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Mason CS, Avis T, Hu C, Nagalingam N, Mudaliar M, Coward C, Begum K, Gajewski K, Alam MJ, Bassères E, Moss S, Reich S, Duperchy E, Fox KR, Garey KW, Powell DJ. The Novel DNA Binding Mechanism of Ridinilazole, a Precision Clostridiodes difficile Antibiotic. Antimicrob Agents Chemother 2023; 67:e0156322. [PMID: 37093023 PMCID: PMC10246881 DOI: 10.1128/aac.01563-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 03/22/2023] [Indexed: 04/25/2023] Open
Abstract
Clostridioides difficile infection (CDI) causes substantial morbidity and mortality worldwide with limited antibiotic treatment options. Ridinilazole is a precision bisbenzimidazole antibiotic being developed to treat CDI and reduce unacceptably high rates of infection recurrence in patients. Although in late clinical development, the precise mechanism of action by which ridinilazole elicits its bactericidal activity has remained elusive. Here, we present conclusive biochemical and structural data to demonstrate that ridinilazole has a primary DNA binding mechanism, with a co-complex structure confirming binding to the DNA minor groove. Additional RNA-seq data indicated early pleiotropic changes to transcription, with broad effects on multiple C. difficile compartments and significant effects on energy generation pathways particularly. DNA binding and genomic localization was confirmed through confocal microscopy utilizing the intrinsic fluorescence of ridinilazole upon DNA binding. As such, ridinilazole has the potential to be the first antibiotic approved with a DNA minor groove binding mechanism of action.
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Affiliation(s)
| | - Tim Avis
- Summit Therapeutics, Cambridge, United Kingdom
| | - Chenlin Hu
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
| | | | | | | | - Khurshida Begum
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
| | - Kathleen Gajewski
- Department of Biology & Biochemistry, University of Houston Colleges of Natural Sciences and Mathematics, Houston, Texas, USA
| | - M. Jahangir Alam
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
| | - Eugenie Bassères
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
| | | | | | | | - Keith R. Fox
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Kevin W. Garey
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
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2
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Le D, Akiyama T, Weiss D, Kim M. Dissociation kinetics of small-molecule inhibitors in Escherichia coli is coupled to physiological state of cells. Commun Biol 2023; 6:223. [PMID: 36841892 PMCID: PMC9968327 DOI: 10.1038/s42003-023-04604-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 02/16/2023] [Indexed: 02/27/2023] Open
Abstract
Bioactive small-molecule inhibitors represent a treasure chest for future drugs. In vitro high-throughput screening is a common approach to identify the small-molecule inhibitors that bind tightly to purified targets. Here, we investigate the inhibitor-target binding/unbinding kinetics in E. coli cells using a benzimidazole-derivative DNA inhibitor as a model system. We find that its unbinding rate is not constant but depends on cell growth rate. This dependence is mediated by the cellular activity, forming a feedback loop with the inhibitor's activity. In accordance with this feedback, we find cell-to-cell heterogeneity in inhibitor-target interaction, leading to co-existence of two distinct subpopulations: actively growing cells that dissociate the inhibitors from the targets and non-growing cells that do not. We find similar heterogeneity for other clinical DNA inhibitors. Our studies reveal a mechanism that couples inhibitor-target kinetics to cell physiology and demonstrate the significant effect of this coupling on drug efficacy.
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Affiliation(s)
- Dai Le
- Department of Physics, Emory University, Atlanta, GA, 30322, USA
- Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA, 30322, USA
| | - Tatsuya Akiyama
- Department of Physics, Emory University, Atlanta, GA, 30322, USA
- Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA, 30322, USA
| | - David Weiss
- Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA, 30322, USA
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, GA, 30322, USA
- Antibiotic Research Center, Emory University, Atlanta, GA, 30322, USA
| | - Minsu Kim
- Department of Physics, Emory University, Atlanta, GA, 30322, USA.
- Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA, 30322, USA.
- Antibiotic Research Center, Emory University, Atlanta, GA, 30322, USA.
