Structural Impact Assessment of Cytochrome P450 2A13 Polymorphisms Using Molecular Dynamics Simulations.

One of the members of CYP, a monooxygenase, CYP2A13 is involved in the metabolism of nicotine, coumarin, and tobacco-specific nitrosamine. Genetic polymorphisms have been identified in CYP2A13, with reported loss or reduction in enzymatic activity in CYP2A13 allelic variants. This study aimed to unravel the mechanism underlying the diminished enzymatic activity of CYP2A13 variants by investigating their three-dimensional structures through molecular dynamics (MD) simulations. For each variant, MD simulations of 1000 ns were performed, and the obtained results were compared with those of the wild type. The findings indicated alterations in the interaction with heme in CYP2A13.4, .6, .8, and .9. In the case of CYP2A13.5, observable effects on the helix structure related to the interaction with the redox partner were identified. These conformational changes were sufficient to cause a decrease in enzyme activity in the variants. Our findings provide valuable insights into the molecular mechanisms associated with the diminished activity in the CYP2A13 polymorphisms.

Identification of the Most Impactful Asparagine Residues for γS-Crystallin Aggregation by Deamidation.

Crystallin aggregation in the eye lens is involved in the pathogenesis of cataracts. The aggregation is considered to be promoted by non-enzymatic post-translational modifications, such as the deamidation and stereoinversion of amino acid residues. Although in a previous study, the deamidated asparagine residues were detected in γS-crystallin in vivo, it is unclear which deamidated residues have the most impact on the aggregation under physiological conditions. In this study, we investigated the deamidation impacts of all Asn residues in γS-crystallin for the structural and aggregation properties utilizing deamidation mimetic mutants (N14D, N37D, N53D, N76D, and N143D). The structural impacts were investigated using circular dichroism analysis and molecular dynamics simulations, and the aggregation properties were analyzed by gel filtration chromatography and spectrophotometric methods. No significant structural impacts of all mutations were detected. However, the N37D mutation decreased thermal stability and changed some intermolecular hydrogen-bond formations. Aggregation analysis indicated that the superiority of the aggregation rate in each mutant varied with temperature. Deamidation at any Asn residues promoted γS-crystallin aggregation, and the deamidation at Asn37, Asn53, and Asn76 were suggested to be the most impactful in the formation of insoluble aggregations.

Phytochemical investigation of Scutellaria scordiifolia and its trypanocidal activity.

Scutellaria scordiifolia Fisch. ex Schrank is used to treat various inflammatory diseases and other ailments in traditional and contemporary medicine. In this study, 10 undescribed compounds, including a flavanone (1), four chrysin C-glycosides (2-5), a phenanthrene glucoside (6), four iridoid glucosides (7-10) and 31 known compounds were identified from an extract of the aerial parts of S. scordiifolia. The absolute configurations of sugars in C-glycosides were determined by comparing electric circular dichroism spectra with calculated data. The flavanones (1 and 17), flavonols (11-13), flavone (14), and some of the flavone glucuronides (15, 16) exhibited trypanocidal activities against Trypanosoma congolense. The activity data and quantitative HPLC analysis of flavonoids from the aerial parts of S. scordiifolia suggest that they may effectively treat diseases caused by the aforementioned trypanosomes. Other compounds such as novel iridoids and phenanthrene glycosides, which may be useful for chemophenetic and chemoecological discussions, were also identified.

Development of Novel Small Antitumor Compounds Inhibiting PD-1/PD-L1 Binding.

