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Fló M, Pellizza L, Durán R, Alvarez B, Fernández C. The monodomain Kunitz protein EgKU-7 from the dog tapeworm Echinococcus granulosus is a high-affinity trypsin inhibitor with two interaction sites. Biochem J 2024; 481:717-739. [PMID: 38752933 DOI: 10.1042/bcj20230514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 05/10/2024] [Accepted: 05/16/2024] [Indexed: 06/01/2024]
Abstract
Typical Kunitz proteins (I2 family of the MEROPS database, Kunitz-A family) are metazoan competitive inhibitors of serine peptidases that form tight complexes of 1:1 stoichiometry, mimicking substrates. The cestode Echinococcus granulosus, the dog tapeworm causing cystic echinococcosis in humans and livestock, encodes an expanded family of monodomain Kunitz proteins, some of which are secreted to the dog host interface. The Kunitz protein EgKU-7 contains, in addition to the Kunitz domain with the anti-peptidase loop comprising a critical arginine, a C-terminal extension of ∼20 amino acids. Kinetic, electrophoretic, and mass spectrometry studies using EgKU-7, a C-terminally truncated variant, and a mutant in which the critical arginine was substituted by alanine, show that EgKU-7 is a tight inhibitor of bovine and canine trypsins with the unusual property of possessing two instead of one site of interaction with the peptidases. One site resides in the anti-peptidase loop and is partially hydrolyzed by bovine but not canine trypsins, suggesting specificity for the target enzymes. The other site is located in the C-terminal extension. This extension can be hydrolyzed in a particular arginine by cationic bovine and canine trypsins but not by anionic canine trypsin. This is the first time to our knowledge that a monodomain Kunitz-A protein is reported to have two interaction sites with its target. Considering that putative orthologs of EgKU-7 are present in other cestodes, our finding unveils a novel piece in the repertoire of peptidase-inhibitor interactions and adds new notes to the evolutionary host-parasite concerto.
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Affiliation(s)
- Martín Fló
- Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Leonardo Pellizza
- Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Rosario Durán
- Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo and Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Beatriz Alvarez
- Laboratorio de Enzimología, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Cecilia Fernández
- Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, Uruguay
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Sivangi KB, Amilpur S, Dasari CM. ReGen-DTI: A novel generative drug target interaction model for predicting potential drug candidates against SARS-COV2. Comput Biol Chem 2023; 106:107927. [PMID: 37499436 DOI: 10.1016/j.compbiolchem.2023.107927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 07/29/2023]
Abstract
Covid-19 has caused massive numbers of infections and fatalities globally. In response, there has been a large-scale experimental and computational research effort to study and develop drugs. Towards this, Deep learning techniques are used for the generation of potential novel drug candidates that are proven to be effective against exploring large molecular search spaces. Recent advances in reinforcement learning in conjunction with generative techniques has proven to be a promising field in the area of drug discovery. In this regard, we propose a generative drug discovery approach using reinforcement techniques for sampling novel molecules that bind to the main protease of SARS-COV2. The generative method reported significant validity scores for the generated novel molecules and captured the underlying features of the training molecules. Further, the model is fine-tuned on existing re-purposed molecules which are active towards specific target proteins based on similarity metrics. Upon fine tuning the model generated 92.71% valid, 93.55% unique, and 100% novel molecules. Unlike previous methods which are dependent on docking procedures, we proposed a deep learning based novel drug target interaction (DTI) model to find the binding affinity between candidate molecules and target protease sequence. Finally, the binding affinity of the generated molecules is predicted against the 3CLPro main protease by using the proposed DTI model. Most of the generated molecules have shown binding affinity scores <100 nM (lower the better), which are significantly better compared to the existing commercial drugs including Remdesevir.
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Affiliation(s)
- Kaushik Bhargav Sivangi
- Indian Institute of Information Technology, Sri City, Chittoor, 517646, Andhra Pradesh, India
| | - Santhosh Amilpur
- Indian Institute of Information Technology, Sri City, Chittoor, 517646, Andhra Pradesh, India
| | - Chandra Mohan Dasari
- Indian Institute of Information Technology, Sri City, Chittoor, 517646, Andhra Pradesh, India.
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3
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Maz TG, Caliskan HB, Capan I, Caliskan B, Özçelik B, Banoglu E. Design, Synthesis and Evaluation of Aryl‐Tailored Oxadiazole‐thiones as New Urease Inhibitors. ChemistrySelect 2023. [DOI: 10.1002/slct.202204449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Affiliation(s)
- Tugce Gur Maz
- Faculty of Pharmacy Department of Pharmaceutical Chemistry Gazi University 06560 Ankara Turkey
| | - H. Burak Caliskan
- Faculty of Engineering Department of Biomedical Engineering TOBB ETU Economy and Technology University 06560 Ankara Turkey
| | - Irfan Capan
- Technical Science Vocational College Department of Material and Material Processing Technologies Gazi University 06560 Ankara Turkey
| | - Burcu Caliskan
- Faculty of Pharmacy Department of Pharmaceutical Chemistry Gazi University 06560 Ankara Turkey
| | - Berrin Özçelik
- Faculty of Pharmacy Department of Pharmaceutical Microbiology Gazi University 06560 Ankara Turkey
| | - Erden Banoglu
- Faculty of Pharmacy Department of Pharmaceutical Chemistry Gazi University 06560 Ankara Turkey
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4
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Austin MJ, Schunk H, Watkins C, Ling N, Chauvin J, Morton L, Rosales AM. Fluorescent Peptomer Substrates for Differential Degradation by Metalloproteases. Biomacromolecules 2022; 23:4909-4923. [PMID: 36269900 DOI: 10.1021/acs.biomac.2c01077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proteases, especially MMPs, are attractive biomarkers given their central role in both physiological and pathological processes. Distinguishing MMP activity with degradable substrates, however, is a difficult task due to overlapping substrate specificity profiles. Here, we developed a system of peptomers (peptide-peptoid hybrids) to probe the impact of non-natural residues on MMP specificity for an MMP peptide consensus sequence. Peptoids are non-natural, N-substituted glycines with a large side-chain diversity. Given the presence of a hallmark proline residue in the P3 position of MMP consensus sequences, we hypothesized that peptoids may offer N-substituted alternatives to generate differential interactions with MMPs. To investigate this hypothesis, peptomer substrates were exposed to five different MMPs, as well as bacterial collagenase, and monitored by fluorescence resonance energy transfer and liquid chromatography-mass spectrometry to determine the rate of cleavage and the composition of degraded fragments, respectively. We found that peptoid residues are well tolerated in the P3 and P3' substrate sites and that the identity of the peptoid in these sites displays a moderate influence on the rate of cleavage. However, peptoid residues were even better tolerated in the P1 substrate site where activity was more strongly correlated with side-chain identity than side-chain position. All MMPs explored demonstrated similar trends in specificity for the peptomers but exhibited different degrees of variability in proteolytic rate. These kinetic profiles served as "fingerprints" for the proteases and yielded separation by multivariate data analysis. To further demonstrate the practical application of this tunability in degradation kinetics, peptomer substrates were tethered into hydrogels and released over distinct timescales. Overall, this work represents a significant step toward the design of probes that maximize differential MMP behavior and presents design rules to tune degradation kinetics with peptoid substitutions, which has promising implications for diagnostic and prognostic applications using array-based sensors.
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Affiliation(s)
- Mariah J Austin
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas78712, United States
| | - Hattie Schunk
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas78712, United States.,Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas78712, United States
| | - Carolyn Watkins
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas78712, United States
| | - Natalie Ling
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas78712, United States
| | - Jeremy Chauvin
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas78712, United States
| | - Logan Morton
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas78712, United States
| | - Adrianne M Rosales
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas78712, United States
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5
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Cheng H, Orr STM, Bailey S, Brooun A, Chen P, Deal JG, Deng YL, Edwards MP, Gallego GM, Grodsky N, Huang B, Jalaie M, Kaiser S, Kania RS, Kephart SE, Lafontaine J, Ornelas MA, Pairish M, Planken S, Shen H, Sutton S, Zehnder L, Almaden CD, Bagrodia S, Falk MD, Gukasyan HJ, Ho C, Kang X, Kosa RE, Liu L, Spilker ME, Timofeevski S, Visswanathan R, Wang Z, Meng F, Ren S, Shao L, Xu F, Kath JC. Structure-Based Drug Design and Synthesis of PI3Kα-Selective Inhibitor (PF-06843195). J Med Chem 2020; 64:644-661. [PMID: 33356246 DOI: 10.1021/acs.jmedchem.0c01652] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The phosphoinositide 3-kinase (PI3K)/mammalian target of rapamycin (mTOR) signaling pathway is a frequently dysregulated pathway in human cancer, and PI3Kα is one of the most frequently mutated kinases in human cancer. A PI3Kα-selective inhibitor may provide the opportunity to spare patients the side effects associated with broader inhibition of the class I PI3K family. Here, we describe our efforts to discover a PI3Kα-selective inhibitor by applying structure-based drug design (SBDD) and computational analysis. A novel series of compounds, exemplified by 2,2-difluoroethyl (3S)-3-{[2'-amino-5-fluoro-2-(morpholin-4-yl)-4,5'-bipyrimidin-6-yl]amino}-3-(hydroxymethyl)pyrrolidine-1-carboxylate (1) (PF-06843195), with high PI3Kα potency and unique PI3K isoform and mTOR selectivity were discovered. We describe here the details of the design and synthesis program that lead to the discovery of 1.
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Affiliation(s)
- Hengmiao Cheng
- La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Suvi T M Orr
- La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Simon Bailey
- La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Alexei Brooun
- La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Ping Chen
- La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Judith G Deal
- La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Yali L Deng
- La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Martin P Edwards
- La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Gary M Gallego
- La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Neil Grodsky
- La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Buwen Huang
- La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Mehran Jalaie
- La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Stephen Kaiser
- La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Robert S Kania
- La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Susan E Kephart
- La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Jennifer Lafontaine
- La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Martha A Ornelas
- La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Mason Pairish
- La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Simon Planken
- La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Hong Shen
- La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Scott Sutton
- La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Luke Zehnder
- La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Chau D Almaden
- La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Shubha Bagrodia
- La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Matthew D Falk
- La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Hovhannes J Gukasyan
- La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Caroline Ho
- La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Xiaolin Kang
- La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Rachel E Kosa
- La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Ling Liu
- La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Mary E Spilker
- La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Sergei Timofeevski
- La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Ravi Visswanathan
- La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Zhenxiong Wang
- La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States
| | - Fanxiu Meng
- Wuxi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Shijian Ren
- Wuxi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Li Shao
- Wuxi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Feng Xu
- Wuxi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - John C Kath
- La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States
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6
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Reytor Gonzalez ML, Alonso Del Rivero Antigua M. Reviewing the experimental and mathematical factors involved in tight binding inhibitors K i values determination: The bi-functional protease inhibitor SmCI as a test model. Biochimie 2020; 181:86-95. [PMID: 33221375 DOI: 10.1016/j.biochi.2020.11.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/25/2020] [Accepted: 11/14/2020] [Indexed: 10/23/2022]
Abstract
Different methodologies for determining the dissociation equilibrium constant (Ki) of protein tight binding inhibitors are frequently found in the scientific literature. Taking into account that the Ki value is the main parameter characterizing the inhibition strength, its determination often represents the first step during the characterization of a potential drug. The purpose of this review is to summarize the current information related to tight binding inhibitors Ki values determination and discuss about the importance of different factors as the enzyme concentration, the inhibitor concentration dilution series, the enzyme-inhibitor incubation time and the dose-response data mathematical fitting. For this aim, the bi-functional SmCI protease inhibitor is used as a tool for exemplifying the experimental and mathematical steps performed during tight binding inhibitors Ki values determination. In addition, the natural and the different recombinant forms of SmCI were used to go deeply into the comparison of some mathematic approaches that are frequently used in the literature. Finally, other biochemical techniques that could be potentially used for tight binding inhibitors Ki values determination are also commented.
