiotic to align its dipole to the luminal electric field of the porin and form favorable electrostatic interactions with specific, highly-conserved charged residues. The importance of these interactions in permeation was further validated with experimental mutagenesis and whole cell accumulation assays. Overall, this study provides insights on the importance of the primary amine for antibiotic permeation into Gram-negative pathogens that could help the design of future antibiotics. We also offer a new computational approach for calculating free-energy of processes where relevant molecular conformations cannot be efficiently captured.
Collapse
Affiliation(s)
- Nandan Haloi
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Archit Kumar Vasan
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Emily J Geddes
- Department of Chemistry, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Arjun Prasanna
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
- Department of Microbiology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Po-Chao Wen
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - William W Metcalf
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
- Department of Microbiology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Paul J Hergenrother
- Department of Chemistry, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| |
Collapse
|
63
|
Xiao G, Alphey MS, Tran F, Pirrie L, Milbeo P, Zhou Y, Bickel JK, Kempf O, Kempf K, Naismith JH, Westwood NJ. Next generation Glucose-1-phosphate thymidylyltransferase (RmlA) inhibitors: An extended SAR study to direct future design. Bioorg Med Chem 2021; 50:116477. [PMID: 34757294 PMCID: PMC8613358 DOI: 10.1016/j.bmc.2021.116477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/07/2021] [Accepted: 10/11/2021] [Indexed: 11/29/2022]
Abstract
The monosaccharide l-Rhamnose is an important component of bacterial cell walls. The first step in the l-rhamnose biosynthetic pathway is catalysed by glucose-1-phosphate thymidylyltransferase (RmlA), which condenses glucose-1-phosphate (Glu-1-P) with deoxythymidine triphosphate (dTTP) to yield dTDP-d-glucose. In addition to the active site where catalysis of this reaction occurs, RmlA has an allosteric site that is important for its function. Building on previous reports, SAR studies have explored further the allosteric site, leading to the identification of very potent P. aeruginosa RmlA inhibitors. Modification at the C6-NH2 of the inhibitor's pyrimidinedione core structure was tolerated. X-ray crystallographic analysis of the complexes of P. aeruginosa RmlA with the novel analogues revealed that C6-aminoalkyl substituents can be used to position a modifiable amine just outside the allosteric pocket. This opens up the possibility of linking a siderophore to this class of inhibitor with the goal of enhancing bacterial cell wall permeability.
Collapse
Affiliation(s)
- Ganyuan Xiao
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews and EaStCHEM, St Andrews Fife KY16 9ST, UK
| | - Magnus S Alphey
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews and EaStCHEM, St Andrews Fife KY16 9ST, UK
| | - Fanny Tran
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews and EaStCHEM, St Andrews Fife KY16 9ST, UK
| | - Lisa Pirrie
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews and EaStCHEM, St Andrews Fife KY16 9ST, UK
| | - Pierre Milbeo
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews and EaStCHEM, St Andrews Fife KY16 9ST, UK
| | - Yi Zhou
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews and EaStCHEM, St Andrews Fife KY16 9ST, UK
| | - Jasmine K Bickel
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews and EaStCHEM, St Andrews Fife KY16 9ST, UK
| | - Oxana Kempf
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews and EaStCHEM, St Andrews Fife KY16 9ST, UK
| | - Karl Kempf
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews and EaStCHEM, St Andrews Fife KY16 9ST, UK
| | - James H Naismith
- Division of Structural Biology, University of Oxford, and The Rosalind Franklin Institute, Harwell Campus, OX11 0FA, UK.
| | - Nicholas J Westwood
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews and EaStCHEM, St Andrews Fife KY16 9ST, UK.
| |
Collapse
|
64
|
Pandeya A, Yang L, Alegun O, Karunasena C, Risko C, Li Z, Wei Y. Biotinylation as a tool to enhance the uptake of small molecules in Gram-negative bacteria. PLoS One 2021; 16:e0260023. [PMID: 34767592 PMCID: PMC8589159 DOI: 10.1371/journal.pone.0260023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 10/31/2021] [Indexed: 11/22/2022] Open
Abstract
Antibiotic resistance is a major public health concern. The shrinking selection of effective antibiotics and lack of new development is making the situation worse. Gram-negative bacteria more specifically pose serious threat because of their double layered cell envelope and effective efflux systems, which is a challenge for drugs to penetrate. One promising approach to breach this barrier is the "Trojan horse strategy". In this technique, an antibiotic molecule is conjugated with a nutrient molecule that helps the antibiotic to enter the cell through dedicated transporters for the nutrient. Here, we explored the approach using biotin conjugation with a florescent molecule Atto565 to determine if biotinylation enhances accumulation. Biotin is an essential vitamin for bacteria and is obtained through either synthesis or uptake from the environment. We found that biotinylation enhanced accumulation of Atto565 in E. coli. However, the enhancement did not seem to be due to uptake through biotin transporters since the presence of free biotin had no observable impact on accumulation. Accumulated compound was mostly in the periplasm, as determined by cell fractionation studies. This was further confirmed through the observation that expression of streptavidin in the periplasm specifically enhanced the accumulation of biotinylated Atto565. This enhancement was not observed when streptavidin was expressed in the cytoplasm indicating no significant distribution of the compound inside the cytoplasm. Using gene knockout strains, plasmid complementation and mutagenesis studies we demonstrated that biotinylation made the compound a better passenger through OmpC, an outer membrane porin. Density functional theory (DFT)-based evaluation of the three-dimensional geometries showed that biotinylation did not directly stabilize the conformation of the compound to make it favorable for the entry through a pore. Further studies including molecular dynamics simulations are necessary to determine the possible mechanisms of enhanced accumulation of the biotinylated Atto565.
Collapse
Affiliation(s)
- Ankit Pandeya
- Department of Chemistry, College of Arts and Sciences, University of Kentucky, Lexington, KY, United States of America
| | - Ling Yang
- Department of Chemistry, College of Arts and Sciences, University of Kentucky, Lexington, KY, United States of America
| | - Olaniyi Alegun
- Department of Chemistry, College of Arts and Sciences, University of Kentucky, Lexington, KY, United States of America
| | - Chamikara Karunasena
- Department of Chemistry, College of Arts and Sciences, University of Kentucky, Lexington, KY, United States of America
- Centre for Applied Energy and Research, University of Kentucky, Lexington, KY, United States of America
| | - Chad Risko
- Department of Chemistry, College of Arts and Sciences, University of Kentucky, Lexington, KY, United States of America
- Centre for Applied Energy and Research, University of Kentucky, Lexington, KY, United States of America
| | - Zhenyu Li
- Saha Cardiovascular Research Center, College of Medicine, University of Kentucky, Lexington, KY, United States of America
| | - Yinan Wei
- Department of Chemistry, College of Arts and Sciences, University of Kentucky, Lexington, KY, United States of America
| |
Collapse
|
65
|
da Silva TH, Hachigian TZ, Lee J, King MD. Using computers to ESKAPE the antibiotic resistance crisis. Drug Discov Today 2021; 27:456-470. [PMID: 34688913 DOI: 10.1016/j.drudis.2021.10.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 08/01/2021] [Accepted: 10/15/2021] [Indexed: 12/16/2022]
Abstract
Since the discovery of penicillin, the development and use of antibiotics have promoted safe and effective control of bacterial infections. However, the number of antibiotic-resistance cases has been ever increasing over time. Thus, the drug discovery process demands fast, efficient and cost-effective alternative approaches for developing lead candidates with outstanding performance. Computational approaches are appealing techniques to develop lead candidates in an in silico fashion. In this review, we provide an overview of the implementation of current in silico state-of-the-art techniques, including machine learning (ML) and deep learning (DL), in drug discovery. We also discuss the development of quantum computing and its potential benefits for antibiotics research and current bottlenecks that limit computational drug discovery advancement.
Collapse
Affiliation(s)
- Thiago H da Silva
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA
| | - Timothy Z Hachigian
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA
| | - Jeunghoon Lee
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; Department of Chemistry and Biochemistry, Boise State University, Boise, ID 83725, USA
| | - Matthew D King
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; Department of Chemistry and Biochemistry, Boise State University, Boise, ID 83725, USA.
| |
Collapse
|
66
|
Geddes EJ, Li Z, Hergenrother PJ. An LC-MS/MS assay and complementary web-based tool to quantify and predict compound accumulation in E. coli. Nat Protoc 2021; 16:4833-4854. [PMID: 34480129 PMCID: PMC8715754 DOI: 10.1038/s41596-021-00598-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 06/25/2021] [Indexed: 02/08/2023]
Abstract
Novel classes of broad-spectrum antibiotics have been extremely difficult to discover, largely due to the impermeability of the Gram-negative membranes coupled with a poor understanding of the physicochemical properties a compound should possess to promote its accumulation inside the cell. To address this challenge, numerous methodologies for assessing intracellular compound accumulation in Gram-negative bacteria have been established, including classic radiometric and fluorescence-based methods. The recent development of accumulation assays that utilize liquid chromatography-tandem mass spectrometry (LC-MS/MS) have circumvented the requirement for labeled compounds, enabling assessment of a substantially broader range of small molecules. Our unbiased study of accumulation trends in Escherichia coli using an LC-MS/MS-based assay led to the development of the eNTRy rules, which stipulate that a compound is most likely to accumulate in E. coli if it has an ionizable Nitrogen, has low Three-dimensionality and is relatively Rigid. To aid in the implementation of the eNTRy rules, we developed a complementary web tool, eNTRyway, which calculates relevant properties and predicts compound accumulation. Here we provide a comprehensive protocol for analysis and prediction of intracellular accumulation of small molecules in E. coli using an LC-MS/MS-based assay (which takes ~2 d) and eNTRyway, a workflow that is readily adoptable by any microbiology, biochemistry or chemical biology laboratory.
