1
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Sasaki T, Kasama T, Nokihara K. A novel cyclic peptide library immobilized on gel-type beads focusing on rapid construction and characterization for comprehensive drug discovery. Chem Biol Drug Des 2023; 102:1327-1335. [PMID: 37658589 DOI: 10.1111/cbdd.14331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 09/03/2023]
Abstract
Medium sized molecules such as peptides and macrocycles have recently drawn much attention as potent sources of medicinal lead compounds, whereas the possibility of obtaining a practical drug from them remains limited. The present paper describes a concept of discovering novel medicinal targets or binding modes as well as lead compounds by the one-peptide-on-one-bead (OPOB) technology for comprehensive screening. The difficulty and problems in conventional drug discovery methods that generally deal with one predetermined target are considered. The building blocks used for the present libraries were selected based on previous results in development of peptidic drugs. Each constituent has the common structure of cyclic form prepared by disulfide of cysteinyl residues or thioether linkages, additionally a methionine residue was inserted for the site-specific rapid cleavage by cyanogen bromide to liberate the immobilized peptides allowing reliable characterization by MALDI-TOF-MS/MS without LC-purification. Thus, a high throughput construction method for cyclic peptide libraries as well as characterization of single bead are proposed for drug discovery.
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2
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Maciuba S, Bowden GD, Stratton HJ, Wisniewski K, Schteingart CD, Almagro JC, Valadon P, Lowitz J, Glaser SM, Lee G, Dolatyari M, Navratilova E, Porreca F, Rivière PJ. Discovery and characterization of prolactin neutralizing monoclonal antibodies for the treatment of female-prevalent pain disorders. MAbs 2023; 15:2254676. [PMID: 37698877 PMCID: PMC10498814 DOI: 10.1080/19420862.2023.2254676] [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: 06/05/2023] [Revised: 08/19/2023] [Accepted: 08/30/2023] [Indexed: 09/13/2023] Open
Abstract
Prolactin (PRL) has recently been demonstrated to elicit female-selective nociceptor sensitization and increase pain-like behaviors in female animals. Here we report the discovery and characterization of first-in-class, humanized PRL neutralizing monoclonal antibodies (PRL mAbs). We obtained two potent and selective PRL mAbs, PL 200,031 and PL 200,039. PL 200,031 was engineered as human IgG1 whereas PL 200,039 was reformatted as human IgG4. Both mAbs have sub-nanomolar affinity for human PRL (hPRL) and produce concentration-dependent and complete inhibition of hPRL signaling at the hPRL receptor (hPRLR). These two PRL mAbs are selective for hPRL as they do not inhibit other hPRLR agonists such as human growth hormone or placental lactogen. They also cross-react with non-human primate PRL but not with rodent PRL. Further, both mAbs show long clearance half-lives after intravenous administration in FcRn-humanized mice. Consistent with their isotypes, these mAbs only differ in binding affinities to Fcγ receptors, as expected by design. Finally, PL 200,019, the murine parental mAb of PL 200,031 and PL 200,039, fully blocked stress-induced and PRL-dependent pain behaviors in female PRL-humanized mice, thereby providing in vivo preclinical proof-of-efficacy for PRL mAbs in mechanisms relevant to pain in females.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Grace Lee
- Department of Pharmacology, The University of Arizona, Tucson, AZ, USA
| | - Mahdi Dolatyari
- Department of Pharmacology, The University of Arizona, Tucson, AZ, USA
| | - Edita Navratilova
- Department of Pharmacology, The University of Arizona, Tucson, AZ, USA
| | - Frank Porreca
- Department of Pharmacology, The University of Arizona, Tucson, AZ, USA
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3
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Zhang H, Chen S. Cyclic peptide drugs approved in the last two decades (2001-2021). RSC Chem Biol 2022; 3:18-31. [PMID: 35128405 PMCID: PMC8729179 DOI: 10.1039/d1cb00154j] [Citation(s) in RCA: 101] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 11/05/2021] [Indexed: 01/01/2023] Open
Abstract
In contrast to the major families of small molecules and antibodies, cyclic peptides, as a family of synthesizable macromolecules, have distinct biochemical and therapeutic properties for pharmaceutical applications. Cyclic peptide-based drugs have increasingly been developed in the past two decades, confirming the common perception that cyclic peptides have high binding affinities and low metabolic toxicity as antibodies, good stability and ease of manufacture as small molecules. Natural peptides were the major source of cyclic peptide drugs in the last century, and cyclic peptides derived from novel screening and cyclization strategies are the new source. In this review, we will discuss and summarize 18 cyclic peptides approved for clinical use in the past two decades to provide a better understanding of cyclic peptide development and to inspire new perspectives. The purpose of the present review is to promote efforts to resolve the challenges in the development of cyclic peptide drugs that are more effective.
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Affiliation(s)
- Huiya Zhang
- Biotech Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
| | - Shiyu Chen
- Biotech Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai 201203 China
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4
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Furukawa A, Schwochert J, Pye CR, Asano D, Edmondson QD, Turmon AC, Klein VG, Ono S, Okada O, Lokey RS. Drug-Like Properties in Macrocycles above MW 1000: Backbone Rigidity versus Side-Chain Lipophilicity. Angew Chem Int Ed Engl 2020; 59:21571-21577. [PMID: 32789999 PMCID: PMC7719619 DOI: 10.1002/anie.202004550] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 06/10/2020] [Indexed: 12/22/2022]
Abstract
Large macrocyclic peptides can achieve surprisingly high membrane permeability, although the properties that govern permeability in this chemical space are only beginning to come into focus. We generated two libraries of cyclic decapeptides with stable cross-β conformations, and found that peptoid substitutions within the β-turns of the macrocycle preserved the rigidity of the parent scaffold, whereas peptoid substitutions in the opposing β-strands led to "chameleonic" species that were rigid in nonpolar media but highly flexible in water. Both rigid and chameleonic compounds showed high permeability over a wide lipophilicity range, with peak permeabilities differing significantly depending on scaffold rigidity. Our findings indicate that modulating lipophilicity can be used to engineer favorable ADME properties into both rigid and flexible macrocyclic peptides, and that scaffold rigidity can be used to tune optimal lipophilicity.
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Affiliation(s)
- Akihiro Furukawa
- Daiichi Sankyo Co., Ltd., 1-2-58, Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Joshua Schwochert
- Unnatural Products, Inc., 250 Natural Bridges Drive, Santa Cruz, CA 95060 USA
| | - Cameron R. Pye
- Unnatural Products, Inc., 250 Natural Bridges Drive, Santa Cruz, CA 95060 USA
| | - Daigo Asano
- Daiichi Sankyo Co., Ltd., 1-2-58, Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Quinn D. Edmondson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, USA
| | - Alexandra C. Turmon
- Unnatural Products, Inc., 250 Natural Bridges Drive, Santa Cruz, CA 95060 USA
| | - Victoria G. Klein
- Department of Chemistry & Biochemistry, University of California Santa Cruz, Santa Cruz, CA 96064 USA
| | - Satoshi Ono
- Discovery Technology Laboratories, Mitsubishi Tanabe Pharma Corporation, Yokohama, 227-0033, Japan
| | - Okimasa Okada
- Discovery Technology Laboratories, Mitsubishi Tanabe Pharma Corporation, Yokohama, 227-0033, Japan
| | - R. Scott Lokey
- Department of Chemistry & Biochemistry, University of California Santa Cruz, Santa Cruz, CA 96064 USA
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5
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Asad AS, Nicola Candia AJ, Gonzalez N, Zuccato CF, Seilicovich A, Candolfi M. The role of the prolactin receptor pathway in the pathogenesis of glioblastoma: what do we know so far? Expert Opin Ther Targets 2020; 24:1121-1133. [PMID: 32896197 DOI: 10.1080/14728222.2020.1821187] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Introduction: Prolactin (PRL) and its receptor (PRLR) have been associated with the development of hormone-dependent tumors and have been detected in glioblastoma (GBM) biopsies. GBM is the most common and aggressive primary brain tumor in adults and the prognosis for patients is dismal; hence researchers are exploring the PRLR pathway as a therapeutic target in this disease. Areas covered: This paper explores the effects of PRLR activation on the biology of GBM, the correlation between PRL and PRLR expression and GBM progression and survival in male and female patients. Finally, we discuss how a better understanding of the PRLR pathway may allow the development of novel treatments for GBM. Expert opinion: We propose PRL and PRLR as potential prognosis biomarkers and therapeutic targets in GBM. Local administration of PRLR inhibitors using gene therapy may offer a beneficial strategy for targeting GBM cells disseminated in the non-neoplastic brain; however, efficacy and safety require careful and extensive evaluation. The data depicted herein underline the need to (i) improve our understanding of sexual dimorphism in GBM, and (ii) develop accurate preclinical models that take into consideration different hormonal contexts, specific genetic alterations, and tumor grades.
