Potent macrocyclic antagonists to the motilin receptor presenting novel unnatural amino acids

Beyond Rule-of-five: Permeability Assessment of Semipeptidic Macrocycles

Compounds beyond the rule-of-five are generating interest as they expand the molecular toolbox for modulating targets previously considered "undruggable". Macrocyclic peptides are an efficient class of molecules for modulating protein-protein interactions. However, predicting their permeability is difficult as they differ from small molecules. Although constrained by macrocyclization, they generally retain some conformational flexibility associated with an enhanced ability to cross biological membranes. In this study, we investigated the relationship between the structure of semi-peptidic macrocycles and their membrane permeability through structural modifications. Based on a scaffold of four amino acids and a linker, we synthesized 56 macrocycles incorporating modifications in either stereochemistry, N-methylation, or lipophilicity and assessed their passive permeability using the parallel artificial membrane permeability assay (PAMPA). Our results show that some semi-peptidic macrocycles have adequate passive permeability even with properties outside the Lipinski rule of five. We found that N-methylation in position 2 and the addition of lipophilic groups to the side chain of tyrosine led to an improvement in permeability with a decrease in tPSA and 3D-PSA. This enhancement could be attributed to the shielding effect of the lipophilic group on some regions of the macrocycle, which in turn, facilitates a favorable macrocycle conformation for permeability, suggesting some degree of chameleonic behavior.

AMPA GluA2 subunit competitive inhibitors for PICK1 PDZ domain: Pharmacophore-based virtual screening, molecular docking, molecular dynamics simulation, and ADME studies

PICK1 (Protein interacting with C kinase-1) plays a key role in the regulation of intracellular trafficking of AMPA GluA2 subunit that is linked with synaptic plasticity. PICK1 is a scaffolding protein and binds numerous proteins through its PDZ domain. Research showed that synaptic plasticity is altered upon disrupting the GluA2-PDZ interactions. Inhibiting PDZ and GluA2 binding lead to beneficial effects in the cure of neurological diseases thus, targeting PDZ domain is proposed as a novel therapeutic target in such diseases. For this, various classes of synthetic peptides were tested. Though small organic molecules have been utilized to prevent these interactions, the number of such molecules is inadequate. Hence, in this study, ten molecular libraries containing large number of molecules were screened against the PDZ domain using pharmacophore-based virtual screening to find the best hits for the PDZ domain. Molecular docking and molecular dynamics simulation studies revealed that Hit_II is a potent inhibitor for the PDZ domain and confirm the allosteric nature of Hit_III. Additionally, ADME analysis suggests the drug-likeness of both Hit_II and Hit_III. This study suggests that tested hits may have potency against the PDZ domain and can be considered effective to treat neurological disorders.Communicated by Ramaswamy H. Sarma.

Heteroaryl sulfonamide synthesis: scope and limitations

Heteroaryl sulfonamides are important structural motifs in the medicinal and agrochemical industries. However, their synthesis often relies on the use of heteroaryl sulfonyl chlorides, which are unstable and toxic reagents. Herein, we report a protocol that allows direct oxidative coupling of heteroaryl thiols and primary amines, readily available and inexpensive commodity chemicals. The transformation proceeds under mild reaction conditions and yields the desired N-alkylated sulfonamides in good yields. N-alkyl heteroaryl sulfonamides can be further transformed using a microwave-promoted Fukuyama-Mitsunobu reaction to N,N-dialkyl heteroaryl sulfonamides. The developed protocols thus enable the preparation of previously difficult to prepare sulfonamides (toxic reagents, harsh conditions, and low yields) under mild conditions.

Unified Approach to Benzo[d]thiazol-2-yl-Sulfonamides

In this paper, we report a unified approach to N-substituted and N,N-disubstituted benzothiazole (BT) sulfonamides. Our approach to BT-sulfonamides starts from simple commercially available building blocks (benzo[d]thiazole-2-thiol and primary and secondary amines) that are connected via (a) a S oxidation/S-N coupling approach, (b) a S-N coupling/S-oxidation sequence, or via (c) a S-oxidation/S-F bond formation/SuFEx approach. The labile N-H bond in N-monoalkylated BT-sulfonamides (pK_a (BTSO₂N(H)Bn) = 3.34 ± 0.05) further allowed us to develop a simple weak base-promoted N-alkylation method and a stereoselective microwave-promoted Fukuyama-Mitsunobu reaction. N-Alkyl-N-aryl BT-sulfonamides were accessed with the help of the Chan-Lam coupling reaction. Developed methods were further used in stereo and chemoselective transformations of podophyllotoxin and several amino alcohols.

Crystal structures of (E)-2-amino-4-methyl-sulfanyl-6-oxo-1-(1-phenyl-ethyl-idene-amino)-1,6-di-hydro-pyrimidine-5-carbo-nitrile and (E)-2-amino-4-methyl-sulfanyl-6-oxo-1-[1-(pyridin-2-yl)ethyl-idene-amino]-1,6-di-hydro-pyrimidine-5-carbo-nitrile

The title compounds 3a, C14H13N5OS, and 3b, C13H12N6OS, both show an E configuration about the N=C bond and a planar NH2 group. The mol-ecules, which only differ in the presence of a phenyl (in 3a) or pyridyl (in 3b) substituent, are closely similar except for the different orientations of these groups. The amino hydrogen atoms form classical hydrogen bonds; in 3a the acceptors are the oxygen atom and the cyano nitro-gen atom, leading to ribbons of mol-ecules parallel to the b axis, whereas in 3b the acceptors are the oxygen atom and the pyridyl nitro-gen, leading to a layer structure perpendicular to (01).