Collapse
Affiliation(s)
- Emily J Geddes
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | - Zhong Li
- Metabolomics Lab, Roy J. Carver Biotechnology Center, University of Illinois, Urbana, IL, USA
| | - Paul J Hergenrother
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA.
| |
Collapse
|
67
|
Kell DB. The Transporter-Mediated Cellular Uptake and Efflux of Pharmaceutical Drugs and Biotechnology Products: How and Why Phospholipid Bilayer Transport Is Negligible in Real Biomembranes. Molecules 2021; 26:5629. [PMID: 34577099 PMCID: PMC8470029 DOI: 10.3390/molecules26185629] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/03/2021] [Accepted: 09/14/2021] [Indexed: 12/12/2022] Open
Abstract
Over the years, my colleagues and I have come to realise that the likelihood of pharmaceutical drugs being able to diffuse through whatever unhindered phospholipid bilayer may exist in intact biological membranes in vivo is vanishingly low. This is because (i) most real biomembranes are mostly protein, not lipid, (ii) unlike purely lipid bilayers that can form transient aqueous channels, the high concentrations of proteins serve to stop such activity, (iii) natural evolution long ago selected against transport methods that just let any undesirable products enter a cell, (iv) transporters have now been identified for all kinds of molecules (even water) that were once thought not to require them, (v) many experiments show a massive variation in the uptake of drugs between different cells, tissues, and organisms, that cannot be explained if lipid bilayer transport is significant or if efflux were the only differentiator, and (vi) many experiments that manipulate the expression level of individual transporters as an independent variable demonstrate their role in drug and nutrient uptake (including in cytotoxicity or adverse drug reactions). This makes such transporters valuable both as a means of targeting drugs (not least anti-infectives) to selected cells or tissues and also as drug targets. The same considerations apply to the exploitation of substrate uptake and product efflux transporters in biotechnology. We are also beginning to recognise that transporters are more promiscuous, and antiporter activity is much more widespread, than had been realised, and that such processes are adaptive (i.e., were selected by natural evolution). The purpose of the present review is to summarise the above, and to rehearse and update readers on recent developments. These developments lead us to retain and indeed to strengthen our contention that for transmembrane pharmaceutical drug transport "phospholipid bilayer transport is negligible".
Collapse
Affiliation(s)
- Douglas B. Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St, Liverpool L69 7ZB, UK;
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs Lyngby, Denmark
- Mellizyme Biotechnology Ltd., IC1, Liverpool Science Park, Mount Pleasant, Liverpool L3 5TF, UK
| |
Collapse
|
68
|
Schütz C, Hodzic A, Hamed M, Abdelsamie AS, Kany AM, Bauer M, Röhrig T, Schmelz S, Scrima A, Blankenfeldt W, Empting M. Divergent synthesis and biological evaluation of 2-(trifluoromethyl)pyridines as virulence-attenuating inverse agonists targeting PqsR. Eur J Med Chem 2021; 226:113797. [PMID: 34520957 DOI: 10.1016/j.ejmech.2021.113797] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 08/10/2021] [Accepted: 08/22/2021] [Indexed: 11/19/2022]
Abstract
A short and divergent route towards new derivatives of 2-(trifluoromethyl)pyridines as potent inverse agonists of the bacterial target PqsR against Pseudomonas aeruginosa (PA) infections is described. This Gram-negative pathogen causes severe nosocomial infections and common antibiotic treatment options are rendered ineffective due to resistance issues. Based on an earlier identified optimized hit, we conducted derivatization and rigidification attempts employing two central building blocks. The western part of the molecule is built up via a 2-(trifluoromethyl)pyridine head group equipped with a terminal alkyne. The eastern section is then introduced through aryliode motifs exploiting Sonogashira as well as Suzuki-type chemistry. Subsequent modification provided quick access to an array of compounds, allowed for deep SAR insights, and enabled to optimize the hit scaffold into a lead structure of nanomolar potency combined with favorable in vitro ADME/T features.
Collapse
Affiliation(s)
- Christian Schütz
- Department of Drug Design and Optimization (DDOP), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany; Department of Pharmacy, Saarland University, Campus E8.1, 66123, Saarbrücken, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 66123, Saarbrücken, Germany
| | - Amir Hodzic
- Department of Drug Design and Optimization (DDOP), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany
| | - Mostafa Hamed
- Department of Drug Design and Optimization (DDOP), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany; Department of Pharmacy, Saarland University, Campus E8.1, 66123, Saarbrücken, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 66123, Saarbrücken, Germany
| | - Ahmed S Abdelsamie
- Department of Drug Design and Optimization (DDOP), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany; Department of Pharmacy, Saarland University, Campus E8.1, 66123, Saarbrücken, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 66123, Saarbrücken, Germany; Chemistry of Natural and Microbial Products Department, National Research Centre, Dokki, 12622, Cairo, Egypt
| | - Andreas M Kany
- Department of Drug Design and Optimization (DDOP), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany; Department of Pharmacy, Saarland University, Campus E8.1, 66123, Saarbrücken, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 66123, Saarbrücken, Germany
| | - Maximilian Bauer
- Department of Drug Design and Optimization (DDOP), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany
| | - Teresa Röhrig
- Department of Drug Design and Optimization (DDOP), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany; Department of Pharmacy, Saarland University, Campus E8.1, 66123, Saarbrücken, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 66123, Saarbrücken, Germany
| | - Stefan Schmelz
- Department of Structure and Function of Proteins (SFPR), Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Andrea Scrima
- Department of Structure and Function of Proteins (SFPR), Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Wulf Blankenfeldt
- Department of Structure and Function of Proteins (SFPR), Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, 38124, Braunschweig, Germany; Biotechnology and Bioinformatics, Institute for Biochemistry, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Martin Empting
- Department of Drug Design and Optimization (DDOP), Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123, Saarbrücken, Germany; Department of Pharmacy, Saarland University, Campus E8.1, 66123, Saarbrücken, Germany; German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 66123, Saarbrücken, Germany.
| |
Collapse
|
69
|
Advances in metabolic engineering of Corynebacterium glutamicum to produce high-value active ingredients for food, feed, human health, and well-being. Essays Biochem 2021; 65:197-212. [PMID: 34096577 PMCID: PMC8313993 DOI: 10.1042/ebc20200134] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 12/12/2022]
Abstract
The soil microbe Corynebacterium glutamicum is a leading workhorse in industrial biotechnology and has become famous for its power to synthetise amino acids and a range of bulk chemicals at high titre and yield. The product portfolio of the microbe is continuously expanding. Moreover, metabolically engineered strains of C. glutamicum produce more than 30 high value active ingredients, including signature molecules of raspberry, savoury, and orange flavours, sun blockers, anti-ageing sugars, and polymers for regenerative medicine. Herein, we highlight recent advances in engineering of the microbe into novel cell factories that overproduce these precious molecules from pioneering proofs-of-concept up to industrial productivity.
Collapse
|
70
|
Santi C, Scimmi C, Sancineto L. Ebselen and Analogues: Pharmacological Properties and Synthetic Strategies for Their Preparation. Molecules 2021; 26:4230. [PMID: 34299505 PMCID: PMC8306772 DOI: 10.3390/molecules26144230] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 02/06/2023] Open
Abstract
Ebselen is the leader of selenorganic compounds, and starting from its identification as mimetic of the key antioxidant enzyme glutathione peroxidase, several papers have appeared in literature claiming its biological activities. It was the subject of several clinical trials and it is currently in clinical evaluation for the treatment of COVID-19 patients. Given our interest in the synthesis and pharmacological evaluation of selenorganic derivatives with this review, we aimed to collect all the papers focused on the biological evaluation of ebselen and its close analogues, covering the timeline between 2016 and most of 2021. Our analysis evidences that, even if it lacks specificity when tested in vitro, being able to bind to every reactive cysteine, it proved to be always well tolerated in vivo, exerting no sign of toxicity whatever the administered doses. Besides, looking at the literature, we realized that no review article dealing with the synthetic approaches for the construction of the benzo[d][1,2]-selenazol-3(2H)-one scaffold is available; thus, a section of the present review article is completely devoted to this specific topic.
