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Hillebrand L, Liang XJ, Serafim RAM, Gehringer M. Emerging and Re-emerging Warheads for Targeted Covalent Inhibitors: An Update. J Med Chem 2024; 67:7668-7758. [PMID: 38711345 DOI: 10.1021/acs.jmedchem.3c01825] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Covalent inhibitors and other types of covalent modalities have seen a revival in the past two decades, with a variety of new targeted covalent drugs having been approved in recent years. A key feature of such molecules is an intrinsically reactive group, typically a weak electrophile, which enables the irreversible or reversible formation of a covalent bond with a specific amino acid of the target protein. This reactive group, often called the "warhead", is a critical determinant of the ligand's activity, selectivity, and general biological properties. In 2019, we summarized emerging and re-emerging warhead chemistries to target cysteine and other amino acids (Gehringer, M.; Laufer, S. A. J. Med. Chem. 2019, 62, 5673-5724; DOI: 10.1021/acs.jmedchem.8b01153). Since then, the field has rapidly evolved. Here we discuss the progress on covalent warheads made since our last Perspective and their application in medicinal chemistry and chemical biology.
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Affiliation(s)
- Laura Hillebrand
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Xiaojun Julia Liang
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
| | - Ricardo A M Serafim
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Matthias Gehringer
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
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2
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Xie X, Lan Q, Zhao J, Zhang S, Liu L, Zhang Y, Xu W, Shao M, Peng J, Xia S, Zhu Y, Zhang K, Zhang X, Zhang R, Li J, Dai W, Ge Z, Hu S, Yu C, Wang J, Ma D, Zheng M, Yang H, Xiao G, Rao Z, Lu L, Zhang L, Bai F, Zhao Y, Jiang S, Liu H. Structure-based design of pan-coronavirus inhibitors targeting host cathepsin L and calpain-1. Signal Transduct Target Ther 2024; 9:54. [PMID: 38443334 PMCID: PMC10914734 DOI: 10.1038/s41392-024-01758-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 01/19/2024] [Accepted: 01/25/2024] [Indexed: 03/07/2024] Open
Abstract
Respiratory disease caused by coronavirus infection remains a global health crisis. Although several SARS-CoV-2-specific vaccines and direct-acting antivirals are available, their efficacy on emerging coronaviruses in the future, including SARS-CoV-2 variants, might be compromised. Host-targeting antivirals provide preventive and therapeutic strategies to overcome resistance and manage future outbreak of emerging coronaviruses. Cathepsin L (CTSL) and calpain-1 (CAPN1) are host cysteine proteases which play crucial roles in coronaviral entrance into cells and infection-related immune response. Here, two peptidomimetic α-ketoamide compounds, 14a and 14b, were identified as potent dual target inhibitors against CTSL and CAPN1. The X-ray crystal structures of human CTSL and CAPN1 in complex with 14a and 14b revealed the covalent binding of α-ketoamide groups of 14a and 14b to C25 of CTSL and C115 of CAPN1. Both showed potent and broad-spectrum anticoronaviral activities in vitro, and it is worth noting that they exhibited low nanomolar potency against SARS-CoV-2 and its variants of concern (VOCs) with EC50 values ranging from 0.80 to 161.7 nM in various cells. Preliminary mechanistic exploration indicated that they exhibited anticoronaviral activity through blocking viral entrance. Moreover, 14a and 14b exhibited good oral pharmacokinetic properties in mice, rats and dogs, and favorable safety in mice. In addition, both 14a and 14b treatments demonstrated potent antiviral potency against SARS-CoV-2 XBB 1.16 variant infection in a K18-hACE2 transgenic mouse model. And 14b also showed effective antiviral activity against HCoV-OC43 infection in a mouse model with a final survival rate of 60%. Further evaluation showed that 14a and 14b exhibited excellent anti-inflammatory effects in Raw 264.7 mouse macrophages and in mice with acute pneumonia. Taken together, these results suggested that 14a and 14b are promising drug candidates, providing novel insight into developing pan-coronavirus inhibitors with antiviral and anti-inflammatory properties.
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Affiliation(s)
- Xiong Xie
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiaoshuai Lan
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, 200032, China
| | - Jinyi Zhao
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Sulin Zhang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lu Liu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Yumin Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Wei Xu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, 200032, China
| | - Maolin Shao
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Jingjing Peng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuai Xia
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, 200032, China
| | - Yan Zhu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Keke Zhang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xian Lin Road, Jiangsu, 210023, Nanjing, China
| | - Xianglei Zhang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Ruxue Zhang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Jian Li
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xian Lin Road, Jiangsu, 210023, Nanjing, China
| | - Wenhao Dai
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhen Ge
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xian Lin Road, Jiangsu, 210023, Nanjing, China
| | - Shulei Hu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Changyue Yu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiang Wang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dakota Ma
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Mingyue Zheng
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xian Lin Road, Jiangsu, 210023, Nanjing, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, 310024, China
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Gengfu Xiao
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Zihe Rao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, 200032, China
| | - Leike Zhang
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Fang Bai
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Yao Zhao
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, 518112, China.
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, 200032, China.
| | - Hong Liu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xian Lin Road, Jiangsu, 210023, Nanjing, China.
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, 310024, China.
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3
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Das B, Baidya ATK, Devi B, Rom T, Paul AK, Thakur B, Darreh-Shori T, Kumar R. Synthesis, single crystal X-ray, DFT, spectroscopic, molecular docking studies and in vitro biological evaluation of compound N-benzyl-4-(4-chlorophenyl)-2-oxobutanamide. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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4
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Li L, Chenna BC, Yang KS, Cole TR, Goodall ZT, Giardini M, Moghadamchargari Z, Hernandez EA, Gomez J, Calvet CM, Bernatchez JA, Mellott DM, Zhu J, Rademacher A, Thomas D, Blankenship LR, Drelich A, Laganowsky A, Tseng CTK, Liu WR, Wand AJ, Cruz-Reyes J, Siqueira-Neto JL, Meek TD. Self-Masked Aldehyde Inhibitors: A Novel Strategy for Inhibiting Cysteine Proteases. J Med Chem 2021; 64:11267-11287. [PMID: 34288674 PMCID: PMC10504874 DOI: 10.1021/acs.jmedchem.1c00628] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cysteine proteases comprise an important class of drug targets, especially for infectious diseases such as Chagas disease (cruzain) and COVID-19 (3CL protease, cathepsin L). Peptide aldehydes have proven to be potent inhibitors for all of these proteases. However, the intrinsic, high electrophilicity of the aldehyde group is associated with safety concerns and metabolic instability, limiting the use of aldehyde inhibitors as drugs. We have developed a novel class of self-masked aldehyde inhibitors (SMAIs) for cruzain, the major cysteine protease of the causative agent of Chagas disease-Trypanosoma cruzi. These SMAIs exerted potent, reversible inhibition of cruzain (Ki* = 18-350 nM) while apparently protecting the free aldehyde in cell-based assays. We synthesized prodrugs of the SMAIs that could potentially improve their pharmacokinetic properties. We also elucidated the kinetic and chemical mechanism of SMAIs and applied this strategy to the design of anti-SARS-CoV-2 inhibitors.
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Affiliation(s)
- Linfeng Li
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
| | - Bala C Chenna
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
| | - Kai S Yang
- Department of Chemistry, Texas A&M University, 580 Ross Street, College Station, Texas 77843, United States
| | - Taylor R Cole
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
| | - Zachary T Goodall
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
| | - Miriam Giardini
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr, La Jolla, California 92093, United States
| | - Zahra Moghadamchargari
- Department of Chemistry, Texas A&M University, 580 Ross Street, College Station, Texas 77843, United States
| | - Elizabeth A Hernandez
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
| | - Jana Gomez
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
| | - Claudia M Calvet
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr, La Jolla, California 92093, United States
| | - Jean A Bernatchez
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr, La Jolla, California 92093, United States
| | - Drake M Mellott
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
| | - Jiyun Zhu
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
| | - Andrew Rademacher
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
| | - Diane Thomas
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr, La Jolla, California 92093, United States
| | - Lauren R Blankenship
- Department of Chemistry, Texas A&M University, 580 Ross Street, College Station, Texas 77843, United States
| | - Aleksandra Drelich
- Department of Microbiology and Immunology, University of Texas Medical Branch, 301 University Blvd, Galveston, Texas 77555, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, 580 Ross Street, College Station, Texas 77843, United States
| | - Chien-Te K Tseng
- Department of Microbiology and Immunology, University of Texas Medical Branch, 301 University Blvd, Galveston, Texas 77555, United States
| | - Wenshe R Liu
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
- Department of Chemistry, Texas A&M University, 580 Ross Street, College Station, Texas 77843, United States
| | - A Joshua Wand
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
| | - Jorge Cruz-Reyes
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
| | - Jair L Siqueira-Neto
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr, La Jolla, California 92093, United States
| | - Thomas D Meek
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, Texas 77843, United States
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5
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Chen R, Jia RL, Li W, Zhao W, Wang KK, Wang ZY, Ma X, Dai W, Sun A. A copper iodide-catalyzed coupling reaction of benzofuran-3(2H)-ones with amines: an approach to α-ketoamides. Org Biomol Chem 2021; 19:5294-5297. [PMID: 34085691 DOI: 10.1039/d1ob00715g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A CuI-catalyzed coupling reaction of benzofuran-3(2H)-ones with amines has been well established for the direct synthesis of α-ketoamides. This process involves C-O bond cleavage and C[double bond, length as m-dash]O/C-N bond formation. Mechanism studies indicated that this α-ketoamide formation reaction may involve a free radical process.
