Design and synthesis of substrate analogue inhibitors of peptide deformylase

Series of substrates derivatives of peptide deformylase were systematically synthesized and studied for their capacities to undergo hydrolysis. Data analysis indicated the requirement for a hydrophobic first side chain and for at least two main chain carbonyl groups in the substrate. For instance, Fo-Met-OCH3 and Fo-Nle-OCH3 were the minimal substrates of peptide deformylase obtained in this study, while positively charged Fo-Nle-ArgNH2 was the most efficient substrate (kcat/Km = 4.5 x 10(5) M-1.s-1). On the basis of this knowledge, 3-mercapto-2-benzylpropanoylglycine (thiorphan), a known inhibitor of thermolysin, could be predicted and further shown to inhibit the deformylation reaction. The inhibition by this compound was competitive and proved to depend on the hydrophobicity at the P1' position. Spectroscopic evidence that the sulfur group of thiorphan binds next to the active site metal ion on the enzyme could be obtained. Consequently, a small thiopseudopeptide derived from Fo-Nle-OCH3 was designed and synthesized. This compound behaved as a competitive inhibitor of peptide deformylase with KI = 52 +/- 5 microM. Introduction of a positive charge to this thiopeptide via addition of an arginine at P2' improved the inhibition constant up to 2.5 +/- 0.5 microM, a value 4 orders of magnitude smaller than that of the starting inhibitors. Evidence that this inhibitor, imino[(5-methoxy-5-oxo-4-[[2-(sulfanylmethyl)hexanoyl]amino]pentyl )am ino]methanamine, binds inside the active site cavity of peptide deformylase, while keeping intact the 3D fold of the protein, was provided by NMR. A fingerprint of the interaction of the inhibitor with the residues of the enzyme was obtained.     

Design and synthesis of macrocyclic peptidyl hydroxamates as peptide deformylase inhibitors

Macrocyclic peptidyl hydroxamates were designed, synthesized, and evaluated as peptide deformylase (PDF) inhibitors. The most potent compound exhibited tight, slow-binding inhibition of Escherichia coli PDF (K(I)(*)=4.4 nM) and had potent antibacterial activity against Gram-positive bacterium Bacillus subtilis (MIC=2-4 microg/mL).     

Design, synthesis and evaluation of peptide inhibitors of Mycobacterium tuberculosis ribonucleotide reductase.

Mycobacterium tuberculosis ribonucleotide reductase (RNR) is a potential target for new antitubercular drugs. Herein we describe the synthesis and evaluation of peptide inhibitors of RNR derived from the C-terminus of the small subunit of M. tuberculosis RNR. An N-terminal truncation, an alanine scan and a novel statistical molecular design (SMD) approach based on the heptapeptide Ac-Glu-Asp-Asp-Asp-Trp-Asp-Phe-OH were applied in this study. The alanine scan showed that Trp5 and Phe7 were important for inhibitory potency. A quantitative structure relationship (QSAR) model was developed based on the synthesized peptides which showed that a negative charge in positions 2, 3, and 6 is beneficial for inhibitory potency. Finally, in position 5 the model coefficients indicate that there is room for a larger side chain, as compared to Trp5.     

Design and synthesis of thrombin inhibitors

Summary As part of our programme directed at the development of enzyme inhibitors based on transition-state mimics, we discovered in the early 1980s that P3-P3 fragments of human fibrinogen A, containing the ketomethylene isostere Arg--[COCH₂]Gly at P1-P1, were potent inhibitors of thrombin. Such low-molecular-weight inhibitors are expected to be clinically useful as anticoagultant drugs. In our more recent investigations, the P1-P1 moiety has been replaced with various arginine or lysine ketones. The resulting compounds showed the following order of thrombin inhibitory potency: -ketoesters > fluoroketones >alkoxymethylketones > difluoro--ketoamides >-ketoesters >alkyl ketones. In contrast to all other lysine/arginine pairs studied previously, the inhibitor based on a lysine -ketoester proved superior to the corresponding arginine analogue. A possible explanation for this finding is discussed. All the highly electrophilic ketones (e.g., fluoroketones) were found to exhibit slow-binding kinetics with thrombin, which is likely to be a disadvantage in clinical use. Alkoxymethyl ketones were devoid of such behaviour and have been developed further to yield nanomolar inhibitors of low molecular weight and good selectivity for thrombin. One of these ketones was found to compare favourably with known thrombin inhibitors in anticoagulant assays. The synthesis of various types of inhibitor mentioned above is described, together with structure-activity correlations for inhibition of thrombin.     

