Cyclic peptide inhibitors of lysine-specific demethylase 1 with improved potency identified by alanine scanning mutagenesis.

Lysine-specific demethylase 1 (LSD1) is a chromatin-remodeling enzyme that plays an important role in cancer. Over-expression of LSD1 decreases methylation at histone 3 lysine 4, and aberrantly silences tumor suppressor genes. Inhibitors of LSD1 have been designed as chemical probes and potential antitumor agents. We recently reported the cyclic peptide 9, which potently and reversibly inhibits LSD1 (IC50 2.1 µM; Ki 385 nM). Systematic alanine mutagenesis of 9 revealed residues that are critical for LSD1 inhibition, and these mutated peptides were evaluated as LSD1 inhibitors. Alanine substitution at positions 2, 3, 4, 6 and 11-17 preserved inhibition, while substitution of alanine at positions 8 and 9 resulted in complete loss of activity. Cyclic mutant peptides 11 and 16 produced the greatest LSD1 inhibition, and 11, 16, 27 and 28 increased global H3K4me2 in K562 cells. In addition, 16, 27 and 28 promoted significant increases in H3K4me2 levels at the promoter sites of the genes IGFBP2 and FEZ1. Data from these LSD1 inhibitors will aid in the design of peptidomimetics with improved stability and pharmacokinetics.

Synthesis and evaluation of novel cyclic Peptide inhibitors of lysine-specific demethylase 1.

Lysine specific demethylase 1 (LSD1) selectively removes methyl groups from mono- and dimethylated histone 3 lysine 4 (H3K4), resulting in gene silencing. LSD1 is overexpressed in many human cancers, resulting in aberrant silencing of tumor suppressor genes. Thus, LSD1 is a validated target for the discovery of antitumor agents. Using a ligand-based approach, we designed and synthesized a series of cyclic and linear peptides that are effective inhibitors of LSD1. Linear peptide 7 and cyclic peptide 9 inhibited LSD1 in vitro by 91 and 94%, respectively, at a concentration of 10 µM. Compound 9 was a potent LSD1 inhibitor (IC50 2.1 µM; K i 385 nM) and had moderate antitumor activity in the MCF-7 and Calu-6 cell lines in vitro. Importantly, 9 is significantly more stable to hydrolysis in rat plasma than the linear analogue 7. The cyclic peptides described herein represent important lead structures in the search for inhibitors of flavin-dependent histone demethylases.

Novel peptide ligands with dual acting pharmacophores designed for the pathophysiology of neuropathic pain.

The conventional design of high affinity drugs targeted to a single molecule has not resulted in clinically useful therapies for pain relief. Recent reviews have suggested that newly designed analgesic drugs should incorporate multiple targets. The distributions of cholecystokinin (CCK) and CCK receptors in the central nervous system (CNS) overlap significantly with endogenous opioid systems and can be dually targeted. CCK has been shown to act as an endogenous "anti-analgesic" peptide and neuropathic pain conditions promote endogenous CCK release in CNS regions of pain modulation. Administration of CCK into nuclei of the rostral ventromedial medulla induces pronociceptive behaviors in rats. RSA 504 and RSA 601 are novel bifunctional compounds developed to target neuropathic pain by simultaneously acting as agonists at two distinct opioid receptors and antagonizing CCK receptors in the CNS. RSA 504 and RSA 601 demonstrate agonist activity in vitro and antihypersensitivity to mechanical and thermal stimuli in vivo using the spinal nerve ligation model of neuropathic pain. Intrathecal administration of RSA 504 and RSA 601 did not demonstrate antinociceptive tolerance over 7 days of administration and did not display motor impairment or sedation using a rotarod. These are the first behavioral studies that demonstrate how multi-targeted molecule design can address the pathology of neuropathic pain. These compounds with δ and µ opioid agonist activity and CCK antagonist activity within one molecule offer a novel approach with efficacy for neuropathic pain while lacking the side effects typically caused by conventional opioid therapies.

3-[1-(4-Sulfamoylphenyl)-5-p-tolyl-1H-pyrazol-3-yl]propanoic acid and 3-[5-(4-bromophenyl)-1-(4-sulfamoylphenyl)-1H-pyrazol-3-yl]propanoic acid-dichloromethane-diethyl ether-water (2/0.72/1/1).

The syntheses of 3-[1-(4-sulfamoylphenyl)-5-p-tolyl-1H-pyrazol-3-yl]propanoic acid, C(19)H(19)N(3)O(4)S, (I), and 3-[5-(4-bromophenyl)-1-(4-sulfamoylphenyl)-1H-pyrazol-3-yl]propanoic acid-dichloromethane-diethyl ether-water (2/0.72/1/1), 2C(18)H(16)BrN(3)O(4)S.0.72CH(2)Cl(2).C(4)H(10)O.H(2)O, (II), are regiospecific. However, correct identification by spectroscopic techniques of the regioisomer formed is not trivial and single-crystal X-ray analysis provided the only means of unambiguous structure determination. Both structures make extensive use of hydrogen bonding and while compound (I) forms a straightforward unsolvated Z' = 1 structure, compound (II) crystallizes as an unusual mixed solvate, with two crystallographically unique molecules of the pyrazole derivative present in the asymmetric unit. The structure of (II) also features Br...Br interactions.

3-[5-(4-Chlorophenyl)-1-(4-methoxyphenyl)-1H-pyrazol-3-yl]propionic acid and the corresponding methyl ester.

The synthesis of 3-[5-(4-chlorophenyl)-1-(4-methoxyphenyl)-1H-pyrazol-3-yl]propionic acid, C(19)H(17)ClN(2)O(3), (I), and its corresponding methyl ester, methyl 3-[5-(4-chlorophenyl)-1-(4-methoxyphenyl)-1H-pyrazol-3-yl]propionate, C(20)H(19)ClN(2)O(3), (II), is regiospecific. However, correct identification of the regioisomer formed by spectroscopic techniques is not trivial and single-crystal X-ray analysis provided the only means of unambiguous structure determination. Compound (I) crystallizes with Z' = 2. The propionic acid groups of the two crystallographically unique molecules form a hydrogen-bonded dimer, as is typical of carboxylic acid groups in the solid state. Conformational differences between the methoxybenzene and pyrazole rings give rise to two unique molecules. The structure of (II) features just one molecule in the asymmetric unit and the crystal packing makes greater use than (I) of weak C-H...A interactions, despite the lack of any functional groups for classical hydrogen bonding.

1-(4-Methoxy-phen-yl)-3-phenyl-1H-pyrazol-5-amine.

The synthesis of the title compound, C(16)H(15)N(3)O, is regiospecific and single-crystal X-ray diffraction provides the only means of unambiguous structural analysis, with the benzene ring bonded to the imine C atom. The phenyl ring and the essentially planar (r.m.s. deviation 0.0354 Å) methoxy-benzene group are rotated by 29.41 (5) and 37.01 (5)°, respectively, from the central pyrazole ring. An inter-molecular N-H⋯N hydrogen bond links symmetry-related mol-ecules into a C(5) chain, which runs parallel to the b axis.