1
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Yokomine M, Morimoto J, Fukuda Y, Ueda T, Takeuchi K, Umezawa K, Ago H, Matsuura H, Ueno G, Senoo A, Nagatoishi S, Tsumoto K, Sando S. A high-resolution structural characterization and physicochemical study of how a peptoid binds to an oncoprotein MDM2. Chem Sci 2024; 15:7051-7060. [PMID: 38756815 PMCID: PMC11095393 DOI: 10.1039/d4sc01540a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 04/16/2024] [Indexed: 05/18/2024] Open
Abstract
Peptoids are a promising drug modality targeting disease-related proteins, but how a peptoid engages in protein binding is poorly understood. This is primarily due to a lack of high-resolution peptoid-protein complex structures and systematic physicochemical studies. Here, we present the first crystal structure of a peptoid bound to a protein, providing high-resolution structural information about how a peptoid binds to a protein. We previously reported a rigid peptoid, oligo(N-substituted alanine) (oligo-NSA), and developed an oligo-NSA-type peptoid that binds to MDM2. X-ray crystallographic analysis of the peptoid bound to MDM2 showed that the peptoid recognizes the MDM2 surface predominantly through the interaction of the N-substituents, while the main chain acts as a scaffold. Additionally, conformational, thermodynamic, and kinetic analysis of the peptoid and its derivatives with a less rigid main chain revealed that rigidification of the peptoid main chain contributes to improving the protein binding affinity. This improvement is thermodynamically attributed to an increased magnitude of the binding enthalpy change, and kinetically to an increased association rate and decreased dissociation rate. This study provides invaluable insights into the design of protein-targeting peptoids.
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Affiliation(s)
- Marin Yokomine
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
| | - Jumpei Morimoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
| | - Yasuhiro Fukuda
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
| | - Takumi Ueda
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Koh Takeuchi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Koji Umezawa
- Department of Biomedical Engineering, Graduate School of Science and Technology, Shinshu University 8304 Minami-Minowa, Kami-Ina Nagano 399-4598 Japan
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University 8304 Minami-Minowa, Kami-Ina Nagano 399-4598 Japan
| | - Hideo Ago
- RIKEN SPring-8 Center 1-1-1 Kouto Sayo Hyogo 679-5148 Japan
| | | | - Go Ueno
- RIKEN SPring-8 Center 1-1-1 Kouto Sayo Hyogo 679-5148 Japan
| | - Akinobu Senoo
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
| | - Satoru Nagatoishi
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
| | - Kouhei Tsumoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
- Institute of Medical Science, The University of Tokyo 4-6-1 Shirokanedai Minato-ku Tokyo 108-8639 Japan
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
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2
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Feng Y, Qirjollari A, Fawaz MV, Cancilla MT, Gonzalez RJ, Pearson K. Rapid and Definitive Identification of Cyclic Peptide Soft Spots by Isotope-Labeled Reductive Dimethylation and Mass Spectrometry Fragmentation. Anal Chem 2024; 96:7756-7762. [PMID: 38690743 DOI: 10.1021/acs.analchem.4c01372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Cyclic peptides are an emerging therapeutic modality over the past few decades. To identify drug candidates with sufficient proteolytic stability for oral administration, it is critical to pinpoint the amide bond hydrolysis sites, or soft spots, to better understand their metabolism and provide guidance on further structure optimization. However, the unambiguous characterization of cyclic peptide soft spots remains a significant challenge during early stage discovery studies, as amide bond hydrolysis forms a linearized isobaric sequence with the addition of a water molecule, regardless of the amide hydrolysis location. In this study, an innovative strategy was developed to enable the rapid and definitive identification of cyclic peptide soft spots by isotope-labeled reductive dimethylation and mass spectrometry fragmentation. The dimethylated immonium ion with enhanced MS signal at a distinctive m/z in MS/MS fragmentation spectra reveals the N-terminal amino acid on a linearized peptide sequence definitively and, thus, significantly simplifies the soft spot identification workflow. This approach has been evaluated to demonstrate the potential of isotope-labeled dimethylation to be a powerful analytical tool in cyclic peptide drug discovery and development.
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Affiliation(s)
- Yu Feng
- Nonclinical Drug Safety, MRL, Merck & Co., Inc., 770 Sumneytown Pike, West Point, Pennsylvania 19486, United States
| | - Athanasia Qirjollari
- Nonclinical Drug Safety, MRL, Merck & Co., Inc., 770 Sumneytown Pike, West Point, Pennsylvania 19486, United States
| | - Maria V Fawaz
- Pharmacokinetics, Dynamics, Metabolism, and Bioanalytics, MRL, Merck & Co., Inc., 770 Sumneytown Pike, West Point, Pennsylvania 19486, United States
| | - Mark T Cancilla
- Pharmacokinetics, Dynamics, Metabolism, and Bioanalytics, MRL, Merck & Co., Inc., 770 Sumneytown Pike, West Point, Pennsylvania 19486, United States
| | - Raymond J Gonzalez
- Nonclinical Drug Safety, MRL, Merck & Co., Inc., 770 Sumneytown Pike, West Point, Pennsylvania 19486, United States
| | - Kara Pearson
- Nonclinical Drug Safety, MRL, Merck & Co., Inc., 770 Sumneytown Pike, West Point, Pennsylvania 19486, United States
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3
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Chen S, Lin T, Basu R, Ritchey J, Wang S, Luo Y, Li X, Pei D, Kara LB, Cheng X. Design of target specific peptide inhibitors using generative deep learning and molecular dynamics simulations. Nat Commun 2024; 15:1611. [PMID: 38383543 PMCID: PMC10882002 DOI: 10.1038/s41467-024-45766-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 02/04/2024] [Indexed: 02/23/2024] Open
Abstract
We introduce a computational approach for the design of target-specific peptides. Our method integrates a Gated Recurrent Unit-based Variational Autoencoder with Rosetta FlexPepDock for peptide sequence generation and binding affinity assessment. Subsequently, molecular dynamics simulations are employed to narrow down the selection of peptides for experimental assays. We apply this computational strategy to design peptide inhibitors that specifically target β-catenin and NF-κB essential modulator. Among the twelve β-catenin inhibitors, six exhibit improved binding affinity compared to the parent peptide. Notably, the best C-terminal peptide binds β-catenin with an IC50 of 0.010 ± 0.06 μM, which is 15-fold better than the parent peptide. For NF-κB essential modulator, two of the four tested peptides display substantially enhanced binding compared to the parent peptide. Collectively, this study underscores the successful integration of deep learning and structure-based modeling and simulation for target specific peptide design.
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Affiliation(s)
- Sijie Chen
- College of Pharmacy, The Ohio State University, 281 W Lane Ave, Columbus, OH, USA
| | - Tong Lin
- Mechanical Engineering Department, Carnegie Mellon University, 5000 Forbes Ave, Pittsburgh, PA, USA
- Machine Learning Department, Carnegie Mellon University, 5000 Forbes Ave, Pittsburgh, PA, USA
| | - Ruchira Basu
- Department of Chemistry and Biochemistry, The Ohio State University, 281 W Lane Ave, Columbus, OH, USA
| | - Jeremy Ritchey
- Department of Chemistry and Biochemistry, The Ohio State University, 281 W Lane Ave, Columbus, OH, USA
| | - Shen Wang
- College of Pharmacy, The Ohio State University, 281 W Lane Ave, Columbus, OH, USA
| | - Yichuan Luo
- Electrical and Computer Engineering Department, Carnegie Mellon University, 5000 Forbes Ave, Pittsburgh, PA, USA
| | - Xingcan Li
- Department of Radiology, Affiliated Hospital and Medical School of Nantong University, 20 West Temple Road, Nantong, Jiangsu, China
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 281 W Lane Ave, Columbus, OH, USA.
| | - Levent Burak Kara
- Mechanical Engineering Department, Carnegie Mellon University, 5000 Forbes Ave, Pittsburgh, PA, USA.
| | - Xiaolin Cheng
- College of Pharmacy, The Ohio State University, 281 W Lane Ave, Columbus, OH, USA.
- Translational Data Analytics Institute, The Ohio State University, 1760 Neil Ave, Columbus, OH, USA.
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4
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Ito T, Yokoo H, Kato T, Doi M, Demizu Y. Sculpting Secondary Structure of a Cyclic Peptide: Conformational Analysis of a Cyclic Hexapeptide Containing a Combination of l-Leu, d-Leu, and Aib Residues. ACS OMEGA 2023; 8:44106-44111. [PMID: 38027316 PMCID: PMC10666233 DOI: 10.1021/acsomega.3c06397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 10/23/2023] [Accepted: 10/31/2023] [Indexed: 12/01/2023]
Abstract
We have previously reported that cyclo(l-Leu-d-Leu-Aib-l-Leu-d-Leu-Aib) (2), a cyclic hexapeptide consisting of heterochiral l-Leu and d-Leu (l-Leu-d-Leu) residues with achiral 2-aminoisobutyric acid (Aib) residues, forms a figure-8 conformation. In this study, we newly designed cyclo(l-Leu-d-Leu-Aib-d-Leu-l-Leu-Aib)+ (4), an epimer of 2, and examined the conformational differences between 2 and 4 by X-ray crystallographic analysis. Peptide 4 formed a planar cyclic conformation with an antiparallel β-sheet hydrogen-bonding pattern. This investigation demonstrates the potential to manipulate the molecular conformation of cyclic peptides by simply arranging the l- and d-amino acids and emphasizes that diverse conformations can be obtained by using cyclic peptides. Harnessing cyclic peptides as platforms for distinct molecular structures is a promising approach to expanding the chemical space for various applications.
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Affiliation(s)
- Takahito Ito
- Division
of Organic Chemistry, National Institute
of Health Sciences, Kawasaki, Kanagawa 210-9501, Japan
- Graduate
School of Medical Life Science, Yokohama
City University, Yokohama, Kanagawa 236-0027, Japan
| | - Hidetomo Yokoo
- Division
of Organic Chemistry, National Institute
of Health Sciences, Kawasaki, Kanagawa 210-9501, Japan
| | - Takuma Kato
- Faculty
of Pharmacy, Osaka Medical and Pharmaceutical
University, Takatsuki, Osaka 569-8686, Japan
| | - Mitsunobu Doi
- Faculty
of Pharmacy, Osaka Medical and Pharmaceutical
University, Takatsuki, Osaka 569-8686, Japan
| | - Yosuke Demizu
- Division
of Organic Chemistry, National Institute
of Health Sciences, Kawasaki, Kanagawa 210-9501, Japan
- Graduate
School of Medical Life Science, Yokohama
City University, Yokohama, Kanagawa 236-0027, Japan
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5
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Zhu J, Chen S, Liu Z, Guo J, Cao S, Long S. Recent advances in anticancer peptoids. Bioorg Chem 2023; 139:106686. [PMID: 37399616 DOI: 10.1016/j.bioorg.2023.106686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 05/07/2023] [Accepted: 06/15/2023] [Indexed: 07/05/2023]
Abstract
Since most tumors become resistant to drugs in a gradual and irreversible manner, making treatment less effective over time, anticancer drugs require continuous development. Peptoids are a class of peptidomimetics that can be easily synthesized and optimized. They exhibit a number of unique characteristics, including protease resistance, non-immunogenicity, do not interfere with peptide functionality and skeleton polarity, and can adopt different conformations. They have been studied for their efficacy in different cancer therapies, and can be considered as a promising alternative molecular category for the development of anticancer drugs. Herein, we discuss the extensive recent advances in peptoids and peptoid hybrids in the treatment of cancers such as prostate, breast, lung, and other ones, in the hope of providing a reference for the further development of peptoid anticancer drugs.
