Recent Advances in Macrocyclic Drugs and Microwave-Assisted and/or Solid-Supported Synthesis of Macrocycles

Macrocycles represent attractive candidates in organic synthesis and drug discovery. Since 2014, nineteen macrocyclic drugs, including three radiopharmaceuticals, have been approved by FDA for the treatment of bacterial and viral infections, cancer, obesity, immunosuppression, etc. As such, new synthetic methodologies and high throughput chemistry (e.g., microwave-assisted and/or solid-phase synthesis) to access various macrocycle entities have attracted great interest in this chemical space. This article serves as an update on our previous review related to macrocyclic drugs and new synthetic strategies toward macrocycles (Molecules, 2013, 18, 6230). In this work, I first reviewed recent FDA-approved macrocyclic drugs since 2014, followed by new advances in macrocycle synthesis using high throughput chemistry, including microwave-assisted and/or solid-supported macrocyclization strategies. Examples and highlights of macrocyclization include macrolactonization and macrolactamization, transition-metal catalyzed olefin ring-closure metathesis, intramolecular C–C and C–heteroatom cross-coupling, copper- or ruthenium-catalyzed azide–alkyne cycloaddition, intramolecular S_NAr or S_N2 nucleophilic substitution, condensation reaction, and multi-component reaction-mediated macrocyclization, and covering the literature since 2010.     

Bridging the synthetic and biopolymer worlds with peptide-drug conjugates

Roberts and Li break the standard library mold by generating hybrid libraries of small molecules tethered to peptides. Hybrid libraries harness larger chemical and structural diversities and thus represent a new frontier in lead drug discovery.     

Parallel synthesis of 19-membered ring macro-heterocycles via intramolecular thioether formation

Starting from resin-bound orthogonally protected lysine, the generation of 19-membered ring macro-heterocycles via intramolecular thioether formation is described. The on resin cyclization occurred by the coupling of p-fluoro-m-nitro benzoic acid or bromo acetic acid followed by intramolecular substitution S_NAr or S_N2 displacement of the fluoro and bromo groups, respectively. The described approaches present versatile synthetic routes toward the synthesis of libraries of macro-heterocycles in an attempt to establish lead drug candidates. The desired cyclic products were obtained in good yields and good purities.     

Three overlooked chemical approaches toward 3-naphthalimide amonafide N-derivatives

Three efficient strategies for derivatization of the anticancer drug candidate amonafide (Quinamed, originally AS1413) are described. Unprecedented reductive amination of aryl aldehydes, S_NAr, and addition–elimination reactions, while using readily available starting materials, give quick entry to potential libraries of novel 3-aryl, 3-benzyl N-derivatives of amonafide. The selective anticancer activity of this important DNA intercalation agent is expected to be enhanced by expanding the diversity of amonafide N-derivatives. The synthetic routes reported in this work are general and readily applicable.     

Synthesis and screening of peptoid arrays on cellulose membranes

Rapid synthesis and screening of compound libraries enables the accelerated identification of novel protein ligands in order to support processes like analysis of protein interactions, drug target discovery or lead structure discovery. SPOT synthesis—a well established method for the rapid preparation of peptide arrays—has recently been extended to the field of nonpeptides. In this contribution we report on the systematic evaluation of the SPOT technique for the assembly of N-alkylglycine (peptoid) library arrays. In the course of this investigation bromoacetic acid 2,4-dinitrophenylester (1a) was identified to be the most suited agent for bromoacetylation in terms of yield and N-selectivity enabling straightforward submonomer synthesis on hydroxy-group rich cellulose membranes. The potential of this method for the rapid identification of novel nonpeptidic protein ligands was demonstrated by synthesis and screening of a library consisting of 8000 peptoids and peptomers (i.e. their hybrids with α-substituted amino acids) allowing the identification of micromolar ligands for the monoclonal antibody Tab-2.     

