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Discoidin domain receptor 1 (DDR1) inhibitors with a desired pharmacophore were designed using deep generative models (DGMs). DDR1 is a receptor tyrosine kinase activated by matrix collagens and implicated in diseases such as cancer, fibrosis and hypoxia. Herein we describe the synthesis and inhibitory activity of compounds generated from DGMs. Three compounds were found to have sub‐micromolar inhibitory activity. The most potent of which, compound 3 (N‐(4‐chloro‐3‐((pyridin‐3‐yloxy)methyl)phenyl)‐3‐(trifluoromethyl)benzamide), had an IC50 value of 92.5 nM. Furthermore, these compounds were predicted to interact with DDR1, which have a desired pharmacophore derived from a known DDR1 inhibitor. The results of synthesis and experiments indicated that our de novo design strategy is practical for hit identification and scaffold hopping., Helpful for scaffold hopping: DDR1 inhibitors were designed using a deep generative model that generates chemical structures with the desired pharmacophore. In structure sampling, about 10,000 generated structures from the agent network have pharmacophore scores greater than 0.8. After filtering the structures, nine compounds were synthesized and their inhibitory activities were evaluated against DDR1. The results of this study show that our de novo design strategy is practical for hit identification and scaffold hopping.

Evidence indicates that hepatitis C virus (HCV) utilizes cellular cyclophilin proteins in its replication, and cyclophilin inhibitors represent a new class of anti-HCV agents. We have established an efficient synthetic methodology to generate FR901459 derivatives via N, O-acyl migration reaction while avoiding total synthesis. Through a detailed structure-activity relationship study, we improved anti-HCV activity while decreasing immunosuppressive activity. Additionally, we discovered the importance of substitution at the 3 position for not only improving anti-HCV activity but also pharmacokinetic profile. Finally, by striking an appropriate balance between potency, solubility, and permeability, we discovered ASP5286 (13) as a potential clinical candidate for anti-HCV therapy.

The ras oncogene products (H-Ras, K-Ras, and N-Ras) have been regarded as some of the most promising targets for anticancer drug discovery because their activating mutations are frequently found in human cancers. Nonetheless, molecular targeted therapy for them is currently unavailable. Here, we report the discovery of a small-molecule compound carrying a naphthalene ring, named KBFM123, which binds to the GTP-bound form of H-Ras. The solution structure of its complex with the guanosine 5'-(β,γ-imide) triphosphate-bound form of H-RasT35S (H-RasT35S·GppNHp) indicates that the naphthalene ring of KBFM123 interacts directly with a hydrophobic pocket located between switch I and switch II and allosterically inhibits the effector interaction by inducing conformational changes in switch I and its flanking region in strand β2, which are directly involved in recognition of the effector molecules, including c-Raf-1. In particular, Asp38 of H-Ras, a crucial residue for the interaction with c-Raf-1 via the formation of a salt bridge with Arg89 of the Ras-binding domain (RBD) of c-Raf-1, shows a drastic conformational change: its side chain orients toward the opposite direction. Consistent with these results, KBFM123 exhibits an activity to inhibit, albeit weakly, the association of H-RasG12V·GppNHp with the c-Raf-1 RBD. The binding of the naphthalene ring to the hydrophobic pocket of H-RasT35S·GppNHp is further supported by nuclear magnetic resonance analyses showing that two other naphthalene-containing compounds with distinct structures also exhibit similar binding properties with KBFM123. These results indicate that the naphthalene ring could become a promising scaffold for the development of Ras inhibitors.

Vascular Adhesion Protein-1 (VAP-1) is a promising therapeutic target for the treatment of several inflammatory-related diseases including diabetic microvascular complication. We identified glycine amide derivative 3 as a novel structure with moderate VAP-1 inhibitory activity. Structure-activity relationship studies of glycine amide derivatives revealed that the tertiary amide moiety is important for stability in rat blood and that the position of substituents on the left phenyl ring plays an important role in VAP-1 inhibitory activity. We also found that low TPSA values and weak basicity are both important for high PAMPA values for glycine amide derivatives. These findings led to the identification of a series of orally active compounds with enhanced VAP-1 inhibitory activity. Of these compounds, 4g exhibited the most potent ex vivo efficacy, with plasma VAP-1 inhibitory activity of 60% after oral administration at 1mg/kg.

A series of pyrazolopyridazine compounds were briefly investigated as ERK2 inhibitors. The crystal structure of ERK2 complexed with an allyl derivative was determined. The compound induces structural change including movement of the glycine-rich loop and peptide flip between Met108-Glu109. As a result, the newly formed subsite can recognize small hydrophobic substituents but not hydrophilic ones.