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Affiliation(s)
- Jidan Zhu
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Hubei Engineering Research Center for Advanced Fine Chemicals, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, 206 1st Rd Optics Valley, East Lake New Technology Development District, Wuhan, Hubei 430205, China
| | - Siyu Chen
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Hubei Engineering Research Center for Advanced Fine Chemicals, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, 206 1st Rd Optics Valley, East Lake New Technology Development District, Wuhan, Hubei 430205, China
| | - Ziwei Liu
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Hubei Engineering Research Center for Advanced Fine Chemicals, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, 206 1st Rd Optics Valley, East Lake New Technology Development District, Wuhan, Hubei 430205, China
| | - Ju Guo
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Hubei Engineering Research Center for Advanced Fine Chemicals, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, 206 1st Rd Optics Valley, East Lake New Technology Development District, Wuhan, Hubei 430205, China
| | - Shuang Cao
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Hubei Engineering Research Center for Advanced Fine Chemicals, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, 206 1st Rd Optics Valley, East Lake New Technology Development District, Wuhan, Hubei 430205, China.
| | - Sihui Long
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Hubei Engineering Research Center for Advanced Fine Chemicals, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, 206 1st Rd Optics Valley, East Lake New Technology Development District, Wuhan, Hubei 430205, China.
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6
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Bu H, Lan X, Cheng H, Pei C, Ouyang M, Chen Y, Huang X, Yu L, Tan Y. Development of an interfering peptide M1-20 with potent anti-cancer effects by targeting FOXM1. Cell Death Dis 2023; 14:533. [PMID: 37598210 PMCID: PMC10439915 DOI: 10.1038/s41419-023-06056-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 08/01/2023] [Accepted: 08/09/2023] [Indexed: 08/21/2023]
Abstract
Disrupting protein-protein interactions (PPIs) has emerged as a promising strategy for cancer drug development. Interfering peptides disrupting PPIs can be rationally designed based on the structures of natural sequences mediating these interactions. Transcription factor FOXM1 overexpresses in multiple cancers and is considered an effective target for cancer therapeutic drug development. Using a rational design approach, we have generated a peptide library from the FOXM1 C-terminal sequence and screened FOXM1-binding peptides. Combining FOXM1 binding and cell inhibitory results, we have obtained a FOXM1-targeting interfering peptide M1-20 that is optimized from the natural parent peptide to the D-retro-inverso peptide. With improved stability characteristics, M1-20 inhibits proliferation and migration, and induces apoptosis of cancer cells. Mechanistically, M1-20 inhibits FOXM1 transcriptional activities by disrupting its interaction between the MuvB complex and the transcriptional co-activator CBP. These are consistent with the results that M1-20 suppresses cancer progression and metastasis without noticeable toxic and side effects in wild-type mice. These findings reveal that M1-20 has the potential to be developed as an anti-cancer drug candidate targeting FOXM1.
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Affiliation(s)
- Huitong Bu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Engineering Research Center for Anticancer Targeted Protein Pharmaceuticals, Hunan University, Changsha, Hunan, 410082, China
| | - Xianling Lan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Engineering Research Center for Anticancer Targeted Protein Pharmaceuticals, Hunan University, Changsha, Hunan, 410082, China
| | - Haojie Cheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Engineering Research Center for Anticancer Targeted Protein Pharmaceuticals, Hunan University, Changsha, Hunan, 410082, China
| | - Chaozhu Pei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Engineering Research Center for Anticancer Targeted Protein Pharmaceuticals, Hunan University, Changsha, Hunan, 410082, China
| | - Min Ouyang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Engineering Research Center for Anticancer Targeted Protein Pharmaceuticals, Hunan University, Changsha, Hunan, 410082, China
| | - Yan Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Engineering Research Center for Anticancer Targeted Protein Pharmaceuticals, Hunan University, Changsha, Hunan, 410082, China
| | - Xiaoqin Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Engineering Research Center for Anticancer Targeted Protein Pharmaceuticals, Hunan University, Changsha, Hunan, 410082, China
| | - Li Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Engineering Research Center for Anticancer Targeted Protein Pharmaceuticals, Hunan University, Changsha, Hunan, 410082, China
| | - Yongjun Tan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Engineering Research Center for Anticancer Targeted Protein Pharmaceuticals, Hunan University, Changsha, Hunan, 410082, China.
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7
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Cheng H, Yuan J, Pei C, Ouyang M, Bu H, Chen Y, Huang X, Zhang Z, Yu L, Tan Y. The development of an anti-cancer peptide M1-21 targeting transcription factor FOXM1. Cell Biosci 2023; 13:114. [PMID: 37344857 DOI: 10.1186/s13578-023-01059-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/26/2023] [Indexed: 06/23/2023] Open
Abstract
BACKGROUND Transcription factor FOXM1 is a potential target for anti-cancer drug development. An interfering peptide M1-21, targeting FOXM1 and FOXM1-interacting proteins, is developed and its anti-cancer efficacy is evaluated. METHODS FOXM1 C-terminus-binding peptides are screened by in silico protocols from the peptide library of FOXM1 (1-138aa) and confirmed by cellular experiments. The selected peptide is synthesized into its D-retro-inverso (DRI) form by fusing a TAT cell-penetrating sequence. Anti-cancer activities are evaluated in vitro and in vivo with tumor-grafted nude mice, spontaneous breast cancer mice, and wild-type metastasis-tracing mice. Anti-cancer mechanisms are analyzed. Distribution and safety profiles in mice are evaluated. RESULTS With improved stability and cell inhibitory activity compared to the parent peptide, M1-21 binds to multiple regions of FOXM1 and interferes with protein-protein interactions between FOXM1 and its various known partner proteins, including PLK1, LIN9 and B-MYB of the MuvB complex, and β-catenin. Consequently, M1-21 inhibits FOXM1-related transcriptional activities and FOXM1-mediated nuclear importation of β-catenin and β-catenin transcriptional activities. M1-21 inhibits multiple types of cancer (20 µM in vitro or 30 mg/kg in vivo) by preventing proliferation, migration, and WNT signaling. Distribution and safety profiles of M1-21 are favorable (broad distribution and > 15 h stability in mice) and the tested non-severely toxic dose reaches 200 mg/kg in mice. M1-21 also has low hemolytic toxicity and immunogenicity in mice. CONCLUSIONS M1-21 is a promising interfering peptide targeting FOXM1 for the development of anti-cancer drugs.
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Affiliation(s)
- Haojie Cheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Engineering Research Center for Anticancer Targeted Protein Pharmaceuticals, Hunan University, 410082, Changsha, Hunan, China
| | - Jie Yuan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Engineering Research Center for Anticancer Targeted Protein Pharmaceuticals, Hunan University, 410082, Changsha, Hunan, China
| | - Chaozhu Pei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Engineering Research Center for Anticancer Targeted Protein Pharmaceuticals, Hunan University, 410082, Changsha, Hunan, China
| | - Min Ouyang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Engineering Research Center for Anticancer Targeted Protein Pharmaceuticals, Hunan University, 410082, Changsha, Hunan, China
| | - Huitong Bu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Engineering Research Center for Anticancer Targeted Protein Pharmaceuticals, Hunan University, 410082, Changsha, Hunan, China
| | - Yan Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Engineering Research Center for Anticancer Targeted Protein Pharmaceuticals, Hunan University, 410082, Changsha, Hunan, China
| | - Xiaoqin Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Engineering Research Center for Anticancer Targeted Protein Pharmaceuticals, Hunan University, 410082, Changsha, Hunan, China
| | - Zhenwang Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Engineering Research Center for Anticancer Targeted Protein Pharmaceuticals, Hunan University, 410082, Changsha, Hunan, China.
- Medicine Research Institute, Hubei Key Laboratory of Diabetes and Angiopathy, Xianning Medical College, Hubei University of Science and Technology, 437000, Xianning, Hubei, China.
| | - Li Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Engineering Research Center for Anticancer Targeted Protein Pharmaceuticals, Hunan University, 410082, Changsha, Hunan, China.
| | - Yongjun Tan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Engineering Research Center for Anticancer Targeted Protein Pharmaceuticals, Hunan University, 410082, Changsha, Hunan, China.
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8
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Fujita M, Tsuchiya K, Kurohara T, Fukuhara K, Misawa T, Demizu Y. In silico optimization of peptides that inhibit Wnt/β-catenin signaling. Bioorg Med Chem 2023; 84:117264. [PMID: 37003158 DOI: 10.1016/j.bmc.2023.117264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 04/03/2023]
Abstract
The Wnt/β-catenin signaling pathway causes transcriptional activation through the interaction between β-catenin and T cell-specific transcription factor (TCF) and regulates a wide variety of cellular responses, including proliferation, differentiation and cell motility. Excessive transcriptional activation of the Wnt/β-catenin pathway is implicated in developing or exacerbating various cancers. We have recently reported that liver receptor homolog-1 (LRH-1)-derived peptides inhibit the β-catenin/TCF interaction. In addition, we developed a cell-penetrating peptide (CPP)-conjugated LRH-1-derived peptide that inhibits the growth of colon cancer cells and specifically inhibits the Wnt/β-catenin pathway. Nonetheless, the inhibitory activity of the CPP-conjugated LRH-1-derived peptide was unsatisfactory (ca. 20 μM), and improving the bioactivity of peptide inhibitors is required for their in vivo applications. In this study, we optimized the LRH-1-derived peptide using in silico design to enhance its activity further. The newly designed peptides showed binding affinity toward β-catenin comparable to the parent peptide. In addition, the CPP-conjugated stapled peptide, Penetratin-st6, showed excellent inhibition (ca. 5 μM). Thus, the combination of in silico design by MOE and MD calculations has revealed that logical molecular design of PPI inhibitory peptides targeting β-catenin is possible. This method can be also applied to the rational design of peptide-based inhibitors targeting other proteins.
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Affiliation(s)
- Minami Fujita
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; Division of Organic Chemistry, National Institute of Health Sciences, Kanagawa 210-9501, Japan
| | - Keisuke Tsuchiya
- Division of Organic Chemistry, National Institute of Health Sciences, Kanagawa 210-9501, Japan; Graduate School of Pharmacy, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan.
| | - Takashi Kurohara
- Division of Organic Chemistry, National Institute of Health Sciences, Kanagawa 210-9501, Japan
| | - Kiyoshi Fukuhara
- Graduate School of Pharmacy, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan
| | - Takashi Misawa
- Division of Organic Chemistry, National Institute of Health Sciences, Kanagawa 210-9501, Japan
| | - Yosuke Demizu
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; Division of Organic Chemistry, National Institute of Health Sciences, Kanagawa 210-9501, Japan; Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushimanaka, Kita-ku, Okayama 700-8530, Japan.