Design, synthesis and structure-activity study of shorter hexa peptide analogues as HIV-1 protease inhibitors

Inhibition of HIV-1 protease enzyme can render the Human Immunodeficiency Virus (HIV-1) non-infectious in vitro. Previous studies have shown that several shorter peptides were discovered as HIV-1 protease inhibitors. In this context, a series of shorter synthetic hexapeptides, Leu-Leu-Glu-Tyr-Val-Xaa (Xaa=Phe, Met, Tyr and Trp), were designed. The synthesized hexa peptides were screened for their HIV-1 protease inhibition. These peptides showed moderately good HIV-1 protease inhibition when compared to acetyl pepstatin.     

Design,synthesis and activity evaluation of novel peptide fusion inhibitors targeting HIV-1 gp41

Human immunodeficiency virus type 1 (HIV-1), the pathogen of acquired immunodeficiency syndrome (AIDS), causes about 2 million people to death every year. Fusion inhibitors targeted the envelope protein (gp41) represent a novel and alternative approach for anti-AIDS therapy, which terminates the HIV-1 life cycle at an early stage. Using CP621-652 as a template, a series of peptides were designed, synthesized and evaluated in vitro assays. An interesting phenomenon was found that the substitution of hydrophobic residues at solvent accessible sites could increase the anti-HIV activity when the C-terminal sequence was extended with an enough numbers of amino acids. After the active peptides was synthesized and evaluated, peptide 8 showed the best anti-HIV-1 IIIB whole cell activity (MAGI IC₅₀ = 53.02 nM). Further study indicated that peptide 8 bound with the gp41 NHR helix, and then blocked the conformation of 6-helix, thus inhibited virus–cell membrane fusion. The results would be helpful for the design of peptide fusion inhibitors against HIV-1 infection.     

Solid phase synthesis of selective caspase-3 peptide inhibitors

A robust method for the solid phase synthesis of a series of selective caspase-3 peptide inhibitors is described. The inhibitors can be obtained after cleavage from the solid support without further purification.     

Design and synthesis of novel metalloproteinase inhibitors

A series of N-benzoyl 4-aminobutyric acid hydroxamate analogs were synthesized and evaluated as matrix metalloproteinase inhibitors. Synthetic work was focused on the chemical modification of the 4-aminobutyric acid part using easily available starting materials. As such, chemical modification was carried out using commercially available starting materials such as 4-aminobutyric acid, (+)- and (-)-malic acid, and D- and L-glutamic acid derivatives. Among the compounds tested, N-[4-(benzofuran-2-yl)benzoyl] 4-amino-4S-hydroxymethylbutyric acid hydroxamates derived from L-glutamic acid demonstrated more potent inhibitory activity against MMP-2 and MMP-9 compared with the corresponding 2S-hydroxy analogs or 3S-hydroxy analogs, respectively, which were derived from (-)-malic acid. Structure-activity relationship study is presented.     

Design and synthesis of statine-containing BACE inhibitors

Utilizing structure-based techniques and solid-phase synthesis, statine-based tetrapeptide BACE inhibitors were designed and synthesized using a heptapeptide BACE transition-state mimetic, 1, as the starting point. Structure–activity relationship studies at the P₃, P₂, and P₂′ positions as well as the N-terminal capping group on scaffold 5 led to the discovery of potent inhibitors 27, 32, and 34 (IC₅₀ <100 nM). In addition, computational analysis and the X-ray structure of BACE–inhibitor 38 are discussed.     

Design and synthesis of dye-conjugated hepsin inhibitors

Hepsin is a type II serine protease that is highly expressed in neoplastic prostate. It is an attractive biomarker for imaging metastatic prostate cancer because of its overexpression in advanced prostate cancer and the location of its active site on the cell surface. We designed and synthesized novel hepsin-targeted imaging probes by conjugating the hepsin-binding ligand with near-infrared (NIR) optical dyes. The Leu-Arg dipeptides, attached to BODIPY or SulfoCy7, exhibited strong hepsin-inhibitory activities with K_i values of 21 and 22 nM, respectively. Compound 2 showed selective uptake and retention in hepsin-overexpressing cells. This is the first report of hepsin-targeted optical probes with strong binding affinities and high selectivity over matriptase. Compound 2 has the potential to be used for developing hepsin-based imaging probes and be as a prototype molecule in the design of new hepsin inhibitors.     

Design and synthesis of procollagen C-proteinase inhibitors

Non-peptidic inhibitors of procollagen C-proteinase (PCP) were designed from substrate leads. Compounds were optimized for potency and selectivity, with N-substituted aryl sulfonamide hydroxamates having the best combination of these properties. Compounds 89 and 60 have IC₅₀ values of 10 and 80 nM, respectively, against PCP; excellent selectivity over MMP’s 1, 2, and 9; and activity in cell-based collagen deposition assays.     

