Bicyclic Analogues Research Articles

Proline Analogues in Drug Design: Current Trends and Future Prospects.

Proline analogues are versatile chemical building blocks that enable modular construction of small-molecule drugs and pharmaceutical peptides. Over the past 15 years, the FDA has approved over 15 drugs containing proline analogues in their structures, five in the last three years alone (daridorexant, trofinetide, nirmatrelvir, rezafungin, danicopan). This perspective offers an analysis of the most common types of proline analogues currently trending in drug design. We focus on examples of fluoroprolines, α-methylproline, bicyclic proline analogues, and aminoprolines, while also highlighting proline analogues that remain underrepresented. We supplement our analysis with physicochemical information regarding the specific molecular properties of these moieties. Additionally, we discuss several intriguing cases where nonproline residues were replaced with proline analogues as a strategy to eliminate unwanted hydrogen bond donor sites. In conclusion, we present some suggestions for the future exploration of this promising class of molecular entities in drug discovery.

Synthesis of Antitumor Bicyclic Hexapeptide RA-VII Analogues Possessing an Aromatic Amino Acid at Residue 2.

RA-III acetate was treated with Lawesson's reagent to afford [Tyr-3-Ψ(CS-NH)-Ala-4]RA-III acetate. Treatment of this product with Hg(OAc)2/Li2CO3 and then methanol gave an oxazole intermediate. Acid-catalyzed arylation of the methylene carbon atom on the oxazole ring and subsequent partial hydrolysis of the oxazole ring in the resultant compounds afforded RA-VII analogues having an aromatic amino acid at residue 2. [5-Fluoro-d-Trp-2]RA-VII showed IC50 values of 0.038 and 0.077 μM against the HL-60 and HCT-116 cell lines, respectively.

A Bicyclic Analog of the Linear Peptide Arodyn Is a Potent and Selective Kappa Opioid Receptor Antagonist.

Kappa opioid receptor (KOR) antagonists have potential therapeutic applications in the treatment of stress-induced relapse to substance abuse and mood disorders. The dynorphin A analog arodyn (Ac[Phe1,2,3,Arg4,D-Ala8]dynorphin A-(1-11)-NH2) exhibits potent and selective kappa opioid receptor antagonism. Multiple cyclizations in longer peptides, such as dynorphin and its analogs, can extend the conformational constraint to additional regions of the peptide beyond what is typically constrained by a single cyclization. Here, we report the design, synthesis, and pharmacological evaluation of a bicyclic arodyn analog with two constraints in the opioid peptide sequence. The peptide, designed based on structure-activity relationships of monocyclic arodyn analogs, was synthesized by solid-phase peptide synthesis and cyclized by sequential ring-closing metathesis (RCM) in the C- and N-terminal sequences. Molecular modeling studies suggest similar interactions of key aromatic and basic residues in the bicyclic peptide with KOR as found in the cryoEM structure of KOR-bound dynorphin, despite substantial differences in the backbone conformations of the two peptides. The bicyclic peptide's affinities at KOR and mu opioid receptors (MOR) were determined in radioligand binding assays, and its KOR antagonism was determined in the [35S]GTPγS assay in KOR-expressing cells. The bicyclic analog retains KOR affinity and selectivity (Ki = 26 nM, 97-fold selectivity over MOR) similar to arodyn and exhibits potent KOR antagonism in the dynorphin-stimulated [35S]GTPγS assay. This bicyclic peptide represents a promising advance in preparing cyclic opioid peptide ligands and opens avenues for the rational design of additional bicyclic opioid peptide analogs.

Syntheses and Structure-Activity Relationship Studies of Antitumor Bicyclic Hexapeptide RA-VII Analogues

A series of antitumor bicyclic hexapeptide RA-VII analogues modified at residue 2, 3, or 6 were prepared by the chemical transformation of the hydroxy, methoxy, or carboxy groups or the aromatic rings of natural peptides RA-II, III, V, VII, and X. Analogues with modified side chains or peptide backbones, which cannot be prepared by the chemical transformation of their natural peptides, and newly isolated peptides from Rubia cordifolia roots were synthesized by using protected cycloisodityrosines prepared by the degradation of bis(thioamide) obtained from RA-VII or the diphenyl ether formation of boronodipeptide under the modified Chan-Lam coupling reaction conditions. Studies of the conformational features of the analogues and the newly isolated peptides and their relationships with cytotoxic activities against the HCT-116, HL-60, KATO-III, KB, L1210, MCF-7, and P-388 cell lines revealed the following: the methoxy group at residue 3 is essential for the potent cytotoxic activity; the methyl group at Ala-2 and Ala-4 but not at D-Ala-1 is required to establish the bioactive conformation; the N-methyl group at Tyr-5 is necessary for the peptides to adopt the active conformation preferentially; and the orientation of Tyr-5 and/or Tyr-6 phenyl rings has a significant effect on the cytotoxic activity.