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9
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Eastwood JRB, Weisberg EI, Katz D, Zuckermann RN, Kirshenbaum K. Guidelines for designing peptoid structures: Insights from the
Peptoid Data Bank. Pept Sci (Hoboken) 2023. [DOI: 10.1002/pep2.24307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Affiliation(s)
| | | | - Dana Katz
- Department of Chemistry New York University New York New York USA
| | | | - Kent Kirshenbaum
- Department of Chemistry New York University New York New York USA
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10
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Zhang H, Liu C, Zhu D, Zhang Q, Li J. Medicinal Chemistry Strategies for the Development of Inhibitors Disrupting β-Catenin's Interactions with Its Nuclear Partners. J Med Chem 2023; 66:1-31. [PMID: 36583662 DOI: 10.1021/acs.jmedchem.2c01016] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Dysregulation of the Wnt/β-catenin signaling pathway is strongly associated with various aspects of cancer, including tumor initiation, proliferation, and metastasis as well as antitumor immunity, and presents a promising opportunity for cancer therapy. Wnt/β-catenin signaling activation increases nuclear dephosphorylated β-catenin levels, resulting in β-catenin binding to TCF and additional cotranscription factors, such as BCL9, CBP, and p300. Therefore, directly disrupting β-catenin's interactions with these nuclear partners holds promise for the effective and selective suppression of the aberrant activation of Wnt/β-catenin signaling. Herein, we summarize recent advances in biochemical techniques and medicinal chemistry strategies used to identify potent peptide-based and small-molecule inhibitors that directly disrupt β-catenin's interactions with its nuclear binding partners. We discuss the challenges involved in developing drug-like inhibitors that target the interactions of β-catenin and its nuclear binding partner into therapeutic agents.
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Affiliation(s)
- Hao Zhang
- School of Pharmacy, Fudan University, Shanghai 201203, China.,Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai 201203, China
| | - Chenglong Liu
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Di Zhu
- School of Pharmacy, Fudan University, Shanghai 201203, China.,Department of Pharmacology, School of Basic Medical Science, Fudan University, Shanghai 201100, China
| | - Qingwei Zhang
- Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai 201203, China
| | - Jianqi Li
- Novel Technology Center of Pharmaceutical Chemistry, Shanghai Institute of Pharmaceutical Industry Co., Ltd., China State Institute of Pharmaceutical Industry, Shanghai 201203, China
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11
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Abstract
Deregulation of transcription factors is critical to hallmarks of cancer. Genetic mutations, gene fusions, amplifications or deletions, epigenetic alternations, and aberrant post-transcriptional modification of transcription factors are involved in the regulation of various stages of carcinogenesis, including cancer initiation, progression, and metastasis. Thus, targeting the dysfunctional transcription factors may lead to new cancer therapeutic strategies. However, transcription factors are conventionally considered as "undruggable." Here, we summarize the recent progresses in understanding the regulation of transcription factors in cancers and strategies to target transcription factors and co-factors for preclinical and clinical drug development, particularly focusing on c-Myc, YAP/TAZ, and β-catenin due to their significance and interplays in cancer.
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12
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Austin MJ, Schunk H, Watkins C, Ling N, Chauvin J, Morton L, Rosales AM. Fluorescent Peptomer Substrates for Differential Degradation by Metalloproteases. Biomacromolecules 2022; 23:4909-4923. [PMID: 36269900 DOI: 10.1021/acs.biomac.2c01077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proteases, especially MMPs, are attractive biomarkers given their central role in both physiological and pathological processes. Distinguishing MMP activity with degradable substrates, however, is a difficult task due to overlapping substrate specificity profiles. Here, we developed a system of peptomers (peptide-peptoid hybrids) to probe the impact of non-natural residues on MMP specificity for an MMP peptide consensus sequence. Peptoids are non-natural, N-substituted glycines with a large side-chain diversity. Given the presence of a hallmark proline residue in the P3 position of MMP consensus sequences, we hypothesized that peptoids may offer N-substituted alternatives to generate differential interactions with MMPs. To investigate this hypothesis, peptomer substrates were exposed to five different MMPs, as well as bacterial collagenase, and monitored by fluorescence resonance energy transfer and liquid chromatography-mass spectrometry to determine the rate of cleavage and the composition of degraded fragments, respectively. We found that peptoid residues are well tolerated in the P3 and P3' substrate sites and that the identity of the peptoid in these sites displays a moderate influence on the rate of cleavage. However, peptoid residues were even better tolerated in the P1 substrate site where activity was more strongly correlated with side-chain identity than side-chain position. All MMPs explored demonstrated similar trends in specificity for the peptomers but exhibited different degrees of variability in proteolytic rate. These kinetic profiles served as "fingerprints" for the proteases and yielded separation by multivariate data analysis. To further demonstrate the practical application of this tunability in degradation kinetics, peptomer substrates were tethered into hydrogels and released over distinct timescales. Overall, this work represents a significant step toward the design of probes that maximize differential MMP behavior and presents design rules to tune degradation kinetics with peptoid substitutions, which has promising implications for diagnostic and prognostic applications using array-based sensors.
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Affiliation(s)
- Mariah J Austin
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas78712, United States
| | - Hattie Schunk
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas78712, United States.,Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas78712, United States
| | - Carolyn Watkins
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas78712, United States
| | - Natalie Ling
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas78712, United States
| | - Jeremy Chauvin
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas78712, United States
| | - Logan Morton
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas78712, United States
| | - Adrianne M Rosales
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas78712, United States
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13
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Li X, Craven TW, Levine PM. Cyclic Peptide Screening Methods for Preclinical Drug Discovery. J Med Chem 2022; 65:11913-11926. [PMID: 36074956 DOI: 10.1021/acs.jmedchem.2c01077] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyclic peptides are among the most diverse architectures for current drug discovery efforts. Their size, stability, and ease of synthesis provide attractive scaffolds to engage and modulate some of the most challenging targets, including protein-protein interactions and those considered to be "undruggable". With a variety of sophisticated screening technologies to produce libraries of cyclic peptides, including phage display, mRNA display, split intein circular ligation of peptides, and in silico screening, a new era of cyclic peptide drug discovery is at the forefront of modern medicine. In this perspective, we begin by discussing cyclic peptides approved for clinical use in the past two decades. Particular focus is placed around synthetic chemistries to generate de novo libraries of cyclic peptides and novel methods to screen them. The perspective culminates with future prospects for generating cyclic peptides as viable therapeutic options and discusses the advantages and disadvantages currently being faced with bringing them to market.
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Affiliation(s)
- Xinting Li
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Timothy W Craven
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Paul M Levine
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
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14
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Kim J, Kobayashi H, Yokomine M, Shiratori Y, Ueda T, Takeuchi K, Umezawa K, Kuroda D, Tsumoto K, Morimoto J, Sando S. Residue-based program of a β-peptoid twisted strand shape via a cyclopentane constraint. Org Biomol Chem 2022; 20:6994-7000. [PMID: 35993969 DOI: 10.1039/d2ob01300b] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
N-Substituted peptides, such as peptoids and β-peptoids, have been reported to have unique structures with diverse functions, like catalysis and manipulation of biomolecular functions. Recently, the preorganization of monomer shape by restricting bond rotations about all backbone dihedral angles has been demonstrated to be useful for de novo design of peptoid structures. Such design strategies are hitherto unexplored for β-peptoids; to date, no preorganized β-peptoid monomers have been reported. Here, we report the first design strategy for β-peptoids, in which all four backbone dihedral angles (ω, ϕ, θ, ψ) are rotationally restricted on a per-residue basis. The introduction of a cyclopentane constraint realized the preorganized monomer structure and led to a β-peptoid with a stable twisted strand shape.
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Affiliation(s)
- Jungyeon Kim
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
| | - Hiroka Kobayashi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
| | - Marin Yokomine
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
| | - Yota Shiratori
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Takumi Ueda
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Koh Takeuchi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Koji Umezawa
- Department of Biomedical Sciences, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan.,Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Matsumoto, Nagano 390-8621, Japan
| | - Daisuke Kuroda
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan. .,Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Kouhei Tsumoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan. .,Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Jumpei Morimoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan. .,Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
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15
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Zou J, Zhou M, Xiao X, Liu R. Advance in Hybrid Peptides Synthesis. Macromol Rapid Commun 2022; 43:e2200575. [PMID: 35978269 DOI: 10.1002/marc.202200575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 07/24/2022] [Indexed: 11/08/2022]
Abstract
Hybrid peptides with heterogeneous backbone are a class of peptide mimics with adjustable proteolytic stability obtained from incorporating unnatural amino acid residues into peptide backbone. α/β-peptides and peptide/peptoid hybrids are two types of hybrid peptides that are widely studied for diverse applications, and several synthetic methods have been developed. In this mini review, the advance in hybrid peptide synthesis is summarized, including solution-phase method, solid-phase method, and novel polymerization method. Conventional solution-phase method and solid-phase method generally result in oligomers with defined sequences, while polymerization methods have advantages in preparing peptide hybrid polymers with high molecular weight with simple operation and low cost. In addition, the future development of polymerization method to realize the control of the peptide hybrid polymer sequence is discussed.
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Affiliation(s)
- Jingcheng Zou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Min Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Ximian Xiao
- Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Research Center for Biomedical Materials of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Runhui Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.,Key Laboratory for Ultrafine Materials of Ministry of Education, Frontiers Science Center for Materiobiology and Dynamic Chemistry, Research Center for Biomedical Materials of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai, 200237, China
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16
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Yao Q, Zhang X, Chen D. The emerging potentials of lncRNA DRAIC in human cancers. Front Oncol 2022; 12:867670. [PMID: 35992823 PMCID: PMC9386314 DOI: 10.3389/fonc.2022.867670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 07/11/2022] [Indexed: 12/24/2022] Open
Abstract
Long non-coding RNA (lncRNA) is a subtype of noncoding RNA that has more than 200 nucleotides. Numerous studies have confirmed that lncRNA is relevant during multiple biological processes through the regulation of various genes, thus affecting disease progression. The lncRNA DRAIC, a newly discovered lncRNA, has been found to be abnormally expressed in a variety of diseases, particularly cancer. Indeed, the dysregulation of DRAIC expression is closely related to clinicopathological features. It was also reported that DRAIC is key to biological functions such as cell proliferation, autophagy, migration, and invasion. Furthermore, DRAIC is of great clinical significance in human disease. In this review, we discuss the expression signature, clinical characteristics, biological functions, relevant mechanisms, and potential clinical applications of DRAIC in several human diseases.
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Affiliation(s)
- Qinfan Yao
- Kidney Disease Center, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou, China
- National Key Clinical Department of Kidney Diseases, Institute of Nephrology, Zhejiang University, Hangzhou, China
- Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Hangzhou, China
| | - Xiuyuan Zhang
- Kidney Disease Center, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou, China
- National Key Clinical Department of Kidney Diseases, Institute of Nephrology, Zhejiang University, Hangzhou, China
- Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Hangzhou, China
| | - Dajin Chen
- Kidney Disease Center, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou, China
- National Key Clinical Department of Kidney Diseases, Institute of Nephrology, Zhejiang University, Hangzhou, China
- Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Hangzhou, China
- *Correspondence: Dajin Chen,
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17
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Zúñiga L, Cayo A, González W, Vilos C, Zúñiga R. Potassium Channels as a Target for Cancer Therapy: Current Perspectives. Onco Targets Ther 2022; 15:783-797. [PMID: 35899081 PMCID: PMC9309325 DOI: 10.2147/ott.s326614] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 07/08/2022] [Indexed: 12/18/2022] Open
Abstract
Potassium (K+) channels are highly regulated membrane proteins that control the potassium ion flux and respond to different cellular stimuli. These ion channels are grouped into three major families, Kv (voltage-gated K+ channel), Kir (inwardly rectifying K+ channel) and K2P (two-pore K+ channels), according to the structure, to mediate the K+ currents. In cancer, alterations in K+ channel function can promote the acquisition of the so-called hallmarks of cancer – cell proliferation, resistance to apoptosis, metabolic changes, angiogenesis, and migratory capabilities – emerging as targets for the development of new therapeutic drugs. In this review, we focus our attention on the different K+ channels associated with the most relevant and prevalent cancer types. We summarize our knowledge about the potassium channels structure and function, their cancer dysregulated expression and discuss the K+ channels modulator and the strategies for designing new drugs.
