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Park J, Yamashita E, Yu J, Lee SJ, Hyun S. De Novo Designed Cell-Penetrating Peptide Self-Assembly Featuring Distinctive Tertiary Structure. ACS OMEGA 2024; 9:32991-32999. [PMID: 39100342 PMCID: PMC11292830 DOI: 10.1021/acsomega.4c04004] [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: 04/26/2024] [Revised: 07/04/2024] [Accepted: 07/09/2024] [Indexed: 08/06/2024]
Abstract
Recent attention has focused on the de novo design of proteins, paralleling advancements in biopharmaceuticals. Achieving protein designs with both structure and function poses a significant challenge, particularly considering the importance of quaternary structures, such as oligomers, in protein function. The cell penetration properties of peptides are of particular interest as they involve the penetration of large molecules into cells. We previously suggested a link between the oligomerization propensity of amphipathic peptides and their cell penetration abilities, yet concrete evidence at cellular-relevant concentrations was lacking due to oligomers' instability. In this study, we sought to characterize oligomerization states using various techniques, including X-ray crystallography, acceptor photobleaching Förster resonance energy transfer (FRET), native mass spectrometry (MS), and differential scanning calorimetry (DSC), while exploring the function related to oligomer status. X-ray crystallography revealed the atomic structures of oligomers formed by LK-3, a bis-disulfide bridged dimer with amino acid sequence LKKLCLKLKKLCKLAG, and its derivatives, highlighting the formation of hexamers, specifically the trimer of dimers, which exhibited a stable hydrophobic core. FRET experiments showed that LK-3 oligomer formation was associated with cell penetration. Native MS confirmed higher-order oligomers of LK-3, while an intriguing finding was the enhanced cell-penetrating capability of a 1:1 mixture of l/d-peptide dimers compared to pure enantiomers. DSC analysis supported the notion that this enantiomeric mixture promotes the formation of functional oligomers, crucial for cell penetration. In conclusion, our study provides direct evidence that amphipathic peptide LK-3 forms oligomers at low nanomolar concentrations, underscoring their significance in cell penetration behavior.
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Affiliation(s)
- Jaehui Park
- College
of Pharmacy, Chungbuk National University, Cheongju 28160, Korea
| | - Eiki Yamashita
- Institute
for Protein Research, Osaka University, 3-2 Yamada-koa, Suita Osaka 565-0871, Japan
| | - Jaehoon Yu
- Department
of Chemistry & Education, Seoul National
University, Seoul 08826, Korea
- CAMP
Therapeutics Co., Ltd., Seoul 08826, Korea
| | - Soo Jae Lee
- College
of Pharmacy, Chungbuk National University, Cheongju 28160, Korea
| | - Soonsil Hyun
- College
of Pharmacy, Chungbuk National University, Cheongju 28160, Korea
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2
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Dongrui Z, Miyamoto M, Yokoo H, Demizu Y. Innovative peptide architectures: advancements in foldamers and stapled peptides for drug discovery. Expert Opin Drug Discov 2024; 19:699-723. [PMID: 38753534 DOI: 10.1080/17460441.2024.2350568] [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: 02/27/2024] [Accepted: 04/29/2024] [Indexed: 05/18/2024]
Abstract
INTRODUCTION Peptide foldamers play a critical role in pharmaceutical research and biomedical applications. This review highlights recent (post-2020) advancements in novel foldamers, synthetic techniques, and their applications in pharmaceutical research. AREAS COVERED The authors summarize the structures and applications of peptide foldamers such as α, β, γ-peptides, hydrocarbon-stapled peptides, urea-type foldamers, sulfonic-γ-amino acid foldamers, aromatic foldamers, and peptoids, which tackle the challenges of traditional peptide drugs. Regarding antimicrobial use, foldamers have shown progress in their potential against drug-resistant bacteria. In drug development, peptide foldamers have been used as drug delivery systems (DDS) and protein-protein interaction (PPI) inhibitors. EXPERT OPINION These structures exhibit resistance to enzymatic degradation, are promising for therapeutic delivery, and disrupt crucial PPIs associated with diseases such as cancer with specificity, versatility, and stability, which are useful therapeutic properties. However, the complexity and cost of their synthesis, along with the necessity for thorough safety and efficacy assessments, necessitate extensive research and cross-sector collaboration. Advances in synthesis methods, computational modeling, and targeted delivery systems are essential for fully realizing the therapeutic potential of foldamers and integrating them into mainstream medical treatments.
