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Li SS, Liu QJ, Bao JX, Lu MT, Deng BQ, Li WW, Cao CC. Counteracting TGM2 by a Fibroin peptide ameliorated Adriamycin-induced nephropathy via regulation of lipid metabolism through PANX1-PPAR α/PANK1 pathway. Transl Res 2024; 271:26-39. [PMID: 38734063 DOI: 10.1016/j.trsl.2024.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 04/28/2024] [Accepted: 05/08/2024] [Indexed: 05/13/2024]
Abstract
Peptide drug discovery for the treatment of chronic kidney disease (CKD) has attracted much attention in recent years due to the urge to find novel drugs and mechanisms to delay the progression of the disease. In this study, we identified a novel short peptide (named YR-7, primary sequence 'YEVEDYR') from the natural Fibroin protein, and demonstrated that it significantly alleviated pathological renal changes in ADR-induced nephropathy. PANX1 was identified as the most notably upregulated component by RNA-sequencing. Further analysis showed that YR-7 alleviated the accumulation of lipid droplets via regulation of the lipid metabolism-related proteins PPAR α and PANK1. Using chemical proteomics, fluorescence polarization, microscale thermophoresis, surface plasmon resonance, and molecular docking, YR-7 was proven to directly bind to β-barrel domains of TGM2 protein to inhibit lipid accumulation. TGM2 knockdown in vivo increased the protein levels of PPAR α and PANK1 while decreased the levels of fibrotic-related proteins to alleviate nephropathy. In vitro, overexpression TGM2 reversed the protective effects of YR-7. Co-immunoprecipitation indicated that TGM2 interacted with PANX1 to promote lipid deposition, and pharmacological inhibition or knockdown of PANX1 decreased the levels of PPAR α and PANK1 induced by ADR. Taken together, our findings revealed that TGM2-PANX1 interaction in promoting lipid deposition may be a new signaling in promoting ADR-induced nephropathy. And a novel natural peptide could ameliorate renal fibrosis through TGM2-PANX1-PPAR α/PANK1 pathway, which highlight the potential of it in the treatment of CKD.
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Affiliation(s)
- Shan-Shan Li
- Department of Nephrology, Sir Run Run hospital, Nanjing Medical University, Nanjing, China
| | - Qiao-Juan Liu
- Department of Nephrology, Sir Run Run hospital, Nanjing Medical University, Nanjing, China
| | - Jia-Xin Bao
- Department of Nephrology, Sir Run Run hospital, Nanjing Medical University, Nanjing, China
| | - Meng-Ting Lu
- Department of Nephrology, Sir Run Run hospital, Nanjing Medical University, Nanjing, China
| | - Bing-Quan Deng
- Department of Nephrology, Sir Run Run hospital, Nanjing Medical University, Nanjing, China
| | - Wen-Wen Li
- Department of Nephrology, Sir Run Run hospital, Nanjing Medical University, Nanjing, China
| | - Chang-Chun Cao
- Department of Nephrology, Sir Run Run hospital, Nanjing Medical University, Nanjing, China.
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2
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Resina L, Esteves T, Pérez-Rafael S, García JIH, Ferreira FC, Tzanov T, Bonardd S, Díaz DD, Pérez-Madrigal MM, Alemán C. Dual electro-/pH-responsive nanoparticle/hydrogel system for controlled delivery of anticancer peptide. BIOMATERIALS ADVANCES 2024; 162:213925. [PMID: 38908101 DOI: 10.1016/j.bioadv.2024.213925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 05/24/2024] [Accepted: 06/09/2024] [Indexed: 06/24/2024]
Abstract
An electro-chemo-responsive carrier has been engineered for the controlled release of a highly hydrophilic anticancer peptide, CR(NMe)EKA (Cys-Arg- N-methyl-Glu-Lys-Ala). Remotely controlled on demand release of CR(NMe)EKA, loaded in electro-responsive poly(3,4-ethylenedioxythiophene) (PEDOT) nanoparticles, has been achieved by applying electrical stimuli consisting of constant positive (+0.50 V) or negative voltages (-0.50 V) at pre-defined time intervals. In addition, after loading CR(NMe)EKA/PEDOT nanoparticles into an injectable pH responsive hydrogel formed by phenylboronic acid grafted to chitosan (PBA-CS), the efficiency of the controlled peptide release has increased approximately by a factor of 2.6. The hydration ratio of such hydrogel is significantly lower in acidic environments than in neutral and basic media, which has been attributed to the dissociation of the boronate bonds between polymer chains. Hence, the electro-controlled peptide release from PBA-CS/CR(NMe)EKA/PEDOT hydrogels, in the acidic environment of tumors, combines the effects of the oxidation and reduction of PEDOT chains on the interactions with the peptide and the carrier, with the peptide concentration gradient at the interface between the collapsed hydrogel and the release medium. Furthermore, the peptide released by electro-stimulation preserved its bioactivity assessed by promoting human prostate cancer cells death. Overall, this work is a promising attempt to develop a carrier platform for small hydrophilic anticancer peptides, which delivery rationale is synergistically regulated by the electrical and pH responsiveness of the carrier.
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Affiliation(s)
- Leonor Resina
- Departament d'Enginyeria Química and Barcelona Research Center for Multiscale Science and Engineering, EEBE, Universitat Politècnica de Catalunya, C/ Eduard Maristany 10-14, 08019 Barcelona, Spain; iBB - Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico - Universidade de Lisboa, Avenida Rovisco Pais 1, 1049-001 Lisboa, Portugal; Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Avenida Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - Teresa Esteves
- iBB - Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico - Universidade de Lisboa, Avenida Rovisco Pais 1, 1049-001 Lisboa, Portugal; Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Avenida Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - Sílvia Pérez-Rafael
- Grup de Biotecnologia Molecular i Industrial, Department of Chemical Engineering, Universitat Politècnica de Catalunya, Rambla Sant Nebridi 22, Terrassa 08222, Spain
| | - José Ignacio Hernández García
- Departmento de Química Orgánica, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez 3, La Laguna 38206, Tenerife, Spain; Instituto Universitario de Bio-Orgánica Antonio González, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez 2, La Laguna 38206, Tenerife, Spain
| | - Frederico Castelo Ferreira
- iBB - Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico - Universidade de Lisboa, Avenida Rovisco Pais 1, 1049-001 Lisboa, Portugal; Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Avenida Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - Tzanko Tzanov
- Grup de Biotecnologia Molecular i Industrial, Department of Chemical Engineering, Universitat Politècnica de Catalunya, Rambla Sant Nebridi 22, Terrassa 08222, Spain
| | - Sebastian Bonardd
- Departmento de Química Orgánica, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez 3, La Laguna 38206, Tenerife, Spain; Instituto Universitario de Bio-Orgánica Antonio González, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez 2, La Laguna 38206, Tenerife, Spain
| | - David Díaz Díaz
- Departmento de Química Orgánica, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez 3, La Laguna 38206, Tenerife, Spain; Instituto Universitario de Bio-Orgánica Antonio González, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez 2, La Laguna 38206, Tenerife, Spain.
| | - Maria M Pérez-Madrigal
- Departament d'Enginyeria Química and Barcelona Research Center for Multiscale Science and Engineering, EEBE, Universitat Politècnica de Catalunya, C/ Eduard Maristany 10-14, 08019 Barcelona, Spain.
| | - Carlos Alemán
- Departament d'Enginyeria Química and Barcelona Research Center for Multiscale Science and Engineering, EEBE, Universitat Politècnica de Catalunya, C/ Eduard Maristany 10-14, 08019 Barcelona, Spain; Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain.
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3
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Registre C, Silva LM, Registre F, Soares RDDOA, Rubio KTS, Carneiro SP, Dos Santos ODH. Targeting Leishmania Promastigotes and Amastigotes Forms through Amino Acids and Peptides: A Promising Therapeutic Strategy. ACS Infect Dis 2024. [PMID: 38950147 DOI: 10.1021/acsinfecdis.4c00089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
Millions of people worldwide are affected by leishmaniasis, caused by the Leishmania parasite. Effective treatment is challenging due to the biological complexity of the parasite, drug toxicity, and increasing resistance to conventional drugs. To combat this disease, the development of specific strategies to target and selectively eliminate the parasite is crucial. This Review highlights the importance of amino acids in the developmental stages of Leishmania as a factor determining whether the infection progresses or is suppressed. It also explores the use of peptides as alternatives in parasite control and the development of novel targeted treatments. While these strategies show promise for more effective and targeted treatment, further studies to address the remaining challenges are imperative.
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Affiliation(s)
- Charmante Registre
- Phytotechnology Laboratory, School of Pharmacy, Federal University of Ouro Preto, Ouro Preto, Minas Gerais 35400000, Brazil
| | - Luciana Miranda Silva
- Phytotechnology Laboratory, School of Pharmacy, Federal University of Ouro Preto, Ouro Preto, Minas Gerais 35400000, Brazil
| | - Farah Registre
- School of Medicine, Goiás Federal University, Goiânia, Goiás 74605-050, Brazil
| | - Rodrigo Dian de Oliveira Aguiar Soares
- Immunopathology Laboratory, Center for Research in Biological Sciences/NUPEB, Federal University of Ouro Preto, Ouro Preto, Minas Gerais 35400000, Brazil
| | - Karina Taciana Santos Rubio
- Toxicology Laboratory, School of Pharmacy, Federal University of Ouro Preto, Ouro Preto, Minas Gerais 35400000, Brazil
| | - Simone Pinto Carneiro
- Department of Pharmacy, Pharmaceutical Technology and Biopharmaceutics, Ludwig-Maximilians-University of Munich, 81377 Munich, Germany
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Wang T, Fu ZY, Li YJ, Zi L, Song CZ, Tao YX, Zhang M, Gu W, Yu J, Yang XX. Recognition on pharmacodynamic ingredients of natural products. Saudi Pharm J 2024; 32:102124. [PMID: 38933713 PMCID: PMC11201352 DOI: 10.1016/j.jsps.2024.102124] [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: 10/30/2023] [Accepted: 05/31/2024] [Indexed: 06/28/2024] Open
Abstract
Natural products (NPs) play an irreplaceable role in the intervention of various diseases and have been considered a critical source of drug development. Many new pharmacodynamic compounds with potential clinical applications have recently been derived from NPs. These compounds range from small molecules to polysaccharides, polypeptides, proteins, self-assembled nanoparticles, and extracellular vesicles. This review summarizes various active substances found in NPs. The investigation of active substances in NPs can potentiate new drug development and promote the in-depth comprehension of the mechanism of action of NPs that can be beneficial in the prevention and treatment of human diseases.
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Affiliation(s)
- Tao Wang
- College of Pharmaceutical Science, Yunnan University of Chinese Medicine, 1076 Yuhua Road, Kunming 650500, China
- Yunnan Key Laboratory of Southern Medicine Utilization, 1076 Yuhua Road, Kunming 650500, China
| | - Zhong-Yu Fu
- College of Pharmaceutical Science, Yunnan University of Chinese Medicine, 1076 Yuhua Road, Kunming 650500, China
- Yunnan Key Laboratory of Southern Medicine Utilization, 1076 Yuhua Road, Kunming 650500, China
| | - Yan-Juan Li
- College of Pharmaceutical Science, Yunnan University of Chinese Medicine, 1076 Yuhua Road, Kunming 650500, China
- Yunnan Key Laboratory of Southern Medicine Utilization, 1076 Yuhua Road, Kunming 650500, China
| | - Lei Zi
- College of Pharmaceutical Science, Yunnan University of Chinese Medicine, 1076 Yuhua Road, Kunming 650500, China
- Yunnan Key Laboratory of Southern Medicine Utilization, 1076 Yuhua Road, Kunming 650500, China
| | - Cheng-Zhu Song
- College of Pharmaceutical Science, Yunnan University of Chinese Medicine, 1076 Yuhua Road, Kunming 650500, China
- Yunnan Key Laboratory of Southern Medicine Utilization, 1076 Yuhua Road, Kunming 650500, China
| | - Yu-Xuan Tao
- College of Pharmaceutical Science, Yunnan University of Chinese Medicine, 1076 Yuhua Road, Kunming 650500, China
- Yunnan Key Laboratory of Southern Medicine Utilization, 1076 Yuhua Road, Kunming 650500, China
| | - Mei Zhang
- College of Pharmaceutical Science, Yunnan University of Chinese Medicine, 1076 Yuhua Road, Kunming 650500, China
- Yunnan Key Laboratory of Southern Medicine Utilization, 1076 Yuhua Road, Kunming 650500, China
| | - Wen Gu
- College of Pharmaceutical Science, Yunnan University of Chinese Medicine, 1076 Yuhua Road, Kunming 650500, China
- Yunnan Key Laboratory of Southern Medicine Utilization, 1076 Yuhua Road, Kunming 650500, China
| | - Jie Yu
- College of Pharmaceutical Science, Yunnan University of Chinese Medicine, 1076 Yuhua Road, Kunming 650500, China
- Yunnan Key Laboratory of Southern Medicine Utilization, 1076 Yuhua Road, Kunming 650500, China
| | - Xing-Xin Yang
- College of Pharmaceutical Science, Yunnan University of Chinese Medicine, 1076 Yuhua Road, Kunming 650500, China
- Yunnan Key Laboratory of Southern Medicine Utilization, 1076 Yuhua Road, Kunming 650500, China
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5
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Zeng P, Wang H, Zhang P, Leung SSY. Unearthing naturally-occurring cyclic antibacterial peptides and their structural optimization strategies. Biotechnol Adv 2024; 73:108371. [PMID: 38704105 DOI: 10.1016/j.biotechadv.2024.108371] [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: 11/10/2023] [Revised: 03/08/2024] [Accepted: 04/29/2024] [Indexed: 05/06/2024]
Abstract
Natural products with antibacterial activity are highly desired globally to combat against multidrug-resistant (MDR) bacteria. Antibacterial peptide (ABP), especially cyclic ABP (CABP), is one of the abundant classes. Most of them were isolated from microbes, demonstrating excellent bactericidal effects. With the improved proteolytic stability, CABPs are normally considered to have better druggability than linear peptides. However, most clinically-used CABP-based antibiotics, such as colistin, also face the challenges of drug resistance soon after they reached the market, urgently requiring the development of next-generation succedaneums. We present here a detail review on the novel naturally-occurring CABPs discovered in the past decade and some of them are under clinical trials, exhibiting anticipated application potential. According to their chemical structures, they were broadly classified into five groups, including (i) lactam/lactone-based CABPs, (ii) cyclic lipopeptides, (iii) glycopeptides, (iv) cyclic sulfur-rich peptides and (v) multiple-modified CABPs. Their chemical structures, antibacterial spectrums and proposed mechanisms are discussed. Moreover, engineered analogs of these novel CABPs are also summarized to preliminarily analyze their structure-activity relationship. This review aims to provide a global perspective on research and development of novel CABPs to highlight the effectiveness of derivatives design in identifying promising antibacterial agents. Further research efforts in this area are believed to play important roles in fighting against the multidrug-resistance crisis.