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Affiliation(s)
- Leandro Zúñiga
- Laboratorio de Fisiología Molecular, Escuela de Medicina, Universidad de Talca, Talca, Chile.,Centro de Nanomedicina, Diagnóstico y Desarrollo de Fármacos (ND3), Escuela de Medicina, Universidad de Talca, Talca, Chile
| | - Angel Cayo
- Laboratorio de Fisiología Molecular, Escuela de Medicina, Universidad de Talca, Talca, Chile.,Centro de Nanomedicina, Diagnóstico y Desarrollo de Fármacos (ND3), Escuela de Medicina, Universidad de Talca, Talca, Chile
| | - Wendy González
- Centro de Bioinformática y Simulación Molecular, Universidad de Talca, Talca, Chile.,Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Universidad de Talca, Talca, Chile
| | - Cristian Vilos
- Centro de Nanomedicina, Diagnóstico y Desarrollo de Fármacos (ND3), Escuela de Medicina, Universidad de Talca, Talca, Chile.,Laboratory of Nanomedicine and Targeted Delivery, School of Medicine, Universidad de Talca, Talca, 3460000, Chile.,Center for The Development of Nanoscience & Nanotechnology (CEDENNA), Universidad de Santiago de Chile, Santiago, 8350709, Chile
| | - Rafael Zúñiga
- Laboratorio de Fisiología Molecular, Escuela de Medicina, Universidad de Talca, Talca, Chile.,Centro de Nanomedicina, Diagnóstico y Desarrollo de Fármacos (ND3), Escuela de Medicina, Universidad de Talca, Talca, Chile
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18
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Eastwood JRB, Jiang L, Bonneau R, Kirshenbaum K, Renfrew PD. Evaluating the Conformations and Dynamics of Peptoid Macrocycles. J Phys Chem B 2022; 126:5161-5174. [PMID: 35820178 DOI: 10.1021/acs.jpcb.2c01669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptoid macrocycles are versatile and chemically diverse peptidomimetic oligomers. However, the conformations and dynamics of these macrocycles have not been evaluated comprehensively and require extensive further investigation. Recent studies indicate that two degrees of freedom, and four distinct conformations, adequately describe the behavior of each monomer backbone unit in most peptoid oligomers. On the basis of this insight, we conducted molecular dynamics simulations of model macrocycles using an exhaustive set of idealized possible starting conformations. Simulations of various sizes of peptoid macrocycles yielded a limited set of populated conformations. In addition to reproducing all relevant experimentally determined conformations, the simulations accurately predicted a cyclo-octamer conformation for which we now present the first experimental observation. Sets of three adjacent dihedral angles (ϕi, ψi, ωi+1) exhibited correlated crankshaft motions over the course of simulation for peptoid macrocycles of six residues and larger. These correlated motions may occur in the form of an inversion of one amide bond and the concerted rotation of the preceding ϕ and ψ angles to their mirror-image conformation, a variation on "crankshaft flip" motions studied in polymers and peptides. The energy landscape of these peptoid macrocycles can be described as a network of conformations interconnected by transformations of individual crankshaft flips. For macrocycles of up to eight residues, our mapping of the landscape is essentially complete.
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Affiliation(s)
- James R B Eastwood
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Linhai Jiang
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Richard Bonneau
- Center for Data Science, New York University, New York, New York 10011, United States.,Center for Computational Biology, Flatiron Institute, New York, New York 10010 United States
| | - Kent Kirshenbaum
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - P Douglas Renfrew
- Center for Computational Biology, Flatiron Institute, New York, New York 10010 United States
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19
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Koelman EMR, Yeste-Vázquez A, Grossmann TN. Targeting the interaction of β-catenin and TCF/LEF transcription factors to inhibit oncogenic Wnt signaling. Bioorg Med Chem 2022; 70:116920. [PMID: 35841828 DOI: 10.1016/j.bmc.2022.116920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 11/02/2022]
Abstract
The Wnt/β-catenin signaling pathway is crucially involved in embryonic development, stem cell maintenance and tissue renewal. Hyperactivation of this pathway is associated with the development and progression of various types of cancers. The transcriptional coactivator β-catenin represents a pivotal component of the pathway and its interaction with transcription factors of the TCF/LEF family is central to pathway activation. Inhibition of this crucial protein-protein interaction via direct targeting of β-catenin is considered a promising strategy for the inactivation of oncogenic Wnt signaling. This review summarizes advances in the development of Wnt antagonists that have been shown to directly bind β-catenin.
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Affiliation(s)
- Emma M R Koelman
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, NL, The Netherlands
| | - Alejandro Yeste-Vázquez
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, NL, The Netherlands; Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, Amsterdam, NL, The Netherlands
| | - Tom N Grossmann
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, NL, The Netherlands; Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, Amsterdam, NL, The Netherlands.
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20
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Affiliation(s)
- Assunta D'Amato
- University of Salerno: Universita degli Studi di Salerno Chemistry and Biology "A. Zambelli" Via Giovanni Paolo II, 132 84084 Fisciano ITALY
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21
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Helical Foldamers and Stapled Peptides as New Modalities in Drug Discovery: Modulators of Protein-Protein Interactions. Processes (Basel) 2022. [DOI: 10.3390/pr10050924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A “foldamer” is an artificial oligomeric molecule with a regular secondary or tertiary structure consisting of various building blocks. A “stapled peptide” is a peptide with stabilized secondary structures, in particular, helical structures by intramolecular covalent side-chain cross-linking. Helical foldamers and stapled peptides are potential drug candidates that can target protein-protein interactions because they enable multipoint molecular recognition, which is difficult to achieve with low-molecular-weight compounds. This mini-review describes a variety of peptide-based foldamers and stapled peptides with a view to their applications in drug discovery, including our recent progress.
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22
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Rational Discovery of Antiviral Whey Protein-Derived Small Peptides Targeting the SARS-CoV-2 Main Protease. Biomedicines 2022; 10:biomedicines10051067. [PMID: 35625804 PMCID: PMC9139167 DOI: 10.3390/biomedicines10051067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 04/30/2022] [Accepted: 04/30/2022] [Indexed: 11/17/2022] Open
Abstract
In the present work, and for the first time, three whey protein-derived peptides (IAEK, IPAVF, MHI), endowed with ACE inhibitory activity, were examined for their antiviral activity against the SARS-CoV-2 3C-like protease (3CLpro) and Human Rhinovirus 3C protease (3Cpro) by employing molecular docking. Computational studies showed reliable binding poses within 3CLpro for the three investigated small peptides, considering docking scores as well as the binding free energy values. Validation by in vitro experiments confirmed these results. In particular, IPAVF exhibited the highest inhibitory activity by returning an IC50 equal to 1.21 μM; it was followed by IAEK, which registered an IC50 of 154.40 μM, whereas MHI was less active with an IC50 equal to 2700.62 μM. On the other hand, none of the assayed peptides registered inhibitory activity against 3Cpro. Based on these results, the herein presented small peptides are introduced as promising molecules to be exploited in the development of “target-specific antiviral” agents against SARS-CoV-2.
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23
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Gupta S, Azadvari N, Hosseinzadeh P. Design of Protein Segments and Peptides for Binding to Protein Targets. BIODESIGN RESEARCH 2022; 2022:9783197. [PMID: 37850124 PMCID: PMC10521657 DOI: 10.34133/2022/9783197] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/16/2022] [Indexed: 10/19/2023] Open
Abstract
Recent years have witnessed a rise in methods for accurate prediction of structure and design of novel functional proteins. Design of functional protein fragments and peptides occupy a small, albeit unique, space within the general field of protein design. While the smaller size of these peptides allows for more exhaustive computational methods, flexibility in their structure and sparsity of data compared to proteins, as well as presence of noncanonical building blocks, add additional challenges to their design. This review summarizes the current advances in the design of protein fragments and peptides for binding to targets and discusses the challenges in the field, with an eye toward future directions.
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Affiliation(s)
- Suchetana Gupta
- Knight Campus Center for Accelerating Scientific Impact, University of Oregon, Eugene OR 97403, USA
| | - Noora Azadvari
- Knight Campus Center for Accelerating Scientific Impact, University of Oregon, Eugene OR 97403, USA
| | - Parisa Hosseinzadeh
- Knight Campus Center for Accelerating Scientific Impact, University of Oregon, Eugene OR 97403, USA
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24
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Buyanova M, Pei D. Targeting intracellular protein-protein interactions with macrocyclic peptides. Trends Pharmacol Sci 2022; 43:234-248. [PMID: 34911657 PMCID: PMC8840965 DOI: 10.1016/j.tips.2021.11.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/23/2021] [Accepted: 11/09/2021] [Indexed: 01/07/2023]
Abstract
Intracellular protein-protein interactions (PPIs) are challenging targets for traditional drug modalities. Macrocyclic peptides (MPs) prove highly effective PPI inhibitors in vitro and can be rapidly discovered against PPI targets by rational design or screening combinatorial libraries but are generally impermeable to the cell membrane. Recent advances in MP science and technology are allowing for the development of 'drug-like' MPs that potently and specifically modulate intracellular PPI targets in cell culture and animal models. In this review, we highlight recent progress in generating cell-permeable MPs that enter the mammalian cell by passive diffusion, endocytosis followed by endosomal escape, or as-yet unknown mechanisms.
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Affiliation(s)
- Marina Buyanova
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA.
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25
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Therapeutic peptides: current applications and future directions. Signal Transduct Target Ther 2022; 7:48. [PMID: 35165272 PMCID: PMC8844085 DOI: 10.1038/s41392-022-00904-4] [Citation(s) in RCA: 437] [Impact Index Per Article: 218.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 02/08/2023] Open
Abstract
Peptide drug development has made great progress in the last decade thanks to new production, modification, and analytic technologies. Peptides have been produced and modified using both chemical and biological methods, together with novel design and delivery strategies, which have helped to overcome the inherent drawbacks of peptides and have allowed the continued advancement of this field. A wide variety of natural and modified peptides have been obtained and studied, covering multiple therapeutic areas. This review summarizes the efforts and achievements in peptide drug discovery, production, and modification, and their current applications. We also discuss the value and challenges associated with future developments in therapeutic peptides.