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Affiliation(s)
- Mey Ling Reytor Gonzalez
- Center for Protein Studies, Faculty of Biology, University of Havana, Cuba.Calle 25, #455, Vedado, Ciudad de La Habana, CP 104000
| | - Maday Alonso Del Rivero Antigua
- Center for Protein Studies, Faculty of Biology, University of Havana, Cuba.Calle 25, #455, Vedado, Ciudad de La Habana, CP 104000.
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7
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Nagy ZA, Szakács D, Boros E, Héja D, Vígh E, Sándor N, Józsi M, Oroszlán G, Dobó J, Gál P, Pál G. Ecotin, a microbial inhibitor of serine proteases, blocks multiple complement dependent and independent microbicidal activities of human serum. PLoS Pathog 2019; 15:e1008232. [PMID: 31860690 PMCID: PMC6944378 DOI: 10.1371/journal.ppat.1008232] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 01/06/2020] [Accepted: 11/21/2019] [Indexed: 12/20/2022] Open
Abstract
Ecotin is a serine protease inhibitor produced by hundreds of microbial species, including pathogens. Here we show, that ecotin orthologs from Escherichia coli, Yersinia pestis, Pseudomonas aeruginosa and Leishmania major are potent inhibitors of MASP-1 and MASP-2, the two key activator proteases of the complement lectin pathway. Factor D is the key activator protease of another complement activation route, the alternative pathway. We show that ecotin inhibits MASP-3, which is the sole factor D activator in resting human blood. In pathway-specific ELISA tests, we found that all ecotin orthologs are potent lectin pathway inhibitors, and at high concentration, they block the alternative pathway as well. In flow cytometry experiments, we compared the extent of complement-mediated opsonization and lysis of wild-type and ecotin-knockout variants of two E. coli strains carrying different surface lipopolysaccharides. We show, that endogenous ecotin provides significant protections against these microbicidal activities for both bacteria. By using pathway specific complement inhibitors, we detected classical-, lectin- and alternative pathway-driven complement attack from normal serum, with the relative contributions of the activation routes depending on the lipopolysaccharide type. Moreover, in cell proliferation experiments we observed an additional, complement-unrelated antimicrobial activity exerted by heat-inactivated serum. While ecotin-knockout cells are highly vulnerable to these activities, endogenous ecotin of wild-type bacteria provides complete protection against the lectin pathway-related and the complement-unrelated attack, and partial protection against the alternative pathway-related damage. In all, ecotin emerges as a potent, versatile self-defense tool that blocks multiple antimicrobial activities of the serum. These findings suggest that ecotin might be a relevant antimicrobial drug target. Bloodstream infections are major cause of morbidity and mortality in many countries around the globe. As the number of multi-drug resistant pathogenic strains is growing, it is urgent to identify their virulence factors and unveil the corresponding mechanisms of action that enable the pathogen to avoid potent immune response. A microbial inhibitor of serine proteases, ecotin was previously implicated in protecting various pathogenic bacteria and eukaryotic Leishmania species against the host immune system by inhibiting leukocyte elastase. However, the interaction of ecotin with the complement system, which provides a first line defense against pathogens, remained unexplored. We found that ecotin blocks activation of the complement lectin pathway by inhibiting its key activator enzymes, MASP-1 and MASP-2. Furthermore, by inhibiting MASP-3, ecotin also disrupts a fundamental link between the lectin- and the alternative pathways. We provide evidence that E. coli cells devoid of ecotin are extremely vulnerable to complement-mediated lysis and they are also potently killed by some complement-independent antimicrobial factors of human serum. These findings could explain the observations of other research groups reporting that ecotin is crucial for the survival of pathogenic microbes in the host. Our results therefore also highlight ecotin as a potential target of future antimicrobial therapies.
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Affiliation(s)
- Zoltán Attila Nagy
- Department of Biochemistry, ELTE, Eötvös Loránd University, Budapest, Hungary
| | - Dávid Szakács
- Department of Biochemistry, ELTE, Eötvös Loránd University, Budapest, Hungary
| | - Eszter Boros
- Department of Biochemistry, ELTE, Eötvös Loránd University, Budapest, Hungary
| | - Dávid Héja
- Department of Biochemistry, ELTE, Eötvös Loránd University, Budapest, Hungary
- Department of Nephrology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Eszter Vígh
- Department of Biochemistry, ELTE, Eötvös Loránd University, Budapest, Hungary
| | - Noémi Sándor
- Department of Immunology, ELTE, Eötvös Loránd University, Budapest, Hungary
| | - Mihály Józsi
- Department of Immunology, ELTE, Eötvös Loránd University, Budapest, Hungary
| | - Gábor Oroszlán
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - József Dobó
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Péter Gál
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Gábor Pál
- Department of Biochemistry, ELTE, Eötvös Loránd University, Budapest, Hungary
- * E-mail:
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8
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Noell SE, Giovannoni SJ. SAR11 bacteria have a high affinity and multifunctional glycine betaine transporter. Environ Microbiol 2019; 21:2559-2575. [PMID: 31090982 DOI: 10.1111/1462-2920.14649] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 05/06/2019] [Indexed: 11/29/2022]
Abstract
Marine bacterioplankton face stiff competition for limited nutrient resources. SAR11, a ubiquitous clade of very small and highly abundant Alphaproteobacteria, are known to devote much of their energy to synthesizing ATP-binding cassette periplasmic proteins that bind substrates. We hypothesized that their small size and relatively large periplasmic space might enable them to outcompete other bacterioplankton for nutrients. Using uptake experiments with 14 C-glycine betaine, we discovered that two strains of SAR11, Candidatus Pelagibacter sp. HTCC7211 and Cand. P. ubique HTCC1062, have extraordinarily high affinity for glycine betaine (GBT), with half-saturation (K s ) values around 1 nM and specific affinity values between 8 and 14 L mg cell-1 h-1 . Competitive inhibition studies indicated that the GBT transporters in these strains are multifunctional, transporting multiple substrates in addition to GBT. Both strains could use most of the transported compounds for metabolism and ATP production. Our findings indicate that Pelagibacter cells are primarily responsible for the high affinity and multifunctional GBT uptake systems observed in seawater. Maximization of whole-cell affinities may enable these organisms to compete effectively for nutrients during periods when the gross transport capacity of the heterotrophic plankton community exceeds the supply, depressing ambient concentrations.
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Affiliation(s)
- Stephen E Noell
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
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9
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Pichon MM, Stauffert F, Bodlenner A, Compain P. Tight-binding inhibition of jack bean α-mannosidase by glycoimidazole clusters. Org Biomol Chem 2019; 17:5801-5817. [DOI: 10.1039/c9ob00826h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Examples of multimeric inhibitors displaying tight binding inhibition of a carbohydrate-processing enzyme are presented.
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Affiliation(s)
- Maëva M. Pichon
- Laboratoire d'Innovation Moléculaire et Applications (LIMA)
- Univ. de Strasbourg
- Univ. de Haute-Alsace
- CNRS (UMR 7042)
- Equipe de Synthèse Organique et Molécules Bioactives (SYBIO)
- ECPM
- 67000 Strasbourg
| | - Fabien Stauffert
- Laboratoire d'Innovation Moléculaire et Applications (LIMA)
- Univ. de Strasbourg
- Univ. de Haute-Alsace
- CNRS (UMR 7042)
- Equipe de Synthèse Organique et Molécules Bioactives (SYBIO)
- ECPM
- 67000 Strasbourg
| | - Anne Bodlenner
- Laboratoire d'Innovation Moléculaire et Applications (LIMA)
- Univ. de Strasbourg
- Univ. de Haute-Alsace
- CNRS (UMR 7042)
- Equipe de Synthèse Organique et Molécules Bioactives (SYBIO)
- ECPM
- 67000 Strasbourg
| | - Philippe Compain
- Laboratoire d'Innovation Moléculaire et Applications (LIMA)
- Univ. de Strasbourg
- Univ. de Haute-Alsace
- CNRS (UMR 7042)
- Equipe de Synthèse Organique et Molécules Bioactives (SYBIO)
- ECPM
- 67000 Strasbourg
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10
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Lee Y, Park HG, Kim V, Cho MA, Kim H, Ho TH, Cho KS, Lee IS, Kim D. Inhibitory effect of α-terpinyl acetate on cytochrome P450 2B6 enzymatic activity. Chem Biol Interact 2018; 289:90-97. [PMID: 29723517 DOI: 10.1016/j.cbi.2018.04.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/16/2018] [Accepted: 04/25/2018] [Indexed: 10/17/2022]
Abstract
Human cytochrome P450 2B6 is an important hepatic enzyme for the metabolism of xenobiotics and clinical drugs. Recently, more attention has been paid to P450 2B6 because of the increasing number of drugs it metabolizes. It has been known to interact with terpenes, the major constituents of the essential oils used for various medicinal purposes. In this study, the effect of monoterpenes on P450 2B6 catalytic activity was investigated. Recombinant P450 2B6 was expressed in Escherichia coli and purified using Ni-affinity chromatography. The purified P450 2B6 enzyme displayed bupropion hydroxylation activity in gas-mass spectrometry (GC-MS) analysis with a kcat of 0.5 min-1 and a Km of 47 μM. Many terpenes displayed the type I binding spectra to purified P450 2B6 enzyme and α-terpinyl acetate showed strong binding affinity with a Kd value of 5.4 μM. In GC-MS analysis, P450 2B6 converted α-terpinyl acetate to a putative oxidative product. The bupropion hydroxylation activity of P450 2B6 was inhibited by α-terpinyl acetate and its IC50 value was 10.4 μM α-Terpinyl acetate was determined to be a competitive inhibitor of P450 2B6 with a Ki value of 7.6 μM. The molecular docking model of the binding site of the P450 2B6 complex with α-terpinyl acetate was constructed. It showed the tight binding of α-terpinyl acetate in the active site of P450 2B6, which suggests that it could be a competitive substrate for P450 2B6.
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Affiliation(s)
- Yejin Lee
- Department of Biological Sciences, Konkuk University, Seoul 05025 Republic of Korea
| | - Hyoung-Goo Park
- Department of Biological Sciences, Konkuk University, Seoul 05025 Republic of Korea
| | - Vitchan Kim
- Department of Biological Sciences, Konkuk University, Seoul 05025 Republic of Korea
| | - Myung-A Cho
- Department of Biological Sciences, Konkuk University, Seoul 05025 Republic of Korea
| | - Harim Kim
- Department of Biological Sciences, Konkuk University, Seoul 05025 Republic of Korea
| | - Thien-Hoang Ho
- Department of Biological Sciences, Konkuk University, Seoul 05025 Republic of Korea
| | - Kyoung Sang Cho
- Department of Biological Sciences, Konkuk University, Seoul 05025 Republic of Korea
| | - Im-Soon Lee
- Department of Biological Sciences, Konkuk University, Seoul 05025 Republic of Korea
| | - Donghak Kim
- Department of Biological Sciences, Konkuk University, Seoul 05025 Republic of Korea.
