Pyridyl Benzamides as a Novel Class of Potent Inhibitors for the Kinetoplastid Trypanosoma brucei

Pd-catalyzed Suzuki-type cross-coupling of 2-pyridyl carbamoyl fluorides

We describe a palladium-catalyzed Suzuki-type cross-coupling reaction of 2-pyridyl carbamoyl fluorides with boronic acids, which provides entry to medicinally relevant pyridyl amides. Mechanistic studies, including the synthesis and reactivity of carbamoyl Pd-F complexes, reveal the importance of both the fluoride electrophile and nitrogen directing group for aiding reactivity.

Aminopyridines in the development of drug candidates against protozoan neglected tropical diseases

Neglected tropical diseases (NTDs) pose a major threat in tropical zones for impoverished populations. Difficulty of access, adverse effects or low efficacy limit the use of current therapeutic options. Therefore, development of new drugs against NTDs is a necessity. Compounds containing an aminopyridine (AP) moiety are of great interest for the design of new anti-NTD drugs due to their intrinsic properties compared with their closest chemical structures. Currently, over 40 compounds with an AP moiety are on the market, but none is used against NTDs despite active research on APs. The aim of this review is to present the medicinal chemistry work carried out with these scaffolds, against protozoan NTDs: Trypanosoma cruzi, Trypanosoma brucei or Leishmania spp.

Novel aroyl guanidine anti-trypanosomal compounds that exert opposing effects on parasite energy metabolism

Human African trypanosomiasis (HAT), or sleeping sickness, is a neglected tropical disease with current treatments marred by severe side effects or delivery issues. To identify novel classes of compounds for the treatment of HAT, high throughput screening (HTS) had previously been conducted on bloodstream forms of T. b. brucei, a model organism closely related to the human pathogens T. b. gambiense and T. b. rhodesiense. This HTS had identified a number of structural classes with potent bioactivity against T. b. brucei (IC50 ≤ 10 μM) with selectivity over mammalian cell-lines (selectivity index of ≥10). One of the confirmed hits was an aroyl guanidine derivative. Deemed to be chemically tractable with attractive physicochemical properties, here we explore this class further to develop the SAR landscape. We also report the influence of the elucidated SAR on parasite metabolism, to gain insight into possible modes of action of this class. Of note, two sub-classes of analogues were identified that generated opposing metabolic responses involving disrupted energy metabolism. This knowledge may guide the future design of more potent inhibitors, while retaining the desirable physicochemical properties and an excellent selectivity profile of the current compound class.

Quantitative Structure-Toxicity Relationship in Bioactive Molecules from a Conceptual DFT Perspective

The preclinical drug discovery stage often requires a large amount of costly and time-consuming experiments using huge sets of chemical compounds. In the last few decades, this process has undergone significant improvements by the introduction of quantitative structure-activity relationship (QSAR) modelling that uses a certain percentage of experimental data to predict the biological activity/property of compounds with similar structural skeleton and/or containing a particular functional group(s). The use of machine learning tools along with it has made life even easier for pharmaceutical researchers. Here, we discuss the toxicity of certain sets of bioactive compounds towards Pimephales promelas and Tetrahymena pyriformis in terms of the global conceptual density functional theory (CDFT)-based descriptor, electrophilicity index (ω). We have compared the results with those obtained by using the commonly used hydrophobicity parameter, logP (where P is the n-octanol/water partition coefficient), considering the greater ease of computing the ω descriptor. The Human African trypanosomiasis (HAT) curing activity of 32 pyridyl benzamide derivatives is also studied against Tryphanosoma brucei. In this review article, we summarize these multiple linear regression (MLR)-based QSAR studies in terms of electrophilicity (ω, ω2) and hydrophobicity (logP, (logP)2) parameters.