Collapse
Affiliation(s)
| | | | - Luca Sancineto
- Group of Catalysis and Green Organic Chemistry, Department of Pharmaceutical Sciences, University of Perugia Via del Liceo 1, 06122 Perugia, Italy; (C.S.); (C.S.)
| |
Collapse
|
71
|
Richter R, Lehr CM. Extracellular vesicles as novel assay tools to study cellular interactions of anti-infective compounds - A perspective. Adv Drug Deliv Rev 2021; 173:492-503. [PMID: 33857554 DOI: 10.1016/j.addr.2021.04.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/21/2021] [Accepted: 04/08/2021] [Indexed: 12/13/2022]
Abstract
Sudden outbreaks of novel infectious diseases and the persistent evolution of antimicrobial resistant pathogens make it necessary to develop specific tools to quickly understand pathogen-cell interactions and to study appropriate drug delivery strategies. Extracellular vesicles (EVs) are cell-specific biogenic transport systems, which are gaining more and more popularity as either diagnostic markers or drug delivery systems. Apart from that, there are emerging possibilities for EVs as tools to study drug penetration, drug-membrane interactions as well as pathogen-membrane interactions. However, it appears that the potential of EVs for such applications has not been fully exploited yet. Considering the vast variety of cells that can be involved in an infection, vesicle-based analytical methods are just emerging and the number of reported applications is still relatively small. Aim of this review is to discuss the current state of the art of EV-based assays, especially in the context of antimicrobial research and therapy, and to present some new perspectives for a more exhaustive and creative exploration in the future.
Collapse
Affiliation(s)
- Robert Richter
- Department of Drug Delivery Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz-Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
| | - Claus-Michael Lehr
- Department of Drug Delivery Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz-Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany; Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.
| |
Collapse
|
72
|
Schütz C, Ho D, Hamed MM, Abdelsamie AS, Röhrig T, Herr C, Kany AM, Rox K, Schmelz S, Siebenbürger L, Wirth M, Börger C, Yahiaoui S, Bals R, Scrima A, Blankenfeldt W, Horstmann JC, Christmann R, Murgia X, Koch M, Berwanger A, Loretz B, Hirsch AKH, Hartmann RW, Lehr C, Empting M. A New PqsR Inverse Agonist Potentiates Tobramycin Efficacy to Eradicate Pseudomonas aeruginosa Biofilms. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2004369. [PMID: 34165899 PMCID: PMC8224453 DOI: 10.1002/advs.202004369] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/21/2021] [Indexed: 05/21/2023]
Abstract
Pseudomonas aeruginosa (PA) infections can be notoriously difficult to treat and are often accompanied by the development of antimicrobial resistance (AMR). Quorum sensing inhibitors (QSI) acting on PqsR (MvfR) - a crucial transcriptional regulator serving major functions in PA virulence - can enhance antibiotic efficacy and eventually prevent the AMR. An integrated drug discovery campaign including design, medicinal chemistry-driven hit-to-lead optimization and in-depth biological profiling of a new QSI generation is reported. The QSI possess excellent activity in inhibiting pyocyanin production and PqsR reporter-gene with IC50 values as low as 200 and 11 × 10-9 m, respectively. Drug metabolism and pharmacokinetics (DMPK) as well as safety pharmacology studies especially highlight the promising translational properties of the lead QSI for pulmonary applications. Moreover, target engagement of the lead QSI is shown in a PA mucoid lung infection mouse model. Beyond that, a significant synergistic effect of a QSI-tobramycin (Tob) combination against PA biofilms using a tailor-made squalene-derived nanoparticle (NP) formulation, which enhance the minimum biofilm eradicating concentration (MBEC) of Tob more than 32-fold is demonstrated. The novel lead QSI and the accompanying NP formulation highlight the potential of adjunctive pathoblocker-mediated therapy against PA infections opening up avenues for preclinical development.
Collapse
|
73
|
Wang W, Zhang YW, Hu SJ, Niu WP, Zhang GN, Zhu M, Wang MH, Zhang F, Li XM, Wang JX. Design, synthesis, and antibacterial evaluation of PFK-158 derivatives as potent agents against drug-resistant bacteria. Bioorg Med Chem Lett 2021; 41:127980. [PMID: 33766773 DOI: 10.1016/j.bmcl.2021.127980] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 03/06/2021] [Accepted: 03/16/2021] [Indexed: 10/21/2022]
Abstract
Infections caused by antibiotic resistant bacteria are a major health concern throughout the world. It is well known that PFK-158 can enhance the antibacterial effect of polymyxin, but its own anti-bactericidal effect is rarely discussed. In order to investigate the anti-bactericidal effect of PFK-158 and its derivatives, PFK-158 and 35 derivatives were designed, synthesized, and evaluated for their antibacterial activities. Compounds A1, A3, A14, A15 and B6 exhibited potent antibacterial effect against both clinical drug sensitive and resistant Gram-positive bacteria, and they are 2-8 folds more potent than levofloxacin against Methicillin-resistant staphylococcus epidermidis (MRSE). A significant synergistic effect of these compounds and polymyxin against drug-resistant Gram-negative bacteria, which is similar to PFK-158 was also observed. The result can provided a new and broader prospect for the development of new medicine against drug-resistant bacteria.
Collapse
Affiliation(s)
- Wei Wang
- School of Pharmacy, Jinzhou Medical University, Jinzhou 121001, PR China
| | - You-Wen Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Shang-Jiu Hu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Wei-Ping Niu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Guo-Ning Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Mei Zhu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Ming-Hua Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Fan Zhang
- School of Pharmacy, Jinzhou Medical University, Jinzhou 121001, PR China.
| | - Xue-Mei Li
- Center for Drug Evaluation, National Medical Products Administration, Beijing 100022, PR China.
| | - Ju-Xian Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China.
| |
Collapse
|
74
|
Blindheim FH, Olsen CE, Krogh Søgaard C, Otterlei M, Sundby E, Hoff BH. Synthetic Strategies towards Imidazopyridinones and 7‐Azaoxindoles and their Evaluation as Antibacterial Agents. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Fredrik Heen Blindheim
- Department of Chemistry Norwegian University of Science and Technology (NTNU) 7491 Trondheim Norway
| | - Cecilie Elisabeth Olsen
- Department of Chemistry Norwegian University of Science and Technology (NTNU) 7491 Trondheim Norway
| | - Caroline Krogh Søgaard
- Department of Clinical and Molecular Medicine Norwegian University of Science and Technology (NTNU) 7489 Trondheim Norway
| | - Marit Otterlei
- Department of Clinical and Molecular Medicine Norwegian University of Science and Technology (NTNU) 7489 Trondheim Norway
| | - Eirik Sundby
- Department of Material Science Norwegian University of Science and Technology (NTNU) 7491 Trondheim Norway
| | - Bård Helge Hoff
- Department of Chemistry Norwegian University of Science and Technology (NTNU) 7491 Trondheim Norway
| |
Collapse
|
75
|
Chitosan/heparin blends in ionic liquid produce polyelectrolyte complexes that quickly adsorb citrate-capped silver nanoparticles, forming bactericidal composites. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115548] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
76
|
Mastering the Gram-negative bacterial barrier - Chemical approaches to increase bacterial bioavailability of antibiotics. Adv Drug Deliv Rev 2021; 172:339-360. [PMID: 33705882 DOI: 10.1016/j.addr.2021.02.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/08/2021] [Accepted: 02/18/2021] [Indexed: 02/07/2023]
Abstract
To win the battle against resistant, pathogenic bacteria, novel classes of anti-infectives and targets are urgently needed. Bacterial uptake, distribution, metabolic and efflux pathways of antibiotics in Gram-negative bacteria determine what we here refer to as bacterial bioavailability. Understanding these mechanisms from a chemical perspective is essential for anti-infective activity and hence, drug discovery as well as drug delivery. A systematic and critical discussion of in bacterio, in vitro and in silico assays reveals that a sufficiently accurate holistic approach is still missing. We expect new findings based on Gram-negative bacterial bioavailability to guide future anti-infective research.
Collapse
|
77
|
Ropponen HK, Diamanti E, Siemens A, Illarionov B, Haupenthal J, Fischer M, Rottmann M, Witschel M, Hirsch AKH. Assessment of the rules related to gaining activity against Gram-negative bacteria. RSC Med Chem 2021; 12:593-601. [PMID: 34046630 PMCID: PMC8128065 DOI: 10.1039/d0md00409j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/30/2021] [Indexed: 11/21/2022] Open
Abstract
In the search for new antibacterial compounds, we repositioned an antimalarial compound class by derivatising it based on the so-called "eNTRy" rules for enhanced accumulation into Gram-negative bacteria. We designed, synthesised and evaluated a small library of amino acid modified compounds together with the respective Boc-protected analogues, leading to no substantial improvement in antibacterial activity against Escherichia coli wild-type K12, whereas more distinct activity differences were observed in E. coli mutant strains ΔtolC, D22, ΔacrB and BL21(DE3)omp8. A comparison of the activity results of the E. coli mutants with respect to the known rules related to enhanced activity against Gram-negative bacteria revealed that applicability of the rules is not always ensured. Out of the four amino acids used in this study, glycine derivatives showed highest antibacterial activity, although still suffering from efflux issues.