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11
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Roellecke K, Jäger VD, Gyurov VH, Kowalski JP, Mielke S, Rettie AE, Hanenberg H, Wiek C, Girhard M. Ligand characterization of CYP4B1 isoforms modified for high-level expression in Escherichia coli and HepG2 cells. Protein Eng Des Sel 2017; 30:205-216. [PMID: 28073960 PMCID: PMC5421619 DOI: 10.1093/protein/gzw075] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 12/06/2016] [Indexed: 01/25/2023] Open
Abstract
Human CYP4B1, a cytochrome P450 monooxygenase predominantly expressed in the lung, inefficiently metabolizes classical CYP4B1 substrates, such as the naturally occurring furan pro-toxin 4-ipomeanol (4-IPO). Highly active animal forms of the enzyme convert 4-IPO to reactive alkylating metabolite(s) that bind(s) to cellular macromolecules. By substitution of 13 amino acids, we restored the enzymatic activity of human CYP4B1 toward 4-IPO and this modified cDNA is potentially valuable as a suicide gene for adoptive T-cell therapies. In order to find novel pro-toxins, we tested numerous furan analogs in in vitro cell culture cytotoxicity assays by expressing the wild-type rabbit and variants of human CYP4B1 in human liver-derived HepG2 cells. To evaluate the CYP4B1 substrate specificities and furan analog catalysis, we optimized the N-terminal sequence of the CYP4B1 variants by modification/truncation and established their heterologous expression in Escherichia coli (yielding 70 and 800 nmol·l-1 of recombinant human and rabbit enzyme, respectively). Finally, spectral binding affinities and oxidative metabolism of the furan analogs by the purified recombinant CYP4B1 variants were analyzed: the naturally occurring perilla ketone was found to be the tightest binder to CYP4B1, but also the analog that was most extensively metabolized by oxidative processes to numerous non-reactive reaction products.
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Affiliation(s)
- Katharina Roellecke
- Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Vera D Jäger
- Institute of Biochemistry, Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Veselin H Gyurov
- Institute of Biochemistry, Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - John P Kowalski
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, WA 98195, USA
| | - Stephanie Mielke
- Institute of Biochemistry, Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Allan E Rettie
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, WA 98195, USA
| | - Helmut Hanenberg
- Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich-Heine University, 40225 Düsseldorf, Germany.,Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, 45122 Essen, Germany
| | - Constanze Wiek
- Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Marco Girhard
- Institute of Biochemistry, Heinrich-Heine University, 40225 Düsseldorf, Germany
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12
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Wilch C, Talbiersky P, Berchner‐Pfannschmidt U, Schaller T, Kirsch M, Klärner F, Schrader T. Molecular Tweezers Inhibit PARP‐1 by a New Mechanism. European J Org Chem 2017. [DOI: 10.1002/ejoc.201601596] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Constanze Wilch
- Faculty of Chemistry University of Duisburg‐Essen Universitätsstr. 7 45117 Essen Germany
| | - Peter Talbiersky
- Faculty of Chemistry University of Duisburg‐Essen Universitätsstr. 7 45117 Essen Germany
| | | | - Torsten Schaller
- Faculty of Chemistry University of Duisburg‐Essen Universitätsstr. 7 45117 Essen Germany
| | - Michael Kirsch
- Institute of Physiological Chemistry University Hospital Essen Hufelandstr. 55 45122 Essen Germany
| | - Frank‐Gerrit Klärner
- Faculty of Chemistry University of Duisburg‐Essen Universitätsstr. 7 45117 Essen Germany
| | - Thomas Schrader
- Faculty of Chemistry University of Duisburg‐Essen Universitätsstr. 7 45117 Essen Germany
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13
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Hohl M, Stintzi A, Schaller A. A novel subtilase inhibitor in plants shows structural and functional similarities to protease propeptides. J Biol Chem 2017; 292:6389-6401. [PMID: 28223360 DOI: 10.1074/jbc.m117.775445] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 02/13/2017] [Indexed: 12/24/2022] Open
Abstract
The propeptides of subtilisin-like serine proteinases (subtilases, SBTs) serve dual functions as intramolecular chaperones that are required for enzyme folding and as inhibitors of the mature proteases. SBT propeptides are homologous to the I9 family of protease inhibitors that have only been described in fungi. Here we report the identification and characterization of subtilisin propeptide-like inhibitor 1 (SPI-1) from Arabidopsis thaliana Sequence similarity and the shared β-α-β-β-α-β core structure identified SPI-1 as a member of the I9 inhibitor family and as the first independent I9 inhibitor in higher eukaryotes. SPI-1 was characterized as a high-affinity, tight-binding inhibitor of Arabidopsis subtilase SBT4.13 with Kd and Ki values in the picomolar range. SPI-1 acted as a stable inhibitor of SBT4.13 over the physiologically relevant range of pH, and its inhibitory profile included many other SBTs from plants but not bovine chymotrypsin or bacterial subtilisin A. Upon binding to SBT4.13, the C-terminal extension of SPI-1 was proteolytically cleaved. The last four amino acids at the newly formed C terminus of SPI-1 matched both the cleavage specificity of SBT4.13 and the consensus sequence of Arabidopsis SBTs at the junction of the propeptide with the catalytic domain. The data suggest that the C terminus of SPI-1 acts as a competitive inhibitor of target proteases as it remains bound to the active site in a product-like manner. SPI-1 thus resembles SBT propeptides with respect to its mode of protease inhibition. However, in contrast to SBT propeptides, SPI-1 could not substitute as a folding assistant for SBT4.13.
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Affiliation(s)
- Mathias Hohl
- From the Institute of Plant Physiology and Biotechnology, University of Hohenheim, D-70593 Stuttgart, Germany
| | - Annick Stintzi
- From the Institute of Plant Physiology and Biotechnology, University of Hohenheim, D-70593 Stuttgart, Germany
| | - Andreas Schaller
- From the Institute of Plant Physiology and Biotechnology, University of Hohenheim, D-70593 Stuttgart, Germany
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14
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Fló M, Margenat M, Pellizza L, Graña M, Durán R, Báez A, Salceda E, Soto E, Alvarez B, Fernández C. Functional diversity of secreted cestode Kunitz proteins: Inhibition of serine peptidases and blockade of cation channels. PLoS Pathog 2017; 13:e1006169. [PMID: 28192542 PMCID: PMC5325619 DOI: 10.1371/journal.ppat.1006169] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 02/24/2017] [Accepted: 01/06/2017] [Indexed: 01/01/2023] Open
Abstract
We previously reported a multigene family of monodomain Kunitz proteins from Echinococcus granulosus (EgKU-1-EgKU-8), and provided evidence that some EgKUs are secreted by larval worms to the host interface. In addition, functional studies and homology modeling suggested that, similar to monodomain Kunitz families present in animal venoms, the E. granulosus family could include peptidase inhibitors as well as channel blockers. Using enzyme kinetics and whole-cell patch-clamp, we now demonstrate that the EgKUs are indeed functionally diverse. In fact, most of them behaved as high affinity inhibitors of either chymotrypsin (EgKU-2-EgKU-3) or trypsin (EgKU-5-EgKU-8). In contrast, the close paralogs EgKU-1 and EgKU-4 blocked voltage-dependent potassium channels (Kv); and also pH-dependent sodium channels (ASICs), while showing null (EgKU-1) or marginal (EgKU-4) peptidase inhibitory activity. We also confirmed the presence of EgKUs in secretions from other parasite stages, notably from adult worms and metacestodes. Interestingly, data from genome projects reveal that at least eight additional monodomain Kunitz proteins are encoded in the genome; that particular EgKUs are up-regulated in various stages; and that analogous Kunitz families exist in other medically important cestodes, but not in trematodes. Members of this expanded family of secreted cestode proteins thus have the potential to block, through high affinity interactions, the function of host counterparts (either peptidases or cation channels) and contribute to the establishment and persistence of infection. From a more general perspective, our results confirm that multigene families of Kunitz inhibitors from parasite secretions and animal venoms display a similar functional diversity and thus, that host-parasite co-evolution may also drive the emergence of a new function associated with the Kunitz scaffold.
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Affiliation(s)
- Martín Fló
- Cátedra de Inmunología, Facultad de Química, Universidad de la República, Montevideo, Uruguay
- Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Mariana Margenat
- Cátedra de Inmunología, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Leonardo Pellizza
- Cátedra de Inmunología, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Martín Graña
- Unidad de Bioinformática, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Rosario Durán
- Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo and Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Adriana Báez
- Instituto de Fisiología, Benemérita Universidad Autónoma de Puebla, Puebla, México
| | - Emilio Salceda
- Instituto de Fisiología, Benemérita Universidad Autónoma de Puebla, Puebla, México
| | - Enrique Soto
- Instituto de Fisiología, Benemérita Universidad Autónoma de Puebla, Puebla, México
| | - Beatriz Alvarez
- Laboratorio de Enzimología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Cecilia Fernández
- Cátedra de Inmunología, Facultad de Química, Universidad de la República, Montevideo, Uruguay
- * E-mail:
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15
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de Groot CO, Hsia JE, Anzola JV, Motamedi A, Yoon M, Wong YL, Jenkins D, Lee HJ, Martinez MB, Davis RL, Gahman TC, Desai A, Shiau AK. A Cell Biologist's Field Guide to Aurora Kinase Inhibitors. Front Oncol 2015; 5:285. [PMID: 26732741 PMCID: PMC4685510 DOI: 10.3389/fonc.2015.00285] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 12/03/2015] [Indexed: 01/19/2023] Open
Abstract
Aurora kinases are essential for cell division and are frequently misregulated in human cancers. Based on their potential as cancer therapeutics, a plethora of small molecule Aurora kinase inhibitors have been developed, with a subset having been adopted as tools in cell biology. Here, we fill a gap in the characterization of Aurora kinase inhibitors by using biochemical and cell-based assays to systematically profile a panel of 10 commercially available compounds with reported selectivity for Aurora A (MLN8054, MLN8237, MK-5108, MK-8745, Genentech Aurora Inhibitor 1), Aurora B (Hesperadin, ZM447439, AZD1152-HQPA, GSK1070916), or Aurora A/B (VX-680). We quantify the in vitro effect of each inhibitor on the activity of Aurora A alone, as well as Aurora A and Aurora B bound to fragments of their activators, TPX2 and INCENP, respectively. We also report kinome profiling results for a subset of these compounds to highlight potential off-target effects. In a cellular context, we demonstrate that immunofluorescence-based detection of LATS2 and histone H3 phospho-epitopes provides a facile and reliable means to assess potency and specificity of Aurora A versus Aurora B inhibition, and that G2 duration measured in a live imaging assay is a specific readout of Aurora A activity. Our analysis also highlights variation between HeLa, U2OS, and hTERT-RPE1 cells that impacts selective Aurora A inhibition. For Aurora B, all four tested compounds exhibit excellent selectivity and do not significantly inhibit Aurora A at effective doses. For Aurora A, MK-5108 and MK-8745 are significantly more selective than the commonly used inhibitors MLN8054 and MLN8237. A crystal structure of an Aurora A/MK-5108 complex that we determined suggests the chemical basis for this higher specificity. Taken together, our quantitative biochemical and cell-based analyses indicate that AZD1152-HQPA and MK-8745 are the best current tools for selectively inhibiting Aurora B and Aurora A, respectively. However, MK-8745 is not nearly as ideal as AZD1152-HQPA in that it requires high concentrations to achieve full inhibition in a cellular context, indicating a need for more potent Aurora A-selective inhibitors. We conclude with a set of “good practice” guidelines for the use of Aurora inhibitors in cell biology experiments.