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Affiliation(s)
- Antonela S Asad
- Instituto de Investigaciones Biomédicas (INBIOMED, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires , Buenos Aires, Argentina
| | - Alejandro J Nicola Candia
- Instituto de Investigaciones Biomédicas (INBIOMED, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires , Buenos Aires, Argentina
| | - Nazareno Gonzalez
- Instituto de Investigaciones Biomédicas (INBIOMED, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires , Buenos Aires, Argentina
| | - Camila F Zuccato
- Instituto de Investigaciones Biomédicas (INBIOMED, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires , Buenos Aires, Argentina
| | - Adriana Seilicovich
- Instituto de Investigaciones Biomédicas (INBIOMED, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires , Buenos Aires, Argentina.,departamento de Biología Celular e Histología, Facultad de Medicina, Universidad de Buenos Aires , Buenos Aires, Argentina
| | - Marianela Candolfi
- Instituto de Investigaciones Biomédicas (INBIOMED, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires , Buenos Aires, Argentina
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6
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Furukawa A, Schwochert J, Pye CR, Asano D, Edmondson QD, Turmon AC, Klein VG, Ono S, Okada O, Lokey RS. Drug‐Like Properties in Macrocycles above MW 1000: Backbone Rigidity versus Side‐Chain Lipophilicity. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004550] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Akihiro Furukawa
- Daiichi Sankyo Co., Ltd. 1-2-58, Hiromachi, Shinagawa-ku Tokyo 140-8710 Japan
| | - Joshua Schwochert
- Unnatural Products, Inc. 250 Natural Bridges Drive Santa Cruz CA 95060 USA
| | - Cameron R. Pye
- Unnatural Products, Inc. 250 Natural Bridges Drive Santa Cruz CA 95060 USA
| | - Daigo Asano
- Daiichi Sankyo Co., Ltd. 1-2-58, Hiromachi, Shinagawa-ku Tokyo 140-8710 Japan
| | - Quinn D. Edmondson
- Department of Pharmaceutical Chemistry University of California, San Francisco San Francisco California 94158 USA
| | | | - Victoria G. Klein
- Department of Chemistry & Biochemistry University of California Santa Cruz Santa Cruz CA 96064 USA
| | - Satoshi Ono
- Discovery Technology Laboratories Mitsubishi Tanabe Pharma Corporation Yokohama 227-0033 Japan
| | - Okimasa Okada
- Discovery Technology Laboratories Mitsubishi Tanabe Pharma Corporation Yokohama 227-0033 Japan
| | - R. Scott Lokey
- Department of Chemistry & Biochemistry University of California Santa Cruz Santa Cruz CA 96064 USA
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Shinbara K, Liu W, van Neer RHP, Katoh T, Suga H. Methodologies for Backbone Macrocyclic Peptide Synthesis Compatible With Screening Technologies. Front Chem 2020; 8:447. [PMID: 32626683 PMCID: PMC7314982 DOI: 10.3389/fchem.2020.00447] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 04/28/2020] [Indexed: 12/23/2022] Open
Abstract
Backbone macrocyclic structures are often found in diverse bioactive peptides and contribute to greater conformational rigidity, peptidase resistance, and potential membrane permeability compared to their linear counterparts. Therefore, such peptide scaffolds are an attractive platform for drug-discovery endeavors. Recent advances in synthetic methods for backbone macrocyclic peptides have enabled the discovery of novel peptide drug candidates against diverse targets. Here, we overview recent technical advancements in the synthetic methods including 1) enzymatic synthesis, 2) chemical synthesis, 3) split-intein circular ligation of peptides and proteins (SICLOPPS), and 4) in vitro translation system combined with genetic code reprogramming. We also discuss screening methodologies compatible with those synthetic methodologies, such as one-beads one-compound (OBOC) screening compatible with the synthetic method 2, cell-based assay compatible with 3, limiting-dilution PCR and mRNA display compatible with 4.
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Affiliation(s)
| | | | | | | | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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Nagano M, Suga H. Expansion of Modality: Peptides to Pseudo-Natural Macrocyclic Peptides. J SYN ORG CHEM JPN 2020. [DOI: 10.5059/yukigoseikyokaishi.78.516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo
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9
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Dandawate P, Kaushik G, Ghosh C, Standing D, Sayed AAA, Choudhury S, Subramaniam D, Manzardo A, Banerjee T, Santra S, Ramamoorthy P, Butler M, Padhye SB, Baranda J, Kasi A, Sun W, Tawfik O, Coppola D, Malafa M, Umar S, Soares MJ, Saha S, Weir SJ, Dhar A, Jensen RA, Thomas SM, Anant S. Diphenylbutylpiperidine Antipsychotic Drugs Inhibit Prolactin Receptor Signaling to Reduce Growth of Pancreatic Ductal Adenocarcinoma in Mice. Gastroenterology 2020; 158:1433-1449.e27. [PMID: 31786131 PMCID: PMC7103550 DOI: 10.1053/j.gastro.2019.11.279] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 11/04/2019] [Accepted: 11/19/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Prolactin (PRL) signaling is up-regulated in hormone-responsive cancers. The PRL receptor (PRLR) is a class I cytokine receptor that signals via the Janus kinase (JAK)-signal transducer and activator of transcription and mitogen-activated protein kinase pathways to regulate cell proliferation, migration, stem cell features, and apoptosis. Patients with pancreatic ductal adenocarcinoma (PDAC) have high plasma levels of PRL. We investigated whether PRLR signaling contributes to the growth of pancreatic tumors in mice. METHODS We used immunohistochemical analyses to compare levels of PRL and PRLR in multitumor tissue microarrays. We used structure-based virtual screening and fragment-based drug discovery to identify compounds likely to bind PRLR and interfere with its signaling. Human pancreatic cell lines (AsPC-1, BxPC-3, Panc-1, and MiaPaCa-2), with or without knockdown of PRLR (clustered regularly interspaced short palindromic repeats or small hairpin RNA), were incubated with PRL or penfluridol and analyzed in proliferation and spheroid formation. C57BL/6 mice were given injections of UNKC-6141 cells, with or without knockdown of PRLR, into pancreas, and tumor development was monitored for 4 weeks, with some mice receiving penfluridol treatment for 21 days. Human pancreatic tumor tissues were implanted into interscapular fat pads of NSG mice, and mice were given injections of penfluridol daily for 28 days. Nude mice were given injections of Panc-1 cells, xenograft tumors were grown for 2 weeks, and mice were then given intraperitoneal penfluridol for 35 days. Tumors were collected from mice and analyzed by histology, immunohistochemistry, and immunoblots. RESULTS Levels of PRLR were increased in PDAC compared with nontumor pancreatic tissues. Incubation of pancreatic cell lines with PRL activated signaling via JAK2-signal transducer and activator of transcription 3 and extracellular signal-regulated kinase, as well as formation of pancospheres and cell migration; these activities were not observed in cells with PRLR knockdown. Pancreatic cancer cells with PRLR knockdown formed significantly smaller tumors in mice. We identified several diphenylbutylpiperidine-class antipsychotic drugs as agents that decreased PRL-induced JAK2 signaling; incubation of pancreatic cancer cells with these compounds reduced their proliferation and formation of panco spheres. Injections of 1 of these compounds, penfluridol, slowed the growth of xenograft tumors in the different mouse models, reducing proliferation and inducing autophagy of the tumor cells. CONCLUSIONS Levels of PRLR are increased in PDAC, and exposure to PRL increases proliferation and migration of pancreatic cancer cells. Antipsychotic drugs, such as penfluridol, block PRL signaling in pancreatic cancer cells to reduce their proliferation, induce autophagy, and slow the growth of xenograft tumors in mice. These drugs might be tested in patients with PDAC.
