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3. The dipeptidyl peptidase IV inhibitors vildagliptin and K-579 inhibit a phospholipase C: a case of promiscuous scaffolds in proteins

Author

Chakraborty, Sandeep, Rendón-Ramírez, Adela, Ásgeirsson, Bjarni, Dutta, Mouparna, Ghosh, Anindya S, Oda, Masataka, Venkatramani, Ravindra, Rao, Basuthkar J, Dandekar, Abhaya M, and Goñi, Félix M

Subjects
Development of treatments and therapeutic interventions, 5.1 Pharmaceuticals, Bacillus cereus, PI-PLC, diabetes, lipase, serine protease, Biochemistry and Cell Biology, Clinical Sciences, Oncology and Carcinogenesis
Abstract

The long term side effects of any newly introduced drug is a subject of intense research, and often raging controversies. One such example is the dipeptidyl peptidase-IV (DPP4) inhibitor used for treating type 2 diabetes, which is inconclusively implicated in increased susceptibility to acute pancreatitis. Previously, based on a computational analysis of the spatial and electrostatic properties of active site residues, we have demonstrated that phosphoinositide-specific phospholipase C (PI-PLC) from Bacillus cereus is a prolyl peptidase using in vivo experiments. In the current work, we first report the inhibition of the native activity of PI-PLC by two DPP4 inhibitors - vildagliptin (LAF-237) and K-579. While vildagliptin inhibited PI-PLC at micromolar concentrations, K-579 was a potent inhibitor even at nanomolar concentrations. Subsequently, we queried a comprehensive, non-redundant set of 5000 human proteins (50% similarity cutoff) with known structures using serine protease (SPASE) motifs derived from trypsin and DPP4. A pancreatic lipase and a gastric lipase are among the proteins that are identified as proteins having promiscuous SPASE scaffolds that could interact with DPP4 inhibitors. The presence of such scaffolds in human lipases is expected since they share the same catalytic mechanism with PI-PLC. However our methodology also detects other proteins, often with a completely different enzymatic mechanism, that have significantly congruent domains with the SPASE motifs. The reported elevated levels of serum lipase, although contested, could be rationalized by inhibition of lipases reported here. In an effort to further our understanding of the spatial and electrostatic basis of DPP4 inhibitors, we have also done a comprehensive analysis of all 76 known DPP4 structures liganded to inhibitors till date. Also, the methodology presented here can be easily adopted for other drugs, and provide the first line of filtering in the identification of pathways that might be inadvertently affected due to promiscuous scaffolds in proteins.

Published
2013

4. A computational module assembled from different protease family motifs identifies PI PLC from Bacillus cereus as a putative prolyl peptidase with a serine protease scaffold.

Author

Rendón-Ramírez, Adela, Shukla, Manish, Oda, Masataka, Chakraborty, Sandeep, Minda, Renu, Dandekar, Abhaya M, Ásgeirsson, Bjarni, Goñi, Félix M, and Rao, Basuthkar J

Subjects
Bacillus cereus, Serine Endopeptidases, Bacterial Proteins, Amino Acid Motifs, Catalytic Domain, Models, Molecular, Computer Simulation, Phosphoinositide Phospholipase C, Models, Molecular, General Science & Technology
Abstract

Proteolytic enzymes have evolved several mechanisms to cleave peptide bonds. These distinct types have been systematically categorized in the MEROPS database. While a BLAST search on these proteases identifies homologous proteins, sequence alignment methods often fail to identify relationships arising from convergent evolution, exon shuffling, and modular reuse of catalytic units. We have previously established a computational method to detect functions in proteins based on the spatial and electrostatic properties of the catalytic residues (CLASP). CLASP identified a promiscuous serine protease scaffold in alkaline phosphatases (AP) and a scaffold recognizing a β-lactam (imipenem) in a cold-active Vibrio AP. Subsequently, we defined a methodology to quantify promiscuous activities in a wide range of proteins. Here, we assemble a module which encapsulates the multifarious motifs used by protease families listed in the MEROPS database. Since APs and proteases are an integral component of outer membrane vesicles (OMV), we sought to query other OMV proteins, like phospholipase C (PLC), using this search module. Our analysis indicated that phosphoinositide-specific PLC from Bacillus cereus is a serine protease. This was validated by protease assays, mass spectrometry and by inhibition of the native phospholipase activity of PI-PLC by the well-known serine protease inhibitor AEBSF (IC50 = 0.018 mM). Edman degradation analysis linked the specificity of the protease activity to a proline in the amino terminal, suggesting that the PI-PLC is a prolyl peptidase. Thus, we propose a computational method of extending protein families based on the spatial and electrostatic congruence of active site residues.