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3
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Rep V, Štulić R, Koštrun S, Kuridža B, Crnolatac I, Radić Stojković M, Paljetak HČ, Perić M, Matijašić M, Raić-Malić S. Novel tetrahydropyrimidinyl-substituted benzimidazoles and benzothiazoles: synthesis, antibacterial activity, DNA interactions and ADME profiling. RSC Med Chem 2022; 13:1504-1525. [PMID: 36561067 PMCID: PMC9749923 DOI: 10.1039/d2md00143h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 07/12/2022] [Indexed: 12/25/2022] Open
Abstract
A series of tetrahydropyrimidinyl-substituted benzimidazoles attached to various aliphatic or aromatic residues via phenoxymethylene were synthesised to investigate their antibacterial activities against selected Gram-positive and Gram-negative bacteria. The influence of the type of substituent at the C-3 and C-4 positions of the phenoxymethylene linker on the antibacterial activity was observed, showing that the aromatic moiety improved the antibacterial potency. Of all the evaluated compounds, benzoyl-substituted benzimidazole derivative 15a was the most active compound, particularly against the Gram-negative pathogens E. coli (MIC = 1 μg mL-1) and M. catarrhalis (MIC = 2 μg mL-1). Compound 15a also exhibited the most promising antibacterial activity against sensitive and resistant strains of S. pyogenes (MIC = 2 μg mL-1). Significant stabilization effects and positive induced CD bands strongly support the binding of the most biologically active benzimidazoles inside the minor grooves of AT-rich DNA, in line with docking studies. The predicted physico-chemical and ADME properties lie within drug-like space except for low membrane permeability, which needs further optimization. Our findings encourage further development of novel structurally related 5(6)-tetrahydropyrimidinyl substituted benzimidazoles in order to optimize their antibacterial effect against common respiratory pathogens.
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Affiliation(s)
- Valentina Rep
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of ZagrebMarulićev trg 1910000 ZagrebCroatia
| | - Rebeka Štulić
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of ZagrebMarulićev trg 1910000 ZagrebCroatia
| | - Sanja Koštrun
- Selvita d.o.oPrilaz baruna Filipovića 2910000 ZagrebCroatia
| | - Bojan Kuridža
- Ruđer Bošković Institute, Division of Organic Chemistry and BiochemistryBijenička cesta 5410000 ZagrebCroatia
| | - Ivo Crnolatac
- Ruđer Bošković Institute, Division of Organic Chemistry and BiochemistryBijenička cesta 5410000 ZagrebCroatia
| | - Marijana Radić Stojković
- Ruđer Bošković Institute, Division of Organic Chemistry and BiochemistryBijenička cesta 5410000 ZagrebCroatia
| | - Hana Čipčić Paljetak
- Department for Intercellular Communication, Center for Translational and Clinical Research, University of Zagreb School of MedicineŠalata 210000 ZagrebCroatia
| | - Mihaela Perić
- Department for Intercellular Communication, Center for Translational and Clinical Research, University of Zagreb School of MedicineŠalata 210000 ZagrebCroatia
| | - Mario Matijašić
- Department for Intercellular Communication, Center for Translational and Clinical Research, University of Zagreb School of MedicineŠalata 210000 ZagrebCroatia
| | - Silvana Raić-Malić
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of ZagrebMarulićev trg 1910000 ZagrebCroatia
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4
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Dale AG, Porcu A, Mann J, Neidle S. The mechanism of resistance in Escherichia coli to ridinilazole and other antibacterial head-to-head bis-benzimidazole compounds. Med Chem Res 2022. [DOI: 10.1007/s00044-022-02918-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AbstractThe appY gene has been characterised as conferring resistance to a novel series of antimicrobial benzimidazole derivatives in E. coli MC1061 cells when expressed in high copy-number. A microarray approach was used to identify genes involved in the mechanism of appY-mediated antibacterial resistance, that were up- or down-regulated following induction of the gene in the appY knockout strain JW0553. In total, expression of 90 genes was induced and 48 repressed greater than 2.5-fold (P < 0.05), 45 min after appY induction. Over half the genes up-regulated