Collapse
Affiliation(s)
- Henni-Karoliina Ropponen
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus Building E8.1 66123 Saarbrücken Germany
- Department of Pharmacy, Saarland University Campus Building E8.1 66123 Saarbrücken Germany
| | - Eleonora Diamanti
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus Building E8.1 66123 Saarbrücken Germany
| | - Alexandra Siemens
- Hamburg School of Food Science, University of Hamburg Grindelallee 117 20146 Hamburg Germany
| | - Boris Illarionov
- Hamburg School of Food Science, University of Hamburg Grindelallee 117 20146 Hamburg Germany
| | - Jörg Haupenthal
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus Building E8.1 66123 Saarbrücken Germany
| | - Markus Fischer
- Hamburg School of Food Science, University of Hamburg Grindelallee 117 20146 Hamburg Germany
| | - Matthias Rottmann
- Swiss Tropical and Public Health Institute Socinstrasse 57 4002 Basel Switzerland
- Universität Basel Petersplatz 1 4003 Basel Switzerland
| | | | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) Campus Building E8.1 66123 Saarbrücken Germany
- Department of Pharmacy, Saarland University Campus Building E8.1 66123 Saarbrücken Germany
| |
Collapse
|
78
|
Rimpiläinen T, Nunes A, Calado R, Fernandes AS, Andrade J, Ntungwe E, Spengler G, Szemerédi N, Rodrigues J, Gomes JP, Rijo P, Candeias NR. Increased antibacterial properties of indoline-derived phenolic Mannich bases. Eur J Med Chem 2021; 220:113459. [PMID: 33915373 DOI: 10.1016/j.ejmech.2021.113459] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/06/2021] [Accepted: 04/07/2021] [Indexed: 01/22/2023]
Abstract
The search for antibacterial agents for the combat of nosocomial infections is a timely problem, as antibiotic-resistant bacteria continue to thrive. The effect of indoline substituents on the antibacterial properties of aminoalkylphenols was studied, leading to the development of a library of compounds with minimum inhibitory concentrations (MICs) as low as 1.18 μM. Two novel aminoalkylphenols were identified as particularly promising, after MIC and minimum bactericidal concentrations (MBC) determination against a panel of reference strain Gram-positive bacteria, and further confirmed against 40 clinical isolates (Staphylococcus aureus, Staphylococcus epidermidis, Enterococcus faecalis, Enterococcus faecium, and Listeria monocytogenes). The same two aminoalkylphenols displayed low toxicity against two in vivo models (Artemia salina brine shrimp and Saccharomyces cerevisiae). The in vitro cytotoxicity evaluation (on human keratinocytes and human embryonic lung fibroblast cell lines) of the same compounds was also carried out. They demonstrated a particularly toxic effect on the fibroblast cell lines, with IC50 in the 1.7-5.1 μM range, thus narrowing their clinical use. The desired increase in the antibacterial properties of the aminoalkylphenols, particularly indoline-derived phenolic Mannich bases, was reached by introducing an additional nitro group in the indolinyl substituent or by the replacement of a methyl by a bioisosteric trifluoromethyl substituent in the benzyl group introduced through use of boronic acids in the Petasis borono-Mannich reaction. Notably, the introduction of an additional nitro moiety did not confer added toxicity to the aminoalkylphenols.
Collapse
Affiliation(s)
- Tatu Rimpiläinen
- Faculty of Engineering and Natural Sciences, Tampere University, Korkeakoulunkatu 8, 33101, Tampere, Finland
| | - Alexandra Nunes
- Department of Infectious Diseases, National Institute of Health, Avenida Padre Cruz, 1649-016, Lisboa, Portugal; Faculty of Veterinary Medicine, Lusófona University, Campo Grande 376, 1749-024, Lisboa, Portugal; CBIOS-Universidade Lusófona Research Center for Biosciences & Health Technologies, Campo Grande 376, 1749-024, Lisboa, Portugal.
| | - Rita Calado
- Department of Infectious Diseases, National Institute of Health, Avenida Padre Cruz, 1649-016, Lisboa, Portugal
| | - Ana S Fernandes
- CBIOS-Universidade Lusófona Research Center for Biosciences & Health Technologies, Campo Grande 376, 1749-024, Lisboa, Portugal
| | - Joana Andrade
- CBIOS-Universidade Lusófona Research Center for Biosciences & Health Technologies, Campo Grande 376, 1749-024, Lisboa, Portugal
| | - Epole Ntungwe
- CBIOS-Universidade Lusófona Research Center for Biosciences & Health Technologies, Campo Grande 376, 1749-024, Lisboa, Portugal
| | - Gabriella Spengler
- Department of Medical Microbiology and Immunobiology, Faculty of Medicine, University of Szeged, Dóm tér 10, 6720, Szeged, Hungary
| | - Nikoletta Szemerédi
- Department of Medical Microbiology and Immunobiology, Faculty of Medicine, University of Szeged, Dóm tér 10, 6720, Szeged, Hungary
| | - João Rodrigues
- Department of Infectious Diseases, National Institute of Health, Avenida Padre Cruz, 1649-016, Lisboa, Portugal
| | - João Paulo Gomes
- Department of Infectious Diseases, National Institute of Health, Avenida Padre Cruz, 1649-016, Lisboa, Portugal
| | - Patricia Rijo
- CBIOS-Universidade Lusófona Research Center for Biosciences & Health Technologies, Campo Grande 376, 1749-024, Lisboa, Portugal; Instituto de Investigação do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - Nuno R Candeias
- Faculty of Engineering and Natural Sciences, Tampere University, Korkeakoulunkatu 8, 33101, Tampere, Finland; LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193, Aveiro, Portugal.
| |
Collapse
|
79
|
Chan LW, Hern KE, Ngambenjawong C, Lee K, Kwon EJ, Hung DT, Bhatia SN. Selective Permeabilization of Gram-Negative Bacterial Membranes Using Multivalent Peptide Constructs for Antibiotic Sensitization. ACS Infect Dis 2021; 7:721-732. [PMID: 33689277 PMCID: PMC8043124 DOI: 10.1021/acsinfecdis.0c00805] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The drug-impermeable bacterial membrane in Gram-negative pathogens limits antibiotic access to intracellular drug targets. To expand our rapidly waning antibiotic arsenal, one approach is to improve the intracellular delivery of drugs with historically poor accumulation in Gram-negative bacteria. To do so, we engineered macromolecular potentiators to permeabilize the Gram-negative membrane to facilitate drug influx. Potentiators, known as WD40, were synthesized by grafting multiple copies of a cationic α-helical antimicrobial peptide, WLBU2, onto a dextran polymer scaffold. WD40 enabled drug uptake in the model pathogen P. aeruginosa, a capability that was not observed with unmodified WLBU2 peptide. WD40 was able to reduce minimum inhibitory concentrations of a drug panel by up to 3 orders of magnitude. Hydrophobic and highly three-dimensional antibiotics exhibited the greatest potentiation. Antibiotic activity was potentiated in several clinical strains and resulted in sensitization of drug-resistant strains to rifampin, a drug not previously used for Gram-negative infections.
Collapse
Affiliation(s)
- Leslie W. Chan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Kelsey E. Hern
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Chayanon Ngambenjawong
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Katie Lee
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02139, United States
| | - Ester J. Kwon
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Deborah T. Hung
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02139, United States
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Sangeeta N. Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02139, United States
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| |
Collapse
|
80
|
Myers AG, Clark RB. Discovery of Macrolide Antibiotics Effective against Multi-Drug Resistant Gram-Negative Pathogens. Acc Chem Res 2021; 54:1635-1645. [PMID: 33691070 DOI: 10.1021/acs.accounts.1c00020] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Macrolides are among the most widely prescribed antibiotics, particularly for bacterial lung infections, due to their favorable safety, oral bioavailability, and spectrum of activity against Gram-positive pathogens such as Streptococcus pneumoniae, the most common cause of bacterial pneumonia. Their utility against Gram-negative bacteria is extremely limited and does not include the Enterobacteriaceae or other ESKAPE pathogens. With the increasing development of resistance to current therapies and the lack of safe, oral options to treat Gram-negative infections, extended-spectrum macrolides have the potential to provide valuable treatment options. While the bacterial ribosome, the target of macrolides, is highly conserved across Gram-positive and Gram-negative bacteria, traditional macrolides do not possess the proper physicochemical properties to cross the polar Gram-negative outer membrane and are highly susceptible to efflux. As with most natural product-derived compounds, macrolides are generally prepared through semisynthesis, which is limited in scope and lacks the ability to make the drastic physicochemical property changes necessary to overcome these hurdles.By using a fully synthetic platform technology to greatly expand structural diversity, novel macrolides were prepared with a focus on lowering the MW and increasing the polarity to achieve a physicochemical property profile more similar to that of traditional Gram-negative drug classes. In addition to the removal of lipophilic groups, a critical structural feature for obtaining Gram-negative activity in the macrolide class proved to be the introduction of small secondary or tertiary amines to yield polycationic species potentially capable of self-promoted uptake. Within the azithromycin-like 15-membered azalides, potent activity was seen when small alkyl amines were introduced at the 6'-position of desosamine. The biggest gains, however, were made by replacing the entire C10-C13 fragment of the macrolactone ring with commercially available or readily synthesized 1,2-aminoalcohols, leading to 13-membered azalides. The introduction of a tethered basic amine at the C10-position and systematic optimization of substitution and tether length and flexibility ultimately provided new macrolides that for the first time exhibit clinically relevant antibacterial activity against multi-drug resistant Gram-negative bacteria. A retrospective computational analysis of >1800 fully synthetic macrolides prepared during this effort identified key drivers and optimum ranges for improving permeability and avoiding efflux. In contrast to standard Gram-negative drugs which generally have MWs below 600 and clogD7.4 values below 0, we found that the ideal ranges for Gram-negative macrolides were MW between 600 and 720 and cLogD7.4 between -1 and 3. A total charge of between 2.5 and 3 was also required to provide optimal permeability and efflux avoidance. Thus, Gram-negative macrolides occupy a unique physicochemical property space that lies between traditional Gram-negative drug classes and Gram-positive macrolides.