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26
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Warnock TMC, Rajkumar S, Fitzpatrick MP, Serpell CJ, Dingwall P, Knipe PC. Chiral, sequence-definable foldamer-derived macrocycles. Chem Sci 2021; 12:15632-15636. [PMID: 35003593 PMCID: PMC8654020 DOI: 10.1039/d1sc05021d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/03/2021] [Indexed: 12/22/2022] Open
Abstract
Nature's oligomeric macromolecules have been a long-standing source of inspiration for chemists producing foldamers. Natural systems are frequently conformationally stabilised by macrocyclisation, yet this approach has been rarely adopted in the field of foldamer chemistry. Here we present a new class of chiral cyclic trimers and tetramers formed by macrocyclisation of open-chain foldamer precursors. Symmetrical products are obtained via a [2 + 2] self-assembly approach, while full sequence control is demonstrated through linear synthesis and cyclisation of an unsymmetrical trimer. Structural characterisation is achieved through a combined X-ray and DFT approach, which indicates the tetramers adopt a near-planar conformation, while the trimers adopt a shallow bowl-like shape. Finally, a proof-of-concept experiment is conducted to demonstrate the macrocycles' capacity for cation binding. Dipole-controlled pre-organization enables the cyclization of sequence-defined foldamers into macrocycles. The structure and properties of trimeric and tetrameric macrocycles are explored, and their ability to bind cationic guests is demonstrated.![]()
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Affiliation(s)
- Toyah M C Warnock
- School of Chemistry and Chemical Engineering, Queen's University Belfast David Keir Building Belfast BT9 5AG UK
| | | | - Matthew P Fitzpatrick
- School of Chemistry and Chemical Engineering, Queen's University Belfast David Keir Building Belfast BT9 5AG UK
| | - Christopher J Serpell
- School of Physical Sciences, University of Kent Ingram Building Canterbury Kent CT2 7NH UK
| | - Paul Dingwall
- School of Chemistry and Chemical Engineering, Queen's University Belfast David Keir Building Belfast BT9 5AG UK
| | - Peter C Knipe
- School of Chemistry and Chemical Engineering, Queen's University Belfast David Keir Building Belfast BT9 5AG UK
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27
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Murali A, Lokhande G, Deo KA, Brokesh A, Gaharwar AK. Emerging 2D Nanomaterials for Biomedical Applications. MATERIALS TODAY (KIDLINGTON, ENGLAND) 2021; 50:276-302. [PMID: 34970073 PMCID: PMC8713997 DOI: 10.1016/j.mattod.2021.04.020] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Two-dimensional (2D) nanomaterials are an emerging class of biomaterials with remarkable potential for biomedical applications. The planar topography of these nanomaterials confers unique physical, chemical, electronic and optical properties, making them attractive candidates for therapeutic delivery, biosensing, bioimaging, regenerative medicine, and additive manufacturing strategies. The high surface-to-volume ratio of 2D nanomaterials promotes enhanced interactions with biomolecules and cells. A range of 2D nanomaterials, including transition metal dichalcogenides (TMDs), layered double hydroxides (LDHs), layered silicates (nanoclays), 2D metal carbides and nitrides (MXenes), metal-organic framework (MOFs), covalent organic frameworks (COFs) and polymer nanosheets have been investigated for their potential in biomedical applications. Here, we will critically evaluate recent advances of 2D nanomaterial strategies in biomedical engineering and discuss emerging approaches and current limitations associated with these nanomaterials. Due to their unique physical, chemical, and biological properties, this new class of nanomaterials has the potential to become a platform technology in regenerative medicine and other biomedical applications.
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Affiliation(s)
- Aparna Murali
- Biomedical Engineering, Dwight Look College of Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Giriraj Lokhande
- Biomedical Engineering, Dwight Look College of Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Kaivalya A. Deo
- Biomedical Engineering, Dwight Look College of Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Anna Brokesh
- Biomedical Engineering, Dwight Look College of Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Akhilesh K. Gaharwar
- Biomedical Engineering, Dwight Look College of Engineering, Texas A&M University, College Station, TX 77843, USA
- Material Science and Engineering, Dwight Look College of Engineering, Texas A&M University, College Station, TX 77843, USA
- Center for Remote Health Technologies and Systems, Texas A&M University, College Station, TX 77843, USA
- Interdisciplinary Graduate Program in Genetics, Texas A&M University, College Station, TX 77843, USA
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28
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Fukuda Y, Yokomine M, Kuroda D, Tsumoto K, Morimoto J, Sando S. Peptoid-based reprogrammable template for cell-permeable inhibitors of protein-protein interactions. Chem Sci 2021; 12:13292-13300. [PMID: 34777747 PMCID: PMC8528041 DOI: 10.1039/d1sc01560e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 08/02/2021] [Indexed: 12/27/2022] Open
Abstract
The development of inhibitors of intracellular protein–protein interactions (PPIs) is of great significance for drug discovery, but the generation of a cell-permeable molecule with high affinity to protein is challenging. Oligo(N-substituted glycines) (oligo-NSGs), referred to as peptoids, are attractive as potential intracellular PPI inhibitors owing to their high membrane permeability. However, their intrinsically flexible backbones make the rational design of inhibitors difficult. Here, we propose a peptoid-based rational approach to develop cell-permeable PPI inhibitors using oligo(N-substituted alanines) (oligo-NSAs). The rigid structures of oligo-NSAs enable independent optimization of each N-substituent to improve binding affinity and membrane permeability, while preserving the backbone shape. A molecule with optimized N-substituents inhibited a target PPI in cells, which demonstrated the utility of oligo-NSA as a reprogrammable template to develop intracellular PPI inhibitors. A peptoid-based modular approach using oligo(N-substituted alanine) as a reprogrammable template enables independent optimization of N-substituents and facile development of cell-permeable inhibitors of protein–protein interactions.![]()
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Affiliation(s)
- Yasuhiro Fukuda
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Marin Yokomine
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Daisuke Kuroda
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan .,Department of Bioengineering, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Kouhei Tsumoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan .,Department of Bioengineering, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan.,Institute of Medical Science, The University of Tokyo 4-6-1, Shirokanedai, Minato-ku Tokyo 108-8639 Japan
| | - Jumpei Morimoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan .,Department of Bioengineering, Graduate School of Engineering, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
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29
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Rajale T, Miner JC, Michalczyk R, Phipps ML, Schmidt JG, Gilbertson RD, Williams RF, Strauss CEM, Martinez JS. Conformational control via sequence for a heteropeptoid in water: coupled NMR and Rosetta modelling. Chem Commun (Camb) 2021; 57:9922-9925. [PMID: 34498621 DOI: 10.1039/d1cc01992a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We report a critical advance in the generation and characterization of peptoid hetero-oligomers. A library of sub-monomers with amine and carboxylate side-chains are combined in different sequences using microwave-assisted synthesis. Their sequence-structure propensity is confirmed by circular dichroism, and conformer subtypes are enumerated by NMR. Biasing the ψ-angle backbone to trans (180°) in Monte Carlo modelling favors i to i + 3 naphthyl-naphthyl stacking, and matches experimental ensemble distributions. Taken together, high-yield synthesis of heterooligomers and NMR with structure prediction enables rapid determination of sequences that induce secondary structural propensities for predictive design of hydrophilic peptidomimetic foldamers and their future libraries.
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Affiliation(s)
- Trideep Rajale
- Center for Integrated Nanotechnologies, (CINT), Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Jacob C Miner
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.,Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Ryszard Michalczyk
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - M Lisa Phipps
- Center for Integrated Nanotechnologies, (CINT), Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Jurgen G Schmidt
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Robert D Gilbertson
- Materials Science and Technology Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Robert F Williams
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Charlie E M Strauss
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Jennifer S Martinez
- Center for Materials Interfaces in Research and Applications, Northern Arizona University, Flagstaff, Arizona 86011, USA. .,Department of Applied Physics and Materials Science, Northern Arizona University, Flagstaff, Arizona 86011, USA
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30
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Blosser SL, Sawyer N, Maksimovic I, Ghosh B, Arora PS. Covalent and Noncovalent Targeting of the Tcf4/β-Catenin Strand Interface with β-Hairpin Mimics. ACS Chem Biol 2021; 16:1518-1525. [PMID: 34286954 DOI: 10.1021/acschembio.1c00389] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
β-Strands are a fundamental component of protein structure, and these extended peptide regions serve as binding epitopes for numerous protein-protein complexes. However, synthetic mimics that capture the conformation of these epitopes and inhibit selected protein-protein interactions are rare. Here we describe covalent and noncovalent β-hairpin mimics of an extended strand region mediating the Tcf4/β-catenin interaction. Our efforts afford a rationally designed lead for an underexplored region of β-catenin, which has been the subject of numerous ligand discovery campaigns.
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Affiliation(s)
- Sarah L. Blosser
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Nicholas Sawyer
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Igor Maksimovic
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Brahma Ghosh
- Discovery Chemistry, Janssen Research and Development, LLC, Spring House, Pennsylvania 19477, United States
| | - Paramjit S. Arora
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
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31
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Wendt M, Bellavita R, Gerber A, Efrém NL, van Ramshorst T, Pearce NM, Davey PRJ, Everard I, Vazquez-Chantada M, Chiarparin E, Grieco P, Hennig S, Grossmann TN. Bicyclic β-Sheet Mimetics that Target the Transcriptional Coactivator β-Catenin and Inhibit Wnt Signaling. Angew Chem Int Ed Engl 2021; 60:13937-13944. [PMID: 33783110 PMCID: PMC8252567 DOI: 10.1002/anie.202102082] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Indexed: 12/29/2022]
Abstract
Protein complexes are defined by the three-dimensional structure of participating binding partners. Knowledge about these structures can facilitate the design of peptidomimetics which have been applied for example, as inhibitors of protein-protein interactions (PPIs). Even though β-sheets participate widely in PPIs, they have only rarely served as the basis for peptidomimetic PPI inhibitors, in particular when addressing intracellular targets. Here, we present the structure-based design of β-sheet mimetics targeting the intracellular protein β-catenin, a central component of the Wnt signaling pathway. Based on a protein binding partner of β-catenin, a macrocyclic peptide was designed and its crystal structure in complex with β-catenin obtained. Using this structure, we designed a library of bicyclic β-sheet mimetics employing a late-stage diversification strategy. Several mimetics were identified that compete with transcription factor binding to β-catenin and inhibit Wnt signaling in cells. The presented design strategy can support the development of inhibitors for other β-sheet-mediated PPIs.
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Affiliation(s)
- Mathias Wendt
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Rosa Bellavita
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Alan Gerber
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Nina-Louisa Efrém
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Thirza van Ramshorst
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Nicholas M Pearce
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Paul R J Davey
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Isabel Everard
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | | | | | - Paolo Grieco
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Sven Hennig
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Tom N Grossmann
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
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32
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Connolly MD, Xuan S, Molchanova N, Zuckermann RN. Submonomer synthesis of sequence defined peptoids with diverse side-chains. Methods Enzymol 2021; 656:241-270. [PMID: 34325788 DOI: 10.1016/bs.mie.2021.04.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Peptoids are a diverse family of sequence-defined oligomers of N-substituted glycine monomers, that can be readily accessed by the solid-phase submonomer synthesis method. Due to the versatility and efficiency of this chemistry, and the easy access to hundreds of potential monomers, there is an enormous potential sequence space that can be explored. This has enabled researchers from many different fields to custom-design peptoid sequences tailored to a wide variety of problems in biomedicine, nanoscience and polymer science. Here we provide detailed protocols for the synthesis of peptoids, using optimized protocols that can be performed by non-chemists. The submonomer method is fully compatible with Fmoc-peptide synthesis conditions, so the method is readily automated on existing automated peptide synthesizers using protocols provided here. Although the submonomer synthesis for peptoids is well established, there are special considerations required in order to access many of the most useful and desirable sidechains. Here we provide methods to include most of the amino-acid-like side chains, some of the most important non-natural monomer classes, as well as the creation of peptoid conjugates and peptide-peptoid hybrids.
