New direct inhibitors of InhA with antimycobacterial activity based on a tetrahydropyran scaffold

doi:10.1016/j.ejmech.2016.02.008

European Journal of Medicinal Chemistry

Volume 112, 13 April 2016, Pages 252-257

https://doi.org/10.1016/j.ejmech.2016.02.008 Get rights and content

Highlights

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New tetrahydropyran inhibitor (1) of mycobacterial InhA was discovered.
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It exhibits good InhA inhibitory potency and moderate antimycobacterial activity.
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SAR study was initiated and a focused library of analogs of hit 1 was synthesized.
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Crystal structure of inhibitor 1 bound to InhA revealed the binding mode.

Abstract

Tetrahydropyran derivative 1 was discovered in a high-throughput screening campaign to find new inhibitors of mycobacterial InhA. Following initial in-vitro profiling, a structure-activity relationship study was initiated and a focused library of analogs was synthesized and evaluated. This yielded compound 42 with improved antimycobacterial activity and low cytotoxicity. Additionally, the crystal structure of InhA in complex with inhibitor 1 was resolved, to reveal the binding mode and provide hints for further optimization.

Graphical abstract

Introduction

Tuberculosis (TB) remains a major global health problem, with an estimated 9 million new cases and 1.5 million deaths per year [1]. Although progress has been made to reduce the global incidence of TB, the emergence and spread of drug resistance threatens to undermine these efforts. This includes both multi-drug resistant TB, which is resistant to isoniazid and rifampicin, and extensively drug-resistant TB, which is resistant to isoniazid, rifampicin, any fluoroquinolone, and an injectable drug (i.e., one of capraomycin, kanamycin, amikacin) [2], [3], [4].

The mycobacterial fatty-acid biosynthesis pathway II (FAS-II) represents a validated target for drug discovery, as fatty acids are essential for bacterial growth and can only be synthesized de novo. In addition, the bacterial FAS-II system is fundamentally distinct from that of mammals, thus providing the possibility to selectively target bacteria [5]. One of the enzymes involved in the FAS-II pathway in Mycobacterium tuberculosis (Mtb) is InhA, a NADH-dependent, enoyl-acyl carrier protein reductase. This is the target of isoniazid, a first-line drug for treatment of TB. Isoniazid is a pro-drug that is enzymatically activated by KatG, a mixed function catalase/peroxidase; this transforms isoniazid into an unstable species that reacts with the NAD cofactor to form a covalent adduct, which subsequently inhibits InhA activity. Resistance to isoniazid is mainly the result of mutations in KatG that reduce its activation of isoniazid, and to a lesser extent, to mutations in the InhA active site. Therefore, compounds that directly target InhA and do not require activation by the mycobacterial catalase/peroxidase KatG are promising candidates for treatment of infections caused by isonoazid-resistant strains [6], [7]. As a follow-up of previous reports, we present here the synthesis, physicochemical characterization, biological profiling, and initial structure-activity relationships (SARs) of new tetrahydropyran derivatives of hit compound 1 (Fig. 1) that was identified by GlaxoSmithKline in a high-throughput screening (HTS) campaign against InhA.

Section snippets

Hit validation

Hit compound 1 was identified by high-throughput screening against InhA with the GlaxoSmithKline compound collection. First, compound 1 was re-synthesized (see below), to complete the initial round of in-vitro profiling, where it had good InhA inhibitory potency (IC₅₀ = 0.020 μM), moderate in-vitro antimycobacterial activity (MIC = 11.7 μM), and killed Mtb inside macrophages (Table 1). In terms of early safety profiling, compound 1 showed modest hERG inhibition, with an IC₅₀ of 50.1 μM, and low

Conclusions

The tetrahydropyran compound 1 was identified in a high-throughput screen of the GlaxoSmithKline collection, and it showed good InhA inhibitory potency (IC₅₀ = 0.020 μM), moderate in-vitro antimycobacterial activity (MIC = 11.7 μM), modest hERG inhibition, and low cytotoxicity against the HepG2 human cell line. Following initial in-vitro profiling, a SAR study was initiated and a series of 18 analogs was synthesized and evaluated. Based on the SAR data generated, it appears that rings C and D

Materials and methods

Chemicals from Sigma-Aldrich, TCI, and Acros were used without further purification. All reactions were performed under argon atmosphere, unless otherwise stated. Analytical TLC was performed on Merck silica gel (60 F₂₅₄) plates (0.25 mm) and visualized with ultraviolet light. Melting points were determined on a Reichert hot-stage microscope and are uncorrected. ¹H and ¹³C NMR spectra were recorded on a Bruker AVANCE III 400 MHz NMR spectrometer in CDCl₃ and DMSO-d₆ solution, with TMS or

Funding sources

The research leading to these data has received funding from the Global Alliance for TB Drug Development, and from the European Union 7th Framework Program (FP7- 2007–2013) under Orchid Grant agreement No. 261378. The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Acknowledgment

We thank Dr. Chris Berrie for critical reading of the manuscript. We are grateful to Rubén González del Río, Delia Blanco Ruano, Pedro A. Torres Gómez, Lydia Mata, Francisco de Dios, and Vanessa Barroso for the biological evaluation, and Bill McDowell for preparation of the protein.