BACKGROUND/AIM: Anti-programmed death-1 (PD-1)/PD-ligand 1 (PD-L1) antibody is a successful treatment for patients with solid cancers; however, there are several disadvantages that need to be resolved. Oral small molecule anti-PD-1/PD-L1 inhibitors have been developed and have good bioavailability. MATERIALS AND METHODS: Potent anti-PD-1/PD-L1 inhibitor candidates from the Shizuoka small compound library were screened and investigated for their antitumor activities in vitro and in vivo using a humanized mouse model. A search for small compounds that inhibit PD-1/PD-L1 binding among 67,395 compounds through three rounds of screening procedures identified six compounds. RESULTS: The two compounds (SCL-1 and SCL-2), which have as a key chemical structure of triazolopyridazin backbone with a piperazine residue on the aromatic ring and 1,3-diphenyl pyrazoline with hydrazinylphthalazine were selected based on in vitro assays and absorption, distribution, metabolism, and excretion (ADME) scoring and subjected to in vivo experiments using a humanized NOG mouse model. SCL-1 and SCL-2 exhibited moderate inhibitory activities against PD-1/PD-L1 binding compared to an anti-PD-1 antibody, with SCL-1 exerting markedly weaker cytotoxic effects on target cells than the other compounds. In in vivo experiments, SCL-1 exerted significant antitumor effects on PD-L1+ SCC-3 tumors, which were dependent on CD8+ T cell infiltration and PD-L1 expression in tumors. A pharmacokinetic study revealed that it has good bioavailability and distribution as an oral reagent. CONCLUSION: SCL-1 is a novel small compound that inhibits PD-1/PD-L1 binding and exerts potent antitumor effects. Thus, it has potential as an oral reagent for cancer immunotherapy.

Structural basis for peptide recognition by archaeal oligopeptide permease A.

Oligopeptide permease A (OppA) plays an important role in the nutrition of cells and various signaling processes. In archaea, OppA is a major protein present in membrane vesicles of Thermococcales. Because there being no crystal structures of archaeal OppAs determined to date, we report the crystal structure of archaeal OppA from Thermococcus kodakaraensis (TkOppA) at 2.3 Å resolution by the single-wavelength anomalous dispersion method. TkOppA consists of three domains similarly to bacterial OppAs, and the inserted regions not present in bacterial OppAs are at the periphery of the core region. An endogenous pentapeptide was bound in the pocket of domains I and III of TkOppA by hydrogen bonds of main-chain atoms of the peptide and hydrophobic interactions. No hydrogen bonds of side-chain atoms of the peptide were observed; thus, TkOppA may have low peptide selectivity but some preference for residues 2 and 3. TkOppA has a relatively large pocket and can bind a nonapeptide; therefore, it is suitable for the binding of large peptides similarly to OppAs of Gram-positive bacteria.

Benzophenone Glucosides and B-Type Proanthocyanidin Dimers from Zambian Cassia abbreviata and Their Trypanocidal Activities.

Two benzophenone glucosides (1 and 2), five flavan-3-ol dimers (5-9), and 17 known compounds (3, 4, and 10-24) were identified from the bark extract of Cassia abbreviata. The chemical structures display two points of interest. First, as an unusual characteristic feature of the 1H NMR spectra of 1 and 2, the signals for the protons on glucosidic carbons C-2 are shielded as compared to those generally observed for glucosyl moieties. The geometrically optimized 3D structures derived from conformational analysis and density functional theory (DFT) calculations revealed that this shielding effect originates from intramolecular hydrogen bonds in 1 and 2. Additionally, 3-15 were identified as dimeric B-type proanthocyanidins, which have 2R,3S-absolute-configured C-rings and C-4-C-8″ linkages, as evidenced by X-ray crystallography and by NMR and ECD spectroscopy. These results suggest the structure-determining procedures for some reported dimers need to be reconsidered. The trypanocidal activities of the isolated compounds against Trypanosoma brucei brucei, T. b. gambiense, T. b. rhodesiense, T. congolense, and T. evansi were evaluated, and the active compounds were identified.

Computational Analysis of the Mechanism of Nonenzymatic Peptide Bond Cleavage at the C-Terminal Side of an Asparagine Residue.