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Affiliation(s)
- Rongxiang Chen
- School of Pharmacy, Xinxiang University, Xinxiang 453000, P.R. of China.
| | - Ruo-Ling Jia
- School of Pharmacy, Xinxiang University, Xinxiang 453000, P.R. of China.
| | - Wenbo Li
- School of Chemistry and Materials Engineering, Xinxiang University, Xinxiang 453000, P.R. of China
| | - Wei Zhao
- School of Pharmacy, Xinxiang University, Xinxiang 453000, P.R. of China.
| | - Kai-Kai Wang
- School of Pharmacy, Xinxiang University, Xinxiang 453000, P.R. of China.
| | - Zhan-Yong Wang
- School of Pharmacy, Xinxiang University, Xinxiang 453000, P.R. of China.
| | - Xueji Ma
- School of Pharmacy, Xinxiang University, Xinxiang 453000, P.R. of China.
| | - Wei Dai
- School of Pharmacy, Xinxiang University, Xinxiang 453000, P.R. of China.
| | - Aili Sun
- School of Pharmacy, Xinxiang University, Xinxiang 453000, P.R. of China.
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6
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Robello M, Barresi E, Baglini E, Salerno S, Taliani S, Settimo FD. The Alpha Keto Amide Moiety as a Privileged Motif in Medicinal Chemistry: Current Insights and Emerging Opportunities. J Med Chem 2021; 64:3508-3545. [PMID: 33764065 PMCID: PMC8154582 DOI: 10.1021/acs.jmedchem.0c01808] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Over the years, researchers in drug discovery have taken advantage of the use of privileged structures to design innovative hit/lead molecules. The α-ketoamide motif is found in many natural products, and it has been widely exploited by medicinal chemists to develop compounds tailored to a vast range of biological targets, thus presenting clinical potential for a plethora of pathological conditions. The purpose of this perspective is to provide insights into the versatility of this chemical moiety as a privileged structure in drug discovery. After a brief analysis of its physical-chemical features and synthetic procedures to obtain it, α-ketoamide-based classes of compounds are reported according to the application of this motif as either a nonreactive or reactive moiety. The goal is to highlight those aspects that may be useful to understanding the perspectives of employing the α-ketoamide moiety in the rational design of compounds able to interact with a specific target.
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Affiliation(s)
- Marco Robello
- Synthetic Bioactive Molecules Section, LBC, NIDDK, NIH, 8 Center Drive, Room 404, Bethesda, Maryland 20892, United States
| | - Elisabetta Barresi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Emma Baglini
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Silvia Salerno
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Sabrina Taliani
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Federico Da Settimo
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
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7
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Spinozzi S, Albini S, Best H, Richard I. Calpains for dummies: What you need to know about the calpain family. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140616. [PMID: 33545367 DOI: 10.1016/j.bbapap.2021.140616] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/29/2021] [Accepted: 01/30/2021] [Indexed: 12/17/2022]
Abstract
This review was written in memory of our late friend, Dr. Hiroyuki Sorimachi, who, following the steps of his mentor Koichi Suzuki, a pioneer in calpain research, has made tremendous contributions to the field. During his career, Hiro also wrote several reviews on calpain, the last of which, published in 2016, was comprehensive. In this manuscript, we decided to put together a review with the basic information a novice may need to know about calpains. We also tried to avoid similarities with previous reviews and reported the most significant new findings, at the same time highlighting Hiro's contributions to the field. The review will cover a short history of calpain discovery, the presentation of the family, the life of calpain from transcription to activity, human diseases caused by calpain mutations and therapeutic perspectives.
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Affiliation(s)
- Simone Spinozzi
- Genethon, 1 bis, Rue de l'Internationale - 91000 Evry, France; Université Paris-Saclay, Univ Evry, Inserm, Genethon, Integrare Research Unit UMR_S951, 91000, Evry, France
| | - Sonia Albini
- Genethon, 1 bis, Rue de l'Internationale - 91000 Evry, France; Université Paris-Saclay, Univ Evry, Inserm, Genethon, Integrare Research Unit UMR_S951, 91000, Evry, France
| | - Heather Best
- Genethon, 1 bis, Rue de l'Internationale - 91000 Evry, France; Université Paris-Saclay, Univ Evry, Inserm, Genethon, Integrare Research Unit UMR_S951, 91000, Evry, France
| | - Isabelle Richard
- Genethon, 1 bis, Rue de l'Internationale - 91000 Evry, France; Université Paris-Saclay, Univ Evry, Inserm, Genethon, Integrare Research Unit UMR_S951, 91000, Evry, France.
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8
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Jastaniah A, Gaisina IN, Knopp RC, Thatcher GRJ. Synthesis of α-Ketoamide-Based Stereoselective Calpain-1 Inhibitors as Neuroprotective Agents. ChemMedChem 2020; 15:2280-2285. [PMID: 32840034 DOI: 10.1002/cmdc.202000385] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/23/2020] [Indexed: 01/05/2023]
Abstract
Calpain inhibitors have been proposed as drug candidates for neurodegenerative disorders, with ABT-957 entering clinical trials for Alzheimer's disease and mild cognitive impairment. The structure of ABT-957 was very recently disclosed, and trials were terminated owing to inadequate CNS concentrations to obtain a pharmacodynamic effect. The multistep synthesis of an α-ketoamide peptidomimetic inhibitor series potentially including ABT-957 was optimized to yield diastereomerically pure compounds that are potent and selective for calpain-1 over papain and cathepsins B and K. As the final oxidation step, with its optimized synthesis protocol, does not alter the configuration of the substrate, the synthesis of the diastereomeric pair (R)-1-benzyl-N-((S)-4-((4-fluorobenzyl)amino)-3,4-dioxo-1-phenylbutan-2-yl)-5-oxopyrrolidine-2-carboxamide (1 c) and (R)-1-benzyl-N-((R)-4-((4-fluorobenzyl)amino)-3,4-dioxo-1-phenylbutan-2-yl)-5-oxopyrrolidine-2-carboxamide (1 g) was feasible. This allowed the exploration of stereoselective inhibition of calpain-1, with 1 c (IC50 =78 nM) being significantly more potent than 1 g. Moreover, inhibitor 1 c restored cognitive function in amnestic mice.
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Affiliation(s)
- Ammar Jastaniah
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL., 60612, USA
| | - Irina N Gaisina
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL., 60612, USA
| | - Rachel C Knopp
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL., 60612, USA
| | - Gregory R J Thatcher
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL., 60612, USA
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9
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Velez G, Sun YJ, Khan S, Yang J, Herrmann J, Chemudupati T, MacLaren RE, Gakhar L, Wakatsuki S, Bassuk AG, Mahajan VB. Structural Insights into the Unique Activation Mechanisms of a Non-classical Calpain and Its Disease-Causing Variants. Cell Rep 2020; 30:881-892.e5. [PMID: 31968260 PMCID: PMC7001764 DOI: 10.1016/j.celrep.2019.12.077] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/26/2019] [Accepted: 12/19/2019] [Indexed: 12/12/2022] Open
Abstract
Increased calpain activity is linked to neuroinflammation including a heritable retinal disease caused by hyper-activating mutations in the calcium-activated calpain-5 (CAPN5) protease. Although structures for classical calpains are known, the structure of CAPN5, a non-classical calpain, remains undetermined. Here we report the 2.8 Å crystal structure of the human CAPN5 protease core (CAPN5-PC). Compared to classical calpains, CAPN5-PC requires high calcium concentrations for maximal activity. Structure-based phylogenetic analysis and multiple sequence alignment reveal that CAPN5-PC contains three elongated flexible loops compared to its classical counterparts. The presence of a disease-causing mutation (c.799G>A, p.Gly267Ser) on the unique PC2L2 loop reveals a function in this region for regulating enzymatic activity. This mechanism could be transferred to distant calpains, using synthetic calpain hybrids, suggesting an evolutionary mechanism for fine-tuning calpain function by modifying flexible loops. Further, the open (inactive) conformation of CAPN5-PC provides structural insight into CAPN5-specific residues that can guide inhibitor design.