Development of Novel Isoindolone-Based Compounds against Trypanosoma brucei rhodesiense

This study identified the isoindolone ring as a scaffold for novel agents against Trypanosoma brucei rhodesiense and explored the structure-activity relationships of various aromatic ring substitutions. The compounds were evaluated in an integrated in vitro screen. Eight compounds exhibited selective activity against T. b. rhodesiense (IC50 <2.2 μm) with no detectable side activity against T. cruzi and Leishmania infantum. Compound 20 showed low nanomolar potency against T. b. rhodesiense (IC50 =40 nm) and no toxicity against MRC-5 and PMM cell lines and may be regarded as a new lead template for agents against T. b. rhodesiense. The isoindolone-based compounds have the potential to progress into lead optimization in view of their highly selective in vitro potency, absence of cytotoxicity and acceptable metabolic stability. However, the solubility of the compounds represents a limiting factor that should be addressed to improve the physicochemical properties that are required to proceed further in the development of in vivo-active derivatives.

Co2(CO)8 as a Solid CO (g) Source for the Amino Carbonylation of (Hetero)aryl Halides with Highly Deactivated (Hetero)arylamines

Carbonylation of (hetero)aryl iodides/bromides with highly deactivated 2-aminopyridines using Pd-Co(CO)₄ bimetallic catalysis is accomplished. The use of Co₂(CO)₈ as a solid CO(g) source enhanced reaction rates observed when compared to CO(g), and excellent yields highlight the versatility of the developed protocol. A wide range of electronically and sterically demanding heterocyclic amines and (hetero)aryl iodides/bromides employed for this study resulted in excellent yields of amino carbonylated products. The developed methodology was further extended to synthesize Trypanosome brucie and luciferase inhibitors.

Metal-free oxidative decarbonylative halogenation of fused imidazoles

An efficient strategy has been developed for the deformylative halogenation of carbaldehyde imidazo-fused heterocycles in the presence of TBHP controlled by temperature.

Investigation of thiazolyl-benzothiophenamides as potential agents for African sleeping sickness

African sleeping sickness is a potentially fatal neglected disease affecting sub-Saharan Africa. High-throughput screening identified the thiazolyl-benzothiophenamide 1 to be active against the causative parasite, Trypanosoma brucei. This work establishes structure-activity relationships of 1, guiding the design of second generation derivatives. After screening against the clinically relevant species T. b. rhodesiense, the derivative 16 was identified as a suitable candidate for further investigation.

Unveiling six potent and highly selective antileishmanial agents via the open source compound collection 'Pathogen Box' against antimony-sensitive and -resistant Leishmania braziliensis

Despite all efforts to provide new chemical entities to tackle leishmaniases, we are still dependent on a the limited drug arsenal, together with drawbacks like toxicity and drug-resistant parasites. Collaborative drug discovery emerged as an option to speed up the way to find alternative antileishmanial agents. This is the case of Medicines for Malaria Ventures - MMV, that promotes an open source drug discovery initiative to fight diseases worldwide. Here, we screened 400 compounds from 'Pathogen Box' (PBox) collection against Leishmania braziliensis, the main etiological agent of cutaneous leishmaniasis in Brazil. Twenty-three compounds were able to inhibit ≥ 80 % L. braziliensis growth at 5 μM. Six out of the PBox selected 23 compounds were found to be highly selective against L. braziliensis intracellular amastigotes with selectivity index varying from > 104 to > 746 and IC₅₀s ranging from 47 to 480 nM. The compounds were also active against antimony-resistant L. braziliensis isolated from the field or laboratory selected mutants, revealing the potential on treating patients infected with drug resistant parasites. Most of the selected compounds were known to be active against kinetoplastids, however, two compounds (MMV688703 and MMV676477) were part of toxoplasmosis and tuberculosis 'PBox' disease set, reinforcing the potential of phenotyping screening to unveil drug repurposing. Here we applied a computational prediction of pharmacokinetic properties using the ADMET predictor pkCSM (http://biosig.unimelb.edu.au/pkcsm/). The tool offered clues on potential drug development needs and can support further in vivo studies. Molecular docking analysis identified CRK3 (LbrM.35.0660), CYP450 (LbrM.30.3580) and PKA (LbrM.18.1180) as L. braziliensis targets for MMV676604, MMV688372 and MMV688703, respectively. Compounds from 'Pathogen Box' thus represents a new hope for novel (or repurposed) small molecules source to tackle leishmaniases.

Singlet oxygen mediated dual C–C and C–N bond cleavage in visible light

A tandem cleavage of carbon–carbon and carbon–nitrogen bonds in imidazo[1,2-a]pyridines and imidazo[1,2-a]quinolines is reported in the presence of eosin Y and visible light.