The nonenzymatic peptide bond cleavage at the C-terminal side of Asn residues is a protein post-translational modification that occurs under physiological conditions. This reaction proceeds much slower than the deamidation of the Asn side chain and causes denaturation and hypofunction of proteins. The peptide bond cleavage of Asn is detected primarily in crystallins and aquaporin 0 in the eye lens. Therefore, cleavage is thought to be involved in age-related cataracts. In this study, to clarify the mechanism underlying succinimide formation for the peptide bond cleavage of the Asn residue, we performed quantum chemical calculations on the model compound Ace-Asn-Gly-Nme (Ace = acetyl and Nme = methylamino). The density functional theory with the B3LYP/6-31+G(d,p) level of theory was used to obtain optimized geometries. The results suggested that the reaction proceeds through two steps, cyclization and C-terminal fragment release, and the required proton transfers can be mediated by H2PO4 - and HCO3 - ions. The conformational change of the main chain on the N-terminal side of Asn was needed for the C-terminal fragmentation step, and a separate conformational change at the C-terminal side was required for the cyclization step. Furthermore, the calculated activation barriers of the reactions catalyzed by the H2PO4 - ion (130 kJ mol-1) and the HCO3 - ion (123 kJ mol-1) were sufficiently low for the reactions to occur under normal physiological conditions.

Deciphering Structural Alterations Associated with Activity Reductions of Genetic Polymorphisms in Cytochrome P450 2A6 Using Molecular Dynamics Simulations.

Cytochrome P450 (CYP) 2A6 is a monooxygenase involved in the metabolism of various endogenous and exogenous chemicals, such as nicotine and therapeutic drugs. The genetic polymorphisms in CYP2A6 are a cause of individual variation in smoking behavior and drug toxicities. The enzymatic activities of the allelic variants of CYP2A6 were analyzed in previous studies. However, the three-dimensional structures of the mutants were not investigated, and the mechanisms underlying activity reduction remain unknown. In this study, to investigate the structural changes involved in the reduction in enzymatic activities, we performed molecular dynamics simulations for ten allelic mutants of CYP2A6. For the calculated wild type structure, no significant structural changes were observed in comparison with the experimental structure. On the other hand, the mutations affected the interaction with heme, substrates, and the redox partner. In CYP2A6.44, a structural change in the substrate access channel was also observed. Those structural effects could explain the alteration of enzymatic activity caused by the mutations. The results of simulations provide useful information regarding the relationship between genotype and phenotype.

Increase in Toxicity of Anticancer Drugs by PMTPV, a Claudin-1-Binding Peptide, Mediated via Down-Regulation of Claudin-1 in Human Lung Adenocarcinoma A549 Cells.

Claudin-1 (CLDN1), a tight junctional protein, is highly expressed in lung cancer cells and may contribute to chemoresistance. A drug which decreases CLDN1 expression could be a chemosensitizer for enhancing the efficacy of anticancer drugs, but there is no such drug known. We found that PMTPV, a short peptide, which mimics the structure of second extracellular loop (ECL2) of CLDN1, can reduce the protein level of CLDN1 without affecting the mRNA level in A549 cells derived from human lung adenocarcinoma. The PMTPV-induced decrease in CLDN1 expression was inhibited by monodansylcadaverine, a clathrin-mediated endocytosis inhibitor, and chloroquine, a lysosome inhibitor. Quartz crystal microbalance assay showed that PMTPV can directly bind to the ECL2 of CLDN1. In transwell assay, PMTPV increased fluxes of Lucifer yellow (LY), a paracellular flux marker, and doxorubicin (DXR), an anthracycline anticancer drug, without affecting transepithelial electrical resistance. In three-dimensional spheroid culture, the size and cell viability were unchanged by short peptides, but the fluorescence intensity of hypoxia probe LOX-1 was decreased by PMTPV. PMTPV elevated the accumulation and cytotoxicity of DXR in the spheroids. Similar results were observed by knockdown of CLDN1. Furthermore, the sensitivities to cisplatin (CDDP), docetaxel, and gefitinib were enhanced by PMTPV. The level of CLDN1 expression in CDDP-resistant cells was higher than that in parental A549 cells, which was reduced by PMTPV. PMTPV restored the toxicity to DXR in the CDDP-resistant cells. Our data suggest that PMTPV may become a novel chemosensitizer for lung adenocarcinoma.

Isolation and evaluation of trypanocidal activity of sesquiterpenoids, flavonoids, and lignans in Artemisia sieversiana collected in Mongolia.