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Affiliation(s)
- Ping Zeng
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Honglan Wang
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Pengfei Zhang
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Sharon Shui Yee Leung
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong.
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6
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Li X, Kuchinski LM, Park A, Murphy GS, Soto KC, Schuster BS. Enzyme purification and sustained enzyme activity for pharmaceutical biocatalysis by fusion with phase-separating intrinsically disordered protein. Biotechnol Bioeng 2024. [PMID: 38951956 DOI: 10.1002/bit.28787] [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: 12/06/2023] [Revised: 06/11/2024] [Accepted: 06/16/2024] [Indexed: 07/03/2024]
Abstract
In recent decades, biocatalysis has emerged as an important alternative to chemical catalysis in pharmaceutical manufacturing. Biocatalysis is attractive because enzymatic cascades can synthesize complex molecules with incredible selectivity, yield, and in an environmentally benign manner. Enzymes for pharmaceutical biocatalysis are typically used in their unpurified state, since it is time-consuming and cost-prohibitive to purify enzymes using conventional chromatographic processes at scale. However, impurities present in crude enzyme preparations can consume substrate, generate unwanted byproducts, as well as make the isolation of desired products more cumbersome. Hence, a facile, nonchromatographic purification method would greatly benefit pharmaceutical biocatalysis. To address this issue, here we have captured enzymes into membraneless compartments by fusing enzymes with an intrinsically disordered protein region, the RGG domain from LAF-1. The RGG domain can undergo liquid-liquid phase separation, forming liquid condensates triggered by changes in temperature or salt concentration. By centrifuging these liquid condensates, we have successfully purified enzyme-RGG fusions, resulting in significantly enhanced purity compared to cell lysate. Furthermore, we performed enzymatic reactions utilizing purified fusion proteins to assay enzyme activity. Results from the enzyme assays indicate that enzyme-RGG fusions purified by the centrifugation method retain enzymatic activity, with greatly reduced background activity compared to crude enzyme preparations. Our work focused on three different enzymes-a kinase, a phosphorylase, and an ATP-dependent ligase. The kinase and phosphorylase are components of the biocatalytic cascade for manufacturing molnupiravir, and we demonstrated facile co-purification of these two enzymes by co-phase separation. To conclude, enzyme capture by RGG tagging promises to overcome difficulties in bioseparations and biocatalysis for pharmaceutical synthesis.
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Affiliation(s)
- Xinyi Li
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Liam M Kuchinski
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Augene Park
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Grant S Murphy
- Department of Process Research and Development, Process Research and Development, Merck & Co., Inc., Rahway, New Jersey, USA
| | - Karla Camacho Soto
- Department of Process Research and Development, Process Research and Development, Merck & Co., Inc., Rahway, New Jersey, USA
| | - Benjamin S Schuster
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
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7
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Biji CA, Balde A, Nazeer RA. Anti-inflammatory peptide therapeutics and the role of sulphur containing amino acids (cysteine and methionine) in inflammation suppression: A review. Inflamm Res 2024; 73:1203-1221. [PMID: 38769154 DOI: 10.1007/s00011-024-01893-6] [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: 02/01/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND Inflammation serves as our body's immune response to combat infections, pathogens, viruses, and external stimuli. Inflammation can be classified into two types: acute inflammation and chronic inflammation. Non-steroidal anti-inflammatory medications (NSAIDs) are used to treat both acute and chronic inflammatory disorders. However, these treatments have various side effects such as reduced healing efficiency, peptic ulcers, gastrointestinal toxicities, etc. METHOD: This review assesses the potential of anti-inflammatory peptides (AIPs) derived from various natural sources, such as algae, fungi, plants, animals, and marine organisms. Focusing on peptides rich in cysteines and methionine, sulphur-containing amino acids known for their role in suppression of inflammation. RESULT Due to their varied biological activity, ability to penetrate cells, and low cytotoxicity, bioactive peptides have garnered interest as possible therapeutic agents. The utilisation of AIPs has shown great potential in the treatment of disorders associated with inflammation. AIPs can be obtained from diverse natural sources such as algae, fungi, plants, and animals. Cysteine and methionine are sulphur-containing amino acids that aid in the elimination of free radicals, hence assisting in the treatment of inflammatory diseases. CONCLUSION This review specifically examines several sources of AIPs including peptides that contain numerous cysteines and methionine. In addition, the biological characteristics of these amino acids and advancements in peptide delivery are also discussed.
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Affiliation(s)
- Catherin Ann Biji
- Biopharmaceuticals Lab, Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Chennai, 603 203, Tamilnadu, India
| | - Akshad Balde
- Biopharmaceuticals Lab, Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Chennai, 603 203, Tamilnadu, India
| | - Rasool Abdul Nazeer
- Biopharmaceuticals Lab, Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Chennai, 603 203, Tamilnadu, India.
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8
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Liu G, Liang J, Li W, Jiang S, Song M, Xu S, Du Q, Wang L, Wang X, Liu X, Tang L, Yang Z, Zhou M, Meng H, Zhang L, Yang Y, Zhang B. The protective effect of erythropoietin and its novel derived peptides in peripheral nerve injury. Int Immunopharmacol 2024; 138:112452. [PMID: 38943972 DOI: 10.1016/j.intimp.2024.112452] [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: 03/28/2024] [Revised: 05/23/2024] [Accepted: 06/07/2024] [Indexed: 07/01/2024]
Abstract
Peripheral nerve injury seriously endangers human life and health, but there is no clinical drug for the treatment of peripheral nerve injury, so it is imperative to develop drugs to promote the repair of peripheral nerve injury. Erythropoietin (EPO) not only has the traditional role of promoting erythropoiesis, but also has a tissue-protective effect. Over the past few decades, researchers have confirmed that EPO has neuroprotective effects. However, side effects caused by long-term use of EPO limited its clinical application. Therefore, EPO derivatives with low side effects have been explored. Among them, ARA290 has shown significant protective effects on the nervous system, but the biggest disadvantage of ARA290, its short half-life, limits its application. To address the short half-life issue, the researchers modified ARA290 with thioether cyclization to generate a thioether cyclized helical B peptide (CHBP). ARA290 and CHBP have promising applications as peptide drugs. The neuroprotective effects they exhibit have attracted continuous exploration of their mechanisms of action. This article will review the research on the role of EPO, ARA290 and CHBP in the nervous system around this developmental process, and provide a certain reference for the subsequent research.
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Affiliation(s)
- Guixian Liu
- Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, Shandong 266071, PR China
| | - Jie Liang
- Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, Shandong 266071, PR China
| | - Wei Li
- Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, Shandong 266071, PR China
| | - Suli Jiang
- Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, Shandong 266071, PR China
| | - Meiying Song
- Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, Shandong 266071, PR China
| | - Shuo Xu
- Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, Shandong 266071, PR China
| | - Qiaochu Du
- Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, Shandong 266071, PR China
| | - Luoyang Wang
- Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, Shandong 266071, PR China
| | - Xiao Wang
- Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, Shandong 266071, PR China
| | - Xiaoli Liu
- Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, Shandong 266071, PR China
| | - Lei Tang
- Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, Shandong 266071, PR China
| | - Zijie Yang
- Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, Shandong 266071, PR China
| | - Mengting Zhou
- Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, Shandong 266071, PR China
| | - Haining Meng
- Department of Emergency Medicine, Medical College of Qingdao University, Qingdao, Shandong 266071, PR China
| | - Li Zhang
- Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, Shandong 266071, PR China
| | - Yanyan Yang
- Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, Shandong 266071, PR China
| | - Bei Zhang
- Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, Shandong 266071, PR China.
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Yamada T. Iron-Catalyzed C-H Alkylamination of Tyrosine Derivatives. Org Lett 2024; 26:5358-5363. [PMID: 38875349 DOI: 10.1021/acs.orglett.4c01764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2024]
Abstract
An efficient method for the direct alkylamination of tyrosine derivatives via iron-catalyzed C-H amination has been developed. The method, using O-benzoyl-N,N-dialkylhydroxylamines as aminating agents, provides various C-amino-functionalized tyrosine derivatives in up to 77% yield. The utility of this method is showcased by its application to the direct introduction of drug molecules into tyrosine, facilitating access to structurally diverse amino-functionalized tyrosine derivatives.
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Affiliation(s)
- Takahiro Yamada
- Showa Pharmaceutical University, Machida, Tokyo 194-8543, Japan
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10
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Ullrich S, Somathilake U, Shang M, Nitsche C. Phage-encoded bismuth bicycles enable instant access to targeted bioactive peptides. Commun Chem 2024; 7:143. [PMID: 38937646 PMCID: PMC11211329 DOI: 10.1038/s42004-024-01232-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 06/20/2024] [Indexed: 06/29/2024] Open
Abstract
Genetically encoded libraries play a crucial role in discovering structurally rigid, high-affinity macrocyclic peptide ligands for therapeutic applications. Bicyclic peptides with metal centres like bismuth were recently developed as a new type of constrained peptide with notable affinity, stability and membrane permeability. This study represents the genetic encoding of peptide-bismuth and peptide-arsenic bicycles in phage display. We introduce bismuth tripotassium dicitrate (gastrodenol) as a water-soluble bismuth(III) reagent for phage library modification and in situ bicyclic peptide preparation, eliminating the need for organic co-solvents. Additionally, we explore arsenic(III) as an alternative thiophilic element that is used analogously to our previously introduced bicyclic peptides with a bismuth core. The modification of phage libraries and peptides with these elements is instantaneous and entirely biocompatible, offering an advantage over conventional alkylation-based methods. In a pilot display screening campaign aimed at identifying ligands for the biotin-binding protein streptavidin, we demonstrate the enrichment of bicyclic peptides with dissociation constants two orders of magnitude lower than those of their linear counterparts, underscoring the impact of structural constraint on binding affinity.
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Affiliation(s)
- Sven Ullrich
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Upamali Somathilake
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Minghao Shang
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
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11
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Cai G, Bao Y, Li Q, Hsu PH, Xia J, Ngo JCK. Design of a covalent protein-protein interaction inhibitor of SRPKs to suppress angiogenesis and invasion of cancer cells. Commun Chem 2024; 7:144. [PMID: 38937565 PMCID: PMC11211491 DOI: 10.1038/s42004-024-01230-2] [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: 02/18/2024] [Accepted: 06/19/2024] [Indexed: 06/29/2024] Open
Abstract
Serine-arginine (SR) proteins are splicing factors that play essential roles in both constitutive and alternative pre-mRNA splicing. Phosphorylation of their C-terminal RS domains by SR protein kinases (SRPKs) regulates their localization and diverse cellular activities. Dysregulation of phosphorylation has been implicated in many human diseases, including cancers. Here, we report the development of a covalent protein-protein interaction inhibitor, C-DBS, that targets a lysine residue within the SRPK-specific docking groove to block the interaction and phosphorylation of the prototypic SR protein SRSF1. C-DBS exhibits high specificity and conjugation efficiency both in vitro and in cellulo. This self-cell-penetrating inhibitor attenuates the phosphorylation of endogenous SR proteins and subsequently inhibits the angiogenesis, migration, and invasion of cancer cells. These findings provide a new foundation for the development of covalent SRPK inhibitors for combatting diseases such as cancer and viral infections and overcoming the resistance encountered by ATP-competitive inhibitors.
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Affiliation(s)
- Gongli Cai
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Yishu Bao
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Qingyun Li
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou, 450001, China
| | - Pang-Hung Hsu
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Jiang Xia
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Jacky Chi Ki Ngo
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.
- Center of Novel Biomaterials, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.
- Center for Protein Science and Crystallography, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.
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12
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Smith FR, Meehan D, Griffiths RC, Knowles HJ, Zhang P, Williams HEL, Wilson AJ, Mitchell NJ. Peptide macrocyclisation via intramolecular interception of visible-light-mediated desulfurisation. Chem Sci 2024; 15:9612-9619. [PMID: 38939126 PMCID: PMC11206203 DOI: 10.1039/d3sc05865d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 04/30/2024] [Indexed: 06/29/2024] Open
Abstract
Synthetic methods that enable the macrocyclisation of peptides facilitate the development of effective therapeutic and diagnostic tools. Herein we report a peptide cyclisation strategy based on intramolecular interception of visible-light-mediated cysteine desulfurisation. This method allows cyclisation of unprotected peptides in an aqueous solution via the installation of a hydrocarbon linkage. We explore the limits of this chemistry using a range of model peptides of increasing length and complexity, including peptides of biological/therapeutic relevance. The method is applied to replace the native disulfide of the peptide hormone, oxytocin, with a proteolytically/redox-stable hydrocarbon, and internal macrocyclisation of an MCL-1-binding peptide.