Reversible Small Molecule Inhibitors of MAO A and MAO B with Anilide Motifs

BACKGROUND

Ligands consisting of two aryl moieties connected via a short spacer were shown to be potent inhibitors of monoamine oxidases (MAO) A and B, which are known as suitable targets in treatment of neurological diseases. Based on this general blueprint, we synthesized a series of 66 small aromatic amide derivatives as novel MAO A/B inhibitors.

METHODS

The compounds were synthesized, purified and structurally confirmed by spectroscopic methods. Fluorimetric enzymological assays were performed to determine MAO A/B inhibition properties. Mode and reversibility of inhibition was determined for the most potent MAO B inhibitor. Docking poses and pharmacophore models were generated to confirm the in vitro results.

RESULTS

N-(2,4-Dinitrophenyl)benzo[d][1,3]dioxole-5-carboxamide (55, ST-2043) was found to be a reversible competitive moderately selective MAO B inhibitor (IC₅₀ = 56 nM, K_i = 6.3 nM), while N-(2,4-dinitrophenyl)benzamide (7, ST-2023) showed higher preference for MAO A (IC₅₀ = 126 nM). Computational analysis confirmed in vitro binding properties, where the anilides examined possessed high surface complementarity to MAO A/B active sites.

CONCLUSION

The small molecule anilides with different substitution patterns were identified as potent MAO A/B inhibitors, which were active in nanomolar concentrations ranges. These small and easily accessible molecules are promising motifs, especially for newly designed multitargeted ligands taking advantage of these fragments.

The Synthesis of N-(Pyridin-2-yl)-Benzamides from Aminopyridine and Trans-Beta-Nitrostyrene by Fe2Ni-BDC Bimetallic Metal–Organic Frameworks

A bimetallic metal–organic framework material, which was generated by bridging iron (III) cations and nickel (II) cations with 1,4-Benzenedicarboxylic anions (Fe2Ni-BDC), was synthesized by a solvothermal approach using nickel (II) nitrate hexahydrate and iron (III) chloride hexahydrate as the mixed metal source and 1,4-Benzenedicarboxylic acid (H2BDC) as the organic ligand source. The structure of samples was determined by X-ray powder diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), Raman spectroscopy, and nitrogen physisorption measurements. The catalytic activity and recyclability of the Fe2Ni-BDC catalyst for the Michael addition amidation reaction of 2-aminopyridine and nitroolefins were estimated. The results illustrated that the Fe2Ni-BDC catalyst demonstrated good efficiency in the reaction under optimal conditions. Based on these results, a reaction mechanism was proposed. When the molar ratio of 2-aminopyridine and trans-β-nitrostyrene was 1:1, and the solvent was dichloromethane, the isolated yield of pyridyl benzamide reached 82%; at 80 °C over 24 h. The catalyst can be reused without a substantial reduction in catalytic activity with 77% yield after six times of reuse.

N-substituted noscapine derivatives as new antiprotozoal agents: Synthesis, antiparasitic activity and molecular docking study

Novel N-substituted noscapine derivatives were synthesized by a three-component Strecker reaction of cyclic ether of N-nornoscapine with varied aldehydes, in the presence of cyanide ion. Moreover, the corresponding amides were synthesized by the oxidation of cyanide moieties in good yields. The in vitro antiprotozoal activity of the products was also investigated. Interestingly, some analogues did put on display promising antiparasitic activity against Trypanosoma brucei rhodesiense with IC₅₀ values between 2.5 and 10.0 µM and selectivity index (SI) ranged from 0.8 to 13.2. Eight compounds exhibited activity against Plasmodium falciparum K1 strain with IC₅₀ ranging 1.7-6.4 µM, and SI values between 2.8 and 10.5 against L6 rat myoblast cell lines. Molecular docking was carried out on trypanothione reductase (TbTR, PDB ID: 2WOW) and UDP-galactose 4' epimerase (TbUDPGE PDB: 1GY8) as targets for studying the envisaged mechanism of action. Compounds 6j₂ and 6b₂ displayed excellent docking scores with -8.59 and -8.86 kcal/mol for TbTR and TbUDPGE, respectively.