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Affiliation(s)
- Prasad Dandawate
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160
| | - Gaurav Kaushik
- Department of Surgery, University of Kansas Medical Center, Kansas City, KS 66160
| | - Chandrayee Ghosh
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160
| | - David Standing
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160
| | - Afreen Asif Ali Sayed
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160
| | - Sonali Choudhury
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160
| | | | - Ann Manzardo
- Department of Psychiatry and Behavioral Sciences, University of Kansas Medical Center, Kansas City, KS 66160
| | - Tuhina Banerjee
- Department of Chemistry, Pittsburg State University, Pittsburg, KS 66762, USA
| | - Santimukul Santra
- Department of Chemistry, Pittsburg State University, Pittsburg, KS 66762, USA
| | - Prabhu Ramamoorthy
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160
| | - Merlin Butler
- Department of Psychiatry and Behavioral Sciences, University of Kansas Medical Center, Kansas City, KS 66160
| | - Subhash B. Padhye
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, Interdisciplinary Science and Technology Research Academy, Abeda Inamdar College, University of Pune, Pune 411001
| | - Joaquina Baranda
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS 66160
| | - Anup Kasi
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS 66160
| | - Weijing Sun
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS 66160
| | - Ossama Tawfik
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160
| | - Domenico Coppola
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612
| | - Mokenge Malafa
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612
| | - Shahid Umar
- Department of Surgery, University of Kansas Medical Center, Kansas City, KS 66160
| | - Michael J. Soares
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS 66160, Department of Pediatrics, University of Kansas Medical Center, Kansas City, KS 66160, Center for Perinatal Research, Children’s Research Institute, Children’s Mercy-Kansas City, MO 64108
| | - Subhrajit Saha
- Department of Radiation Oncology, University of Kansas Medical Center, Kansas City, KS 66160
| | - Scott J. Weir
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, KS 66160
| | - Animesh Dhar
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160
| | - Roy A. Jensen
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160
| | - Sufi Mary Thomas
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, Department of Otolaryngology, University of Kansas Medical Center, Kansas City, KS 66160
| | - Shrikant Anant
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas; Department of Surgery, University of Kansas Medical Center, Kansas City, Kansas; Interdisciplinary Science and Technology Research Academy, Abeda Inamdar College, University of Pune, Pune.
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10
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Asif K, O'Brien GL, Goodman SM, Suwal S. Solid phase syntheses of peptoid like arylureido compounds and sequencing of isobars without molecular encoding. Org Biomol Chem 2019; 17:4204-4207. [PMID: 30938397 DOI: 10.1039/c9ob00205g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Arylureido-backbone containing peptoid-like trimers were prepared using the one-bead-one-compound approach. Isobaric molecules were synthesized from isocyanate precursors that contain alkyl halide handles at the ortho and para-positions in the phenyl ring. After chain extension with a primary amine, the piperazine-capped molecules were sequenced using tandem mass spectrometry and successfully identified based on their fragmentation pattern without a need for internal molecular encoding.
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Affiliation(s)
- Kanwal Asif
- Department of Chemistry, SUNY Buffalo State, 1300 Elmwood Ave, Buffalo, NY 14222, USA.
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11
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Iegre J, Gaynord JS, Robertson NS, Sore HF, Hyvönen M, Spring DR. Two-Component Stapling of Biologically Active and Conformationally Constrained Peptides: Past, Present, and Future. ADVANCED THERAPEUTICS 2018. [DOI: 10.1002/adtp.201800052] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Jessica Iegre
- Department of Chemistry; University of Cambridge; Cambridge CB2 1EW UK
| | | | | | - Hannah F. Sore
- Department of Chemistry; University of Cambridge; Cambridge CB2 1EW UK
| | - Marko Hyvönen
- Department of Biochemistry; University of Cambridge; Cambridge CB2 1GA UK
| | - David R. Spring
- Department of Chemistry; University of Cambridge; Cambridge CB2 1EW UK
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12
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Kish WS, Roach MK, Sachi H, Naik AD, Menegatti S, Carbonell RG. Purification of human erythropoietin by affinity chromatography using cyclic peptide ligands. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1085:1-12. [DOI: 10.1016/j.jchromb.2018.03.039] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 03/12/2018] [Accepted: 03/24/2018] [Indexed: 10/17/2022]
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13
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Kish WS, Sachi H, Naik AD, Roach MK, Bobay BG, Blackburn RK, Menegatti S, Carbonell RG. Design, selection, and development of cyclic peptide ligands for human erythropoietin. J Chromatogr A 2017; 1500:105-120. [DOI: 10.1016/j.chroma.2017.04.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/28/2017] [Accepted: 04/10/2017] [Indexed: 11/26/2022]
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14
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Donald JR, Unsworth WP. Ring-Expansion Reactions in the Synthesis of Macrocycles and Medium-Sized Rings. Chemistry 2017; 23:8780-8799. [DOI: 10.1002/chem.201700467] [Citation(s) in RCA: 147] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Indexed: 01/20/2023]
Affiliation(s)
- James R. Donald
- Department of Chemistry; University of York; Heslington, York YO10 5DD UK
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15
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Wu H, An H, Mo SC, Kodadek T. Asymmetric synthesis of vinylogous β-amino acids and their incorporation into mixed backbone oligomers. Org Biomol Chem 2017; 15:3255-3264. [PMID: 28346549 PMCID: PMC7243482 DOI: 10.1039/c7ob00333a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chiral vinylogous β-amino acids (VBAA) were synthesized using enantioselective Mannich reactions of aldehydes with in situ generated N-carbamoyl imines followed by a Horner-Wadsworth-Emmons reaction. The efficiency with which these units could be incorporated into oligomers with different moieties on the C- and N-terminal sides was established, as was the feasibility of sequencing oligomers containing VBAAs by tandem mass spectrometry. The data show that VBAAs will be useful building blocks for the construction of combinatorial libraries of peptidomimetic compounds.
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Affiliation(s)
- Hao Wu
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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16
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Morimoto J, Kodadek T. Synthesis of a large library of macrocyclic peptides containing multiple and diverse N-alkylated residues. MOLECULAR BIOSYSTEMS 2016; 11:2770-9. [PMID: 26067000 DOI: 10.1039/c5mb00308c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Large combinatorial libraries of macrocyclic peptides are a useful source of bioactive compounds. However, peptides are not generally cell permeable, so there is great interest in the development of methods to create large libraries of modified peptides. In particular, N-alkylation of peptides is known to improve their bioavailability significantly. Incorporation of some level of N-methylated amino acids into peptide libraries has been accomplished with ribosome display or related methods, but the modest efficiency and the inability to employ more diverse N-alkylated amino acids in this type of system argue for the development of synthetic libraries. Here we present optimized procedures for synthesizing macrocyclic peptides containing multiple N-alkylated units and show that this chemistry is efficient enough for the creation of high quality combinatorial libraries by split and pool solid-phase synthesis.