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Affiliation(s)
- Christian O de Groot
- Small Molecule Discovery Program, Ludwig Institute for Cancer Research , La Jolla, CA , USA
| | - Judy E Hsia
- Small Molecule Discovery Program, Ludwig Institute for Cancer Research , La Jolla, CA , USA
| | - John V Anzola
- Small Molecule Discovery Program, Ludwig Institute for Cancer Research , La Jolla, CA , USA
| | - Amir Motamedi
- Small Molecule Discovery Program, Ludwig Institute for Cancer Research , La Jolla, CA , USA
| | - Michelle Yoon
- Small Molecule Discovery Program, Ludwig Institute for Cancer Research , La Jolla, CA , USA
| | - Yao Liang Wong
- Laboratory of Chromosome Biology, Ludwig Institute for Cancer Research, La Jolla, CA, USA; Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - David Jenkins
- Small Molecule Discovery Program, Ludwig Institute for Cancer Research , La Jolla, CA , USA
| | - Hyun J Lee
- Small Molecule Discovery Program, Ludwig Institute for Cancer Research , La Jolla, CA , USA
| | - Mallory B Martinez
- Small Molecule Discovery Program, Ludwig Institute for Cancer Research , La Jolla, CA , USA
| | - Robert L Davis
- Small Molecule Discovery Program, Ludwig Institute for Cancer Research , La Jolla, CA , USA
| | - Timothy C Gahman
- Small Molecule Discovery Program, Ludwig Institute for Cancer Research , La Jolla, CA , USA
| | - Arshad Desai
- Laboratory of Chromosome Biology, Ludwig Institute for Cancer Research, La Jolla, CA, USA; Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Andrew K Shiau
- Small Molecule Discovery Program, Ludwig Institute for Cancer Research , La Jolla, CA , USA
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16
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Active compounds from Schisandra chinensis exhibiting tyrosinase activity and melanin content inhibition in B16 melanoma cells. BIOTECHNOL BIOPROC E 2015. [DOI: 10.1007/s12257-014-0867-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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17
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Borišek J, Vizovišek M, Sosnowski P, Turk B, Turk D, Mohar B, Novič M. Development of N-(Functionalized benzoyl)-homocycloleucyl-glycinonitriles as Potent Cathepsin K Inhibitors. J Med Chem 2015; 58:6928-37. [PMID: 26280490 DOI: 10.1021/acs.jmedchem.5b00746] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cathepsin K is a major drug target for osteoporosis and related-bone disorders. Using a combination of virtual combinatorial chemistry, QSAR modeling, and molecular docking studies, a series of cathepsin K inhibitors based on N-(functionalized benzoyl)-homocycloleucyl-glycinonitrile scaffold was developed. In order to avoid previous problems of cathepsin K inhibitors associated with lysosomotropism of compounds with basic character that resulted in off-target effects, a weakly- to nonbasic moiety was incorporated into the P3 position. Compounds 5, 6, and 9 were highly selective for cathepsin K when compared with cathepsins L and S, with the Ki values in the 10-30 nM range. The kinetic studies revealed that the new compounds exhibited reversible tight binding to cathepsin K, while the X-ray structural studies showed covalent and noncovalent binding between the nitrile group and the catalytic cysteine (Cys25) site.
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Affiliation(s)
- Jure Borišek
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Matej Vizovišek
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute , Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Piotr Sosnowski
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute , Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Boris Turk
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute , Jamova cesta 39, SI-1000 Ljubljana, Slovenia.,Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Dušan Turk
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute , Jamova cesta 39, SI-1000 Ljubljana, Slovenia.,Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova cesta 39, SI-1000 Ljubljana, Slovenia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana , Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Barbara Mohar
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Marjana Novič
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
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18
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Hu T, Zhou X, Wang L, Or PM, Yeung JH, Kwan YW, Cho CH. Effects of tanshinones from Salvia miltiorrhiza on CYP2C19 activity in human liver microsomes: Enzyme kinetic and molecular docking studies. Chem Biol Interact 2015; 230:1-8. [DOI: 10.1016/j.cbi.2015.02.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Revised: 01/20/2015] [Accepted: 02/06/2015] [Indexed: 10/24/2022]
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19
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Silver NW, King BM, Nalam MNL, Cao H, Ali A, Kiran Kumar Reddy GS, Rana TM, Schiffer CA, Tidor B. Efficient Computation of Small-Molecule Configurational Binding Entropy and Free Energy Changes by Ensemble Enumeration. J Chem Theory Comput 2013; 9:5098-5115. [PMID: 24250277 PMCID: PMC3827837 DOI: 10.1021/ct400383v] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2013] [Indexed: 01/02/2023]
Abstract
![]()
Here
we present a novel, end-point method using the dead-end-elimination
and A* algorithms to efficiently and accurately calculate the change
in free energy, enthalpy, and configurational entropy of binding for
ligand–receptor association reactions. We apply the new approach
to the binding of a series of human immunodeficiency virus (HIV-1)
protease inhibitors to examine the effect ensemble reranking has on
relative accuracy as well as to evaluate the role of the absolute
and relative ligand configurational entropy losses upon binding in
affinity differences for structurally related inhibitors. Our results
suggest that most thermodynamic parameters can be estimated using
only a small fraction of the full configurational space, and we see
significant improvement in relative accuracy when using an ensemble
versus single-conformer approach to ligand ranking. We also find that
using approximate metrics based on the single-conformation enthalpy
differences between the global minimum energy configuration in the
bound as well as unbound states also correlates well with experiment.
Using a novel, additive entropy expansion based on conditional mutual
information, we also analyze the source of ligand configurational
entropy loss upon binding in terms of both uncoupled per degree of
freedom losses as well as changes in coupling between inhibitor degrees
of freedom. We estimate entropic free energy losses of approximately
+24 kcal/mol, 12 kcal/mol of which stems from loss of translational
and rotational entropy. Coupling effects contribute only a small fraction
to the overall entropy change (1–2 kcal/mol) but suggest differences
in how inhibitor dihedral angles couple to each other in the bound
versus unbound states. The importance of accounting for flexibility
in drug optimization and design is also discussed.
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Affiliation(s)
- Nathaniel W Silver
- Department of Chemistry and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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20
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Avrutina O, Fittler H, Glotzbach B, Kolmar H, Empting M. Between two worlds: a comparative study on in vitro and in silico inhibition of trypsin and matriptase by redox-stable SFTI-1 variants at near physiological pH. Org Biomol Chem 2013; 10:7753-62. [PMID: 22903577 DOI: 10.1039/c2ob26162f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A comparative study on in vitro and in silico inhibition of trypsin and matriptase by derivatives of the sunflower trypsin inhibitor-1 at near physiological pH is reported. Besides wild-type bicyclic SFTI-1, monocyclic variants possessing native cystine as well as redox-stable triazolyl side-chain macrocyclization motifs were studied for the first time in matriptase inhibition assays. Interestingly, monocyclic SFTI-1[1,14] demonstrated higher potency against this pharmacologically relevant protease compared to its bicyclic counterpart. Structural analysis of binding/inhibition of investigated SFTI-1 derivatives was performed using a combination of molecular dynamics simulations and docking experiments. In silico data were in good accordance with in vitro results, indicating the importance of the terminal inhibitor regions for the affinity towards matriptase. Presented work gives new perspectives for the optimization of the SFTI-1 framework towards in vivo applications.
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Affiliation(s)
- Olga Avrutina
- Clemens-Schöpf Institute of Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Petersenstr. 22, 64287 Darmstadt, Germany
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21
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Hum RJ, Jha P, McGahan AM, Cheng YL. Global divergence in critical income for adult and childhood survival: analyses of mortality using Michaelis-Menten. eLife 2012; 1:e00051. [PMID: 23240081 PMCID: PMC3510452 DOI: 10.7554/elife.00051] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 09/25/2012] [Indexed: 11/13/2022] Open
Abstract
Life expectancy has risen sharply in the last 50 years. We applied the classic Michaelis-Menten enzyme kinetics to demonstrate a novel mathematical relationship of income to childhood (aged 0-5 years) and adult (aged 15-60 years) survival. We treat income as a substrate that is catalyzed to increase survival (from technologies that income buys) for 180 countries from 1970 and 2007. Michaelis-Menten kinetics permit estimates of maximal survival and, uniquely, the critical income needed to achieve half of the period-specific maximum. Maximum child and adult survival rose by about 1% per year. Critical incomes fell by half for children, but doubled for men. HIV infection and smoking account for some, but not all, of the rising critical incomes for adult survival. Altering the future cost curve for adult survival will require more widespread use of current interventions, most notably tobacco control, but also research to identify practicable low-cost drugs, diagnostics, and strategies.DOI:http://dx.doi.org/10.7554/eLife.00051.001.
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Affiliation(s)
- Ryan J Hum
- Department of Chemical Engineering and Applied Chemistry and Centre for Global Engineering, University of Toronto, Toronto, Canada
| | - Prabhat Jha
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
- Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, Canada
| | - Anita M McGahan
- Rotman School of Management, University of Toronto, Toronto, Canada
| | - Yu-Ling Cheng
- Department of Chemical Engineering and Applied Chemistry and Centre for Global Engineering, University of Toronto, Toronto, Canada
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22
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Parai MK, Huggins DJ, Cao H, Nalam MNL, Ali A, Schiffer CA, Tidor B, Rana TM. Design, synthesis, and biological and structural evaluations of novel HIV-1 protease inhibitors to combat drug resistance. J Med Chem 2012; 55:6328-41. [PMID: 22708897 PMCID: PMC3409094 DOI: 10.1021/jm300238h] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A series of new HIV-1 protease inhibitors (PIs) were designed using a general strategy that combines computational structure-based design with substrate-envelope constraints. The PIs incorporate various alcohol-derived P2 carbamates with acyclic and cyclic heteroatomic functionalities into the (R)-hydroxyethylamine isostere. Most of the new PIs show potent binding affinities against wild-type HIV-1 protease and three multidrug resistant (MDR) variants. In particular, inhibitors containing the 2,2-dichloroacetamide, pyrrolidinone, imidazolidinone, and oxazolidinone moieties at P2 are the most potent with K(i) values in the picomolar range. Several new PIs exhibit nanomolar antiviral potencies against patient-derived wild-type viruses from HIV-1 clades A, B, and C and two MDR variants. Crystal structure analyses of four potent inhibitors revealed that carbonyl groups of the new P2 moieties promote extensive hydrogen bond interactions with the invariant Asp29 residue of the protease. These structure-activity relationship findings can be utilized to design new PIs with enhanced enzyme inhibitory and antiviral potencies.