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Affiliation(s)
- Gabriel Velez
- Omics Laboratory, Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA; Medical Scientist Training Program, University of Iowa, Iowa City, IA 52242, USA
| | - Young Joo Sun
- Omics Laboratory, Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
| | - Saif Khan
- Protein and Crystallography Facility, University of Iowa, Iowa City, IA 52242, USA; Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA; Department of Biology and Biochemistry, University of Bath, Bath BA2 7AX, UK
| | - Jing Yang
- Omics Laboratory, Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
| | - Jonathan Herrmann
- Department of Structural Biology, Stanford University, Palo Alto, CA 94305, USA; Photon Science, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Teja Chemudupati
- Omics Laboratory, Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
| | - Robert E MacLaren
- NIHR Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford EC1V 2PD, UK; Oxford Eye Hospital, University of Oxford NHS Trust, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Lokesh Gakhar
- Protein and Crystallography Facility, University of Iowa, Iowa City, IA 52242, USA; Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Soichi Wakatsuki
- Department of Structural Biology, Stanford University, Palo Alto, CA 94305, USA; Photon Science, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - Vinit B Mahajan
- Omics Laboratory, Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA; Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA.
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10
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Fournier J, Chen K, Mailyan AK, Jackson JJ, Buckman BO, Emayan K, Yuan S, Rajagopalan R, Misialek S, Adler M, Blaesse M, Griessner A, Zakarian A. Total Synthesis of Covalent Cysteine Protease Inhibitor N-Desmethyl Thalassospiramide C and Crystallographic Evidence for Its Mode of Action. Org Lett 2019; 21:508-512. [DOI: 10.1021/acs.orglett.8b03821] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jeremy Fournier
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93111, United States
| | - Karen Chen
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93111, United States
| | - Artur K. Mailyan
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93111, United States
| | - Jeffrey J. Jackson
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93111, United States
| | - Brad O. Buckman
- Blade Therapeutics, 442 Littlefield Avenue, South San Francisco, California 94080, United States
| | - Kumar Emayan
- Bayside Pharma, 2600 Hilltop Drive, Richmond, California 94806, United States
| | - Shendong Yuan
- Bayside Pharma, 2600 Hilltop Drive, Richmond, California 94806, United States
| | - Ravi Rajagopalan
- Blade Therapeutics, 442 Littlefield Avenue, South San Francisco, California 94080, United States
| | - Shawn Misialek
- Blade Therapeutics, 442 Littlefield Avenue, South San Francisco, California 94080, United States
| | - Marc Adler
- ChemPartner, 280 Utah Avenue Suite 100, South San Francisco, California 94080, United States
| | - Michael Blaesse
- Proteros Biostructures GmbH, Bunsenstraße 7 a, 82152 Planegg-Martinsried, Germany
| | - Andreas Griessner
- Proteros Biostructures GmbH, Bunsenstraße 7 a, 82152 Planegg-Martinsried, Germany
| | - Armen Zakarian
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93111, United States
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11
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Tripeptide analogues of MG132 as protease inhibitors. Bioorg Med Chem 2018; 27:436-441. [PMID: 30581047 DOI: 10.1016/j.bmc.2018.12.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 12/12/2018] [Accepted: 12/13/2018] [Indexed: 12/17/2022]
Abstract
The 26S proteasome and calpain are linked to a number of important human diseases. Here, we report a series of analogues of the prototypical tripeptide aldehyde inhibitor MG132 that show a unique combination of high activity and selectivity for calpains over proteasome. Tripeptide aldehydes (1-3) with an aromatic P3 substituent show enhanced activity and selectivity against ovine calpain 2 relative to chymotrypsin-like activity of proteasome. Docking studies reveal the key contacts between inhibitors and calpain to confirm the importance of the S3 pocket with respect to selectivity between calpains 1 and 2 and the proteasome.
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12
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McCartney CSE, Ye Q, Campbell RL, Davies PL. Insertion sequence 1 from calpain-3 is functional in calpain-2 as an internal propeptide. J Biol Chem 2018; 293:17716-17730. [PMID: 30254072 DOI: 10.1074/jbc.ra118.004803] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 09/18/2018] [Indexed: 11/06/2022] Open
Abstract
Calpains are intracellular, calcium-activated cysteine proteases. Calpain-3 is abundant in skeletal muscle, where its mutation-induced loss of function causes limb-girdle muscular dystrophy type 2A. Unlike the small subunit-containing calpain-1 and -2, the calpain-3 isoform homodimerizes through pairing of its C-terminal penta-EF-hand domain. It also has two unique insertion sequences (ISs) not found in the other calpains: IS1 within calpain-3's protease core and IS2 just prior to the penta-EF-hand domain. Production of either native or recombinant full-length calpain-3 to characterize the function of these ISs is challenging. Therefore, here we used recombinant rat calpain-2 as a stable surrogate and inserted IS1 into its equivalent position in the protease core. As it does in calpain-3, IS1 occupied the catalytic cleft and restricted the enzyme's access to substrate and inhibitors. Following activation by Ca2+, IS1 was rapidly cleaved by intramolecular autolysis, permitting the enzyme to freely accept substrate and inhibitors. The surrogate remained functional until extensive intermolecular autoproteolysis inactivated the enzyme, as is typical of calpain-2. Although the small-molecule inhibitors E-64 and leupeptin limited intermolecular autolysis of the surrogate, they did not block the initial intramolecular cleavage of IS1, establishing its role as a propeptide. Surprisingly, the large-molecule calpain inhibitor, calpastatin, completely blocked enzyme activity, even with IS1 intact. We suggest that calpastatin is large enough to oust IS1 from the catalytic cleft and take its place. We propose an explanation for why calpastatin can inhibit calpain-2 bearing the IS1 insertion but cannot inhibit WT calpain-3.
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Affiliation(s)
- Christian-Scott E McCartney
- From the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Qilu Ye
- From the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Robert L Campbell
- From the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Peter L Davies
- From the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada.
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13
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Romo-Mancillas A, Lemus R, Pérez-Estrada R, Kuribreña-Romero de Terreros F, Domínguez-Ramírez L. Molecular dynamic simulations of the catalytic subunit of calpains 1, 2, 5, and 10: Structural analysis with an aim toward drug design. Chem Biol Drug Des 2018; 93:38-49. [PMID: 30107087 DOI: 10.1111/cbdd.13376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 05/21/2018] [Accepted: 07/07/2018] [Indexed: 12/14/2022]
Abstract
Calpains are cysteine proteases involved in the development of several human chronic illnesses such as neurodegenerative diseases, cardiovascular ailments, diabetes, and obesity which constitutes them into possible therapeutic targets. Here, using molecular dynamic simulations and docking, we studied the binding of known inhibitors to representative members of classical and nonclassical calpains. Our aim is to gain better understanding on the inhibition mechanism of calpains and to develop better and more specific inhibitors. Our atomistic models confirmed the importance of calcium ions for the structure of calpains and, as a consequence, their functionality. With these models and their subsequent use in molecular docking, essential structural requirements were identified for the binding of ligands to the calpain catalytic site that provide useful information for the design of new selective calpain inhibitors.
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Affiliation(s)
- Antonio Romo-Mancillas
- División de Estudios de Posgrado, Facultad de Química, Universidad Autónoma de Querétaro, Santiago de Querétaro, México.,Dirección de Nuevos Desarrollos, Landsteiner Scientific, Parque Industrial, Toluca, Mexico
| | - Roselyn Lemus
- Dirección de Nuevos Desarrollos, Landsteiner Scientific, Parque Industrial, Toluca, Mexico
| | - Raúl Pérez-Estrada
- Dirección de Nuevos Desarrollos, Landsteiner Scientific, Parque Industrial, Toluca, Mexico
| | | | - Lenin Domínguez-Ramírez
- Departamento de Ciencias Químico-Biológicas, Escuela de Ciencias, Universidad de las Américas Puebla, Santa Catarina Mártir Cholula, Puebla, Mexico
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14
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Ni K, Meng LG, Wang K, Wang L. Visible-Light-Promoted Oxidative Amidation of Bromoalkynes with Anilines: An Approach to α-Ketoamides. Org Lett 2018; 20:2245-2248. [PMID: 29600860 DOI: 10.1021/acs.orglett.8b00586] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A convenient and practical synthetic route to α-ketoamides from bromoalkynes and anilines through phototriggered organic transformations via a C-N cross-coupling and an oxidation of C≡C was developed. The reaction could be furnished without an external photocatalyst at ambient conditions, and a wide range of α-ketoamides were obtained in good yields.