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Affiliation(s)
- Jumpei Morimoto
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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17
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Camperi SA, Giudicessi SL, Martínez‐Ceron MC, Gurevich‐Messina JM, Saavedra SL, Acosta G, Cascone O, Erra‐Balsells R, Albericio F. Combinatorial Library Screening Coupled to Mass Spectrometry to Identify Valuable Cyclic Peptides. ACTA ACUST UNITED AC 2016; 8:109-130. [DOI: 10.1002/cpch.2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Silvia A. Camperi
- NANOBIOTEC Institute, UBA‐CONICET, Cathedra of Biotechnology, School of Pharmacy and Biochemistry, University of Buenos Aires Buenos Aires Argentina
- National Scientific and Technological Research Council (CONICET) Buenos Aires Argentina
| | - Silvana L. Giudicessi
- NANOBIOTEC Institute, UBA‐CONICET, Cathedra of Biotechnology, School of Pharmacy and Biochemistry, University of Buenos Aires Buenos Aires Argentina
- National Scientific and Technological Research Council (CONICET) Buenos Aires Argentina
| | - María C. Martínez‐Ceron
- NANOBIOTEC Institute, UBA‐CONICET, Cathedra of Biotechnology, School of Pharmacy and Biochemistry, University of Buenos Aires Buenos Aires Argentina
- National Scientific and Technological Research Council (CONICET) Buenos Aires Argentina
| | - Juan M. Gurevich‐Messina
- NANOBIOTEC Institute, UBA‐CONICET, Cathedra of Biotechnology, School of Pharmacy and Biochemistry, University of Buenos Aires Buenos Aires Argentina
- National Scientific and Technological Research Council (CONICET) Buenos Aires Argentina
| | - Soledad L. Saavedra
- NANOBIOTEC Institute, UBA‐CONICET, Cathedra of Biotechnology, School of Pharmacy and Biochemistry, University of Buenos Aires Buenos Aires Argentina
| | - Gerardo Acosta
- Department of Organic Chemistry, Barcelona Science Park, University of Barcelona Barcelona Spain
- CIBER‐BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park Barcelona Spain
| | - Osvaldo Cascone
- NANOBIOTEC Institute, UBA‐CONICET, Cathedra of Biotechnology, School of Pharmacy and Biochemistry, University of Buenos Aires Buenos Aires Argentina
- National Scientific and Technological Research Council (CONICET) Buenos Aires Argentina
| | - Rosa Erra‐Balsells
- National Scientific and Technological Research Council (CONICET) Buenos Aires Argentina
- CIHDECAR‐CONICET, Department of Organic Chemistry, School of Exact and Natural Sciences, University of Buenos Aires Buenos Aires Argentina
| | - Fernando Albericio
- Department of Organic Chemistry, Barcelona Science Park, University of Barcelona Barcelona Spain
- CIBER‐BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park Barcelona Spain
- School of Chemistry & Physics, University of Kwazulu‐Natal Durban South Africa
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18
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Kitsiou C, Hindes JJ, I'Anson P, Jackson P, Wilson TC, Daly EK, Felstead HR, Hearnshaw P, Unsworth WP. The Synthesis of Structurally Diverse Macrocycles By Successive Ring Expansion. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201509153] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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19
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Kitsiou C, Hindes JJ, I'Anson P, Jackson P, Wilson TC, Daly EK, Felstead HR, Hearnshaw P, Unsworth WP. The Synthesis of Structurally Diverse Macrocycles By Successive Ring Expansion. Angew Chem Int Ed Engl 2015; 54:15794-8. [PMID: 26768697 DOI: 10.1002/anie.201509153] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 10/28/2015] [Indexed: 11/10/2022]
Abstract
Structurally diverse macrocycles and medium-sized rings (9-24 membered scaffolds, 22 examples) can be generated through a telescoped acylation/ring-expansion sequence, leading to the insertion of linear fragments into cyclic β-ketoesters without performing a discrete macrocyclization step. The key β-ketoester motif is regenerated in the ring-expanded product, meaning that the same sequence of steps can then be repeated (in theory indefinitely) with other linear fragments, allowing macrocycles with precise substitution patterns to be "grown" from smaller rings using the successive ring-expansion (SuRE) method.
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20
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Mendes K, Ndungu JM, Clark LF, Kodadek T. Optimization of the Magnetic Recovery of Hits from One-Bead-One-Compound Library Screens. ACS COMBINATORIAL SCIENCE 2015. [PMID: 26221913 DOI: 10.1021/acscombsci.5b00090] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
On-bead screening of one-bead-one-compound (OBOC) libraries is a useful procedure for the identification of protein ligands. An important aspect of this experiment is the method by which beads that bind the target protein are separated from those that do not. Ideally, such a method would be rapid and convenient and result in the isolation of 100% of the "hits" with no false positives (beads that display compounds that are not good ligands for the target). We introduced a technique in which beads that have bound a labeled target protein can be magnetized, thus allowing their convenient isolation ( Astle et al. Chem. Biol. 2010 , 17 , 38 - 45 ). However, recent work in our laboratory and others has shown that magnetic hit recovery can result in the isolation of large numbers of false positives and has also suggested that many true hit beads are missed. In this study, we employ a well-defined model system to examine the efficiency of various magnetic hit isolation protocols. We show that the choice of reagents and the particular operations employed are critical for optimal results.
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Affiliation(s)
- Kimberly Mendes
- Opko Health, Inc., RF Building, Jupiter, Florida 33458, United States
| | - J. M. Ndungu
- Opko Health, Inc., RF Building, Jupiter, Florida 33458, United States
| | - Lorraine F. Clark
- Departments
of Chemistry and Cancer Biology, The Scripps Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United States
| | - Thomas Kodadek
- Departments
of Chemistry and Cancer Biology, The Scripps Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United States
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21
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Jee JE, Lim J, Hyun H, Oon J, Ong YS, Massif C, Chang YT, Choi HS, Lee SS. Investigating fluorescent dyes in fluorescence-assisted screenings. Chem Commun (Camb) 2015; 50:15220-3. [PMID: 25340456 DOI: 10.1039/c4cc07008a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Screening of bead-based peptide libraries against fluorescent dye-labeled target proteins was found to be significantly influenced by the dye characteristics. Commercially available red fluorescent dyes with net negative charges adversely showed strong interactions with library beads. The introduction of zwitterionic dyes significantly reduced the unwanted interactions, which sheds light upon using the right fluorescent probe for acquisition of reliable results in various fluorescence-assisted applications.
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Affiliation(s)
- Joo-Eun Jee
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669.
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22
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Schwochert J, Turner R, Thang M, Berkeley RF, Ponkey AR, Rodriguez KM, Leung SSF, Khunte B, Goetz G, Limberakis C, Kalgutkar AS, Eng H, Shapiro MJ, Mathiowetz AM, Price DA, Liras S, Jacobson MP, Lokey RS. Peptide to Peptoid Substitutions Increase Cell Permeability in Cyclic Hexapeptides. Org Lett 2015; 17:2928-31. [PMID: 26046483 DOI: 10.1021/acs.orglett.5b01162] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The effect of peptide-to-peptoid substitutions on the passive membrane permeability of an N-methylated cyclic hexapeptide is examined. In general, substitutions maintained permeability but increased conformational heterogeneity. Diversification with nonproteinogenic side chains increased permeability up to 3-fold. Additionally, the conformational impact of peptoid substitutions within a β-turn are explored. Based on these results, the strategic incorporation of peptoid residues into cyclic peptides can maintain or improve cell permeability, while increasing access to diverse side-chain functionality.