Artemisia sieversiana is an annual herbaceous plant distributed throughout Central and East Eurasia and is regarded as an undesirable forage plant in Mongolia. It affects livestock, so information about its chemical composition is needed. We isolated three new sesquiterpenoids (1-3) and known compounds from A. sieversiana and investigated their activities. The absolute configuration of 1 was established using single-crystal X-ray diffraction crystallography, and its configuration differed from those of reported compounds with similar structures. Two additional new sesquiterpenoids (2 and 3) with similar structures were identified, and their configurations were determined. The trypanocidal activities of the isolated compounds (1-18) against Trypanosoma congolense and the pathogen responsible for fatal trypanosomosis in animals were estimated. Flavonoids and lignans were identified as active compounds with IC50 values ranging from 2.9 to 90.2 µM.

Impact of single nucleotide polymorphisms (R132Q and W120R) on the binding affinity and metabolic activity of CYP2C19 toward some therapeutically important substrates.

Although CYP2C19 is minor human liver enzyme, it is responsible for the metabolism of many clinically important drugs. In this work, CYP2C19 wild type and its SNP mutants (R132Q and W120R) were prepared using over-expression system in E. coli, purified by column chromatography and their biological activities were compared. The enzyme activity toward certain drugs (amitriptyline, imipramine, lansoprazole and omeprazole) was investigated. Resonance Raman and UV-VIS spectroscopies revealed a minimal effect of SNP mutations on the heme structure. However, the mutation greatly affected the drug metabolism activities of CYP2C19. The degree of these effects was dependent on both the mutation and the chemical structure of the substrate. Surprisingly, the affected amino acid residue is located remotely from the heme center. Therefore, the direct effect of the mutation on the metabolic center is excluded. Alternatively, the significant impairment in the drug metabolism of these mutants could be attributed to a decrease in the electron flow to the iron center. Accordingly, understanding the effect of SNPs of CYP2C19, and the extents in which they participate in the drug metabolism, are important pillars that can enhance the therapeutic drugs efficacy and improve the patient outcomes toward the development of patient's tailored medicine.

Total Synthesis of Sophoraflavanone H and Confirmation of Its Absolute Configuration.

Sophoraflavanone H (1) is a polyphenol with a hybrid-type structure containing 2,3-diaryl-2,3-dihydrobenzofuran and flavanone ring moieties. This compound and related analogues are promising leads for antimicrobial and antitumor drug development. Here we describe a total synthesis of 1 and its diastereomer. The dihydrobenzofuran and flavanone rings were constructed by a Rh-catalyzed asymmetric C-H insertion reaction and selective oxy-Michael reaction. The absolute configuration of 1 was established by X-ray crystallographic analysis and CD spectral investigation of synthetic derivatives.

Claudin-2 binding peptides, VPDSM and DSMKF, down-regulate claudin-2 expression and anticancer resistance in human lung adenocarcinoma A549 cells.

Claudin-2 (CLDN2), a tight junctional protein, is involved in the chemoresistance in spheroid culture models of human lung adenocarcinoma A549 cells. However, there is no chemical which can improve the sensitivity to anticancer drugs. So far, we reported that DFYSP, a short peptide which mimics the second extracellular loop (ECL2) of CLDN2, decreases CLDN2 expression in A549 cells, but the concentration is relatively high. Here, we found that the effects of VPDSM and DSMKF are stronger than that of DFYSP. Both VPDSM and DSMKF decreased the protein levels of CLDN2 without affecting the mRNA levels of CLDN2. The peptide-induced decrease in CLDN2 expression was suppressed by monodansylcadaverine (MDC), a clathrin-dependent endocytosis (CDE) inhibitor, and chloroquine, a lysosome inhibitor. CLDN2 was colocalized with ZO-1, an adapter protein, in tight junctions (TJs) under control conditions, whereas it disappeared from the TJs in the peptide-treated cells. Quartz crystal microbalance assay showed that both peptides can bind to recombinant CLDN2 protein. Both peptides increased permeability to paracellular transport marker lucifer yellow. In three-dimensional spheroid culture models, both peptides enhanced the sensitivity to doxorubicin, a cytotoxic anticancer drug, which was inhibited by MDC. We suggest that VPDSM and DSMKF enhance the chemosensitivity to anticancer drugs in aggregated adenocarcinoma cells mediated by the CDE pathway and lysosomal degradation of CLDN2 in lung adenocarcinoma cells. VPDSM and DSMKF, which mimic the ECL2 of CLDN2, may become novel adjuvant therapeutic drugs for lung adenocarcinoma.