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Affiliation(s)
- Zhou Dongrui
- Division of Organic Chemistry, National Institute of Health Sciences, Kawasaki, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Maho Miyamoto
- Division of Organic Chemistry, National Institute of Health Sciences, Kawasaki, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Hidetomo Yokoo
- Division of Organic Chemistry, National Institute of Health Sciences, Kawasaki, Japan
| | - Yosuke Demizu
- Division of Organic Chemistry, National Institute of Health Sciences, Kawasaki, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Division of Pharmaceutical Science of Okayama University, Kita, Japan
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Shin G, Hyun S, Kim D, Choi Y, Kim KH, Kim D, Kwon S, Kim YS, Yang SH, Yu J. Cyclohexylalanine-Containing α-Helical Amphipathic Peptide Targets Cardiolipin, Rescuing Mitochondrial Dysfunction in Kidney Injury. J Med Chem 2024; 67:3385-3399. [PMID: 38112308 PMCID: PMC10945481 DOI: 10.1021/acs.jmedchem.3c01578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/21/2023]
Abstract
Mitochondrial dysfunction is linked to degenerative diseases, resulting from cardiolipin (CL)-induced disruption of cristae structure in the inner mitochondrial membrane (IMM); therefore, preserving cristae and preventing CL remodeling offer effective strategies to maintain mitochondrial function. To identify reactive oxygen species (ROS)-blocking agents against mitochondrial dysfunction, a library of cyclohexylamine-containing cell-penetrating α-helical amphipathic "bundle" peptides were screened. Among these, CMP3013 is selectively bound to abnormal mitochondria, preserving the cristae structure impaired by mitochondria-damaging agents. With a stronger affinity for CL compared with other IMM lipid components, CMP3013 exhibited high selectivity. Consequently, it protected cristae, reduced ROS production, and enhanced adenosine triphosphate (ATP) generation. In mouse models of acute kidney injury, a 1 mg/kg dose of CMP3013 demonstrated remarkable efficacy, highlighting its potential as a therapeutic agent for mitochondrial dysfunction-related disorders. Overall, CMP3013 represents a promising agent for mitigating mitochondrial dysfunction and associated diseases.
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Affiliation(s)
- Gwangsu Shin
- Department
of Chemistry & Education, Seoul National
University, Seoul 08826, Korea
| | - Soonsil Hyun
- Department
of Chemistry & Education, Seoul National
University, Seoul 08826, Korea
| | - Dongwoo Kim
- Department
of Chemistry & Education, Seoul National
University, Seoul 08826, Korea
| | | | - Kyu Hong Kim
- Department
of Biomedical Sciences, Seoul National University
Graduate School, Seoul 03080, Korea
| | - Dongmin Kim
- CAMP
Therapeutics Co., Ltd., Seoul 08826, Korea
| | - Soie Kwon
- Department
of Internal Medicine, Seoul National University
Hospital, Seoul 03080, Korea
| | - Yon Su Kim
- Department
of Internal Medicine, Seoul National University
Hospital, Seoul 03080, Korea
- Kidney
Research Institute, Seoul National University, Seoul 03080, Korea
- Biomedical
Research Institute, Seoul National University
Hospital, Seoul 03080, Republic of Korea
| | - Seung Hee Yang
- Kidney
Research Institute, Seoul National University, Seoul 03080, Korea
- Biomedical
Research Institute, Seoul National University
Hospital, Seoul 03080, Republic of Korea
| | - Jaehoon Yu
- Department
of Chemistry & Education, Seoul National
University, Seoul 08826, Korea
- CAMP
Therapeutics Co., Ltd., Seoul 08826, Korea
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Choi Y, Choe HW, Kook M, Choo S, Park TW, Bae S, Kim H, Yang J, Jeong WS, Yu J, Lee KR, Kim YS, Yu J. Proline-Hinged α-Helical Peptides Sensitize Gram-Positive Antibiotics, Expanding Their Physicochemical Properties to Be Used as Gram-Negative Antibiotics. J Med Chem 2024; 67:1825-1842. [PMID: 38124427 PMCID: PMC10860147 DOI: 10.1021/acs.jmedchem.3c01473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/13/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023]
Abstract
The outer membrane (OM) of Gram-negative bacteria is the most difficult obstacle for small-molecule antibiotics to reach their targets in the cytosol. The molecular features of Gram-negative antibiotics required for passing through the OM are that they should be positively charged rather than neutral, flat rather than globular, less flexible, or more increased amphiphilic moment. Because of these specific molecular characteristics, developing Gram-negative antibiotics is difficult. We focused on sensitizer peptides to facilitate the passage of hydrophobic Gram-positive antibiotics through the OM. We explored ways of improving the sensitizing ability of proline-hinged α-helical peptides by adjusting their length, hydrophobicity, and N-terminal groups. A novel peptide, 1403, improves the potentiation of rifampicin in vitro and in vivo and potentiates most Gram-positive antibiotics. The "sensitizer" approach is more plausible than those that rely on conventional drug discovery methods concerning drug development costs and the development of drug resistance.