Quality, not quantity: the role of natural products and chemical proteomics in modern drug discovery

Chemical genetics and reverse chemical genetics parallel classical genetics but target genes at the protein level and have proven useful in recent years for screening combinatorial libraries for compounds of biological interest. However, the performance of combinatorial chemistry in filling pharmaceutical pipelines has been lower than anticipated and the tide may be turning back to Nature in the search for new drug candidates. Even though diversity oriented synthesis is now producing molecules that are natural product-like in terms of size and complexity, these molecules have not evolved to interact with biomolecules. Natural products, on the other hand, have evolved to interact with biomolecules, which is why so many can be found in pharmacopoeias. However, the cellular targets and modes of action of these fascinating compounds are seldom known, hindering the drug development process. This review focuses on the emergence of chemical proteomics and reverse chemical proteomics as tools for the discovery of cellular receptors for natural products, thereby generating protein/ligand pairs that will prove useful in identifying new drug targets and new biologically active small molecule scaffolds. Such a system-wide approach to identifying new drugable targets and their small molecule ligands will help unblock the pharmaceutical product pipelines by speeding the process of target and lead identification.     

X-ray photoelectron emission studies of mixed selenides AgGaSe2 and Ag9GaSe6

Auger and direct electron specta from crystalline AgGaSe₂ and Ag₉GaSe₆ have been studied with X-ray photoelectron spectroscopy. It is shown that the AgM₅N_4,5N_4,5 and M₄N_4,5N_4,5 Auger spectra are more sensitive to the chemical environment than the Ag 3d direct photoelectron spectra. Furthermore the Auger parameter as defined by Wagner is used in order to characterize the chemical state of these compounds. Last, the XPS spectra of the valence-band region are investigated and chalcogen s and p and noble-metal d bands are clearly identified. The electronic structure of these two selenides does not seem to be determined predominantly by the crystal structure. As a whole, the spectral features are discussed in connection with the character of the chemical bonding and the physical properties of these compounds.     

A new A431/cell membrane chromatography and online high performance liquid chromatography/mass spectrometry method for screening epidermal growth factor receptor antagonists from Radix sophorae flavescentis

The intracellular kinase domains of epidermal growth factor receptor (EGFR) in some tumor cells such as human epidermal squamous cells (A₄₃₁ cells) are an important target for drug discovery. We have developed a new A₄₃₁/cell membrane chromatography (A₄₃₁/CMC)-online–high performance liquid chromatography/mass spectrometry (HPLC/MS) method for screening EGFR antagonists from medicinal herbs such as traditional Chinese medicines (TCMs). In this study, A₄₃₁ cells with high EGFR expression levels were used to prepare cell membrane stationary phase (CMSP) in an A₄₃₁/CMC model. The retention fractions eluted from the CMSP column were enriched onto an ODS pre-column and then switched into an HPLC/MS system by combining a 10 port columns switching valve. The screening results found that oxymatrine and matrine from Radix sophorae flavescentis (RSF) were the targeted components which could act on EGFR in similar manner of gefitinib as a control drug. There was a good relationship of their inhibiting effects on EGFR secretion and A₄₃₁ cell growth in vitro. This new A₄₃₁/CMC-online-HPLC/MS method can be applied for screening EGFR antagonists from TCMs such as RSF. It will be a useful method for drug discovery with natural medicinal herbs as a leading compound resource.     

Why Matter Matters: Fast-Tracking Mycobacterium abscessus Drug Discovery

Unlike Tuberculosis (TB), Mycobacterium abscessus lung disease is a highly drug-resistant bacterial infection with no reliable treatment options. De novo M. abscessus drug discovery is urgently needed but is hampered by the bacterium’s extreme drug resistance profile, leaving the current drug pipeline underpopulated. One proposed strategy to accelerate de novo M. abscessus drug discovery is to prioritize screening of advanced TB-active compounds for anti-M. abscessus activity. This approach would take advantage of the greater chance of homologous drug targets between mycobacterial species, increasing hit rates. Furthermore, the screening of compound series with established structure–activity-relationship, pharmacokinetic, and tolerability properties should fast-track the development of in vitro anti-M. abscessus hits into lead compounds with in vivo efficacy. In this review, we evaluated the effectiveness of this strategy by examining the literature. We found several examples where the screening of advanced TB chemical matter resulted in the identification of anti-M. abscessus compounds with in vivo proof-of-concept, effectively populating the M. abscessus drug pipeline with promising new candidates. These reports validate the screening of advanced TB chemical matter as an effective means of fast-tracking M. abscessus drug discovery.     