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Affiliation(s)
- Ke Ni
- Department of Chemistry , Huaibei Normal University , Huaibei , Anhui 235000 , P. R. China
| | - Ling-Guo Meng
- Department of Chemistry , Huaibei Normal University , Huaibei , Anhui 235000 , P. R. China
| | - Kuai Wang
- Department of Chemistry , Huaibei Normal University , Huaibei , Anhui 235000 , P. R. China
| | - Lei Wang
- Department of Chemistry , Huaibei Normal University , Huaibei , Anhui 235000 , P. R. China.,State Key Laboratory of Organometallic Chemistry , Shanghai Institute of Organic Chemistry , Shanghai 200032 , P. R. China
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15
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A Synopsis of the Properties and Applications of Heteroaromatic Rings in Medicinal Chemistry. ADVANCES IN HETEROCYCLIC CHEMISTRY 2017. [DOI: 10.1016/bs.aihch.2016.11.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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16
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Gakhar L, Bassuk AG, Velez G, Khan S, Yang J, Tsang SH, Mahajan VB. Small-angle X-ray scattering of calpain-5 reveals a highly open conformation among calpains. J Struct Biol 2016; 196:309-318. [PMID: 27474374 PMCID: PMC5118095 DOI: 10.1016/j.jsb.2016.07.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 07/22/2016] [Accepted: 07/26/2016] [Indexed: 10/21/2022]
Abstract
Calpain-5 is a calcium-activated protease expressed in the retina. Mutations in calpain-5 cause autosomal dominant neovascular inflammatory vitreoretinopathy (ADNIV, OMIM#193235). The structure of calpain-5 has not been determined, thus hindering the investigation of its proteolytic targets and pathological role in ADNIV. Herein, we report models of the proteolytic core of calpain-5 (mini-calpain-5) containing two globular domains (termed DIIa-IIb) connected by a short, flexible linker, consistent with small-angle X-ray scattering (SAXS) data. Structural modeling in the absence of calcium suggests that mini-calpain-5 adopts a more open conformation when compared to previously determined structures of other calpain cores. This open conformation, achieved by a rotation of DIIa and DIIb with respect to each other, prevents formation of the active site and constrains the enzyme in an inactivated form. The relative domain rotation of 60-100° we found for mini-calpain-5 (a non-classical calpain) is significantly greater than the largest rotation previously observed for a classical calpain (i.e., 55.0° for mini-calpain-9). Together with our prediction that, in the full-length form, a long loop in DIIb (loop C1), a few residues downstream of the inter-domain linker, likely interacts with the shorter, acidic, inactivating loop on domain-III (DIII), these structural insights illuminate the complexity of calpain regulation. Moreover, our studies argue that pursuing higher resolution structural studies are necessary to understand the complex activity regulation prevalent in the calpain family and for the design of specific calpain inhibitors.
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Affiliation(s)
- Lokesh Gakhar
- Department of Biochemistry, University of Iowa, Iowa City, IA, USA; Protein Crystallography Facility, University of Iowa, Iowa City, IA, USA
| | - Alexander G Bassuk
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA; Omics Lab, University of Iowa, Iowa City, IA, USA
| | - Gabriel Velez
- Omics Lab, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, USA; Medical Scientist Training Program, University of Iowa, Iowa City, IA, USA
| | - Saif Khan
- Protein Crystallography Facility, University of Iowa, Iowa City, IA, USA
| | - Jing Yang
- Protein Crystallography Facility, University of Iowa, Iowa City, IA, USA
| | - Stephen H Tsang
- Barbara and Donald Jonas Laboratory of Stem Cells and Regenerative Medicine and Bernard & Shirlee Brown Glaucoma Laboratory, Edward S. Harkness Eye Institute, Columbia University, New York, NY, USA; Department of Pathology & Cell Biology, College of Physicians & Surgeons, Columbia University, New York, NY, USA
| | - Vinit B Mahajan
- Omics Lab, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, USA.
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17
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Ono Y, Saido TC, Sorimachi H. Calpain research for drug discovery: challenges and potential. Nat Rev Drug Discov 2016; 15:854-876. [PMID: 27833121 DOI: 10.1038/nrd.2016.212] [Citation(s) in RCA: 191] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Calpains are a family of proteases that were scientifically recognized earlier than proteasomes and caspases, but remain enigmatic. However, they are known to participate in a multitude of physiological and pathological processes, performing 'limited proteolysis' whereby they do not destroy but rather modulate the functions of their substrates. Calpains are therefore referred to as 'modulator proteases'. Multidisciplinary research on calpains has begun to elucidate their involvement in pathophysiological mechanisms. Therapeutic strategies targeting malfunctions of calpains have been developed, driven primarily by improvements in the specificity and bioavailability of calpain inhibitors. Here, we review the calpain superfamily and calpain-related disorders, and discuss emerging calpain-targeted therapeutic strategies.
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Affiliation(s)
- Yasuko Ono
- Calpain Project, Department of Advanced Science for Biomolecules, Tokyo Metropolitan Institute of Medical Science (IGAKUKEN), 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Takaomi C Saido
- Laboratory for Proteolytic Neuroscience, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hiroyuki Sorimachi
- Calpain Project, Department of Advanced Science for Biomolecules, Tokyo Metropolitan Institute of Medical Science (IGAKUKEN), 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
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18
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Pandey AK, Shukla SC, Bhattacharya P, Patnaik R. A possible therapeutic potential of quercetin through inhibition of μ-calpain in hypoxia induced neuronal injury: a molecular dynamics simulation study. Neural Regen Res 2016; 11:1247-53. [PMID: 27651771 PMCID: PMC5020822 DOI: 10.4103/1673-5374.189186] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2015] [Indexed: 12/24/2022] Open
Abstract
The neuroprotective property of quercetin is well reported against hypoxia and ischemia in past studies. This property of quercetin lies in its antioxidant property with blood-brain barrier permeability and anti-inflammatory capabilities. µ-Calpain, a calcium ion activated intracellular cysteine protease causes serious cellular insult, leading to cell death in various pathological conditions including hypoxia and ischemic stroke. Hence, it may be considered as a potential drug target for the treatment of hypoxia induced neuronal injury. As the inhibitory property of µ-calpain is yet to be explored in details, hence, in the present study, we investigated the interaction of quercetin with µ-calpain through a molecular dynamics simulation study as a tool through clarifying the molecular mechanism of such inhibition and determining the probable sites and modes of quercetin interaction with the µ-calpain catalytic domain. In addition, we also investigated the structure-activity relationship of quercetin with μ-calpain. Affinity binding of quercetin with µ-calpain had a value of -28.73 kJ/mol and a Ki value of 35.87 µM that may be a probable reason to lead to altered functioning of µ-calpain. Hence, quercetin was found to be an inhibitor of µ-calpain which might have a possible therapeutic role in hypoxic injury.
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Affiliation(s)
- Anand Kumar Pandey
- School of Biomedical Engineering, Indian Institute of Technology, Banaras Hindu University, Varanasi, India
| | - Swet Chand Shukla
- School of Biochemical Engineering, Indian Institute of Technology, Banaras Hindu University, Varanasi, India
| | - Pallab Bhattacharya
- School of Biomedical Engineering, Indian Institute of Technology, Banaras Hindu University, Varanasi, India
- Department of Neurology, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Ranjana Patnaik
- School of Biomedical Engineering, Indian Institute of Technology, Banaras Hindu University, Varanasi, India
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19
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Low KE, Ler S, Chen KJ, Campbell RL, Hickey JL, Tan J, Scully CCG, Davies PL, Yudin AK, Zaretsky S. Rational Design of Calpain Inhibitors Based on Calpastatin Peptidomimetics. J Med Chem 2016; 59:5403-15. [DOI: 10.1021/acs.jmedchem.6b00267] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Kristin E. Low
- Department
of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Spencer Ler
- Department
of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Kevin J. Chen
- Department
of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Robert L. Campbell
- Department
of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Jennifer L. Hickey
- Encycle Therapeutics Inc., 101
College Street, Suite 314, Toronto, Ontario M5G 1L7, Canada
| | - Joanne Tan
- Department
of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Conor C. G. Scully
- Department
of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Peter L. Davies
- Department
of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Andrei K. Yudin
- Department
of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Serge Zaretsky
- Department
of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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20
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Wert KJ, Bassuk AG, Wu WH, Gakhar L, Coglan D, Mahajan M, Wu S, Yang J, Lin CS, Tsang SH, Mahajan VB. CAPN5 mutation in hereditary uveitis: the R243L mutation increases calpain catalytic activity and triggers intraocular inflammation in a mouse model. Hum Mol Genet 2015; 24:4584-98. [PMID: 25994508 DOI: 10.1093/hmg/ddv189] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 05/18/2015] [Indexed: 12/21/2022] Open
Abstract
A single amino acid mutation near the active site of the CAPN5 protease was linked to the inherited blinding disorder, autosomal dominant neovascular inflammatory vitreoretinopathy (ADNIV, OMIM #193235). In homology modeling with other calpains, this R243L CAPN5 mutation was situated in a mobile loop that gates substrate access to the calcium-regulated active site. In in vitro activity assays, the mutation increased calpain protease activity and made it far more active at low concentrations of calcium. To test whether the disease allele could yield an animal model of ADNIV, we created transgenic mice expressing human (h) CAPN5(R243L) only in the retina. The resulting hCAPN5(R243L) transgenic mice developed a phenotype consistent with human uveitis and ADNIV, at the clinical, histological and molecular levels. The fundus of hCAPN5(R243L) mice showed enhanced autofluorescence (AF) and pigment changes indicative of reactive retinal pigment epithelial cells and photoreceptor degeneration. Electroretinography showed mutant mouse eyes had a selective loss of the b-wave indicating an inner-retina signaling defect. Histological analysis of mutant mouse eyes showed protein extravasation from dilated vessels into the anterior chamber and vitreous, vitreous inflammation, vitreous and retinal fibrosis and retinal degeneration. Analysis of gene expression changes in the hCAPN5(R243L) mouse retina showed upregulation of several markers, including members of the Toll-like receptor pathway, chemokines and cytokines, indicative of both an innate and adaptive immune response. Since many forms of uveitis share phenotypic characteristics of ADNIV, this mouse offers a model with therapeutic testing utility for ADNIV and uveitis patients.
