1
|
Singh SB, Tan CM, Kaelin D, Meinke PT, Miesel L, Olsen DB, Fukuda H, Kishii R, Takei M, Ohata K, Takeuchi T, Shibue T, Takano H, Nishimura A, Fukuda Y. Structure activity relationship of N-1 substituted 1,5-naphthyrid-2-one analogs of oxabicyclooctane-linked novel bacterial topoisomerase inhibitors as broad-spectrum antibacterial agents (Part-9). Bioorg Med Chem Lett 2022; 75:128808. [PMID: 35609741 DOI: 10.1016/j.bmcl.2022.128808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 05/13/2022] [Accepted: 05/17/2022] [Indexed: 11/02/2022]
Abstract
Novel bacterial topoisomerase inhibitors (NBTIs) are the newest members of gyrase inhibitor broad-spectrum antibacterial agents, represented by the most advanced member, gepotidacin, a 4-amino-piperidine linked NBTI, which is undergoing phase III clinical trials for treatment of urinary tract infections (UTI). We have extensively reported studies on oxabicyclooctane linked NBTIs, including AM-8722. The present study summarizes structure activity relationship (SAR) of AM-8722 leading to identification of 7-fluoro-1-cyanomethyl-1,5-naphthyridin-2-one based NBTI (16, AM-8888) with improved potency and spectrum (MIC values of 0.016-4 μg/mL), with Pseudomonas aeruginosa being the least sensitive strain (MIC 4 μg/mL).
Collapse
Affiliation(s)
| | | | | | | | - Lynn Miesel
- Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | | | - Hideyuki Fukuda
- Kyorin Pharmaceutical Co., Ltd., 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Ryuta Kishii
- Kyorin Pharmaceutical Co., Ltd., 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Masaya Takei
- Kyorin Pharmaceutical Co., Ltd., 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Kohei Ohata
- Kyorin Pharmaceutical Co., Ltd., 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Tomoko Takeuchi
- Kyorin Pharmaceutical Co., Ltd., 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Taku Shibue
- Kyorin Pharmaceutical Co., Ltd., 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Hisashi Takano
- Kyorin Pharmaceutical Co., Ltd., 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Akinori Nishimura
- Kyorin Pharmaceutical Co., Ltd., 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Yasumichi Fukuda
- Kyorin Pharmaceutical Co., Ltd., 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan.
| |
Collapse
|
2
|
Creanza TM, Delre P, Ancona N, Lentini G, Saviano M, Mangiatordi GF. Structure-Based Prediction of hERG-Related Cardiotoxicity: A Benchmark Study. J Chem Inf Model 2021; 61:4758-4770. [PMID: 34506150 PMCID: PMC9282647 DOI: 10.1021/acs.jcim.1c00744] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
![]()
Drug-induced blockade of the human
ether-à-go-go-related
gene (hERG) channel is today considered the main
cause of cardiotoxicity in postmarketing surveillance. Hence, several
ligand-based approaches were developed in the last years and are currently
employed in the early stages of a drug discovery process for in silico cardiac safety assessment of drug candidates.
Herein, we present the first structure-based classifiers able to discern hERG binders from nonbinders. LASSO regularized support
vector machines were applied to integrate docking scores and protein–ligand
interaction fingerprints. A total of 396 models were trained and validated
based on: (i) high-quality experimental bioactivity information returned
by 8337 curated compounds extracted from ChEMBL (version 25) and (ii)
structural predictor data. Molecular docking simulations were performed
using GLIDE and GOLD software programs and four different hERG structural models, namely, the recently published structures
obtained by cryoelectron microscopy (PDB codes: 5VA1 and 7CN1) and
two published homology models selected for comparison. Interestingly,
some classifiers return performances comparable to ligand-based models
in terms of area under the ROC curve (AUCMAX = 0.86 ±
0.01) and negative predictive values (NPVMAX = 0.81 ±
0.01), thus putting forward the herein proposed computational workflow
as a valuable tool for predicting hERG-related cardiotoxicity
without the limitations of ligand-based models, typically affected
by low interpretability and a limited applicability domain. From a
methodological point of view, our study represents the first example
of a successful integration of docking scores and protein–ligand
interaction fingerprints (IFs) through a support vector machine (SVM)
LASSO regularized strategy. Finally, the study highlights the importance
of using hERG structural models accounting for ligand-induced
fit effects and allowed us to select the best-performing protein conformation
(made available in the Supporting Information, SI) to be employed
for a reliable structure-based prediction of hERG-related cardiotoxicity.