Collapse
Affiliation(s)
- Andrew G. Myers
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Roger B. Clark
- Zikani Therapeutics, 480 Arsenal Way, Watertown, Massachusetts 02472, United States
| |
Collapse
|
81
|
In Vivo Targeting of Escherichia coli with Vancomycin-Arginine. Antimicrob Agents Chemother 2021; 65:AAC.02416-20. [PMID: 33468474 PMCID: PMC8097466 DOI: 10.1128/aac.02416-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 12/25/2020] [Indexed: 12/20/2022] Open
Abstract
The ability of vancomycin-arginine (V-r) to extend the spectrum of activity of glycopeptides to Gram-negative bacteria was investigated. Its MIC toward Escherichia coli, including β-lactamase expressing Ambler classes A, B, and D, was 8 to 16 μg/ml. The ability of vancomycin-arginine (V-r) to extend the spectrum of activity of glycopeptides to Gram-negative bacteria was investigated. Its MIC towards Escherichia coli, including β-lactamase expressing Ambler classes A, B, and D, was 8 to 16 μg/ml. Addition of 8 times the MIC of V-r to E. coli was acutely bactericidal and associated with a low frequency of resistance (<2.32 × 10−10). In vivo, V-r markedly reduced E. coli burden by >7 log10 CFU/g in a thigh muscle model. These data warrant further development of V-r in combatting E. coli, including resistant forms.
Collapse
|
82
|
Prajapati JD, Kleinekathöfer U, Winterhalter M. How to Enter a Bacterium: Bacterial Porins and the Permeation of Antibiotics. Chem Rev 2021; 121:5158-5192. [PMID: 33724823 DOI: 10.1021/acs.chemrev.0c01213] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Despite tremendous successes in the field of antibiotic discovery seen in the previous century, infectious diseases have remained a leading cause of death. More specifically, pathogenic Gram-negative bacteria have become a global threat due to their extraordinary ability to acquire resistance against any clinically available antibiotic, thus urging for the discovery of novel antibacterial agents. One major challenge is to design new antibiotics molecules able to rapidly penetrate Gram-negative bacteria in order to achieve a lethal intracellular drug accumulation. Protein channels in the outer membrane are known to form an entry route for many antibiotics into bacterial cells. Up until today, there has been a lack of simple experimental techniques to measure the antibiotic uptake and the local concentration in subcellular compartments. Hence, rules for translocation directly into the various Gram-negative bacteria via the outer membrane or via channels have remained elusive, hindering the design of new or the improvement of existing antibiotics. In this review, we will discuss the recent progress, both experimentally as well as computationally, in understanding the structure-function relationship of outer-membrane channels of Gram-negative pathogens, mainly focusing on the transport of antibiotics.
Collapse
Affiliation(s)
| | | | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen 28759, Germany
| |
Collapse
|
83
|
Muñoz KA, Hergenrother PJ. Facilitating Compound Entry as a Means to Discover Antibiotics for Gram-Negative Bacteria. Acc Chem Res 2021; 54:1322-1333. [PMID: 33635073 DOI: 10.1021/acs.accounts.0c00895] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
It has been over half a century since the last class of antibiotics active against the most problematic Gram-negative bacteria was approved by the Food and Drug Administration (FDA). The major challenge with developing antibiotics to treat these infections is not drug-target engagement but rather the inability of most small molecules to traverse the Gram-negative membranes, be retained, and accumulate within the cell. Despite an abundance of lead compounds, limited understanding of the physicochemical properties needed for compound accumulation (or avoidance of efflux) in Gram-negative bacteria has precluded a generalizable approach for developing Gram-negative antibiotics. Indeed, in many instances, despite years of intensive derivatization efforts and the synthesis of hundreds of compounds aimed at building in Gram-negative activity, little or no progress has been made in expanding the spectrum of activity for many Gram-positive-only antibiotics. In this Account, we describe the discovery and successful applications of a promising strategy for enhancing the accumulation of Gram-positive-only antibiotics as a means of imbuing compounds with broad-spectrum activity.Utilizing a prospective approach examining the accumulation in Escherichia coli for more than 180 diverse compounds, we found that small molecules have an increased likelihood to accumulate in E. coli when they contain an ionizable Nitrogen, have low Three-dimensionality, and are Rigid. Implementing these guidelines, codified as the "eNTRy rules" and assisted by web application www.entry-way.org, we have facilitated compound entry and systematically built Gram-negative activity into Gram-positive-only antibiotics. Though each antibiotic will have case-specific considerations, we describe a set of important criteria to consider when selecting candidate Gram-positive-only antibiotics for conversion to Gram-negative-active versions via the eNTRy rules. As detailed herein, using this blueprint the spectrum of activity was expanded for three antibiotic classes that engage three different biological targets: DNA gyrase inhibitor 6DNM, FabI inhibitor Debio-1452, and FMN riboswitch inhibitor Ribocil C. In each scenario, the eNTRy rules guided the synthesis of key analogues predisposed to accumulate in Gram-negative bacteria leading to compounds that display antibiotic activity (minimum inhibitory concentrations (MIC) ≤8 μg mL-1) against E. coli and other Gram-negative ESKAPE pathogens. While the eNTRy rules will continue to be refined and enhanced as more accumulation data is gathered, on the basis of these collective results and on other examples not covered herein it is clear that the eNTRy rules are actionable for the development of novel broad-spectrum antibiotics from Gram-positive-only compounds. By enabling the prediction of compound accumulation, the eNTRy rules should facilitate the process of discovering and developing novel antibiotics active against Gram-negative bacteria.
Collapse
Affiliation(s)
- Kristen A. Muñoz
- Department of Chemistry Institute for Genomic Biology, University of Illinois, Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Paul J. Hergenrother
- Department of Chemistry Institute for Genomic Biology, University of Illinois, Urbana−Champaign, Urbana, Illinois 61801, United States
| |
Collapse
|
84
|
Toscani A, Hind C, Clifford M, Kim SH, Gucic A, Woolley C, Saeed N, Rahman KM, Sutton JM, Castagnolo D. Development of photoactivable phenanthroline-based manganese(I) CO-Releasing molecules (PhotoCORMs) active against ESKAPE bacteria and bacterial biofilms. Eur J Med Chem 2021; 213:113172. [PMID: 33516984 DOI: 10.1016/j.ejmech.2021.113172] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 01/06/2021] [Accepted: 01/07/2021] [Indexed: 02/02/2023]
Abstract
The synthesis and biological evaluation of a series of phenanthroline-based visible-light-activated manganese(I) carbon-monoxide-releasing molecules (PhotoCORMs) against ESKAPE bacteria and bacterial biofilms is reported. Four carbonyl compounds of general formula fac-[Mn(N∧N)(CO)3(L)] have been synthesized and characterized. Despite being thermally stable in the absence of light, these PhotoCORMs readily release CO upon blue (435-450 nm) LED light irradiation as confirmed by spectrophotometric CO releasing experiments (Mb Assay). The antibacterial activity of the four PhotoCORMs has been investigated against a panel of ESKAPE bacteria. The compounds 1-3 were found to be effective antibacterials at low concentrations against multidrug-resistant Klebsiella pneumoniae and Acinetobacter baumannii when photoactivated with blue-light. In addition, the PhotoCORMs 1-2 were found to inhibit the formation of Klebsiella pneumoniae and Acinetobacter baumannii bacterial biofilms at low concentrations (MIC = 4-8 μg/mL), turning out to be promising candidates to combat antimicrobial resistance. The antibacterial and biofilm inhibitory effect of the PhotoCORMs is plausibly due to the release of CO as well as the formation of phenanthroline photo-by-products as revealed by spectroscopy and microbiology experiments.
Collapse
Affiliation(s)
- Anita Toscani
- School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 1DB, United Kingdom
| | - Charlotte Hind
- Research and Development Institute, National Infections Service, Porton Down, Public Health England, Salisbury SP4 0JG, Wiltshire, United Kingdom
| | - Melanie Clifford
- Research and Development Institute, National Infections Service, Porton Down, Public Health England, Salisbury SP4 0JG, Wiltshire, United Kingdom
| | - Seong-Heun Kim
- School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 1DB, United Kingdom
| | - Antonia Gucic
- School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 1DB, United Kingdom
| | - Charlotte Woolley
- Research and Development Institute, National Infections Service, Porton Down, Public Health England, Salisbury SP4 0JG, Wiltshire, United Kingdom
| | - Naima Saeed
- School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 1DB, United Kingdom
| | - Khondaker Miraz Rahman
- School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 1DB, United Kingdom
| | - J Mark Sutton
- Research and Development Institute, National Infections Service, Porton Down, Public Health England, Salisbury SP4 0JG, Wiltshire, United Kingdom.
| | - Daniele Castagnolo
- School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 1DB, United Kingdom.
| |
Collapse
|
85
|
Hobson C, Chan AN, Wright GD. The Antibiotic Resistome: A Guide for the Discovery of Natural Products as Antimicrobial Agents. Chem Rev 2021; 121:3464-3494. [PMID: 33606500 DOI: 10.1021/acs.chemrev.0c01214] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The use of life-saving antibiotics has long been plagued by the ability of pathogenic bacteria to acquire and develop an array of antibiotic resistance mechanisms. The sum of these resistance mechanisms, the antibiotic resistome, is a formidable threat to antibiotic discovery, development, and use. The study and understanding of the molecular mechanisms in the resistome provide the basis for traditional approaches to combat resistance, including semisynthetic modification of naturally occurring antibiotic scaffolds, the development of adjuvant therapies that overcome resistance mechanisms, and the total synthesis of new antibiotics and their analogues. Using two major classes of antibiotics, the aminoglycosides and tetracyclines as case studies, we review the success and limitations of these strategies when used to combat the many forms of resistance that have emerged toward natural product-based antibiotics specifically. Furthermore, we discuss the use of the resistome as a guide for the genomics-driven discovery of novel antimicrobials, which are essential to combat the growing number of emerging pathogens that are resistant to even the newest approved therapies.