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Affiliation(s)
- Katherine J Wert
- Barbara and Donald Jonas Laboratory of Stem Cells and Regenerative Medicine and Bernard and Shirlee Brown Glaucoma Laboratory, Edward S. Harkness Eye Institute, Institute of Human Nutrition, College of Physicians and Surgeons
| | | | - Wen-Hsuan Wu
- Barbara and Donald Jonas Laboratory of Stem Cells and Regenerative Medicine and Bernard and Shirlee Brown Glaucoma Laboratory, Edward S. Harkness Eye Institute
| | - Lokesh Gakhar
- Department of Biochemistry, Protein Crystallography Facility
| | - Diana Coglan
- Omics Laboratory and Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, USA
| | - MaryAnn Mahajan
- Omics Laboratory and Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, USA
| | - Shu Wu
- Department of Pediatrics and Neurology
| | - Jing Yang
- Protein Crystallography Facility, Omics Laboratory and
| | | | - Stephen H Tsang
- Barbara and Donald Jonas Laboratory of Stem Cells and Regenerative Medicine and Bernard and Shirlee Brown Glaucoma Laboratory, Edward S. Harkness Eye Institute, Institute of Human Nutrition, College of Physicians and Surgeons, Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY, USA,
| | - Vinit B Mahajan
- Omics Laboratory and Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, USA
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21
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Mechanism of action of thalassospiramides, a new class of calpain inhibitors. Sci Rep 2015; 5:8783. [PMID: 25740631 PMCID: PMC4350077 DOI: 10.1038/srep08783] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 02/04/2015] [Indexed: 11/10/2022] Open
Abstract
Thalassospiramides comprise a large family of lipopeptide natural products produced by Thalassospira and Tistrella marine bacteria. Here we provide further evidence of their nanomolar inhibitory activity against the human calpain 1 protease. Analysis of structure-activity relationship data supported our hypothesis that the rigid 12-membered ring containing an α,β-unsaturated carbonyl moiety is the pharmacologically active functional group, in contrast to classic electrophilic “warheads” in known calpain inhibitors. Using a combination of chemical modifications, mass spectrometric techniques, site-directed mutagenesis, and molecular modeling, we show the covalent binding of thalassospiramide's α,β-unsaturated carbonyl moiety to the thiol group of calpain's catalytic Cys115 residue by a Michael 1,4-addition reaction. As nanomolar calpain inhibitors with promising selectivity and low toxicity from natural sources are rare, we consider thalassospiramides as promising drug leads.
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22
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Understanding the interaction determinants of CAPN1 inhibition by CAST4 from bovines using molecular modeling techniques. Molecules 2014; 19:14316-51. [PMID: 25215589 PMCID: PMC6271145 DOI: 10.3390/molecules190914316] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 08/21/2014] [Accepted: 09/01/2014] [Indexed: 11/17/2022] Open
Abstract
HCV-induced CAPN activation and its effects on virus-infected cells in a host-immune system have been studied recently. It has been shown that the HCV-nonstructural 5A protein acts as both an inducer and a substrate for host CAPN protease; it participates in suppressing the TNF-α-induced apoptosis response and downstream IFN-induced antiviral processes. However, little is known regarding the disturbance of antiviral responses generated by bovine CAPN activation by BVDV, which is a surrogate model of HCV and is one of the most destructive diseases leading to great economic losses in cattle herds worldwide. This is also thought to be associated with the effects of either small CAPN inhibitors or the natural inhibitor CAST. They mainly bind to the binding site of CAPN substrate proteins and competitively inhibit the binding of the enzyme substrates to possibly defend against the two viruses (HCV and BVDV) for anti-viral immunity. To devise a new stratagem to discover lead candidates for an anti-BVDV drug, we first attempted to understand the bovine CAPN-CAST interaction sites and the interaction constraints of local binding architectures, were well reflected in the geometry between the pharmacophore features and its shape constraints identified using our modeled bovine CAPN1/CAST4 complex structures. We propose a computer-aided molecular design of an anti-BVDV drug as a mimetic CAST inhibitor to develop a rule-based screening function for adjusting the puzzle of relationship between bovine CAPN1 and the BVDV nonstructural proteins from all of the data obtained in the study.
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23
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Low KE, Karunan Partha S, Davies PL, Campbell RL. Allosteric inhibitors of calpains: Reevaluating inhibition by PD150606 and LSEAL. Biochim Biophys Acta Gen Subj 2014; 1840:3367-73. [PMID: 25196359 DOI: 10.1016/j.bbagen.2014.08.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 08/26/2014] [Accepted: 08/28/2014] [Indexed: 10/24/2022]
Abstract
BACKGROUND The mercaptoacrylate calpain inhibitor, PD150606, has been shown by X-ray crystallography to bind to a hydrophobic groove in the enzyme's penta-EF-hand domains far away from the catalytic cleft and has been previously described as an uncompetitive inhibitor of calpains. The penta-peptide LSEAL has been reported to be an inhibitor of calpain and was predicted to bind in the same hydrophobic groove. The X-ray crystal structure of calpain-2 bound to its endogenous calpain inhibitor, calpastatin, shows that calpastatin also binds to the hydrophobic grooves in the two penta-EF-hand domains, but its inhibitory domain binds to the protease core domains and blocks the active site cleft directly. METHODS The mechanisms of inhibition by PD150606 and LSEAL were investigated using steady-state kinetics of cleavage of a fluorogenic substrate by calpain-2 and the protease core of calpain1, as well as by examining the inhibition of casein hydrolysis by calpain and the autoproteolysis of calpain. RESULTS PD150606 inhibits both full-length calpain-2 and the protease core of calpain-1 with an apparent noncompetitive kinetic model. The penta-peptide LSEAL failed to inhibit either whole calpain or its protease core in vitro. CONCLUSIONS PD150606 cannot inhibit cleavage by calpain-2 of small substrates via binding to the penta-EF-hand domain. GENERAL SIGNIFICANCE PD150606 is often described as a calpain-specific inhibitor due to its ability to target the penta-EF-hand domains of calpain, but we show that it must be acting at a site on the protease core domain instead.
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Affiliation(s)
- Kristin E Low
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada.
| | - Sarathy Karunan Partha
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada.
| | - Peter L Davies
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada.
| | - Robert L Campbell
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada.
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Rosenberger TA. Targeting calpain-mediated proteolysis and peptide signaling as a strategy to reduce injury in multiple sclerosis. J Neurochem 2014; 130:161-4. [PMID: 24844646 DOI: 10.1111/jnc.12732] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Revised: 04/01/2014] [Accepted: 04/02/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Thad A Rosenberger
- University of North Dakota School of Medicine and Health Sciences, Department of Basic Sciences, Grand Forks, North Dakota
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25
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Virtual screening based on pharmacophoric features of known calpain inhibitors to identify potent inhibitors of calpain. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0842-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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26
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Analysis of the structure of calpain-10 and its interaction with the protease inhibitor SNJ-1715. Comput Biol Med 2013; 43:1334-40. [DOI: 10.1016/j.compbiomed.2013.07.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 07/07/2013] [Accepted: 07/11/2013] [Indexed: 01/24/2023]
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27
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Schiefer IT, Tapadar S, Litosh V, Siklos M, Scism R, Wijewickrama GT, Chandrasena EP, Sinha V, Tavassoli E, Brunsteiner M, Fa' M, Arancio O, Petukhov P, Thatcher GRJ. Design, synthesis, and optimization of novel epoxide incorporating peptidomimetics as selective calpain inhibitors. J Med Chem 2013; 56:6054-68. [PMID: 23834438 DOI: 10.1021/jm4006719] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Hyperactivation of the calcium-dependent cysteine protease calpain 1 (Cal1) is implicated as a primary or secondary pathological event in a wide range of illnesses and in neurodegenerative states, including Alzheimer's disease (AD). E-64 is an epoxide-containing natural product identified as a potent nonselective, calpain inhibitor, with demonstrated efficacy in animal models of AD. By use of E-64 as a lead, three successive generations of calpain inhibitors were developed using computationally assisted design to increase selectivity for Cal1. First generation analogues were potent inhibitors, effecting covalent modification of recombinant Cal1 catalytic domain (Cal1cat), demonstrated using LC-MS/MS. Refinement yielded second generation inhibitors with improved selectivity. Further library expansion and ligand refinement gave three Cal1 inhibitors, one of which was designed as an activity-based protein profiling probe. These were determined to be irreversible and selective inhibitors by kinetics studies comparing full length Cal1 with the general cysteine protease papain.