Published
2013

11. Suitable Stereoisomers of Vibrioferrin Probes for Iron Uptake of Vibrio Parahaemolyticus

Author

Sumida, Ryuichi, Okuda, Misa, Mera, Akane, Inoue, Masaki, Karanjit, Sangita, Niwa, Kanji, Tsutsumi, Tomohiro, Sato, Ryota, Nakayama, Atsushi, Tanaka, Naonobu, Oda, Masataka, Namba, Kosuke, Sumida, Ryuichi, Okuda, Misa, Mera, Akane, Inoue, Masaki, Karanjit, Sangita, Niwa, Kanji, Tsutsumi, Tomohiro, Sato, Ryota, Nakayama, Atsushi, Tanaka, Naonobu, Oda, Masataka, and Namba, Kosuke

Abstract

Suitable Stereostructures of vibrioferrin probes for iron uptake of Vibrio parahaemolyticus was revealed. Stereoisomers of dansyl labeled vibrioferrin at the 2′′-position were synthesized and their uptake activities were evaluated. Vibrio parahaemolyticus take in both isomers at the 2′′-position. In addition to Vibrio parahaemolyticus, several bacteria have also taken up the (R)-isomer.

Published
2023

22. The inhibition of lipopolysaccharide-induced tumor necrosis factor-α and nitric oxide production by Clostridium perfringens α-toxin and its relation to α-toxin-induced intracellular ceramide generation

Author

Tumurkhuu, Gantsetseg, Koide, Naoki, Dagvadorj, Jargalsaikhan, Shadat Mohammod Noman, Abu, Iftekar-E-Khuda, Imtiaz, Naiki, Yoshikazu, Komatsu, Takayuki, Yoshida, Tomoaki, Oda, Masataka, Nagahama, Masahiro, Sakurai, Jun, and Yokochi, Takashi

Published
2009
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24. List of Contributors