Structure of the RAD9-RAD1-HUS1 checkpoint clamp bound to RHINO sheds light on the other side of the DNA clamp.

DNA clamp, a highly conserved ring-shaped protein, binds dsDNA within its central pore. Also, DNA clamp interacts with various nuclear proteins on its front, thereby stimulating their enzymatic activities and biological functions. It has been assumed that the DNA clamp is a functionally single-faced ring from bacteria to humans. Here, we report the crystal structure of the heterotrimeric RAD9-RAD1-HUS1 (9-1-1) checkpoint clamp bound to a peptide of RHINO, a recently identified cancer-related protein that interacts with 9-1-1 and promotes activation of the DNA damage checkpoint. This is the first structure of 9-1-1 bound to its partner. The structure reveals that RHINO is unexpectedly bound to the edge and around the back of the 9-1-1 ring through specific interactions with the RAD1 subunit of 9-1-1. Our finding indicates that 9-1-1 is a functionally double-faced DNA clamp.

Antitumor activity of the PD-1/PD-L1 binding inhibitor BMS-202 in the humanized MHC-double knockout NOG mouse.

Recently, the first series of small molecule inhibitors of PD-1/PD-L1 were reported by Bristol-Myers Squibb (BMS), which were developed using a homogeneous time-resolved fluorescence (HTRF)-based screening investigation of the PD-1/PD-L1 interaction. Additional crystallographic and biophysical studies showed that these compounds inhibited the interaction of PD-1/PD-L1 by inducing the dimerization of PD-L1, in which each dimer binds one molecule of the stabilizer at its interface. However, the immunological mechanism of the antitumor effect of these compounds remains to be elucidated. In the present study, we focused on BMS-202 (a representative of the BMS compounds) and investigated its antitumor activity using in vitro and in vivo experiments. BMS-202 inhibited the proliferation of strongly PD-L1-positive SCC-3 cells (IC50 15 µM) and anti-CD3 antibody-activated Jurkat cells (IC50 10 µM) in vitro. Additionally, BMS-202 had no regulatory effect on the PD-1 or PD-L1 expression level on the cell surface of these cells. In an in vivo study using humanized MHC-double knockout (dKO) NOG mice, BMS-202 showed a clear antitumor effect compared with the controls; however, a direct cytotoxic effect was revealed to be involved in the antitumor mechanism, as there was no lymphocyte accumulation in the tumor site. These results suggest that the antitumor effect of BMS-202 might be partly mediated by a direct off-target cytotoxic effect in addition to the immune response-based mechanism. Also, the humanized dKO NOG mouse model used in this study was shown to be a useful tool for the screening of small molecule inhibitors of PD-1/PD-L1 binding that can inhibit tumor growth via an immune-response-mediated mechanism.

Inhibitory Effects of Phenylpropanoid Derivatives from Oenanthe javanica on Antigen-Stimulated Degranulation in RBL-2H3 Cells.

Two diacyldaucic acids (1 and 2), an α,ß-unsaturated γ-lactone-type lignan (3) and its derivatives (4-6), and 12 known compounds were isolated from a traditional East Asian vegetable, Oenanthe javanica. The absolute configuration of 1 was validated by obtaining (+)-osbeckic acid through acid hydrolysis. The absolute configurations of 3-5 were determined by comparing their experimental and computed ECD data. The conclusion was supported by applying the phenylglycine methyl ester method to 3. Compound 6 was obtained as an interconverting mixture of isomers in a 3:1 trans- cis ratio. Several water-soluble components (1, 3, and 6) showed concentration-dependent inhibitory effects on antigen-stimulated degranulation in RBL-2H3 cells without producing any direct cytotoxicity against RBL-2H3 or HeLa cells.