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Affiliation(s)
- Yoonhwa Choi
- Department
of Chemistry & Education, Seoul National
University, Seoul 08826, Republic
of Korea
- CAMP
Therapeutics, Seoul 08826, Republic of Korea
| | - Hyeong Woon Choe
- Department
of Chemistry & Education, Seoul National
University, Seoul 08826, Republic
of Korea
| | - Minsoo Kook
- Department
of Infectious Disease, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Seolah Choo
- Department
of Chemistry & Education, Seoul National
University, Seoul 08826, Republic
of Korea
| | - Tae Woo Park
- Department
of Chemistry & Education, Seoul National
University, Seoul 08826, Republic
of Korea
| | - Soeun Bae
- Department
of Chemistry & Education, Seoul National
University, Seoul 08826, Republic
of Korea
| | - Heeseung Kim
- Department
of Infectious Disease, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Jihye Yang
- Department
of Infectious Disease, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Woo-Seong Jeong
- Laboratory
Animal Resource Center, Korea Research Institute
of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Jiyoung Yu
- Asan
Medical Center, Seoul 05505, Republic
of Korea
| | - Kyeong-Ryoon Lee
- Laboratory
Animal Resource Center, Korea Research Institute
of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Yang Soo Kim
- Department
of Infectious Disease, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Jaehoon Yu
- Department
of Chemistry & Education, Seoul National
University, Seoul 08826, Republic
of Korea
- CAMP
Therapeutics, Seoul 08826, Republic of Korea
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Gori A, Lodigiani G, Colombarolli SG, Bergamaschi G, Vitali A. Cell Penetrating Peptides: Classification, Mechanisms, Methods of Study, and Applications. ChemMedChem 2023; 18:e202300236. [PMID: 37389978 DOI: 10.1002/cmdc.202300236] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/28/2023] [Accepted: 06/28/2023] [Indexed: 07/02/2023]
Abstract
Cell-penetrating peptides (CPPs) encompass a class of peptides that possess the remarkable ability to cross cell membranes and deliver various types of cargoes, including drugs, nucleic acids, and proteins, into cells. For this reason, CPPs are largely investigated in drug delivery applications in the context of many diseases, such as cancer, diabetes, and genetic disorders. While sharing this functionality and some common structural features, such as a high content of positively charged amino acids, CPPs represent an extremely diverse group of elements, which can differentiate under many aspects. In this review, we summarize the most common characteristics of CPPs, introduce their main distinctive features, mechanistic aspects that drive their function, and outline the most widely used techniques for their structural and functional studies. We highlight current gaps and future perspectives in this field, which have the potential to significantly impact the future field of drug delivery and therapeutics.
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Affiliation(s)
- Alessandro Gori
- SCITEC - Istituto di Scienze e Tecnologie Chimiche "Giulio Natta", National Research Council of Italy, Via Mario Bianco 9, 20131, Milano, Italy
| | - Giulia Lodigiani
- SCITEC - Istituto di Scienze e Tecnologie Chimiche "Giulio Natta", National Research Council of Italy, Via Mario Bianco 9, 20131, Milano, Italy
| | - Stella G Colombarolli
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta", National Research Council of Italy, L.go F. Vito 1, 00168, Roma, Italy
| | - Greta Bergamaschi
- SCITEC - Istituto di Scienze e Tecnologie Chimiche "Giulio Natta", National Research Council of Italy, Via Mario Bianco 9, 20131, Milano, Italy
| | - Alberto Vitali
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta", National Research Council of Italy, L.go F. Vito 1, 00168, Roma, Italy
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