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Affiliation(s)
- Joshua Schwochert
- †Chemistry and Biochemistry University of California, Santa Cruz, California 95064, United States
| | - Rushia Turner
- †Chemistry and Biochemistry University of California, Santa Cruz, California 95064, United States
| | - Melissa Thang
- †Chemistry and Biochemistry University of California, Santa Cruz, California 95064, United States
| | - Ray F Berkeley
- †Chemistry and Biochemistry University of California, Santa Cruz, California 95064, United States
| | - Alexandra R Ponkey
- †Chemistry and Biochemistry University of California, Santa Cruz, California 95064, United States
| | - Kelsie M Rodriguez
- †Chemistry and Biochemistry University of California, Santa Cruz, California 95064, United States
| | - Siegfried S F Leung
- ‡Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Bhagyashree Khunte
- ∥World Wide Medicinal Chemistry, Groton Laboratories, Pfizer Inc. Groton, Connecticut 06340, United States
| | - Gilles Goetz
- ∥World Wide Medicinal Chemistry, Groton Laboratories, Pfizer Inc. Groton, Connecticut 06340, United States
| | - Chris Limberakis
- ∥World Wide Medicinal Chemistry, Groton Laboratories, Pfizer Inc. Groton, Connecticut 06340, United States
| | - Amit S Kalgutkar
- §Pharmacokinetics and Drug Metabolism, Cambridge Laboratories, Pfizer Inc. Cambridge, Massachusetts 02139, United States
| | - Heather Eng
- ⊥Pharmacokinetics and Drug Metabolism, Groton Laboratories, Pfizer Inc. Groton, Connecticut 06340, United States
| | - Michael J Shapiro
- ∥World Wide Medicinal Chemistry, Groton Laboratories, Pfizer Inc. Groton, Connecticut 06340, United States
| | - Alan M Mathiowetz
- ○World Wide Medicinal Chemistry, Cambridge Laboratories, Pfizer Inc. Cambridge, Massachusetts 02139, United States
| | - David A Price
- ○World Wide Medicinal Chemistry, Cambridge Laboratories, Pfizer Inc. Cambridge, Massachusetts 02139, United States
| | - Spiros Liras
- ○World Wide Medicinal Chemistry, Cambridge Laboratories, Pfizer Inc. Cambridge, Massachusetts 02139, United States
| | - Matthew P Jacobson
- ‡Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - R Scott Lokey
- †Chemistry and Biochemistry University of California, Santa Cruz, California 95064, United States
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23
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Giguère S, Laviolette F, Marchand M, Tremblay D, Moineau S, Liang X, Biron É, Corbeil J. Machine learning assisted design of highly active peptides for drug discovery. PLoS Comput Biol 2015; 11:e1004074. [PMID: 25849257 PMCID: PMC4388847 DOI: 10.1371/journal.pcbi.1004074] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 12/05/2014] [Indexed: 01/15/2023] Open
Abstract
The discovery of peptides possessing high biological activity is very challenging due to the enormous diversity for which only a minority have the desired properties. To lower cost and reduce the time to obtain promising peptides, machine learning approaches can greatly assist in the process and even partly replace expensive laboratory experiments by learning a predictor with existing data or with a smaller amount of data generation. Unfortunately, once the model is learned, selecting peptides having the greatest predicted bioactivity often requires a prohibitive amount of computational time. For this combinatorial problem, heuristics and stochastic optimization methods are not guaranteed to find adequate solutions. We focused on recent advances in kernel methods and machine learning to learn a predictive model with proven success. For this type of model, we propose an efficient algorithm based on graph theory, that is guaranteed to find the peptides for which the model predicts maximal bioactivity. We also present a second algorithm capable of sorting the peptides of maximal bioactivity. Extensive analyses demonstrate how these algorithms can be part of an iterative combinatorial chemistry procedure to speed up the discovery and the validation of peptide leads. Moreover, the proposed approach does not require the use of known ligands for the target protein since it can leverage recent multi-target machine learning predictors where ligands for similar targets can serve as initial training data. Finally, we validated the proposed approach in vitro with the discovery of new cationic antimicrobial peptides. Source code freely available at http://graal.ift.ulaval.ca/peptide-design/. Part of the complexity of drug discovery is the sheer chemical diversity to explore combined to all requirements a compound must meet to become a commercial drug. Hence, it makes sense to automate this chemical exploration endeavor in a wise, informed, and efficient fashion. Here, we focused on peptides as they have properties that make them excellent drug starting points. Machine learning techniques may replace expensive in-vitro laboratory experiments by learning an accurate model of it. However, computational models also suffer from the combinatorial explosion due to the enormous chemical diversity. Indeed, applying the model to every peptides would take an astronomical amount of computer time. Therefore, given a model, is it possible to determine, using reasonable computational time, the peptide that has the best properties and chance for success? This exact question is what motivated our work. We focused on recent advances in kernel methods and machine learning to learn a model that already had excellent results. We demonstrate that this class of model has mathematical properties that makes it possible to rapidly identify and sort the best peptides. Finally, in-vitro and in-silico results are provided to support and validate this theoretical discovery.
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Affiliation(s)
- Sébastien Giguère
- Department of Computer Science and Software Engineering, Université Laval, Québec, Canada
- * E-mail:
| | - François Laviolette
- Department of Computer Science and Software Engineering, Université Laval, Québec, Canada
| | - Mario Marchand
- Department of Computer Science and Software Engineering, Université Laval, Québec, Canada
| | - Denise Tremblay
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, Canada
| | - Sylvain Moineau
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, Canada
| | - Xinxia Liang
- Faculty of Pharmacy, Université Laval, Québec, Canada
| | - Éric Biron
- Faculty of Pharmacy, Université Laval, Québec, Canada
| | - Jacques Corbeil
- Department of Molecular Medicine, Université Laval, Québec, Canada
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24
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Foster AD, Ingram JD, Leitch EK, Lennard KR, Osher EL, Tavassoli A. Methods for the Creation of Cyclic Peptide Libraries for Use in Lead Discovery. ACTA ACUST UNITED AC 2015; 20:563-76. [DOI: 10.1177/1087057114566803] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 12/11/2014] [Indexed: 12/23/2022]
Abstract
The identification of initial hits is a crucial stage in the drug discovery process. Although many projects adopt high-throughput screening of small-molecule libraries at this stage, there is significant potential for screening libraries of macromolecules created using chemical biology approaches. Not only can the production of the library be directly interfaced with a cell-based assay, but these libraries also require significantly fewer resources to generate and maintain. In this context, cyclic peptides are increasingly viewed as ideal scaffolds and have proven capability against challenging targets such as protein-protein interactions. Here we discuss a range of methods used for the creation of cyclic peptide libraries and detail examples of their successful implementation.