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Affiliation(s)
- Frances R Smith
- School of Chemistry, University of Nottingham, University Park Nottingham NG7 2RD UK
| | - Declan Meehan
- School of Chemistry, University of Nottingham, University Park Nottingham NG7 2RD UK
| | - Rhys C Griffiths
- School of Chemistry, University of Nottingham, University Park Nottingham NG7 2RD UK
| | - Harriet J Knowles
- School of Chemistry, University of Nottingham, University Park Nottingham NG7 2RD UK
| | - Peiyu Zhang
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Huw E L Williams
- Biodiscovery Institute, University of Nottingham, University Park Nottingham NG7 2RD UK
| | - Andrew J Wilson
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- School of Chemistry, University of Birmingham Edgbaston Birmingham B15 2TT UK
| | - Nicholas J Mitchell
- School of Chemistry, University of Nottingham, University Park Nottingham NG7 2RD UK
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13
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Zeng Q, Meng G, Zhao B, Lin H, Guan Y, Qin X, Yuan Y, Li Y, Wang Q. Peptide Drug Design Using Alchemical Free Energy Calculation: An Application and Validation on Agonists of Ghrelin Receptor. J Chem Inf Model 2024; 64:4863-4876. [PMID: 38836743 DOI: 10.1021/acs.jcim.4c00414] [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: 06/06/2024]
Abstract
With recent large-scale applications and validations, the relative binding free energy (RBFE) calculated using alchemical free energy methods has been proven to be an accurate measure to probe the binding of small-molecule drug candidates. On the other hand, given the flexibility of peptides, it is of great interest to find out whether sufficient sampling could be achieved within the typical time scale of such calculation, and a similar level of accuracy could be reached for peptide drugs. However, the systematic evaluation of such calculations on protein-peptide systems has been less reported. Most reported studies of peptides were restricted to a limited number of data points or lacking experimental support. To demonstrate the applicability of the alchemical free energy method for protein-peptide systems in a typical real-world drug discovery project, we report an application of the thermodynamic integration (TI) method to the RBFE calculation of ghrelin receptor and its peptide agonists. Along with the calculation, the synthesis and in vitro EC50 activity of relamorelin and 17 new peptide derivatives were also reported. A cost-effective criterion to determine the data collection time was proposed for peptides in the TI simulation. The average of three TI repeats yielded a mean absolute error of 0.98 kcal/mol and Pearson's correlation coefficient (R) of 0.77 against the experimental free energy derived from the in vitro EC50 activity, showing good repeatability of the proposed method and a slightly better agreement than the results obtained from the arbitrary time frames up to 20 ns. Although it is limited by having one target and a deduced binding pose, we hope that this study can add some insights into alchemical free energy calculation of protein-peptide systems, providing theoretical assistance to the development of peptide drugs.
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Affiliation(s)
- Qin Zeng
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Guangpeng Meng
- Chengdu Sintanovo Biotechnology Co., Ltd., Chengdu 610000, China
| | - Bingyu Zhao
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Haodian Lin
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Yuqing Guan
- Chengdu Sintanovo Biotechnology Co., Ltd., Chengdu 610000, China
| | - Xiaobin Qin
- Chengdu Sintanovo Biotechnology Co., Ltd., Chengdu 610000, China
| | - Yu Yuan
- Chengdu Sintanovo Biotechnology Co., Ltd., Chengdu 610000, China
| | - Yuanbo Li
- Chengdu Sintanovo Biotechnology Co., Ltd., Chengdu 610000, China
| | - Qiantao Wang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
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14
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Song L, Liu H, Li M, Yang Y, Dong H, Li J, Shao J, Zhi L, Sun H, Li Z, Sui H, Zhang Y, Wu C, Yin Y. Ribosomal Incorporation of Lithocholic Acid into Peptides for the De Novo Discovery Of Peptide-Lithocholic Acid Hybrid Macrocyclic Peptides. ACS Chem Biol 2024. [PMID: 38901034 DOI: 10.1021/acschembio.4c00298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Peptide-bile acid hybrids offer promising drug candidates due to enhanced pharmacological properties, such as improved protease resistance and oral bioavailability. However, it remains unknown whether bile acids can be incorporated into peptide chains by the ribosome to produce a peptide-bile acid hybrid macrocyclic peptide library for target-based de novo screening. In this study, we achieved the ribosomal incorporation of lithocholic acid (LCA)-d-tyrosine into peptide chains. This led to the construction of a peptide-LCA hybrid macrocyclic peptide library, which enabled the identification of peptides TP-2C-4L3 (targeting Trop2) and EP-2C-4L5 (targeting EphA2) with strong binding affinities. Notably, LCA was found to directly participate in binding to EphA2 and confer on the peptides improved stability and resistance to proteases. Cell staining experiments confirmed the high specificity of the peptides for targeting Trop2 and EphA2. This study highlights the benefits of LCA in peptides and paves the way for de novo discovery of stable peptide-LCA hybrid drugs.
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Affiliation(s)
- Lulu Song
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Hongtan Liu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P.R. China
| | - Maolin Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yawen Yang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Huilei Dong
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P.R. China
| | - Jinjing Li
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P.R. China
| | - Jiaqi Shao
- College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lixu Zhi
- College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Hao Sun
- College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhifeng Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Haiyan Sui
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Chuanliu Wu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P.R. China
| | - Yizhen Yin
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
- Shandong Research Institute of Industrial Technology, Jinan 250101, China
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15
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Bohley M, Leroux JC. Gastrointestinal Permeation Enhancers Beyond Sodium Caprate and SNAC - What is Coming Next? ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2400843. [PMID: 38884149 DOI: 10.1002/advs.202400843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/13/2024] [Indexed: 06/18/2024]
Abstract
Oral peptide delivery is trending again. Among the possible reasons are the recent approvals of two oral peptide formulations, which represent a huge stride in the field. For the first time, gastrointestinal (GI) permeation enhancers (PEs) are leveraged to overcome the main limitation of oral peptide delivery-low permeability through the intestinal epithelium. Despite some success, the application of current PEs, such as salcaprozate sodium (SNAC), sodium caprylate (C8), and sodium caprate (C10), is generally resulting in relatively low oral bioavailabilities (BAs)-even for carefully selected therapeutics. With several hundred peptide-based drugs presently in the pipeline, there is a huge unmet need for more effective PEs. Aiming to provide useful insights for the development of novel PEs, this review summarizes the biological hurdles to oral peptide delivery with special emphasis on the epithelial barrier. It describes the concepts and action modes of PEs and mentions possible new targets. It further states the benchmark that is set by current PEs, while critically assessing and evaluating emerging PEs regarding translatability, safety, and efficacy. Additionally, examples of novel PEs under preclinical and clinical evaluation and future directions are discussed.
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Affiliation(s)
- Marilena Bohley
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, 8093, Switzerland
| | - Jean-Christophe Leroux
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, 8093, Switzerland
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16
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Cristofori-Armstrong B, Budusan E, Smith JJ, Reynaud S, Voll K, Chassagnon IR, Durek T, Rash LD. Revealing molecular determinants governing mambalgin-3 pharmacology at acid-sensing ion channel 1 variants. Cell Mol Life Sci 2024; 81:266. [PMID: 38880807 DOI: 10.1007/s00018-024-05276-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/19/2024] [Accepted: 05/12/2024] [Indexed: 06/18/2024]
Abstract
Acid-sensing ion channels (ASICs) are trimeric proton-gated cation channels that play a role in neurotransmission and pain sensation. The snake venom-derived peptides, mambalgins, exhibit potent analgesic effects in rodents by inhibiting central ASIC1a and peripheral ASIC1b. Despite their distinct species- and subtype-dependent pharmacology, previous structure-function studies have focussed on the mambalgin interaction with ASIC1a. Currently, the specific channel residues responsible for this pharmacological profile, and the mambalgin pharmacophore at ASIC1b remain unknown. Here we identify non-conserved residues at the ASIC1 subunit interface that drive differences in the mambalgin pharmacology from rat ASIC1a to ASIC1b, some of which likely do not make peptide binding interactions. Additionally, an amino acid variation below the core binding site explains potency differences between rat and human ASIC1. Two regions within the palm domain, which contribute to subtype-dependent effects for mambalgins, play key roles in ASIC gating, consistent with subtype-specific differences in the peptides mechanism. Lastly, there is a shared primary mambalgin pharmacophore for ASIC1a and ASIC1b activity, with certain peripheral peptide residues showing variant-specific significance for potency. Through our broad mutagenesis studies across various species and subtype variants, we gain a more comprehensive understanding of the pharmacophore and the intricate molecular interactions that underlie ligand specificity. These insights pave the way for the development of more potent and targeted peptide analogues required to advance our understating of human ASIC1 function and its role in disease.
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Affiliation(s)
- Ben Cristofori-Armstrong
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Elena Budusan
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Jennifer J Smith
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- Genentech, 1 DNA Way, South San Francisco, CA, 94080, United States
| | - Steve Reynaud
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- In Extenso Innovation Growth, Lyon, France
| | - Kerstin Voll
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88397, Biberach an der Riß, Germany
| | - Irène R Chassagnon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- Servatus Ltd. Coolum Beach, Coolum Beach, QLD, Australia
| | - Thomas Durek
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Lachlan D Rash
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia.
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17
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You S, McIntyre G, Passioura T. The coming of age of cyclic peptide drugs: an update on discovery technologies. Expert Opin Drug Discov 2024:1-13. [PMID: 38872502 DOI: 10.1080/17460441.2024.2367024] [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: 04/25/2024] [Accepted: 06/07/2024] [Indexed: 06/15/2024]
Abstract
INTRODUCTION Cyclic peptides are an established class of pharmaceuticals, with the ability to bind to a broader range of protein targets than traditional small molecules while also being capable of oral availability and cell penetration. Historically, cyclic peptide drugs have been discovered almost exclusively through natural product mining approaches; however, the last two decades have seen the development of display screening approaches capable of rapidly identifying de novo (i.e. not natural product derived) cyclic peptide ligands to targets of interest. AREAS COVERED In this review, the authors describe the current clinical landscape for cyclic peptide pharmaceuticals. This article focuses on the discovery approaches that have led to the development of different classes of molecules and how the development of newer technologies, particularly phage and mRNA display, has broadened the clinical applicability of such molecules. EXPERT OPINION The field of de novo cyclic peptide drug discovery is reaching maturity, with the first drugs identified through display screening approaches reaching the market in recent years. Many more are in clinical trials; however, significant technical challenges remain. Technological improvements will be required over the coming years to facilitate the identification of membrane permeable cyclic peptides capable of oral availability and targeting intracellular proteins.
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Affiliation(s)
- Sophia You
- Insamo South, Chippendale, NSW, Australia
| | | | - Toby Passioura
- School of Chemistry, The University of Sydney, Camperdown, NSW, Australia
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18
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Su J, Chen W, Zhou F, Li R, Tong Z, Wu S, Ye Z, Zhang Y, Lin B, Yu X, Guan B, Feng Z, Chen K, Chen Q, Chen L. Inhibitory mechanisms of decoy receptor 3 in cecal ligation and puncture-induced sepsis. mBio 2024; 15:e0052124. [PMID: 38700314 DOI: 10.1128/mbio.00521-24] [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: 02/21/2024] [Accepted: 04/02/2024] [Indexed: 05/05/2024] Open
Abstract
Despite its high mortality, specific and effective drugs for sepsis are lacking. Decoy receptor 3 (DcR3) is a potential biomarker for the progression of inflammatory diseases. The recombinant human DcR3-Fc chimera protein (DcR3.Fc) suppresses inflammatory responses in mice with sepsis, which is critical for improving survival. The Fc region can exert detrimental effects on the patient, and endogenous peptides are highly conducive to clinical application. However, the mechanisms underlying the effects of DcR3 on sepsis are unknown. Herein, we aimed to demonstrate that DcR3 may be beneficial in treating sepsis and investigated its mechanism of action. Recombinant DcR3 was obtained in vitro. Postoperative DcR3 treatment was performed in mouse models of lipopolysaccharide- and cecal ligation and puncture (CLP)-induced sepsis, and their underlying molecular mechanisms were explored. DcR3 inhibited sustained excessive inflammation in vitro, increased the survival rate, reduced the proinflammatory cytokine levels, changed the circulating immune cell composition, regulated the gut microbiota, and induced short-chain fatty acid synthesis in vivo. Thus, DcR3 protects against CLP-induced sepsis by inhibiting the inflammatory response and apoptosis. Our study provides valuable insights into the molecular mechanisms associated with the protective effects of DcR3 against sepsis, paving the way for future clinical studies. IMPORTANCE Sepsis affects millions of hospitalized patients worldwide each year, but there are no sepsis-specific drugs, which makes sepsis therapies urgently needed. Suppression of excessive inflammatory responses is important for improving the survival of patients with sepsis. Our results demonstrate that DcR3 ameliorates sepsis in mice by attenuating systematic inflammation and modulating gut microbiota, and unveil the molecular mechanism underlying its anti-inflammatory effect.