Collapse
Affiliation(s)
- Christian Hobson
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Andrew N Chan
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| | - Gerard D Wright
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada
| |
Collapse
|
86
|
Zgurskaya HI, Walker JK, Parks JM, Rybenkov VV. Multidrug Efflux Pumps and the Two-Faced Janus of Substrates and Inhibitors. Acc Chem Res 2021; 54:930-939. [PMID: 33539084 PMCID: PMC8208102 DOI: 10.1021/acs.accounts.0c00843] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Antibiotics are miracle drugs that can cure infectious bacterial diseases. However, their utility is challenged by antibiotic-resistant bacteria emerging in clinics and straining modern medicine and our ways of life. Certain bacteria such as Gram-negative (Gram(-)) and Mycobacteriales species are intrinsically resistant to most clinical antibiotics and can further gain multidrug resistance through mutations and plasmid acquisition. These species stand out by the presence of an additional external lipidic membrane, the outer membrane (OM), that is composed of unique glycolipids. Although formidable, the OM is a passive permeability barrier that can reduce penetration of antibiotics but cannot affect intracellular steady-state concentrations of drugs. The two-membrane envelopes are further reinforced by active efflux transporters that expel antibiotics from cells against their concentration gradients. The major mechanism of antibiotic resistance in Gram(-) pathogens is the active efflux of drugs, which acts synergistically with the low permeability barrier of the OM and other mutational and plasmid-borne mechanisms of antibiotic resistance.The synergy between active efflux and slow uptake offers Gram(-) bacteria an impressive degree of protection from potentially harmful chemicals, but it is also their Achilles heel. Kinetic studies have revealed that even small changes in the efficiency of either of the two factors can have dramatic effects on drug penetration into the cell. In line with these expectations, two major approaches to overcome this antibiotic resistance mechanism are currently being explored: (1) facilitation of antibiotic penetration across the outer membranes and (2) avoidance and inhibition of clinically relevant multidrug efflux pumps. Herein we summarize the progress in the latter approach with a focus on efflux pumps from the resistance-nodulation-division (RND) superfamily. The ability to export various substrates across the OM at the expense of the proton-motive force acting on the inner membrane and the engagement of accessory proteins for their functions are the major mechanistic advantages of these pumps. Both the RND transporters and their accessory proteins are being targeted in the discovery of efflux pump inhibitors, which in combination with antibiotics can potentiate antibacterial activities. We discuss intriguing relationships between substrates and inhibitors of efflux pumps, as these two types of ligands face similar barriers and binding sites in the transporters and accessory proteins and both types of activities often occur with the same chemical scaffold. Several distinct chemical classes of efflux inhibitors have been discovered that are as structurally diverse as the substrates of efflux pumps. Recent mechanistic insights, both empirical and computational, have led to the identification of features that distinguish OM permeators and efflux pump avoiders as well as efflux inhibitors from substrates. These findings suggest a path forward for optimizing the OM permeation and efflux-inhibitory activities in antibiotics and other chemically diverse compounds.
Collapse
Affiliation(s)
- Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - John K Walker
- Department of Pharmacological and Physiological Science, Saint Louis University School of Medicine, St. Louis, Missouri 63104, United States
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Valentin V Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| |
Collapse
|
87
|
Veale CGL. Into the Fray! A Beginner's Guide to Medicinal Chemistry. ChemMedChem 2021; 16:1199-1225. [PMID: 33591595 DOI: 10.1002/cmdc.202000929] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Indexed: 12/31/2022]
Abstract
Modern medicinal chemistry is a complex, multidimensional discipline that operates at the interface of the chemical and biological sciences. The medicinal chemistry contribution to drug discovery is typically described in the context of the well-recited linear progression of the drug discovery pipeline. However, compound optimization is idiosyncratic to each project, and clear definitions of hit and lead molecules and the subsequent progress along the pipeline becomes easily blurred. In addition, this description lacks insight into the entangled relationship between chemical and pharmacological properties, and thus provides limited guidance on how innovative medicinal chemistry strategies can be applied to solve optimization problems, regardless of the stage in the pipeline. Through discussion and illustrative examples, this article seeks to provide insights into the finesse of medicinal chemistry and the subtlety of balancing chemical properties pharmacology. In so doing, it aims to serve as an accessible and simple-to-digest guide for anyone who wishes to learn about the underlying principles of medicinal chemistry, in a context that has been decoupled from the pipeline description.
Collapse
Affiliation(s)
- Clinton G L Veale
- School of Chemistry and Physics, Pietermaritzburg Campus, University of KwaZulu-Natal, Private Bag X01, Pietermaritzburg, Scottsville, 3209, South Africa
| |
Collapse
|
88
|
Varney AM, Smitten KL, Thomas JA, McLean S. Transcriptomic Analysis of the Activity and Mechanism of Action of a Ruthenium(II)-Based Antimicrobial That Induces Minimal Evolution of Pathogen Resistance. ACS Pharmacol Transl Sci 2021; 4:168-178. [PMID: 33615170 PMCID: PMC7887750 DOI: 10.1021/acsptsci.0c00159] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Indexed: 01/30/2023]
Abstract
Increasing concern over rising levels of antibiotic resistance among pathogenic bacteria has prompted significant research into developing efficacious alternatives to antibiotic treatment. Previously, we have reported on the therapeutic activity of a dinuclear ruthenium(II) complex against pathogenic, multi-drug-resistant bacterial pathogens. Herein, we report that the solubility properties of this lead are comparable to those exhibited by orally available therapeutics that in comparison to clinically relevant antibiotics it induces very slow evolution of resistance in the uropathogenic, therapeutically resistant, E. coli strain EC958, and this resistance was lost when exposure to the compound was temporarily removed. With the aim of further investigating the mechanism of action of this compound, the regulation of nine target genes relating to the membrane, DNA damage, and other stress responses provoked by exposure to the compound was also studied. This analysis confirmed that the compound causes a significant transcriptional downregulation of genes involved in membrane transport and the tricarboxylic acid cycle. By contrast, expression of the chaperone protein-coding gene, spy, was significantly increased suggesting a requirement for repair of damaged proteins in the region of the outer membrane. The complex was also found to display activity comparable to that in E. coli in a range of other therapeutically relevant Gram-negative pathogens.
Collapse
Affiliation(s)
- Adam M. Varney
- School
of Science and Technology, Nottingham Trent
University, Nottingham NG11 8NS, United Kingdom
| | - Kirsty L. Smitten
- Department
of Chemistry, The University of Sheffield, Western Bank, Sheffield S3 7HF, United
Kingdom
| | - Jim A. Thomas
- Department
of Chemistry, The University of Sheffield, Western Bank, Sheffield S3 7HF, United
Kingdom
| | - Samantha McLean
- School
of Science and Technology, Nottingham Trent
University, Nottingham NG11 8NS, United Kingdom
| |
Collapse
|
89
|
Cyanidin-3-glucoside Lipophilic Conjugates for Topical Application: Tuning the Antimicrobial Activities with Fatty Acid Chain Length. Processes (Basel) 2021. [DOI: 10.3390/pr9020340] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background: Natural anthocyanins present a low solubility in lipophilic media, which compromises their effective application in lipophilic systems. In this work, cyanidin-3-O-glucoside (Cy3glc) was esterified by the addition of fatty acids with increasing chain-lengths and a structure-activity relationship was performed towards the description of the best analog for skin-care applications. Methods: By enzymatic hemi-synthesis, it was possible to obtain 5 structurally related derivatives of cyanidin-3-O-glucoside with successive C2 increments in the aliphatic chain. The stability in hanks buffer and DMEM with or without FBS was followed by HPLC. The cytotoxicity against keratinocytes was evaluated by MTT assay. The antioxidant capacity was determined by using the fluorescent probe DCF-DA. The effect on enzyme activity was evaluated towards tyrosinase, collagenase, and elastase enzymes by colorimetric assays. MIC and MBC values were obtained against reference strains and against multidrug-resistant isolates. Results: In physiological conditions, cy3glc−fatty acid derivatives are more stable and may be converted to the native anthocyanin. The 5 conjugates showed lower antioxidant capacity and enzymatic inhibitory activities in comparison to the anthocyanin precursor. However, concerning the antibacterial activity, the insertion of a fatty acid chain sprouted the antibacterial activity, showing a clear biphasic effect and a more effective effect on Gram-positive bacteria. Conclusions: Cy3glc-C10 was the most effective compound considering the antimicrobial activity, although a general reduction was observed among the other activities evaluated. This work prompt further assays with a different panoply of derivatives ranging other features including saturation vs. unsaturation, even vs. odd carbon content and linear vs. branched.