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Affiliation(s)
| | | | | | | | | | - Ali Tavassoli
- Chemistry, University of Southampton, Southampton, UK
- Cancer Sciences, University of Southampton, Southampton, UK
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25
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Hewitt WM, Leung SSF, Pye CR, Ponkey AR, Bednarek M, Jacobson MP, Lokey RS. Cell-Permeable Cyclic Peptides from Synthetic Libraries Inspired by Natural Products. J Am Chem Soc 2015; 137:715-21. [DOI: 10.1021/ja508766b] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- William M. Hewitt
- Department
of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Siegfried S. F. Leung
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, United States
| | - Cameron R. Pye
- Department
of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Alexandra R. Ponkey
- Department
of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - Maria Bednarek
- Department of Antibody Discovery & Protein Engineering, Medimmune Ltd., Cambridge CB21 6GH, U.K
| | - Matthew P. Jacobson
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, United States
| | - R. Scott Lokey
- Department
of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
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26
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Joo SH. Cyclic peptides as therapeutic agents and biochemical tools. Biomol Ther (Seoul) 2014; 20:19-26. [PMID: 24116270 PMCID: PMC3792197 DOI: 10.4062/biomolther.2012.20.1.019] [Citation(s) in RCA: 218] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 10/10/2011] [Accepted: 10/28/2011] [Indexed: 01/08/2023] Open
Abstract
There are many cyclic peptides with diverse biological activities, such as antibacterial activity, immunosuppressive activity, and anti-tumor activity, and so on. Encouraged by natural cyclic peptides with biological activity, efforts have been made to develop cyclic peptides with both genetic and synthetic methods. The genetic methods include phage display, intein-based cyclic peptides, and mRNA display. The synthetic methods involve individual synthesis, parallel synthesis, as well as split-and-pool synthesis. Recent development of cyclic peptide library based on split-and-pool synthesis allows on-bead screening, in-solution screening, and microarray screening of cyclic peptides for biological activity. Cyclic peptides will be useful as receptor agonist/antagonist, RNA binding molecule, enzyme inhibitor and so on, and more cyclic peptides will emerge as therapeutic agents and biochemical tools.
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Affiliation(s)
- Sang Hoon Joo
- Laboratory of Biochemistry, College of Pharmacy, Catholic University of Daegu, Gyeongsan 712-702, Republic of Korea
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27
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The hidden potential of small synthetic molecules and peptides as affinity ligands for bioseparations. ACTA ACUST UNITED AC 2013. [DOI: 10.4155/pbp.13.54] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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28
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Giudicessi SL, Gurevich-Messina JM, Martínez-Ceron MC, Erra-Balsells R, Albericio F, Cascone O, Camperi SA. Friendly strategy to prepare encoded one bead-one compound cyclic peptide library. ACS COMBINATORIAL SCIENCE 2013; 15:525-9. [PMID: 23971518 DOI: 10.1021/co400039a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
One bead-one peptide libraries allow the screening of suitable ligands for any target protein. Short cyclic peptides are ideal ligands for affinity chromatography because of their high affinity and selectivity for the target protein and stability against proteases. We designed a library synthesis strategy to facilitate the identification of cyclic peptides by MS consisting of (a) sequential incorporation of a mixture of Fmoc-Ala-OH and Fmoc-Asp[2-phenylisopropyl (OPp)]-OH (15:85) to Gly-oxymethylbenzamide-ChemMatrix (Gly-HMBA-CM) resin, (b) synthesis of the combinatorial library on the resin by the divide-couple-recombine method, (c) removal of OPp with 4% TFA, (d) peptide cyclization on solid phase through side-chain Asp and amino terminus, and (e) removal of side chain protecting groups with a 95% TFA cocktail. Peptides were cleaved from the beads with ammonia and the linear code was sequenced by MALDI-TOF MS/MS. The high capacity of ChemMatrix resin together with the sensitivity of MS allows code sequencing from a single bead.
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Affiliation(s)
- Silvana L. Giudicessi
- Cathedra of Industrial Microbiology and Biotechnology, School of Pharmacy and Biochemistry, University of Buenos Aires, Junín 956, (1113) Buenos Aires, Argentina
- National Scientific and Technological Research Council (CONICET), Rivadavia 1917, (1033) Buenos Aires, Argentina
| | - Juan M. Gurevich-Messina
- Cathedra of Industrial Microbiology and Biotechnology, School of Pharmacy and Biochemistry, University of Buenos Aires, Junín 956, (1113) Buenos Aires, Argentina
| | - María C. Martínez-Ceron
- Cathedra of Industrial Microbiology and Biotechnology, School of Pharmacy and Biochemistry, University of Buenos Aires, Junín 956, (1113) Buenos Aires, Argentina
- National Scientific and Technological Research Council (CONICET), Rivadavia 1917, (1033) Buenos Aires, Argentina
| | - Rosa Erra-Balsells
- National Scientific and Technological Research Council (CONICET), Rivadavia 1917, (1033) Buenos Aires, Argentina
- CIHDECAR-CONICET, Department of Organic Chemistry, School of Exact and Natural Sciences, University of Buenos Aires, (1428) Buenos Aires, Argentina
| | - Fernando Albericio
- Institute for Research in Biomedicine, Baldiri Reixac 10, (08028) Barcelona, Spain
- Department of Organic Chemistry, University of Barcelona, Martí i Franquès 1-11, (08028) Barcelona, Spain
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, Baldiri Reixac 10, (08028) Barcelona, Spain
- School of Chemistry and Physics, University of KwaZulu-Natal, University Road Westville 3630, Durban 4001, South Africa
| | - Osvaldo Cascone
- Cathedra of Industrial Microbiology and Biotechnology, School of Pharmacy and Biochemistry, University of Buenos Aires, Junín 956, (1113) Buenos Aires, Argentina
- National Scientific and Technological Research Council (CONICET), Rivadavia 1917, (1033) Buenos Aires, Argentina
| | - Silvia A. Camperi
- Cathedra of Industrial Microbiology and Biotechnology, School of Pharmacy and Biochemistry, University of Buenos Aires, Junín 956, (1113) Buenos Aires, Argentina
- National Scientific and Technological Research Council (CONICET), Rivadavia 1917, (1033) Buenos Aires, Argentina
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29
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Menegatti S, Ward KL, Naik AD, Kish WS, Blackburn RK, Carbonell RG. Reversible cyclic peptide libraries for the discovery of affinity ligands. Anal Chem 2013; 85:9229-37. [PMID: 24000940 DOI: 10.1021/ac401954k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A novel strategy is presented for the identification of cyclic peptide ligands from combinatorial libraries of reversible cyclic depsipeptides. A method for the solid-phase synthesis of individual cyclic depsipeptides and combinatorial libraries of these compounds is proposed, which employs lactic acid (Lact) and the dipeptide ester (Nα-Ac)-Ser(Ala)- as linkers for dilactonization. Upon alkaline treatment of the beads selected by screening a model library, the cyclic depsipeptides are linearized and released from the solid support to the liquid phase, to be sequenced via single-step tandem mass spectrometry (MS/MS). The protocol presented for library synthesis provides for wide structural diversity. Two model sequences, VVWVVK and AAWAAR, were chosen to present different structural examples for depsipeptide libraries and demonstrate the process of sequence determination by mass spectrometry. Further, a case study using the IgG binding cyclic depsipeptide cyclo[(Nα-Ac)-S(A)-RWHYFK-Lact-E] is presented to demonstrate the process of library screening and sequence determination on the selected beads. Finally, a method is shown for synthesis of the irreversible cyclic peptide corresponding to the proposed depsipeptide structure, to make the ligand stable to the aqueous acid and alkaline conditions encountered in affinity chromatographic applications. The cyclic peptide ligand was synthesized on a poly(methacrylate) resin and used for chromatographic binding of the target IgG.
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Affiliation(s)
- Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, ‡Department of Molecular and Structural Biochemistry, and §Biomanufacturing Training and Education Center, North Carolina State University , Raleigh, North Carolina 27695, United States
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30
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Makley LN, Gestwicki JE. Expanding the number of 'druggable' targets: non-enzymes and protein-protein interactions. Chem Biol Drug Des 2013; 81:22-32. [PMID: 23253128 DOI: 10.1111/cbdd.12066] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Following sequencing and assembly of the human genome, the preferred methods for identification of new drug targets have changed dramatically. Modern tactics such as genome-wide association studies (GWAS) and deep sequencing are fundamentally different from the pharmacology-guided approaches used previously, in which knowledge of small molecule ligands acting at their cellular targets was the primary discovery engine. A consequence of the 'target-first, pharmacology-second' strategy is that many predicted drug targets are non-enzymes, such as scaffolding, regulatory or structural proteins, and their activities are often dependent on protein-protein interactions (PPIs). These types of targets create unique challenges to drug discovery efforts because enzymatic turnover cannot be used as a convenient surrogate for compound potency. Moreover, it is often challenging to predict how ligand binding to non-enzymes might affect changes in protein function and/or pathobiology. Thus, in the postgenomic era, targets might be strongly implicated by molecular biology-based methods, yet they often later earn the designation of 'undruggable'. Can the scope of available targets be widened to include these promising, but challenging, non-enzymes? In this review, we discuss advances in high-throughput screening (HTS) technology and chemical library design that are emerging to deal with these challenges.