following appY expression had confirmed or putative roles in acid resistance (AR) and response to oxidative and antibiotic stresses. These included the genes for MdtE and MdtF, which form a multi-drug transporter with TolC and have been implicated in resistance to several antibiotics including erythromycin. Amongst the acid resistance genes were gadAB and adiAC encoding the glutamate-dependant (AR2) and arginine-dependant (AR3) acid resistance systems respectively, in addition to the transcriptional activators of these systems gadE and gadX. In agreement with earlier studies, appA, appCB and hyaA-F were also up-regulated following induction of appY. This study has also confirmed that over-expression of mdtEF confers resistance to these antibacterial benzimidazoles, indicating that the observation of appY conferring resistance to these compounds, proceeds through an appY-mediated up-regulation of this efflux transporter. To assess the importance of the AppY enzyme to acid stress responses, the percentage survival of bacteria in acidified media (pH ≤ 2) was measured. From an initial input of 1 × 106 CFU/ml, the wild-type strain MG1655 showed 7.29% and 0.46% survival after 2 and 4 h, respectively. In contrast, strain JW0553 in which appY is deleted was completely killed by the treatment. Transformation of JW0553 with a plasmid carrying appY returned survival to wild-type levels (7.85% and 1.03% survival at 2 and 4 h). Further dissection of the response by prior induction of each of the three AR systems has revealed that AR1 and AR3 were most affected by the absence of appY. This work highlights an important and previously unidentified role for the AppY enzyme in mediating the responses to several stress conditions. It is likely that the appY gene fits into a complex transcriptional regulatory network involving σS and gadE and gadX. Further work to pinpoint its position in such a hierarchy and to assess the contribution of appY to oxidative stress responses should help determine its full significance. This work is also consistent with recent studies in C. difficile showing that the mechanism of action of ridinilazole involves AT-rich DNA minor groove binding.
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Baron A, Sann CL, Mann J. Symmetric bis-benzimidazoles as DNA minor groove-binding agents with anti-tumour and antibacterial activity, and the evolution of the drug ridinilazole for the treatment of Clostridium difficile infections. Bioorg Med Chem 2022; 58:116656. [PMID: 35183028 DOI: 10.1016/j.bmc.2022.116656] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/07/2022] [Indexed: 11/02/2022]
Abstract
We report the synthesis of a range of symmetrical bis-benzimidazoles (BBZ) which possess anticancer and antibacterial activities. One of these BBZs has specific activity against Clostridium difficile and is currently in a phase 3 clinical evaluation as the drug ridinilazole. X-ray and computer modelling studies showed that BBZs typically exhibit high specificity for oligonucleotide sequences that occur in the minor groove of DNA.
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Affiliation(s)
- Anne Baron
- School of Chemistry, Queen's University Belfast, Belfast BT9 5AG, UK
| | - Christine Le Sann
- School of Chemistry, Queen's University Belfast, Belfast BT9 5AG, UK
| | - John Mann
- School of Chemistry, Queen's University Belfast, Belfast BT9 5AG, UK.
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6
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Bisbenzimidazole Derivatives as Potential Antimicrobial Agents: Design, Synthesis, Biological Evaluation and Pharmacophore Analysis. Pharm Chem J 2021. [DOI: 10.1007/s11094-021-02389-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Caymaz B, Yıldız U, Akkoç S, Gerçek Z, Şengül A, Coban B. Synthesis, Characterization, and Antiproliferative Activity Studies of Novel Benzimidazole‐Imidazopyridine Hybrids as DNA Groove Binders. ChemistrySelect 2020. [DOI: 10.1002/slct.202001580] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Bahar Caymaz
- Zonguldak Bülent Ecevit UniversityFaculty of Arts and SciencesDepartment of Chemistry 67100 Zonguldak Turkey
| | - Ufuk Yıldız
- Zonguldak Bülent Ecevit UniversityFaculty of Arts and SciencesDepartment of Chemistry 67100 Zonguldak Turkey
| | - Senem Akkoç