Author

Abel-Santos, Ernesto, primary, Abraham, Soman N., additional, Aizawa, Shin-Ichi, additional, Aldape, Michael J., additional, Alexander, David C., additional, Allison, David G., additional, Amyes, Sebastian G.B., additional, Anderson, Burt E., additional, Anderson, Frank J., additional, Antelmann, Haike, additional, Austin, Frank W., additional, Ayllón, Nieves, additional, Bai, Fang, additional, Barbosa, Angela Silva, additional, Barer, Michael R., additional, Basarab, Gregory S., additional, Beaman, Blaine L., additional, Beard, Matthew, additional, Black, Carolyn M., additional, Blakely, Garry W., additional, Boiron, Patrick, additional, Bouabe, Hicham, additional, Bozue, Joel A., additional, Brinkman, Cassandra L., additional, Brubaker, Robert R., additional, Bryant, Amy E., additional, Cain, Robert J., additional, Calvo, Ana Cristina, additional, Carvalho, Eneas, additional, Capo, Christian, additional, Castillo-Ramirez, Santiago, additional, Chaddock, John A., additional, Chamberland, Robin R., additional, Clarridge, Jill E., additional, Cote, Christopher K., additional, Cox, Sarah L., additional, Cutler, Sally J., additional, Davidson, Donald J., additional, Day, Nicholas P.J., additional, de la Fuente, José, additional, De Jesus, Magdia, additional, Dorin, Julia R., additional, Dorman, Charles J., additional, Eakin, Ann E., additional, Egland, Paul G., additional, Ellis, Simon, additional, Enright, Mark C., additional, Evans, Benjamin A., additional, Everett, Jake A., additional, Falkinham, Joseph O., additional, Fan, Feinan, additional, Fan, Huizhou, additional, Faulds-Pain, Alexandra, additional, Feil, Edward J., additional, Figueroa, Cesar J., additional, Forsberg, Åke, additional, Foster, Timothy J., additional, Fox-Moon, Sandra M., additional, Fraga, Tatiana Rodrigues, additional, Fredricks, David N., additional, Freitag, Nancy E., additional, García-López, María-Luisa, additional, Garzetti, Debora, additional, Gemmell, Curtis G., additional, Geoghegan, Joan A., additional, Gillis, Thomas P., additional, Gilmore, Michael S., additional, Goldstone, Robert J., additional, Gray-Owen, Scott D., additional, Guiso, Nicole, additional, Hallstrom, Kelly N., additional, Harper, David R., additional, Harrington, Amanda T., additional, Harris, Jason B., additional, Hays, John P., additional, He, Yongqun, additional, Heffron, Jared D., additional, Heimer, Susan R., additional, High, Nicola J., additional, Hobot, Jan A., additional, Hultgren, Scott, additional, Humphreys, Tricia L., additional, Hunstad, David A., additional, Igietseme, Joseph U., additional, Inglis, Neil F., additional, Inglis, Tim J.J., additional, Isaac, Lourdes, additional, Janowicz, Diane M., additional, Jin, Shouguang, additional, Jin, Yongxin, additional, Johansson, Anna-Lena, additional, Johnston, Randal N., additional, Jones, Jessica L., additional, Justice, Sheryl S., additional, Kaakoush, Nadeem O., additional, Kalas, Vasilios, additional, Khare, Reeti, additional, Jordan, I. King, additional, Kobayashi, Keiko, additional, Kocan, Katherine M., additional, Könönen, Eija, additional, Kumar, Purnima S., additional, Lambert, Peter A., additional, Lamont, Richard J., additional, Lan, Ruiting, additional, Lang, Sue, additional, Lereclus, Didier, additional, Levett, Paul N., additional, Li, Xuefeng, additional, Liu, Dongyou, additional, Liu, Shu-Lin, additional, Ma, Lin, additional, Mahlen, Steven D., additional, Man, Si Ming, additional, Margolis, Elisa, additional, Marrie, Thomas J., additional, Martin, Melissa J., additional, Mayer, Leonard W., additional, McConville, Malcolm, additional, McCormick, Beth A., additional, McDowell, Andrew, additional, McHugh, Brian J., additional, McMullen, P. David, additional, McSheffrey, Gordon G., additional, Mege, Jean-Louis, additional, Merritt, Adam J., additional, Minnick, Michael F., additional, Mitchell, Hazel M., additional, Morrison, Donald, additional, Musser, Kimberlee A., additional, Nagahama, Masahiro, additional, Nagao, Prescilla Emy, additional, Nagy, István, additional, Salomonsson, Emelie Näslund, additional, Nazarian, Elizabeth J., additional, Nichols, Wright W., additional, Noppa, Laila, additional, Octavia, Sophie, additional, Oda, Masataka, additional, Ofek, Itzhak, additional, Oliver, James D., additional, Olson, Patrick D., additional, Omosun, Yusuf, additional, Ong, Edmund, additional, Osta, Rosario, additional, Otero, Andrés, additional, Oyston, Petra C.F., additional, Paris, Daniel H., additional, Patel, Robin, additional, Patrick, Sheila, additional, Pedra, Joao H.F., additional, Posteraro, Brunella, additional, Posteraro, Patrizia, additional, Poxton, Ian R., additional, Pujic, Petar, additional, Raffa, Brittany J., additional, Rakin, Alexander, additional, Ramarao, Nalini, additional, Ramirez, Mario, additional, Ravalison, Miora, additional, Reed, Kurt D., additional, Reglinski, Mark, additional, Richards, Allen L., additional, Riesbeck, Kristian, additional, Riley, Thomas V., additional, Rodríguez-Calleja, José-María, additional, Rodríguez-Nava, Verónica, additional, Rumbaugh, Kendra P., additional, Sanderson, Kenneth E., additional, Sanguinetti, Maurizio, additional, Santos, Jesús A., additional, Santos, Renato L., additional, Schaar, Viveka, additional, Scheld, W. Michael, additional, Schmitz, Jonathan E., additional, Schwartzman, Joseph D., additional, Severo, Maiara S., additional, Sharon, Nathan, additional, Shirtliff, Mark E., additional, Simner, Patricia J., additional, Šmajs, David, additional, Smith, David G.E., additional, Sorokin, Alexei, additional, Sprague, Lisa D., additional, Sriskandan, Shiranee, additional, Stevens, Dennis L., additional, Stratton, Charles W., additional, Strouhal, Michal, additional, Su, Yu Ching, additional, Sussman, Max, additional, Talbot, Elizabeth A., additional, Tang, Le, additional, Tang, Yi-Wei, additional, Taur, Ying, additional, Tessier, Jeffrey M., additional, Textoris, Julien, additional, Thirumalapura, Nagaraja R., additional, Tsuge, Hideaki, additional, Turenne, Christine Y., additional, Valvano, Miguel A., additional, Vázquez-Boland, José A., additional, Verhaegh, Suzanne J.C., additional, Volkan, Ender, additional, Vollmer, Waldemar, additional, Wade, William F., additional, Waites, Ken B., additional, Walker, Alan W., additional, Walker, David H., additional, Wang, Guiqing, additional, Wang, Qinning, additional, Wang, Xin, additional, Ward, Bruce, additional, Watson, Eleanor, additional, Weil, Ana A., additional, Welkos, Susan L., additional, Wen, Zhensong, additional, Wengenack, Nancy L., additional, Westblade, Lars F., additional, Wexler, Hannah M., additional, Wren, Brendan W., additional, Wu, Min, additional, Wu, Shangwei, additional, Wu, Weihui, additional, Xiao, Li, additional, Zhang, Jing-Ren, additional, Zhao, Zuotao, additional, and Zhong, Guangming, additional

