Constrained Analogues Research Articles

Enantioselective Synthesis of Tetrahydrocarbazoles through a Michael Addition/Ciamician–Plancher Rearrangement Sequence: Asymmetric Synthesis of a Potent Constrained Analogue of MS‐245

Awakening an ancient rearrangement: A one-pot sequential Friedel–Crafts-type Michael addition/Ag+-mediated Ciamician–Plancher rearrangement reaction on C2,C3-nonsubstituted indoles can be used for accessing enantiomerically enriched pharmaceutically relevant 1,2,3,4-tetrahydrocarbazoles. The methodology was applied in an enantioselective total synthesis of a highly potent serotonin 5-HT6 receptor antagonist (see scheme). Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

Structure‐Based Design of a Highly Constrained Nucleic Acid Analogue: Improved Duplex Stabilization by Restricting Sugar Pucker and Torsion Angle γ

Dual conformational restriction: a new, highly constrained modification of the α-L-locked nucleic acid (α-L-LNA) scaffold that locks the sugar furanose ring in an N-type configuration and also restricts rotation around torsion angle γ was synthesized. This new modification increases the thermostability of an oligonucleotide duplex compared to using a single mode of constraint alone.

Structure‐Based Design of a Highly Constrained Nucleic Acid Analogue: Improved Duplex Stabilization by Restricting Sugar Pucker and Torsion Angle γ

Doppelt eingeschränkt: Eine neue, konformativ stark eingeschränkte α-L-LNA-Modifikation (α-L-LNA=α-L-locked nucleic acid) wurde synthetisiert, in welcher der Zucker-Furanosering in einer N-Typ-Konfiguration fixiert und die Rotation um den Torsionswinkel γ eingeschränkt ist (siehe Schema). Diese neue Modifikation erhöht die Thermostabilität eines Oligonucleotidduplex gegenüber dem Einsatz nur einer Einschränkung.

Extensive Rigid Analogue Design Maps the Binding Conformation of Potent N-Benzylphenethylamine 5-HT2A Serotonin Receptor Agonist Ligands

Based on the structure of the superpotent 5-HT(2A) agonist 2-(4-bromo-2,5-dimethoxyphenyl)-N-[(2-methoxyphenyl)methyl]ethanamine, which consists of a ring-substituted phenethylamine skeleton modified with an N-benzyl group, we designed and synthesized a small library of constrained analogues to identify the optimal arrangement of the pharmacophoric elements of the ligand. Structures consisted of diversely substituted tetrahydroisoquinolines, piperidines, and one benzazepine. Based on the structure of (S,S)-9b, which showed the highest affinity of the series, we propose an optimal binding conformation. (S,S)-9b also displayed 124-fold selectivity for the 5-HT(2A) over the 5-HT(2C) receptor, making it the most selective 5-HT(2A) receptor agonist ligand currently known.

Towards a KCC2 blocker pharmacophore model

A multi-disciplinary approach was used to identify the first pharmacophore model for KCC2 blockers: several physico-chemical studies such as XRD and NMR were combined to molecular modelling techniques, SAR analysis and synthesis of constrained analogues in order to determine a minimal conformational space regrouping few potential bioactive conformations. These conformations were further compared to the conformational space of a different series of KCC2 blockers in order to identify the common pharmacophoric features. The synthesis of more potent analogues in this second series confirmed the usefulness of this KCC2 blocker pharmacophore model.

The cis-4-Amino-l-proline Residue as a Scaffold for the Synthesis of Cyclic and Linear Endomorphin-2 Analogues

Endomorphin-2 (EM-2: Tyr-Pro-Phe-Phe-NH(2)) is an endogenous tetrapeptide that combines potency and efficacy with high affinity and selectivity toward the μ opioid receptor, the most responsible for analgesic effects in the central nervous system. The presence of the Pro(2) represents a crucial factor for the ligand structural and conformational properties. Proline is in fact an efficient stereochemical spacer, capable of inducing favorable spatial orientation of aromatic rings, a key factor for ligand recognition and interaction with receptors. Here the Pro(2) has been replaced by 4(S)-NH(2)-2(S)-proline (cAmp), a proline/GABA cis-chimera residue. This bivalent amino acid maintains the capacity to influenc the tetrapeptide conformation and offers the opportunity to generate new linear models and unusually constrained cyclic analogues characterized by an N-terminal Tyr bearing a free α-amino group. The results indicate that the new analogues do not show affinity for both δ and κ opioid receptors and bind only poorly to the μ receptors (for cyclopeptide 9: K(i)(μ) = 660 nM; GPI (IC(50)) = 1.4% at 1 μM; for linear tetrapeptide acid 13: K(i)(μ) = 2000 nM; GPI (IC(50)) = 0% at 1 μM; for linear tetrapeptide amide 15: K(i)(μ) = 310 nM; GPI (IC(50)) = 894 nM).