- Department of Basic Pharmaceutical SciencesFaculty of PharmacySüleyman Demirel University Isparta 32260 Turkey
| | - Zuhal Gerçek
- Zonguldak Bülent Ecevit UniversityFaculty of Arts and SciencesDepartment of Chemistry 67100 Zonguldak Turkey
| | - Abdurrahman Şengül
- Zonguldak Bülent Ecevit UniversityFaculty of Arts and SciencesDepartment of Chemistry 67100 Zonguldak Turkey
| | - Burak Coban
- Zonguldak Bülent Ecevit UniversityFaculty of Arts and SciencesDepartment of Chemistry 67100 Zonguldak Turkey
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8
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Matos de Opitz CL, Sass P. Tackling antimicrobial resistance by exploring new mechanisms of antibiotic action. Future Microbiol 2020; 15:703-708. [DOI: 10.2217/fmb-2020-0048] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Cruz L Matos de Opitz
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology & Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Peter Sass
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology & Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Germany
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9
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Carro L. Recent Progress in the Development of Small-Molecule FtsZ Inhibitors as Chemical Tools for the Development of Novel Antibiotics. Antibiotics (Basel) 2019; 8:E217. [PMID: 31717975 PMCID: PMC6963470 DOI: 10.3390/antibiotics8040217] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/26/2019] [Accepted: 11/05/2019] [Indexed: 01/20/2023] Open
Abstract
Antibiotics are potent pharmacological weapons against bacterial pathogens, nevertheless their efficacy is becoming compromised due to the worldwide emergence and spread of multidrug-resistant bacteria or "superbugs". Antibiotic resistance is rising to such dangerous levels that the treatment of bacterial infections is becoming a clinical challenge. Therefore, urgent action is needed to develop new generations of antibiotics that will help tackle this increasing and serious public health problem. Due to its essential role in bacterial cell division, the tubulin-like protein FtsZ has emerged as a promising target for the development of novel antibiotics with new mechanisms of action. This review highlights the medicinal chemistry efforts towards the identification of small-molecule FtsZ inhibitors with antibacterial activity in the last three years.
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Affiliation(s)
- Laura Carro
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Facultad de Farmacia, Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain;
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
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10
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Carlson TJ, Endres BT, Bassères E, Gonzales-Luna AJ, Garey KW. Ridinilazole for the treatment of Clostridioides difficile infection. Expert Opin Investig Drugs 2019; 28:303-310. [PMID: 30767587 DOI: 10.1080/13543784.2019.1582640] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 02/11/2019] [Indexed: 12/23/2022]
Abstract
INTRODUCTION Ridinilazole is a novel antibiotic being developed for the treatment of Clostridioides difficile infection (CDI). Ridinilazole has completed two phase II trials and phase III trials which are denoted Ri-CoDIFy 1 and 2, are planned (ClinicalTrials.gov identifiers: NCT03595553 and NCT03595566). Areas covered: This article covers the chemistry, mechanism of action, in vitro microbiology versus C. difficile and host microbiota, pre-clinical and clinical efficacy, pharmacokinetics, pharmacodynamics and safety and tolerability of ridinilazole. Expert opinion: Ridinilazole is a novel antibiotic with ideal properties for the treatment of CDI. Given the promising results from the phase II clinical trial, ridinilazole may have the capability to lower the risk for CDI recurrence thus improving sustained clinical response rates - a current unmet medical need. Assuming a positive phase III trial, ridinilazole will enter a market with heightened awareness on the importance of prevention of CDI. This along with further research into the economic consequences and decreased patient quality of life associated with recurrent CDI, should provide clinicians with further evidence for the need for therapy that limits CDI recurrence and improves sustained clinical cure.