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Affiliation(s)
- Leah N Makley
- Departments of Pathology, Biological Chemistry and the Interdisciplinary Program in Medicinal Chemistry, The Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, USA
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31
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Hintersteiner M, Auer M. A two-channel detection method for autofluorescence correction and efficient on-bead screening of one-bead one-compound combinatorial libraries using the COPAS fluorescence activated bead sorting system. Methods Appl Fluoresc 2013; 1:017001. [PMID: 29148437 DOI: 10.1088/2050-6120/1/1/017001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
One-bead one-compound combinatorial library beads exhibit varying levels of autofluorescence after solid phase combinatorial synthesis. Very often this causes significant problems for automated on-bead screening using TentaGel beads and fluorescently labeled target proteins. Herein, we present a method to overcome this limitation when fluorescence activated bead sorting is used as the screening method. We have equipped the COPAS bead sorting instrument with a high-speed profiling unit and developed a spectral autofluorescence correction method. The correction method is based on a simple algebraic operation using the fluorescence data from two detection channels and is applied on-the-fly in order to reliably identify hit beads by COPAS bead sorting. Our method provides a practical tool for the fast and efficient isolation of hit beads from one-bead one-compound library screens using either fluorescently labeled target proteins or biotinylated target proteins. This method makes hit bead identification easier and more reliable. It reduces false positives and eliminates the need for time-consuming pre-sorting of library beads in order to remove autofluorescent beads.
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32
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Chung BKW, Hickey JL, Scully CCG, Zaretsky S, Yudin AK. Bicycle synthesis through peptide macrocyclization using aziridine aldehydes followed by late stage disulfide bond installation. MEDCHEMCOMM 2013. [DOI: 10.1039/c3md00054k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We present a method that can be applied to generate medium-sized peptidomimetic macrocycles equipped with disulfide bonds.
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Affiliation(s)
| | | | | | - Serge Zaretsky
- Department of Chemistry
- University of Toronto
- Toronto
- Canada
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33
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Li Y, Dooley CT, Misler JA, Debevec G, Giulianotti MA, Cazares ME, Maida L, Houghten RA. Fluorescent mu selective opioid ligands from a mixture based cyclic peptide library. ACS COMBINATORIAL SCIENCE 2012; 14:673-9. [PMID: 23110623 DOI: 10.1021/co300110t] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A positional scanning cyclic peptide library was generated using a penta-peptide thioester scaffold. Glycine was fixed at position R(1). Diaminopropionic acid was fixed at position R(3), with its γ-amino attaching to an anthraniloyl group. Positions R(2) and R(4) contained 36 L- and D- amino acids and position R(5) contained 19 L- amino acids. Cyclization was performed in a mixture of acetonitrile and 1.5 M aqueous imidazole solution (7:1 v/v) at room temperature for 5 days. No significant cross-oligomerization was detected under the cyclization conditions. The library was screened in a binding assay for mu opioid receptor, identifying the active amino acid mixture at each position. A total of 40 individual cyclic peptides were identified and synthesized by the combinations of the most active amino acid mixtures found at three positions 5 × 4 × 2. Two cyclic peptides exhibited high binding affinities to opioid receptor. The most active cyclic peptide in the library was yielded to have Tyr at R(2), D-Lys at R(4), and Tyr at R(5). Further investigation on this compound revealed the side chain-to-tail isomer to have greater binding affinity (14 nM) than the head-to-tail isomer (39 nM). Both isomers were selective for the mu-opioid receptor.
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Affiliation(s)
- Yangmei Li
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port Saint Lucie, Florida 34987, United
States
| | - Colette T. Dooley
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port Saint Lucie, Florida 34987, United
States
| | - Jaime A. Misler
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port Saint Lucie, Florida 34987, United
States
| | - Ginamarie Debevec
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port Saint Lucie, Florida 34987, United
States
| | - Marc A. Giulianotti
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port Saint Lucie, Florida 34987, United
States
| | - Margaret E. Cazares
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port Saint Lucie, Florida 34987, United
States
| | - Laura Maida
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port Saint Lucie, Florida 34987, United
States
| | - Richard A. Houghten
- Torrey Pines Institute for Molecular Studies, 11350 SW Village Parkway, Port Saint Lucie, Florida 34987, United
States
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Menegatti S, Hussain M, Naik AD, Carbonell RG, Rao BM. mRNA display selection and solid-phase synthesis of Fc-binding cyclic peptide affinity ligands. Biotechnol Bioeng 2012; 110:857-70. [DOI: 10.1002/bit.24760] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 10/09/2012] [Accepted: 10/12/2012] [Indexed: 12/25/2022]
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Bédard F, Girard A, Biron É. A Convenient Approach to Prepare Topologically Segregated Bilayer Beads for One-Bead Two-Compound Combinatorial Peptide Libraries. Int J Pept Res Ther 2012. [DOI: 10.1007/s10989-012-9316-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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36
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Dewan V, Liu T, Chen KM, Qian Z, Xiao Y, Kleiman L, Mahasenan KV, Li C, Matsuo H, Pei D, Musier-Forsyth K. Cyclic peptide inhibitors of HIV-1 capsid-human lysyl-tRNA synthetase interaction. ACS Chem Biol 2012; 7:761-9. [PMID: 22276994 PMCID: PMC3330833 DOI: 10.1021/cb200450w] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
The human immunodeficiency virus type 1 (HIV-1) capsid
protein
(CA) plays a critical role in the viral life cycle. The C-terminal
domain (CTD) of CA binds to human lysyl-tRNA synthetase (hLysRS),
and this interaction facilitates packaging of host cell tRNALys,3, which serves as the primer for reverse transcription. Here, we
report the library synthesis, high-throughput screening, and identification
of cyclic peptides (CPs) that bind HIV-1 CA. Scrambling or single-residue
changes of the selected peptide sequences eliminated binding, suggesting
a sequence-specific mode of interaction. Two peptides (CP2 and CP4)
subjected to detailed analysis also inhibited hLysRS/CA interaction in vitro. Nuclear magnetic resonance spectroscopy and mutagenesis
studies revealed that both CPs bind to a site proximal to helix 4
of the CA-CTD, which is the known site of hLysRS interaction. These
results extend the current repertoire of CA-binding molecules to a
new class of peptides targeting a novel site with potential for development
into novel antiviral agents.
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Affiliation(s)
| | | | - Kuan-Ming Chen
- Biochemistry, Molecular
Biology
and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | | | - Yong Xiao
- Lady Davis Institute for Medical
Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec, Canada H3T 1E2
| | - Lawrence Kleiman
- Lady Davis Institute for Medical
Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec, Canada H3T 1E2
| | | | | | - Hiroshi Matsuo
- Biochemistry, Molecular
Biology
and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
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Simpson LS, Kodadek T. A Cleavable Scaffold Strategy for the Synthesis of One-Bead One-Compound Cyclic Peptoid Libraries That Can Be Sequenced By Tandem Mass Spectrometry. Tetrahedron Lett 2012; 53:2341-2344. [PMID: 22736872 DOI: 10.1016/j.tetlet.2012.02.112] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Many macrocyclic depsipeptides or related compounds have interesting medicinal properties and often display more favorable pharmacokinetic properties than linear analogues. Therefore, there is considerable interest in the development of large combinatorial libraries of macrocyclic peptidomimetic compounds. However, such molecules cannot be easily sequenced by tandem mass spectrometry, making it difficult to identify hits isolated from library screens using one bead one compound libraries. Here we report a strategy to solve this problem by placing a methionine in both the linker connecting the cyclic molecule to the bead as well as within the cycle itself. Treatment with CNBr both linearizes the molecule at a specific position and releases the molecule from the bead, making its characterization by tandem MALDI mass spectrometry straightforward.