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Citation Excerpt :
The right side of the molecule (rings C and D) is placed in a deep pocket in the protein, not having any known specific interactions. The tetrahydropyran ring appears to be pointing out of the binding site [27]. Triclosan (Fig. 1) is an antibacterial compound used as an additive in personal care products, acting as a membrane disrupter.
Tuberculosis (TB) remains a major health problem worldwide. The infectious agent, Mycobacterium tuberculosis, has a unique ability to survive within the host, alternating between active and latent disease states, and escaping the immune system defences. The extended duration of anti-TB regimens and the increasing prevalence of multidrug- (MDR) and extensively drug-resistant (XDR) M. tuberculosis strains have created an urgent need for new antibiotics active against drug-resistant organisms and that can shorten standard therapy. However, despite success in identifying active compounds through phenotypic screens, the conversion of hits into novel chemical series and ultimately into clinical candidates is hampered by the poor efficacy in eliminating M. tuberculosis within different host compartments, including macrophages, as well as a lack of knowledge about the specific target(s) inhibited and/or upregulated.
The current status of anti-TB lead generation has much improved over the last decade, as exemplified by the recent approval of bedaquiline and delamanid to treat MDR-TB and XDR-TB. This review provides a critical analysis on the strategies used to progress hit compounds into viable lead candidates, and how emerging targets may play a role in TB drug discovery in the near future. Four new relevant targets are addressed: the enoyl-acyl carrier protein reductase, InhA; the transmembrane transport protein large, MmpL3; the decaprenylphospho-beta-d-ribofuranose 2-oxidase, DprE1; and the ubiquinol-cytochrome C reductase, QcrB. Validated hit compounds for each target are presented and explored, and the medicinal chemistry strategies to expand SAR around novel chemotypes analyzed. In addition, very recent emerging targets are also discussed.

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European Journal of Medicinal Chemistry

Highlights

Abstract

Graphical abstract

Introduction

Section snippets

Hit validation

Conclusions

Materials and methods

Funding sources

Acknowledgment

References (17)

Multidrug-resistant and extensively drug-resistant tuberculosis: a threat to global control of tuberculosis

Lancet

Global tuberculosis drug development pipeline: the need and the reality

Lancet

Targeting tuberculosis and malaria through inhibition of enoyl reductase: compound activity and structural data

J. Biol. Chem.

WHO Global Tuberculosis Report 2014

Worldwide emergence of extensively drug-resistant tuberculosis

Emerg. Infect. Dis.

Inhibitors of FabI, an enzyme drug target in the bacterial fatty acid biosynthesis pathway

Accounts Chem. Res.

Molecular basis and mechanisms of drug resistance in Mycobacterium tuberculosis: classical and new drugs

J. Antimicrob. Chemoth

The mechanism of isoniazid killing: clarity through the scope of genetics

Annu. Rev. Microbiol.

Cited by (23)

Discovery of 1,2,3-triazole incorporated indole-piperazines as potent antitubercular agents: Design, synthesis, in vitro biological evaluation, molecular docking and ADME studies

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Novel 2-arylthiazolidin-4-one-thiazole hybrids with potent activity against Mycobacterium tuberculosis

Indole chalcones: Design, synthesis, in vitro and in silico evaluation against Mycobacterium tuberculosis

Improved multicomponent, one-pot synthesis of functionalized tetrahydropyrans cardiovascular dysfunction regulators

Drug discovery in tuberculosis. New drug targets and antimycobacterial agents

Short communicationNew direct inhibitors of InhA with antimycobacterial activity based on a tetrahydropyran scaffold

Highlights

Abstract

Graphical abstract

Introduction

Section snippets

Hit validation

Conclusions

Materials and methods

Funding sources

Acknowledgment

Lancet

Lancet

J. Biol. Chem.

WHO Global Tuberculosis Report 2014

Worldwide emergence of extensively drug-resistant tuberculosis

Emerg. Infect. Dis.

Inhibitors of FabI, an enzyme drug target in the bacterial fatty acid biosynthesis pathway

Accounts Chem. Res.

Molecular basis and mechanisms of drug resistance in Mycobacterium tuberculosis: classical and new drugs

J. Antimicrob. Chemoth

The mechanism of isoniazid killing: clarity through the scope of genetics

Annu. Rev. Microbiol.

Short communication
New direct inhibitors of InhA with antimycobacterial activity based on a tetrahydropyran scaffold