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Affiliation(s)
- Travis J Carlson
- a Department of Pharmacy Practice and Translational Research , University of Houston College of Pharmacy , Houston , TX , USA
| | - Bradley T Endres
- a Department of Pharmacy Practice and Translational Research , University of Houston College of Pharmacy , Houston , TX , USA
| | - Eugénie Bassères
- a Department of Pharmacy Practice and Translational Research , University of Houston College of Pharmacy , Houston , TX , USA
| | - Anne J Gonzales-Luna
- a Department of Pharmacy Practice and Translational Research , University of Houston College of Pharmacy , Houston , TX , USA
| | - Kevin W Garey
- a Department of Pharmacy Practice and Translational Research , University of Houston College of Pharmacy , Houston , TX , USA
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11
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Cationic biaryl 1,2,3-triazolyl peptidomimetic amphiphiles targeting Clostridioides (Clostridium) difficile: Synthesis, antibacterial evaluation and an in vivo C. difficile infection model. Eur J Med Chem 2019; 170:203-224. [PMID: 30901686 DOI: 10.1016/j.ejmech.2019.02.068] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/25/2019] [Accepted: 02/25/2019] [Indexed: 12/30/2022]
Abstract
Clostridioides (formerly Clostridium) difficile is a Gram-positive anaerobic bacterial pathogen that causes severe gastrointestinal infection in humans. The current chemotherapeutic options are vastly inadequate, expensive and limited; this results in an exorbitant medical and financial burden. New, inexpensive chemotherapeutic treatments for C. difficile infection with improved efficacy are urgently needed. A streamlined synthetic pathway was developed to allow access to 38 novel mono- and di-cationic biaryl 1,2,3-triazolyl peptidomimetics with increased synthetic efficiency, aqueous solubility and enhanced antibacterial efficacy. The monocationic arginine derivative 28 was identified as a potent, Gram-positive selective antibacterial with MIC values of 4 μg/mL against methicillin-resistant Staphylococcus aureus and 8 μg/mL against C. difficile. Furthermore, the dicationic bis-triazole analogue 50 was found to exhibit broad-spectrum activity with substantial Gram-negative efficacy against Acinetobacter baumannii (8 μg/mL), Pseudomonas aeruginosa (8 μg/mL) and Klebsiella pneumoniae (16 μg/mL); additionally, compound 50 displayed reduced haemolytic activity (<13%) in an in vitro haemolysis assay. Membrane-disruption assays were conducted on selected derivatives to confirm the membrane-active mechanism of action inherent to the synthesized amphiphilic compounds. A comparative solubility assay was developed and utilized to optimize the aqueous solubility of the compounds for in vivo studies. The biaryl peptidomimetics 28 and 67 were found to exhibit significant efficacy in an in vivo murine model of C. difficile infection by reducing the severity and slowing the onset of disease.
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12
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Bistrović A, Krstulović L, Stolić I, Drenjančević D, Talapko J, Taylor MC, Kelly JM, Bajić M, Raić-Malić S. Synthesis, anti-bacterial and anti-protozoal activities of amidinobenzimidazole derivatives and their interactions with DNA and RNA. J Enzyme Inhib Med Chem 2018; 33:1323-1334. [PMID: 30165753 PMCID: PMC6127852 DOI: 10.1080/14756366.2018.1484733] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 05/18/2018] [Accepted: 05/31/2018] [Indexed: 02/09/2023] Open
Abstract
Amidinobenzimidazole derivatives connected to 1-aryl-substituted 1,2,3-triazole through phenoxymethylene linkers 7a-7e, 8a-8e, and 9a-9e were designed and synthesised with the aim of evaluating their anti-bacterial and anti-trypanosomal activities and DNA/RNA binding affinity. Results from anti-bacterial evaluations of antibiotic-resistant pathogenic bacteria revealed that both o-chlorophenyl-1,2,3-triazole and N-isopropylamidine moieties in 8c led to strong inhibitory activity against resistant Gram-positive bacteria, particularly the MRSA strain. Furthermore, the non-substituted amidine and phenyl ring in 7a induced a marked anti-bacterial effect, with potency against ESBL-producing Gram-negative E. coli better than those of the antibiotics ceftazidime and ciprofloxacin. UV-Vis and CD spectroscopy, as well as thermal denaturation assays, indicated that compounds 7a and 8c showed also binding affinities towards ctDNA. Anti-trypanosomal evaluations showed that the p-methoxyphenyl-1,2,3-triazole moiety in 7b and 9b enhanced inhibitory activity against T. brucei, with 8b being more potent than nifurtimox, and having minimal toxicity towards mammalian cells.