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Affiliation(s)
- Michael D Connolly
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Sunting Xuan
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Natalia Molchanova
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Ronald N Zuckermann
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
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33
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Voelz VA, Ge Y, Raddi RM. Reconciling Simulations and Experiments With BICePs: A Review. Front Mol Biosci 2021; 8:661520. [PMID: 34046431 PMCID: PMC8144449 DOI: 10.3389/fmolb.2021.661520] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 04/12/2021] [Indexed: 02/04/2023] Open
Abstract
Bayesian Inference of Conformational Populations (BICePs) is an algorithm developed to reconcile simulated ensembles with sparse experimental measurements. The Bayesian framework of BICePs enables population reweighting as a post-simulation processing step, with several advantages over existing methods, including the proper use of reference potentials, and the estimation of a Bayes factor-like quantity called the BICePs score for model selection. Here, we summarize the theory underlying this method in context with related algorithms, review the history of BICePs applications to date, and discuss current shortcomings along with future plans for improvement.
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Affiliation(s)
- Vincent A. Voelz
- Department of Chemistry, Temple University, Philadelphia, PA, United States
| | - Yunhui Ge
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, United States
| | - Robert M. Raddi
- Department of Chemistry, Temple University, Philadelphia, PA, United States
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34
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Wendt M, Bellavita R, Gerber A, Efrém N, Ramshorst T, Pearce NM, Davey PRJ, Everard I, Vazquez‐Chantada M, Chiarparin E, Grieco P, Hennig S, Grossmann TN. Bicyclic β‐Sheet Mimetics that Target the Transcriptional Coactivator β‐Catenin and Inhibit Wnt Signaling. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Mathias Wendt
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
| | - Rosa Bellavita
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
- Department of Pharmacy University of Naples Federico II Naples Italy
| | - Alan Gerber
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
| | - Nina‐Louisa Efrém
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
| | - Thirza Ramshorst
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
| | - Nicholas M. Pearce
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
| | | | - Isabel Everard
- Mechanistic Biology and Profiling Discovery Sciences, R&D AstraZeneca Cambridge UK
| | | | | | - Paolo Grieco
- Department of Pharmacy University of Naples Federico II Naples Italy
| | - Sven Hennig
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
| | - Tom N. Grossmann
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
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35
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Liu Z, Wang P, Wold EA, Song Q, Zhao C, Wang C, Zhou J. Small-Molecule Inhibitors Targeting the Canonical WNT Signaling Pathway for the Treatment of Cancer. J Med Chem 2021; 64:4257-4288. [PMID: 33822624 DOI: 10.1021/acs.jmedchem.0c01799] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Canonical WNT signaling is an important developmental pathway that has attracted increased attention for anticancer drug discovery. From the production and secretion of WNT ligands, their binding to membrane receptors, and the β-catenin destruction complex to the expansive β-catenin transcriptional complex, multiple components have been investigated as drug targets to modulate WNT signaling. Significant progress in developing WNT inhibitors such as porcupine inhibitors, tankyrase inhibitors, β-catenin/coactivators, protein-protein interaction inhibitors, casein kinase modulators, DVL inhibitors, and dCTPP1 inhibitors has been made, with several candidates (e.g., LGK-974, PRI-724, and ETC-159) in human clinical trials. Herein we summarize recent progress in the drug discovery and development of small-molecule inhibitors targeting the canonical WNT pathway, focusing on their specific target proteins, in vitro and in vivo activities, physicochemical properties, and therapeutic potential. The relevant opportunities and challenges toward maintaining the balance between efficacy and toxicity in effectively targeting this pathway are also highlighted.
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Affiliation(s)
- Zhiqing Liu
- Institute of Evolution and Marine Biodiversity, College of Food Science and Technology, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Pingyuan Wang
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, Texas 77555, United States
| | - Eric A Wold
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, Texas 77555, United States
| | - Qiaoling Song
- Institute of Evolution and Marine Biodiversity, College of Food Science and Technology, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Chenyang Zhao
- Institute of Evolution and Marine Biodiversity, College of Food Science and Technology, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Changyun Wang
- Institute of Evolution and Marine Biodiversity, College of Food Science and Technology, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, Texas 77555, United States
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36
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Wang Z, Li Z, Ji H. Direct targeting of β-catenin in the Wnt signaling pathway: Current progress and perspectives. Med Res Rev 2021; 41:2109-2129. [PMID: 33475177 DOI: 10.1002/med.21787] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 08/30/2020] [Accepted: 01/05/2021] [Indexed: 12/28/2022]
Abstract
Aberrant activation of the Wnt/β-catenin signaling circuit is associated with cancer recurrence and relapse, cancer invasion and metastasis, and cancer immune evasion. Direct targeting of β-catenin, the central hub in this signaling pathway, is a promising strategy to suppress the hyperactive β-catenin signaling but has proven to be highly challenging. Substantial efforts have been made to discover compounds that bind with β-catenin, block β-catenin-mediated protein-protein interactions, and suppress β-catenin signaling. Herein, we characterize potential small-molecule binding sites in β-catenin, summarize bioactive small molecules that directly target β-catenin, and review structure-based inhibitor optimization, structure-activity relationship, and biological activities of reported inhibitors. This knowledge will benefit future inhibitor development and β-catenin-related drug discovery.
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Affiliation(s)
- Zhen Wang
- Department of Drug Discovery, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Zilu Li
- Department of Chemistry, University of South Florida, Tampa, Florida, USA
| | - Haitao Ji
- Department of Drug Discovery, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA.,Department of Chemistry, University of South Florida, Tampa, Florida, USA
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37
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González-Muñiz R, Bonache MÁ, Pérez de Vega MJ. Modulating Protein-Protein Interactions by Cyclic and Macrocyclic Peptides. Prominent Strategies and Examples. Molecules 2021; 26:445. [PMID: 33467010 PMCID: PMC7830901 DOI: 10.3390/molecules26020445] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 12/11/2022] Open
Abstract
Cyclic and macrocyclic peptides constitute advanced molecules for modulating protein-protein interactions (PPIs). Although still peptide derivatives, they are metabolically more stable than linear counterparts, and should have a lower degree of flexibility, with more defined secondary structure conformations that can be adapted to imitate protein interfaces. In this review, we analyze recent progress on the main methods to access cyclic/macrocyclic peptide derivatives, with emphasis in a few selected examples designed to interfere within PPIs. These types of peptides can be from natural origin, or prepared by biochemical or synthetic methodologies, and their design could be aided by computational approaches. Some advances to facilitate the permeability of these quite big molecules by conjugation with cell penetrating peptides, and the incorporation of β-amino acid and peptoid structures to improve metabolic stability, are also commented. It is predicted that this field of research could have an important future mission, running in parallel to the discovery of new, relevant PPIs involved in pathological processes.
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Affiliation(s)
- Rosario González-Muñiz
- Instituto de Química Médica (IQM-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain; (M.Á.B.); (M.J.P.d.V.)
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38
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Kessler D, Mayer M, Zahn SK, Zeeb M, Wöhrle S, Bergner A, Bruchhaus J, Ciftci T, Dahmann G, Dettling M, Döbel S, Fuchs JE, Geist L, Hela W, Kofink C, Kousek R, Moser F, Puchner T, Rumpel K, Scharnweber M, Werni P, Wolkerstorfer B, Breitsprecher D, Baaske P, Pearson M, McConnell DB, Böttcher J. Getting a Grip on the Undrugged: Targeting β-Catenin with Fragment-Based Methods. ChemMedChem 2021; 16:1420-1424. [PMID: 33275320 PMCID: PMC8247886 DOI: 10.1002/cmdc.202000839] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Indexed: 12/20/2022]
Abstract
Aberrant WNT pathway activation, leading to nuclear accumulation of β‐catenin, is a key oncogenic driver event. Mutations in the tumor suppressor gene APC lead to impaired proteasomal degradation of β‐catenin and subsequent nuclear translocation. Restoring cellular degradation of β‐catenin represents a potential therapeutic strategy. Here, we report the fragment‐based discovery of a small molecule binder to β‐catenin, including the structural elucidation of the binding mode by X‐ray crystallography. The difficulty in drugging β‐catenin was confirmed as the primary screening campaigns identified only few and very weak hits. Iterative virtual and NMR screening techniques were required to discover a compound with sufficient potency to be able to obtain an X‐ray co‐crystal structure. The binding site is located between armadillo repeats two and three, adjacent to the BCL9 and TCF4 binding sites. Genetic studies show that it is unlikely to be useful for the development of protein–protein interaction inhibitors but structural information and established assays provide a solid basis for a prospective optimization towards β‐catenin proteolysis targeting chimeras (PROTACs) as alternative modality.
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Affiliation(s)
- Dirk Kessler
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Moriz Mayer
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Stephan K Zahn
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Markus Zeeb
- Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Straße 65, 88397, Biberach, Germany
| | - Simon Wöhrle
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Andreas Bergner
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Jens Bruchhaus
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Tuncay Ciftci
- Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Straße 65, 88397, Biberach, Germany
| | - Georg Dahmann
- Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Straße 65, 88397, Biberach, Germany
| | - Maike Dettling
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Sandra Döbel
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Julian E Fuchs
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Leonhard Geist
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Wolfgang Hela
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Christiane Kofink
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Roland Kousek
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Franziska Moser
- Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Straße 65, 88397, Biberach, Germany
| | - Teresa Puchner
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Klaus Rumpel
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | | | - Patrick Werni
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | | | - Dennis Breitsprecher
- NanoTemper Technologies GmbH, Floessergasse 4, 81369, Muenchen, Germany.,Leica Microsystems AG, Max Schmidheiny-Strasse 201, 9435, Heerbrugg, Switzerland
| | - Philipp Baaske
- NanoTemper Technologies GmbH, Floessergasse 4, 81369, Muenchen, Germany
| | - Mark Pearson
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Darryl B McConnell
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Jark Böttcher
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
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39
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Amawi H, Aljabali AAA, Boddu SHS, Amawi S, Obeid MA, Ashby CR, Tiwari AK. The use of zebrafish model in prostate cancer therapeutic development and discovery. Cancer Chemother Pharmacol 2021; 87:311-325. [PMID: 33392639 DOI: 10.1007/s00280-020-04211-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/26/2020] [Indexed: 12/24/2022]
Abstract
Zebrafish is now among the leading in vivo model for cancer research, including prostate cancer. They are an alternative economic model being used to study cancer development, proliferation, and metastasis. They can also be effectively utilized for the development of cancer drugs at all levels, including target validation, and high-throughput screening for possible lead molecules. In this review, we provide a comprehensive overview of the role of zebrafish as an in vivo model in prostate cancer research. Globally, prostate cancer is a leading cause of death in men. Although many molecular mechanisms have been identified as playing a role in the pathogenesis of prostate cancer, there is still a significant need to understand the initial events of the disease. Furthermore, current treatments are limited by the emergence of severe toxicities and multidrug resistance. There is an essential need for economical and relevant research tools to improve our understanding and overcome these problems. This review provides a comprehensive summary of studies that utilized zebrafish for different aims in prostate cancer research. We discuss the use of zebrafish in prostate cancer cell proliferation and metastasis, defining signaling pathways, drug discovery and therapeutic development against prostate cancer, and toxicity studies. Finally, this review highlights limitations in this field and future directions to efficiently use zebrafish as a robust model for prostate cancer therapeutics development.
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Affiliation(s)
- Haneen Amawi
- Department of Pharmacy Practice, Faculty of Pharmacy, Yarmouk University, P.O.BOX 566, Irbid, 21163, Jordan.
| | - Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Yarmouk University, Irbid, Jordan
| | - Sai H S Boddu
- College of Pharmacy and Health Sciences, Ajman University, Ajman, UAE
| | - Sadam Amawi
- Department of Urology and General Surgery, Faculty of Medicine, King Abdullah University Hospital, Jordan University of Science and Technology, Irbid, 22110, Jordan
| | - Mohammad A Obeid
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Yarmouk University, Irbid, Jordan
| | - Charles R Ashby
- Department of Pharmaceutical Sciences, St. John's University, Queens, USA
| | - Amit K Tiwari
- Department of Pharmacology and Experimental Therapeutics, The University of Toledo, Toledo, OH, USA.