FR255031 (2-[(7S)-7-[5-(4-ethylphenyl)-2-thienyl]-1,1-dioxido-4-(2-pyridinylcarbonyl)hexahydro-1,4-thiazepin-7-yl]-N-hydroxyacetamide) is a novel synthetic matrix metalloproteinase (MMP) inhibitor that inhibits human collagenases (MMP-1, MMP-8 and MMP-13), gelatinases (MMP-2 and MMP-9) and membrane type 1 MMP (MT1-MMP/MMP-14). FR255031 also inhibits rat collagenase and gelatinase. We studied the effect of FR255031 and Trocade, an inhibitor of collagenase and MMP-14, on a rat collagen-induced arthritis (CIA) model. Rat CIA was induced by intradermal injection of type II collagen (IIC) and oral administration of FR255031 or Trocade was performed for 28 days. Body weight loss, hind paw swelling, elevation of serum anti-IIC antibody, and histological and radiographic scores were evaluated. FR255031 markedly inhibited cartilage degradation in a dose-dependent manner in the CIA model, but Trocade failed to prevent the degradation. FR255031 at a dose of 100 mg kg(-1) also had statistically significant effects on bone destruction and pannus formation and on the recovery of body weight loss on day 28. These results indicate that FR255031 is effective for rat CIA, especially on joint cartilage destruction. These data suggest that as well as collagenases or MT-MMP, gelatinases are also involved in joint destruction in arthritis.

Novel cyclic pentapeptides, WS7338A, B, C and D (cyclo-(AAl -AA2-D- Trp-D-Glu-Ala)) were isolated as Endothelin (ET) receptor antagonists from the culture broth of Sfreptomyces sp. No. 7338. Based on conformational analysis of these seeds, we defined the minimum structural requirements for binding affinity and prepared a series of acylated tripeptides with ETA receptor binding affinity. Through extensive chemical modification of the lead tripeptide, we have discovered a highly potent and selective ETA receptor antagonist FR139317. Further modification of this series of tripeptide ET antagonists has led to the discovery of a highly potent and selective ETB receptor antagonist FR164343. The discovery and structure-activity relationship of these ET antagonists and the pharmacological profile of FR139317 and FR164343 are described.

The overall crystal quality as well as the harvest period of bovine adenosine deaminase containing a zinc ion at the active centre has been compared in three different environments: crystallization as a control, crystallization with agarose gel and crystallization in a high magnetic field. In crystallization with agarose gel, the probability of obtaining high-quality crystals was somewhat increased, but the harvest period was elongated. On the other hand, in crystallization in a magnetic field, the probability of obtaining high-quality crystals was greatly increased. Furthermore, the harvest period for crystal growth in a magnetic field was much shorter than that with agarose gel.

The soil-borne bacterial pathogen Ralstonia solanacearum invades a broad range of plants through their roots, resulting in wilting of the plant, but no effective protection against this disease has been developed. Two bacterial wilt disease-inhibiting compounds were biochemically isolated from tobacco and identified as sclareol and cis-abienol, labdane-type diterpenes. When exogenously applied to their roots, sclareol and cis-abienol inhibited wilt disease in tobacco, tomato and Arabidopsis plants without exhibiting any antibacterial activity. Microarray analysis identified many sclareol-responsive genes in Arabidopsis roots, including genes encoding or with a role in ATP-binding cassette (ABC) transporters, and biosynthesis and signaling of defense-related molecules and mitogen-activated protein kinase (MAPK) cascade components. Inhibition of wilt disease by sclareol was attenuated in Arabidopsis mutants defective in the ABC transporter AtPDR12, the MAPK MPK3, and ethylene and abscisic acid signaling pathways, and also in transgenic tobacco plants with reduced expression of NtPDR1, a tobacco homolog of AtPDR12. These results suggest that multiple host factors are involved in the inhibition of bacterial wilt disease by sclareol-related compounds.

The phenacyl esters of peptide segments were efficiently cleaved by zinc reduction using a chelating compound, acetylacetone, in the presence of pyridine.

Selective inhibition of extracellular signal-regulated kinase (ERK) represents a potential approach for the treatment of cancer and other diseases; however, no selective inhibitors are currently available. Here, we describe an ERK-selective inhibitor, FR180204, and determine the structural basis of its selectivity. FR180204 inhibited the kinase activity of ERK1 and ERK2, with Ki values 0.31 and 0.14 μM, respectively. Lineweaver–Burk analysis of the binding interaction revealed that FR180204 acted as competitive inhibitor of ATP. In mink lung epithelial Mv1Lu cells, FR180204 inhibited TGFβ-induced luciferase-expression. X-ray crystal structure analysis of the human ERK2/FR180204 complex revealed that Q105, D106, L156, and C166, which form the ATP-binding pocket on ERK, play important roles in the drug/protein interaction. These results suggest that FR180204 is an ERK-selective and cell-permeable inhibitor, and could be useful for elucidating the roles of ERK as well as for drug development.