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Affiliation(s)
- Isaac T Schiefer
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL 60612-7231, USA
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Pehere AD, Pietsch M, Gütschow M, Neilsen PM, Pedersen DS, Nguyen S, Zvarec O, Sykes MJ, Callen DF, Abell AD. Synthesis and extended activity of triazole-containing macrocyclic protease inhibitors. Chemistry 2013; 19:7975-81. [PMID: 23606616 DOI: 10.1002/chem.201204260] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 03/12/2013] [Indexed: 12/26/2022]
Abstract
Peptide-derived protease inhibitors are an important class of compounds with the potential to treat a wide range of diseases. Herein, we describe the synthesis of a series of triazole-containing macrocyclic protease inhibitors pre-organized into a β-strand conformation and an evaluation of their activity against a panel of proteases. Acyclic azido-alkyne-based aldehydes are also evaluated for comparison. The macrocyclic peptidomimetics showed considerable activity towards calpain II, cathepsin L and S, and the 20S proteasome chymotrypsin-like activity. Some of the first examples of highly potent macrocyclic inhibitors of cathepsin S were identified. These adopt a well-defined β-strand geometry as shown by NMR spectroscopy, X-ray analysis, and molecular docking studies.
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Affiliation(s)
- Ashok D Pehere
- School of Chemistry & Physics, The University of Adelaide, North Terrace, Adelaide, SA 5005, Australia
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Abstract
Calpains are a family of complex multi-domain intracellular enzymes that share a calcium-dependent cysteine protease core. These are not degradative enzymes, but instead carry out limited cleavage of target proteins in response to calcium signalling. Selective cutting of cytoskeletal proteins to facilitate cell migration is one such function. The two most abundant and extensively studied members of this family in mammals, calpains 1 and 2, are heterodimers of an isoform-specific 80 kDa large subunit and a common 28 kDa small subunit. Structures of calpain-2, both Ca2+-free and bound to calpastatin in the activated Ca2+-bound state, have provided a wealth of information about the enzyme's structure-function relationships and activation. The main association between the subunits is the pairing of their C-terminal penta-EF-hand domains through extensive intimate hydrophobic contacts. A lesser contact is made between the N-terminal anchor helix of the large subunit and the penta-EF-hand domain of the small subunit. Up to ten Ca2+ ions are co-operatively bound during activation. The anchor helix is released and individual domains change their positions relative to each other to properly align the active site. Because calpains 1 and 2 require ~30 and ~350 μM Ca2+ ions for half-maximal activation respectively, it has long been argued that autoproteolysis, subunit dissociation, post-translational modifications or auxiliary proteins are needed to activate the enzymes in the cell, where Ca2+ levels are in the nanomolar range. In the absence of robust support for these mechanisms, it is possible that under normal conditions calpains are transiently activated by high Ca2+ concentrations in the microenvironment of a Ca2+ influx, and then return to an inactive state ready for reactivation.
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Metabolic stress response implicated in diabetic retinopathy: The role of calpain, and the therapeutic impact of calpain inhibitor. Neurobiol Dis 2012; 48:556-67. [DOI: 10.1016/j.nbd.2012.07.025] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 07/12/2012] [Accepted: 07/25/2012] [Indexed: 12/30/2022] Open
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Stuart BG, Coxon JM, Morton JD, Abell AD, McDonald DQ, Aitken SG, Jones MA, Bickerstaffe R. Molecular Modeling: A Search for a Calpain Inhibitor as a New Treatment for Cataractogenesis. J Med Chem 2011; 54:7503-22. [DOI: 10.1021/jm200471r] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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32
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Synthesis of cinnamoyl ketoamides as hybrid structures of antioxidants and calpain inhibitors. Bioorg Med Chem Lett 2011; 21:2850-4. [DOI: 10.1016/j.bmcl.2011.03.077] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Revised: 03/04/2011] [Accepted: 03/23/2011] [Indexed: 11/18/2022]
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33
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Donkor IO. Calpain inhibitors: a survey of compounds reported in the patent and scientific literature. Expert Opin Ther Pat 2011; 21:601-36. [DOI: 10.1517/13543776.2011.568480] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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34
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Ma H, Tochigi A, Shearer TR, Azuma M. Calpain inhibitor SNJ-1945 attenuates events prior to angiogenesis in cultured human retinal endothelial cells. J Ocul Pharmacol Ther 2010; 25:409-14. [PMID: 19857102 DOI: 10.1089/jop.2009.0030] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
PURPOSE Vascular endothelial growth factor (VEGF) is an important regulator of angiogenesis and microvascular permeability. VEGF-induced cytoskeletal reorganization plays a crucial role in angiogenesis. Cytoskeletal organization in endothelial cells is regulated by calpain proteases (EC 3.4.22.17). Calpains are a family of 14 calcium-regulated, intracellular cysteine proteases, which modulate cellular functions by limited, specific proteolysis. Calpain 1 (mu-calpain) and calpain 2 (m-calpain) are the 2 major typical calpain isoforms and are responsible for most calpain activity in endothelial cells. The purpose of the present study was to determine if an orally available form of calpain inhibitor, SNJ-1945, prevented angiogenesis induced by VEGF in cultured retinal endothelial cells. METHODS Human retinal microvascular endothelial cells (HRMEC) were incubated with VEGF (60-100 ng/mL) for 24 h. Calcium uptake was measured with Fluo8. Total calpain activity was measured using fluorescent-labeled casein substrate, and separate activities for calpains 1 and 2 were assessed by casein zymography. Proteolysis of endogenous calpain substrate alpha-spectrin in situ was analyzed by immunoblotting. Angiogenesis in vitro was evaluated by measuring cell migration and tube formation into Matrigel. RESULTS Incubation of HRMEC with VEGF resulted in calcium uptake, increased activity of mainly calpain 2, and increased calpain proteolysis of alpha-spectrin. Treatment of endothelial cells with calpain inhibitor SNJ-1945 reversed VEGF-mediated tube formation and cell motility. CONCLUSIONS Inhibition of angiogenesis by specific calpain inhibitor in the presence of VEGF supported our hypothesis that calpains may be involved in VEGF-mediated angiogenesis in retinal endothelial cells. Therefore, manipulating calpain activity by calpain inhibitor SNJ-1945 might provide a promising therapy for management of pathological angiogenesis, such as that occurring in proliferative retinopathy and age-related macular degeneration with neovascularization.
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Affiliation(s)
- Hong Ma
- Department of Integrative Biosciences, Oregon Health and Science University, Portland, Oregon 97239-3097, USA
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35
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Profiling of calpain activity with a series of FRET-based substrates. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:1505-9. [DOI: 10.1016/j.bbapap.2009.06.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2008] [Revised: 06/15/2009] [Accepted: 06/16/2009] [Indexed: 11/21/2022]
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36
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Kang DH, Jun KY, Lee JP, Pak CS, Na Y, Kwon Y. Identification of 3-Acetyl-2-aminoquinolin-4-one as a Novel, Nonpeptidic Scaffold for Specific Calpain Inhibitory Activity. J Med Chem 2009; 52:3093-7. [DOI: 10.1021/jm8014734] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Da-Hye Kang
- College of Pharmacy & Division of Life & Pharmaceutical Sciences, Ewha Womans University, Seoul 120-750, Korea, Department of Chemistry, Chungnam National University, Daejeon 305-764, Korea, Drug Discovery Division, Korea Research Institute of Chemical Technology, Daejeon 305-600, Korea, College of Pharmacy, Catholic University of Daegu, Gyeongsan, Gyeongbuk 712-702, Korea
| | - Kyu-Yeon Jun
- College of Pharmacy & Division of Life & Pharmaceutical Sciences, Ewha Womans University, Seoul 120-750, Korea, Department of Chemistry, Chungnam National University, Daejeon 305-764, Korea, Drug Discovery Division, Korea Research Institute of Chemical Technology, Daejeon 305-600, Korea, College of Pharmacy, Catholic University of Daegu, Gyeongsan, Gyeongbuk 712-702, Korea
| | - Jin Pyo Lee
- College of Pharmacy & Division of Life & Pharmaceutical Sciences, Ewha Womans University, Seoul 120-750, Korea, Department of Chemistry, Chungnam National University, Daejeon 305-764, Korea, Drug Discovery Division, Korea Research Institute of Chemical Technology, Daejeon 305-600, Korea, College of Pharmacy, Catholic University of Daegu, Gyeongsan, Gyeongbuk 712-702, Korea
| | - Chwang Siek Pak
- College of Pharmacy & Division of Life & Pharmaceutical Sciences, Ewha Womans University, Seoul 120-750, Korea, Department of Chemistry, Chungnam National University, Daejeon 305-764, Korea, Drug Discovery Division, Korea Research Institute of Chemical Technology, Daejeon 305-600, Korea, College of Pharmacy, Catholic University of Daegu, Gyeongsan, Gyeongbuk 712-702, Korea
| | - Younghwa Na
- College of Pharmacy & Division of Life & Pharmaceutical Sciences, Ewha Womans University, Seoul 120-750, Korea, Department of Chemistry, Chungnam National University, Daejeon 305-764, Korea, Drug Discovery Division, Korea Research Institute of Chemical Technology, Daejeon 305-600, Korea, College of Pharmacy, Catholic University of Daegu, Gyeongsan, Gyeongbuk 712-702, Korea
| | - Youngjoo Kwon
- College of Pharmacy & Division of Life & Pharmaceutical Sciences, Ewha Womans University, Seoul 120-750, Korea, Department of Chemistry, Chungnam National University, Daejeon 305-764, Korea, Drug Discovery Division, Korea Research Institute of Chemical Technology, Daejeon 305-600, Korea, College of Pharmacy, Catholic University of Daegu, Gyeongsan, Gyeongbuk 712-702, Korea
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37
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Abell AD, Jones MA, Coxon JM, Morton JD, Aitken SG, McNabb SB, Lee HYY, Mehrtens JM, Alexander NA, Stuart BG, Neffe AT, Bickerstaffe R. Molecular modeling, synthesis, and biological evaluation of macrocyclic calpain inhibitors. Angew Chem Int Ed Engl 2009; 48:1455-8. [PMID: 19145612 DOI: 10.1002/anie.200805014] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The design and elaboration of a series of macrocyclic templates that exhibit a propensity to adopt a beta-strand-like peptide-backbone conformation led to potent and selective inhibitors of calpain 2. Macrocycle 1 retarded calcium-induced opacification in an ovine-lens culture assay and is a lead compound for the development of a drug for cataract treatment. Cbz=carbobenzyloxy.