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Affiliation(s)
- Jingqian Su
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University, Fuzhou, China
| | - Wenzhi Chen
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University, Fuzhou, China
- Institute of Edible Fungi, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
| | - Fen Zhou
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University, Fuzhou, China
| | - Rui Li
- Department of Neurosurgery & Neurocritical Care, Huashan Hospital, Fudan University, Shanghai, China
| | - Zhiyong Tong
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University, Fuzhou, China
| | - Shun Wu
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University, Fuzhou, China
| | - Zhen Ye
- Department of Neurosurgery & Neurocritical Care, Huashan Hospital, Fudan University, Shanghai, China
| | - Yichao Zhang
- Department of Neurosurgery & Neurocritical Care, Huashan Hospital, Fudan University, Shanghai, China
| | - Ben Lin
- Department of Neurosurgery & Neurocritical Care, Huashan Hospital, Fudan University, Shanghai, China
| | - Xing Yu
- Department of Gastroenterology, the First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Biyun Guan
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University, Fuzhou, China
| | - Zhihua Feng
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University, Fuzhou, China
| | - Kunsen Chen
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University, Fuzhou, China
| | - Qi Chen
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University, Fuzhou, China
| | - Long Chen
- Department of Neurosurgery & Neurocritical Care, Huashan Hospital, Fudan University, Shanghai, China
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19
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Li Z, Feng Y, Han H, Jiang X, Chen W, Ma X, Mei Y, Yuan D, Zhang D, Shi J. A Stapled Peptide Inhibitor Targeting the Binding Interface of N6-Adenosine-Methyltransferase Subunits METTL3 and METTL14 for Cancer Therapy. Angew Chem Int Ed Engl 2024; 63:e202402611. [PMID: 38607929 DOI: 10.1002/anie.202402611] [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: 02/05/2024] [Revised: 04/08/2024] [Accepted: 04/11/2024] [Indexed: 04/14/2024]
Abstract
METTL3, a primary methyltransferase catalyzing the RNA N6-methyladenosine (m6A) modification, has been identified as an oncogene in several cancer types and thus nominated as a potentially effective target for therapeutic inhibition. However, current options using this strategy are limited. In this study, we targeted protein-protein interactions at the METTL3-METTL14 binding interface to inhibit complex formation and subsequent catalysis of the RNA m6A modification. Among candidate peptides, RM3 exhibited the highest anti-cancer potency, inhibiting METTL3 activity while also facilitating its proteasomal degradation. We then designed a stapled peptide inhibitor (RSM3) with enhanced peptide stability and formation of the α-helical secondary structure required for METTL3 interaction. Functional and transcriptomic analysis in vivo indicated that RSM3 induced upregulation of programmed cell death-related genes while inhibiting cancer-promoting signals. Furthermore, tumor growth was significantly suppressed while apoptosis was enhanced upon RSM3 treatment, accompanied by increased METTL3 degradation, and reduced global RNA methylation levels in two in vivo tumor models. This peptide inhibitor thus exploits a mechanism distinct from other small-molecule competitive inhibitors to inhibit oncogenic METTL3 activity. Our findings collectively highlight the potential of targeting METTL3 in cancer therapies through peptide-based inhibition of complex formation and proteolytic degradation.
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Affiliation(s)
- Zenghui Li
- Hunan Provincial Key Laboratory of Animal Models and Molecular Medicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, School of Biomedical Sciences, Hunan University Changsha, Hunan, 410082, China
- Greater Bay Area Institute for Innovation Institution, Guangzhou, 511300, Guangdong Province, China
| | - Yuqing Feng
- Hunan Provincial Key Laboratory of Animal Models and Molecular Medicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, School of Biomedical Sciences, Hunan University Changsha, Hunan, 410082, China
- Shenzhen Research Institute, Hunan University, Shenzhen, 518000, Guangdong Province, China
| | - Hong Han
- Hunan Provincial Key Laboratory of Animal Models and Molecular Medicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, School of Biomedical Sciences, Hunan University Changsha, Hunan, 410082, China
- Greater Bay Area Institute for Innovation Institution, Guangzhou, 511300, Guangdong Province, China
| | - Xingyue Jiang
- Hunan Provincial Key Laboratory of Animal Models and Molecular Medicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, School of Biomedical Sciences, Hunan University Changsha, Hunan, 410082, China
- Greater Bay Area Institute for Innovation Institution, Guangzhou, 511300, Guangdong Province, China
| | - Weiyu Chen
- Hunan Provincial Key Laboratory of Animal Models and Molecular Medicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, School of Biomedical Sciences, Hunan University Changsha, Hunan, 410082, China
- Greater Bay Area Institute for Innovation Institution, Guangzhou, 511300, Guangdong Province, China
| | - Xuezhen Ma
- Hunan Provincial Key Laboratory of Animal Models and Molecular Medicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, School of Biomedical Sciences, Hunan University Changsha, Hunan, 410082, China
| | - Yang Mei
- Hunan Provincial Key Laboratory of Animal Models and Molecular Medicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, School of Biomedical Sciences, Hunan University Changsha, Hunan, 410082, China
| | - Dan Yuan
- Hunan Provincial Key Laboratory of Animal Models and Molecular Medicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, School of Biomedical Sciences, Hunan University Changsha, Hunan, 410082, China
- Greater Bay Area Institute for Innovation Institution, Guangzhou, 511300, Guangdong Province, China
| | - Dingxiao Zhang
- Hunan Provincial Key Laboratory of Animal Models and Molecular Medicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, School of Biomedical Sciences, Hunan University Changsha, Hunan, 410082, China
- Shenzhen Research Institute, Hunan University, Shenzhen, 518000, Guangdong Province, China
| | - Junfeng Shi
- Hunan Provincial Key Laboratory of Animal Models and Molecular Medicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, School of Biomedical Sciences, Hunan University Changsha, Hunan, 410082, China
- Greater Bay Area Institute for Innovation Institution, Guangzhou, 511300, Guangdong Province, China
- Shenzhen Research Institute, Hunan University, Shenzhen, 518000, Guangdong Province, China
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20
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Quintieri L, Caputo L, Nicolotti O. Recent Advances in the Discovery of Novel Drugs on Natural Molecules. Biomedicines 2024; 12:1254. [PMID: 38927461 PMCID: PMC11200856 DOI: 10.3390/biomedicines12061254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
Natural products (NPs) are always a promising source of novel drugs for tackling unsolved diseases [...].
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Affiliation(s)
- Laura Quintieri
- Institute of Sciences of Food Production, National Research Council (CNR), Via G. Amendola, 122/O, 70126 Bari, Italy;
| | - Leonardo Caputo
- Institute of Sciences of Food Production, National Research Council (CNR), Via G. Amendola, 122/O, 70126 Bari, Italy;
| | - Orazio Nicolotti
- Dipartimento di Farmacia—Scienze del Farmaco, Università degli Studi di Bari “Aldo Moro”, Via E. Orabona, 4, 70125 Bari, Italy;
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21
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Zhang P, Ye X, Wang JCK, Baddock HT, Jensvold Z, Foe IT, Loas A, Eaton DL, Hao Q, Nile AH, Pentelute BL. Reversibly Reactive Affinity Selection-Mass Spectrometry Enables Identification of Covalent Peptide Binders. J Am Chem Soc 2024; 146:15627-15639. [PMID: 38771982 DOI: 10.1021/jacs.4c05571] [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: 05/23/2024]
Abstract
Covalent peptide binders have found applications as activity-based probes and as irreversible therapeutic inhibitors. Currently, there is no rapid, label-free, and tunable affinity selection platform to enrich covalent reactive peptide binders from synthetic libraries. We address this challenge by developing a reversibly reactive affinity selection platform termed ReAct-ASMS enabled by tandem high-resolution mass spectrometry (MS/MS) to identify covalent peptide binders to native protein targets. It uses mixed disulfide-containing peptides to build reversible peptide-protein conjugates that can enrich for covalent variants, which can be sequenced by MS/MS after reduction. Using this platform, we identified covalent peptide binders against two oncoproteins, human papillomavirus 16 early protein 6 (HPV16 E6) and peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 protein (Pin1). The resulting peptide binders efficiently and selectively cross-link Cys58 of E6 at 37 °C and Cys113 of Pin1 at room temperature, respectively. ReAct-ASMS enables the identification of highly selective covalent peptide binders for diverse molecular targets, introducing an applicable platform to assist preclinical therapeutic development pipelines.
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Affiliation(s)
- Peiyuan Zhang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Xiyun Ye
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - John C K Wang
- Calico Life Sciences LLC, 1170 Veterans Boulevard, South San Francisco, California 94080, United States
| | - Hannah T Baddock
- Calico Life Sciences LLC, 1170 Veterans Boulevard, South San Francisco, California 94080, United States
| | - Zena Jensvold
- Calico Life Sciences LLC, 1170 Veterans Boulevard, South San Francisco, California 94080, United States
| | - Ian T Foe
- Calico Life Sciences LLC, 1170 Veterans Boulevard, South San Francisco, California 94080, United States
| | - Andrei Loas
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Dan L Eaton
- Calico Life Sciences LLC, 1170 Veterans Boulevard, South San Francisco, California 94080, United States
| | - Qi Hao
- Calico Life Sciences LLC, 1170 Veterans Boulevard, South San Francisco, California 94080, United States
| | - Aaron H Nile
- Calico Life Sciences LLC, 1170 Veterans Boulevard, South San Francisco, California 94080, United States
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, Massachusetts 02142, United States
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
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22
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Koehbach J, Muratspahić E, Ahmed ZM, White AM, Tomašević N, Durek T, Clark RJ, Gruber CW, Craik DJ. Chemical synthesis of grafted cyclotides using a "plug and play" approach. RSC Chem Biol 2024; 5:567-571. [PMID: 38846076 PMCID: PMC11151825 DOI: 10.1039/d4cb00008k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 04/23/2024] [Indexed: 06/09/2024] Open
Abstract
Cyclotides are a diverse class of plant-derived cyclic, disulfide-rich peptides with a unique cyclic cystine knot topology. Their remarkable structural stability and resistance to proteolytic degradation can lead to improved pharmacokinetics and oral activity as well as selectivity and high enzymatic stability. Thus, cyclotides have emerged as powerful scaffold molecules for designing peptide-based therapeutics. The chemical engineering of cyclotides has generated novel peptide ligands of G protein-coupled receptors (GPCRs), today's most exploited drug targets. However key challenges potentially limit the widespread use of cyclotides in molecular grafting applications. Folding of cyclotides containing bioactive epitopes remains a major bottleneck in cyclotide synthesis. Here we present a modular 'plug and play' approach that effectively bypasses problems associated with the oxidative folding of cyclotides. By grafting onto a pre-formed acyclic cyclotide-like scaffold we show that difficult-to-graft sequences can be easily obtained and can target GPCRs with nanomolar affinities and potencies. We further show the suitability of this new method to graft other complex epitopes including structures with additional disulfide bonds that are not readily available via currently employed chemical methods, thus fully unlocking cyclotides to be used in drug design applications.
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Affiliation(s)
- Johannes Koehbach
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland Brisbane Queensland Australia
- School of Biomedical Sciences, The University of Queensland Brisbane Queensland Australia
| | - Edin Muratspahić
- Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna Vienna Austria
| | - Zakaria M Ahmed
- School of Biomedical Sciences, The University of Queensland Brisbane Queensland Australia
| | - Andrew M White
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland Brisbane Queensland Australia
- Research School of Chemistry, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Australian National University Australia
| | - Nataša Tomašević
- Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna Vienna Austria
| | - Thomas Durek
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland Brisbane Queensland Australia
| | - Richard J Clark
- School of Biomedical Sciences, The University of Queensland Brisbane Queensland Australia
| | - Christian W Gruber
- Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna Vienna Austria
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland Brisbane Queensland Australia
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23
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Gruber CW. Plant-Derived Peptides: (Neglected) Natural Products for Drug Discovery. PLANTA MEDICA 2024; 90:627-630. [PMID: 38843800 PMCID: PMC11156498 DOI: 10.1055/a-2219-9724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/21/2023] [Indexed: 06/10/2024]
Abstract
Peptides have emerged as key regulators in various physiological processes, including growth, development, stress, and defense responses within plants as well as ecological interactions of plants with microbes and animals. Understanding and harnessing plant peptides can lead to the development of innovative strategies for crop improvement, increasing agricultural productivity, and enhancing resilience to environmental challenges such as drought, pests, and diseases. Moreover, some plant peptides have shown promise in human health applications, with potential therapeutic benefits as ingredients in herbal medicines as well as novel drug leads. The exploration of plant peptides is essential for unraveling the mysteries of plant biology and advancing peptide drug discovery. This short personal commentary provides a very brief overview about the field of plant-derived peptides and a personal word of motivation to increase the number of scientists in pharmacognosy working with these fascinating biomolecules.
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Affiliation(s)
- Christian W. Gruber
- Center for Physiology and Pharmacology, Medical University of Vienna, Austria
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24
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Wang Q, Jin D, Liu C, Shi L, Li T. A Tumor-Specific Cascade-Activating Smart Prodrug System for Enhanced Targeted Therapy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2309482. [PMID: 38150668 DOI: 10.1002/smll.202309482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/28/2023] [Indexed: 12/29/2023]
Abstract
Developing intelligently targeted drugs with low side effects is urgent for cancer treatment. Toward this goal, a tumor-specific cascade-activating smart prodrug system consisting of a G-quadruplex(G4)-modulated tumor-targeted DNA vehicle and a well-designed cellular stimuli-responsive ligand-drug conjugates (LDCs) is proposed. An original "donor-acceptor" binary fluorescent ligand, with ultrahigh affinity, brightness, and photostability, is engineered to tightly bind G4 structures and significantly improve the nuclease resistance of the DNA vehicle, which serves as a bridge contributing to the construction of the prodrug system, named ApG4/LDCs. Sodium nitroprusside and doxorubicin are loaded into ApG4/LDCs in one pot and generate nitric oxide and superoxide anion in response to cancer cellular environments, which in cascade generates peroxynitrite to cause DNA damage while promoting the self-monitored drug release to achieve enhanced targeted therapy. Such a cascade activation and self-reinforcement process is executed only when the prodrug system targets the tumor tissue followed by cell uptake, showing significant antitumor efficacy and greatly weakening the damage to normal tissues. Given the unique features, the innovative strategy for prodrug design may open a new door to precision disease treatment.