Design and synthesis of potent RSK inhibitors

Utilizing the already described 3,4-bi-aryl pyridine series as a starting point, incorporation of a second ring system with a hydrogen bond donor and additional hydrophobic contacts yielded the azaindole series which exhibited potent, picomolar RSK2 inhibition and the most potent in vitro target modulation seen thus far for a RSK inhibitor. In the context of the more potent core, several changes at the phenol moiety were assessed to potentially find a tool molecule appropriate for in vivo evaluation.     

Design and synthesis of CK2 inhibitors

A series of new polybrominated benzimidazoles and benzotriazoles has been synthesized and their influence on the activity of protein kinase CK2 was evaluated. It was revealed that the most active inhibitors are those with methyl or ethyl substituent at benzene ring, namely 5,6,7-tribromo-4-methyl-1H-benzotriazole (38, IC(50) 0.51 μM) and 5,6,7-tribromo-4-ethyl-1H-benzotriazole (40, IC(50) 0.16 μM). The derivatives with large aromatic or heterocyclic substituents connected to benzimidazole or benzotriazole scaffold appeared to be less potent inhibitors.     

Stimulation of atrial natriuretic peptide secretion and synthesis by Na-K-ATPase inhibitors

Ouabain has been reported to increase the secretion of ANP in vitro. In this study, we focused on whether this action is common in Na-K-ATPase inhibitors (ATPI) and whether ATPI simply increase the release of ANP or stimulate both its biosynthesis and release. The effects of ouabain and digoxin on secretion of ANP and accumulation of ANP mRNA were investigated in the rat cardiocyte superfusion system. Ouabain and digoxin increased the immunoreactive ANP (iANP) output into perfusate and accumulation of ANP mRNA significantly. These results suggest that ATPI may stimulate both ANP biosynthesis and release in vitro.     

Design, synthesis and antibacterial activity of 3-methylenepyrrolidine formyl hydroxyamino derivatives as novel peptide deformylase inhibitors

The synthesis and antibacterial activity of 3-methylenepyrrolidine formyl hydroxyamino derivatives are reported. The antibacterial activities of these derivatives were evaluated to discover SAR at P^1′ and P^3′ positions, and most of these derivatives exhibit better in vitro antibacterial activity than existing drugs against drug-resistant clinical isolates including MRSA, PRSP, and Haemophilus influenzae.     

Design and synthesis of fluorescent SGLT2 inhibitors

The design and synthesis of the first fluorophore-conjugated SGLT2 inhibitors is described. The mode of linking the fluorophore to the SGLT2 pharmacophore was found to be crucial in achieving optimum potency. Superior potency to phlorizin was provided by examples containing TAMRA, BODIPY, Cy3B and NBD fluorophores.     

Design and synthesis of heterocyclic malonyl-CoA decarboxylase inhibitors

We have previously reported the discovery of small molecule inhibitors of malonyl-CoA decarboxylase (MCD) as novel metabolic modulators, which inhibited fatty acid oxidation and consequently increased the glucose oxidation rates in the isolated working rat hearts. MCD inhibitors were also shown to improve cardiac efficiency in rat and pig demand-induced ischemic models through the mechanism-based modulation of energy metabolism. Herein, we describe the design and synthesis of a series of novel heterocyclic MCD inhibitors with a preference for substituted imidazole and isoxazole.     

Design and synthesis of aminophenol-based factor Xa inhibitors

A novel potent and selective aminophenol scaffold for fXa inhibitors was developed from a previously reported benzimidazole-based naphthylamidine template. The aminophenol template is more synthetically accessible than the benzimidazole template, which simplified the introduction of carboxylic acid groups. Substitution of a propenyl-para-hydroxy-benzamidine group on the aminophenol template produced selective, sub-nanomolar fXa inhibitors. The potency of the inhibitors is partially explained with the aid of a trypsin complex crystal structure.     

Design and synthesis of phthalimide-type histone deacetylase inhibitors

Several hydroxamic acid derivatives with a substituted phthalimide group as a linker and/or cap structure, prepared during structural development studies based on thalidomide, were found to have histone deacetylase (HDAC)-inhibitory activity. Structure-activity relationship studies indicated that nature of the substituent introduced at the phthalimide nitrogen atom, introduction of a hydroxamic acid structure, and distance between the N-hydroxyl group and the cap structure are important for HDAC-inhibitory activity.     

Design and synthesis of lignostilbene-alpha,beta-dioxygenase inhibitors

Lignostilbene-alpha,beta-dioxygenase cleaves the olefinic double bond of phenolic stilbenes by a mechanism similar to that of 9-cis-epoxycarotenoid dioxygenase, a key enzyme in abscisic acid biosynthesis. Several analogues of stilbene were designed and synthesized, and their efficacy as inhibitors of lignostilbene-alpha,beta-dioxygenase was examined. The compound (Z)-1-(4-hydroxyphenyl)-1-fluoro-2-phenylethene (2) was found to be a potent inhibitor of this enzyme with an IC(50) of 3 microM.