Synthesis and Biological Evaluation of a Highly Constrained Analogue of Methylthioadenosine (MTA)

We describe the synthesis and the antibacterial evaluation 2’,N3-cyclonucleoside 3 analogue of MTA that is characterized by the presence of an additional linkage between the heterocyclic ring and the sugar moiety.

Omegatides: constrained analogs of peptide primary sequence

Omegatides: constrained analogs of peptide primary sequence

Synthesis, biological activity and molecular modeling studies of 1,2,3,4-tetrahydroisoquinoline derivatives as conformationally constrained analogues of KN62, a potent antagonist of the P2X7-receptor containing a tyrosine moiety.

A new series of ring constrained analogues of the P2X7 receptor antagonist KN62 (1-[N,O-bis(1,5-isoquinolinesulfonyl)-N-methyl-L-tyrosyl]-4- phenylpiperazine, CAS 127191-97-3) containing the 1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid core with S configuration in position 3 was synthesised and their antagonist activities were tested on human macrophage cells. While KN62 is a potent antagonist of the P2X7 receptor, these novel compounds are weak antagonists of the purinergic P2X7 receptor and only one compound (5) showed appreciable activity as P2X7 antagonist, which was 30 times weaker than that reported for KN62. Along with compound 5, the derivatives 11 and 25 were the most active inhibitors in this synthesised series. A molecular modeling study confirmed that an extended rather than folded conformation seems to be crucial for the antagonistic activity at the P2X7 receptor.

Synthesis, Biological Evaluation, and Automated Docking of Constrained Analogues of the Opioid Peptide H-Dmt-d-Ala-Phe-Gly-NH2 Using the 4- or 5-Methyl Substituted 4-Amino-1,2,4,5-tetrahydro-2-benzazepin-3-one Scaffold

The Phe(3) residue of the N-terminal tetrapeptide of dermorphin (H-Dmt-d-Ala-Phe-Gly-NH(2)) was conformationally constrained using 4- or 5-methyl-substituted 4-amino-1,2,4,5-tetrahydro-2-benzazepin-3-one (Aba) stereoisomeric scaffolds. Several of the synthesized peptides were determined to be high affinity agonists for the μ opioid receptor (OPRM) with selectivity over the δ opioid receptor (OPRD). Interesting effects of the Aba configuration on ligand binding affinity were observed. H-Dmt-d-Ala-erythro-(4S,5S)-5-Me-Aba-Gly-NH(2)9 and H-Dmt-threo-(4R,5S)-5-Me-Aba-Gly-NH(2)12 exhibited subnanomolar affinity for OPRM, while they possess an opposite absolute configuration at position 4 of the Aba ring. However, in the 4-methyl substituted analogues, H-Dmt-d-Ala-(4R)-Me-Aba-Gly-NH(2)14 was significantly more potent than the (4S)-derivative 13. These unexpected results were rationalized using the binding poses predicted by molecular docking simulations. Interestingly, H-Dmt-d-Ala-(4R)-Me-Aba-Gly-NH(2)14 is proposed to bind in a different mode compared with the other analogues. Moreover, in contrast to Ac-4-Me-Aba-NH-Me, which adopts a β-turn in solution and in the crystal structure, the binding mode of this analogue suggests an alternative receptor-bound conformation.