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40
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Meng F, Liang Z, Zhao K, Luo C. Drug design targeting active posttranslational modification protein isoforms. Med Res Rev 2020; 41:1701-1750. [PMID: 33355944 DOI: 10.1002/med.21774] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/29/2020] [Accepted: 12/03/2020] [Indexed: 12/11/2022]
Abstract
Modern drug design aims to discover novel lead compounds with attractable chemical profiles to enable further exploration of the intersection of chemical space and biological space. Identification of small molecules with good ligand efficiency, high activity, and selectivity is crucial toward developing effective and safe drugs. However, the intersection is one of the most challenging tasks in the pharmaceutical industry, as chemical space is almost infinity and continuous, whereas the biological space is very limited and discrete. This bottleneck potentially limits the discovery of molecules with desirable properties for lead optimization. Herein, we present a new direction leveraging posttranslational modification (PTM) protein isoforms target space to inspire drug design termed as "Post-translational Modification Inspired Drug Design (PTMI-DD)." PTMI-DD aims to extend the intersections of chemical space and biological space. We further rationalized and highlighted the importance of PTM protein isoforms and their roles in various diseases and biological functions. We then laid out a few directions to elaborate the PTMI-DD in drug design including discovering covalent binding inhibitors mimicking PTMs, targeting PTM protein isoforms with distinctive binding sites from that of wild-type counterpart, targeting protein-protein interactions involving PTMs, and hijacking protein degeneration by ubiquitination for PTM protein isoforms. These directions will lead to a significant expansion of the biological space and/or increase the tractability of compounds, primarily due to precisely targeting PTM protein isoforms or complexes which are highly relevant to biological functions. Importantly, this new avenue will further enrich the personalized treatment opportunity through precision medicine targeting PTM isoforms.
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Affiliation(s)
- Fanwang Meng
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Zhongjie Liang
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Kehao Zhao
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China
| | - Cheng Luo
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
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41
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Furukawa A, Schwochert J, Pye CR, Asano D, Edmondson QD, Turmon AC, Klein VG, Ono S, Okada O, Lokey RS. Drug-Like Properties in Macrocycles above MW 1000: Backbone Rigidity versus Side-Chain Lipophilicity. Angew Chem Int Ed Engl 2020; 59:21571-21577. [PMID: 32789999 PMCID: PMC7719619 DOI: 10.1002/anie.202004550] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 06/10/2020] [Indexed: 12/22/2022]
Abstract
Large macrocyclic peptides can achieve surprisingly high membrane permeability, although the properties that govern permeability in this chemical space are only beginning to come into focus. We generated two libraries of cyclic decapeptides with stable cross-β conformations, and found that peptoid substitutions within the β-turns of the macrocycle preserved the rigidity of the parent scaffold, whereas peptoid substitutions in the opposing β-strands led to "chameleonic" species that were rigid in nonpolar media but highly flexible in water. Both rigid and chameleonic compounds showed high permeability over a wide lipophilicity range, with peak permeabilities differing significantly depending on scaffold rigidity. Our findings indicate that modulating lipophilicity can be used to engineer favorable ADME properties into both rigid and flexible macrocyclic peptides, and that scaffold rigidity can be used to tune optimal lipophilicity.
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Affiliation(s)
- Akihiro Furukawa
- Daiichi Sankyo Co., Ltd., 1-2-58, Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Joshua Schwochert
- Unnatural Products, Inc., 250 Natural Bridges Drive, Santa Cruz, CA 95060 USA
| | - Cameron R. Pye
- Unnatural Products, Inc., 250 Natural Bridges Drive, Santa Cruz, CA 95060 USA
| | - Daigo Asano
- Daiichi Sankyo Co., Ltd., 1-2-58, Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Quinn D. Edmondson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, USA
| | - Alexandra C. Turmon
- Unnatural Products, Inc., 250 Natural Bridges Drive, Santa Cruz, CA 95060 USA
| | - Victoria G. Klein
- Department of Chemistry & Biochemistry, University of California Santa Cruz, Santa Cruz, CA 96064 USA
| | - Satoshi Ono
- Discovery Technology Laboratories, Mitsubishi Tanabe Pharma Corporation, Yokohama, 227-0033, Japan
| | - Okimasa Okada
- Discovery Technology Laboratories, Mitsubishi Tanabe Pharma Corporation, Yokohama, 227-0033, Japan
| | - R. Scott Lokey
- Department of Chemistry & Biochemistry, University of California Santa Cruz, Santa Cruz, CA 96064 USA
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Zhang W, Sviripa VM, Xie Y, Yu T, Haney MG, Blackburn JS, Adeniran CA, Zhan CG, Watt DS, Liu C. Epigenetic Regulation of Wnt Signaling by Carboxamide-Substituted Benzhydryl Amines that Function as Histone Demethylase Inhibitors. iScience 2020; 23:101795. [PMID: 33305174 PMCID: PMC7718485 DOI: 10.1016/j.isci.2020.101795] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/24/2020] [Accepted: 11/09/2020] [Indexed: 01/01/2023] Open
Abstract
Aberrant activation of Wnt signaling triggered by mutations in either Adenomatous Polyposis Coli (APC) or CTNNB1 (β-catenin) is a hallmark of colorectal cancers (CRC). As part of a program to develop epigenetic regulators for cancer therapy, we developed carboxamide-substituted benzhydryl amines (CBAs) bearing either aryl or heteroaryl groups that selectively targeted histone lysine demethylases (KDMs) and functioned as inhibitors of the Wnt pathway. A biotinylated variant of N-((5-chloro-8-hydroxyquinolin-7-yl) (4-(diethylamino)phenyl)-methyl)butyramide (CBA-1) identified KDM3A as a binding partner. KDM3A is a Jumonji (JmjC) domain-containing demethylase that is significantly upregulated in CRC. KDM3A regulates the demethylation of histone H3's lysine 9 (H3K9Me2), a repressive marker for transcription. Inhibiting KDM3 increased H3K9Me2 levels, repressed Wnt target genes, and curtailed in vitro CRC cell proliferation. CBA-1 also exhibited in vivo inhibition of Wnt signaling in a zebrafish model without displaying in vivo toxicity. A class of carboxamide-substituted benzhydryl amine (CBA) Wnt inhibitors A biological active, biotinylated CBA to identify KDM3A as a direct target CBA-1 interacted with the Mn2+ ion in the JmjC domains of KDM3A/3B CBA-1 inhibited Wnt signaling in colon cancer cells and in zebrafish models
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Affiliation(s)
- Wen Zhang
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536-0509, USA
- Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY 40536-0093, USA
| | - Vitaliy M. Sviripa
- Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY 40536-0093, USA
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596, USA
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596, USA
| | - Yanqi Xie
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536-0509, USA
- Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY 40536-0093, USA
| | - Tianxin Yu
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536-0509, USA
- Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY 40536-0093, USA
| | - Meghan G. Haney
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536-0509, USA
- Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY 40536-0093, USA
| | - Jessica S. Blackburn
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536-0509, USA
- Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY 40536-0093, USA
| | - Charles A. Adeniran
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596, USA
- Molecular Modeling and Pharmaceutical Center, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596, USA
| | - Chang-Guo Zhan
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596, USA
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596, USA
- Molecular Modeling and Pharmaceutical Center, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596, USA
| | - David S. Watt
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536-0509, USA
- Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY 40536-0093, USA
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596, USA
- Corresponding author
| | - Chunming Liu
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536-0509, USA
- Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY 40536-0093, USA
- Corresponding author
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43
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Khan I, Eklund EE, Gartel AL. Therapeutic Vulnerabilities of Transcription Factors in AML. Mol Cancer Ther 2020; 20:229-237. [PMID: 33158995 DOI: 10.1158/1535-7163.mct-20-0115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 08/13/2020] [Accepted: 10/19/2020] [Indexed: 11/16/2022]
Abstract
Acute myeloid leukemia (AML) is characterized by impaired myeloid lineage differentiation, uncontrolled proliferation, and inhibition of proapoptotic pathways. In spite of a relatively homogeneous clinical disease presentation, risk of long-term survival in AML varies from 20% to 80% depending on molecular disease characteristics. In recognition of the molecular heterogeneity of AML, the European Leukemia Net (ELN) and WHO classification systems now incorporate cytogenetics and increasing numbers of gene mutations into AML prognostication. Several of the genomic AML subsets are characterized by unique transcription factor alterations that are highlighted in this review. There are many mechanisms of transcriptional deregulation in leukemia. We broadly classify transcription factors based on mechanisms of transcriptional deregulation including direct involvement of transcription factors in recurrent translocations, loss-of-function mutations, and intracellular relocalization. Transcription factors, due to their pleiotropic effects, have been attractive but elusive targets. Indirect targeting approaches include inhibition of upstream kinases such as TAK1 for suppression of NFκB signaling and downstream effectors such as FGF signaling in HOXA-upregulated leukemia. Other strategies include targeting scaffolding proteins like BrD4 in the case of MYC or coactivators such as menin to suppress HOX expression; disrupting critical protein interactions in the case of β-catenin:TCF/LEF, and preventing transcription factor binding to DNA as in the case of PU.1 or FOXM1. We comprehensively describe the mechanism of deregulation of transcription factors in genomic subsets of AML, consequent pathway addictions, and potential therapeutic strategies.
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Affiliation(s)
- Irum Khan
- Department of Medicine, University of Illinois, Chicago, Illinois
| | - Elizabeth E Eklund
- Feinberg School of Medicine and Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois.,Jesse Brown VA Medical Center, Chicago, Illinois
| | - Andrei L Gartel
- Department of Medicine, University of Illinois, Chicago, Illinois.
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44
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Morimoto J, Sando S. Peptoids with Substituents on the Backbone Carbons as Conformationally Constrained Synthetic Oligoamides. J SYN ORG CHEM JPN 2020. [DOI: 10.5059/yukigoseikyokaishi.78.1076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo
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45
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Wise DR, Schneider JA, Armenia J, Febles VA, McLaughlin B, Brennan R, Thoren KL, Abida W, Sfanos KS, De Marzo AM, Yegnasubramanian S, Fox JJ, Haas M, Heath H, Kagey MH, Newman W, Sirard CA, Fleisher M, Morris MJ, Chen Y, Larson SM, Haffner MC, Nelson PS, Schultz N, Garabedian MJ, Scher HI, Logan SK, Sawyers CL. Dickkopf-1 Can Lead to Immune Evasion in Metastatic Castration-Resistant Prostate Cancer. JCO Precis Oncol 2020; 4:2000097. [PMID: 33015525 DOI: 10.1200/po.20.00097] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/12/2020] [Indexed: 12/31/2022] Open
Abstract
PURPOSE Metastatic castration-resistant prostate cancer (mCRPC) with low androgen receptor (AR) and without neuroendocrine signaling, termed double-negative prostate cancer (DNPC), is increasingly prevalent in patients treated with AR signaling inhibitors and is in need of new biomarkers and therapeutic targets. METHODS Candidate genes enriched in DNPC were determined using differential gene expression analysis of discovery and validation cohorts of mCRPC biopsies. Laboratory studies were carried out in human mCRPC organoid cultures, prostate cancer (PCa) cell lines, and mouse xenograft models. Epigenetic studies were carried out in a rapid autopsy cohort. RESULTS Dickkopf-1 (DKK1) expression is increased in DNPC relative to prostate-specific antigen (PSA)-expressing mCRPC in the Stand Up to Cancer/Prostate Cancer Foundation discovery cohort (11.2 v 0.28 reads per kilobase per million mapped reads; q < 0.05; n = 117) and in the University of Washington/Fred Hutchinson Cancer Research Center cohort (9.2 v 0.99 fragments per kilobase of transcript per million mapped reads; P < .0001). DKK1 expression can be regulated by activated Wnt signaling in vitro and correlates with activating canonical Wnt signaling mutations and low PSA mRNA in mCRPC biopsies (P < .05). DKK1 hypomethylation was associated with increased DKK1 mRNA expression (Pearson r = -0.66; P < .0001) in a rapid autopsy cohort (n = 7). DKK1-high mCRPC biopsies are infiltrated with significantly higher numbers of quiescent natural killer (NK) cells (P < .005) and lower numbers of activated NK cells (P < .0005). Growth inhibition of the human PCa model PC3 by the anti-DKK1 monoclonal antibody DKN-01 depends on the presence of NK cells in a severe combined immunodeficient xenograft mouse model. CONCLUSION These results support DKK1 as a contributor to the immunosuppressive tumor microenvironment of DNPC. These data have provided the rationale for a clinical trial targeting DKK1 in mCRPC (ClinicalTrials.gov identifier: NCT03837353).