Topologically engineering of π-conjugated macrocycles: Tunable emission and photochemical reaction toward multi-cyclic polymers

The topology of conjugated macrocycles had significant impacts on their photo-physical and photo-chemical properties. Herein, a series of π-conjugated macrocycles with diverse topology were synthesized via intramolecular McMurry coupling. Their chemical structure and macrocyclic topology were unambiguously confirmed via NMR, MALDI-TOF mass spectra, crystal analysis and scanning tunneling microscopy (STM). Depending on the structural topology and structural rigidity, these cyclic compounds display obviously distinctive emission behavior and photochemical reactions in the solution and in the solid state. Monocyclic phenylene vinylene macrocycle (denoted as MST) exhibiting aggregation-induced emission behavior, was more vulnerable to photo-cyclization in solution and triplet sensitizer promoted photo-dimerization due to lower strain and more flourishing intramolecular motions. After UV light irradiation, relatively more flexible MST could yield the anti-dimer via triplet excimer on the HOPG surface confirmed by STM investigation. By contrast, highly constrained bicyclic analogue (named as DMTPE) with central tetraphenylethene core, displayed high emission quantum yields of 68% both in solution and in the solid state, and was relatively inert to photochemical reactions and yield syn-dimer on the surface via singlet excimer involved [2 + 2] photo-dimerization. Based on the solution-mediated photo-polymerization of MST moiety, multicyclic porous carbon-rich ribbon connected with four-membered ring was successfully constructed and validated via STM imaging.

Identification of novel Nrf2-activating neuroprotective agents: Elucidation of structural congeners of (-)-galiellalactone and congener-based novel Nrf2 activators

Herein, (-)-galiellalactone 1 congeners responsible for the nuclear factor erythroid 2-related factor 2 (Nrf2)-activating neuroprotective effects were elucidated. Additionally, novel congener-based Nrf2 activators were identified using a drug repositioning strategy. (-)-Galiellalactone, which comprises a tricyclic lactone skeleton, significantly activates antioxidant response element (ARE)-mediated transcription in neuroblastoma SH-SY5Y cells. Interestingly, two cyclohexene-truncated [3.3] bicyclic lactone analogs, which possess an exocyclic α-methylene-γ-butyrolactone moiety, exhibited higher Nrf2/ARE transcriptional activities than the parent (-)-galiellalactone. We confirmed that the cyclohexene moiety embedding the [3.3] bicyclic lactone congener does not play the essential role of (-)-galiellalactone for Nrf2/ARE activation. Nrf2/ARE activation by novel analogs resulted in the upregulation of downstream antioxidative and phase II detoxifying enzymes, heme oxygenase-1, and NAD(P)H quinone oxidoreductase 1, which are closely related to the cytoprotective effects on neurodegenerative diseases. (-)-Galiellalactone and its [3.3] bicyclic variants 3l and 3p increased the expression of antioxidant genes and exhibited neuroprotective effects against 6-hydroxydopamine-mediated neurotoxicity in the neuroblastoma SH-SY5Y cell line.

Synthesis and cytotoxicity evaluation of retro-inverso analogue of antitumor bicyclic hexapeptide RA-VII

A retro-inverso analogue of antitumor bicyclic hexapeptide RA-VII was designed and synthesized. A cycloisodityrosine unit was synthesized by the intramolecular diphenyl ether formation of Boc-3-borono-d-Tyr(Me)-d-Tyr-OMe mediated by copper(II) acetate and 4-(dimethylamino)pyridine. After the N-methylation, Boc-Ala-OH and the tripeptide segment were sequentially coupled to the N-terminus of the cycloisodityrosine unit, affording a hexapeptide. After removal of the C- and N-terminal protecting groups, the hexapeptide was subjected to macrocyclization using diphenylphosphoryl azide and NaHCO3 in N,N-dimethylformamide to afford a bicyclic hexapeptide analogue. X-ray crystallography and NMR experiments showed that the analogue had different structural features from RA-VII, which were responsible for the lack of cytotoxic activity of the analogue.