Collapse
Affiliation(s)
- Teresa Maria Creanza
- CNR-Institute of Intelligent Industrial Technologies and Systems for Advanced Manufacturing, Via Amendola 122/o, 70126 Bari, Italy
| | - Pietro Delre
- Chemistry Department, University of Bari "Aldo Moro", via E. Orabona, 4, I-70125 Bari, Italy.,CNR-Institute of Crystallography, Via Amendola 122/o, 70126 Bari, Italy
| | - Nicola Ancona
- CNR-Institute of Intelligent Industrial Technologies and Systems for Advanced Manufacturing, Via Amendola 122/o, 70126 Bari, Italy
| | - Giovanni Lentini
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari "Aldo Moro", via E. Orabona, 4, I-70125 Bari, Italy
| | - Michele Saviano
- CNR-Institute of Crystallography, Via Amendola 122/o, 70126 Bari, Italy
| | | |
Collapse
|
3
|
Recent advances in DNA gyrase-targeted antimicrobial agents. Eur J Med Chem 2020; 199:112326. [DOI: 10.1016/j.ejmech.2020.112326] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 12/16/2022]
|
4
|
Synthetic Strategies, Reactivity and Applications of 1,5-Naphthyridines. Molecules 2020; 25:molecules25143252. [PMID: 32708796 PMCID: PMC7397193 DOI: 10.3390/molecules25143252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/11/2020] [Accepted: 07/15/2020] [Indexed: 11/17/2022] Open
Abstract
This review covers the synthesis and reactivity of 1,5-naphthyridine derivatives published in the last 18 years. These heterocycles present a significant importance in the field of medicinal chemistry because many of them exhibit a great variety of biological activities. First, the published strategies related to the synthesis of 1,5-naphthyridines are presented followed by the reactivity of these compounds with electrophilic or nucleophilic reagents, in oxidations, reductions, cross-coupling reactions, modification of side chains or formation of metal complexes. Finally, some properties and applications of these heterocycles studied during this period are examined.
Collapse
|
5
|
Kolarič A, Anderluh M, Minovski N. Two Decades of Successful SAR-Grounded Stories of the Novel Bacterial Topoisomerase Inhibitors (NBTIs). J Med Chem 2020; 63:5664-5674. [PMID: 32027491 PMCID: PMC7307926 DOI: 10.1021/acs.jmedchem.9b01738] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The emergence of bacterial resistance against life-saving medicines has forced the scientific community and pharmaceutical industry to take actions in the quest for novel antibacterials. These should not only overcome the existing bacterial resistance but also provide at least interim effective protection against emerging bacterial infections. Research into DNA gyrase and topoisomerase IV inhibitors has become a particular focus, with the description of a new class of bacterial topoisomerase type II inhibitors known as "novel bacterial topoisomerase inhibitors", NBTIs. Elucidation of the key structural modifications incorporated into these inhibitors and the impact these can have on their general physicochemical properties are detailed in this review. This defines novel bacterial topoisomerase inhibitors with promising antibacterial activities and potencies, which thus represent one potential example of the future "drugs for bad bugs", as identified by the World Health Organization.