FR255031 (2-[(7S)-7-[5-(4-ethylphenyl)-2-thienyl]-1,1-dioxido-4-(2-pyridinylcarbonyl)hexahydro-1,4-thiazepin-7-yl]-N-hydroxyacetamide) is a novel synthetic matrix metalloproteinase (MMP) inhibitor that inhibits human collagenases (MMP-1, MMP-8 and MMP-13), gelatinases (MMP-2 and MMP-9) and membrane type 1 MMP (MT1-MMP/MMP-14). FR255031 also inhibits rat collagenase and gelatinase. We studied the effect of FR255031 and Trocade, an inhibitor of collagenase and MMP-14, on a rat collagen-induced arthritis (CIA) model. Rat CIA was induced by intradermal injection of type II collagen (IIC) and oral administration of FR255031 or Trocade was performed for 28 days. Body weight loss, hind paw swelling, elevation of serum anti-IIC antibody, and histological and radiographic scores were evaluated. FR255031 markedly inhibited cartilage degradation in a dose-dependent manner in the CIA model, but Trocade failed to prevent the degradation. FR255031 at a dose of 100 mg kg(-1) also had statistically significant effects on bone destruction and pannus formation and on the recovery of body weight loss on day 28. These results indicate that FR255031 is effective for rat CIA, especially on joint cartilage destruction. These data suggest that as well as collagenases or MT-MMP, gelatinases are also involved in joint destruction in arthritis.

Matrix metalloproteinase (MMP) has been implicated in joint destruction of chronic arthritis diseases, such as rheumatoid arthritis. FR217840 (2R)-1-([5-(4-fluorophenyl)-2-thienyl]sulfonyl)-N-hydroxy-4-(methylsulfonyl)-2-piperazinecarboxamide is a potent, orally active synthetic MMP inhibitor that inhibits human collagenases (MMP-1, MMP-8 and MMP-13), gelatinases (MMP-2 and MMP-9) and membrane type MMP (MT-MMP) (MT1-MMP/MMP-14). FR217840 also inhibits rat collagenase and gelatinase. We studied the effect of FR217840 on a rat adjuvant induced arthritis model. Although oral administration (days 1-21) of FR217840 (3.2, 10, 32 mg/kg) to adjuvant injected Lewis rats did not affect inflammation, as indicated by both hind paw swelling and histological inflammatory infiltration, FR217840 suppressed both bone destruction and serum pyridinoline content in a dose-dependent manner. Also, FR217840 (32 mg/kg) reduced tartrate-resistant acid phosphatase (TRAP) cell number in the ankle joints of rats with arthritis. These results indicate that FR217840 successfully suppressed joint destruction and suggest that FR217840 may have potential as a novel anti-rheumatic drug.

Direct synthesis of peptides containing 1-benzyloxycarbonyl-2-aziridinecarboxylic acid were carried out by the reaction of β-hydroxy-α-amino acid peptides with DEAD–TPP reagents, and key O-peptide intermediates of actinomycin D synthesis were prepared via a ring-opening reaction of the aziridine with N-protected dipeptide. Peptide lactone was prepared by the DCC–HOBt method, and the subsequent debenzyl procedure and oxydation procedure gave the title compounds in good yields.

threo-3-Methyl-D-cysteine as a moiety of β-methyllanthionine in the peptide antibiotic nisin was synthesized stereospecifically. The reaction of (2R,3R)-3-methyl-2-aziridinecarboxylic acid derivative prepared from D-threonine with thiobenzoic acid gave the β-mercapto α-amino acid derivative of the same configuration as the starting material. A stereochemistry of the product was retained as a result of double inversion mechanism through the reactions. Thus, we could prepare threo-3-methyl-D-cysteine, i.e., (2S,3S)-2-amino-3-mercaptobutanoic acid which is required for the synthetic study of nisin.

The 2-aziridinecarboxylic acid residue in peptides was isomerized with NaI in an acetone solution into the corresponding dehydroalanine or dehydro-2-aminobutyric acid derivatives, but not into the corresponding 2-oxazoline derivatives.

threo-3-Methyl-D-cysteine as a moiety of β-methyllanthionine in the peptide antibiotic nisin was synthesized stereospecifically. The reaction of (2R,3R)-3-methyl-2-aziridinecarboxylic acid derivative prepared from D-threonine with thiobenzoic acid gave the β-mercapto α-amino acid derivative of the same configuration as the starting material. A stereochemistry of the product was retained as a result of double inversion mechanism through the reactions. Thus, we could prepare threo-3-methyl-D-cysteine, i.e., (2S,3S)-2-amino-3-mercaptobutanoic acid which is required for the synthetic study of nisin.

The reaction of aziridine derivatives having a urethane-type protecting group with several alcohols in the presence of boron trifluoride etherate afford the corresponding optically pure O-alkylserine and O-alkylthreonine derivatives via a ring-opening reaction of aziridine in good yield.

The reaction of aziridine derivatives having a urethane-type protecting group with several alcohols in the presence of boron trifluoride etherate afford the corresponding optically pure O-alkylserine and O-alkylthreonine derivatives via a ring-opening reaction of aziridine in good yield.

The first total synthesis of urogastrone (h-EGF)has been achieved by the segment condensation method in solution applying the maximum protection strategy.