Published
2015
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28. Structural basis of actin recognition and arginine ADP-ribosylation by Clostridium perfringens [iota]-toxin

Author

Tsuge, Hideaki, Nagahama, Masahiro, Oda, Masataka, Iwamoto, Shinobu, Utsunomiya, Hiroko, Marquez, Victor E., Katunuma, Nobuhiko, Nishizawa, Mugio, and Sakurai, Jun

Subjects
Clostridium -- Physiological aspects, Actin -- Properties, Ribose -- Properties, Microbiological chemistry -- Research, Crystals -- Structure, Crystals -- Evaluation, Protein research, Science and technology
Abstract

The ADP-ribosylating toxins (ADPRTs) produced by pathogenic bacteria modify intracellular protein and affect eukaryotic cell function. Actin-specific ADPRTs (including Clostridium perfringens L-toxin and Clostridium botulinum C2 toxin) ADP-ribosylate G-actin at Arg-177, leading to disorganization of the cytoskeleton and cell death. Although the structures of many actin-specific ADPRTs are available, the mechanisms underlying actin recognition and selective ADP-ribosylation of Arg-177 remain unknown. Here we report the crystal structure of actin-la in complex with the nonhydrolyzable NAD analog [beta]TAD at 2.8 A resolution. The structure indicates that la recognizes actin via five loops around NAD: loop I (Tyr-60--Tyr-62 in the N domain), loop II (active-site loop), loop III, loop IV (PN loop), and loop V (ADP-ribosylating turn-turn loop). We used site-directed mutagenesis to confirm that loop I on the N domain and loop II are essential for the ADP-ribosyltransferase activity. Furthermore, we revealed that Glu-378 on the EXE loop is in close proximity to Arg-177 in actin, and we proposed that the ADP-ribosylation of Arg-177 proceeds by an SN1 reaction via first an oxocarbenium ion intermediate and second a cationic intermediate by alleviating the strained conformation of the first oxocarbenium ion. Our results suggest a common reaction mechanism for ADPRTs. Moreover, the structure might be of use in rational drug design to block toxin-substrate recognition. complex | crystal structure | protein recognition

Published
2008

29. Asymmetric Total Syntheses and Structure Revisions of Eurotiumide A and Eurotiumide B, and Evaluation of their Fluorescent Properties as Natural Probes