7-Aminoalkoxy-Quinazolines from Epigenetic Focused Libraries Are Potent and Selective Inhibitors of DNA Methyltransferase 1

Inhibitors of epigenetic writers such as DNA methyltransferases (DNMTs) are attractive compounds for epigenetic drug and probe discovery. To advance epigenetic probes and drug discovery, chemical companies are developing focused libraries for epigenetic targets. Based on a knowledge-based approach, herein we report the identification of two quinazoline-based derivatives identified in focused libraries with sub-micromolar inhibition of DNMT1 (30 and 81 nM), more potent than S-adenosylhomocysteine. Also, both compounds had a low micromolar affinity of DNMT3A and did not inhibit DNMT3B. The enzymatic inhibitory activity of DNMT1 and DNMT3A was rationalized with molecular modeling. The quinazolines reported in this work are known to have low cell toxicity and be potent inhibitors of the epigenetic target G9a. Therefore, the quinazoline-based compounds presented are attractive not only as novel potent inhibitors of DNMTs but also as dual and selective epigenetic agents targeting two families of epigenetic writers.     

High‐expression β1 adrenergic receptor/cell membrane chromatography method based on a target receptor to screen active ingredients from traditional Chinese medicines

β‐Adrenergic receptors are important targets for drug discovery. We have developed a new β₁‐adrenergic receptor cell membrane chromatography (β₁AR‐CMC) with offline ultra‐performance LC (UPLC) and MS method for screening active ingredients from traditional Chinese medicines. In this study, Chinese hamster ovary‐S cells with high β₁AR expression levels were established and used to prepare a cell membrane stationary phase in a β₁AR‐CMC model. The retention fractions were separated and identified by the UPLC–MS system. The screening results found that isoimperatorin from Rhizoma et Radix Notopterygii was the targeted component that could act on β₁AR in similar manner of metoprolol as a control drug. In addition, the biological effects of active component were also investigated in order to search for a new type of β₁AR antagonist. It will be a useful method for drug discovery as a leading compound resource.     

组合化学、分子库与新药研究

组合化学是进入90 年代以来寻找及优化新药先导化合物的主要研究方法, 其特点是改变了传统的逐一合成、逐一纯化、逐一筛选的模式, 而是以合成和筛选化学库的形式完成寻找及优化药物先导化合物, 极大地加快了药物先导化合物出现的速度。本文就目前有关组合化学研究的基本理论、基本方法、发展趋势、研究成果以及我国应当采取的措施进行了综述。     

Mapping the DNA Damaging Effects of Polypyridyl Copper Complexes with DNA Electrochemical Biosensors

Several classes of copper complexes are known to induce oxidative DNA damage that mediates cell death. These compounds are potentially useful anticancer agents and detailed investigation can reveal the mode of DNA interaction, binding strength, and type of oxidative lesion formed. We recently reported the development of a DNA electrochemical biosensor employed to quantify the DNA cleavage activity of the well-studied [Cu(phen)₂]²⁺ chemical nuclease. However, to validate the broader compatibility of this sensor for use with more diverse—and biologically compatible—copper complexes, and to probe its use from a drug discovery perspective, analysis involving new compound libraries is required. Here, we report on the DNA binding and quantitative cleavage activity of the [Cu(TPMA)(N,N)]²⁺ class (where TPMA = tris-2-pyridylmethylamine) using a DNA electrochemical biosensor. TPMA is a tripodal copper caging ligand, while N,N represents a bidentate planar phenanthrene ligand capable of enhancing DNA interactions through intercalation. All complexes exhibited electroactivity and interact with DNA through partial (or semi-) intercalation but predominantly through electrostatic attraction. Although TPMA provides excellent solution stability, the bulky ligand enforces a non-planar geometry on the complex, which sterically impedes full interaction. [Cu(TPMA)(phen)]²⁺ and [Cu(TPMA)(DPQ)]²⁺ cleaved 39% and 48% of the DNA strands from the biosensor surface, respectively, while complexes [Cu(TPMA)(bipy)]²⁺ and [Cu(TPMA)(PD)]²⁺ exhibit comparatively moderate nuclease efficacy (ca. 26%). Comparing the nuclease activities of [Cu(TPMA)(phen)] ²⁺ and [Cu(phen)₂]²⁺ (ca. 23%) confirms the presence of TPMA significantly enhances chemical nuclease activity. Therefore, the use of this DNA electrochemical biosensor is compatible with copper(II) polypyridyl complexes and reveals TPMA complexes as a promising class of DNA damaging agent with tuneable activity due to coordinated ancillary phenanthrene ligands.     