Modulation of the Passive Permeability of Semipeptidic Macrocycles: N- and C-Methylations Fine-Tune Conformation and Properties

Incorporating small modifications to peptidic macrocycles can have a major influence on their properties. For instance, N-methylation has been shown to impact permeability. A better understanding of the relationship between permeability and structure is of key importance as peptidic drugs are often associated with unfavorable pharmacokinetic profiles. Starting from a semipeptidic macrocycle backbone composed of a tripeptide tethered head-to-tail with an alkyl linker, we investigated two small changes: peptide-to-peptoid substitution and various methyl placements on the nonpeptidic linker. Implementing these changes in parallel, we created a collection of 36 compounds. Their permeability was then assessed in parallel artificial membrane permeability assay (PAMPA) and Caco-2 assays. Our results show a systematic improvement in permeability associated with one peptoid position in the cycle, while the influence of methyl substitution varies on a case-by-case basis. Using a combination of molecular dynamics simulations and NMR measurements, we offer hypotheses to explain such behavior.

Macrocycles as protein-protein interaction inhibitors

Macrocyclic compounds such as cyclic peptides have emerged as a new and exciting class of drug candidates for inhibition of intracellular protein-protein interactions, which are challenging targets for conventional drug modalities (i.e. small molecules and proteins). Over the past decade, several complementary technologies have been developed to synthesize macrocycle libraries and screen them for binding to therapeutically relevant targets. Two different approaches have also been explored to increase the membrane permeability of cyclic peptides. In this review, we discuss these methods and their applications in the discovery of macrocyclic compounds against protein-protein interactions.

Macrocyclic Inhibitors of GPCR's, Integrins and Protein–Protein Interactions

This chapter summarizes some highlights of macrocyclic drug discovery in the area of GPCRs, integrins, and protein–protein interactions spanning roughly the last 30 years. Several examples demonstrate that incorporation of pharmacophores derived from natural peptide ligands into the context of a constrained macrocycle (“lock of the bioactive conformation”) has proven a powerful approach for the discovery of potent and selective macrocyclic drugs. In addition, it will be shown that macrocycles, due to their semi-rigid nature, can exhibit unique properties that can be beneficially exploited by medicinal chemists. Macrocycles can adapt their conformation during binding to a flexible protein target surface (“induced fit”), and due to their size, can interact with larger protein interfaces (“hot spots”). Also, macrocycles can display favorable ADME properties well beyond the rule of 5 in particular exhibiting favorable cell penetrating properties and oral bioavailability.

Application of dimethyl N-cyanodithioiminocarbonate in synthesis of fused heterocycles and in biological chemistry

The synthetic chemistry of dimethyl

Importance and synthesis of benzannulated medium-sized and macrocyclic rings (BMRs)

Cyclic molecular frameworks, especially the benzannulated medium-sized and macrocyclic ring (BMR) systems, constitute an integral component of a large number of biologically significant natural or synthetic molecules.

Concise route to the chiral pyrrolidine core of selective inhibitors of neuronal nitric oxide

2-(((3R,4R)-4-(Allyloxy)-1-benzylpyrrolidin-3-yl)methyl)-6-(2,5-dimethyl-1H-pyrrol-1-yl)-4-methylpyridine (2), a key intermediate for the preparation of novel neuronal nitric oxide synthase (nNOS) inhibitors, is synthesized using diisopropyl (R)-(+)-malate as the starting material. The key steps involve a Frater-Seebach diastereoselective alkylation and a fast intramolecular cyclization.

Efficient parallel synthesis of macrocyclic peptidomimetics

A new method for solid phase parallel synthesis of chemically and conformationally diverse macrocyclic peptidomimetics is reported. A key feature of the method is access to broad chemical and conformational diversity. Synthesis and mechanistic studies on the macrocyclization step are reported.

Motilin, ghrelin and related neuropeptides as targets for the treatment of GI diseases

Motilin and ghrelin are released from the upper gut during fasting, to stimulate gastric motility. Additional actions of ghrelin (e.g. changes in appetite, nausea or endocrine functions) improve the possibility of using ghrelin receptor agonists to treat complex disorders such as functional dyspepsia. However, changes in endocrine functions increase the risk of unacceptable side effects. By comparison, the more restricted prokinetic activity of motilin limits the therapeutic possibilities but improves the risk:benefit ratio. Compounds targeting both receptors are in development. Recently, additional peptides have been identified from preproghrelin (obestatin) and prepromotilin. These exert biological activity but their pathophysiological significance is unknown.

Motilin

PURPOSE OF REVIEW

Motilin is a hormone produced from endocrine cells of the duodenal mucosa to help regulate motility of the digestive tract. This review discusses new findings on the potential impact of motilin in human medicine.

RECENT FINDINGS

Motilin is a member of the peptide family that includes ghrelin whose cDNA also encodes a new candidate peptide, obestatin. Physiological interactions between these products will have to be explored. Pharmacological agents, agonists as well as antagonists, to motilin receptors are now emerging for clinical application. Motilin-receptor characterization, regarding its localization on nerves or muscles, as well as its biochemical mechanisms to sensitization for example, will be important steps in the design of future motilin agonists or antagonists.

SUMMARY

Motilin is a fascinating hormone for the physiologist. Its interaction with the family member ghrelin and with obestatin will open new areas for basic research. Motilin-receptor agonists or antagonists could soon be part of the therapeutic arsenal of the clinician to improve digestive dysmotility.