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Affiliation(s)
- Maloy Kumar Parai
- Program for RNA Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037
| | - David J. Huggins
- Department of Biological Engineering and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Hong Cao
- Chemical Biology Program, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Madhavi N. L. Nalam
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Akbar Ali
- Chemical Biology Program, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Bruce Tidor
- Department of Biological Engineering and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Tariq M. Rana
- Program for RNA Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037
- Chemical Biology Program, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
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Bartlett CW, Cheong SY, Hou L, Paquette J, Lum PY, Jäger G, Battke F, Vehlow C, Heinrich J, Nieselt K, Sakai R, Aerts J, Ray WC. An eQTL biological data visualization challenge and approaches from the visualization community. BMC Bioinformatics 2012; 13 Suppl 8:S8. [PMID: 22607587 PMCID: PMC3355334 DOI: 10.1186/1471-2105-13-s8-s8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
In 2011, the IEEE VisWeek conferences inaugurated a symposium on Biological Data Visualization. Like other domain-oriented Vis symposia, this symposium's purpose was to explore the unique characteristics and requirements of visualization within the domain, and to enhance both the Visualization and Bio/Life-Sciences communities by pushing Biological data sets and domain understanding into the Visualization community, and well-informed Visualization solutions back to the Biological community. Amongst several other activities, the BioVis symposium created a data analysis and visualization contest. Unlike many contests in other venues, where the purpose is primarily to allow entrants to demonstrate tour-de-force programming skills on sample problems with known solutions, the BioVis contest was intended to whet the participants' appetites for a tremendously challenging biological domain, and simultaneously produce viable tools for a biological grand challenge domain with no extant solutions. For this purpose expression Quantitative Trait Locus (eQTL) data analysis was selected. In the BioVis 2011 contest, we provided contestants with a synthetic eQTL data set containing real biological variation, as well as a spiked-in gene expression interaction network influenced by single nucleotide polymorphism (SNP) DNA variation and a hypothetical disease model. Contestants were asked to elucidate the pattern of SNPs and interactions that predicted an individual's disease state. 9 teams competed in the contest using a mixture of methods, some analytical and others through visual exploratory methods. Independent panels of visualization and biological experts judged entries. Awards were given for each panel's favorite entry, and an overall best entry agreed upon by both panels. Three special mention awards were given for particularly innovative and useful aspects of those entries. And further recognition was given to entries that correctly answered a bonus question about how a proposed "gene therapy" change to a SNP might change an individual's disease status, which served as a calibration for each approaches' applicability to a typical domain question. In the future, BioVis will continue the data analysis and visualization contest, maintaining the philosophy of providing new challenging questions in open-ended and dramatically underserved Bio/Life Sciences domains.
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Ee K, Zhao J, Rehman A, Agboola S. Glycosylation, amino acid analysis and kinetic properties of a major Kunitz-type trypsin inhibitor from Acacia victoriae Bentham seeds. Food Chem 2011; 129:1224-7. [DOI: 10.1016/j.foodchem.2011.05.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Revised: 03/16/2011] [Accepted: 05/04/2011] [Indexed: 10/18/2022]
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Mechanical influence of static versus dynamic loadings on parametrical analysis of plasticized ethyl cellulose films. Int J Pharm 2011; 408:1-8. [DOI: 10.1016/j.ijpharm.2010.11.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Accepted: 11/15/2010] [Indexed: 11/22/2022]
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Ali A, Kiran Kumar Reddy GS, Nalam MNL, Anjum SG, Cao H, Schiffer CA, Rana TM. Structure-based design, synthesis, and structure-activity relationship studies of HIV-1 protease inhibitors incorporating phenyloxazolidinones. J Med Chem 2010; 53:7699-708. [PMID: 20958050 PMCID: PMC2996262 DOI: 10.1021/jm1008743] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A series of new HIV-1 protease inhibitors with the hydroxyethylamine core and different phenyloxazolidinone P2 ligands were designed and synthesized. Variation of phenyl substitutions at the P2 and P2' moieties significantly affected the binding affinity and antiviral potency of the inhibitors. In general, compounds with 2- and 4-substituted phenyloxazolidinones at P2 exhibited lower binding affinities than 3-substituted analogues. Crystal structure analyses of ligand-enzyme complexes revealed different binding modes for 2- and 3-substituted P2 moieties in the protease S2 binding pocket, which may explain their different binding affinities. Several compounds with 3-substituted P2 moieties demonstrated picomolar binding affinity and low nanomolar antiviral potency against patient-derived viruses from HIV-1 clades A, B, and C, and most retained potency against drug-resistant viruses. Further optimization of these compounds using structure-based design may lead to the development of novel protease inhibitors with improved activity against drug-resistant strains of HIV-1.
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Affiliation(s)
- Akbar Ali
- Chemical Biology Program, University of Massachusetts Medical School, Worcester, Massachusetts 01605
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - G. S. Kiran Kumar Reddy
- Chemical Biology Program, University of Massachusetts Medical School, Worcester, Massachusetts 01605
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Madhavi N. L. Nalam
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Saima Ghafoor Anjum
- Chemical Biology Program, University of Massachusetts Medical School, Worcester, Massachusetts 01605
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Hong Cao
- Chemical Biology Program, University of Massachusetts Medical School, Worcester, Massachusetts 01605
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Tariq M. Rana
- Chemical Biology Program, University of Massachusetts Medical School, Worcester, Massachusetts 01605
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
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A human surfactant peptide-elastase inhibitor construct as a treatment for emphysema. Proc Natl Acad Sci U S A 2010; 107:10661-6. [PMID: 20534582 DOI: 10.1073/pnas.1001349107] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two million Americans suffer from pulmonary emphysema, costing $2.5 billion/year and contributing to 100,000 deaths/year. Emphysema is thought to result from an imbalance between elastase and endogenous inhibitors of elastase, leading to tissue destruction and a loss of alveoli. Decades of research have still not resulted in an effective treatment other than stopping cigarette smoking, a highly addictive behavior. On the basis of our previous work, we hypothesize that small molecule inhibitors of human neutrophil elastase are ineffective because of rapid clearance from the lungs. To develop a long-acting elastase inhibitor with a lung pharmacodynamic profile that has minimal immunogenicity, we covalently linked an elastase inhibitor, similar to a trifluoro inhibitor that was used in clinical trials, to a 25-amino-acid fragment of human surfactant peptide B. We used this construct to prevent human neutrophil elastase-induced emphysema in a rodent model. The elastase inhibitor alone, although in a 70-fold molar excess to elastase in a mixture with <0.6% residual elastase activity, provided no protection from elastase-induced emphysema. Covalently combining an endogenous peptide from the target organ with a synthetic small molecule inhibitor is a unique way of endowing an active compound with the pharmacodynamic profile needed to create in vivo efficacy.
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Pegolo S, Merlanti R, Giantin M, Dacasto M, Montesissa C, Capolongo F. High performance liquid chromatography determination of cytochrome P450 1A and 2C activities in bovine liver microsomes. Vet J 2010; 183:81-88. [DOI: 10.1016/j.tvjl.2008.08.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Revised: 07/24/2008] [Accepted: 08/07/2008] [Indexed: 10/21/2022]
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A family of diverse Kunitz inhibitors from Echinococcus granulosus potentially involved in host-parasite cross-talk. PLoS One 2009; 4:e7009. [PMID: 19759914 PMCID: PMC2740865 DOI: 10.1371/journal.pone.0007009] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Accepted: 08/03/2009] [Indexed: 11/19/2022] Open
Abstract
The cestode Echinococcus granulosus, the agent of hydatidosis/echinococcosis, is remarkably well adapted to its definitive host. However, the molecular mechanisms underlying the successful establishment of larval worms (protoscoleces) in the dog duodenum are unknown. With the aim of identifying molecules participating in the E. granulosus-dog cross-talk, we surveyed the transcriptomes of protoscoleces and protoscoleces treated with pepsin at pH 2. This analysis identified a multigene family of secreted monodomain Kunitz proteins associated mostly with pepsin/H(+)-treated worms, suggesting that they play a role at the onset of infection. We present the relevant molecular features of eight members of the E. granulosus Kunitz family (EgKU-1 - EgKU-8). Although diverse, the family includes three pairs of close paralogs (EgKU-1/EgKU-4; EgKU-3/EgKU-8; EgKU-6/EgKU-7), which would be the products of recent gene duplications. In addition, we describe the purification of EgKU-1 and EgKU-8 from larval worms, and provide data indicating that some members of the family (notably, EgKU-3 and EgKU-8) are secreted by protoscoleces. Detailed kinetic studies with native EgKU-1 and EgKU-8 highlighted their functional diversity. Like most monodomain Kunitz proteins, EgKU-8 behaved as a slow, tight-binding inhibitor of serine proteases, with global inhibition constants (K(I) (*)) versus trypsins in the picomolar range. In sharp contrast, EgKU-1 did not inhibit any of the assayed peptidases. Interestingly, molecular modeling revealed structural elements associated with activity in Kunitz cation-channel blockers. We propose that this family of inhibitors has the potential to act at the E. granulosus-dog interface and interfere with host physiological processes at the initial stages of infection.
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Jorissen RN, Reddy GSKK, Ali A, Altman MD, Chellappan S, Anjum SG, Tidor B, Schiffer CA, Rana TM, Gilson MK. Additivity in the analysis and design of HIV protease inhibitors. J Med Chem 2009; 52:737-54. [PMID: 19193159 DOI: 10.1021/jm8009525] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We explore the applicability of an additive treatment of substituent effects to the analysis and design of HIV protease inhibitors. Affinity data for a set of inhibitors with a common chemical framework were analyzed to provide estimates of the free energy contribution of each chemical substituent. These estimates were then used to design new inhibitors whose high affinities were confirmed by synthesis and experimental testing. Derivations of additive models by least-squares and ridge-regression methods were found to yield statistically similar results. The additivity approach was also compared with standard molecular descriptor-based QSAR; the latter was not found to provide superior predictions. Crystallographic studies of HIV protease-inhibitor complexes help explain the perhaps surprisingly high degree of substituent additivity in this system, and allow some of the additivity coefficients to be rationalized on a structural basis.
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Affiliation(s)
- Robert N Jorissen
- Center for Advanced Research in Biotechnology, UMBI, 9600 Gudelsky Drive, Rockville, Maryland 20850, USA
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31
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Ribeiro C, Esteves da Silva JCG. Kinetics of inhibition of firefly luciferase by oxyluciferin and dehydroluciferyl-adenylate. Photochem Photobiol Sci 2008; 7:1085-90. [PMID: 18754056 DOI: 10.1039/b809935a] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The inhibition mechanisms of the firefly luciferase (Luc) by the two major products of the reactions catalysed by Luc, oxyluciferin and dehydroluciferyl-adenylate (L-AMP), were investigated. Light production in the presence and absence of these inhibitors (0.5 to 2 microM oxyluciferin; 0.0025 to 1.25 microM L-AMP) has been measured in 50 mM Hepes buffer (pH=7.5), 10 nM Luc, 250 microM ATP and D-Luciferin (from 3.75 up to 120 microM). Nonlinear regression analysis with the appropriate kinetic models (Henri-Michaelis-Menten and William-Morrison equations) reveals that oxyluciferin is a competitive inhibitor of luciferase (Ki=0.50+/-0.03 microM) while L-AMP act as a tight-binding competitive inhibitor (Ki=3.8+/-0.7 nM). The Km values obtained both for oxyluciferin and L-AMP were 14.7+/-0.7 and 14.9+/-0.2 microM, respectively. L-AMP is a stronger inhibitor of Luc than oxyluciferin and the major responsible for the characteristic flash profile of in vitro Luc bioluminescence.