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Affiliation(s)
- Qiwei Wang
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Duo Jin
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Chengbin Liu
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
| | - Lili Shi
- Department of Chemistry, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China
| | - Tao Li
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui, 230026, China
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25
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Song M, Liu Q, Yao JF, Wang YT, Ma YN, Xu H, Yu QY, Li Z, Du SS, Qi YK. Synthesis and structural optimization of oncolytic peptide LTX-315. Bioorg Med Chem 2024; 107:117760. [PMID: 38762978 DOI: 10.1016/j.bmc.2024.117760] [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: 04/13/2024] [Revised: 05/07/2024] [Accepted: 05/13/2024] [Indexed: 05/21/2024]
Abstract
Oncolytic peptides represented potential novel candidates for anticancer treatments especially drug-resistant cancer cell lines. One of the most promising and extensively studied is LTX-315, which is considered as the first in class oncolytic peptide and has entered phase I/II clinical trials. Nevertheless, the shortcomings including poor proteolytic stability, moderate anticancer durability and high synthesis costs may hinder the widespread clinical applications of LTX-315. In order to reduce the synthesis costs, as well as develop derivatives possessing both high protease-stability and durable anticancer efficiency, twenty LTX-315-based derived-peptides were designed and efficiently synthesized. Especially, through solid-phase S-alkylation, as well as the optimized peptide cleavage condition, the derived peptides could be prepared with drastically reduced synthesis cost. The in vitro anticancer efficiency, serum stability, anticancer durability, anti-migration activity, and hemolysis effect were systematically investigated. It was found that derived peptide MS-13 exhibited comparable anticancer efficiency and durability to those of LTX-315. Strikingly, the D-type peptide MS-20, which is the enantiomer of MS-13, was demonstrated to possess significantly high proteolytic stability and sustained anticancer durability. In general, the cost-effective synthesis and stability-guided structural optimizations were conducted on LTX-315, affording the highly hydrolysis resistant MS-20 which possessed durable anticancer activity. Meanwhile, this study also provided a reliable reference for the future optimization of anticancer peptides through the solid-phase S-alkylation and L-type to D-type amino acid substitutions.
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Affiliation(s)
- Min Song
- State Key Laboratory Base for Eco-Chemical Engineering in College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Qing Liu
- State Key Laboratory Base for Eco-Chemical Engineering in College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Jing-Fang Yao
- Department of Natural Medicinal Chemistry and Pharmacognosy, School of Pharmacy, Qingdao University, #1 Ningde Road, Qingdao 266073, China
| | - Yu-Tao Wang
- State Key Laboratory Base for Eco-Chemical Engineering in College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Yan-Nan Ma
- Department of Natural Medicinal Chemistry and Pharmacognosy, School of Pharmacy, Qingdao University, #1 Ningde Road, Qingdao 266073, China
| | - Huan Xu
- State Key Laboratory Base for Eco-Chemical Engineering in College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Qian-Yao Yu
- Department of Natural Medicinal Chemistry and Pharmacognosy, School of Pharmacy, Qingdao University, #1 Ningde Road, Qingdao 266073, China
| | - Zhibo Li
- State Key Laboratory Base for Eco-Chemical Engineering in College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Shan-Shan Du
- State Key Laboratory Base for Eco-Chemical Engineering in College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China; Department of Natural Medicinal Chemistry and Pharmacognosy, School of Pharmacy, Qingdao University, #1 Ningde Road, Qingdao 266073, China.
| | - Yun-Kun Qi
- Department of Natural Medicinal Chemistry and Pharmacognosy, School of Pharmacy, Qingdao University, #1 Ningde Road, Qingdao 266073, China.
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26
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Matsuda K, Wakimoto T. Penicillin-binding protein-type thioesterases: An emerging family of non-ribosomal peptide cyclases with biocatalytic potentials. Curr Opin Chem Biol 2024; 80:102465. [PMID: 38759287 DOI: 10.1016/j.cbpa.2024.102465] [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: 02/28/2024] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/19/2024]
Abstract
Macrocyclization of peptides reduces conformational flexibilities, potentially leading to improved drug-like properties, such as target specificities and metabolic stabilities. As chemical methodologies often allow side reactions like epimerization and oligomerization, keen attention has been directed toward enzymatic peptide cyclization using peptide cyclases from specialized metabolic pathways. Penicillin-binding protein-type thioesterases (PBP-type TEs) are a recently identified family of peptide cyclases involved in the biosynthesis of non-ribosomal peptides in actinobacteria. PBP-type TEs have undergone intensive investigation due to their outstanding potential as biocatalysts. This review summarizes the rapidly growing knowledge on PBP-type TEs, with special emphasis on their functions, scopes, and structures, and efforts towards their biocatalytic applications.
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Affiliation(s)
- Kenichi Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan.
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan.
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27
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Wang M, Li WW, Cao Z, Sun J, Xiong J, Tao SQ, Lv T, Gao K, Luo S, Dong SH. Genome mining of sulfonated lanthipeptides reveals unique cyclic peptide sulfotransferases. Acta Pharm Sin B 2024; 14:2773-2785. [PMID: 38828142 PMCID: PMC11143521 DOI: 10.1016/j.apsb.2024.02.016] [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: 10/31/2023] [Revised: 01/31/2024] [Accepted: 02/07/2024] [Indexed: 06/05/2024] Open
Abstract
Although sulfonation plays crucial roles in various biological processes and is frequently utilized in medicinal chemistry to improve water solubility and chemical diversity of drug leads, it is rare and underexplored in ribosomally synthesized and post-translationally modified peptides (RiPPs). Biosynthesis of RiPPs typically entails modification of hydrophilic residues, which substantially increases their chemical stability and bioactivity, albeit at the expense of reducing water solubility. To explore sulfonated RiPPs that may have improved solubility, we conducted co-occurrence analysis of RiPP class-defining enzymes and sulfotransferase (ST), and discovered two distinctive biosynthetic gene clusters (BGCs) encoding both lanthipeptide synthetase (LanM) and ST. Upon expressing these BGCs, we characterized the structures of novel sulfonated lanthipeptides and determined the catalytic details of LanM and ST. We demonstrate that SslST-catalyzed sulfonation is leader-independent but relies on the presence of A ring formed by LanM. Both LanM and ST are promiscuous towards residues in the A ring, but ST displays strict regioselectivity toward Tyr5. The recognition of cyclic peptide by ST was further discussed. Bioactivity evaluation underscores the significance of the ST-catalyzed sulfonation. This study sets up the starting point to engineering the novel lanthipeptide STs as biocatalysts for hydrophobic lanthipeptides improvement.
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Affiliation(s)
| | | | - Zhe Cao
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Jianong Sun
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Jiang Xiong
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Si-Qin Tao
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Tinghong Lv
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Kun Gao
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Shangwen Luo
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Shi-Hui Dong
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
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28
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Chen Z, Wang R, Guo J, Wang X. The role and future prospects of artificial intelligence algorithms in peptide drug development. Biomed Pharmacother 2024; 175:116709. [PMID: 38713945 DOI: 10.1016/j.biopha.2024.116709] [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: 03/10/2024] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 05/09/2024] Open
Abstract
Peptide medications have been more well-known in recent years due to their many benefits, including low side effects, high biological activity, specificity, effectiveness, and so on. Over 100 peptide medications have been introduced to the market to treat a variety of illnesses. Most of these peptide medications are developed on the basis of endogenous peptides or natural peptides, which frequently required expensive, time-consuming, and extensive tests to confirm. As artificial intelligence advances quickly, it is now possible to build machine learning or deep learning models that screen a large number of candidate sequences for therapeutic peptides. Therapeutic peptides, such as those with antibacterial or anticancer properties, have been developed by the application of artificial intelligence algorithms.The process of finding and developing peptide drugs is outlined in this review, along with a few related cases that were helped by AI and conventional methods. These resources will open up new avenues for peptide drug development and discovery, helping to meet the pressing needs of clinical patients for disease treatment. Although peptide drugs are a new class of biopharmaceuticals that distinguish them from chemical and small molecule drugs, their clinical purpose and value cannot be ignored. However, the traditional peptide drug research and development has a long development cycle and high investment, and the creation of peptide medications will be substantially hastened by the AI-assisted (AI+) mode, offering a new boost for combating diseases.
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Affiliation(s)
- Zhiheng Chen
- School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China.
| | - Ruoxi Wang
- School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China.
| | - Junqi Guo
- School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China.
| | - Xiaogang Wang
- Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, The Third Affiliated Hospital of Southern Medical University, Guangzhou, Guangdong 510630, China.
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29
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Downey ML, Peralta-Yahya P. Technologies for the discovery of G protein-coupled receptor-targeting biologics. Curr Opin Biotechnol 2024; 87:103138. [PMID: 38728825 DOI: 10.1016/j.copbio.2024.103138] [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: 03/04/2024] [Accepted: 04/13/2024] [Indexed: 05/12/2024]
Abstract
G protein-coupled receptors (GPCRs) are important pharmaceutical targets, working as entry points for signaling pathways involved in metabolic, neurological, and cardiovascular diseases. Although small molecules remain the major GPCR drug type, biologic therapeutics, such as peptides and antibodies, are increasingly found among clinical trials and Food and Drug Administration (FDA)-approved drugs. Here, we review state-of-the-art technologies for the engineering of biologics that target GPCRs, as well as proof-of-principle technologies that are ripe for this application. Looking ahead, inexpensive DNA synthesis will enable the routine generation of computationally predesigned libraries for use in display assays for the rapid discovery of GPCR binders. Advances in synthetic biology are enabling the increased throughput of functional GPCR assays to the point that they can be used to directly identify biologics that modulate GPCR activity. Finally, we give an overview of adjacent technologies that are ripe for application to discover biologics that target human GPCRs.
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Affiliation(s)
- McKenna L Downey
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Pamela Peralta-Yahya
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA; School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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30
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Zhang Z, Yi Y, Wang Z, Zhang H, Zhao Y, He R, Luo Y, Cui Z. LncRNA MAGI2-AS3-Encoded Polypeptide Restrains the Proliferation and Migration of Breast Cancer Cells. Mol Biotechnol 2024; 66:1409-1423. [PMID: 37358745 DOI: 10.1007/s12033-023-00801-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 06/20/2023] [Indexed: 06/27/2023]
Abstract
Accumulating articles have reported the coding potential of long non-coding RNAs (lncRNAs). However, only a few lncRNAs-encoded peptides have been studied. Breast cancer (BRCA) progression-related gene modules were determined by weighted gene co-expression network analysis (WGCNA). Cell viability, proliferation, and migration capacities were assessed by Cell counting kit-8 (CCK8), 5-ethynyl-2'-deoxyuridine (EdU), and transwell assays. Immunofluorescence (IF) assay was implemented to observe protein expression. Co-immunoprecipitation (Co-IP) and high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) were employed to analyze MAGI2 antisense RNA 3 (MAGI2-AS3)-ORF5-interacted proteins. WGCNA identified that MEpurple and MEblack modules were significantly negatively correlated with T stage in BRCA patients. MAGI2-AS3 was screened as one of the differentially expressed (DE) lncRNAs with translational potential in MEblack and MEpurple modules in BRCA. The data in The Cancer Genome Atlas (TCGA) uncovered that MAGI2-AS3 abundance was significantly decreased in invasive BRCA patients, and it had high diagnostic and prognostic values. MAGI2-AS3-ORF5 notably restrained BRCA cell viability, proliferation, and migration. Mechanically, MAGI2-AS3-ORF5 might affect the progression of BRCA cells by binding to extracellular matrix (ECM)-related proteins. MAGI2-AS3-ORF5 played an anti-tumor role by inhibiting BRCA cell viability, proliferation, and migration. MAGI2-AS3-ORF5 might modulate BRCA cell migration through ECM-associated proteins.
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Affiliation(s)
- Zhiwei Zhang
- Department of Oncology, Affiliated Hospital of Hebei University of Engineering, Handan, 056000, Hebei, China
| | - Yanli Yi
- Department of Breast Surgery, Affiliated Hospital of Hebei University of Engineering, Handan, 056000, Hebei, China
| | - Zai Wang
- Science and Education Division, Affiliated Hospital of Hebei University of Engineering, Handan, 056000, Hebei, China
| | - Haoyun Zhang
- Department of Breast Surgery, Affiliated Hospital of Hebei University of Engineering, Handan, 056000, Hebei, China
| | - Yanchun Zhao
- Department of Breast Surgery, Affiliated Hospital of Hebei University of Engineering, Handan, 056000, Hebei, China
| | - Ruijing He
- Department of Breast Surgery, Affiliated Hospital of Hebei University of Engineering, Handan, 056000, Hebei, China
| | - Yan Luo
- Department of Reproductive Genetic, Hebei General Hospital, Shijiazhuang, 050000, Hebei, China
| | - Zhiqiang Cui
- Department of Breast Surgery, Affiliated Hospital of Hebei University of Engineering, Handan, 056000, Hebei, China.
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31
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Aslan A, Ari Yuka S. Therapeutic peptides for coronary artery diseases: in silico methods and current perspectives. Amino Acids 2024; 56:37. [PMID: 38822212 PMCID: PMC11143054 DOI: 10.1007/s00726-024-03397-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 05/06/2024] [Indexed: 06/02/2024]
Abstract
Many drug formulations containing small active molecules are used for the treatment of coronary artery disease, which affects a significant part of the world's population. However, the inadequate profile of these molecules in terms of therapeutic efficacy has led to the therapeutic use of protein and peptide-based biomolecules with superior properties, such as target-specific affinity and low immunogenicity, in critical diseases. Protein‒protein interactions, as a consequence of advances in molecular techniques with strategies involving the combined use of in silico methods, have enabled the design of therapeutic peptides to reach an advanced dimension. In particular, with the advantages provided by protein/peptide structural modeling, molecular docking for the study of their interactions, molecular dynamics simulations for their interactions under physiological conditions and machine learning techniques that can work in combination with all these, significant progress has been made in approaches to developing therapeutic peptides that can modulate the development and progression of coronary artery diseases. In this scope, this review discusses in silico methods for the development of peptide therapeutics for the treatment of coronary artery disease and strategies for identifying the molecular mechanisms that can be modulated by these designs and provides a comprehensive perspective for future studies.