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Affiliation(s)
- Andrea Bistrović
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Zagreb, Croatia
| | - Luka Krstulović
- Department of Chemistry and Biochemistry, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Ivana Stolić
- Department of Chemistry and Biochemistry, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Domagoj Drenjančević
- Department of Transfusion Medicine, Osijek University Hospital, Osijek, Croatia
- Department of Microbiology and Parasitology, Faculty of Medicine, University of Osijek, Osijek, Croatia
| | - Jasminka Talapko
- Department of Microbiology and Parasitology, Faculty of Medicine, University of Osijek, Osijek, Croatia
| | - Martin C. Taylor
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - John M. Kelly
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Miroslav Bajić
- Department of Chemistry and Biochemistry, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Silvana Raić-Malić
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Zagreb, Croatia
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13
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Petrosillo N, Granata G, Cataldo MA. Novel Antimicrobials for the Treatment of Clostridium difficile Infection. Front Med (Lausanne) 2018; 5:96. [PMID: 29713630 PMCID: PMC5911476 DOI: 10.3389/fmed.2018.00096] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/26/2018] [Indexed: 12/17/2022] Open
Abstract
The current picture of Clostridium difficile infection (CDI) is alarming with a mortality rate ranging between 3% and 15% and a CDI recurrence rate ranging from 12% to 40%. Despite the great efforts made over the past 10 years to face the CDI burden, there are still gray areas in our knowledge on CDI management. The traditional anti-CDI antimicrobials are not always adequate in addressing the current needs in CDI management. The aim of our review is to give an update on novel antimicrobials for the treatment of CDI, considering the currently available evidences on their efficacy, safety, molecular mechanism of action, and their probability to be successfully introduced into the clinical practice in the near future. We identified, through a PubMed search, 16 novel antimicrobial molecules under study for CDI treatment: cadazolid, surotomycin, ridinilazole, LFF571, ramoplanin, CRS3123, fusidic acid, nitazoxanide, rifampin, rifaximin, tigecycline, auranofin, NVB302, thuricin CD, lacticin 3147, and acyldepsipeptide antimicrobials. In comparison with the traditional anti-CDI antimicrobial treatment, some of the novel antimicrobials reviewed in this study offer several advantages, i.e., the favorable pharmacokinetic and pharmacodynamic profile, the narrow-spectrum activity against CD that implicates a low impact on the gut microbiota composition, the inhibitory activity on CD sporulation and toxins production. Among these novel antimicrobials, the most active compounds in reducing spore production are cadazolid, ridinilazole, CRS3123, ramoplanin and, potentially, the acyldepsipeptide antimicrobials. These antimicrobials may potentially reduce CD environment spread and persistence, thus reducing CDI healthcare-associated acquisition. However, some of them, i.e., surotomycin, fusidic acid, etc., will not be available due to lack of superiority versus standard of treatment. The most CD narrow-spectrum novel antimicrobials that allow to preserve microbiota integrity are cadazolid, ridinilazole, auranofin, and thuricin CD. In conclusion, the novel antimicrobial molecules under development for CDI have promising key features and advancements in comparison to the traditional anti-CDI antimicrobials. In the near future, some of these new molecules might be effective alternatives to fight CDI.
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Affiliation(s)
- Nicola Petrosillo
- Clinical and Research Department for Infectious Diseases, Unit Systemic and Immunedepression-Associated Infections, National Institute for Infectious Diseases L. Spallanzani, Rome, Italy
| | - Guido Granata
- Clinical and Research Department for Infectious Diseases, Unit Systemic and Immunedepression-Associated Infections, National Institute for Infectious Diseases L. Spallanzani, Rome, Italy
| | - Maria Adriana Cataldo
- Clinical and Research Department for Infectious Diseases, Unit Systemic and Immunedepression-Associated Infections, National Institute for Infectious Diseases L. Spallanzani, Rome, Italy
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14
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Mo CY, Culyba MJ, Selwood T, Kubiak JM, Hostetler ZM, Jurewicz AJ, Keller PM, Pope AJ, Quinn A, Schneck J, Widdowson KL, Kohli RM. Inhibitors of LexA Autoproteolysis and the Bacterial SOS Response Discovered by an Academic-Industry Partnership. ACS Infect Dis 2018; 4:349-359. [PMID: 29275629 DOI: 10.1021/acsinfecdis.7b00122] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The RecA/LexA axis of the bacterial DNA damage (SOS) response is a promising, yet nontraditional, drug target. The SOS response is initiated upon genotoxic stress, when RecA, a DNA damage sensor, induces LexA, the SOS repressor, to undergo autoproteolysis, thereby derepressing downstream genes that can mediate DNA repair and accelerate mutagenesis. As genetic inhibition of the SOS response sensitizes bacteria to DNA damaging antibiotics and decreases acquired resistance, inhibitors of the RecA/LexA axis could potentiate our current antibiotic arsenal. Compounds targeting RecA, which has many mammalian homologues, have been reported; however, small-molecules targeting LexA autoproteolysis, a reaction unique to the prokaryotic SOS response, have remained elusive. Here, we describe the logistics and accomplishments of an academic-industry partnership formed to pursue inhibitors against the RecA/LexA axis. A novel fluorescence polarization assay reporting on RecA-induced self-cleavage of LexA enabled the screening of 1.8 million compounds. Follow-up studies on select leads show distinct activity patterns in orthogonal assays, including several with activity in cell-based assays reporting on SOS activation. Mechanistic assays demonstrate that we have identified first-in-class small molecules that specifically target the LexA autoproteolysis step in SOS activation. Our efforts establish a realistic example for navigating academic-industry partnerships in pursuit of anti-infective drugs and offer starting points for dedicated lead optimization of SOS inhibitors that could act as adjuvants for current antibiotics.