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Affiliation(s)
- César Ribeiro
- Centro de Investigação em Química (UP), Departamento de Química, Faculdade de Ciências da Universidade do Porto, R. Campo Alegre 687, 4169-007, Porto, Portugal
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32
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Altman MD, Ali A, Reddy GSKK, Nalam MNL, Anjum SG, Cao H, Chellappan S, Kairys V, Fernandes MX, Gilson MK, Schiffer CA, Rana TM, Tidor B. HIV-1 protease inhibitors from inverse design in the substrate envelope exhibit subnanomolar binding to drug-resistant variants. J Am Chem Soc 2008; 130:6099-113. [PMID: 18412349 PMCID: PMC3465729 DOI: 10.1021/ja076558p] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The acquisition of drug-resistant mutations by infectious pathogens remains a pressing health concern, and the development of strategies to combat this threat is a priority. Here we have applied a general strategy, inverse design using the substrate envelope, to develop inhibitors of HIV-1 protease. Structure-based computation was used to design inhibitors predicted to stay within a consensus substrate volume in the binding site. Two rounds of design, synthesis, experimental testing, and structural analysis were carried out, resulting in a total of 51 compounds. Improvements in design methodology led to a roughly 1000-fold affinity enhancement to a wild-type protease for the best binders, from a Ki of 30-50 nM in round one to below 100 pM in round two. Crystal structures of a subset of complexes revealed a binding mode similar to each design that respected the substrate envelope in nearly all cases. All four best binders from round one exhibited broad specificity against a clinically relevant panel of drug-resistant HIV-1 protease variants, losing no more than 6-13-fold affinity relative to wild type. Testing a subset of second-round compounds against the panel of resistant variants revealed three classes of inhibitors: robust binders (maximum affinity loss of 14-16-fold), moderate binders (35-80-fold), and susceptible binders (greater than 100-fold). Although for especially high-affinity inhibitors additional factors may also be important, overall, these results suggest that designing inhibitors using the substrate envelope may be a useful strategy in the development of therapeutics with low susceptibility to resistance.
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Affiliation(s)
- Michael D. Altman
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Akbar Ali
- Chemical Biology Program, Department of Biochemistry and Molecular Pharmacology, University of Massachuetts Medical School, Worcester, MA 01605, USA
| | - G. S. Kiran Kumar Reddy
- Chemical Biology Program, Department of Biochemistry and Molecular Pharmacology, University of Massachuetts Medical School, Worcester, MA 01605, USA
| | - Madhavi N. L. Nalam
- Department of Biochemistry and Molecular Pharmacology, University of Massachuetts Medical School, Worcester, MA 01605, USA
| | - Saima Ghafoor Anjum
- Chemical Biology Program, Department of Biochemistry and Molecular Pharmacology, University of Massachuetts Medical School, Worcester, MA 01605, USA
| | - Hong Cao
- Chemical Biology Program, Department of Biochemistry and Molecular Pharmacology, University of Massachuetts Medical School, Worcester, MA 01605, USA
| | - Sripriya Chellappan
- Center for Advanced Research in Biotechnology, University of Maryland, Biotechnology Institute, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Visvaldas Kairys
- Center for Advanced Research in Biotechnology, University of Maryland, Biotechnology Institute, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Miguel X. Fernandes
- Center for Advanced Research in Biotechnology, University of Maryland, Biotechnology Institute, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Michael K. Gilson
- Center for Advanced Research in Biotechnology, University of Maryland, Biotechnology Institute, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachuetts Medical School, Worcester, MA 01605, USA
| | - Tariq M. Rana
- Chemical Biology Program, Department of Biochemistry and Molecular Pharmacology, University of Massachuetts Medical School, Worcester, MA 01605, USA
| | - Bruce Tidor
- Department of Biological Engineering, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Mihelic M, Dobersek A, Guncar G, Turk D. Inhibitory fragment from the p41 form of invariant chain can regulate activity of cysteine cathepsins in antigen presentation. J Biol Chem 2008; 283:14453-60. [PMID: 18362148 DOI: 10.1074/jbc.m801283200] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cysteine cathepsins play an indispensable role in proteolytic processing of the major histocompatibility complex class II-associated invariant chain (Ii) and foreign antigens in a number of antigen presenting cells. Previously it was shown that a fragment of 64 residues present in the p41 form of the Ii (p41 fragment) selectively inhibits the endopeptidase cathepsin L, whereas the activity of cathepsin S remains unaffected. Comparison of structures indicated that the selectivity of interactions between cysteine cathepsins and the p41 fragment is far from being understood and requires further investigation. The p41 fragment has now been shown also to inhibit human cathepsins V, K, and F (also, presumably, O) and mouse cathepsin L with K(i) values in the low nanomolar range. These K(i) values are sufficiently low to ensure complex formation at physiological concentrations. In addition we have found that the p41 fragment can inhibit cathepsin S too. These findings suggest that regulation of the proteolytic activity of most of the cysteine cathepsins by the p41 fragment is an important and widespread control mechanism of antigen presentation.
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Affiliation(s)
- Marko Mihelic
- Department of Biochemistry and Molecular and Structural Biology, J Stefan Institute, Ljubljana, Slovenia
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Kiran Kumar Reddy GS, Ali A, Nalam MNL, Anjum SG, Cao H, Nathans RS, Schiffer CA, Rana TM. Design and synthesis of HIV-1 protease inhibitors incorporating oxazolidinones as P2/P2' ligands in pseudosymmetric dipeptide isosteres. J Med Chem 2007; 50:4316-28. [PMID: 17696512 PMCID: PMC3862176 DOI: 10.1021/jm070284z] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A series of novel HIV-1 protease inhibitors based on two pseudosymmetric dipeptide isosteres have been synthesized and evaluated. The inhibitors were designed by incorporating N-phenyloxazolidinone-5-carboxamides into the hydroxyethylene and (hydroxyethyl)hydrazine dipeptide isosteres as P2 and P2' ligands. Compounds with (S)-phenyloxazolidinones attached at a position proximal to the central hydroxyl group showed low nM inhibitory activities against wild-type HIV-1 protease. Selected compounds were further evaluated for their inhibitory activities against a panel of multidrug-resistant protease variants and for their antiviral potencies in MT-4 cells. The crystal structures of lopinavir (LPV) and two new inhibitors containing phenyloxazolidinone-based ligands in complex with wild-type HIV-1 protease have been determined. A comparison of the inhibitor-protease structures with the LPV-protease structure provides valuable insight into the binding mode of the new inhibitors to the protease enzyme. Based on the crystal structures and knowledge of structure-activity relationships, new inhibitors can be designed with enhanced enzyme inhibitory and antiviral potencies.
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Affiliation(s)
- G. S. Kiran Kumar Reddy
- Chemical Biology Program, University of Massachusetts Medical School, Worcester, Massachusetts 01605
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Akbar Ali
- Chemical Biology Program, University of Massachusetts Medical School, Worcester, Massachusetts 01605
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Madhavi N. L. Nalam
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Saima Ghafoor Anjum
- Chemical Biology Program, University of Massachusetts Medical School, Worcester, Massachusetts 01605
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Hong Cao
- Chemical Biology Program, University of Massachusetts Medical School, Worcester, Massachusetts 01605
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Robin S. Nathans
- Chemical Biology Program, University of Massachusetts Medical School, Worcester, Massachusetts 01605
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Tariq M. Rana
- Chemical Biology Program, University of Massachusetts Medical School, Worcester, Massachusetts 01605
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
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Ali A, Reddy GSKK, Cao H, Anjum SG, Nalam MNL, Schiffer CA, Rana TM. Discovery of HIV-1 Protease Inhibitors with Picomolar Affinities Incorporating N-Aryl-oxazolidinone-5-carboxamides as Novel P2 Ligands. J Med Chem 2006; 49:7342-56. [PMID: 17149864 DOI: 10.1021/jm060666p] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Here, we describe the design, synthesis, and biological evaluation of novel HIV-1 protease inhibitors incorporating N-phenyloxazolidinone-5-carboxamides into the (hydroxyethylamino)sulfonamide scaffold as P2 ligands. Series of inhibitors with variations at the P2 phenyloxazolidinone and the P2' phenylsulfonamide moieties were synthesized. Compounds with the (S)-enantiomer of substituted phenyloxazolidinones at P2 show highly potent inhibitory activities against HIV-1 protease. The inhibitors possessing 3-acetyl, 4-acetyl, and 3-trifluoromethyl groups at the phenyl ring of the oxazolidinone fragment are the most potent in each series, with K(i) values in the low picomolar (pM) range. The electron-donating groups 4-methoxy and 1,3-dioxolane are preferred at P2' phenyl ring, as compounds with other substitutions show lower binding affinities. Attempts to replace the isobutyl group at P1' with small cyclic moieties caused significant loss of affinities in the resulting compounds. Crystal structure analysis of the two most potent inhibitors in complex with the HIV-1 protease provided valuable information on the interactions between the inhibitor and the protease enzyme. In both inhibitor - enzyme complexes, the carbonyl group of the oxazolidinone ring makes hydrogenbond interactions with relatively conserved Asp29 residue of the protease. Potent inhibitors from each series incorporating various phenyloxazolidinone based P2 ligands were selected and their activities against a panel of multidrug-resistant (MDR) protease variants were determined. Interestingly, the most potent protease inhibitor starts out with extremely tight affinity for the wild-type enzyme (K(i) = 0.8 pM), and even against the MDR variants it retains picomolar to low nanomolar K(i), which is highly comparable with the best FDA-approved protease inhibitors.
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Affiliation(s)
- Akbar Ali
- Chemical Biology Program, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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Mihelic M, Teuscher C, Turk V, Turk D. Mouse stefins A1 and A2 (Stfa1 and Stfa2) differentiate between papain-like endo- and exopeptidases. FEBS Lett 2006; 580:4195-9. [PMID: 16831429 DOI: 10.1016/j.febslet.2006.06.076] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2006] [Revised: 06/13/2006] [Accepted: 06/28/2006] [Indexed: 10/24/2022]
Abstract
Stefin A (Stfa) acts as a competitive inhibitor of intracellular papain-like cysteine proteases which play important roles in normal cellular functions such as general protein turnover, antigen processing and ovarian follicular growth and maturation. In the mouse there are at least three different variants of Stfa (Stfa1, Stfa2 and Stfa3). Recent genetic studies identified structural polymorphisms in Stfa1 and Stfa2 as candidates for Aod1b, a locus controlling susceptibility to day three thymectomy (D3Tx)-induced autoimmune ovarian disease (AOD). To evaluate the functional significance of these polymorphisms, recombinant allelic proteins were expressed in Escherichia coli, purified and characterized. The polymorphisms do not markedly alter the folding characteristics of the two proteins. Stfa1 and Stfa2 both act as fast and tight binding inhibitors of endopeptidases papain and cathepsins L and S, however their interaction with exopeptidases cathepsins B, C and H was several orders of magnitude weaker compared to human, porcine and bovine Stfa. Notwithstanding, the K(i) values for the interactions of Stfa1-b from AOD resistant C57BL/6J mice was 10-fold higher than that of the Stfa1-a allele from susceptible A/J mice for papain, cathepsins B, C and H but not L and S. In contrast, the inhibitory activities of Stfa2-a and Stfa2-b were found to be roughly equivalent for all targets peptidases.