Collaborative drug discovery and the Tres Cantos Antimalarial Set (TCAMS)

Malaria affects a population of over 200 million people worldwide. New drugs are needed because of widespread resistance, and the hunt for such drugs involves a coordinated research effort from the scientific community. The release of the Tres Cantos Antimalarial Set (TCAMS) in 2010 represented a landmark in the field of collaborative drug discovery for malaria. This set of >13 000 molecules with confirmed activity against several strains of Plasmodium falciparum was publicly released with the goal of fostering additional research beyond the GlaxoSmithKline (GSK) network of collaborators. Here, we examine the outcomes realized from TCAMS over the past 8 years and whether the expectations surrounding this initiative have become a reality.

A facile tandem decyanation/cyanation reaction of α-iminonitriles toward cyano-substituted amides

A new tandem decyanation/cyanation reaction of α-iminonitriles has been developed. A variety of cyano-substituted aryl amides and heteroaryl amides are synthesized in good yields. Both electron-rich and electron-deficient groups are compatible with the standard conditions. This reaction features a nonmetallic cyano source, tandem decyanation and cyanation reaction, waste utilization of the HCN from the hydrolysis of α-iminonitriles, formation of two important functional groups in one-step operation, etc.

Ce(iii)-catalyzed highly efficient synthesis of pyridyl benzamides from aminopyridines and nitroolefins without external oxidants

An efficient synthesis of a variety of pyridyl benzamides from 2-aminopyridines and nitroolefins is described. This rare-earth-metal-catalyzed reaction provides the corresponding products with broad substrate scope in moderate to excellent yields, in the absence of additives and external oxidants. Water is used as the source of the carbonyl oxygen atom in pyridyl benzamides. Furthermore, 2-substituted oxazolo[4,5-b]pyridines are formed in good yields under the standard conditions when 2-aminopyridin-3-ols are used as the substrates.

Unpacking the Pathogen Box-An Open Source Tool for Fighting Neglected Tropical Disease

The Pathogen Box is a 400-strong collection of drug-like compounds, selected for their potential against several of the world's most important neglected tropical diseases, including trypanosomiasis, leishmaniasis, cryptosporidiosis, toxoplasmosis, filariasis, schistosomiasis, dengue virus and trichuriasis, in addition to malaria and tuberculosis. This library represents an ensemble of numerous successful drug discovery programmes from around the globe, aimed at providing a powerful resource to stimulate open source drug discovery for diseases threatening the most vulnerable communities in the world. This review seeks to provide an in-depth analysis of the literature pertaining to the compounds in the Pathogen Box, including structure-activity relationship highlights, mechanisms of action, related compounds with reported activity against different diseases, and, where appropriate, discussion on the known and putative targets of compounds, thereby providing context and increasing the accessibility of the Pathogen Box to the drug discovery community.

CuI incorporated cobalt ferrite nanoparticles as a magnetically separable catalyst for oxidative amidation reaction

A Cu-incorporated magnetic nanocatalyst has been developed for oxidative amidation of aryl aldehydes with 2-aminopyridine in the presence of TBHP.

Chemodivergent synthesis of N-(pyridin-2-yl)amides and 3-bromoimidazo[1,2-a]pyridines from α-bromoketones and 2-aminopyridines

N-(Pyridin-2-yl)amides and 3-bromoimidazo[1,2-a]pyridines were synthesized respectively from α-bromoketones and 2-aminopyridine under different reaction conditions.

Screening of the Pathogen Box reveals new starting points for anti-trypanosomal drug discovery

This study aimed to uncover new starting points for anti-trypansomal drug discovery through the screening of the Pathogen Box against Trypanosoma brucei brucei. Our study identified compounds 35, 39, 46, 53 and 56 whose activity and selectivity highlighted them as promising candidates with potential for further study and optimisation.