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Affiliation(s)
- Charlie Y. Mo
- Department of Medicine, Department of Biochemistry and Biophysics, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, Pennsylvania 19104, United States
| | - Matthew J. Culyba
- Department of Medicine, Department of Biochemistry and Biophysics, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, Pennsylvania 19104, United States
| | - Trevor Selwood
- Department of Medicine, Department of Biochemistry and Biophysics, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, Pennsylvania 19104, United States
| | - Jeffrey M. Kubiak
- Department of Medicine, Department of Biochemistry and Biophysics, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, Pennsylvania 19104, United States
| | - Zachary M. Hostetler
- Department of Medicine, Department of Biochemistry and Biophysics, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, Pennsylvania 19104, United States
| | - Anthony J. Jurewicz
- Screening, Profiling, and Mechanistic Biology, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Paul M. Keller
- Screening, Profiling, and Mechanistic Biology, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Andrew J. Pope
- Discovery Partnerships with Academia, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Amy Quinn
- Screening, Profiling, and Mechanistic Biology, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Jessica Schneck
- Screening, Profiling, and Mechanistic Biology, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Katherine L. Widdowson
- Discovery Partnerships with Academia, GlaxoSmithKline, 1250 S. Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Rahul M. Kohli
- Department of Medicine, Department of Biochemistry and Biophysics, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, Pennsylvania 19104, United States
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15
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Picconi P, Hind C, Jamshidi S, Nahar K, Clifford M, Wand ME, Sutton JM, Rahman KM. Triaryl Benzimidazoles as a New Class of Antibacterial Agents against Resistant Pathogenic Microorganisms. J Med Chem 2017. [PMID: 28650661 DOI: 10.1021/acs.jmedchem.7b00108] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A new class of nontoxic triaryl benzimidazole compounds, derived from existing classes of DNA minor groove binders, were designed, synthesized, and evaluated for their antibacterial activity against multidrug resistant (MDR) Gram-positive and Gram-negative species. Molecular modeling experiments suggest that the newly synthesized class cannot be accommodated within the minor groove of DNA due to a change in the shape of the molecules. Compounds 8, 13, and 14 were found to be the most active of the series, with MICs in the range of 0.5-4 μg/mL against the MDR Staphylococci and Enterococci species. Compound 13 showed moderate activity against the MDR Gram-negative strains, with MICs in the range of 16-32 μg/mL. Active compounds showed a bactericidal mode of action, and a mechanistic study suggested the inhibition of bacterial gyrase as the mechanism of action (MOA) of this chemical class. The MOA was further supported by the molecular modeling study.