An environmentally-friendly one-pot synthesis of 4-sulfonyl benzoic acids

This Letter reports an environmentally-friendly one-pot S_NAr reaction of thiols to 4-halobenzoic acid methyl esters to provide 4-substituted sulfone benzoic acids and picolinic acids after bleach-mediated oxidative workup. These acid intermediates were synthesized on gram scale, are perfect partners for library synthesis, and have good physical chemical properties useful for drug discovery.     

Iron/copper co-catalyzed highly selective arylation of sulfinamides with aryl iodides

In the present study, an inexpensive but efficient Iron(III) and Copper(II) co-catalyst without ligands catalyzed arylation of sulfinamides with aryl iodide was primarily reported. In brief, in the presence of Fe(NO₃)₃·9H₂O, CuO and K₃PO₄, the highly selective C–N cross coupling of several sulfinamides and aryl iodides was achieved in high chemical yield, while the aryl chlorides and bromides could not yield coupling products. It is noteworthy that through the arylation of chiral tert-butanesulfinamide with aryl iodides, N-aryl tert-butanesulfinamides are provided without racemization, even in gram-scale. The possible mechanism was that This oxidative addition process between copper catalyst and aryl-iodides might be significantly accelerated by active Fe(III) species. Moreover, using this synthetic method, a facile and efficient access was developed for the derivatives of N-phenyl sulfinamides, which might help to develop new drug molecules and material chemicals.     

Synthesis,biochemical evaluation and computational simulations of new cytochrome bc1 complex inhibitors based on N-(4-aryloxyphenyl) phthalimides

A series of N-(4-aryloxyphenyl)phthalimides were synthesized and identified as new inhibitors of the cytochrome bc1 complex. Furthermore, results obtained from computational simulations indicated that 3e' should bind to the Q_o site of the bc1 complex.     

Decoding Split and Pool Combinatorial Libraries with Electron-Transfer Dissociation Tandem Mass Spectrometry

Screening of bead-based split and pool combinatorial chemistry libraries is a powerful approach to aid the discovery of new chemical compounds able to interact with, and modulate the activities of, protein targets of interest. Split and pool synthesis provides for large and well diversified chemical libraries, in this case comprised of oligomers generated from a well-defined starting set. At the end of the synthesis, each bead in the library displays many copies of a unique oligomer sequence. Because the sequence of the oligomer is not known at the time of screening, methods for decoding of the sequence of each screening “hit” are essential. Here we describe an electron-transfer dissociation (ETD) based tandem mass spectrometry approach for the decoding of mass-encoded split and pool libraries. We demonstrate that the newly described “chiral oligomers of pentenoic amides (COPAs)” yield non-sequence-specific product ions upon collisional activated dissociation; however, complete sequence information can be obtained with ETD. To aid in the decoding of libraries from MS and MS/MS data, we have incorporated ⁷⁹Br/⁸¹Br isotope “tags” to differentiate N- and C-terminal product ions. In addition, we have created “Hit-Find,” a software program that allows users to generate libraries in silico. The user can then search all possible members of the chemical library for those that fall within a user-defined mass error.      

Amidomethylation of amodiaquine: antimalarial N-Mannich base derivatives

Novel N-Mannich base-type derivatives of the antimalarial drug amodiaquine were synthesised by reaction with tertiary N-chloromethylamides. With the exception of the derivative of ethyl hippurate, all the so-formed (1-amidomethyl-1H-quinolin-4-ylidene)arylamines displayed high chemical and enzymatic stability. These compounds displayed antimalarial activity against the multi-drug resistant Plasmodium falciparum strain Dd2 (IC₅₀ values 15-31 nM) and demonstrated no significant loss in activity compared to amodiaquine (IC₅₀ 30 nM).     

6,7,14,15-Tetrahydro-15aH-azocino[1,2-a:6,5-b′]diindole. Synthesis of a novel pentacyclic ring system

In search of new lead structures for potent allosteric enhancers of antagonist binding to muscarinic M₂ receptors, a novel heterocyclic ring system, 6,7,14,15-tetrahydro-15aH-azocino[1,2-a:6,5-b′]diindole, has been synthesized. The new ring skeleton was obtained from indol-2-yl-acetic acid in three steps.