Collapse
Affiliation(s)
- Anja Kolarič
- Laboratory for Cheminformatics, Theory Department, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia.,Chair of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Marko Anderluh
- Chair of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Nikola Minovski
- Laboratory for Cheminformatics, Theory Department, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| |
Collapse
|
6
|
Yi L, Lü X. New Strategy on Antimicrobial-resistance: Inhibitors of DNA Replication Enzymes. Curr Med Chem 2019; 26:1761-1787. [PMID: 29110590 DOI: 10.2174/0929867324666171106160326] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 08/31/2017] [Accepted: 10/30/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND Antimicrobial resistance is found in all microorganisms and has become one of the biggest threats to global health. New antimicrobials with different action mechanisms are effective weapons to fight against antibiotic-resistance. OBJECTIVE This review aims to find potential drugs which can be further developed into clinic practice and provide clues for developing more effective antimicrobials. METHODS DNA replication universally exists in all living organisms and is a complicated process in which multiple enzymes are involved in. Enzymes in bacterial DNA replication of initiation and elongation phases bring abundant targets for antimicrobial development as they are conserved and indispensable. In this review, enzyme inhibitors of DNA helicase, DNA primase, topoisomerases, DNA polymerase and DNA ligase were discussed. Special attentions were paid to structures, activities and action modes of these enzyme inhibitors. RESULTS Among these enzymes, type II topoisomerase is the most validated target with abundant inhibitors. For type II topoisomerase inhibitors (excluding quinolones), NBTIs and benzimidazole urea derivatives are the most promising inhibitors because of their good antimicrobial activity and physicochemical properties. Simultaneously, DNA gyrase targeted drugs are particularly attractive in the treatment of tuberculosis as DNA gyrase is the sole type II topoisomerase in Mycobacterium tuberculosis. Relatively, exploitation of antimicrobial inhibitors of the other DNA replication enzymes are primeval, in which inhibitors of topo III are even blank so far. CONCLUSION This review demonstrates that inhibitors of DNA replication enzymes are abundant, diverse and promising, many of which can be developed into antimicrobials to deal with antibioticresistance.
Collapse
Affiliation(s)
- Lanhua Yi
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Xin Lü
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| |
Collapse
|
7
|
Kolaric A, Minovski N. Structure-based design of novel combinatorially generated NBTIs as potential DNA gyrase inhibitors against various Staphylococcus aureus mutant strains. MOLECULAR BIOSYSTEMS 2018; 13:1406-1420. [PMID: 28590495 DOI: 10.1039/c7mb00168a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Although intercalating agents such as quinolones have had proven therapeutic success as antibacterial agents for more than 40 years, new forms of quinolone-based resistance in bacteria are continually emerging. To alleviate this problem, a new class of antibacterials is urgently needed; recently, novel bacterial topoisomerase inhibitors (NBTIs) have been found to be particularly important. Based on 67 experimentally evaluated NBTIs against wild-type (WT) DNA gyrase originating from Staphylococcus aureus, a predictive QSAR model was initially constructed and validated and was later used for in silico prediction of biological activities for an in house designed compound library of 548 novel drug-like NBTI combinatorial analogs. To evaluate the influence of gyrA alterations on NBTI resistance, various mutant homology models were constructed; meanwhile, their resistance profiles were assessed and validated relative to that of WT enzyme by structure-based virtual screening (VS) of known NBTIs. Surprisingly, the M121K mutant model was recognized as the most selective due to an additional established cation-π interaction between K121-NH3+ (not found in the WT) and the aromatic moiety of the NBTI right-hand site (RHS) fragment; this finding was additionally supported by VS of our combinatorially generated NBTIs. Moreover, we identified several attractive, synthetically feasible RHS building blocks that may enable the development of new NBTIs.
Collapse
Affiliation(s)
- Anja Kolaric
- Department of Cheminformatics, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.
| | | |
Collapse
|
8
|
Franco-Ulloa S, La Sala G, Miscione GP, De Vivo M. Novel Bacterial Topoisomerase Inhibitors Exploit Asp83 and the Intrinsic Flexibility of the DNA Gyrase Binding Site. Int J Mol Sci 2018; 19:ijms19020453. [PMID: 29401640 PMCID: PMC5855675 DOI: 10.3390/ijms19020453] [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: 01/24/2018] [Revised: 01/29/2018] [Accepted: 01/30/2018] [Indexed: 11/19/2022] Open
Abstract
DNA gyrases are enzymes that control the topology of DNA in bacteria cells. This is a vital function for bacteria. For this reason, DNA gyrases are targeted by widely used antibiotics such as quinolones. Recently, structural and biochemical investigations identified a new class of DNA gyrase inhibitors called NBTIs (i.e., novel bacterial topoisomerase inhibitors). NBTIs are particularly promising because they are active against multi-drug resistant bacteria, an alarming clinical issue. Structural data recently demonstrated that these NBTIs bind tightly to a newly identified pocket at the dimer interface of the DNA–protein complex. In the present study, we used molecular dynamics (MD) simulations and docking calculations to shed new light on the binding of NBTIs to this site. Interestingly, our MD simulations demonstrate the intrinsic flexibility of this binding site, which allows the pocket to adapt its conformation and form optimal interactions with the ligand. In particular, we examined two ligands, AM8085 and AM8191, which induced a repositioning of a key aspartate (Asp83B), whose side chain can rotate within the binding site. The conformational rearrangement of Asp83B allows the formation of a newly identified H-bond interaction with an NH on the bound NBTI, which seems important for the binding of NBTIs having such functionality. We validated these findings through docking calculations using an extended set of cognate oxabicyclooctane-linked NBTIs derivatives (~150, in total), screened against multiple target conformations. The newly identified H-bond interaction significantly improves the docking enrichment. These insights could be helpful for future virtual screening campaigns against DNA gyrase.