Synthesis and Structure–Activity Relationships of Constrained Heterocyclic Analogues of Combretastatin A4

A series of combretastatin A4 (CA4) analogues with a lactam or lactone ring fused to the trimethoxyphenyl or the B-phenyl moiety were synthesized in an efficient and stereoselective manner by using a domino Heck-Suzuki-Miyaura coupling reaction. The vascular-disrupting potential of these conformationally restricted CA4 analogues was assessed by various in vitro assays: inhibition of tubulin polymerization, modification of endothelial cell morphology, and disruption of endothelial cell cords. Compounds were also evaluated for their growth inhibitory effects against murine and human tumor cells. B-ring-constrained derivatives that contain an oxindole ring (in contrast to compounds with a benzofuranone ring) as well as analogues bearing a six-membered lactone core fused to the trimethoxyphenyl ring are endowed with significant biological activity. The most potent compound of this series (oxindole 9 b) is of particular interest, as it combines chemical stability and a biological activity profile characteristic of a vascular-disrupting agent.

Regioselective Suzuki Coupling of Dihaloheteroaromatic Compounds as a Rapid Strategy To Synthesize Potent Rigid Combretastatin Analogues

Combretastatin A-4 (CA-4) is a potent tubulin depolymerizing agent able to inhibit tumor growth and with antivascular effects. Although it is in clinical trials, the search for novel analogues that may display better/different features is still ongoing. In this manuscript we describe the synthesis of novel constrained analogues of CA-4 obtained in only two synthetic steps exploiting a regioselective Suzuki coupling of dihalogenated heteroaromatic and alicyclic compounds. All the compounds synthesized have been evaluated for cytotoxicity and for their ability to inhibit tubulin assembly. One of them, 38, displayed low nanomolar cytotoxicity and proved to have a pharmacodynamic profile similar to that of CA-4 and a better pharmacokinetic profile, but most important of all, this synthetic strategy may pave the way for the easy and rapid generation of novel rigid analogues of combretastatins.

Phenylpropenamide derivatives: Anti-hepatitis B virus activity of the Z isomer, SAR and the search for novel analogs

Phenylpropenamides have been reported to be a class of non-nucleoside inhibitors of the hepatitis B virus (HBV). This class of compounds was explored with the objective of developing potent anti-HBV agents, with a novel mechanism of action, that could be combined with nucleos(t)ide analogs currently used to treat HBV infection. To accomplish this objective a series of substituted arylpropenamide derivatives were prepared and the E and Z geometrical isomers were separated. The structural identity of each of the E and Z isomers was determined by single crystal X-ray crystallography. Contrary to previous reports, the activity of this class of molecules resides in the Z isomer. Further structure-activity relationship studies around the active Z isomer identified compounds that displayed potent antiviral activity against HBV with EC(90) value of approximately 0.5 μM in vitro. Attempts to develop ring constrained analogs did not lead to active HBV inhibitors.

Conformational constraints in angiotensin IV to probe the role of Tyr2, Pro5 and Phe6

The aromatic amino acids Tyr and Phe in angiotensin IV (Ang IV) were conformationally constrained by the use of β-Me substituted analogs, or cyclic constrained analogs. None of these modifications was allowed for Tyr¹, while only e-β-MePhe⁶ substitution resulted in an AngIV analog with high IRAP potency and selectivity versus AP-N or the AT₁ receptor. This indicates an important role of the orientation of the Phe⁶ for inducing selectivity. Pro⁵ replacement with 2-aminocyclopentanecarboxylic acid maintained IRAP potency and abolished AT₁ affinity. These results confirm the importance of conformational constrained amino acids to generate selectivity in bioactive peptides.

Luminescence studies of copper(I)-containing [2]pseudorotaxanes

This report describes photoluminescence studies of copper-containing [2]pseudorotaxanes that mimic elements of functioning molecular machines. Excitation with visible light induces a formal oxidation of the metal center and simulates an actuation process. In all four [2]pseudorotaxanes studied, the ring ligand is the same, but the thread ligand is variable, namely 2,9-di(anisol-4-yl)-1,10-phenanthroline (dap), 6,6′-di(anisol-4-yl)-2,2′-bipyridine (o-dabipy), 5,5′-di(anisol-4-yl)-2,2′-bipyridine (m-dabipy), or 8,8′-di(anisol-4-yl)-3,3′-bi-isoquinoline (dabiiq). The absorbance bandshapes suggest that aryl substituents extending from the core ligands engage in stacking interactions and induce a partially flattened structure in the ground state. More severe flattening occurs in the excited state and precludes the observation of emission if inter-ligand steric forces do not limit the distortion. Thus, the [2]pseudorotaxanes containing dap or o-dabipy as the thread ligand exhibit uncorrected emission maxima at around 720 nm in room-temperature dichloromethane, while the less constrained analogues, containing dabiiq or m-dabipy, are not emissive in fluid solution and barely exhibit a signal in rigid media. In dichloromethane, the luminescence quantum yields of the dap- and o-dabipy-containing systems are 6 × 10−4 and 4 × 10−4, and the excited-state lifetimes are 98 ns and 90 ns, respectively.