Author

Nakayama, Atsushi, Sato, Hideo, Karanjit, Sangita, Hayashi, Naoki, Oda, Masataka, and Namba, Kosuke

Subjects
natural products, fluorescent probes, total synthesis
Abstract

Asymmetric total syntheses and structure revisions of dihydroisocoumarin-type natural products, eurotiumide A and eurotiumide B have been described. The key features of these total syntheses are the asymmetric Shi epoxidation, regio and stereo-selective epoxide opening, C1 insertion/lactonization cascade reaction for constructing 4-methoxyisochroman-1-one skeleton. We confirmed the structures and configurations of eurotiumide A and B on the basis of X-ray crystallographic analysis of the key intermediate, and revealed that eurotiumide A and B have cis and trans configurations at H3/H4 positions, which are the opposite relationship of the stereochemistry from the previous report, respectively. The absolute configurations of them are also determined. These natural products exhibited highly fluorescence in several solvents with large Stokes shifts involving the excited-state intramolecular proton transfer mechanism, which is supported by time-dependent density functional theory. Eurotiumide A also emitted fluorescence in Bacillus cereus.

Published
2018

35. Clostridium perfringens alpha-toxin induces rabbit neutrophil adhesion

Author

Ochi, Sadayuki, Miyawaki, Toshihumi, Matsuda, Hisaaki, Oda, Masataka, Nagahama, Masahiro, and Sakurai, Jun

Subjects
Neutrophils -- Physiological aspects, Cell adhesion molecules -- Physiological aspects, Phospholipids -- Physiological aspects, Protein kinases -- Physiological aspects, Fibrinogen -- Physiological aspects, Biological sciences
Abstract

Results indicate that rabbit neutrophils adhere to the matrix by alpha-toxin stimulation with concomitant oxygen production facilitated by diacylglycerol formed via phospholipid metabolism and protein kinase C activation.

Published
2002

36. Effects of Erythromycin on Osteoclasts and Bone Resorption via DEL-1 Induction in Mice

Author

Tamura, Hikaru, primary, Maekawa, Tomoki, additional, Domon, Hisanori, additional, Hiyoshi, Takumi, additional, Hirayama, Satoru, additional, Isono, Toshihito, additional, Sasagawa, Karin, additional, Yonezawa, Daisuke, additional, Takahashi, Naoki, additional, Oda, Masataka, additional, Maeda, Takeyasu, additional, Tabeta, Koichi, additional, and Terao, Yutaka, additional

Published
2021
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39. Erythromycin inhibits neutrophilic inflammation and mucosal disease by upregulating DEL-1

Author

Maekawa, Tomoki, primary, Tamura, Hikaru, additional, Domon, Hisanori, additional, Hiyoshi, Takumi, additional, Isono, Toshihito, additional, Yonezawa, Daisuke, additional, Hayashi, Naoki, additional, Takahashi, Naoki, additional, Tabeta, Koichi, additional, Maeda, Takeyasu, additional, Oda, Masataka, additional, Ziogas, Athanasios, additional, Alexaki, Vasileia Ismini, additional, Chavakis, Triantafyllos, additional, Terao, Yutaka, additional, and Hajishengallis, George, additional

Published
2020
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41. Lipopolysaccharide-Deficient Acinetobacter baumannii Due to Colistin Resistance Is Killed by Neutrophil-Produced Lysozyme

Author

Kamoshida, Go, primary, Akaji, Takuya, additional, Takemoto, Norihiko, additional, Suzuki, Yusuke, additional, Sato, Yoshinori, additional, Kai, Daichi, additional, Hibino, Taishi, additional, Yamaguchi, Daiki, additional, Kikuchi-Ueda, Takane, additional, Nishida, Satoshi, additional, Unno, Yuka, additional, Tansho-Nagakawa, Shigeru, additional, Ubagai, Tsuneyuki, additional, Miyoshi-Akiyama, Tohru, additional, Oda, Masataka, additional, and Ono, Yasuo, additional

Published
2020
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43. Additional file 9 of Sulfated vizantin causes detachment of biofilms composed mainly of the genus Streptococcus without affecting bacterial growth and viability

Author

Hasegawa, Taisuke, Takenaka, Shoji, Oda, Masataka, Domon, Hisanori, Hiyoshi, Takumi, Sasagawa, Karin, Ohsumi, Tatsuya, Hayashi, Naoki, Okamoto, Yasuko, Yamamoto, Hirofumi, Ohshima, Hayato, Terao, Yutaka, and Noiri, Yuichiro

Abstract

Additional file 9: Table S4 Primer sequences used for analyzing the genes associated with bacterial adhesion by real-time PCR.