Collapse
Affiliation(s)
- Sebastian Franco-Ulloa
- COBO Computational Bio-Organic Chemistry Bogotá, Chemistry Department, Universidad de los Andes, Cra 1 No 18A-12, 111711 Bogotá, Colombia.
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy.
| | - Giuseppina La Sala
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy.
| | - Gian Pietro Miscione
- COBO Computational Bio-Organic Chemistry Bogotá, Chemistry Department, Universidad de los Andes, Cra 1 No 18A-12, 111711 Bogotá, Colombia.
| | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy.
- IAS-5/INM-9 Computational Biomedicine Forschungszentrum Jülich Wilhelm-Johnen-Straße, 52428 Jülich, Germany.
| |
Collapse
|
9
|
Mitton-Fry MJ, Brickner SJ, Hamel JC, Barham R, Brennan L, Casavant JM, Ding X, Finegan S, Hardink J, Hoang T, Huband MD, Maloney M, Marfat A, McCurdy SP, McLeod D, Subramanyam C, Plotkin M, Reilly U, Schafer J, Stone GG, Uccello DP, Wisialowski T, Yoon K, Zaniewski R, Zook C. Novel 3-fluoro-6-methoxyquinoline derivatives as inhibitors of bacterial DNA gyrase and topoisomerase IV. Bioorg Med Chem Lett 2017; 27:3353-3358. [PMID: 28610977 DOI: 10.1016/j.bmcl.2017.06.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 05/31/2017] [Accepted: 06/02/2017] [Indexed: 10/19/2022]
Abstract
Novel (non-fluoroquinolone) inhibitors of bacterial type II topoisomerases (NBTIs) are an emerging class of antibacterial agents. We report an optimized series of cyclobutylaryl-substituted NBTIs. Compound 14 demonstrated excellent activity both in vitro (S. aureus MIC90=0.125μg/mL) and in vivo (systemic and tissue infections). Enhanced inhibition of Topoisomerase IV correlated with improved activity in S. aureus strains with mutations conferring resistance to NBTIs. Compound 14 also displayed an improved hERG IC50 of 85.9μM and a favorable profile in the anesthetized guinea pig model.
Collapse
Affiliation(s)
| | | | - Judith C Hamel
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Rose Barham
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Lori Brennan
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | | | - Xiaoyuan Ding
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Steven Finegan
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Joel Hardink
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Thuy Hoang
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Michael D Huband
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Meghan Maloney
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Anthony Marfat
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Sandra P McCurdy
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Dale McLeod
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | | | - Michael Plotkin
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Usa Reilly
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - John Schafer
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Gregory G Stone
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Daniel P Uccello
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Todd Wisialowski
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Kwansik Yoon
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | | | - Christopher Zook
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| |
Collapse
|
10
|
In Vitro and In Vivo Characterization of the Novel Oxabicyclooctane-Linked Bacterial Topoisomerase Inhibitor AM-8722, a Selective, Potent Inhibitor of Bacterial DNA Gyrase. Antimicrob Agents Chemother 2016; 60:4830-9. [PMID: 27246784 DOI: 10.1128/aac.00619-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 05/25/2016] [Indexed: 01/08/2023] Open
Abstract
Oxabicyclooctane-linked novel bacterial topoisomerase inhibitors (NBTIs) represent a new class of recently described antibacterial agents with broad-spectrum activity. NBTIs dually inhibit the clinically validated bacterial targets DNA gyrase and topoisomerase IV and have been shown to bind distinctly from known classes of antibacterial agents directed against these targets. Herein we report the molecular, cellular, and in vivo characterization of AM-8722 as a representative N-alkylated-1,5-naphthyridone left-hand-side-substituted NBTI. Consistent with its mode of action, macromolecular labeling studies revealed a specific effect of AM-8722 to dose dependently inhibit bacterial DNA synthesis. AM-8722 displayed greater intrinsic enzymatic potency than levofloxacin versus both DNA gyrase and topoisomerase IV from Staphylococcus aureus and Escherichia coli and displayed selectivity against human topoisomerase II. AM-8722 was rapidly bactericidal and exhibited whole-cell activity versus a range of Gram-negative and Gram-positive organisms, with no whole-cell potency shift due to the presence of DNA or human serum. Frequency-of-resistance studies demonstrated an acceptable rate of resistance emergence in vitro at concentrations 16- to 32-fold the MIC. AM-8722 displayed acceptable pharmacokinetic properties and was shown to be efficacious in mouse models of bacterial septicemia. Overall, AM-8722 is a selective and potent NBTI that displays broad-spectrum antimicrobial activity in vitro and in vivo.