Acylated Lignans Isolated from Brachanthemum gobicum and Their Trypanocidal Activity.

Eight isovaleryllignans (1-4 and 8-11), three isovalerylphenylpropanoids (5-7), three known lignans (12-14), and four known compounds were isolated from an extract of the aerial part of Brachanthemum gobicum. The structures of the isolated compounds were elucidated based on NMR and MS data analyses. The enantiomers of compounds 1-3, 5, 8, and 9 were isolated using chiral-phase HPLC, and the absolute configurations of 1a/1b-3a/3b, 5a/5b, 8a/8b, and 9a/9b were elucidated from their optical rotations and ECD spectra; the other lignans were assumed to be racemic or scalemic by chiral-phase HPLC analyses and optical rotation data. Some of the acylated lignans (racemic mixtures) (1-4, 8, 9, and 12-14) exhibited moderate inhibitory activities against Trypanosoma congolense, the causative agent of nagana disease in animals.

Propolis Components from Stingless Bees Collected on South Sulawesi, Indonesia, and Their Xanthine Oxidase Inhibitory Activity.

Three new compounds, namely, 4-(4'-hydroxy-3'-methoxyphenyl)-3,5,7-trihydroxycoumarin (1) and sulawesins A (2) and B (3), were isolated from the propolis of stingless bees ( Tetragonula aff. biroi) collected on South Sulawesi, Indonesia. In addition, five known compounds, glyasperin A, broussoflavonol F, (2 S)-5,7-dihydroxy-4'-methoxy-8-prenylflavanone, (1' S)-2- trans,4- trans-abscisic acid, and (1' S)-2- cis,4- trans-abscisic acid, were identified. The structures of the new compounds were determined by a combination of methods that included mass spectrometry and NMR spectroscopy. The absolute configuration of sulawesin A (2), a new podophyllotoxin derivative, was determined by X-ray crystallography. The absolute configuration of sulawesin B (3) was also determined by the ECD calculation. 4-(4'-Hydroxy-3'-methoxyphenyl)-3,5,7-trihydroxycoumarin (1) and sulawesin A (2) were examined for xanthine oxidase (XO) inhibitory activity; 1 exhibited XO inhibitory activity, with an IC50 value of 3.9 µM.

Investigation on drug-binding in heme pocket of CYP2C19 with UV-visible and resonance Raman spectroscopies.

Cytochrome P450 (CYP) is a class of heme-containing enzymes which mainly catalyze a monooxygenation reaction of various chemicals, and hence CYP plays a key role in the drug metabolism. Although CYP2C19 isoform is a minor hepatic CYP, it metabolizes clinically important drugs such as omeprazole and S­mephenytoin. In this work, the interaction of purified CYP2C19 WT (CYP2C19) with seven drugs (phenytoin, S­mephenytoin, omeprazole, lansoprazole, cimetidine, propranolol, and warfarin) was investigated using spectroscopic methods. The binding of each drug and the induced structural change in the heme distal environment were evaluated. Ferric form of CYP2C19 was revealed to contain a six-coordinate low-spin heme with a water molecule as a sixth ligand in a distal site, and the addition of each drug caused varied minor fraction of five-coordinate heme. It was suggested that the ligated water molecule was partly moved away from the heme distal environment and that the degree of water removal was dependent on the type of drugs. The effect on the coordination was varied with the studied drugs with wide variation in the dissociation constants from 2.6 µM for lansoprazole to 5400 µM for warfarin. Phenytoin and S­mephenytoin showed that binding to CYP2C19 occurred in a stepwise manner and that the coordination of a water molecule was facilitated in the second binding step. In the ferrous CO-bound state, ν(FeCO) stretching mode was clearly observed at 471 cm-1 in the absence of drugs. The Raman line was greatly up-shifted by omeprazole (487 cm-1) and lansoprazole (477 cm-1) but was minimally affected by propranolol, phenytoin, and S­mephenytoin. These results indicate that slight chemical modification of a drug greatly affects the heme distal environments upon binding.