Published
2020
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44. Additional file 8 of Sulfated vizantin causes detachment of biofilms composed mainly of the genus Streptococcus without affecting bacterial growth and viability

Author

Hasegawa, Taisuke, Takenaka, Shoji, Oda, Masataka, Domon, Hisanori, Hiyoshi, Takumi, Sasagawa, Karin, Ohsumi, Tatsuya, Hayashi, Naoki, Okamoto, Yasuko, Yamamoto, Hirofumi, Ohshima, Hayato, Terao, Yutaka, and Noiri, Yuichiro

Subjects
biochemical phenomena, metabolism, and nutrition
Abstract

Additional file 8: Table S3 Primer sequences used for analyzing the genes associated with biofilm formation by real-time PCR.

Published
2020
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45. Additional file 6 of Sulfated vizantin causes detachment of biofilms composed mainly of the genus Streptococcus without affecting bacterial growth and viability

Author

Hasegawa, Taisuke, Takenaka, Shoji, Oda, Masataka, Domon, Hisanori, Hiyoshi, Takumi, Sasagawa, Karin, Ohsumi, Tatsuya, Hayashi, Naoki, Okamoto, Yasuko, Yamamoto, Hirofumi, Ohshima, Hayato, Terao, Yutaka, and Noiri, Yuichiro

Abstract

Additional file 6: Table S1 Two-step PCR protocol used in this study.

Published
2020
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46. Additional file 3 of Sulfated vizantin causes detachment of biofilms composed mainly of the genus Streptococcus without affecting bacterial growth and viability

Author

Hasegawa, Taisuke, Takenaka, Shoji, Oda, Masataka, Domon, Hisanori, Hiyoshi, Takumi, Sasagawa, Karin, Ohsumi, Tatsuya, Hayashi, Naoki, Okamoto, Yasuko, Yamamoto, Hirofumi, Ohshima, Hayato, Terao, Yutaka, and Noiri, Yuichiro

Subjects
fungi, human activities
Abstract

Additional file 3:Fig. S2 Production of inflammatory cytokines in THP-1 cells following Viz-S treatment (n = 5). *p

Published
2020
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47. Synthesis and Antimicrobial Evaluation of Side-Chain Derivatives based on Eurotiumide A

Author

Nakayama, Atsushi, Sato, Hideo, Nakamura, Tenta, Hamada, Mai, Nagano, Shuji, Kameyama, Shuhei, Furue, Yui, Hayashi, Naoki, Kamoshida, Go, Karanjit, Sangita, Oda, Masataka, Namba, Kosuke, Nakayama, Atsushi, Sato, Hideo, Nakamura, Tenta, Hamada, Mai, Nagano, Shuji, Kameyama, Shuhei, Furue, Yui, Hayashi, Naoki, Kamoshida, Go, Karanjit, Sangita, Oda, Masataka, and Namba, Kosuke

Abstract

Side-chain derivatives of eurotiumide A, a dihydroisochroman-type natural product, have been synthesized and their antimicrobial activities described. Sixteen derivatives were synthesized from a key intermediate of the total synthesis of eurotiumide A, and their antimicrobial activities against two Gram-positive bacteria, methicillin-susceptible and methicillin-resistant Staphylococcus aureus (MSSA and MRSA), and a Gram-negative bacterium, Porphyromonas gingivalis, were evaluated. The results showed that derivatives having an iodine atom on their aromatic ring instead of the prenyl moiety displayed better antimicrobial activity than eurotiumide A against MSSA and P. gingivalis. Moreover, we discovered that a derivative with an isopentyl side chain, which is a hydrogenated product of eurotiumide A, is the strongest antimicrobial agent against all three strains, including MRSA.

Published
2020

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