Collapse
|
11
|
Abstract
DNA gyrase and topoisomerase IV are type IIA bacterial topoisomerases that are targeted by highly effective antibiotics. However, resistance via multiple mechanisms arises to limit the efficacies of these drugs. Continued research on type IIA bacterial topoisomerases has provided novel approaches to counter the most common resistance mechanism for utilization of these proven targets in antibacterial therapy. Bacterial topoisomerase I is being explored as an alternative target that is not expected to show cross-resistance. Dual targeting or combination therapy could be strategies for circumventing the development of resistance to topoisomerase-targeting antibiotics. Bacterial topoisomerases are high-value bactericidal targets that could continue to be exploited for antibacterial therapy, if new tactics to counter resistance can be adopted.
Collapse
|
12
|
Miles TJ, Hennessy AJ, Bax B, Brooks G, Brown BS, Brown P, Cailleau N, Chen D, Dabbs S, Davies DT, Esken JM, Giordano I, Hoover JL, Jones GE, Kusalakumari Sukmar SK, Markwell RE, Minthorn EA, Rittenhouse S, Gwynn MN, Pearson ND. Novel tricyclics (e.g., GSK945237) as potent inhibitors of bacterial type IIA topoisomerases. Bioorg Med Chem Lett 2016; 26:2464-2469. [PMID: 27055939 DOI: 10.1016/j.bmcl.2016.03.106] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 03/28/2016] [Accepted: 03/29/2016] [Indexed: 01/06/2023]
Abstract
During the course of our research on the lead optimisation of the NBTI (Novel Bacterial Type II Topoisomerase Inhibitors) class of antibacterials, we discovered a series of tricyclic compounds that showed good Gram-positive and Gram-negative potency. Herein we will discuss the various subunits that were investigated in this series and report advanced studies on compound 1 (GSK945237) which demonstrates good PK and in vivo efficacy properties.
Collapse
Affiliation(s)
- Timothy J Miles
- Diseases of the Developing World CEDD, GlaxoSmithKline, Calle Severo Ochoa, 2, 28760 Tres Cantos, Madrid, Spain.
| | - Alan J Hennessy
- Infectious Diseases CEDD, GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Ben Bax
- Platform Technology & Science, GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Gerald Brooks
- Infectious Diseases CEDD, GlaxoSmithKline, Third Avenue, Harlow CM19 5AW, UK
| | - Barry S Brown
- Infectious Diseases CEDD, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, USA
| | - Pamela Brown
- Infectious Diseases CEDD, GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Nathalie Cailleau
- Infectious Diseases CEDD, GlaxoSmithKline, Third Avenue, Harlow CM19 5AW, UK
| | - Dongzhao Chen
- Infectious Diseases CEDD, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, USA
| | - Steven Dabbs
- Infectious Diseases CEDD, GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - David T Davies
- Infectious Diseases CEDD, GlaxoSmithKline, Third Avenue, Harlow CM19 5AW, UK
| | - Joel M Esken
- Infectious Diseases CEDD, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, USA
| | - Ilaria Giordano
- Diseases of the Developing World CEDD, GlaxoSmithKline, Calle Severo Ochoa, 2, 28760 Tres Cantos, Madrid, Spain
| | - Jennifer L Hoover
- Infectious Diseases CEDD, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, USA
| | - Graham E Jones
- Infectious Diseases CEDD, GlaxoSmithKline, Third Avenue, Harlow CM19 5AW, UK
| | | | - Roger E Markwell
- Infectious Diseases CEDD, GlaxoSmithKline, Third Avenue, Harlow CM19 5AW, UK
| | - Elisabeth A Minthorn
- Oncology TA, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, USA
| | - Steve Rittenhouse
- Infectious Diseases CEDD, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, USA
| | - Michael N Gwynn