ω-(3-Trifluoromethylpyrazol-4-yl)alkanoic acids via (3 + 2)-cycloaddition of nitrile imines with cyclic enones and deacylative aromatization

A series of ω-substituted alkanoic acids functionalized with 1-aryl-3-trifluoromethylpyrazol-4-yl group was synthesized via two-step protocol using in situ generated CF3-nitrile imines and cyclic enones as key building blocks. The first 1,3-dipolar cycloaddition step proceeded in a fully selective manner either in solutions or under solvent-free mechanochemical activation. Treatment of the first formed cycloadducts derived from 2-cyclopentenone or 2-cyclohexenone with DDQ afforded corresponding bicyclic pyrazoles formed via dehydrogenative oxidation pathway, whereas MnO2-mediated deacylative aromatization led to desired propionic or butyric acid derivatives, respectively. In contrast, oxidation of model 2-cycloheptenone-derived (3 + 2)-cycloadduct yielded bicyclic analogue irrespectively to the applied conditions.

A novel genetically-encoded bicyclic peptide inhibitor of human urokinase-type plasminogen activator with better cross-reactivity toward the murine orthologue

The inhibition of human urokinase-type plasminogen activator (huPA), a serine protease that plays an important role in pericellular proteolysis, is a promising strategy to decrease the invasive and metastatic activity of tumour cells. However, the generation of selective small molecule huPA inhibitors has proven to be challenging due to the high structural similarity of huPA to other paralogue serine proteases. Efforts to generate more specific therapies have led to the development of cyclic peptide-based inhibitors with much higher selectivity against huPA. While this latter property is desired, the sparing of the orthologue murine poses difficulties for the testing of the inhibitor in preclinical mouse model. In this work, we have applied a Darwinian evolution-based approach to identify phage-encoded bicyclic peptide inhibitors of huPA with better cross-reactivity towards murine uPA (muPA). The best selected bicyclic peptide (UK132) inhibited huPA and muPA with Ki values of 0.33 and 12.58 µM, respectively. The inhibition appears to be specific for uPA, as UK132 only weakly inhibits a panel of structurally similar serine proteases. Removal or substitution of the second loop with one not evolved in vitro led to monocyclic and bicyclic peptide analogues with lower potency than UK132. Moreover, swapping of 1,3,5-tris-(bromomethyl)-benzene with different small molecules not used in the phage selection, resulted in an 80-fold reduction of potency, revealing the important structural role of the branched cyclization linker. Further substitution of an arginine in UK132 to a lysine resulted in a bicyclic peptide UK140 with enhanced inhibitory potency against both huPA (Ki = 0.20 µM) and murine orthologue (Ki = 2.79 µM). By combining good specificity, nanomolar affinity and a low molecular mass, the bicyclic peptide inhibitor developed in this work may provide a novel human and murine cross-reactive lead for the development of a potent and selective anti-metastatic therapy.

The design, synthesis, and inhibition of Clostridioides difficile spore germination by acyclic and bicyclic tertiary amide analogs of cholate

Clostridioides difficile infection (CDI) is a major identifiable cause of antibiotic-associated diarrhea. In our previous study (J. Med. Chem., 2018, 61, 6759–6778), we have identified N-phenyl-cholan-24-amide as a potent inhibitor of spore germination. The most potent compounds in our previous work are N-arylamides. We were interested in the role that the conformation of the amide plays in activity. Previous research has shown that secondary N-arylamides exist exclusively in the coplanar trans conformation while tertiary N-methyl-N-arylamides exist in a non-planar, cis conformation. The N-methyl-N-phenyl-cholan-24-amide was 17-fold less active compared to the parent compounds suggesting the importance of the orientation of the phenyl ring. To lock the phenyl ring into a trans conformation, cyclic tertiary amides were prepared. Indoline and quinoline cholan-24-amides were both inhibitors of spore germination; however, the indoline analogs were most potent. Isoindoline and isoquinoline amides were inactive. We found that the simple indoline derivative gave an IC50 value of 1 μM, while the 5′-fluoro-substituted compound (5d) possessed an IC50 of 400 nM. To our knowledge, 5d is the most potent known spore germination inhibitor described to date. Taken together, our results indicate that the trans, coplanar conformation of the phenyl ring is required for potent inhibition.

Chemoenzymatic synthesis of bridged homolyxofuranosyl pyrimidine nucleosides: Bicyclic AZT analogues

A greener chemo-enzymatic methodology has been developed for the synthesis of conformationally restricted diastereomeric homolyxofuranosyl pyrimidines (AZT analogue), i.e., (5′R)-3′-azido-3′-deoxy-2′-O,5′-C-bridged-β-d-homolyxofuranosyl-uracil and thymine starting from inexpensive diacetone-d-glucofuranose in 18% and 21% overall yields, respectively. In one of the key steps in multistep synthesis of bicyclic AZT analogues, the primary hydroxyl group of 3′-azido-3′-deoxy-β-d-glucofuranosyl pyrimidines has been acetylated using Novozyme® 435 in THF in 92% and 97% yields, respectively. The monoacetylated nucleoside was converted to desired bicyclic AZT analogue in two steps in an overall yield of 82% and 83%, respectively.