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Affiliation(s)
- Andrew D Abell
- Department of Chemistry, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
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38
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Abell A, Jones M, Coxon J, Morton J, Aitken S, McNabb S, Lee H, Mehrtens J, Alexander N, Stuart B, Neffe A, Bickerstaffe R. Molecular Modeling, Synthesis, and Biological Evaluation of Macrocyclic Calpain Inhibitors. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200805014] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Andrew D. Abell
- Department of Chemistry, University of Canterbury, Private Bag 4800, Christchurch (New Zealand)
- Present address: School of Chemistry & Physics, The University of Adelaide, North Terrace, Adelaide, SA 5005 (Australia), Fax: (+61) 8‐8303‐4358
| | - Matthew A. Jones
- Department of Chemistry, University of Canterbury, Private Bag 4800, Christchurch (New Zealand)
| | - James M. Coxon
- Department of Chemistry, University of Canterbury, Private Bag 4800, Christchurch (New Zealand)
| | - James D. Morton
- Agriculture and Life Sciences Division, Lincoln University, Post Office Box 84, Canterbury (New Zealand), Fax: (+64) 3‐325‐3851
| | - Steven G. Aitken
- Department of Chemistry, University of Canterbury, Private Bag 4800, Christchurch (New Zealand)
| | - Stephen B. McNabb
- Department of Chemistry, University of Canterbury, Private Bag 4800, Christchurch (New Zealand)
| | - Hannah Y.‐Y. Lee
- Agriculture and Life Sciences Division, Lincoln University, Post Office Box 84, Canterbury (New Zealand), Fax: (+64) 3‐325‐3851
| | - Janna M. Mehrtens
- Department of Chemistry, University of Canterbury, Private Bag 4800, Christchurch (New Zealand)
| | - Nathan A. Alexander
- Department of Chemistry, University of Canterbury, Private Bag 4800, Christchurch (New Zealand)
| | - Blair G. Stuart
- Department of Chemistry, University of Canterbury, Private Bag 4800, Christchurch (New Zealand)
| | - Axel T. Neffe
- Department of Chemistry, University of Canterbury, Private Bag 4800, Christchurch (New Zealand)
- Present address: Institute of Polymer Research, GKSS Research, Centre Geesthacht GmbH, Kantstrasse 55, 14513 Teltow (Germany)
| | - Roy Bickerstaffe
- Agriculture and Life Sciences Division, Lincoln University, Post Office Box 84, Canterbury (New Zealand), Fax: (+64) 3‐325‐3851
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Shirasaki Y, Takahashi H, Yamaguchi M, Inoue J. Molecular design to enhance the penetration into the retina via ocular instillation. Bioorg Med Chem Lett 2008; 18:5174-7. [DOI: 10.1016/j.bmcl.2008.08.089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2008] [Revised: 08/11/2008] [Accepted: 08/26/2008] [Indexed: 01/24/2023]
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40
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Donkor IO, Korukonda R. Synthesis and calpain inhibitory activity of peptidomimetic compounds with constrained amino acids at the P2 position. Bioorg Med Chem Lett 2008; 18:4806-8. [PMID: 18694642 PMCID: PMC2575414 DOI: 10.1016/j.bmcl.2008.07.094] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Revised: 07/21/2008] [Accepted: 07/24/2008] [Indexed: 10/21/2022]
Abstract
The effect of incorporating alpha,alpha'-diethylglycine and alpha-aminocyclopentane carboxylic acid at the P(2) position of inhibitors on mu-calpain inhibition was studied. Compound 3 with alpha,alpha'-diethylglycine was over 20-fold more potent than 2 with alpha-aminocyclopentane carboxylic acid. Additionally, 3 was over 35-fold selective for mu-calpain compared to cathepsin B, while 2 was 3-fold selective for cathepsin B compared to mu-calpain. Thus, the conformation induced by the P(2) residue influenced the activities of the compounds versus the closely related cysteine proteases, and suggests an approach to the discovery of selective mu-calpain inhibitors.
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Affiliation(s)
- Isaac O Donkor
- Department of Pharmaceutical Sciences, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
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41
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Donkor IO, Assefa H, Liu J. Structural basis for the potent calpain inhibitory activity of peptidyl alpha-ketoacids. J Med Chem 2008; 51:4346-50. [PMID: 18636690 DOI: 10.1021/jm800182c] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of peptidyl alpha-ketoacids and alpha-ketoesters was synthesized and studied as mu-calpain inhibitors. Docking studies revealed that the mu-calpain inhibitory activity of the compounds is influenced by hydrogen bonding interactions and the potential for ionic interaction with active site residues as well as placement of a planar N-terminal capping group into the S 3 pocket of the enzyme.
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Affiliation(s)
- Isaac O Donkor
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA.
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Qian J, Cuerrier D, Davies PL, Li Z, Powers JC, Campbell RL. Cocrystal structures of primed side-extending alpha-ketoamide inhibitors reveal novel calpain-inhibitor aromatic interactions. J Med Chem 2008; 51:5264-70. [PMID: 18702462 DOI: 10.1021/jm800045t] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Calpains are intracellular cysteine proteases that catalyze the cleavage of target proteins in response to Ca(2+) signaling. When Ca(2+) homeostasis is disrupted, calpain overactivation causes unregulated proteolysis, which can contribute to diseases such as postischemic injury and cataract formation. Potent calpain inhibitors exist, but of these many cross-react with other cysteine proteases and will need modification to specifically target calpain. Here, we present crystal structures of rat calpain 1 protease core (muI-II) bound to two alpha-ketoamide-based calpain inhibitors containing adenyl and piperazyl primed-side extensions. An unexpected aromatic-stacking interaction is observed between the primed-side adenine moiety and the Trp298 side chain. This interaction increased the potency of the inhibitor toward muI-II and heterodimeric m-calpain. Moreover, stacking orients the adenine such that it can be used as a scaffold for designing novel primed-side address regions, which could be incorporated into future inhibitors to enhance their calpain specificity.
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Affiliation(s)
- Jin Qian
- Department of Biochemistry, Queen's University, Kingston, Ontario, K7L 3N6, Canada
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43
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Gonçalves BT, Esteves PM, Pinto AC, Kaiser CR, da Silva FL, Miguez E, da Silva JFM. Anisotropic and hydrogen bonding effects in phenylglyoxamides and mandelamides: theoretical and NMR conformational evaluation. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2008; 46:418-426. [PMID: 18327891 DOI: 10.1002/mrc.2192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Interesting anisotropic effects were observed for phenylglyoxamides and their respective mandelamides. Such effects were observed in experimental (1)H and (13)C NMR (in CDCl(3), CD(3)OD, and DMSO-d(6) solvents) and in some cases with good correlation to theoretical (1)H and (13)C NMR DFT-GIAO (B3LYP/6-311++G**//B3LYP/6-31G*) calculations. A systematic conformational analysis of these compounds was performed in a two-step methodology, using PM3 and DFT (B3LYP/6-31G*) calculations; with good accomplishment and computational time economy. It was observed that intramolecular hydrogen bonding plays a significant role in the conformation of such compounds. Finally, a geminal nonequivalence of an N-CH(2) moiety, in one of the alkyl side chain (R1 = R2), was found for the tertiary mandelamides studied.
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Affiliation(s)
- Biank T Gonçalves
- Departamento de Química Orgânica, Instituto de Química, Bloco A, 6 a Andar do CT, Universidade Federal do Rio de Janeiro, Cidade Universitária, Ilha do Fundão, RJ, Brazil, 21949900
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The role of calcium-activated protease calpain in experimental retinal pathology. Surv Ophthalmol 2008; 53:150-63. [PMID: 18348880 DOI: 10.1016/j.survophthal.2007.12.006] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The purpose of this review is to present the recent evidence linking the family of ubiquitous proteases called calpains (EC 3.4.22.17) to neuropathologies of the retina. The hypothesis being tested in such studies is that over-activation of calpains by elevated intracellular calcium contributes to retinal cell death produced by conditions such as elevated intraocular pressure and hypoxia. Recent x-ray diffraction studies have provided insight into the molecular events causing calpain activation. Further, x-ray diffraction data has provided details on how side chains on calpain inhibitors affect docking into the active site of calpain 1. This opens the possibility of testing calpain-specific inhibitors, such as SJA6017 and SNJ1945, for human safety and as a site-directed form of treatment for retinal pathologies.