- Infectious Diseases CEDD, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, USA
| | - Neil D Pearson
- Infectious Diseases CEDD, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, USA
| |
Collapse
|
13
|
Singh SB, Kaelin DE, Meinke PT, Wu J, Miesel L, Tan CM, Olsen DB, Lagrutta A, Fukuda H, Kishii R, Takei M, Takeuchi T, Takano H, Ohata K, Kurasaki H, Nishimura A, Shibata T, Fukuda Y. Structure activity relationship of C-2 ether substituted 1,5-naphthyridine analogs of oxabicyclooctane-linked novel bacterial topoisomerase inhibitors as broad-spectrum antibacterial agents (Part-5). Bioorg Med Chem Lett 2015; 25:3630-5. [PMID: 26152426 DOI: 10.1016/j.bmcl.2015.06.061] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 06/12/2015] [Accepted: 06/15/2015] [Indexed: 02/02/2023]
Abstract
Oxabicyclooctane linked novel bacterial topoisomerase inhibitors (NBTIs) are new class of recently reported broad-spectrum antibacterial agents. They target bacterial DNA gyrase and topoisomerase IV and bind to a site different than quinolones. They show no cross-resistance to known antibiotics and provide opportunity to combat drug-resistant bacteria. A structure activity relationship of the C-2 substituted ether analogs of 1,5-naphthyridine oxabicyclooctane-linked NBTIs are described. Synthesis and antibacterial activities of a total of 63 analogs have been summarized representing alkyl, cyclo alkyl, fluoro alkyl, hydroxy alkyl, amino alkyl, and carboxyl alkyl ethers. All compounds were tested against three key strains each of Gram-positive and Gram-negative bacteria as well as for hERG binding activities. Many key compounds were also tested for the functional hERG activity. Six compounds were evaluated for efficacy in a murine bacteremia model of Staphylococcus aureus infection. Significant tolerance for the ether substitution (including polar groups such as amino and carboxyl) at C-2 was observed for S. aureus activity however the same was not true for Enterococcus faecium and Gram-negative strains. Reduced clogD generally showed reduced hERG activity and improved in vivo efficacy but was generally associated with decreased overall potency. One of the best compounds was hydroxy propyl ether (16), which mainly retained the potency, spectrum and in vivo efficacy of AM8085 associated with the decreased hERG activity and improved physical property.
Collapse
Affiliation(s)
- Sheo B Singh
- Merck Research Laboratories, Kenilworth, NJ 07033, United States.
| | - David E Kaelin
- Merck Research Laboratories, Kenilworth, NJ 07033, United States
| | - Peter T Meinke
- Merck Research Laboratories, Kenilworth, NJ 07033, United States
| | - Jin Wu
- Merck Research Laboratories, Kenilworth, NJ 07033, United States
| | - Lynn Miesel
- Merck Research Laboratories, Kenilworth, NJ 07033, United States
| | | | - David B Olsen
- Merck Research Laboratories, West Point, PA 19486, United States
| | - Armando Lagrutta
- Merck Research Laboratories, West Point, PA 19486, United States
| | - Hideyuki Fukuda
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Ryuta Kishii
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Masaya Takei
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Tomoko Takeuchi
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Hisashi Takano
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Kohei Ohata
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Haruaki Kurasaki
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Akinori Nishimura
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Takeshi Shibata
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Yasumichi Fukuda
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan.