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Affiliation(s)
- David R Wise
- Department of Medicine, Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY
| | | | - Joshua Armenia
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Victor Adorno Febles
- Department of Medicine, Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY
| | - Bridget McLaughlin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ryan Brennan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Katie L Thoren
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Wassim Abida
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Karen S Sfanos
- Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, MD.,Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, MD.,Brady Urological Institute, School of Medicine, Johns Hopkins University, Baltimore, MD
| | - Angelo M De Marzo
- Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, MD.,Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, MD.,Brady Urological Institute, School of Medicine, Johns Hopkins University, Baltimore, MD
| | - Srinivasan Yegnasubramanian
- Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, MD.,Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, MD
| | - Josef J Fox
- Molecular Imaging and Therapy Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | | | - Martin Fleisher
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael J Morris
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yu Chen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Steven M Larson
- Molecular Imaging and Therapy Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael C Haffner
- Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, MD.,Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, MD
| | - Peter S Nelson
- Departments of Medicine and Pathology, University of Washington, and Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Nikolaus Schultz
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael J Garabedian
- Department of Urology, NYU Langone Medical Center, New York, NY.,Department of Microbiology, NYU Langone Medical Center, New York, NY
| | - Howard I Scher
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Susan K Logan
- Department of Urology, NYU Langone Medical Center, New York, NY
| | - Charles L Sawyers
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY.,Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY
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46
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Furukawa A, Schwochert J, Pye CR, Asano D, Edmondson QD, Turmon AC, Klein VG, Ono S, Okada O, Lokey RS. Drug‐Like Properties in Macrocycles above MW 1000: Backbone Rigidity versus Side‐Chain Lipophilicity. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004550] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Akihiro Furukawa
- Daiichi Sankyo Co., Ltd. 1-2-58, Hiromachi, Shinagawa-ku Tokyo 140-8710 Japan
| | - Joshua Schwochert
- Unnatural Products, Inc. 250 Natural Bridges Drive Santa Cruz CA 95060 USA
| | - Cameron R. Pye
- Unnatural Products, Inc. 250 Natural Bridges Drive Santa Cruz CA 95060 USA
| | - Daigo Asano
- Daiichi Sankyo Co., Ltd. 1-2-58, Hiromachi, Shinagawa-ku Tokyo 140-8710 Japan
| | - Quinn D. Edmondson
- Department of Pharmaceutical Chemistry University of California, San Francisco San Francisco California 94158 USA
| | | | - Victoria G. Klein
- Department of Chemistry & Biochemistry University of California Santa Cruz Santa Cruz CA 96064 USA
| | - Satoshi Ono
- Discovery Technology Laboratories Mitsubishi Tanabe Pharma Corporation Yokohama 227-0033 Japan
| | - Okimasa Okada
- Discovery Technology Laboratories Mitsubishi Tanabe Pharma Corporation Yokohama 227-0033 Japan
| | - R. Scott Lokey
- Department of Chemistry & Biochemistry University of California Santa Cruz Santa Cruz CA 96064 USA
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47
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Ghosh P, Maayan G. A rationally designed peptoid for the selective chelation of Zn 2+ over Cu 2. Chem Sci 2020; 11:10127-10134. [PMID: 34094275 PMCID: PMC8162371 DOI: 10.1039/d0sc03391j] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The selective removal of Zn2+ from proteins by using a synthetic chelator is a promising therapeutic approach for the treatment of various diseases including cancer. Although the chelation of Zn2+ is well known, its removal from a protein in the presence of potential competing biologically relevant ions such as Cu2+ is hardly explored. Herein we present a peptoid - N-substituted glycine trimer - incorporating a picolyl group at the N-terminus, a non-coordinating but structurally directing benzyl group at the C-terminus and a 2,2':6',2''-terpyridine group in the second position, that selectively binds Zn2+ ions in the presence of excess Cu2+ ions in water. We further demonstrate that this chelator can selectively bind Zn2+ from a pool of excess biologically relevant and competitive ions (Cu2+, Fe3+, Ca2+, Mg2+, Na+, and K+) in a simulated body fluid (SBF), and also its ability to remove Zn2+ from a natural zinc protein domain (PYKCPECGKSFSQKSDLVKHQRTHTG) in a SBF.
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Affiliation(s)
- Pritam Ghosh
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology Technion City Haifa 3200008 Israel
| | - Galia Maayan
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology Technion City Haifa 3200008 Israel
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48
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Integrated Dissection of lncRNA-Perturbated Triplets Reveals Novel Prognostic Signatures Across Cancer Types. Int J Mol Sci 2020; 21:ijms21176087. [PMID: 32846981 PMCID: PMC7503457 DOI: 10.3390/ijms21176087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/13/2020] [Accepted: 08/20/2020] [Indexed: 11/20/2022] Open
Abstract
Long noncoding RNA (lncRNA)/microRNA(miRNA)/mRNA triplets contribute to cancer biology. However, identifying significative triplets remains a major challenge for cancer research. The dynamic changes among factors of the triplets have been less understood. Here, by integrating target information and expression datasets, we proposed a novel computational framework to identify the triplets termed as “lncRNA-perturbated triplets”. We applied the framework to five cancer datasets in The Cancer Genome Atlas (TCGA) project and identified 109 triplets. We showed that the paired miRNAs and mRNAs were widely perturbated by lncRNAs in different cancer types. LncRNA perturbators and lncRNA-perturbated mRNAs showed significantly higher evolutionary conservation than other lncRNAs and mRNAs. Importantly, the lncRNA-perturbated triplets exhibited high cancer specificity. The pan-cancer perturbator OIP5-AS1 had higher expression level than that of the cancer-specific perturbators. These lncRNA perturbators were significantly enriched in known cancer-related pathways. Furthermore, among the 25 lncRNA in the 109 triplets, lncRNA SNHG7 was identified as a stable potential biomarker in lung adenocarcinoma (LUAD) by combining the TCGA dataset and two independent GEO datasets. Results from cell transfection also indicated that overexpression of lncRNA SNHG7 and TUG1 enhanced the expression of the corresponding mRNA PNMA2 and CDC7 in LUAD. Our study provides a systematic dissection of lncRNA-perturbated triplets and facilitates our understanding of the molecular roles of lncRNAs in cancers.
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49
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Computational methods-guided design of modulators targeting protein-protein interactions (PPIs). Eur J Med Chem 2020; 207:112764. [PMID: 32871340 DOI: 10.1016/j.ejmech.2020.112764] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/09/2020] [Accepted: 08/16/2020] [Indexed: 12/15/2022]
Abstract
Protein-protein interactions (PPIs) play a pivotal role in extensive biological processes and are thus crucial to human health and the development of disease states. Due to their critical implications, PPIs have been spotlighted as promising drug targets of broad-spectrum therapeutic interests. However, owing to the general properties of PPIs, such as flat surfaces, featureless conformations, difficult topologies, and shallow pockets, previous attempts were faced with serious obstacles when targeting PPIs and almost portrayed them as "intractable" for decades. To date, rapid progress in computational chemistry and structural biology methods has promoted the exploitation of PPIs in drug discovery. These techniques boost their cost-effective and high-throughput traits, and enable the study of dynamic PPI interfaces. Thus, computational methods represent an alternative strategy to target "undruggable" PPI interfaces and have attracted intense pharmaceutical interest in recent years, as exemplified by the accumulating number of successful cases. In this review, we first introduce a diverse set of computational methods used to design PPI modulators. Herein, we focus on the recent progress in computational strategies and provide a comprehensive overview covering various methodologies. Importantly, a list of recently-reported successful examples is highlighted to verify the feasibility of these computational approaches. Finally, we conclude the general role of computational methods in targeting PPIs, and also discuss future perspectives on the development of such aids.
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Matos B, Howl J, Jerónimo C, Fardilha M. The disruption of protein-protein interactions as a therapeutic strategy for prostate cancer. Pharmacol Res 2020; 161:105145. [PMID: 32814172 DOI: 10.1016/j.phrs.2020.105145] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 08/11/2020] [Accepted: 08/11/2020] [Indexed: 12/14/2022]
Abstract
Prostate cancer (PCa) is one of the most common male-specific cancers worldwide, with high morbidity and mortality rates associated with advanced disease stages. The current treatment options of PCa are prostatectomy, hormonal therapy, chemotherapy or radiotherapy, the selection of which is usually dependent upon the stage of the disease. The development of PCa to a castration-resistant phenotype (CRPC) is associated with a more severe prognosis requiring the development of a new and effective therapy. Protein-protein interactions (PPIs) have been recognised as an emerging drug modality and targeting PPIs is a promising therapeutic approach for several diseases, including cancer. The efficacy of several compounds in which target PPIs and consequently impair disease progression were validated in phase I/II clinical trials for different types of cancer. In PCa, various small molecules and peptides proved successful in inhibiting important PPIs, mainly associated with the androgen receptor (AR), Bcl-2 family proteins, and kinases/phosphatases, thus impairing the growth of PCa cells in vitro. Moreover, a majority of these compounds require further validation in vivo and, preferably, in clinical trials. In addition, several other PPIs associated with PCa progression have been identified and now require experimental validation as potential therapeutic loci. In conclusion, we consider the disruption of PPIs to be a promising though challenging therapeutic strategy for PCa. Agents which modulate PPIs might be employed as a monotherapy or as an adjunct to classical chemotherapeutics to overcome drug resistance and improve efficacy. The discovery of new PPIs with important roles in disease progression, and of novel optimized strategies to target them are major challenges for the scientific and pharmacological communities.
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Affiliation(s)
- Bárbara Matos
- Laboratory of Signal Transduction, Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193, Aveiro, Portugal
| | - John Howl
- Molecular Pharmacology Group, Research Institute in Healthcare Science, University of Wolverhampton, Wolverhampton WV1 1LY, UK
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Institute of Oncology of Porto (IPO Porto), Research Center-LAB 3, F Bdg., 1st Floor, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar- University of Porto (ICBAS-UP), Porto, Portugal
| | - Margarida Fardilha
- Laboratory of Signal Transduction, Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193, Aveiro, Portugal.
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