Synthesis of Jacaranone-Derived Nitrogenous Cyclohexadienones and Their Antiproliferative and Antiprotozoal Activities

The cytotoxic and antiprotozoal activities of the phytoquinoide, jacaranone, and related compounds have been an ongoing topic in recent drug discovery. Starting from the natural product-derived cyclohexadienone scaffold, a series of nitrogen-containing derivatives were synthesized and subsequently evaluated for their antiproliferative and antiprotozoal activity. Anticancer potency was analyzed using different types of cancer cell lines: MDA-MB-231 breast cancer, CCRF-CEM leukemia, HCT-116 colon cancer, U251 glioblastoma, and, in addition, non-tumorigenic MRC-5 lung fibroblasts. Antiproliferative activities at micromolar concentrations could be shown. Antiprotozoal activity was assessed against Plasmodium falciparum NF54 and Trypanosoma brucei rhodesiense STIB900. For all compounds, selectivity indices (SI) were calculated based on assessed cytotoxicity towards L6 cells. In addition, the structure-activity-relationships and physicochemical parameters of these compounds are discussed.

Optimization and Evaluation of Antiparasitic Benzamidobenzoic Acids as Inhibitors of Kinetoplastid Hexokinase 1

Kinetoplastid-based infections are neglected diseases that represent a significant human health issue. Chemotherapeutic options are limited due to toxicity, parasite susceptibility, and poor patient compliance. In response, we studied a molecular-target-directed approach involving intervention of hexokinase activity-a pivotal enzyme in parasite metabolism. A benzamidobenzoic acid hit with modest biochemical inhibition of Trypanosoma brucei hexokinase 1 (TbHK1, IC50 =9.1 μm), low mammalian cytotoxicity (IMR90 cells, EC50 >25 μm), and no appreciable activity on whole bloodstream-form (BSF) parasites was optimized to afford a probe with improved TbHK1 potency and, significantly, efficacy against whole BSF parasites (TbHK1, IC50 =0.28 μm; BSF, ED50 =1.9 μm). Compounds in this series also inhibited the hexokinase enzyme from Leishmania major (LmHK1), albeit with less potency than toward TbHK1, suggesting that inhibition of the glycolytic pathway may be a promising opportunity to target multiple disease-causing trypanosomatid protozoa.

Screening the Medicines for Malaria Venture Pathogen Box across Multiple Pathogens Reclassifies Starting Points for Open-Source Drug Discovery

Open-access drug discovery provides a substantial resource for diseases primarily affecting the poor and disadvantaged. The open-access Pathogen Box collection is comprised of compounds with demonstrated biological activity against specific pathogenic organisms. The supply of this resource by the Medicines for Malaria Venture has the potential to provide new chemical starting points for a number of tropical and neglected diseases, through repurposing of these compounds for use in drug discovery campaigns for these additional pathogens. We tested the Pathogen Box against kinetoplastid parasites and malaria life cycle stages in vitro Consequently, chemical starting points for malaria, human African trypanosomiasis, Chagas disease, and leishmaniasis drug discovery efforts have been identified. Inclusive of this in vitro biological evaluation, outcomes from extensive literature reviews and database searches are provided. This information encompasses commercial availability, literature reference citations, other aliases and ChEMBL number with associated biological activity, where available. The release of this new data for the Pathogen Box collection into the public domain will aid the open-source model of drug discovery. Importantly, this will provide novel chemical starting points for drug discovery and target identification in tropical disease research.

Discovery of N-(2-aminoethyl)-N-benzyloxyphenyl benzamides: New potent Trypanosoma brucei inhibitors

A phenotypic screen of a compound library for antiparasitic activity on Trypanosoma brucei, the causative agent of Human African Trypanosomiasis (HAT), led to the identification of N-(2-aminoethyl)-N-phenyl benzamides as a starting point for hit-to-lead medicinal chemistry. Eighty two analogues were prepared, which led to the identification of a set of highly potent N-(2-aminoethyl)-N-benzyloxyphenyl benzamides with the most potent compound 73 having an in vitro EC50=0.001μM. The compounds displayed drug-like properties when tested in a number of in vitro assays. Compound 73 was orally bioavailable and displayed good plasma and brain exposure in mice, cured 2 out of 3 mice infected with Trypanosoma brucei in acute model when dosed orally at 50mg/kg once per day for 4days. Given its potent antiparasitic properties and its ease of synthesis, compound 73 represents a potential lead for the development of drug to treat Human African Trypanosomiasis.