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Abstract
The eukaryotic calpains are a family of calcium-dependent papain-like proteases and their non-enzymatic relatives whose varied physiological functions are beginning to be fully explored. The calpain family is named for the calcium dependence of the papain-like, thiol protease activity of the well-studied ubiquitous vertebrate enzymes calpain-1 (μ-calpain) and calpain-2 (m-calpain). Proteins showing sequence relatedness to the catalytic core domains of these enzymes are included in this ancient and diverse eukaryotic protein family. Calpains are examples of highly modular organization, with several varieties of amino-terminal or carboxy-terminal modules flanking a conserved core. Acquisition of the penta-EF-hand module involved in calcium binding (and the formation of heterodimers for some calpains) seems to be a relatively late event in calpain evolution. Several alternative mechanisms for binding calcium and associating with membranes/phospholipids are found throughout the family. The gene family is expanded in mammals, trypanosomes and ciliates, with up to 26 members in Tetrahymena, for example; in striking contrast to this, only a single calpain gene is present in many other protozoa and in plants. The many isoforms of calpain and their multiple splice variants complicate the discussion and analysis of the family, and challenge researchers to ascertain the relationships between calpain gene sequences, protein isoforms and their distinct or overlapping functions. In mammals and plants it is clear that a calpain plays an essential role in development. There is increasing evidence that ubiquitous calpains participate in a variety of signal transduction pathways and function in important cellular processes of life and death. In contrast to relatively promiscuous degradative proteases, calpains cleave only a restricted set of protein substrates and use complex substrate-recognition mechanisms, involving primary and secondary structural features of target proteins. The detailed physiological significance of both proteolytically active calpains and those lacking key catalytic residues requires further study.
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Affiliation(s)
- Dorothy E Croall
- Department of Biochemistry, Microbiology and Molecular Biology, University of Maine, Orono, ME 04469-5735, USA
| | - Klaus Ersfeld
- Department of Biological Sciences, University of Hull, Hull HU6 7RX, UK
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Lorenzo HK, Susin SA. Therapeutic potential of AIF-mediated caspase-independent programmed cell death. Drug Resist Updat 2008; 10:235-55. [PMID: 18180198 DOI: 10.1016/j.drup.2007.11.001] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2007] [Accepted: 11/01/2007] [Indexed: 01/15/2023]
Abstract
Resistance to anticancer drugs is often related to deficient cell death execution pathways in cancer cells. Apoptosis, which denotes a form of cell death executed by caspases, was traditionally considered as the only physiological and programmed form of cell death. However, recent evidence indicates that programmed cell death (PCD) can occur in complete absence of caspase activation. Indeed, a large number of caspase-independent models are now defined and a key protein implicated in this type of PCD, apoptosis-inducing factor (AIF), has been identified. AIF is a mitochondrial protein with two faces looking in opposite life/death directions. Recently, the identification of five different isoforms allowed a better characterization of AIFs life/mitochondrial versus death/nuclear functions, as well as definition of its pro-apoptotic region and some of its nuclear partners. Importantly, much work on caspase-independent PCD has revealed that AIF participates in more PCD systems than initially thought. A wider molecular knowledge of AIF, and of the caspase-independent PCDs in which it is involved, are key to provide new insights into the role of PCD. There is no doubt that these insights will lead to the development of more selective and efficient drugs against cancer, degenerative diseases, and other pathological disorders implicating AIF.
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Affiliation(s)
- Hans K Lorenzo
- INSERM U542, Institut André Lwoff, Lavoisier Building, 94803 Villejuif, France.
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Guttmann R. Recent developments in the therapeutic targeting of calpains in neurodegeneration. Expert Opin Ther Pat 2007. [DOI: 10.1517/13543776.17.10.1203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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48
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Abell AD, Jones MA, Neffe AT, Aitken SG, Cain TP, Payne RJ, McNabb SB, Coxon JM, Stuart BG, Pearson D, Lee HYY, Morton JD. Investigation into the P3 Binding Domain of m-Calpain Using Photoswitchable Diazo- and Triazene-dipeptide Aldehydes: New Anticataract Agents. J Med Chem 2007; 50:2916-20. [PMID: 17497840 DOI: 10.1021/jm061455n] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The photoswitchable N-terminal diazo and triazene-dipeptide aldehydes 8a-d, 10a,b, and 17a,b present predominantly as the (E)-isomer, which purportedly binds deep in the S3 pocket of calpain. All compounds are potent inhibitors of m-calpain, with 8b being the most active (IC50 of 35 nM). The diazo-containing inhibitors 8a, 8c, and 10a were irradiated at 340 nm to give a photostationary state enriched in the (Z)-isomer, and in all cases, these were less active. The most water soluble triazene 17a (IC50 of 90 nM) retards calpain-induced cataract formation in lens culture.
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Affiliation(s)
- Andrew D Abell
- Department of Chemistry, University of Canterbury, Private Bag 4800, Christchurch, New Zealand.
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Mitzel T, Wzorek J, Troutman A, Allegue K. Control of Skeletal Connectivity in Indium Promoted Reactions: 1,2-Additions and Cope Rearrangements En Route to Lactol Formation. J Org Chem 2007; 72:3042-52. [PMID: 17348712 DOI: 10.1021/jo070020k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Indium promoted coupling reactions between propargyl aldehydes (3) and allyl halides under aqueous and organic conditions are reported. Coupling reactions under aqueous conditions occur via 1,2-addition with excellent yields to afford 4-hydroxy-1-ene-5-ynes (8). Coupling reactions under organic conditions also add in a 1,2-fashion, but the initial products can be induced to undergo oxy-Cope rearrangements giving 2,5-hexadienals (9). Oxy-Cope rearrangement of 8 followed by a secondary addition step under highly basic conditions leads to lactol formation (10) in good to excellent yields. This paper reveals the versatility and control of product formation which may be attained when working with propargyl aldehyde (3) and allyl halide systems under indium promoted coupling conditions.
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Affiliation(s)
- Thomas Mitzel
- Department of Chemistry, Trinity College, 300 Summit Street, Hartford, Connecticut 06106, USA.
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Cuerrier D, Moldoveanu T, Campbell RL, Kelly J, Yoruk B, Verhelst SHL, Greenbaum D, Bogyo M, Davies PL. Development of Calpain-specific Inactivators by Screening of Positional Scanning Epoxide Libraries. J Biol Chem 2007; 282:9600-9611. [PMID: 17218315 DOI: 10.1074/jbc.m610372200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Calpains are calcium-dependent proteases that are required for numerous intracellular processes but also play an important role in the development of pathologies such as ischemic injury and neurodegeneration. Many current small molecule calpain inhibitors also inhibit other cysteine proteases, including cathepsins, and need improved selectivity. The specificity of inhibition of several calpains and papain was profiled using synthetic positional scanning libraries of epoxide-based compounds that target the active-site cysteine. These peptidomimetic libraries probe the P4, P3, and P2 positions, display (S,S)- or (R,R)-epoxide stereochemistries, and incorporate both natural and non-natural amino acids. To facilitate library screening, an SDS-PAGE assay that measures the extent of hydrolysis of an inactive recombinant m-calpain was developed. Individual epoxide inhibitors were synthesized guided by calpain-specific preferences observed from the profiles and tested for inhibition against calpain. The most potent compounds were assayed for specificity against cathepsins B, L, and K. Several compounds demonstrated high inhibition specificity for calpains over cathepsins. The best of these inhibitors, WRH(R,R), irreversibly inactivates m- and mu-calpain rapidly (k(2)/K(i) = 131,000 and 16,500 m(-1) s(-1), respectively) but behaves exclusively as a reversible and less potent inhibitor toward the cathepsins. X-ray crystallography of the proteolytic core of rat mu-calpain inactivated by the epoxide compounds WR gamma-cyano-alpha-aminobutyric acid (S,S) and WR allylglycine (R,R) reveals that the stereochemistry of the epoxide influences positioning and orientation of the P2 residue, facilitating alternate interactions within the S2 pocket. Moreover, the WR gamma-cyano-alpha-aminobutyric acid (S,S)-complexed structure defines a novel hydrogen-bonding site within the S2 pocket of calpains.
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Affiliation(s)
- Dominic Cuerrier
- Department of Biochemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Tudor Moldoveanu
- Department of Biochemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Robert L Campbell
- Department of Biochemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Jacqueline Kelly
- Department of Biochemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Bilge Yoruk
- Department of Biochemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Steven H L Verhelst
- Department of Pathology, Stanford University School of Medicine, Stanford, Califorina 94305
| | - Doron Greenbaum
- Department of Pathology, Stanford University School of Medicine, Stanford, Califorina 94305
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, Califorina 94305
| | - Peter L Davies
- Department of Biochemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada; Protein Function Discovery Group, Queen's University, Kingston, Ontario K7L 3N6, Canada.
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