Rupturing aromaticity by periphery overcrowding

The balance between strain relief and aromatic stabilization dictates the form and function of non-planar π-aromatics. Overcrowded systems are known to undergo geometric deformations, but the energetically favourable π-electron delocalization of their aromatic ring(s) is typically preserved. In this study we incremented the strain energy of an aromatic system beyond its aromatic stabilization energy, causing it to rearrange and its aromaticity to be ruptured. We noted that increasing the steric bulk around the periphery of π-extended tropylium rings leads them to deviate from planarity to form contorted conformations in which aromatic stabilization and strain are close in energy. Under increasing strain, the aromatic π-electron delocalization of the system is broken, leading to the formation of a non-aromatic, bicyclic analogue referred to as ‘Dewar tropylium’. The aromatic and non-aromatic isomers have been found to exist in rapid equilibrium with one another. This investigation demarcates the extent of steric deformation tolerated by an aromatic carbocycle and thus provides direct experimental insights into the fundamental nature of aromaticity.

The development of BVDU: An odyssey.

Brivudin, ((E)-5-(2-bromovinyl)-2'-deoxyuridine (BVDU) can be considered the gold standard for the treatment of varicella-zoster virus (VZV) infections, such as herpes zoster (shingles). It is available for clinical use in most European countries (except for the UK) and over the whole world (except for the US and Canada). Besides VZV its activity spectrum also includes various other herpesviruses, such as herpes simplex virus type 1 (HSV-1). Its activity against VZV and HSV-1 depends on phosphorylation by the virus-encoded thymidine kinase (TK). In its active form (BVDU TP or BVDU 5'-triphosphate), it can act as both substrate and inhibitor of the viral (i.e., HSV-1) DNA polymerase. It has proven to be effective against herpes zoster, including post-herpetic neuralgia (PHN). It is contra-indicated in patients concomitantly treated by 5-fluorouracil (FU), since its degradation product, (E)-5-(2-bromovinyl)uracil, is inhibitory to the catabolism of FU, which may enhance the toxicity of the latter. A new compound, the bicyclic nucleoside analogue (BCNA) Cf-1743, has been described, which is a more potent inhibitor of VZV replication than BVDU and which does not interfere with the catabolism of FU. It is applicable orally, as its 5'-valine ester FV-100 (Fermavir), but has not (yet) been marketed for clinical use.

Annulated bicyclic isothioureas: identification of active and selective butyrylcholinesterase inhibitors

Structural optimization of butyrylcholinesterase inhibitors, 5-bromomethyl- and 5-iodomethyl-N,N-disubstituted 2-aminothiazolines, led to a series of their annulated bicyclic analogues, obtained by intramolecular cyclization of cycloalkenylthioureas. The most active compound in this series, cyclohepta[d]thiazol-2-amine, is a mixed-type butyryl-cholinesterase inhibitor with IC50 = 130 nm, highly selective compared to acetylcholinesterase and non-toxic at 100 μm concentrations.

Live-Cell RNA Imaging with Metabolically Incorporated Fluorescent Nucleosides.

Fluorescence imaging is a powerful method for probing macromolecular dynamics in biological systems; however, approaches for cellular RNA imaging are limited to the investigation of individual RNA constructs or bulk RNA labeling methods compatible primarily with fixed samples. Here, we develop a platform for fluorescence imaging of bulk RNA dynamics in living cells. We show that fluorescent bicyclic and tricyclic cytidine analogues can be metabolically incorporated into cellular RNA by overexpression of uridine-cytidine kinase 2. In particular, metabolic feeding with the tricyclic cytidine-derived nucleoside tC combined with confocal imaging enables the investigation of RNA synthesis, degradation, and trafficking at single-cell resolution. We apply our imaging modality to study RNA metabolism and localization during the oxidative stress response and find that bulk RNA turnover is greatly accelerated upon NaAsO2 treatment. Furthermore, we identify cytoplasmic RNA granules containing RNA transcripts generated during oxidative stress that are distinct from canonical stress granules and P-bodies and co-localize with the RNA helicase DDX6. Taken together, our work provides a powerful approach for live-cell RNA imaging and reveals how cells reshape RNA transcriptome dynamics in response to oxidative stress.