| |
Collapse
|
14
|
Singh SB, Kaelin DE, Wu J, Miesel L, Tan CM, Meinke PT, Olsen DB, Lagrutta A, Wei C, Liao Y, Peng X, Wang X, Fukuda H, Kishii R, Takei M, Yajima M, Shibue T, Shibata T, Ohata K, Nishimura A, Fukuda Y. Structure activity relationship of pyridoxazinone substituted RHS analogs of oxabicyclooctane-linked 1,5-naphthyridinyl novel bacterial topoisomerase inhibitors as broad-spectrum antibacterial agents (Part-6). Bioorg Med Chem Lett 2015; 25:3636-43. [PMID: 26141771 DOI: 10.1016/j.bmcl.2015.06.057] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 06/12/2015] [Accepted: 06/15/2015] [Indexed: 12/30/2022]
Abstract
Oxabicyclooctane linked 1,5-naphthyridinyl-pyridoxazinones are novel broad-spectrum bacterial topoisomerase inhibitors (NBTIs) targeting bacterial DNA gyrase and topoisomerase IV at a site different than quinolones. Due to lack of cross-resistance to known antibiotics they present excellent opportunity to combat drug-resistant bacteria. A structure activity relationship of the pyridoxazinone moiety is described in this Letter. Chemical synthesis and activities of NBTIs with substitutions at C-3, C-4 and C-7 of the pyridoxazinone moiety with halogens, alkyl groups and methoxy group has been described. In addition, substitutions of the linker NH proton and its transformation into amide analogs of AM-8085 and AM-8191 have been reported. Fluoro, chloro, and methyl groups at C-3 of the pyridoxazinone moiety retained the potency and spectrum. In addition, a C-3 fluoro analog showed 4-fold better oral efficacy (ED50 3.9 mg/kg) as compared to the parent AM-8085 in a murine bacteremia model of infection of Staphylococcus aureus. Even modest polarity (e.g., methoxy) is not tolerated at C-3 of the pyridoxazinone unit. The basicity and NH group of the linker is important for the activity when CH2 is at the linker position-8. However, amides (with linker position-8 ketone) with a position-7 NH or N-methyl group retained potency and spectrum suggesting that neither basicity nor hydrogen-donor properties of the linker amide NH is essential for the activity. This would suggest likely an altered binding mode of the linker position-7,8 amide containing compounds. The amides showed highly improved hERG (functional IC50 >30 μM) profile.
Collapse
Affiliation(s)
- Sheo B Singh
- Merck Research Laboratories, Kenilworth, NJ 07033, United States.
| | - David E Kaelin
- Merck Research Laboratories, Kenilworth, NJ 07033, United States
| | - Jin Wu
- Merck Research Laboratories, Kenilworth, NJ 07033, United States
| | - Lynn Miesel
- Merck Research Laboratories, Kenilworth, NJ 07033, United States
| | | | - Peter T Meinke
- Merck Research Laboratories, Kenilworth, NJ 07033, United States
| | - David B Olsen
- Merck Research Laboratories, West Point, PA 19486, United States
| | - Armando Lagrutta
- Merck Research Laboratories, West Point, PA 19486, United States
| | | | | | - Xuanjia Peng
- WuXi AppTec, Shanghai, People's Republic of China
| | - Xiu Wang
- WuXi AppTec, Shanghai, People's Republic of China
| | - Hideyuki Fukuda
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Ryuta Kishii
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Masaya Takei
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Masanobu Yajima
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Taku Shibue
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Takeshi Shibata
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Kohei Ohata
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Akinori Nishimura
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Yasumichi Fukuda
- Kyorin Pharmaceutical Co., Ltd, 1848 Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan.
| |
Collapse
|
15
|
Singh SB, Kaelin DE, Wu J, Miesel L, Tan CM, Meinke PT, Olsen DB, Lagrutta A, Wei C, Liao Y, Peng X, Wang X, Fukuda H, Kishii R, Takei M, Shibata T, Takeuchi T, Ohata K, Nishimura A, Fukuda Y. C1–C2-linker substituted 1,5-naphthyridine analogues of oxabicyclooctane-linked NBTIs as broad-spectrum antibacterial agents (part 7). MEDCHEMCOMM 2015. [DOI: 10.1039/c5md00297d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Substitutions around linker positions C-1 and C-2 suggest that the C-2α hydroxy group is the best for activity.
Collapse
Affiliation(s)
| | | | - Jin Wu
- Merck Research Laboratories
- Kenilworth
- USA
| | | | | | | | | | | | | | | | | | - Xiu Wang
- WuXi AppTec
- Shanghai
- People's Republic of China
| | | | - Ryuta Kishii
- Kyorin Pharmaceutical Co., Ltd
- Tochigi
- 329-0114 Japan
| | - Masaya Takei
- Kyorin Pharmaceutical Co., Ltd
- Tochigi
- 329-0114 Japan
| | | | | | - Kohei Ohata
- Kyorin Pharmaceutical Co., Ltd
- Tochigi
- 329-0114 Japan
| | | | | |
Collapse
|