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Affiliation(s)
- Ayca Aslan
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yildiz Technical University, Esenler, Istanbul, Turkey
- Health Biotechnology Joint Research and Application Center of Excellence, Esenler, Istanbul, Turkey
| | - Selcen Ari Yuka
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yildiz Technical University, Esenler, Istanbul, Turkey.
- Health Biotechnology Joint Research and Application Center of Excellence, Esenler, Istanbul, Turkey.
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32
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Yamada A, Takei T, Kawakami T, Taniguchi Y, Sekiguchi K, Hojo H. Application of cysteinyl prolyl ester for the synthesis of cyclic peptides containing an RGD sequence and their biological activity measurement. Front Chem 2024; 12:1391678. [PMID: 38873405 PMCID: PMC11169864 DOI: 10.3389/fchem.2024.1391678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 05/01/2024] [Indexed: 06/15/2024] Open
Abstract
Cysteinyl RGD-peptidyl cysteinyl prolyl esters, which have different configurations at the cysteine and proline residues, were synthesized by the solid-phase method and cyclized by the native chemical ligation reaction. Cyclization efficiently proceeded to give cyclic peptides, regardless of the difference in the configuration. The peptides were further derivatized to the corresponding desulfurized or methylated cyclic peptides at the Cys residues. The inhibition activity to αvβ6 integrin binding was then analyzed by ELISA. The results showed that the activity varied depending on the difference in the configuration and modification of the cysteinyl prolyl ester (CPC) moiety, demonstrating the usefulness of this method in the search for a good inhibitor of the protein-protein interaction.
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Affiliation(s)
| | | | | | | | | | - Hironobu Hojo
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
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33
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Hsiao MH, Miao Y, Liu Z, Schütze K, Limjunyawong N, Chien DCC, Monteiro WD, Chu LS, Morgenlander W, Jayaraman S, Jang SE, Gray JJ, Zhu H, Dong X, Steinegger M, Larman HB. Molecular Display of the Animal Meta-Venome for Discovery of Novel Therapeutic Peptides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.27.595990. [PMID: 38854075 PMCID: PMC11160688 DOI: 10.1101/2024.05.27.595990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Animal venoms, distinguished by their unique structural features and potent bioactivities, represent a vast and relatively untapped reservoir of therapeutic molecules. However, limitations associated with extracting or expressing large numbers of individual venoms and venom-like molecules have precluded their therapeutic evaluation via high throughput screening. Here, we developed an innovative computational approach to design a highly diverse library of animal venoms and "metavenoms". We employed programmable M13 hyperphage display to preserve critical disulfide-bonded structures for highly parallelized single-round biopanning with quantitation via high-throughput DNA sequencing. Our approach led to the discovery of Kunitz type domain containing proteins that target the human itch receptor Mas-related G protein-coupled receptor X4 (MRGPRX4), which plays a crucial role in itch perception. Deep learning-based structural homology mining identified two endogenous human homologs, tissue factor pathway inhibitor (TFPI) and serine peptidase inhibitor, Kunitz type 2 (SPINT2), which exhibit agonist-dependent potentiation of MRGPRX4. Highly multiplexed screening of animal venoms and metavenoms is therefore a promising approach to uncover new drug candidates.
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Affiliation(s)
- Meng-Hsuan Hsiao
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- These authors contributed equally to this work
| | - Yang Miao
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- These authors contributed equally to this work
| | - Zixing Liu
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biology, Zanvyl Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Konstantin Schütze
- School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Nathachit Limjunyawong
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Center of Research Excellence in Allergy and Immunology, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand
| | - Daphne Chun-Che Chien
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Wayne Denis Monteiro
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Lee-Shin Chu
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - William Morgenlander
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sahana Jayaraman
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sung-eun Jang
- School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Viral Oncology Program, Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Xinzhong Dong
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Martin Steinegger
- School of Biological Sciences, Seoul National University, Seoul, South Korea
- Artificial Intelligence Institute, Seoul National University, Seoul, South Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - H. Benjamin Larman
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Li Y, Li L, Wang X, Zhao F, Yang Y, Zhou Y, Zhang J, Wang L, Jiang Z, Zhang Y, Chen Y, Wu C, Li K, Zhang T, Wang P, Mao Z, Zhu W, Xu X, Liang S, Lou Z, Yuan J. USP25 Elevates SHLD2-Mediated DNA Double-Strand Break Repair and Regulates Chemoresponse in Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2403485. [PMID: 38803048 DOI: 10.1002/advs.202403485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Indexed: 05/29/2024]
Abstract
DNA damage plays a significant role in the tumorigenesis and progression of the disease. Abnormal DNA repair affects the therapy and prognosis of cancer. In this study, it is demonstrated that the deubiquitinase USP25 promotes non-homologous end joining (NHEJ), which in turn contributes to chemoresistance in cancer. It is shown that USP25 deubiquitinates SHLD2 at the K64 site, which enhances its binding with REV7 and promotes NHEJ. Furthermore, USP25 deficiency impairs NHEJ-mediated DNA repair and reduces class switch recombination (CSR) in USP25-deficient mice. USP25 is overexpressed in a subset of colon cancers. Depletion of USP25 sensitizes colon cancer cells to IR, 5-Fu, and cisplatin. TRIM25 is also identified, an E3 ligase, as the enzyme responsible for degrading USP25. Downregulation of TRIM25 leads to an increase in USP25 levels, which in turn induces chemoresistance in colon cancer cells. Finally, a peptide that disrupts the USP25-SHLD2 interaction is successfully identified, impairing NHEJ and increasing sensitivity to chemotherapy in PDX model. Overall, these findings reveal USP25 as a critical effector of SHLD2 in regulating the NHEJ repair pathway and suggest its potential as a therapeutic target for cancer therapy.
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Affiliation(s)
- Yunhui Li
- Medical Innovation Center, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
- Cancer Center, Tongji University School of Medicine, Shanghai, 200331, China
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, 200331, China
| | - Lei Li
- Medical Innovation Center, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
- Cancer Center, Tongji University School of Medicine, Shanghai, 200331, China
| | - Xinshu Wang
- Medical Innovation Center, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, 200331, China
| | - Fei Zhao
- College of Biology, Hunan University, Changsha, 410082, China
| | - Yuntong Yang
- Medical Innovation Center, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, 200331, China
| | - Yujuan Zhou
- Medical Innovation Center, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, 200331, China
| | - Jiyuan Zhang
- Medical Innovation Center, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, 200331, China
| | - Li Wang
- Medical Innovation Center, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, 200331, China
| | - Zeshan Jiang
- Medical Innovation Center, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, 200331, China
| | - Yuanyuan Zhang
- Department of General Surgery and Colorectal Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Yuping Chen
- Cancer Center, Tongji University School of Medicine, Shanghai, 200331, China
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, 200331, China
- Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200080, China
| | - Chenming Wu
- Medical Innovation Center, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
- Cancer Center, Tongji University School of Medicine, Shanghai, 200331, China
| | - Ke Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Tingting Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Ping Wang
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Shanghai, 200072, China
| | - Zhiyong Mao
- Shanghai Key Laboratory of Maternal-Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, Tongji University School of Medicine, Shanghai, 200040, China
| | - Weiguo Zhu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen, 518037, China
| | - Xingzhi Xu
- The Sixth Affiliated Hospital of Shenzhen University, Guangdong Key Laboratory for Genome Stability and Disease Prevention and Carson International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University School of Medicine, Shenzhen, 518055, China
| | - Shikang Liang
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, 999077, Hong Kong
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Jian Yuan
- Medical Innovation Center, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
- Cancer Center, Tongji University School of Medicine, Shanghai, 200331, China
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, 200331, China
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35
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Bekker GJ, Oshima K, Araki M, Okuno Y, Kamiya N. Binding Mechanism between Platelet Glycoprotein and Cyclic Peptide Elucidated by McMD-Based Dynamic Docking. J Chem Inf Model 2024; 64:4158-4167. [PMID: 38751042 DOI: 10.1021/acs.jcim.4c00100] [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: 05/28/2024]
Abstract
The cyclic peptide OS1 (amino acid sequence: CTERMALHNLC), which has a disulfide bond between both termini cysteine residues, inhibits complex formation between the platelet glycoprotein Ibα (GPIbα) and the von Willebrand factor (vWF) by forming a complex with GPIbα. To study the binding mechanism between GPIbα and OS1 and, therefore, the inhibition mechanism of the protein-protein GPIbα-vWF complex, we have applied our multicanonical molecular dynamics (McMD)-based dynamic docking protocol starting from the unbound state of the peptide. Our simulations have reproduced the experimental complex structure, although the top-ranking structure was an intermediary one, where the peptide was bound in the same location as in the experimental structure; however, the β-switch of GPIbα attained a different conformation. Our analysis showed that subsequent refolding of the β-switch results in a more stable binding configuration, although the transition to the native configuration appears to take some time, during which OS1 could dissociate. Our results show that conformational changes in the β-switch are crucial for successful binding of OS1. Furthermore, we identified several allosteric binding sites of GPIbα that might also interfere with vWF binding, and optimization of the peptide to target these allosteric sites might lead to a more effective inhibitor, as these are not dependent on the β-switch conformation.
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Affiliation(s)
- Gert-Jan Bekker
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kanji Oshima
- Bio-Pharma Research Laboratories, Kaneka Corporation, 1-8 Miyamae-cho, Takasago-cho, Takasago, Hyogo 676-8688, Japan
| | - Mitsugu Araki
- Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Yasushi Okuno
- Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Narutoshi Kamiya
- Graduate School of Information Science, University of Hyogo, 7-1-28 minatojima Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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36
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Gatto MS, Johnson MP, Najahi-Missaoui W. Targeted Liposomal Drug Delivery: Overview of the Current Applications and Challenges. Life (Basel) 2024; 14:672. [PMID: 38929656 PMCID: PMC11204409 DOI: 10.3390/life14060672] [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: 03/30/2024] [Revised: 05/14/2024] [Accepted: 05/20/2024] [Indexed: 06/28/2024] Open
Abstract
In drug development, it is not uncommon that an active substance exhibits efficacy in vitro but lacks the ability to specifically reach its target in vivo. As a result, targeted drug delivery has become a primary focus in the pharmaceutical sciences. Since the approval of Doxil® in 1995, liposomes have emerged as a leading nanoparticle in targeted drug delivery. Their low immunogenicity, high versatility, and well-documented efficacy have led to their clinical use against a wide variety of diseases. That being said, every disease is accompanied by a unique set of physiological conditions, and each liposomal product must be formulated with this consideration. There are a multitude of different targeting techniques for liposomes that can be employed depending on the application. Passive techniques such as PEGylation or the enhanced permeation and retention effect can improve general pharmacokinetics, while active techniques such as conjugating targeting molecules to the liposome surface may bring even further specificity. This review aims to summarize the current strategies for targeted liposomes in the treatment of diseases.
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Affiliation(s)
| | | | - Wided Najahi-Missaoui
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA; (M.S.G.); (M.P.J.)
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37
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Goles M, Daza A, Cabas-Mora G, Sarmiento-Varón L, Sepúlveda-Yañez J, Anvari-Kazemabad H, Davari MD, Uribe-Paredes R, Olivera-Nappa Á, Navarrete MA, Medina-Ortiz D. Peptide-based drug discovery through artificial intelligence: towards an autonomous design of therapeutic peptides. Brief Bioinform 2024; 25:bbae275. [PMID: 38856172 PMCID: PMC11163380 DOI: 10.1093/bib/bbae275] [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: 02/08/2024] [Revised: 04/23/2024] [Accepted: 06/04/2024] [Indexed: 06/11/2024] Open
Abstract
With their diverse biological activities, peptides are promising candidates for therapeutic applications, showing antimicrobial, antitumour and hormonal signalling capabilities. Despite their advantages, therapeutic peptides face challenges such as short half-life, limited oral bioavailability and susceptibility to plasma degradation. The rise of computational tools and artificial intelligence (AI) in peptide research has spurred the development of advanced methodologies and databases that are pivotal in the exploration of these complex macromolecules. This perspective delves into integrating AI in peptide development, encompassing classifier methods, predictive systems and the avant-garde design facilitated by deep-generative models like generative adversarial networks and variational autoencoders. There are still challenges, such as the need for processing optimization and careful validation of predictive models. This work outlines traditional strategies for machine learning model construction and training techniques and proposes a comprehensive AI-assisted peptide design and validation pipeline. The evolving landscape of peptide design using AI is emphasized, showcasing the practicality of these methods in expediting the development and discovery of novel peptides within the context of peptide-based drug discovery.