Synthesis and cytotoxic evaluation of cis-locked and constrained analogues of combretastatin and combretastatin A4

A series of cis-locked stilbenic compounds related to combretastatin and combretastatin A4 has been designed and synthesized. The cytotoxic effects of these rigid analogues were evaluated as well as their abilities to inhibit tubulin polymerization.

Synthesis and cannabinoid-1 receptor binding affinity of conformationally constrained analogs of taranabant

The design, synthesis, and binding activity of ring constrained analogs of the acyclic cannabinoid-1 receptor (CB1R) inverse agonist taranabant 1 are described. The initial inspiration for these taranabant derivatives was its conformation 1a, determined by 1H NMR, X-ray, and molecular modeling. The constrained analogs were all much less potent than their acyclic parent structure. The results obtained are discussed in the context of a predicted binding of 1 to a homology model of CB1R.

ChemInform Abstract: Ring Constrained Analogues of β-Alanine-Containing GPIIb/IIIa Receptor Antagonists.

A series of ring constrained analogues of the GPIIb/IIIa receptor antagonist XR299 (1) was investigated as potential inhibitors of glycoprotein IIb/IIIa, a platelet receptor that plays a key role in platelet aggregation and platelet adhesion. Ring size was found to have a large effect on in vitro potency. Selected compounds showed good in vitro activity, a preference for binding to activated platelets, and modest duration of action when dosed iv as a racemate in a canine model.

Constrained cycloalkyl analogues of glutamic acid: stereocontrolled synthesis of (+)-2-aminobicyclo[3.1.0]hexane-2,6-dicarboxylic acid (LY354740) and its 6-phosphonic acid analogue

A new stereocontrolled synthesis of (+)-2-aminobicyclo[3.1.0]hexane-2.6-dicarboxylic acid (LY354740) 1, a potent and selective 2mGluR agonist, has been accomplished in four steps with an overall yield of 27% starting from the enantiopure (+)-( R)-2-( p-tolylsulfinyl)cyclopent-2-enone 3. The key steps include asymmetric cyclopropanation of 3 with (dimethylsulfuranylidene)acetate (EDSA) and removal of the chiral p-tolylsulfinyl auxiliary from the cycloadduct ent- 4c upon treatment with iso-propylmagnesium chloride. The stereoselective hydantoin formation from the bicyclic ketone 6 formed (Bucherer–Bergs reaction) and subsequent hydrolysis completed the synthesis of 1. The same reaction sequence has been applied in the first synthesis of enantiopure (+)-2-amino-6-phosphonobicyclo[3.0.1]hexane-2-carboxylic acid 2, a structural 6-phosphono analogue of 1. The starting bicyclic ketophosphonates 9–11 have been obtained by asymmetric cyclopropanation of (−)-( S)- 3 with phosphoryl sulfonium ylides, producing only two endo-isomers. The major endo-isomer (+)- 11a containing the 6-diisopropoxyphosphoryl group has been converted in three steps into (+)- endo- 2 in 46% overall yield.

Design and synthesis of conformationally constrained N,N-disubstituted 1,4-diazepanes as potent orexin receptor antagonists

Orexins are neuropeptides that regulate wakefulness and arousal. Small molecule antagonists of orexin receptors may provide a novel therapy for the treatment of insomnia and other sleep disorders. In this Letter we describe the design and synthesis of conformationally constrained N,N-disubstituted 1,4-diazepanes as orexin receptor antagonists. The design of these constrained analogs was guided by an understanding of the preferred solution and solid state conformation of the diazepane central ring.