Collapse
|
90
|
New dual ATP-competitive inhibitors of bacterial DNA gyrase and topoisomerase IV active against ESKAPE pathogens. Eur J Med Chem 2021; 213:113200. [PMID: 33524686 DOI: 10.1016/j.ejmech.2021.113200] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/10/2020] [Accepted: 01/12/2021] [Indexed: 11/21/2022]
Abstract
The rise in multidrug-resistant bacteria defines the need for identification of new antibacterial agents that are less prone to resistance acquisition. Compounds that simultaneously inhibit multiple bacterial targets are more likely to suppress the evolution of target-based resistance than monotargeting compounds. The structurally similar ATP binding sites of DNA gyrase and topoisomerase Ⅳ offer an opportunity to accomplish this goal. Here we present the design and structure-activity relationship analysis of balanced, low nanomolar inhibitors of bacterial DNA gyrase and topoisomerase IV that show potent antibacterial activities against the ESKAPE pathogens. For inhibitor 31c, a crystal structure in complex with Staphylococcus aureus DNA gyrase B was obtained that confirms the mode of action of these compounds. The best inhibitor, 31h, does not show any in vitro cytotoxicity and has excellent potency against Gram-positive (MICs: range, 0.0078-0.0625 μg/mL) and Gram-negative pathogens (MICs: range, 1-2 μg/mL). Furthermore, 31h inhibits GyrB mutants that can develop resistance to other drugs. Based on these data, we expect that structural derivatives of 31h will represent a step toward clinically efficacious multitargeting antimicrobials that are not impacted by existing antimicrobial resistance.
Collapse
|
91
|
Kong Q, Yang Y. Recent advances in antibacterial agents. Bioorg Med Chem Lett 2021; 35:127799. [PMID: 33476772 DOI: 10.1016/j.bmcl.2021.127799] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/10/2021] [Accepted: 01/11/2021] [Indexed: 12/12/2022]
Abstract
Antimicrobial resistance is a global challenge and the effectiveness of old antibiotics is decreasing. Discovery and development of antibacterial agents have been accelerated to replenish the arsenal of antibiotics which is limited and shrinking. In recent years, significant advances have achieved in the antibacterial area, including new compounds of known classes and new compounds with new mechanisms. This review summarizes these advances and provides perspective on future directions of antibacterial agents.
Collapse
Affiliation(s)
- Qidi Kong
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Beijing 100049, China
| | - Yushe Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Beijing 100049, China.
| |
Collapse
|
92
|
Abstract
Antibiotic-resistant bacteria rapidly spread in clinical and natural environments and challenge our modern lifestyle. A major component of defense against antibiotics in Gram-negative bacteria is a drug permeation barrier created by active efflux across the outer membrane. We identified molecular determinants defining the propensity of small peptidomimetic molecules to avoid and inhibit efflux pumps in Pseudomonas aeruginosa, a human pathogen notorious for its antibiotic resistance. Combining experimental and computational protocols, we mapped the fate of the compounds from structure-activity relationships through their dynamic behavior in solution, permeation across both the inner and outer membranes, and interaction with MexB, the major efflux transporter of P. aeruginosa We identified predictors of efflux avoidance and inhibition and demonstrated their power by using a library of traditional antibiotics and compound series and by generating new inhibitors of MexB. The identified predictors will enable the discovery and optimization of antibacterial agents suitable for treatment of P. aeruginosa infections.IMPORTANCE Efflux pump avoidance and inhibition are desired properties for the optimization of antibacterial activities against Gram-negative bacteria. However, molecular and physicochemical interactions defining the interface between compounds and efflux pumps remain poorly understood. We identified properties that correlate with efflux avoidance and inhibition, are predictive of similar features in structurally diverse compounds, and allow researchers to distinguish between efflux substrates, inhibitors, and avoiders in P. aeruginosa The developed predictive models are based on the descriptors representative of different clusters comprising a physically intuitive combination of properties. Molecular shape (represented by acylindricity), amphiphilicity (anisotropic polarizability), aromaticity (number of aromatic rings), and the partition coefficient (LogD) are physicochemical predictors of efflux inhibitors, whereas interactions with Pro668 and Leu674 residues of MexB distinguish between inhibitors/substrates and efflux avoiders. The predictive models and efflux rules are applicable to compounds with unrelated chemical scaffolds and pave the way for development of compounds with the desired efflux interface properties.
Collapse
|
93
|
Pereira CDS, Enes KB, de Almeida AM, de Mendonça CC, da Silva VL, Gallupo Diniz C, Couri MRC, Silva H. Syntheses and biological activity of platinum(II) and palladium(II) complexes with phenyl-oxadiazole-ethylenediamine ligands. J COORD CHEM 2021. [DOI: 10.1080/00958972.2021.1871608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
| | - Karine Braga Enes
- Departamento de Química, Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | | | | | - Vânia Lúcia da Silva
- Departamento de Parasitologia, Microbiologia e Imunologia, Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Cláudio Gallupo Diniz
- Departamento de Parasitologia, Microbiologia e Imunologia, Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Mara Rubia Costa Couri
- Departamento de Química, Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Heveline Silva
- Departamento de Química, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| |
Collapse
|
94
|
Perlmutter SJ, Geddes EJ, Drown BS, Motika SE, Lee MR, Hergenrother PJ. Compound Uptake into E. coli Can Be Facilitated by N-Alkyl Guanidiniums and Pyridiniums. ACS Infect Dis 2021; 7:162-173. [PMID: 33228356 PMCID: PMC7796962 DOI: 10.1021/acsinfecdis.0c00715] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Multidrug-resistant Gram-negative bacterial infections are on the rise, and with no FDA approvals for new classes of broad-spectrum antibiotics in over 50 years, these infections constitute a major threat to human health. A significant challenge is the inability of most compounds to accumulate in Gram-negative bacteria. Recently developed predictive guidelines show that appending a primary amine to an appropriately shaped compound can enhance Gram-negative accumulation. Here, we report that other positively charged nitrogen functional groups, namely, N-alkyl guanidiniums and pyridiniums, can also facilitate compound uptake into Gram-negative bacteria. The accumulation of a set of 60 nonantibiotic compounds, consisting of 20 primary amines and their corresponding guanidiniums and pyridiniums, was assessed in Escherichia coli. We also installed these alternate functional groups onto antibiotic scaffolds and assessed their accumulation and antibacterial activity in Gram-negative bacteria. The results suggest that other positively-charged, nitrogen-containing functional groups should be considered when designing antibiotics with Gram-negative activity.
Collapse
Affiliation(s)
- Sarah J Perlmutter
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801, United States
| | - Emily J Geddes
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801, United States
| | - Bryon S Drown
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801, United States
| | - Stephen E Motika
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801, United States
| | - Myung Ryul Lee
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801, United States
| | - Paul J Hergenrother
- Roger Adams Laboratory, Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois 61801, United States
| |
Collapse
|
95
|
Zhao S, Adamiak JW, Bonifay V, Mehla J, Zgurskaya HI, Tan DS. Defining new chemical space for drug penetration into Gram-negative bacteria. Nat Chem Biol 2020; 16:1293-1302. [PMID: 33199906 PMCID: PMC7897441 DOI: 10.1038/s41589-020-00674-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 09/11/2020] [Indexed: 12/24/2022]
Abstract
We live in the era of antibiotic resistance, and this problem will progressively worsen if no new solutions emerge. In particular, Gram-negative pathogens present both biological and chemical challenges that hinder the discovery of new antibacterial drugs. First, these bacteria are protected from a variety of structurally diverse drugs by a low-permeability barrier composed of two membranes with distinct permeability properties, in addition to active drug efflux, making this cell envelope impermeable to most compounds. Second, chemical libraries currently used in drug discovery contain few compounds that can penetrate Gram-negative bacteria. As a result of these challenges, intensive screening campaigns have led to few successes, highlighting the need for new approaches to identify regions of chemical space that are specifically relevant to antibacterial drug discovery. Herein we provide an overview of emerging insights into this problem and outline a general approach to addressing it using prospective analysis of chemical libraries for the ability of compounds to accumulate in Gram-negative bacteria. The overall goal is to develop robust cheminformatic tools to predict Gram-negative permeation and efflux, which can then be used to guide medicinal chemistry campaigns and the design of antibacterial discovery libraries.