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Affiliation(s)
- Montserrat Goles
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Av. Pdte. Manuel Bulnes 01855, 6210427, Punta Arenas, Chile
- Departamento de Ingeniería Química, Biotecnología y Materiales, Universidad de Chile, Beauchef 851, 8370456, Santiago, Chile
| | - Anamaría Daza
- Centre for Biotechnology and Bioengineering, CeBiB, Universidad de Chile, Beauchef 851, 8370456, Santiago, Chile
| | - Gabriel Cabas-Mora
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Av. Pdte. Manuel Bulnes 01855, 6210427, Punta Arenas, Chile
| | - Lindybeth Sarmiento-Varón
- Centro Asistencial de Docencia e Investigación, CADI, Universidad de Magallanes, Av. Los Flamencos 01364, 6210005, Punta Arenas, Chile
| | - Julieta Sepúlveda-Yañez
- Facultad de Ciencias de la Salud, Universidad de Magallanes, Av. Pdte. Manuel Bulnes 01855, 6210427, Punta Arenas, Chile
| | - Hoda Anvari-Kazemabad
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Av. Pdte. Manuel Bulnes 01855, 6210427, Punta Arenas, Chile
| | - Mehdi D Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Germany
| | - Roberto Uribe-Paredes
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Av. Pdte. Manuel Bulnes 01855, 6210427, Punta Arenas, Chile
| | - Álvaro Olivera-Nappa
- Centre for Biotechnology and Bioengineering, CeBiB, Universidad de Chile, Beauchef 851, 8370456, Santiago, Chile
| | - Marcelo A Navarrete
- Centro Asistencial de Docencia e Investigación, CADI, Universidad de Magallanes, Av. Los Flamencos 01364, 6210005, Punta Arenas, Chile
- Escuela de Medicina, Universidad de Magallanes, Av. Pdte. Manuel Bulnes 01855, 6210427, Punta Arenas, Chile
| | - David Medina-Ortiz
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Av. Pdte. Manuel Bulnes 01855, 6210427, Punta Arenas, Chile
- Centre for Biotechnology and Bioengineering, CeBiB, Universidad de Chile, Beauchef 851, 8370456, Santiago, Chile
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38
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Chen N, Yu J, Zhe L, Wang F, Li X, Wong KC. TP-LMMSG: a peptide prediction graph neural network incorporating flexible amino acid property representation. Brief Bioinform 2024; 25:bbae308. [PMID: 38920345 PMCID: PMC11200197 DOI: 10.1093/bib/bbae308] [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: 04/08/2024] [Revised: 05/28/2024] [Accepted: 06/10/2024] [Indexed: 06/27/2024] Open
Abstract
Bioactive peptide therapeutics has been a long-standing research topic. Notably, the antimicrobial peptides (AMPs) have been extensively studied for its therapeutic potential. Meanwhile, the demand for annotating other therapeutic peptides, such as antiviral peptides (AVPs) and anticancer peptides (ACPs), also witnessed an increase in recent years. However, we conceive that the structure of peptide chains and the intrinsic information between the amino acids is not fully investigated among the existing protocols. Therefore, we develop a new graph deep learning model, namely TP-LMMSG, which offers lightweight and easy-to-deploy advantages while improving the annotation performance in a generalizable manner. The results indicate that our model can accurately predict the properties of different peptides. The model surpasses the other state-of-the-art models on AMP, AVP and ACP prediction across multiple experimental validated datasets. Moreover, TP-LMMSG also addresses the challenges of time-consuming pre-processing in graph neural network frameworks. With its flexibility in integrating heterogeneous peptide features, our model can provide substantial impacts on the screening and discovery of therapeutic peptides. The source code is available at https://github.com/NanjunChen37/TP_LMMSG.
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Affiliation(s)
- Nanjun Chen
- Department of Computer Science, City University of Hong Kong, 83 Tat Chee Ave, Kowloon Tong, Kowloon, Hong Kong SAR
| | - Jixiang Yu
- Department of Computer Science, City University of Hong Kong, 83 Tat Chee Ave, Kowloon Tong, Kowloon, Hong Kong SAR
| | - Liu Zhe
- Department of Computer Science, City University of Hong Kong, 83 Tat Chee Ave, Kowloon Tong, Kowloon, Hong Kong SAR
| | - Fuzhou Wang
- Department of Computer Science, City University of Hong Kong, 83 Tat Chee Ave, Kowloon Tong, Kowloon, Hong Kong SAR
| | - Xiangtao Li
- School of Artificial Intelligence, Jilin University, Chang Chun, Ji Lin, China
| | - Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, 83 Tat Chee Ave, Kowloon Tong, Kowloon, Hong Kong SAR
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen, Guang Dong, China
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39
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Zhao X, Liu H, Zhang JC, Cai J. Helical sulfonyl-γ-AApeptides for the inhibition of HIV-1 fusion and HIF-1α signaling. RSC Med Chem 2024; 15:1418-1423. [PMID: 38784464 PMCID: PMC11110726 DOI: 10.1039/d4md00110a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 03/19/2024] [Indexed: 05/25/2024] Open
Abstract
Synthetic helical peptidic foldamers show promising applications in chemical biology and biomedical sciences by mimicking protein helical segments. Sulfonyl-γ-AApeptide helices developed by our group exhibit good chemodiversity, predictable folding structures, proteolytic resistance, favorable cell permeability, and enhanced bioavailability. Herein, in this minireview, we highlight two recent examples of homogeneous left-handed sulfonyl-γ-AApeptide helices to modulate protein-protein interactions (PPIs). One is sulfonyl-γ-AApeptides as anti-HIV-1 fusion inhibitors mimicking the helical C-terminal heptad repeat (CHR), which show excellent anti-HIV-1 activities through tight binding with the N-terminal heptad repeat (NHR) and inhibiting the formation of the 6-helical bundle (HB) structure. Another example is helical sulfonyl-γ-AApeptides disrupting hypoxia-inducible factor 1α (HIF-1α) and p300 PPI, thus selectively inhibiting the relevant signaling cascade. We hope these findings could help to elucidate the principles of the structural design of sulfonyl-γ-AApeptides and inspire their future applications in PPI modulations.
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Affiliation(s)
- Xue Zhao
- Department of Chemistry, University of South Florida Tampa FL 33620 USA
| | - Heng Liu
- Department of Chemistry, University of South Florida Tampa FL 33620 USA
| | - Justin C Zhang
- Department of Chemistry, University of South Florida Tampa FL 33620 USA
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida Tampa FL 33620 USA
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40
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Wang N, Mcneer NA, Eton E, Fass J, Kentsis A. Proteomic Barcoding Platform for Macromolecular Screening and Delivery. J Proteome Res 2024. [PMID: 38776430 DOI: 10.1021/acs.jproteome.4c00068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Engineered macromolecules offer compelling means for the therapy of conventionally undruggable interactions in human disease. However, their efficacy is limited by barriers to tissue and intracellular delivery. Inspired by recent advances in molecular barcoding and evolution, we developed BarcodeBabel, a generalized method for the design of libraries of peptide barcodes suitable for high-throughput mass spectrometry proteomics. Combined with PeptideBabel, a Monte Carlo sampling algorithm for the design of peptides with evolvable physicochemical properties and sequence complexity, we developed a barcoded library of cell penetrating peptides (CPPs) with distinct physicochemical features. Using quantitative targeted mass spectrometry, we identified CPPS with improved nuclear and cytoplasmic delivery exceeding hundreds of millions of molecules per human cell while maintaining minimal membrane disruption and negligible toxicity in vitro. These studies provide a proof of concept for peptide barcoding as a homogeneous high-throughput method for macromolecular screening and delivery. BarcodeBabel and PeptideBabel are available open-source from https://github.com/kentsisresearchgroup/.
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Affiliation(s)
- Ning Wang
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Nicole A Mcneer
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Elliot Eton
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Josh Fass
- Tri-I PhD Program in Computational Biology and Medicine, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Departments of Pediatrics, Pharmacology, and Physiology & Biophysics, Weill Cornell Medical College, Cornell University, New York, New York 10065, United States
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41
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Zhong H, Zhang X, Wu Y, Li L, Zhang Z, Chi X, Cui X, Ji C. The dairy-derived peptide Miltin exerts anti-obesity effects by increasing adipocyte thermogenesis. Food Funct 2024; 15:5300-5314. [PMID: 38669145 DOI: 10.1039/d3fo05704f] [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: 04/28/2024]
Abstract
Growing research has highlighted that the consumption of dairy products improves the metabolic health in obese individuals by functioning as regulatory modulators. However, the molecular basis of this effect remains largely unknown. Herein, we report a dairy-derived peptide, which we named Miltin, that activates the thermogenesis of brown adipocytes and increases white adipocyte browning. Previously, Miltin was merely identified for its antioxidant capacity, although it is commonly present in different dairy products. In this study, we revealed the effect of Miltin in modulating adipose thermogenesis and further explored its potential in treating obesity through in vivo and in vitro strategies. The administration of Miltin in mice fed with a high-fat diet resulted in enhanced thermogenesis, improved glucose homeostasis, and reduced body mass and lipid accumulation, indicating the anti-obesity effect of Miltin. Genomic analysis revealed that Miltin modulates thermogenesis by inducing the activation of the MAPK signaling pathway by preferentially interacting with GADD45γ to promote its stability. Together, our findings indicate that Miltin's role in initiating the thermogenesis of adipocytes makes it a potential anti-obesity therapy for future development.
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Affiliation(s)
- Hong Zhong
- Nanjing Maternal and Child Health Institute, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, 123 Tianfei Alley, Mochou Road, Nanjing, China.
| | - Xiaoxiao Zhang
- Nanjing Maternal and Child Health Institute, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, 123 Tianfei Alley, Mochou Road, Nanjing, China.
| | - Yangyang Wu
- Nanjing Maternal and Child Health Institute, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, 123 Tianfei Alley, Mochou Road, Nanjing, China.
| | - Lu Li
- Nanjing Maternal and Child Health Institute, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, 123 Tianfei Alley, Mochou Road, Nanjing, China.
| | - Zhuo Zhang
- Nanjing Maternal and Child Health Institute, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, 123 Tianfei Alley, Mochou Road, Nanjing, China.
| | - Xia Chi
- Nanjing Maternal and Child Health Institute, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, 123 Tianfei Alley, Mochou Road, Nanjing, China.
| | - Xianwei Cui
- Nanjing Maternal and Child Health Institute, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, 123 Tianfei Alley, Mochou Road, Nanjing, China.
| | - Chenbo Ji
- Nanjing Maternal and Child Health Institute, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, 123 Tianfei Alley, Mochou Road, Nanjing, China.
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42
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Mukherjee S, Rogers A, Creech G, Hang C, Ramirez A, Dummeldinger M, Brueggemeier S, Mapelli C, Zaretsky S, Huang M, Black R, Peddicord MB, Cuniere N, Kempson J, Pawluczyk J, Allen M, Parsons R, Sfouggatakis C. Process Development of a Macrocyclic Peptide Inhibitor of PD-L1. J Org Chem 2024; 89:6651-6663. [PMID: 38663026 DOI: 10.1021/acs.joc.4c00430] [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: 05/18/2024]
Abstract
This article outlines the process development leading to the manufacture of 800 g of BMS-986189, a macrocyclic peptide active pharmaceutical ingredient. Multiple N-methylated unnatural amino acids posed challenges to manufacturing due to the lability of the peptide to cleavage during global side chain deprotection and precipitation steps. These issues were exacerbated upon scale-up, resulting in severe yield loss and necessitating careful impurity identification, understanding the root cause of impurity formation, and process optimization to deliver a scalable synthesis. A systematic study of macrocyclization with its dependence on concentration and pH is presented. In addition, a side chain protected peptide synthesis is discussed where the macrocyclic protected peptide is extremely labile to hydrolysis. A computational study explains the root cause of the increased lability of macrocyclic peptide over linear peptide to hydrolysis. A process solution involving the use of labile protecting groups is discussed. Overall, the article highlights the advancements achieved to enable scalable synthesis of an unusually labile macrocyclic peptide by solid-phase peptide synthesis. The sustainability metric indicates the final preparative chromatography drives a significant fraction of a high process mass intensity (PMI).
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Affiliation(s)
- Subha Mukherjee
- Chemical Process Development, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Amanda Rogers
- Chemical Process Development, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Gardner Creech
- Chemical Process Development, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Chao Hang
- Chemical Process Development, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Antonio Ramirez
- Chemical Process Development, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Michael Dummeldinger
- Chemical Process Development, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Shawn Brueggemeier
- Chemical Process Development, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Claudio Mapelli
- Discovery Chemistry, Bristol Myers Squibb, Princeton, New Jersey 08540, United States
| | - Serge Zaretsky
- Chemical Process Development, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Masano Huang
- Chemical Process Development, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Regina Black
- Chemical Process Development, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Michael B Peddicord
- Chemical Process Development, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Nicolas Cuniere
- Chemical Process Development, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - James Kempson
- Discovery Chemistry, Bristol Myers Squibb, Princeton, New Jersey 08540, United States
| | - Joseph Pawluczyk
- Discovery Chemistry, Bristol Myers Squibb, Princeton, New Jersey 08540, United States
| | - Martin Allen
- Discovery Chemistry, Bristol Myers Squibb, Princeton, New Jersey 08540, United States
| | - Rodney Parsons
- Chemical Process Development, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
| | - Chris Sfouggatakis
- Chemical Process Development, Bristol Myers Squibb, New Brunswick, New Jersey 08903, United States
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43
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Ansari M, White AD. Learning peptide properties with positive examples only. DIGITAL DISCOVERY 2024; 3:977-986. [PMID: 38756224 PMCID: PMC11094695 DOI: 10.1039/d3dd00218g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 03/30/2024] [Indexed: 05/18/2024]
Abstract
Deep learning can create accurate predictive models by exploiting existing large-scale experimental data, and guide the design of molecules. However, a major barrier is the requirement of both positive and negative examples in the classical supervised learning frameworks. Notably, most peptide databases come with missing information and low number of observations on negative examples, as such sequences are hard to obtain using high-throughput screening methods. To address this challenge, we solely exploit the limited known positive examples in a semi-supervised setting, and discover peptide sequences that are likely to map to certain antimicrobial properties via positive-unlabeled learning (PU). In particular, we use the two learning strategies of adapting base classifier and reliable negative identification to build deep learning models for inferring solubility, hemolysis, binding against SHP-2, and non-fouling activity of peptides, given their sequence. We evaluate the predictive performance of our PU learning method and show that by only using the positive data, it can achieve competitive performance when compared with the classical positive-negative (PN) classification approach, where there is access to both positive and negative examples.