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Affiliation(s)
- Levi S Simpson
- Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9185
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38
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Liu T, Qian Z, Xiao Q, Pei D. High-throughput screening of one-bead-one-compound libraries: identification of cyclic peptidyl inhibitors against calcineurin/NFAT interaction. ACS COMBINATORIAL SCIENCE 2011; 13:537-46. [PMID: 21848276 DOI: 10.1021/co200101w] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
One-bead-one-compound (OBOC) libraries provide a powerful tool for drug discovery as well as biomedical research. However, screening a large number of beads/compounds (>1 million) and rank ordering the initial hits (which are covalently attached to a solid support) according to their potencies still post significant technical challenges. In this work, we have integrated some of the latest technical advances from our own as well as other laboratories to develop a general methodology for rapidly screening large OBOC libraries. The methodology has been applied to synthesize and screen a cyclic peptide library that features: (1) spatially segregated beads containing cyclic peptides on the surface layer and linear encoding peptides in their interior; (2) rapid on-bead screening of the library (>1 million) by a multistage procedure (magnetic bead sorting, enzyme-linked assay, and fluorescence based screening); (3) selective release of cyclic peptides from single positive beads for solution-phase determination of their binding affinities; and (4) hit identification by partial Edman degradation/mass spectrometry (PED/MS). Screening of the library against protein phosphatase calcineurin (Cn) identified a series of cyclic peptides that bind to the substrate-docking site for nuclear factor of activated T cells (NFAT) with K(D) values of ∼1 μM. Further improvement of the affinity and specificity of these compounds may lead to a new class of immunosuppressive agents that are more selective and therefore less toxic than cyclosporine A and FK506.
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Affiliation(s)
- Tao Liu
- Department of Chemistry and Ohio State Biochemistry Program, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Ziqing Qian
- Department of Chemistry and Ohio State Biochemistry Program, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Qing Xiao
- Department of Chemistry and Ohio State Biochemistry Program, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Dehua Pei
- Department of Chemistry and Ohio State Biochemistry Program, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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39
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Feliu L, Oliveras G, Cirac AD, Besalú E, Rosés C, Colomer R, Bardají E, Planas M, Puig T. Antimicrobial cyclic decapeptides with anticancer activity. Peptides 2010; 31:2017-26. [PMID: 20708052 DOI: 10.1016/j.peptides.2010.07.027] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Revised: 07/30/2010] [Accepted: 07/30/2010] [Indexed: 11/27/2022]
Abstract
Antimicrobial peptides have been considered as potential candidates for cancer therapy. We report here the cytotoxicity of a library of 66 antibacterial cyclodecapeptides on human carcinoma cell lines, and their effects on apoptosis [as assessed by cleavage of poly(ADP-ribose) polymerase (PARP)] and cell signaling proteins (p53 and ERK1/2) in cultured human cervical carcinoma cells. A design of experiments approach permitted to analyze the results of a subset of 16 peptides and define rules for high anticancer activity against MDA-MB-231 breast carcinoma cells. Eight peptides were identified with IC(50) values ranging from 18.5 to 57.5 μM against the five cell lines tested, being HeLa cells the most sensitive. Among these sequences, BPC88, BPC96, BPC98, and BPC194 displayed specificity and high cytotoxicity against HeLa cells (IC(50) of 22.5-38.5 μM), showed low hemolytic activity and low cytotoxicity to non-malignant fibroblasts, and were stable to proteases in human serum. Induction of apoptosis by these peptides was observed and the apoptotic effect of BPC88 and BPC96 caused a marked decrease on the activated form of ERK1/2 kinase and an induction of p53. We further showed that BPC96 at low doses synergized the cytotoxic effect of cisplatin. These findings suggest that cyclic decapeptides may represent novel anticancer agents providing a new strategy in cancer therapy.
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Affiliation(s)
- Lidia Feliu
- LIPPSO, Department of Chemistry, University of Girona, Campus Montilivi, E-17071 Girona, Spain
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40
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Jacobson EM, Hugo ER, Tuttle TR, Papoian R, Ben-Jonathan N. Unexploited therapies in breast and prostate cancer: blockade of the prolactin receptor. Trends Endocrinol Metab 2010; 21:691-8. [PMID: 20846877 PMCID: PMC2967606 DOI: 10.1016/j.tem.2010.08.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Revised: 08/18/2010] [Accepted: 08/18/2010] [Indexed: 01/27/2023]
Abstract
Breast and prostate cancers are hormone-sensitive malignancies that afflict millions of women and men. Although prolactin (PRL) is known as a survival factor that supports tumor growth and confers chemoresistance in both cancers, its precise role in these tumors has not been studied extensively. Growth hormone and placental lactogen also bind PRL receptor (PRLR) and mimic some of the actions of PRL. Blockade of the PRLR represents a novel treatment for patients with advanced breast or prostate cancer with limited therapeutic options. This review discusses different approaches for generating PRLR antagonists. Emphasis is placed on technological advances which enable high-throughput screening for small molecule inhibitors of PRLR signaling that could serve as oral medications.
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Affiliation(s)
- Eric M Jacobson
- Division of Endocrinology, Diabetes and Metabolism, University of Cincinnati, Cincinnati, OH 45267-0567, USA
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41
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Liu T, Liu Y, Kao HY, Pei D. Membrane permeable cyclic peptidyl inhibitors against human Peptidylprolyl Isomerase Pin1. J Med Chem 2010; 53:2494-501. [PMID: 20180533 DOI: 10.1021/jm901778v] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Peptidylprolyl isomerase Pin1 regulates the function and/or stability of phosphoproteins by altering the conformation of specific pSer/pThr-Pro peptide bonds. In this work, a cyclic peptide library was synthesized and screened against the catalytic domain of human Pin1. The selected inhibitors contained a consensus motif of D-pThr-Pip-Nal (where Pip is L-piperidine-2-carboxylic acid and Nal is L-2-naphthylalanine). Representative compounds were tested for binding to Pin1 by isothermal titration calorimetry and inhibition of Pin1 activity, and the most potent inhibitors had K(D) (and K(I)) values in the low nanomolar range. Treatment of breast cancer cells with the inhibitors, which were rendered membrane permeable by attachment of an octaarginine sequence, inhibited cell proliferation and increased the protein levels of two previously established Pin1 substrates, PML and SMRT. Finally, a second generation of cell permeable Pin1 inhibitors was designed by replacing the noncritical residues within the cyclic peptide ring with arginine residues and shown to have antiproliferative activity against the cancer cells.
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Affiliation(s)
- Tao Liu
- The Ohio State University, Columbus, Ohio 43210, USA
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42
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Dewkar GK, Carneiro PB, Hartman MCT. Synthesis of Novel Peptide Linkers: Simultaneous Cyclization and Labeling. Org Lett 2009; 11:4708-11. [DOI: 10.1021/ol901662c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gajanan K. Dewkar
- Department of Chemistry and Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, Virginia 23298-0037
| | - Pedro B. Carneiro
- Department of Chemistry and Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, Virginia 23298-0037
| | - Matthew C. T. Hartman
- Department of Chemistry and Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, Virginia 23298-0037
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