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Affiliation(s)
- Pietro Picconi
- Institute of Pharmaceutical Science, King's College London , London SE1 1DB, U.K
| | - Charlotte Hind
- National Infections Service, Porton Down, Public Health England , Salisbury SP4 0JG, Wiltshire U.K
| | - Shirin Jamshidi
- Institute of Pharmaceutical Science, King's College London , London SE1 1DB, U.K
| | - Kazi Nahar
- Institute of Pharmaceutical Science, King's College London , London SE1 1DB, U.K
| | - Melanie Clifford
- National Infections Service, Porton Down, Public Health England , Salisbury SP4 0JG, Wiltshire U.K
| | - Matthew E Wand
- National Infections Service, Porton Down, Public Health England , Salisbury SP4 0JG, Wiltshire U.K
| | - J Mark Sutton
- National Infections Service, Porton Down, Public Health England , Salisbury SP4 0JG, Wiltshire U.K
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16
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Freedman S, Mullane K. The academic-industrial complex: navigating the translational and cultural divide. Drug Discov Today 2017; 22:976-993. [PMID: 28336175 DOI: 10.1016/j.drudis.2017.03.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 02/11/2017] [Accepted: 03/13/2017] [Indexed: 12/26/2022]
Abstract
In general, the fruits of academic discoveries can only be realized through joint efforts with industry. However, the poor reproducibility of much academic research has damaged credibility and jeopardized translational efforts that could benefit patients. Meanwhile, journals are rife with articles bemoaning the limited productivity and increasing costs of the biopharmaceutical industry and its resultant predilection for mergers and reorganizations while decreasing internal research efforts. The ensuing disarray and uncertainty has created tremendous opportunities for academia and industry to form even closer ties, and to embrace new operational and financial models to their joint benefit. This review article offers a personal perspective on the opportunities, models and approaches that harness the increased interface and growing interdependency between biomedical research institutes, the biopharmaceutical industry and the technological world.
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Affiliation(s)
- Stephen Freedman
- Gladstone Institutes,1650 Owens Street, San Francisco, CA 94158, USA
| | - Kevin Mullane
- Gladstone Institutes,1650 Owens Street, San Francisco, CA 94158, USA.
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17
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Moloney MG. Natural Products as a Source for Novel Antibiotics. Trends Pharmacol Sci 2016; 37:689-701. [DOI: 10.1016/j.tips.2016.05.001] [Citation(s) in RCA: 161] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/02/2016] [Accepted: 05/02/2016] [Indexed: 01/04/2023]
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18
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Slayton ET, Hay AS, Babcock CK, Long TE. New antibiotics in clinical trials for Clostridium difficile. Expert Rev Anti Infect Ther 2016; 14:789-800. [PMID: 27410763 DOI: 10.1080/14787210.2016.1211931] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
INTRODUCTION There are limited number of approved therapies for C. difficile infections (CDIs) and new treatments are needed to decrease recurrence rates. Over the past 5 years, four novel antibiotics have been evaluated in clinical trials that offer distinct advantages over existing therapies for the treatment of CDI. AREAS COVERED This article reviews the preclinical and clinical studies of cadazolid, LFF571, ridinilazole, and surotomycin. The advantages that these antibiotics may have in the treatment of CDI is compared with current therapies metronidazole, vancomycin, and fidaxomicin. Expert commentary: The antibiotics examined have the potential to improve rates of CDI treatment without recurrence. We anticipate that one or more of these medications will be approved within five years.
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Affiliation(s)
- Eric T Slayton
- a Department of Pharmaceutical Science and Research, School of Pharmacy , Marshall University , Huntington , WV , USA
| | - Abigail S Hay
- b Department of Pharmacy Practice, Administration, and Research, School of Pharmacy , Marshall University , Huntington , WV , USA.,c Department of Pharmacy , St. Mary's Medical Center , Huntington , WV , USA
| | - Charles K Babcock
- b Department of Pharmacy Practice, Administration, and Research, School of Pharmacy , Marshall University , Huntington , WV , USA
| | - Timothy E Long
- a Department of Pharmaceutical Science and Research, School of Pharmacy , Marshall University , Huntington , WV , USA.,d Department of Biochemistry and Microbiology, Joan C. Edwards School of Medicine , Marshall University , Huntington , WV , USA
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19
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Abstract
The practice of medicine was profoundly transformed by the introduction of the antibiotics (compounds isolated from Nature) and the antibacterials (compounds prepared by synthesis) for the control of bacterial infection. As a result of the extraordinary success of these compounds over decades of time, a timeless biological activity for these compounds has been presumed. This presumption is no longer. The inexorable acquisition of resistance mechanisms by bacteria is retransforming medical practice. Credible answers to this dilemma are far better recognized than they are being implemented. In this perspective we examine (and in key respects, reiterate) the chemical and biological strategies being used to address the challenge of bacterial resistance.
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Affiliation(s)
- Jed F. Fisher
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame IN 46556–5670, USA
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame IN 46556–5670, USA
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