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Affiliation(s)
- Marko Mihelic
- Department of Biochemistry and Molecular Biology, J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
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37
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Kapoor M, Reddy C, Krishnasastry M, Surolia N, Surolia A. Slow-tight-binding inhibition of enoyl-acyl carrier protein reductase from Plasmodium falciparum by triclosan. Biochem J 2004; 381:719-24. [PMID: 15086316 PMCID: PMC1133881 DOI: 10.1042/bj20031821] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2003] [Revised: 03/05/2004] [Accepted: 04/16/2004] [Indexed: 11/17/2022]
Abstract
Triclosan is a potent inhibitor of FabI (enoyl-ACP reductase, where ACP stands for acyl carrier protein), which catalyses the last step in a sequence of four reactions that is repeated many times with each elongation step in the type II fatty acid biosynthesis pathway. The malarial parasite Plasmodium falciparum also harbours the genes and is capable of synthesizing fatty acids by utilizing the enzymes of type II FAS (fatty acid synthase). The basic differences in the enzymes of type I FAS, present in humans, and type II FAS, present in Plasmodium, make the enzymes of this pathway a good target for antimalarials. The steady-state kinetics revealed time-dependent inhibition of FabI by triclosan, demonstrating that triclosan is a slow-tight-binding inhibitor of FabI. The inhibition followed a rapid equilibrium step to form a reversible enzyme-inhibitor complex (EI) that isomerizes to a second enzyme-inhibitor complex (EI*), which dissociates at a very slow rate. The rate constants for the isomerization of EI to EI* and the dissociation of EI* were 5.49x10(-2) and 1x10(-4) s(-1) respectively. The K(i) value for the formation of the EI complex was 53 nM and the overall inhibition constant K(i)* was 96 pM. The results match well with the rate constants derived independently from fluorescence analysis of the interaction of FabI and triclosan, as well as those obtained by surface plasmon resonance studies [Kapoor, Mukhi, N. Surolia, Sugunda and A. Surolia (2004) Biochem. J. 381, 725-733].
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Affiliation(s)
- Mili Kapoor
- *Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India
| | | | | | - Namita Surolia
- ‡Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, India
| | - Avadhesha Surolia
- *Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India
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Murphy DJ. Determination of accurate KI values for tight-binding enzyme inhibitors: an in silico study of experimental error and assay design. Anal Biochem 2004; 327:61-7. [PMID: 15033511 DOI: 10.1016/j.ab.2003.12.018] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2003] [Indexed: 11/25/2022]
Abstract
Determination of accurate K(I) values for tight-binding enzyme inhibitors is important from both a basic biochemistry point of view (understanding the differences in affinity of related molecules) and a medicinal chemistry vantage (developing structure-activity relationships (SAR)). It is advantageous to directly fit the quadratic equation describing tight-binding behavior, known commonly as the Morrison equation, to obtain these K(I) values. The results of simulated experiments that examine the effect of assay design and experimental error on the ability to accurately determine K(I) values at several [E]0/K(I-app) ratios are described. Input ("true") values of the uninhibited velocity, inhibition constant, and total enzyme concentration were used to calculate the velocity at various inhibitor concentrations. Gaussian error was introduced into the velocities and the simulated reactions were fit to estimate upsilon0, K(I), and [E]0. Recommendations for optimizing the inhibitor dilutions within the context of a 96-well-plate format and simple serial dilution steps are made. These include using three points to determine the enzyme concentration ([I]=0, 0.5[E]0, and [E]0), using a narrow dilution series with only two or three points to determine the asymptote at high inhibitor concentration, and avoiding fixing [E]0 to a constant value in the fitting if at all possible. The risks and rewards of fixing [E]0 to a constant value, especially the effect on SAR, are also examined.
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Affiliation(s)
- Dennis J Murphy
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, USA
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39
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Fonovic M, Brömme D, Turk V, Turk B. Human cathepsin F: expression in baculovirus system, characterization and inhibition by protein inhibitors. Biol Chem 2004; 385:505-9. [PMID: 15255182 DOI: 10.1515/bc.2004.059] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Recombinant full-length human procathepsin F, produced in the baculovirus expression system, was partially processed during the purification procedure to a form lacking the N-terminal cystatin-like domain and activated with pepsin. Active cathepsin F efficiently hydrolyzed Z-FR-MCA (kcat/Km=106 mM(-1) s(-1)) and Bz-FVR-MCA (kcat/Km=8 mM(-1) s(-1)), whereas hydrolysis of Z-RR-MCA was very slow (kcat/Km<0.2 mM(-1) s(-1)). Cathepsin F was rapidly and tightly inhibited by cystatin C, chicken cystatin and equistatin with Ki values in the subnanomolar range (0.03-0.47 nM), whereas L-kininogen was a less strong inhibitor of the enzyme (Ki=4.7 nM). Stefin A inhibited cathepsin F slowly (kass=1.6 x 10(5) M(-1) s(-1)) and with a lower affinity (Ki=25 nM). These data suggest that cathepsin F differs from other related endopeptidases by considerably weaker inhibition by stefins.
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Affiliation(s)
- Marko Fonovic
- Department of Biochemistry and Molecular Biology, J. Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
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40
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Abstract
Exploiting the principle of bivalent binding, we have designed symmetrical, bifunctional inhibitors to simultaneously occupy both active sites of cytosolic glutathione S-transferase, with enhanced specificity for the P1-1 isoform. We have prepared two series of compounds that differ in their binding domains-the first is a series of bis-glutathione conjugates, and the second is a series of compounds each possessing two equivalents of Uniblue A, an analogue of Cibacron Blue. For each series, a monofunctional reference compound was also prepared to determine the relative advantage of the bivalent inhibitors. Within each series, the most potent inhibitors exhibited IC(50) values 2 orders of magnitude lower than the relevant reference compounds. Moreover, within the bis-glutathionyl series, a 10-fold increase in selectivity was achieved for GST P1-1 over the A1-1 isoform. Isothermal titration calorimetry with a representative bis-glutathione conjugate and a monofunctional reference compound indicates that the bivalent inhibitor exhibits the expected increase in intrinsic affinity and decrease in stoichiometry relative to the monofunctional compound, supporting the overall design strategy.
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Affiliation(s)
- Robert P Lyon
- Department of Medicinal Chemistry, Box 357610, University of Washington, Seattle, Washington 98195-7610, USA
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41
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Rozman-Pungercar J, Kopitar-Jerala N, Bogyo M, Turk D, Vasiljeva O, Stefe I, Vandenabeele P, Brömme D, Puizdar V, Fonović M, Trstenjak-Prebanda M, Dolenc I, Turk V, Turk B. Inhibition of papain-like cysteine proteases and legumain by caspase-specific inhibitors: when reaction mechanism is more important than specificity. Cell Death Differ 2003; 10:881-8. [PMID: 12867995 DOI: 10.1038/sj.cdd.4401247] [Citation(s) in RCA: 159] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
We report here that a number of commonly used small peptide caspase inhibitors consisting of a caspase recognition sequence linked to chloromethylketone, fluoromethylketone or aldehyde reactive group efficiently inhibit other cysteine proteases than caspases. The in vitro studies included cathepsins B, H, L, S, K, F, V, X and C, papain and legumain. Z-DEVD-cmk was shown to be the preferred irreversible inhibitor of most of the cathepsins in vitro, followed by Z-DEVD-fmk, Ac-YVAD-cmk, Z-YVAD-fmk and Z-VAD-fmk. Inactivation of legumain by all the inhibitors investigated was moderate, whereas cathepsins H and C were poorly inhibited or not inhibited at all. Inhibition by aldehydes was not very potent. All the three fluoromethylketones efficiently inhibited cathepsins in Jurkat and human embryonic kidney 293 cells at concentrations of 100 microM. Furthermore, they completely inhibited cathepsins B and X activity in tissue extracts at concentrations as low as 1 microM. These results suggest that data based on the use of these inhibitors should be taken with caution and that other proteases may be implicated in the processes previously ascribed solely to caspases.
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Affiliation(s)
- J Rozman-Pungercar
- Department of Biochemistry and Molecular Biology, J. Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
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42
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Kuzmic P, Elrod KC, Cregar LM, Sideris S, Rai R, Janc JW. High-throughput screening of enzyme inhibitors: simultaneous determination of tight-binding inhibition constants and enzyme concentration. Anal Biochem 2000; 286:45-50. [PMID: 11038272 DOI: 10.1006/abio.2000.4685] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Active site titration by a reversible tight-binding inhibitor normally depends on prior knowledge of the inhibition constant. Conversely, the determination of tight-binding inhibition constants normally requires prior knowledge of the active enzyme concentration. Often, neither of these quantities is known with sufficient accuracy. This paper describes experimental conditions under which both the enzyme active site concentration and the tight-binding inhibition constant can be determined simultaneously from a single dose-response curve. Representative experimental data are shown for the inhibition of human kallikrein.
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Affiliation(s)
- P Kuzmic
- BioKin, Ltd., 1652 South Grand Avenue, Suite 337, Pullman, Washington 99163, USA.
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43
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Kuzmic P, Sideris S, Cregar LM, Elrod KC, Rice KD, Janc JW. High-throughput screening of enzyme inhibitors: automatic determination of tight-binding inhibition constants. Anal Biochem 2000; 281:62-7. [PMID: 10847611 DOI: 10.1006/abio.2000.4501] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Determination of tight-binding inhibition constants by nonlinear least-squares regression requires sufficiently good initial estimates of the best-fit values. Normally an initial estimate of the inhibition constant must be provided by the investigator. This paper describes an automatic procedure for the estimation of tight-binding inhibition constants directly from dose-response data. Because the procedure does not require human intervention, it was incorporated into an algorithm for high-throughput screening of enzyme inhibitors. A suitable computer program is available electronically (http://www.biokin.com). Representative experimental data are shown for the inhibition of human mast-cell tryptase.
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Affiliation(s)
- P Kuzmic
- BioKin, Ltd., Madison, Wisconsin 53708, USA.
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44
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Galesa K, Strukelj B, Bavec S, Turk V, Lenarcic B. Cloning and expression of functional equistatin. Biol Chem 2000; 381:85-8. [PMID: 10722055 DOI: 10.1515/bc.2000.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Equistatin is a 199-residue protein composed of three thyroglobulin type-1 domains. It strongly inhibits cysteine proteinases as well as the aspartic proteinase cathepsin D. In order to initiate structure-function studies by protein engineering, a cDNA library from sea anemone, Actinia equina, was screened. A positive clone of 888 nucleotides was shown to encode a protein of 231 amino acids, including the signal sequence. The mature protein region was amplified by PCR, cloned into the pET22b(+)cas expression vector and expressed in Escherichia coli. Isolation of active recombinant equistatin required only one purification step, the His-tag affinity column. The protein displays physical and inhibitory properties closely similar to the native inhibitor.