Collapse
Affiliation(s)
- Shibin Zhao
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Justyna W Adamiak
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Vincent Bonifay
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Jitender Mehla
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA.
| | - Derek S Tan
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
96
|
Dalberto PF, de Souza EV, Abbadi BL, Neves CE, Rambo RS, Ramos AS, Macchi FS, Machado P, Bizarro CV, Basso LA. Handling the Hurdles on the Way to Anti-tuberculosis Drug Development. Front Chem 2020; 8:586294. [PMID: 33330374 PMCID: PMC7710551 DOI: 10.3389/fchem.2020.586294] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 09/25/2020] [Indexed: 12/17/2022] Open
Abstract
The global epidemic of tuberculosis (TB) imposes a sustained epidemiologic vigilance and investments in research by governments. Mycobacterium tuberculosis, the main causative agent of TB in human beings, is a very successful pathogen, being the main cause of death in the population among infectious agents. In 2018, ~10 million individuals were contaminated with this bacillus and became ill with TB, and about 1.2 million succumbed to the disease. Most of the success of the M. tuberculosis to linger in the population comes from its ability to persist in an asymptomatic latent state into the host and, in fact, the majority of the individuals are unaware of being contaminated. Even though TB is a treatable disease and is curable in most cases, the treatment is lengthy and laborious. In addition, the rise of resistance to first-line anti-TB drugs elicits a response from TB research groups to discover new chemical entities, preferably with novel mechanisms of action. The pathway to find a new TB drug, however, is arduous and has many barriers that are difficult to overcome. Fortunately, several approaches are available today to be pursued by scientists interested in anti-TB drug development, which goes from massively testing chemical compounds against mycobacteria, to discovering new molecular targets by genetic manipulation. This review presents some difficulties found along the TB drug development process and illustrates different approaches that might be used to try to identify new molecules or targets that are able to impair M. tuberculosis survival.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Luiz A. Basso
- Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF) and Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| |
Collapse
|
97
|
Cruz CD, Wrigstedt P, Moslova K, Iashin V, Mäkkylä H, Ghemtio L, Heikkinen S, Tammela P, Perea-Buceta JE. Installation of an aryl boronic acid function into the external section of N-aryl-oxazolidinones: Synthesis and antimicrobial evaluation. Eur J Med Chem 2020; 211:113002. [PMID: 33223262 DOI: 10.1016/j.ejmech.2020.113002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/02/2020] [Accepted: 11/04/2020] [Indexed: 10/23/2022]
Abstract
N-aryl-oxazolidinones is a prominent family of antimicrobials used for treating infections caused by clinically prevalent Gram-positive bacteria. Recently, boron-containing compounds have displayed intriguing potential in the antibiotic discovery setting. Herein, we report the unprecedented introduction of a boron-containing moiety such as an aryl boronic acid in the external region of the oxazolidinone structure via a chemoselective acyl coupling reaction. As a result, we accessed a series of analogues with a distal aryl boronic pharmacophore on the oxazolidinone scaffold. We identified that a peripheric linear conformation coupled with freedom of rotation and no further substitution on the external aryl boronic ring, an amido linkage with hydrogen bonding character, in addition to a para-relative disposition between boronic group and linker, are the optimal combination of structural features in this series for antimicrobial activity. In comparison to linezolid, the analogue comprising all those features, compound 20b, displayed levels of antimicrobial activity augmented by an eight-fold to a thirty-two-fold against a panel of Gram-positive strains, and a near one hundred-fold against Escherichia coli JW5503, a Gram-negative mutant strain with a defective efflux capability.
Collapse
Affiliation(s)
- Cristina D Cruz
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, 00014, Finland
| | - Pauli Wrigstedt
- Department of Chemistry, Faculty of Science, University of Helsinki, P.O. Box 55, 00014, Finland
| | - Karina Moslova
- Department of Chemistry, Faculty of Science, University of Helsinki, P.O. Box 55, 00014, Finland
| | - Vladimir Iashin
- Department of Chemistry, Faculty of Science, University of Helsinki, P.O. Box 55, 00014, Finland
| | - Heidi Mäkkylä
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, 00014, Finland
| | - Léo Ghemtio
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, 00014, Finland
| | - Sami Heikkinen
- Department of Chemistry, Faculty of Science, University of Helsinki, P.O. Box 55, 00014, Finland
| | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, 00014, Finland
| | - Jesus E Perea-Buceta
- Department of Chemistry, Faculty of Science, University of Helsinki, P.O. Box 55, 00014, Finland.
| |
Collapse
|
98
|
Discovery of small-molecule inhibitors of multidrug-resistance plasmid maintenance using a high-throughput screening approach. Proc Natl Acad Sci U S A 2020; 117:29839-29850. [PMID: 33168749 DOI: 10.1073/pnas.2005948117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Carbapenem-resistant Enterobacteriaceae (CRE) are multidrug-resistant pathogens for which new treatments are desperately needed. Carbapenemases and other types of antibiotic resistance genes are carried almost exclusively on large, low-copy-number plasmids (pCRE). Accordingly, small molecules that efficiently evict pCRE plasmids should restore much-needed treatment options. We therefore designed a high-throughput screen to identify such compounds. A synthetic plasmid was constructed containing the plasmid replication machinery from a representative Escherichia coli CRE isolate as well as a fluorescent reporter gene to easily monitor plasmid maintenance. The synthetic plasmid was then introduced into an E. coli K12 tolC host. We used this screening strain to test a library of over 12,000 known bioactive agents for molecules that selectively reduce plasmid levels relative to effects on bacterial growth. From 366 screen hits we further validated the antiplasmid activity of kasugamycin, an aminoglycoside; CGS 15943, a nucleoside analog; and Ro 90-7501, a bibenzimidazole. All three compounds exhibited significant antiplasmid activity including up to complete suppression of plasmid replication and/or plasmid eviction in multiple orthogonal readouts and potentiated activity of the carbapenem, meropenem, against a strain carrying the large, pCRE plasmid from which we constructed the synthetic screening plasmid. Additionally, we found kasugamycin and CGS 15943 blocked plasmid replication, respectively, by inhibiting expression or function of the plasmid replication initiation protein, RepE. In summary, we validated our approach to identify compounds that alter plasmid maintenance, confer resensitization to antimicrobials, and have specific mechanisms of action.
Collapse
|
99
|
Miller LM, Herman R, Gyulev I, Krauss TF, Thomas GH, Duhme-Klair AK. Synthesis and biochemical evaluation of cephalosporin analogues equipped with chemical tethers. RSC Adv 2020; 10:36485-36494. [PMID: 35517937 PMCID: PMC9056950 DOI: 10.1039/d0ra04893c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 09/25/2020] [Indexed: 02/04/2023] Open
Abstract
Molecular probes typically require structural modifications to allow for the immobilisation or bioconjugation with a desired substrate but the effects of these changes are often not evaluated. Here, we set out to determine the effects of attaching functional handles to a first-generation cephalosporin. A series of cephalexin derivatives was prepared, equipped with chemical tethers suitable for the site-selective conjugation of antibiotics to functionalised surfaces. The tethers were positioned remotely from the β-lactam ring to ensure minimal effect to the antibiotic's pharmacophore. Herein, the activity of the modified antibiotics was evaluated for binding to the therapeutic target, the penicillin binding proteins, and shown to maintain binding interactions. In addition, the deactivation of the modified drugs by four β-lactamases (TEM-1, CTX-M-15, AmpC, NDM-1) was investigated and the effect of the tethers on the catalytic efficiencies determined. CTX-M-15 was found to favour hydrolysis of the parent antibiotic without a tether, whereas AmpC and NDM-1 were found to favour the modified analogues. Furthermore, the antimicrobial activity of the derivatives was evaluated to investigate the effect of the structural modifications on the antimicrobial activity of the parent drug, cephalexin. Tethered β-lactam antibiotics provide insights into designing chemical tools to target specific β-lactamases.![]()
Collapse
Affiliation(s)
- Lisa M Miller
- Department of Chemistry, University of York Heslington York YO10 5DD UK
| | - Reyme Herman
- Department of Biology, University of York Heslington York YO10 5DD UK
| | - Ivan Gyulev
- Department of Biology, University of York Heslington York YO10 5DD UK
| | - Thomas F Krauss
- Department of Physics, University of York Heslington York YO10 5DD UK
| | - Gavin H Thomas
- Department of Biology, University of York Heslington York YO10 5DD UK
| | | |
Collapse
|
100
|
Pandeya A, Ojo I, Alegun O, Wei Y. Periplasmic Targets for the Development of Effective Antimicrobials against Gram-Negative Bacteria. ACS Infect Dis 2020; 6:2337-2354. [PMID: 32786281 PMCID: PMC8187054 DOI: 10.1021/acsinfecdis.0c00384] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Antibiotic resistance has emerged as a serious threat to global public health in recent years. Lack of novel antimicrobials, especially new classes of compounds, further aggravates the situation. For Gram-negative bacteria, their double layered cell envelope and an array of efflux pumps act as formidable barriers for antimicrobials to penetrate. While cytoplasmic targets are hard to reach, proteins in the periplasm are clearly more accessible, as the drug only needs to breach the outer membrane. In this review, we summarized recent efforts on the validation and testing of periplasmic proteins as potential antimicrobial targets and the development of related inhibitors that either inhibit the growth of a bacterial pathogen or reduce its virulence during interaction with host cells. We conclude that the periplasm contains a promising pool of novel antimicrobial targets that should be scrutinized more closely for the development of effective treatment against multidrug-resistant Gram-negative bacteria.
Collapse
Affiliation(s)
- Ankit Pandeya
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Isoiza Ojo
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Olaniyi Alegun
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Yinan Wei
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| |
Collapse
|