QSAR analysis for 6-arylpyrazine-2-carboxamides as Trypanosoma brucei inhibitors

Human African trypanosomiasis (HAT) is prevalent in African countries, covering 37 countries, mostly sub-Saharan. A limited number of drugs are available to cure this neglected disease. In the present work, quantitative structure-activity (toxicity) relationships (QSA(T)R) analysis has been performed for a dataset of 54 6-arylpyrazine-2-carboxamides as Trypanosoma brucei inhibitors to identify the important structural features required for future optimization of lead candidates. The QSA(T)R models satisfy OECD guidelines and have high statistical robustness. The QSA(T)R models are based on easily interpretable molecular descriptors. The QSA(T)R models indicate that Trypanosoma brucei inhibitory activity of 6-arylpyrazine-2-carboxamides has correlation with the presence of N-sec-butylformamide and substituted benzene. The results could be beneficial for further optimization of 6-arylpyrazine-2-carboxamides as Trypanosoma brucei inhibitors. Some potential candidate molecules have been proposed.

Ligand-Enabled, Copper-Promoted Regio- and Chemoselective Hydroxylation of Arenes, Aryl Halides, and Aryl Methyl Ethers

We report here a practical method for the ortho C-H hydroxylation of benzamides with inexpensive copper(II) acetate monohydrate and a pyridine ligand. An intra- and intermolecular ligand combination was explored to achieve regio- and chemoselective hydroxylation. Interestingly, typical regiochemical scrambling associated with the C-H activation was further resolved by introducing a ligand-directed ortho hydroxylation of haloarenes and aryl methyl ethers.

Microwave-assisted heteropolyanion-based ionic liquid promoted sustainable protocol to N-heteroaryl amides via N-directing dual catalyzed oxidative amidation of aldehydes

A procedure for the synthesis of N-heteroaryl amides directly from oxidative amidation of aldehydes catalyzed by heteropolyanion-based ionic liquids has been reported. The proposed N-directing dual-catalysis mechanism was briefly investigated.

Copper(i)-catalysed oxidative C–N coupling of 2-aminopyridine with terminal alkynes featuring a CC bond cleavage promoted by visible light

An efficient and eco-friendly approach to aerobic oxidative C–N coupling of 2-aminopyridine with terminal alkynes for preparation of biologically important pyridyl-amides via CC triple bond cleavage at room temperature.

The total synthesis and functional evaluation of fourteen stereoisomers of yaku'amide B. The importance of stereochemistry for hydrophobicity and cytotoxicity

Yaku'amide B is a highly unsaturated linear tridecapeptide and an extremely potent cytotoxin.

6-Arylpyrazine-2-carboxamides: A New Core for Trypanosoma brucei Inhibitors

From a whole-organism high throughput screen of approximately 87000 compounds against Trypanosoma brucei brucei, we recently identified eight new unique compounds for the treatment of human African trypanosomiasis. In an effort to understand the structure-activity relationships around these compounds, we report for the first time our results on a new class of trypanocides, the pyrazine carboxamides. Attracted by the low molecular weight (270 g·mol(-1)) of our starting hit (9) and its potency (0.49 μM), the SAR around the core was explored, leading to compounds having an EC50 as low as 25 nM against T. b. brucei and being more than 1500 times less toxic against mammalian L6 and HEK293 cell lines. The most potent compounds in the series were exquisitely selective for T. brucei over a panel of other protozoan parasites, showing an excellent correlation with the human infective parasite Trypanosoma brucei rhodesiense, the most potent compound (65) having an EC50 of 24 nM. The compounds are highly drug-like and are able to penetrate the CNS, their only limitation currently being their rate of microsomal metabolism. To that effect, efforts to identify potential metabolites of selected compounds are also reported.

Antiprotozoal Selectivity of Diimidazoline N-Phenylbenzamides

We discovered three diimidazolines with high antiplasmodial selectivity that had IC50 values of 1.9-28 nM against cultured Plasmodium falciparum. We also identified a gem-dimethyl diimidazoline with high antitrypanosomal selectivity that had an IC50 value of 26 nM against cultured Trypanosoma brucei rhodesiense. Two 2-imidazoline heterocycles in a para orientation on a N-phenylbenzamide or similar core structure were required for high antiprotozoal activity. Ring expansion of the imidazoline as well as heterocyclic variants with pKa values of <7 all decreased activity significantly.