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Affiliation(s)
- K Galesa
- Department of Biochemistry and Molecular Biology, J. Stefan Institute, Ljubljana, Slovenia
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45
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Lenarcic B, Turk V. Thyroglobulin type-1 domains in equistatin inhibit both papain-like cysteine proteinases and cathepsin D. J Biol Chem 1999; 274:563-6. [PMID: 9872988 DOI: 10.1074/jbc.274.2.563] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Equistatin from sea anemone is a protein composed of three thyroglobulin-type 1 domains known to inhibit papain-like cysteine proteinases, papain, and cathepsins B and L. Limited proteolysis was used to dissect equistatin into a first domain, eq d-1, and a combined second and third domain, eq d-2,3. Only the N-terminal domain inhibits papain (Ki = 0.61 nM). Remarkably, equistatin also strongly inhibits cathepsin D with Ki = 0.3 nM but not other aspartic proteinases such as pepsin, chymosin, and HIV-PR. This activity resides on the eq d-2,3 domains (Ki = 0.4 nM). Papain and cathepsin D can be bound and inhibited simultaneously by equistatin at pH 4.5, confirming the physical separation of the two binding sites. Equistatin is the first inhibitor of animal origin known to inhibit cathepsin D. The obtained results demonstrate that the widely distributed thyroglobulin type-1 domains can support a variety of functions.
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Affiliation(s)
- B Lenarcic
- Department of Biochemistry and Molecular Biology, J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia.
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46
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Sham HL, Kempf DJ, Molla A, Marsh KC, Kumar GN, Chen CM, Kati W, Stewart K, Lal R, Hsu A, Betebenner D, Korneyeva M, Vasavanonda S, McDonald E, Saldivar A, Wideburg N, Chen X, Niu P, Park C, Jayanti V, Grabowski B, Granneman GR, Sun E, Japour AJ, Leonard JM, Plattner JJ, Norbeck DW. ABT-378, a highly potent inhibitor of the human immunodeficiency virus protease. Antimicrob Agents Chemother 1998; 42:3218-24. [PMID: 9835517 PMCID: PMC106025 DOI: 10.1128/aac.42.12.3218] [Citation(s) in RCA: 331] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/1998] [Accepted: 09/11/1998] [Indexed: 11/20/2022] Open
Abstract
The valine at position 82 (Val 82) in the active site of the human immunodeficiency virus (HIV) protease mutates in response to therapy with the protease inhibitor ritonavir. By using the X-ray crystal structure of the complex of HIV protease and ritonavir, the potent protease inhibitor ABT-378, which has a diminished interaction with Val 82, was designed. ABT-378 potently inhibited wild-type and mutant HIV protease (Ki = 1.3 to 3.6 pM), blocked the replication of laboratory and clinical strains of HIV type 1 (50% effective concentration [EC50], 0.006 to 0.017 microM), and maintained high potency against mutant HIV selected by ritonavir in vivo (EC50, =0. 06 microM). The metabolism of ABT-378 was strongly inhibited by ritonavir in vitro. Consequently, following concomitant oral administration of ABT-378 and ritonavir, the concentrations of ABT-378 in rat, dog, and monkey plasma exceeded the in vitro antiviral EC50 in the presence of human serum by >50-fold after 8 h. In healthy human volunteers, coadministration of a single 400-mg dose of ABT-378 with 50 mg of ritonavir enhanced the area under the concentration curve of ABT-378 in plasma by 77-fold over that observed after dosing with ABT-378 alone, and mean concentrations of ABT-378 exceeded the EC50 for >24 h. These results demonstrate the potential utility of ABT-378 as a therapeutic intervention against AIDS.
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Affiliation(s)
- H L Sham
- Departments of Infectious Diseases Research, Abbott Laboratories, Abbott Park, Illinois 60064, USA.
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47
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Berri M, Rouchon P, Zabari M, Ouali A. Purification and characterization of a new potential in vivo inhibitor of cathepsin L from bovine skeletal muscle. Comp Biochem Physiol B Biochem Mol Biol 1998; 119:283-8. [PMID: 9629660 DOI: 10.1016/s0305-0491(97)00326-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Four papain-inhibiting peaks, labeled F-I, F-II, F-III, and F-IV, were fractionated from a crude bovine muscle extract by gel filtration chromatography on Sephadex G100, and the F-III fraction was analyzed. From F-III, a cysteine proteinase inhibitor was purified by two successive anionic exchange chromatography steps on Q-Sepharose and Mono-Q columns. This inhibitor has a molecular weight of about 30 kDa. Regarding its specificity toward different proteinases, the purified 30 kDa inhibitor was inactive against serine (trypsin and chymotrypsin) and aspartyl (pepsin) families. In contrast, cathepsin L, H, B, and papain, four enzymes of the cysteine class were strongly inhibited suggesting that this inhibitor was specific to the cysteine proteinase group. However, no inhibitory activity was shown against calpains. Kinetic parameters, including inhibition constants (Ki), rate constant for association (kass) and time required for almost complete inhibition of proteinase in vivo were determined. The values are consistent with a possible physiological function for this inhibitor protein in controlling in vivo cathepsin L activity.
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Affiliation(s)
- M Berri
- Muscle Biochemistry Laboratory, SRV, INRA, St Genès Champanelle, France
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48
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Mc Cormack T, Baumeister W, Grenier L, Moomaw C, Plamondon L, Pramanik B, Slaughter C, Soucy F, Stein R, Zühl F, Dick L. Active site-directed inhibitors of Rhodococcus 20 S proteasome. Kinetics and mechanism. J Biol Chem 1997; 272:26103-9. [PMID: 9334174 DOI: 10.1074/jbc.272.42.26103] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We have studied the mechanism of inhibition of the recombinant Rhodococcus proteasome by four different chemical classes of active site-directed small molecule inhibitors. Clasto-lactacystin beta-lactone is a time-dependent inhibitor of the Rhodococcus proteasome's ability to hydrolyze Suc-Leu-Leu-Val-Tyr-AMC, a substrate for this proteasome's single type of active site, and proceeds with a kinact/[I] of 1,700 M-1 s-1. Using peptide mapping of tryptic digests, LC/MS, and amino acid sequence analysis, we have established that the Ogamma of the hydroxyl group on the N-terminal threonine of the beta-subunit is the sole modification made by the beta-lactone. Active site titrations of the Rhodococcus proteasome with reversible peptide aldehydes show the expected stoichiometry of one inhibitor molecule per beta-subunit. Prior modification with beta-lactone completely abrogates the binding of peptidyl boronic acid inhibitors, suggesting that these inhibitors also inactivate the enzyme by reacting with the Ogamma moiety on Thr1. High performance liquid chromatography analysis of peptidyl vinyl sulfone-modified intact Rhodococcus proteasome beta-subunit and its tryptic peptides suggests that the peptidyl vinyl sulfone modifies a residue in the N-terminal 20 amino acids. This modification is also blocked by prior treatment with beta-lactone.
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Affiliation(s)
- T Mc Cormack
- ProScript Inc., Cambridge, Massachusetts 02139, USA
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49
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Marchot P, Prowse CN, Kanter J, Camp S, Ackermann EJ, Radić Z, Bougis PE, Taylor P. Expression and activity of mutants of fasciculin, a peptidic acetylcholinesterase inhibitor from mamba venom. J Biol Chem 1997; 272:3502-10. [PMID: 9013597 DOI: 10.1074/jbc.272.6.3502] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Fasciculin, a selective peptidic inhibitor of acetylcholinesterase, is a member of the three-fingered peptide toxin superfamily isolated from snake venoms. The availability of a crystal structure of a fasciculin 2 (Fas2)-acetylcholinesterase complex affords an opportunity to examine in detail the interaction of this toxin with its target site. To this end, we constructed a synthetic fasciculin gene with an appropriate leader peptide for expression and secretion from mammalian cells. Recombinant wild-type Fas2, expressed and amplified in Chinese hamster ovary cells, was purified to homogeneity and found to be identical in composition and biological activities to the venom-derived toxin. Sixteen mutations at positions where the crystal structure of the complex indicates a significant interfacial contact point or determinant of conformation were generated. Two mutants of loop I, T8A/T9A and R11Q, ten mutants of the longest loop II, R24T, K25L, R27W, R28D, H29D, DeltaPro30, P31R, K32G, M33A, and V34A/L35A, and two mutants of loop III, D45K and K51S, were expressed transiently in human embryonic kidney cells. Inhibitory potencies of the Fas2 mutants toward mouse AChE were established, based on titration of the mutants with a polyclonal anti-Fas2 serum. The Arg27, Pro30, and Pro31 mutants each lost two or more orders of magnitude in Fas2 activity, suggesting that this subset of three residues, at the tip of loop II, dominates the loop conformation and interaction of Fas2 with the enzyme. The Arg24, Lys32, and Met33 mutants lost about one order of magnitude, suggesting that these residues make moderate contributions to the strength of the complex, whereas the Lys25, Arg28, Val34-Leu35, Asp45, and Lys51 mutants appeared as active as Fas2. The Thr8-Thr9, Arg11, and His29 mutants showed greater ratios of inhibitory activity to immunochemical titer than Fas2. This may reflect immunodominant determinants in these regions or intramolecular rearrangements in conformation that enhance the interaction. Of the many Fas2 residues that lie at the interface with acetylcholinesterase, only a few appear to provide substantial energetic contributions to the high affinity of the complex.
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Affiliation(s)
- P Marchot
- Department of Pharmacology, University of California at San Diego, La Jolla, California 92093-0636, USA
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50
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Farazi T, Leichman J, Harris T, Cahoon M, Hedstrom L. Isolation and characterization of mycophenolic acid-resistant mutants of inosine-5'-monophosphate dehydrogenase. J Biol Chem 1997; 272:961-5. [PMID: 8995388 DOI: 10.1074/jbc.272.2.961] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Mycophenolic acid (MPA) is a potent and specific inhibitor of mammalian inosine-monophosphate dehydrogenases (IMPDH); most microbial IMPDHs are not sensitive to MPA. MPA-resistant mutants of human IMPDH type II were isolated in order to identify the structural features that determine the species selectivity of MPA. Three mutant IMPDHs were identified with decreased affinity for MPA The mutation of Gln277 --> Arg causes a 9-fold increase in the Ki of MPA, a 5-6-fold increase in the Km values for IMP and NAD, and a 3-fold decrease in kcat relative to wild type. The mutation of Ala462 --> Thr causes a 3-fold increase in the Ki for MPA, a 2.5-fold increase in the Km for NAD, and a 1.5-fold increase in kcat. The combination of these two mutations does not increase the Ki for MPA, but does increase the Km for NAD 3-fold relative to Q277R and restores kcat to wild type levels. Q277R/A462T is the first human IMPDH mutant with increased Ki for MPA and wild type activity. The third mutant IMPDH contains two mutations, Phe465 --> Ser and Asp470 --> Gly. Ki for MPA is increased 3-fold in this mutant enzyme, and Km for IMP is also increased 3-fold, while the Km for NAD and kcat are unchanged. Thus increases in the Ki for MPA do not correlate with changes in Km for either IMP or NAD, nor to changes in kcat. All four of these mutations are in regions of the IMPDH that differ in mammalian and microbial enzymes, and thus can be structural determinants of MPA selectivity.
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Affiliation(s)
- T Farazi
- Graduate Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02254, USA
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