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Affiliation(s)
- Mehrad Ansari
- Department of Chemical Engineering, University of Rochester Rochester NY 14627 USA
| | - Andrew D White
- Department of Chemical Engineering, University of Rochester Rochester NY 14627 USA
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44
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Tran DVH, Luong HX, Kim DH, Lee BJ, Kim YW. Lysine-homologue substitution: Impact on antimicrobial activity and proteolytic stability of cationic stapled heptapeptides. Bioorg Med Chem 2024; 106:117735. [PMID: 38714021 DOI: 10.1016/j.bmc.2024.117735] [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: 02/22/2024] [Revised: 04/19/2024] [Accepted: 04/19/2024] [Indexed: 05/09/2024]
Abstract
Numerous natural antimicrobial peptides (AMPs) exhibit a cationic amphipathic helical conformation, wherein cationic amino acids, such as lysine and arginine, play pivotal roles in antimicrobial activity by aiding initial attraction to negatively charged bacterial membranes. Expanding on our previous work, which introduced a de novo design of amphipathic helices within cationic heptapeptides using an 'all-hydrocarbon peptide stapling' approach, we investigated the impact of lysine-homologue substitution on helix formation, antimicrobial activity, hemolytic activity, and proteolytic stability of these novel AMPs. Our results demonstrate that substituting lysine with ornithine enhances both the antimicrobial activity and proteolytic stability of the stapled heptapeptide AMP series, while maintaining low hemolytic activity. This finding underscores lysine-homologue substitution as a valuable strategy for optimizing the therapeutic potential of diverse cationic AMPs.
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Affiliation(s)
- Duc V H Tran
- College of Pharmacy, Dongguk University-Seoul, Goyang 10326, Republic of Korea; Intergrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Huy X Luong
- College of Pharmacy, Dongguk University-Seoul, Goyang 10326, Republic of Korea; Intergrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Do-Hee Kim
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Bong-Jin Lee
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Young-Woo Kim
- College of Pharmacy, Dongguk University-Seoul, Goyang 10326, Republic of Korea; Intergrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang 10326, Republic of Korea.
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45
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Holzenkamp C, Wennrich JP, Muema JM, Ashrafi S, Maier W, Stadler M, Ebada SS. Laburnicotides A-F: Acyclic N-Acetyl Oligopeptides from the Nematode-Cyst-Associated Fungus Laburnicola nematophila. ACS OMEGA 2024; 9:21658-21667. [PMID: 38764662 PMCID: PMC11097168 DOI: 10.1021/acsomega.4c02719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/17/2024] [Accepted: 04/23/2024] [Indexed: 05/21/2024]
Abstract
Nematode-associated fungi revealed the potential to produce a broad spectrum of chemical scaffolds. In this study, a mycelial extract of Laburnicola nematophila, a fungal strain derived from the cereal cyst nematode Heterodera filipjevi, was chemically explored and afforded six unprecedentedly reported acylic N-acetyl oligopeptides, laburnicotides A-F (1-6). Structure elucidation of the isolated compounds was established based on comprehensive 1D and 2D NMR spectroscopic analyses together with the acquired HR-ESI-MS spectrometric data. The absolute configuration of amino acid residues in 1-6 was established by performing advanced Marfey's derivatization method. All isolated compounds were assessed for their cytotoxic, antimicrobial, antiviral, and nematicidal activities with no potential activity observed.
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Affiliation(s)
- Caren Holzenkamp
- Department
of Microbial Drugs, Helmholtz Centre
for Infection Research (HZI) and German Centre for Infection Research, Inhoffenstrasse 7, Braunschweig 38124, Germany
- Institute
of Microbiology, Technische Universität
Braunschweig, Spielmannstraße
7, Braunschweig 38106, Germany
| | - Jan-Peer Wennrich
- Department
of Microbial Drugs, Helmholtz Centre
for Infection Research (HZI) and German Centre for Infection Research, Inhoffenstrasse 7, Braunschweig 38124, Germany
- Institute
of Microbiology, Technische Universität
Braunschweig, Spielmannstraße
7, Braunschweig 38106, Germany
| | - Jackson M. Muema
- Compound
Profiling and Screening (COPS), Helmholtz
Centre for Infection Research (HZI), Inhoffenstrasse 7, Braunschweig 38124, Germany
| | - Samad Ashrafi
- Institute
for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI)−Federal Research Center
for Cultivated Plants, Messeweg 11-12, Braunschweig 38104, Germany
- Institute
for Crop and Soil Science, Julius Kühn
Institute (JKI)−Federal Research Centre for Cultivated Plants, Bundesallee 58, Braunschweig 38116, Germany
| | - Wolfgang Maier
- Institute
for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI)−Federal Research Center
for Cultivated Plants, Messeweg 11-12, Braunschweig 38104, Germany
| | - Marc Stadler
- Department
of Microbial Drugs, Helmholtz Centre
for Infection Research (HZI) and German Centre for Infection Research, Inhoffenstrasse 7, Braunschweig 38124, Germany
- Institute
of Microbiology, Technische Universität
Braunschweig, Spielmannstraße
7, Braunschweig 38106, Germany
| | - Sherif S. Ebada
- Department
of Microbial Drugs, Helmholtz Centre
for Infection Research (HZI) and German Centre for Infection Research, Inhoffenstrasse 7, Braunschweig 38124, Germany
- Department
of Pharmacognosy, Faculty of Pharmacy, Ain
Shams University, Cairo 11566, Egypt
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46
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Zhang Q, Li H, Jia D, Chen W, Jia X, Lin Q, Zhang J, Tang Y. Protective Effect of Deer Heart Peptide on Cardiac Injury in Mice. Int J Inflam 2024; 2024:6661371. [PMID: 38938287 PMCID: PMC11208793 DOI: 10.1155/2024/6661371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 03/10/2024] [Accepted: 03/20/2024] [Indexed: 06/29/2024] Open
Abstract
Peptides are widely used as natural bio-small molecules because of their various pharmacological activities such as enhancing immunity, promoting wound healing, and improving inflammation. Alcoholic heart injury has become one of the major health problems worldwide, and alcohol consumption is now the main cause of alcoholic cardiomyopathy. In this study, deer heart peptides were extracted from deer hearts by enzymatic digestion and the antioxidant activity of deer heart peptides extracted at different times was evaluated by three in vitro antioxidant methods, and the active peptide with the best enzymatic effect has been selected for in vivo animal experiments. The anti-inflammatory and antioxidant properties of deer heart enzymatic extracts were evaluated in in vivo experiments in mice. In this study, mice were orally gavaged with white wine (12 mL/kg body weight) to induce a mouse model of cardiac injury, while mice were orally administered a single dose of 100 mg/kg/bw and 200 mg/kg/bw of deer heart enzyme digest and were examined for body weight, dietary intake, water intake, and coat gloss, as well as for general behaviors, adverse effects, and mortality. Histology, serum, anti-inflammatory factors, and oxidative stress parameters were subsequently assessed. In all modeled mice, no four-way or any significant behavioral changes were observed in all groups, but in the modeled group, mice showed weight loss, decreased diet and water intake, and decreased cardiac index. For in vivo tests, the extract inhibited the anti-inflammatory activity with a significant decrease in inflammatory factors of TNF-α, IL-6, and IL-1β in cardiac tissues, a significant increase in serum levels of both CAT and SOD, an increase in MDA content, and a remarkable increase in the level of the marker CK in the cardiac myocardial enzyme profile. Significant improvement in myocardial disorders by deer heart peptide could be observed from heart tissue sections. The present study emphasizes the anti-inflammatory and antioxidant activity of deer heart peptide, an enzymatic digest of deer heart, which provides empirical as well as supportive role for the anti-inflammatory properties of traditional medicine.
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Affiliation(s)
- Qun Zhang
- School of Life Sciences, Changchun Sci-Tech University, Changchun 130600, Jilin, China
- Department of Food Science and Nutrition, College of Health Science, Dong-A University, Busan 49315, Republic of Korea
- Jilin Sino-ROK Institute of Animal Science, Changchun 130600, Jilin, China
| | - Hongjin Li
- School of Vocational and Technical Education, Changchun Sci-Tech University, Changchun 130600, Jilin, China
| | - Dongshu Jia
- School of Life Sciences, Changchun Sci-Tech University, Changchun 130600, Jilin, China
| | - Wei Chen
- School of Life Sciences, Changchun Sci-Tech University, Changchun 130600, Jilin, China
| | - Xinao Jia
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Qi Lin
- School of Life Sciences, Changchun Sci-Tech University, Changchun 130600, Jilin, China
| | - Jiyi Zhang
- School of Life Sciences, Changchun Sci-Tech University, Changchun 130600, Jilin, China
| | - Yujiao Tang
- School of Life Sciences, Changchun Sci-Tech University, Changchun 130600, Jilin, China
- Jilin Sino-ROK Institute of Animal Science, Changchun 130600, Jilin, China
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47
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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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48
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Huang J, Xue S, Xie YQ, Teixeira AP, Fussenegger M. Ultrashort-Peptide-Responsive Gene Switches for Regulation of Therapeutic Protein Expression in Mammalian Cells. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2309411. [PMID: 38741284 DOI: 10.1002/advs.202309411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 03/04/2024] [Indexed: 05/16/2024]
Abstract
Despite the array of mammalian transgene switches available for regulating therapeutic protein expression in response to small molecules or physical stimuli, issues remain, including cytotoxicity of chemical inducers and limited biocompatibility of physical cues. This study introduces gene switches driven by short peptides comprising eight or fewer amino acid residues. Utilizing a competence regulator (ComR) and sigma factor X-inducing peptide (XIP) from Streptococcus vestibularis as the receptor and inducer, respectively, this study develops two strategies for a peptide-activated transgene control system. The first strategy involves fusing ComR with a transactivation domain and utilizes ComR-dependent synthetic promoters to drive expression of the gene-of-interest, activated by XIP, thereby confirming its membrane penetrability and intracellular functionality. The second strategy features an orthogonal synthetic receptor exposing ComR extracellularly (ComREXTRA), greatly increasing sensitivity with exceptional responsiveness to short peptides. In a proof-of-concept study, peptides are administered to type-1 diabetic mice with microencapsulated engineered human cells expressing ComREXTRA for control of insulin expression, restoring normoglycemia. It is envisioned that this system will encourage the development of short peptide drugs and promote the introduction of non-toxic, orthogonal, and highly biocompatible personalized biopharmaceuticals for gene- and cell-based therapies.
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Affiliation(s)
- Jinbo Huang
- Department of Biosystems Science and Engineering, ETH Zurich, Klingelbergstrasse 48, Basel, CH-4056, Switzerland
| | - Shuai Xue
- Department of Biosystems Science and Engineering, ETH Zurich, Klingelbergstrasse 48, Basel, CH-4056, Switzerland
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Yu-Qing Xie
- Department of Biosystems Science and Engineering, ETH Zurich, Klingelbergstrasse 48, Basel, CH-4056, Switzerland
| | - Ana Palma Teixeira
- Department of Biosystems Science and Engineering, ETH Zurich, Klingelbergstrasse 48, Basel, CH-4056, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Klingelbergstrasse 48, Basel, CH-4056, Switzerland
- Faculty of Science, University of Basel, Klingelbergstrasse 48, Basel, CH-4056, Switzerland
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49
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Nichols C, Do-Thi VA, Peltier DC. Noncanonical microprotein regulation of immunity. Mol Ther 2024:S1525-0016(24)00324-1. [PMID: 38734902 DOI: 10.1016/j.ymthe.2024.05.021] [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: 02/08/2024] [Revised: 04/19/2024] [Accepted: 05/09/2024] [Indexed: 05/13/2024] Open
Abstract
The immune system is highly regulated but, when dysregulated, suboptimal protective or overly robust immune responses can lead to immune-mediated disorders. The genetic and molecular mechanisms of immune regulation are incompletely understood, impeding the development of more precise diagnostics and therapeutics for immune-mediated disorders. Recently, thousands of previously unrecognized noncanonical microprotein genes encoded by small open reading frames have been identified. Many of these microproteins perform critical functions, often in a cell- and context-specific manner. Several microproteins are now known to regulate immunity; however, the vast majority are uncharacterized. Therefore, illuminating what is often referred to as the "dark proteome," may present opportunities to tune immune responses more precisely. Here, we review noncanonical microprotein biology, highlight recently discovered examples regulating immunity, and discuss the potential and challenges of modulating dysregulated immune responses by targeting microproteins.
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Affiliation(s)
- Cydney Nichols
- Morris Green Scholars Program, Department of Pediatrics, Riley Hospital for Children, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Van Anh Do-Thi
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Daniel C Peltier
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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50
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Akintelu SA, Zhang Q, Yao B. Postassembly Modification of Peptides by Histidine-Directed β-C(sp 3)-H Arylation of Alanine at the Internal Positions: Overcoming the Inhibitory Effect of Peptide Bonds. Org Lett 2024; 26:3991-3996. [PMID: 38691578 DOI: 10.1021/acs.orglett.4c01250] [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
Peptide modification by C(sp3)-H functionalization of residues at the internal positions remains underdeveloped due to the inhibitory effect of backbone amides. In this study, using histidine (His) as an endogenous directing group, we developed a novel method for the β-C(sp3)-H functionalization of alanine (Ala) at diverse positions of peptides. Through this approach, a wide range of linear peptides were modified on the side-chain of Ala adjacent to His to afford the functionalized peptides in moderate to good yield and excellent position selectivity. Furthermore, conjugation of peptides with functional molecules such as glucuronide, oleanolic acid, dipeptide, and fluorophore derivatives was achieved.
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Affiliation(s)
- Sunday A Akintelu
- MOE Key Laboratory of Cluster Science, Beijing Key Laboratory of Photoelectronic-Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, P. R. China
| | - Qi Zhang
- MOE Key Laboratory of Cluster Science, Beijing Key Laboratory of Photoelectronic-Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, P. R. China
| | - Bo Yao
- MOE Key Laboratory of Cluster Science, Beijing Key Laboratory of Photoelectronic-Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, P. R. China
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