1,3-Dioxane-Linked Novel Bacterial Topoisomerase Inhibitors: Expanding Structural Diversity and the Antibacterial Spectrum.

Antibacterial resistance continues its devastation of available therapies. Novel bacterial topoisomerase inhibitors (NBTIs) offer one solution to this critical issue. Two series of amine NBTIs bearing tricyclic DNA-binding moieties as well as amide NBTIs with a bicyclic DNA-binding moiety were synthesized and evaluated against methicillin-resistant Staphylococcus aureus (MRSA). Additionally, these compounds and a series of bicyclic amine analogues displayed high activity against susceptible and drug-resistant Neisseria gonorrhoeae, expanding the spectrum of these dioxane-linked NBTIs.

FV-100 for the Treatment of Varicella-Virus (VZV) Infections: Quo Vadis?

The bicyclic nucleoside analogue (BCNA) Cf1743 and its orally bioavailable prodrug FV-100 have unique potential as varicella-zoster virus (VZV) inhibitors to treat herpes zoster (shingles) and the therewith associated pain, including post-herpetic neuralgia (PHN). The anti-VZV activity of Cf1743 depends on a specific phosphorylation by the VZV-encoded thymidine kinase (TK). The target of antiviral action is assumed to be the viral DNA polymerase (or DNA synthesis in the virus-infected cells).

Synthesis of Novel Pyrazine-Substituted 1H-Pyrrole-2-carboxamides and Related Tethered Heterocycles

AbstractAs part of a drug discovery program, 4-pyrazin-2-yl-1H-pyrrole-2-carboxamides were accessed along with a number of bicyclic analogues. Routes to these compounds were largely absent from the scientific literature. The synthesis of a 4-(pyrazin-2-yl)-1H-pyrrole-2-carboxamide and several fused bicyclic analogues all using standard procedures (SNAr, borylation, C–C cross couplings, hydrolysis, amide bond formation, cyclisation, halogenation, and alkylation) from readily available starting materials is reported. The synthetic sequences range from 4–12 steps per final compound, with yields of isolated intermediates ranging from 20 to ∼100%.

Chemical and chemoenzymatic routes to bridged homoarabinofuranosylpyrimidines: Bicyclic AZT analogues.

Conformationally restricted diastereomeric homoarabinofuranosylpyrimidines (AZT analogue), i.e., (5′R)-3′-azido-3′-deoxy-2′-O,5′-C-bridged-β-ᴅ-homoarabinofuranosylthymine and -uracil had been synthesized starting from diacetone ᴅ-glucofuranose following chemoenzymatic and chemical routes in 34–35% and 24–25% overall yields, respectively. The quantitative and diastereoselective acetylation of primary hydroxy over two secondary hydroxy groups present in the key nucleoside precursor was mediated with Lipozyme® TL IM in 2-methyltetrahydrofuran following a chemoenzymatic pathway. Whereas, the protection of the primary hydroxy over the lone secondary hydroxy group in the key azido sugar precursor was achieved using bulky tert-butyldiphenylsilyl chloride (TBDPS-Cl) in pyridine in 92% yield following a chemical synthetic pathway. The chemoenzymatic method was found to be superior over the chemical method in respect of the number of synthetic steps and overall yield of the final product.

EVALUATION OF PARAMETERS IN SOFTWARE IMPLEMENTATION BAR GRAPH DISPLAY DEVICES

The work is devoted to the estimation of resource consumption of the microcontroller for the synthesis of bar graph discrete-analog data display on the LED information field in bicyclic mode. The paper compares the programs of multicycle information output and its bicyclic analogue for discrete-analog means for the information display systems. The significance of the influence of bicyclic information models on the minimization of machine time resources of a single-chip microcontroller is shown. It is determined that in order to reduce resource consumption in the developed solutions it is necessary to focus on the maximum possible optimization of program blocks that are executed during interrupts and serve the I / O subsystem of the microcontroller. In this sense the bar graph displays based on the bicyclic additive information model has the best results. It was found that the traditional approach to assessing the effectiveness of programs using special benchmark programs, with subsequent measurement of code and execution time of the entire program does not allow to correctly assess the effectiveness of the program and the work of microcontroller at the device design stage. Therefore, as an alternative, it was proposed to use the size of the bytecode of the program and the speed of the main cycle - the procedure of information output to assess the effectiveness of the program. It was found that in terms of speed of execution and consumption of resources, the multicycle version significantly loses to the bicyclic program. Also, reducing the number of image formation cycles in the information field is one of the most effective way to minimize the consumption of microcontroller resources for display services.